Report summary
Explore the associations between microbiota composition of data and external factors provided by the user.
Created | 07/10/2019 |
---|---|
Updated | 13/11/2020 |
Type | Factor analysis report |
Project | NIIOR CCI (Neurorehabilitation) and ACI (Pneumonia) groups |
Uploaded samples | 82 |
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:
IonXpress.019.run0, IonXpress.006.run1
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
Description of pathways
Plots of relative abundance by factor
Patient_group
Total relative abundance of the genes involved in vitamins biosynthesis summed across the respective pathways.
KEGG 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
Patient_group
Total relative abundance of the genes involved in butyrate synthesis summed across the respective pathways.
KEGG pathways
Synthesis of propionate
Description of pathways
Plots of relative abundance by factor
Patient_group
Total relative abundance of the genes involved in propionate synthesis summed across the respective pathways.
KEGG 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 |
---|---|---|---|---|
Patient_group | 0.046648 | 0.078663 | False | 0.132598 |
Benzoic_acid | 0.029249 | 0.078663 | False | 0.086512 |
Phenyllactic_acid | 0.040948 | 0.078663 | False | 0.080622 |
Hydroxyphenylacetic_acid | 0.056597 | 0.078663 | False | 0.074518 |
Homovanilic_acid | 0.021649 | 0.078663 | False | 0.094858 |
Hydroxyhenyllactic_acid | 0.058997 | 0.078663 | False | 0.073405 |
Hydroxybenzoic_acid | 0.229939 | 0.262787 | False | 0.047412 |
Phenylpropionic_acid | 0.542073 | 0.542073 | False | 0.028714 |
parameter | value |
---|---|
sample size | 21 |
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 |
---|---|---|---|---|
Hydroxyphenylacetic_acid | 0.006550 | 0.052397 | False | 0.177000 |
Hydroxyhenyllactic_acid | 0.016349 | 0.065397 | False | 0.134930 |
Patient_group | 0.097345 | 0.159459 | False | 0.120605 |
Benzoic_acid | 0.112844 | 0.159459 | False | 0.064506 |
Phenylpropionic_acid | 0.110794 | 0.159459 | False | 0.064176 |
Phenyllactic_acid | 0.119594 | 0.159459 | False | 0.061483 |
Homovanilic_acid | 0.272236 | 0.311127 | False | 0.038259 |
Hydroxybenzoic_acid | 0.543623 | 0.543623 | False | 0.019697 |
parameter | value |
---|---|
sample size | 21 |
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).
Phenylpropionic_acid
taxon | taxa level | covariate | coefficient | p-value | adjusted p-value |
---|---|---|---|---|---|
c__Deltaproteobacteria | class | Phenylpropionic_acid | -7.961759 | 2.406830e-03 | 1.856697e-02 |
c__Gemm-1 | class | Phenylpropionic_acid | -53.820416 | 2.046476e-04 | 1.841828e-03 |
o__Pasteurellales | order | Phenylpropionic_acid | 19.503801 | 4.851663e-03 | 3.022959e-02 |
o__u(c__Gemm-1) | order | Phenylpropionic_acid | -53.820416 | 2.046476e-04 | 2.550224e-03 |
f__Prevotellaceae | family | Phenylpropionic_acid | 29.890095 | 4.868477e-04 | 5.842173e-03 |
f__Pasteurellaceae | family | Phenylpropionic_acid | 19.503801 | 4.851663e-03 | 3.472265e-02 |
f__Enterococcaceae | family | Phenylpropionic_acid | -20.224839 | 3.398867e-03 | 2.651733e-02 |
f__u(c__Gemm-1) | family | Phenylpropionic_acid | -53.820416 | 2.046476e-04 | 2.833582e-03 |
g__Prevotella | genus | Phenylpropionic_acid | 29.571692 | 5.094321e-04 | 5.393987e-03 |
g__Dialister | genus | Phenylpropionic_acid | 19.905537 | 1.977507e-06 | 5.932520e-05 |
g__Haemophilus | genus | Phenylpropionic_acid | 18.647642 | 1.096158e-02 | 4.932709e-02 |
g__u(f__Enterococcaceae) | genus | Phenylpropionic_acid | -10.392364 | 1.220859e-13 | 1.648160e-11 |
g__u(f__Planococcaceae) | genus | Phenylpropionic_acid | -13.733566 | 8.892665e-03 | 4.326162e-02 |
g__SMB53 | genus | Phenylpropionic_acid | -19.428554 | 4.599005e-03 | 2.508548e-02 |
g__Enterococcus | genus | Phenylpropionic_acid | -19.902288 | 4.287092e-03 | 2.411489e-02 |
g__u(c__Gemm-1) | genus | Phenylpropionic_acid | -53.820416 | 2.046476e-04 | 2.695358e-03 |
s__u(g__Leuconostoc) | species | Phenylpropionic_acid | 75.921006 | 3.470923e-03 | 2.473033e-02 |
g__Bifidobacterium s__adolescentis | species | Phenylpropionic_acid | 47.548119 | 1.221242e-05 | 2.983319e-04 |
g__Prevotella s__copri | species | Phenylpropionic_acid | 32.277510 | 2.815220e-03 | 2.093055e-02 |
s__u(g__Dialister) | species | Phenylpropionic_acid | 19.905537 | 1.977507e-06 | 6.763073e-05 |
s__u(f__Enterococcaceae) | species | Phenylpropionic_acid | -10.392364 | 1.220859e-13 | 2.087669e-11 |
s__u(f__Planococcaceae) | species | Phenylpropionic_acid | -13.733566 | 8.892665e-03 | 4.985724e-02 |
s__u(g__SMB53) | species | Phenylpropionic_acid | -19.428554 | 4.599005e-03 | 2.939925e-02 |
s__u(g__Enterococcus) | species | Phenylpropionic_acid | -19.838277 | 4.426026e-03 | 2.856040e-02 |
g__[Eubacterium] s__dolichum | species | Phenylpropionic_acid | -28.088237 | 2.004462e-04 | 3.110643e-03 |
s__u(c__Gemm-1) | species | Phenylpropionic_acid | -53.820416 | 2.046476e-04 | 3.110643e-03 |
Benzoic_acid
taxon | taxa level | covariate | coefficient | p-value | adjusted p-value |
---|---|---|---|---|---|
c__Betaproteobacteria | class | Benzoic_acid | 2.234197 | 4.307688e-05 | 5.169226e-04 |
