mSystems最新文献

{"title":"A comprehensive two-hybrid analysis to explore the <i>Legionella pneumophila</i> effector-effector interactome.","authors":"Harley O'Connor Mount, Malene L Urbanus, Dayag Sheykhkarimli, Atina G Coté, Florent Laval, Georges Coppin, Nishka Kishore, Roujia Li, Kerstin Spirohn-Fitzgerald, Morgan O Petersen, Jennifer J Knapp, Dae-Kyum Kim, Jean-Claude Twizere, Michael A Calderwood, Marc Vidal, Frederick P Roth, Alexander W Ensminger","doi":"10.1128/msystems.01004-24","DOIUrl":"10.1128/msystems.01004-24","url":null,"abstract":"<p><p><i>Legionella pneumophila</i> uses over 300 translocated effector proteins to rewire host cells during infection and create a replicative niche for intracellular growth. To date, several studies have identified <i>L. pneumophila</i> effectors that indirectly and directly regulate the activity of other effectors, providing an additional layer of regulatory complexity. Among these are \"metaeffectors,\" a special class of effectors that regulate the activity of other effectors once inside the host. A defining feature of metaeffectors is direct, physical interaction with a target effector. Metaeffector identification, to date, has depended on phenotypes in heterologous systems and experimental serendipity. Using a multiplexed, recombinant barcode-based yeast two-hybrid technology we screened for protein-protein interactions among all <i>L. pneumophila</i> effectors and 28 components of the Dot/Icm type IV secretion system (>167,000 protein combinations). Of the 52 protein interactions identified by this approach, 44 are novel protein interactions, including 10 novel effector-effector interactions (doubling the number of known effector-effector interactions).</p><p><strong>Importance: </strong>Secreted bacterial effector proteins are typically viewed as modulators of host activity, entering the host cytosol to physically interact with and modify the activity of one or more host proteins in support of infection. A growing body of evidence suggests that a subset of effectors primarily function to modify the activities of other effectors inside the host. These \"effectors of effectors\" or metaeffectors are often identified through experimental serendipity during the study of canonical effector function against the host. We previously performed the first global effector-wide genetic interaction screen for metaeffectors within the arsenal of <i>Legionella pneumophila</i>, an intracellular bacterial pathogen with over 300 effectors. Here, using a high-throughput, scalable methodology, we present the first global interaction network of physical interactions between <i>L. pneumophila</i> effectors. This data set serves as a complementary resource to identify and understand both the scope and nature of non-canonical effector activity within this important human pathogen.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0100424"},"PeriodicalIF":5.0,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11651115/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142624245","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":"Description of the first marine-isolated member of the under-represented phylum <i>Gemmatimonadota</i>, and the environmental distribution and ecogenomics of <i>Gaopeijiales</i> ord. nov.","authors":"Yu-Qi Ye, Meng-Qi Ye, Xin-Yue Zhang, You-Zhi Huang, Zi-Yang Zhou, Yan-Jun Feng, Zong-Jun Du","doi":"10.1128/msystems.00535-24","DOIUrl":"10.1128/msystems.00535-24","url":null,"abstract":"<p><p>The phylum <i>Gemmatimonadota</i> is widespread but rarely cultured and, in fact, there are only six described species isolated from soil, freshwater, and wastewater treatment. However, no isolates of <i>Gemmatimonadota</i> from marine environment have been described; thus, little is known about the physiology and metabolism of members of the marine lineages. In this study, four novel facultatively anaerobic bacterial strains belonging to <i>Gemmatimonadota</i> were isolated from marine sediments collected from Xiaoshi Island in Weihai, China, using an aerobic enrichment method. The integrated results of phylogenetic and phenotypic characteristics supported that these four strains represent one novel species in a novel genus, for which the name <i>Gaopeijia maritima</i> gen. nov., sp. nov. is proposed, as the first representative of novel taxa, <i>Gaopeijiales</i> ord. nov., <i>Gaopeijiaceae</i> fam. nov. in the class <i>Longimicrobiia. Gaopeijiales</i> was detected in 22,884 out of 95,549 amplicon data sets, mainly from soil. However, the highest mean relative abundances were in sponge (0.7%) and marine sediment (0.35%), showing salt-related character. Most of the <i>Gaopeijiales</i> subgroups potentially belong to the rare bacterial biosphere. The aerobic enrichment in this study could significantly increase the relative abundance of <i>Gaopeijiales</i> (from 0.37% to 