Clostridioides difficile infection (CDI) has been recognized as a leading cause of healthcare-associated infections and a considerable threat to public health globally. Increasing evidence suggests that the gut microbiota plays a key role in the pathogenesis of CDI. The taxonomic composition and functional capacity of the gut microbiota associated with CDI have not been studied systematically. Here, we performed a comprehensive shotgun metagenomic sequencing in a well-characterized human cohort to reveal distinct patterns of gut microbiota and potential functional features associated with CDI. Fecal samples were collected from 104 inpatients, including : (1) patients with clinically significant diarrhea and positive nucleic acid amplification testing (NAAT) and received CDI treatment (CDI, n = 47); (2) patients with positive stool NAAT but without diarrhea (Carrier, n = 17); (3) patients with negative stool NAAT but with diarrhea (Diarrhea, n = 14); and (4) patients with negative stool NAAT and without diarrhea (Control, n = 26). Downstream statistical analyses (including alpha and beta diversity analysis, differential abundance analysis, correlation network analysis, and potential functional analysis) were then performed. The gut microbiota in the Control group showed higher Chao1 index (p < 0.05), while Shannon index at KEGG module level was higher in CDI than in Carrier and Control (p < 0.05). Beta diversity for species composition differed significantly between CDI vs Carrier/Control cohorts (p < 0.05). Microbial Linear discriminant analysis Effect Size and ANCOM analysis both identified 8 species (unclassified_f_Enterobacteriaceae, Veillonella_parvula, unclassified_g_Klebsiella and etc.) were enriched in CDI, Enterobacter_aerogenes was enriched in Diarrhea, Collinsella_aerofaciens, Collinsella_sp_4_8_47FAA, Collinsella_tanakaei and Collinsella_sp_CAG_166 were enriched in Control (LDA >3.0, adjusted p < 0.05). Correlation network complexity was higher in CDI with more negative correlations than in other three cohorts. Modules involved in iron complex transport system (M00240) was enriched in CDI, ABC-2 type transport system (M00254), aminoacyl-tRNA biosynthesis (M00359), histidine biosynthesis (M00026) and inosine monophosphate biosynthesis (M00048) were enriched in Carrier, ribosome (M00178 and M00179) was enriched in Diarrhea, fluoroquinolone resistance (M00729) and aminoacyl-tRNA biosynthesis (M00360) were enriched in Control (LDA > 2.5, adjusted p < 0.05). Resistance functions of acriflavine and glycylcycline were enriched in CDI, while resistance function of bacitracin was enriched in Carrier (LDA > 3.0, adjusted p < 0.05), and the contributions of phylum and species to resistance functions differed among the four groups. Our results reveal alterations of gut microbiota composition and potential functions among four groups of differential colonization/infection status of Clostridioides difficile. These findings support the potential roles of gut microbiota and their potential functions in the pathogenesis of CDI.

This review explores the emerging term "gut-skin axis" (GSA), describing the bidirectional signaling that occurs between the skin and the gastrointestinal tract under both homeostatic and disease conditions. Central to GSA communication are the gut and skin microbiota, the microbial communities that colonize these barrier surfaces. By influencing diverse host pathways, including innate immune, vitamin D receptor, and Aryl hydrocarbon receptor signaling, a balanced microbiota contributes to both tissue homeostasis and host defense. In contrast, microbiota imbalance, or dysbiosis at one site, can lead to local barrier dysfunction, resulting in the activation of signaling pathways that can disrupt tissue homeostasis at the other site, potentially leading to inflammatory skin conditions such as atopic dermatitis and psoriasis, or gut diseases like Inflammatory Bowel Disease. To date, most research on the GSA has examined the impact of the gut microbiota and diet on skin health, but recent studies show that exposing the skin to ultraviolet B-light can beneficially modulate both the gut microbiome and intestinal health. Thus, despite the traditional focus of clinicians and researchers on these organ systems as distinct, the GSA offers new opportunities to better understand the pathogenesis of cutaneous and gastrointestinal diseases and promote health at both sites.

Restriction of dietary carbohydrates, fat and/or protein is often used to reduce body weight and/or treat (metabolic) diseases. Since diet is a key modulator of the human gut microbiome, which plays an important role in health and disease, this review aims to provide an overview of current knowledge of the effects of macronutrient-restricted diets on gut microbial composition and metabolites. A structured search strategy was performed in several databases. After screening for inclusion and exclusion criteria, thirty-six articles could be included. Data are included in the results only when supported by at least three independent studies to enhance the reliability of our conclusions. Low-carbohydrate (<30 energy%) diets tended to induce a decrease in the relative abundance of several health-promoting bacteria, including Bifidobacterium, as well as a reduction in short-chain fatty acid (SCFA) levels in faeces. In contrast, low-fat diets (<30 energy%) increased alpha diversity, faecal SCFA levels and abundance of some beneficial bacteria, including Faecalibacterium prausnitzii. There were insufficient data to draw conclusions concerning the effects of low-protein (<10 energy%) diets on gut microbiota. Although the data of included studies unveil possible benefits of low-fat and potential drawbacks of low-carbohydrate diets for human gut microbiota, the diversity in study designs made it difficult to draw firm conclusions. Using a more uniform methodology in design, sample processing and sharing raw sequence data could foster our understanding of the effects of macronutrient restriction on gut microbiota composition and metabolic dynamics relevant to health. This systematic review was registered at https://www.crd.york.ac.uk/prospero as CRD42020156929.

The gut microbiome supports both gut and overall health. Diet is known to be one of the driving factors that influences the gut microbiome. The foods we eat, the dietary and nondietary components they contain, various food consumption patterns, and the ratio of nutrients consumed have been shown to impact gut microbiome composition and function. Studies indicate that many acute and chronic diseases are associated with alterations to the gut microbiome. There are many patients who rely on enteral tube feeding for their nutrition support. More recently, enteral tube feeding formulations of "real food" have become commercially available. However, little is known about how enteral tube feeding impacts the gut microbiome in patients requiring this specialized form of nutrition therapy. This review summarizes the existing evidence regarding the food sources of commonly consumed macronutrients and their impact on the gut microbiome. Also presented is what is known regarding "standard" and real food enteral formulations on the gut microbiome. Existing evidence is suggestive that real food enteral formulations positively impact the gut microbiome. Still, more research is needed on ready-to-feed formulations, particularly in patients with various clinical conditions, and how gut microbiome modulation impacts clinical outcomes.

