Paired analysis report for 20180822 Tomsk SibGMU opisthorchiasis

Report summary

Perform comparison of paired datasets (e.g., taken from the same subjects before and after the treatment).

Created16/10/2018
Updated31/12/2019
TypePaired analysis report
Project20180822 Tomsk SibGMU opisthorchiasis
Uploaded samples152

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 change the way of major composition display between the top features in the selected sample and the top features across all samples on the average.

Analysis of outliers

Automatic filtering of the user samples with extreme taxonomic composition (based on the combined analysis of user and external data). Analysis of outliers: samples in upper 1% tail of distribution of median distance between each sample and closest 50% of neighbours approximated by normal distribution. List of outliers:

TGU.11460114, TGU.11200114, TGU.09100414, TGU.11410114

PCoA visualization based on taxonomic composition

Distribution of the samples by their taxonomic composition in reduced dimensionality. The closer the samples (points) on the plot, the more similar their composition. Vectors show the directions in which the levels of the respective major taxa increase. Method of dimension reduction: PCoA (Principal Coordinate Analysis); dissimilarity metric: weighted UniFrac. Clicking on a dot “freezes” the detailed information about the sample on the right of the plot (click again or on the cross near sample name to “unfreeze”). Switch between the display modes with or without outliers and with or without vectors showing major microbial “drivers” using the respective controls.

Alpha-diversity

The measure describes the conditional number of taxa in each sample. Metric: Shannon index.

Сomparison

Wilcoxon signed-rank test is applied to compare the alpha-diversity between the two groups.

Alpha-diversity does not vary significantly between groups (p= 0.4588443639352483)

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.

Taxa co-occurence analysis

Co-occurence graph

Co-occurrence of microbial genera was analyzed basing on correlation analysis of their relative abundance using SPIEC-EASI software. In the graph, vertices show genera; pairs of highly co-occurring genera are connected with blue lines. The graph shows the members of the cooperatives - groups of highly co-occurring genera corresponding to isolated components (singleton vertices are omitted). Parameters of SPIEC-EASI algorithm: Meinshausen and Bühlmann neighbourhood selection method (MB), minimum lambda ratio= 0.1, number of lambda iterations = 20, model selection using StARS algorithm (number of StARS subsamples = 50).

No cooperatives detected. Possible reasons: too few or too many co-occurring taxa or insufficient number of samples to perform the analysis.

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.

parameter value
sample size 91
number of permutations 20000
significance level 0.05
group variations equal (p = 0.319)
R-squared 0.018
p-value 0.119

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.

parameter value
sample size 94
number of permutations 20000
significance level 0.05
group variations equal (p = 0.154)
R-squared 0.028
p-value 0.017

Taxonomic composition

Individual microbial taxa for which relative abundance is significantly different between two groups are identified.

Wilcoxon test comparison

Method: Wilcoxon signed rank test. The analysis includes the following steps: filtration of rare taxa (taxon must be present in at least 10% of the samples at the level of >0.2%), Wilcoxon signed rank test applied to each taxon to detect the taxa differentially abundant between the groups. Multiple testing adjustment is performed using Benjamini–Hochberg procedure. Contribution of each taxon to the inter-group difference is estimated using LDA method. Samples-outliers listed in the taxonomic composition section are excluded from this analysis.

Differentially abundant taxa

Tables of differentially abundant taxa overpresented in the groups

Nothing to show

Cladogram of differences

Tree-like summary of the taxa differentially abundant in two groups constructed using LefSe.

List of differentially abundant taxa

Nothing to show

Cladogram

Nothing to show

Excluded features

Nothing to show

All results of the test

All features were discarded during the filtering.

Generalized linear mixed effect model

A generalized mixed effects linear model is fitted for each taxon to identify if it is differentially abundant between the groups. "Subject_id", is treated as a random effect. The specific probability distribution is selected heuristically depending on the number of samples. For >100 samples, a zero-inflated negative binomial regression is fitted; in other cases - a negative binomial model. 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. Contribution of each taxon to the inter-group difference is estimated using LDA method. The information about distribution family, terms of the model and sample size is displayed in "Model details" section.

Differentially abundant taxa

Tables of differentially abundant taxa overpresented in the groups

Overpresented in group: 2_opisth

taxon taxa level 3_treat mean, % 3_treat sd, % 2_opisth mean, % 2_opisth sd, % p-value adjusted p-value lda score sample size
p__Proteobacteria phylum 1.182 1.610 7.300 13.764 0.000 0.000 4.774 94
c__Gammaproteobacteria class 0.775 1.376 6.805 13.827 0.000 0.000 4.796 94
o__Enterobacteriales order 0.678 1.355 5.975 12.920 0.000 0.000 4.840 94
f__Enterobacteriaceae family 0.678 1.355 5.975 12.920 0.000 0.000 4.773 94
g__u(f__Enterobacteriaceae) genus 0.670 1.337 5.950 12.911 0.000 0.000 4.763 94
s__u(f__Enterobacteriaceae) species 0.670 1.337 5.950 12.911 0.000 0.000 4.496 94
g__Prevotella s__stercorea species 0.013 0.062 0.230 0.636 0.001 0.022 4.438 94

Overpresented in group: 3_treat

taxon taxa level 3_treat mean, % 3_treat sd, % 2_opisth mean, % 2_opisth sd, % p-value adjusted p-value lda score sample size
p__Firmicutes phylum 74.317 9.326 65.642 17.455 0.009 0.033 4.804 94
g__[Ruminococcus] s__torques species 0.671 1.963 0.088 0.183 0.001 0.022 3.973 94

Cladogram of differences

Tree-like summary of the taxa differentially abundant in two groups constructed using LefSe.

