Microbiome最新文献

Background: Understanding how metabolic capabilities diverge across microbial species is essential for deciphering community function, ecological interactions, and the design of synthetic microbiomes. Despite shared core pathways, microbial phenotypes can differ markedly due to evolutionary adaptations and metabolic specialization. Genome-scale metabolic models (GEMs) provide a systems-level framework to explore these differences; however, their complexity hinders direct comparison.

Results: We introduce NIS (Neidhardt-Ingraham-Schaechter), a computational workflow that integrates the redGEM, lumpGEM, and redGEMX algorithms to systematically reduce genome-scale models into biologically interpretable modules. This approach enables direct, quantitative comparison of fueling pathways, biomass biosynthetic routes, and environmental exchange processes while retaining essential metabolic information. We first demonstrate the utility of NIS by analyzing Escherichia coli and Saccharomyces cerevisiae, which revealed both conserved and divergent strategies in central metabolism, biosynthetic cost, and substrate utilization. We then applied NIS to the core honeybee gut microbiome, uncovering distinct metabolic traits, functional redundancy, and complementarity that help explain auxotrophy, cross-feeding interactions, and microbial coexistence.

Conclusions: NIS provides an automated, scalable, and reproducible framework for dissecting microbial metabolic networks beyond gene content or taxonomy. By linking metabolism to ecological function, NIS offers new opportunities to interpret microbial community dynamics and to support the rational design of microbiomes in health, agriculture, and environmental applications. Video Abstract.

Background: Microorganisms in groundwater ecosystems exist either as planktonic cells or as attached communities on aquifer rock surfaces. Attached cells outnumber planktonic ones by at least three orders of magnitude, suggesting a critical role in aquifer ecosystem function. However, particularly in consolidated carbonate aquifers, where research has predominantly focused on planktonic microbes, the metabolic potential and ecological roles of attached communities remain poorly understood.

Results: To investigate the differences between attached and planktonic communities, we sampled the attached microbiome from passive samplers filled with crushed carbonate rock exposed to oxic and anoxic groundwater in the Hainich Critical Zone Exploratory and compared it to a previously published, extensive dataset of planktonic communities from the same aquifer ecosystem. Microbial lifestyle (attached vs. planktonic) explained more variance in community composition than redox conditions, prompting us to further investigate its role in shaping functional and activity profiles. Metagenomic analysis revealed a striking taxonomic and functional segregation: the 605 metagenome-assembled genomes (MAGs) from attached communities were dominated by Proteobacteria (358 MAGs) and were enriched in genes for biofilm formation, chemolithoautotrophy, and redox cycling (e.g., iron and sulfur metabolism). In contrast, the 891 MAGs from planktonic communities were dominated by Cand. Patescibacteria (464 MAGs) and Nitrospirota (60 MAGs) and showed lower functional versatility. Only a few genera were shared, and even closely related MAGs (> 90% average nucleotide identity) differed in assembly size and metabolic traits, demonstrating lifestyle-specific functional adaptation. Analysis of active replication indicated that the active fraction of the attached community was primarily represented by the most abundant MAGs. Planktonic communities featured a higher fraction of active MAGs compared to attached communities, but overall with lower relative abundances.

Conclusions: The high abundance, metabolic specialization, and carbon fixation potential of attached microbes suggest that they are key drivers of subsurface biogeochemical processes. Carbonate aquifers may act as much larger inorganic carbon sinks than previously estimated based on CO₂ fixation rates of the planktonic communities alone. Our findings underscore the need to incorporate attached microbial communities into models of subsurface ecosystem function. Video Abstract.

Background: The role of gut microbiome in predicting diet response and developing personalized dietary recommendations has been increasingly recognized. Yet, we still lack comprehensive, genome-based insights into which gut microbes metabolize specific dietary compounds.