The gut microbiota constitutes a complex ecosystem essential for host health, offering metabolic support, modulating the immune system, and protecting against pathogens. However, this community faces constant destabilizing challenges, including dietary changes, antibiotics, and enteric infection. Prolonged microbiota imbalance or dysbiosis can exacerbate intestinal disease states, including inflammatory bowel disease and colorectal cancer. Understanding the mechanisms that sustain microbiota resilience in the face of these imbalances is crucial for maintaining host health and developing effective therapeutics. This review explores microbiota resilience through the lens of an ecological model, emphasizing the interplay between microbial communities and host-driven environmental controls. We highlight two critical factors shaping microbiota resilience: oxygen tension and iron availability-challenges encountered by ancient anaerobic organisms during early evolutionary history, from which the predominant members of the microbiota have descended. Disruptions in intestinal anaerobiosis during inflammation increase luminal oxygen levels, favoring pro-inflammatory facultative anaerobes and depleting obligately anaerobic commensals. Simultaneously, host nutritional immunity restricts iron availability, further challenging commensal survival. This dual environmental challenge of rising oxygen tension and reduced iron availability is a convergent outcome of a diverse array of perturbations, from pathogen invasion to antibiotic treatment. By highlighting these conserved downstream environmental challenges rather than the specific upstream perturbations, this ecological view offers a focused framework for understanding microbiota resilience. This perspective not only enhances our understanding of host-microbiota interactions but also informs therapeutic strategies to foster resilience and support host health.

The Qinghai-Tibetan Plateau (QTP) offers one of the most extreme environments for yaks (Bos grunniens). The yak is an indigenous species, and the wild yak was domesticated on the QTP. The gut microbiota plays a vital role in health and animal performance. However, little is known about the progression of gut microbes in different age developmental stages of domesticated yaks.

We used the 16 S rRNA gene sequencing method to explore the progression of the fecal bacterial microbiota of 18 different confined domestic yaks at two developmental stages: 3 to 5 years (GT35) and 6 to 8 years (GT68).

We found significant differences in gut bacterial communities between the two age groups. The diversity of the gut bacterial community was significantly lower in the GT35 group, which reached stability with age. Bacteroidetes and Firmicutes were the two dominant phyla between the two age groups. Phylum Firmicutes was significantly higher in the GT68 group, and Proteobacteria, Spirochaetes, Tenericutes, and Actinobacteria were highly abundant in the GT35 age group. Genera Bacteroides, Alloprevotella, and Anaerovibrio were abundant in the GT35 group. The short-chain fatty acid (SCFA) producing bacteria Rikenellaceae showed higher abundance in GT35. The core bacterial microbiota of the GT68 age group was dominated by Ruminococcaceae and Rikenellaceae. The gut bacterial community has a great variation between the groups. Based on the exploration of dynamic changes in the gut bacterial community at different ages, our results illustrate that yaks undergo a process of reaching stability and maturity as they age.

A wide variety of human diseases are associated with loss of microbial diversity in the human gut, inspiring a great interest in the diagnostic or therapeutic potential of the microbiota. However, the ecological forces that drive diversity reduction in disease states remain unclear, rendering it difficult to ascertain the role of the microbiota in disease emergence or severity. One hypothesis to explain this phenomenon is that microbial diversity is diminished as disease states select for microbial populations that are more fit to survive environmental stress caused by inflammation or other host factors. Here, we tested this hypothesis on a large scale, by developing a software framework to quantify the enrichment of microbial metabolisms in complex metagenomes as a function of microbial diversity. We applied this framework to over 400 gut metagenomes from individuals who are healthy or diagnosed with inflammatory bowel disease (IBD). We found that high metabolic independence (HMI) is a distinguishing characteristic of microbial communities associated with individuals diagnosed with IBD. A classifier we trained using the normalized copy numbers of 33 HMI-associated metabolic modules not only distinguished states of health vs IBD, but also tracked the recovery of the gut microbiome following antibiotic treatment, suggesting that HMI is a hallmark of microbial communities in stressed gut environments.

The fruit fly Drosophila melanogaster is a vital model for studying the microbiome due to the availability of genetic resources and procedures. To understand better the importance of microbial composition in shaping immune modulation, we can investigate the role of the microbiota through parasitic infection. For this, we use entomopathogenic nematodes (EPN) of the genus Steinernema which exhibit remarkable ability to efficiently infect a diverse array of insect species, facilitated by the mutualistic bacteria Xenorhabdus found within their gut. To examine the microbiome changes in D. melanogaster larvae in response to Steinernema nematode infection, D. melanogaster late second to early third instar larvae were exposed separately to S. carpocapsae and S. hermaphroditum infective juveniles. We have found that S. carpocapsae infective juveniles are more pathogenic to D. melanogaster larvae compared to the closely related S. hermaphroditum. Our microbiome analysis also indicates substantial changes in the size and composition of the D. melanogaster larval microbiome during infection with either nematode species compared to the uninfected controls. Our results serve as a foundation for future studies to elucidate the entomopathogenic-specific effector molecules that alter the D. melanogaster microbiome and understand the role of the microbiome in regulating insect anti-nematode immune processes.

The interplay among antibiotics, gut microbiota, and disease pathogenesis remains poorly understood, particularly in the context of rare gut bacteria. This study identifies a novel correlation between erythromycin-induced stress and the production of antiangiogenic metabolites in Aneurinibacillus aneurinilyticus, a human gut bacterium. We report the isolation and structural characterization of aneuristatin (1), a metabolite featuring a unique pyrrolo[1,2-a]pyrazine scaffold, along with seven structurally related metabolites (2-8) from A. aneurinilyticus ATCC 12856T. These metabolites were upregulated via the erythromycin-induced activation of the arnA biosynthetic gene. Aneuristatin (1) enhanced prolyl hydroxylase activity, promoting hypoxia-inducible factor-1α (HIF-1α) degradation and reducing downstream targets, including VEGF and EPO. It also exhibited antioxidant effects by reducing ROS levels under hypoxia. Additionally, it inhibited angiogenesis in HUVECs and zebrafish and effectively reduced inflammation, fibrosis, and angiogenesis in a mouse corneal injury model. Our study establishes a molecular basis for the potential of erythromycin-induced aneuristatin (1) to prevent or treat angiogenesis-related diseases such as cancer.

The role of Blastocystis, a common intestinal parasitic protist of humans and other animals, in human health and disease remains elusive. Recent studies suggest a connection between Blastocystis colonization, healthier lifestyles, and high-diversity gut microbiota. Nevertheless, studies concerning the relationship between Blastocystis colonization, its intensity, and gut microbiota composition -involving both bacterial and eukaryotic communities- remain limited.

This study examines the impact of Blastocystis carriage and colonization intensity on gut microbiota composition in a rural community in Colombia. A total of 88 human samples were collected from the rural population of Las Guacas village, located in the Cauca department in southwest Colombia. We utilized 16S and 18S rDNA sequencing to analyze both bacterial and eukaryotic microbiota, comparing Blastocystis-positive and -negative individuals, as well as groups with varying Blastocystis colonization intensity (low, medium, high), to identify distinct microbiota profiles and differentially abundant taxa linked to each condition.

