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Li S, Wang H, Li B, Lu H, Zhao J, Gao A, An Y, Yang J, Ma T. Multi-Omics Analysis Reveals the Negative Effects of High-Concentrate Diets on the Colonic Epithelium of Dumont Lambs. Animals (Basel) 2025; 15:749. [PMID: 40076032 PMCID: PMC11898968 DOI: 10.3390/ani15050749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2025] [Revised: 03/03/2025] [Accepted: 03/03/2025] [Indexed: 03/14/2025] Open
Abstract
Feeding HC diets has been found to induce metabolic dysregulation in the colon. However, the mechanisms by which changes in colonic flora and metabolites damage the colonic epithelium are poorly studied. Therefore, the present experiment used a multi-omics technique to investigate the mechanism of colonic injury induced by high-concentrate diets in lambs. Twelve male Dumont lambs were randomly split into two groups: a low-concentrate diet (LC = concentrate/forage = 30:70) group and a high-concentrate diet (HC = concentrate/forage = 70:30) group. The results showed that the HC group presented significantly increased lipopolysaccharide (LPS) concentrations in the colonic epithelium and significantly decreased serum total cholesterol (TC), superoxide dismutase (SOD), and glutathione peroxidase (GSH-Px) levels (p < 0.05), which led to cavities and inflammatory cell infiltration in the colonic epithelium. The HC group had significantly lower pH and less VFAs in colon contents, as well as a significantly increased abundance of bacteria of the genera [Eubacterium]_coprostanoligenes_group, Rikenellaceae_RC9_gut_group, Treponema, Clostridia_UCG-014, Alistipes, Ruminococcus, Christensenellaceae_R-7_group, UCG-002, Bacteroidales_RF16_group and Lachnospiraceae_AC2044_group compared to the LC diet group. These microorganisms significantly increased the level of metabolites of cholic acid, chenodeoxycholic acid, LysoPA (P-16:0/0:0), methapyrilene, and fusaric acid. A transcriptome analysis showed that cytokine-cytokine receptor interaction, glutathione metabolism, and the peroxisome signaling pathway were downregulated in the colon epithelium of the lambs fed the HC diet. Therefore, the HC diet caused epithelial inflammation and oxidative damage by affecting the interaction between the microbial flora of the colon and metabolites and the host epithelium, which eventually disrupted colon homeostasis and had a negative impact on sheep health.
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Affiliation(s)
- Shufang Li
- Animal Nutrition and Feed Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (S.L.); (B.L.); (H.L.); (J.Z.); (J.Y.); (T.M.)
| | - Hairong Wang
- Animal Nutrition and Feed Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (S.L.); (B.L.); (H.L.); (J.Z.); (J.Y.); (T.M.)
| | - Boyang Li
- Animal Nutrition and Feed Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (S.L.); (B.L.); (H.L.); (J.Z.); (J.Y.); (T.M.)
| | - Henan Lu
- Animal Nutrition and Feed Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (S.L.); (B.L.); (H.L.); (J.Z.); (J.Y.); (T.M.)
| | - Jianxin Zhao
- Animal Nutrition and Feed Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (S.L.); (B.L.); (H.L.); (J.Z.); (J.Y.); (T.M.)
| | - Aiwu Gao
- Food Science, Inner Mongolia Agricultural University, Hohhot 010018, China;
| | - Yawen An
- Veterinary Research Institute, Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010018, China;
| | - Jinli Yang
- Animal Nutrition and Feed Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (S.L.); (B.L.); (H.L.); (J.Z.); (J.Y.); (T.M.)
| | - Tian Ma
- Animal Nutrition and Feed Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (S.L.); (B.L.); (H.L.); (J.Z.); (J.Y.); (T.M.)
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Xie S, Ying Z, Xiu Z, Sun Y, Yang Q, Gao H, Fan W, Wu Y. Zinc oxide nanoparticles improve lactation and metabolism in dairy goats by modulating the rumen microbiota. Front Microbiol 2024; 15:1483680. [PMID: 39654678 PMCID: PMC11625748 DOI: 10.3389/fmicb.2024.1483680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2024] [Accepted: 10/18/2024] [Indexed: 12/12/2024] Open
Abstract
This study aimed to investigate the effects of dietary supplementation with zinc oxide nanoparticles (ZnONPs) on lactation, rumen microbiota, and metabolomics in dairy goats. Twenty Guanzhong dairy goats, with comparable milk yields and in the mid-lactation stage, were randomly divided into two groups, with 10 goats in each group. The control group was fed a standard diet, while the ZnONP group received the control diet plus 30 mg ZnONPs/kg DM. The pre-trial period lasted for 7 days, followed by a trial period of 30 days. The results showed that the addition of ZnONPs increased the milk yield and milk fat content (p < 0.05). The results of rumen microbial sequencing showed that the Chao1, Observed species, and PD_whole_tree indices of the ZnONP group were higher than those of the control group. The addition of ZnONPs altered the composition of the rumen microbiota, increasing the abundance of beneficial bacteria (Prevotella and Rikenellaceae_RC9_gut_group) and decreasing the abundance of the harmful bacterium Sediminispirochaeta. Non-targeted metabolomics analysis identified a total of 261 differential metabolites between the two groups, indicating changes in rumen metabolism. Further correlation analysis revealed a positive correlation between beneficial bacteria (Rikenellaceae RC9 gut group and Anaeroplasma) and metabolites such as nicotinamide riboside, inosine, and guanosine (p < 0.05). In addition, a positive correlation was observed between milk yield and beneficial bacteria (RF39 and Clostridia vadinBB60 group), as well as between milk fat content and Quinella (p < 0.05). In summary, ZnONP supplementation can improve the structure of the rumen microbiota in dairy goats, positively influencing milk yield, milk composition, and metabolism.
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Affiliation(s)
- Shan Xie
- College of Smart Agriculture, Chongqing University of Arts and Sciences, Yongchuan, China
- College of Biology and Food Engineering, Chongqing Three Gorges University, Wanzhou, China
| | - Zaixiang Ying
- College of Smart Agriculture, Chongqing University of Arts and Sciences, Yongchuan, China
- College of Biology and Food Engineering, Chongqing Three Gorges University, Wanzhou, China
| | - Ziqing Xiu
- College of Animal Science and Technology, Southwest University, Beibei, China
| | - Yawang Sun
- College of Animal Science and Technology, Southwest University, Beibei, China
| | - Qinlin Yang
- Chongqing Institute of Medicinal Plant Cultivation, Nanchuan, China
| | - Hanyu Gao
- College of Smart Agriculture, Chongqing University of Arts and Sciences, Yongchuan, China
- College of Biology and Food Engineering, Chongqing Three Gorges University, Wanzhou, China
| | - Wenqiao Fan
- College of Smart Agriculture, Chongqing University of Arts and Sciences, Yongchuan, China
| | - Yongjiang Wu
- College of Smart Agriculture, Chongqing University of Arts and Sciences, Yongchuan, China
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de la Sovera V, Bovio-Winkler P, Zinola G, Etchebehere C. Microbial community evolution in a lab-scale reactor operated to obtain biomass for biochemical methane potential assays. Appl Microbiol Biotechnol 2024; 108:519. [PMID: 39549075 PMCID: PMC11568993 DOI: 10.1007/s00253-024-13305-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 07/11/2024] [Accepted: 09/05/2024] [Indexed: 11/18/2024]
Abstract
Biochemical methane potential (BMP) test is an important tool to evaluate the methane production biodegradability and toxicity of different wastes or wastewaters. This is a key parameter for assessing design and feasibility issues in the full-scale implementation of anaerobic digestion processes. A standardized and storable inoculum is the key to obtain reproducible results. In Uruguay, a local enterprise dedicated to design and install anaerobic digesters operated a lab-scale bioreactor as a source of biomass for BMP tests, using a protocol previously described. This reactor was controlled and fed with a mixture of varied organic compounds (lipids, cellulolytic wastes, proteins). Biomass was reintroduced into the reactor after BMP assays to maintain a constant volume and biomass concentration. The aim of this work was to evaluate how the microbial community evolved during this operation and the effect of storing biomass in the refrigerator. The composition of the microbial communities was analyzed by 16S rRNA amplicon sequencing using primers for Bacteria and Archaea. The methanogenic activity was determined, and the methanogens were quantified by mcrA qPCR. One sample was stored for a 5-month period in the refrigerator (4 °C); the activity and the microbial community composition were analyzed before and after storage. Results showed that applying the reported methodology, a reliable methanogenic sludge with an acceptable SMA was obtained even though the reactor suffered biomass alterations along the evaluated period. Refrigerating the acclimatized biomass for 5 months did not affect its activity nor its microbial composition according to the 16S rRNA gene sequence analysis, even though changes in the mcrA abundance were observed. KEY POINTS: • The applied methodology was successful to obtain biomass suitable to perform BMP assays. • The microbial community was resilient to external biomass addition. • Biomass storage at 4 °C for 5 months did not alter the methanogenic activity.
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Affiliation(s)
- Victoria de la Sovera
- Microbial Ecology Laboratory, Biological Research Institute "Clemente Estable" (IIBCE), Department of Biochemistry and Microbial Genomics, Av. Italia 3318, Montevideo, Uruguay
| | - Patricia Bovio-Winkler
- Microbial Ecology Laboratory, Biological Research Institute "Clemente Estable" (IIBCE), Department of Biochemistry and Microbial Genomics, Av. Italia 3318, Montevideo, Uruguay
| | - Guillermo Zinola
- Microbial Ecology Laboratory, Biological Research Institute "Clemente Estable" (IIBCE), Department of Biochemistry and Microbial Genomics, Av. Italia 3318, Montevideo, Uruguay
| | - Claudia Etchebehere
- Microbial Ecology Laboratory, Biological Research Institute "Clemente Estable" (IIBCE), Department of Biochemistry and Microbial Genomics, Av. Italia 3318, Montevideo, Uruguay.
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Mao K, Lu G, Zang Y, Qiu Q, Zhao X, Ouyang K, Qu M, Li Y. Hydrogen-rich water 400ppb as a potential strategy for improving ruminant nutrition and mitigating methane emissions. BMC Microbiol 2024; 24:469. [PMID: 39528942 PMCID: PMC11555914 DOI: 10.1186/s12866-024-03638-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2024] [Accepted: 11/07/2024] [Indexed: 11/16/2024] Open
Abstract
The objective of this study was to evaluate the effects of different concentrations of hydrogen-rich water (HRW) on in vitro rumen fermentation characteristics and the dynamics of bacterial communities. The experiment included four treatment groups: a control (CON) and hydrogen-rich water (HRW) at 200, 400, and 800 ppb. Each group was analyzed at 12-hour (h) and 48-hour (h) time points with five replicates, totaling 40 samples. The experimental results highlighted the HRW800ppb group as the top production in terms of gas production and CH4 content. In contrast, the HRW200ppb group exhibited significantly lower methane levels at both 12 h and 48 h (P < 0.05). Regarding rumen fermentation, the HRW400ppb group significantly increased the levels of ammonia nitrogen (NH3-N) and microbial crude protein (MCP) at 12 h fermentation, but reduced the dry matter degradation rate (P < 0.05). After 48 h, the HRW400ppb group had highest MCP content (P < 0.05), but no significant differences in NH3-N and dry matter degradation rate compared with the CON group (P > 0.05). Although HRW did not significantly benefit the synthesis of total volatile fatty acids (TVFA) and individual VFA, the HRW800ppb group significantly increased the ratio of acetate to propionate (P < 0.05). Based on CH4 emissions and MCP synthesis, we selected the HRW400ppb group for subsequent bacterial community analysis. Bacterial community analysis showed that at 12 h, compared with the CON group, the Bacterial community analysis revealed that the HRW400ppb group had significant increases in the Simpson index, Firmicutes, Streptococcus, Schwartzia, Prevotellaceae_YAB2003_group, and Oribacterium, and decreases in Prevotella, Ruminobacter, Succinivibrio, unclassified_Succinivibrionaceae, and Prevotellaceae_UCG-003 (P < 0.05). At 48 h, the Prevotellaceae_YAB2003_group and Oribacterium abundances continued to rise significantly, while Rikenellaceae_RC9_gut_group and Succiniclasticum abundances fell in the HRW400ppb group (P < 0.05). Correlation analysis indicated a negative link between CH4 and Streptococcus, and a positive correlation between the abundance of Rikenellaceae_RC9_gut_group and CH4. Collectively, these results indicate that HRW can modulate rumen fermentation and microbial community structure to reduce methane emissions without significantly affecting VFA synthesis, highlighting its potential as drinking water for enhancing ruminant nutrition and mitigating the environmental impact of livestock farming.
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Affiliation(s)
- Kang Mao
- Jiangxi Province Key Laboratory of Animal Nutrition/Animal Nutrition and Feed Safety Innovation Team, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Guwei Lu
- Jiangxi Province Key Laboratory of Animal Nutrition/Animal Nutrition and Feed Safety Innovation Team, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Yitian Zang
- Jiangxi Province Key Laboratory of Animal Nutrition/Animal Nutrition and Feed Safety Innovation Team, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Qinghua Qiu
- Jiangxi Province Key Laboratory of Animal Nutrition/Animal Nutrition and Feed Safety Innovation Team, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Xianghui Zhao
- Jiangxi Province Key Laboratory of Animal Nutrition/Animal Nutrition and Feed Safety Innovation Team, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Kehui Ouyang
- Jiangxi Province Key Laboratory of Animal Nutrition/Animal Nutrition and Feed Safety Innovation Team, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Mingren Qu
- Jiangxi Province Key Laboratory of Animal Nutrition/Animal Nutrition and Feed Safety Innovation Team, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Yanjiao Li
- Jiangxi Province Key Laboratory of Animal Nutrition/Animal Nutrition and Feed Safety Innovation Team, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China.
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Liu Q, Chen B, Li X, Zhou M, Xiong T, Hu X, Mao H, Liu S. Dietary supplementation of Sida rhombifolia enhances the plasma antioxidation and modulates gut microbiota in Anyi tile-like grey chickens. J Anim Physiol Anim Nutr (Berl) 2024; 108:1712-1722. [PMID: 38943520 DOI: 10.1111/jpn.14013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 05/06/2024] [Accepted: 06/19/2024] [Indexed: 07/01/2024]
Abstract
Sida rhombifolia (S. rhombifolia) is a widely used herbal plant for humans because of its antioxidant and antibacterial effects, but its potential use as a feed additive for livestock has not been investigated. Twenty 350 days-old Anyi tile-like grey chickens were randomly divided into a control group (fed basal diet) and a treatment group (fed basal diet + 3% of S. rhombifolia), and these chickens were feed for 31 days. Dietary S. rhombifolia remarkably enhanced plasma antioxidants, including the significantly increased total antioxidant capability (p < 0.01), catalase (p = 0.04), and superoxide dismutase (p < 0.01) in the treatment group. Furthermore, dietary S. rhombifolia also modulated chicken cecal microbiota, including an increased microbial diversity (Shannon, p = 0.03; Chao1, p = 0.03) in the treatment group. Regarding taxonomic analysis, 34 microbial taxa showed significant differences between the two groups. Meanwhile, the dominant phylum Actinobacteriota (p = 0.04), and dominant genera Desulfovibrio (p = 0.04) and Olsenella (p = 0.02) were significantly increased after treatment, whereas the pathogenic genus Escherichia-Shigella (p = 0.04) was significantly decreased after feeding S. rhombifolia. The results indicating that S. rhombifolia has potential for use as a natural plant feed additive for chickens.
