Long-read 16S rRNA amplicon sequencing reveals microbial characteristics in patients with colorectal adenomas and carcinoma lesions in Egypt

Abstract

Background: Colorectal cancer (CRC) is among the five leading causes of cancer incidence and mortality. During the past decade, the role of the gut microbiota and its dysbiosis in colorectal tumorigenesis has been emphasized. Metagenomics and amplicon-based microbiome profiling provided insights into the potential role of microbial dysbiosis in the development of CRC.

Aim: To address the scarcity of information on differential microbiome composition of tumor tissue in comparison to adenomas and the lack of such data from Egyptian patients with CRC.

Materials and methods: Long-read nanopore sequencing of 16S rRNA amplicons was used to profile the colonic microbiota from fresh colonoscopic biopsy samples of Egyptian patients with CRC and patients with colonic polyps.

Results: Species richness of CRC lesions was significantly higher than that in colonic polyps (p-value = 0.0078), while evenness of the CRC group was significantly lower than the colonic polyps group (p-value = 0.0055). Both species richness and Shannon diversity index of the late onset CRC samples were significantly higher than those of the early onset ones. The Firmicutes-to-Bacteroidetes (F/B) ratio was significantly higher in the CRC group than in the colonic polyps group (p-value = 0.0054), and significantly higher in samples from early-onset CRC. The Enterococcus spp. were significantly overabundant in patients with rectal cancer and early-onset CRC, while Staphylococcus spp. were significantly higher in patients with sigmoid cancer and late-onset CRC. In addition, the relative abundance of Fusobacterium nucleatum was significantly higher in CRC patients.

Conclusion: Differentiating trends were identified at phylum, genus, and species levels, despite the inter-individual differences. In summary, this study addressed the microbial dysbiosis associated with CRC and colonic polyps groups, paving the way for a better understanding of the pathogenesis of early and late-onset CRC in Egyptian patients.

Keywords: 16S rRNA; Colonic polyps; Colorectal cancer; Microbiome.

Fig. 1

Distribution of bacterial phyla and families in CRC and colonic polyps groups. Y axis: relative abundance (% of total reads) of reads assigned to the indicated phyla, after unassigned sequences were excluded. X axis: different samples from patients with CRC, polyps, and one ambiguous, undiagnosed case

Fig. 2

Genus distribution (Top panel) and the top 50 species (bottom panel) of the current studied samples

Fig. 3

A color-coded correlation plot indicates five clusters of correlated relative abundance within the microbiome profiles of samples from CRC tissue and colonic polyps

Fig. 4

Alpha diversity analysis: species richness index (A and C), Shannon evenness index (B), and Shannon diversity index (D) in CRC and colonic polyp groups. Differencess between early and late-onset tumors are specifically shown in panels C and D. All differences were tested for significance by the non-parametric Mann-Whitney test. p-values are shown

Fig. 5

Firmicutes/Bacteroidetes(F/B) ratio (A) between CRC and colonic polyps groups, and (B) between the early and late onset of CRC and colonic polyps. p-values were calculated by Mann-Whitney test. (Yes) refers to early onset, and (No) refers to late onset, while the patient age is used as color gradient for each sample point

Fig. 6

Taxon abundance in CRC and colonic polyps groups split by anatomical site

Fig. 7

(A) Taxon abundance at the genus level in CRC and colonic polyps groups split by age; (B) Taxon abundance at the species level in CRC and colonic polyps groups split by age: p-values were calculated by Mann-Whitney test; (Yes) refers to early onset, and (No) refers to late-onset