mSphere最新文献

{"title":"Not all is lost: resilience of microbiome samples to freezer failures and long-term storage.","authors":"M Fabiola Pulido Barriga, James W J Randolph, Sydney I Glassman","doi":"10.1128/msphere.00603-24","DOIUrl":"10.1128/msphere.00603-24","url":null,"abstract":"<p><p>Advances in technology have facilitated extensive sample collection to explore microbiomes across diverse systems, leading to a growing reliance on ultracold freezers for storing both samples and extracted DNA. However, freezer malfunctions can jeopardize data integrity. To evaluate the impact of an unexpected -80°C freezer failure and the recoverability of thawed soil samples, we extracted DNA and compared it to long-term DNA stored at -20°C and original 16S and ITS2 sequencing data collected before the malfunction. Using Illumina MiSeq, we assessed how the freezer failure and long-term storage influenced the resilience of bacterial or fungal richness or community composition and our ability to accurately determine experimental treatment effects. Our results reveal substantial resilience in fungal richness and both bacterial and fungal beta-diversity to soil sample thawing and extended frozen DNA storage. This resilience facilitated biological inferences that closely mirrored those observed in the original study. Notably, fungi exhibited greater resilience to short-term thawing compared to bacteria, which showed sensitivity to both thawing and long-term freezing. Moreover, taxonomic composition analysis revealed the persistence of dominant microbial taxa under thawing and prolonged freezing, suggesting that dominant microbes remain viable for tracking across temporal studies. In conclusion, our study highlights that beta-diversity is more robust than alpha-diversity and fungi are more resilient to freezer failure than bacteria. Furthermore, our findings underscore the effectiveness of soil storage at -80°C compared to storage of extracted DNA at -20°C, despite potential freezer failures, as the most robust method for long-term storage in microbiome studies.</p><p><strong>Importance: </strong>Microbiome studies heavily rely on ultracold freezers for sample storage. Unfortunately, these freezers are prone to frequent malfunctions, resulting in the loss of invaluable samples at laboratories worldwide. Such losses can halt research progress due to potential issues with sample reliability. Our research demonstrates that not all is lost when an unforeseen freezer failure occurs. Samples can still be reliably used to assess treatment effects, which is particularly important for long-term temporal studies where samples cannot be readily obtained again.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0060324"},"PeriodicalIF":3.7,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11774026/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142864889","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":"Small RNA CjNC110 regulates the activated methyl cycle to enable optimal chicken colonization by <i>Campylobacter jejuni</i>.","authors":"Brandon Ruddell, Alan Hassall, Orhan Sahin, Paul J Plummer, Qijing Zhang, Amanda J Kreuder","doi":"10.1128/msphere.00832-24","DOIUrl":"10.1128/msphere.00832-24","url":null,"abstract":"<p><p>Post-transcriptional gene regulation by non-coding small RNAs (sRNAs) is critical for colonization and survival of enteric pathogens, including the zoonotic pathogen <i>Campylobacter jejuni</i>. In this study, we utilized <i>C. jejuni</i> IA3902 (a representative isolate of the sheep abortion clone) and <i>C. jejuni</i> W7 (a highly motile variant of NCTC 11168, a human gastroenteritis strain) to further investigate regulation by sRNA CjNC110. Both motility and autoagglutination ability were confirmed to be phenotypes of conserved regulation by CjNC110. However, we demonstrated that W7∆CjNC110 does not change chicken colonization levels compared to W7 wild type, directly contrasting IA3902∆CjNC110, which had decreased colonization ability. Subsequently, we determined strain-specific phenotype variation between W7∆CjNC110 and IA3902∆CjNC110 when examining intracellular L-methionine (L-met) levels controlled by the activated methyl cycle (AMC). We hypothesized that the presence of a secondary system for L-met production conferred by MetAB in W7 but not IA3902 might explain the difference in both chicken colonization and L-met availability. Insertion of <i>metAB</i> within IA3902∆CjNC110 (naturally absent) restored intracellular L-met levels in IA3902∆CjNC110::metAB and overcame the colonization defect that resulted from mutagenesis of CjNC110 in IA3902. Deletion of metAB in W7∆CjNC110 (naturally present) led to a decrease in L-met in W7∆CjNC110∆metAB and a colonization defect which was otherwise masked in W7∆CjNC110. Our results indicate that regulation of the AMC leading to altered L-met availability is a conserved regulatory function of CjNC110 in <i>C. jejuni</i> and confirm that L-met generation via the AMC as activated by CjNC110 is critical for optimal