mSystems最新文献

{"title":"Clade-specific long-read sequencing increases the accuracy and specificity of the <i>gyrB</i> phylogenetic marker gene.","authors":"Robert G Nichols, Emily R Davenport","doi":"10.1128/msystems.01480-24","DOIUrl":"10.1128/msystems.01480-24","url":null,"abstract":"<p><p>Phylogenetic marker gene sequencing is often used as a quick and cost-effective way of evaluating microbial composition within a community. While 16S rRNA gene sequencing (16S) is commonly used for bacteria and archaea, other marker genes are preferable in certain situations, such as when 16S sequences cannot distinguish between taxa within a group. Another situation is when researchers want to study cospeciation of host taxa that diverged much more recently than the slowly evolving 16S rRNA gene. For example, the bacterial gyrase subunit B (<i>gyrB</i>) gene has been used to investigate cospeciation between the microbiome and various hominid species. However, to date, only primers that generate short-read Illumina MiSeq-length amplicons exist to investigate <i>gyrB</i> of the Bacteroidaceae, Bifidobacteriaceae, and Lachnospiraceae families. Here, we update this methodology by creating <i>gyrB</i> primers for the Bacteroidaceae, Bifidobacteriaceae, and Lachnospiraceae families for long-read PacBio sequencing and characterize them against established short-read <i>gyrB</i> primer sets. We demonstrate both bioinformatically and analytically that these longer amplicons offer more sequence space for greater taxonomic resolution, lower off-target amplification rates, and lower error rates with PacBio CCS sequencing versus established short-read sequencing. The availability of these long-read <i>gyrB</i> primers will prove to be integral to the continued analysis of cospeciation between bacterial members of the gut microbiome and recently diverging host species.</p><p><strong>Importance: </strong>Previous studies have shown that the marker gene gyrase subunit B (<i>gyrB</i>) can be used to study codiversification between the gut microbiome and hominids. However, only primers for short-read sequencing have been developed which have limited resolution for subspecies assignment. In the present study, we create new <i>gyrB</i> primer sets for long-read sequencing approaches and compare them to the existing short-read <i>gyrB</i> primers. We show that using longer reads leads to better taxonomic resolution, lower off-target amplification, and lower error rates, which are vital for accurate estimates of codiversification.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0148024"},"PeriodicalIF":5.0,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11748558/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142829442","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Systematic identification of secondary bile acid production genes in global microbiome.","authors":"Yuwei Yang, Wenxing Gao, Ruixin Zhu, Liwen Tao, Wanning Chen, Xinyue Zhu, Mengping Shen, Tingjun Xu, Tingting Zhao, Xiaobai Zhang, Lixin Zhu, Na Jiao","doi":"10.1128/msystems.00817-24","DOIUrl":"10.1128/msystems.00817-24","url":null,"abstract":"<p><p>Microbial metabolism of bile acids (BAs) is crucial for maintaining homeostasis in vertebrate hosts and environments. Although certain organisms involved in bile acid metabolism have been identified, a global, comprehensive elucidation of the microbes, metabolic enzymes, and bile acid remains incomplete. To bridge this gap, we employed hidden Markov models to systematically search in a large-scale and high-quality search library comprising 28,813 RefSeq multi-kingdom microbial complete genomes, enabling us to construct a secondary bile acid production gene catalog. This catalog greatly expanded the distribution of secondary bile acid production genes across 11 phyla, encompassing bacteria, archaea, and fungi, and extended to 14 habitats spanning hosts and environmental contexts. Furthermore, we highlighted the associations between secondary bile acids (SBAs) and gastrointestinal and hepatic disorders, including inflammatory bowel disease (IBD), colorectal cancer (CRC), and nonalcoholic fatty liver disease (NAFLD), further elucidating disease-specific alterations in secondary bile acid production genes. Additionally, we proposed the pig as a particularly suitable animal model for investigating secondary bile acid production in humans, given its closely aligned secondary bile acid production gene composition. This gene catalog provides a comprehensive and reliable foundation for future studies on microbial bile acid metabolism, offering new insights into the microbial contributions to health and disease.