The analysis revealed significant differences between Blastocystis-positive and -negative individuals. In terms of bacterial composition and structure, Blastocystis-positive individuals exhibited distinct microbiota profiles, as shown by beta diversity analysis. Taxa associated with colonization included Bacteroides, Prevotella, Oscillibacter, Faecalibacterium, and Alistipes. Higher Blastocystis colonization intensity was associated with an increased abundance of taxa such as Alistipes and Lachnospira, while lower intensities correlated with beneficial bacteria such as Akkermansia. Regarding eukaryotic composition, beta diversity analysis revealed distinct profiles associated with Blastocystis colonization. Differentially abundant taxa, including Entamoeba coli, were more prevalent in Blastocystis-positive individuals, while Blastocystis-negative individuals exhibited a higher abundance of opportunistic fungi, such as Candida albicans. Machine learning models, including random forest classifiers, supported these findings, identifying Faecalibacterium and Bacteroides as predictors of Blastocystis colonization.

These findings suggest that Blastocystis may modulate gut microbiota, contributing to microbial balance providing new insights into the ecological implications of Blastocystis in rural populations.

Ionic liquids (ILs), which are expanding produced and applied as alternatives to volatile organic solvents, have shown the ability to deteriorate the anaerobic biotransformation of organics. It is unclear, nevertheless, how ILs affect different functional anaerobes during anaerobic digestion, leaving a knowledge gap in the environmental risks of ILs. Here, we revealed that the differences of Gram-staining bacteria probably were the part drivers of a shift in methanogenic pathway from acetoclastic to hydrogenotrophic methanogenesis in anaerobic microcosms exposed to a typical IL (Tetrakis (hydroxymethyl) phosphonium chloride, [P(CH2OH)4]Cl). The results showed that 0.1-4 mg/L [P(CH2OH)4]Cl respectively decreased methane production rate and carbon-use efficiency by 4.43-43.90 % and 0.52-57.23 % during anaerobic digestion. Microbial community and microscopic examination analysis indicated that most Gram-positive bacteria were more likely to survive in the [P(CH2OH)4]Cl-present environment than Gram-negative bacteria. Mechanistically, [P(CH2OH)4]Cl distorted cell walls of anaerobes, and then perturbed protein homeostasis in the periplasm by breaking disulfide bonds and disrupting disulfide-bond-forming pathways. Moreover, Gram-positive bacteria exhibited a higher tolerance than Gram-negative bacteria, potentially due to their thicker peptidoglycan structures and reliance less on disulfide bonds to stabilize proteins, leading to the remodeling of microbiome function and carbon-transport pathway. This study is the first to reveal the differential impact of [P(CH2OH)4]Cl on Gram-positive vs. Gram-negative anaerobes during methanogenesis, providing new insights into the ecological risks of ILs and contributing to their optimal design.

The relatively limited availability of genetic tools has hampered mechanistic studies of Bacteroides fragilis, an opportunistic anaerobe that constitutes 1%-5% of the gut microbiota in healthy humans. Here we describe novel vectors for B. fragilis gene deletion and expression as well as a semi-defined media for cultivation of B. fragilis str. P207.

This study aims to evaluate the concordance between the disc diffusion test (DDT) and custom-designed Sensititre® Broth Microdilution plates and to estimate their respective sensitivity (Se) and specificity (Sp) for antimicrobial susceptibility testing (AST) of Bacteroides fragilis group (BFG) clinical isolates.

AST was performed on 126 BFG isolates using both DDT and Sensititre® methods according to the 2024 CA-SFM guidelines. Cohen's kappa coefficients were used to assess concordance, while a Bayesian approach estimated Se and Sp with 95% confidence intervals (95% CIs) for amoxicillin-clavulanate (AMC), piperacillin-tazobactam (PTZ), imipenem (IPM), clindamycin (CLI), metronidazole (MTR), and moxifloxacin (MXF).

Cohen's kappa coefficients with 95% CIs for AMC, PTZ, IPM, CLI, MTR, and MXF were 0.92 (0.85-1.00), 0.70 (0.56-0.83), 0.96 (0.92-1.00), 0.98 (0.94-1.00), 0.96 (0.89-1.00), and 0.70 (0.58-0.82), respectively. DDT demonstrated Se > 0.8 for all antibiotics, and Sp > 0.8 except for PTZ (0.51; 0.37-0.65) and CLI (0.71; 0.58-0.82). Sensititre® exhibited Se > 0.9 for all antibiotics except for PTZ (0.86; 0.70-0.99), and Sp > 0.9 except for MXF (0.88; 0.75-0.99).

DDT and Sensititre® Broth Microdilution demonstrated strong concordance for most antibiotics. Predictive values estimated using Bayesian model showed that Sensititre® offered the highest overall Se and Sp.

Intestinal transit time has been recognized as an important factor in shaping the gut microbiota, although causality remains to be firmly demonstrated. The aim of this study was to evaluate the effect of different loperamide doses on the mouse intestinal transit time and to investigate the effects of increasing transit time on the gut microbial community. Loperamide significantly increased the transit time in a dose-dependent manner. Additionally, we observed a significant difference between the control group and the loperamide-treated groups in the abundance of the bacterial families Bacteroidaceae, Erysipelotrichaceae, Porphyromonadaceae, and Akkermansiaceae after 7 days of loperamide treatment, with the bacterial families responding to the increased transit time at different rates. Fermentation of faeces obtained from the same mice, with or without loperamide, demonstrated that the observed effects on gut microbiota in vivo were not a result of direct interactions between loperamide and the gut microbiota but rather a consequence of loperamide-induced increased intestinal transit time. In the cecum of the mice, we found higher levels of propionate in the high-dose group compared to the control and low-dose groups. Collectively, our findings establish that an altered transit time is causal to changes in the composition and activity of the microbiome.

Chitosan, is a natural bio-based polymer with known prebiotic properties. However, its potential in the management of spermatogenic disorders remains largely unexplored. By utilizing a busulfan-treated mouse model and integrated multi-omics analysis, this study explored the potential mechanisms through which chitosan improves impaired spermatogenesis. The results showed that chitosan treatment can improve testicular function and significantly reshape the gut microbiota composition in busulfan-treated mice. Metabolomics revealed that docosahexaenoic acid (DHA) transport was significantly dysregulated in busulfan-treated mice, but chitosan reversed this dysfunction by modulating tight junction proteins and fatty acid transporters in the intestine. Fecal microbiota transplantation experiments further highlighted the critical role of gut microbiota in DHA transport and spermatogenesis. Additionally, DHA supplementation alleviated busulfan-induced ferroptosis in testicular tissues. Hence, owing to its prebiotic effects chitosan could serve as a novel therapeutic strategy for improving busulfan-induced spermatogenic disorders by restoring the homeostasis of the gut-testis axis.

