Draft genome and description of Mixta mediterraneensis strain Marseille-Q2057T sp.nov., a new bacterium isolated from human healthy skin

Antezack, Angéline; Magnien, S.; Cassir, Nadim; Scola, Bernard La

doi:10.1016/j.nmni.2021.100840

Cited by 4 publications

(5 citation statements)

References 26 publications

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“…This species cluster was effectively published as "Mixta mediterraneensis" (Boxberger et al, 2021). However, both our phylogenetic analysis and GTDB place this taxon in the genus Pantoea.…”

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

confidence: 78%

“…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%

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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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“…This species cluster was effectively published as "Mixta mediterraneensis" (Boxberger et al, 2021). However, both our phylogenetic analysis and GTDB place this taxon in the genus Pantoea.…”

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

confidence: 78%

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

confidence: 99%

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

confidence: 99%

See 1 more Smart Citation

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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“…We identified the genome as M. mediterraneensis . We then used the original genome of Mixta ( Erwinia ) mediterraneensis (Boxberger et al 2021 ) as a database and mapped the reads again in the same way as above. The reassembled genome and transcriptome were improved using Pilon (Walker et al 2014 ).…”

Section: Methodsmentioning

confidence: 99%

“…Based on the mite metagenomic DNA samples, we assembled the genome of Erwiniaceae bacteria. The next comparison of the assembled genome revealed that it belongs to Mixta mediterraneensis according to high similarity to M. mediterraneensis strain Marseille-Q2057 T that was previously isolated from skin swabs from the hand of a 30-year-old healthy woman (Boxberger et al 2021 ). We focused on describing interactions between mites and bacterial symbionts using functional metagenomics, meta-transcriptomics, and proteomics.…”

Section: Introductionmentioning

confidence: 99%

Mixta mediterraneensis as a novel and abundant gut symbiont of the allergen-producing domestic mite Blomia tropicalis

Erban,

Sopko,

Klimov

et al. 2024

Exp Appl Acarol

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Blomia tropicalis is an allergen-producing mite in the human environment in tropical regions. The microbiome of B. tropicalis was described using the barcode sequencing region of V4 16S rDNA and genome assemblage. Mixta mediterraneensis, previously isolated from human skin swabs, was identified as a B. tropicalis gut symbiont based on genome assembly. The microbiome contains two bacteria, Staphylococcus and M. mediterraneensis. The number of M. mediterraneensis 16S DNA copies was 106 per mite and 109 per feces in the rearing chamber based on qPCR quantification. The profile of this bacterium reached 50% of reads in the mite gut and feces. Genomic analyses revealed that the bacterium has several metabolic pathways that suggest metabolic cooperation with the mite host in vitamin and amino acid synthesis, nitrogen recycling, and antimicrobial defense. Lysozyme is present in the symbiotic bacterium but absent in the mite. The B. tropicalis microbiome contained Staphylococcus, which accelerates mite population growth. Mites can digest Staphylococcus by using specific enzymes with hydrolytic functions against bacterial cell walls (chitinases and cathepsin D), leading to endocytosis of bacteria and their degradation in lysosomes and phagosomes. Gene expression analysis of B. tropicalis indicated that phagocytosis was mediated by the PI3-kinase/Akt pathway interacting with the invasins produced by M. mediterraneensis. Moreover, the symbiont had metabolic pathways that allowed it to recycle the mite metabolic waste product guanine, known as a mite attractant. The mite host symbiont enhances mite aggregation in the feces, and the fecal–oral transmission route is excepted.

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Pantoea

Palmer

Coutinho

2022

Bergey's Manual of Systematics of Archaea and Bacteria

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Pan.toe'a. Gr. masc. adj. pantoios , of all sorts and sources; N.L. fem. n. Pantoea , [bacteria] from diverse [geographical and ecological] sources. Pseudomonadota / Gammaproteobacteria / Enterobacterales / Enterobacteriaceae / Pantoea The genus Pantoea comprises a versatile assemblage of Gram‐negative and facultatively anaerobic bacteria. These bacteria occur in association with plant and animal hosts, as beneficial or pathogenic members of the communities or as free‐living in various environments. Cells of the members of this genus are non‐spore‐forming and nonencapsulated rods, ranging between 0.5 and 1.3 by 1.0 and 3.8 μm. The formation of symplasmata occurs in some members of the genus. Most are motile by means of peritrichous flagella, with some members producing a yellow pigment. The genus currently consists of 23 validly and effectively published species, ranging widely in isolation source and apparent pathogenic ability. The genomes of these organisms range markedly in size, with the median genome size being 4.85 Mb. The genomic pool of these organisms is diverse, contributing to their ecological versatility. Conserved genes within the genus are mainly involved in core housekeeping functions. This genus forms part of the family Enterobacteriaceae , with a close evolutionary relationship to Erwinia , Izhakiella , Mixta , Phaseolibacter , Rosenbergiella , and Tatumella . The G + C content of their DNA, as determined from genome sequences, ranges between 51.80 and 59.60%. Various members of this genus are considered pathogens or opportunistic pathogens, while some isolates display biotechnological and agricultural potential. DNA G + C content based on genome (mol%) : 51.90–59.60. Type species : Pantoea agglomerans (Beijerinck 1988) Gavini et al. 1989 VP .

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Draft genome and description of Mixta mediterraneensis strain Marseille-Q2057T sp.nov., a new bacterium isolated from human healthy skin

Cited by 4 publications

References 26 publications

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

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

Mixta mediterraneensis as a novel and abundant gut symbiont of the allergen-producing domestic mite Blomia tropicalis

Pantoea

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