Non-contiguous finished genome sequence and description of Anaerococcus senegalensis sp. nov.

Lagier, Jean‐Christophe; Karkouri, Khalid El; Nguyen, Thi Hong Van; Armougom, Fabrice; Raoult, Didier; Fournier, Pierre‐Edouard

doi:10.4056/sigs.2415480

Cited by 105 publications

(74 citation statements)

References 17 publications

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“…This suggest a different oxidative stress resistance level among anaerobic prokaryotes. Indeed, while Methanobrevibacter smithii and Faecalibacterium prausnitzii are prokaryotes among the most sensitive ones to oxygen (F. prausnitzii loses its viability within 2 min after exposure to ambient air [35]), we observed a trace but nonsignificant growth of A. rubiinfantis in microaerophilic conditions, as previously reported for A. senegalensis [12]. These results suggest that the aerobic/anaerobic bacterial culture dichotomy is no longer relevant [36] and that there is a continuum between species whose growth is not affected by a normal (ambient air) partial pressure of oxygen and/or positive redox potential, and species that only grow in total absence of oxygen and/or when redox potential is very low [37].…”

Section: Discussionsupporting

confidence: 75%

“…Differences between strain mt16 and A. vaginalis (its closest neighbor) also included the production of alkaline phosphatase as well as the production of acids from the following carbohydrates: arabinose, mannitol and sucrose [38]. Strain mt16 was classified among the Anaerococcus genus that currently contains eight validated species [5] which are Gram-positive, strictly anaerobic, non-motile, and mostly non-sporeforming species [6,12]. The phylogenetic relationship between several members of the family Peptoniphilaceae to which the genus Anaerococcus belongs, displayed in Fig.…”

Section: Discussionmentioning

confidence: 99%

“…Thanks to the decreasing cost of genome sequencing, a new concept of bacterial description [10], taxonogenomics, was created in our laboratory allying classical bacterial classification features to a proteomic description with the MALDI-TOF profile [11] and a description of the complete annotated genome of the described species [12].…”

Section: Introductionmentioning

confidence: 99%

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Anaerococcus rubiinfantis sp. nov., isolated from the gut microbiota of a Senegalese infant with severe acute malnutrition

Alou¹,

Khelaifia²,

Michelle³

et al. 2016

Anaerobe

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Anaerococcus rubiinfantis sp. nov. strain mt16(T) is a new species within the genus Anaerococcus, which was isolated by the culturomics approach from the gut microbiota of an infant suffering from kwashiorkor. A phenotypic, biochemical and proteomic description of this strain is hereby presented alongside a complete annotation of its genome. This strictly anaerobic species forms Gram-positive non-sporeforming cocci. The major fatty acid was hexadecanoic acid. The phylogenetic analysis of strain mt16(T) showed a 97.9% similarity level with Anaerococcus vaginalis, the closest validly published species. Its genome is 1,929,161 bp long with 29.5% G + C content and contains 1808 protein-coding genes and 56 RNA genes, among which are six rRNA genes. Genomic analysis identified 41/1864 coding genes as ORFans (2.2%) and at least 620/1808 (34.9%) orthologous proteins which are not shared with the closest phylogenetic species. We believe that the extension of the human anaerobic gut compendium by culturomics is one of the first steps that will improve the understanding of the links between the microbiome and health or disease.

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Section: Discussionsupporting

confidence: 75%

Section: Discussionmentioning

confidence: 99%

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Anaerococcus rubiinfantis sp. nov., isolated from the gut microbiota of a Senegalese infant with severe acute malnutrition

Alou¹,

Khelaifia²,

Michelle³

et al. 2016

Anaerobe

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“…This strategy combines phenotypic characteristics with MALDI-TOF MS spectrum and genomic analysis (Lagier et al, 2012b;Mishra et al, 2012). Using this method, we isolated the strain S5 T belonging to the genus Oceanobacillus.…”

Section: Introductionmentioning

confidence: 99%

Microbial Culturomics to Map Halophilic Bacterium in Human Gut: Genome Sequence and Description of Oceanobacillus jeddahense sp. nov.