List of differentially abundant taxa

increased in 2_opisth

denotation feature
a g__u(f__Enterobacteriaceae)
b f__Enterobacteriaceae
c o__Enterobacteriales
d c__Gammaproteobacteria

Excluded features

phylum

p__Planctomycetes, p__Synergistetes, p__Lentisphaerae, p__Chlorobi, p__OP8, p__Aquificae, p__Fusobacteria, p__Chloroflexi, p__Crenarchaeota, p__Cyanobacteria, p__OP3, p__[Thermi], p__Acidobacteria, p__Spirochaetes

class

c__Aquificae, c__Acidobacteriia, c__Thermoplasmata, c__Sphingobacteriia, c__OP8_1, c__Flavobacteriia, c__Chloroflexi, c__Alphaproteobacteria, c__Planctomycetia, c__Methanomicrobia, c__koll11, c__u(p__Cyanobacteria), c__Thermomicrobia, c__Deinococci, c__MB-A2-108, c__Cytophagia, c__Thaumarchaeota, c__Halobacteria, c__Spirochaetes, c__Anaerolineae, c__OPB56, c__Opitutae, c__Synergistia, c__Thermoleophilia, c__Acidimicrobiia, c__4C0d-2, c__[Lentisphaeria], c__Epsilonproteobacteria, c__[Chloracidobacteria], c__TK17, c__[Saprospirae], c__Chloroplast, c__Acidobacteria-5, c__RF3, c__Acidobacteria-6, c__[Spartobacteria], c__Fusobacteriia

order

o__u(c__Betaproteobacteria), o__Caulobacterales, o__Anaerolineales, o__Streptophyta, o__[Cerasicoccales], o__Gemmatales, o__iii1-15, o__Myxococcales, o__GIF10, o__Halobacteriales, o__u(c__Alphaproteobacteria), o__Sphingomonadales, o__Pasteurellales, o__Xanthomonadales, o__SBla14, o__Bdellovibrionales, o__[Saprospirales], o__Neisseriales, o__Campylobacterales, o__Victivallales, o__Hydrogenophilales, o__Opitutales, o__Bacillales, o__Acholeplasmatales, o__Rickettsiales, o__Rhodobacterales, o__[Roseiflexales], o__Desulfurellales, o__Sphingobacteriales, o__OPB95, o__Anaeroplasmatales, o__u(c__Acidobacteria-5), o__Acidithiobacillales, o__Gallionellales, o__Oceanospirillales, o__Thermales, o__Thermoplasmatales, o__Acidobacteriales, o__Solirubrobacterales, o__Rhodocyclales, o__Caldilineales, o__Desulfobacterales, o__JG30-KF-CM45, o__u(c__Mollicutes), o__Rhizobiales, o__Alteromonadales, o__Pseudomonadales, o__u(c__Gammaproteobacteria), o__Gaiellales, o__[Chthoniobacterales], o__u(c__OPB56), o__Cardiobacteriales, o__ML615J-28, o__HOC36, o__Aeromonadales, o__Spirochaetales, o__Stramenopiles, o__Flavobacteriales, o__mle1-48, o__Acidimicrobiales, o__SHA-98, o__Rhodospirillales, o__Nitrososphaerales, o__Aquificales, o__0319-7L14, o__Cytophagales, o__Thiobacterales, o__RB41, o__RF32, o__Chlorophyta, o__Synergistales, o__u(p__Cyanobacteria), o__Thermoanaerobacterales, o__Methanomicrobiales, o__YS2, o__Gemellales, o__Fusobacteriales