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Affiliation(s)
- Qiuhong Liu
- Department of Poultry Genetics and Breeding, Poultry Institute, Jiangxi Agricultural University, Nanchang, P. R. China
- Department of Animal Science, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, P. R. China
| | - Biao Chen
- Department of Poultry Genetics and Breeding, Poultry Institute, Jiangxi Agricultural University, Nanchang, P. R. China
- Department of Animal Science, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, P. R. China
| | - Xinghui Li
- Department of Animal Husbandry and Veterinary, Agriculture and Rural Affairs Bureau of Ningdu County, Ganzhou, P. R. China
| | - Mingfang Zhou
- Department of Poultry Genetics and Breeding, Poultry Institute, Jiangxi Agricultural University, Nanchang, P. R. China
- Department of Animal Science, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, P. R. China
| | - Ting Xiong
- Department of Poultry Genetics and Breeding, Poultry Institute, Jiangxi Agricultural University, Nanchang, P. R. China
- Department of Animal Science, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, P. R. China
| | - Xiaolong Hu
- Department of Poultry Genetics and Breeding, Poultry Institute, Jiangxi Agricultural University, Nanchang, P. R. China
- Department of Animal Science, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, P. R. China
| | - Huirong Mao
- Department of Poultry Genetics and Breeding, Poultry Institute, Jiangxi Agricultural University, Nanchang, P. R. China
- Department of Animal Science, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, P. R. China
| | - Sanfeng Liu
- Department of Poultry Genetics and Breeding, Poultry Institute, Jiangxi Agricultural University, Nanchang, P. R. China
- Department of Animal Science, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, P. R. China
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Miccoli F, Galarza R, Juliano N, Ferreyra S, Maresca S, López-Valiente S, Guerrero L, Palladino R, Albornoz R. Oro-ruminal sampling device and technique for rapid collection of rumen content and improved recovery of solid fractions for microbiome analysis. JDS COMMUNICATIONS 2024; 5:563-567. [PMID: 39650028 PMCID: PMC11624337 DOI: 10.3168/jdsc.2023-0536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 05/16/2024] [Indexed: 12/11/2024]
Abstract
Rumen fistulation is a widely used procedure that allows for collection of ruminal contents. However, fistulation is an invasive and costly procedure that generally limits the number of animals that can be recruited for experiments, thus encouraging the use of alternative techniques such as the intra-esophageal tube technique. One of the challenges of this technique is the limited ability to collect solid fractions from the rumen content pool, which may affect the microbial community structure in the sample, particularly affecting the recovery and characterization of solid adherent bacteria. We developed an intra-esophageal tube rumen sampling technique and device referred to as the "Rumen Sampler MG" with the aim of increasing the recovery of solid fractions from rumen content compared with other oro-ruminal sampling methods. The Rumen Sampler MG device consists of a manual pump fitted with a barometer and an intra-esophageal flexible polyvinyl chloride (PVC) tube with beveled terminal edge allowing for minimal clogging of the sampling tubing and a rapid flux of contents being sampled. Nine lactating Holstein-Friesian dairy cows (554.6 ± 25.2 kg of BW; 8.3 ± 3.3 DIM; ± SD) were recruited to evaluate the proposed method. During the procedure, animals were safely restrained in a chute and administered with a low dosage of a neuroleptic drug to reduce animal stress during sampling. An endoscopic camera was inserted into the reticulo-rumen through the esophagus to identify the sampling location and determine the length of the sampling tube necessary to reach the desired location. Following, the intra-esophageal sampling tube connected to a manual pump was inserted for collection of rumen contents. Samples collected did not present visual evidence of saliva contamination (e.g., high viscosity) and their pH ranged within expected values (6.33-7.04) for samples collected from the reticulo-rumen. Each sample contained 35% to 40% wet solids volume. Individual dry matter intake and milk production of cows continued to increase after sampling as expected for cows in the early postpartum period, suggesting that the sampling procedure did not affect cow performance. Results from microbiome analysis of rumen content samples suggest that the relative abundances of the main bacterial phyla are consistent with those from samples collected from dairy cows via rumen fistula in previous studies. The device and technique proposed allow for adequate samples of ruminal liquid and solid contents to be collected for microbiome analysis without disruption of animal performance.
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Affiliation(s)
- F.E. Miccoli
- Facultad de Ciencias Agrarias, Instituto de Investigacion en Produccion Agropecuaria, Ambiente y Salud (IIPAAS), Universidad Nacional de Lomas de Zamora (UNLZ), Llavallol, 1836, Buenos Aires, Argentina
- Departamento de Producción Animal, Universidad de Buenos Aires (UBA), Caba, C1417DSE, Argentina
| | - R.I. Galarza
- Estacion Experimental Agropecuaria del Instituto Nacional de Tecnología Agropecuaria, EEA Cuenca del Salado–INTA, Rauch 7203, Buenos Aires, Argentina
| | - N. Juliano
- Departamento de Producción Animal, Universidad de Buenos Aires (UBA), Caba, C1417DSE, Argentina
| | - S. Ferreyra
- Facultad de Ciencias Agrarias, Instituto de Investigacion en Produccion Agropecuaria, Ambiente y Salud (IIPAAS), Universidad Nacional de Lomas de Zamora (UNLZ), Llavallol, 1836, Buenos Aires, Argentina
| | - S. Maresca
- Estacion Experimental Agropecuaria del Instituto Nacional de Tecnología Agropecuaria, EEA Cuenca del Salado–INTA, Rauch 7203, Buenos Aires, Argentina
| | - S. López-Valiente
- Estacion Experimental Agropecuaria del Instituto Nacional de Tecnología Agropecuaria, EEA Cuenca del Salado–INTA, Rauch 7203, Buenos Aires, Argentina
| | - L.D. Guerrero
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Caba, C1417DSE, Argentina
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres” (INGEBI), CABA, C1428ADN, Buenos Aires, Argentina
| | - R.A. Palladino
- Facultad de Ciencias Agrarias, Instituto de Investigacion en Produccion Agropecuaria, Ambiente y Salud (IIPAAS), Universidad Nacional de Lomas de Zamora (UNLZ), Llavallol, 1836, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Caba, C1417DSE, Argentina
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Zhang K, Teng Z, Meng Q, Liu S, Yuan L, Fu T, Zhang N, Gao T. Dynamics of Fermentation Parameters and Bacterial Community in Rumen of Calves During Dietary Protein Oscillation. Microorganisms 2024; 12:2123. [PMID: 39597513 PMCID: PMC11596580 DOI: 10.3390/microorganisms12112123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2024] [Revised: 10/18/2024] [Accepted: 10/21/2024] [Indexed: 11/29/2024] Open
Abstract
Dietary crude protein concentration oscillation can improve the nitrogen utilization efficiency of ruminants. However, little is known about the dynamic changes in microbiota and fermentation in the rumen of calves during the oscillation period. In this study, six calves were fed an oscillating diet at 2-day intervals, including a high-protein diet (HP) and a low-protein diet (LP). The rumen fermentation parameters, plasma urea-N concentration, and rumen bacterial diversity were characterized throughout the oscillation period. The concentrations of volatile fatty acids, NH3-N, and plasma urea-N in rumen changed significantly with an oscillating diet. The abundance of Prevotella_1, Selenomonadales, Succiniclasticum, Clostridiales, Ruminococcaceae, Lachnospiraceae, and Rikenellaceae_RC9_gut_group showed significant changes with diet. Prevotella_1 was positively correlated, and Lachnospiraceae_AC2044_group and Saccharofermentans were negatively correlated with NH3-N. The abundance of Amino Acid Metabolism, Metabolism of Other Amino Acids, and Glycan Biosynthesis and Metabolism pathways, annotated by bacterial functional genes, decreased when the diet changed from HP to LP. The abundance of the Carbohydrate Metabolism pathway increased after the two dietary changes. In conclusion, the plasma urea-N concentration was not as sensitive and quick to adapt to diet changes as the rumen fermentation parameters. Rumen bacteria were responsible for increasing the nitrogen utilization efficiency of calves fed an oscillating diet.
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Affiliation(s)
- Kun Zhang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Zhanwei Teng
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Qing Meng
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Shuai Liu
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Liping Yuan
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Tong Fu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Ningning Zhang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Tengyun Gao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
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Bukhari SM, Andleeb S, Alghamdi HA, Rehman KU, Javid A, Ali W, Abbas Y, Nokhaiz K. Exploration of gut microbial diversity of pheasants through pyrosequencing of 16S rRNA gene. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART A, ECOLOGICAL AND INTEGRATIVE PHYSIOLOGY 2024; 341:950-959. [PMID: 38966934 DOI: 10.1002/jez.2855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 06/04/2024] [Accepted: 06/24/2024] [Indexed: 07/06/2024]
Abstract
Despite the diversity of microbiota in birds is similar to that of other animals, there is a lack of research on the gut microbial diversity of nondomesticated bird species. This study aims to address this gap in knowledge by analyzing the bacterial communities present in the gut of two important game bird species, the Ring-necked pheasant (Phasianus colchicus) and the Green pheasant (Phasianus versicolor) to understand the gut microbial diversity of these species. The gut microbiome of 10 individual pheasants from two different species was studied using pooled fecal samples. We used 16S rRNA gene sequencing on the Ion S5 XL System next-generation sequencing with Mothur and SILVA Database for taxonomic division. An average of 141 different operational taxonomic units were detected in the gut microbiome. Analysis of microbial classification revealed the presence of 191 genera belonging to 12 different phyla in both pheasants. Alpha diversity indices revealed that P. colchicus exhibited most prevalence firmicutes with bacillus species microbial community than P. versicolor. Alpha diversity indices indicated that P. colchicus had a more diverse community and P. versicolor had a greater diversity of evolutionary lineages, while both species had similar levels of species richness and sample inclusiveness. These findings may have implications for the health and well-being of pheasants, serving as a reference for their bacterial diversity. Additionally, they provide a baseline for future research and conservation efforts aimed at improving the health and well-being of these and possibly other avian species.
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Affiliation(s)
- Syed M Bukhari
- Department of Wildlife and Ecology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Shahla Andleeb
- Department of Environmental Sciences, Faculty of Natural Sciences, GC Women University, Sialkot, Pakistan
| | - Huda A Alghamdi
- Department of Biology, College of Science, King Khalid University, Abha, Saudi Arabia
| | - Khalil Ur Rehman
- Department of Environmental Sciences, Faculty of Natural Sciences, GC Women University, Sialkot, Pakistan
| | - Arshad Javid
- Department of Wildlife and Ecology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Waqas Ali
- Department of Wildlife and Ecology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Yassar Abbas
- Department of Animal Sciences, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Kashaf Nokhaiz
- Department of Wildlife and Ecology, University of Veterinary and Animal Sciences, Lahore, Pakistan
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9
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Shah T, Guo X, Song Y, Fang Y, Ding L. Comparative Analysis of Gut Bacterial Diversity in Wild and Domestic Yaks on the Qinghai-Tibetan Plateau. Animals (Basel) 2024; 14:2380. [PMID: 39199914 PMCID: PMC11350814 DOI: 10.3390/ani14162380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 08/01/2024] [Accepted: 08/02/2024] [Indexed: 09/01/2024] Open
Abstract
The gut microbiota is a diverse and complex population, and it has a key role in the host's health and adaptability to the environment. The present study investigated the fecal bacterial community of wild grazing (WG) and domestic grazing (DG) yaks on natural grazing pastures, analyzing the gut microbiota using 16S rRNA sequencing to assess bacterial diversity. A total of 48 yak fecal samples were selected from two different grazing habitats. The DG group had more crude proteins and non-fiber carbohydrates. The WG group had more OM, insoluble dietary fiber such as NDF, ADF, ether extract, and TC. There were 165 and 142 unique operational taxonomic units (OTUs) in the WG and DG groups, respectively. Shannon index analysis revealed a higher bacterial diversity in the WG group than in the DG group. At the phylum level, Firmicutes were the dominant bacterial taxa in both groups. The relative abundance of Firmicutes in the WG group was higher than in the DG group. At the family level, the WG group had a significantly higher abundance of Ruminococcaceae (p < 0.001) and Rikenellaceae (p < 0.001) than the DG group. The abundances of Alloprevotella and Succinivibrio were more pronounced in the DG group than in the WG group at the genus level. This study presents a novel understanding of the bacterial communities of ruminants and their potential applications for livestock production.
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Affiliation(s)
- Tariq Shah
- Sichuan Provincial Forest and Grassland Key Laboratory of Alpine Grassland Conservation and Utilization of Tibetan Plateau, Institute of Qinghai–Tibetan Plateau, College of Grassland Resources, Southwest Minzu University, Chengdu 610041, China;
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
| | - Xusheng Guo
- Probiotics and Biological Feed Research Centre, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yongwu Song
- Animal Husbandry and Veterinary Station, Gangcha County, Haibei 812399, China
| | - Yonggui Fang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Luming Ding
- Sichuan Provincial Forest and Grassland Key Laboratory of Alpine Grassland Conservation and Utilization of Tibetan Plateau, Institute of Qinghai–Tibetan Plateau, College of Grassland Resources, Southwest Minzu University, Chengdu 610041, China;
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Zhang F, Zhang Y, He T, Ji Q, Hou S, Gui L. Changes in Rumen Microbiology and Metabolism of Tibetan Sheep with Different Lys/Met Ratios in Low-Protein Diets. Animals (Basel) 2024; 14:1533. [PMID: 38891581 PMCID: PMC11171176 DOI: 10.3390/ani14111533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/14/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024] Open
Abstract
In ruminants, supplementing appropriate amounts of amino acids improves growth, feed utilization efficiency, and productivity. This study aimed to assess the effects of different Lys/Met ratios on the ruminal microbial community and the metabolic profiling in Tibetan sheep using 16S rDNA sequencing and non-target metabolomics. Ninety-two-month-old Tibetan rams (initial weight = 15.37 ± 0.92 kg) were divided into three groups and fed lysine/methionine (Lys/Met) of 1:1 (LP-L), 2:1 (LP-M), and 3:1 (LP-H) in low-protein diet, respectively. Results: The T-AOC, GSH-Px, and SOD were significantly higher in the LP-L group than in LP-H and LP-M groups (p < 0.05). Cellulase activity was significantly higher in the LP-L group than in the LP-H group (p < 0.05). In the fermentation parameters, acetic acid concentration was significantly higher in the LP-L group than in the LP-H group (p < 0.05). Microbial sequencing analysis showed that Ace and Chao1 indicators were significantly higher in LP-L than in LP-H and LP-M (p < 0.05). At the genus level, the abundance of Rikenellaceae RC9 gut group flora and Succiniclasticum were significantly higher in LP-L than in LP-M group (p < 0.05). Non-target metabolomics analyses revealed that the levels of phosphoric acid, pyrocatechol, hydrocinnamic acid, banzamide, l-gulono-1,4-lactone, cis-jasmone, Val-Asp-Arg, and tropinone content were higher in LP-L. However, l-citrulline and purine levels were lower in the LP-L group than in the LP-M and LP-H groups. Banzamide, cis-jasmone, and Val-Asp-Arg contents were positively correlated with the phenotypic contents, including T-AOC, SOD, and cellulase. Phosphoric acid content was positively correlated with cellulase and lipase activities. In conclusion, the Met/Lys ratio of 1:1 in low-protein diets showed superior antioxidant status and cellulase activity in the rumen by modulating the microbiota and metabolism of Tibetan sheep.
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Affiliation(s)
| | | | | | | | | | - Linsheng Gui
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810000, China; (F.Z.); (Y.Z.); (Q.J.); (S.H.)
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11
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Ma X, Li Z, Cai L, Xiao M, He F, Liu Z, Chen D, Wang Y, Shen L, Gu Y. Analysis of fungal diversity in the gut feces of wild takin ( Budorcas taxicolor). Front Microbiol 2024; 15:1364486. [PMID: 38699479 PMCID: PMC11063333 DOI: 10.3389/fmicb.2024.1364486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/08/2024] [Indexed: 05/05/2024] Open
Abstract
Introduction The composition of the intestinal microbiome correlates significantly with an animal's health status. Hence, this indicator is highly important and sensitive for protecting endangered animals. However, data regarding the fungal diversity of the wild Budorcas taxicolor (takin) gut remain scarce. Therefore, this study analyzes the fungal diversity, community structure, and pathogen composition in the feces of wild B. taxicolor. Methods To ensure comprehensive data analyses, we collected 82 fecal samples from five geographical sites. Amplicon sequencing of the internal transcribed spacer (ITS) rRNA was used to assess fecal core microbiota and potential pathogens to determine whether the microflora composition is related to geographical location or diet. We further validated the ITS rRNA sequencing results via amplicon metagenomic sequencing and culturing of fecal fungi. Results and discussion The fungal diversity in the feces of wild Budorcas taxicolor primarily comprised three phyla (99.69%): Ascomycota (82.19%), Fungi_unclassified (10.37%), and Basidiomycota (7.13%). At the genus level, the predominant fungi included Thelebolus (30.93%), Functional_unclassified (15.35%), and Ascomycota_unclassified (10.37%). Within these genera, certain strains exhibit pathogenic properties, such as Thelebolus, Cryptococcus, Trichosporon, Candida, Zopfiella, and Podospora. Collectively, this study offers valuable information for evaluating the health status of B. taxicolor and formulating protective strategies.