The gut microbiota is amenable to early nutrition including micronutrients but intake above and below the recommendations commonly occur with unknown consequences. Serotonin (5-hydroxytryptamine [5-HT]) is a monoamine found centrally and peripherally with diverse functions such as food intake regulation via the hypothalamic 5-HT receptor 2C (5-HTR2C). This study determined the impact of prenatal micronutrients on the gut microbiota and serotonergic system in offspring. Pregnant Wistar rats were fed either recommended vitamins (RV), high vitamins (HV), high folic acid with recommended choline (HFRC), or high folic acid with no choline (HFNC). Offspring were fed a high-fat diet for 12 weeks postweaning. HV, HFRC, and HFNC males and females had lower hypothalamic 5-HTR2C protein expression compared to RV. Brain 5-HT concentrations were lower but colon 5-HT concentrations were higher in HV and HFNC males and females and HFRC males compared to RV. Refeeding response after 5-HTR2C agonist was negatively correlated with hypothalamic 5-HTR2C protein expression in males and with brain 5-HT concentrations in females. Random forest revealed top bacterial taxa, which Lactococcus, Ruminococcus, Bacteroides, and Oscillospira showed significant correlations with refeeding response and concentrations of brain and colon 5-HT. In conclusion, excess or imbalanced prenatal consumption of micronutrients leads to gut microbiota-associated disturbances in the serotonergic system in offspring.

Ochratoxin A (OTA) is a toxic fungal secondary metabolite that triggers liver inflammation in animals. OTA could disrupt intestinal microbiota balance by promoting Gram-negative bacteria growth and activating the Toll-like receptor 4 (TLR4)/Nuclear factor-kappa B (NF-κB) signaling pathway, thereby inducing liver inflammation. Ginsenoside Rg1 (Rg1) is an active component of ginseng, exhibits anti-inflammatory, antibacterial, and antioxidative properties, particularly against gram-negative bacteria. Rg1 has been shown to maintain intestinal microbiota homeostasis and inhibit the TLR4 signaling pathway to alleviate liver inflammation. Given these established mechanisms, the aim of this study was to explore the preventive effect of Rg1 in countering OTA-induced liver inflammation through modulation of intestinal microbiota and the TLR4/NF-κB signaling pathway. The results revealed that Rg1 reduced OTA residues in the cecum and enhanced intestinal barrier function. Moreover, Rg1 ameliorated the intestinal microbiota composition in OTA-treated ducklings by decreasing the relative abundance of lipopolysaccharide (LPS)-related bacteria. Rg1 also increases the abundance of short-chain fatty acid (SCFA)-producing bacteria. Additionally, Rg1 supplementation with OTA decreased the accumulation of LPS in tissues and inhibited the TLR4/NF-κB signaling pathway. Intriguingly, Rg1 maintained its beneficial effects in OTA-treated ducklings even after antibiotic treatment by inhibiting the TLR4/NF-κB pathway. These findings emphasized the importance of intestinal microbiota homeostasis and TLR4/NF-κB pathway suppression in the anti-inflammatory action of Rg1 during OTA-induced liver inflammation.

BackgroundProbiotics, as common regulators of the gut microbiota, have been used in research to alleviate clinical symptoms of atopic dermatitis (AD).ObjectiveOur research team has previously identified a potential relieving effect of Clostridium butyricum on the treatment of AD, but the specific mechanism of how Clostridium butyricum alleviates AD has not yet been confirmed.MethodsIn this study, we explored the relieving effect of Clostridium butyricum on AD through in vivo and in vitro experiments. AD mice induced by 2,4-dinitrofluorobenzene (DNFB) were orally administered with 1 × 108 CFU of Clostridium butyricum for three consecutive weeks.ResultsOral administration of Clostridium butyricum reduced ear swelling, alleviated back skin lesions, decreased mast cell and inflammatory cell infiltration, and regulated the levels of inflammation-related cytokines. Clostridium butyricum activated the intestinal immune system through the TLR4/MyD88/NF-κB signaling pathway, suppressed the expression of inflammatory factors IL-10 and IL-13, and protected the damaged intestinal mucosa.ConclusionClostridium butyricum administration improved the diversity and abundance of the gut microbiota, enhanced the functionality of the immune system, and protected the epidermal barrier.

The weaning period is a critical phase for nursery pigs that is characterized by rapid growth and alterations in the intestinal microbiome associated with nutrient utilization. The present study aimed to investigate the efficacy of halquinol, when used as an antibiotic (ABO), on the growth performance, diarrhea incidence, coefficient of apparent total tract digestibility (CATTD), fecal volatile fatty acids (VFAs), and microbiota in pigs. A total of 210 healthy weaned pigs with an average initial weight of 6.9 kg and aged 28 ± 2 days were assigned to five treatments (six pens/treatment) in a complete randomized design, including a control group (T1, CON; feed with no ABO), a colistin group (T2, CLT; feed containing 120 ppm colistin), and three halquinol groups (T3 to T5, HAL; feed containing 180, 240, and 360 ppm halquinol, respectively). The experiment period lasted for 10 days. Field recordings, observation, and feces collection were performed on D1, D5, and D10. CATTD and VFA assessments were conducted on D10. The composition of the fecal microbiota was analyzed via 16S rRNA gene sequencing using the Illumina Miseq platform. The results demonstrated that the in-feed ABO groups exhibited a significantly lower ADFI (p < 0.01). Pigs fed the T3 and T4 diets had the lowest FCR (p < 0.01) on D5 and D10 and, thus, had reduced ADFI (p < 0.01). A quadratic contrast was found in ADFI and FCR on D5 and D10, indicating a negative correlation with HAL concentration (p < 0.01). Pigs fed CLT and HAL had significantly reduced levels of coliform (p < 0.01) and E. coli (p < 0.01). Moreover, pigs receiving ABO also had a lower fecal score compared to those on the CON diet (p < 0.01). Dietary in-feed ABO had no effect on all the parameters of the CATTD on D10 (p > 0.05), except for fat digestibility in pigs that received T4 (p < 0.01). Pigs fed the T4 and T5 diets had higher propionate concentrations and lower A/P ratios than pigs fed T1, T2, and T3 (p < 0.01). The microbial diversity shifted quickly through the early weaning period. The relative abundance of beneficial Enterococcus microbes increased in pigs fed in-feed ABO, whereas the relative prevalence of pathogenic bacteria, such as Escherichia and Klebsiella, decreased. Escherichia and Bacteroides were negatively correlated with carbohydrate digestibility and butyric and valeric acid production (p < 0.05). Overall, the appropriate HAL dosage was 240 ppm (T4), and this antimicrobial can potentially be characterized as an in-feed colistin replacer that improves feed efficiency and fat digestion, enhancing VFA production, alleviating post-weaning diarrhea, and protecting ABO-resistant piglets.