c__Deltaproteobacteria | class | Benzoic_acid | -4.393386 | 5.764295e-08 | 1.556360e-06 |
o__Pseudomonadales | order | Benzoic_acid | 3.994871 | 2.594638e-09 | 2.101657e-07 |
o__Bacillales | order | Benzoic_acid | 2.991335 | 2.188247e-03 | 1.683042e-02 |
o__Burkholderiales | order | Benzoic_acid | 1.829423 | 1.315708e-03 | 1.209666e-02 |
f__u(o__Lactobacillales) | family | Benzoic_acid | 8.638305 | 4.648336e-07 | 1.859334e-05 |
f__Moraxellaceae | family | Benzoic_acid | 6.484438 | 4.844008e-10 | 8.719215e-08 |
f__Staphylococcaceae | family | Benzoic_acid | 4.044193 | 2.926093e-05 | 6.196432e-04 |
f__Clostridiaceae | family | Benzoic_acid | -4.959147 | 7.026369e-04 | 8.159654e-03 |
g__u(o__Lactobacillales) | genus | Benzoic_acid | 8.638305 | 4.648336e-07 | 1.792929e-05 |
g__u(f__Enterococcaceae) | genus | Benzoic_acid | 7.141643 | 5.101006e-17 | 1.377272e-14 |
g__Acinetobacter | genus | Benzoic_acid | 6.692847 | 2.310106e-07 | 1.039548e-05 |
g__Staphylococcus | genus | Benzoic_acid | 4.096773 | 5.421629e-05 | 8.871756e-04 |
g__u(f__[Mogibacteriaceae]) | genus | Benzoic_acid | -2.792287 | 9.964931e-04 | 8.340756e-03 |
g__[Eubacterium] | genus | Benzoic_acid | -4.154815 | 5.982283e-03 | 3.076602e-02 |
g__Coprobacillus | genus | Benzoic_acid | -6.931576 | 5.113653e-03 | 2.707228e-02 |
g__SMB53 | genus | Benzoic_acid | -7.233358 | 4.852715e-04 | 5.376877e-03 |
g__u(f__Clostridiaceae) | genus | Benzoic_acid | -9.528443 | 7.625435e-06 | 1.960826e-04 |
g__Desulfovibrio | genus | Benzoic_acid | -14.551666 | 3.051534e-04 | 3.880240e-03 |
g__Bifidobacterium s__adolescentis | species | Benzoic_acid | 14.829775 | 3.463986e-07 | 1.579578e-05 |
s__u(o__Lactobacillales) | species | Benzoic_acid | 8.638305 | 4.648336e-07 | 1.987164e-05 |
s__u(f__Enterococcaceae) | species | Benzoic_acid | 7.141643 | 5.101006e-17 | 1.744544e-14 |
s__u(g__Acinetobacter) | species | Benzoic_acid | 6.917941 | 3.236464e-06 | 1.054162e-04 |
g__Staphylococcus s__aureus | species | Benzoic_acid | 5.107119 | 1.956799e-04 | 3.110643e-03 |
s__u(f__[Mogibacteriaceae]) | species | Benzoic_acid | -2.792287 | 9.964931e-04 | 9.737161e-03 |
g__Bacteroides s__uniformis | species | Benzoic_acid | -4.413446 | 8.029990e-03 | 4.577094e-02 |
s__u(g__SMB53) | species | Benzoic_acid | -7.233358 | 4.852715e-04 | 6.383186e-03 |
s__u(f__Clostridiaceae) | species | Benzoic_acid | -9.528443 | 7.625435e-06 | 2.173249e-04 |
s__u(g__Collinsella) | species | Benzoic_acid | -18.470681 | 7.789748e-03 | 4.477469e-02 |
Hydroxyhenyllactic_acid
taxon | taxa level | covariate | coefficient | p-value | adjusted p-value |
---|---|---|---|---|---|
p__Proteobacteria | phylum | Hydroxyhenyllactic_acid | -2.822900 | 1.909307e-04 | 3.436752e-03 |
c__Deltaproteobacteria | class | Hydroxyhenyllactic_acid | 3.420558 | 1.083594e-07 | 2.340563e-06 |
c__Gammaproteobacteria | class | Hydroxyhenyllactic_acid | -3.228993 | 7.752779e-05 | 7.611819e-04 |
o__Burkholderiales | order | Hydroxyhenyllactic_acid | 2.623787 | 7.584024e-03 | 4.312791e-02 |
o__Clostridiales | order | Hydroxyhenyllactic_acid | 2.030824 | 7.567451e-03 | 4.312791e-02 |
o__Pseudomonadales | order | Hydroxyhenyllactic_acid | -2.350896 | 1.047022e-03 | 1.130783e-02 |
o__Enterobacteriales | order | Hydroxyhenyllactic_acid | -3.712437 | 2.263045e-06 | 5.080191e-05 |
o__Pasteurellales | order | Hydroxyhenyllactic_acid | -7.047295 | 6.625149e-06 | 1.073274e-04 |
f__[Paraprevotellaceae] | family | Hydroxyhenyllactic_acid | 4.653515 | 3.707442e-03 | 2.780581e-02 |
f__u(o__Clostridiales) | family | Hydroxyhenyllactic_acid | 3.869347 | 1.325812e-08 | 7.954870e-07 |
f__[Mogibacteriaceae] | family | Hydroxyhenyllactic_acid | 2.884096 | 1.834956e-03 | 1.651460e-02 |
f__Lachnospiraceae | family | Hydroxyhenyllactic_acid | 2.644187 | 4.079871e-03 | 2.997456e-02 |
f__Pseudomonadaceae | family | Hydroxyhenyllactic_acid | -2.639135 | 3.461985e-03 | 2.651733e-02 |
f__Enterobacteriaceae | family | Hydroxyhenyllactic_acid | -3.712437 | 2.263045e-06 | 6.789134e-05 |
f__Moraxellaceae | family | Hydroxyhenyllactic_acid | -3.850282 | 2.775503e-03 | 2.270866e-02 |
f__Pasteurellaceae | family | Hydroxyhenyllactic_acid | -7.047295 | 6.625149e-06 | 1.703610e-04 |
g__Desulfovibrio | genus | Hydroxyhenyllactic_acid | 13.694593 | 6.243698e-04 | 6.243698e-03 |
g__SMB53 | genus | Hydroxyhenyllactic_acid | 7.603796 | 1.318936e-03 | 1.017465e-02 |
g__Blautia | genus | Hydroxyhenyllactic_acid | 5.711964 | 1.348603e-03 | 1.025698e-02 |
g__u(f__Clostridiaceae) | genus | Hydroxyhenyllactic_acid | 4.825021 | 2.958845e-03 | 1.836524e-02 |
g__Coprobacillus | genus | Hydroxyhenyllactic_acid | 4.732232 | 1.328107e-04 | 1.887310e-03 |
g__Clostridium | genus | Hydroxyhenyllactic_acid | 4.261404 | 9.268746e-03 | 4.408802e-02 |
g__u(o__Clostridiales) | genus | Hydroxyhenyllactic_acid | 3.869347 | 1.325812e-08 | 8.949228e-07 |
g__Coprococcus | genus | Hydroxyhenyllactic_acid | 3.591224 | 1.896006e-03 | 1.315472e-02 |
g__u(f__Erysipelotrichaceae) | genus | Hydroxyhenyllactic_acid | 3.588981 | 1.752619e-03 | 1.251892e-02 |
g__Oscillospira | genus | Hydroxyhenyllactic_acid | 3.326935 | 3.291136e-04 | 3.949363e-03 |
