mSphere最新文献

{"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}

{"title":"Advancing dental biofilm models: the integral role of pH in predicting <i>S. mutans</i> colonization.","authors":"Jay S Sangha, Valentina Gogulancea, Thomas P Curtis, Nicholas S Jakubovics, Paul Barrett, Aline Metris, Irina D Ofiţeru","doi":"10.1128/msphere.00743-24","DOIUrl":"10.1128/msphere.00743-24","url":null,"abstract":"<p><p>Mathematical models can provide insights into complex interactions and dynamics within microbial communities to complement and extend experimental laboratory approaches. For dental biofilms, they can give a basis for evaluating biofilm growth or the transition from health to disease. We have developed mathematical models to simulate the transition toward a cariogenic microbial biofilm, modeled as the overgrowth of <i>Streptococcus mutans</i> within a five-species dental community. This work builds on experimental data from a continuous flow reactor with hydroxyapatite coupons for biofilm growth, in a chemically defined medium with varying concentrations of glucose and lactic acid. The biofilms formed on the coupons were simulated using individual-based models (IbMs), with bacterial growth modeled using experimentally measured kinetic parameters. The IbM assumes that the maximum theoretical growth yield for biomass is dependent on the local concentration of reactants and products, while the growth rates were described using traditional Monod equations. We have simulated all the conditions studied experimentally, considering different initial relative abundance of the five species, and also different initial clustering in the biofilm. The simulation results only reproduced the experimental dominance of <i>S. mutans</i> at high glucose concentration after we considered the species-specific effect of pH on growth rates. This highlights the significance of the aciduric property of <i>S. mutans</i> in the development of caries. Our study demonstrates the potential of combining <i>in vitro</i> and <i>in silico</i> studies to gain a new understanding of the factors that influence dental biofilm dynamics.IMPORTANCEWe have developed <i>in silico</i> models able to reproduce the relative abundance measured <i>in vitro</i> in the synthetic dental biofilm communities growing in a chemically defined medium. The advantage of this combination of <i>in vitro</i> and <i>in silico</i> models is that we can study the influence of one parameter at a time and aim for direct validation. Our work demonstrates the utility of individual-based models for simulating diverse conditions affecting dental biofilm scenarios, such as the frequency of glucose intake, sucrose pulsing, or integration of pathogenic or probiotic species. Although <i>in silico</i> models are reductionist approaches, they have the advantage of not being limited in the scenarios they can test by the ethical consideration of an <i>in vivo</i> system, thus significantly contributing to dental biofilm research.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0074324"},"PeriodicalIF":3.7,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11774048/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142807862","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":"Protein kinases MpkA and SepH transduce crosstalk between CWI and SIN pathways to activate protective hyphal septation under echinocandin cell wall stress.","authors":"Alexander G Doan, Jessica E Schafer, Casey M Douglas, Matthew S Quintanilla, Meredith E Morse, Harley Edwards, Walker D Huso, Kelsey J Gray, JungHun Lee, Joshua K Dayie, Steven D Harris, Mark R Marten","doi":"10.1128/msphere.00641-24","DOIUrl":"10.1128/msphere.00641-24","url":null,"abstract":"<p><p>This study investigates a previously unreported stress signal transduced as crosstalk between the cell wall integrity (CWI) pathway and the septation initiation network (SIN). Echinocandins, which target cell wall synthesis, are widely used to treat mycoses. Their efficacy, however, is species specific. Our findings suggest that this is due largely to CWI-SIN crosstalk and the ability of filamentous species to fortify with septa in response to echinocandin stress. To better understand this crosstalk, we used a microscopy-based assay to measure septum density, aiming to understand the septation response to cell wall stress. The echinocandin micafungin, an inhibitor of β-(1,3)-glucan synthase, was employed to induce this stress. We observed a strong positive correlation between micafungin treatment and septum density in wild-type strains. This finding suggests that CWI activates SIN under cell wall stress, increasing septum density to protect against cell wall failure. More detailed investigations, with targeted knockouts of CWI and SIN signaling proteins, enabled us to identify crosstalk occurring between the CWI kinase, MpkA, and the SIN kinase, SepH. This discovery of the previously unknown crosstalk between the CWI and SIN pathways not only reshapes our understanding of fungal stress responses, but also unveils a promising new target pathway for the development of novel antifungal strategies.