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Table 1 Shared functional dysbiosis between two type 2 diabetes (T2D) cohorts and two Crohn’s disease (CD) cohorts

From: Carnelian uncovers hidden functional patterns across diverse study populations from whole metagenome sequencing reads

IDPathwayCarnelianmi-faserHUMAnN2Kraken2Fisher’s p (Carnelian)
(a) Common pathways between Chinese and European T2D cohorts
00030Pentose phosphate pathwaySBNBNBNB6.59E −03
00040Pentose and gluconerate interconversionsSBNBNBNB9.88E −03
00051Fructose and mannose metabolismSBSENBNB4.94E −04
00052Galactose metabolismSBNBNBNB4.71E −03
00061Fatty acid biosynthesisSBSCNBSC6.56E −03
00190Oxidative phosphorylationSBSESCSE4.97E −04
00250Alanine, aspartate, and glutamate metabolismSBNBNBNB1.48E −04
00290Valine, leucine, and isoleucine biosynthesisSBSENBNB1.68E −05
00590Arachidonic acid metabolismSBNBNBNB2.11E −03
00600Sphingolipid metabolismSBSENBSC8.86E −05
00730Thiamine metabolismSBNBNBNB2.62E −03
00983Drug metabolism—other enzymesSBNBNBNB2.62E −03
00195PhotosynthesisSBSBSCSB2.74E −03
00254Aflatoxin biosynthesisSCSCNBSB1.03E −02
(b) Common pathways between US and Swedish CD cohorts
00500Starch and sucrose metabolismSBNBSSSS4.91E −06
00620Pyruvate metabolismSBNBNBSS4.05E −04
00640Propanoate metabolismSBNBNBNB9.04E −03
00290Valine, leucine, and isoleucine biosynthesisSBSSNBSS5.03E −03
00450Selenocompound metabolismSBNBNBNB8.95E −03
00460Cyanoamino acid metabolismSBNBSSSS8.33E −05
00513Various types of N-glycan biosynthesisSBNBNBNB5.79E −03
00710Carbon fixation in photosynthetic organismsSBNBNBSS1.09E −05
00410Beta-alanine metabolismNBSSNBSB5.79E −01
  1. (a) Common pathways between Chinese and European T2D cohorts which have significantly altered read abundances. We found 13 shared pathways of which 12 are highly relevant to T2D; these pathways are significant in individual cohorts (BH-corrected Wilcoxon rank-sum test p value <0.05) as well as in Fisher’s combined test at p value <0.05 cutoff. On the other hand, mi-faser finds only the photosynthesis pathway and Kraken2 finds the photosynthesis and aflatoxin biosynthesis pathways to be commonly disrupted between both the cohorts; with HUMAnN2-profiles, no overlap at the pathway level was found (Additional file 2: Tables S11–S16). (b) Common pathways between the US and Swedish CD cohorts which have significantly altered read abundances. We identify shared dysbiosis in 8 pathways between the two study cohorts; these pathways are significant in individual cohorts as well as in Fisher’s combined test at p value <0.05 cutoff. On the other hand, only Kraken2 finds the beta-alanine metabolism pathway to be commonly disrupted between both the cohorts; with mi-faser- and HUMAnN2-profiles, no overlap at the pathway level was found (Additional file 3: Tables S23, S24, S27, S28, S31, and S32). SB significant in both the studies, NB detected but not significant in both the studies, SC significant in the Chinese cohort only, SE significant in European cohort only, SU significant in the US cohort only, SS significant in the Swedish cohort only