family

f__Bdellovibrionaceae, f__Promicromonosporaceae, f__Ellin6075, f__u(o__SHA-98), f__Acidobacteriaceae, f__u(o__Solirubrobacterales), f__Corynebacteriaceae, f__Xanthomonadaceae, f__Streptomycetaceae, f__Opitutaceae, f__Comamonadaceae, f__Acidithiobacillaceae, f__Cryptosporangiaceae, f__SUP05, f__[Chthoniobacteraceae], f__Trebouxiophyceae, f__Peptostreptococcaceae, f__u(o__GIF10), f__u(o__Rhodospirillales), f__Alcanivoracaceae, f__Hyphomicrobiaceae, f__Gallionellaceae, f__Caldilineaceae, f__u(o__Sphingobacteriales), f__u(o__OPB95), f__Thermoanaerobacteraceae, f__Synergistaceae, f__Spirochaetaceae, f__Pseudomonadaceae, f__Sphingomonadaceae, f__Halomonadaceae, f__u(o__Bacillales), f__Sinobacteraceae, f__Rhodobacteraceae, f__Acetobacteraceae, f__mitochondria, f__Sporolactobacillaceae, f__u(o__Acidimicrobiales), f__Cardiobacteriaceae, f__Nocardioidaceae, f__Conexibacteraceae, f__u(o__RF32), f__Koribacteraceae, f__EtOH8, f__[Tissierellaceae], f__C111, f__Rhodospirillaceae, f__u(o__Actinomycetales), f__Thiobacteraceae, f__Aeromonadaceae, f__u(o__Stramenopiles), f__Carnobacteriaceae, f__Shewanellaceae, f__Methanocorpusculaceae, f__u(c__Gammaproteobacteria), f__Staphylococcaceae, f__Kineosporiaceae, f__Bacillaceae, f__Mycobacteriaceae, f__Isosphaeraceae, f__Flavobacteriaceae, f__Eubacteriaceae, f__u(o__iii1-15), f__u(c__OPB56), f__Sphingobacteriaceae, f__Victivallaceae, f__Cryomorphaceae, f__Chitinophagaceae, f__Aerococcaceae, f__Polyangiaceae, f__Burkholderiaceae, f__[Weeksellaceae], f__Nitrososphaeraceae, f__Gemellaceae, f__u(o__Lactobacillales), f__Anaeroplasmataceae, f__BSLdp215, f__Beijerinckiaceae, f__Aquificaceae, f__Oxalobacteraceae, f__u(o__Burkholderiales), f__Rhodocyclaceae, f__u(o__mle1-48), f__Leuconostocaceae, f__Xanthobacteraceae, f__Nannocystaceae, f__u(c__Acidobacteria-5), f__u(c__Alphaproteobacteria), f__Gemmataceae, f__Neisseriaceae, f__Saprospiraceae, f__u(o__HOC36), f__u(o__YS2), f__Brucellaceae, f__Hyphomonadaceae, f__Bradyrhizobiaceae, f__u(o__SBla14), f__Ruaniaceae, f__Anaerolinaceae, f__u(o__Myxococcales), f__u(p__Cyanobacteria), f__Intrasporangiaceae, f__Halobacteriaceae, f__Cyclobacteriaceae, f__u(o__Rickettsiales), f__u(o__JG30-KF-CM45), f__Dehalobacteriaceae, f__u(c__Mollicutes), f__u(c__Betaproteobacteria), f__Rhizobiaceae, f__Methylocystaceae, f__Succinivibrionaceae, f__Hydrogenophilaceae, f__Cellulomonadaceae, f__Alicyclobacillaceae, f__Moraxellaceae, f__Thermaceae, f__Pasteurellaceae, f__Desulfurellaceae, f__[Cerasicoccaceae], f__Cytophagaceae, f__u(o__0319-7L14), f__u(o__Rhizobiales), f__Erythrobacteraceae, f__Acholeplasmataceae, f__Methylobacteriaceae, f__Hydrogenothermaceae, f__[Roseiflexaceae], f__Campylobacteraceae, f__Microbacteriaceae, f__Dethiosulfovibrionaceae, f__Pseudonocardiaceae, f__u(o__Bacteroidales), f__Caulobacteraceae, f__u(o__ML615J-28), f__Micrococcaceae, f__u(o__Streptophyta), f__Fusobacteriaceae, f__Desulfobulbaceae, f__Planococcaceae, f__Gaiellaceae

