“Intestinimonas gabonensis” sp. nov., a new bacterium detected from a Gabonese stool specimen

There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

Abstract

Detection of new bacteria becomes a major part of culturomics studies coupled with taxonogenomics. Using these strategies, we report here the main characteristics of a new species, “Intestinimonas gabonensis” strain GM5. It is a bacterium isolated from a stool specimen from a 27-year-old man from Gabon.

Related collections

Most cited references 7

Record: found
Abstract: found
Article: not found

The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota.

Jean-Christophe Lagier, Perrine Hugon, Saber Khelaifia … (2015)

Bacterial culture was the first method used to describe the human microbiota, but this method is considered outdated by many researchers. Metagenomics studies have since been applied to clinical microbiology; however, a "dark matter" of prokaryotes, which corresponds to a hole in our knowledge and includes minority bacterial populations, is not elucidated by these studies. By replicating the natural environment, environmental microbiologists were the first to reduce the "great plate count anomaly," which corresponds to the difference between microscopic and culture counts. The revolution in bacterial identification also allowed rapid progress. 16S rRNA bacterial identification allowed the accurate identification of new species. Mass spectrometry allowed the high-throughput identification of rare species and the detection of new species. By using these methods and by increasing the number of culture conditions, culturomics allowed the extension of the known human gut repertoire to levels equivalent to those of pyrosequencing. Finally, taxonogenomics strategies became an emerging method for describing new species, associating the genome sequence of the bacteria systematically. We provide a comprehensive review on these topics, demonstrating that both empirical and hypothesis-driven approaches will enable a rapid increase in the identification of the human prokaryote repertoire.

0 comments Cited 373 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: not found

Intestinimonas butyriciproducens gen. nov., sp. nov., a butyrate-producing bacterium from the mouse intestine.

Karoline Kläring, Laura Hanske, Nam Bui … (2013)

A Gram-positive, spore-forming, non-motile, strictly anaerobic rod-shaped bacterium was isolated from the caecal content of a TNF(deltaARE) mouse. The isolate, referred to as strain SRB-521-5-I(T), was originally cultured on a reduced agar medium containing yeast extract, rumen fluid and lactic acid as main energy and carbon sources. Phylogenetic analysis of partial 16S rRNA genes revealed that the species most closely related to strain SRB-521-5-I(T) were Flavonifractor plautii and Pseudoflavonifractor capillosus (<95 % sequence similarity; 1436 bp). In contrast to F. plautii and P. capillosus, strain SRB-521-5-I(T) contained a substantial amount of C18 : 0 dimethylacetal. Additional major fatty acids were C14 : 0 methyl ester, C16 : 0 dimethylacetal and C18 : 0 aldehyde. Strain SRB-521-5-I(T) differed in its enzyme profile from F. plautii and P. capillosus by being positive for dextrin, maltotriose, turanose, dl-lactic acid and d-lactic acid methyl ester but negative for d-fructose. In reduced Wilkins-Chalgren-Anaerobe broth, strain SRB-521-5-I(T) produced approximately 8 mM butyrate and 4 mM acetate. In contrast to F. plautii, the strain did not metabolize flavonoids. It showed intermediate resistance towards the antibiotics ciprofloxacin, colistin and tetracycline. Based on genotypic and phenotypic characteristics, we propose the name Intestinimonas butyriciproducens gen. nov., sp. nov. to accommodate strain SRB-521-5-I(T) ( = DSM 26588(T) = CCUG 63529(T)) as the type strain.

0 comments Cited 37 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: not found

Rise of Microbial Culturomics: Noncontiguous Finished Genome Sequence and Description of Beduini massiliensis gen. nov., sp. nov.

Gaël Mourembou, Muhammad Yasir, Esam Ibraheem Azhar … (2015)

Microbial culturomics is a new field of omics sciences that examines the bacterial diversity of human gut coupled with a taxono-genomic strategy. Using microbial culturomics, we report here for the first time a novel Gram negative, catalase- and oxidase-negative, strict anaerobic bacilli named Beduini massiliensis gen. nov., sp nov. strain GM1 (= CSUR P1440 = DSM 100188), isolated from the stools of a female nomadic Bedouin from Saudi Arabia. With a length of 2,850,586 bp, the Beduini massiliensis genome exhibits a G + C content of 35.9%, and contains 2819 genes (2744 protein-coding and 75 RNA genes including 57 tRNA and 18 rRNA genes). It is composed of 6 scaffolds (composed of 6 contigs). A total of 1859 genes (67.75%) were assigned a putative function (by COGs or by NR blast). At least 1457 (53%) orthologous proteins were not shared with the closest phylogenetic species. 274 genes (10.0%) were identified as ORFans. These results show that microbial culturomics can dramatically improve the characterization of the human microbiota repertoire, deciphering new bacterial species and new genes. Further studies will clarify the geographic specificity and the putative role of these new microbes and their related functional genetic content in health and disease. Microbial culturomics is an emerging frontier of omics systems sciences and integrative biology and thus, warrants further consideration as part of the postgenomics methodology toolbox.

0 comments Cited 9 times – based on 0 reviews      Review now

Bookmark

All references

Author and article information

Contributors

J.C. Lagier

Journal

Journal ID (nlm-ta): New Microbes New Infect

Journal ID (iso-abbrev): New Microbes New Infect

Title: New Microbes and New Infections

Publisher: Elsevier

ISSN (Electronic): 2052-2975

Publication date PMC-release: 20 October 2016

Publication date Collection: January 2017

Publication date (Electronic): 20 October 2016

Volume: 15

Pages: 24-26

Affiliations

[1) ]Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France

[2) ]Ecole Doctorale Régionale d’Afrique Centrale, Gabon

[3) ]Unité de Parasitologie Médicale (UPARAM) CIRMF, Franceville, Gabon

[4) ]Département de Microbiologie, Laboratoire national de référence IST/SIDA, Faculté de Médecine, Gabon

[5) ]Département de Parasitologie Mycologie et de Médecine Tropicale, Université des Sciences de la Santé, Libreville, Gabon

Author notes

[∗ ] Corresponding author: J.C. Lagier, Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, FranceAix Marseille UniversitéURMITEUM63CNRS 7278IRD 198INSERM 1095MarseilleFrance jclagier@ 123456yahoo.fr

Article

Publisher ID: S2052-2975(16)30111-1

DOI: 10.1016/j.nmni.2016.10.005

PMC ID: 5237755

SO-VID: 5c573004-3e76-4845-8391-dec75898f9e4

License:

This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

History

Date received : 29 August 2016

Date revision received : 29 September 2016

Date accepted : 14 October 2016

“Intestinimonas gabonensis” sp. nov., a new bacterium detected from a Gabonese stool specimen

Read this article at

Abstract

Related collections

Phytosauria

Most cited references 7

The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota.

Intestinimonas butyriciproducens gen. nov., sp. nov., a butyrate-producing bacterium from the mouse intestine.

Rise of Microbial Culturomics: Noncontiguous Finished Genome Sequence and Description of Beduini massiliensis gen. nov., sp. nov.

Author and article information

Contributors

Journal

Affiliations

Author notes

Article

History

Categories

Comments

Comment on this article

Similar content 28

Most referenced authors 86