Additional file 3: of The contribution of culturomics to the repertoire of isolated human bacterial and archaeal species

This table represents all the bacterial species isolated at least once from the human being, classified according to its phylum and combining the present work and the previous species reported by Hugon et al., in 2015. (XLSX 73 kb

Additional file 1: Table S1. of Non-contiguous finished genome sequence and description of Clostridium ihumii sp. nov.

Differential characteristics of C. ihumii AP5T, Clostridium beijerinckii strain NCIMB 8052, Clostridium botulinum strain ATCC 3502, Clostridium carboxidivorans strain P7, Clostridium dakarensestrain FF1, Clostridium difficile strain B1, Clostridium perfringens strain ATCC 13124, and C. senegalense strain JC122

MALDI-TOF Identification of the Human Gut Microbiome in People with and without Diarrhea in Senegal

<div><p>Background</p><p>In Africa, there are several problems with the specific identification of bacteria. Recently, MALDI-TOF mass spectrometry has become a powerful tool for the routine microbial identification in many clinical laboratories.</p><p>Methodology/Principal Findings</p><p>This study was conducted using feces from 347 individuals (162 with diarrhea and 185 without diarrhea) sampled in health centers in Dakar, Senegal. Feces were transported from Dakar to Marseille, France, where they were cultured using different culture conditions. The isolated colonies were identified using MALDI-TOF. If a colony was unidentified, 16S rRNA sequencing was performed. Overall, 2,753 isolates were tested, allowing for the identification of 189 bacteria from 5 phyla, including 2 previously unknown species, 11 species not previously reported in the human gut, 10 species not previously reported in humans, and 3 fungi. 2,718 bacterial isolates (98.8%) out of 2,750 yielded an accurate identification using mass spectrometry, as did the 3 <i>Candida albicans</i> isolates. Thirty-two bacterial isolates not identified by MALDI-TOF (1.2%) were identified by sequencing, allowing for the identification of 2 new species. The number of bacterial species per fecal sample was significantly higher among patients without diarrhea (8.6±3) than in those with diarrhea (7.3±3.4; <i>P</i> = 0.0003). A modification of the gut microbiota was observed between the two groups. In individuals with diarrhea, major commensal bacterial species such as <i>E. coli</i> were significantly decreased (85% versus 64%), as were several <i>Enterococcus</i> spp. (<i>E. faecium</i> and <i>E. casseliflavus</i>) and anaerobes, such as <i>Bacteroides</i> spp. (<i>B. uniformis</i> and <i>B. vulgatus</i>) and <i>Clostridium</i> spp. (<i>C. bifermentans</i>, <i>C. orbiscindens</i>, <i>C. perfringens</i>, and <i>C. symbosium</i>). Conversely, several <i>Bacillus</i> spp. (<i>B. licheniformis</i>, <i>B. mojavensis</i>, and <i>B. pumilus</i>) were significantly more frequent among patients with diarrhea.</p><p>Conclusions/Significance</p><p>MALDI-TOF is a potentially powerful tool for routine bacterial identification in Africa, allowing for a quick identification of bacterial species.</p></div

Population description.

<p>Population description.</p

Culture media and conditionings used in this study.

<p>BCYE: Buffered Charcoal Yeast Extract; BCP: Bromocresol Purple; LAMVAB: Lactobacillus Anaerobic MRS with Vancomycin and Bromocresol green. *from Hartemink <i>et al</i>. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087419#pone.0087419-Hartemink1" target="_blank">[15]</a>.</p

Relative abundance of anaerobic and aerobic genera of the duodenal microbiota.

<p>The source black nodes are the obese and the normal weight groups (five individuals by group). The blue and red nodes are the aerobic and anaerobic genera identified in the groups, respectively. The genus node is linked by an edge to it source node. The genus relative abundance is given by the node size. Finally, two genera shared by the obese and normal weight groups are linked by an additional edge. The Cytoscape network visualization tool version 3.1.0 was used for building this figure.</p

Bacterial species for which significant differences have been observed between individuals with diarrhea and those without diarrhea.

<p>Bacterial species for which significant differences have been observed between individuals with diarrhea and those without diarrhea.</p

Primers used for 16S rRNA PCR and sequencing.

<p>Primers used for 16S rRNA PCR and sequencing.</p

Fatty acid beta-oxidation by duodenal microbiota in obese individuals.

<p>The degradation of fatty acids involves their conversion into Acyl-CoA followed by multiple repetitions of the fatty acid beta-oxidation cycle that leads to the removal each round of two carbon atoms from the acyl chain and to the release of one Acetyl-CoA molecule entering in the Krebs’ cycle. Four key enzymes are involved in the beta-oxidation process, including Acyl-CoA dehydrogenase (FAD), enoyl CoA hydratase, 3-hydroxy acyl CoA dehydrogenase and 3-ketoacyl CoA thiolase. FAD, the first enzyme of fatty acid beta-oxidation, was found to be enriched in the microbiota of obese subjects, suggesting a higher beta-oxidation capacity and energy mobilization in these subjects.</p

Isolates from individuals with diarrhea (D; top) and without diarrhea (ND; bottom).

<p>Each bacterial species corresponds to a node. The edge color represents the phylum (blue: <i>Firmicutes</i>; red: <i>Proteobacteria</i>; green: <i>Bacteroidetes</i>; yellow: <i>Actinobacteria</i>; pink: <i>Fusobacteria</i>). The common and specific bacteria detected from patients with diarrhea and those without are provided.</p