Report summary
Explore the associations between microbiota composition of data and external factors provided by the user.
| Created | 30/12/2019 |
|---|---|
| Updated | 31/12/2019 |
| Type | Factor analysis report |
| Project | 20180822 Tomsk SibGMU opisthorchiasis |
| Uploaded samples | 152 |
Metadata
Taxonomic composition
Heatmap of taxonomic composition
The interactive heatmap represents relative abundance of major microbial taxa (columns) in the samples (rows). Using the drop-down list “Heatmap settings” on the right of the heatmap, users can select taxonomic rank of interest. For convenience of comparison between close values, clicking on a cell “freezes” the displayed value of cell on the Legend and additionally the displayed abundance of top 10 taxa of corresponding sample (click again or on the cross near sample name to “unfreeze”). Use the Top control to switch the way of major composition display between the top features in the selected sample and the top features across all samples on the average. Controls at the top and bottom-right allow to change the display of rows and columns.
Analysis of outliers
Automatic filtering of the user samples with extreme taxonomic composition (based on the combined analysis of user and all available external datasets). Analysis of outliers: samples in the upper 1% tail of distribution of median distance between each sample and closest 50% of neighbours approximated by normal distribution. List of outliers:
TGU.11460114, TGU.11200114, TGU.09100414, TGU.11410114
PCoA visualization based on taxonomic composition
Distribution of the samples by their taxonomic composition in reduced dimensionality. The closer the samples (points) on the plot, the more similar their composition. Vectors show the directions in which the levels of the respective major taxa increase. Method of dimension reduction: PCoA (Principal Coordinate Analysis); dissimilarity metric: weighted UniFrac. Clicking on a dot “freezes” the detailed information about the sample on the right of the plot (click again or on the cross near sample name to “unfreeze”). Switch between the display modes with or without outliers and with or without vectors showing major microbial “drivers” using the respective controls.
Alpha-diversity
The measure describes the conditional number of taxa in each sample. Metric: Shannon index. Clicking on a dot “freezes” the displayed value on Y axis and additionally the abundance of top 10 taxa (click on it or on the cross near the sample name to “unfreeze”). In addition, the mean and confidence interval value appear when the mouse is over the boxplot. Controls at the top and bottom-right allow to change the displayed data.
Reconstruction of metabolic potential
Predicted functional composition of microbiota.
Vitamins synthesis
Plots of relative abundance by factor
group
Total relative abundance of the genes involved in vitamins biosynthesis summed across the respective pathways.
KEGG pathways
gender
Total relative abundance of the genes involved in vitamins biosynthesis summed across the respective pathways.
KEGG pathways
Description of pathways
Synthesis of short-chain fatty acids (SCFAs)
Gut microbes are known to produce SCFAs. The boxplots represent median, standard deviation and quartiles of the SCFAs biosynthesis pathways in the samples.
Synthesis of butyrate
Description of pathways
Plots of relative abundance by factor
group
Total relative abundance of the genes involved in butyrate synthesis summed across the respective pathways.
KEGG pathways
gender
Total relative abundance of the genes involved in butyrate synthesis summed across the respective pathways.
KEGG pathways
Synthesis of propionate
Plots of relative abundance by factor
group
Total relative abundance of the genes involved in propionate synthesis summed across the respective pathways.
KEGG pathways
gender
Total relative abundance of the genes involved in propionate synthesis summed across the respective pathways.
KEGG pathways
Description of pathways
Statistical analysis
General difference of community structure between two groups
Test if there are significant differences in overall community composition between the samples of two groups. Method: permutational multivariate analysis of variance (PERMANOVA), beta-diversity metric: weighted UniFrac. The result includes the total number of samples, number of PERMANOVA permutations, p-value for the null hypothesis that there is no difference between the groups, as well as information on the equality of group dispersions (obtained using PERMDISP method with same number of permutations). If the group variations are not equal, the results should be interpreted with caution. Samples-outliers listed in the taxonomic composition section are excluded from this analysis.
| factor | p-value | adjusted p-value | significant | R-squared |
|---|---|---|---|---|
| group | 0.00065 | 0.00065 | True | 0.043396 |
| parameter | value |
|---|---|
| sample size | 141 |
| number of permutations | 20000 |
| significance level | 0.05 |
General difference of metabolic potential structure between two groups
Test if there are significant differences in overall metabolic structure between the samples of two groups. Method: permutational multivariate analysis of variance (PERMANOVA), beta-diversity metric: Bray-Curtis distance. The result includes the total number of samples, number of PERMANOVA permutations, p-value for the null hypothesis that there is no difference between the groups, as well as information on the equality of group dispersions (obtained using PERMDISP method with same number of permutations). If the group variations are not equal, the results should be interpreted with caution. Samples-outliers listed in the taxonomic composition section are excluded from this analysis.
| factor | p-value | adjusted p-value | significant | R-squared |
|---|---|---|---|---|
| group | 0.00005 | 0.00005 | True | 0.053211 |
| parameter | value |
|---|---|
| sample size | 145 |
| number of permutations | 20000 |
| significance level | 0.05 |
Taxonomic composition
Individual microbial taxa for which relative abundance is significantly different between two groups are identified.