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Affiliation(s)
- Xiaoping Ma
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Zhiguo Li
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Lijun Cai
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Management Office of Tangjiahe National Nature Reserve, Qingchuan, China
| | - Mei Xiao
- Management Office of Tangjiahe National Nature Reserve, Qingchuan, China
| | - Fang He
- Management Office of Tangjiahe National Nature Reserve, Qingchuan, China
| | - Zhen Liu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Dong Chen
- Sichuan Provincial Center for Animal Disease Prevention and Control, Chengdu, China
| | - Ya Wang
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Limin Shen
- Management Office of Tangjiahe National Nature Reserve, Qingchuan, China
| | - Yu Gu
- College of Life Sciences, Sichuan Agricultural University, Chengdu, China
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12
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Murtaza N, Nawaz M, Yaqub T, Mehmood AK. Impact of Limosilactobacillus fermentum probiotic treatment on gut microbiota composition in sahiwal calves with rotavirus diarrhea: A 16S metagenomic analysis study". BMC Microbiol 2024; 24:114. [PMID: 38575861 PMCID: PMC10993544 DOI: 10.1186/s12866-024-03254-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 03/08/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Diarrhea poses a major threat to bovine calves leading to mortality and economic losses. Among the causes of calf diarrhea, bovine rotavirus is a major etiological agent and may result in dysbiosis of gut microbiota. The current study was designed to investigate the effect of probiotic Limosilactobacillus fermentum (Accession No.OR504458) on the microbial composition of rotavirus-infected calves using 16S metagenomic analysis technique. Screening of rotavirus infection in calves below one month of age was done through clinical signs and Reverse Transcriptase PCR. The healthy calves (n = 10) were taken as control while the infected calves (n = 10) before treatment was designated as diarrheal group were treated with Probiotic for 5 days. All the calves were screened for the presence of rotavirus infection on each day and fecal scoring was done to assess the fecal consistency. Infected calves after treatment were designated as recovered group. Fecal samples from healthy, recovered and diarrheal (infected calves before sampling) were processed for DNA extraction while four samples from each group were processed for 16S metagenomic analysis using Illumina sequencing technique and analyzed via QIIME 2. RESULTS The results show that Firmicutes were more abundant in the healthy and recovered group than in the diarrheal group. At the same time Proteobacteria was higher in abundance in the diarrheal group. Order Oscillospirales dominated healthy and recovered calves and Enterobacterials dominated the diarrheal group. Alpha diversity indices show that diversity indices based on richness were higher in the healthy group and lower in the diarrheal group while a mixed pattern of clustering between diarrheal and recovered groups samples in PCA plots based on beta diversity indices was observed. CONCLUSION It is concluded that probiotic Limosilactobacillus Fermentum N-30 ameliorate the dysbiosis caused by rotavirus diarrhea and may be used to prevent diarrhea in pre-weaned calves after further exploration.
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Affiliation(s)
- Nadeem Murtaza
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan
| | - Muhammad Nawaz
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan.
| | - Tahir Yaqub
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan
| | - Asim Khalid Mehmood
- Department of Veterinary Surgery and Pet Sciences, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan
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Olaniyi OO, Oriade B, Lawal OT, Ayodeji AO, Olorunfemi YO, Igbe FO. Purification and biochemical characterization of pullulanase produced from Bacillus sp. modified by ethyl-methyl sulfonate for improved applications. Prep Biochem Biotechnol 2024; 54:455-469. [PMID: 37587838 DOI: 10.1080/10826068.2023.2245884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Strain improvement via chemical mutagen could impart traits with better enzyme production or improved characteristics. The present study sought to investigate the physicochemical properties of pullulanase produced from the wild Bacillus sp and the mutant. The pullulanases produced from the wild and the mutant Bacillus sp. (obtained via induction with ethyl methyl sulfonate) were purified in a-three step purification procedure and were also characterized. The wild and mutant pullulanases, which have molecular masses of 40 and 43.23 kDa, showed yields of 2.3% with 6.0-fold purification and 2.0% with 5.0-fold purification, respectively, and were most active at 50 and 40 °C and pH 7 and 8, respectively. The highest stability of the wild and mutant was between 40 and 50 °C after 1 h, although the mutant retained greater enzymatic activity between pH 6 and 9 than the wild. The mutant had a decreased Km of 0.03 mM as opposed to the wild type of 1.6 mM. In comparison to the wild, the mutant demonstrated a better capacity for tolerating metal ions and chelating agents. These exceptional characteristics of the mutant pullulanase may have been caused by a single mutation, which could improve its utility in industrial and commercial applications.
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Affiliation(s)
- Oladipo O Olaniyi
- Microbiology Department, Federal University of Technology, Akure, Nigeria
| | - Blessing Oriade
- Microbiology Department, Federal University of Technology, Akure, Nigeria
| | - Olusola T Lawal
- Biochemistry Department, Federal University of Technology, Akure, Nigeria
| | - Adeyemi O Ayodeji
- Department of Biological Sciences, Joseph Ayo-Babalola University, Arakeji, Nigeria
| | | | - Festus O Igbe
- Biochemistry Department, Federal University of Technology, Akure, Nigeria
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14
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Keum GB, Pandey S, Kim ES, Doo H, Kwak J, Ryu S, Choi Y, Kang J, Kim S, Kim HB. Understanding the Diversity and Roles of the Ruminal Microbiome. J Microbiol 2024; 62:217-230. [PMID: 38662310 DOI: 10.1007/s12275-024-00121-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/16/2024] [Accepted: 02/16/2024] [Indexed: 04/26/2024]
Abstract
The importance of ruminal microbiota in ruminants is emphasized, not only as a special symbiotic relationship with ruminants but also as an interactive and dynamic ecosystem established by the metabolites of various rumen microorganisms. Rumen microbial community is essential for life maintenance and production as they help decompose and utilize fiber that is difficult to digest, supplying about 70% of the energy needed by the host and 60-85% of the amino acids that reach the small intestine. Bacteria are the most abundant in the rumen, but protozoa, which are relatively large, account for 40-50% of the total microorganisms. However, the composition of these ruminal microbiota is not conserved or constant throughout life and is greatly influenced by the host. It is known that the initial colonization of calves immediately after birth is mainly influenced by the mother, and later changes depending on various factors such as diet, age, gender and breed. The initial rumen microbial community contains aerobic and facultative anaerobic bacteria due to the presence of oxygen, but as age increases, a hypoxic environment is created inside the rumen, and anaerobic bacteria become dominant in the rumen microbial community. As calves grow, taxonomic diversity increases, especially as they begin to consume solid food. Understanding the factors affecting the rumen microbial community and their effects and changes can lead to the early development and stabilization of the microbial community through the control of rumen microorganisms, and is expected to ultimately help improve host productivity and efficiency.
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Affiliation(s)
- Gi Beom Keum
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Sriniwas Pandey
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Eun Sol Kim
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Hyunok Doo
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Jinok Kwak
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Sumin Ryu
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Yejin Choi
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Juyoun Kang
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Sheena Kim
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea.
| | - Hyeun Bum Kim
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea.
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15
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Pfau AP, Henniger MT, Samuelson KL, Hales KE, Löest CA, Hubbert ME, Lindholm-Perry AK, Egert-McLean AM, Mason KM, Shepherd EA, Voy BH, Myer PR. Effects of protein concentration and beta-adrenergic agonists on ruminal bacterial communities in finishing beef heifers. PLoS One 2024; 19:e0296407. [PMID: 38422047 PMCID: PMC10903865 DOI: 10.1371/journal.pone.0296407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 12/12/2023] [Indexed: 03/02/2024] Open
Abstract
To improve animal performance and modify growth by increasing lean tissue accretion, beef cattle production has relied on use of growth promoting technologies such as beta-adrenergic agonists. These synthetic catecholamines, combined with the variable inclusion of rumen degradable (RDP) and undegradable protein (RUP), improve feed efficiency and rate of gain in finishing beef cattle. However, research regarding the impact of beta-adrenergic agonists, protein level, and source on the ruminal microbiome is limited. The objective of this study was to determine the effect of different protein concentrations and beta-adrenergic agonist (ractopamine hydrochloride; RAC) on ruminal bacterial communities in finishing beef heifers. Heifers (n = 140) were ranked according to body weight and assigned to pens in a generalized complete block design with a 3 × 2 factorial arrangement of treatments of 6 different treatment combinations, containing 3 protein treatments (Control: 13.9% CP, 8.9% RDP, and 5.0% RUP; High RDP: 20.9% CP, 14.4% RDP, 6.5% RUP; or High RUP: 20.9% CP, 9.7% RDP, 11.2% RUP) and 2 RAC treatments (0 and 400 mg/day). Rumen samples were collected via orogastric tubing 7 days before harvest. DNA from rumen samples were sequenced to identify bacteria based on the V1-V3 hypervariable regions of the 16S rRNA gene. Reads from treatments were analyzed using the packages 'phyloseq' and 'dada2' within the R environment. Beta diversity was analyzed based on Bray-Curtis distances and was significantly different among protein and RAC treatments (P < 0.05). Alpha diversity metrics, such as Chao1 and Shannon diversity indices, were not significantly different (P > 0.05). Bacterial differences among treatments after analyses using PROC MIXED in SAS 9 were identified for the main effects of protein concentration (P < 0.05), rather than their interaction. These results suggest possible effects on microbial communities with different concentrations of protein but limited impact with RAC. However, both may potentially act synergistically to improve performance in finishing beef cattle.
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Affiliation(s)
- Alison P. Pfau
- Department of Animal Science, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Madison T. Henniger
- Department of Animal Science, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Kendall L. Samuelson
- Department of Agricultural Sciences, West Texas A&M University, Canyon, Texas, United States of America
| | - Kristin E. Hales
- Department of Animal and Food Sciences, Texas Tech University, Lubbock, Texas, United States of America
| | - Clint A. Löest
- Department of Animal and Range Sciences, New Mexico State University, Las Cruces, New Mexico, United States of America
| | - Mike E. Hubbert
- Department of Animal and Range Sciences, Clayton Livestock Research Center, New Mexico State University, Clayton, New Mexico, United States of America
| | | | - Amanda M. Egert-McLean
- Department of Animal Science, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Katie M. Mason
- Department of Animal Science, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Elizabeth A. Shepherd
- Department of Animal Science, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Brynn H. Voy
- Department of Animal Science, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Phillip R. Myer
- Department of Animal Science, University of Tennessee, Knoxville, Tennessee, United States of America
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Min BR, Wang W, Pitta DW, Indugu N, Patra AK, Wang HH, Abrahamsen F, Hilaire M, Puchala R. Characterization of the ruminal microbiota in sheep and goats fed different levels of tannin-rich Sericea lespedeza hay. J Anim Sci 2024; 102:skae198. [PMID: 39018107 PMCID: PMC11484804 DOI: 10.1093/jas/skae198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 07/15/2024] [Indexed: 07/18/2024] Open
Abstract
Understanding ruminal microbiota and diet-host breed interactions under forage feeding conditions is essential for optimizing rumen fermentation and improving feed efficiency in small ruminants. This study aimed to investigate the effects of different ratios of condensed tannin-rich Sericea lespedeza (SL; Lespedeza cuneata) in the diets on changes and interactions of ruminal microbiota and host species (i.e., sheep and goats). Katahdin sheep (n = 12) and Alpine goats (n = 12) at approximately 10 to 12 mo of age were blocked by body weight (BW = 30.3 and 25.5 kg, respectively) and randomly assigned to one of the 3 treatments. Diets contained 75% coarsely ground forage and 25% concentrate. The forages were 1) 100% alfalfa hay (AL), 2) 100% SL, and 3) 50% AL + 50% SL (ASL). In the present study, the diversity and composition of ruminal microbiota differed between sheep and goats fed similar diets. Based on the taxonomic analysis, there was a distinct clustering pattern (P < 0.05) for sheep by diets, but such a pattern was not observed for goats (P > 0.1). The most predominant phyla were Firmicutes, Bacteroidetes, Ascomycota, and methanogen species of Methanobrevibactor sp. in the rumen of sheep and goats, regardless of diets. The Bacteroidetes and Ascomycota were enriched in sheep fed AL and ASL. In contrast, these microbial phyla were enhanced in goats fed tannin-rich SL diets, with the diet-by-host species interaction (P < 0.02) for the Bacteroidetes phylum. Sheep rumen fluid samples showed a higher degree of variability in microbial community composition compared to goat rumen fluid samples. The relative proportion of the Aspergillus fungi population was reduced to 90.7% in the SL group compared with the AL group, regardless of host species. The antimicrobial activity of tannins and greater sensitivities of selected microbiota species to these tannin compounds during SL feeding in sheep and goats perhaps caused this difference. The results from this study suggest that differences in the microbiota were associated with differences in diets and host species. Therefore, this study provides a better understanding of ruminal microbiota and diet-host species interactions under various tannin-rich diets, which could advance consolidative information on rumen microbiome community diversity changes and may improve sheep and goat production.
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Affiliation(s)
- Byeng R Min
- Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL 36064, USA
| | - Wei Wang
- American Institute for Goat Research, Langston University, Langston, OK 73050, USA
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Dipti W Pitta
- Department of Clinical Studies, School of Veterinary Medicine, Pennsylvania State University, University Park, PA 16802, USA
| | - Nagaraju Indugu
- Department of Clinical Studies, School of Veterinary Medicine, Pennsylvania State University, University Park, PA 16802, USA
| | - Amlan K Patra
- American Institute for Goat Research, Langston University, Langston, OK 73050, USA
| | - Hong He Wang
- Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL 36064, USA
| | - Frank Abrahamsen
- Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL 36064, USA
| | - Mariline Hilaire
- Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL 36064, USA
| | - Ryszard Puchala
- American Institute for Goat Research, Langston University, Langston, OK 73050, USA
- Military Institute of Hygiene and Epidemiology, 01-001 Warsaw, Poland
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17
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Majhi S, Kerry RG, Sahoo L. Profiling of microbiome diversity in cattle: present status and future prospectives. APPLICATIONS OF METAGENOMICS 2024:129-142. [DOI: 10.1016/b978-0-323-98394-5.00003-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2025]
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18
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Chen M, Xie W, Zhou S, Ma N, Wang Y, Huang J, Shen X, Chang G. A high-concentrate diet induces colonic inflammation and barrier damage in Hu sheep. J Dairy Sci 2023; 106:9644-9662. [PMID: 37641289 DOI: 10.3168/jds.2023-23359] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/15/2023] [Indexed: 08/31/2023]
Abstract
Long-term feeding of a high-concentrate diet can induce subacute ruminal acidosis (SARA) in ruminants, which further leads to systemic inflammatory response. However, few studies have examined the effects of feeding a high-concentrate diet on the hindgut of ruminants. The purpose of this study was to investigate the effects of a high-concentrate diet on the composition of gut microbiota in colonic contents, inflammatory response, and barrier damage in the colon tissue of ruminants. A total of 12 healthy multiparous lactating Hu sheep were randomly allotted into the following 2 groups: a high-concentrate (HC) group (concentrate:forage = 7:3) and a low-concentrate (LC) group (concentrate:forage = 3:7). All sheep were fitted with ruminal fistulas. The formal feeding experiment lasted for 8 wk. After the feeding experiment, rumen fluid, portal vein blood, hepatic vein blood, colonic contents, and colon tissue samples were collected. The results showed that feeding the HC diet induced SARA in Hu sheep and significantly reduced pH in the colonic contents. The abundances of Firmicutes, Verrucomicrobiota, and Actinobacteriota decreased significantly, whereas those of Bacteroidota, Spirochaetota, and Fibrobacterota significantly increased in colonic contents. At the genus level, the relative abundances of 29 genera were significantly altered depending on the different type of diets. Analysis of the 10 bacterial genera with high relative abundance revealed that feeding the HC diet significantly reduced the abundance of UCG-005, Christensenellaceae R-7 group, UCG-010-norank, Monoglobus, [Eubacterium] coprostanoligenes group_norank, and Alistipes, whereas the abundances of Rikenellaceae RC9 gut group, Treponema, Bacteroides, and Prevotella increased. Compared with the LC group, feeding the HC diet significantly increased the concentration of LPS in rumen fluid, portal vein blood, hepatic vein blood, and colonic contents, and significantly upregulated the mRNA expression levels of proinflammatory cytokines in colon tissue, including TNF-α, IL-1β, IL-6, and IL-8, indicating the occurrence of inflammatory response in the colon tissue. In addition, the structure of colonic epithelial cells was loose, the intercellular space became larger, epithelial cells were exfoliated, and the mRNA and protein abundances of ZO-1, occludin, claudin-1, claudin-3, and claudin-4 were significantly decreased in the HC group, which was consistent with the results of immunohistochemistry. Furthermore, feeding the HC diet increased the ratios of DNA methylation and chromatin compaction in the promoter regions of occludin and claudin-1, which in turn inhibited their transcriptional expression. Therefore, the present study demonstrated that feeding an HC diet induced SARA in Hu sheep, altered the composition and structure of the microbial community in the colonic contents, induced an inflammatory response, and disrupted the intestinal mucosal barrier in the colonic tissue.
