Meta-analysis of 16S rRNA Microbial Data Identified Distinctive and Predictive Microbiota Dysbiosis in Colorectal Carcinoma Adjacent Tissue

Abstract

As research focusing on the colorectal cancer fecal microbiome using shotgun sequencing continues, increasing evidence has supported correlations between colorectal carcinomas (CRCs) and fecal microbiome dysbiosis. However, large-scale on-site and off-site (surrounding adjacent) tissue microbiome characterization of CRC was underrepresented. Here, considering each taxon as a feature, we demonstrate a machine learning-based method to investigate tissue microbial differences among CRC, colorectal adenoma (CRA), and healthy control groups using 16S rRNA data sets retrieved from 15 studies. A total of 2,099 samples were included and analyzed in case-control comparisons. Multiple methods, including differential abundance analysis, random forest classification, cooccurrence network analysis, and Dirichlet multinomial mixture analysis, were conducted to investigate the microbial signatures. We showed that the dysbiosis of the off-site tissue of colonic cancer was distinctive and predictive. The AUCs (areas under the curve) were 80.7%, 96.0%, and 95.8% for CRC versus healthy control random forest models using stool, tissue, and adjacent tissue samples and 69.9%, 91.5%, and 89.5% for the corresponding CRA models, respectively. We also found that the microbiota ecologies of the surrounding adjacent tissues of CRC and CRA were similar to their on-site counterparts according to network analysis. Furthermore, based on the enterotyping of tissue samples, the cohort-specific microbial signature might be the crux in addressing classification generalization problems. Despite cohort heterogeneity, the dysbiosis of lesion-adjacent tissues might provide us with further perspectives in demonstrating the role of the microbiota in colorectal cancer tumorigenesis. IMPORTANCE Turbulent fecal and tissue microbiome dysbiosis of colorectal carcinoma and adenoma has been identified, and some taxa have been proven to be carcinogenic. However, the microbiomes of surrounding adjacent tissues of colonic cancerous tissues were seldom investigated uniformly on a large scale. Here, we characterize the microbiome signatures and dysbiosis of various colonic cancer sample groups. We found a high correlation between colorectal carcinoma adjacent tissue microbiomes and their on-site counterparts. We also discovered that the microbiome dysbiosis in adjacent tissues could discriminate colorectal carcinomas from healthy controls effectively. These results extend our knowledge on the microbial profile of colorectal cancer tissues and highlight microbiota dysbiosis in the surrounding tissues. They also suggest that microbial feature variations of cancerous lesion-adjacent tissues might help to reveal the microbial etiology of colonic cancer and could ultimately be applied for diagnostic and screening purposes.

Identification of microbial markers across populations in early detection of colorectal cancer

“…11), indicating the non-invasive clinical screening tests could be used as complementary characteristics of gut microbiota for early screening of adenoma. Recently, a 16s rRNA analysis showed that microbiome dysbiosis in adjacent tissues could discriminate colorectal adenomas from healthy controls effectively(13), providing a new insight for following research of adenoma biomarkers.…”

“…Furthermore, current knowledge of the associations between microbiome and biomarkers for colorectal adenoma early-detection is poor as well. Only a few studies have investigated the microbial alterations in colorectal adenoma(4, 7, 11-13). However, a substantial variation exists among microbial makers in these studies, and its cause could be various biological factors influencing gut microbiome composition and inconsistent processing of microbial sequencing data.…”

“…Meta-analysis offers a set of tools that is powerful, informative and unbiased to improve the robustness of microbiome alterations and reduce the noise of biological and technical confounders so that consistent alterations across multiple studies could be identified. Recently, several meta-analysis of multi-studies have identified universal microbial markers across multiple diseases, such as CRC(11, 13-15), obese(16), Inflammatory bowel disease (IBD)(17), via 16S rRNA sequencing or whole metagenome shotgun sequencing (WMS) technique. However, previous researches based on meta-analysis(11, 13) still could not identify universal stool-based microbial markers for colorectal cancer across multiple cohorts (Supplementary Note 1).…”

“…Recently, several meta-analysis of multi-studies have identified universal microbial markers across multiple diseases, such as CRC(11, 13-15), obese(16), Inflammatory bowel disease (IBD)(17), via 16S rRNA sequencing or whole metagenome shotgun sequencing (WMS) technique. However, previous researches based on meta-analysis(11, 13) still could not identify universal stool-based microbial markers for colorectal cancer across multiple cohorts (Supplementary Note 1). Additionally, the commonly used non-invasive stool-based screening test, Faecal Immunochemical Test (FIT), has drawbacks such as poor sensitivity to early and advanced adenoma (7.6% and 38%, respectively)(18).…”

Fecal microbiota changes with fermented kimchi intake regulated either formation or advancement of colon adenoma

“…(37) Since better understanding of the role of gut microbiota in either colon adenoma progression or CRC carcinogenesis could provide promising new directions to either prevention or treatment, the discovery of novel biomarkers of the gut microbiome might be of outmost importance. (38)(39)(40) Microorganisms affected the onset and progression of CRC via acceleration of chronic mutagenic inflammation, the biosynthesis of genotoxins that interfere with cell cycle regulation, the production of toxic metabolites, activation of carcinogenic diet compounds, and robust oxidative genotoxic stress, by which altered gut microbiota may allow the outgrowth of bacterial populations that induce genomic mutations or exacerbate tumor-promoting inflammation, concluding large metagenomic studies in CRC-associated microbiome signature significantly tells fundamental role of intestinal microbiota in adenoma-carcinoma sequence. (41) As like in the current investigation denoted in advanced colon adenoma, S. bovis, Helicobacter pylori, B. fragilis, E. faecalis, C. septicum, Fusobacterium spp., and Escherichia coli were reported to be pathogen responsible for colon tumorigenesis including adenocarcinoma.…”