</p><p><strong>Importance: </strong>Bile acid metabolism is an important function in both host and environmental microorganisms. The existing functional annotations from single source pose limitations on cross-habitat analysis. Our construction of a systematic secondary bile acid production gene catalog encompassing numerous high-quality reference sequences propelled research on bile acid metabolism in the global microbiome, holding significance for the concept of One Health. We further highlighted the potential of the microbiota-secondary bile acid axis as a target for the treatment of hepatic and intestinal diseases, as well as the varying feasibility of using animal models for studying human bile acid metabolism. This gene catalog offers a solid groundwork for investigating microbial bile acid metabolism across different compartments, including humans, animals, plants, and environments, shedding light on the contributions of microorganisms to One Health.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0081724"},"PeriodicalIF":5.0,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11748489/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142837796","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Soil microbiome interventions for carbon sequestration and climate mitigation.","authors":"Gwyn A Beattie, Anna Edlund, Nwadiuto Esiobu, Jack Gilbert, Mette Haubjerg Nicolaisen, Janet K Jansson, Paul Jensen, Marco Keiluweit, Jay T Lennon, Jennifer Martiny, Vanessa R Minnis, Dianne Newman, Raquel Peixoto, Christopher Schadt, Jan Roelof van der Meer","doi":"10.1128/msystems.01129-24","DOIUrl":"10.1128/msystems.01129-24","url":null,"abstract":"<p><p>Mitigating climate change in soil ecosystems involves complex plant and microbial processes regulating carbon pools and flows. Here, we advocate for the use of soil microbiome interventions to help increase soil carbon stocks and curb greenhouse gas emissions from managed soils. Direct interventions include the introduction of microbial strains, consortia, phage, and soil transplants, whereas indirect interventions include managing soil conditions or additives to modulate community composition or its activities. Approaches to increase soil carbon stocks using microbially catalyzed processes include increasing carbon inputs from plants, promoting soil organic matter (SOM) formation, and reducing SOM turnover and production of diverse greenhouse gases. Marginal or degraded soils may provide the greatest opportunities for enhancing global soil carbon stocks. Among the many knowledge gaps in this field, crucial gaps include the processes influencing the transformation of plant-derived soil carbon inputs into SOM and the identity of the microbes and microbial activities impacting this transformation. As a critical step forward, we encourage broadening the current widespread screening of potentially beneficial soil microorganisms to encompass functions relevant to stimulating soil carbon stocks. Moreover, in developing these interventions, we must consider the potential ecological ramifications and uncertainties, such as incurred by the widespread introduction of homogenous inoculants and consortia, and the need for site-specificity given the extreme variation among soil habitats. Incentivization and implementation at large spatial scales could effectively harness increases in soil carbon stocks, helping to mitigate the impacts of climate change.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0112924"},"PeriodicalIF":5.0,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11748500/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142847031","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bisphenol S impairs oocyte quality by inducing gut microbiota dysbiosis.","authors":"Jiaming Zhang, Xiaoxia Yu, Weidong Li, Yunjing Jiang, Liangran Zhang, Shunxin Wang","doi":"10.1128/msystems.00912-24","DOIUrl":"10.1128/msystems.00912-24","url":null,"abstract":"<p><p>A good quality egg is essential for a successful pregnancy and early embryo development. Oocyte development is vulnerable to environmental exposures. Bisphenol S (BPS) is widely used as a replacement for its analog bisphenol A, but the reproductive toxicity of BPS has been of great concern. In this study, we showed that BPS exposure induces dysbiosis of the gut microbiota, which further leads to intestinal permeability and inflammation, and ultimately impairs oocyte quality. More importantly, we found that alginate oligosaccharide reshapes the gut microbiota to improve gut homeostasis, thereby preventing the deleterious effects of BPS on the gut and oocytes. Overall, this study not only demonstrates that BPS exposure impairs the intestine and oocytes by inducing dysbiosis of the gut microbiota but also develops a preventive strategy.