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Affiliation(s)
- Mengru Chen
- Ministry of Education Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, P. R. China 210095
| | - Wan Xie
- Ministry of Education Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, P. R. China 210095
| | - Shendong Zhou
- Ministry of Education Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, P. R. China 210095
| | - Nana Ma
- Ministry of Education Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, P. R. China 210095
| | - Yan Wang
- Ministry of Education Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, P. R. China 210095
| | - Jie Huang
- Huzhou Research Institute of Hu Sheep, Huzhou Academy of Agricultural Science, Huzhou, Zhejiang, P. R. China 313099
| | - Xiangzhen Shen
- Ministry of Education Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, P. R. China 210095
| | - Guangjun Chang
- Ministry of Education Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, P. R. China 210095.
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Dahl SA, Seifert J, Camarinha-Silva A, Hernández-Arriaga A, Windisch W, König A. "Get the best out of what comes in" - adaptation of the microbiota of chamois ( Rupicapra rupicapra) to seasonal forage availability in the Bavarian Alps. Front Microbiol 2023; 14:1238744. [PMID: 37849922 PMCID: PMC10577445 DOI: 10.3389/fmicb.2023.1238744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/11/2023] [Indexed: 10/19/2023] Open
Abstract
As an inhabitant of the Alps, chamois are exposed to significant climatic changes throughout the year and are also strongly confronted with changing forage availability. Besides horizontal and vertical migratory movements as an adaptation, it undergoes physiological transformations and dynamic changes in the ruminal microbiota. The following study used 48 chamois of different ages and genders to investigate to which extent the ingested food plants, the resulting crude nutrients in the rumen (reticulorumen) contents, and the bacterial microbiota in the rumen and their fermentation products were influenced by the changes over the seasons. Very little is known about the microbiota of wild ruminants, and many bacterial taxa could only be determined to certain taxonomic levels in this study. However, adapted microbiota reflects the significant changes in the ingested forage and the resulting crude nutrients. For some taxa, our results indicated potential functional relationships. In addition, 15 genera were identified, representing almost 90% of the relative abundance, forming the central part of the microbial community throughout the year. The successful and flexible adaptation of chamois is reflected in the chamois rumen's nutrient and microbial profile. This is also the first study that analyzes the microbiota of the chamois using rumen samples and considers the microbiota in a seasonal comparison.
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Affiliation(s)
- Sarah-Alica Dahl
- Wildlife Biology and Management Unit, Chair of Animal Nutrition and Metabolism, Technical University of Munich, Freising, Germany
| | - Jana Seifert
- HoLMiR – Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Amélia Camarinha-Silva
- HoLMiR – Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Angélica Hernández-Arriaga
- HoLMiR – Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Wilhelm Windisch
- TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Andreas König
- Wildlife Biology and Management Unit, Chair of Animal Nutrition and Metabolism, Technical University of Munich, Freising, Germany
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Cai Y, Li H, Qu G, Hu Y, Zou H, Zhao S, Cheng M, Chu X, Ren N. Responses of applied voltages on the archaea microbial distribution in sludge digestion. CHEMOSPHERE 2023; 339:139639. [PMID: 37495052 DOI: 10.1016/j.chemosphere.2023.139639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 07/18/2023] [Accepted: 07/22/2023] [Indexed: 07/28/2023]
Abstract
As the development of urban population led to the increase of domestic water consumption, consequently the generation of surplus sludge (SS) produced increasingly during sewage treatment processes. In order to enhance the SS resource utilization efficiency, an electricity-assisted anaerobic digestion (EAAD) system was employed to examine the alterations in the digestion broth and the characteristics of gas production. Additionally, the response of applied voltages on the distribution of archaeal community near various electrodes within the sludge was explored. The results revealed that the application of high voltages exceeding 3.0 V hindered the CH4 production but stimulated the CO2 generation. Subsequently, both CH4 and CO2 production were impeded by the applied voltages. Furthermore, the increased voltages significantly decreased the abundance of Methanomicrobia, Methanosaeta, and Methanosarcina, which were crucial determinants of CH4 content in biogas. Notably, the excessively high voltages intensities caused the AD process to halt and even inactivate the microbial flora. Interestingly, the distribution characteristics of archaeal community were influenced not only by the voltages intensity but also exhibited variations between the anode and cathode regions. Moreover, as the applied voltage intensified, the discrepancy of responses between the cathode and anode regions became more pronounced, offering novel theoretical and technical foundations for the advancement of electricity-assisted with AD technology.
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Affiliation(s)
- Yingying Cai
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China; National-Regional Engineering Center for Recovery of Waste Gases from Metallurgical and Chemical Industries, Kunming, 650500, Yunnan, China
| | - Heng Li
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China; Yunnan Yuntianhua Environmental Protection Technology Co., LTD, Kunming, 650228, Yunnan, China
| | - Guangfei Qu
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China; National-Regional Engineering Center for Recovery of Waste Gases from Metallurgical and Chemical Industries, Kunming, 650500, Yunnan, China.
| | - Yinghui Hu
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China; National-Regional Engineering Center for Recovery of Waste Gases from Metallurgical and Chemical Industries, Kunming, 650500, Yunnan, China
| | - Hongmei Zou
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China; National-Regional Engineering Center for Recovery of Waste Gases from Metallurgical and Chemical Industries, Kunming, 650500, Yunnan, China
| | - Shiqiang Zhao
- Yunnan Shunfeng Erhai Environmental Protection Technology Co., LTD, Dali, 671000, Yunnan, China
| | - Minhua Cheng
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China; National-Regional Engineering Center for Recovery of Waste Gases from Metallurgical and Chemical Industries, Kunming, 650500, Yunnan, China
| | - Xiaomei Chu
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China; National-Regional Engineering Center for Recovery of Waste Gases from Metallurgical and Chemical Industries, Kunming, 650500, Yunnan, China
| | - Nanqi Ren
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China; School of Environment, Harbin Institute of Technology, Harbin, 150000, Heilongjiang, China
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21
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Sha Y, He Y, Liu X, Shao P, Wang F, Xie Z, Li W, Wang J, Li S, Zhao S, Chen G. Interactions of rumen microbiota and metabolites with meat quality-related genes to regulate meat quality and flavor of Tibetan sheep under nutrient stress in the cold season. J Appl Microbiol 2023; 134:lxad182. [PMID: 37567778 DOI: 10.1093/jambio/lxad182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/26/2023] [Accepted: 08/10/2023] [Indexed: 08/13/2023]
Abstract
AIM The meat of Tibetan sheep has a unique flavor, delicious taste, and superior nutritional value. However, the change of grass will lead to a change in meat quality. This study aimed to explore the potential regulatory mechanisms of microbial metabolites with respect to meat quality traits of Tibetan sheep under nutrient stress in the cold season. METHODS AND RESULTS We determined and analyzed the longissimus dorsi quality, fatty acid composition, expression of genes, and rumen microbial metabolites of Tibetan sheep in cold and warm seasons. The shear force was decreased (P < .05), the meat color a*24 h value was increased (P < .05), and the contents of crude fat (EE) and protein (CP) were decreased in the cold season. Polyunsaturated fatty acids (PUFAs)-linoleic acid and docosahexaenoic acid increased significantly in the cold season (P < .05). The expressions of meat quality genes MC4R, CAPN1, H-FABP, and LPL were significantly higher in the warm season (P < .05), and the CAST gene was significantly expressed in the cold season (P < .01). The different microbial metabolites of Tibetan sheep in the cold and warm seasons were mainly involved in amino acid metabolism, lipid metabolism, and digestive system pathway, and there was some correlation between microbiota and meat quality traits. There are similarities between microbial metabolites enriched in the lipid metabolism pathway and muscle metabolites. CONCLUSION Under nutritional stress in the cold season, the muscle tenderness of Tibetan sheep was improved, and the fat deposition capacity was weakened, but the levels of beneficial fatty acids were higher than those in the warm season, which was more conducive to healthy eating.
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Affiliation(s)
- Yuzhu Sha
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China
| | - Yanyu He
- School of Fundamental Sciences, Massey University, Palmerston North 4410, New Zealand
| | - Xiu Liu
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China
| | - Pengyang Shao
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China
| | - Fanxiong Wang
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China
| | - Zhuanhui Xie
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China
| | - Wenhao Li
- Academy of Animal Science and Veterinary medicine, Qinghai University, Xining 810000, China
| | - Jiqing Wang
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China
| | - Shaobin Li
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China
| | - Shengguo Zhao
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China
| | - Guoshun Chen
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China
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Choi Y, Lee SJ, Kim HS, Eom JS, Jo SU, Guan LL, Seo J, Park T, Lee Y, Lee SS, Lee SS. Oral administration of Pinus koraiensis cone essential oil reduces rumen methane emission by altering the rumen microbial composition and functions in Korean native goat ( Capra hircus coreanae). Front Vet Sci 2023; 10:1168237. [PMID: 37275608 PMCID: PMC10234127 DOI: 10.3389/fvets.2023.1168237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/21/2023] [Indexed: 06/07/2023] Open
Abstract
This study aimed to investigate Pinus koraiensis cone essential oil (PEO) as a methane (CH4) inhibitor and determine its impact on the taxonomic and functional characteristics of the rumen microbiota in goats. A total of 10 growing Korean native goats (Capra hircus coreanae, 29.9 ± 1.58 kg, male) were assigned to different dietary treatments: control (CON; basal diet without additive) and PEO (basal diet +1 g/d of PEO) by a 2 × 2 crossover design. Methane measurements were conducted every 4 consecutive days for 17-20 days using a laser CH4 detector. Samples of rumen fluid and feces were collected during each experimental period to evaluate the biological effects and dry matter (DM) digestibility after PEO oral administration. The rumen microbiota was analyzed via 16S rRNA gene amplicon sequencing. The PEO oral administration resulted in reduced CH4 emission (eructation CH4/body weight0.75, p = 0.079) without affecting DM intake; however, it lowered the total volatile fatty acids (p = 0.041), molar proportion of propionate (p = 0.075), and ammonia nitrogen (p = 0.087) in the rumen. Blood metabolites (i.e., albumin, alanine transaminase/serum glutamic pyruvate transaminase, creatinine, and triglyceride) were significantly affected (p < 0.05) by PEO oral administration. The absolute fungal abundance (p = 0.009) was reduced by PEO oral administration, whereas ciliate protozoa, total bacteria, and methanogen abundance were not affected. The composition of rumen prokaryotic microbiota was altered by PEO oral administration with lower evenness (p = 0.054) observed for the PEO group than the CON group. Moreover, PICRUSt2 analysis revealed that the metabolic pathways of prokaryotic bacteria, such as pyruvate metabolism, were enriched in the PEO group. We also identified the Rikenellaceae RC9 gut group as the taxa potentially contributing to the enriched KEGG modules for histidine biosynthesis and pyruvate oxidation in the rumen of the PEO group using the FishTaco analysis. The entire co-occurrence networks showed that more nodes and edges were detected in the PEO group. Overall, these findings provide an understanding of how PEO oral administration affects CH4 emission and rumen prokaryotic microbiota composition and function. This study may help develop potential manipulation strategies to find new essential oils to mitigate enteric CH4 emissions from ruminants.
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Affiliation(s)
- Youyoung Choi
- Division of Applied Life Science (BK21), Gyeongsang National University, Jinju, Republic of Korea
- Institute of Agriculture and Life Science (IALS), Gyeongsang National University, Jinju, Republic of Korea
| | - Shin Ja Lee
- Institute of Agriculture and Life Science (IALS), Gyeongsang National University, Jinju, Republic of Korea
- Institute of Agriculture and Life Science and University-Centered Labs, Gyeongsang National University, Jinju, Republic of Korea
| | - Hyun Sang Kim
- Institute of Agriculture and Life Science (IALS), Gyeongsang National University, Jinju, Republic of Korea
| | - Jun Sik Eom
- Institute of Agriculture and Life Science (IALS), Gyeongsang National University, Jinju, Republic of Korea
| | - Seong Uk Jo
- Division of Applied Life Science (BK21), Gyeongsang National University, Jinju, Republic of Korea
- Institute of Agriculture and Life Science (IALS), Gyeongsang National University, Jinju, Republic of Korea
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Jakyeom Seo
- Department of Animal Science, Life and Industry Convergence Research Institute, Pusan National University, Miryang, Republic of Korea
| | - Tansol Park
- Department of Animal Science and Technology, Chung-Ang University, Anseong, Republic of Korea
| | - Yookyung Lee
- Animal Nutrition and Physiology Team, National Institute of Animal Science, RDA, Jeonju, Republic of Korea
| | - Sang Suk Lee
- Ruminant Nutrition and Anaerobe Laboratory, Department of Animal Science and Technology, Sunchon National University, Sunchon, Republic of Korea
| | - Sung Sill Lee
- Division of Applied Life Science (BK21), Gyeongsang National University, Jinju, Republic of Korea
- Institute of Agriculture and Life Science (IALS), Gyeongsang National University, Jinju, Republic of Korea
- Institute of Agriculture and Life Science and University-Centered Labs, Gyeongsang National University, Jinju, Republic of Korea
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Zhang J, Shang J, Hao Y, Wang Y, Cao Z, Yang H, Wang W, Li S. Growth performance, blood metabolites, ruminal fermentation, and bacterial community in preweaning dairy calves fed corn silage-included starter and total mixed ration. J Dairy Sci 2023:S0022-0302(23)00208-4. [PMID: 37164844 DOI: 10.3168/jds.2022-22476] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 12/14/2022] [Indexed: 05/12/2023]
Abstract
The objective of this study was to evaluate the effects of the inclusion of whole-plant corn silage (WPCS) in a starter or total mixed ration (TMR) on growth, blood metabolites, ruminal fermentation, and microbial community in preweaning dairy calves. A total of 45 healthy dairy calves were blocked by date of birth and randomly assigned to 1 of 3 treatments: 100% calf starter (CONS), a mix of 85% calf starter and 15% WPCS [dry matter (DM) basis; CSCS], or 100% WPCS-based lactation TMR (CTMR). Pasteurized normal milk was fed to all the animals under the same regimen. The experiment ran from when the calves were 2 d old to weaning at 63 d. Milk and feed intakes were recorded daily. Growth performance data and blood samples were collected on wk 3, 5, 7, and 9 of the experiment. Rumen fluid was sampled at 40 and 60 d. The 3 treatments had different particle size fractions. The CSCS group had greater medium fraction (<19 mm, >8 mm) and particles retained on 8-mm sieves than the other 2 groups, whereas the CTMR group had the greatest long (>19 mm) and fine (<4 mm) fractions and physically effective neutral detergent fiber (NDF) on 8- and 4-mm sieves, but had the smallest short fraction (<8 mm, >4 mm) and particles retained on 4-mm sieves. The 24-h in vitro digestibility of DM, crude protein (CP), NDF, and acid detergent fiber (ADF) were decreased in order by the CONS, CSCS, and CTMR groups. Compared with the CONS group, the digestibility of ether extract (EE) was lower in the CSCS and CTMR groups, whereas the digestibility of starch was similar among treatments. During the experimental period, the DM, CP, and metabolizable energy intakes from milk, solid feed, and total feed were not affected by treatments. The NDF, ADF, and EE intakes and potentially digestible intakes were greater in the CTMR group than in the other 2 groups. With the exception that body barrel was greater for calves fed CSCS, growth parameters and blood metabolites were similar among treatments. Compared with the CSCS group, the CTMR group had greater rumen pH and total volatile fatty acids, propionate, and isovalerate concentrations, but a lower acetate:propionate ratio. The CTMR group had greater relative abundances of some cellulolytic bacteria (Rikenellaceae RC9 gut group, Christensenellaceae R7, Ruminococcaceae NK4A214, Ruminococcaceae UCG, Ruminococcus, and Erysipelotrichaceae UCG) in the rumen, which may be beneficial for the early acquisition of specific adult-associated microorganisms. In summary, a WPCS-based lactation TMR, but not the WPCS-included starter, had the potential to be an alternative starter in preweaning calves without having significant adverse effects. These findings provide theoretical and practical implications for the rational application of TMR in the early life of dairy calves.