Generalized linear mixed effect model
A generalized mixed effects linear model is fitted for each taxon to identify associations with each factor from metadata. If on the average there is >50 samples per each fixed factor coefficient then a zero-inflated negative binomial distribution family is used; in other cases - a negative binomial one. Rare taxa are excluded from the analysis (a taxon must be present in at least 10% of the samples at the level of >0.2%). Multiple testing adjustment is performed using Benjamini–Hochberg procedure. The information about distribution family, terms of the model and sample size is displayed in "Model details" section.
Significant results
The column 'coefficient' contains the value of linear model coefficient. Its sign shows the direction of association between a microbial taxon and a factor - positive or negative. If a factor is categorical (for example, group), it is first decomposed into several factors - one per each value/group. Each of these is viewed as a separate factor relative to the first group (sorted by alphabet).
group
| taxon | taxa level | covariate | group, compared with | coefficient | p-value | adjusted p-value |
|---|---|---|---|---|---|---|
| p__Proteobacteria | phylum | group2_opisth | 1_control | 1.556824 | 2.180910e-09 | 3.053275e-08 |
| p__Bacteroidetes | phylum | group2_opisth | 1_control | 0.639110 | 6.647970e-03 | 3.102386e-02 |
| p__Firmicutes | phylum | group2_opisth | 1_control | -0.140995 | 1.592844e-03 | 1.114990e-02 |
| c__Gammaproteobacteria | class | group2_opisth | 1_control | 1.663769 | 7.704294e-08 | 1.849030e-06 |
| c__Coriobacteriia | class | group3_treat | 1_control | -0.601543 | 3.865960e-03 | 4.639152e-02 |
| o__Enterobacteriales | order | group2_opisth | 1_control | 1.650319 | 1.756915e-06 | 4.919363e-05 |
| o__Actinomycetales | order | group3_treat | 1_control | 0.758452 | 7.584191e-04 | 1.061787e-02 |
| o__Bacteroidales | order | group2_opisth | 1_control | 0.639086 | 6.655221e-03 | 4.658655e-02 |
| o__Coriobacteriales | order | group3_treat | 1_control | -0.601543 | 3.865960e-03 | 3.608229e-02 |
| f__[Barnesiellaceae] | family | group3_treat | 1_control | 1.655771 | 3.239760e-06 | 4.859640e-05 |
| f__Enterobacteriaceae | family | group2_opisth | 1_control | 1.650319 | 1.756915e-06 | 3.513831e-05 |
| f__[Barnesiellaceae] | family | group2_opisth | 1_control | 1.533720 | 1.503000e-05 | 1.503000e-04 |
| f__Porphyromonadaceae | family | group3_treat | 1_control | 1.392214 | 1.685192e-06 | 3.513831e-05 |
| f__Rikenellaceae | family | group2_opisth | 1_control | 1.338708 | 3.951103e-04 | 3.386660e-03 |
| f__[Paraprevotellaceae] | family | group2_opisth | 1_control | 1.179590 | 2.965704e-03 | 1.482852e-02 |
| f__[Odoribacteraceae] | family | group2_opisth | 1_control | 1.085656 | 1.378873e-03 | 8.273237e-03 |
| f__Rikenellaceae | family | group3_treat | 1_control | 1.084456 | 4.312791e-03 | 1.725116e-02 |
| f__Porphyromonadaceae | family | group2_opisth | 1_control | 0.995753 | 5.873588e-04 | 4.405191e-03 |
| f__Bacteroidaceae | family | group2_opisth | 1_control | 0.886295 | 1.266242e-03 | 8.273237e-03 |
| f__Bacteroidaceae | family | group3_treat | 1_control | 0.862616 | 1.800302e-03 | 9.819831e-03 |
| f__Actinomycetaceae | family | group3_treat | 1_control | 0.737600 | 3.763379e-03 | 1.656840e-02 |
| f__Lachnospiraceae | family | group2_opisth | 1_control | -0.292091 | 1.182136e-02 | 4.172245e-02 |
| f__Coriobacteriaceae | family | group3_treat | 1_control | -0.601543 | 3.865960e-03 | 1.656840e-02 |
| f__Veillonellaceae | family | group3_treat | 1_control | -0.824033 | 7.630117e-03 | 2.861294e-02 |
| f__Streptococcaceae | family | group3_treat | 1_control | -1.397689 | 1.119780e-05 | 1.343736e-04 |
| f__Streptococcaceae | family | group2_opisth | 1_control | -1.797006 | 1.477419e-08 | 8.864516e-07 |
| g__u(f__[Barnesiellaceae]) | genus | group3_treat | 1_control | 1.655771 | 3.239760e-06 | 5.291607e-05 |
| g__u(f__Enterobacteriaceae) | genus | group2_opisth | 1_control | 1.654883 | 1.954525e-06 | 4.568115e-05 |
