Distinct gut microbiomes in Thai patients with colorectal polyps

Figure 1 Flowchart of participant enrollment. CRC: Colorectal cancer; CT: Control group; HP: Hyperplastic polyps; TA: Tubular adenoma.

Figure 2 Microbial diversity of the gut microbiome in control, hyperplastic polyps, and tubular adenoma groups. A: Box plots show α-diversity between the control (CT) and hyperplastic polyps (HP) groups; B: Box plots show α-diversity between the CT and tubular adenoma (TA) groups; C: Principal coordinate analysis (PCoA) plots show β-diversity between the CT and HP groups; D: PCoA plots show β-diversity the CT and TA groups. PD: Phylogenetic diversity.

Figure 3 Linear discriminant analysis effect size and DESeq2 identified the most enriched microbial species in the control, hyperplastic polyps, and tubular adenoma groups. A: Linear discriminant analysis (LDA) effect size (LEfSe) showed significant microbial differences between the control (CT) and hyperplastic polyps (HP) groups; B: LEfSe showed significant microbial differences the CT and tubular adenoma (TA) groups (LDA score > 2); C: DESeq2 analysis graphs illustrate the log₂ fold differential abundances of microbial species between the CT and HP groups; D: DESeq2 analysis graphs illustrate the log₂ fold differential abundances of microbial species between the CT and TA groups. In the graphs, log₂ fold changes > 0 indicate an increase in the corresponding microbial species, whereas log₂ fold changes < 0 indicate a decrease. Microbial species positioned above the zero threshold demonstrated higher relative abundance in either the HP or TA group compared to the CT group.

Figure 4 Functional differences in the gut microbiome among control, hyperplastic polyps, and tubular adenoma groups. A: PICRUSt2 demonstrated significant differences in the gut microbiome within MetaCyc pathways between the control (CT) and hyperplastic polyps (HP) groups; B: PICRUSt2 demonstrated significant differences in the gut microbiome within MetaCyc pathways between the CT and tubular adenoma (TA) groups.

Figure 5 Microbial interaction network of the gut microbiome. A: Co-occurrence networks were constructed at the species level using abundance data from the control (CT) group; B: Co-occurrence networks were constructed at the species level using abundance data from hyperplastic polyps (HP); C: Co-occurrence networks were constructed at the species level using abundance data from tubular adenoma (TA) group. The figure shows that all nodes had more than five connections. Each node in the network represents a single microbial species. The color of each node corresponds to its degree (i.e. number of connections with other nodes). Nodes are represented as follows, according to their degree: > 20, red; 16-19, orange; 10-15, yellow; and 6-9, pink. Edges between nodes represent correlations between those nodes; blue indicates a positive correlation, whereas red indicates a negative correlation.

Figure 6 Co-occurrence networks and DyNet visualization of synchronized co-occurrence networks. A: The control (CT) and hyperplastic polyps (HP) networks; B: The CT and tubular adenoma (TA) networks. Nodes represent microbial species, whereas edges represent correlation coefficients between microbial species. Green edges are only present in the CT network; red nodes and edges are exclusive to the HP and TA groups; and white nodes and gray edges are shared between the CT and HP groups, as well as the CT and TA groups.