Microbial culturomics: paradigm shift in the human gut microbiome study. Clin Microbiol Infect

Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095  Service de Nutrition, Maladies Métaboliques et Endocrinologie, UMR-INRA U1260, CHU de la Timone, Marseille, France  IRD, UMR CNRS 7278-IRD 198, Route des Pères Maristes, Dakar, Sénégal  National Centre for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Clinical Microbiology and Infection (Impact Factor: 5.77). 09/2012; 449(12). DOI: 10.1111/1469-0691.12023
Source: PubMed


Clin Microbiol Infect 2012; 18: 1185–1193
Comprehensive determination of the microbial composition of the gut microbiota and the relationships with health and disease are major challenges in the 21st century. Metagenomic analysis of the human gut microbiota detects mostly uncultured bacteria. We studied stools from two lean Africans and one obese European, using 212 different culture conditions (microbial culturomics), and tested the colonies by using mass spectrometry and 16S rRNA amplification and sequencing. In parallel, we analysed the same three samples by pyrosequencing 16S rRNA amplicons targeting the V6 region. The 32 500 colonies obtained by culturomics have yielded 340 species of bacteria from seven phyla and 117 genera, including two species from rare phyla (Deinococcus-Thermus and Synergistetes, five fungi, and a giant virus (Senegalvirus). The microbiome identified by culturomics included 174 species never described previously in the human gut, including 31 new species and genera for which the genomes were sequenced, generating c. 10 000 new unknown genes (ORFans), which will help in future molecular studies. Among these, the new species Microvirga massiliensis has the largest bacterial genome so far obtained from a human, and Senegalvirus is the largest virus reported in the human gut. Concurrent metagenomic analysis of the same samples produced 698 phylotypes, including 282 known species, 51 of which overlapped with the microbiome identified by culturomics. Thus, culturomics complements metagenomics by overcoming the depth bias inherent in metagenomic approaches.

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Available from: Catherine Robert, Sep 17, 2014
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    • "Culturomics was developed in 2012 in order to extend the human gut repertoire. In the first study, by multiplying the number of culture conditions (212 different culture conditions) with rapid identification of the colonies using MALDI-TOF, we were able to identify 340 different bacterial species including 31 new bacterial species (Lagier et al. 2012a,b,c,d). In addition, we demonstrated a complementarity with metagenomics (the usual gold standard for studying complex ecosystems) because only 15% of the species were concomitantly detected by culture and metagenomics applied to the same samples. "
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    ABSTRACT: Microvirga massiliensis sp. nov. strain JC119(T) is a bacteria isolated in Marseille from a stool sample collected in Senegal. The 16S rRNA (JF824802) of M. massiliensis JC119(T) revealed 95% sequence identity with Microvirga lotononidis WSM3557(T) (HM362432). This bacterium is aerobic, gram negative, catalase positive, and oxidase negative. The draft genome of M. massiliensis JC119(T) comprises a 9,207,211-bp-long genome that is the largest bacterial genome of an isolate in humans. The genome exhibits a G+C content of 63.28% and contains 8685 protein-coding genes and 77 RNA genes, including 21 rRNA genes. Here, we describe the features of M. massiliensis JC119(T) , together with the genome sequence information and its annotation.
    Full-text · Article · Jan 2016 · MicrobiologyOpen
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    • "This number remains insufficient as a result of the lack of comprehensive culture methods. To enhance the isolation of bacteria, our laboratory performed an efficient method called culturomics [4]. Since then, several new bacteria, including new genera and species, have been reported in the human gut [5] [6] [7] [8]. "
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    ABSTRACT: Taxonogenomics coupled with culturomics promotes the isolation and characterization of bacteria. Kallipyga gabonensis sp. nov. strain GM4 is a strictly anaerobic, Gram-positive, and non motile coccus isolated from the stool of a Gabonese male teenager. The genome is 1,621,211 bp long with 50.01% G+C content and two scaffolds. Of the 1,536 predicted genes, 1,475 were protein-coding genes and 61 were RNA genes. A total of 931 genes were assigned a putative function, and 79 genes were identified as ORFans.
    Full-text · Article · Nov 2015
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    • "This long, fastidious and costly method was gradually abandoned in favour of metagenomic studies [1]. More recently, by culture-dependent studies using dilution method [5] or microbial culturomics [6] [7], designing techniques mimicking the natural environment of the bacteria, the human gut repertoire, composed preferentially of anaerobic bacteria, was dramatically extended [8]. Nevertheless, these techniques remain frequently reserved for specialized laboratories. "
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    ABSTRACT: In the mid-19th century, the dichotomy between aerobic and anaerobic bacteria was introduced. Nevertheless, the aerobic growth of strictly anaerobic bacterial species such as Ruminococcus gnavus and Fusobacterium necrophorum, in a culture medium containing antioxidants, was recently demonstrated. We tested aerobically the culture of 623 bacterial strains from 276 bacterial species including 82 strictly anaerobic, 154 facultative anaerobic, 31 aerobic and nine microaerophilic bacterial species as well as ten fungi. The basic culture medium was based on Schaedler agar supplemented with 1 g/L ascorbic acid and 0.1 g/L glutathione (R-medium). We successively optimized this media, adding 0.4 g/L uric acid, using separate autoclaving of the component, or adding haemin 0.1 g/L or α-ketoglutarate 2 g/L. In the basic medium, 237 bacterial species and ten fungal species grew but with no growth of 36 bacterial species, including 22 strict anaerobes. Adding uric acid allowed the growth of 14 further species including eight strict anaerobes, while separate autoclaving allowed the growth of all tested bacterial strains. To extend its potential use for fastidious bacteria, we added haemin for Haemophilus influenzae, Haemophilus parainfluenzae and Eikenella corrodens and α-ketoglutarate for Legionella pneumophila. This medium allowed the growth of all tested strains with the exception of Mycobacterium tuberculosis and Mycobacterium bovis. Testing primoculture and more fastidious species will constitute the main work to be done, but R-medium coupled with a rapid identification method (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry) will facilitate the anaerobic culture in clinical microbiology laboratories.
    Full-text · Article · Nov 2015 · Clinical Microbiology and Infection
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