Excess amino acids from a protein-rich diet are mainly catabolized in the liver. However, it is still unclear to what extent the gut microbiota may be involved in the mechanisms governing this catabolism. Therefore, the aim of this study was to investigate whether consumption of different dietary protein concentrations induces changes in the taxonomy of the gut microbiota, which may contribute to the regulation of hepatic amino acid catabolism. Consumption of a high-protein diet caused overexpression of HIF-1α in the colon and increase in mitochondrial activity, creating a more anaerobic environment that was associated with changes in the taxonomy of the gut microbiota promoting an increase in the synthesis of secondary bile acids, increased secretion of pancreatic glucagon. This effect was demonstrated in pancreatic islets, where secondary bile acids stimulated the expression of the PC2 enzyme that promotes glucagon formation. The increase in circulating glucagon was associated with an induction of the expression of hepatic amino acid-degrading enzymes, an effect attenuated by antibiotics. Thus, high protein intake in mice and humans induced the increase of different species in the gut microbiota with the capacity to produce secondary bile acids leading to an increase in secondary bile acids and glucagon levels, promoting amino acid catabolism.

In health, the gut microbiome functions as a stable ecosystem maintaining overall balance and ensuring its own survival against environmental stressors through complex microbial interaction. This balance and protection from stressors is maintained through interactions both within the bacterial ecosystem as well as with its host. As a consequence, the gut microbiome plays a critical role in various physiological processes including maintaining the structure and function of the gut barrier, educating the gut immune system, and modulating the gut motor, digestive/absorptive, as well as neuroendocrine system all of which are crucial for human health and disease pathogenesis. Pre- and probiotics, widely available and clinically established, offer various health benefits primarily by beneficially modulating the gut microbiome. However, their clinical outcomes can vary significantly due to differences in host physiology, diets, individual microbiome compositions, and other environmental factors. This perspective paper highlights emerging scientific insights into the importance of microbial micronutrient sharing, gut redox balance, keystone species, and the gut barrier in maintaining a diverse and functional microbial ecosystem, and their relevance to human health. We propose a novel approach that targets microbial ecosystems and keystone taxa performance by supplying microbial micronutrients in the form of colon-delivered vitamins, and precision prebiotics [e.g. human milk oligosaccharides (HMOs) or synthetic glycans] as components of precisely tailored ingredient combinations to optimize human health. Such a strategy may effectively support and stabilize microbial ecosystems, providing a more robust and consistent approach across various individuals and environmental conditions, thus, overcoming the limitations of current single biotic solutions.

Partial RAG deficiency (pRD) can manifest with systemic and tissue-specific immune dysregulation, with inflammatory bowel disease (IBD) in 15% of the patients. We aimed at identifying the immunopathological and microbial signatures associated with IBD in patients with pRD and in a mouse model of pRD (Rag1w/w) with spontaneous development of colitis. pRD patients with IBD and Rag1w/w mice showed a systemic and colonic Th1/Th17 inflammatory signature. Restriction of fecal microbial diversity, abundance of pathogenic bacteria, and depletion of microbial species producing short-chain fatty acid were observed, which were associated with impaired induction of lamina propria peripheral Treg cells in Rag1w/w mice. The use of vedolizumab in Rag1w/w mice and of ustekinumab in a pRD patient were ineffective. Antibiotics ameliorated gut inflammation in Rag1w/w mice, but only bone marrow transplantation (BMT) rescued the immunopathological and microbial signatures. Our findings shed new light in the pathophysiology of gut inflammation in pRD and establish a curative role for BMT to resolve the disease phenotype.

Bladder cancer is a common malignancy of the genitourinary system. Recent studies have confirmed the existence of microorganisms in urine. This study aimed to characterize changes in the urinary microbiota of Chinese bladder cancer patients and determine differences between patients with muscle-invasive bladder cancer (MIBC) and those with non-muscle-invasive bladder cancer (NMIBC).

Urine samples were collected from 64 patients with bladder cancer and 94 disease-free controls using the clean catch method and sequenced by 16S rRNA gene sequencing. Sequencing reads were filtered by VSEARCH and clustered by UPARSE.

Significant associations were found between urinary microbiota and factors such as sex, age, and disease status. After age adjustment, differences in beta diversity were observed between healthy men and women, cancer patients and healthy controls, and NMIBC and MIBC patients. The cancer patients had an increased abundance of 14 bacterial genera, including Stenotrophomonas, Propionibacterium, and Acinetobacter. Notably, Peptoniphilus spp. were enriched in high-risk MIBC patients, indicating their potential as a risk marker. Functional prediction via PICRUSt analysis suggested enriched metabolic pathways in specific disease groups. Furthermore, molecular ecological network analysis revealed differences based on sex and disease type.

This significant microbial diversity indicates a potential correlation between urinary microbiota dysbiosis and bladder cancer, with implications for risk stratification and disease management. The identified urinary microbiota may serve as noninvasive markers for bladder cancer, warranting further validation in larger cohorts. This study provides a foundation for further research on the mechanisms of bladder cancer progression.

The gut microbiota plays a vital role in nutrient and energy utilization, as well as in the host's ability to adapt its immune system to environmental changes. As a biological control agent for the invasive Parthenium weed, the Parthenium beetle Zygogramma bicolorata (Z. bicolorata) Pallister is often exposed to fluctuating temperatures, which may induce stress in its natural habitat. This study utilized 16S amplicon sequencing to explore the impact of temperature stress on the gut microbiome of Z. bicolorata under cold (15°C), control (27°C), and hot (35°C) conditions. A total of 11 bacterial phyla and 149 genera were identified, with Firmicutes, Proteobacteria, and Cyanobacteria being the most abundant. Temperature treatments significantly influenced the diversity of the gut microbiota, as evidenced by alpha diversity measures. Principal coordinate analysis further revealed substantial variations in microbiome composition across the different temperature conditions. Additionally, PICRUSt2 analysis suggested that the gut microbiota is linked to metagenomic functions related to amino acid and carbohydrate transport, inorganic ion metabolism, and cellular processes. Our findings suggest that thermal stress alters the gut microbiome of Parthenium beetles, offering new insights into how these beetles may have ecologically adapted to temperature fluctuations, while also highlighting the potential role of gut microbes in maintaining beetle health under environmental stress.

