Table 2 Comparative genomics of the taxa containing MAGs negatively associated with IA seroconversion.
Major species containing negative MAGs (Negative MAGs/Total MAGs) | Module ID | Function description | Enrichment analysisb | Phylogenetic regression analysisc | ||
|---|---|---|---|---|---|---|
Effect size | Q value | Estimate | Q value | |||
Comparison of f__Enterococcaceae (a #4) and f__Lactobacillaceae (a #6) versus f__Streptococcaceae (a #5) | ||||||
Enterococcus faecalis(228/245) | M00550 | Ascorbate degradation, ascorbate => D-xylulose−5P | 1.07 | 3.78E–125 | 3.92 | 1.97E–10 |
Enterococcus_A avium(76/79) | M00061 | D-Glucuronate degradation, D-glucuronate => pyruvate + D-glyceraldehyde 3P | 0.79 | 4.94E–89 | 4.95 | 8.80E–18 |
Enterococcus_B faecium(51/55) | M00631 | D-Galacturonate degradation (bacteria), D-galacturonate => pyruvate + D-glyceraldehyde 3P | 0.76 | 1.40E–83 | 6.43 | 2.15E–18 |
Enterococcus_B faecium_B(18/20) | M00008 | Entner-Doudoroff pathway, glucose-6P => glyceraldehyde-3P + pyruvate | 0.73 | 1.48E–76 | 5.45 | 1.25E-12 |
Enterococcus_D casseliflavus (19/21) | M00006 | Pentose phosphate pathway, oxidative phase, glucose 6P => ribulose 5P | 0.68 | 1.85E–67 | 8.24 | 4.79E–28 |
Enterococcus_D gallinarum (40/42) | M00003 | Gluconeogenesis, oxaloacetate => fructose-6P | 0.65 | 1.68E–75 | 6.53 | 1.12E–15 |
Enterococcus_D sp002850555 (12/12) | M00116 | Menaquinone biosynthesis, chorismate => menaquinol | 0.61 | 4.76E−50 | 10.07 | 2.55E–10 |
Lacticaseibacillus paracasei(100/111) | M00153 | Cytochrome bd ubiquinol oxidase | 0.60 | 3.42E–59 | 9.35 | 1.31E–05 |
Lacticaseibacillus rhamnosus(153/165) | M00308 | Semi-phosphorylative Entner-Doudoroff pathway, gluconate => glycerate-3eP | 0.54 | 9.00E–48 | 6.59 | 3.99E–21 |
Lactiplantibacillus plantarum (33/33) | M00004 | Pentose phosphate pathway (Pentose phosphate cycle) | 0.53 | 2.15E–51 | 14.10 | 1.88E–28 |
Lactobacillus gasseri (19/21) | M00165 | Reductive pentose phosphate cycle (Calvin cycle) | 0.52 | 1.99E–47 | 7.70 | 3.94E–18 |
Lactobacillus paragasseri (8/13) | M00011 | Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate | 0.47 | 7.77E–32 | 7.83 | 7.86E–28 |
Limosilactobacillus fermentum (44/49) | M00532 | Photorespiration | 0.46 | 1.02E–36 | 6.28 | 6.63E–39 |
`Limosilactobacillus oris (16/16) | M00001 | Glycolysis (Embden-Meyerhof pathway), glucose => pyruvate | 0.46 | 1.63E–43 | 19.39 | 7.62E–26 |
Lactococcus lactis (16/28) | M00167 | Reductive pentose phosphate cycle, glyceraldehyde-3P => ribulose-5P | 0.43 | 6.08E–28 | 13.87 | 1.93E–19 |
M00345 | Formaldehyde assimilation, ribulose monophosphate pathway | 0.43 | 5.47E–31 | 19.86 | 6.85E–10 | |
Comparison of o__Burkholderiales (a #3) and o__Enterobacterales (a #2) versus o__Verrucomicrobiales (a #1) | ||||||
Parasutterella excrementihominis(45/45) | M00529 | Denitrification, nitrate => nitrogen | 1.20 | 1.15E–137 | 20.59 | 9.55E–08 |