The gut microbiome contributes to chronic inflammatory responses in ulcerative colitis (UC), but molecular mechanisms and disease-relevant effectors remain unclear. Here we analyze the pro-inflammatory properties of colonic fluid obtained during colonoscopy from UC and control patients. In patients with UC, we find that the pelletable effector fraction is composed mostly of bacterial extracellular vesicles (BEVs) that exhibit high IgA-levels and incite strong pro-inflammatory responses in IgA receptor-positive (CD89+) immune cells. Biopsy analyses reveal higher infiltration of CD89+ immune cells in the colonic mucosa from patients with UC than control individuals. Further studies show that IgA-coated BEVs, but not host-derived vesicles nor soluble IgA, are potent activators of pro-inflammatory responses in CD89+ cells. IgA-coated BEVs also exacerbate intestinal inflammation in a dextran sodium sulfate colitis model using transgenic mice expressing human CD89. Our data thus implicate a link between IgA-coated BEVs and intestinal inflammation via CD89+ immune cells, and also hint a potential new therapeutic target for UC.

End-stage liver disease is associated with disruptions in gut microbiota composition and function, which may facilitate gut-to-liver bacterial translocation, impacting liver graft integrity and clinical outcomes following liver transplantation. This study aimed to assess the impact of two liver graft preservation methods on fecal microbiota and changes in fecal and breath organic acids following liver transplantation.

This single-center, non-randomized prospective pilot study enrolled liver transplant patients whose grafts were preserved using either static cold storage or ex situ normothermic machine perfusion (NMP). Fresh stool and breath samples were collected immediately before surgery and at postoperative months 3, 6, and 12. Stool microbiota was profiled via 16S rRNA gene sequencing, stool short-chain fatty acids were measured using gas chromatography/-mass spectrometry, and breath volatile organic compounds (VOCs) were analyzed with selected-ion flow-tube mass spectrometry.

Both cohorts experienced a loss of microbiota diversity and dominance by single taxa. The NMP cohort demonstrated enrichment of several beneficial gut taxa, while the static cold storage cohort showed depletion of such taxa. Various gut bacteria were found to correlate with stool short-chain fatty acids (e.g., lactic acid, butyric acid) and several VOCs.

Fecal microbiota alterations associated with end-stage liver disease do not fully normalize to a healthy control profile following liver transplantation. However, notable differences in microbiota composition and function were observed between liver graft preservation methods. Future research with larger randomized cohorts is needed to explore whether the NMP-associated shift in gut microbiota impacts clinical outcomes and if breath VOCs could serve as biomarkers of the clinical trajectory in liver transplant patients.

The increasing global prevalence of inflammatory diseases, such as ulcerative colitis and irritable bowel syndrome, represents a challenging task for healthcare systems. Several approaches to disease management target the intestinal microbiome, which plays a key role in health and disease. One promising approach is modulating the microbiome using human milk oligosaccharides (HMOs). Originating from human milk, HMOs are indigestible carbohydrates that act in a host-optimized prebiotic fashion by providing an energy source for health-promoting intestinal bacteria and exhibiting systemic effects. Commercial products supporting infant health and development have been the primary fields of HMO application. Advancements in the large-scale production of HMOs through bioengineering and precision fermentation have led to evaluation of their potential for managing inflammatory diseases. Several in vitro studies and observations on model systems have been clinically validated in infants, resulting in a large body of evidence supporting the safety and efficacy of HMOs in inflammatory disorders. Although novel approaches seek to explore interventions in adults, the primary goal for the future is to provide cost-efficient, safe, and reliable healthcare compounds across all age groups.

Emerging evidence suggests that changes in the blood microbes might be associated with cardiovascular disease, especially myocardial infarction (MI). However, some researchers are questioning whether a true "blood microbiome" actually exists. They hypothesized that these microbes may translocate into the bloodstream from the gut or oral cavities. To test this hypothesis, we analyzed the microbial composition, diversity, and potential role in disease progression by comparing blood, gut, and oral microbiota profiles in a cohort of MI patients and healthy controls.

In this study, 144 samples, including blood, fecal, and saliva, were collected from twenty-four myocardial infarction patients and twenty-four healthy controls. These samples were analyzed using 16 S rRNA sequencing to characterize the microbial profiles across the three distinct microbial compartments. Differential analyses were conducted to find key differential microbiota for MI. Spearman's rank correlation analysis was used to study the association between microbiota and clinical indicators.

Our findings revealed striking microbial shifts across blood, gut, and oral compartments in MI patients compared to healthy controls. In the blood, we observed significant enrichment of the phyla Armatimonadota and Caldatribacteriota, alongside the genera Bacillus, Pedobacter, and Odoribacter. The gut microbiota of MI patients showed a notable increase in the phyla Proteobacteria, Verrucomicrobiota, Cyanobacteria, Synergistota, and Crenarchaeota, as well as the genera Eubacterium_coprostanoligenes_group, Rothia, Akkermansia, Lachnospiraceae_ NK4A136_ group, and Eubacterium_ruminantium_group. Meanwhile, the oral microbiota of MI patients was uniquely enriched with the phylum Elusimicrobiota and the genera Streptococcus, Rothia, and Granulicatella. These distinct microbial signatures highlight compartment-specific alterations that may play a role in the pathophysiology of MI. Additionally, LEfSe analysis identified 64 distinct taxa that differed across the three compartments. Of these, eight taxa were unique to blood, eighteen to the gut, and thirty-eight to the oral microbiota, all of which demonstrated significant associations with clinical markers of MI. Functional pathways were predicted and analyzed via KEGG annotation, but no statistically significant differences were found between MI patients and healthy controls in any of the microbiome compartments.

This study demonstrates significant alterations in the blood, gut, and oral microbiome profiles of MI patients, identifying specific bacterial taxa strongly associated with key markers of myocardial infarction. The unique microbial patterns detected in the blood provide compelling evidence for the existence of a stable core blood microbiome, highlighting its importance as a key contributor to cardiovascular health and disease progression.

Traditional Chinese Medicine (TCM) theory posits a close relationship between an individual's constitutional types and the overall health. Variations in metabolic processes and microbial composition have been observed across different constitution types. This study aims to explore the relationship between TCM constitutions, intestinal flora, and metabolites to devise personalized TCM treatment strategies, enhancing evidence-based guidance for clinical practice.

The research investigated differences in microbial diversity and composition among three TCM constitution types: yin-deficiency constitution (PA), balanced constitution (PH), and yang-deficiency constitution (PI). A significant elevation of the Chao1 metric was noted in the PH group compared to the PI group.

PCoA and CPCoA analyses demonstrated distinct group separation based on floral samples. Dominant phyla included Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Fusobacteria, with varying abundance at the genus level. Metabolic pathway analysis unveiled disparities in metabolites associated with different pathways among constitution groups. KEGG pathway enrichment analysis emphasized pathways such as steroid hormone biosynthesis, ovarian steroidogenesis, and tryptophan metabolism. Furthermore, correlation analysis revealed associations between specific bacterial taxa and metabolites.

