mSystems最新文献

{"title":"Embracing the systems complexity of microbial ecology and evolution: call for papers.","authors":"Leonora Bittleston, Jack Gilbert, Jonathan Klassen, Rachel Mackelprang, Mark J Mandel, Ryan J Newton, Atmika Paudel, Alejandra Rodriguez-Verdugo, Ashley Shade, Roland C Wilhelm, Ying Zhang","doi":"10.1128/msystems.00091-25","DOIUrl":"https://doi.org/10.1128/msystems.00091-25","url":null,"abstract":"","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0009125"},"PeriodicalIF":5.0,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143458629","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":"Investigating the influence of <i>Diadematidae</i> scuticociliatosis on host microbiome composition.","authors":"Brayan Vilanova-Cuevas, Christopher M DeRito, Isabella T Ritchie, Christina A Kellogg, James S Evans, Alizee Zimmerman, Stacey M Williams, Marilyn Brandt, Moriah Sevier, Samuel Gittens, Kayla A Budd, Matthew Warham, William C Sharp, Gabriel A Delgado, Alwin Hylkema, Kimani Kitson-Walters, Jean-Pascal Quod, Mya Breitbart, Ian Hewson","doi":"10.1128/msystems.01418-24","DOIUrl":"https://doi.org/10.1128/msystems.01418-24","url":null,"abstract":"<p><p>Mass mortality of Diadematidae urchins, caused by the <i>Diadema antillarum</i> scuticociliatosis Philaster clade (DScPc)<i>,</i> affected the Caribbean in spring 2022 and subsequently spread to the eastern Mediterranean, Red Sea, and western Indian Ocean. A key question around Diadematidae scuticociliatosis (DSc), the disease caused by the scuticociliate, is whether the urchin microbiome varies between scuticociliatosis-affected and grossly normal urchins. Tissue samples from both grossly normal and abnormal <i>Diadema antillarum</i> were collected in the field during the initial assessment of the DSc causative agent and from an experimental challenge of DScPc culture on aquacultured <i>D. antillarum</i>. Specimens were analyzed using 16S rRNA gene amplicon sequencing. Additional abnormal urchin samples were collected from the most recent outbreak site in the western Indian Ocean (Réunion Island). At reference (i.e., unaffected by DSc) sites, <i>Kistimonas</i> spp.<i>, Propionigenium</i> spp., and <i>Endozoicomonas</i> spp. were highly represented in amplicon libraries. DSc-affected urchin amplicon libraries had lower taxonomic richness and a greater representation of taxa related to <i>Fangia hongkongensis</i> and <i>Psychrobium</i> spp. Amplicon libraries of urchins experimentally challenged with the DSc pathogen had some shifts in microbial composition, but <i>F. hongkongensis</i> was not a part of the core bacteria in DSc-challenged specimens. DSc-affected <i>Echinothrix diadema</i> from Réunion Island showed a similar high representation of <i>F. hongkongensis</i> as that seen on Caribbean <i>D. antillarum</i>. Our results suggest that DSc alters <i>Diadematidae</i> microbiomes and that <i>F. hongkongensis</i> may be a candidate bacterial biomarker for DSc in environmental samples. The mechanism driving microbiome variation in host-pathogen interactions remains to be explored.IMPORTANCEThe mass mortality of Diadematidae urchins due to <i>Diadema antillarum</i> scuticociliatosis (DSc) has had significant ecological impacts, spreading from the Caribbean to the eastern Mediterranean, Red Sea, and western Indian Ocean. This study investigates whether the microbiome of urchins varies between those affected by DSc and those that are not. Using 16S rRNA gene amplicon sequencing, researchers found that DSc-affected urchins had lower taxonomic richness and a greater representation of <i>Fangia hongkongensis</i> and <i>Psychrobium</i> spp. The findings indicate that <i>F. hongkongensis</i> could serve as a bacterial biomarker for DSc in environmental samples, providing a potential tool for early detection and management of the disease. Understanding these microbiome changes is crucial for developing strategies to mitigate the spread and impact of DSc on marine ecosystems.