Microbial Genomics最新文献

{"title":"Inferior <i>Caballeronia</i> symbiont lacks conserved symbiosis genes.","authors":"Kaisy Martinez, Patrick T Stillson, Alison Ravenscraft","doi":"10.1099/mgen.0.001333","DOIUrl":"10.1099/mgen.0.001333","url":null,"abstract":"<p><p>Pentatomomorphan bugs can form symbiotic associations with bacteria belonging to the supergenus <i>Burkholderia sensu lato</i>. This relationship has become a model for understanding environmental symbiont acquisition. Host insects can utilize various symbiont strains from across <i>Burkholderia sensu lato</i>; however, host colonization success and benefits conferred vary by bacterial clade. Therefore, we conducted a meta-analysis aimed at identifying candidate genes that underpin beneficial symbioses within this system. We scanned the entire Burkholderiaceae family for the presence of 17 colonization-associated genes, as well as 88 candidate genes that are differentially expressed during symbiosis. There was no difference in the distribution of the 17 colonization-associated genes between symbiotic (<i>Caballeronia</i> and insect-associated plant beneficial and environmental clade) and non-symbiotic lineages; however, there was a higher prevalence of the 88 candidate genes in the insect symbiont lineages. We subsequently analysed the genomes of nine symbiotic <i>Caballeronia</i> species that confer varying fitness benefits to their insect hosts. One symbiont species was significantly worse, one was significantly better and the remaining seven were intermediate in terms of conferred host fitness benefits. We found that species possessing a higher number of the candidate genes conferred faster host development time. Furthermore, we identified two candidate genes that were missing in the least beneficial species but present in the other eight, suggesting that these genes may be important in modulating symbiont quality. Our study suggests that the mechanisms required for host colonization are broadly distributed across Burkholderiaceae, but the genes that determine symbiont quality are more prevalent in insect-associated species. This work helps to identify genes that influence this highly specialized yet diverse symbiosis between Pentatomomorphan insects and Burkholderiaceae bacteria.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 12","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142829345","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A prospective cohort study to investigate the transmission and burden of <i>Staphylococcus aureus</i> in Sri Lanka.","authors":"T Locke, S Siribaddana, J A A S Jayaweera, C M Suligoy, T I de Silva, R M Corrigan, T C Darton","doi":"10.1099/mgen.0.001336","DOIUrl":"10.1099/mgen.0.001336","url":null,"abstract":"<p><p>Methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) is a common cause of infection in both community and healthcare settings, and the household may be a central component linking these two environments. Strategies to prevent <i>S. aureus</i> transmission and thereby reduce the risk of infection must be informed by a detailed understanding of local epidemiology. These data are typically lacking in many low- and middle-income countries. Therefore, we aimed to investigate the circulation of infecting <i>S. aureus</i> strains in Sri Lanka, with a focus on the community and healthcare interface. A prospective longitudinal cohort study was performed between July and December 2021. Index patients with <i>S. aureus</i> infection and up to four of their household contacts were enrolled in the study. Colonization was assessed by sampling participants' nose and axilla at two time points over 3 months of follow-up. Whole-genome sequencing (WGS) was used to characterize isolates and assess strain similarity to identify transmission episodes and environmental clusters. A total of 153 participants were recruited, including 42 <i>S</i>. <i>aureus</i>-positive index patients and 111 household contacts. The baseline prevalence of <i>S. aureus</i> colonization amongst household contacts was 11.7% (13/111), of which 30.8% (4/13) were methicillin-resistant. A total of 88 <i>S</i>. <i>aureus</i> isolates underwent WGS and three multilocus sequence types predominated: ST672, ST5 and ST6. Each type had unique virulence characteristics but was identified in both community and healthcare environments. Colonization of household members with the index's infecting strain was not detected. <i>S. aureus</i> is a major cause of morbidity and mortality in low-resource settings such as Sri Lanka, yet little is known about risk factors and transmission networks. In this descriptive study, we have identified a small number of strains that appear to be well established and capable of causing both severe infection and asymptomatic colonization. Transmission of <i>S. aureus</i> did not appear to be occurring frequently in the household, and, therefore, preventative strategies that target high-risk groups may be more successful than universal community-based measures.