g__Dorea | genus | Hydroxyhenyllactic_acid | 3.314311 | 1.003980e-03 | 8.340756e-03 |
g__u(f__[Mogibacteriaceae]) | genus | Hydroxyhenyllactic_acid | 2.765707 | 1.954628e-03 | 1.315472e-02 |
g__Ruminococcus | genus | Hydroxyhenyllactic_acid | 2.279228 | 4.762940e-03 | 2.549282e-02 |
g__u(f__Enterobacteriaceae) | genus | Hydroxyhenyllactic_acid | -3.501788 | 9.247691e-06 | 2.171197e-04 |
g__Acinetobacter | genus | Hydroxyhenyllactic_acid | -4.514676 | 3.757440e-03 | 2.247184e-02 |
g__Erwinia | genus | Hydroxyhenyllactic_acid | -5.893127 | 2.803499e-03 | 1.786995e-02 |
g__Serratia | genus | Hydroxyhenyllactic_acid | -6.634214 | 8.542222e-06 | 2.096727e-04 |
g__Haemophilus | genus | Hydroxyhenyllactic_acid | -6.876743 | 1.991352e-05 | 3.931660e-04 |
g__Klebsiella | genus | Hydroxyhenyllactic_acid | -7.366464 | 2.184256e-05 | 3.931660e-04 |
s__u(g__SMB53) | species | Hydroxyhenyllactic_acid | 7.603796 | 1.318936e-03 | 1.219125e-02 |
s__u(g__Blautia) | species | Hydroxyhenyllactic_acid | 5.464113 | 4.249770e-03 | 2.822177e-02 |
s__u(f__Clostridiaceae) | species | Hydroxyhenyllactic_acid | 4.825021 | 2.958845e-03 | 2.130368e-02 |
s__u(g__Clostridium) | species | Hydroxyhenyllactic_acid | 4.577019 | 6.407081e-03 | 3.878268e-02 |
s__u(o__Clostridiales) | species | Hydroxyhenyllactic_acid | 3.869347 | 1.325812e-08 | 8.244138e-07 |
s__u(f__Erysipelotrichaceae) | species | Hydroxyhenyllactic_acid | 3.588981 | 1.752619e-03 | 1.498489e-02 |
s__u(g__Coprococcus) | species | Hydroxyhenyllactic_acid | 3.585301 | 1.972510e-03 | 1.575744e-02 |
s__u(g__Dorea) | species | Hydroxyhenyllactic_acid | 3.484300 | 7.793402e-04 | 8.461408e-03 |
s__u(g__Oscillospira) | species | Hydroxyhenyllactic_acid | 3.326935 | 3.291136e-04 | 4.502274e-03 |
s__u(f__[Mogibacteriaceae]) | species | Hydroxyhenyllactic_acid | 2.765707 | 1.954628e-03 | 1.575744e-02 |
s__u(f__Enterobacteriaceae) | species | Hydroxyhenyllactic_acid | -3.501788 | 9.247691e-06 | 2.530168e-04 |
g__Serratia s__marcescens | species | Hydroxyhenyllactic_acid | -5.932271 | 1.405659e-04 | 2.345051e-03 |
s__u(g__Erwinia) | species | Hydroxyhenyllactic_acid | -6.331635 | 5.826650e-04 | 6.991979e-03 |
s__u(g__Serratia) | species | Hydroxyhenyllactic_acid | -6.948419 | 7.293152e-04 | 8.045994e-03 |
s__u(g__Haemophilus) | species | Hydroxyhenyllactic_acid | -6.959580 | 4.847679e-05 | 9.752389e-04 |
s__u(g__Klebsiella) | species | Hydroxyhenyllactic_acid | -7.366464 | 2.184256e-05 | 4.980103e-04 |
g__Bifidobacterium s__adolescentis | species | Hydroxyhenyllactic_acid | -17.544006 | 2.667302e-09 | 2.027150e-07 |
Phenyllactic_acid
taxon | taxa level | covariate | coefficient | p-value | adjusted p-value |
---|---|---|---|---|---|
c__Deltaproteobacteria | class | Phenyllactic_acid | -12.642070 | 2.406918e-09 | 2.599472e-07 |
o__Pasteurellales | order | Phenyllactic_acid | 15.734853 | 9.198400e-05 | 1.354673e-03 |
o__Pseudomonadales | order | Phenyllactic_acid | 6.156024 | 2.285612e-03 | 1.683042e-02 |
o__Burkholderiales | order | Phenyllactic_acid | -8.349144 | 1.183436e-03 | 1.198229e-02 |
f__Pasteurellaceae | family | Phenyllactic_acid | 15.734853 | 9.198400e-05 | 1.655712e-03 |
f__Moraxellaceae | family | Phenyllactic_acid | 10.199586 | 3.069759e-03 | 2.455807e-02 |
f__Lachnospiraceae | family | Phenyllactic_acid | -7.993247 | 7.288475e-03 | 4.603247e-02 |
f__[Mogibacteriaceae] | family | Phenyllactic_acid | -9.289656 | 2.180455e-03 | 1.868962e-02 |
f__u(o__Clostridiales) | family | Phenyllactic_acid | -9.815726 | 1.018422e-05 | 2.444212e-04 |
f__u(o__Lactobacillales) | family | Phenyllactic_acid | -11.556871 | 1.642176e-03 | 1.515855e-02 |
f__[Paraprevotellaceae] | family | Phenyllactic_acid | -13.092014 | 5.360609e-03 | 3.641168e-02 |
f__Alcaligenaceae | family | Phenyllactic_acid | -18.599852 | 3.795817e-04 | 4.880336e-03 |
g__Haemophilus | genus | Phenyllactic_acid | 15.989579 | 1.669303e-04 | 2.253559e-03 |
g__Acinetobacter | genus | Phenyllactic_acid | 12.068977 | 3.942719e-03 | 2.264966e-02 |
g__Ruminococcus | genus | Phenyllactic_acid | -7.491525 | 5.622213e-03 | 2.919226e-02 |
g__u(f__Enterococcaceae) | genus | Phenyllactic_acid | -8.101321 | 5.688220e-09 | 4.388055e-07 |
g__u(f__[Mogibacteriaceae]) | genus | Phenyllactic_acid | -8.886087 | 2.390909e-03 | 1.555531e-02 |
g__Dorea | genus | Phenyllactic_acid | -9.307245 | 2.812863e-03 | 1.786995e-02 |
g__Oscillospira | genus | Phenyllactic_acid | -9.731724 | 7.144988e-04 | 7.004096e-03 |
g__u(o__Clostridiales) | genus | Phenyllactic_acid | -9.815726 | 1.018422e-05 | 2.291449e-04 |
g__Coprococcus | genus | Phenyllactic_acid | -10.504428 | 5.466271e-03 | 2.865812e-02 |
g__u(o__Lactobacillales) | genus | Phenyllactic_acid | -11.556871 | 1.642176e-03 | 1.231632e-02 |
g__u(f__Erysipelotrichaceae) | genus | Phenyllactic_acid | -12.437351 | 5.350209e-04 | 5.451157e-03 |
g__Coprobacillus | genus | Phenyllactic_acid | -14.072155 | 5.315233e-04 | 5.451157e-03 |
g__u(f__Rikenellaceae) | genus | Phenyllactic_acid | -14.196658 | 9.307472e-03 | 4.408802e-02 |
g__Blautia | genus | Phenyllactic_acid | -20.070512 | 1.761922e-03 | 1.251892e-02 |