2.6%). Furthermore, the metabolic capabilities inferred from high-quality representative <i>Gaopeijiales</i> genomes/MAGs suggest that this group primarily performs chemoorganoheterotrophic metabolism with facultatively anaerobic characteristics and possesses various secondary metabolite biosynthesis gene clusters (BGCs), mirroring those observed in the four novel strains.IMPORTANCEDespite rapid advances in molecular and sequencing technologies, obtaining pure cultures remains a crucial research goal in microbiology, as it is essential for a deeper understanding of microbial metabolism. <i>Gemmatimonadota</i> is a widespread but rarely cultured bacterial phylum. Currently, there are only six cultured strains of this interesting group, all isolated from non-marine environments. Little is known about the physiology and metabolism of members of the marine lineages. Here we isolated and characterized four novel marine strains, and proposed a new order <i>Gaopeijiales</i> within <i>Gemmatimonadota</i>. Furthermore, the global distribution, environmental preference, and metabolic potential of <i>Gaopeijiales</i> are analyzed using public data. Our work enriches the resources available for the under-represented phylum <i>Gemmatimonadota</i> and provides insights into the physiological and metabolic characteristics of the marine lineage (<i>Gaopeijiales</i>) through culturology and omics.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0053524"},"PeriodicalIF":5.0,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11651109/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142668034","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":"Evolution of copper resistance in <i>Xanthomonas euvesicatoria</i> pv. <i>perforans</i> population.","authors":"Amandeep Kaur, Gerald V Minsavage, Neha Potnis, Jeffrey B Jones, Erica M Goss","doi":"10.1128/msystems.01427-24","DOIUrl":"10.1128/msystems.01427-24","url":null,"abstract":"<p><p>The widespread use of antimicrobials that target bacterial pathogens has driven evolution of resistance, compromising the efficacy of these bactericides. Understanding the emergence and spread of resistance genes via mobile genetic elements is crucial for combating antimicrobial resistance. Copper resistance (CuR) in <i>Xanthomonas euvesicatoria</i> pv. <i>perforans</i> has severely affected the efficacy of copper-based bactericides for controlling bacterial leaf spot disease of tomato and pepper. Here, we investigated the evolutionary pathways of CuR acquisition and dissemination in <i>X. euvesicatoria</i> pv. <i>perforans</i> using an extensive collection of strains. We determined that chromosomally encoded CuR predominates over plasmid-borne CuR in multiple distinct phylogenetic groups of <i>X. euvesicatoria</i> pv. <i>perforans</i>. Our analysis revealed a single site of chromosomal integration by a CuR genomic island, although the genomic island showed sequence variation among phylogenetic groups. While chromosomal CuR was more prevalent, strains with plasmid-borne resistance conferred greater copper tolerance. Additionally, we identified strains carrying two copies of CuR genes, on plasmid and chromosome, that exhibited increased copper tolerance. Strains of <i>X. euvesicatoria</i> pv. <i>perforans</i> from the USA shared identical CuR gene sequences whether on plasmids or chromosome while different alleles were found in strains from other countries. In contrast to <i>X. euvesicatoria</i> pv. <i>perforans</i>, plasmid-borne CuR predominated in closely related pathovar, <i>X. euvesicatoria</i> pv. <i>euvesicatoria</i>. Overall, these findings contribute to a better understanding of the evolution and persistence of CuR in <i>X. euvesicatoria</i> pv. <i>perforans</i> and its closest relatives.IMPORTANCEThe emergence of antimicrobial resistance is a significant threat to agricultural production as it reduces the efficacy of various antimicrobials including copper-based bactericides that are widely used to control plant diseases. The challenge of increasing antimicrobial resistance entering a production system necessitates a deeper understanding of the dynamics and mechanisms by which pathogens acquire resistance. As a result of this research, we have identified different mechanisms of copper resistance acquisition as well as levels of copper resistance in a devastating plant pathogen, <i>X. euvesicatoria</i> pv. <i>perforans</i>. The evolution and dissemination of copper resistance in strains through plasmid or chromosomally integrated genomic island or both presents barriers to current management approaches, where growers rely heavily on copper-based bactericides to manage disease outbreaks. This knowledge is crucial when considering the continued use of existing antimicrobials or adopting alternative antimicrobials in efforts to implement enhanced antimicrobial stewardship strategies in agriculture.