</p><p><strong>Importance: </strong>Oocyte development is vulnerable to stimulation by intrinsic and extrinsic factors, particularly many environmental pollutants and chemicals in daily life. The reproductive toxicity of bisphenol S has been of great concern, although it is widely used as a safe substitute for its analog bisphenol A. However, it is not known how bisphenol S impairs oocyte quality. This work presents the exciting finding that bisphenol S induces gut microbiota dysbiosis, which further leads to increased intestinal permeability and inflammation and ultimately damages oocytes. More importantly, we show that alginate oligosaccharide improves gut homeostasis by reshaping the gut microbiota, therefore preventing the bisphenol S-induced gut microbiota dysbiosis and gut and oocyte damage. These findings present a major advance in the understanding of bisphenol S toxicity to oocytes and also provide a preventive strategy.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0091224"},"PeriodicalIF":5.0,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11748550/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142864370","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hindguts of <i>Kyphosus sydneyanus</i> harbor phylogenetically and genomically distinct <i>Alistipes</i> capable of degrading algal polysaccharides and diazotrophy.","authors":"Cesar T Facimoto, Kendall D Clements, W Lindsey White, Kim M Handley","doi":"10.1128/msystems.01007-24","DOIUrl":"10.1128/msystems.01007-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;The genus &lt;i&gt;Alistipes&lt;/i&gt; (&lt;i&gt;Bacteroidota&lt;/i&gt;) is most often associated with human clinical samples and livestock. However, &lt;i&gt;Alistipes&lt;/i&gt; are also prevalent in the hindgut of the marine herbivorous fish &lt;i&gt;Kyphosus sydneyanus&lt;/i&gt; (Silver Drummer), and analysis of their carbohydrate-active enzyme (CAZyme) encoding gene repertoires suggests &lt;i&gt;Alistipes&lt;/i&gt; degrade macroalgal biomass to support fish nutrition. To further explore host-associated traits unique to &lt;i&gt;K. sydneyanus&lt;/i&gt;-derived &lt;i&gt;Alistipes&lt;/i&gt;, we compared 445 high-quality genomes of &lt;i&gt;Alistipes&lt;/i&gt; available in public databases (e.g., human and ruminant associated) with 99 metagenome-assembled genomes (MAGs) from the &lt;i&gt;K. sydneyanus&lt;/i&gt; gut. Analyses showed that &lt;i&gt;Alistipes&lt;/i&gt; from &lt;i&gt;K. sydneyanus&lt;/i&gt; are phylogenetically distinct from other hosts and comprise 26 species based on genomic average nucleotide identity (ANI) analyses. Ruminant- and fish-derived &lt;i&gt;Alistipes&lt;/i&gt; had significantly smaller genomes than human-derived strains, and lower GC contents, possibly reflecting a symbiotic relationship with their hosts. The fish-derived &lt;i&gt;Alistipes&lt;/i&gt; were further delineated by their genetic capacity to fix nitrogen, biosynthesize cobalamin (vitamin B12), and utilize marine polysaccharides (e.g., alginate and carrageenan). The distribution of CAZymes encoded by &lt;i&gt;Alistipes&lt;/i&gt; from &lt;i&gt;K. sydneyanus&lt;/i&gt; was not phylogenetically conserved. Distinct CAZyme gene compositions were observed between closely related species. Conversely, CAZyme gene clusters (operons) targeting the same substrates were found across diverse species. Nonetheless, transcriptional data suggest that closely related &lt;i&gt;Alistipes&lt;/i&gt; target specific groups of substrates within the fish hindgut. Results highlight host-specific adaptations among &lt;i&gt;Alistipes&lt;/i&gt; in the fish hindgut that likely contribute to &lt;i&gt;K. sydneyanus&lt;/i&gt; digesting their seaweed diet, and diverse and redundant carbohydrate-degrading capabilities across these &lt;i&gt;Alistipes&lt;/i&gt; species.IMPORTANCEDespite numerous reports of the &lt;i&gt;Alistipes&lt;/i&gt; genus in