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. 2020 Nov 20;11(11):1374.
doi: 10.3390/genes11111374.

Classification of Changes in the Fecal Microbiota Associated with Colonic Adenomatous Polyps Using a Long-Read Sequencing Platform

Po-Li Wei  1   2   3   4   5 , Ching-Sheng Hung  6   7 , Yi-Wei Kao  8 , Ying-Chin Lin  9   10 , Cheng-Yang Lee  11   12 , Tzu-Hao Chang  12 , Ben-Chang Shia  8 , Jung-Chun Lin  6   13   14
Affiliations

Classification of Changes in the Fecal Microbiota Associated with Colonic Adenomatous Polyps Using a Long-Read Sequencing Platform

Po-Li Wei et al. Genes (Basel). .

Abstract

The microbiota is the community of microorganisms that colonizes the oral cavity, respiratory tract, and gut of multicellular organisms. The microbiota exerts manifold physiological and pathological impacts on the organism it inhabits. A growing body of attention is being paid to host-microbiota interplay, which is highly relevant to the development of carcinogenesis. Adenomatous polyps are considered a common hallmark of colorectal cancer, the second leading cause of carcinogenesis-mediated death worldwide. In this study, we examined the relevance between targeted operational taxonomic units and colonic polyps using short- and long-read sequencing platforms. The gut microbiota was assessed in 132 clinical subjects, including 53 healthy participants, 36 patients with occult blood in the gut, and 43 cases with adenomatous polyps. An elevation in the relative abundance of Klebsiella pneumonia, Fusobacterium varium, and Fusobacterium mortiferum was identified in patients with adenomatous polyps compared with the other groups using long-read sequencing workflow. In contrast, the relatively high abundances of Blautia luti, Bacteroides plebeius, and Prevotella copri were characterized in the healthy groups. The diversities in gut microbiota communities were similar in all recruited samples. These results indicated that alterations in gut microbiota were characteristic of participants with adenomatous polyps, which might be relevant to the further development of CRC. These findings provide a potential contribution to the early prediction and interception of CRC occurrence.

Keywords: Oxford nanopore technology; adenomatous polyp; colorectal cancer; gut microbiota.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Diversity of taxonomic identification between three groups of participants. (A) The α-diversity in all groups was estimated using Shannon indices. (B) Weighted Unifrac principal component analysis (PCA) was performed to evaluate the β-diversity in all groups of participants.
Figure 1
Figure 1
Diversity of taxonomic identification between three groups of participants. (A) The α-diversity in all groups was estimated using Shannon indices. (B) Weighted Unifrac principal component analysis (PCA) was performed to evaluate the β-diversity in all groups of participants.
Figure 2
Figure 2
Distinct composition of microbial community of the healthy group and the OB group with short-read sequencing results. (A) Increases (red bar) or decreases (green bar) in the differential abundance of identified taxa in OB group as compared to the healthy group. (B) The relative abundances of top 20 classified taxa in two groups.
Figure 2
Figure 2
Distinct composition of microbial community of the healthy group and the OB group with short-read sequencing results. (A) Increases (red bar) or decreases (green bar) in the differential abundance of identified taxa in OB group as compared to the healthy group. (B) The relative abundances of top 20 classified taxa in two groups.
Figure 3
Figure 3
Distinct composition of microbial community of the healthy group and the OB group with long-read sequencing results. (A) Increases (red bar) or decreases (green bar) in the differential abundance of identified taxa in OB group as compared to the healthy group. (B) The relative levels of top 20 classified taxa in two groups with MinION results.
Figure 4
Figure 4
Distinct composition of microbial community of the healthy group and the case group with short- and long-read sequencing results. (A) The relative levels of top 25 classified taxa in these two groups with short-read sequencing data. (B) Increases (red bar) or decreases (green bar) in the differential abundance of identified taxa in Case group as compared to the healthy group with MiSeq data. (C) Increases (red bar) or decreases (green bar) in the differential abundance of identified taxa in Case group as compared to the healthy group with MinION results.
Figure 4
Figure 4
Distinct composition of microbial community of the healthy group and the case group with short- and long-read sequencing results. (A) The relative levels of top 25 classified taxa in these two groups with short-read sequencing data. (B) Increases (red bar) or decreases (green bar) in the differential abundance of identified taxa in Case group as compared to the healthy group with MiSeq data. (C) Increases (red bar) or decreases (green bar) in the differential abundance of identified taxa in Case group as compared to the healthy group with MinION results.
Figure 5
Figure 5
Characterization of identified taxa in adenomatous polyp participants and healthy subjects using LEfSe analysis. (A) The relative abundances of the top 30 classified OTUs to species level in healthy group (left) and adenomatous group (right) with MinION data. (B) Histogram of the LDA scores computed for OTUs with differential abundance in the healthy subjects and the participants with adenomatous polyp (case group).
Figure 6
Figure 6
Area under the ROC curve (AUC; red line: ROC curve) for the prediction of (A) adenomatous polyp or (B) occult blood based on the relative abundance of F. mortiferum in fecal samples with the MinION sequencing results.
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