A signature of Prevotella copri and Faecalibacterium prausnitzii depletion, and a link with bacterial glutamate degradation in the Kenyan colorectal cancer patients

Colorectal cancer (CRC) is the fifth most diagnosed cancer in Sub-Saharan Africa. In Kenya, CRC incidence rates tripled from 1997 to 2017. In the Moi Teaching and Referral Hospital, Moi University, there has been an increase in CRC cases, notably for younger patients. A suggested pathobiology for this increase is gut microbiome dysbiosis. Since, for the Kenyan CRC patient population, microbiome studies are rare, there is a need for a better understanding of how microbiome dysbiosis influences CRC epidemiology in Kenya. In this single-center study, the focus was on profiling the gut microbiome of Kenyan CRC patients and healthy volunteers and evaluating associations between microbiome profiles and the age of CRC patients.Colonic tissues from 18 CRC patients and 18 healthy controls were collected during colonoscopy. The inclusion criteria for CRC patients were being FOLFOX chemotherapy-naive, having undergone colonoscopy from a clinicians indication, and having pathologically confirmed CRC at the Moi Teaching and Referral Hospital, Moi University (MTRH/MU). All participants who had taken any probiotic or antibiotic within 4 weeks prior to colonoscopy, and those who previously had resectable CRC were excluded. Study data were collected at the MTRH/MU, which mainly serves residents of the Western Kenya region (representing at least 22 counties) during the period of June-2018 to June-2019. DNA was extracted from tissues collected from 18 CRC patients and 18 healthy controls, using QIAamp DNA Microbiome kits (Qiagen, Hilden, Germany), according to the manufacturers instructions. For all samples, the V4 hypervariable region of the 16S rRNA gene was amplified using 16S V4 amplification primers and sequenced with an Illumina MiSeq platform at the UAB Genomic Core.