Microorganisms drive essential biogeochemical processes in aquatic ecosystems and are sensitive to both salinity and hydrological changes. As climate change and anthropogenic activities alter hydrology and salinity worldwide, understanding microbial ecology and metabolism becomes increasingly important for managing aquatic ecosystems. Biogeochemical processes were investigated on sediment microbial communities during a significant flood event in the hypersaline Coorong lagoon, South Australia (the largest in the Murray-Darling Basin since 1956). Samples from six sites across a salinity gradient were collected before and during flooding in 2022. To assess changes in microbial taxonomy and metabolic function, 16S rRNA amplicon sequencing was employed alongside untargeted liquid chromatography-mass spectrometry (LC-MS) to assess changes in microbial taxonomy and metabolic function. Results showed a decrease in microbial richness and diversity during flooding, especially in hypersaline conditions. Pre-flood communities were enriched with osmolyte-degrading and methanogenic taxa, alongside osmoprotectant metabolites, such as glycine betaine and choline. Flood conditions favored taxa such as Halanaerobiaceae and Beggiatoaceae, inducing inferred metagenomic shifts indicative of sulfur cycling and nitrogen reduction pathways, while also enriching a greater diversity of metabolites including Gly-Phe dipeptides and guanine. This study demonstrates that integrating metabolomics with microbial community analysis enhances understanding of ecosystem responses to disturbance. These findings suggest microbial communities rapidly change in response to salinity reductions while maintaining key biogeochemical functions. Such insights are valuable for ecosystem management and predictive modelling under environmental stressors such as flooding.

This study focuses on treating phenolic wastewater with a novel closed fixed-bed bacteria-algae biofilm reactor (CF-BABR) to enhance resource transformation for phenolic substances. The CF-BABR showed strong impact - load resistance and stable degradation efficiency, fully degrading phenolic compounds at concentrations from 0 to 150 mg/L. From the inflow to the outflow, the effective sequences, abundance, and diversity of bacteria decreased. Chlorobaculum was the dominant bacterium for phenolic pollutant degradation. The abundance of fungi decreased gradually, while their diversity increased. Kalenjinia and Cutaneotrichosporon played a synergistic role in reducing pollutant toxicity. The high - concentration pollutants at the influent led to a higher abundance of microalgal communities, and Scenedesmaceae became the most dominant algal family, which was positively correlated with the degradation of phenolic compounds. Functional gene prediction indicated that the abundance of functional genes in bacteria decreased overall along the wastewater flow. Carbohydrate metabolism and amino acid metabolism were the most active secondary pathways. In fungi, the predicted gene functions had the highest abundance in the upstream region. Metabolic intermediates such as organic acids and derivatives, lipids and lipid - like molecules, and carboxylic acids and derivatives demonstrated the degradation effect of CF-BABR on phenolic compounds.

Uranium (U), recognized as a significant health risk in groundwater, has become a key focus in environmental remediation efforts. While numerous electron donors have been investigated for the removal of U(VI) through microbial processes, the potential of abundant and economical Fe(II)-containing minerals remains unexplored. Here, a new inorganic electron donor, siderite (FeCO3) was proposed. Although siderite demonstrates a lesser electron-donating capacity than Fe(0) and S(0), the Siderite-B bioreactor successfully enriched microbes belonging to the Azotobacter genus, which are known for their nitrogen-fixing ability. Within this system, Azotobacter facilitated the oxidation of Fe(II) coupled with the reduction of U(VI). Initially, Fe(II) donated electrons to the NAD+/NADH couple. Subsequently, NADH transferred these electrons to the Rnf/Fix complex, which in turn donated them to ferredoxin, catalyzing the reduction of U(VI) to U(IV). The Siderite-B autotrophic bioreactor achieved a U(VI) removal efficiency of 93.40 ± 0.47 % over 144 h, which was slightly lower than the S(0)-B bioreactor (97.12 ± 0.50 %) and the Fe(0)-B bioreactor (95.58 ± 0.95 %). In contrast, S(0)-B and Fe(0)-B bioreactors were enriched with microbes belonging to the Thiobacillus genus, which reduced U(VI) mainly through Fe-S oxidoreductase and Cytochrome C mediated electron transfer. Over a 90-day continuous-flow experiment, the Siderite-B bioreactor exhibited high U(VI) removal efficiencies of 96.83 ± 1.12 %, 95.92 ± 1.84 %, and 85.28 ± 1.41 % at influent U(VI) concentrations of 10, 20, and 30 mg/L, respectively. The findings highlight the potential of siderite as an effective and autotrophic electron donor for U(VI) reduction, offering a cost-effective and environmentally friendly alternative for groundwater uranium remediation.