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 12","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11657565/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142854691","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":"Zoonotic transmission of asymptomatic carriage <i>Staphylococcus aureus</i> on dairy farms in Canterbury, New Zealand.","authors":"Christina Straub, William Taylor, Nigel P French, David R Murdoch, Patricia Priest, Trevor Anderson, Pippa Scott","doi":"10.1099/mgen.0.001318","DOIUrl":"10.1099/mgen.0.001318","url":null,"abstract":"<p><p>Zoonotic pathogen transmission is of growing concern globally, with agricultural intensification facilitating interactions between humans, livestock and wild animals. <i>Staphylococcus aureus</i> is a major human pathogen, but it also causes mastitis in dairy cattle, leading to an economic burden on the dairy industry. Here, we investigated transmission within and between cattle and humans, including potential zoonotic transmission of <i>S. aureus</i> isolated from cattle and humans from three dairy farms and an associated primary school in New Zealand. Nasal swabs (<i>N</i>=170) were taken from healthy humans. Inguinal and combined nasal/inguinal swabs were taken from healthy cattle (<i>N</i>=1163). Whole-genome sequencing was performed for 96 <i>S</i>. <i>aureus</i> isolates (44 human and 52 cattle). Multilocus sequence typing and assessments of antimicrobial resistance and virulence were carried out. Potential within- and across-species transmission events were determined based on single nucleotide polymorphisms (SNPs). Thirteen potential transmission clusters were detected, with 12 clusters restricted to within-species and one potential zoonotic transmission cluster (ST5). Potential transmission among cattle was mostly limited to single age groups, likely because different age groups are managed separately on farms. While the prevalence of antimicrobial resistance (AMR) was low among both bovine and human isolates, the discovery of an extended-spectrum beta-lactamase gene (<i>bla</i> _TEM-116) in a bovine isolate was concerning. This study provides evidence around frequency and patterns of potential transmission of <i>S. aureus</i> on dairy farms and highlights the AMR and virulence profile of asymptomatic carriage <i>S. aureus</i> isolates.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 12","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11616781/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142770389","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":"Retraction notice: Comparative genomic analysis of <i>Escherichia coli</i> isolates from cases of bovine clinical mastitis identifies nine specific pathotype marker genes.","authors":"The Microbiology Society","doi":"10.1099/mgen.0.001343","DOIUrl":"https://doi.org/10.1099/mgen.0.001343","url":null,"abstract":"","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 12","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142854694","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chromosome architecture as a determinant for biosynthetic diversity in <i>Micromonospora</i>.","authors":"David R Mark, Nicholas P Tucker, Paul R Herron","doi":"10.1099/mgen.0.001313","DOIUrl":"10.1099/mgen.0.001313","url":null,"abstract":"<p><p>Natural products - small molecules generated by organisms to facilitate ecological interactions - are of great importance to society and are used as antibacterial, antiviral, antifungal and anticancer drugs. However, the role and evolution of these molecules and the fitness benefits they provide to their hosts in their natural habitat remain an outstanding question. In bacteria, the genes that encode the biosynthetic proteins that generate these molecules are organised into discrete loci termed biosynthetic gene clusters (BGCs). In this work, we asked the following question: How are biosynthetic gene clusters organised at the chromosomal level? We sought to answer this using publicly available high-quality assemblies of <i>Micromonospora</i>, an actinomycete genus with members responsible for biosynthesizing notable natural products, such as gentamicin and calicheamicin. By orienting the <i>Micromonospora</i> chromosome around the origin of replication, we demonstrated that <i>Micromonospora</i> has a conserved origin-proximal region, which becomes progressively more disordered towards the antipodes of the origin. We then demonstrated through genome mining of these organisms that the conserved origin-proximal region and the origin-distal region of <i>Micromonospora</i> have distinct populations of BGCs and, in this regard, parallel the organization of <i>Streptomyces</i>, which possesses linear chromosomes. Specifically, the origin-proximal region contains highly syntenous, conserved BGCs predicted to biosynthesize terpenes and a type III polyketide synthase. In contrast, the ori-distal region contains a highly diverse population of BGCs, with many BGCs belonging to unique gene cluster families. These data highlight that genomic plasticity in <i>Micromonospora</i> is locus-specific, and highlight the importance of using high-quality genome assemblies for natural product discovery and guide future natural product discovery by highlighting that biosynthetic novelty may be enriched in specific chromosomal neighbourhoods.