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0141824"},"PeriodicalIF":5.0,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143448277","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":"Comparison of different microbiome analysis pipelines to validate their reproducibility of gastric mucosal microbiome composition.","authors":"Konrad Lehr, Baptiste Oosterlinck, Chee Kin Then, Matthew R Gemmell, Rolandas Gedgaudas, Jan Bornschein, Juozas Kupcinskas, Annemieke Smet, Georgina Hold, Alexander Link","doi":"10.1128/msystems.01358-24","DOIUrl":"10.1128/msystems.01358-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Microbiome analysis has become a crucial tool for basic and translational research due to its potential for translation into clinical practice. However, there is ongoing controversy regarding the comparability of different bioinformatic analysis platforms and a lack of recognized standards, which might have an impact on the translational potential of results. This study investigates how the performance of different microbiome analysis platforms impacts the final results of mucosal microbiome signatures. Across five independent research groups, we compared three distinct and frequently used microbiome analysis bioinformatic packages (DADA2, MOTHUR, and QIIME2) on the same subset of fastQ files. The source data set encompassed 16S rRNA gene raw sequencing data (V1-V2) from gastric biopsy samples of clinically well-defined gastric cancer (GC) patients (&lt;i&gt;n&lt;/i&gt; = 40; with and without &lt;i&gt;Helicobacter pylori&lt;/i&gt; [&lt;i&gt;H. pylori&lt;/i&gt;] infection) and controls (&lt;i&gt;n&lt;/i&gt; = 39, with and without &lt;i&gt;H. pylori&lt;/i&gt; infection). Independent of the applied protocol, &lt;i&gt;H. pylori&lt;/i&gt; status, microbial diversity and relative bacterial abundance were reproducible across all platforms, although differences in performance were detected. Furthermore, alignment of the filtered sequences to the old and new taxonomic databases (i.e., Ribosomal Database Project, Greengenes, and SILVA) had only a limited impact on the taxonomic assignment and thus on global analytical outcomes. Taken together, our results clearly demonstrate that different microbiome analysis approaches from independent expert groups generate comparable results when applied to the same data set. This is crucial for interpreting respective studies and underscores the broader applicability of microbiome analysis in clinical research, provided that robust pipelines are utilized and thoroughly documented to ensure reproducibility.IMPORTANCEMicrobiome analysis is one of the most important tools for basic and translational research due to its potential for translation into clinical practice. However, there is an ongoing controversy about the comparability of different bioinformatic analysis platforms and a lack of recognized standards. In this study, we investigate how the performance of different microbiome analysis platforms affects the final results of mucosal microbiome signatures. Five independent research groups used three different and commonly used bioinformatics packages for microbiome analysis on the same data set and compared the results. This data set included microbiome sequencing data from gastric biopsy samples of GC patients. Regardless of the protocol used, &lt;i&gt;Helicobacter pylori&lt;/i&gt; status, microbial diversity, and relative bacterial abundance were reproducible across all platforms. The results show that different microbiome analysis approaches provide comparable results. This is crucial for the interpretation of corresponding studies and underlines the broader applicability of microbiome ana","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0135824"},"PeriodicalIF":5.0,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11834405/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143053040","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":"Genomic re-sequencing reveals mutational divergence across genetically engineered strains of model archaea.","authors":"Andrew L Soborowski, Rylee K Hackley, Sungmin Hwang, Guangyin Zhou, Keely A Dulmage, Peter Schönheit, Charles Daniels, Alexandre W Bisson-Filho, Anita Marchfelder, Julie A Maupin-Furlow, Thorsten Allers, Amy K Schmid","doi":"10.1128/msystems.01084-24","DOIUrl":"10.1128/msystems.01084-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Archaeal molecular biology has been a topic of intense research in recent decades as their role in global ecosystems, nutrient cycles, and eukaryotic evolution comes to light. The hypersaline-adapted archaeal species &lt;i&gt;Halobacterium salinarum&lt;/i&gt; and &lt;i&gt;Haloferax volcanii&lt;/i&gt; serve as important model organisms for understanding archaeal genomics, genetics, and biochemistry, in part because efficient tools enable genetic manipulation. As a result, the number of strains in circulation among the haloarchaeal