‘Collinsella provencensis’  sp. nov.,  ‘Parabacteroides bouchesdurhonensis’  sp. nov. and  ‘Sutterella seckii,’  sp. nov., three new bacterial species identified from human gut microbiota

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Abstract

We report here the main characteristics of ‘Collinsella provencensis’ strain Marseille-P3740 (CSUR P3740), ‘Parabacteroides bouchesdurhonensis’ strain Marseille-P3763 (CSUR P3763) and ‘Sutterella seckii’ strain Marseille-P3660 (CSUR P3660), which were isolated using culturomics from the human gut microbiota of healthy individuals living in Marseille.

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Ongoing revolution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

Piseth Seng, Michel Drancourt, Frédérique Gouriet … (2009)

Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry accurately identifies both selected bacteria and bacteria in select clinical situations. It has not been evaluated for routine use in the clinic. We prospectively analyzed routine MALDI-TOF mass spectrometry identification in parallel with conventional phenotypic identification of bacteria regardless of phylum or source of isolation. Discrepancies were resolved by 16S ribosomal RNA and rpoB gene sequence-based molecular identification. Colonies (4 spots per isolate directly deposited on the MALDI-TOF plate) were analyzed using an Autoflex II Bruker Daltonik mass spectrometer. Peptidic spectra were compared with the Bruker BioTyper database, version 2.0, and the identification score was noted. Delays and costs of identification were measured. Of 1660 bacterial isolates analyzed, 95.4% were correctly identified by MALDI-TOF mass spectrometry; 84.1% were identified at the species level, and 11.3% were identified at the genus level. In most cases, absence of identification (2.8% of isolates) and erroneous identification (1.7% of isolates) were due to improper database entries. Accurate MALDI-TOF mass spectrometry identification was significantly correlated with having 10 reference spectra in the database (P=.01). The mean time required for MALDI-TOF mass spectrometry identification of 1 isolate was 6 minutes for an estimated 22%-32% cost of current methods of identification. MALDI-TOF mass spectrometry is a cost-effective, accurate method for routine identification of bacterial isolates in or =10 reference spectra per bacterial species and a 1.9 identification score (Brucker system). It may replace Gram staining and biochemical identification in the near future.

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16S ribosomal DNA sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates.

M Drancourt, C Bollet, A Carlioz … (2000)

Some bacteria are difficult to identify with phenotypic identification schemes commonly used outside reference laboratories. 16S ribosomal DNA (rDNA)-based identification of bacteria potentially offers a useful alternative when phenotypic characterization methods fail. However, as yet, the usefulness of 16S rDNA sequence analysis in the identification of conventionally unidentifiable isolates has not been evaluated with a large collection of isolates. In this study, we evaluated the utility of 16S rDNA sequencing as a means to identify a collection of 177 such isolates obtained from environmental, veterinary, and clinical sources. For 159 isolates (89.8%) there was at least one sequence in GenBank that yielded a similarity score of > or =97%, and for 139 isolates (78.5%) there was at least one sequence in GenBank that yielded a similarity score of > or =99%. These similarity score values were used to defined identification at the genus and species levels, respectively. For isolates identified to the species level, conventional identification failed to produce accurate results because of inappropriate biochemical profile determination in 76 isolates (58.7%), Gram staining in 16 isolates (11.6%), oxidase and catalase activity determination in 5 isolates (3.6%) and growth requirement determination in 2 isolates (1.5%). Eighteen isolates (10.2%) remained unidentifiable by 16S rDNA sequence analysis but were probably prototype isolates of new species. These isolates originated mainly from environmental sources (P = 0.07). The 16S rDNA approach failed to identify Enterobacter and Pantoea isolates to the species level (P = 0.04; odds ratio = 0.32 [95% confidence interval, 0.10 to 1.14]). Elsewhere, the usefulness of 16S rDNA sequencing was compromised by the presence of 16S rDNA sequences with >1% undetermined positions in the databases. Unlike phenotypic identification, which can be modified by the variability of expression of characters, 16S rDNA sequencing provides unambiguous data even for rare isolates, which are reproducible in and between laboratories. The increase in accurate new 16S rDNA sequences and the development of alternative genes for molecular identification of certain taxa should further improve the usefulness of molecular identification of bacteria.

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Phylogenetic and phenotypic evidence for the transfer of Eubacterium aerofaciens to the genus Collinsella as Collinsella aerofaciens gen. nov., comb. nov.

T Nakase, Y Benno, A Kageyama (1999)

Three strains of Eubacterium aerofacien, JCM 10188T, JCM 7790 and JCM 7791, and 178 freshly isolated strains of the Eubacterium aerofaciens group from human faeces were characterized by biochemical tests, cell wall peptidoglycan type and 16S rRNA analysis. The Eubacterium aerofaciens group was divided into four groups by fermentation patterns of sucrose and cellobiose, and were further divided into 16 sub-groups by fermentation patterns of aesculin, salicin and amygdalin. All of the strains of the Eubacterium aerofaciens group were shown to be phylogenetically distantly related to Eubacterium limosum, which is the type species of genus Eubacterium. Eubacterium aerofaciens was shown to have a specific phylogenetic association with Coriobacterium glomerans. All the strains belonging to Eubacterium aerofaciens resembled Coriobacterium glomerans in possessing a high G + C content (60 mol%). Cell wall analysis, however, revealed the presence of different A4 beta (L-Ala)-D-Glu-L-Orn-L-Asp peptidoglycan types. Based on a 16S rRNA sequence divergence of greater than 9% with Coriobacterium glomerans and the presence of a unique peptidoglycan type, a new genus, Collinsella, is proposed for Eubacterium aerofaciens, with one species, Collinsella aerofaciens. The type strain of Collinsella aerofaciens is JCM 10188T.

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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: 22 February 2018

Publication date Collection: May 2018

Publication date (Electronic): 22 February 2018

Volume: 23

Pages: 44-47

Affiliations

[1]Aix-Marseille Université, IRD, MEPHI, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France

Author notes

[∗ ]Corresponding author: J.C. Lagier, Aix-Marseille Université, IRD, AP-HM, IHU-Méditerranée Infection, UMR, Microbes Evolution Phylogénie (MEPHI), 19-21 Boulevard Jean Moulin, 13005 Marseille, France.Aix-Marseille UniversitéIRDAP-HMIHU-Méditerranée InfectionUMRMicrobes Evolution Phylogénie (MEPHI)19-21 Boulevard Jean MoulinMarseille13005France jclagier@ 123456yahoo.fr

Article

Publisher ID: S2052-2975(18)30009-X

DOI: 10.1016/j.nmni.2018.02.003

PMC ID: 5854914

SO-VID: 04333451-7141-4aa0-afa6-9fb6b20fa3e5

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 December 2017

Date revision received : 31 January 2018

Date accepted : 9 February 2018

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‘Collinsella provencensis’ sp. nov., ‘Parabacteroides bouchesdurhonensis’ sp. nov. and ‘Sutterella seckii,’ sp. nov., three new bacterial species identified from human gut microbiota

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Role of Microbes in Soil Fertility and Human Health

Most cited references 4

Ongoing revolution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

16S ribosomal DNA sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates.

Phylogenetic and phenotypic evidence for the transfer of Eubacterium aerofaciens to the genus Collinsella as Collinsella aerofaciens gen. nov., comb. nov.

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