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 11","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11537254/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142583674","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":"Identifying gene-level mechanisms of successful dispersal of <i>Vibrio parahaemolyticus</i> during El Niño events.","authors":"Amy Marie Campbell, Ronnie G Gavilan, Chris Hauton, Ronny van Aerle, Jaime Martinez-Urtaza","doi":"10.1099/mgen.0.001317","DOIUrl":"10.1099/mgen.0.001317","url":null,"abstract":"<p><p>El Niño events, the warm phase of the El Niño Southern Oscillation, facilitate the movement of warm surface waters eastwards across the Pacific Ocean. Marine organisms transported by these waters can act as biological corridors for water-borne bacteria with attachment abilities. El Niño events have been hypothesized as driving the recent emergence of <i>Vibrio parahaemolyticus</i> (Vp) variants, marine bacterium causing gastroenteritis, in South America, but the lack of a robust methodological framework limited any further exploration. Here, we introduce two new analysis approaches to explore Vp dynamics in South America, which will be central to uncovering Vp dynamics in the future. Distributed non-linear lag models found that strong El Niño events increase the relative probability of Vp detection in Peru, with a 3-4-month lag time. Machine learning found that the presence of a specific gene (<i>vopZ</i>) involved in attachment to plankton in a pandemic Vp clone in South America was temporally associated with strong El Niño events, offering a possible strategy for survival over long-range dispersal, such as that offered by El Niño events. Robust surveillance of marine pathogens and methodological development are necessary to produce resolute conclusions on the effect of El Niño events on water-borne diseases.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 11","pages":""},"PeriodicalIF":5.4,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11547132/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142605277","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":"Delineating bacterial genera based on gene content analysis: a case study of the <i>Mycoplasmatales-Entomoplasmatales</i> clade within the class <i>Mollicutes</i>.","authors":"Xiao-Hua Yan, Shen-Chian Pei, Hsi-Ching Yen, Alain Blanchard, Pascal Sirand-Pugnet, Vincent Baby, Gail E Gasparich, Chih-Horng Kuo","doi":"10.1099/mgen.0.001321","DOIUrl":"10.1099/mgen.0.001321","url":null,"abstract":"<p><p>Genome-based analysis allows for large-scale classification of diverse bacteria and has been widely adopted for delineating species. Unfortunately, for higher taxonomic ranks such as genus, establishing a generally accepted approach based on genome analysis is challenging. While core-genome phylogenies depict the evolutionary relationships among species, determining the correspondence between clades and genera may not be straightforward. For genotypic divergence, the percentage of conserved proteins and genome-wide average amino acid identity are commonly used, but often do not provide a clear threshold for classification. In this work, we investigated the utility of global comparisons and data visualization in identifying clusters of species based on their overall gene content and rationalized that such patterns can be integrated with phylogeny and other information such as phenotypes for improving taxonomy. As a proof of concept, we selected 177 representative genome sequences from the <i>Mycoplasmatales-Entomoplasmatales</i> clade within the class <i>Mollicutes</i> for a case study. We found that the clustering patterns corresponded to the current understanding of these organisms, namely the split into three above-genus groups: Hominis, Pneumoniae and <i>Spiroplasma-Entomoplasmataceae</i>-Mycoides. However, at the genus level, several important issues were found. For example, recent taxonomic revisions that split the Hominis group into three genera and <i>Entomoplasmataceae</i> into five genera are problematic, as those newly described or emended genera lack clear differentiations in gene content from one another. Moreover, several cases of misclassification were identified. These findings demonstrated the utility of this approach and its potential application to other bacteria.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 11","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11567158/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142639280","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":"Pangenomic insights into <i>Dehalobacter</i> evolution and acquisition of functional genes for bioremediation.","authors":"Olivia Bulka, Radhakrishnan Mahadevan, Elizabeth A Edwards","doi":"10.1099/mgen.0.001324","DOIUrl":"10.1099/mgen.0.001324","url":null,"abstract":"<p><p><i>Dehalobacter</i> is a genus of organohalide-respiring bacteria that is recognized for its fastidious growth using reductive dehalogenases (RDases). In the SC05 culture, however, a <i>Dehalobacter</i> population also mineralizes dichloromethane (DCM) produced by chloroform dechlorination using the <i>mec</i> cassette, just downstream of its active RDase. A closed genome of this DCM-mineralizing lineage has previously evaded assembly. Here, we present the genomes of two novel <i>Dehalobacter</i> strains, each of which was assembled from the