g__Desulfovibrio | genus | Phenyllactic_acid | -38.583618 | 3.161677e-04 | 3.880240e-03 |
g__Bifidobacterium s__adolescentis | species | Phenyllactic_acid | 54.676727 | 2.212641e-10 | 3.026892e-08 |
s__u(g__Haemophilus) | species | Phenyllactic_acid | 15.869765 | 5.775299e-04 | 6.991979e-03 |
s__u(g__Erwinia) | species | Phenyllactic_acid | 10.389094 | 4.667731e-03 | 2.956230e-02 |
s__u(f__Enterococcaceae) | species | Phenyllactic_acid | -8.101321 | 5.688220e-09 | 3.890742e-07 |
s__u(f__[Mogibacteriaceae]) | species | Phenyllactic_acid | -8.886087 | 2.390909e-03 | 1.817091e-02 |
s__u(g__Oscillospira) | species | Phenyllactic_acid | -9.731724 | 7.144988e-04 | 8.045994e-03 |
s__u(o__Clostridiales) | species | Phenyllactic_acid | -9.815726 | 1.018422e-05 | 2.679233e-04 |
s__u(g__Dorea) | species | Phenyllactic_acid | -9.896778 | 1.619716e-03 | 1.457745e-02 |
s__u(g__Coprococcus) | species | Phenyllactic_acid | -10.483624 | 5.664514e-03 | 3.522298e-02 |
s__u(o__Lactobacillales) | species | Phenyllactic_acid | -11.556871 | 1.642176e-03 | 1.458764e-02 |
s__u(f__Erysipelotrichaceae) | species | Phenyllactic_acid | -12.437351 | 5.350209e-04 | 6.776932e-03 |
s__u(g__Blautia) | species | Phenyllactic_acid | -18.596241 | 7.705251e-03 | 4.477469e-02 |
Hydroxybenzoic_acid
taxon | taxa level | covariate | coefficient | p-value | adjusted p-value |
---|---|---|---|---|---|
c__Gammaproteobacteria | class | Hydroxybenzoic_acid | 15.489656 | 0.005895 | 0.037452 |
c__Bacilli | class | Hydroxybenzoic_acid | -12.464043 | 0.002242 | 0.018567 |
o__Enterobacteriales | order | Hydroxybenzoic_acid | 15.239778 | 0.002650 | 0.018665 |
o__Desulfovibrionales | order | Hydroxybenzoic_acid | 12.277046 | 0.009118 | 0.047647 |
o__Bacillales | order | Hydroxybenzoic_acid | -15.580186 | 0.002851 | 0.019246 |
o__Actinomycetales | order | Hydroxybenzoic_acid | -21.102770 | 0.001038 | 0.011308 |
f__Enterobacteriaceae | family | Hydroxybenzoic_acid | 15.239778 | 0.002650 | 0.022186 |
f__Veillonellaceae | family | Hydroxybenzoic_acid | 13.623764 | 0.005145 | 0.035622 |
f__Planococcaceae | family | Hydroxybenzoic_acid | -14.919938 | 0.005817 | 0.038075 |
f__Carnobacteriaceae | family | Hydroxybenzoic_acid | -19.667860 | 0.005712 | 0.038075 |
f__Enterococcaceae | family | Hydroxybenzoic_acid | -21.210594 | 0.000067 | 0.001341 |
g__Faecalibacterium | genus | Hydroxybenzoic_acid | 25.258935 | 0.001973 | 0.013155 |
g__Bilophila | genus | Hydroxybenzoic_acid | 24.872088 | 0.000021 | 0.000393 |
g__Phascolarctobacterium | genus | Hydroxybenzoic_acid | 21.084824 | 0.001712 | 0.012490 |
g__Erwinia | genus | Hydroxybenzoic_acid | 19.293833 | 0.000932 | 0.008118 |
g__u(f__Enterobacteriaceae) | genus | Hydroxybenzoic_acid | 14.771435 | 0.003534 | 0.021618 |
g__Ruminococcus | genus | Hydroxybenzoic_acid | 10.441188 | 0.003563 | 0.021618 |
g__u(f__Planococcaceae) | genus | Hydroxybenzoic_acid | -15.361156 | 0.002958 | 0.018365 |
g__Enterococcus | genus | Hydroxybenzoic_acid | -21.330801 | 0.000063 | 0.001005 |
g__Granulicatella | genus | Hydroxybenzoic_acid | -21.588769 | 0.004419 | 0.024348 |
g__Bifidobacterium s__adolescentis | species | Hydroxybenzoic_acid | 49.928473 | 0.000035 | 0.000725 |
g__Faecalibacterium s__prausnitzii | species | Hydroxybenzoic_acid | 25.258935 | 0.001973 | 0.015757 |
s__u(g__Bilophila) | species | Hydroxybenzoic_acid | 24.872088 | 0.000021 | 0.000498 |
s__u(g__Erwinia) | species | Hydroxybenzoic_acid | 22.664876 | 0.000070 | 0.001257 |
s__u(g__Phascolarctobacterium) | species | Hydroxybenzoic_acid | 21.084824 | 0.001712 | 0.014981 |
g__Serratia s__marcescens | species | Hydroxybenzoic_acid | 17.956278 | 0.006481 | 0.038886 |
s__u(f__Enterobacteriaceae) | species | Hydroxybenzoic_acid | 14.771435 | 0.003534 | 0.024918 |
s__u(g__Ruminococcus) | species | Hydroxybenzoic_acid | 10.867578 | 0.002956 | 0.021304 |
s__u(f__Planococcaceae) | species | Hydroxybenzoic_acid | -15.361156 | 0.002958 | 0.021304 |
s__u(g__Enterococcus) | species | Hydroxybenzoic_acid | -21.317420 | 0.000064 | 0.001210 |
s__u(g__Granulicatella) | species | Hydroxybenzoic_acid | -21.588769 | 0.004419 | 0.028560 |
Patient_group
taxon | taxa level | covariate | group, compared with | coefficient | p-value | adjusted p-value |
---|---|---|---|---|---|---|
c__Deltaproteobacteria | class | Patient_groupTrauma | Neurorehabilitation | 5.600123 | 4.092050e-08 | 1.473138e-06 |
c__Betaproteobacteria | class | Patient_groupPneumonia | Neurorehabilitation | 2.092439 | 4.944731e-07 | 8.900515e-06 |
c__Deltaproteobacteria | class | Patient_groupPneumonia | Neurorehabilitation | 1.759088 | 3.981395e-06 | 6.066713e-05 |
o__Desulfovibrionales | order | Patient_groupTrauma | Neurorehabilitation | 5.773398 | 1.642004e-04 | 2.216705e-03 |
o__Desulfovibrionales | order | Patient_groupPneumonia | Neurorehabilitation | 3.627081 | 6.525986e-06 | 1.073274e-04 |
o__Burkholderiales | order | Patient_groupPneumonia | Neurorehabilitation | 2.260611 | 1.178411e-06 | 3.181709e-05 |
o__Gemellales | order | Patient_groupPneumonia | Neurorehabilitation | 1.911572 | 1.486337e-03 | 1.267298e-02 |
o__Burkholderiales | order | Patient_groupTrauma | Neurorehabilitation | 1.552510 | 7.899790e-03 | 4.312791e-02 |
