Lysinibacillus timonensis sp. nov., Microbacterium timonense sp. nov., and Erwinia mediterraneensis sp. nov., three new species isolated from the human skin

Ndiaye, Codou; Lo, Cheikh Ibrahima; Basséne, Hubert; Raoult, Didier; Lagier, Jean-Christophe; Sokhna, Cheikh

doi:10.1016/j.nmni.2019.100579

Cited by 6 publications

(3 citation statements)

References 14 publications

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“…Sequencing of the gDNA from each strain was carried out with a MiSeq sequencer using the mate pair strategy (Illumina Inc., San Diego, CA, USA) as previously executed [ 4 ]. Then, assembly and annotation of the genomes of each strain were carried out using several softwares similar to those previously used [ 22 ].…”

Section: Methodsmentioning

confidence: 99%

Two new bacteria isolated from vagina of a patient with vaginosis: Atopobium massiliense sp. nov. and Butyricimonas vaginalis sp. nov.

Bordigoni

Yimagou

et al. 2020

New Microbes and New Infections

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Two new bacterial strains, Marseille-P4126 (=CSURP4126) and Marseille-P4593 (=CSURP4593), were isolated from the vaginal sample of a French woman with vaginosis. These strains were identified and characterized using the taxonogenomics method. The findings from phylogenetic tree interpretation, phenotypic criteria and genomic analysis provided here distinctly display that Atopobium massiliense sp. nov. and Butyricimonas vaginalis sp. nov. are new members of the genus Atopobium and Butyricimonas , respectively.

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Section: Methodsmentioning

confidence: 99%

Two new bacteria isolated from vagina of a patient with vaginosis: Atopobium massiliense sp. nov. and Butyricimonas vaginalis sp. nov.

Bordigoni

Yimagou

et al. 2020

New Microbes and New Infections

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“…However, both our phylogenetic analysis and GTDB place this taxon in the genus Pantoea. The species cluster currently consists of the genome of a single strain, Marseille-Q2057, which was isolated from the skin swabs of a healthy human (Ndiaye et al, 2019;Boxberger et al, 2021). As stated above, P. "mediterraneensis_A" shares an MRCA with P. bituminis sp.…”

Section: Pantoea "Mediterraneensis_a" ( a B C D E F )mentioning

confidence: 99%

“…This species consists of the genome of a single strain, the type strain Marseille-P5165 T , isolated from human skin swabs (Ndiaye et al, 2019;Boxberger et al, 2021). Based on GTDB, previous phylogenomic analyses of the Erwiniaceae family Stavrinides, 2019, 2022), and our core genome tree, this species, whose basonym is "Erwinia mediterraneensis", belongs to the genus Pantoea.…”

Section: Pantoea "Mediterraneensis" ( a B C D E F )mentioning

confidence: 99%

Genomic delineation and description of species and within-species lineages in the genus Pantoea

Crosby,

Rojas,

Sharma

et al. 2023

Front. Microbiol.

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As the name of the genus Pantoea (“of all sorts and sources”) suggests, this genus includes bacteria with a wide range of provenances, including plants, animals, soils, components of the water cycle, and humans. Some members of the genus are pathogenic to plants, and some are suspected to be opportunistic human pathogens; while others are used as microbial pesticides or show promise in biotechnological applications. During its taxonomic history, the genus and its species have seen many revisions. However, evolutionary and comparative genomics studies have started to provide a solid foundation for a more stable taxonomy. To move further toward this goal, we have built a 2,509-gene core genome tree of 437 public genome sequences representing the currently known diversity of the genus Pantoea. Clades were evaluated for being evolutionarily and ecologically significant by determining bootstrap support, gene content differences, and recent recombination events. These results were then integrated with genome metadata, published literature, descriptions of named species with standing in nomenclature, and circumscriptions of yet-unnamed species clusters, 15 of which we assigned names under the nascent SeqCode. Finally, genome-based circumscriptions and descriptions of each species and each significant genetic lineage within species were uploaded to the LINbase Web server so that newly sequenced genomes of isolates belonging to any of these groups could be precisely and accurately identified.

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Erwinia

Coutinho,

Shin

2023

Bergey's Manual of Systematics of Archaea and Bacteria

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er.win'i.a. N.L. fem. n. Erwinia , named after Erwin F. Smith. Proteobacteria / Gammaproteobacteria / Enterobacterales / Erwiniaceae / Erwinia Cells of the genus Erwinia are Gram‐stain‐negative rods, 0.5–1.0 × 1.0–3.0 μm, and occur alone or in pairs, sometimes in chains. Cells are motile by means of peritrichous flagella. They do not produce indole. They are mostly facultatively anaerobic, catalase‐positive, and oxidase‐ and urease‐negative. They utilize d ‐arabinose, fructose, fumarate, galactose, gluconate, glucose, glycerol, malate, β‐methyl‐glucoside, N‐ acetyl‐ d ‐glucosamine, ribose, trehalose, and succinate but not benzoate, butanol, l ‐fucose, glycogen, methanol, oxalate, propionate, or sorbose as the sole carbon sources. The major fatty acids are C 12:0 , C 14:0 , and C 16:0 . The known habitats are plants, where they cause vascular wilts and soft rots. They are also part of the epiphytic flora. They have also been isolated from insects and in one case from human skin. DNA G + C content (mol%) : 51.1–56.4%. Type species : Erwinia amylovora Winslow et al. 1920 AL (basonym: Micrococcus amylovorus Burrill 1882).

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Lysinibacillus timonensis sp. nov., Microbacterium timonense sp. nov., and Erwinia mediterraneensis sp. nov., three new species isolated from the human skin

Abstract: Lysinibacillus timonensis strain Marseille-P5727 T (=CSURP5727), Microbacterium timonense strain Marseille-P5731 T (=CSURP5731) and Erwinia mediterraneensis strain Marseille-P5165 T (=CSURP5165) are three new species isolated from the human skin.

Cited by 6 publications

References 14 publications

Two new bacteria isolated from vagina of a patient with vaginosis: Atopobium massiliense sp. nov. and Butyricimonas vaginalis sp. nov.

Two new bacteria isolated from vagina of a patient with vaginosis: Atopobium massiliense sp. nov. and Butyricimonas vaginalis sp. nov.

Genomic delineation and description of species and within-species lineages in the genus Pantoea

Erwinia

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