| g__u(f__[Barnesiellaceae]) | genus | group2_opisth | 1_control | 1.533720 | 1.503000e-05 | 1.841174e-04 |
| g__Lachnospira | genus | group2_opisth | 1_control | 1.412889 | 2.330671e-06 | 4.568115e-05 |
| g__Parabacteroides | genus | group3_treat | 1_control | 1.402793 | 1.543734e-06 | 4.568115e-05 |
| g__u(f__Rikenellaceae) | genus | group2_opisth | 1_control | 1.338708 | 3.951103e-04 | 3.872081e-03 |
| g__u(f__Rikenellaceae) | genus | group3_treat | 1_control | 1.084456 | 4.312791e-03 | 2.486197e-02 |
| g__Parabacteroides | genus | group2_opisth | 1_control | 1.006489 | 5.384089e-04 | 4.520836e-03 |
| g__Bacteroides | genus | group2_opisth | 1_control | 0.886295 | 1.266242e-03 | 9.545517e-03 |
| g__Bacteroides | genus | group3_treat | 1_control | 0.862616 | 1.800302e-03 | 1.176198e-02 |
| g__Ruminococcus | genus | group3_treat | 1_control | 0.629764 | 3.492878e-03 | 2.139388e-02 |
| g__[Ruminococcus] | genus | group3_treat | 1_control | 0.595647 | 8.448705e-03 | 4.139865e-02 |
| g__Oscillospira | genus | group3_treat | 1_control | 0.567935 | 1.697020e-03 | 1.176198e-02 |
| g__u(f__Ruminococcaceae) | genus | group3_treat | 1_control | 0.378525 | 9.278835e-03 | 4.330123e-02 |
| g__Clostridium | genus | group3_treat | 1_control | -0.458325 | 4.827906e-03 | 2.628527e-02 |
| g__Blautia | genus | group2_opisth | 1_control | -0.548440 | 5.535717e-04 | 4.520836e-03 |
| g__SMB53 | genus | group2_opisth | 1_control | -0.668148 | 6.541530e-03 | 3.374053e-02 |
| g__u(f__Coriobacteriaceae) | genus | group3_treat | 1_control | -0.940494 | 1.638619e-04 | 1.784274e-03 |
| g__Streptococcus | genus | group3_treat | 1_control | -1.494948 | 5.852839e-06 | 8.193974e-05 |
| g__Streptococcus | genus | group2_opisth | 1_control | -1.770003 | 7.253989e-08 | 7.108909e-06 |
| g__Megasphaera | genus | group3_treat | 1_control | -6.013718 | 1.184401e-06 | 4.568115e-05 |
| g__Bacteroides s__plebeius | species | group2_opisth | 1_control | 2.868277 | 8.190190e-04 | 6.166731e-03 |
| g__Bacteroides s__uniformis | species | group3_treat | 1_control | 2.025598 | 4.781102e-08 | 4.283258e-06 |
| s__u(f__[Barnesiellaceae]) | species | group3_treat | 1_control | 1.655771 | 3.239760e-06 | 5.183616e-05 |
| s__u(f__Enterobacteriaceae) | species | group2_opisth | 1_control | 1.654883 | 1.954525e-06 | 4.261798e-05 |
| g__Parabacteroides s__distasonis | species | group3_treat | 1_control | 1.604829 | 4.774434e-07 | 2.037092e-05 |
| s__u(f__[Barnesiellaceae]) | species | group2_opisth | 1_control | 1.533720 | 1.503000e-05 | 1.748945e-04 |
| g__[Ruminococcus] s__torques | species | group3_treat | 1_control | 1.532031 | 1.579279e-03 | 1.123043e-02 |
| g__Parabacteroides s__distasonis | species | group2_opisth | 1_control | 1.421555 | 7.789630e-06 | 1.018000e-04 |
| s__u(g__Lachnospira) | species | group2_opisth | 1_control | 1.412889 | 2.330671e-06 | 4.261798e-05 |
| g__Bacteroides s__ovatus | species | group3_treat | 1_control | 1.376904 | 2.221761e-06 | 4.261798e-05 |
| s__u(g__Parabacteroides) | species | group3_treat | 1_control | 1.358941 | 6.116395e-05 | 6.524154e-04 |
| s__u(f__Rikenellaceae) | species | group2_opisth | 1_control | 1.338708 | 3.951103e-04 | 3.371608e-03 |
| g__Bacteroides s__ovatus | species | group2_opisth | 1_control | 1.154916 | 6.762329e-05 | 6.658294e-04 |
| g__Bacteroides s__uniformis | species | group2_opisth | 1_control | 1.098751 | 2.950193e-03 | 1.888124e-02 |
| s__u(f__Rikenellaceae) | species | group3_treat | 1_control | 1.084456 | 4.312791e-03 | 2.509260e-02 |
| s__u(g__Parabacteroides) | species | group2_opisth | 1_control | 0.901820 | 7.592293e-03 | 3.737744e-02 |
| s__u(g__Ruminococcus) | species | group3_treat | 1_control | 0.635343 | 3.265886e-03 | 1.990635e-02 |
| s__u(g__Oscillospira) | species | group3_treat | 1_control | 0.567935 | 1.697020e-03 | 1.143255e-02 |
| s__u(f__Ruminococcaceae) | species | group3_treat | 1_control | 0.378525 | 9.278835e-03 | 4.398855e-02 |