genus

g__u(f__Sphingomonadaceae), g__Dechloromonas, g__Haemophilus, g__u(f__Bifidobacteriaceae), g__Oxalobacter, g__u(f__Moraxellaceae), g__Rhodobacter, g__u(o__Solirubrobacterales), g__Comamonas, g__u(f__Cryptosporangiaceae), g__u(o__GIF10), g__Butyrivibrio, g__u(f__Alcaligenaceae), g__Porphyromonas, g__u(o__Acidimicrobiales), g__u(o__RF32), g__Pseudochrobactrum, g__u(f__Thermoanaerobacteraceae), g__u(f__Leuconostocaceae), g__u(o__Bacillales), g__Atopobium, g__u(o__Streptophyta), g__u(o__Myxococcales), g__Psychrobacter, g__Opitutus, g__Devosia, g__ph2, g__u(f__Streptomycetaceae), g__Holdemania, g__Staphylococcus, g__Pseudoramibacter_Eubacterium, g__u(f__Aerococcaceae), g__u(f__Rhodospirillaceae), g__WAL_1855D, g__Cloacibacillus, g__Methanosphaera, g__Salinicoccus, g__Dysgonomonas, g__Salmonella, g__u(f__Trebouxiophyceae), g__Hyphomonas, g__u(f__Nocardioidaceae), g__Granulicatella, g__u(f__Desulfovibrionaceae), g__Hydrogenobaculum, g__u(f__Chitinophagaceae), g__Anaerofustis, g__Pullulanibacillus, g__YRC22, g__Geobacillus, g__u(f__[Paraprevotellaceae]), g__Caldilinea, g__Proteus, g__Lysinibacillus, g__u(c__OPB56), g__u(o__YS2), g__Polynucleobacter, g__Sporosarcina, g__Ochrobactrum, g__Pseudomonas, g__Citrobacter, g__u(o__Stramenopiles), g__Sphingomonas, g__Leuconostoc, g__Ralstonia, g__Candidatus Nitrososphaera, g__Trichococcus, g__u(o__Bacteroidales), g__Aggregatibacter, g__u(f__Acidobacteriaceae), g__Lactococcus, g__u(f__Saprospiraceae), g__u(f__Pseudomonadaceae), g__Rhodoplanes, g__u(f__Conexibacteraceae), g__Adlercreutzia, g__u(o__Rhizobiales), g__Bilophila, g__Synergistes, g__Rummeliibacillus, g__Desulfurella, g__Hyphomicrobium, g__Slackia, g__u(f__Anaeroplasmataceae), g__u(f__Lactobacillaceae), g__u(p__Cyanobacteria), g__Janibacter, g__Gallionella, g__Moryella, g__Kribbella, g__Anaerococcus, g__u(f__Aeromonadaceae), g__u(o__Actinomycetales), g__Achromobacter, g__u(f__Sphingobacteriaceae), g__u(f__Streptococcaceae), g__Christensenella, g__u(f__Rhodobacteraceae), g__Parvimonas, g__u(f__Burkholderiaceae), g__Pediococcus, g__Mogibacterium, g__Pyramidobacter, g__Xanthobacter, g__Thiobacter, g__Pseudonocardia, g__u(f__Hyphomicrobiaceae), g__u(f__Pasteurellaceae), g__u(f__BSLdp215), g__u(f__Rhodocyclaceae), g__Anaerotruncus, g__Halomicrobium, g__u(f__Anaerolinaceae), g__Veillonella, g__Treponema, g__u(f__Acetobacteraceae), g__Polaromonas, g__u(f__Peptococcaceae), g__Actinomyces, g__u(f__Actinomycetaceae), g__Corynebacterium, g__Gallicola, g__1-68, g__u(f__Kineosporiaceae), g__Cardiobacterium, g__Mobiluncus, g__Thermus, g__Megasphaera, g__Alloiococcus, g__CF231, g__u(f__Synergistaceae), g__Selenomonas, g__Scardovia, g__Burkholderia, g__Bacillus, g__u(f__Isosphaeraceae), g__u(c__Alphaproteobacteria), g__Candidatus