host colonization.IMPORTANCEDuring this study, the regulatory action and conservation of function of CjNC110 between two different zoonotically important <i>Campylobacter jejuni</i> strains were examined. Critically, this work for the first time reveals regulation of L-methionine (L-met) production within the activated methyl cycle (AMC) by small RNA (sRNA) CjNC110 as a key factor driving <i>C. jejuni</i> optimal chicken colonization. As a growing body of evidence suggests that maintenance of L-met homeostasis appears to be critical for <i>C. jejuni</i> colonization, interventions targeting the AMC could provide a critical control point for therapeutic drug options to combat this zoonotic pathogen. Our results also indicate that even for conserved sRNAs such as CjNC110, strain-specific differences in phenotypes regulated by sRNAs may exist, independent of conserved regulatory action. Depending on the strain examined and accessory genomic content present, conserved regulatory actions might be masked, thus investigation in multiple strains may be warranted.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0083224"},"PeriodicalIF":3.7,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11774046/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142952314","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":"Preliminary clinical performance of a Cas13a-based lateral flow assay for detecting <i>Neisseria gonorrhoeae</i> in urine specimens.","authors":"Lao-Tzu Allan-Blitz, Gordon Adams, Gabriela Sanders, Palak Shah, Krithik Ramesh, Jana Jarolimova, Kevin L Ard, John A Branda, Jeffrey D Klausner, Pardis C Sabeti, Jacob E Lemieux","doi":"10.1128/msphere.00677-24","DOIUrl":"10.1128/msphere.00677-24","url":null,"abstract":"<p><p>Nucleic acid amplification testing (NAAT) for <i>N. gonorrhoeae</i> is unavailable in resource-limited settings. We previously developed a CRISPR-based lateral flow assay for detecting <i>N. gonorrhoeae</i>. We aimed to pair that assay with point-of-care DNA extraction, assess performance in clinical urine specimens, and optimize assay kinetics. We collected urine specimens among men presenting with urethritis enrolling in a clinical trial at the Massachusetts General Hospital Sexual Health Clinic. We assessed the quantified DNA yield of detergent-based extractions with and without heat. We selected one detergent for extracting all specimens, paired with isothermal recombinase polymerase amplification for 90 minutes and lateral flow Cas13a detection, interpreted via pixel intensity analysis. We also trained a smartphone-based machine-learning model on 1,008 images to classify lateral flow results. We used the model to interpret lateral flow results from the clinical specimens. We also tested a modified amplification chemistry with a second forward primer lacking the T7-promoter to accelerate reaction kinetics. Extraction with 0.02% Triton X resulted in an average DNA yield of 2.6 × 10⁶ copies/µL (SD ± 6.7 × 10⁵). We treated 40 urine specimens (<i>n</i> = 12 positive) with 0.02% Triton X, and using quantified pixel intensity analysis, the Cas13a-based assay correctly classified all specimens (100% agreement; 95% CI 91.2%-100%). The machine-learning model correctly classified 45/45 strips in the validation data set and all 40 lateral flow strips from clinical specimens. Including the second forward primer reduced incubation time to 60 minutes. Using point-of-care DNA extraction, our Cas13a-based lateral flow <i>N. gonorrhoeae</i> assay demonstrated promising performance among clinical urine specimens.IMPORTANCEUsing a CRISPR-based assay we previously developed for <i>Neisseria gonorrhoeae</i> detection, we developed new techniques to facilitate point-of-care use. We then demonstrated the promising performance of that assay in clinical specimens. Furthermore, we developed a smartphone-based machine learning application for assisting interpretation of lateral flow strip results. Such an assay has the potential to transform the care of sexually transmitted infections in low-resource settings where diagnostic tests are unavailable. A point-of-care pathogen-specific assay, paired with the connectivity offered by a smartphone application, can also support public health surveillance efforts in such areas.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0067724"},"PeriodicalIF":3.7,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11774021/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142837888","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":"When HSFs bring the heat-mapping the transcriptional circuitries of HSF-type regulators in <i>Candida albicans</i>.","authors":"Sadri Znaidi","doi":"10.1128/msphere.00644-23","DOIUrl":"10.1128/msphere.00644-23","url":null,"abstract":"<p><p>Heat shock factor (HSF)-type regulators are stress-responsive transcription factors widely distributed among eukaryotes, including fungi. They carry a four-stranded winged helix-turn-helix DNA-binding domain considered as the signature domain for HSFs. The