| s__u(g__Coprococcus) | species | group2_opisth | 1_control | -0.411024 | 6.957268e-03 | 3.562121e-02 |
| s__u(g__Clostridium) | species | group3_treat | 1_control | -0.445901 | 6.251504e-03 | 3.479098e-02 |
| s__u(g__Blautia) | species | group2_opisth | 1_control | -0.549855 | 6.663562e-04 | 5.330850e-03 |
| s__u(g__SMB53) | species | group2_opisth | 1_control | -0.668148 | 6.541530e-03 | 3.488816e-02 |
| s__u(f__Coriobacteriaceae) | species | group3_treat | 1_control | -0.940494 | 1.638619e-04 | 1.498166e-03 |
| s__u(g__Streptococcus) | species | group3_treat | 1_control | -1.498924 | 7.953129e-06 | 1.018000e-04 |
| s__u(g__Streptococcus) | species | group2_opisth | 1_control | -1.805757 | 6.692590e-08 | 4.283258e-06 |
| s__u(g__Megasphaera) | species | group3_treat | 1_control | -6.013718 | 1.184401e-06 | 3.790084e-05 |
All results of the test
Data filtration summary
Information about filtration of factors and features during the analysis
Metadata after NAs removement
Metadata after removement of NAs, factors with unique or all distinct values
Excluded features
Model details
| trait | state |
|---|---|
| distribution | negative binomial |
| formula | feature_abundance ~ group |
| link function | log |
| number of samples | 145 |
Functional composition
Individual microbial taxa for which relative abundance is significantly different between two groups are identified.
Generalized linear mixed effect model
A generalized mixed effects linear model is fitted for each taxon to identify associations with each factor from metadata. If on the average there is >50 samples per each fixed factor coefficient then a zero-inflated negative binomial distribution family is used; in other cases - a negative binomial one. Rare taxa are excluded from the analysis (a taxon must be present in at least 10% of the samples at the level of >0.2%). Multiple testing adjustment is performed using Benjamini–Hochberg procedure. The information about distribution family, terms of the model and sample size is displayed in "Model details" section.
Significant results
The column 'coefficient' contains the value of linear model coefficient. Its sign shows the direction of association between a microbial taxon and a factor - positive or negative. If a factor is categorical (for example, group), it is first decomposed into several factors - one per each value/group. Each of these is viewed as a separate factor relative to the first group (sorted by alphabet).
group
| pathway | metabolic level | covariate | group, compared with | coefficient | p-value | adjusted p-value |
|---|---|---|---|---|---|---|
| ko03070 : Bacterial secretion system | KEGG pathways | group[T.2_opisth] | 1_control | 0.001485 | 0.000022 | 0.001710 |
| ko00540 : Lipopolysaccharide biosynthesis | KEGG pathways | group[T.2_opisth] | 1_control | 0.001481 | 0.000255 | 0.005060 |
| ko03020 : RNA polymerase | KEGG pathways | group[T.3_treat] | 1_control | 0.001381 | 0.003006 | 0.021043 |
| ko00130 : Ubiquinone and other terpenoid-quinone biosynthesis | KEGG pathways | group[T.2_opisth] | 1_control | 0.001063 | 0.000019 | 0.001710 |
| ko00720 : Carbon fixation pathways in prokaryotes | KEGG pathways | group[T.3_treat] | 1_control | 0.000844 | 0.002544 | 0.018653 |
| ko00061 : Fatty acid biosynthesis | KEGG pathways | group[T.2_opisth] | 1_control | 0.000508 | 0.000137 | 0.004393 |
| ko00620 : Pyruvate metabolism | KEGG pathways | group[T.3_treat] | 1_control | 0.000499 | 0.000143 | 0.004393 |
| ko00620 : Pyruvate metabolism | KEGG pathways | group[T.2_opisth] | 1_control | 0.000449 | 0.000550 | 0.008965 |
| ko01040 : Biosynthesis of unsaturated fatty acids | KEGG pathways | group[T.2_opisth] | 1_control | 0.000391 | 0.001492 | 0.013627 |
| ko00260 : Glycine, serine and threonine metabolism | KEGG pathways | group[T.2_opisth] | 1_control | 0.000340 | 0.000683 | 0.008965 |
| ko00750 : Vitamin B6 metabolism | KEGG pathways | group[T.2_opisth] | 1_control | 0.000335 | 0.000988 | 0.010863 |