This study delineated the variations in intestinal flora and metabolic profiles among individuals with PA, PH, and PI constitution types, providing valuable insights for the development of personalized TCM treatment approaches.

Dysbiosis of the microbiome correlates with many neurological disorders, yet very little is known about the chemistry that controls the production of neuromodulatory molecules by gut microbes. Here, we found that an enzyme glutamate decarboxylase (BfGAD) of a gut microbe Bacteroides fragilis forms multiple neuromodulatory molecules such as γ-aminobutyric acid (GABA), hypotaurine, taurine, homotaurine, and β-alanine. We evolved BfGAD and doubled its taurine productivity. Additionally, we increased its specificity toward the substrate L-glutamate. Here, we provide a chemical strategy via which the BfGAD activity could be fine-tuned. In future, this strategy could be used to modulate the production of neuromodulatory molecules by gut microbes.

Microbial succession during postnatal gut development in mice is likely impacted by site of sampling, time, intestinal injury, and host genetics. We investigated this in wild-type and Sigirr transgenic mice that encode the p.Y168X mutation identified in a neonate with necrotizing enterocolitis (NEC). Temporal profiling of the ileal and colonic microbiome after birth to weaning revealed a clear pattern of progression from a less diverse, Proteobacteria/Escherichia_Shigella dominant community to a more diverse, Firmicutes/Bacteroidetes dominant community. Formula milk feeding, a risk factor for necrotizing enterocolitis, decreased Firmicutes and increased Proteobacteria leading to enrichment of bacterial genes denoting exaggerated glycolysis and increased production of acetate and lactate. Sigirr transgenic mice exhibited modest baseline differences in microbiota composition but exaggerated formula feeding-induced dysbiosis, mucosal inflammation, and villus injury. Postnatal intestinal microbiota succession in mice resembles human neonates and is shaped by developmental maturity, ileal vs. colonic sampling, formula feeding, and Sigirr genotype.

Liver abscesses in cattle reduce animal performance, increase the environmental footprint of beef production, and cause significant economic losses. The low pH of the rumen resulting from the consumption of high grain diets damages the rumen epithelium and facilitates the translocation of opportunistic pathogens from the gastrointestinal tract into the bloodstream where they can colonize the liver, causing infection. Recently, 16s rRNA sequencing has revealed that 25%-50% of liver abscess microbiomes have prominent levels of Bacteroides. Due to the inability to reliably classify amplicon sequences beyond the genus level, the identity of these microbes remains unknown. We have employed a combination of culture-independent and culture-based methods to isolate and identify the Bacteroides associated with liver abscesses in cattle. Shotgun metagenomic sequencing and assembly of metagenome-assembled genomes generated four high-quality genomes, two of which were putatively identified as Bacteroides. These microbes were subsequently isolated from the purulent material of liver abscesses. Whole-genome sequencing conclusively identified these isolates as Bacteroides pyogenes and a previously unknown species of Bacteroides, revealing distinct differences from Bacteroides typically found in the gut. Carbohydrate utilization assays revealed that both organisms metabolize glycogen and glycosaminoglycans found in the extracellular matrix of the liver but display differences in substrate specificity. These data not only identify Bacteroides found in bovine liver abscesses but also provide new insights into the potential role that these organisms may play in this production-limiting disease.

Liver abscesses (LAs) are commonly found in cattle raised in feedlots and result from a bacterial infection of the liver. Not only are LAs a concern for animal health, but they also impact growth efficiency, animal welfare, and cost the North American beef industry upwards of $120 million per annum. Recently, it has been found that 25%-50% of liver abscess microbiomes have prominent levels of Bacteroides; however, to date, the biological relevance in LA pathogenesis and the identity of these bacteria are unknown. This research describes the isolation, identification, and genomic characterization of the Bacteroides found in bovine liver abscesses. These data provide a critical foundation for expanding our knowledge of the potential role Bacteroides play in liver abscess development and could contribute to the identification of novel targets for developing treatments to prevent this important production-limiting disease.

Testing differences in mean vectors is a fundamental task in the analysis of high-dimensional microbiome compositional data. Existing methods may suffer from low power if the underlying signal pattern is in a situation that does not favor the deployed test. In this work, we develop 2-sample power-enhanced mean tests for high-dimensional compositional data based on the combination of $P$-values, which integrates strengths from 2 popular types of tests: the maximum-type test and the quadratic-type test. We provide rigorous theoretical guarantees on the proposed tests, showing accurate Type-I error rate control and enhanced testing power. Our method boosts the testing power toward a broader alternative space, which yields robust performance across a wide range of signal pattern settings. Our methodology and theory also contribute to the literature on power enhancement and Gaussian approximation for high-dimensional hypothesis testing. We demonstrate the performance of our method on both simulated data and real-world microbiome data, showing that our proposed approach improves the testing power substantially compared to existing methods.

Antioxidants are organic molecules that scavenge reactive oxygen species (ROS) and reactive nitrogen species (RNS), thereby maintaining cellular redox balance in living organisms. The human body synthesizes endogenous antioxidants, whereas humans obtain exogenous antioxidants from other organisms such as plants, animals, fungi, and bacteria. This review primarily focuses on the antioxidant potential of natural metabolites and extracts from five major bacterial phyla, including the well-studied Actinobacteria and Cyanobacteria, as well as less-studied Bacteroides, Firmicutes, and Proteobacteria. The literature survey revealed that the metabolites and the extracts with antioxidant activity can be obtained from bacterial cells and their culture supernatants. The metabolites with antioxidant activity include pigments, phycobiliproteins, polysaccharides, mycosporins-like amino acids, peptides, phenolic compounds, and alkaloids. Both metabolites and extracts demonstrate in vitro antioxidant capacity through radical-scavenging, metal-reducing, and metal-chelating activity assays. In in vivo models, they can scavenge ROS and RNS directly and/or indirectly eliminate them by enhancing the activities of antioxidant enzymes, such as catalase, superoxide dismutase, and glutathione peroxidase. Due to their antioxidant activities, they may find applications in the cosmetic industry as anti-aging agents for the skin and in medicine as drugs or supplements for combating oxidative stress-related disorders, such as neurodegenerative diseases and diabetes. The literature survey also elucidated that some metabolites and extracts with antioxidant activity also exhibited strong antimicrobial properties. Therefore, we consider that they may have future applications in the treatment of infectious diseases, the preparation of pathogen-free healthy foods, and the extension of food shelf life.

Bacteroides fragilis is one of the most frequently isolated pathogenic anaerobic bacteria. Infections caused by B. fragilis are commonly treated with carbapenems or tazobactam/piperacillin. However, there is no evidence for the optimal antibiotic choice against infections caused by B. fragilis as an empirical therapy owing to its varied antibiotic resistance mechanisms. Hence, we compared the effectiveness of carbapenems and tazobactam/piperacillin as an antibiotic therapy in patients infected with B. fragilis.