Portiera, g__Anoxybacillus, g__u(c__Mollicutes), g__Cellulosimicrobium, g__02d06, g__u(o__OPB95), g__u(f__Veillonellaceae), g__Peptostreptococcus, g__u(f__Bacillaceae), g__Carnobacterium, g__Erwinia, g__Trabulsiella, g__Fusobacterium, g__u(o__JG30-KF-CM45), g__Thauera, g__TG5, g__Paracoccus, g__u(f__Oxalobacteraceae), g__Bulleidia, g__u(f__Victivallaceae), g__u(c__Acidobacteria-5), g__Allobaculum, g__Streptomyces, g__Neisseria, g__Dehalobacterium, g__Aerococcus, g__u(o__ML615J-28), g__DA101, g__RFN20, g__Rothia, g__u(f__Gemellaceae), g__Facklamia, g__u(f__EtOH8), g__Megamonas, g__u(o__Rickettsiales), g__Acidovorax, g__Solibacillus, g__Micrococcus, g__Beijerinckia, g__Terracoccus, g__Arcobacter, g__u(f__[Cerasicoccaceae]), g__u(o__mle1-48), g__u(c__Gammaproteobacteria), g__Halomonas, g__u(o__iii1-15), g__Methylibium, g__u(f__Prevotellaceae), g__Campylobacter, g__u(o__SBla14), g__Schwartzia, g__Roseiflexus, g__Succinivibrio, g__u(f__Micrococcaceae), g__u(o__Lactobacillales), g__Ramlibacter, g__Rhodoferax, g__Varibaculum, g__Bradyrhizobium, g__u(o__Rhodospirillales), g__Acidaminococcus, g__Mycobacterium, g__Shewanella, g__u(o__Burkholderiales), g__Methanocalculus, g__Lautropia, g__u(f__Planococcaceae), g__u(o__Sphingobacteriales), g__u(f__Peptostreptococcaceae), g__Cellulomonas, g__Bdellovibrio, g__Flavobacterium, g__u(f__Desulfobulbaceae), g__Acidithiobacillus, g__Brevundimonas, g__Coprobacillus, g__Alicyclobacillus, g__Alcanivorax, g__u(o__SHA-98), g__u(o__HOC36), g__u(f__Gaiellaceae), g__Plesiocystis, g__u(f__Microbacteriaceae), g__u(f__Hydrogenothermaceae), g__u(f__Sinobacteraceae), g__Methylobacterium, g__Gemella, g__u(c__Betaproteobacteria), g__u(f__Rhizobiaceae), g__Alloscardovia, g__u(f__Cyclobacteriaceae), g__Candidatus Koribacter, g__Gallibacterium, g__Arenimonas, g__Zoogloea, g__u(f__Neisseriaceae), g__u(f__Enterococcaceae), g__u(f__Ellin6075), g__u(f__Methylobacteriaceae), g__Acholeplasma, g__Serratia, g__u(f__mitochondria), g__Actinobacillus, g__Sterolibacterium, g__Balneimonas, g__u(f__Ruaniaceae), g__Meiothermus, g__u(f__Polyangiaceae), g__u(f__Gemmataceae), g__u(f__Promicromonosporaceae), g__rc4-4, g__Vagococcus, g__cc_115, g__u(f__Caulobacteraceae), g__Succiniclasticum, g__Stenotrophomonas, g__Klebsiella, g__Chryseobacterium, g__u(o__0319-7L14), g__u(f__Methylocystaceae), g__Thiobacillus, g__Macrococcus, g__Morganella, g__u(f__Erythrobacteraceae), g__Mitsuokella, g__Finegoldia, g__Anaerovibrio, g__Oribacterium, g__u(f__SUP05), g__Weissella, g__Peptoniphilus, g__Lysobacter, g__Fluviicola, g__Acinetobacter, g__u(f__Xanthomonadaceae), g__Epulopiscium, g__u(f__Comamonadaceae), g__Xylanimicrobium, g__p-75-a5, g__u(f__Cytophagaceae), g__u(f__C111)