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Affiliation(s)
- Jun Zhang
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Jiaqi Shang
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yangyi Hao
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yajing Wang
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Zhijun Cao
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Hongjian Yang
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Wei Wang
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Shengli Li
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
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Yu S, Li L, Zhao H, Tu Y, Liu M, Jiang L, Zhao Y. Characterization of the Dynamic Changes of Ruminal Microbiota Colonizing Citrus Pomace Waste during Rumen Incubation for Volatile Fatty Acid Production. Microbiol Spectr 2023; 11:e0351722. [PMID: 36862010 PMCID: PMC10101060 DOI: 10.1128/spectrum.03517-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 02/03/2023] [Indexed: 03/03/2023] Open
Abstract
Rumen microorganisms are promising for efficient bioconversion of lignocellulosic wastes to biofuels and industrially relevant products. Investigating the dynamic changes of the rumen microbial community colonizing citrus pomace (CtP) will advance our understanding of the utilization of citrus processing waste by rumen fluid. Citrus pomace in nylon bags was incubated in the rumen of three ruminally cannulated Holstein cows for 1, 2, 4, 8, 12, 24, and 48 h. Results showed that total volatile fatty acids concentrations and proportions of valerate and isovalerate were increased over time during the first 12 h. Three major cellulose enzymes attached to CtP rose initially and then decreased during the 48-h incubation. Primary colonization happened during the initial hours of CtP incubation, and microbes compete to attach CtP for degrading easily digestible components and/or utilizing the waste. The 16S rRNA gene sequencing data revealed the diversity and structure of microbiota adhered to CtP were distinctly different at each time point. The increased abundance of Fibrobacterota, Rikenellaceae_RC9_gut_group, and Butyrivibrio may explain the elevated volatile fatty acids concentrations. This study highlighted key metabolically active microbial taxa colonizing citrus pomace in a 48-h in situ rumen incubation, which could have implications for promoting the biotechnological process of CtP. IMPORTANCE As a natural fermentation system, the rumen ecosystem of ruminants can efficiently degrade plant cellulose, indicating that the rumen microbiome offers an opportunity for anaerobic digestion to utilize biomass wastes containing cellulose. Knowledge of the response of the in situ microbial community to citrus pomace during anaerobic fermentation will help improve the current understanding of citrus biomass waste utilization. Our results demonstrated that a highly diverse rumen bacterial community colonized citrus pomace rapidly and continuously changed during a 48-h incubation period. These findings may provide a deep understanding of constructing, manipulating, and enriching rumen microorganisms to improve the anaerobic fermentation efficiency of citrus pomace.
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Affiliation(s)
- Shiqiang Yu
- Beijing Key Laboratory of Dairy Cow Nutrition, Animal Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Liuxue Li
- Beijing Key Laboratory of Dairy Cow Nutrition, Animal Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Huiying Zhao
- Beijing Key Laboratory of Dairy Cow Nutrition, Animal Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Yan Tu
- Beijing Key Laboratory of Dairy Cow Nutrition, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ming Liu
- Beijing Key Laboratory of Dairy Cow Nutrition, Animal Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Linshu Jiang
- Beijing Key Laboratory of Dairy Cow Nutrition, Animal Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Yuchao Zhao
- Beijing Key Laboratory of Dairy Cow Nutrition, Animal Science and Technology College, Beijing University of Agriculture, Beijing, China
- Beijing Beinong Enterprise Management Co., Ltd., Beijing, China
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Neha SA, Salazar-Bravo J. Fine-scale spatial variation shape fecal microbiome diversity and composition in black-tailed prairie dogs (Cynomys ludovicianus). BMC Microbiol 2023; 23:51. [PMID: 36858951 PMCID: PMC9979494 DOI: 10.1186/s12866-023-02778-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 01/19/2023] [Indexed: 03/03/2023] Open
Abstract
BACKGROUND Host associated gut microbiota are important in understanding the coevolution of host-microbe, and how they may help wildlife populations to adapt to rapid environmental changes. Mammalian gut microbiota composition and diversity may be affected by a variety of factors including geographic variation, seasonal variation in diet, habitat disturbance, environmental conditions, age, and sex. However, there have been few studies that examined how ecological and environmental factors influence gut microbiota composition in animals' natural environments. In this study, we explore how host habitat, geographical location and environmental factors affect the fecal microbiota of Cynomys ludovicianus at a small spatial scale. We collected fecal samples from five geographically distinct locations in the Texas Panhandle classified as urban and rural areas and analyzed them using high throughput 16S rRNA gene amplicon sequencing. RESULTS The results showed that microbiota of these fecal samples was largely dominated by the phylum Bacteroidetes. Fecal microbiome diversity and composition differed significantly across sampling sites and habitats. Prairie dogs inhabiting urban areas showed reduced fecal diversity due to more homogenous environment and, likely, anthropogenic disturbance. Urban prairie dog colonies displayed greater phylogenetic variation among replicates than those in rural habitats. Differentially abundant analysis revealed that bacterial species pathogenic to humans and animals were highly abundant in urban areas which indicates that host health and fitness might be negatively affected. Random forest models identified Alistipes shahii as the important species driving the changes in fecal microbiome composition. Despite the effects of habitat and geographic location of host, we found a strong correlation with environmental factors and that- average maximum temperature was the best predictor of prairie dog fecal microbial diversity. CONCLUSIONS Our findings suggest that reduction in alpha diversity in conjunction with greater dispersion in beta diversity could be indicative of declining host health in urban areas; this information may, in turn, help determine future conservation efforts. Moreover, several bacterial species pathogenic to humans and other animals were enriched in prairie dog colonies near urban areas, which may in turn adversely affect host phenotype and fitness.
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Affiliation(s)
- Sufia Akter Neha
- International Center for Arid and Semi-Arid Land Studies, Texas Tech University, Lubbock, TX, 79409, USA.
- Department of Biological Sciences, Texas Tech University, Lubbock, 79409, USA.
| | - Jorge Salazar-Bravo
- International Center for Arid and Semi-Arid Land Studies, Texas Tech University, Lubbock, TX, 79409, USA
- Department of Biological Sciences, Texas Tech University, Lubbock, 79409, USA
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Cui X, Wang Z, Guo P, Li F, Chang S, Yan T, Zheng H, Hou F. Shift of Feeding Strategies from Grazing to Different Forage Feeds Reshapes the Rumen Microbiota To Improve the Ability of Tibetan Sheep (Ovis aries) To Adapt to the Cold Season. Microbiol Spectr 2023; 11:e0281622. [PMID: 36809032 PMCID: PMC10100778 DOI: 10.1128/spectrum.02816-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 01/22/2023] [Indexed: 02/23/2023] Open
Abstract
The dynamics of ruminant-rumen microbiome symbiosis associated with feeding strategies in the cold season were examined. Twelve pure-grazing adult Tibetan sheep (Ovis aries) (18 months old; body weight, 40 ± 0.23 kg) were transferred from natural pasture to two indoor feedlots and fed either a native-pasture diet (NPF group) or an oat hay diet (OHF group) (n = 6 per treatment), and then the flexibility of rumen microbiomes to adapt to these compositionally different feeding strategies was examined. Principal-coordinate analysis and similarity analysis indicated that the rumen bacterial composition correlated with altered feeding strategies. Microbial diversity was higher in the grazing group than in those fed with native pasture and an oat hay diet (P < 0.05). The dominant microbial phyla were Bacteroidetes and Firmicutes, and the core bacterial taxa comprised mostly (42.49% of shared operational taxonomic units [OTUs]) Ruminococcaceae (408 taxa), Lachnospiraceae (333 taxa), and Prevotellaceae (195 taxa), which were relatively stable across different treatments. Greater relative abundances of Tenericutes at the phylum level, Pseudomonadales at the order level, Mollicutes at the class level, and Pseudomonas at the genus level were observed in a grazing period than in the other two treatments (NPF and OHF) (P < 0.05). In the OHF group, due to the high nutritional quality of the forage, Tibetan sheep can produce high concentrations of short-chain fatty acids (SCFAs) and NH3-N by increasing the relative abundances of key bacteria in the rumen, such as Lentisphaerae, Negativicutes, Selenomonadales, Veillonellaceae, Ruminococcus 2, Quinella, Bacteroidales RF16 group, and Prevotella 1, to aid in nutrients degradation and energy utilization. The levels of beneficial bacteria were increased by the oat hay diet; these microbiotas are likely to help improve and maintain host health and metabolic ability in Tibetan sheep to adapt to cold environments. The rumen fermentation parameters were significantly influenced by feeding strategy in the cold season (P < 0.05). Overall, the results of this study demonstrate the strong effect of feeding strategies on the rumen microbiota of Tibetan sheep, which provided a new idea for the nutrition regulation of Tibetan sheep grazing in the cold season on the Qinghai-Tibetan Plateau. IMPORTANCE During the cold season, like other high-altitude mammals, Tibetan sheep have to adapt their physiological and nutritional strategies, as well as the structure and function of their rumen microbial community, to the seasonal variation of lower food availability and quality. This study focused on the changes and adaptability in the rumen microbiota of Tibetan sheep when they adapted from grazing to a high-efficiency feeding strategy during the cold season by analyzing the rumen microbiota of Tibetan sheep raised under the different management systems, and it shows the linkages among the rumen core and pan-bacteriomes, nutrient utilization, and rumen short-chain fatty acids. The findings from this study suggest that the feeding strategies potentially contribute to variations in the pan-rumen bacteriome, together with the core bacteriome. Fundamental knowledge on the rumen microbiomes and their roles in nutrient utilization furthers our understanding of how rumen microbial adaptation to harsh environments may function in hosts. The facts obtained from the present trial clarified the possible mechanisms of the positive effects of feeding strategy on nutrient utilization and rumen fermentation in harsh environments.
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Affiliation(s)
- Xiongxiong Cui
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Zhaofeng Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Penghui Guo
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Fuhou Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Shenghua Chang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Tianhai Yan
- Livestock Production Science Branch, Agri-Food and Biosciences Institute, Hillsborough, County Down, United Kingdom
| | - Huiru Zheng
- School of Computing, University of Ulster, Belfast, United Kingdom
| | - Fujiang Hou
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
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The Effect of Combining Millet and Corn Straw as Source Forage for Beef Cattle Diets on Ruminal Degradability and Fungal Community. Animals (Basel) 2023; 13:ani13040548. [PMID: 36830335 PMCID: PMC9951761 DOI: 10.3390/ani13040548] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/29/2023] [Accepted: 01/30/2023] [Indexed: 02/09/2023] Open
Abstract
Three ruminal cannulated Simmental crossbreed bulls (approximately 3 years of age and with 380 ± 20 kg live weight at initiation of the experiment) were used in a 3 × 3 Latin square experiment in order to determine the effects of the treatments on ruminal pH and degradability of nutrients, as well as the rumen fungal community. The experimental periods were 21 d, with 18 d of adjustment to the respective dietary treatments and 3 d of sample collection. Treatments consisted of a basal diet containing a 47.11% composition of two sources of forage as follows: (1) 100% millet straw (MILLSTR), (2) 50:50 millet straw and corn straw (COMB), and (3) 100% corn straw (CORNSTR). Dry matter (DM), crude protein (CP), neutral detergent fiber (NDF), and acid detergent fiber (ADF) were tested for ruminal degradability using the nylon bag method, which was incubated for 6, 12, 24, 36, 48, and 72 h, and rumen fungal community in rumen fluid was determined by high-throughput gene sequencing technology. Ruminal pH was not affected by treatments. At 72 h, compared to MILLSTR, DM degradability of CORNSTR was 4.8% greater (p < 0.05), but when corn was combined with millet straw, the difference in DM degradability was 9.4%. During the first 24 h, degradability of CP was lower for CORNSTR, intermediate for MILLSTR, and higher for COMB. However, at 72 h, MILLSTR and COMB had a similar CP degradability value, staying greater than the CP degradability value of the CORNSTR treatment. Compared to MILLSTR, the rumen degradability of NDF was greater for CORNSTR and intermediate for the COMB. There was a greater degradability for ADF in CORNSTR, intermediate for COMB, and lower for MILLSTR. In all treatments, Ascomycota and Basidiomycota were dominant flora. Abundance of Basidiomycota in the group COMB was higher (p < 0.05) than that in the group CORNSTR at 12 h. Relative to the fungal genus level, the Thelebolus, Cladosporium, and Meyerozyma were the dominant fungus, and the abundance of Meyerozyma in COMB and CORNSTR were greater (p < 0.05) than MILLSTR at 12, 24, and 36 h of incubation. In conclusion, it is suggested to feed beef cattle with different proportions of millet straw and corn straw combinations.
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Kibegwa FM, Bett RC, Gachuiri CK, Machuka E, Stomeo F, Mujibi FD. Diversity and functional analysis of rumen and fecal microbial communities associated with dietary changes in crossbreed dairy cattle. PLoS One 2023; 18:e0274371. [PMID: 36638091 PMCID: PMC9838872 DOI: 10.1371/journal.pone.0274371] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 12/29/2022] [Indexed: 01/14/2023] Open
Abstract
The objective of this study was to investigate the effect of varying roughage and concentrate proportions, in diet of crossbreed dairy cattle, on the composition and associated functional genes of rumen and fecal microbiota. We also explored fecal samples as a proxy for rumen liquor samples. Six crossbred dairy cattle were reared on three diets with an increasing concentrate and reducing roughage amount in three consecutive 10-day periods. After each period, individual rumen liquor and fecal samples were collected and analyzed through shotgun metagenomic sequencing. Average relative abundance of identified Operational Taxonomic Units (OTU) and microbial functional roles from all animals were compared between diets and sample types (fecal and rumen liquor). Results indicated that dietary modifications significantly affected several rumen and fecal microbial OTUs. In the rumen, an increase in dietary concentrate resulted in an upsurge in the abundance of Proteobacteria, while reducing the proportions of Bacteroidetes and Firmicutes. Conversely, changes in microbial composition in fecal samples were not consistent with dietary modification patterns. Microbial functional pathway classification identified that carbohydrate metabolism and protein metabolism pathways dominated microbial roles. Assessment of dietary effects on the predicted functional roles of these microbiota revealed that a high amount of dietary concentrate resulted in an increase in central carbohydrate metabolism and a corresponding reduction in protein synthesis. Moreover, we identified several microbial stress-related responses linked to dietary changes. Bacteroides and Clostridium genera were the principal hosts of these microbial functions. Therefore, the roughage to concentrate proportion has more influence on the microbial composition and microbial functional genes in rumen samples than fecal samples. As such, we did not establish a significant relationship between the rumen and fecal metagenome profiles, and the rumen and fecal microbiota from one animal did not correlate more than those from different animals.
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Affiliation(s)
- Felix M. Kibegwa
- Department of Animal Production, Faculty of Veterinary Medicine, University of Nairobi, Nairobi, Kenya
- * E-mail:
| | - Rawlynce C. Bett
- Department of Animal Production, Faculty of Veterinary Medicine, University of Nairobi, Nairobi, Kenya
| | - Charles K. Gachuiri
- Department of Animal Production, Faculty of Veterinary Medicine, University of Nairobi, Nairobi, Kenya
| | - Eunice Machuka
- Biosciences Eastern and Central Africa—International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - Francesca Stomeo
- Biosciences Eastern and Central Africa—International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
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The improvement of parturition duration by high intake of dietary fibre in late gestation is associated with gut microbiota and metabolome in sows. Br J Nutr 2022; 128:2341-2352. [PMID: 35152932 DOI: 10.1017/s0007114522000502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Prolonged parturition duration has been widely demonstrated to be a risk factor for incidence of stillbirth. This study evaluated the supply of dietary fibre on the parturition duration, gut microbiota and metabolome using sows as a model. A total of 40 Yorkshire sows were randomly given diet containing normal level of dietary fibre (NDF, 17·5 % dietary fibre) or high level of dietary fibre (HDF, 33·5 % dietary fibre). Faecal microbiota profiled with 16S rRNA amplicon sequencing, SCFA and metabolome in the faeces and plasma around parturition were compared between the dietary groups. Correlation analysis was conducted to further explore the potential associations between specific bacterial taxa and metabolites. Results showed that HDF diet significantly improved the parturition process as presented by the shorter parturition duration. HDF diet increased the abundance of the phyla Bacteroidetes and Synergistetes and multiple genera. Except for butyrate, SCFA levels in the faeces and plasma of sows at parturition were elevated in HDF group. The abundances of fifteen and twelve metabolites in the faeces and plasma, respectively, markedly differ between HDF and NDF sows. These metabolites are involved in energy metabolism and bacterial metabolism. Correlation analysis also showed associations between specific bacteria taxa and metabolites. Collectively, our study indicates that the improvement of parturition duration by high fibre intake in late gestation is associated with gut microbiota, production of SCFA and other metabolites, potentially serving for energy metabolism.