Results: Here, we leveraged the metabolic networks constructed from well-annotated microbial genomes to characterize the potential interactions between microbes and metabolites, specifically emphasizing the interactions between microbes and dietary compounds. We revealed a substantial, approximately fourfold variation in both the number of metabolites and dietary compounds in the microbial genome-scale metabolic networks across different genera, whereas species within the same genus showed a high metabolic similarity (mean coefficient of variation in microbial network degree $\overline{\mathrm{CV}}$ = 0.023 for metabolites and 0.015 for dietary compounds). We found that the number of species that can utilize a metabolite drastically varies, ranging from 1 to 818 species, with some metabolites being used by a wide range of species (211 out of 1390 metabolites used by more than 95% of species) and others only by a few species (435 metabolites used by less than 5% of species). Leveraging a longitudinal microbiome study, we observed that microbial taxa with similar metabolic capacity tend to have positively correlated abundances, and the gut microbiome's capacity to process dietary compounds is functionally stable. Finally, we propose a network-based method to identify the dietary compounds that are specific to no more than 10 microbial species, offering a new strategy for combining a dietary compound and its linked microbial species to design synbiotics.

Conclusions: Our results quantitatively reveal large-scale variation and redundancy in gut microbial metabolism and identify dietary compounds linked to only a few microbial species. These findings improve understanding of microbe-metabolite interactions and provide a foundation for the rational design of microbiome-based interventions for healthy benefits. Video Abstract.

Background: Dietary fibre is an important regulator of the gut microbiome and is associated with many health benefits. However, high levels of fibre intake have also been reported to exacerbate some diseases.

Results: Here, we show that mice fed semi-synthetic diets supplemented with purified inulin fibre develop chronic infections with the parasitic whipworm Trichuris muris, concomitant with dysregulated innate antimicrobial defences, exacerbated mucosal inflammation, and altered tryptophan metabolism. Inhibition of tryptophan catabolism or neutralizing either IL-27 or IL-18 restored infection resistance. Inulin-fed mice developed gut microbiota dysbiosis during parasite infection, with Proteobacteria becoming dominant. However, despite drastic differences in gut microbiota compositions in control- and inulin-fed mice, microbiota transfer and depletion experiments demonstrated that dietary inulin triggered chronic T. muris infection in a microbiota-independent manner. Importantly, removing inulin from the diet within a critical immune development window rapidly restored anti-parasite immunity, indicating direct, time-dependent modulation of mucosal immune responses.

Conclusions: These data reveal T. muris-induced dysbiosis as a consequence rather than a causative factor of diet-driven changes in host susceptibility, and establish a direct link between dietary fibre and host defence at mucosal surfaces. Video Abstract.

Background: Bacterial antiphage defense systems play essential roles in microbial ecology, yet their dynamics within urban wastewater systems (UWS) remain poorly characterized.

Results: In this study, we performed comprehensive metagenomic and plasmidome analyses on 78 wastewater samples collected during two seasons and four sampling points across UWS from three European countries. We observed a significant reduction in the abundance, diversity, and mobility potential of defense systems during biological treatment. However, these reductions were not directly correlated with changes in microbial abundance. Defense systems were significantly enriched on plasmids, particularly conjugative plasmids, where their gene density was approximately twice as high as on chromosomes and remained relatively stable across compartments. In contrast to chromosomal defense systems, plasmid-borne systems exhibited more frequent co-localization with a wide range of mobile genetic elements (MGEs)-associated genes, thereby facilitating multilayered dissemination networks. Furthermore, we detected a strong correlation between phage abundance and host defense system profiles, indicating ongoing phage-host co-evolutionary dynamics in these environments.

Conclusions: In summary, our results demonstrate that UWS reduce the abundance and diversity of bacterial defense system genes. However, plasmid-associated defense systems can persist through shared mobile genetic reservoirs. These findings underscore the critical role of plasmids in bacterial immunity and provide new insights into defense system dynamics within urban wastewater environments.

Background: Bovine metritis is associated with uterine microbiota dysbiosis, characterized by the proliferation of Gram-negative anaerobes, including Fusobacterium necrophorum, Bacteroides pyogenes, and Porphyromonas levii. However, the mechanisms by which these opportunistic pathogens proliferate together and contribute to disease remain unclear. This study aimed to identify the interactions among these bacteria and to elucidate their role in the development of metritis.