Maternal probiotic supplementation altered the microbial composition in infants' gut, yet its effect on the functional pathways of the microbiota remains unclear. This study aimed to explore the potential impact of maternal probiotic intake on the predicted functional pathways of the gut microbiome in healthy infants. A total of 24 pregnant women were randomly allocated to either the control group or the probiotic group. The women in the probiotic group began receiving probiotics at the 32nd week of pregnancy and continued until delivery. Meconium and fecal samples were collected from infants at birth, as well as on the 3rd day, 14th day, and 6th month after birth. The functional characteristics of the microbial community were inferred using 16S rRNA gene analysis, processed with PICRUSt software, and cross-referenced with the KEGG database. The probiotic group had lower levels of Actinobacteria and Bacteroidetes, while Bifidobacterium growth was notably increased in the infant gut microbiota. At day 0 postpartum, the control group exhibited higher levels of Prevotellaceae compared to the probiotic group (P < 0.05). However, no significant differences were found by day 3. At day 14, the control group exhibited higher levels of Bacteroidaceae and Bacteroides, while Bacteroides_thetaiotaomicron was more abundant in the probiotic group (P < 0.05). By 6 months, the control group showed a higher abundance of Firmicutes (P < 0.05). On day 0 postpartum, maternal probiotic consumption increased the Environmental information processing pathway at KEGG Level 1, and increased Energy metabolism, Metabolism of cofactors and vitamins, and Cell growth and death pathways at KEGG Level 2. It also increased Histidine metabolism, One carbon pool by folate, and Folate biosynthesis at KEGG Level 3. No changes were observed in the infant gut microbiota's functional metabolic pathways at 3 days postpartum. At 14 days postpartum, probiotics reduced Lipid metabolism pathways at KEGG Level 2 and the Citrate cycle at KEGG Level 3. At 6 months postpartum, probiotics decreased Carbohydrate metabolism pathways at KEGG Level 2. Our findings suggest that probiotic supplementation during pregnancy affects the functional metabolism of the gut microbiota in healthy infants. This, in turn, may influence the development of the infant's immune system, metabolism, and overall health by modifying the gut microbial environment.

Polychlorinated biphenyls (PCBs) are neurotoxic hazardous materials that may cause toxicity via the gut-liver-brain axis. This study investigated PCB × microbiome interactions in adult female mice exposed orally to an environmental PCB mixture. Female mice (6-week-old) were exposed daily for 7 weeks to peanut butter containing 0, 0.1, 1, or 6 mg/kg/day of PCBs. Twenty hours after the final exposure, the cecal content was collected to characterize the microbiome composition and predicted function. PCB and its metabolites in feces were analyzed using gas chromatography-tandem mass spectrometry (GC-MS/MS), while cecal content was assessed with liquid chromatography-high resolution mass spectrometry (LC-HRMS). PCB exposure influenced the abundance of microbial taxa and predicted functions within the cecal content. Complex PCB and metabolite mixtures were detected in the gastrointestinal tract. Network analysis revealed associations between specific parent PCBs and metabolites with changes in the abundance of bacteria in the gastrointestinal tract. These findings demonstrate that individual PCBs and their metabolites significantly influence the abundance of specific bacteria in the gastrointestinal tract following oral PCB exposure. These findings inform further research targeting the microbiome to attenuate the adverse health outcomes of PCB exposure.

As important methane hydrate storage sites, cold seep areas are threatened by microplastics (MPs) contamination. To assess the environmental impact of MPs on microbial communities in cold seep sediments, an incubation experiment was conducted using cold seep sediment amended with different concentration of polyamide (PA), polyethylene (PE), polyethylene terephthalate (PET), and polypropylene (PP) microplastics. The results showed that the different type and concentration of MPs significantly altered the prokaryotic community structures. The PE and PET addition highly changed the relative abundance of bacterial taxa in the bacterial community, while the proportion of archaeal species in the archaeal community was significantly altered in 0.5 % MPs treatments. All of the MPs reduced the network complexity of the bacterial and archaeal communities, such as the lower average degree and greater average path length. Furthermore, the MPs treatments also significantly decreased the network stability of prokaryotic communities. The lower network complexity led to lower network stability was observed in the archaeal community. The formation of oxidative functional groups on PE and PET MP surface based on FTIR analysis suggested that biodegradation could occur in cold seep sediment. Together, these results provide new evidence that MPs could change the structures and species coexistence of prokaryotic communities in cold seep sediments.

The biodegradation of microplastics in river sediments was subject to the prior photodegradation in surface water and can be greatly affected by polymers and additives. However, the understanding of the effects of additives on the cascade photo- and biodegradation processes remains limited. In this study, the characteristics of morphology, functional groups, and indictive degrading bacteria of polyethylene (PE) and polypropylene (PP) were detected to analyze the effects of Dioctyl phthalate (DOP), Bisphenol A (BPA) and Benzotriazole (BTA), on the single and cascade photo- and biodegradation processes of PP/PE films (PP/PEP, PP/PEB, PP/PEPB). The results showed that photodegradation enhanced the biodegradation, by creating smaller fractions which induced the proliferation of new PP/PE-degrading bacteria (P-bacteria). Compared to the general PP/PE-degrading bacteria, P-bacteria displayed higher standard betweenness centrality and carbon metabolism. Among the three additives, DOP most obviously promoted photo- and biodegradation processes, followed by BPA. BTA inhibited the photodegradation to biodegradation by absorbing UV light. Overall, these findings provide insights into the nonnegligible joint influence of photodegradation and additives on the biodegradation of PP/PE resins in natural rivers.

There is currently increased interest in nanocellulose as a food emulsifier and dietary supplement. It was hypothesized that nanocellulose could modulate behaviors and glucose homeostasis in female mice using mechanisms of altered gut microbiome and immune modulation. An initial experiment was conducted with the objective of examining whether three common types of nanocellulose affected the gut microbiome of female C57BL/6 mice on a Western diet. Cellulose nanofibrils (CNF), TEMPO-CNF and cellulose nanocrystals were administered at the physiologically relevant dose of 30 mg/kg/day for 30 days by gavage, with cellulose and water groups as the positive and negative controls, respectively. Findings suggested that CNF had the strongest effect on the gut microbiome. CNF was therefore selected for a chronic 6-month study on the gut microbiome, immune system and behaviors in female NOD mice, a model for type 1 diabetes. Gut microbiome analysis suggested that there might be some beneficial changes following subchronic exposure (e.g., at the two-month timepoint), however, this effect was no longer seen after chronic consumption (e.g., at the six-month timepoint). CNF treatment also altered the immune homeostasis, including decreases in the splenic Mac-3+ population and serum level of proinflammatory chemokine LIX. Additionally, CNF consumption decreased diabetic incidences but had no effect on the depressive-like behavior and grip strength. However, further analysis, e.g., the insulin tolerance test, indicated that CNF-treated NOD mice might exhibit signs of insulin resistance. Taken together, nanocellulose dysregulated glucose homeostasis in female mice on a Western diet involving mechanisms related to alteration of the gut microbiome.

