Draft Genome Sequence of Micrococcus luteus (Schroeter) Cohn (ATCC 12698)

Putonti, Catherine; Cudone, Evan; Kalesinskas, Laurynas; Engelbrecht, Kathleen; Koenig, David W.; Wolfe, Alan J.

doi:10.1128/genomea.00576-17

Cited by 3 publications

(1 citation statement)

References 10 publications

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“…Given this, Yang et al had further speculated that its primary adaptation is to mammalian skin, and that its occasional presence elsewhere might possibly arise from contamination by skin akes; and the transposable elements could have played a part in the contraction of the M. luteus genome [3]. Now genome sequences of more than 70 M. luteus strains have been published and/or are available at the NCBI GenBank database [34][35][36][37][38][39], providing rich resources for the study of the genetic diversity, evolutionary history, and the potential ecological differentiation of the species.…”

Section: Introductionmentioning

confidence: 99%

Comparative Genomics Reveals Broad Genetic Diversity, Extensive Recombination and Nascent Ecological Adaptation in Micrococcus luteus

Sun

Rong

et al. 2020

Preprint

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Background: Micrococcus luteus is a group of actinobacteria that is widely used in biotechnology and is being thought as an emerging nosocomial pathogen. With one of the smallest genomes of free-living actinobacteria, it is found in a wide range of environments, but intraspecies genetic diversity and adaptation strategies to various environments remain unclear. Here, comparative genomics, phylogenomics, and genome-wide association studies (GWAS) were used to investigate the genomic diversity, evolutionary history, and the potential ecological differentiation of the species.Results: High-quality genomes of 66 M. luteus strains were downloaded from the NCBI GenBank database and core and pangenome analysis revealed a considerable intraspecies heterogeneity. Phylogenomic analysis, gene content comparison, and average nucleotide identity calculation consistently indicated that the species has diverged into three well-differentiated clades. Population structure analysis revealed four admixed ancestral subpopulations, with three of them corresponding to the three clades, respectively, and the fourth corresponding to an unknown ancestor or the fourth, yet unsampled, clade. Reconstruction of gene gain/loss events along the evolutionary history revealed both early events that contributed to the inter-clade divergence and recent events leading to the intra-clade diversity. We also found convincing evidence that recombination has played a key role of the evolutionary process of the species, with upto two-thirds of the core genes have been affected by recombination. Furthermore, distribution of mammal-associated strains (including pathogens) on the phylogenetic tree strongly suggested that the last common ancestor had a free-living lifestyle, and a few recently diverged lineages have developed a mammal-associated lifestyle separately. Consistently, genome-wide association studies revealed that mammal-associated strains from different lineages shared genes functionally relevant to the host-associated lifestyle, indicating a recent ecological adaption to the new host-associated habitats.Conclusions: These results revealed high intraspecies genomic diversity of M. luteus and highlighted that gene gain/loss events and extensive recombination events played key roles in the genome evolution. Our study also indicated that, as a free-living species, some lineages have recently developed or are developing a mammal-associated lifestyle. This study provides insights into the mechanisms that drive the genome evolution and adaption to various environments of a bacterial species.

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Section: Introductionmentioning

confidence: 99%

Comparative Genomics Reveals Broad Genetic Diversity, Extensive Recombination and Nascent Ecological Adaptation in Micrococcus luteus

Sun

Rong

et al. 2020

Preprint

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Cataloging the Phylogenetic Diversity of Human Bladder Bacterial Isolates

Wolfe

Khemmani

et al. 2023

Preprint

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Although the human bladder is reported to harbor unique microbiota, our understanding of how these microbial communities interact with their human hosts is limited, mostly owing to the lack of isolates to test mechanistic hypotheses. Niche-specific bacterial collections and associated reference genome databases have been instrumental in expanding knowledge of the microbiota of other anatomical sites, e.g., the gut and oral cavity. To facilitate genomic, functional, and experimental analyses of the human bladder microbiota, here we present a bladder-specific bacterial reference collection comprised of 1134 genomes. These genomes were culled from bacterial isolates obtained by a metaculturomic method from bladder urine collected by transurethral catheterization. This bladder-specific bacterial reference collection includes 196 different species, including representatives of major aerobes and facultative anaerobes, as well as some anaerobes. It captures 72.2 % of the genera found when we reexamined previously published 16S rRNA gene sequencing of 392 adult female bladder urine samples. Comparative genomic analysis found that the taxonomies and functions of the bladder microbiota shared more similarities with the vaginal microbiota than the gut microbiota. Whole-genome phylogenetic and functional analyses of 186 bladderE. coliisolates and 387 gutE. coliisolates supports the hypothesis that phylogroup distribution and functions ofE. colistrains differ dramatically between these two very different niches. This bladder-specific bacterial reference collection is a unique resource that will enable hypothesis-driven bladder microbiota research and comparison to isolates from other anatomical sites.

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Cataloging the phylogenetic diversity of human bladder bacterial isolates

Du,

Khemmani,

Halverson

et al. 2024

Genome Biol

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Background Although the human bladder is reported to harbor unique microbiota, our understanding of how these microbial communities interact with their human hosts is limited, mostly owing to the lack of isolates to test mechanistic hypotheses. Niche-specific bacterial collections and associated reference genome databases have been instrumental in expanding knowledge of the microbiota of other anatomical sites, such as the gut and oral cavity. Results To facilitate genomic, functional, and experimental analyses of the human bladder microbiota, we present a bladder-specific bacterial isolate reference collection comprising 1134 genomes, primarily from adult females. These genomes were culled from bacterial isolates obtained by a metaculturomic method from bladder urine collected by transurethral catheterization. This bladder-specific bacterial isolate reference collection includes 196 different species, including representatives of major aerobes and facultative anaerobes, as well as some anaerobes. It captures 72.2% of the genera found when re-examining previously published 16S rRNA gene sequencing of 392 adult female bladder urine samples. Comparative genomic analysis finds that the taxonomies and functions of the bladder microbiota share more similarities with the vaginal microbiota than the gut microbiota. Whole-genome phylogenetic and functional analyses of 186 bladder Escherichia coli isolates and 387 gut Escherichia coli isolates support the hypothesis that phylogroup distribution and functions of Escherichia coli strains differ dramatically between these two very different niches. Conclusions This bladder-specific bacterial isolate reference collection is a unique resource that will enable bladder microbiota research and comparison to isolates from other anatomical sites.

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Draft Genome Sequence of Micrococcus luteus (Schroeter) Cohn (ATCC 12698)

Abstract: The actinobacterium Micrococcus luteus can be found in a wide variety of habitats. Here, we report the 2,411,958-bp draft genome sequence of the type strain M. leuteus (Schroeter) Cohn (ATCC 12698). Characteristic of this taxa, the genome sequence has a high G+C content, 73.14%.

Cited by 3 publications

References 10 publications

Comparative Genomics Reveals Broad Genetic Diversity, Extensive Recombination and Nascent Ecological Adaptation in Micrococcus luteus

Comparative Genomics Reveals Broad Genetic Diversity, Extensive Recombination and Nascent Ecological Adaptation in Micrococcus luteus

Cataloging the Phylogenetic Diversity of Human Bladder Bacterial Isolates

Cataloging the phylogenetic diversity of human bladder bacterial isolates

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