mSystems最新文献

{"title":"Machine learning reveals proteome-encoded growth determinants underlying metabolic versatility of <i>Rhodopseudomonas palustris</i> on lignin-derived aromatics.","authors":"Abraham Osinuga, Mark Kathol, Rajib Saha","doi":"10.1128/msystems.00383-26","DOIUrl":"https://doi.org/10.1128/msystems.00383-26","url":null,"abstract":"<p><p>Lignin depolymerization generates mixtures of aromatic compounds that are promising carbon sources for microbial bioconversion, yet the constraints governing microbial growth on these substrates remain unclear. Here, we investigated how <i>Rhodopseudomonas palustris</i> CGA009 organizes metabolism to grow on chemically distinct lignin-derived aromatics under aerobic and anaerobic conditions. Quantitative proteomics across 14 substrate-oxygen environments revealed extensive oxygen-dependent proteome remodeling, consistent with shifts between respiratory and photoheterotrophic programs. Despite this reorganization, predictive modeling showed that growth rate is encoded by a relatively small subset of proteins whose abundance tracks physiological performance across environments. Using CorePredX, a machine-learning framework that combines global importance analysis with dependence-aware redundancy filtering, we identified 118 high-confidence proteins whose variation made conditionally non-redundant contributions to growth-rate prediction among 1,857 quantified proteins. These proteins are organized into a hierarchical architecture comprising a cross-condition core, adaptive regulators, substrate-specific specialists, and conditional hubs. The cross-condition core linked translational capacity, sulfur assimilation, redox buffering, and carbon storage cycling, highlighting conserved proteomic features associated with growth across oxygen regimes and substrate chemistries. Notably, an uncharacterized cystathionine beta-synthase domain protein, RPA3416, emerged as a strong predictive component of this core, raising the hypothesis of an adenylate-responsive process associated with aerobic growth on lignin-derived aromatics. Together, these results suggest that the metabolic versatility of <i>R. palustris</i> arises from flexible regulation layered onto partially conserved proteome-encoded growth-associated constraints, providing candidate targets for lignin bioconversion engineering and metabolic model refinement.IMPORTANCELignin is an abundant part of plant waste that is notoriously difficult to break down and turn into valuable products. While certain microbes, like <i>Rhodopseudomonas palustris</i>, can consume lignin byproducts, scientists do not fully understand how they do it. In this study, we discovered that we can predict how well this microbe will grow simply by tracking a small, specific group of its core proteins-even when its environment changes. We also identified a new, unstudied protein that is a strong candidate for future research. By pinpointing the specific biological tools microbes use to process lignin, this research provides a clear roadmap for engineering bacteria to efficiently turn plant waste into useful, sustainable materials.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0038326"},"PeriodicalIF":4.6,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147840332","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial genetic screen identifies bacterial genes that compromise <i>Caenorhabditis elegans</i> reproductive fitness.","authors":"Ziling Yang, Huigui Guo, Yudong Zhang, Xinzhou Jia, Yalun Wu, Tao Zhu, Ying Li, Jinyue Wang, Dianshuang Zhou, Zuobin Zhu","doi":"10.1128/msystems.01698-25","DOIUrl":"https://doi.org/10.1128/msystems.01698-25","url":null,"abstract":"<p><p>The mechanisms by which microbial genetic variation governs host reproductive fitness remain to be determined. Defining the causal relationship between specific microbial genes and host reproduction not only facilitates understanding of the microbe-host interaction mechanism but also provides new insights for reproductive health interventions. However, the complexity of the gut microbial community poses a challenge, and related research has been constrained by a lack of systematic approaches. In the present study, we utilized the <i>Escherichia coli</i> Keio collection that comprises 3,467 strains to screen for three mutant strains <i>ΔcrcB</i>, <i>ΔpurE</i>, and <i>ΔyojI</i> that markedly inhibit the reproductive fitness of <i>Caenorhabditis elegans</i>. These mutants reduce offspring number and prolong the time to first reproduction, specifically inhibiting spermatogenesis, while exerting no impact on locomotor function or lifespan. Multi-omics analyses revealed that these gene deletions trigger bacterial metabolic