Biofilms drive all biogeochemical processes and represent the main mode of existence for active microbial life. Many past studies examined biofilm formation under static and eutrophic conditions, but those conditions are not representative of typical groundwater environments. In this study, we developed in situ bioreactors and methodologies to examine the influence of subsurface properties such as redox condition and lithology on the properties of naturally formed biofilms in two adjacent wells, a 30-m deep well completed in alluvium and a 120-m deep well in gneiss bedrock. The bulk chemistry of groundwater from the wells was similar, with neutral pH and abundant nitrate (21.9-24.6 mg/L), but redox conditions differed with depth (alluvial: oxic, gneiss bedrock: anoxic). Microbial community analysis revealed distinct clustering of biofilm community composition with the groundwater environment. Biofilm communities were consistently assembled by deterministic processes whereas planktonic communities had a higher influence of stochastic processes. Alluvial biofilms exhibited more diverse communities mainly composed of organotrophic aerobes capable of nitrate utilization. Bedrock biofilms indicated similar community compositions with groundwater where anaerobic denitrifiers coupled with sulfur oxidizers were dominant. Visualization and biomass quantification revealed distinct morphologies and development of biofilm along rock types and groundwater environments. Biofilm on gneiss surface had more biomass and formed a thin layered structure, compared to sandstone biofilm which had a randomly distributed pattern, implying that the morphology of biofilm was governed by the properties of the rock. Attached to unattached (planktonic) microbe ratios ranged from 3.9 × 103 to 1.2 × 104: 1 in the gneiss surface and 3.4 × 102 to 4.2 × 102: 1 in the sandstone surface in bedrock groundwater environment. Taken together, this study advances our understanding of subsurface biomass abundance and demonstrates that the in-situ bioreactors are effective for cultivating and analyzing of subsurface biofilms. Based on the specific field conditions tested, we found that biofilm can form stably on fractured rock surfaces within a year, with groundwater redox conditions shaping community composition and rock types determining biofilm volume and morphology. The methodologies presented here can be extended to other subsurface environments with varying groundwater geochemistry and lithology, which will help further refine estimates of microbial life and its role in subsurface ecosystems.

Changes in soil characteristics due to varying farming practices can modify the structure of bacterial communities. However, it remains uncertain whether bacterial groups that break down organic material are similarly impacted. We examined changes in the bacterial community by pyrosequencing the 16S rRNA gene when young maize plants, their neutral detergent fibre fraction, or urea were applied to an Australian Vertisol. This soil was managed with either conventional tillage with continuous cotton, minimum tillage with continuous cotton, or a wheat-cotton rotation. The soil organic carbon content was 1.4 times higher in the wheat-cotton rotation than in the conventional tillage with continuous cotton treatment. Approximately 41.6% of the organic carbon was added with maize plants, and 13.1% of the neutral detergent fibre fraction was mineralized after 28 days. The application of young maize plants and the neutral detergent fibre fraction significantly altered the bacterial community and the presumed metabolic functional structure, but urea did not. Many bacterial groups, such as Streptomyces, Nocardioides, and Kribbella, and presumed metabolic functions were enriched by the application of organic material, but less so by urea. We found that a limited number of bacterial groups and presumed metabolic functions were affected in an irrigated Vertisol by the different cotton farming systems, but many were strongly affected by the application of maize plants or its neutral detergent fibre.

Lignocellulosic composting has been widely promoted in the utilization of agricultural wastes, while few focus on orchard lignocellulosic wastes in the fruit industry. Peniophora is a laccase hyper-producer highly efficient in lignin degradation, yet its application in lignocellulosic composting has not been investigated. Here, an aerobic composting experiment was conducted to investigate the effects of inoculation with Peniophora crassitunicata and a commercial microbial inoculant (mainly Bacillus and Aspergillus) on grape (Vitis Vinifera L.) orchard lignocellulosic wastes degradation and the underlying mechanisms. The inoculation with P. crassitunicata, both individually (H) and in combination with the commercial microbial inoculant (HS), enhanced lignocellulose degradation efficiency. Notably, the co-inoculation exhibited higher lignocellulose degradation ratios and higher lignocellulosic enzyme activities compared to other treatments. The compost piles with co-inoculation experienced a more rapid temperature rise, a longer duration (15 days) of high temperatures, lower pH, and lower electrical conductivity (EC). Firmicutes (e.g. Bacillus, Paenibacillus) and Ascomycota (e.g. Aspergillus) along with Bacteroidota, Actinobacteriota, and Basidiomycota (e.g. Peniophora) dominated the microbial community in compost; carbohydrate metabolism dominated microbial metabolic pathways at the thermophilic phase, highlighting an active microbial community. As compost processed, highly mature and non-toxic compost products were finally obtained for the co-inoculation, with a pH of 7.87, C/N ratio of 13.5, NH4+-N/NO3‾-N ratio of 0.21-0.41, EC of 0.90 mS cm-1, and germination index of 149 %. The co-inoculation of P. crassitunicata with the commercial microbial inoculant effectively accelerated lignocellulose degradation and compost maturation, producing a friendly and non-toxic organic fertilizer for agricultural applications and thereby providing a new strategy for orchard wastes management and agricultural applications.

