Microbiome最新文献

{"title":"SubCom analysis: dissecting microbial community functions into taxon-specific contributions and interaction contexts.","authors":"Hidehiro Ishizawa, Miku Kito, Sunao Noguchi, Kodai Kimura, Masahiro Takeo","doi":"10.1186/s40168-026-02460-3","DOIUrl":"10.1186/s40168-026-02460-3","url":null,"abstract":"<p><strong>Background: </strong>Microbial communities play fundamental roles in industrial processes and ecosystem stability. However, understanding how individual members and their interactions give rise to community-level function remains challenging because such functions emerge from complex interactions among diverse members.</p><p><strong>Results: </strong>In this study, we developed SubCom analysis, a subcommunity-based experimental-computational workflow for inferring candidate taxon-specific contributions and interaction contexts underlying microbial community function. Using an aniline-degrading microbial community, we generated paired composition-function data from 558 randomly assembled, low-complexity subcommunities constructed using a dilution-and-dispense strategy. We then trained decision-tree-based models to predict community function from composition, achieving high predictive performance (r = 0.77-0.89). Interpretation of the learned decision rules identified taxa with consistent functional association: specific Pseudomonas and Acinetobacter taxa were associated with increased community-level aniline utilization, whereas an Achromobacter taxon exhibited a negative association despite its presumed role in downstream metabolism. The models further suggested potential functional interactions, including attenuation of the positive contributions of Pseudomonas and Acinetobacter in the presence of a Corynebacterium taxon, highlighting functional relationships that are not readily inferred from genome-based approaches alone. An augmentation assay using representative isolates supported the predicted direction of several effects and enabled targeted improvement of community function.</p><p><strong>Conclusions: </strong>These results demonstrate the potential of SubCom analysis as a practical framework for inferring taxon-specific contributions and interaction contexts in complex, nonsynthetic microbial communities. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13374233/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148422352","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Conserved 3' stem-loop structures enable comprehensive analysis of bacterial transcription termination in metagenomes.","authors":"Yunfan Jin, Jiyun Cui, Rulong Liu, Hongli Ma, Xiaomin Xu, Shufang Wu, Fei Gan, Zhi John Lu, Zhenjiang Zech Xu","doi":"10.1186/s40168-026-02454-1","DOIUrl":"10.1186/s40168-026-02454-1","url":null,"abstract":"<p><strong>Background: </strong>Bacterial transcription termination is a critical yet underexplored layer of gene regulation in microbial ecosystems. Existing computational tools, however, primarily focus on predicting transcript 3' ends generated by Rho-independent terminators (RITs) in a few model species, leaving gaps in understanding those generated by Rho-dependent terminators (RDTs) and their diversity across Bacteria.</p><p><strong>Results: </strong>We developed BATTER (Bacteria Transcript Three Prime End Recognizer), a deep learning-based framework for predicting bacterial transcript 3' termini. BATTER leverages the observation that conserved stem-loop structures are frequently associated with 3' ends of primary transcripts terminated by both RIT and RDT mechanisms across diverse bacterial clades. Compared with existing approaches, BATTER demonstrated superior performance and scalability, enabling a comprehensive analysis of 42,905 representative bacterial genomes. This large-scale application revealed that stem-loop structures exhibit clade-specific properties with greater variations between species than between gene families. Notably, BATTER uncovered that certain Cyanobacteria lineages, despite lacking rho homologs, harbor Rho utilization (RUT)-like sequences near 3' ends, and preliminary experimental validation in E. coli supports their partial functionality in transcription termination. Additionally, BATTER systematically identified pervasive premature termination events in antimicrobial resistance (AMR) genes.</p><p><strong>Conclusions: </strong>BATTER enables large-scale comparative genomic analyses of transcription termination, providing a powerful framework to investigate termination-associated transcriptional regulation in microbial communities. The BATTER tool is available at https://github.com/xu-research-lab/BATTER . Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13613805/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148391290","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction: Heat stress suppresses lactation through potential rumen-mammary communication mediated by extracellular vesicles: integrated analysis of microbiome, metabolome, and miRNA profiles.","authors":"Qi Huang, Dewei Du, Jia Guo, Jiaqi Liu, Peng Sun","doi":"10.1186/s40168-026-02471-0","DOIUrl":"10.1186/s40168-026-02471-0","url":null,"abstract":"","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"14 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13321500/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148369063","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Museomics reveals uncultured symbionts with biosynthetic potential in nudibranchs.","authors":"Dafne Porcel Sanchis, Marta Pola, J Pamela Engelberts, Oleanna Guerra-Font, Lauren Messer, Inés Alberola-Mora, Lucía Escobar Sáez, Néstor Pérez Gómez, Álvaro Portolés Campo, Juan Valero-Tebar, Luis María Naya Garmendia, Jesús Carlos Preciado Barahona, Rosario Gil García, Vicente Arnau, Simon J McIlroy, Mária Džunková","doi":"10.1186/s40168-026-02456-z","DOIUrl":"10.1186/s40168-026-02456-z","url":null,"abstract":"<p><strong>Background: </strong>Museum specimens are widely used for PCR-based pathogen detection, yet their potential for metagenomic discovery of beneficial microbes remains underexplored, largely due to difficulties in distinguishing true symbionts from contaminants. Here, we use metagenomics of museum specimens to uncover symbioses in endangered or difficult-to-collect animals, such as nudibranchs. To date, Doriopsilla is the only nudibranch demonstrated to harbor an uncultured symbiont involved in chemical defense, leaving it unclear whether comparable associations occur in other nudibranchs. We hypothesized that bona fide symbionts should belong to abundant, uncultured lineages consistently present across individuals of the same host taxon collected across space and time.</p><p><strong>Results: </strong>Using ethanol-preserved specimens archived for up to 30 years, we doubled the number of available nudibranch microbiome datasets and found that dominant uncultured symbionts are rare, with most nudibranchs likely relying on alternative chemical defense mechanisms. An exception were Polycera and Felimare that contained two previously unknown symbionts, Candidatus Polyceribacter and Candidatus Felimaribacter, from distinct uncultured orders that are globally rare in marine metagenomes. These symbionts encode diverse biosynthetic gene clusters exhibiting strain- and species-level microdiversity consistent with metabolites previously reported from their hosts. Their restricted host distribution, phylogenetic distinctiveness, and phylogenetic similarity to symbionts of sponges or corals that are not nudibranch prey, support long-term evolutionary specialization and functional convergence. Fine-scale diversification further suggests host-driven microbial adaptation following symbiosis establishment.</p><p><strong>Conclusions: </strong>Overall, this study establishes museomics as a robust framework for symbiosis research and advances understanding of the evolutionary and chemical ecology of host-microbe interactions in rare marine invertebrates. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13393909/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148360762","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Population-based characterisation of child and adolescent oral bacterial microbiomes.","authors":"Robyn J Wright, Vanessa DeClercq, Christie L Burton, Nicole M Roslin, Alex W Y Chan, Paul D Arnold, Paul Peters, Russell Schachar, Jennifer Crosbie, Morgan G I Langille","doi":"10.1186/s40168-026-02452-3","DOIUrl":"10.1186/s40168-026-02452-3","url":null,"abstract":"<p><strong>Background: </strong>The factors influencing the oral microbiome during childhood and adolescence remain under-explored at the population level. Furthermore, details on how the oral microbiome differs with age, varies between individuals of different ethnicities, or is associated with socioeconomic factors and diet in children and adolescents are almost entirely unknown. Saliva samples and detailed demographic, health, diet and socioeconomic data were collected from children and adolescents that attended the Ontario Science Centre (Toronto, Canada) and were enrolled in the Spit for Science cohort. We characterised the bacterial microbiota of 4812 samples using 16S rRNA gene sequencing to make this the largest population cohort of the paediatric oral microbiome to date.</p><p><strong>Results: </strong>Exploration of limited participant genotyping information and more than 50 variables encompassing the demographics, health, diet, socioeconomic status and living environment of participants revealed that almost all of the investigated variables were associated with overall community structure and/or the abundance of specific bacterial genera. However, most of these associations were modest (R² < 0.01) and the correlation between genetic relatedness and salivary bacteriome similarity was weak (R² = -0.014), while the strongest determinants of oral bacteriome composition were shared family/household environment (R² = 0.61 in the subset of participants from multi-child households), age (R² = 0.014) and ethnicity (R² = 0.01). We show that older children and adolescents have higher richness but lower evenness than younger children, suggesting that their oral bacteriome changes as they are exposed to more influences outside the home, and that the oral bacteriome is more consistent with more core taxa among children and adolescents than adults. We also find that diet variables related to the frequency of sugar consumption have the largest impact on the oral bacteriome of children and adolescents, and that microbial differences attributed to ethnicity and diet are likely intertwined.