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0142724"},"PeriodicalIF":5.0,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11651105/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142710487","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":"Phenotypic and genomic characterization of ST11-K1 CR-hvKP with highly homologous <i>bla</i>_KPC-2-bearing plasmids in China.","authors":"Yu-Ling Han, Hua Wang, Hong-Zhe Zhu, Ying-Ying Lv, Wen Zhao, Yan-Yan Wang, Jian-Xun Wen, Zhi-De Hu, Jun-Rui Wang, Wen-Qi Zheng","doi":"10.1128/msystems.01101-24","DOIUrl":"10.1128/msystems.01101-24","url":null,"abstract":"<p><p>Carbapenem-resistant hypervirulent <i>Klebsiella pneumoniae</i> (CR-hvKP) strains present a significant global public health threat due to their high mortality rates. This study investigated the genomic characteristics of seven ST11-K1 CR-hvKP isolates harboring highly homologous KPC-2-encoding multidrug-resistance plasmids. The strains were isolated from a Chinese tertiary hospital between 2017 and 2020. Whole-genome sequencing and bioinformatic analysis revealed various antibiotic resistance genes (ARGs) and virulence determinants. The <i>bla</i>_KPC-2-bearing plasmids that contain multiple antibiotic-resistance genes were also identified in these strains. ISfinder and Orifinder were applied to identify insertion sequences (IS) and conjugation-related factors among these <i>bla</i>_KPC-2-bearing plasmids. The <i>bla</i>_KPC-2 was highly consistent in seven <i>bla</i>_KPC-2-bearing plasmids (IS<i>Kpn6-bla</i>_KPC-2-IS<i>Kpn27</i>-IS<i>Yps3</i>-IS<i>26</i>). In addition, we found a region composed of IS<i>IR</i>, Tn<i>5393</i>, and IS<i>26</i>. It was located upstream of the <i>bla</i>_CTX-M-15 gene and presented in six <i>bla</i>_KPC-2-bearing plasmids, with pCR-hvKP221-KPC-P3 as an exception. Conjugation experiments demonstrated the horizontal transfer of resistance plasmids pCR-hvKP128-KPC-P1 and pCR-hvKP132-KPC-P1 across species. Notably, pLVPK-like virulence plasmids carrying virulence gene clusters pCR-hvKP173-Vir-P1, and pCR-hvKP221-Vir-P1 were also detected. A fusional plasmid pCR-hvKP221-Vir-P2, which carries virulence gene clusters and ARGs, was also identified. Five CR-hvKP strains displayed enhanced biofilm formation and high virulence <i>in vivo</i> infection models. Phylogenetic and single nucleotide polymorphism (SNP) analyses indicated a close genetic relationship among the isolates, suggesting a subclade. These findings highlight the complex genetic profiles and potential transmission mechanisms of CR-hvKP strains.</p><p><strong>Importance: </strong>We reported seven CR-hvKP strains all carried a highly homologous <i>bla</i>_KPC-2 integrated IncFⅡ-resistant plasmid, and two strains harbored virulence plasmids. Conjugation experiments confirmed the transferability of these plasmids, indicating a potential for resistance spread. Phylogenetic analysis clarified the relationship among the CR-hvKP isolates. This study provides insights into the phenotypic and genomic characteristics of seven ST11-K1 CR-hvKP strains. The high prevalence and potential for local outbreaks emphasize the need for effective control measures.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0110124"},"PeriodicalIF":5.0,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11651102/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142648311","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":"Metabolic capabilities are highly conserved among human nasal-associated <i>Corynebacterium</i> species in pangenomic analyses.","authors":"Tommy H Tran, Isabel F Escapa, Ari Q Roberts, Wei Gao, Abiola C Obawemimo, Julia A Segre, Heidi H Kong, Sean Conlan, Matthew S Kelly, Katherine P Lemon","doi":"10.1128/msystems.01132-24","DOIUrl":"10.1128/msystems.01132-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;i&gt;Corynebact&lt;/i&gt;e&lt;i&gt;rium&lt;/i&gt; species are globally ubiquitous in human nasal microbiota across the lifespan. Moreover, nasal microbiota profiles typified by higher relative abundances of &lt;i&gt;Corynebacterium&lt;/i&gt; are often positively associated with health. Among the most common human nasal &lt;i&gt;Corynebacterium&lt;/i&gt; species are &lt;i&gt;C. propinquum&lt;/i&gt;, &lt;i&gt;C. pseudodiphtheriticum, C. accolens&lt;/i&gt;, and &lt;i&gt;C. tuberculostearicum&lt;/i&gt;. To gain insight into the functions of these four species, we identified genomic, phylogenomic, and pangenomic properties and estimated the metabolic capabilities of 87 distinct human nasal &lt;i&gt;Corynebacterium&lt;/i&gt; strain genomes: 31 from Botswana and 56 from the United States. &lt;i&gt;C. pseudodiphtheriticum&lt;/i&gt; had geographically distinct clades consistent with localized strain circulation, whereas some strains from the other species had wide geographic distribution spanning Africa and North America. All