humans and ruminants, its diversity and function remain understudied, and there is no clear consensus on whether it positively or negatively impacts host health. Given the symbiotic role of gut communities in the &lt;i&gt;Kyphosus sydneyanus&lt;/i&gt; hindgut, where &lt;i&gt;Alistipes&lt;/i&gt; are prevalent, and the diversity of carbohydrate-active enzymes (CAZymes) encoded that likely contribute to the breakdown of important substrates in the host diet, it is likely that this genus provides essential services to the fish host. Therefore, considering its metabolism in various contexts and hosts is crucial for understanding the ecology of the genus. Our study highlights the distinct genetic traits of &lt;i&gt;Alistipes&lt;/i&gt; based on host association, and the potential of fish-associated &lt;i&gt;Alistipes&lt;/i&gt; to transform macroalgae biomass into nutraceuticals (alginate oligosaccharides, β-glucans, sulfated galactans, a","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0100724"},"PeriodicalIF":5.0,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11748540/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142877482","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cigarette smoke-induced disordered microbiota aggravates the severity of influenza A virus infection.","authors":"Tsering Wüthrich, Simone de Brot, Veronica Richina, Nadja Mostacci, Zora Baumann, Nathan G F Leborgne, Aurélie Godel, Marco P Alves, Mohamed Bentires-Alj, Charaf Benarafa, Markus Hilty","doi":"10.1128/msystems.00790-24","DOIUrl":"10.1128/msystems.00790-24","url":null,"abstract":"<p><p>Cigarette smoke (CS) promotes the development of chronic pulmonary disease and has been associated with increased risk for influenza-related illness. Here, we directly addressed the impact of CS disordered microbiota on the severity of influenza A virus (IAV) infection. Specific and opportunistic pathogen-free (SOPF) C57BL/6J mice were exposed to CS or room air (RA) for 5.5 months. Each exposed mouse was then cohoused with a group of recipient germ-free (GF) mice for 1 month for microbial transfer. Colonized GF mice were then infected intranasally with IAV and disease development was monitored. Upper and lower airway and fecal microbiota were longitudinally investigated by 16S rRNA gene sequencing and bacterial cultures in donor and recipient mice. The bacterial family <i>Streptococcaceae</i> accounted for the largest difference between CS- and RA-exposed microbiota in the oropharynx. Analysis of the oropharynx and fecal microbiota indicated an efficient transfer to coprophagic recipient mice, which replicated the differences in microbiota composition observed in donor mice. Subsequent IAV infection revealed significantly higher weight loss for CS microbiota recipient mice at 8-10 days post infection (dpi) compared to control recipient mice. In addition, H1N1 infection inflicted substantial changes in the microbiota composition, especially at days 4 and 8 after infection. In conclusion, mice with a CS-associated microbiota suffer from higher disease severity upon IAV infection compared to mice colonized with a normal SOPF microbiota. Our data suggest that independently of CS exposure and concomitant structural lung damage, microbial distortion due to CS exposure may impact the severity of IAV disease course.IMPORTANCEIt has been reported that chronic exposure to CS is associated with a disordered microbiota composition. In this study, we colonized germ-free (GF) mice with the microbiota from SOPF mice which were chronically exposed to CS or RA. This allowed disentangling the effect of the disordered microbiota from the immune-modulating effects of actual CS exposure. We observed a successful transfer of the microbiotas after cohousing including specific microbiota differences induced by CS exposure in formerly GF mice, which were never exposed to CS. We then investigated the effects of IAV infection on the disease course and microbiotas of formerly GF mice. We found that mice with CS-associated microbiota reveal worse disease course compared to the control group. We hypothesize that CS-induced disordering of the microbiota may, indeed, impact the severity of influenza A disease.