remodeling, characterized by the accumulation of cytidine diphosphate-diacylglycerol (CDP-DG) and disturbances in nucleotide and glycerophospholipid metabolism. These changes further regulate oxidative phosphorylation (with gene upregulation) and cell cycle pathways (with gene downregulation) in the host nematode, thereby inducing a \"high metabolism, low proliferation\" state and ultimately reducing reproductive fitness. This study delineates the one-to-one correspondence between gene deletions in <i>Escherichia coli</i> and alterations in nematode reproduction at the single-gene level, providing a novel framework for dissecting the molecular basis of host reproductive disorders from a microbial genetics perspective.IMPORTANCEThis study identifies a direct causal link between a specific bacterial gene and host reproductive fitness. Systematic screening of <i>Escherichia coli</i> mutants showed that deleting one gene severely impairs <i>Caenorhabditis elegans</i> reproduction. Using a controllable model, we achieved precise microbe gene-host reproductive phenotype mapping, revealing the mechanism: bacterial gene deficiency induces host \"high metabolism, low proliferation\" to reduce fertility. It offers a new genetic perspective for understanding microbe-mediated reproductive disorders and a framework for dissecting single-gene microbe-host interactions and developing targeted interventions.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0169825"},"PeriodicalIF":4.6,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147840334","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Seasonal thawing of high Arctic soils triggers selective microbial growth and predation.","authors":"Margaret A Cramm, Ömer K Coskun, Francesco Montemagno, Matteo Selci, Daniel S Read, Tim Goodall, Brianna Green, Sayali A Mulay, Katie Sipes, Andrey A Abramov, Catherine M Heppell, Julia Boike, Donato Giovannelli, Tatiana A Vishnivetskaya, Robert L Hettich, Andrew D Steen, Karen G Lloyd, William D Orsi, Anne D Jungblut, James A Bradley","doi":"10.1128/msystems.00738-25","DOIUrl":"https://doi.org/10.1128/msystems.00738-25","url":null,"abstract":"<p><p>Climate warming threatens Arctic permafrost with seasonal cycles of freezing and thawing. Arctic soil microorganisms regulate carbon stocks and greenhouse gas exchanges with the atmosphere, yet their precise seasonal growth and dormancy dynamics, and their responses to permafrost thaw, are not well understood. We thawed frozen Svalbard active layer soil and traced microbial growth using DNA quantitative stable isotope probing with H₂¹⁸O. We observed temporal growth patterns resulting in distinct early (21-day) and late-stage (98-day) growing microbial populations. In particular, Acidobacteriota, Actinobacteriota, Bacteroidota, Proteobacteria, and predatory and epibiont bacterial taxa (such as those affiliated to Bdellovibrionota and Patescibacteria) were identified in the soil active layer as clades that were growing following thawing. Methane concentrations in our microcosms remained low, yet <i>pmoA</i> genes were ¹⁸O-labeled, indicating growth of aerobic methane-oxidizing bacteria. Approximately half of the microbial taxa detected did not grow, suggesting that Arctic soils constitute sizeable reservoirs of dormant microorganisms. Our results reveal complex and temporal microbial dormancy, growth, death, predation, and parasitism dynamics in seasonally changing Arctic soils. These processes likely regulate the exchange and storage of soil carbon across the increasingly vulnerable Arctic region.IMPORTANCEMicroorganisms play key roles in transforming soil carbon into greenhouse gases. As Arctic soils warm as a result of climate change, greater depths and expanses of permanently frozen soil are experiencing seasonal thaw. Despite the importance of active soil microorganisms in transforming soil carbon, the seasonal freezing and thawing of Arctic soils and associated dormancy and re-activation of microbial populations are not well constrained. Here, we thawed and incubated active layer (i.e., seasonally thawing) Arctic soil with a stable isotope to directly label the DNA of growing soil microorganisms. We found that half of the microbial diversity did not grow after thaw and that some groups, including the Bacteroidota and predatory bacteria, grew disproportionately. The growing microbial community shifted over time, and bacteria capable of oxidizing methane grew more after prolonged thaw. These findings highlight that dormancy, predation, and variable growth dynamics are important factors determining ecological and biogeochemical processes in thawing Arctic soil.