</p><p><strong>Importance: </strong>Echinocandin-resistant species pose a major challenge in clinical mycology by rendering one of only four lines of treatment, notably one of the two that are well-tolerated, ineffective in treating systemic mycoses of these species. Previous studies have demonstrated that echinocandins fail against highly polarized fungi because they target only apical septal compartments. It is known that many filamentous species respond to cell wall stress with hyperseptation. In this work, we show that echinocandin resistance hinges on this dynamic response, rather than on innate septation alone. We also describe, for the first time, the signaling pathway used to deploy the hyperseptation response. By disabling this pathway, we were able to render mycelia susceptible to echinocandin stress. This work enhances our microbiological understanding of filamentous fungi and introduces a potential target to overcome echinocandin-resistant species.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0064124"},"PeriodicalIF":3.7,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11774030/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142818796","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":"Genome evolution following an ecological shift in nectar-dwelling <i>Acinetobacter</i>.","authors":"Vivianna A Sanchez, Tanya Renner, Lydia J Baker, Tory A Hendry","doi":"10.1128/msphere.01010-24","DOIUrl":"10.1128/msphere.01010-24","url":null,"abstract":"<p><p>The bacterial genus <i>Acinetobacter</i> includes species found in environmental habitats like soil and water, as well as taxa adapted to be host-associated or pathogenic. High genetic diversity may allow for this habitat flexibility, but the specific genes underlying switches between habitats are poorly understood. One lineage of <i>Acinetobacter</i> has undergone a substantial habitat change by evolving from a presumed soil-dwelling ancestral state to thrive in floral nectar. Here, we compared the genomes of floral-dwelling and pollinator-associated <i>Acinetobacter</i>, including newly described species, with genomes from relatives found in other environments to determine the genomic changes associated with this ecological shift. Following one evolutionary origin of floral nectar adaptation, nectar-dwelling <i>Acinetobacter</i> taxa have undergone reduction in genome size compared with relatives and have experienced dynamic gene gains and losses as they diversified. Gene content changes suggest a shift to metabolism of monosaccharides rather than diverse carbohydrates, and scavenging of nitrogen sources, which we predict to be beneficial in nectar environments. Gene gains appear to result from duplication events, evolutionary divergence, and horizontal gene transfer. Most notably, nectar-dwelling <i>Acinetobacter</i> acquired the ability to degrade pectin from plant pathogens, and the genes underlying this ability have duplicated and are under selection within the clade. We hypothesize that this ability was a key trait for adaptation to floral nectar, as it could improve access to nutrients in the nutritionally unbalanced habitat of nectar. These results identify the genomic changes and traits coinciding with a dramatic habitat switch from soil to floral nectar.</p><p><strong>Importance: </strong>Many bacteria, including the genus <i>Acinetobacter</i>, commonly evolve to exploit new habitats. However, the genetic changes that underlie habitat switches are often unknown. Floral nectar is home to specialized microbes that can grow in this nutritionally unbalanced habitat. Several specialized <i>Acinetobacter</i> species evolved from soil-dwelling relatives to become common and abundant in floral nectar. Here, we investigate the genomic adaptations required to successfully colonize a novel habitat like floral nectar. We performed comparative genomics analyses between nectar-dwelling <i>Acinetobacter</i> and <i>Acinetobacter</i> species from other environments, like soil and water. We find that although gene loss coincided with the switch to living in nectar, gains of specific genes from other bacteria may have been particularly important for this ecological change. <i>Acinetobacter</i> living in nectar gained genes for degrading pectin, a plant polysaccharide, which may improve access to nutrients in their environment. These findings shed light on how evolutionary novelty evolves in bacteria.