species had similar genomic and pangenomic structures. Gene clusters assigned to all COG metabolic categories were overrepresented in the persistent versus accessory genome of each species indicating limited strain-level variability in metabolic capacity. Based on prevalence data, at least two &lt;i&gt;Corynebacterium&lt;/i&gt; species likely coexist in the nasal microbiota of 82% of adults. So, it was surprising that core metabolic capabilities were highly conserved among the four species indicating limited species-level metabolic variation. Strikingly, strains in the U.S. clade of &lt;i&gt;C. pseudodiphtheriticum&lt;/i&gt; lacked genes for assimilatory sulfate reduction present in most of the strains in the Botswana clade and in the other studied species, indicating a recent, geographically related loss of assimilatory sulfate reduction. Overall, the minimal species and strain variability in metabolic capacity implies coexisting strains might have limited ability to occupy distinct metabolic niches.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;Pangenomic analysis with estimation of functional capabilities facilitates our understanding of the full biologic diversity of bacterial species. We performed systematic genomic, phylogenomic, and pangenomic analyses with qualitative estimation of the metabolic capabilities of four common human nasal &lt;i&gt;Corynebacterium&lt;/i&gt; species, along with focused experimental validations, generating a foundational resource. The prevalence of each species in human nasal microbiota is consistent with the common coexistence of at least two species. We identified a notably high level of metabolic conservation within and among species indicating limited options for species to occupy distinct metabolic niches, highlighting the importance of investigating interactions among nasal &lt;i&gt;Corynebacterium&lt;/i&gt; species. Comparing strains from two continents, &lt;i&gt;C. pseudodiphtheriticum&lt;/i&gt; had restricted geographic strain distribution characterized by an evolutionarily recent loss of assimilatory sulfate reduction in U.S. strains. Our findings contrib","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0113224"},"PeriodicalIF":5.0,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11651106/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142604711","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":"Dispersal shapes compositional and functional diversity in aquatic microbial communities.","authors":"Angel Rain-Franco, Alizée Le Moigne, Lucas Serra Moncadas, Marisa O D Silva, Adrian-Stefan Andrei, Jakob Pernthaler","doi":"10.1128/msystems.01403-24","DOIUrl":"10.1128/msystems.01403-24","url":null,"abstract":"<p><p>Segregation and mixing shape the structure and functioning of aquatic microbial communities, but their respective roles are challenging to disentangle in field studies. We explored the hypothesis that functional differences and beta diversity among stochastically assembled communities would increase in the absence of dispersal. Contrariwise, we expected biotic selection during homogenizing dispersal to reduce beta and gamma diversity as well as functional variability. This was experimentally addressed by examining the compositional and functional changes of 20 freshwater bacterial assemblages maintained at identical conditions over seven growth cycles for 34 days and subjected to two consecutive dispersal regimes. Initial dispersal limitation generated high beta diversity and led to the repeated emergence of community types that were dominated by particular taxa. Compositional stability and evenness of the community types varied over successive growth cycles, reflecting differences in functional properties. Carbon use efficiency increased during cultivation, with some communities of unique composition outperforming the replicate community types. Homogenizing dispersal led to high compositional similarity and reduced gamma diversity. While a neutral and a competition-based (Elo-rating) model together largely explained community assembly, a pseudomonad disproportionally dominated across communities, possibly due to interaction-related genomic traits. In conclusion, microbial assemblages stochastically generated by dispersal limitation can be gradually \"refined\" into distinct community types by subsequent deterministic processes. Segregation of communities represented an insurance mechanism for highly productive but competitively weak microbial taxa that were excluded during community coalescence.