research community has increased in recent decades. However, the degree of genetic divergence and effects on genetic integrity resulting from the creation and inter-lab transfer of novel lab stock strains remain unclear. To address this, we performed whole-genome re-sequencing on a cross-section of wild-type, parental, and knockout strains in both model species. Integrating these data with existing repositories of re-sequencing data, we identify mutations that have arisen in a collection of 60 strains, sampled from two species across eight different labs. Independent of sequencing, we construct strain lineages, identifying branch points and significant genetic events in strain history. Combining this with our sequencing data, we identify small clusters of mutations that definitively separate lab strains. Additionally, an analysis of gene knockout strains suggests that roughly one in three strains currently in use harbors second-site mutations of potential phenotypic impact. Overall, we find that divergence among lab strains is thus far minimal, though as the archaeal research community continues to grow, careful strain provenance and genomic re-sequencing are required to keep inter-lab divergence to a minimum, prevent the compounding of mutations into fully independent lineages, and maintain the current high degree of reproducible research between lab groups.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;Archaea are a domain of microbial life whose member species play a critical role in the global carbon cycle, climate regulation, the human microbiome, and persistence in extreme habitats. In particular, hypersaline-adapted archaea are important, genetically tractable model organisms for studying archaeal genetics, genomics, and biochemistry. As the archaeal research community grows, keeping track of the genetic integrity of strains of interest is necessary. In particular, routine genetic manipulations and the common practice of sharing strains between labs allow mutations to arise in lab stocks. If these mutations affect cellular processes, they may jeopardize the reproducibility of work between research groups and confound the results of future studies. In this work, we examine DNA sequences from 60 strains across two species of archaea. We identify shared and unique mutations occurring between and within strains. Independently, we trace the lineage of each strain, identifying which genetic manipulations lead to observed off-target mutations. While","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0108424"},"PeriodicalIF":5.0,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11834397/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142951966","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":"Discovery of viruses and bacteria associated with swine respiratory disease on farms at a nationwide scale in China using metatranscriptomic and metagenomic sequencing.","authors":"Xi Huang, Xinzhi Yao, Wenbo Song, Mengfei Zhao, Zhanwei Zhu, Hanyuan Liu, Xiaorong Song, Jingwen Huang, Yongrun Chen, Zihao Wang, Changjiang Peng, Wenqing Wu, Hao Yang, Lin Hua, Huanchun Chen, Bin Wu, Zhong Peng","doi":"10.1128/msystems.00025-25","DOIUrl":"10.1128/msystems.00025-25","url":null,"abstract":"<p><p>Respiratory disease (RD) is a worldwide leading threat to the pig industry, but there is still limited understanding of the pathogens associated with swine RD. In this study, we conducted a nationwide genomic surveillance on identifying viruses, bacteria, and antimicrobial resistance genes (ARGs) from the lungs of pigs with RD in China. By performing metatranscriptomic sequencing combined with metagenomic sequencing, we identified 21 viral species belonging to 12 viral families. Among them, porcine reproductive and respiratory syndrome virus, influenza A virus, herpes virus, adenovirus, and parvovirus were commonly identified. However, emerging viruses, such as Getah virus and porcine respiratory coronaviruses, were also characterized. Apart from viruses, a total of 164 bacterial species were identified, with <i>Streptococcus</i> suis, <i>Mycoplasma hyorhinis</i>, <i>Mycoplasma hyopneumoniae</i>, <i>Glaesserella parasuis</i>, and <i>Pasteurella multocida</i> being frequently detected in high abundances. Notably, <i>Escherichia coli</i>, <i>Enterococcus faecalis</i>, <i>Staphylococcus aureus</i>, and <i>Klebsiella pneumoniae</i> were also highly detected. Our further analysis revealed a complex interaction