| ko00524 : Neomycin, kanamycin and gentamicin biosynthesis | KEGG pathways | group[T.3_treat] | 1_control | 0.000218 | 0.001558 | 0.013627 |
| ko00960 : Tropane, piperidine and pyridine alkaloid biosynthesis | KEGG pathways | group[T.2_opisth] | 1_control | 0.000215 | 0.000073 | 0.003768 |
| ko03410 : Base excision repair | KEGG pathways | group[T.2_opisth] | 1_control | -0.000228 | 0.002518 | 0.018653 |
| ko00290 : Valine, leucine and isoleucine biosynthesis | KEGG pathways | group[T.3_treat] | 1_control | -0.000319 | 0.001593 | 0.013627 |
| ko00523 : Polyketide sugar unit biosynthesis | KEGG pathways | group[T.2_opisth] | 1_control | -0.000362 | 0.000699 | 0.008965 |
| ko00660 : C5-Branched dibasic acid metabolism | KEGG pathways | group[T.2_opisth] | 1_control | -0.000513 | 0.000194 | 0.004986 |
| ko00300 : Lysine biosynthesis | KEGG pathways | group[T.2_opisth] | 1_control | -0.000702 | 0.000263 | 0.005060 |
| ko00680 : Methane metabolism | KEGG pathways | group[T.2_opisth] | 1_control | -0.001853 | 0.000884 | 0.010473 |
| ko00860 : Porphyrin and chlorophyll metabolism | KEGG pathways | group[T.2_opisth] | 1_control | -0.002613 | 0.000648 | 0.008965 |
| ko02010 : ABC transporters | KEGG pathways | group[T.3_treat] | 1_control | -0.004482 | 0.002535 | 0.018653 |
| ko02010 : ABC transporters | KEGG pathways | group[T.2_opisth] | 1_control | -0.004697 | 0.001499 | 0.013627 |
| M00620 : Incomplete reductive citrate cycle, acetyl-CoA => oxoglutarate | KEGG modules | group[T.3_treat] | 1_control | 0.001106 | 0.002221 | 0.014523 |
| M00060 : KDO2-lipid A biosynthesis, Raetz pathway, LpxL-LpxM type | KEGG modules | group[T.2_opisth] | 1_control | 0.000975 | 0.000555 | 0.004630 |
| M00116 : Menaquinone biosynthesis, chorismate => menaquinol | KEGG modules | group[T.2_opisth] | 1_control | 0.000911 | 0.000045 | 0.002164 |
| M00144 : NADH:quinone oxidoreductase, prokaryotes | KEGG modules | group[T.2_opisth] | 1_control | 0.000728 | 0.006841 | 0.027138 |
| M00362 : Nucleotide sugar biosynthesis, prokaryotes | KEGG modules | group[T.2_opisth] | 1_control | 0.000679 | 0.002155 | 0.014487 |
| M00532 : Photorespiration | KEGG modules | group[T.2_opisth] | 1_control | 0.000677 | 0.000031 | 0.002164 |
| M00331 : Type II general secretion pathway | KEGG modules | group[T.2_opisth] | 1_control | 0.000569 | 0.005335 | 0.022652 |
| M00362 : Nucleotide sugar biosynthesis, prokaryotes | KEGG modules | group[T.3_treat] | 1_control | 0.000547 | 0.013387 | 0.044997 |
| M00572 : Pimeloyl-ACP biosynthesis, BioC-BioH pathway, malonyl-ACP => pimeloyl-ACP | KEGG modules | group[T.3_treat] | 1_control | 0.000513 | 0.000124 | 0.002305 |
| M00242 : Zinc transport system | KEGG modules | group[T.2_opisth] | 1_control | 0.000507 | 0.003220 | 0.017314 |
| M00572 : Pimeloyl-ACP biosynthesis, BioC-BioH pathway, malonyl-ACP => pimeloyl-ACP | KEGG modules | group[T.2_opisth] | 1_control | 0.000493 | 0.000205 | 0.002911 |
| M00242 : Zinc transport system | KEGG modules | group[T.3_treat] | 1_control | 0.000490 | 0.004561 | 0.020438 |
| M00124 : Pyridoxal biosynthesis, erythrose-4P => pyridoxal-5P | KEGG modules | group[T.2_opisth] | 1_control | 0.000457 | 0.000050 | 0.002164 |
| M00133 : Polyamine biosynthesis, arginine => agmatine => putrescine => spermidine | KEGG modules | group[T.3_treat] | 1_control | 0.000441 | 0.000155 | 0.002348 |
| M00307 : Pyruvate oxidation, pyruvate => acetyl-CoA | KEGG modules | group[T.3_treat] | 1_control | 0.000416 | 0.000100 | 0.002164 |
| M00549 : Nucleotide sugar biosynthesis, glucose => UDP-glucose | KEGG modules | group[T.2_opisth] | 1_control | 0.000397 | 0.002348 | 0.014952 |
| M00083 : Fatty acid biosynthesis, elongation | KEGG modules | group[T.2_opisth] | 1_control | 0.000378 | 0.000440 | 0.003942 |
| M00035 : Methionine degradation | KEGG modules | group[T.3_treat] | 1_control | 0.000355 | 0.004477 | 0.020438 |
| M00549 : Nucleotide sugar biosynthesis, glucose => UDP-glucose | KEGG modules | group[T.3_treat] | 1_control | 0.000347 | 0.007800 | 0.029779 |