genome of the opportunistic yeast <i>Candida albicans</i> encodes four HSF members, namely, Sfl1, Sfl2, Skn7, and the essential regulator, Hsf1. <i>C. albicans</i> HSFs do not only respond to heat shock and/or temperature variation but also to CO₂ levels, oxidative stress, and quorum sensing, acting this way as central decision makers. In this minireview, I follow on the heels of my mSphere of Influence commentary (2020) to provide an overview of the repertoire of HSF regulators in <i>Saccharomyces cerevisiae</i> and <i>C. albicans</i> and describe how their genetic perturbation in <i>C. albicans</i>, coupled with genome-wide expression and location analyses, allow to map their transcriptional circuitry. I highlight how they can regulate, in common, a crucial developmental program: filamentous growth.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0064423"},"PeriodicalIF":3.7,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11774045/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142864887","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":"Perforin-2 is dispensable for host defense against <i>Aspergillus fumigatus</i> and <i>Candida albicans</i>.","authors":"Mariano A Aufiero, Li-Yin Hung, De'Broski R Herbert, Tobias M Hohl","doi":"10.1128/msphere.00803-24","DOIUrl":"10.1128/msphere.00803-24","url":null,"abstract":"<p><p>Myeloid phagocytes are essential for antifungal immunity against pulmonary <i>Aspergillus fumigatus</i> and systemic <i>Candida albicans</i> infections. However, the molecular mechanisms underlying fungal clearance by phagocytes remain incompletely understood. In this study, we investigated the role of Perforin-2 (<i>Mpeg1</i>) in antifungal immunity. We found that <i>Mpeg1</i>^-/- mice generated on a mixed C57BL/6J-DBA/2 background exhibited enhanced survival, reduced lung fungal burden, and greater neutrophil fungal killing activity compared to wild-type C57BL/6J (B6) mice, suggesting that Perforin-2 may impair antifungal immune responses. However, when we compared <i>Mpeg1</i>^-/- mice with co-housed <i>Mpeg</i>^+/+ littermate controls, these differences were no longer observed, indicating that initial findings were likely influenced by differences in the murine genetic background or the microbiota composition. Furthermore, Perforin-2 was dispensable for antifungal immunity during <i>C. albicans</i> bloodstream infection. These results suggest that Perforin-2 is not essential for host defense against fungal infections in otherwise immune-competent mice.</p><p><strong>Importance: </strong>Humans encounter fungal pathogens daily and rely on innate immune cells to clear <i>Aspergillus fumigatus</i>, the leading cause of mold pneumonia worldwide, and <i>Candida albicans</i>, the most common cause of fungal bloodstream infections. The World Health Organization has classified <i>A. fumigatus</i> and <i>C. albicans</i> as critical priority fungal pathogens due to the emergence of drug resistance and the increasing number of susceptible individuals across the globe. The mechanisms by which innate immune cells clear these fungal pathogens remain incompletely defined. In this study, we examined the role of a pore-forming protein called Perforin-2 in host defense against these fungal pathogens, in part because Perforin-2 has been implicated in antibacterial host defense. Our findings reveal that Perforin-2 is dispensable for antifungal immunity against respiratory <i>A. fumigatus</i> and systemic <i>C. albicans</i> infections in mice, suggesting that the antimicrobial activity of Perforin-2 does not extend to these two fungal pathogens.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0080324"},"PeriodicalIF":3.7,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11774031/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142864891","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":"Decomposition of the pangenome matrix reveals a structure in gene distribution in the <i>Escherichia coli</i> species.","authors":"Siddharth M Chauhan, Omid Ardalani, Jason C Hyun, Jonathan M Monk, Patrick V Phaneuf, Bernhard O Palsson","doi":"10.1128/msphere.00532-24","DOIUrl":"10.1128/msphere.00532-24","url":null,"abstract":"<p><p>Thousands of complete genome sequences for strains of a species that are now available enable the advancement of pangenome analytics to a new level of sophistication. We collected 2,377 publicly available complete genomes of <i>Escherichia coli</i> for detailed pangenome analysis. The core genome and accessory genomes consisted of 2,398 and 5,182 genes, respectively. We developed a machine learning approach to define the accessory genes characterizing the major phylogroups of <i>E. coli</i> plus <i>Shigella</i>: A, B1, B2, C, D, E, F, G, and <i>Shigella</i>. The analysis resulted in a detailed structure of the genetic basis of the phylogroups' differential traits. This pangenome structure was largely consistent with a housekeeping-gene-based MLST distribution, sequence-based Mash distance, and the Clermont quadruplex classification. The rare genome (consisting of genes found in <6.8% of all strains) consisted of 163,619 genes, about 79% of which represented variations of 315 underlying transposon elements. This analysis generated a mathematical definition of the genetic basis for a species.