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. 2019 Sep 5;9(1):12807.
doi: 10.1038/s41598-019-49189-8.

Metagenomic and culturomic analysis of gut microbiota dysbiosis during Clostridium difficile infection

Sophie Amrane  1 , Marie Hocquart  1 , Pamela Afouda  1 , Edmond Kuete  1 , Thi-Phuong-Thao Pham  1 , Niokhor Dione  1 , Issa Isaac Ngom  1 , Camille Valles  1 , Dipankar Bachar  1 , Didier Raoult  1 , Jean Christophe Lagier  2
Affiliations

Metagenomic and culturomic analysis of gut microbiota dysbiosis during Clostridium difficile infection

Sophie Amrane et al. Sci Rep. .

Abstract

Recently, cocktail of bacteria were proposed in order to treat Clostridium difficile infection (CDI), but these bacteriotherapies were selected more by chance than experimentation. We propose to comprehensively explore the gut microbiota of patients with CDI compared to healthy donors in order to propose a consortium of bacteria for treating C. difficile. We compared stool samples composition from 11 CDI patients and 8 healthy donors using two techniques: metagenomics, 16S V3-V4 region amplification and sequencing and culturomics, high throughout culture using six culture conditions and MALDI-TOF identification. By culturomics, we detected 170 different species in the CDI group and 275 in the control group. Bacteroidetes were significantly underrepresented in the CDI group (p = 0.007). By metagenomics, 452 different operational taxonomic units assigned to the species level were detected in the CDI group compared to 522 in the control group. By these two techniques, we selected 37 bacteria only found in control group in more than 75% of the samples and/or with high relative abundance, 10 of which have already been tested in published bacteriotherapies against CDI, and 3 of which (Bifidobacterium adolescentis, Bifidobacterium longum and Bacteroides ovatus) have been detected by these two techniques. This controlled number of bacteria could be administrated orally in a non-invasive way in order to treat CDI.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
(A) Phyla repartition between bacteria detected in culturomic analysis in CDI and control group. (B) Proportion of bacteria in both group identified by culturomics and already known in human gut microbiota composition (H(GUT)), already known in human other site (H), first isolated in human (NH) and new species discovered by culturomic studies.
Figure 2
Figure 2
(A) Shannon index, p = 9.0334e-06 (t-test), (B) PCoA, (C) Phyla repartition between CDI group and control group in metagenomic analysis.
Figure 3
Figure 3
Bacteria associated to healthy microbiota, found by culturomics, metagenomics, culturomics and metagenomics, and compared to other published bacteriotherapies.
See this image and copyright information in PMC

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