Skip to main content
Fig. 3 | BMC Genomics

Fig. 3

From: The taxonomic distribution of histamine-secreting bacteria in the human gut microbiome

Fig. 3

Differential abundance analysis of putative histamine-secreting bacteria. The analysis was performed on stool metagenomic samples between patients with colorectal cancer (CRC), inflammatory bowel disease (IBD) and healthy controls by DESeq2 (A), MaAslin2 (B) and LefSe (C). Relative abundances (counts) were calculated using Kraken2 (2.0.8-beta) (see methods section for more details). The criteria for enriched species for DEseq2 are log2FC > 1 (the Integrative Human Microbiome Project, i.e. HMP2 > 0.5) and q < 0.05, for MaAsLin2 are coef > 0.2 (HMP2 > 0) and q < 0.05, and for LefSe are LDA > 2 and q < 0.001. The statistical differences between all bacteria and histamine-secreting bacteria (HSB) were determined by one-tailed two-proportion Z-test with continuity correction and the p values were converted to asterisks (n.s. for p > 0.05; * for p ≤ 0.05; ** for p ≤ 0.01; *** for p ≤ 0.001 and **** for p ≤ 0.0001). Number of samples by disease state for each study are: Feng 2015 [51]: control = 61, CRC = 46; Vogtmann 2016 [52]: control = 52, CRC = 52; Yu 2017 [53]: control = 75, CRC = 53; Zeller 2014 [54]: control = 66, CRC = 91; Hall 2017 [55]: control = 74, IBD = 188; Franzosa 2019 (discovery cohorts) [56]: control = 34, IBD = 121; HMP2 [57, 58]: control = 429, IBD = 1209; Nielsen 0214 [59]: control = 248, IBD = 148. See also Table S4 for the enrichment of individual species and Table S5 for the detailed results of Z-test

Back to article page