Microbiome signatures associated with clinical stages of gastric Cancer: whole metagenome shotgun sequencing study

Abstract

Background: Gastric cancer is one of the global health concerns. A series of studies on the stomach have confirmed the role of the microbiome in shaping gastrointestinal diseases. Delineation of microbiome signatures to distinguish chronic gastritis from gastric cancer will provide a non-invasive preventative and treatment strategy. In this study, we performed whole metagenome shotgun sequencing of fecal samples to enhance the detection of rare bacterial species and increase genome sequence coverage. Additionally, we employed multiple bioinformatics approaches to investigate the potential targets of the microbiome as an indicator of differentiating gastric cancer from chronic gastritis.

Results: A total of 65 patients were enrolled, comprising 33 individuals with chronic gastritis and 32 with gastric cancer. Within each group, the chronic gastritis group was sub-grouped into intestinal metaplasia (n = 15) and non-intestinal metaplasia (n = 18); the gastric cancer group, early stage (stages 1 and 2, n = 13) and late stage (stages 3 and 4, n = 19) cancer. No significant differences in alpha and beta diversities were detected among the patient groups. However, in a two-group univariate comparison, higher Fusobacteria abundance was identified in phylum; Fusobacteria presented higher abundance in gastric cancer (LDA scored 4.27, q = 0.041 in LEfSe). Age and sex-adjusted MaAsLin and Random Forest variable of importance (VIMP) analysis in species provided meaningful features; Bacteria_caccae was the most contributing species toward gastric cancer and late-stage cancer (beta:2.43, se:0.891, p:0.008, VIMP score:2.543). In contrast, Bifidobacterium_longum significantly contributed to chronic gastritis (beta:-1.8, se:0.699, p:0.009, VIMP score:1.988). Age, sex, and BMI-adjusted MasAsLin on metabolic pathway analysis showed that GLCMANNANAUT-PWY degradation was higher in gastric cancer and one of the contributing species was Fusobacterium_varium.

Conclusion: Microbiomes belonging to the pathogenic phylum Fusobacteria and species Bacteroides_caccae and Streptococcus_anginosus can be significant targets for monitoring the progression of gastric cancer. Whereas Bifidobacterium_longum and Lachnospiraceae_bacterium_5_1_63FAA might be protection biomarkers against gastric cancer.

Keywords: Bacteroides_caccae; Bifidobacterium_longum; Fusobacteria; GLCMANNANAUT-PWY; Lachnospiraceae_bacterium_5_1_63FAA; Streptococcus_anginosus.

Fig. 1

Differential abundance in phylum between chronic gastritis and gastric cancer. Footnote: (A) Y axis: relative abundance by percent value

Fig. 2

LEfSe analysis between chronic gastritis and gastric cancer in the genus

Fig. 3

Heat Tree by Wilcox-Rank Sum test. Footnote: Red color means higher abundance in chronic gastritis (CG). Green color means higher abundance in gastric cancer (GCA)

Fig. 4

Top 30 features by Variable importance by Random Forest. Footnote: Red-colored bars are significant species within 95% CI of VIMP scores

Fig. 5

Important species between chronic gastritis and gastric cancer by MaAsLin and VIMP (VIMP score > 2) A Bacteroides_caccae B Bifidobacterium_longum C Streptococcus_aginosus D Lactobacillus_fermentum E Parabacteroides_distasonis F Oscillibacter_unclassified

Fig. 6

Distribution of microbiome abundance across 4 groups in important 4 species A Bacteroides_caccae B Bifidobacterium_longum C Lactobacillus_mucosae D Eubacterium_rectale