We investigated mortality, clinical and antimicrobial efficacy, and the percentage of patients who switched to broad-spectrum antibiotics, such as carbapenems or tazobactam/piperacillin, due to the aggravated symptoms of infection in patients receiving carbapenems or tazobactam/piperacillin from 2019 to 2024.

A total of 60 patients were included in the study; 24 patients received carbapenems and 36 received tazobactam-piperacillin as an empirical treatment against B. fragilis infections. None of the patients in either group died. Compared to carbapenem treatment, tazobactam/piperacillin treatment significantly improved inflammatory markers, including body temperature and C-reactive protein (45.8 % vs. 72.2 %, p = 0.039 and 37.5 % vs. 63.4 %, p = 0.045, respectively; carbapenem vs. tazobactam/piperacillin). The percentage of patients switching from carbapenems to tazobactam/piperacillin or vice versa was significantly lower in the tazobactam/piperacillin group than in the carbapenem group (41.7 % vs. 11.1 %, p < 0.001).

Our findings suggest that tazobactam/piperacillin can be used as the first-line empirical treatment for patients infected with B. fragilis.

Ports are hot spots of pollution; they receive pollution from land-based sources, marine traffic and port infrastructures. Marine ecosystems of nearby areas can be strongly affected by pollution from port-related activities. Here, we investigated the microbiomes present in sea floor sediments along a transect from the harbour of Livorno (Central Italy) to a nearby marine protected area. Results of 16S rRNA amplicon sequencing and metagenome assembled genomes (MAGs) analyses indicated the presence of different trends of specific bacterial groups (e.g. phyla NB1-j, Acidobacteriota and Desulfobulbales) along the transect, correlating with the measured pollution levels. Human pathogenic bacteria and antibiotic resistance genes (ARGs) were also found. These results demonstrate a pervasive impact of human port activities and highlight the importance of microbiological surveillance of marine sediments, which may constitute a reservoir of ARGs and pathogenic bacteria.

Bacteroides are potential candidates  for next-generation probiotics (NGPs), which require preclinical safety and efficacy evaluations to ensure their rational use. This study aimed to verify the safety of two Bacteroides strains isolated from human fecal samples, Bacteroides dorei CK16 (B. dorei CK16) and Bacteroides vulgatus CK29 (B. vulgatus CK29), using genomic analysis and in vivo experiments. Whole-genome sequencing analysis of B. dorei CK16 revealed a predicted 4,898 protein-coding sequences (CDS), about 5.5 Mb of total genome length with a G + C content of 42.08%, and B. vulgatus CK29 revealed a predicted 4,610 CDS, about 5.3 Mb of total genome length with a G + C content of 42.56%. Moreover, the genome demonstrated the absence of virulence factors, and insertion sequences related to clinically relevant strains in either strain. A 42-day in vivo experiment was conducted on BALB/c and BALB/c nude mice, with each mouse receiving a daily dose of 1 × 108 colony forming units (CFU) /mL of B. dorei CK16 or B. vulgatus CK29. No significant in vivo pathogenic characteristics were observed based on body weight, organ index, hematological, serum biochemical, or histological analyses, particularly in nude mice. Therefore, the initial safety assessment of the two novel Bacteroides strains exhibited no notable adverse effects in both immunocompetent and immunodeficient mice models.

The oral and gastrointestinal (GI) tract microbiota in humans is susceptible to geographical influences and represents vital factors impacting healthy aging. The northeastern region of China, characterized by distinct dietary and climatic conditions, significantly influences the human microbiome composition. However, the microbial structure of the entire long-lived population in this area has not been evaluated. This study recruited a cohort of 142 individuals aged 55-102 residing in Northeast China, and their oral and gut microbiota were evaluated using full-length 16S rRNA gene amplicon sequencing. The results indicate that the oral and GI tract microbiota of long-lived individuals showed reduced microbial taxonomic richness and evenness compared to sub-longevity individuals. With aging, the core species experience a gradual decline in abundance, while subordinate species show an increase. The long-lived population exhibited a heightened ability to enrich beneficial bacteria including Akkermansia, Alistipes, Parabacteroides, and Eubacterium coprostanoligenes in the GI tract, which are associated with host metabolism and have the potential to act as probiotics, reducing the risks of unhealthy aging in the northeast population. Bifidobacterium sp. and Lactobacillus salivarius have been found to coexist in both the oral cavity and the GI tract of long-lived individuals. We hypothesize that beneficial bacterial taxa from the oral cavity colonize the GI tract more extensively in long-lived individuals compared to those with a shorter lifespan. These findings pave the way for identifying probiotic strains that can promote healthy aging in Northeast China.

Portal vein thrombosis (PVT) is a common complication in patients with end-stage liver disease (ESLD). The portal vein in patients with ESLD is proposedly an inflammatory vascular bed due to translocation of endotoxins and cytokines from the gut. We hypothesized that a proinflammatory gut microbiome and elevated trimethylamine N-oxide (TMAO), a driver of thrombosis, may contribute to PVT development.

We investigated whether gut microbiome diversity, bacterial species, metabolic pathways, and TMAO levels are associated with PVT in patients with ESLD.

Fecal samples, plasma samples, and data from patients with ESLD and healthy controls were collected through the TransplantLines Biobank and Cohort Study. PVT was defined as a thrombus in the portal vein within a year prior to or after fecal sample collection. Fecal samples were analyzed using Shotgun Metagenomic Sequencing, and TMAO levels were measured in plasma using a Vantera Clinical Analyzer.

One hundred two patients with ESLD, of which 23 with PVT, and 246 healthy controls were included. No significant difference in gut microbiome diversity was found between patients with PVT and without PVT (P = .18). Both ESLD groups had significantly lower alpha diversity than controls. Bacteroides fragilis and 3 Clostridiales species were increased in patients with PVT compared with without PVT. TMAO levels between the 3 groups were not significantly different.

We observed profound differences in gut microbiota between patients with ESLD and controls, but minimal differences between patients with ESLD with or without PVT. In our cohort, a gut-derived proinflammatory state was not associated with presence of PVT in patients with ESLD.