between the identified pathogens in swine RD. We also conducted retrospectively analyses to demonstrate the prevalent viral genotypes or bacterial serotypes associated with swine RD in China. Finally, we identified 48 ARGs, which conferred resistance to 13 predicted antimicrobial classes, and many of these ARGs were significantly associated with a substantial number of mobile genetic elements, including transposons (e.g., <i>tnp</i>AIS1, <i>tnp</i>A1353, <i>int</i>3, and <i>IS</i>Cau1) and plasmids (e.g., Col(BS512), Col(YC)]. These findings will contribute to further understanding the etiology, epidemiology, and microbial interactions in swine RD, and may also shed a light on the development of effective vaccines.IMPORTANCEIn this study, we identified viruses and bacteria from the lungs of pigs with RD in China at a nationwide farm scale by performing metatranscriptomic sequencing combined with metagenomic sequencing. We also demonstrated the complex interactions between different viral and/or bacterial species in swine RD. Our work provides a comprehensive knowledge about the etiology, epidemiology, and microbial interactions in swine RD and data reference for the research and development of effective vaccines against the disease.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0002525"},"PeriodicalIF":5.0,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11834406/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143066816","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":"Multi-omics investigation of <i>Porphyromonas gingivalis</i> exacerbating acute kidney injury through the gut-kidney axis.","authors":"Ling Dong, Zhaoxin Ji, Jing Sun, Jiangqi Hu, Qingsong Jiang, Wei Wei","doi":"10.1128/msystems.01136-24","DOIUrl":"10.1128/msystems.01136-24","url":null,"abstract":"<p><p>Periodontitis is closely related to renal health, but the specific influence of <i>Porphyromonas gingivalis</i> (<i>P. gingivalis</i>), a key pathogen in periodontitis, on the development of acute kidney injury (AKI) in mice has not been fully elucidated. In our study, AKI was induced in mice through ischemia-reperfusion injury while administering oral infection with <i>P. gingivalis</i>. Comprehensive analyses were conducted, including 16S rRNA sequencing, liquid chromatography-mass spectrometry (LC-MS) metabolomics, and transcriptome sequencing. <i>In vitro</i>, the identified metabolite was used to stimulate mouse neutrophils. Subsequently, these modified neutrophils were co-cultured with mouse renal tubular epithelial cells. The results showed that oral infection with <i>P. gingivalis</i> significantly exacerbated AKI in mice. 16S rRNA sequencing revealed notable shifts in gut microbiota composition. LC-MS metabolomics analysis identified significant metabolic alterations, particularly the upregulation of 3-indoleacrylic acid in the serum. Transcriptome sequencing showed an increased expression of neutrophilic granule protein (<i>Ngp</i>), which was closely associated with 3-indoleacrylic acid, and the presence of <i>Porphyromonas</i>. Cellular experiments demonstrated that 3-indoleacrylic acid could activate neutrophils, leading to an elevation in NGP protein levels, a response that was associated with renal epithelial cell injury. Oral infection with <i>P. gingivalis</i> exacerbated AKI through the gut-kidney axis, involving gut microbiota dysbiosis, metabolic disturbances, and increased renal expression of <i>Ngp</i>.</p><p><strong>Importance: </strong>This study provides novel insights into the relationship between periodontal health and renal function. <i>Porphyromonas gingivalis</i> oral infection disrupted the balance of gut microbiota and was an important modifier determining the severity of acute kidney injury. Under the \"gut-kidney axis,\" <i>P. gingivalis</i> might cause an increase in the level of the gut microbial metabolite 3-indoleacrylic acid, interfering with kidney immunity and disrupting the maintenance of kidney epithelium.