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Choi Y, Lee SJ, Kim HS, Eom JS, Jo SU, Guan LL, Park T, Seo J, Lee Y, Bae D, Lee SS. Red seaweed extracts reduce methane production by altering rumen fermentation and microbial composition in vitro. Front Vet Sci 2022; 9:985824. [PMID: 36467635 PMCID: PMC9709288 DOI: 10.3389/fvets.2022.985824] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/26/2022] [Indexed: 06/27/2024] Open
Abstract
A series of in vitro batch culture incubations were carried out to investigate changes in rumen fermentation characteristics, methane (CH4) production, and microbial composition in response to supplementation with five different red seaweed species (Amphiroa anceps, AANC; Asparagopsis taxiformis, ATAX; Chondracanthus tenellus, CTEN; Grateloupia elliptica, GELL; and Gracilaria parvispora, GPAR). Prior to the incubations, the total flavonoid and polyphenol content of the red seaweed extracts was quantified. The incubated substrate consisted of timothy hay and corn grain [60:40 dry matter (DM) basis]. Treatments were substrate mixtures without seaweed extract (CON) or substrate mixtures supplemented with 0.25 mg/mL of red seaweed extract. Samples were incubated for 6, 12, 24, 36, and 48 h. Each sample was incubated in triplicates in three separate runs. In vitro DM degradability, fermentation parameters (i.e., pH, volatile fatty acids, and ammonia nitrogen), total gas production, and CH4 production were analyzed for all time points. Microbial composition was analyzed using 16S rRNA amplicon sequencing after 24 h of incubation. The highest CH4 reduction (mL/g DM, mL/g digested DM, and % of total gas production) was observed in ATAX (51.3, 50.1, and 51.5%, respectively, compared to CON; P < 0.001) after 12 h of incubation. The other red seaweed extracts reduced the CH4 production (mL/g DM; P < 0.001) in the range of 4.6-35.0% compared to CON after 24 h of incubation. After 24 h of incubation, supplementation with red seaweed extracts tended to increase the molar proportion of propionate (P = 0.057) and decreased the acetate to propionate ratio (P = 0.033) compared to the CON. Abundances of the genus Methanobrevibacter and total methanogens were reduced (P = 0.050 and P = 0.016) by red seaweed extract supplementation. The linear discriminant analysis effect size (P < 0.05, LDA ≥ 2.0) showed that UG Succinivibrionaceae, Anaeroplasma, and UG Ruminococcaceae, which are associated with higher propionate production, starch degradation, and amylase activity were relatively more abundant in red seaweed extracts than in the CON. Our results suggest that supplementation with red seaweed extracts altered the microbiota, leading to the acceleration of propionate production and reduction in CH4 production.
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Affiliation(s)
- Youyoung Choi
- Division of Applied Life Science (BK21), Gyeongsang National University, Jinju, South Korea
- Institute of Agriculture & Life Science (IALS), Gyeongsang National University, Jinju, South Korea
| | - Shin Ja Lee
- Institute of Agriculture & Life Science (IALS), Gyeongsang National University, Jinju, South Korea
- Institute of Agriculture and Life Science & University-Centered Labs, Gyeongsang National University, Jinju, South Korea
| | - Hyun Sang Kim
- Institute of Agriculture & Life Science (IALS), Gyeongsang National University, Jinju, South Korea
| | - Jun Sik Eom
- Institute of Agriculture & Life Science (IALS), Gyeongsang National University, Jinju, South Korea
| | - Seong Uk Jo
- Division of Applied Life Science (BK21), Gyeongsang National University, Jinju, South Korea
- Institute of Agriculture & Life Science (IALS), Gyeongsang National University, Jinju, South Korea
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Tansol Park
- Department of Animal Science and Technology, Chung-Ang University, Anseong, South Korea
| | - Jakyeom Seo
- Department of Animal Science, Life and Industry Convergence Research Institute, Pusan National University, Miryang, South Korea
| | - Yookyung Lee
- Animal Nutrition and Physiology Team, National Institute of Animal Science, Rural Development of Administration (RDA), Jeonju, South Korea
| | - Dongryeoul Bae
- College of Pharmacy and Research Institute of Pharmaceutical Science, PMBBRC, Gyeongsang National University, Jinju, South Korea
| | - Sung Sill Lee
- Division of Applied Life Science (BK21), Gyeongsang National University, Jinju, South Korea
- Institute of Agriculture & Life Science (IALS), Gyeongsang National University, Jinju, South Korea
- Institute of Agriculture and Life Science & University-Centered Labs, Gyeongsang National University, Jinju, South Korea
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Tan C, Zhao W, Wen W, Chen X, Ma Z, Yu G. Unraveling the effects of sulfamethoxazole on the composition of gut microbiota and immune responses in Stichopus variegatus. Front Microbiol 2022; 13:1032873. [DOI: 10.3389/fmicb.2022.1032873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/18/2022] [Indexed: 11/09/2022] Open
Abstract
The aim of this work was to reveal the changes in gut microbiota composition and immune responses of sea cucumber (Stichopus variegatus) after being affected by different doses of sulfamethoxazole. In this study, the bacterial 16S rRNA of gut microbiota were analyzed by high-throughput sequencing, and the activities of immune enzymes [lysozyme (LZM), phenoloxidase (PO), alkaline phosphatase (AKP), and acid phosphatase (ACP)] in the gut of S. variegatus were determined. The results showed that the gut microbiota presented a lower richness in the antibiotic treatment groups compared with the control group, and there were significant differences among the dominant bacteria of different concentration treatments. At the genus level, the abundance of Escherichia, Exiguobacterium, Acinetobacter, Pseudomonas, and Thalassotalea were significantly decreased in the 3 mg/L treatment group, while Vibrio was significantly increased. Furthermore, the 6 mg/L treatment group had less effect on these intestinal dominant bacteria, especially Vibrio. The changes in relative abundance of Vibrio at the species level indicated that lower concentrations of sulfamethoxazole could enhance the enrichment of Vibrio mediterranei and Vibrio fortis in S. variegatus more than higher concentrations of sulfamethoxazole. Meanwhile, the 3 mg/L treatment group significantly increased the activities of PO, AKP, and ACP, and decreased the activity of LZM. These results suggested that lower doses of sulfamethoxazole have a greater effect on the gut microbiota composition and immune responses in S. variegatus and may increase the risk of host infection.
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In Vitro Fermentation and Degradation Characteristics of Rosemary Extract in Total Mixed Ration of Lactating Dairy Cows. FERMENTATION 2022. [DOI: 10.3390/fermentation8090461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Rosemary extract (RE) is characterized as an antioxidant, and it has the potential to reduce methane emission and change microbial fermentation. Hence, to the extent of the evaluation of RE in ruminant nutrition, the in vitro fermentation technique was used to investigate the effects of RE on the fermentation characteristics of a total mixed ration (TMR) fed to dairy cows. Different doses of RE were added to the TMR to obtain different concentrations of antioxidants, including 0 (CON), 0.05 (LRE), and 0.10 g/kg (HRE). A total of 500 mg ground TMR was incubated in buffer solution and rumen fluid for 48 h at 39 °C. Nutrient degradability, gas production parameters, gas composition, fermentation parameters, and microbial composition were analyzed. The results showed that nutrient degradability and total volatile fatty acid concentration were not affected by the treatments. Furthermore, total methane production and proportion were depressed in a dose-dependent way. The RE increased the propionate concentration and proportion linearly and decreased the acetate concentration and proportion linearly. Finally, microbial diversity analysis showed that the richness and evenness indexes were unchanged by different treatments, while Prevotella_1 was decreased and Prevotella_7 was increased with RE supplementation. In conclusion, RE is an effective inhibitor of methane emission of microbial fermentation and changed the profile of volatile fatty acids with no disadvantageous effects on diet utilization.
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Zhu X, Liu B, Xiao J, Guo M, Zhao S, Hu M, Cui Y, Li D, Wang C, Ma S, Shi Y. Effects of Different Roughage Diets on Fattening Performance, Meat Quality, Fatty Acid Composition, and Rumen Microbe in Steers. Front Nutr 2022; 9:885069. [PMID: 35799586 PMCID: PMC9253607 DOI: 10.3389/fnut.2022.885069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
This study aimed to evaluate different roughages on fatting performance, muscle fatty acids, rumen fermentation and rumen microbes of steers. Seventy-five Simmental crossbred steers were randomly divided into wheat straw group (WG), peanut vine group (PG) and alfalfa hay group (AG), with 5 replicates of 5 steers each. The results showed a highest average daily gain and lowest feed/gain ratio in AG group (P = 0.001). Steers fed alfalfa hay had the highest muscle marbling score and n-3 polyunsaturated fatty acid (PUFA), and also the rumen NH3-N and microbial protein (MCP) concentration among the three groups (P < 0.05). Correlation analysis showed that ruminal NH3-N and MCP were negatively correlated with muscle saturated fatty acid (SFA), while ruminal MCP was positively correlated with muscle PUFA and n-3 PUFA (P < 0.05). 16S rRNA analysis indicated that fed alfalfa hay decreased the abundance of Ruminococcaceae_UCG-001(P = 0.005). More importantly, muscle SFA deposition were positively correlated to the abundance of Ruminococcaceae_UCG-001 (P < 0.05), while the muscle PUFA and n-3 PUFA deposition were negatively correlated to it (P < 0.01). Therefore, alfalfa hay provides a better fattening effect on steers. Alfalfa rich in n-3 PUFA would reduce the abundance of Ruminococcaceae_UCG-001 involved in hydrogenation, increase the rumen protective effect of C18:3 n-3, which is beneficial to the deposition of muscle n-3 PUFA and PUFA.
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Affiliation(s)
- Xiaoyan Zhu
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Key Laboratory of Grassland Resources Innovation and Utilization, Henan Agricultural University, Zhengzhou, China
- Henan Herbage Engineering Technology Research Center, Henan Agricultural University, Zhengzhou, China
| | - Boshuai Liu
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Junnan Xiao
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Ming Guo
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Shumin Zhao
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Menglin Hu
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Yalei Cui
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Key Laboratory of Grassland Resources Innovation and Utilization, Henan Agricultural University, Zhengzhou, China
- Henan Herbage Engineering Technology Research Center, Henan Agricultural University, Zhengzhou, China
| | - Defeng Li
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Key Laboratory of Grassland Resources Innovation and Utilization, Henan Agricultural University, Zhengzhou, China
- Henan Herbage Engineering Technology Research Center, Henan Agricultural University, Zhengzhou, China
| | - Chengzhang Wang
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Key Laboratory of Grassland Resources Innovation and Utilization, Henan Agricultural University, Zhengzhou, China
- Henan Herbage Engineering Technology Research Center, Henan Agricultural University, Zhengzhou, China
| | - Sen Ma
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Key Laboratory of Grassland Resources Innovation and Utilization, Henan Agricultural University, Zhengzhou, China
- Henan Herbage Engineering Technology Research Center, Henan Agricultural University, Zhengzhou, China
| | - Yinghua Shi
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Key Laboratory of Grassland Resources Innovation and Utilization, Henan Agricultural University, Zhengzhou, China
- Henan Herbage Engineering Technology Research Center, Henan Agricultural University, Zhengzhou, China
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Dynamic Variations in Rumen Fermentation Characteristics and Bacterial Community Composition during In Vitro Fermentation. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8060276] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
This study aimed to explore the dynamic variations of rumen fermentation characteristics and bacterial community composition during a 24 h in vitro fermentation. A total of twenty-three samples were collected from original rumen fluid (ORF, n = 3), fermentation at 12 h (R12, n = 10), and fermentation at 24 h (R24, n = 10). Results showed that gas production, concentrations of microbial crude protein, ammonia nitrogen, and individual volatile fatty acids (VFA), as well as total VFA and branched-chain VFA concentrations, were higher in R24 when compared with R12 (p < 0.05). However, no significant differences were observed in acetate to propionate ratio and fermentation efficiency between R12 and R24 (p > 0.05). Bacterial diversity analysis found that Shannon index and Simpson index were higher in R24 (p < 0.05), and obvious clusters were observed in rumen bacterial community between R12 and R24. Taxonomic analysis at the phylum level showed that the abundances of Proteobacteria and Fibrobacteres were higher in R12 than that in R24, and inverse results were observed in Bacteroidetes, Firmicutes, Cyanobacteria, Verrucomicrobia, Lentisphaerae, and Synergistetes abundances. Taxonomic analysis at the genus level revealed that the abundances of Rikenellaceae RC9 gut group, Succiniclasticum, Prevotellaceae UCG-003, Christensenellaceae R-7 group, Ruminococcaceae UCG-002, Veillonellaceae UCG-001, and Ruminococcaceae NK4A214 group were higher in R24, whereas higher abundances of Succinivibrionaceae UCG-002, Ruminobacter, and Fibrobacter, were found in R12. Correlation analysis revealed the negative associations between gas production and abundances of Proteobacteria, Succinivibrionaceae UCG-002, and Ruminobacter. Moreover, the abundances of Firmicutes, Rikenellaceae RC9 gut group, Christensenellaceae R-7 group, and Ruminococcaceae UCG-002 positively correlated with VFA production. These results indicate that both rumen fermentation characteristics and bacterial community composition were dynamic during in vitro fermentation, whereas the fermentation pattern, efficiency, and bacterial richness remained similar. This study provide insight into the dynamics of rumen fermentation characteristics and bacterial composition during in vitro fermentation. This study may also provide a reference for decision-making for the sampling time point when conducting an in vitro fermentation for bacterial community investigation.
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Su M, Hao Z, Shi H, Li T, Wang H, Li Q, Zhang Y, Ma Y. Metagenomic Analysis Revealed Differences in Composition and Function Between Liquid-Associated and Solid-Associated Microorganisms of Sheep Rumen. Front Microbiol 2022; 13:851567. [PMID: 35711780 PMCID: PMC9197192 DOI: 10.3389/fmicb.2022.851567] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 04/11/2022] [Indexed: 11/24/2022] Open
Abstract
The rumen microbiota plays a key role in the utilization of plant materials by ruminants, yet little is known about the key taxa and their genetic functions of the rumen sub-environment involved in the ruminal degradation process. Understanding the differences in the composition and function of ruminal microbiota in the liquid-associated (LA) and solid-associated (SA) systems is needed to further study and regulate rumen function and health. In this study, rumen contents of nine sheep were collected to separate LA and SA systems with elution and centrifugal precipitation. Metagenome sequencing was used to investigate the differences in microbial composition and genetic functions of LA and SA systems, with special emphasis on their degradational potential toward carbohydrates. Results showed that the dominant species composition was similar between the two systems, but SA microorganisms had a higher relative abundance than LA microorganisms in all taxa. The concentration of fiber-degrading bacteria, such as Ruminococcus, Treponema, and Fibrobacter, was higher and Prevotella was lower in the SA vs. LA system. Additionally, SA microorganisms dominated in cellulose degradation, while LA microorganisms were more important in starch utilization based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology (KO)'s functional categories and Carbohydrate-Active Enzymes (CAZymes). In general, SA microorganisms are more abundant and important in metabolic functions than LA, such as carbohydrate and amino acid metabolisms. In summary, the key differential biomarkers between LA and SA systems were Prevotella, Ruminococcus, Treponema, and Fibrobacter. Ruminal microbes degraded carbohydrates synergistically with SA, thus, more focusing on cellulose and hemicellulose, while LA is more important to starch.