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0079024"},"PeriodicalIF":5.0,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11651097/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142676164","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gut microbiota dysbiosis induced by alcohol exposure in pubertal and adult mice.","authors":"Jinlong Yang, Haoyu Wang, Xiaoqian Lin, Jincen Liu, Yue Feng, Yuyin Bai, Hewei Liang, Tongyuan Hu, Zhinan Wu, Jianghua Lai, Jianmei Liu, Yuanqiang Zou, Shuguang Wei, Peng Yan","doi":"10.1128/msystems.01366-24","DOIUrl":"10.1128/msystems.01366-24","url":null,"abstract":"<p><p>Alcohol intake causes many diseases including neuropsychiatric symptoms, nutritional deficiency, progressive pancreatitis, liver cirrhosis, and ischemic heart disease. The gut microbiota changes significantly after alcohol exposure. Alcohol consumption tends to increase in underage and young people, but the feature of the gut microbiota in puberty remains largely unexplored. In this study, we conducted alcohol-exposed pubertal and adult mice model to investigate the intestinal damage and gut microbiota change. Interestingly, the responses of pubertal mice and adult mice after alcohol exposure were different. We found that alcohol dehydrogenase decreased and aldehyde dehydrogenase increased in the liver of pubertal mice, thus reducing the accumulation of toxic acetaldehyde. Furthermore, alcohol exposure caused less intestinal injury in pubertal mice. Through the analysis of metagenome assembly genome, we obtained many unrecognized bacterial genomes. <i>Limosillactobacillus reuteri</i> (cluster_56) and <i>Lactobacillus intestinalis</i> (cluster_57) were assembled from the samples of pubertal mice, which were involved in the production of indole acetic acid and the transformation of bile acids in response to alcohol exposure. This study provided a new insight to investigate the gut microbiota change and explained the difference of the gut microbiota after alcohol exposure between pubertal mice and adult mice.</p><p><strong>Importance: </strong>This study elucidates the significant impact of alcohol exposure on the gut microbiota and metabolic pathways in mice, highlighting the differential responses between adolescent and adult stages. Alcohol exposure was found to damage the intestinal barrier, alter the microbial composition by decreasing beneficial bacteria like <i>Lactobacillus</i>, and increase harmful bacteria such as <i>Alistipes</i>. The study also discovered unique microbial changes and resilience in pubertal mice. Species-level metagenomic analysis revealed specific microbial taxa and metabolic functions affected by alcohol. Metagenome-assembled genomes (MAGs) found many species that could not be annotated by conventional methods including many members of <i>Lachnospiraceae</i>, greatly expanding our understanding of the gut microbiota composition. These findings underscore the need for further research on alcohol's effects on various organs and the implications of microbial metabolites on disease progression.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0136624"},"PeriodicalIF":5.0,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11651099/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142729264","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metabolomic profiles of stony coral species from the Dry Tortugas National Park display inter- and intraspecies variation.","authors":"Jessica M Deutsch, Alyssa M Demko, Olakunle A Jaiyesimi, Gabriel Foster, Adelaide Kindler, Kelly A Pitts, Tessa Vekich, Gareth J Williams, Brian K Walker, Valerie J Paul, Neha Garg","doi":"10.1128/msystems.00856-24","DOIUrl":"10.1128/msystems.00856-24","url":null,"abstract":"<p><p>Coral reefs are experiencing unprecedented loss in coral cover due to increased incidence of disease and bleaching events. Thus, understanding mechanisms of disease susceptibility and resilience, which vary by species, is important. In this regard, untargeted metabolomics serves as an important hypothesis-building tool enabling the delineation of molecular factors underlying disease susceptibility or resilience. In this study, we characterize metabolomes of four species of visually healthy stony corals, including <i>Meandrina meandrites</i>, <i>Orbicella faveolata</i>, <i>Colpophyllia natans</i>, and <i>Montastraea cavernosa</i>, collected at least a year before stony coral tissue loss disease reached the Dry Tortugas, Florida, and demonstrate that both symbiont and host-derived biochemical pathways vary by species. Metabolomes of <i>Meandrina meandrites</i> displayed minimal intraspecies variability and the highest biological activity against coral pathogens when compared to other species in this study. The application of advanced metabolite annotation methods enabled the delineation of several pathways underlying interspecies variability. Specifically, endosymbiont-derived vitamin E family compounds, betaine lipids, and host-derived acylcarnitines were among the top predictors of interspecies variability. Since several metabolite features that contributed to inter- and intraspecies variation are synthesized by the endosymbiotic Symbiodiniaceae, which could be a major source of these compounds in corals, our data will guide further investigations into these Symbiodiniaceae-derived pathways.