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0073825"},"PeriodicalIF":4.6,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147840260","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Depth-associated selection and drift shape persistent microbial populations in Holocene lake sediments.","authors":"Paula Rodríguez, Sophie A Simon, Alexander J Probst, Cara Magnabosco","doi":"10.1128/msystems.01500-25","DOIUrl":"https://doi.org/10.1128/msystems.01500-25","url":null,"abstract":"<p><p>Cosmopolitan microbial lineages are found in anoxic sediments worldwide, but the details about their ecology and evolution remain underexplored. In this study, we identified persistent populations from these cosmopolitan lineages belonging to <i>Planctomycetes</i>, <i>Chloroflexi Atribacteria</i>, and <i>Candidatus</i> Bathyarchaeia from an ~8,000-year sedimentary sequence. To investigate the genomic variations within these persistent populations, a pangenome of each population was constructed using all non-redundant metagenome-assembled genomes (MAGs) recovered from the sedimentary sequence and was screened for enriched functional genes, single-nucleotide polymorphism (SNP) density, <i>dN</i>/<i>DS</i> ratios, and pseudogene content. Our results show that the majority of persistent populations studied possess large variable genomes enriched for energy conservation and transcriptional regulation functions with increasing depth, whereas <i>Planctomycetes</i> retain a highly conserved, SNP-poor core genome. Analysis of SNPs across depths indicates progressive isolation with burial, while a subset of core genes shows signatures of positive selection. Collectively, the data support depth-associated selection acting alongside drift across Lake Cadagno's persistent sedimentary lineages.IMPORTANCEThroughout the subsurface, multiple examples of \"evolutionary stasis\" have been reported in microbial lineages that exhibit lower rates of metabolic activity and cellular turnover. This study uses an ~8,000-year sedimentary record of Lake Cadagno to evaluate how persistent populations of cosmopolitan bacteria and archaea have changed with burial and identifies signals of progressive genetic isolation along with positive selection of population-specific subsets of core genes with depth. Together, these changes show that Lake Cadagno's persistent populations are not in stasis but diverge over time and burial.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0150025"},"PeriodicalIF":4.6,"publicationDate":"2026-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147840307","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chronic intermittent hypoxia exacerbates hepatic steatosis in a microbiota-dependent manner in lean mice.","authors":"Xiaoman Zhang, Anyuan Zhong, Yupu Liu, Jianyin Zou, Meizhen Gu, Xiaoyue Zhu, Huajun Xu, Shankai Yin","doi":"10.1128/msystems.00163-26","DOIUrl":"https://doi.org/10.1128/msystems.00163-26","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Chronic intermittent hypoxia (CIH), a hallmark pathological feature of obstructive sleep apnea (OSA), is extensively linked to hepatic steatosis in high-fat-diet-induced mice. However, the association between CIH and hepatic steatosis in lean mice, as well as the potential involvement of gut microbiota-related mechanisms, remains poorly understood. Four hundred participants in the Shanghai Sleep Health Study were included to assess the association between apnea-hypopnea index (AHI) and hepatic steatosis index (HSI). To characterize CIH-associated phenotypes and explore microbiota-related alterations in lean mice, liver histology, inflammatory cytokine profiling, metagenomic sequencing with antibiotic intervention, plasma untargeted metabolomics, and liver transcriptomics were performed. As a result, AHI was positively associated with HSI in non-obese participants. In lean mice, 16-week CIH alone induced hepatic steatosis and inflammation, accompanied by significant alterations in gut microbiota composition. Antibiotic treatment attenuated hepatic steatosis and inflammation in 16-week CIH-exposed mice. Metagenomic analysis revealed CIH-associated depletion of &lt;i&gt;Bacteroides uniformis&lt;/i&gt;, which was reversed by antibiotic treatment. Plasma metabolomic profiling identified deoxycholic acid as a metabolite exhibiting opposite, phenotype-aligned alterations between CIH and CIH plus antibiotic groups and showing the strongest correlation with &lt;i&gt;Bacteroides uniformis&lt;/i&gt; abundance. In parallel, liver transcriptomics revealed coordinated alterations in bile acid-related metabolic pathways and PPAR signaling consistent with CIH-induced and antibiotic-sensitive metabolic remodeling. Together, these findings indicate that prolonged CIH exposure induces hepatic lipid accumulation in lean mice and