</p><p><strong>Importance: </strong>The comprehensive analysis of the pangenome of <i>Escherichia coli</i> presented in this study marks a significant advancement in understanding bacterial genetic diversity. By employing machine learning techniques to analyze 2,377 complete <i>E. coli</i> genomes, the study provides a detailed mapping of core, accessory, and rare genes. This approach reveals the genetic basis for differential traits across phylogroups, offering insights into pathogenicity, antibiotic resistance, and evolutionary adaptations. The findings enhance the potential for genome-based diagnostics and pave the way for future studies aimed at achieving a global genetic definition of bacterial phylogeny.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0053224"},"PeriodicalIF":3.7,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11774025/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142915435","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":"Skin-associated <i>Corynebacterium amycolatum</i> shares cobamides.","authors":"M H Swaney, N Henriquez, T Campbell, J Handelsman, L R Kalan","doi":"10.1128/msphere.00606-24","DOIUrl":"10.1128/msphere.00606-24","url":null,"abstract":"<p><p>The underlying interactions that occur to maintain skin microbiome composition, function, and overall skin health are largely unknown. Often, these types of interactions are mediated by microbial metabolites. Cobamides, the vitamin B₁₂ family of cofactors, are essential for metabolism in many bacteria but are only synthesized by a fraction of prokaryotes, including certain skin-associated species. Therefore, we hypothesize that cobamide sharing mediates skin community dynamics. Preliminary work predicts that several skin-associated <i>Corynebacterium</i> species encode <i>de novo</i> cobamide biosynthesis and that their abundance is associated with skin microbiome diversity. Here, we show that commensal <i>Corynebacterium amycolatum</i> produces cobamides and that this synthesis can be tuned by cobalt limitation. To demonstrate cobamide sharing by <i>C. amycolatum</i>, we employed a co-culture assay using an <i>E. coli</i> cobamide auxotroph and showed that <i>C. amycolatum</i> produces sufficient cobamides to support <i>Escherichia coli</i> growth, both in liquid co-culture and when separated spatially on solid medium. We also generated a <i>C. amycolatum</i> non-cobamide-producing strain (cob^-) using UV mutagenesis that contains mutated cobamide biosynthesis genes <i>cobK</i> (precorrin-6X reductase) and <i>cobO</i> (corrinoid adenosyltransferase) and confirm that disruption of cobamide biosynthesis abolishes the support of <i>E. coli</i> growth through cobamide sharing. Our study provides a unique model to study metabolite sharing by microorganisms, which will be critical for understanding the fundamental interactions that occur within complex microbiomes and for developing approaches to target the human microbiota for health advances.</p><p><strong>Importance: </strong>The human skin serves as a crucial barrier for the body and hosts a diverse community of microbes known as the skin microbiome. The interactions that occur to maintain a healthy skin microbiome are largely unknown but are thought to be driven in part, by nutrient sharing between species in close association. Here we show that the skin-associated bacteria <i>Corynebacterium amycolatum</i> produces and shares cobalamin, a cofactor essential for survival in organisms across all domains of life. This study provides a unique model to study metabolite sharing by skin microorganisms, which will be critical for understanding the fundamental interactions that occur within the skin microbiome and for developing therapeutic approaches aiming to engineer and manipulate the skin microbiota.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0060624"},"PeriodicalIF":3.7,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11774034/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142846543","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":"Identification of novel fructo-oligosaccharide bacterial consumers by pulse metatranscriptomics in a human stool sample.","authors":"Catherine Prattico, Emmanuel Gonzalez, Lharbi Dridi, Shiva Jazestani, Kristin E Low, D Wade Abbott, Corinne F Maurice, Bastien Castagner","doi":"10.1128/msphere.00668-24","DOIUrl":"10.1128/msphere.00668-24","url":null,"abstract":"<p><p>Dietary fibers influence the composition of the human gut microbiota and directly contribute to its downstream effects on host health. As more research supports the use of glycans as prebiotics for therapeutic applications, the need to identify the gut bacteria that metabolize glycans of interest increases. Fructo-oligosaccharide (FOS) is a common diet-derived glycan that is fermented by the gut microbiota and has been used as a prebiotic. Despite being well studied, we do not yet have a complete picture of all FOS-consuming gut bacterial taxa. To identify new bacterial consumers, we used a short exposure of microbial communities in a stool sample to FOS or galactomannan as the sole carbon source to induce glycan metabolism genes. We then performed metatranscriptomics, paired with whole metagenomic sequencing, and 16S amplicon sequencing. The short incubation was sufficient to cause induction of genes involved in carbohydrate metabolism, like carbohydrate-active enzymes (CAZymes), including glycoside hydrolase family 32 genes, which hydrolyze fructan polysaccharides like FOS and inulin. Interestingly, FOS metabolism transcripts were notably overexpressed in <i>Blautia</i> species not previously reported to be fructan consumers. We therefore validated the ability of different <i>Blautia</i> species to ferment fructans by monitoring their growth and fermentation in defined media. This pulse metatranscriptomics approach is a useful method to find novel consumers of prebiotics and increase our understanding of prebiotic metabolism by CAZymes in the gut microbiota.</p><p><strong>Importance: </strong>Complex carbohydrates are key contributors to the composition of the human gut microbiota and play an essential role in the microbiota's effects on host health. Understanding which bacteria consume complex carbohydrates, or glycans, provides a mechanistic link between dietary prebiotics and their beneficial health effects, an essential step for their therapeutic application. Here, we used a pulse metatranscriptomics pipeline to identify bacterial consumers based on glycan metabolism induction in a human stool sample. We identified novel consumers of fructo-oligosaccharide among <i>Blautia</i> species, expanding our understanding of this well-known glycan. Our approach can be applied to identify consumers of understudied glycans and expand our prebiotic repertoire. It can also be used to study prebiotic glycans directly in stool samples in distinct patient populations to help delineate the prebiotic mechanism.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0066824"},"PeriodicalIF":3.7,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11774028/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142854554","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":"Dextran sodium sulfate-induced colitis alters the proportion and composition of replicating gut bacteria.","authors":"Eve T Beauchemin, Claire Hunter, Corinne F Maurice","doi":"10.1128/msphere.00825-24","DOIUrl":"10.1128/msphere.00825-24","url":null,"abstract":"<p><p>The bacteria living in the human gut are essential for host health. Though the composition and metabolism of these bacteria are well described in both healthy hosts and those with intestinal disease, less is known about the metabolic activity of the gut bacteria prior to, and during, disease development-especially regarding gut bacterial replication. Here, we use a recently developed single-cell technique alongside existing metagenomics-based tools to identify, track, and quantify replicating gut bacteria both <i>ex vivo</i> and <i>in situ</i> in the dextran sodium sulfate (DSS) mouse model of colitis. We show that the proportion of replicating gut bacteria decreases when mice have the highest levels of inflammation and returns to baseline levels as mice begin recovering. In addition, we report significant alterations in the composition of the replicating gut bacterial community <i>ex vivo</i> during colitis development. On the taxa level, we observe significant changes in the abundance of taxa such as the mucus-degrading <i>Akkermansia</i> and the poorly described <i>Erysipelatoclostridium</i> genus. We further demonstrate that many taxa exhibit variable replication rates <i>in situ</i> during colitis, including <i>Akkermansia muciniphila</i>. Lastly, we show that colitis development is positively correlated with increases in the presence and abundance of bacteria <i>in situ</i> which are predicted to be fast replicators. This could suggest that taxa with the potential to replicate quickly may have an advantage during intestinal inflammation. These data support the need for additional research using activity-based approaches to further characterize the gut bacterial response to intestinal inflammation and its consequences for both the host and the gut microbial community.IMPORTANCEIt is well known that the bacteria living inside the gut are important for human health. Indeed, the type of bacteria that are present and their metabolism are different in healthy people versus those with intestinal disease. However, less is known about how these gut bacteria are replicating, especially as someone begins to develop intestinal disease. This is particularly important as it is thought that metabolically active gut bacteria may be more relevant to health. Here, we begin to address this gap using several complementary approaches to characterize the replicating gut bacteria in a mouse model of intestinal inflammation. We reveal which gut bacteria are replicating, and how quickly, as mice develop and recover from inflammation. This work can serve as a model for future research to identify how actively growing gut bacteria may be impacting health, or why these particular bacteria tend to thrive during intestinal inflammation.