mSystems最新文献

{"title":"Deciphering temporal antifungal dynamics of a rare actinomycete via integrated omics.","authors":"Hildah Amutuhaire, Michael Dubovis, Ivan Plyushchenko, Judith Kraut-Cohen, Tal Luzzatto-Knaan, Jonathan Friedman, Eddie Cytryn","doi":"10.1128/msystems.00694-26","DOIUrl":"10.1128/msystems.00694-26","url":null,"abstract":"<p><p>Fungal phytopathogens pose a persistent threat to global crop production, and widespread use of fungicides has driven resistance development and environmental concerns, necessitating sustainable alternatives. Actinomycetes produce diverse bioactive metabolites, yet natural product discovery has disproportionately focused on <i>Streptomyces</i>, leaving rare actinomycete taxa underexplored. <i>Saccharomonospora xinjiangensis</i> XJ-54 is a rare actinomycete exhibiting antifungal activity against Fusarium phytopathogens, including <i>Fusarium oxysporum</i> f. sp<i>. cucumerinum</i> (FORC), and harbors numerous biosynthetic gene clusters (BGCs) whose products remain uncharacterized. However, as in many rare actinomycetes, BGCs may be transcriptionally silent under standard laboratory conditions, and their expression dynamics remain poorly understood. To elucidate the molecular basis of antifungal activity in <i>S. xinjiangensis</i> XJ-54, we integrated genomic, transcriptomic, and metabolomic analyses. Cell-free supernatants inhibited FORC after 5 days of fermentation, with activity increasing by day 7. Time-resolved RNA sequencing demonstrated that all genomically identified BGCs were transcriptionally active but exhibited distinct growth-phase-dependent expression patterns, with approximately half upregulated during exponential growth and the remainder following transition to stationary phase. We observed temporal variations in transcriptional coupling between cluster-specific regulators and biosynthetic genes. Liquid chromatography-mass spectrometry-based metabolomics showed growth-phase-dependent metabolite shifts, including stationary phase accumulation of secoiridoid-like monoterpenoids, N-acyl amines, and alkaloids (imidazoles, pyridines, and indoles), correlating with the observed antifungal phenotype. Bioactivity-guided fractionation subsequently yielded an active fraction containing a predicted halogenated alkaloid that induced hyphal damage in FORC. These findings indicate that antifungal activity in <i>S. xinjiangensis</i> XJ-54 arises from temporally coordinated biosynthetic programs, providing a framework for optimizing growth conditions and prioritizing BGCs for functional characterization.IMPORTANCEThe discovery of new antifungal compounds is critical for sustainable agriculture, yet most natural product research has focused on a narrow range of well-studied microorganisms. Rare actinomycetes represent an untapped reservoir of chemical diversity, but their biosynthetic potential often remains hidden. By integrating time-resolved transcriptomics with metabolomics, we show that the rare actinomycete <i>Saccharomonospora xinjiangensis</i> XJ-54 produces antifungal metabolites through temporally coordinated biosynthetic programs. Contrary to the prevailing assumption that the majority of biosynthetic gene clusters (BGCs) are silent, all BGCs in this strain showed detectable transcriptional activity under standard laboratory conditi","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0069426"},"PeriodicalIF":5.2,"publicationDate":"2026-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149069993","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":"Tryptophan-driven metabolomic shift in <i>Acidobacteriaceae</i> reveals phytohormones and antifungal metabolites.","authors":"Celine M Zumkeller, Christoph Hartwig, Walter Lanzalonga, Maria A Patras, Yang Liu, Michael Marner, Sanja Mihajlovic, Marius S Spohn, Till F Schäberle","doi":"10.1128/msystems.00828-26","DOIUrl":"10.1128/msystems.00828-26","url":null,"abstract":"<p><p><i>Acidobacteriota</i> is one of the most abundant phyla in soils and has recently attracted attention for its potential role in promoting phytosanitary benefits. The metabolomic capabilities of this phylum remain poorly characterized, with few experimentally confirmed metabolites described. To address these gaps, we combined untargeted metabolomic profiling with comparative genomic analyses to explore the functional potential of newly isolated <i>Acidobacteriaceae</i> strains. Genome mining across the <i>Acidobacteriota</i> phylum revealed the presence and taxon-specific enrichment of genes associated with plant-related traits, including phytohormone biosynthesis. In parallel, metabolomic analyses of OSMAC-derived extracts uncovered pronounced condition-dependent metabolic variation. Tryptophan supplementation was associated with marked metabolomic reprogramming, including changes in indole-derived metabolites, such as indole-3-acetic acid. Subsequent analyses linked these metabolic shifts to the suppression of phytopathogenic fungi and enabled the identification of malassezindoles and pityriacitrins as active compounds, confirmed by structure elucidation using NMR spectroscopy. Overall, these findings shed light on the previously unexplored metabolic potential of the <i>Acidobacteriota</i> phylum, emphasizing its ecological importance for phytosanitary applications.</p><p><strong>Importance: </strong>Despite their ubiquity and genomic diversity, the functional metabolism of members of the <i>Acidobacteriota</i> has largely remained uncharacterized. This study links genomic predictions to experimentally verified metabolomic outputs of <i>Acidobacteriaceae</i>, demonstrating tryptophan-responsive metabolic shifts translating to phytohormones and metabolites suppressing fungal growth. Our work underscores the emerging role of <i>Acidobacteriota</i> as important contributors to soil ecosystem functioning and plant-microbe interactions.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0082826"},"PeriodicalIF":5.2,"publicationDate":"2026-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148963572","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":"A robustness-first cross-disease framework supports a candidate shared microbial redox axis and disease-specific metabolic divergence in colorectal cancer, Crohn's disease, and liver cirrhosis.","authors":"Kartika Sahu, Palok Aich","doi":"10.1128/msystems.00836-26","DOIUrl":"10.1128/msystems.00836-26","url":null,"abstract":"<p><p>Gut microbiome dysbiosis is associated with colorectal cancer (CRC), Crohn's disease (CD), and liver cirrhosis (LC), yet whether these diseases share conserved microbial vulnerabilities remains unresolved. Analytical pipeline choices alone can shift apparent performance from near-zero to near-perfect on identical data, rendering cross-disease comparison unreliable. Here, in a secondary cross-sectional analysis of public data sets, maximin optimization is introduced as a proposed pipeline-selection criterion guaranteeing worst-case performance across all tasks simultaneously. Benchmarking 1,152 preprocessing-model configurations across six tasks using gut metagenomics and serum metabolomics from CRC, CD, and LC reveals a candidate 19-species microbiome signature in which <i>Firmicutes</i> bacterium CAG:41 is the sole threshold-stable cross-disease taxon, depleted in all three diseases. Microbiome pathway enrichment converges on sulfur-selenium redox metabolism and B-vitamin biosynthesis, while host metabolomic responses are predominantly disease-specific. CD and LC are dominated by single discriminative taxa; CRC requires community-level integration. Exploratory external evaluation was adequately powered only for CRC (AUC = 0.769, 95% bootstrap CI 0.678-0.849); CD and LC assessments were exploratory only.</p><p><strong>Importance: </strong>Cross-disease microbiome comparison has lacked a principled analytical foundation: arbitrary preprocessing choices can shift apparent classification performance from near-random to near-perfect on identical data, making biological conclusions unreliable when pooled across diseases. Maximin optimization addresses this by providing a decision-theoretic guarantee that every classification task contributes valid signal, enabling the first analytically controlled cross-disease comparison of gut metagenomics and serum metabolomics across three major gut-associated diseases. The identification of <i>Firmicutes</i> bacterium CAG:41 as the sole threshold-stable cross-disease taxon, harboring predicted functions in sulfur-selenium metabolism, offers a concrete target for experimental characterization and prospective screening validation. The two-layer dysbiosis architecture-universal microbial vulnerability with disease-specific host metabolic responses-provides a conceptual template for cross-disease microbiome study design in other gut-associated conditions, pending prospective confirmation.