| M00035 : Methionine degradation | KEGG modules | group[T.2_opisth] | 1_control | 0.000334 | 0.007081 | 0.027640 |
| M00021 : Cysteine biosynthesis, serine => cysteine | KEGG modules | group[T.3_treat] | 1_control | 0.000333 | 0.014845 | 0.049213 |
| M00114 : Ascorbate biosynthesis, plants, glucose-6P => ascorbate | KEGG modules | group[T.3_treat] | 1_control | 0.000308 | 0.006711 | 0.027068 |
| M00173 : Reductive citrate cycle (Arnon-Buchanan cycle) | KEGG modules | group[T.2_opisth] | 1_control | 0.000301 | 0.000383 | 0.003710 |
| M00307 : Pyruvate oxidation, pyruvate => acetyl-CoA | KEGG modules | group[T.2_opisth] | 1_control | 0.000297 | 0.004699 | 0.020677 |
| M00017 : Methionine biosynthesis, apartate => homoserine => methionine | KEGG modules | group[T.2_opisth] | 1_control | 0.000286 | 0.000414 | 0.003856 |
| M00628 : beta-Lactam resistance, AmpC system | KEGG modules | group[T.2_opisth] | 1_control | 0.000221 | 0.003218 | 0.017314 |
| M00740 : Methylaspartate cycle | KEGG modules | group[T.3_treat] | 1_control | 0.000180 | 0.008615 | 0.031113 |
| M00432 : Leucine biosynthesis, 2-oxoisovalerate => 2-oxoisocaproate | KEGG modules | group[T.3_treat] | 1_control | 0.000160 | 0.000233 | 0.002911 |
| M00552 : D-galactonate degradation, De Ley-Doudoroff pathway, D-galactonate => glycerate-3P | KEGG modules | group[T.2_opisth] | 1_control | 0.000158 | 0.002659 | 0.016086 |
| M00552 : D-galactonate degradation, De Ley-Doudoroff pathway, D-galactonate => glycerate-3P | KEGG modules | group[T.3_treat] | 1_control | 0.000158 | 0.002893 | 0.017077 |
| M00394 : RNA degradosome | KEGG modules | group[T.2_opisth] | 1_control | 0.000137 | 0.000537 | 0.004630 |
| M00005 : PRPP biosynthesis, ribose 5P => PRPP | KEGG modules | group[T.2_opisth] | 1_control | -0.000150 | 0.003593 | 0.017883 |
| M00271 : PTS system, beta-glucoside-specific II component | KEGG modules | group[T.2_opisth] | 1_control | -0.000193 | 0.008126 | 0.030188 |
| M00271 : PTS system, beta-glucoside-specific II component | KEGG modules | group[T.3_treat] | 1_control | -0.000213 | 0.003708 | 0.017949 |
| M00016 : Lysine biosynthesis, succinyl-DAP pathway, aspartate => lysine | KEGG modules | group[T.3_treat] | 1_control | -0.000240 | 0.007875 | 0.029779 |
| M00582 : Energy-coupling factor transport system | KEGG modules | group[T.2_opisth] | 1_control | -0.000279 | 0.000017 | 0.002164 |
| M00429 : Competence-related DNA transformation transporter | KEGG modules | group[T.2_opisth] | 1_control | -0.000304 | 0.008233 | 0.030188 |
| M00052 : Pyrimidine ribonucleotide biosynthesis, UMP => UDP/UTP,CDP/CTP | KEGG modules | group[T.2_opisth] | 1_control | -0.000318 | 0.004084 | 0.019379 |
| M00579 : Phosphate acetyltransferase-acetate kinase pathway, acetyl-CoA => acetate | KEGG modules | group[T.2_opisth] | 1_control | -0.000319 | 0.000139 | 0.002348 |
| M00434 : PhoR-PhoB (phosphate starvation response) two-component regulatory system | KEGG modules | group[T.2_opisth] | 1_control | -0.000326 | 0.001673 | 0.012270 |
| M00018 : Threonine biosynthesis, aspartate => homoserine => threonine | KEGG modules | group[T.3_treat] | 1_control | -0.000348 | 0.003595 | 0.017883 |
| M00228 : Aspartate/glutamate/glutamine transport system | KEGG modules | group[T.3_treat] | 1_control | -0.000350 | 0.005486 | 0.022889 |
| M00199 : L-Arabinose/lactose transport system | KEGG modules | group[T.2_opisth] | 1_control | -0.000368 | 0.004181 | 0.019458 |
| M00567 : Methanogenesis, CO2 => methane | KEGG modules | group[T.2_opisth] | 1_control | -0.000381 | 0.001762 | 0.012543 |
| M00250 : Lipopolysaccharide transport system | KEGG modules | group[T.2_opisth] | 1_control | -0.000407 | 0.001148 | 0.008683 |
| M00345 : Formaldehyde assimilation, ribulose monophosphate pathway | KEGG modules | group[T.2_opisth] | 1_control | -0.000426 | 0.009324 | 0.032701 |
| M00793 : dTDP-L-rhamnose biosynthesis | KEGG modules | group[T.2_opisth] | 1_control | -0.000460 | 0.003621 | 0.017883 |