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0082524"},"PeriodicalIF":3.7,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11774032/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142896462","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":"Molecular epidemiology of carbapenem-resistant <i>Acinetobacter baumannii</i> group in Taiwan.","authors":"Tran Lam Tu Quyen, Yu-Chia Hsieh, Shiao-Wen Li, Lii-Tzu Wu, Ya-Zhu Liu, Yi-Jiun Pan","doi":"10.1128/msphere.00793-24","DOIUrl":"10.1128/msphere.00793-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;i&gt;Acinetobacter,&lt;/i&gt; particularly the &lt;i&gt;Acinetobacter baumannii&lt;/i&gt; group, is a major cause of nosocomial infections, and carbapenem-resistant &lt;i&gt;Acinetobacter&lt;/i&gt; spp. are important human pathogens. We collected 492 &lt;i&gt;Acinetobacter&lt;/i&gt; spp. strains from two hospitals in Taiwan and classified them using MALDI-TOF MS and &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;OXA-51-like&lt;/sub&gt; PCR; 94.5% were &lt;i&gt;A. baumannii,&lt;/i&gt; and 5.5% were non-&lt;i&gt;A&lt;/i&gt;. &lt;i&gt;baumannii&lt;/i&gt; (NAB). We confirmed their identity by &lt;i&gt;rpo&lt;/i&gt;B gene sequencing of 239 randomly selected &lt;i&gt;A. baumannii&lt;/i&gt; strains and all 27 NAB strains. Our analysis revealed that the &lt;i&gt;rpo&lt;/i&gt;B alleles of OXA51-like-negative strains matched those of two NAB species, &lt;i&gt;A. seifertii&lt;/i&gt; and &lt;i&gt;A. nosocomialis&lt;/i&gt;, while all OXA51-like-positive strains matched &lt;i&gt;A. baumannii&lt;/i&gt;, as per the Pasteur MLST scheme database. Among the 492 strains, 240 exhibited carbapenem resistance, including 237 carbapenem-resistant &lt;i&gt;A. baumannii&lt;/i&gt; (CRAB) strains and three CR-NAB strains. All CRAB strains were positive for &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;OXA-51-like&lt;/sub&gt;; 72.6% also carried &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;OXA-23-like&lt;/sub&gt;, 22.8% carried &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;OXA-24-like&lt;/sub&gt;, 3.4% co-carried &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;OXA-23-like&lt;/sub&gt;+&lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;OXA-24-like&lt;/sub&gt;, and 1.27% carried &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;OXA-51-like&lt;/sub&gt; alone. Among the three CR-NAB strains, one carried &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM-1&lt;/sub&gt;, and two co-carried &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;OXA-58-like&lt;/sub&gt;+&lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;IMP&lt;/sub&gt;. We also established a new multiplex PCR method for rapid screening of common capsular types (KL), which showed a difference between CRAB and carbapenem-susceptible &lt;i&gt;A. baumannii&lt;/i&gt; (CSAB). KL2, KL10, KL22, and KL52 accounted for 76.6% of CRAB strains, whereas about half of the CSAB strains were other KL types. Of the remaining CSAB strains, KL14 was the most predominant type at 10.3%. We further conducted MLST Pasteur typing for 262 isolates and found that the carbapenemase genes were correlated with either ST or KL types. Additionally, KL types showed correlations with ST types, carbapenem resistance, and certain clinical records. Whole-genome sequencing of a &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM-1&lt;/sub&gt;-carrying &lt;i&gt;A. seifertii&lt;/i&gt; strain revealed a plasmid transferable via &lt;i&gt;in vitro&lt;/i&gt; conjugation, suggesting &lt;i&gt;A. seifertii&lt;/i&gt; may be a reservoir for NDM-1 plasmids.IMPORTANCECarbapenem-resistant &lt;i&gt;Acinetobacter&lt;/i&gt; spp. have been identified by the World Health Organization as a top priority for new antibiotic development. We established a rapid KL-typing method for efficient screening of &lt;i&gt;Acinetobacter baumannii&lt;/i&gt; strains to enable epidemiological surveillance and provide a foundation for effective infection control. Our investigation of the molecular epidemiology of the &lt;i&gt;A. baumannii&lt;/i&gt; group isolates revealed the prevalence of carbapenemase genes and major KL types among CR and CS strains of &lt;i&gt;A. baumannii&lt;/i&gt; and NAB. We identified an &lt;i&gt;A. seifertii&lt;/i&gt; strain carrying a Ti-type conjugative op","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0079324"},"PeriodicalIF":3.7,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11774041/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142915440","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}