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0083626"},"PeriodicalIF":5.2,"publicationDate":"2026-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148963612","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":"Experimental benchmarking remains crucial to the interpretation of sequence annotation data.","authors":"Claire M Palmer","doi":"10.1128/msystems.00772-26","DOIUrl":"10.1128/msystems.00772-26","url":null,"abstract":"<p><p>Determining the distribution and origin of bacterial synthesis of metabolites of interest relies on computational prediction of protein function. In their recent study, Lawrence and colleagues employed a rigorous pipeline for benchmarking their annotation methods (E. C. Lawrence, H. Pan, N. Ollikainen, and B. J. Belin, mSystems 11:e00619-26, 2026, https://doi.org/10.1128/msystems.00619-26). This allowed them to distinguish between related yet functionally distinct proteins, thereby refining their understanding of bacterial hopanoid production. They find that the ability to synthesize these compounds likely arose in marine alphaproteobacteria and is related to osmotic stress tolerance. This study additionally provides new insights into the extracellular transport of hopanoids. The combination of large-scale computational analysis with experimentally based benchmarking that they describe provides a useful model for any researcher interested in understanding bacterial biosynthetic capability.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0077226"},"PeriodicalIF":5.2,"publicationDate":"2026-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149075311","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":"Gut microbiome and metabolite profiles are associated with subsequent histologic MASH in a longitudinal mouse model.","authors":"Stephany Flores Ramos, Kelly Fogelson, Valentina B Muti, Allegra T Aron, Rodolfo A Salido, R Alexander Richter, Helena Mannochio-Russo, Jingjing Hu, Mojgan Hosseini, Rohit Loomba, Pieter C Dorrestein, Rob Knight, Amir Zarrinpar","doi":"10.1128/msystems.00720-26","DOIUrl":"10.1128/msystems.00720-26","url":null,"abstract":"<p><p>Detecting metabolic dysfunction-associated steatohepatitis (MASH) before fibrosis develops remains a major challenge. We used a longitudinal streptozotocin/high-fat diet (STAM/HFD) mouse model to identify microbial and metabolic features that emerge before histological MASH onset. Integrative 16S rRNA and untargeted LC-MS/MS analyses revealed microbial and metabolite shifts weeks before disease development. Lachnospiraceae and Oscillospiraceae were enriched in non-MASH mice and were negatively correlated with fatty acids elevated under MASH conditions. Bile acid and fatty acid metabolites enriched under MASH and non-MASH states varied with collection time, showing that diurnal variation strongly shapes biomarker profiles. Analysis of a human MAFLD cohort confirmed higher abundances of Lachnospiraceae bacteria in healthy participants. Our results identify early microbial and metabolic features that are associated with subsequent histologic MASH onset and reveal how temporal factors influence biomarker detection. These time-sensitive features, together with cross-species concordance in a human MAFLD cohort, lay the groundwork for developing and validating microbiome-based diagnostics and circadian-informed interventions that target the gut-liver axis to prevent metabolic liver disease.</p><p><strong>Importance: </strong>Metabolic dysfunction-associated steatohepatitis (MASH) often develops silently, limiting opportunities for early intervention before fibrosis occurs. In this study, we identify gut microbial taxa and stool metabolites that are associated with future histologic MASH development in a longitudinal mouse model. We show that members of the Lachnospiraceae and Oscillospiraceae families are enriched in mice that remain disease-free and that members of the Lachnospiraceae family exhibit similar patterns in a human MAFLD cohort. Importantly, we demonstrate that time of sample collection has a strong effect on metabolomic profiles, with disease-associated lipid and bile acid signals detectable only at specific sampling times. These findings highlight circadian timing as a critical variable in microbiome-based biomarker discovery and support the development of time-aware diagnostic strategies for early MASH risk assessment.