Factor analysis report for NIIOR CCI (Neurorehabilitation) and ACI (Pneumonia) groups

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Explore the associations between microbiota composition of data and external factors provided by the user.

Created07/10/2019
Updated13/11/2020
TypeFactor analysis report
ProjectNIIOR CCI (Neurorehabilitation) and ACI (Pneumonia) groups
Uploaded samples82

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

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

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

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

Download metadata_after_na_filtration.csv

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

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

Download metadata_after_na_filtration.csv

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

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

Download metadata_after_na_filtration.csv

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).

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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

Download metadata_after_na_filtration.csv

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