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0101024"},"PeriodicalIF":3.7,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11774029/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142895717","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":"Comparative analysis of the human microbiome from four different regions of China and machine learning-based geographical inference.","authors":"Yinlei Lei, Min Li, Han Zhang, Yu Deng, Xinyu Dong, Pengyu Chen, Ye Li, Suhua Zhang, Chengtao Li, Shouyu Wang, Ruiyang Tao","doi":"10.1128/msphere.00672-24","DOIUrl":"10.1128/msphere.00672-24","url":null,"abstract":"<p><p>The human microbiome, the community of microorganisms that reside on and inside the human body, is critically important for health and disease. However, it is influenced by various factors and may vary among individuals residing in distinct geographic regions. In this study, 220 samples, consisting of sterile swabs from palmar skin and oral and nasal cavities were collected from Chinese Han individuals living in Shanghai, Chifeng, Kunming, and Urumqi, representing the geographic regions of east, northeast, southwest, and northwest China. The full-length 16S rRNA gene of the microbiota in each sample was sequenced using the PacBio single-molecule real-time sequencing platform, followed by clustering the sequences into operational taxonomic units (OTUs). The analysis revealed significant differences in microbial communities among the four regions. <i>Cutibacterium</i> was the most abundant bacterium in palmar samples from Shanghai and Kunming, <i>Psychrobacter</i> in Chifeng samples, and <i>Psychrobacillus</i> in Urumqi samples. Additionally, <i>Streptococcus</i> and <i>Staphylococcus</i> were the dominant bacteria in the oral and nasal cavities. Individuals from the four regions could be distinguished and predicted based on a model constructed using the random forest algorithm, with the predictive effect of palmar microbiota being better than that of oral and nasal cavities. The prediction accuracy using hypervariable regions (V3-V4 and V4-V5) was comparable with that of using the entire 16S rRNA. Overall, our study highlights the distinctiveness of the human microbiome in individuals living in these four regions. Furthermore, the microbiome can serve as a biomarker for geographic origin inference, which has immense application value in forensic science.IMPORTANCEMicrobial communities in human hosts play a significant role in health and disease, varying in species, quantity, and composition due to factors such as gender, ethnicity, health status, lifestyle, and living environment. The characteristics of microbial composition at various body sites of individuals from different regions remain largely unexplored. This study utilized single-molecule real-time sequencing technology to detect the entire 16S rRNA gene of bacteria residing in the palmar skin, oral, and nasal cavities of Han individuals from four regions in China. The composition and structure of the bacteria at these three body sites were well characterized and found to differ regionally. The results elucidate the differences in bacterial communities colonizing these body sites across different regions and reveal the influence of geographical factors on human bacteria. These findings not only contribute to a deeper understanding of the diversity and geographical distribution of human bacteria but also enrich the microbiome data of the Asian population for further studies.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0067224"},"PeriodicalIF":3.7,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11774049/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142854367","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":"Strain-limited biofilm regulation through the Brg1-Rme1 circuit in <i>Candida albicans</i>.","authors":"Min-Ju Kim, Aaron P Mitchell","doi":"10.1128/msphere.00980-24","DOIUrl":"10.1128/msphere.00980-24","url":null,"abstract":"<p><p>Prominent virulence traits of <i>Candida albicans</i> include its ability to produce filamentous hyphal cells and grow as a biofilm. These traits are under control of numerous transcription factors (TFs), including Brg1 and Rme1. In the reference strain SC5314, a <i>brg1</i>Δ/Δ mutant has reduced levels of biofilm/filament production; a <i>brg1</i>Δ/Δ <i>rme1</i>Δ/Δ double mutant has wild-type levels of biofilm/filament production. Here, we asked whether this suppression relationship is preserved in four additional strain backgrounds: P76067, P57055, P87, and P75010. These strains represent diverse clades and biofilm/filament production abilities. We find that a <i>rme1</i>Δ/Δ mutation restores biofilm/filament production in a <i>brg1</i>Δ/Δ mutant of P76067, but not in <i>brg1</i>Δ/Δ mutants of P57055, P87, and P75010. We speculate that variation in activities of two functionally related TFs, Nrg1, and Ume6, may cause the strain-limited impact of the <i>rme1</i>Δ/Δ mutation.