mSphere最新文献

{"title":"Combined mutations in nonstructural protein 14, envelope, and membrane proteins mitigate the neuropathogenicity of SARS-CoV-2 Omicron BA.1 in K18-hACE2 mice.","authors":"Kotou Sangare, Shufeng Liu, Prabhuanand Selvaraj, Charles B Stauft, Matthew F Starost, Tony T Wang","doi":"10.1128/msphere.00726-24","DOIUrl":"10.1128/msphere.00726-24","url":null,"abstract":"<p><p>We previously reported that mutations outside the spike protein play a role in the attenuation of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron BA.1 variant in human ACE2 transgenic mice (K18-hACE2). Here, we assessed the pathogenicity of SARS-CoV-2 (WA1/2020) containing mutations from the Omicron BA.1 variant in K18-hACE2 mice. At an infection dose of 10⁴ plaque-forming units (PFU), WA1 virus carrying Omicron BA.1 Nsp14(I42V), E(T9I), M(D3G/Q19E/A63T), but not Nsp6(Δ105-107, I189V), substitutions showed significant reduction in lethality. Interestingly, reduction of viral load is more pronounced in the brains than in the lungs. Subsequent analyses suggest that BA.1 E(T9I) and M(D3G/Q19E/A63T) substitutions result in less efficient packaging of virus-like particles. Given that Nsp14(I42V), E(T9I), M(Q19E/A63T) are well preserved in subsequent omicron subvariants, including currently circulating variants, our findings highlight the importance of understanding how non-spike mutations affect the pathogenicity of SARS-CoV-2 variants.</p><p><strong>Importance: </strong>Inoculation of transgenic mice expressing human angiotensin-converting enzyme 2 (hACE2) with SARS-CoV-2 often leads to a fatal brain infection. Omicron BA.1 variant, however, was found to be non-lethal in this model. Here, we systematically assessed the effect of individual mutations of Omicron BA.1 on the pathogenicity of the virus in hACE2 transgenic mice and found that combination of 5 mutations of Nsp14, E, and M of BA.1 variant significantly lowered brain viral load and reduced lethality. These results provide new insights into how SARS-CoV-2 Omicron BA.1 is attenuated.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0072624"},"PeriodicalIF":3.7,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11774043/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142807864","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":"Development of monoclonal antibodies against <i>P. gingivalis</i> Mfa1 and their protective capacity in an experimental periodontitis model.","authors":"Mingya Cao, Siyu Wang, Shengke Zhou, Min Yan, Yu Zou, Yuan Cui, Xinyu Lou, Yichang Gao, Ying Chen, Zijing Han, Yi Qian, Jingying Chen, Xia Li","doi":"10.1128/msphere.00721-24","DOIUrl":"10.1128/msphere.00721-24","url":null,"abstract":"<p><p><i>Porphyromonas gingivalis</i> (<i>P. gingivalis</i>), a gram-negative, black-pigmented anaerobe, is a major etiological agent and a leading cause of periodontitis. Fimbriae protein Mfa1 is a key virulence factor of <i>P. gingivalis</i> and plays a crucial role in bacterial adhesion, colonization, biofilm formation, and persistent inflammation, making it a promising therapeutic target. However, the role of anti-Mfa1 antibodies and the underlying protective mechanisms remain largely unexplored. Here, we developed and characterized the monoclonal antibodies (mAbs) targeting the Mfa1 protein of <i>P. gingivalis</i>. Function analysis showed that anti-Mfa1 mAbs mediated bacterial agglutination and inhibited <i>P. gingivalis</i> adhesion to saliva-coated hydroxyapatite and host cells. Notably, anti-Mfa1 mAbs significantly reduced bacterial burden and alveolar bone loss in a <i>P. gingivalis</i>-induced experimental periodontitis model. These results show that anti-Mfa1 mAbs can be beneficial in alleviating <i>P. gingivalis</i> infections, and provide important insights for the development of adequate adjuvant treatment regimens for Mfa1-targeted therapeutics.