</p><p><strong>Importance: </strong>Previous research profiling gene expression, proteins, and metabolites produced during thermal stress have reported the importance of endosymbiont-derived pathways in coral bleaching resistance. However, our understanding of interspecies variation in these pathways among healthy corals and their role in diseases is limited. We surveyed the metabolomes of four species of healthy corals with differing susceptibilities to the devastating stony coral tissue loss disease and applied advanced annotation approaches in untargeted metabolomics to determine the interspecies variation in host and endosymbiont-derived pathways. Using this approach, we propose the survey of immune markers such as vitamin E family compounds, acylcarnitines, and other metabolites to infer their role in resilience to coral diseases. As time-resolved multi-omics datasets are generated for disease-impacted corals, our approach and findings will be valuable in providing insight into the mechanisms of disease resistance.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0085624"},"PeriodicalIF":5.0,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11651114/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142668040","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Florfenicol administration in piglets co-selects for multiple antimicrobial resistance genes.","authors":"Devin B Holman, Katherine E Gzyl, Arun Kommadath","doi":"10.1128/msystems.01250-24","DOIUrl":"10.1128/msystems.01250-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Antimicrobial use in food-producing animals such as pigs is a significant issue due to its association with antimicrobial resistance. Florfenicol is a broad-spectrum phenicol antibiotic used in swine for various indications; however, its effect on the swine microbiome and resistome is largely unknown. This study investigated these effects in piglets treated intramuscularly with florfenicol at 1 and 7 days of age. Fecal samples were collected from treated (&lt;i&gt;n&lt;/i&gt; = 30) and untreated (&lt;i&gt;n&lt;/i&gt; = 30) pigs at nine different time points up until 140 days of age, and the fecal metagenomes were sequenced. The fecal microbiomes of the two groups of piglets were most dissimilar in the immediate period following florfenicol administration. These differences were driven in part by an increase in the relative abundance of &lt;i&gt;Clostridium scindens&lt;/i&gt;, &lt;i&gt;Enterococcus faecalis&lt;/i&gt;, and &lt;i&gt;Escherichia&lt;/i&gt; spp. in the florfenicol-treated piglets and &lt;i&gt;Fusobacterium&lt;/i&gt; spp., &lt;i&gt;Pauljensenia hyovaginalis&lt;/i&gt;, and &lt;i&gt;Ruminococcus gnavus&lt;/i&gt; in the control piglets. In addition to selecting for florfenicol resistance genes (&lt;i&gt;floR&lt;/i&gt;, &lt;i&gt;fexA&lt;/i&gt;, and &lt;i&gt;fexB&lt;/i&gt;), florfenicol also selected for genes conferring resistance to the aminoglycosides, beta-lactams, or sulfonamides up until weaning at 21 days of age. Florfenicol-resistant &lt;i&gt;Escherichia coli&lt;/i&gt; isolated from these piglets were found to carry a plasmid with &lt;i&gt;floR&lt;/i&gt;, along with &lt;i&gt;tet&lt;/i&gt;(A), &lt;i&gt;aph(6)-Id&lt;/i&gt;, &lt;i&gt;aph(3″)-Ib&lt;/i&gt;, &lt;i&gt;sul2&lt;/i&gt;, and &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;TEM-1&lt;/sub&gt;/&lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;CMY-2&lt;/sub&gt;. A plasmid carrying &lt;i&gt;fexB&lt;/i&gt; and &lt;i&gt;poxtA&lt;/i&gt; (phenicols and oxazolidinones) was identified in florfenicol-resistant &lt;i&gt;Enterococcus avium&lt;/i&gt;, &lt;i&gt;Enterococcus faecium&lt;/i&gt;, and &lt;i&gt;E. faecalis&lt;/i&gt; isolates from the treated piglets. This study highlights the potential for co-selection and perturbation