Nano-selenium fertilizers can promote plant growth and nitrogen availability. However, little information is available on the effects of nano-selenium on tea leaf quality, soil nutrient availability and associated microbe-driven mechanisms. This study examined the effects of nano-selenium on the tea leaf quality and soil nitrogen cycling in 20-year-old tea plantations when the leaves were sprayed with ammonium or nitrate. Leaf selenium and amino acid contents increased ninefold and 9%, respectively, with nano-selenium in "Zhongcha108" and "Longjing43." Rhizosphere bacterial and fungal community compositions were more sensitive to selenium and nitrogen applications in "Longjing43" than in "Zhongcha108." "Zhongcha108" enriched more taxa related to microbial growth, while more taxa related to cellular maintenance and nutrient acquisition enriched in "Longjing43." Nano-selenium application decreased the copy number of AOA and AOB genes, and nosZ and nirK genes by 59%, 53%, 37% and 46% under ammonium, and by 77%, 43%, 38% and 65%, respectively, under nitrate spraying, in "Longjing43." However, the expression of these genes increased by nano-selenium in "Zhongcha108" with ammonium spraying. It is concluded that a nano-selenium application increases tea leaf quality, and this effect on nitrogen cycling and ecological functioning largely depends on the tea cultivar-specific bacterial and fungal composition and function.

The stress resistance of medicinal plants is essential to the accumulation of pharmacological active ingredients, but the regulation mechanism of biological factors and abiotic factors on medicinal plants is still unclear. To investigate the mechanism of soil nutrient and microecology on the stress resistance of C. pilosula, rhizosphere soil and roots were collected across the four seasons in Minxian, Gansu, and their physicochemical properties, as well as root-associated microorganisms, were examined. The results showed that the bacterial α-diversity indexes increased in the endosphere and rhizosphere from summer to autumn. At the same time, the community composition and function changed considerably. The stability of the endophytic bacterial community was higher than that rhizospheric bacteria, and the complexity of the endophytic bacterial community was lower than rhizospheric bacteria. Soil organic matter (OM), water content (WC), total potassium (TK), and total nitrogen (TN) have been identified as the key factors affecting bacterial community diversity and stress resistance of C. pilosula. WC, TN, and OM showed significant differences from summer to autumn (P < 0.5). Four key soil physiochemical factors changed significantly between seasons (P < 0.01). TN and OM change the stress resistance of C. pilosula mainly by changing the activity of antioxidant enzymes. Changes of OM and endophytic bacterial diversity affect the accumulation of soluble sugars to alter stress resistance. These four key soil physicochemical factors significantly influenced the diversity of endophytic bacteria. WC and OM were identified as the most important factors for endophytic and rhizospheric bacteria, respectively. This study provided the research basis for the scientific planting of C. pilosula.

Brain functional changes and gut microbiota dysbiosis have been observed in perimenopausal syndrome (PMS). We evaluated the effects of a plant-based daily diet enriched with Raphanus sativus L. (RSL, radish seed) on the gut microbiota composition, gastrointestinal symptoms, resting-state local spontaneous brain activity, and neuropsychology in perimenopausal women. For 12 weeks, the participants were instructed to adhere to a controlled, Raphanus sativus L.-rich plant-based diet (a mean RSL intake of 5 g/day). Two test days were organized: before and after the nutritional intervention. The fecal microbiota composition, gastrointestinal symptoms, resting-state brain function, and neuropsychology were assessed twice. A longitudinal single-arm study was conducted on 24 perimenopausal women. The Montreal Cognitive Assessment (MoCA) scores tended to improve in the visuospatial/executive function subitem and in the total score after the diet. The participants presented elevated amplitude of low-frequency fluctuation (ALFF) values in the left middle occipital gyrus, the left precentral gyrus, and the left middle cingulum gyrus. The abundances of the phyla Synergistetes and Verrucomicrobia were positively correlated with the ALFF values of the left middle occipital gyrus, left precentral gyrus, and left middle cingulum gyrus. These data suggest that specific gut microbes may modulate intrinsic brain activity and cognitive function in perimenopausal women. A plant-based RSL-rich diet has beneficial effects on the gut microbial composition and brain function of perimenopausal women.

Microplastics (MPs) transport bacteria from rivers to oceans, impacting aquatic ecosystems. In situ incubation, a common method for studying bacterial communities on MPs, cannot reproduce complex and realistic environmental dynamics. Herein, a natural incubation experiment was performed to reproduce the migration of nine different substrates from rivers to the sea and examine the succession of bacterial communities on their surfaces. Furthermore, an in situ sequential incubation experiment and the natural incubation experiment were compared. Substantial structural changes were observed in the bacterial communities on MPs along riverine courses to the ocean, with implications for biosecurity, elemental cycling, and degradation potential in aquatic ecosystems. Rapid fluctuations in salinity were the prevalent factor for the significant changes in the bacterial community on MPs. The type of substrate has a significant effect on the formation and structure of bacterial communities, which depend on substrate structure and composition. Unlike in situ incubation, natural incubation reproduces realistic environmental dynamics, providing more comprehensive information on bacterial species composition, diversity, functional metabolism, and structure on MPs. This study introduces a novel methodological approach for MP research and enhances our understanding of the ecological risks associated with MPs transported from rivers to the ocean.

Fusobacterium nucleatum is an oral bacterium known to colonize colorectal tumors, where it is thought to play an important role in cancer progression. Recent advances in sequencing and phenotyping of F. nucleatum have revealed important differences at the subspecies level, but whether these differences impact the overall tumor ecology, and tumorigenesis itself, remain poorly understood. In this study, we sought to characterize Fusobacteria in the tumor microbiome of a cohort of individuals with CRC through a combination of molecular, spatial, and microbiologic analyses. We assessed for relative abundance of F. nucleatum in tumors compared to paired normal tissue, and correlated abundance with clinical and pathological features. We demonstrate striking enrichment of F. nucleatum and the recently discovered subspecies animalis clade 2 (Fna C2) specifically in colon tumors that have biofilms, highlighting the importance of complex community partnerships in the pathogenesis of this important organism.