</p><p><strong>Importance: </strong><i>Candida albicans</i> is a widespread fungal pathogen. The regulatory circuitry underlying virulence traits is well studied in the reference strain background, but not in other clinical isolate backgrounds. Here, we describe a pronounced example of strain variation in the control of two prominent virulence traits, biofilm formation and filamentation.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0098024"},"PeriodicalIF":3.7,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11774020/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142914457","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":"Establishing a new human pneumococcal standard reference serum, MPRSS-01.","authors":"Joseph M Antonello, Rocio D Murphy, Chitrananda Abeygunawardana, Juliana C Malinverni, Rajam Gowrisankar, Tina Green, Rebecca Greway, Jenna Schmauch, Adrienne Howlett, Cyrille J Bonhomme, Katrina M Nolan","doi":"10.1128/msphere.00404-24","DOIUrl":"10.1128/msphere.00404-24","url":null,"abstract":"<p><p>Measuring the immunogenicity of pneumococcal vaccines involves the use of immunoassays to measure serotype-specific immunoglobulin G (IgG) antibody levels post-vaccination with the current <i>Streptococcus pneumoniae</i> human reference serum standard (007sp) for anti-pneumococcal capsule antibodies. Development of new pneumococcal conjugate vaccines (PCVs) with additional serotypes not in 007sp (e.g., V116, a 21-valent PCV) requires a new reference serum. Antibody concentrations to 33 pneumococcal serotypes were assigned in a new Merck Pneumococcal Reference Serum Standard (MPRSS-01; Merck Pneumococcal Reference Serum Standard) using the pneumococcal electrochemiluminescence assay. MPRSS-01 was generated by pooling high-titer serum samples from adults immunized with either 23-valent pneumococcal polysaccharide vaccine (PPSV23) or V116. For the 24 serotypes with established IgG concentrations, the corresponding antibody concentrations in MPRSS-01 were assigned via direct calibration to 007sp, while a cross-standardization approach was used for the nine novel serotypes. Serotype 7F was initially chosen as the reference calibrator for cross-standardization due to parallelism across dilution-response curves demonstrated across all 33 serotypes, and an evaluation of the single-calibrator approach was conducted for the 24 serotypes. Potential systematic bias from using a unique serotype for calibration was identified and addressed by further adjusting the estimated IgG concentrations of the nine novel serotypes. Using the final MPRSS-01 antibody concentration assignments, and the calibration factor relating MPRSS-01 to 007sp, antibody concentration assignments for 007sp were provided for the nine novel serotypes. This proposal was accepted by the Center for Biologics Evaluation and Research (CBER), enabling V116 to bridge old and new human pneumococcal reference sera.IMPORTANCEImmunogenicity of pneumococcal vaccines is measured using post-vaccination serotype-specific immunoglobulin G (IgG) antibodies in serum using enzyme-linked immunoassays with the 007sp reference serum containing serotype-specific IgG for 24 pneumococcal serotypes. With the development of next-generation PCVs, a new <i>S. pneumoniae</i> reference serum standard was needed to include serotypes beyond the existing 24 in 007sp. In this study, antibody concentrations to 33 pneumococcal serotypes were assigned in a new Merck Pneumococcal Reference Serum Standard (MPRSS-01) using the pneumococcal electrochemiluminescence assay, enabling V116 to maintain the link to the historical human pneumococcal standard reference serum while utilizing the new human pneumococcal reference serum.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0040424"},"PeriodicalIF":3.7,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11774022/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142952310","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}