Methods: F. necrophorum, B. pyogenes, and P. levii were isolated from the uteri of cows with metritis and cultured anaerobically in chopped meat carbohydrate broth. Bacterial growth, coaggregation, biofilm formation, endotoxin production, protease activity, adhesion to bovine endometrial epithelial (BEND) cells, and cytotoxicity were evaluated under single-, dual-, and triple-species culture conditions.

Results: Among the three species, F. necrophorum grew faster and acted as a key species that coaggregated with B. pyogenes and P. levii, promoting multi-species biofilm formation and increasing bacterial adhesion to BEND cells. The growth of B. pyogenes was enhanced by metabolites from P. levii, whereas the growth of P. levii was delayed by metabolites from F. necrophorum. The multi-species biofilm formed by these three bacterial species generated the highest biomass, with P. levii predominantly occupying the basal layer and F. necrophorum and B. pyogenes co-localizing in the upper layer. This spatial arrangement likely reflects the strong biofilm-forming ability of P. levii, which rapidly produces matrix and provides a scaffold for cohabiting species. Endotoxin levels were highest in both F. necrophorum and P. levii, and protease activity was highest in P. levii under mono-culture conditions. However, no synergistic effects were observed for either parameter under co-culture conditions. Interestingly, co-culture with B. pyogenes lowered the endotoxin levels of the other bacteria and attenuated the cytotoxicity of P. levii.

Conclusions: Our findings suggest that these opportunistic uterine pathogens interact synergistically to promote bacterial persistence in the uterus rather than exacerbating disease severity, which likely contributes to uterine microbiota dysbiosis and chronic inflammation. Video Abstract.

Background: Over the past decade, emerging evidence has shed light on the role of the gut microbiota in the interface between diet and brain health. Olive oil, particularly virgin olive oil, a key component and major fat source in the Mediterranean diet, has exhibited widespread healthful benefits, including improvements in gut microbiota and cognitive health. Despite insights from preclinical studies into the relationship between virgin olive oil consumption, gut microbiota, and cognitive function, human research in this area remains limited. Therefore, our study aims to investigate the interplay between total olive oil consumption and its subtypes, gut microbiota, and changes in cognitive function in older adults who were cognitively healthy at baseline but at high risk of cognitive decline.

Methods: In this prospective cohort study, we assessed a total of 656 participants aged 55 to 75y (mean age 65.0 ± 4.9y, 47.9% women) with overweight/obesity and metabolic syndrome who provided stool samples and completed a validated semi-quantitative food frequency questionnaire at baseline and a comprehensive battery of neuropsychological tests at baseline and at a 2-y follow-up.

Results: Results from the multivariable linear regression models showed that higher consumption of virgin olive oil was associated with improved cognitive function over a 2-y follow-up, and a more diverse gut microbiota overall structure at baseline. Conversely, increased consumption of common olive oil is linked to lower alpha diversity of the microbial communities, and accelerated cognitive decline. Mediation analysis suggests that gut microbiota and particularly the Adlercreutzia, may serve as a mediator taxon in the association between virgin olive oil consumption and positive changes in general cognitive function.

Conclusions: Higher consumption of virgin olive oil was associated with cognitive preservation, possibly mediated by favorable alterations in gut microbiota composition. Our study provides novel insights into the complex interplay between different types of olive oil consumption, gut microbiota, and changes in cognitive function. These findings underscore the potential of microbiota-targeted dietary strategies to promote cognitive health in aging populations, though further high-quality and clinical cohort studies are required. Video Abstract.

Background: Urban wastewater systems (UWSs) act as reservoirs and conduits for the dissemination of antibiotic resistance genes (ARGs), with plasmids playing a central role in their spread. Despite their significance, the diversity and persistence of plasmids in UWSs remain underexplored.