</p><p><strong>Conclusions: </strong>This study provides an atlas of the demographic, health and lifestyle factors that are associated with the salivary bacteriome of children and adolescents. These findings highlight the complex interplay between social, environmental, and biological factors in shaping the developing oral microbiome and underscore the importance of inclusive, demographically diverse cohorts in microbiome research. This presents a reference for the variables that are important to account for in paediatric oral microbiome studies. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13520369/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148361106","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Uncovering transcriptional processes in microbial communities adapted to differing saline conditions in salt-weathered historic buildings.","authors":"Lukas Fürnwein, Johannes Tichy, Monika Waldherr, Elias Lehner, Martin Ortbauer, Ylenia Vassallo, Beate Sipek, Katja Sterflinger, Guadalupe Piñar, Alexandra B Graf","doi":"10.1186/s40168-026-02383-z","DOIUrl":"10.1186/s40168-026-02383-z","url":null,"abstract":"<p><strong>Background: </strong>Microbial colonization of architectural surfaces in historic buildings can cause not only aesthetic damage but also biodeterioration. One example is the colonizing microbiome on salt-weathered architectural surfaces. Halotolerant and halophilic communities on such surfaces produce colored pigments that visually alter cultural heritage sites and could potentially degrade organic binders used for mural paintings. Although the microorganisms involved in these deterioration processes have already been described, detailed information about the molecular processes that allow these communities to succeed, survive, and thrive under such extreme conditions is still lacking.</p><p><strong>Results: </strong>A combined metagenome and metatranscriptome approach were employed to investigate three sampling sites located in two Austrian historic buildings displaying different environmental and saline compositions. The chapel of St. Virgil (Vienna) is a subsurface, climate-controlled environment. In contrast, the Charterhouse Mauerbach (Lower Austria) is exposed to natural fluctuations in temperature and humidity. DNA and total RNA were extracted from each sampling site simultaneously and sequenced. Two methods for gene assembly were compared and functionally evaluated. Results showed a minor bias in both methods, with improved results when they were combined. Comparison between DNA and RNA showed interesting variations in the taxonomic composition between the DNA- and RNA-based dataset, distinguishing the dormant from the active microbiome. The annotated halotolerance mechanisms in the metatranscriptomes indicated genome and proteome adaptations, showing high GC content, proteome acidification, with elevated aspartate and glutamate levels, and low isoelectric point profiles. Furthermore, the communities used both \"salt-in\" and \"salt-out\" osmoregulatory mechanisms. Pigment production was confirmed in all sampling points, revealing diverse pathways for carotenoid biosynthesis. Various protective mechanisms against oxidative stress were detected, such as those against reactive oxygen species (ROS), but also detoxification, protein folding, protein and DNA repair, and RNA chaperones. Key metabolic pathways revealed diverse pathways related to carbon, nitrogen, and sulfur cycling, linked to varying oxygen concentrations within biofilms. The results also highlighted the need for an in-depth analysis of the capabilities of the involved microorganisms.</p><p><strong>Conclusions: </strong>The study shows highly specialized and cooperative adaptations, using both \"salt-in\" and \"salt-out\" strategies, diverse phototrophic and redox metabolisms that tightly couple C-N-S cycling.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13326497/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148352427","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"IL-17A deficiency in HLA-DR3 transgenic mice enriches beneficial Prevotella species in gut to promote Tregs and reduce CNS autoimmunity.","authors":"Shailesh K Shahi, Sudeep Ghimire, Samantha N Jensen, Peter C Lehman, Allison G Rux, Souradip Sinha, Nicholas Borcherding, Munir R Tanas, Katherine N Gibson-Corley, Sukirth M Ganesan, Nitin J Karandikar, Ashutosh K Mangalam","doi":"10.1186/s40168-026-02394-w","DOIUrl":"10.1186/s40168-026-02394-w","url":null,"abstract":"<p><strong>Background: </strong>Human Leukocyte Antigen (HLA) class-II genes, particularly HLA-DR2 and HLA-DR3, and the gut microbiota are intricately linked to the pathobiology of multiple sclerosis (MS) through their ability to regulate host immunity, a critical factor in disease pathogenesis. An imbalance between anti-inflammatory CD4⁺ Tregs and pro-inflammatory IL-17A-secreting CD4⁺ Th17 cells is thought to drive disease. However, a key unresolved question is whether HLA-class II-restricted CD4⁺IL-17A cells can influence Treg populations and the extent to which gut microbiota regulate this IL-17A-Treg axis. Therefore, we utilized humanized transgenic mice expressing the HLA class-II gene and deficient in mouse class-II molecules, where all CD4⁺ T cells are selected on the human HLA class-II molecule, closely mimicking human immune responses.