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0072026"},"PeriodicalIF":5.2,"publicationDate":"2026-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148919278","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":"<i>Spiroplasma</i> in <i>Glossina fuscipes fuscipes</i>: a potential manipulator of male reproduction.","authors":"Riccardo Piccinno, Giulia Fiorenza, Francesco Lescai, Simone Carpanzano, Fabian Gstöttenmayer, Kiswend-Sida M Dera, Anna Cleta Croce, Chantel J de Beer, Brian L Weiss, Mariangela Santorsola, Alberta Pinnola, Giuliano Gasperi, Federico Forneris, Serap Aksoy, Adly M M Abd-Alla, Anna Rodolfa Malacrida","doi":"10.1128/msystems.00526-26","DOIUrl":"10.1128/msystems.00526-26","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;i&gt;Glossina fuscipes fuscipes&lt;/i&gt; (&lt;i&gt;Gff&lt;/i&gt;) is a riverine species of the &lt;i&gt;Glossina&lt;/i&gt; genus (tsetse flies). It is one of the principal vector species responsible for transmitting human African trypanosomiasis across a broad swath of sub-Saharan Africa. Consequently, it remains a primary target for vector-control interventions in endemic regions. As with other &lt;i&gt;Glossina&lt;/i&gt; species, &lt;i&gt;G. fuscipes&lt;/i&gt; houses a highly streamlined microbiota, composed of maternally transmitted endosymbionts mandatory for survival, which also significantly impacts the vectorial capacity. Among them, the obligate &lt;i&gt;Wigglesworthia&lt;/i&gt; provides essential nutrients and stimulates maturation of the fly's immune system, providing a refractory effect against &lt;i&gt;Trypanosoma&lt;/i&gt;. It also harbors the commensal &lt;i&gt;Sodalis&lt;/i&gt; and parasitic &lt;i&gt;Wolbachia&lt;/i&gt;, the latter of which induces cytoplasmic incompatibility. In addition, &lt;i&gt;Gff&lt;/i&gt; hosts a &lt;i&gt;Spiroplasma&lt;/i&gt; strain that enhances host refractoriness to trypanosome infection but disrupts female metabolic and reproductive homeostasis. We used high-throughput RNA sequencing to examine the impact of &lt;i&gt;Spiroplasma&lt;/i&gt; on male testes and accessory glands to reveal how this microbe exerts its influence on male reproductive physiology. We found that &lt;i&gt;Spiroplasma&lt;/i&gt; substantially alters testes physiology, downregulating genes involved in energy metabolism and sperm function, suggesting reduced male reproductive fitness. In contrast, accessory gland gene expression was not significantly affected despite the critical role of these organs in semen production and reproductive success, considering also that the bacterium exploits the ejaculate to further increase its population prevalence. &lt;i&gt;Spiroplasma&lt;/i&gt; infection also correlated with increased abundance of other symbionts, including &lt;i&gt;Wigglesworthia&lt;/i&gt;.IMPORTANCEA complex host-symbiont interplay makes the &lt;i&gt;Spiroplasma&lt;/i&gt; harbored in tsetse fly intriguing. The unexpected male-specific energetic costs of &lt;i&gt;Spiroplasma&lt;/i&gt; infection keep open the biological question of why this bacterium is maintained in this species. On the other hand, &lt;i&gt;Spiroplasma&lt;/i&gt; infection correlates with increased abundance of &lt;i&gt;Wigglesworthia&lt;/i&gt;, promoting trypanosome refractoriness. The present work adds a valuable layer to further interpret the ecological and evolutionary narrative of &lt;i&gt;Spiroplasma&lt;/i&gt; interactions, and lays the preliminary groundwork to explore the potential of using &lt;i&gt;Spiroplasma&lt;/i&gt; as a biocontrol agent. While acknowledging that our findings were derived from a long-established laboratory colony, the data on the modulation of fly reproductive fitness and on the possible contribution to trypanosome refractoriness found make &lt;i&gt;Spiroplasma&lt;/i&gt; intriguing for strategic integration into environmentally sustainable vector management programs, potentially in concert with the Sterile Insect Technique. The results provide significant advances in symbiont-host inter","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0052626"},"PeriodicalIF":5.2,"publicationDate":"2026-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148945406","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":"Genome mining and metabolomics reveal context-dependent biosynthetic potential in