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0113624"},"PeriodicalIF":5.0,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11834432/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142979225","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":"Interactions between gut microbes and host promote degradation of various fiber components in Meishan pigs.","authors":"Guang Pu, Liming Hou, Qingbo Zhao, Gensheng Liu, Zhongyu Wang, Wuduo Zhou, Peipei Niu, Chengwu Wu, Pinghua Li, Ruihua Huang","doi":"10.1128/msystems.01500-24","DOIUrl":"10.1128/msystems.01500-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Although metagenomic investigations into microbial fiber-degrading capabilities are currently prevalent, there is a notable gap in research concerning the regulatory mechanisms underpinning host-microbiota interactions that confer tolerance to high-fiber diets in pigs. In this study, 28 Meishan (MS) and 28 Large White (LW) pigs were subjected to feeding experiments involving various fiber levels. Subsequently, multi-omics was employed to investigate the influence of host-microbiota interactions on the fiber degradation of pigs. MS exhibited superior fiber digestibility compared with LW, particularly evident when fed a high-fiber diet. In MS, positive interactions among &lt;i&gt;Treponema bryantii&lt;/i&gt;, &lt;i&gt;Treponema&lt;/i&gt; sp., &lt;i&gt;Rikenellaceae&lt;/i&gt; bacterium, and &lt;i&gt;Bacteroidales&lt;/i&gt; bacterium WCE2004 facilitated the degradation of both cellulose and pectin. The reduced polymerization of polysaccharides and oligosaccharides observed in MS provides compelling evidence for their superior microbial fiber-degrading capability. The concentrations of propionate and butyrate retained in cecal lumen of MS was unchanged, whereas it was significantly increased in LW, indicating a strong absorption of short-chain fatty acids (SCFAs) in MS intestines. Correlation analysis using RNA-seq data revealed distinct patterns in LW and MS. In LW, microbial profiles along with &lt;i&gt;GPR183&lt;/i&gt; and &lt;i&gt;GPR174&lt;/i&gt; exhibited negative correlations with butyrate and propionate, respectively. Conversely, in MS, &lt;i&gt;GPR174&lt;/i&gt; and &lt;i&gt;SLC2A4&lt;/i&gt; were positively correlated with butyrate. Our findings underscore the dynamic collaboration among microbial species in degrading cellulose and pectin, coupled with the synergistic effects of SCFA transport-related genes, as crucial underpinnings for the heightened fiber digestibility observed in MS. These discoveries offer fresh perspectives into the intricate mechanisms governing host-microbiota interactions that influence fiber digestion in pigs.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;Studies on porcine intestinal microbiota have been widely conducted, and some microbial taxa with fiber degradation functions have been identified. However, the mechanisms of division among gut microbes in the degradation of complex fiber components are still unclear. In addition, the regulation of fiber digestion by host through absorption of short-chain fatty acids (SCFAs) needs to be further investigated. Our study used apparent total tract digestibility of dietary fiber to assess the utilization efficiency of dietary fiber between Meishan and Large White pigs. Subsequently, through metagenome sequencing and determination of fiber-degrading products, we found that in Meishan pigs, positive interactions among &lt;i&gt;Treponema bryantii&lt;/i&gt;, &lt;i&gt;Treponema&lt;/i&gt; sp&lt;i&gt;.&lt;/i&gt;, &lt;i&gt;Rikenellaceae&lt;/i&gt; bacterium, and &lt;i&gt;Bacteroidales&lt;/i&gt; bacterium WCE2004 facilitated the degradation of both cellulose and pectin. RNA-seq analysis elucidated breed-specific genes associated with SCFA ","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0150024"},"PeriodicalIF":5.0,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11834408/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143053043","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":"Targeted sequencing of <i>Enterobacterales</i> bacteria using CRISPR-Cas9 enrichment and Oxford Nanopore Technologies.","authors":"Hugh Cottingham, Louise M Judd, Jessica A Wisniewski, Ryan R Wick, Thomas D Stanton, Ben Vezina, Nenad Macesic, Anton Y Peleg, Iruka N Okeke, Kathryn E Holt, Jane Hawkey","doi":"10.1128/msystems.01413-24","DOIUrl":"10.1128/msystems.01413-24","url":null,"abstract":"<p><p>Sequencing DNA directly from patient samples enables faster pathogen characterization compared to traditional culture-based approaches, but often yields insufficient sequence data for effective downstream analysis. CRISPR-Cas9 enrichment is designed to improve the yield of low abundance sequences but has not been thoroughly explored with Oxford Nanopore Technologies (ONT) for use in clinical bacterial epidemiology. We designed CRISPR-Cas9 guide RNAs to enrich the human pathogen <i>Klebsiella pneumoniae</i>, by