Khelaifia

Lagier

Bibi

et al. 2016

OMICS: A Journal of Integrative Biology

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Culturomics is a new omics subspecialty to map the microbial diversity of human gut, coupled with a taxono-genomic strategy. We report here the description of a new bacterial species using microbial culturomics: strain S5T, (= CSUR P1091=DSM 28586) isolated from a stool specimen of a 25-year-old obese patient from Saudi Arabia. The strain S5T was a Gram-positive, strictly aerobic rod, which was motile by a polar flagellum, spore-forming, and exhibited catalase and oxidase activities. It grows optimally at 37°C, with a pH of 7.5 and 10% of NaCl. 16S rRNA gene-based identification revealed that strain S5T has 98.6% 16S rRNA sequence similarity with the reference O. oncorhynchi, phylogenetically the closest validated Oceanobacillus species. Here, we further describe the phenotypic characteristics of this organism and its complete genome sequence and annotation. The 5,388,285 bp long genome exhibits a G+C content of 37.24% and contains 5109 protein-coding genes and 198 RNA genes. Based on the characteristics reported here, we propose classifying this novel bacterium as representative of a new species belonging to the genus Oceanobacillus, Oceanobacillus jeddahense sp. nov. In a broader context, it is noteworthy that halophilic bacteria have long been overlooked in the human gut, and their role in human health and disease has not yet been investigated. This study thus further underscores the usefulness of the culturomics approach exploring the bacterial diversity of the gut.

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“…The Marseilleviridae family contains two more members: Marseillevirus [3] and Senegalvirus [4]. The latter strain was recovered from the stools of an asymptomatic individual in Senegal, demonstrating that humans may be exposed to these large viruses.…”

Section: Introductionmentioning

confidence: 99%

Lausannevirus Seroprevalence among Asymptomatic Young Adults

et al. 2013

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Objectives: The giant Lausannevirus was recently identified as a parasite of amoeba that replicates rapidly in these professional phagocytes. This study aimed at assessing Lausannevirus seroprevalence among asymptomatic young men in Switzerland and hopefully identifying possible sources of contact with this giant virus. Methods: The presence of anti-Lausannevirus antibodies was assessed in sera from 517 asymptomatic volunteers who filled a detailed questionnaire. The coreactivity between Lausannevirus and amoeba-resisting bacteria was assessed. Results: Lausannevirus prevalence ranged from 1.74 to 2.51%. Sporadic condom use or multiple sexual partners, although frequent (53.97 and 60.35%, respectively), were not associated with anti-Lausannevirus antibodies. On the contrary, frequent outdoor sport practice as well as milk consumption were significantly associated with positive Lausannevirus serologies (p = 0.0066 and 0.028, respectively). Coreactivity analyses revealed an association between Criblamydia sequanensis (an amoeba-resisting bacterium present in water environments) and Lausannevirus seropositivity (p = 0.001). Conclusions: Lausannevirus seroprevalence is low in asymptomatic Swiss men. However, the association between virus seropositivity and frequent sport practice suggests that this member of the Megavirales may be transmitted by aerosols and/or exposure to specific outdoor environments. Milk intake was also associated with seropositivity. Whether the coreactivity observed for C. sequanensis and Lausannevirus reflects a common mode of acquisition or some unexpected cross-reactivity remains to be determined.

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Non-contiguous finished genome sequence and description of Anaerococcus senegalensis sp. nov.

Cited by 105 publications

References 17 publications

Anaerococcus rubiinfantis sp. nov., isolated from the gut microbiota of a Senegalese infant with severe acute malnutrition

Anaerococcus rubiinfantis sp. nov., isolated from the gut microbiota of a Senegalese infant with severe acute malnutrition

Microbial Culturomics to Map Halophilic Bacterium in Human Gut: Genome Sequence and Description of Oceanobacillus jeddahense sp. nov.

Lausannevirus Seroprevalence among Asymptomatic Young Adults

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