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Affiliation(s)
- Manchun Su
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, China
- School of Agriculture and Forestry Technology, Longnan Teachers College, Longnan, China
| | - Ziyun Hao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, China
| | - Huibin Shi
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, China
| | - Taotao Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, China
| | - Huihui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, China
| | - Qiao Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, China
| | - Yong Zhang
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, China
| | - Youji Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, China
- *Correspondence: Youji Ma
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Pinnell LJ, Reyes AA, Wolfe CA, Weinroth MD, Metcalf JL, Delmore RJ, Belk KE, Morley PS, Engle TE. Bacteroidetes and Firmicutes Drive Differing Microbial Diversity and Community Composition Among Micro-Environments in the Bovine Rumen. Front Vet Sci 2022; 9:897996. [PMID: 35664853 PMCID: PMC9161295 DOI: 10.3389/fvets.2022.897996] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/28/2022] [Indexed: 01/04/2023] Open
Abstract
Ruminants are a critical human food source and have been implicated as a potentially important source of global methane emissions. Because of their unique digestive physiology, ruminants rely upon a symbiotic relationship with the complex and rich community of microorganism in the foregut to allow digestion of complex carbohydrates. This study used 16S rRNA gene sequencing to investigate the composition of microbial communities from three rumen micro-environments of cattle fed identical diets: (1) free fluid, (2) the fibrous pack, and (3) the mucosa. Community composition analysis revealed that while a phylogenetic core including the most abundant and most common ruminal taxa (members of Bacteroidetes and Firmicutes) existed across micro-environments, the abundances of these taxa differed significantly between fluid- and mucosa-associated communities, and specific lineages were discriminant of individual micro-environments. Members of Firmicutes, specifically Clostridiales, Lachnospiraceae, Mogibacteriaceae, Christenellaceae, and Erysipelotrichaceae were significantly more abundant in fluid communities, while members of Bacteroidetes, namely Muribaculaceae and Prevotellaceae were more abundant in mucosa-associated communities. Additionally, Methanobacteriaceae, a family of methanogenic Archaea, was more abundant in fluid-associated communities. A set of four more diverse lineages were discriminant of pack-associated communities that included Succinivibrionaceae, RFP12 (Verruco-5), Fibrobacteraceae, and Spirochaetaceae. Our findings indicate that different ecological niches within each micro-environment have resulted in significant differences in the diversity and community structure of microbial communities from rumen fluid, pack, and mucosa without the influence of diet that will help contextualize the influence of other environmental factors.
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Affiliation(s)
- Lee J. Pinnell
- Veterinary Education, Research, and Outreach Program, Texas A&M University, Canyon, TX, United States
| | - Arquimides A. Reyes
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, United States
| | - Cory A. Wolfe
- Veterinary Education, Research, and Outreach Program, Texas A&M University, Canyon, TX, United States
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, United States
| | - Maggie D. Weinroth
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, United States
| | - Jessica L. Metcalf
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, United States
| | - Robert J. Delmore
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, United States
| | - Keith E. Belk
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, United States
| | - Paul S. Morley
- Veterinary Education, Research, and Outreach Program, Texas A&M University, Canyon, TX, United States
- *Correspondence: Paul S. Morley
| | - Terry E. Engle
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, United States
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Rumen sampling methods bias bacterial communities observed. PLoS One 2022; 17:e0258176. [PMID: 35511785 PMCID: PMC9070869 DOI: 10.1371/journal.pone.0258176] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 04/10/2022] [Indexed: 01/04/2023] Open
Abstract
The rumen is a complex ecosystem that plays a critical role in our efforts to improve feed efficiency of cattle and reduce their environmental impacts. Sequencing of the 16S rRNA gene provides a powerful tool to survey the bacterial and some archaeal. Oral stomach tubing a cow to collect a rumen sample is a rapid, cost-effective alternative to rumen cannulation for acquiring rumen samples. In this study, we determined how sampling method (oral stomach tubing vs cannulated grab sample), as well as rumen fraction type (liquid vs solid), bias the bacterial and archaeal communities observed. Liquid samples were further divided into liquid strained through cheesecloth and unstrained. Fecal samples were also collected to determine how these differed from the rumen sample types. The abundance of major archaeal communities was not different at the family level in samples acquired via rumen cannula or stomach tube. In contrast to the stable archaeal communities across sample type, the bacterial order WCHB1-41 (phylum Kiritimatiellaeota) was enriched in both liquid strained and unstrained samples as well as the family Prevotellaceae as compared to grab samples. However, these liquid samples had significantly lower abundance of Lachnospiraceae compared with grab samples. Solid samples strained of rumen liquid most closely resembled the grab samples containing both rumen liquid and solid particles obtained directly from the rumen cannula; therefore, inclusion of particulate matter is important for an accurate representation of the rumen bacteria. Stomach tube samples were the most variable and were most representative of the liquid phase. In comparison with a grab sample, stomach tube samples had significantly lower abundance of Lachnospiraceae, Fibrobacter and Treponema. Fecal samples did not reflect the community composition of the rumen, as fecal samples had significantly higher relative abundance of Ruminococcaceae and significantly lower relative abundance of Lachnospiraceae compared with grab samples.
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Shah T, Ding L, Ud Din A, Hassan FU, Ahmad AA, Wei H, Wang X, Yan Q, Ishaq M, Ali N, Fang Y. Differential Effects of Natural Grazing and Feedlot Feeding on Yak Fecal Microbiota. Front Vet Sci 2022; 9:791245. [PMID: 35529830 PMCID: PMC9074760 DOI: 10.3389/fvets.2022.791245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 02/15/2022] [Indexed: 12/25/2022] Open
Abstract
Variation in food and diet shapes the diversity of the gut microbiota of ruminants. The present study investigated the microbial diversity in the fecal microbiota of yaks reared under natural grazing and feedlot system. A total of 48 domestic yaks with an average age of 7.5 years were selected from two different grazing habitats: one group grazed on natural pasture (grazing yaks—GY) while the other group was fed fodder and concentrate (feedlot yaks—FY). Crude protein, non-fiber carbohydrate, hemicelluloses, and digestible dry matter contents of natural pastures were higher than those in the feedlot. The lower insoluble fiber contents were found in grazing land. The 16S rRNA gene sequencing revealed 675 and 348 unique operational taxonomic units (OTUs) in the GY and FY, respectively, in addition to 1,778 common OTUs. Overall, a total of 9,891 OTUs were identified as a whole, of which 6,160 OTUs were from GY and 3,731 were from FY. Shannon index analysis revealed a higher bacterial diversity in GY than FY. At the phylum level, Firmicutes were dominant bacterial taxa in both groups. The relative abundance of Firmicutes in GY (56% ± 0.05) was higher than in FY (41% ± 0.08). At the family level, GY had a significantly higher abundance of Ruminococcaceae (p < 0.001) and Rikenellaceae (p < 0.001) than FY, but FY had a significantly higher abundance of Prevotellaceae than GY (p < 0.001). At the genus level, abundances of Faecalibacterium, Alloprevotella, and Succinivibrio were higher in FY than in GY. This study presents novel information on fecal bacterial composition and diversity in yaks reared under two different production systems.
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Affiliation(s)
- Tariq Shah
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Luming Ding
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
- Qinghai Provincial Key Laboratory of Adaptive Management on Alpine Grassland, Qinghai University, Xining, China
- *Correspondence: Luming Ding
| | - Ahmad Ud Din
- Drug Discovery Research Center, Southwest Medical University, Luzhou, China
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Faiz-ul Hassan
- Faculty of Animal Husbandry, Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Anum Ali Ahmad
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Haiyan Wei
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Xianju Wang
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Qi Yan
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Muhammad Ishaq
- School of Life Sciences, Probiotics and Biological Feed Research Centre, Lanzhou University, Lanzhou, China
| | - Niyaz Ali
- State Key Laboratory of Subtropical Agro Bio–Resource and College of Life Sciences, Guangxi University, Nanning, China
| | - Yougui Fang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
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Debi MR, Wichert BA, Liesegang A. Anaerobic fermentation of rice bran with rumen liquor for reducing their fiber components to use as chicken feed. Heliyon 2022; 8:e09275. [PMID: 35497030 PMCID: PMC9038563 DOI: 10.1016/j.heliyon.2022.e09275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 03/01/2022] [Accepted: 04/11/2022] [Indexed: 10/25/2022] Open
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Bio-Fermentation Improved Rumen Fermentation and Decreased Methane Concentration of Rice Straw by Altering the Particle-Attached Microbial Community. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8020072] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Bio-fermentation technology has been successfully developed for ensiling rice straw; however, its effects on the particle-attached microbial community remains unknown. Therefore, rice straw (RS) and bio-fermented rice straw (BFRS) were used as substrates for in vitro rumen fermentation to investigate the effect of bio-fermentation on particle-attached microbial community, as well as their effects on gas and methane production, fermentation products, and fiber degradation. Our results have shown that total gas production, fiber degradation, and in vitro fermentation products were significantly higher (p < 0.05) for the BFRS than the RS, while methane concentration in total gas volume was significantly lower (p < 0.05) for the BFRS than RS. Linear discriminant effect size (LefSe) analysis revealed that the relative abundance of the phyla Bacteroidetes, Fibrobacteres, Proteobacteria, and Lantisphaerae, as well as the genera Fibrobacter, Saccharofermentans, and [Eubacterium] ruminantium groups in the tightly attached bacterial community, was significantly higher (p < 0.05) for the BFRS than the RS, whereas other microbial communities did not change. Thus, bio-fermentation altered the tightly attached bacterial community, thereby improving gas production, fiber degradation, and fermentation products. Furthermore, bio-fermentation reduced methane concentration in total gas volume without affecting the archaeal community.
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López-García A, Saborío-Montero A, Gutiérrez-Rivas M, Atxaerandio R, Goiri I, García-Rodríguez A, Jiménez-Montero JA, González C, Tamames J, Puente-Sánchez F, Serrano M, Carrasco R, Óvilo C, González-Recio O. Fungal and ciliate protozoa are the main rumen microbes associated with methane emissions in dairy cattle. Gigascience 2022; 11:giab088. [PMID: 35077540 PMCID: PMC8848325 DOI: 10.1093/gigascience/giab088] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/18/2021] [Accepted: 11/30/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Mitigating the effects of global warming has become the main challenge for humanity in recent decades. Livestock farming contributes to greenhouse gas emissions, with an important output of methane from enteric fermentation processes, mostly in ruminants. Because ruminal microbiota is directly involved in digestive fermentation processes and methane biosynthesis, understanding the ecological relationships between rumen microorganisms and their active metabolic pathways is essential for reducing emissions. This study analysed whole rumen metagenome using long reads and considering its compositional nature in order to disentangle the role of rumen microbes in methane emissions. RESULTS The β-diversity analyses suggested a subtle association between methane production and overall microbiota composition (0.01 < R2 < 0.02). Differential abundance analysis identified 36 genera and 279 KEGGs as significantly associated with methane production (Padj < 0.05). Those genera associated with high methane production were Eukaryota from Alveolata and Fungi clades, while Bacteria were associated with low methane emissions. The genus-level association network showed 2 clusters grouping Eukaryota and Bacteria, respectively. Regarding microbial gene functions, 41 KEGGs were found to be differentially abundant between low- and high-emission animals and were mainly involved in metabolic pathways. No KEGGs included in the methane metabolism pathway (ko00680) were detected as associated with high methane emissions. The KEGG network showed 3 clusters grouping KEGGs associated with high emissions, low emissions, and not differentially abundant in either. A deeper analysis of the differentially abundant KEGGs revealed that genes related with anaerobic respiration through nitrate degradation were more abundant in low-emission animals. CONCLUSIONS Methane emissions are largely associated with the relative abundance of ciliates and fungi. The role of nitrate electron acceptors can be particularly important because this respiration mechanism directly competes with methanogenesis. Whole metagenome sequencing is necessary to jointly consider the relative abundance of Bacteria, Archaea, and Eukaryota in the statistical analyses. Nutritional and genetic strategies to reduce CH4 emissions should focus on reducing the relative abundance of Alveolata and Fungi in the rumen. This experiment has generated the largest ONT ruminal metagenomic dataset currently available.
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Affiliation(s)
- Adrián López-García
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Crta. de la Coruña km 7.5, 28040 Madrid, Spain
| | - Alejandro Saborío-Montero
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Crta. de la Coruña km 7.5, 28040 Madrid, Spain
- Escuela de Zootecnia y Centro de Investigación en Nutrición Animal, Universidad de Costa Rica, 11501 San José, Costa Rica
| | - Mónica Gutiérrez-Rivas
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Crta. de la Coruña km 7.5, 28040 Madrid, Spain
| | - Raquel Atxaerandio
- NEIKER – Instituto Vasco de Investigación y Desarrollo Agrario. Basque Research and Technology Alliance (BRTA), Campus Agroalimentario de Arkaute s/n, 01192 Arkaute, Spain
| | - Idoia Goiri
- NEIKER – Instituto Vasco de Investigación y Desarrollo Agrario. Basque Research and Technology Alliance (BRTA), Campus Agroalimentario de Arkaute s/n, 01192 Arkaute, Spain
| | - Aser García-Rodríguez
- NEIKER – Instituto Vasco de Investigación y Desarrollo Agrario. Basque Research and Technology Alliance (BRTA), Campus Agroalimentario de Arkaute s/n, 01192 Arkaute, Spain
| | - Jose A Jiménez-Montero
- Confederación de Asociaciones de Frisona Española (CONAFE), Ctra. de Andalucía km 23600 Valdemoro, 28340 Madrid, Spain
| | - Carmen González
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Crta. de la Coruña km 7.5, 28040 Madrid, Spain
| | - Javier Tamames
- Departamento de Biología de Sistemas, Centro Nacional de Biotecnología, CSIC, Madrid, 28049 Madrid, Spain
| | - Fernando Puente-Sánchez
- Departamento de Biología de Sistemas, Centro Nacional de Biotecnología, CSIC, Madrid, 28049 Madrid, Spain
| | - Magdalena Serrano
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Crta. de la Coruña km 7.5, 28040 Madrid, Spain
| | - Rafael Carrasco
- Departamento de Periodismo y Nuevos Medios, Universidad Complutense de Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
| | - Cristina Óvilo
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Crta. de la Coruña km 7.5, 28040 Madrid, Spain
| | - Oscar González-Recio
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Crta. de la Coruña km 7.5, 28040 Madrid, Spain
- Departamento de Producción Agraria, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
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Responsive changes of rumen microbiome and metabolome in dairy cows with different susceptibility to subacute ruminal acidosis. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2022; 8:331-340. [PMID: 35024470 PMCID: PMC8718735 DOI: 10.1016/j.aninu.2021.10.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 09/29/2021] [Accepted: 10/11/2021] [Indexed: 12/19/2022]
Abstract
Subacute ruminal acidosis (SARA) represents one of the most important digestive disorders in intensive dairy farms, and dairy cows are individually different in the severity of SARA risk. The objectives of the current study were to investigate differences in the ruminal bacterial community and metabolome in dairy cattle with different susceptibility to SARA. In the present study, 12 cows were initially enrolled in the experiment. Based on average ruminal pH, 4 cows with the lowest ruminal pH were assigned to the susceptible group (SUS, pH = 5.76, n = 4) and 4 cows with the highest ruminal pH assigned to the tolerant group (TOL, pH = 6.10, n = 4). Rumen contents from susceptible (SUS, n = 4) and tolerant (TOL, n = 4) dairy cows were collected through rumen fistula to systematically reveal the rumen microbial and metabolic alterations of dairy cows with different susceptibility to SARA using multi-omics approaches (16S and 18S rRNA gene sequencing and metabolome). The results showed that despite being fed the same diet, SUS cows had lower ruminal pH and higher concentrations of total volatile fatty acids (VFA) and propionate than TOL cows (P < 0.05). No significant differences were observed in dry matter intake, milk yield, and other milk compositions between the SUS and TOL groups (P > 0.05). The principal coordinates analysis based on the analysis of molecular variance indicated a significant difference in bacterial composition between the two groups (P = 0.01). More specifically, the relative abundance of starch-degrading bacteria (Prevotella spp.) was greater (P < 0.05), while the proportion of fiber-degrading bacteria (unclassified Ruminococcaceae spp., Ruminococcus spp., Papillibacter, and unclassified Family_XIII) was lower in the rumen of SUS cows compared with TOL cows (P < 0.05). Community analysis of protozoa showed that there were no significant differences in the diversity, richness, and community structure (P > 0.05). Metabolomics analysis revealed that the concentrations of organic acids (such as lactic acid), biogenic amines (such as histamine), and bacterial degradation products (such as hypoxanthine) were significantly higher in the SUS group compared to the TOL group (P < 0.05). These findings revealed that the higher proportion of starch-degrading bacteria/lower fiber-degrading bacteria in the rumen of SUS cows resulted in higher VFA-producing capacity, in particular propionate. This caused a disruption in metabolic homeostasis in the rumen which might be the reason for the higher susceptibility to SARA. Overall, these findings enhanced our understanding of the ruminal microbiome and metabolic changes in cows susceptible to SARA.