a core poplar dark septate endophyte.","authors":"Julian B Cosner, Sameer Mudbhari, Jack A Orebaugh, Robert L Hettich, Paul E Abraham, Tomás A Rush","doi":"10.1128/msystems.00838-26","DOIUrl":"10.1128/msystems.00838-26","url":null,"abstract":"<p><p>Dark septate endophytes (DSEs) are ubiquitous root-colonizing fungi characterized by melanized, septate hyphae and a frequent association with plants in stressful or nutrient-poor environments. Although DSEs are increasingly recognized for context-dependent effects on host stress resilience, the specialized metabolic capacity of many DSE lineages remains poorly resolved. <i>Hyaloscypha finlandica</i> is a recurrent root-associated fungus of <i>Populus</i> and other hosts, making it a useful system for understanding symbiotic mechanisms using multi-omics analyses. Here, we combined comparative biosynthetic gene cluster (BGC) prediction across 41 ascomycete genomes with untargeted metabolomics of <i>H. finlandica</i> PMI 746 grown in a defined minimal medium and a complex plant-derived medium. Benchmarking antiSMASH, FunBGCeX, and BGC-Prophet revealed broad conservation of PKS-, NRPS-, and terpene-associated biosynthetic capacity among DSEs. LC-MS/MS profiling detected strong medium-associated shifts in the extracellular chemical footprint of <i>H. finlandica</i> and identified putative terpenoid-, polyketide-, peptide-, siderophore-, and DHN-melanin-related features through spectral matching and <i>in silico</i> chemical-class inference. Authentic-standard comparison supported a probable assignment of 7-oxodehydroabietic acid, whereas most other annotations remain putative or class-level assignments. Integrating genomic and metabolomic evidence identified representative candidate intersections between encoded biosynthetic capacity and observed chemistry, but definitive BGC-product links remain targets for future genetic and structural validation. Together, these results provide a public paired-omics resource for a core <i>Populus</i>-associated DSE and a conservative framework for interpreting fungal multi-omics in non-model endophytes.<b>IMPORTANCE</b>Dark septate endophytes (DSEs) are widespread fungal symbionts that influence plant performance, yet their encoded and expressed metabolic capacities remain largely uncharacterized. This study provides a paired comparative genome-mining and untargeted metabolomics resource for <i>Hyaloscypha finlandica</i>, a recurrent <i>Populus</i>-associated DSE. By explicitly distinguishing biosynthetic gene cluster (BGC) prediction, spectral annotation, authentic-standard support, and unresolved BGC-Prophet assignment, this work provides a transparent reference for future studies of DSE specialized metabolism. The resulting data sets support comparative analyses across fungal endophytes and help prioritize candidate metabolites and gene clusters for targeted validation.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0083826"},"PeriodicalIF":5.2,"publicationDate":"2026-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149025383","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":"Comparative gut microbiome in diarrheal and non-diarrheal children: an individually matched case-control study.","authors":"Jialiang Xu, Yufeng Fan, Geruo Qu, Jiaqi Li, Yao Peng, Mengyu Wang, Jingyun Zhang, Yuqing Feng, Xiao Liu, Yongfei Hu, Biao Kan, Zhenpeng Li, Mei Zeng, Xin Lu","doi":"10.1128/msystems.00198-26","DOIUrl":"10.1128/msystems.00198-26","url":null,"abstract":"<p><p>Diarrhea, a leading cause of under-five mortality in developing countries, drives therapeutic challenges amid global antibiotic resistance. This study aimed to compare gut microbiota, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and virulence factors (VFs) in diarrheal and non-diarrheal children, explore reasons for asymptomatic pathogen carriage, and develop a microbiome-based model to predict the potential etiology of diarrhea. This individually matched case-control study analyzed 42 paired fecal samples (selected from 716 diarrhea/non-diarrhea cases) to compare gut microbiome profiles, ARGs, MGEs, and VFs using metagenomic sequencing and pathogen-specific PCR. Diarrheal children showed reduced alpha diversity, increased Proteobacteria, and elevated VFs and MGEs. Surprisingly, ARGs were more abundant in non-diarrheal children, suggesting ARG colonization in healthy hosts. <i>Actinomyces</i> was