Leveraging Fecal Bacterial Survey Data to Predict Colorectal Tumors

Abstract

Colorectal cancer (CRC) ranks second in cancer-associated mortality and third in the incidence worldwide. Most of CRC follow adenoma-carcinoma sequence, and have more than 90% chance of survival if diagnosed at early stage. But the recommended screening by colonoscopy is invasive, expensive, and poorly adhered to. Recently, several studies reported that the fecal bacteria might provide non-invasive biomarkers for CRC and precancerous tumors. Therefore, we collected and uniformly re-analyzed these published fecal 16S rDNA sequencing datasets to verify the association and identify biomarkers to classify and predict colorectal tumors by random forest method. A total of 1674 samples (330 CRC, 357 advanced adenoma, 141 adenoma, and 846 control) from 7 studies were analyzed in this study. By random effects model and fixed effects model, we observed significant differences in alpha-diversity and beta-diversity between individuals with CRC and the normal colon, but not between adenoma and the normal. We identified various bacterial genera with significant odds ratios for colorectal tumors at different stages. Through building random forest model with 10-fold cross-validation as well as new test datasets, we classified individuals with CRC, advanced adenoma, adenoma and normal colon. All approaches obtained comparable performance at entire OTU level, entire genus level, and the common genus level as measured using AUC. When combined all samples, the AUC of random forest model based on 12 common genera reached 0.846 for CRC, although the predication performed poorly for advance adenoma and adenoma.

Gut microbial characteristics of adult patients with allergy rhinitis

“…The procedure for DNA extraction of fecal samples (approximately 0.25 g) from non-AR healthy individuals and AR patients, the purity and concentration of the isolated DNAs, the 16S rRNA V3-V4 hypervariable region amplification for the library construction and paired-end sequencing were based on previous procedure [24]. The bioinformatics analysis procedure for raw reads were according to the previously described [24,29].…”

Alteration of the abundance of <em>Parvimonas&nbsp;micra</em> in the gut along the adenoma‑carcinoma sequence

“…Early screening is essential for the prevention of CRC and the survival of patients with CRC, as the 5-year survival rate >90% if CRC is detected at an early stage but decreases to 10% if it is discovered at an advanced metastatic stage (24). Currently, the methods for CRC screening are the fecal occult blood test (FOBT), fecal DNA test, detection of tumor markers and colonoscopy.…”

“…The process of CRC development begins with an aberrant crypt, which evolves into a polyp or adenoma and eventually progresses to CRC over an estimated 10-15 year period (1). Currently, the microbiota associated with CRA have not been consistently identified, and the association between P. micra and CRA remains elusive (23)(24)(25). Therefore, the present study aimed to investigate the association between P. micra and CRA by measuring the changes in the relative abundance of P. micra in stool samples obtained along the adenoma-carcinoma sequence using a qPCR method.…”

Repulsive Guidance Molecule b Deficiency Induces Gut Microbiota Dysbiosis and Increases the Susceptibility to Intestinal Inflammation in Mice

“…The raw paired-end reads were assembled and merged by FLASH ( Magoc and Salzberg, 2011 ; Zhang et al, 2019 ). The PCR primers were subsequently truncated by cutadapt ( Martin, 2011 ).…”