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Zhang J, Wang P, Dingkao R, Du M, Ahmad AA, Liang Z, Zheng J, Shen J, Yan P, Ding X. Fecal Microbiota Dynamics Reveal the Feasibility of Early Weaning of Yak Calves under Conventional Grazing System. BIOLOGY 2021; 11:biology11010031. [PMID: 35053029 PMCID: PMC8773362 DOI: 10.3390/biology11010031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/15/2021] [Accepted: 12/22/2021] [Indexed: 12/22/2022]
Abstract
Simple Summary Yak (Bos grunniens) is the most economically and culturally important domestic bovine species adapted to the extreme ecological environment of the Qinghai–Tibetan Plateau (QTP), which provides milk, meat, transportation, fuel (yak dung), and wool for local nomads as well as major sources of income. Calves are an important part of the sustainable development of the yak industry on the QTP, and the quality of calf rearing directly determines the production performance of adult animals. Under the traditional grazing management, late weaning (>180 days) of yak calves seriously affects the improvement of their production performance. A comparative study of fecal microbiota dynamics of yak and cattle (Bos taurus) calves in different months after weaning will help to understand the changes in intestinal microbiota structure, and will aid in in improving growth rate and survivability of early weaned calves. Our research will contribute to the development of appropriate strategies to regulate the gut microbiome and thus improve the growth and health of the grazing ruminants on the QTP. Abstract Background: The gut microbiota plays an important role in the health and production of animals. However, little information is available on the dynamic variations and comparison of intestinal microbiota in post-weaning yak calves living on the QTP. Methods: We explored the fecal bacterial microbiota succession of yak calves at different months after early weaning (60 d) compared with cattle calves by 16S rRNA gene amplicon sequencing and functional composition prediction. Results: We found no significant difference in blood biochemical parameters related to glucose and lipid metabolism between yaks and calves in different months after weaning. The core fecal bacterial microbiota from both species of calves was dominated by Ruminococcaceae, Rikenellaceae, and Bacteroidaceae. The fecal microbial community has a great alteration within the time after weaning in both cattle and yak calves, but cattle showed a larger change. After five months, the microbiota achieves a stable and concentrated state. This is also similar to the functional profile. Conclusions: Based on the exploration of dynamic changes in the fecal microbiota at an early stage of life, our results illustrated that there were no negative effects of intestinal microbiota succession on yak calves when early weaning was employed.
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Affiliation(s)
- Jianbo Zhang
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (J.Z.); (M.D.); (A.A.A.); (Z.L.); (J.Z.); (J.S.); (P.Y.)
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agricultural and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China;
| | - Peng Wang
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agricultural and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China;
| | - Renqing Dingkao
- Gannan Institute of Animal Husbandry Science, Hezuo 747000, China;
| | - Mei Du
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (J.Z.); (M.D.); (A.A.A.); (Z.L.); (J.Z.); (J.S.); (P.Y.)
| | - Anum Ali Ahmad
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (J.Z.); (M.D.); (A.A.A.); (Z.L.); (J.Z.); (J.S.); (P.Y.)
| | - Zeyi Liang
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (J.Z.); (M.D.); (A.A.A.); (Z.L.); (J.Z.); (J.S.); (P.Y.)
| | - Juanshan Zheng
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (J.Z.); (M.D.); (A.A.A.); (Z.L.); (J.Z.); (J.S.); (P.Y.)
| | - Jiahao Shen
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (J.Z.); (M.D.); (A.A.A.); (Z.L.); (J.Z.); (J.S.); (P.Y.)
| | - Ping Yan
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (J.Z.); (M.D.); (A.A.A.); (Z.L.); (J.Z.); (J.S.); (P.Y.)
| | - Xuezhi Ding
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (J.Z.); (M.D.); (A.A.A.); (Z.L.); (J.Z.); (J.S.); (P.Y.)
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agricultural and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China;
- Correspondence: ; Tel.: +86-0931-2115255
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Fregulia P, Neves ALA, Dias RJP, Campos MM. A review of rumen parameters in bovines with divergent feed efficiencies: What do these parameters tell us about improving animal productivity and sustainability? Livest Sci 2021. [DOI: 10.1016/j.livsci.2021.104761] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Indugu N, Hennessy M, Kaplan-Shabtai V, de Assis Lage C, Räisänen S, Melgar A, Nedelkov K, Chen X, Oh J, Vecchiarelli B, Bender J, Hristov A, Pitta D. Comparing noninvasive sampling techniques with standard cannula sampling method for ruminal microbial analysis. JDS COMMUNICATIONS 2021; 2:329-333. [PMID: 36337103 PMCID: PMC9623630 DOI: 10.3168/jdsc.2021-0094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 08/05/2021] [Indexed: 11/19/2022]
Abstract
Ruminal cannula is the gold standard for sampling rumen contents but is limited to few animals. Noninvasive methods are needed as proxy for cannula to enable sampling larger numbers of cows. Saliva, rumination bolus, tube-derived rumen samples, and feces were compared with cannula samples. Microbial community in the solid fraction of tube samples mirrored that of cannula samples. Rumination bolus may serve as a proxy for cannula samples under certain conditions. Rumen microbes play an important role in the conversion of indigestible plant material to energy and protein in dairy cows. Sampling for ruminal contents via cannula is considered the gold standard technique for microbial analysis, but the technique requires ruminally cannulated animals and specialized animal facilities. The purpose of this study was to determine whether other sampling methods and locations along the digestive tract may serve as noninvasive proxies to the cannula method for microbial analysis. Six ruminally cannulated lactating Holstein dairy cows were adapted to a standard total mixed ration for 2 wk and sampled during the third week. Sampling locations and methods included salivary content, rumination bolus (regurgitated digesta collected from the cow's mouth), feces, and rumen contents via stomach tube and cannula. Stomach tube and cannula samples differ in proportions of solid and liquid material and were therefore separated into whole (as collected), liquid, and solid fractions. Samples were collected at 0 (before feeding), 2, 4, 6, 8, and 12 h after feeding over 2 d. All samples were extracted for total genomic DNA and selected samples for metabolically active DNA (RNA), PCR-amplified for the V1-V2 region of the 16S rRNA bacterial gene, and analyzed for bacterial diversity using the QIIME2 pipeline followed by statistical analysis in R (https://www.R-project.org/). In DNA-based analysis, at the community level, saliva, rumination bolus, and fecal samples clustered in separate groups, whereas all fractions of stomach tube and cannula samples clustered together, indicating that microbial communities of stomach tube and cannula samples were homogeneous. Rumination bolus samples at 6, 8, and 12 h after feeding clustered with stomach tube and cannula samples, indicating that rumination bolus samples may be an alternative for cannula samples; however, time of sampling is critical for sampling of bolus digesta. Results of the RNA-based analysis of rumination bolus samples and solid samples from cannula and stomach tube at 0 and 6 h after feeding were similar. We concluded that the solid fraction of samples obtained via the stomach tube method may serve as a proxy for the solid fraction of whole ruminal contents obtained via cannula for DNA-based microbial investigations. Both rumination bolus and stomach tube solid samples may serve as proxies for cannula solid samples for RNA-based microbial analysis.
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Affiliation(s)
- N. Indugu
- Department of Clinical Studies, University of Pennsylvania, School of Veterinary Medicine, New Bolton Center, Kennett Square 19348
| | - M. Hennessy
- Department of Clinical Studies, University of Pennsylvania, School of Veterinary Medicine, New Bolton Center, Kennett Square 19348
| | - V.S. Kaplan-Shabtai
- Department of Clinical Studies, University of Pennsylvania, School of Veterinary Medicine, New Bolton Center, Kennett Square 19348
| | - C.F. de Assis Lage
- Department of Animal Science, The Pennsylvania State University, University Park 16802
| | - S.E. Räisänen
- Department of Animal Science, The Pennsylvania State University, University Park 16802
| | - A. Melgar
- Department of Animal Science, The Pennsylvania State University, University Park 16802
| | - K. Nedelkov
- Department of Animal Science, The Pennsylvania State University, University Park 16802
| | - X. Chen
- Department of Animal Science, The Pennsylvania State University, University Park 16802
| | - J. Oh
- Department of Animal Science, The Pennsylvania State University, University Park 16802
| | - B. Vecchiarelli
- Department of Clinical Studies, University of Pennsylvania, School of Veterinary Medicine, New Bolton Center, Kennett Square 19348
| | - J.S. Bender
- Department of Clinical Studies, University of Pennsylvania, School of Veterinary Medicine, New Bolton Center, Kennett Square 19348
| | - A.N. Hristov
- Department of Animal Science, The Pennsylvania State University, University Park 16802
| | - D.W. Pitta
- Department of Clinical Studies, University of Pennsylvania, School of Veterinary Medicine, New Bolton Center, Kennett Square 19348
- Corresponding author
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Characteristics of faecal bacterial flora and volatile fatty acids in Min pig, Landrace pig, and Yorkshire pig. ELECTRON J BIOTECHN 2021. [DOI: 10.1016/j.ejbt.2021.05.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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Effects of Condensed Tannins Supplementation on Animal Performance, Phylogenetic Microbial Changes, and In Vitro Methane Emissions in Steers Grazing Winter Wheat. Animals (Basel) 2021; 11:ani11082391. [PMID: 34438848 PMCID: PMC8388732 DOI: 10.3390/ani11082391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 08/04/2021] [Accepted: 08/09/2021] [Indexed: 11/18/2022] Open
Abstract
Simple Summary Grazing wheat pasture is a common practice throughout the southeastern and south-central United States; however, the practice is limited by concerns regarding the occurrence of bloat. In addition, there are few reports concerning methane production by cattle grazing wheat pasture. Naturally occurring plant secondary compounds, including condensed tannins (CT), saponins, and essential oils, are extensively evaluated as natural alternatives to control bloat and to mitigate methane production. However, the effects of CT supplementation on ruminal gas production, rumen microflora community changes, and animal performance in stocker cattle grazing wheat forage are not fully defined. Supplementation with CT induced changes in ruminal bacteria, reduced methane emissions, and increased animal performance. These data indicate that CT supplementation may benefit stocker producers grazing wheat pasture by decreasing the incidence of bloat and increasing animal performance by changing rumen fermentation. Abstract Eighteen growing rumen-cannulated steers, with initial body weight (BW) of 167.4 ± 7.10 kg, were randomly allocated to one of three treatments that included a control (0% CT) and two CT treatment levels (0.05% and 0.07% condensed tannins (CT)/kg BW) with two replicates each. Both in vivo and in vitro experiments were conducted. In Exp. 1, final BW and average daily gain were greater (p < 0.05) for the 0.07% CT treatment compared to either 0.05% CT or control groups. Rumen bacterial populations in steers fed winter wheat in the absence of CT represented large proportions of the moderate-guanines and cytosines (GC) containing bacterial clusters with similarity coefficient (SC) ranging from 64% to 92% In the presence of CT on day 0, day 20, and day 60, however, the SC was 60% or greater (90% SC) with multiple bacterial band clusters as shown by the denaturing gel gradient electrophoresis banding patterns. In Exp. 2, in vitro total gas, potential gas, and CH4 productions decreased (p < 0.01) as CT supplementation increased in steers grazing wheat forage. These results suggested that the administration of CT improved BW gain and induced bacterial community changes in the rumen of steers grazing wheat forage.
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Microbial colonization of the gastrointestinal tract of dairy calves - a review of its importance and relationship to health and performance. Anim Health Res Rev 2021; 22:97-108. [PMID: 34132191 DOI: 10.1017/s1466252321000062] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review aims to explain how microbial colonization of the gastrointestinal tract (GIT) in young dairy calves is related to health and, consequently, to the performance of these animals. The review addresses everything from the fundamental aspects of microbial colonization to the current understanding about the microbiota manipulation to improve performance in adult animals. The ruminal microbiota is the most studied, mainly due to the high interest in the fermentative aspects, the production of short-chain fatty acids, and microbial proteins, and its effects on animal production. However, in recent years, the intestinal microbiota has gained space between studies, mainly due to the relationship to the host health and how it affects performance. Understanding how the GIT's microbiota looks like and how it is colonized may allow future studies to predict the best timing for dietary interventions as a way to manipulate it and, consequently, improve the health and performance of young ruminants.
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Long-Term Effects of Dietary Supplementation with Olive Oil and Hydrogenated Vegetable Oil on the Rumen Microbiome of Dairy Cows. Microorganisms 2021; 9:microorganisms9061121. [PMID: 34067293 PMCID: PMC8224598 DOI: 10.3390/microorganisms9061121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/14/2021] [Accepted: 05/19/2021] [Indexed: 11/30/2022] Open
Abstract
Dietary lipids increase energy density in dairy cow diets and in some cases can increase beneficial fatty acids (FA) in milk and dairy products. However, the degree of FA saturation may affect the rumen microbiome. The objective of this study was to determine the long-term effects of feeding saturated (hydrogenated vegetable oil; HVO) or unsaturated (olive oil; OO) fatty acid (FA) sources on the rumen microbiome of dairy cows. For 63 days, 15 mid-lactating cows were fed with either a basal diet (no fat supplement), or the basal diet supplemented with 3% dry matter (DM), either HVO or OO. Rumen contents were collected on days 21, 42 and 63 for 16S rRNA gene sequencing using the Illumina MiSeq platform. The results reveal dominance of the phyla Firmicutes (71.5%) and Bacteroidetes (26.2%), and their respective prevalent genera Succiniclasticum (19.4%) and Prevotella (16.6%). Succiniclasticum increased with both treatments at all time points. Prevotella was reduced on day 42 in both diets. Bacterial diversity alpha or beta were not affected by diets. Predicted bacterial functions by CowPI showed changes in energy and protein metabolism. Overall, 3% DM of lipid supplementation over 63 days can be used in dairy cow diets without major impacts on global bacterial community structure.
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Zhang K, Qian Q, Mao Y, Xu Y, Yang Y, Chen Y, Wang X. Characterization of growth phenotypes and gastrointestinal tract microbiota in sheep fed with caragana. J Appl Microbiol 2021; 131:2763-2779. [PMID: 33998744 DOI: 10.1111/jam.15138] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/22/2021] [Accepted: 05/10/2021] [Indexed: 01/15/2023]
Abstract
AIMS Using high-protein caragana as an unconventional feed supplement has promising application potential in livestock feeding programmes, and verifying its function is of great importance to guide efficient dietary management of livestock. METHODS AND RESULTS This study investigated the resulting changes in the growth, slaughter performance, serum physiological index, physical and chemical characteristics of meat, ruminal and intestine morphology and gastrointestinal tract microbiota in sheep fed with caragana (CAR), corn straw (COR) and alfalfa (ALF) diets. The CAR group showed an increased abundance of Christensenellaceae R-7 group, Marvinbryantia, Ruminococcaceae NK4A214, Lachnospiraceae UCG-002 and Desulfuromonas in the rumen compared with ALF, and CAR group mainly enhanced starch and sucrose metabolism, fructose and mannose metabolism, photosynthesis and d-alanine metabolism in the rumen compared with ALF. CONCLUSIONS CAR diet positively changed the fatty acid profile of longissimus dorsi muscle and significantly altered the composition and function of the microbiota in the rumen, ileum and cecum. SIGNIFICANCE AND IMPACT OF THE STUDY This study systematically demonstrated the feasibility of CAR as an alternative to ALF for animal fattening in a complete formula granulated feed and provided a fundamental basis for further research and development of CAR as an unconventional feed source for ruminants.
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Affiliation(s)
- K Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Q Qian
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Y Mao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Y Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Y Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Y Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - X Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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