| M00205 : N-Acetylglucosamine transport system | KEGG modules | group[T.2_opisth] | 1_control | -0.000477 | 0.000076 | 0.002164 |
| M00018 : Threonine biosynthesis, aspartate => homoserine => threonine | KEGG modules | group[T.2_opisth] | 1_control | -0.000496 | 0.000039 | 0.002164 |
| M00228 : Aspartate/glutamate/glutamine transport system | KEGG modules | group[T.2_opisth] | 1_control | -0.000500 | 0.000086 | 0.002164 |
| M00197 : Putative fructooligosaccharide transport system | KEGG modules | group[T.2_opisth] | 1_control | -0.000511 | 0.000061 | 0.002164 |
| M00742 : Aminoglycoside resistance, protease FtsH | KEGG modules | group[T.2_opisth] | 1_control | -0.000512 | 0.000221 | 0.002911 |
| M00535 : Isoleucine biosynthesis, pyruvate => 2-oxobutanoate | KEGG modules | group[T.2_opisth] | 1_control | -0.000522 | 0.003153 | 0.017314 |
| M00299 : Spermidine/putrescine transport system | KEGG modules | group[T.2_opisth] | 1_control | -0.000532 | 0.003158 | 0.017314 |
| M00216 : Multiple sugar transport system | KEGG modules | group[T.2_opisth] | 1_control | -0.000578 | 0.000082 | 0.002164 |
| M00022 : Shikimate pathway, phosphoenolpyruvate + erythrose-4P => chorismate | KEGG modules | group[T.2_opisth] | 1_control | -0.000586 | 0.000245 | 0.002911 |
| M00236 : Putative polar amino acid transport system | KEGG modules | group[T.3_treat] | 1_control | -0.000675 | 0.012174 | 0.041496 |
| M00377 : Reductive acetyl-CoA pathway (Wood-Ljungdahl pathway) | KEGG modules | group[T.2_opisth] | 1_control | -0.000707 | 0.000090 | 0.002164 |
| M00565 : Trehalose biosynthesis, D-glucose 1P => trehalose | KEGG modules | group[T.2_opisth] | 1_control | -0.000712 | 0.000694 | 0.005421 |
| M00247 : Putative ABC transport system | KEGG modules | group[T.3_treat] | 1_control | -0.000753 | 0.002565 | 0.015917 |
| M00122 : Cobalamin biosynthesis, cobinamide => cobalamin | KEGG modules | group[T.2_opisth] | 1_control | -0.000756 | 0.008743 | 0.031113 |
| M00221 : Putative simple sugar transport system | KEGG modules | group[T.3_treat] | 1_control | -0.000774 | 0.006383 | 0.026182 |
| M00236 : Putative polar amino acid transport system | KEGG modules | group[T.2_opisth] | 1_control | -0.000787 | 0.003425 | 0.017883 |
| M00246 : Nickel transport system | KEGG modules | group[T.2_opisth] | 1_control | -0.000873 | 0.000343 | 0.003458 |
| M00247 : Putative ABC transport system | KEGG modules | group[T.2_opisth] | 1_control | -0.000949 | 0.000153 | 0.002348 |
| M00221 : Putative simple sugar transport system | KEGG modules | group[T.2_opisth] | 1_control | -0.001045 | 0.000253 | 0.002911 |
| M00258 : Putative ABC transport system | KEGG modules | group[T.2_opisth] | 1_control | -0.001247 | 0.009484 | 0.032789 |
| M00157 : F-type ATPase, prokaryotes and chloroplasts | KEGG modules | group[T.3_treat] | 1_control | -0.001290 | 0.000595 | 0.004797 |
| M00157 : F-type ATPase, prokaryotes and chloroplasts | KEGG modules | group[T.2_opisth] | 1_control | -0.001342 | 0.000338 | 0.003458 |
| M00239 : Peptides/nickel transport system | KEGG modules | group[T.3_treat] | 1_control | -0.001892 | 0.001855 | 0.012823 |
| M00519 : YesM-YesN two-component regulatory system | KEGG modules | group[T.2_opisth] | 1_control | -0.001971 | 0.000107 | 0.002164 |
| M00212 : Ribose transport system | KEGG modules | group[T.2_opisth] | 1_control | -0.002399 | 0.000265 | 0.002911 |
| M00207 : Putative multiple sugar transport system | KEGG modules | group[T.2_opisth] | 1_control | -0.003858 | 0.004850 | 0.020959 |
All results of the test
Data filtration summary
Information about filtration of factors and features during the analysis
Metadata after NAs removement
Metadata after removement of NAs, factors with unique or all distinct values
Excluded features
Model details
| trait | state |
|---|---|
| distribution | gaussian |
| formula | feature_abundance ~ group |
| number of samples | 145 |
| transform | arcsin(sqrt) |
Specific pathways
Individual microbial taxa for which relative abundance is significantly different between two groups are identified.
