Phylogenetic Biodiversity of Bacteria Community in the Gut of Diarrhoeic Patients in Rivers State, Nigeria

Abstract

Background: The microbial ecosystem in the human intestine is complex and it plays a great role in health and nutrition. Cultural techniques have been used over the years to study the gut microbiota but studies suggest that a greater percentage of these bacteria found in the gut cannot be cultivated using the conventional methods of bacteria isolation. Aim: To increase understanding in this area, we characterized the bacterial diversity (both cultivated and non-cultivated bacteria) in the gut of diarrhoeic individuals using 16S rRNA gene (rDNA) sequences. Methodology: PCR amplification, sequencing and phylogenetic analysis of the 16S ribosomal DNA (rDNA) sequences were done on 10 diarrhoeic stool samples. Results: After quality filtering and chimeric sequence removal, 72313 sequences from all 10 diarrhoeic stool samples subjected to clustering generated 2767 Operational Taxonomic Units (OTUs) of which 2073 were new and unassigned. Representative sequences of the bacteria OTUs cluster were used to construct a bacteria phylogenetic tree which revealed a wide variety of bacteria Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Tenericutes and Cyanobacteria and others that could not be detected using the cultural techniques. The evolutionary relationship of the most abundant organisms and their contributions from each sample revealed the phylum Firmicutes to be most abundant and therefore have contributed most in the samples followed by Bacteroidetes. Fewer contributions were made by the other phyla Proteobacteria, Actinobacteria, Tenericutes and Cyanobacteria. Conclusion: This study was able to identify culturable and unculturable bacteria in the gut of diarrhoeic people in Rivers state and also show the biodiversity and interrelatedness of these microorganisms using molecular methods. Therefore, we can say that 16S rRNA techniques for detection and identification of predominant bacteria create new opportunities for non-cultivation studies of the human intestinal microflora, proper diagnosis of infectious diseases and new methods of treatments of diseases.