</p><p><strong>Importance: </strong>Fimbriae (pili) play an important role in bacterial adhesion, invasion of host cells and tissues, and formation of biofilms. Studies have shown that two types of fimbriae of <i>Porphyromonas gingivalis</i>, FimA and Mfa1, are important for colonization and infection through their binding to host tissues and other bacteria. While anti-FimA antibodies have been shown to improve periodontitis, the effect of anti-Mfa1 antibodies on <i>P. gingivalis</i> infection and periodontitis was previously unknown. In this study, we report for the first time that anti-Mfa1 monoclonal antibodies can reduce <i>P. gingivalis</i> infection and improve periodontitis. These findings suggest that Mfa1 represents a promising therapeutic target, and the development of anti-Mfa1 mAbs holds a potential as essential diagnostic and adjunctive therapeutic tools for managing <i>P. gingivalis</i>-related diseases.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0072124"},"PeriodicalIF":3.7,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11774036/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142854564","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The <i>Legionella pneumophila</i> effector PieF modulates mRNA stability through association with eukaryotic CCR4-NOT.","authors":"Harley O'Connor Mount, Malene L Urbanus, Francesco Zangari, Anne-Claude Gingras, Alexander W Ensminger","doi":"10.1128/msphere.00891-24","DOIUrl":"10.1128/msphere.00891-24","url":null,"abstract":"<p><p>The eukaryotic CCR4-NOT deadenylase complex is a highly conserved regulator of mRNA metabolism that influences the expression of the complete transcriptome, representing a prime target for a generalist bacterial pathogen. We show that a translocated bacterial effector protein, PieF (Lpg1972) of <i>Legionella pneumophila</i>, directly interacts with the CNOT7/8 nuclease module of CCR4-NOT, with a dissociation constant in the low nanomolar range. PieF is a robust <i>in vitro</i> inhibitor of the DEDD-type nuclease, CNOT7, acting in a stoichiometric, dose-dependent manner. Heterologous expression of PieF phenocopies knockout of the CNOT7 ortholog (POP2) in <i>Saccharomyces cerevisiae</i>, resulting in 6-azauracil sensitivity. In mammalian cells, expression of PieF leads to a variety of quantifiable phenotypes: PieF silences gene expression and reduces mRNA steady-state levels when artificially tethered to a reporter transcript, and its overexpression results in the nuclear exclusion of CNOT7. PieF expression also disrupts the association between CNOT6/6L EEP-type nucleases and CNOT7. Adding to the complexities of PieF activity <i>in vivo</i>, we identified a separate domain of PieF responsible for binding to eukaryotic kinases. Unlike what we observe for CNOT6/6L, we show that these interactions can occur concomitantly with PieF's binding to CNOT7. Collectively, this work reveals a new, highly conserved target of <i>L. pneumophila</i> effectors and suggests a mechanism by which the pathogen may be modulating host mRNA stability and expression during infection.</p><p><strong>Importance: </strong>The intracellular bacterial pathogen <i>Legionella pneumophila</i> targets conserved eukaryotic pathways to establish a replicative niche inside host cells. With a host range that spans billions of years of evolution (from protists to humans), the interaction between <i>L. pneumophila</i> and its hosts frequently involves conserved eukaryotic pathways (protein translation, ubiquitination, membrane trafficking, autophagy, and the cytoskeleton). Here, we present the identification of a new, highly conserved host target of <i>L. pneumophila</i> effectors: the CCR4-NOT complex. CCR4-NOT modulates mRNA stability in eukaryotes from yeast to humans, making it an attractive target for a generalist pathogen, such as <i>L. pneumophila</i>. We show that the uncharacterized <i>L. pneumophila</i> effector PieF specifically targets one component of this complex, the deadenylase subunit CNOT7/8. We show that the interaction between PieF and CNOT7 is direct, occurs with high affinity, and reshapes the catalytic activity, localization, and composition of the complex across evolutionarily diverse eukaryotic cells.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0089124"},"PeriodicalIF":3.7,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11774319/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142854568","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":"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}