Aquatic environments are frequently contaminated with nanoplastics (NPs) ranging from 1-100 nm generated by plastic aging, but their bio-enrichment and toxicological impacts remain poorly understood. This study investigates how chronic exposure to carboxylated polystyrene nanoplastics (PNPs) alters gut microbiota composition and function in zebrafish (Danio rerio). Adult zebrafish were exposed to 50 nm PNPs at concentrations of 0.1, 1.0, and 10 mg/L for 14 and 28 days, followed by gut microbiota analysis using 16S rRNA gene sequencing. PNP exposure altered gut microbiota composition, including an increase in Proteobacteria abundance and a decrease in Firmicutes, Bacteroidetes, and the inflammation-related genus Alistipes. Beneficial probiotics such as Faecalibacterium, Streptococcus, Bifidobacterium, and Lachnospira were diminished, while pathogenic bacteria proliferated. TEM imaging revealed the internalization of PNP particles within intestinal tissues resulted in vacuolation, suggesting potential epithelial damage. Co-occurrence network patterns of gut microbiota greatly decreased during treatment with NPs. The neutral community model showed that among PNP treatments, 0.1 mg/L led to a less predictable (stochastic assembly process). PNP exposure led to increased predicted microbial functions (via PICRUSt2) related to xenobiotic metabolism, infection pathways, and lipopolysaccharide (LPS) production, while RNA transport and N-glycan biosynthesis were decreased. However, pathways related to microbial antioxidants exhibited significant variation across different PNP levels. These results provide critical insights into the toxicological impacts of chronic PNP exposure on fish gut health, highlighting the potential risks to aquatic ecosystems and human health.

Microsporidians (Microsporidia) are a group of obligate intracellular parasites that commonly infect mosquitoes. Recently, it has been shown that infection by these parasites can alter the composition and functionality of the mosquito-associated microbiome. The host-associated microbiome of the mosquito can play a pivotal role in various physiological processes of this host, including its vector competence for pathogens. Thus, understanding how microsporidians shape the mosquito microbiome may be crucial for elucidating interactions between these parasites and their mosquito hosts, which are also vectors for other parasites and pathogens.

The effects of microsporidian infection on the microbiome structure and functionality of Culex pipiens and Culex torrentium larvae under semi-natural conditions were examined. The host-associated microbiome of Cx. pipiens (n = 498) and Cx. torrentium (n = 465) larvae, including that of the 97 infected individuals of these samples, was analysed using 16S DNA profiling and functional prediction analysis.

Microbiome network analysis revealed that, in the microsporidian-positive larvae, host microbial communities consistently grouped within a common bacterial module that included Aerococcaceae, Lactobacillaceae, Microbacteriaceae, Myxococcaceae, and Polyangiaceae. Indicator species analysis revealed two strong positive correlations between microsporidian infection and the presence of Weissella cf. viridescens and Wolbachia pipientis. Functional predictions of microbiome content showed enrichment in biosynthetic pathways for ansamycin and vancomycin antibiotic groups in infected larvae. Furthermore, the MexJK-OprM multidrug-resistance module was exclusively present in the infected larvae, while carbapenem- and vancomycin-resistance modules were specific to the microsporidian-free larvae.

Our results demonstrate that microsporidian infection alters the microbial community composition in mosquito larvae. Moreover, they show that microsporidian infection can increase the antimicrobial capabilities of the host-associated microbiome. These results provide novel insights into host microbiome-parasite interactions and have potential implications for the vector competencies of mosquitoes.

The intertidal zone is one of the natural systems most vulnerable to threats from polycyclic aromatic hydrocarbons (PAHs). However, the natural attenuation rate of PAHs within intertidal zones is low, posing challenges for the short-term recovery of contaminated environments. This study developed a contaminated intertidal zone simulation system and used a composite bacterial consortium containing Cellulosimicrobium sp. RS and Brucella sp. BZ for bioaugmented remediation. The degradation rate of PAHs (initial concentration: 5000 μg/kg) in the sediments reached 85.37 % after 120 days of restoration, which was significantly higher than the 29.93 % observed in the control group. High-throughput sequencing was used to analyze the structure and function of sediment microbial communities. The exogenous bacteria Cellulosimicrobium became dominant after remediation, whereas Brucella did not dominate but contributed to synergistic degradation. Network analysis and PICRUSt predictions confirmed that the microbial community evolved toward stronger PAHs degradation capabilities and degraded PAHs through ring cleavage, side-chain metabolism, and central metabolism in bioaugmented sediments. This study provides theoretical guidance and data support for bioaugmented remediation of intertidal zone pollution.

Little is known about the dysbiosis of the gut microbiome in patients with mild cognitive impairment (MCI) potentially at risk for the development of Alzheimer's disease (AD). So far, only cross-sectional differences and not longitudinal changes and their prognostic significance have been in the scope of research in MCI. Therefore, we investigated the ability of longitudinal taxonomic and functional gut microbiome data from 100 healthy controls (HC) to predict the progression from normal cognition to MCI over a 4-year follow-up period (4yFU). Logistic regression models were built with baseline features that best discriminated between the two groups using an ANOVA-type statistical analysis. The best model for the discrimination of MCI converters was based on functional data using Gene Ontology (GO), which included 14 features. This model achieved an area under the receiver operating characteristic curve (AUROC) of 0.84 at baseline, 0.78 at the 1-year follow-up (1yFU), and 0.75 at 4yFU. This functional model outperformed the taxonomic model, which included 38 genera features, in terms of descriptive performance and showed comparable efficacy to combined analyses integrating functional, taxonomic, and clinical characteristics. Thus, gut microbiome algorithms have the potential to predict MCI conversion in HCs over a 4-year period, offering a promising innovative supplement for early AD identification.