</p><p><strong>Results: </strong>Utilizing IL-17A-deficient (DR3.IL-17A^-/-) mice expressing HLA-DR3 (HLA-DRβ1*0301), we show that IL-17A deficiency enriches beneficial gut bacteria, including Prevotella species, enhances peroxisome proliferator-activated receptor (PPAR) signaling, and increases FoxP3⁺ regulatory T (Treg) cells and IL-10 production. The importance of gut microbiota in promoting Tregs and anti-inflammatory responses was confirmed by administering Prevotella copri, a common commensal in human gut, which mirrored the effects observed in IL-17A-deficient mice by inducing PPAR signaling and Treg population. Moreover, DR3.IL-17A^-/- mice exhibited a marked reduction in EAE severity compared to IL-17A-sufficient (DR3) mice, underscoring the enhanced functional capacity of the Treg population in mitigating disease progression. Cohousing experiments validated the role of gut microbiota in immune regulation including Treg induction, as demonstrated by the transfer of Prevotella species from IL-17A-deficient mice to IL-17A-sufficient mice, increased Treg populations and attenuated EAE severity in recipient DR3 mice.</p><p><strong>Conclusions: </strong>This study redefines IL-17A's role in immune regulation, emphasizing its ability to directly influence gut microbiota composition and the abundance of Treg-promoting bacteria. Thus, gut microbiota-targeted therapies, particularly those promoting Treg-inducing bacteria like Prevotella species, hold promise for treating autoimmune diseases by modulating host immune responses. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13326294/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148352463","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Differential rumen and hindgut microbiome and metabolome in Holstein female calves with divergent feed efficiency.","authors":"Tianyu Chen, Jianxin Xiao, Shangru Li, Rong Peng, Yiming Xu, Yimin Zhuang, Xinjie Zhao, Mo Sha, Jingjun Wang, Jiaying Ma, Wei Wang, Jian Gao, Mei Ma, Shengli Li, Zhijun Cao, Shuai Liu","doi":"10.1186/s40168-026-02446-1","DOIUrl":"10.1186/s40168-026-02446-1","url":null,"abstract":"<p><strong>Background: </strong>Significant environmental problems have challenged animal agriculture, improving feed efficiency in animals has become a vital research direction for sustainable agriculture. Bacteria play a critical role in the feed efficiency of animals. However, our current understanding of bacteria communities in the gastrointestinal tract of high-feed efficiency animals and their metabolic mechanisms remains unclear.</p><p><strong>Results: </strong>Twenty Holstein female calves were used in this multi-omics study that integrated metagenomic and metabolomic analyses of 20 Holstein female calves to investigate feed efficiency, as measured by residual feed intake (RFI). From an initial cohort of 84 calves, the 10 with the highest RFI (HRFI, low efficiency) and the 10 with the lowest RFI (LRFI, high efficiency) were selected at 84 days of age. Rumen fluid, feces, and serum samples from these calves were collected for subsequent analyses. We found that LRFI calves harbored rumen and fecal microbiomes with significantly different community structures and co-occurrence networks compared to HRFI calves. Multi-omics integration identified robust microbial and metabolite biomarkers discriminating RFI groups. These microbiomes were functionally linked to differential nutrient utilization, LRFI calves were characterized by enhanced starch and protein digestibility coupled with propionate-oriented fermentation, associated with key species like Erysipelotrichaceae_bacterium and Hungatella_sp. Conversely, HRFI calves showed higher fat digestibility and acetate production. Notably, serum glutamate was enriched in LRFI calves despite lower intake, correlating with potential microbial metabolites (ribitol, taurine). Subsequent validation confirmed that glutamate supplementation in mice improved nitrogen metabolism and gut barrier function.</p><p><strong>Conclusions: </strong>In summary, this multi-omics study reveals that high feed efficiency in calves is associated with distinct microbial ecosystems characterized by functions such as starch degradation and propionate production, where glutamate metabolism serves as a central node. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13587403/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148330248","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reconstructing community dynamics from limited observations.","authors":"Chandler Ross, Ville Laitinen, Moein Khalighi, Jarkko Salojärvi, Willem M de Vos, Guilhem Sommeria-Klein, Leo Lahti","doi":"10.1186/s40168-026-02449-y","DOIUrl":"10.1186/s40168-026-02449-y","url":null,"abstract":"<p><strong>Background: </strong>Ecosystems tend to fluctuate around stable equilibria in response to internal dynamics and environmental factors. Occasionally, they enter an unstable tipping region and collapse into an alternative stable state. Being able to quantify and predict these dynamics is key to our understanding of how microbial communities vary over time and respond to perturbations.