targeting multi-locus sequence type (MLST) and transfer RNA (tRNA) genes, as well as common antimicrobial resistance (AMR) genes and the resistance-associated integron gene <i>intI1</i>. We validated enrichment performance in 20 <i>K</i>. <i>pneumoniae</i> isolates, finding that guides generated successful enrichment across all conserved sites except for one AMR gene in two isolates. Enrichment of MLST genes led to a correct allele call in all seven loci for 8 out of 10 isolates that had depth of 30× or more in these regions. We then compared enriched and unenriched sequencing of three human fecal samples spiked with <i>K. pneumoniae</i> at varying abundance. Enriched sequencing generated 56× and 11.3× the number of AMR and MLST reads, respectively, compared to unenriched sequencing, and required approximately one-third of the computational storage space. Targeting the <i>intI1</i> gene often led to detection of 10-20 proximal resistance genes due to the long reads produced by ONT sequencing. We demonstrated that CRISPR-Cas9 enrichment combined with ONT sequencing enabled improved genomic characterization outcomes over unenriched sequencing of patient samples. This method could be used to inform infection control strategies by identifying patients colonized with high-risk strains.</p><p><strong>Importance: </strong>Understanding bacteria in complex samples can be challenging due to their low abundance, which often results in insufficient data for analysis. To improve the detection of harmful bacteria, we implemented a technique aimed at increasing the amount of data from target pathogens when combined with modern DNA sequencing technologies. Our technique uses CRISPR-Cas9 to target specific gene sequences in the bacterial pathogen <i>Klebsiella pneumoniae</i> and improve recovery from human stool samples. We found our enrichment method to significantly outperform traditional methods, generating far more data originating from our target genes. Additionally, we developed new computational techniques to further enhance the analysis, providing a thorough method for characterizing pathogens from complex biological samples.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0141324"},"PeriodicalIF":5.0,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11834407/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142951971","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":"Multi-omic signatures of host response associated with presence, type, and outcome of enterococcal bacteremia.","authors":"Charlie Bayne, Dominic McGrosso, Concepcion Sanchez, Leigh-Ana Rossitto, Maxwell Patterson, Carlos Gonzalez, Courtney Baus, Cecilia Volk, Haoqi Nina Zhao, Pieter Dorrestein, Victor Nizet, George Sakoulas, David J Gonzalez, Warren Rose","doi":"10.1128/msystems.01471-24","DOIUrl":"10.1128/msystems.01471-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Despite the prevalence and severity of enterococcal bacteremia (EcB), the mechanisms underlying systemic host responses to the disease remain unclear. Here, we present an extensive study that profiles molecular differences in plasma from EcB patients using an unbiased multi-omics approach. We performed shotgun proteomics and metabolomics on 105 plasma samples, including those from EcB patients and healthy volunteers. Comparison between healthy volunteer and EcB-infected patient samples revealed significant disparities in proteins and metabolites involved in the acute phase response, inflammatory processes, and cholestasis. Several features distinguish these two groups with remarkable accuracy. Cross-referencing EcB signatures with those of &lt;i&gt;Staphylococcus aureus&lt;/i&gt; bacteremia revealed shared reductions in cholesterol metabolism proteins and differing responses in platelet alpha granule and neutrophil-associated proteins. Characterization of &lt;i&gt;Enterococcus&lt;/i&gt; isolates derived from patients facilitated a nuanced comparison between EcB caused by &lt;i&gt;Enterococcus faecalis&lt;/i&gt; and &lt;i&gt;Enterococcus faecium,&lt;/i&gt; uncovering reduced immunoglobulin abundances in &lt;i&gt;E. faecium&lt;/i&gt; cases and features capable of distinguishing the underlying microbe. Leveraging extensive patient metadata, we now have identified features associated with mortality or survival, revealing significant multi-omic differences and pinpointing histidine-rich glycoprotein and fetuin-B as features capable of distinguishing survival status with excellent accuracy. Altogether, this study aims to culminate in the creation of objective risk stratification algorithms-a pivotal step toward enhancing patient management and care. To facilitate the exploration of this rich data source, we provide a user-friendly interface at https://gonzalezlab.shinyapps.io/EcB_multiomics/.