The APOE ε4 allele (APOE4) is a known risk factor for neurodegenerative and cardiovascular diseases, but its link to body composition and metabolism remains debated. The gut microbiota influences host metabolism and immunity, yet its relationship with APOE genotype in healthy individuals is not well understood. The objective of this work was to examine associations between APOE genotype and gut microbiota composition and function in healthy adults, focusing on microbial and metabolic differences related to the APOE4 allele. Seventy-seven healthy Spanish adults were genotyped for APOE. Fecal microbiota profiles were assessed by 16 S rRNA gene sequencing, and predicted functions were inferred using PICRUSt2. Body composition (DEXA) and physical activity (accelerometry) were also measured. APOE4 carriers exhibited subtle shifts in microbiota composition, including a five-fold reduction in Megamonas and lower abundance of the Eubacterium brachy group-both linked to energy harvest and adiposity-compared to APOE3 homozygotes. An uncharacterized Puniceicoccaceae genus was enriched in APOE4 carriers. Although E. brachy group abundance correlated with adiposity, no significant differences in body composition were observed. Functional predictions showed APOE4-associated microbiota enriched in pathways for carotenoid biosynthesis and trehalose metabolism, and depleted in tryptophan biosynthesis, propionate production, and multidrug resistance mechanisms. APOE4 carriers harbor gut microbiota with distinct taxonomic and functional features, potentially reflecting adaptations to metabolic and oxidative challenges. These findings underscore the relevance of the gut microbiome in shaping APOE4-associated phenotypes and warrant further investigation into its mechanistic contributions to health and disease.

Electro-bioremediation under anaerobic conditions is an effective approach for refractory organic matter removal in groundwater. Bicarbonate (HCO3-) is an inorganic carbon source and electron acceptor in groundwater, however, the influencing mechanism of HCO3- on pollutant removal of electro-bioremediation remains unclear. Herein, the effects of HCO3- concentration on electro-bioremediation of phenanthrene (PHE)-contaminated groundwater were investigated. HCO3- could facilitate the PHE degradation while an HCO3- concentration of higher than 1000 mg L-1 had a significant inhibition effect. Among the HCO3- concentration of 100-5000 mg L-1, the highest PHE degradation efficiency of 75.04-80.18 % was achieved in the electro-biochemical reactor with 500 mg L-1 HCO3-. The PHE removal efficiency was negatively correlated with the current density during the electro-bioremediation process, due to the effect of HCO3- concentrations on the electrolyte conductivity in the reactors. The electro-bioremediation process could increase the richness of diversity of microbes. Methanomethylovorans and the PHE-degrading bacteria including Pelolinea, Clostridium sensu stricto 5, Diaphorobacter, Methyloversatilis and Flavobacterium were the main microbes involved in PHE degradation. Of them, Methanomethylovorans was significantly positively correlated with the PHE removal efficiency. The potential metabolic function analysis revealed that the bacterial chemotaxis, flagellar assembly, carbohydrate metabolism and ABC transporters were prompted with the addition of HCO3-, while they were inhibited with the increasing HCO3- concentration. These findings suggested that electro-bioremediation technology was suitable for the remediation of polycyclic aromatic hydrocarbons such as PHE-contaminated groundwater in low bicarbonate areas.

Immunosuppressant administration subsequent to organ transplantation exerts a substantial influence on gut microbiota composition, thereby affecting patients' prognosis and quality of life.

We conducted a retrospective analysis involving 18 patients who experienced severe diarrhea or recurrent urinary tract infection (rUTI) due to prolonged immunosuppressant usage after kidney transplantation. Following episodes of severe diarrhea or rUTI, these individuals underwent fecal microbiota transplantation (FMT), resulting in notable alleviation of clinical symptoms. No unexpected adverse or serious adverse events were reported. In comparison to the pre-FMT period, the α-diversity of the intestinal microbiota in patients did not exhibit a significant difference following FMT; however, there was a notable distinction in the β-diversity and analysis of similarity (ANOSIM). In addition, our findings indicated a significant decline in the relative abundance of the bacterial genera Veillonella, Enterococcus, and Oribacterium, whereas a marked elevation was observed in the relative abundance of Faecalibacterium, Roseburia, Sutterella, Parasutterella, and Ruminiclostridium 5 after FMT in patients. Furthermore, there was a notable alteration in the metabolic pathway of gut microbiota in patients following FMT, with a significant enrichment observed in pathways such as Flavone and flavonol biosynthesis, Cytoskeleton proteins, Chromosome-related processes, NOD-like receptor signaling pathway, Progesterone-mediated oocyte maturation, and Antigen processing and presentation.

FMT exhibited an effective approach for managing rUTI and diarrhea arising from postoperative immunosuppressant exposure in kidney transplant recipients.

The intratumoral microbe-host interaction plays crucial role in the development of cancer. The microbiome can influence cancer development by modulating inflammation, immune responses and metabolic pathways. Therefore, we aim to delineate the landscape and role of intratumoral microbiota in cervical cancer (CC).

The presence of bacterial community in CC tissues was confirmed by fluorescence in situ hybridization (FISH). Then 16s rRNA and RNA-Seq were used to characterize the composition of intratumoral microbiota. Combined with cervical squamous cell carcinoma (CESC) data from the Tumor Cancer Genome Atlas (TCGA), the clinical signatures of intratumoral microbiota and DEGs were further analyzed. Finally, the effect of the up-regulated Fibrinogen beta chain (FGB) expressed fragment peptide on the biological behavior of cancer was verified in vitro.