is associated with coordinated, antibiotic-sensitive alterations in gut microbiota composition, bile acid metabolism, and hepatic transcriptional programs, suggesting a potential involvement of gut microbiota-bile acid-liver interactions in CIH-associated hepatic steatosis.IMPORTANCEObstructive sleep apnea (OSA) is increasingly recognized as a contributor to metabolic dysfunction, yet its role in hepatic steatosis independent of obesity remains incompletely understood. This study shows that chronic intermittent hypoxia (CIH), a defining pathological feature of OSA, is sufficient to induce hepatic steatosis and inflammation in lean mice, independent of dietary manipulation. These findings broaden current understanding of OSA-associated liver disease beyond the context of obesity and metabolic syndrome. By integrating metagenomic sequencing, plasma metabolomics, and liver transcriptomics, this work highlights coordinated alterations in gut microbial composition, bile acid profiles, and hepatic lipid-related transcriptional programs associated with CIH exposure. Depletion of &lt;i&gt;Bacteroides uniformis&lt;/i&gt; and elevation of deoxycholic acid were linked to CIH-induce","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0016326"},"PeriodicalIF":4.6,"publicationDate":"2026-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147817635","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prophage induction and acetate availability are associated with distinct <i>Lactiplantibacillus plantarum</i> electrode responses.","authors":"Aaron Leininger, Emily Mayo, Yuqing Yan, Wenyu Gu, Harold D May, Zhiyong Jason Ren","doi":"10.1128/msystems.00183-26","DOIUrl":"https://doi.org/10.1128/msystems.00183-26","url":null,"abstract":"<p><p>Lactic acid bacteria can use an electron transport system to pass reducing equivalents to extracellular mediators. This redox flexibility decouples carbon and electron balances and presents the opportunity to use electrodes to engineer fermentations. We show that growth with an anode may be a two-edged sword for the fitness of the model lactic acid bacterium <i>Lactiplantibacillus plantarum</i> grown in a chemically defined medium supplemented with quinones, depending on substrate and cultivation regime. In batch culture on glucose, the anode slows growth despite yielding an over four-fold higher ratio of acetate to lactate than the open-circuit control, a fermentation profile associated with higher ATP yield. In batch culture on the more reduced substrate mannitol, the anode facilitates growth by enabling the dissipation of reducing equivalents. However, when acetate is also present as an alternate electron sink, the anode prolongs the lag phase while maintaining a growth rate similar to the open-circuit control, despite the expected ATP cost of acetate-to-ethanol reduction. Under semi-continuous cultivation on mannitol in the absence of acetate, anode polarization reduces growth yield relative to open-circuit conditions. Although the anode promotes more energetically favorable fermentation patterns during batch growth on both glucose and mannitol, these are likely counterbalanced by prophage induction to affect population growth, as confirmed by transcriptomic analysis, extracellular DNA measurement, and transmission electron microscopy. Together, these results indicate that extracellular electron transfer associated with an anode is not necessarily beneficial for fermenters and prompt further inquiry into the context-dependent nature of this style of metabolism.</p><p><strong>Importance: </strong>A hybrid metabolism has been described in widespread fermenters where energy conservation through substrate level phosphorylation is coupled with electron transfer to external electron acceptors via extracellular redox mediators. This mechanism shapes interactions in microbial systems and presents opportunities in biotechnology. The variable physiological effects observed here of using an electrode as an electron sink highlight both the potential and challenges of applying electrodes to regulate fermentations. We show that polarization of an anode can hinder <i>Lactiplantibacillus plantarum</i> growth and is associated with induction of prophages, increasing the rate of lysis and thereby possibly counteracting the benefits of metabolic flexibility and more energetic fermentation patterns. These results make a new connection between electron balancing and a mobile genetic element and suggest a dynamic, context-dependent role of these mediators as public goods.