enriched in non-diarrheal pathogen carriers and may be associated with asymptomatic bacterial pathogen carriage. A random forest (RF) model incorporating non-pathogenic bacteria achieved high accuracy in predicting diarrheal status and pathogen carriage. This study reveals distinct microbial ecologies between diarrheal and healthy children. The enrichment of specific bacterial taxa in asymptomatic carriers may be associated with pathogen tolerance. The unexpected ARG abundance in healthy children highlights a hidden antimicrobial resistance reservoir. These findings inform microbiome-based diagnostics and antibiotic stewardship in pediatric diarrhea.IMPORTANCEThis study is significant because it provides robust, individually matched case-control evidence linking childhood diarrhea to gut microbiome dysbiosis and the distribution of pathogenic and resistance-related genetic elements. By integrating metagenomic sequencing with pathogen-specific polymerase chain reaction (PCR), it offers a comprehensive comparison of microbial composition, virulence factors (VFs), mobile genetic elements (MHEs), and antibiotic resistance genes (ARGs) between diarrheal and non-diarrheal children. The findings demonstrate reduced microbial diversity and enrichment of Proteobacteria, virulence factors, and mobile genetic elements in diarrheal cases, highlighting microbiome instability during infection. Importantly, the unexpectedly higher abundance of antibiotic resistance genes in non-diarrheal children underscores the underestimated role of healthy populations as reservoirs of resistance. Furthermore, the establishment of predictive models for diarrhea status and pathogen carriage enhances the translational value of the study. Overall, this work advances the understanding of pediatric diarrheal disease and informs prevention, surveillance, and treatment strategies in the context of global antimicrobial resistance.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0019826"},"PeriodicalIF":5.2,"publicationDate":"2026-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149081162","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":"Rarefaction is better than robust Aitchison PCA and other compositional data analysis methods at controlling for uneven sequencing effort.","authors":"Patrick D Schloss","doi":"10.1128/msystems.00930-26","DOIUrl":"10.1128/msystems.00930-26","url":null,"abstract":"<p><p>Amplicon sequencing typically results in a wide distribution in the number of sequences obtained from each sample. How best to account for this variation has been a persistent problem in the microbial ecology literature. Historically, rarefaction has been used in ecology and this practice was adopted by microbial ecologists. However, rarefaction has been strongly criticized, leading to the development of compositional data analysis and normalization methods. Therefore, I reassessed the benchmarking data that were generated by the developers of one such method, robust Aitchison PCA. I found numerous problems in the Python code that led to the support of robust Aitchison PCA. These problems extended to the creation of simulated data sets, implementation of machine learning methods, and choice of analysis parameters. Furthermore, the analysis of the simulated and case study data sets was done in a manner that was foreign to standard microbiome analyses. I corrected the problems in the original code, added data sets with smaller effect sizes, and expanded the collection of methods that purport to correct for uneven sequencing effort. Contrary to the claims of the original analysis, robust Aitchison PCA was not insensitive to uneven sequencing effort and did not perform as well as rarefaction. In fact, even using the benchmarking framework from the original analysis, rarefaction outperformed robust Aitchison PCA, other compositional data analysis methods, and other normalization methods. Rarefaction remains the preferred method of controlling for uneven sampling effort in amplicon sequence studies.