We found the composition heterogeneity of bacteria in CC tumors. Pseudomonas was most highly enriched in CC tissues and grouped according to the relative abundance level. The clinical characteristics of patients with relatively high abundance of Pseudomonas had the higher levels of fibrinogen and lower levels of white blood cell (WBC) and albumin (ALB) expression. Combining transcriptome data from the two our collective CC and TCGA-CESC cohorts, we found that Pseudomonas abundance was significantly associated with fibrinogen beta peptide expression and worse overall survival in CC patients. In vitro experiment revealed that Pseudomonas could promote the proliferation and migration of cervical cancer cells through overexpression of FGB.

We characterized the composition of the intratumoral microbiota in CC tissues and identified the most significantly differentially abundant bacteria between cancerous and non-cancerous tissues. Our findings provide novel insights into the relationship between intratumoral Pseudomonas and the tumorigenesis of CC. A deeper understanding of the tumor microenvironment and its associated microbiota may reveal new potential therapeutic targets and improve clinical outcomes.

Overgrazing (OG) is an important driver of grassland degradation and productivity decline. Highly effective synergy between plants and rhizosphere growth-promoting rhizobacteria (PGPR) may be a major way for grassland plants to effectively cope with OG stress. There have been few reports providing solid evidence on how this synergy occurs.

This study combined with multi-omics analysis and the interaction effect of specific root exudate with PGPR B68, aiming to reveal the synergistic effect and regulatory mechanism of L. chinensis and PGPR under overgrazing stress. The results showed that Leymus chinensis plants with OG history can recruit the beneficial Phyllobacterium sp. B68 by regulating specific root exudate compounds(such as amino acid L-leucyl-L-alanine and alkaloid cordycepin). These compounds enhanced B68 rhizosphere colonization by promoting B68 chemotaxis and biofilm formation. The pot study experiments indicated that the bacterial isolates used as bio inoculants increased L. chinensis growth (mainly including plant height and biomass) by significantly increasing the chlorophyll content, RuBisCO activity, soluble sugar, plant hormones and nutrient content. Metagenomics results show that B68 inoculation significantly altered rhizosphere soil bacterial community composition and function. Additionally, B68 systemically upregulated the expression level of genes involved in plant hormone signaling, nutrient and sugar transporters, nitrogen metabolism, cell division, cell wall modification and photosynthesis to promote plant growth. The above results indicate that the PGPR B68 recruited by the root exudates of L. chinensis under OG helps the plant adapt to stress by promoting nutrient uptake and transport, maintaining hormone homeostasis, and enhancing the expression of genes related to plant growth and nutrient metabolism.

This study provides new insights into the positive interactions between grassland plants and rhizosphere bacteria under OG stress, offering valuable knowledge for developing new fertilizers and better management practices for degraded rangeland restoration and sustainable agriculture development.

Not applicable.

Recent improvements in Nanopore sequencing chemistry has made it a promising platform for long-read 16S rRNA sequencing. This study evaluated its clinical utility in a nationwide collaboration coordinated by Genomic Medicine Sweden.

Thirteen mock samples comprised of various bacterial strains and an External Quality Assessment (EQA) panel from QCMD (Quality Control for Molecular Diagnostics) were analysed by 20 microbiological laboratories across Sweden, using the recent v14 chemistry. Most laboratories generated full-length 16S rRNA sequencing libraries using an optimized protocol for the 16S Barcoding Kit 24, while two laboratories employed in-house PCR coupled with the Ligation Sequencing Kit. The commercial 16S bioinformatic pipeline from 1928 Diagnostics (1928-16S) was evaluated and compared with the open-sourced gms_16S pipeline that is based on the EMU classification tool (GMS-16S).

Seventeen out of 20 laboratories successfully sequenced and analysed the samples. Laboratories that used sodium acetate-containing elution buffers faced compatibility issues during library construction, resulting in reduced read count. High bacterial load samples were generally well-characterized, whereas hard-to-lyse bacteria such as Gram-positive strains were detected at lower abundance. The GMS-16S tool provided improved species-level identification compared to the 1928-16S pipeline, particularly for closely related taxa within the Streptococcus and Staphylococcus genera.

Nanopore sequencing demonstrated promising potential for bacterial identification in a clinical setting. The results prompt further optimization of the protocol to improve detection of a broader range of species. This multicentre study highlights the feasibility of implementing Nanopore sequencing into clinical microbiological laboratories, for improved national precision diagnostics.

The peripartum period is critical for breeding female donkeys (i.e., jennies) and ensuring the delivery of healthy neonatal foals. The gut microbiota deeply influences the host metabolism. This study aimed to investigate the dynamic changes in the gut microbiome during the peripartum period in jennies. Fresh fecal samples of eight adult jennies were collected at the following seven sampling time points: 21, 7, and 3 days prepartum (G21, G7, and G3) and 1, 3, 7, and 14 days postpartum (L1, L3, L7, and L14). Sequencing of the V4 hypervariable regions of the 16S rRNA genes was carried out using fecal samples to identify the differences in the microbiome across the peripartum period. Bacteroidota and Firmicutes were the most abundant bacterial phyla in the feces. Treponema and Lachnospiraceae XPB1014 group significantly increased in the L3 group compared to the G7 group (q < 0.05), and a decline trend was observed in L1 group around parturition. The genus Clostridium sensu stricto 1, family Clostridiaceae, and order Clostridiales were considered to be biomarkers of the L3 group. Among the 25 functional pathways detected by Kyoto Encyclopedia of Genes and Genomes pathway analysis, beta lactam resistance, insulin resistance, and peptidases were the top three important pathways observed in the gut microbiota during the peripartum period in jennies. The gut microbial structure changed significantly at different time points during the peripartum period in jennies. These results contribute to a better understanding of the gut microbiota to ensure health care during important phases from late pregnancy to early lactation in jennies.