240 64-week-old Lohman LSL-Lite laying hens were used to evaluate the effect of ahiflower seed (AS) and its press cake (APC) on egg yolk fatty acid profile, production performance, apparent total tract nutrient digestibility (ATTD), egg quality, eggshell mineral content, and fecal microbiota composition for 12 weeks in a completely randomized design, with 6 replicates of 5 birds in a cage. The diets included a control (CD), CD supplemented with 10 % flaxseed (FS), and CD supplemented with AS at 1, 5, and 10 % inclusion levels and APC at 5, 10, and 15 % inclusion levels. Diet did not affect eggshell Ca (P=0.1168) and P (P=0.8212) levels, and feed conversion ratio (P=0.136), but the 10 % FS reduced body weight gain (P=0.044), hen day egg production (P= 0.000) and feed intake (P<.0001) compared to other treatments. The yolk lightness L* was reduced (P=0.030) by 5 % APC compared to 10 % APC, redness a* was reduced (P= 0.002) by 10 % FS and 15 %APC compared to 10 %APC, CD, and 1 % AS. The 10 % FS and 15 %APC also reduced (P<0.001) yellowness *b compared to 1 %AS and 5 %APC. Apparent metabolizable energy (AME) and nitrogen-corrected apparent metabolizable energy (AMEn) increased (P<0.001) in 10 %FS and all AS and APC levels compared to CD. Compared to CD (87 %), ATTD of energy was increased (P<0.001) in hens fed 10 %FS (93 %), 1 %AS (93 %), and 15 %APC (92 %). However, 10 %FS (78.7 %) and 1 %AS (81.7 %) had higher (P=0.011) ATTD of P than 10 %APC (64.6 %). Similarly, ATTD of Ca was reduced (P<0.001) in hens fed 10 %APC compared to CD and 10 %AS. Compared to other treatments, total n-3 and stearidonic acids were increased (P<0.001) by 10 %FS and 10 %AS, respectively, and the total n-6 FAs and linoleic acid were highest (P=0.001) in 15 %APC. Both 10 %AS and 10 %FS increased (P<0.001) eicosapentaenoic, docosahexaenoic, and alpha-linolenic acid, compared to CD. The n-6/n-3 ratio was reduced (P<0.001) by 10 %FS and 10 %AS compared to APC and CD. Dietary treatments modulated fecal microbiota differently, but notably, Lactobacillus was more abundant when hens were fed 5 %AS compared to other treatments. In conclusion, the dietary supplementation of 10 %AS increased n3-FAs deposition in eggs similar to 10 %FS. However, 10 %FS reduced production performance. All levels of AS and APC increased diet metabolizable energy with no negative effect on production performance.

Introduction. Previous studies have shown vast differences in the skin and oral microbiomes of newborns based on delivery method [Caesarean section (C-section) vs vaginal]. Exposure to or absence of certain bacteria during delivery can impact the neonate's future susceptibility to infections, allergies or autoimmunity by altering immune functions. Few studies have focused on the impact of maternal obesity on the variations of newborn skin and oral microbiomes. Obese pregnant women typically have a higher vaginal microbiome diversity, and their pregnancies are at higher risk for adverse outcomes and complications.Hypothesis. We hypothesized that the skin and oral microbiomes of newborns born to obese mothers would include more diverse, potentially pathogenic bacteria and that the skin and oral microbiome in C-section delivered newborns would be less diverse than vaginally delivered newborns.Aim. We aim to begin to establish maternal obesity and mode of delivery as factors contributing to increased risk for negative newborn outcomes through impacts on newborn bacterial dysbiosis.Methodology. A skin swab was collected immediately following delivery of 39 newborns from 13 healthy weight body mass index (BMI 18.50-24.99), 11 overweight (BMI 25.0-29.99) and 15 obese (BMI ≥30.00) pregnant participants. An oral swab was collected immediately following delivery for 38 of these newborns from 13 healthy weight, 10 overweight and 15 obese pregnant participants. Bacterial genera were identified via 16S rRNA amplicon sequencing.Results. The newborn skin microbiome was comprised of typical skin bacteria (i.e. Corynebacterium). Newborns of obese participants had a higher relative abundance of Peptoniphilus in their skin microbiome compared to newborns of healthy weight participants (P=0.007). Neonates born via C-section had a higher relative abundance of Ureaplasma in their oral microbiome compared to neonates delivered vaginally (P=0.046).Conclusion. We identified differences in the newborn skin and oral microbiomes based on pre-pregnancy BMI and method of delivery. These differences could be linked to an increased risk of allergies, autoimmune disease and infections. Future longitudinal studies will be crucial in determining the long-term impact of these specific genera on newborn outcomes. Understanding these connections could lead to targeted interventions that reduce the risk of adverse outcomes and improve overall health trajectory.

Crohn's disease (CD), also known as cicatrizing enteritis, is an inflammatory bowel disease that occurs in the distal ileum and right colon of unknown cause and is also called inflammatory bowel disease (IBD) with ulcerative colitis (UC). In recent years, intestinal biota have been confirmed to play a significant role in various gastrointestinal diseases. Studies have found that intestinal microbiota disorders are closely associated with the onset and progression of Crohn's disease. Bacteroidetes, the second largest microbiota in the intestine, are crucial for equilibrium in the microbiota and intestinal environment. Certain Bacteroides can induce the development of Crohn's disease and aggravate intestinal inflammation directly or through their metabolites. Conversely, certain Bacteroides can reduce intestinal inflammation and symptoms of Crohn's disease. This article reviews the effect of several intestinal Bacteroides in the onset and progression of Crohn's disease and their impact on its treatment.

Probiotics are pivotal in maintaining or restoring the balance of human intestinal microbiota, a crucial factor in mitigating diseases and preserving the host's health. Exploration into Bacteroides spp. reveals substantial promise in their development as next-generation probiotics due to their profound interaction with host immune cells and capability to regulate the microbiome's metabolism by significantly impacting metabolite production. These beneficial bacteria exhibit potential in ameliorating various health issues such as intestinal disorders, cardiovascular diseases, behavioral disorders, and even cancer. Though it's important to note that a high percentage of them are as well opportunistic pathogens, posing risks under certain conditions. Studies highlight their role in modifying immune responses and improving health conditions by regulating lymphocytes, controlling metabolism, and preventing inflammation and cancer. The safety and efficacy of Bacteroides strains are currently under scrutiny by the European Commission for authorization in food processing, marking a significant step towards their commercialization. The recent advancements in bacterial isolation and sequencing methodologies, coupled with the integration of Metagenome-Assembled Genomes (MAGs) binning from metagenomics data, continue to unveil the potential of Bacteroides spp., aiding in the broader understanding and application of these novel probiotics in health and disease management.

Accumulating data suggest that remodeling aged gut microbiota improves aging-related imbalance in intestinal homeostasis. However, evidence in favor of the beneficial effect of remodeling gut microbiota on intestinal stress and immune responses during aging is scarce. The current study revealed that old mice presented impaired gut barrier integrity. Transcriptome sequencing coupled with bioinformatics analysis revealed that aging altered gene expression profiles of the colon and mesenteric lymph nodes, which are involved mainly in stress and immune responses, respectively. Notably, gut microbiota was closely related to the differentially expressed genes. Microbiota depletion in old mice ameliorated gut barrier integrity and partially reversed the inflammatory factors upregulated in aging mice. Furthermore, fecal microbiota transplantation from young mice to old mice resulted in a significant improvement in intestinal barrier integrity and immune homeostasis. These findings highlight the potential of microbiota-targeted interventions on aging-related physiological processes and call for further investigation.