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

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

Population description.

<p>Population description.</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

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

Representative PFGE patterns of <i>Salmonella</i> Grumpensis from infants with gastroenteritis.

<p>Representative PFGE patterns of <i>Salmonella</i> Grumpensis from infants with gastroenteritis.</p