o__Enterobacteriales | order | Patient_groupPneumonia | Neurorehabilitation | 1.315139 | 7.986650e-03 | 4.312791e-02 |
o__Bacillales | order | Patient_groupTrauma | Neurorehabilitation | -4.608350 | 1.916587e-03 | 1.552435e-02 |
f__Alcaligenaceae | family | Patient_groupTrauma | Neurorehabilitation | 8.338701 | 2.020857e-03 | 1.774411e-02 |
f__Desulfovibrionaceae | family | Patient_groupTrauma | Neurorehabilitation | 5.773398 | 1.642004e-04 | 2.552614e-03 |
f__Desulfovibrionaceae | family | Patient_groupPneumonia | Neurorehabilitation | 3.627081 | 6.525986e-06 | 1.703610e-04 |
f__Alcaligenaceae | family | Patient_groupPneumonia | Neurorehabilitation | 3.295221 | 7.911108e-04 | 8.899996e-03 |
f__Enterobacteriaceae | family | Patient_groupPneumonia | Neurorehabilitation | 1.315139 | 7.986650e-03 | 4.957231e-02 |
f__Leuconostocaceae | family | Patient_groupPneumonia | Neurorehabilitation | -3.587560 | 4.280799e-04 | 5.314095e-03 |
f__Rikenellaceae | family | Patient_groupPneumonia | Neurorehabilitation | -3.916056 | 8.209125e-04 | 8.955409e-03 |
f__Carnobacteriaceae | family | Patient_groupPneumonia | Neurorehabilitation | -4.017464 | 1.772649e-04 | 2.552614e-03 |
f__Staphylococcaceae | family | Patient_groupTrauma | Neurorehabilitation | -5.315829 | 3.429716e-04 | 4.572955e-03 |
f__u(o__Lactobacillales) | family | Patient_groupTrauma | Neurorehabilitation | -10.756858 | 3.353930e-07 | 1.509269e-05 |
g__Desulfovibrio | genus | Patient_groupTrauma | Neurorehabilitation | 18.980071 | 1.175994e-03 | 9.338775e-03 |
g__u(f__Clostridiaceae) | genus | Patient_groupTrauma | Neurorehabilitation | 8.445413 | 7.263507e-04 | 7.004096e-03 |
g__Desulfovibrio | genus | Patient_groupPneumonia | Neurorehabilitation | 7.657947 | 1.077666e-04 | 1.572809e-03 |
g__SMB53 | genus | Patient_groupTrauma | Neurorehabilitation | 7.344928 | 6.784244e-03 | 3.392122e-02 |
g__u(f__Christensenellaceae) | genus | Patient_groupTrauma | Neurorehabilitation | 6.643681 | 3.862302e-03 | 2.247184e-02 |
g__Bilophila | genus | Patient_groupTrauma | Neurorehabilitation | 4.175977 | 1.491380e-04 | 2.064987e-03 |
g__u(f__[Mogibacteriaceae]) | genus | Patient_groupTrauma | Neurorehabilitation | 3.775699 | 8.944289e-04 | 8.049860e-03 |
g__Bilophila | genus | Patient_groupPneumonia | Neurorehabilitation | 3.485782 | 1.543562e-07 | 7.577484e-06 |
g__u(f__Christensenellaceae) | genus | Patient_groupPneumonia | Neurorehabilitation | 3.231958 | 8.538686e-04 | 7.834337e-03 |
g__Faecalibacterium | genus | Patient_groupPneumonia | Neurorehabilitation | 2.367966 | 6.298276e-03 | 3.208556e-02 |
g__u(f__Enterobacteriaceae) | genus | Patient_groupPneumonia | Neurorehabilitation | 1.330261 | 6.935381e-03 | 3.435877e-02 |
g__Dorea | genus | Patient_groupPneumonia | Neurorehabilitation | -1.391704 | 6.758188e-03 | 3.392122e-02 |
g__[Ruminococcus] | genus | Patient_groupPneumonia | Neurorehabilitation | -1.527281 | 1.007655e-02 | 4.684781e-02 |
g__u(f__Erysipelotrichaceae) | genus | Patient_groupPneumonia | Neurorehabilitation | -2.115394 | 4.978590e-04 | 5.376877e-03 |
g__Oscillospira | genus | Patient_groupPneumonia | Neurorehabilitation | -2.769945 | 7.307628e-06 | 1.960826e-04 |
g__Lactococcus | genus | Patient_groupPneumonia | Neurorehabilitation | -3.043558 | 4.768102e-03 | 2.549282e-02 |
g__u(f__Rikenellaceae) | genus | Patient_groupPneumonia | Neurorehabilitation | -3.916056 | 8.209125e-04 | 7.777066e-03 |
g__Granulicatella | genus | Patient_groupPneumonia | Neurorehabilitation | -4.084820 | 4.373116e-04 | 5.024431e-03 |
g__u(f__Planococcaceae) | genus | Patient_groupTrauma | Neurorehabilitation | -4.840741 | 9.703175e-03 | 4.556274e-02 |
g__Staphylococcus | genus | Patient_groupTrauma | Neurorehabilitation | -5.343481 | 4.961609e-04 | 5.376877e-03 |
g__u(f__Enterococcaceae) | genus | Patient_groupTrauma | Neurorehabilitation | -5.873421 | 9.026998e-07 | 3.249719e-05 |
g__u(o__Lactobacillales) | genus | Patient_groupTrauma | Neurorehabilitation | -10.756858 | 3.353930e-07 | 1.393171e-05 |
g__Bifidobacterium s__adolescentis | species | Patient_groupPneumonia | Neurorehabilitation | 8.976274 | 5.126585e-10 | 5.009406e-08 |
s__u(f__Clostridiaceae) | species | Patient_groupTrauma | Neurorehabilitation | 8.445413 | 7.263507e-04 | 8.045994e-03 |
s__u(g__SMB53) | species | Patient_groupTrauma | Neurorehabilitation | 7.344928 | 6.784244e-03 | 4.035150e-02 |
s__u(f__Christensenellaceae) | species | Patient_groupTrauma | Neurorehabilitation | 6.643681 | 3.862302e-03 | 2.620973e-02 |
s__u(g__Bilophila) | species | Patient_groupTrauma | Neurorehabilitation | 4.175977 | 1.491380e-04 | 2.428818e-03 |
g__Streptococcus s__anginosus | species | Patient_groupPneumonia | Neurorehabilitation | 3.792393 | 7.753757e-03 | 4.477469e-02 |
s__u(f__[Mogibacteriaceae]) | species | Patient_groupTrauma | Neurorehabilitation | 3.775699 | 8.944289e-04 | 9.131185e-03 |
s__u(g__Bilophila) | species | Patient_groupPneumonia | Neurorehabilitation | 3.485782 | 1.543562e-07 | 8.121508e-06 |
s__u(f__Christensenellaceae) | species | Patient_groupPneumonia | Neurorehabilitation | 3.231958 | 8.538686e-04 | 8.871001e-03 |