</p><p><strong>Results: </strong>Mechanistic models of microbial community dynamics often fail to characterise observed fluctuations in naturally occurring microbiomes and inform us about key dynamical properties such as stability and resilience. An alternative approach is to characterise the dynamical landscape using non-parametric models. However, the scarcity of long, dense time series data poses a severe bottleneck for characterising community dynamics using existing methods. We overcome this limitation by combining information across multiple short time series using Bayesian inference. By decomposing dynamics into deterministic and stochastic components using Gaussian process priors, we are able to predict stable and tipping regions along a unidimensional stability landscape while simultaneously addressing the associated uncertainty. In particular, we estimate a recently proposed probabilistic metric for resilience in multistable systems: the expected \"exit time\" out of the current stable state under stochastic fluctuations. We validate our approach on simulated data and highlight in particular that our model is able to distinguish bistability from bimodality, which are often conflated in classical potential analyses. We further demonstrate our approach by re-analysing ecological time series data of lake cyanobacteria abundance, for which we recover similar results as a previous study using three orders of magnitude fewer data points. Finally, we use our model to re-evaluate the stability of previously proposed \"tipping elements\" in the human gut microbiota.</p><p><strong>Conclusions: </strong>We introduce a probabilistic non-parametric approach to characterise stationary community dynamics from short time series, which is potentially applicable to a broad range of systems in microbial ecology and beyond. We use this model to clarify the distinction between bistable and bimodal dynamics and to contribute to contemporary debates on the stability and resilience of ecological communities, in particular the human gut microbiota. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13540962/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148330251","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Whole metagenome sequencing: not deep enough for complete microbial function recovery.","authors":"Jia Liu, Modupe Oluseun Coker, Nosayaba Osazuwa-Peters, Oluwaseun Peter, Nosakhare Lawrence Idemudia, Nicolas F Schlecht, Ozoemene Obuekwe, Fidelis E Eki-Udoko, Yana Bromberg","doi":"10.1186/s40168-026-02448-z","DOIUrl":"10.1186/s40168-026-02448-z","url":null,"abstract":"<p><strong>Background: </strong>Whole metagenome shotgun sequencing (WMS) is widely used to profile microbial function. However, technical variability in sequencing and analysis often obscures true biological patterns. Large-scale studies are particularly susceptible to batch effects, such as differences in sequencing depth and platform and annotation strategies, as well as sample-to-flow-cell assignments. However, the relative effects of these factors on functional inference in such studies have yet to be systematically evaluated. We analyzed oral-rinse WMS data from 671 Nigerian youths aged 9-18, sequenced on two Illumina platforms. Microbial molecular functionality encoded in these data was annotated using the mi-faser/Fusion pipeline, to capture the broad functional repertoire, and HUMAnN 3/EC numbers pipeline to characterize curated enzymatic activities. We then quantified how technical factors and batch effects shaped the recovery of microbial functionality.</p><p><strong>Results: </strong>Three findings of our work were most salient. First, we observed that the choice of annotation strategy traded off between breadth and specificity of functional coverage. Second, we found that low-prevalence functions were disproportionately lost at shallow sequencing depths, indicating that in, e.g., case-control studies with few representatives of the minor class, sequencing depth could critically impact study resolution. Finally, using our newly developed model relating sequencing depth to functional recovery, we demonstrated that increasing sequencing depth does not directly or proportionally improve functional recall. That is, at as little as 10% of this study's sequencing depth, 30% of the estimated complete microbiome functional repertoire was detectable. However, even at the full depth used in this study, we were only able to recover an estimated 60% of that complete functional repertoire. We further showed that despite biomes differences in functional diversity and host contamination levels (e.g., soil, fecal), incomplete functional recovery at commonly used sequencing depths was consistently observed.</p><p><strong>Conclusions: </strong>Together, these findings and our depth-to-function mapping framework provide practical guidelines for the design and interpretation of WMS studies. Coordinating sequencing depth planning with annotation strategy, experimental design, and rigorous batch control is thus essential for robust detection of microbial functions and for ensuring reproducible microbiome insights. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13556019/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148330180","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}