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0018326"},"PeriodicalIF":4.6,"publicationDate":"2026-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147776360","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Host genetics shapes the recovery of the gut microbiome after antibiotic treatment: the role of the blood group related <i>B4galnt2</i> gene.","authors":"Aleksa Čepić, Philipp Rausch, Theresa Geese, Astrid Dempfle, Guntram A Grassl, John F Baines","doi":"10.1128/msystems.01640-25","DOIUrl":"https://doi.org/10.1128/msystems.01640-25","url":null,"abstract":"&lt;p&gt;&lt;p&gt;The intestinal microbiota is integral to host health, metabolism, and colonization resistance. Antibiotics can disrupt microbial homeostasis, leading to dysbiosis and altered colonization resistance. While antibiotic-induced microbiota disruption is well-documented, less is known about how host genetics shapes post-antibiotic recovery. Here, we investigate the impact of &lt;i&gt;B4galnt2&lt;/i&gt;, a blood-group-related glycosyltransferase gene, on microbiota recovery following antibiotic treatment. Using a longitudinal, multi-omic approach-including 16S rRNA gene sequencing, metagenomics, and metatranscriptomics-we compare the microbiota dynamics of &lt;i&gt;B4galnt2&lt;sup&gt;+/-&lt;/sup&gt;&lt;/i&gt; and &lt;i&gt;B4galnt2&lt;sup&gt;-/-&lt;/sup&gt;&lt;/i&gt; mice after treatment with streptomycin, kanamycin, and vancomycin. Our findings reveal that &lt;i&gt;B4galnt2&lt;sup&gt;-/-&lt;/sup&gt;&lt;/i&gt; mice exhibit faster recovery of microbial diversity and composition following streptomycin treatment compared to their &lt;i&gt;B4galnt2&lt;sup&gt;+/-&lt;/sup&gt;&lt;/i&gt; counterparts. This accelerated recovery is associated with higher relative abundance of taxa such as &lt;i&gt;Blautia&lt;/i&gt;, &lt;i&gt;Dorea,&lt;/i&gt; and other Lachnospiraceae, and increased expression of motility-related genes, and differential regulation of antibiotic resistance genes (ARGs), including the aminoglycoside nucleotidyltransferase genes &lt;i&gt;aadA&lt;/i&gt; and &lt;i&gt;aadE&lt;/i&gt;. Genotype-dependent differences in recovery were most pronounced following streptomycin and were not consistently observed with kanamycin or vancomycin, indicating an antibiotic-by-genotype interaction shaped by the &lt;i&gt;B4galnt2&lt;/i&gt;-associated microbiota. These results underscore the role of host genetics in shaping microbiota response and recovery following antibiotic exposure. By demonstrating the interplay between glycosylation-mediated microbiota composition, antibiotic response, and microbial recovery, our study may provide insights into the potential for personalized approaches to mitigate dysbiosis-related health outcomes.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;Antibiotic treatments disrupt the gut microbiome, often leading to long-term alterations that potentially affect host health. While much is known about how antibiotics cause microbial dysbiosis, little is understood about the factors that could influence the speed of microbial community recovery, such as host genetic differences. Using a mouse model, this study reveals that genetic variation at the blood group-related &lt;i&gt;B4galnt2&lt;/i&gt; gene significantly alters recovery after streptomycin treatment. Mice lacking intestinal &lt;i&gt;B4galnt2&lt;/i&gt; expression recover faster, with distinct changes in microbial composition, activity, and antibiotic resistance gene expression. These findings highlight how a single host gene can shape microbiota dynamics following antibiotic-induced disruption. The work emphasizes the importance of considering host genetic factors when predicting microbiome responses to antibiotics and suggests potential for genotype-guided strategies to reduce ","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0164025"},"PeriodicalIF":4.6,"publicationDate":"2026-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147775826","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Surviving through a dry spell: microbial responses to drying and rewetting.","authors":"Don A Cowan","doi":"10.1128/msystems.00175-26","DOIUrl":"https://doi.org/10.1128/msystems.00175-26","url":null,"abstract":"<p><p>The issues of how microorganisms survive very long periods of desiccation and how they react during both drying and rehydration phases have long been topics of interest in a range of relevant fields, including desert ecosystem microbiomics, food storage, ancient microbe studies, and even astrobiology. The recently published study by Carini et al., who used a combination of transcriptomics and metabolomics to investigate steady-state gene expression and cellular metabolite profiles at different states of bacterial cellular desiccation, during both drying and rewetting phases, adds some valuable insights into how members of bacterial communities can survive in the driest habitats on earth (P. Carini, A. Gomez-Buckley, C. R. Guerrero, M. R. Kridler, et al., mSystems 11:e00493-25, 2026, https://doi.org/10.1128/msystems.00493-25).