g__Faecalibacterium s__prausnitzii | species | Patient_groupPneumonia | Neurorehabilitation | 2.367966 | 6.298276e-03 | 3.846447e-02 |
s__u(f__Enterobacteriaceae) | species | Patient_groupPneumonia | Neurorehabilitation | 1.330261 | 6.935381e-03 | 4.089483e-02 |
s__u(g__Dorea) | species | Patient_groupPneumonia | Neurorehabilitation | -1.526012 | 2.783625e-03 | 2.092307e-02 |
g__[Ruminococcus] s__gnavus | species | Patient_groupPneumonia | Neurorehabilitation | -1.986540 | 7.023756e-04 | 8.045994e-03 |
s__u(f__Erysipelotrichaceae) | species | Patient_groupPneumonia | Neurorehabilitation | -2.115394 | 4.978590e-04 | 6.425199e-03 |
s__u(g__Oscillospira) | species | Patient_groupPneumonia | Neurorehabilitation | -2.769945 | 7.307628e-06 | 2.173225e-04 |
s__u(g__Lactococcus) | species | Patient_groupPneumonia | Neurorehabilitation | -2.966685 | 5.802135e-03 | 3.575369e-02 |
s__u(g__Collinsella) | species | Patient_groupPneumonia | Neurorehabilitation | -3.651317 | 3.196575e-04 | 4.462157e-03 |
g__[Ruminococcus] s__torques | species | Patient_groupPneumonia | Neurorehabilitation | -3.734830 | 9.761238e-04 | 9.676357e-03 |
s__u(f__Rikenellaceae) | species | Patient_groupPneumonia | Neurorehabilitation | -3.916056 | 8.209125e-04 | 8.773503e-03 |
s__u(g__Granulicatella) | species | Patient_groupPneumonia | Neurorehabilitation | -4.084820 | 4.373116e-04 | 5.865120e-03 |
s__u(f__Enterococcaceae) | species | Patient_groupTrauma | Neurorehabilitation | -5.873421 | 9.026998e-07 | 3.430259e-05 |
g__Staphylococcus s__aureus | species | Patient_groupTrauma | Neurorehabilitation | -5.889024 | 1.930990e-03 | 1.575744e-02 |
s__u(o__Lactobacillales) | species | Patient_groupTrauma | Neurorehabilitation | -10.756858 | 3.353930e-07 | 1.579578e-05 |
Homovanilic_acid
taxon | taxa level | covariate | coefficient | p-value | adjusted p-value |
---|---|---|---|---|---|
p__Proteobacteria | phylum | Homovanilic_acid | 0.169777 | 1.695133e-04 | 0.003437 |
c__Gammaproteobacteria | class | Homovanilic_acid | 0.195911 | 6.797016e-05 | 0.000734 |
c__Deltaproteobacteria | class | Homovanilic_acid | -0.069811 | 4.491400e-03 | 0.030317 |
o__Pasteurellales | order | Homovanilic_acid | 0.392998 | 5.731753e-07 | 0.000023 |
o__Enterobacteriales | order | Homovanilic_acid | 0.225410 | 1.128444e-06 | 0.000032 |
o__Bacillales | order | Homovanilic_acid | -0.156994 | 4.502206e-03 | 0.029174 |
f__Leuconostocaceae | family | Homovanilic_acid | 0.555001 | 7.058785e-03 | 0.045378 |
f__Pasteurellaceae | family | Homovanilic_acid | 0.392998 | 5.731753e-07 | 0.000021 |
f__Prevotellaceae | family | Homovanilic_acid | 0.265052 | 1.368468e-03 | 0.013315 |
f__Enterobacteriaceae | family | Homovanilic_acid | 0.225410 | 1.128444e-06 | 0.000037 |
f__Enterococcaceae | family | Homovanilic_acid | -0.236328 | 7.146152e-05 | 0.001354 |
f__Planococcaceae | family | Homovanilic_acid | -0.636837 | 1.018359e-04 | 0.001746 |
f__u(o__Lactobacillales) | family | Homovanilic_acid | -1.360327 | 2.542920e-05 | 0.000572 |
g__Haemophilus | genus | Homovanilic_acid | 0.390909 | 1.640748e-06 | 0.000055 |
g__Klebsiella | genus | Homovanilic_acid | 0.378392 | 3.124148e-04 | 0.003880 |
g__Serratia | genus | Homovanilic_acid | 0.356441 | 2.138565e-05 | 0.000393 |
g__Erwinia | genus | Homovanilic_acid | 0.291014 | 1.059043e-02 | 0.048465 |
g__Prevotella | genus | Homovanilic_acid | 0.267062 | 1.195163e-03 | 0.009353 |
g__u(f__Enterobacteriaceae) | genus | Homovanilic_acid | 0.219939 | 1.844188e-06 | 0.000059 |
g__u(f__Christensenellaceae) | genus | Homovanilic_acid | -0.197934 | 4.417739e-03 | 0.024348 |
g__SMB53 | genus | Homovanilic_acid | -0.228966 | 1.143451e-03 | 0.009221 |
g__Enterococcus | genus | Homovanilic_acid | -0.236168 | 8.533561e-05 | 0.001295 |
g__u(f__Planococcaceae) | genus | Homovanilic_acid | -0.602330 | 8.634398e-05 | 0.001295 |
g__u(f__Enterococcaceae) | genus | Homovanilic_acid | -1.062715 | 2.608867e-08 | 0.000002 |
g__Alloscardovia | genus | Homovanilic_acid | -1.246850 | 1.089213e-02 | 0.049327 |
g__u(o__Lactobacillales) | genus | Homovanilic_acid | -1.360327 | 2.542920e-05 | 0.000443 |
s__u(g__Haemophilus) | species | Homovanilic_acid | 0.407618 | 3.640729e-06 | 0.000113 |
s__u(g__Serratia) | species | Homovanilic_acid | 0.389390 | 1.525784e-03 | 0.013915 |
s__u(g__Klebsiella) | species | Homovanilic_acid | 0.378392 | 3.124148e-04 | 0.004452 |
g__Serratia s__marcescens | species | Homovanilic_acid | 0.309780 | 3.020574e-04 | 0.004396 |
s__u(g__Erwinia) | species | Homovanilic_acid | 0.309020 | 3.601391e-03 | 0.025136 |
s__u(f__Enterobacteriaceae) | species | Homovanilic_acid | 0.219939 | 1.844188e-06 | 0.000066 |
s__u(g__Collinsella) | species | Homovanilic_acid | 0.201115 | 1.981198e-03 | 0.015757 |
s__u(f__Christensenellaceae) | species | Homovanilic_acid | -0.197934 | 4.417739e-03 | 0.028560 |
s__u(g__SMB53) | species | Homovanilic_acid | -0.228966 | 1.143451e-03 | 0.010869 |
s__u(g__Enterococcus) | species | Homovanilic_acid | -0.235784 | 8.777301e-05 | 0.001501 |
s__u(f__Planococcaceae) | species | Homovanilic_acid | -0.602330 | 8.634398e-05 | 0.001501 |