species

s__u(g__Staphylococcus), s__u(g__Erwinia), g__Parabacteroides s__gordonii, s__u(g__Micrococcus), s__u(g__cc_115), s__u(f__Microbacteriaceae), g__Collinsella s__stercoris, s__u(o__YS2), s__u(g__Lysobacter), g__Bacteroides s__barnesiae, g__Alcanivorax s__dieselolei, s__u(g__Oxalobacter), s__u(g__Alloscardovia), s__u(g__Desulfovibrio), s__u(f__mitochondria), s__u(o__Actinomycetales), s__u(g__Rhodobacter), s__u(f__Oxalobacteraceae), s__u(g__Schwartzia), s__u(o__Rhizobiales), s__u(g__Bulleidia), s__u(g__Achromobacter), g__Hyphomicrobium s__zavarzinii, s__u(f__Rhodospirillaceae), s__u(o__ML615J-28), s__u(o__JG30-KF-CM45), s__u(g__Gallionella), g__Pyramidobacter s__piscolens, s__u(o__GIF10), g__Mitsuokella s__multacida, s__u(g__Lautropia), s__u(g__Opitutus), g__Enterococcus s__sulfureus, g__Alloiococcus s__otitis, g__Peptostreptococcus s__anaerobius, s__u(o__0319-7L14), g__Lactobacillus s__acidipiscis, s__u(g__Synergistes), g__Actinomyces s__europaeus, s__u(g__Oribacterium), s__u(g__Finegoldia), s__u(g__Anaerovibrio), s__u(g__Halomonas), s__u(f__Moraxellaceae), s__u(f__Desulfobulbaceae), s__u(g__YRC22), s__u(o__OPB95), g__Oxalobacter s__formigenes, s__u(g__Megamonas), g__Streptococcus s__minor, s__u(f__Ellin6075), s__u(g__Varibaculum), s__u(o__Acidimicrobiales), s__u(o__Lactobacillales), s__u(g__Shewanella), s__u(g__Adlercreutzia), s__u(g__Bilophila), s__u(f__Anaerolinaceae), s__u(c__Gammaproteobacteria), s__u(g__Janibacter), g__Lactobacillus s__coleohominis, g__Veillonella s__dispar, s__u(f__Streptomycetaceae), s__u(f__Micrococcaceae), g__Neisseria s__subflava, s__u(g__Rhodoplanes), s__u(g__Ochrobactrum), s__u(f__SUP05), s__u(f__Chitinophagaceae), g__Staphylococcus s__epidermidis, s__u(f__Sphingobacteriaceae), s__u(f__Veillonellaceae), g__Corynebacterium s__durum, g__Prevotella s__nigrescens, s__u(c__Alphaproteobacteria), s__u(f__BSLdp215), g__Bulleidia s__moorei, s__u(o__iii1-15), s__u(g__Porphyromonas), s__u(c__Betaproteobacteria), g__Staphylococcus s__succinus, s__u(f__Aeromonadaceae), s__u(f__Rhodocyclaceae), s__u(g__Succinivibrio), s__u(g__Methanocalculus), g__Anoxybacillus s__kestanbolensis, s__u(f__Peptococcaceae), s__u(g__Selenomonas), s__u(f__Enterococcaceae), s__u(g__Xanthobacter), s__u(g__Halomicrobium), s__u(g__Methylibium), g__Macrococcus s__caseolyticus, s__u(g__Actinomyces), s__u(g__Gallibacterium), s__u(g__Dysgonomonas), g__Moryella s__indoligenes, s__u(g__p-75-a5), s__u(g__Atopobium), s__u(g__Pseudomonas), s__u(f__C111), s__u(f__Lactobacillaceae), s__u(g__Dehalobacterium), s__u(g__Caldilinea), s__u(f__Promicromonosporaceae), s__u(f__Methylobacteriaceae), g__Pseudomonas s__stutzeri, g__Morganella s__morganii, s__u(g__Anaerotruncus), s__u(g__Candidatus Nitrososphaera), s__u(g__Zoogloea), s__u(g__Flavobacterium), s__u(f__Kineosporiaceae), s__u(g__Alloiococcus), s__u(o__mle1-48), g__Lysinibacillus s__boronitolerans, s__u(g__Ralstonia), s__u(g__Candidatus Portiera), s__u(g__Methanosphaera), g__Lactobacillus s__agilis, s__u(o__Rickettsiales), g__Clostridium s__butyricum, s__u(g__Klebsiella), s__u(g__Citrobacter), s__u(g__ph2), s__u(g__Collinsella), s__u(f__Planococcaceae), s__u(f__Erythrobacteraceae), s__u(f__Alcaligenaceae), s__u(f__[Cerasicoccaceae]), s__u(g__Acholeplasma), g__Staphylococcus s__haemolyticus, g__Bifidobacterium s__animalis, s__u(f__Pseudomonadaceae), s__u(o__RF32), s__u(g__Pediococcus), s__u(g__Serratia), s__u(g__Xylanimicrobium), s__u(o__Sphingobacteriales), s__u(g__Cellulomonas), g__Clostridium s__perfringens, s__u(g__Weissella), s__u(f__Bacillaceae), s__u(f__Neisseriaceae), s__u(g__Roseiflexus), s__u(g__Carnobacterium), s__u(f__Nocardioidaceae), s__u(g__WAL_1855D), s__u(g__Treponema), s__u(o__Streptophyta), s__u(g__Beijerinckia), g__Streptococcus s__luteciae, s__u(g__Epulopiscium), g__Brevundimonas s__diminuta, s__u(f__Caulobacteraceae), s__u(o__Bacillales), g__Ruminococcus s__bromii, g__Staphylococcus s__sciuri, s__u(g__Dechloromonas), g__Acinetobacter s__johnsonii, g__Salmonella s__enterica, s__u(g__Streptomyces), s__u(g__Mogibacterium), s__u(g__Geobacillus), g__Ruminococcus s__callidus, s__u(f__Bifidobacteriaceae), s__u(g__Acinetobacter), g__Coprobacillus s__cateniformis, g__Streptococcus s__agalactiae, g__Staphylococcus s__aureus, s__u(f__Peptostreptococcaceae), s__u(o__SHA-98), s__u(f__Cryptosporangiaceae), s__u(o__Burkholderiales), s__u(g__RFN20), s__u(c__OPB56), s__u(g__Meiothermus), s__u(g__Devosia), s__u(c__Mollicutes), s__u(g__Anaerococcus), s__u(f__Desulfovibrionaceae), g__Veillonella