</p><p><strong>Importance: </strong>We experimentally assessed the compositional and functional responses of freshwater bacterial assemblages exposed to two consecutive dispersal-related events (dispersal limitation and homogenizing dispersal) under identical growth conditions. While segregation led to a decreased local diversity, high beta diversity sustained regional diversity and functional variability. In contrast, homogenizing dispersal reduced the species pool and functional variability of the metacommunity. Our findings highlight the role of dispersal in regulating both diversity and functional variability of aquatic microbial metacommunities, thereby providing crucial insight to predict changes in ecosystem functioning.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0140324"},"PeriodicalIF":5.0,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11651098/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142648308","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":"Association of body index with fecal microbiome in children cohorts with ethnic-geographic factor interaction: accurately using a Bayesian zero-inflated negative binomial regression model.","authors":"Jian Huang, Yanzhuan Lu, Fengwei Tian, Yongqing Ni","doi":"10.1128/msystems.01345-24","DOIUrl":"10.1128/msystems.01345-24","url":null,"abstract":"<p><p>The exponential growth of high-throughput sequencing (HTS) data on the microbial communities presents researchers with an unparalleled opportunity to delve deeper into the association of microorganisms with host phenotype. However, this growth also poses a challenge, as microbial data are complex, sparse, discrete, and prone to zero inflation. Herein, by utilizing 10 distinct counting models for analyzing simulated data, we proposed an innovative Bayesian zero-inflated negative binomial (ZINB) regression model that is capable of identifying differentially abundant taxa associated with distinctive host phenotypes and quantifying the effects of covariates on these taxa. Our proposed model exhibits excellent accuracy compared with conventional Hurdle and INLA models, especially in scenarios characterized by inflation and overdispersion. Moreover, we confirm that dispersion parameters significantly affect the accuracy of model results, with defects gradually alleviating as the number of analyzed samples increases. Subsequently applying our model to amplicon data in real multi-ethnic children cohort, we found that only a subset of taxa were identified as having zero inflation in real data, suggesting that the prevailing understanding and processing of microbial count data in most previous microbiome studies were overly dogmatic. In practice, our pipeline of integrating bacterial differential abundance in microbiome data and relevant covariates is effective and feasible. Taken together, our method is expected to be extended to the microbiota studies of various multi-cohort populations.</p><p><strong>Importance: </strong>The microbiome is closely associated with physical indicators of the body, such as height, weight, age and BMI, which can be used as measures of human health. Accurately identifying which taxa in the microbiome are closely related to indicators of physical development is valuable as microbial markers of regional child growth trajectory. Zero-inflated negative binomial (ZINB) model, a type of Bayesian generalized linear model, can be effectively modeled in complex biological systems. We present an innovative ZINB regression model that is capable of identifying differentially abundant taxa associated with distinctive host phenotypes and quantifying the effects of covariates on these taxa, and demonstrate that its accuracy is superior to traditional Hurdle and INLA models. Our pipeline of integrating bacterial differential abundance in microbiome data and relevant covariates is effective and feasible.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0134524"},"PeriodicalIF":5.0,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11651110/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142681116","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":"Bacterial community function increases leaf growth in a pitcher plant experimental system.","authors":"Jessica R Bernardin, Erica B Young, Sarah M Gray, Leonora S Bittleston","doi":"10.1128/msystems.01298-24","DOIUrl":"10.1128/msystems.01298-24","url":null,"abstract":"<p><p>Across diverse ecosystems, bacteria and their hosts engage in complex relationships having negative, neutral, or positive interactions. However, the specific effects of leaf-associated bacterial community functions on plant growth are poorly understood. Although microbes can promote plant growth through various biochemical mechanisms, investigating the community's functional contributions to plant growth remains to be explored. To address this gap, we characterized the relationships between bacterial community function and host plant growth in the purple pitcher plant (<i>Sarracenia purpurea</i>). The main aim of our research was to investigate how different bacterial community functions affect the growth and nutrient content in the plant. Previous research has suggested that microbial communities aid in