s__u(f__Enterococcaceae) | species | Homovanilic_acid | -1.062715 | 2.608867e-08 | 0.000001 |
s__u(o__Lactobacillales) | species | Homovanilic_acid | -1.360327 | 2.542920e-05 | 0.000561 |
Hydroxyphenylacetic_acid
taxon | taxa level | covariate | coefficient | p-value | adjusted p-value |
---|---|---|---|---|---|
p__Actinobacteria | phylum | Hydroxyphenylacetic_acid | -3.087679 | 7.069286e-08 | 3.817415e-06 |
c__Gammaproteobacteria | class | Hydroxyphenylacetic_acid | 1.112153 | 6.686724e-03 | 3.800875e-02 |
c__Bacilli | class | Hydroxyphenylacetic_acid | 1.078312 | 6.659021e-03 | 3.800875e-02 |
c__Clostridia | class | Hydroxyphenylacetic_acid | -1.751097 | 4.493861e-06 | 6.066713e-05 |
c__Actinobacteria | class | Hydroxyphenylacetic_acid | -2.266156 | 4.345027e-03 | 3.031695e-02 |
c__Coriobacteriia | class | Hydroxyphenylacetic_acid | -4.578125 | 4.914530e-09 | 2.653846e-07 |
o__Pseudomonadales | order | Hydroxyphenylacetic_acid | 1.719339 | 2.199383e-09 | 2.101657e-07 |
o__Enterobacteriales | order | Hydroxyphenylacetic_acid | 1.275392 | 1.344073e-03 | 1.209666e-02 |
o__Clostridiales | order | Hydroxyphenylacetic_acid | -1.773290 | 2.508737e-06 | 5.080191e-05 |
o__Coriobacteriales | order | Hydroxyphenylacetic_acid | -4.578125 | 4.914530e-09 | 2.653846e-07 |
f__u(o__Lactobacillales) | family | Hydroxyphenylacetic_acid | 3.192057 | 1.280988e-09 | 1.537186e-07 |
f__Moraxellaceae | family | Hydroxyphenylacetic_acid | 2.537322 | 1.874638e-09 | 1.687174e-07 |
f__Enterococcaceae | family | Hydroxyphenylacetic_acid | 1.835069 | 9.755399e-04 | 1.032925e-02 |
f__Pseudomonadaceae | family | Hydroxyphenylacetic_acid | 1.450977 | 1.231647e-04 | 2.015422e-03 |
f__Enterobacteriaceae | family | Hydroxyphenylacetic_acid | 1.275392 | 1.344073e-03 | 1.331483e-02 |
f__Ruminococcaceae | family | Hydroxyphenylacetic_acid | -1.968205 | 1.513041e-03 | 1.433407e-02 |
f__Lachnospiraceae | family | Hydroxyphenylacetic_acid | -2.377785 | 4.481936e-08 | 2.304996e-06 |
f__Alcaligenaceae | family | Hydroxyphenylacetic_acid | -2.756707 | 4.919042e-03 | 3.472265e-02 |
f__Veillonellaceae | family | Hydroxyphenylacetic_acid | -3.071949 | 1.752841e-04 | 2.552614e-03 |
f__u(o__Clostridiales) | family | Hydroxyphenylacetic_acid | -3.255662 | 4.093706e-15 | 1.473734e-12 |
f__Prevotellaceae | family | Hydroxyphenylacetic_acid | -4.389035 | 1.021338e-03 | 1.050519e-02 |
f__Coriobacteriaceae | family | Hydroxyphenylacetic_acid | -4.578125 | 4.914530e-09 | 3.538462e-07 |
g__Vagococcus | genus | Hydroxyphenylacetic_acid | 5.806242 | 9.280718e-04 | 8.118461e-03 |
g__u(f__Enterococcaceae) | genus | Hydroxyphenylacetic_acid | 3.742451 | 4.562643e-24 | 2.463827e-21 |
g__u(o__Lactobacillales) | genus | Hydroxyphenylacetic_acid | 3.192057 | 1.280988e-09 | 1.152889e-07 |
g__Acinetobacter | genus | Hydroxyphenylacetic_acid | 2.847176 | 6.131033e-08 | 3.310758e-06 |
g__Klebsiella | genus | Hydroxyphenylacetic_acid | 2.409054 | 8.805563e-03 | 4.322731e-02 |
g__Enterococcus | genus | Hydroxyphenylacetic_acid | 1.760073 | 1.691520e-03 | 1.248961e-02 |
g__Bilophila | genus | Hydroxyphenylacetic_acid | 1.417622 | 1.144064e-03 | 9.220814e-03 |
g__u(f__Enterobacteriaceae) | genus | Hydroxyphenylacetic_acid | 1.235522 | 1.941837e-03 | 1.315472e-02 |
g__u(f__Ruminococcaceae) | genus | Hydroxyphenylacetic_acid | -1.751901 | 3.828624e-03 | 2.247184e-02 |
g__Ruminococcus | genus | Hydroxyphenylacetic_acid | -1.767072 | 3.961962e-04 | 4.650999e-03 |
g__u(f__Erysipelotrichaceae) | genus | Hydroxyphenylacetic_acid | -1.817481 | 4.072540e-03 | 2.314918e-02 |
g__[Ruminococcus] | genus | Hydroxyphenylacetic_acid | -1.935392 | 1.964417e-03 | 1.315472e-02 |
g__Dorea | genus | Hydroxyphenylacetic_acid | -2.056712 | 1.529947e-05 | 3.177583e-04 |
g__Oscillospira | genus | Hydroxyphenylacetic_acid | -2.154613 | 3.366628e-05 | 5.681185e-04 |
g__Coprococcus | genus | Hydroxyphenylacetic_acid | -2.560747 | 1.071854e-05 | 2.315205e-04 |
g__u(f__Lachnospiraceae) | genus | Hydroxyphenylacetic_acid | -3.200484 | 3.201460e-10 | 3.457577e-08 |
g__u(o__Clostridiales) | genus | Hydroxyphenylacetic_acid | -3.255662 | 4.093706e-15 | 7.368671e-13 |
g__Eggerthella | genus | Hydroxyphenylacetic_acid | -3.405547 | 2.253773e-03 | 1.484192e-02 |
g__Prevotella | genus | Hydroxyphenylacetic_acid | -4.404110 | 9.518966e-04 | 8.159114e-03 |
g__u(f__Clostridiaceae) | genus | Hydroxyphenylacetic_acid | -4.982415 | 8.559738e-04 | 7.834337e-03 |
g__Blautia | genus | Hydroxyphenylacetic_acid | -5.261376 | 6.155800e-06 | 1.749543e-04 |
g__SMB53 | genus | Hydroxyphenylacetic_acid | -5.363021 | 9.281529e-03 | 4.408802e-02 |
g__u(f__Coriobacteriaceae) | genus | Hydroxyphenylacetic_acid | -5.443950 | 3.870151e-03 | 2.247184e-02 |
g__Collinsella | genus | Hydroxyphenylacetic_acid | -14.060887 | 1.015036e-02 | 4.684781e-02 |
s__u(g__Vagococcus) | species | Hydroxyphenylacetic_acid | 5.806242 | 9.280718e-04 | 9.335310e-03 |
s__u(f__Enterococcaceae) | species | Hydroxyphenylacetic_acid | 3.742451 | 4.562643e-24 | 3.120848e-21 |
s__u(o__Lactobacillales) | species | Hydroxyphenylacetic_acid | 3.192057 | 1.280988e-09 | 1.095245e-07 |