s__parvula, g__Lactobacillus s__mucosae, s__u(f__Victivallaceae), s__u(g__Allobaculum), s__u(f__Trebouxiophyceae), g__Weissella s__viridescens, s__u(g__Megasphaera), s__u(g__Psychrobacter), s__u(o__Rhodospirillales), g__Vagococcus s__salmoninarum, s__u(f__Sphingomonadaceae), s__u(g__Kribbella), s__u(g__Holdemania), s__u(g__[Eubacterium]), s__u(g__Thiobacter), s__u(g__Mitsuokella), s__u(g__Acidovorax), s__u(g__Gemella), s__u(g__Acidaminococcus), s__u(g__Thauera), s__u(g__Lysinibacillus), g__Dechloromonas s__fungiphilus, s__u(g__Chryseobacterium), g__[Eubacterium] s__dolichum, g__Bifidobacterium s__longum, s__u(g__Sterolibacterium), s__u(g__Burkholderia), s__u(g__Trichococcus), s__u(g__Paracoccus), s__u(f__[Paraprevotellaceae]), s__u(f__Synergistaceae), s__u(g__Vagococcus), s__u(f__Pasteurellaceae), g__Lactobacillus s__delbrueckii, s__u(g__Arcobacter), s__u(g__Lactococcus), s__u(f__Aerococcaceae), s__u(f__Acetobacteraceae), s__u(g__Alicyclobacillus), s__u(f__Hyphomicrobiaceae), s__u(g__Polaromonas), s__u(f__Xanthomonadaceae), g__Blautia s__producta, s__u(g__1-68), s__u(g__Bradyrhizobium), g__Enterococcus s__casseliflavus, g__Lactococcus s__garvieae, s__u(g__Desulfurella), s__u(g__Polynucleobacter), s__u(g__Ramlibacter), s__u(o__Myxococcales), s__u(g__Campylobacter), s__u(g__TG5), g__Actinobacillus s__parahaemolyticus, s__u(g__Succiniclasticum), s__u(g__Mobiluncus), s__u(g__Sporosarcina), s__u(g__Scardovia), s__u(g__Peptostreptococcus), s__u(g__rc4-4), s__u(g__Pseudoramibacter_Eubacterium), g__[Eubacterium] s__cylindroides, s__u(f__Cytophagaceae), s__u(g__Acidithiobacillus), g__Bacteroides s__caccae, s__u(g__Plesiocystis), s__u(o__Bacteroidales), s__u(f__Saprospiraceae), s__u(g__CF231), s__u(g__Proteus), s__u(o__HOC36), s__u(o__Solirubrobacterales), s__u(g__Veillonella), s__u(g__Roseburia), s__u(g__Rhodoferax), s__u(f__Anaeroplasmataceae), s__u(c__Acidobacteria-5), s__u(p__Cyanobacteria), s__u(f__Leuconostocaceae), g__Acinetobacter s__rhizosphaerae, s__u(g__Butyrivibrio), s__u(o__SBla14), s__u(f__Conexibacteraceae), g__[Prevotella] s__tannerae, s__u(g__Hyphomonas), s__u(f__Prevotellaceae), s__u(g__Stenotrophomonas), s__u(g__Facklamia), s__u(f__Gaiellaceae), g__Rothia s__dentocariosa, s__u(g__Thermus), s__u(g__Methylobacterium), s__u(f__Rhizobiaceae), s__u(g__Hydrogenobaculum), s__u(g__Leuconostoc), g__Streptococcus s__anginosus, s__u(f__Gemellaceae), g__Serratia s__marcescens, g__Streptococcus s__infantis, s__u(g__Macrococcus), g__Haemophilus s__parainfluenzae, s__u(g__Trabulsiella), s__u(f__Burkholderiaceae), s__u(f__Ruaniaceae), s__u(g__Fusobacterium), s__u(f__Isosphaeraceae), s__u(g__Aerococcus), s__u(g__Anaerofustis), g__Rothia s__mucilaginosa, s__u(g__Bdellovibrio), s__u(g__Corynebacterium), g__Leuconostoc s__mesenteroides, s__u(g__Gallicola), g__Bacillus s__muralis, s__u(g__DA101), s__u(f__EtOH8), s__u(g__Solibacillus), s__u(o__Stramenopiles), g__Roseburia s__faecis, s__u(g__Balneimonas), s__u(g__Christensenella), s__u(f__Methylocystaceae), s__u(g__Thiobacillus), s__u(g__Candidatus Koribacter), s__u(f__Hydrogenothermaceae), s__u(f__Thermoanaerobacteraceae), s__u(f__Streptococcaceae), s__u(g__02d06), s__u(g__Parvimonas), s__u(g__Slackia), g__Lactobacillus s__zeae, s__u(g__Bacillus), s__u(f__Polyangiaceae), s__u(f__Rhodobacteraceae), s__u(g__Terracoccus), s__u(g__Fluviicola), s__u(g__Faecalibacterium), g__Bulleidia s__p-1630-c5, s__u(f__Actinomycetaceae), g__Candidatus Nitrososphaera s__SCA1170, g__Bacteroides s__coprophilus, s__u(g__Cellulosimicrobium), s__u(f__Cyclobacteriaceae), s__u(g__Sphingomonas), s__u(g__Arenimonas), s__u(g__Pseudonocardia), s__u(g__Mycobacterium), s__u(f__Sinobacteraceae), s__u(g__Pseudochrobactrum), g__Ruminococcus s__flavefaciens, s__u(g__Comamonas), s__u(f__Comamonadaceae), g__Streptococcus s__sobrinus, g__Pseudomonas s__alcaligenes, g__Streptococcus s__equi, s__u(g__Coprobacillus), s__u(g__Cloacibacillus), s__u(g__Pullulanibacillus), s__u(f__Acidobacteriaceae), g__Bacillus s__flexus, s__u(g__Salinicoccus), g__Bacteroides s__eggerthii, s__u(g__Hyphomicrobium), s__u(g__Granulicatella), s__u(g__Peptoniphilus), s__u(g__Aggregatibacter), s__u(f__Gemmataceae), g__Bifidobacterium s__pseudolongum, s__u(g__Rummeliibacillus), s__u(g__Cardiobacterium)