metagenome of a distinct subculture from SC05. A pangenomic analysis of the <i>Dehalobacter</i> genus, including RDase synteny and phylogenomics, reveals at least five species of <i>Dehalobacter</i> based on average nucleotide identity, RDase and core gene synteny, as well as differential functional genes. An integration hotspot is also pinpointed in the <i>Dehalobacter</i> genome, in which many recombinase islands have accumulated. This nested recombinase island encodes the active RDase and <i>mec</i> cassette in both SC05 <i>Dehalobacter</i> genomes, indicating the transfer of key functional genes between species of <i>Dehalobacter</i>. Horizontal gene transfer between these two novel <i>Dehalobacter</i> strains has implications for the evolutionary history within the SC05 subcultures and of the <i>Dehalobacter</i> genus as a whole, especially regarding adaptation to anthropogenic chemicals.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 11","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11578063/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142676028","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":"Characterization of psychrotrophic and thermoduric bacteria in raw milk using a multi-omics approach.","authors":"Xue Qin, Jingqi Cheng, Yue Qiu, Ning Guan, Tanushree B Gupta, Shuyan Wu, Yujun Jiang, Xinyan Yang, Chaoxin Man","doi":"10.1099/mgen.0.001311","DOIUrl":"10.1099/mgen.0.001311","url":null,"abstract":"<p><p>Psychrotrophic and thermoduric bacteria are the main reasons for the spoilage of dairy products. This study aims to address the composition and function of psychrotrophic and thermoduric bacteria in eight groups of raw milk samples obtained from Heilongjiang Province and Inner Mongolia (China). Microbial enumeration showed an average total bacterial count of 4.63 log c.f.u. ml^-1 and psychrotrophic bacterial counts of 4.82 log c.f.u. ml^-1. The mean counts of mesophilic and thermophilic thermoduric bacteria were 3.68 log and 1.81 log c.f.u. ml^-1, respectively. Isolated psychrotrophic bacteria (26 genera and 50 species) and mesophilic thermoduric bacteria (20 genera and 32 species) showed high microbial diversity. Through metagenomic and proteomic analyses, significant disparities in the concentration and community structure of psychrotrophic and thermoduric bacteria were observed among different locations. A large number of peptidases were annotated by metagenomics, which may result in milk spoilage. They mainly come from some typical psychrotrophic and thermoduric bacteria, such as <i>Chryseobacterium</i>, <i>Epilithonimonas</i>, <i>Pseudomonas</i>, <i>Psychrobacter</i>, <i>Acinetobacter, Lactococcus, Escherichia</i> and <i>Bacillus</i>. However, the main proteins detected in fresh raw milk were associated with bacterial growth, reproduction and adaptation to cold environments. This investigation provides valuable insights into the microbial communities and protein profiles of raw milk, shedding light on the microbial factors contributing to milk deterioration.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 11","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11540130/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142583672","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":"Matching excellence: Oxford Nanopore Technologies' rise to parity with Pacific Biosciences in genome reconstruction of non-model bacterium with high G+C content.","authors":"Axel Soto-Serrano, Wenwen Li, Farhad M Panah, Yan Hui, Pablo Atienza, Alexey Fomenkov, Richard J Roberts, Paulina Deptula, Lukasz Krych","doi":"10.1099/mgen.0.001316","DOIUrl":"10.1099/mgen.0.001316","url":null,"abstract":"<p><p>The reconstruction of complete bacterial genomes is essential for microbial research, offering insights into genetic content, ontology and regulation. While Pacific Biosciences (PacBio) provides high-quality genomes, its cost remains a limitation. Oxford Nanopore Technologies (ONT) offers long reads at a lower cost, yet its error rate raises scepticism. Recent ONT advancements, such as new Flow cells (R10.4.1), chemistry (V14) and duplex mode, improve data quality. Our study compares ONT with PacBio and Illumina, including hybrid data. We used <i>Propionibacterium freudenreichii</i>, a bacterium with a genome known for being difficult to reconstruct. By combining data from ONT's Native Barcoding and a custom-developed BARSEQ method, we achieved high-quality, near-perfect genome assemblies. Our findings demonstrate, for the first time, that the combination of nanopore-only long-native with shorter PCR DNA reads (~3 kb) results in high-quality genome reconstruction, comparable to hybrid data assembly from two sequencing platforms. This endorses ONT as a cost-effective, stand-alone strategy for bacterial genome reconstruction. Additionally, we compared methylated motif detection between PacBio and ONT R10.4.1 data, showing that results comparable to PacBio are achievable using ONT, especially when utilizing the advanced Nanomotif tool.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 11","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11649196/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142621736","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}