of the fecal microbial community in pre-weaned piglets administered florfenicol.IMPORTANCEAntimicrobial use remains a serious challenge in food-animal production due to its linkage with antimicrobial resistance. Antimicrobial resistance can reduce the efficacy of veterinary treatment and can potentially be transferred to humans through the food chain or direct contact with animals and their environment. In this study, early-life florfenicol treatment in piglets altered the composition of the fecal microbiome and selected for many unrelated antimicrobial resistance genes up until weaning at 21 days of age. Part of this co-selection process appeared to involve an &lt;i&gt;Escherichia coli&lt;/i&gt; plasmid carrying a florfenicol resistance gene along with genes conferring resistance to at least four other antimicrobial classes. In addition, florfenicol selected for certain genes that provide resistance to multiple antimicrobial classes, including the oxazolidinones. These results highlight that florfenicol can co-select for multiple antimicrobial resistance genes, and their presence on mobile genetic elements sugg","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0125024"},"PeriodicalIF":5.0,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11651103/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142710514","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The transcriptional response to low temperature is weakly conserved across the <i>Enterobacteriaceae</i>.","authors":"Johnson Hoang, Daniel M Stoebel","doi":"10.1128/msystems.00785-24","DOIUrl":"10.1128/msystems.00785-24","url":null,"abstract":"<p><p>Bacteria respond to changes in their external environment, such as temperature, by changing the transcription of their genes. We know little about how these regulatory patterns evolve. We used RNA-seq to study the transcriptional response to a shift from 37°C to 15°C in wild-type <i>Escherichia coli</i>, <i>Salmonella enterica</i>, <i>Citrobacter rodentium</i>, <i>Enterobacter cloacae</i>, <i>Klebsiella pneumoniae</i>, and <i>Serratia marcescens</i>, as well as ∆<i>rpoS</i> strains of <i>E. coli</i> and <i>S. enterica</i>. We found that these species change the transcription of between 626 and 1057 genes in response to the temperature shift, but there were only 16 differentially expressed genes in common among the six species. Species-specific transcriptional patterns of shared genes were a prominent cause of this lack of conservation. Gene ontology enrichment of regulated genes suggested many species-specific phenotypic responses to temperature changes, but enriched terms associated with iron metabolism, central metabolism, and biofilm formation were implicated in at least half of the species. The alternative sigma factor RpoS regulated about 200 genes between 37°C and 15°C in both <i>E. coli</i> and <i>S. enterica</i>, with only 83 genes in common between the two species. Overall, there was limited conservation of the response to low temperature generally, or the RpoS-regulated part of the response specifically. This study suggests that species-specific patterns of transcription of shared genes, rather than horizontal acquisition of unique genes, are the major reason for the lack of conservation of the transcriptomic response to low temperature.</p><p><strong>Importance: </strong>We studied how different species of bacteria from the same Family (Enterobacteriaceae) change the expression of their genes in response to a decrease in temperature. Using <i>de novo</i>-generated parallel RNA-seq data sets, we found that the six species in this study change the level of expression of many of their genes in response to a shift from human body temperature (37°C) to a temperature that might be found out of doors (15°C). Surprisingly, there were very few genes that change expression in all six species. This was due in part to differences in gene content, and in part due to shared genes with distinct expression profiles between the species. This study is important to the field because it illustrates that closely related species can share many genes but not use those genes in the same way in response to the same environmental change.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0078524"},"PeriodicalIF":5.0,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11651113/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142716595","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}