s__u(g__Acinetobacter) | species | Hydroxyphenylacetic_acid | 2.965725 | 8.390688e-07 | 3.376018e-05 |
s__u(g__Klebsiella) | species | Hydroxyphenylacetic_acid | 2.409054 | 8.805563e-03 | 4.977690e-02 |
g__Parabacteroides s__distasonis | species | Hydroxyphenylacetic_acid | 2.219433 | 2.085624e-03 | 1.639732e-02 |
s__u(g__Enterococcus) | species | Hydroxyphenylacetic_acid | 1.755724 | 1.730277e-03 | 1.498113e-02 |
s__u(g__Bilophila) | species | Hydroxyphenylacetic_acid | 1.417622 | 1.144064e-03 | 1.086861e-02 |
s__u(f__Enterobacteriaceae) | species | Hydroxyphenylacetic_acid | 1.235522 | 1.941837e-03 | 1.575744e-02 |
s__u(g__Ruminococcus) | species | Hydroxyphenylacetic_acid | -1.711420 | 5.931940e-04 | 6.995599e-03 |
s__u(f__Ruminococcaceae) | species | Hydroxyphenylacetic_acid | -1.751901 | 3.828624e-03 | 2.620973e-02 |
s__u(f__Erysipelotrichaceae) | species | Hydroxyphenylacetic_acid | -1.817481 | 4.072540e-03 | 2.730998e-02 |
s__u(g__Dorea) | species | Hydroxyphenylacetic_acid | -1.955919 | 6.743749e-05 | 1.246682e-03 |
s__u(g__Oscillospira) | species | Hydroxyphenylacetic_acid | -2.154613 | 3.366628e-05 | 7.196168e-04 |
g__[Ruminococcus] s__gnavus | species | Hydroxyphenylacetic_acid | -2.181108 | 1.299755e-03 | 1.217853e-02 |
s__u(g__[Ruminococcus]) | species | Hydroxyphenylacetic_acid | -2.226232 | 2.378447e-04 | 3.536647e-03 |
g__Blautia s__producta | species | Hydroxyphenylacetic_acid | -2.307625 | 5.606547e-04 | 6.972506e-03 |
s__u(g__Coprococcus) | species | Hydroxyphenylacetic_acid | -2.559045 | 1.117608e-05 | 2.831273e-04 |
g__Bacteroides s__uniformis | species | Hydroxyphenylacetic_acid | -2.735180 | 2.245142e-03 | 1.732113e-02 |
s__u(f__Lachnospiraceae) | species | Hydroxyphenylacetic_acid | -3.200484 | 3.201460e-10 | 3.649665e-08 |
s__u(o__Clostridiales) | species | Hydroxyphenylacetic_acid | -3.255662 | 4.093706e-15 | 9.333650e-13 |
g__Eggerthella s__lenta | species | Hydroxyphenylacetic_acid | -3.405547 | 2.253773e-03 | 1.732113e-02 |
s__u(f__Clostridiaceae) | species | Hydroxyphenylacetic_acid | -4.982415 | 8.559738e-04 | 8.871001e-03 |
s__u(f__Coriobacteriaceae) | species | Hydroxyphenylacetic_acid | -5.443950 | 3.870151e-03 | 2.620973e-02 |
s__u(g__Blautia) | species | Hydroxyphenylacetic_acid | -5.706295 | 5.210778e-05 | 1.018335e-03 |
g__Blautia s__obeum | species | Hydroxyphenylacetic_acid | -8.253868 | 5.625129e-03 | 3.522298e-02 |
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 ~ Hydroxyhenyllactic_acid + Hydroxybenzoic_acid + Phenylpropionic_acid + Benzoic_acid + Phenyllactic_acid + Patient_group + Homovanilic_acid + Hydroxyphenylacetic_acid |
link function | log |
number of samples | 21 |
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).
Benzoic_acid
pathway | metabolic level | covariate | coefficient | p-value | adjusted p-value |
---|---|---|---|---|---|
M00223 : Phosphonate transport system | KEGG modules | Benzoic_acid | 0.003961 | 0.000021 | 0.015591 |
Hydroxyphenylacetic_acid
pathway | metabolic level | covariate | coefficient | p-value | adjusted p-value |
---|---|---|---|---|---|
ko00400 : Phenylalanine, tyrosine and tryptophan biosynthesis | KEGG pathways | Hydroxyphenylacetic_acid | -0.003502 | 0.000019 | 0.014167 |
M00122 : Cobalamin biosynthesis, cobinamide => cobalamin | KEGG modules | Hydroxyphenylacetic_acid | -0.003836 | 0.000008 | 0.012410 |
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 ~ Hydroxyhenyllactic_acid + Hydroxybenzoic_acid + Phenylpropionic_acid + Benzoic_acid + Phenyllactic_acid + Patient_group + Homovanilic_acid + Hydroxyphenylacetic_acid |
number of samples | 21 |
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).
Nothing to show
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 ~ Hydroxyhenyllactic_acid + Hydroxybenzoic_acid + Phenylpropionic_acid + Benzoic_acid + Phenyllactic_acid + Patient_group + Homovanilic_acid + Hydroxyphenylacetic_acid |
number of samples | 21 |
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).
Nothing to show
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 ~ Hydroxyhenyllactic_acid + Hydroxybenzoic_acid + Phenylpropionic_acid + Benzoic_acid + Phenyllactic_acid + Patient_group + Homovanilic_acid + Hydroxyphenylacetic_acid |
link function | log |
number of samples | 21 |
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 | 21 |
formula | alpha_diversity ~ Patient_group + Benzoic_acid + Phenylpropionic_acid + Phenyllactic_acid + Hydroxybenzoic_acid + Hydroxyphenylacetic_acid + Homovanilic_acid + Hydroxyhenyllactic_acid |
Shapiro-Wilk test for residuals, p-value | 0.273 |
Summary
covariate | Estimate | p-value |
---|---|---|
Intercept | 7.120821 | 6.692155e-08 |
Patient_group[T.Pneumonia] | -0.503170 | 3.883767e-01 |
Patient_group[T.Trauma] | 2.262474 | 9.637508e-02 |
Benzoic_acid | -2.566919 | 2.277205e-02 |
Phenylpropionic_acid | 0.805832 | 8.468750e-01 |
Phenyllactic_acid | -4.130638 | 1.517871e-01 |
Hydroxybenzoic_acid | 3.604231 | 4.283660e-01 |
Hydroxyphenylacetic_acid | -1.269873 | 1.643810e-02 |
Homovanilic_acid | 0.008768 | 8.506093e-01 |
Hydroxyhenyllactic_acid | 1.239736 | 1.942303e-01 |
datalab:
3.10.0
knb_lib:
4.8.51
knb_interactive:
2.0.2