</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0017526"},"PeriodicalIF":4.6,"publicationDate":"2026-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147776423","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Advances and future directions in identifying specific taxa from microbial meta-omics data: from pipeline to deep learning.","authors":"Jingkang Zhang, Xingjie Wang, Di Wang, Zikui Zheng, Hongmei Wang, Liyuan Ma","doi":"10.1128/msystems.00800-25","DOIUrl":"https://doi.org/10.1128/msystems.00800-25","url":null,"abstract":"<p><p>Molecular profiling enabled by meta-omics technologies has significantly expanded our knowledge of microbial catalog across diverse environments. Increasing attention has now been focused on identifying ecologically significant taxa, particularly keystone that stabilize communities, rare taxa that underpin functional redundancy, and indicators that reflect environmental gradients. However, current pipeline methods remain limited in deciphering complex ecological relationships and modeling the evolution of community dynamics. As a transformative computational tool, deep learning (DL) offers novel strategies to address these challenges through autonomous feature extraction, nonlinear interaction modeling, and integration of multi-modal data sets. Nevertheless, there are still obstacles to the widespread adoption of DL for collaborative identification of specific microbial taxa, primarily including the intrinsic heterogeneity and imbalance of data sets, the difficulty of model generalization across diverse ecosystems, and the limited ecological interpretability of model outputs. This review summarizes existing research advances and proposes to build a unified DL framework for multi-modal data, exploring its implementation pathways, challenges, and potential coping strategies. The envisioned framework establishes a multi-task learning architecture for unified identification of keystone, rare, and indicator taxa, incorporating domain knowledge through ecological constraint layers and explainable AI modules, while providing flexible implementation pathways for heterogeneous data integration and model customization across microbial ecosystems. This framework has the potential to form a closed-loop verification in combination with synthetic microbial community experiments, reshape the paradigm of microbial community research, and promote the transition from empirical classification to mechanistic ecological cognition.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0080025"},"PeriodicalIF":4.6,"publicationDate":"2026-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147776650","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unlocking the secret to <i>Staphylococcus aureus</i> survival in serum.","authors":"Warren E Rose, John-Demian Sauer","doi":"10.1128/msystems.01813-25","DOIUrl":"https://doi.org/10.1128/msystems.01813-25","url":null,"abstract":"<p><p><i>Staphylococcus aureus</i> bloodstream infections remain a major clinical challenge. A key knowledge gap is how <i>S. aureus</i> adapts to the hostile, nutrient-limited environment of human serum, where immune pressures, such as complement, antimicrobial peptides, and nutritional immunity, restrict bacterial survival. Recent investigations integrating transcriptomic, proteomic, and metabolomic data across five clinically relevant <i>S. aureus</i> lineages revealed coordinated serum-specific metabolic and stress-response adaptations (W. Mujchariyakul, C. J. Walsh, S. Giulieri, C. Cramond, et al., mSystems 11:e01183-25, 2026, https://doi.org/10.1128/msystems.01183-25). Serum triggered increased gluconeogenic and TCA-cycle activity, expanded carbohydrate, amino acid, and lipid utilization, and induction of iron-acquisition systems, nucleotide biosynthesis, and oxidative-stress defenses, while suppressing ribosome biogenesis. Functional validation confirmed key roles for carbon-metabolism genes (<i>gapdhB, sucA</i>), siderophore and iron-uptake systems (<i>sirA, sstD</i>), and the peroxide regulator <i>perR</i>. These findings highlight the metabolic resourcefulness and stress resilience that enable <i>S. aureus</i> survival and persistence despite antibiotic therapy. This work underscores the importance of multiomic approaches across pathogens and physiologic models to reveal new therapeutic targets for bloodstream infections.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0181325"},"PeriodicalIF":4.6,"publicationDate":"2026-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147776626","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}