Direct Analysis of Genes Encoding 16S rRNA from Complex Communities Reveals Many Novel Molecular Species within the Human Gut

• DOI: 10.1128/aem.65.11.4799-4807.1999
• Publication Date: 2019-12-19T19:43:40Z
• Authors: Antonia Suau; Régis Bonnet; Malène Sutren; Jean-Jacques Godon; Glenn R. Gibson; Matthew D. Collins; Joel Doré
• Keywords: Bacteroides thetaiotaomicron; Human feces; Eubacterium; Faecalibacterium prausnitzii; Bacteroides fragilis

The human intestinal tract harbors a complex microbial ecosystem which plays key role in nutrition and health. Although this microbiota has been studied great detail by culture techniques, microscopic counts on feces suggest that 60 to 80% of the observable bacteria cannot be cultivated. Using comparative analysis cloned 16S rRNA gene (rDNA) sequences, we have investigated bacterial diversity (both cultivated noncultivated bacteria) within an adult-male fecal sample. 284 clones obtained from 10-cycle PCR were classified into 82 molecular species (at least 98% similarity). Three phylogenetic groups contained 95% clones: Bacteroides group, Clostridium coccoides leptum subgroup. remaining distributed among variety clusters. Only 24% recovered corresponded described organisms (those whose sequences available public databases), all these established members dominant flora (e.g., thetaiotaomicron, Fusobacterium prausnitzii, Eubacterium rectale). However, majority generated rDNA (76%) did not correspond known clearly derived hitherto unknown gut microflora.