</p><p><strong>Importance: </strong>Efforts to connect the structure of microbial communities with environmental processes and host health have captured widespread interest among scientists and the general public. The methods used to generate the sequencing data that are fundamental to these efforts result in wide variation in the number of sequences per sample. This variation and how to account for it can have detrimental effects on the ability to draw valid conclusions. Compositional data analysis methods, including robust Aitchison principal component analysis (PCA), have grown in popularity for mitigating these effects and have been proposed as alternatives to rarefaction. In this study, I reviewed and fixed the code that was used to benchmark robust Aitchison PCA and expanded the analysis. With this improved and expanded analysis, I found that rarefaction was still superior to robust Aitchison PCA and other methods of controlling for uneven sequencing effort.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0093026"},"PeriodicalIF":5.2,"publicationDate":"2026-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149081307","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":"Proteomic profiling of the <i>Pseudomonas aeruginosa</i> stringent response highlights global adaptive responses during stationary phase.","authors":"Jacquelyn Rich, Samuel J T Wardell, Dorival Martins, Malika Khakhimova, Gowthami Sampathkumar, Tevy Chan, Thi Tuyet Mai Nguyen, Geoffrey McKay, Lorne Taylor, Daniel Pletzer, Dao Nguyen","doi":"10.1128/msystems.01742-25","DOIUrl":"10.1128/msystems.01742-25","url":null,"abstract":"<p><p><i>Pseudomonas aeruginosa</i> (<i>P.a</i>) is a clinically important opportunistic pathogen capable of adapting and surviving a wide range of environments and stress conditions. A central regulator of this adaptability is the stringent response, mediated by the alarmones (p)ppGpp. Activation of the stringent response triggers a global physiological shift away from active metabolism toward stress management and cellular quiescence, a key transition to stationary phase. To date, few studies have investigated the protein-level processes under stringent response control. In this study, we performed shotgun proteomic profiling (LC-MS/MS) of a (p)ppGpp-null <i>relA spoT</i> double knockout mutant (ΔSR) and its isogenic PAO1 parent during late exponential and stationary phase planktonic growth in rich medium. In this first characterization of the stringent response proteome in <i>P.a</i>, we identified 146 differentially abundant proteins (DAP) in late exponential phase ΔSR cells, and 2.3-fold greater DAP (339) in stationary-phase cells. Functional characterization and system-level analysis of the differentially abundant stationary phase proteome highlighted the key role of (p)ppGpp in shutting down a wide range of metabolic processes while inducing adaptive processes such as responses to oxidative stress. Comparative RNA-seq analysis also uncovered incongruent protein and mRNA responses in the ΔSR relative to wild-type cells in several processes, including iron homeostasis and antioxidant defenses. Transcriptomic analysis of the ΔSR also revealed differential expression of numerous sRNAs, including PrrF1/2, raising the possibility that sRNAs may mediate certain stringent-response-dependent post-transcriptional control. Phenotypic validation of the ΔSR proteome confirmed multiple defects in antioxidant defenses and dysregulated pyoverdine biosynthesis.</p><p><strong>Importance: </strong><i>Pseudomonas aeruginosa</i> is an important opportunistic human pathogen that causes difficult-to-treat infections and is highly adaptable to stressful environments. A key orchestrator of this adaptability is the stringent response, mediated by the signaling molecule (p)ppGpp. In this study, we characterized the extensive proteome remodeling in the (p)ppGpp-null <i>relA spoT</i> mutant during late exponential and stationary phase and provided the first protein-level analysis of the stringent response in <i>P. aeruginosa</i>. These data highlight the role of (p)ppGpp in shutting down broad metabolic functions and activating adaptive pathways, including stress-resistance responses, particularly during stationary phase. Using comparative proteomics and RNA-seq, we also find that several processes-such as iron regulation and oxidative stress responses-show mismatched RNA and protein changes, suggesting additional layers of post-transcriptional control, potentially involving small regulatory RNAs.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0174225"},"PeriodicalIF":5.2,"publicationDate":"2026-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148990647","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}