Parasutterella sp000980495 (26/27) | M00880 | Molybdenum cofactor biosynthesis, GTP => molybdenum cofactor | 1.08 | 3.82E-128 | 11.37 | 2.60E-17 |
Sutterella wadsworthensis (14/14) | M00550 | Ascorbate degradation, ascorbate => D-xylulose-5P | 0.96 | 3.08E–105 | 3.87 | 5.24E–09 |
Enterobacter himalayensis (15/18) | M00804 | Complete nitrification, comammox, ammonia => nitrite => nitrate | 0.81 | 8.55E-83 | 8.19 | 4.38E-29 |
Escherichia coli (226/255) | M00150 | Fumarate reductase, prokaryotes | 0.78 | 2.43E–88 | 15.61 | 9.55E–09 |
Escherichia coli_D (69/76) | M00616 | Sulfate-sulfur assimilation | 0.69 | 1.12E–72 | 4.31 | 1.12E–22 |
Escherichia flexneri (114/130) | M00095 | C5 isoprenoid biosynthesis, mevalonate pathway | 0.69 | 5.94E–71 | 5.76 | 2.92E–16 |
Klebsiella_A oxytoca (12/13) | M00718 | Multidrug resistance, efflux pump MexAB-OprM | 0.67 | 5.63E–61 | 21.27 | 3.85E–43 |
Klebsiella pneumoniae (19/25) | M00546 | Purine degradation, xanthine => urea | 0.65 | 8.20E–58 | 4.92 | 1.44E–19 |
M00167 | Reductive pentose phosphate cycle, glyceraldehyde-3P => ribulose-5P | 0.64 | 2.99E–56 | 16.59 | 1.08E–44 | |
M00879 | Arginine succinyltransferase pathway, arginine => glutamate | 0.63 | 3.97E–64 | 3.93 | 4.92E–21 | |
M00087 | beta-Oxidation | 0.62 | 1.39E–61 | 3.42 | 9.28E–09 | |
M00761 | Undecaprenylphosphate alpha-L-Ara4N biosynthesis, UDP-GlcA => undecaprenyl phosphate alpha-L-Ara4N | 0.56 | 5.70E–51 | 2.89 | 4.27E–08 | |
M00417 | Cytochrome o ubiquinol oxidase | 0.55 | 3.85E–51 | 2.89 | 2.06E–08 | |
M00170 | C4-dicarboxylic acid cycle, phosphoenolpyruvate carboxykinase type | 0.53 | 5.49E–42 | 15.96 | 9.14E–50 | |
M00004 | Pentose phosphate pathway (Pentose phosphate cycle) | 0.52 | 2.09E–40 | 22.59 | 1.10E–17 | |
M00088 | Ketone body biosynthesis, acetyl-CoA => acetoacetate/3-hydroxybutyrate/acetone | 0.51 | 6.75E–43 | 17.61 | 1.11E–11 | |
M00006 | Pentose phosphate pathway, oxidative phase, glucose 6P => ribulose 5P | 0.50 | 7.30E–40 | 5.24 | 5.18E–16 | |
M00615 | Nitrate assimilation | 0.49 | 4.46E–38 | 13.86 | 2.17E–37 | |
M00008 | Entner-Doudoroff pathway, glucose-6P => glyceraldehyde-3P + pyruvate | 0.48 | 7.42E–39 | 9.68 | 7.37E–08 | |
M00165 | Reductive pentose phosphate cycle (Calvin cycle) | 0.48 | 1.03E–38 | 18.87 | 7.92E–22 | |
M00061 | D-Glucuronate degradation, D-glucuronate => pyruvate + D-glyceraldehyde 3P | 0.47 | 2.22E–40 | 2.89 | 8.20E–15 | |
M00345 | Formaldehyde assimilation, ribulose monophosphate pathway | 0.45 | 3.02E–30 | 19.62 | 3.65E–03 | |
M00034 | Methionine salvage pathway | 0.43 | 4.56E–27 | 18.65 | 3.89E–38 | |
M00579 | Phosphate acetyltransferase-acetate kinase pathway, acetyl-CoA => acetate | 0.42 | 2.03E–30 | 4.47 | 1.24E–13 | |
M00631 | D-Galacturonate degradation (bacteria), D-galacturonate => pyruvate + D-glyceraldehyde 3P | 0.41 | 6.69E–31 | 4.41 | 9.77E–26 | |