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;&lt;i&gt;Enterococcus&lt;/i&gt; infections have emerged as the second most common nosocomial infection, with enterococcal bacteremia (EcB) contributing to thousands of patient deaths annually. To address a lack of detailed understanding regarding the specific systemic response to EcB, we conducted a comprehensive multi-omic evaluation of the systemic host response observed in patient plasma. Our findings reveal significant features in the metabolome and proteome associated with the presence of infection, species differences, and survival outcome. We identified features capable of discriminating EcB infection from healthy states and survival from mortality with excellent accuracy, suggesting potential practical clinical utility. However, our study also established that systemic features to distinguish &lt;i&gt;Enterococcus faecalis&lt;/i&gt; from &lt;i&gt;Enterococcus faecium&lt;/i&gt; EcB show only a moderate degree of discriminatory accuracy, unlikely to significantly improve upon current diagnostic methods. Comparisons of differences in the plasma proteome relative to healthy samples between bacteremia caused by &lt;i&gt;","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0147124"},"PeriodicalIF":5.0,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11834471/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143008529","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":"Antiviral defense systems in the rumen microbiome.","authors":"Johan S Sáenz, Bibiana Rios-Galicia, Jana Seifert","doi":"10.1128/msystems.01521-24","DOIUrl":"10.1128/msystems.01521-24","url":null,"abstract":"<p><p>The continuous interaction between phages and their respective hosts has resulted in the evolution of multiple bacterial immune mechanisms. However, the diversity and prevalence of antiviral defense systems in complex communities are still unknown. We therefore investigated the diversity and abundance of viral defense systems in 3,038 high-quality bacterial and archaeal genomes from the rumen. In total, 14,241 defense systems and 31,948 antiviral-related genes were identified. Those genes represented 114 unique system types grouped into 49 families. We observed a high prevalence of defense systems in the genomes. However, the number of defense systems, defense system families, and system density varied widely from genome to genome. Additionally, the number of defense system per genome correlated positively with the number of defense system families and the genome size. Restriction modification, Abi, and cas system families were the most common, but many rare systems were present in only 1% of the genomes. Antiviral defense systems are prevalent and diverse in the rumen, but only a few are dominant, indicating that most systems are rarely present. However, the collection of systems throughout the rumen may represent a pool of mechanisms that can be shared by different members of the community and modulate the phage-host interaction.IMPORTANCEPhages may act antagonistically at the cell level but have a mutualistic interaction at the microbiome level. This interaction shapes the structure of microbial communities and is mainly driven by the defense mechanism. However, the diversity of such mechanism is larger than previously thought. Because of that, we described the abundance and diversity of the antiviral defense system of a collection of genomes, metagenome-assembled genomes (MAGs) and isolates, from the rumen. While defense mechanisms seem to be prevalent among bacteria and archaea, only a few were common. This suggests that most of these defense mechanisms are not present in many rumen microbes but could be shared among different members of the microbial community. This is consistent with the \"pan-immune system\" model, which appears to be common across different environments.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0152124"},"PeriodicalIF":5.0,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11834463/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142979224","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}