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Background  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.    Methodology/Principal Findings  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  Candida albicans  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;  P  = 0.0003). A modification of the gut microbiota was observed between the two groups. In individuals with diarrhea, major commensal bacterial species such as  E. coli  were significantly decreased (85% versus 64%), as were several  Enterococcus  spp. ( E. faecium  and  E. casseliflavus ) and anaerobes, such as  Bacteroides  spp. ( B. uniformis  and  B. vulgatus ) and  Clostridium  spp. ( C. bifermentans ,  C. orbiscindens ,  C. perfringens , and  C. symbosium ). Conversely, several  Bacillus  spp. ( B. licheniformis ,  B. mojavensis , and  B. pumilus ) were significantly more frequent among patients with diarrhea.    Conclusions/Significance  MALDI-TOF is a potentially powerful tool for routine bacterial identification in Africa, allowing for a quick identification of bacterial species.

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