Table 1.
Shared functional dysbiosis between two type 2 diabetes (T2D) cohorts and two Crohn’s disease (CD) cohorts
| ID | Pathway | Carnelian | mi-faser | HUMAnN2 | Kraken2 | Fisher’s p (Carnelian) |
|---|---|---|---|---|---|---|
| (a) Common pathways between Chinese and European T2D cohorts | ||||||
| 00030 | Pentose phosphate pathway | SB | NB | NB | NB | 6.59E −03 |
| 00040 | Pentose and gluconerate interconversions | SB | NB | NB | NB | 9.88E −03 |
| 00051 | Fructose and mannose metabolism | SB | SE | NB | NB | 4.94E −04 |
| 00052 | Galactose metabolism | SB | NB | NB | NB | 4.71E −03 |
| 00061 | Fatty acid biosynthesis | SB | SC | NB | SC | 6.56E −03 |
| 00190 | Oxidative phosphorylation | SB | SE | SC | SE | 4.97E −04 |
| 00250 | Alanine, aspartate, and glutamate metabolism | SB | NB | NB | NB | 1.48E −04 |
| 00290 | Valine, leucine, and isoleucine biosynthesis | SB | SE | NB | NB | 1.68E −05 |
| 00590 | Arachidonic acid metabolism | SB | NB | NB | NB | 2.11E −03 |
| 00600 | Sphingolipid metabolism | SB | SE | NB | SC | 8.86E −05 |
| 00730 | Thiamine metabolism | SB | NB | NB | NB | 2.62E −03 |
| 00983 | Drug metabolism—other enzymes | SB | NB | NB | NB | 2.62E −03 |
| 00195 | Photosynthesis | SB | SB | SC | SB | 2.74E −03 |
| 00254 | Aflatoxin biosynthesis | SC | SC | NB | SB | 1.03E −02 |
| (b) Common pathways between US and Swedish CD cohorts | ||||||
| 00500 | Starch and sucrose metabolism | SB | NB | SS | SS | 4.91E −06 |
| 00620 | Pyruvate metabolism | SB | NB | NB | SS | 4.05E −04 |
| 00640 | Propanoate metabolism | SB | NB | NB | NB | 9.04E −03 |
| 00290 | Valine, leucine, and isoleucine biosynthesis | SB | SS | NB | SS | 5.03E −03 |
| 00450 | Selenocompound metabolism | SB | NB | NB | NB | 8.95E −03 |
| 00460 | Cyanoamino acid metabolism | SB | NB | SS | SS | 8.33E −05 |
| 00513 | Various types of N-glycan biosynthesis | SB | NB | NB | NB | 5.79E −03 |
| 00710 | Carbon fixation in photosynthetic organisms | SB | NB | NB | SS | 1.09E −05 |
| 00410 | Beta-alanine metabolism | NB | SS | NB | SB | 5.79E −01 |
(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