prey decomposition and subsequent nutrient acquisition in carnivorous plants, including <i>S. purpurea</i>. However, the specific functional roles of bacterial communities in plant growth and nutrient uptake are not well known. In this study, sterile, freshly opened pitchers were inoculated with three functionally distinct, pre-assembled bacterial communities. Bacterial community composition and function were measured over 8 weeks using physiological assays, metagenomics, and metatranscriptomics. Distinct community functions affected plant traits; a bacterial community enriched in decomposition was associated with larger leaves with almost double the biomass of control pitchers. Physiological differences in bacterial communities were supported by metatranscriptomics; for example, the bacterial community with the highest chitinase activity had greater expression of transcripts associated with chitinase enzymes. The relationship between bacterial community function and plant growth observed here indicates potential mechanisms, such as chitinase activity, for host-associated bacterial functions to support pitcher plant growth.</p><p><strong>Importance: </strong>This study addresses a gap in understanding the relationships between bacterial community function and plant growth. We inoculated sterile, freshly opened pitcher plant leaves with three functionally distinct bacterial communities to uncover potential mechanisms through which bacterial functions support plant health and growth. Our findings demonstrate that distinct community functions significantly influence plant traits, with some bacterial communities supporting more plant growth than in control pitchers. These results highlight the ecological roles of microbial communities in plants and thus ecosystems and suggest that nutrient cycling is an important pathway through which microbes support host plant health. This research provides valuable insights into plant-microbe interactions and the effects of diverse microbial community functions.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0129824"},"PeriodicalIF":5.0,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11651108/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142710482","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":"Understanding brewing trait inheritance in <i>de novo</i> Lager yeast hybrids.","authors":"Vasni Zavaleta, Laura Pérez-Través, Luis A Saona, Carlos A Villarroel, Amparo Querol, Francisco A Cubillos","doi":"10.1128/msystems.00762-24","DOIUrl":"10.1128/msystems.00762-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Hybridization between &lt;i&gt;Saccharomyces cerevisiae&lt;/i&gt; and &lt;i&gt;Saccharomyces eubayanus&lt;/i&gt; resulted in the emergence of &lt;i&gt;S. pastorianus&lt;/i&gt;, a crucial yeast for lager fermentation. However, our understanding of hybridization success and hybrid vigor between these two species remains limited due to the scarcity of &lt;i&gt;S. eubayanus&lt;/i&gt; parental strains. Here, we explore hybridization success and the impact of hybridization on fermentation performance and volatile compound profiles in newly formed lager hybrids. By selecting parental candidates spanning a diverse array of lineages from both species, we reveal that the Beer and PB-2 lineages exhibit high rates of hybridization success in &lt;i&gt;S. cerevisiae&lt;/i&gt; and &lt;i&gt;S. eubayanus&lt;/i&gt;, respectively. Polyploid hybrids were generated through a spontaneous diploid hybridization technique (rare-mating), revealing a prevalence of triploids and diploids over tetraploids. Despite the absence of heterosis in fermentative capacity, hybrids displayed phenotypic variability, notably influenced by maltotriose consumption. Interestingly, ploidy levels did not significantly correlate with fermentative capacity, although triploids exhibited greater phenotypic variability. The &lt;i&gt;S. cerevisiae&lt;/i&gt; parental lineages primarily influenced volatile compound profiles, with significant differences in aroma production. Interestingly, hybrids emerging from the Beer &lt;i&gt;S. cerevisiae&lt;/i&gt; parental lineages exhibited a volatile compound profile resembling the corresponding &lt;i&gt;S. eubayanus&lt;/i&gt; parent. This pattern may result from the dominant inheritance of the &lt;i&gt;S. eubayanus&lt;/i&gt; aroma profile, as suggested by the over-expression of genes related to alcohol metabolism and acetate synthesis in hybrids including the Beer &lt;i&gt;S. cerevisiae&lt;/i&gt; lineage. Our findings suggest complex interactions between parental lineages and hybridization outcomes, highlighting the potential for creating yeasts with distinct brewing traits through hybridization strategies.