Results: This study applies a multi-omics approach, including metagenomic and direct plasmidome sequencing, high-throughput qPCR array, and whole genome sequencing of plasmid isolates, to comprehensively profile the microbial plasmidome and resistome on 78 samples across UWSs in Denmark, Spain, and the UK. We successfully uncovered an extensive plasmid and ARG diversity that could not be fully captured by a single method, especially identified 78,574 plasmids, including 20,925 plasmids previously unreported. We also observed that plasmids carried a disproportionate share of clinically relevant ARGs, particularly beta-lactamase resistance genes; most importantly, they were preferentially located on transmissible plasmids. Furtherly, plasmids harbor ARG can enhance their persistence in wastewater ecosystems, especially harboring multiple types of ARGs. Moreover, Bacteroides emerged as a unique persistent ARG reservoir not only for harboring and disseminating diverse resistance genes especially in residential-relevant areas, but also emerged as a major driver of antimicrobial resistance dynamics across different wastewater treatment processes.

Conclusions: Overall, this work provides the first attempt at a holistic description of the UWSs' resistome, its structure, dynamics, and mobility and significantly expands the current knowledge. Video Abstract.

Background: Slaughterhouses and meat cutting plants represent potential hotspots for the spread and transfer of spoilage and pathogenic, including antimicrobial resistant, bacteria to meat and meat products. Here, we characterise the progression of the microbiome and resistome of two pork cuts (loin and sirloin) at different stages of processing, from the slaughter line to the end of shelf-life. To this end, we analysed samples from facility surfaces, carcasses, and meat cuts using whole metagenome sequencing.

Results: The taxonomic and antimicrobial resistance gene (ARG) profiles of carcasses and meat cuts were significantly influenced by the point of sampling and the processing room. The facility surfaces were found to be the main source of some abundant genera, such as Anoxybacillus, Acinetobacter, Pseudomonas, and Brochothrix, in carcasses and meat cuts. A total of 1,291 metagenome-assembled genomes were reconstructed, corresponding to the most prevalent species identified in the taxonomic analysis at the read level. A reduction in bacterial and ARGs richness and diversity was observed for carcasses and meat cuts along the production chain, which suggests that processing procedures are effective in reducing bacterial and ARGs loads. Nonetheless, an increase in the ARGs load was observed at two sampling points: the carcass after evisceration and the sirloin at the end of its shelf-life (in this case linked to the increase of a single gene, tet(L)). The ARGs most frequently detected were those associated with resistance to tetracyclines, aminoglycosides, and lincosamides. Acinetobacter (in processing environments and carcass/meat samples) and Staphylococcus (in carcasses and meat) were identified as the main genera associated with the ARGs found.

Conclusions: Overall, our results provide the most detailed metagenomics-based perspective on the microbial successions of pig carcasses and fresh meat cuts during slaughtering, processing, and commercialisation. The observations made suggest that selection pressures imposed by processing steps and contact with facility surfaces contribute to shaping the microbiome and resistome of the two pork products throughout their production line and shelf-life. Video Abstract.

Background: Phytate is the primary phosphorus storage molecule of plants and plays a major role in animal nutrition. To enhance phosphate availability and absorption in livestock, and to reduce eutrophication by liquid manure, bacterial phytases are often added to animal feed. The dephosphorylated form of phytate, the polyol myo-inositol (myo-Ins) with multiple functions in eukaryotes, is metabolized by approximately 30% of all bacterial species.

Results: Here, we employed a culturomics approach to identify possible metabolic interactions between phytase-producing and myo-Ins degrading bacteria in intestinal samples from pigs. Selective cultivation revealed an unexpectedly high abundance of myo-Ins degrading bacteria, suggesting substantial phytate dephosphorylation in the pig gut. Phytase activity assays performed on gut isolates showed a high degree of variability, suggesting the presence of a diverse set of phytases yet to be characterized. Furthermore, using supernatants of phytase-positive gut strains cultivated in the presence of phytate, we observed cross-feeding of myo-Ins from phytase producers to phytase-negative strains, including the pathogen Salmonella enterica serovar Typhimurium.

Conclusions: The data demonstrate that a wide range of commensal bacteria can potentially benefit from phytase activity by utilizing myo-Ins, released through phytate hydrolysis, as a growth substrate. Video Abstract.