In this study first study from South Asia, we assessed the gut microbiome in stool and colonic tissue biopsies of patients with CRC and premalignant lesions, comparing them to the microbiome of healthy age and sex matched individuals and those with diabetes. Interestingly, there were significant differences in the microbiome in colonic tissue samples compared to stool samples in all subgroups, with Fusobacterium, Acinetobacter, Escherichia, Shigella being significantly more abundant in colonic tissue samples with Romboutsia and Prevotella, being the most abundant in stool samples. Although significant variations have been previously observed between stool and colonic biopsy samples, the abundance of bacteria have greatly varied [25, 26]. Bacteroidetes, Fusobacteria and Verrucomicrobia were overabundant in colonic tissue samples of patients with CRC compared to healthy individuals, while Firmicutes and Actinobacteria were the most abundant in tissue samples of healthy individuals. Studies in the US and Sweden also have shown that Actinobacteria and Firmicutes were most abundant in healthy colonic tissue samples, although they did not find a high abundance of Proteobacteria[25] [26]. Fusobacterium have shown to be overabundant in adenomas[9], while many studies have reported a high abundance of Bacteroides species in those with CRC compared to other groups[8, 9].
Interestingly, bacteria belonging to the genus Romboutsia and Prevotella were found to be overabundant in stool samples compared to colonic tissue biopsies. Furthermore, genus Romboutsia was significantly more abundant in stool samples in healthy individuals compared to those with CRC and diabetes. Rombutsia species have shown to be less abundant in individuals with diabetes compared to healthy individuals [27, 28]. However, some have shown that Rombutsia species associate with the presence of non-alcoholic fatty liver disease (NAFLD) and strongly associated with hepatocellular carcinoma (HCC), while it was less abundant in those with diabetes [29, 30]. As many of these studies including ours report associations and patterns of the microbiome in disease and health, it would be important to explore if these bacteria do play a role in NAFLD and HCC and if so, the possible mechanisms involved.
In our cohort, we found that the bacteria of genus Prevotella were one of the most abundant bacteria in stool samples. Prevotella species have shown to associate with plant-based diets, high in fiber and low in fat content, and is highly abundant typically in individuals consuming a non-Western diet [31, 32]. However, there was no difference in the abundance rates of Prevotella species in those with CRC, compared to healthy individuals, those with premalignant lesions or in those with diabetes. This is likely to be due to high consumption of plant-based products in the typical Sri Lankan diet. It would be important to further characterize the different bacteria at species level to understand their roles and to explore the possibility of dietary manipulation to enhance the abundance of favorable microbe species.
As shown in other studies Bacteroides species were found to be overabundant in those with CRC compared to other groups[8, 9]. Although we could not characterize the Bacteriodes species in this study, due to sequencing of the V4 hypervariable region of the 16S RNA, one of our previous studies using quantitative real-time PCR showed that Bacteriodes fragilis was significantly higher in patients with CRC compared to healthy individuals and in those with diabetes [33]. Presence of enterotoxigenic Bacteroides fragilis has shown to be a potential marker for the presence of CRC and was shown to associate with poor prognosis[34, 35]. Bacteroides fragilis has shown to induce tumorigenesis by multiple mechanisms, which include alterations in NFkβ signalling pathways, inducing DNA damage, increasing polyamine metabolism, inducing TH17 cellular responses and by stimulating stem cell activity [35]. Fusobacterium, which has also shown to associate with CRC was found to be enriched especially in colonic tissue samples in those with CRC [10, 36, 37]. We found that those with premalignant lesions had significantly higher frequency of Christensenellaceae, Enterobacteriaceae, Mollicutes and Ruminococcaceae in their stool samples compared to patients with CRC. The presence of Christensenellaceae and Ruminococcaceae were found to be enriched in patients with adenoma previously compared to healthy individuals and have shown to be potential biomarkers for early identification of progression to CRC [38].
In summary, we found that despite marked differences in the Sri Lankan diet compared to the typical Western diet, Bacteroides fragilis and Fusobacterium species were the most abundant in those with CRC, while bacteria of genus Christensenellaceae and Ruminococcaceae were found to be most abundant in those with premalignant lesions. Interestingly, Prevotella species, was one of the most abundant in many individuals, possibly due to the predominant plant-based diet consumed by Sri Lankans. We believe these results pave the way for possible dietary interventions for prevention of CRC in the South Asian population.