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;Our study investigates the principles of lager yeast hybridization between &lt;i&gt;Saccharomyces cerevisiae&lt;/i&gt; and &lt;i&gt;Saccharomyces eubayanus&lt;/i&gt;. This process gave rise to the lager yeast &lt;i&gt;Saccharomyces pastorianus&lt;/i&gt;. By examining how these novel hybrids perform during fermentation and the aromas they produce, we uncover the genetic bases of brewing trait inheritance. We successfully generated polyploid hybrids using diverse strains and lineages from both parent species, predominantly triploids and diploids. Although these hybrids did not show improved fermentation capacity, they exhibited varied traits, especially in utilizing maltotriose, a key sugar in brewing. Remarkably, the aroma profiles of these hybrids were primarily influenced by the &lt;i&gt;S. cerevisiae&lt;/i&gt; parent, with Beer lineage hybrids adopting aroma characteristics from their &lt;i&gt;S. eubayanus&lt;/i&gt; parent. These insights reveal the complex genetic interactions in hybrid yeasts, openin","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0076224"},"PeriodicalIF":5.0,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11651111/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142624254","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":"Dissecting the genetic features and evolution of <i>Staphylococcus aureus</i> sequence type 88: a global perspective.","authors":"Ye Jin, Chenyang Gao, Gaoqin Teng, Zhenchao Zhou, Wangxiao Zhou, Man Huang","doi":"10.1128/msystems.01142-24","DOIUrl":"10.1128/msystems.01142-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;i&gt;Staphylococcus aureus&lt;/i&gt; sequence type (ST) 88, encompassing both methicillin-resistant &lt;i&gt;S. aureus&lt;/i&gt; (MRSA) and methicillin-sensitive &lt;i&gt;S. aureus&lt;/i&gt; (MSSA) phenotypes, is globally prevalent and commonly associated with skin and soft tissue infections. Despite its widespread occurrence, comprehensive genomic studies on this clone remain scarce. In this study, we performed detailed genomic analyses on 130 ST88 isolates derived from severe bloodstream infections alongside 275 publicly available ST88 sequences. Our phylogenetic analysis identified four distinct clades, with evidence suggesting independent evolution and significant clonal expansion of ST88 in China, particularly within clade I, which appeared to have emerged circa 1964. We documented notable interregional, international, and even intercontinental transmission of ST88 isolates. Variability in the distribution of SCC&lt;i&gt;mec&lt;/i&gt; and &lt;i&gt;spa&lt;/i&gt; types was observed across clades. Our &lt;i&gt;in silico&lt;/i&gt; analyses indicated distinct patterns in the distribution of resistance genes, virulence genes, and mobile genetic elements among the clades, with clade I notably harboring the highest prevalence of the intact &lt;i&gt;sraP&lt;/i&gt; gene and an independently acquired novel prophage, φST88-1. Conversely, clade IV exhibited deletions within the &lt;i&gt;sasC&lt;/i&gt; gene, with certain sub-clades lacking the &lt;i&gt;sdrDE&lt;/i&gt; and &lt;i&gt;fnbB&lt;/i&gt; genes, underscoring the superior adhesive capabilities of clade I. &lt;i&gt;In vitro&lt;/i&gt; experiments confirmed enhanced biofilm formation in clade I isolates, although the levels of hemolysis and cytotoxicity were similar across clades. Pan-genome-wide association study revealed that core SNPs, rather than the accessory genome, are the primary contributors to the diversification of the ST88 clades. These findings enrich our understanding of the genetic foundations underpinning the transmission dynamics and phenotypic diversity of ST88 clones globally.IMPORTANCEUnderstanding the evolution and transmission of &lt;i&gt;Staphylococcus aureus&lt;/i&gt; ST88 clones is critically important due to their spread within food, hospital, and community environments, leading to significant health issues. Despite its prevalence, detailed genomic insights into ST88, particularly regarding its diversity and evolutionary dynamics, have been lacking. Our comprehensive genomic analysis of 130 ST88 isolates from severe bloodstream infections, alongside 275 sequences from public databases, significantly advances our understanding of this pathogen. We identified four distinct evolutionary clades, demonstrating the independent evolution and substantial clonal expansion of ST88 in China, as well as its ability to spread across regions and continents. The diversity among the isolates was evident in their unique profiles of &lt;i&gt;SCCmec&lt;/i&gt; elements, antibiotic resistance genes, virulence genes, and mobile genetic elements. Our findings underscore the critical role of core genomic variations over accessory elements in d","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0114224"},"PeriodicalIF":5.0,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11651095/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142624246","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}