Generalized linear mixed effect model
A generalized mixed effects linear model is fitted for each taxon to identify associations with each factor from metadata. If on the average there is >50 samples per each fixed factor coefficient then a zero-inflated negative binomial distribution family is used; in other cases - a negative binomial one. Rare taxa are excluded from the analysis (a taxon must be present in at least 10% of the samples at the level of >0.2%). Multiple testing adjustment is performed using Benjamini–Hochberg procedure. The information about distribution family, terms of the model and sample size is displayed in "Model details" section.
Significant results
The column 'coefficient' contains the value of linear model coefficient. Its sign shows the direction of association between a microbial taxon and a factor - positive or negative. If a factor is categorical (for example, group), it is first decomposed into several factors - one per each value/group. Each of these is viewed as a separate factor relative to the first group (sorted by alphabet).
group
| pathway | metabolic level | covariate | group, compared with | coefficient | p-value | adjusted p-value |
|---|---|---|---|---|---|---|
| Acetyl-CoA | butyrate | group[T.2_opisth] | 1_control | 0.001432 | 0.000061 | 0.000365 |
| 4-aminobutyrate/Succinate | butyrate | group[T.2_opisth] | 1_control | 0.000311 | 0.006955 | 0.020866 |
| Glutarate | butyrate | group[T.2_opisth] | 1_control | 0.000242 | 0.011568 | 0.023136 |
| K_a | vitamin | group[T.2_opisth] | 1_control | 0.000811 | 0.000027 | 0.000494 |
| B7_a | vitamin | group[T.2_opisth] | 1_control | -0.000272 | 0.004390 | 0.026339 |
| B12_a | vitamin | group[T.3_treat] | 1_control | -0.000996 | 0.006982 | 0.031417 |
| B12_a | vitamin | group[T.2_opisth] | 1_control | -0.001414 | 0.000145 | 0.001305 |
All results of the test
Data filtration summary
Information about filtration of factors and features during the analysis
Metadata after NAs removement
Metadata after removement of NAs, factors with unique or all distinct values
Excluded features
Model details
| trait | state |
|---|---|
| distribution | gaussian |
| formula | feature_abundance ~ group |
| number of samples | 145 |
| transform | arcsin(sqrt) |
Taxa co-occurence analysis
Individual microbial taxa for which relative abundance is significantly different between two groups are identified.
Generalized linear mixed effect model
A generalized mixed effects linear model is fitted for each taxon to identify associations with each factor from metadata. If on the average there is >50 samples per each fixed factor coefficient then a zero-inflated negative binomial distribution family is used; in other cases - a negative binomial one. Rare taxa are excluded from the analysis (a taxon must be present in at least 10% of the samples at the level of >0.2%). Multiple testing adjustment is performed using Benjamini–Hochberg procedure. The information about distribution family, terms of the model and sample size is displayed in "Model details" section.
Significant results
The column 'coefficient' contains the value of linear model coefficient. Its sign shows the direction of association between a microbial taxon and a factor - positive or negative. If a factor is categorical (for example, group), it is first decomposed into several factors - one per each value/group. Each of these is viewed as a separate factor relative to the first group (sorted by alphabet).
group
| taxon | taxa level | covariate | group, compared with | coefficient | p-value | adjusted p-value |
|---|---|---|---|---|---|---|
| coop_6 | cooperatives | group2_opisth | 1_control | 1.517519 | 0.000005 | 0.000064 |
| coop_2 | cooperatives | group3_treat | 1_control | -0.668994 | 0.003834 | 0.019604 |
| coop_4 | cooperatives | group3_treat | 1_control | -1.488518 | 0.004901 | 0.019604 |
All results of the test
Data filtration summary
Information about filtration of factors and features during the analysis
Metadata after NAs removement
Metadata after removement of NAs, factors with unique or all distinct values
Excluded features
Model details
| trait | state |
|---|---|
| distribution | negative binomial |
| formula | feature_abundance ~ group |
| link function | log |
| number of samples | 145 |
Alpha-diversity
Linear mixed effect model is applied to find associations of alpha-diversity with each factor from metadata. Normality of the residuals is tested using Shapiro-Wilk test; if p < 0.05 then the results of linear mixed effects model may be unreliable.
Model details
| parameter | value |
|---|---|
| number of samples | 145 |
| formula | alpha_diversity ~ group |
| Shapiro-Wilk test for residuals, p-value | 0 |
Summary
| covariate | Estimate | p-value |
|---|---|---|
| Intercept | 5.500187 | 1.616346e-87 |
| group[T.2_opisth] | -0.046093 | 7.832967e-01 |
| group[T.3_treat] | -0.079358 | 6.376649e-01 |
datalab:
3.10.0
knb_lib:
4.8.45
knb_interactive:
2.0.2