All results of the test

Model details

trait state
distribution negative binomial
formula feature_abundance ~ group + (1|subject_id)
link function log
number of samples 94

Functional composition

Individual microbial taxa for which relative abundance is significantly different between two groups are identified.

Wilcoxon test comparison

Method: Wilcoxon signed rank test. The analysis includes the following steps: filtration of rare taxa (taxon must be present in at least 10% of the samples at the level of >0.2%), Wilcoxon signed rank test applied to each taxon to detect the taxa differentially abundant between the groups. Multiple testing adjustment is performed using Benjamini–Hochberg procedure. Contribution of each taxon to the inter-group difference is estimated using LDA method. Samples-outliers listed in the taxonomic composition section are excluded from this analysis.

Differentially abundant taxa

Tables of differentially abundant taxa overpresented in the groups

Overpresented in group: 3_treat

pathway metabolic level 2_opisth median, % 3_treat median, % p-value adjusted p-value lda score
ko03410 : Base excision repair KEGG pathways 0.848 0.879 0.0 0.031 2.461

Cladogram of differences

Tree-like summary of the taxa differentially abundant in two groups constructed using LefSe.

List of differentially abundant taxa

increased in 3_treat

denotation feature
a ko03410

Excluded features

KEGG pathways

ko00020 : Citrate cycle (TCA cycle), ko00053 : Ascorbate and aldarate metabolism, ko00062 : Fatty acid elongation, ko00100 : Steroid biosynthesis, ko00120 : Primary bile acid biosynthesis, ko00121 : Secondary bile acid biosynthesis, ko00140 : Steroid hormone biosynthesis, ko00196 : Photosynthesis - antenna proteins, ko00232 : Caffeine metabolism, ko00253 : Tetracycline biosynthesis, ko00280 : Valine, leucine and isoleucine degradation, ko00281 : Geraniol degradation, ko00310 : Lysine degradation, ko00311 : Penicillin and cephalosporin biosynthesis, ko00312 : , ko00331 : Clavulanic acid biosynthesis, ko00350 : Tyrosine metabolism, ko00360 : Phenylalanine metabolism, ko00361 : Chlorocyclohexane and chlorobenzene degradation, ko00362 : Benzoate degradation, ko00363 : Bisphenol degradation, ko00364 : Fluorobenzoate degradation, ko00380 : Tryptophan metabolism, ko00401 : Novobiocin biosynthesis, ko00410 : beta-Alanine metabolism, ko00430 : Taurine and hypotaurine metabolism, ko00440 : Phosphonate and phosphinate metabolism, ko00460 : Cyanoamino acid metabolism, ko00471 : D-Glutamine and D-glutamate metabolism, ko00472 : D-Arginine and D-ornithine metabolism, ko00473 : D-Alanine metabolism, ko00510 : N-Glycan biosynthesis, ko00513 : Various types of N-glycan biosynthesis, ko00514 : Other types of O-glycan biosynthesis, ko00521 : Streptomycin biosynthesis, ko00522 : Biosynthesis of 12-, 14- and 16-membered macrolides, ko00531 : Glycosaminoglycan degradation, ko00532 : Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate, ko00534 : Glycosaminoglycan biosynthesis - heparan sulfate / heparin, ko00562 : Inositol phosphate metabolism, ko00563 : Glycosylphosphatidylinositol (GPI)-anchor biosynthesis, ko00565 : Ether lipid metabolism, ko00590 : Arachidonic acid metabolism, ko00591 : Linoleic acid metabolism, ko00592 : alpha-Linolenic acid metabolism, ko00601 : Glycosphingolipid biosynthesis - lacto and neolacto series, ko00604 : Glycosphingolipid biosynthesis - ganglio series, ko00621 : Dioxin degradation, ko00622 : Xylene degradation, ko00623 : Toluene degradation, ko00625 : Chloroalkane and chloroalkene degradation, ko00626 : Naphthalene degradation, ko00627 : Aminobenzoate degradation, ko00633 : Nitrotoluene degradation, ko00642 : Ethylbenzene degradation, ko00643 : Styrene degradation, ko00785 : Lipoic acid metabolism, ko00791 : Atrazine degradation, ko00830 : Retinol metabolism, ko00901 : Indole alkaloid biosynthesis, ko00905 : Brassinosteroid biosynthesis, ko00906 : Carotenoid biosynthesis, ko00908 : Zeatin biosynthesis, ko00909 : Sesquiterpenoid and triterpenoid biosynthesis, ko00930 : Caprolactam degradation, ko00941 : Flavonoid biosynthesis, ko00943 : Isoflavonoid biosynthesis, ko00945 : Stilbenoid, diarylheptanoid and gingerol biosynthesis, ko00950 : Isoquinoline alkaloid biosynthesis, ko00965 : Betalain biosynthesis, ko00980 : Metabolism of xenobiotics by cytochrome P450, ko00982 : Drug metabolism - cytochrome P450, ko01053 : Biosynthesis of siderophore group nonribosomal peptides, ko01055 : Biosynthesis of vancomycin group antibiotics, ko01056 : Biosynthesis of type II polyketide backbone, ko01057 : Biosynthesis of type II polyketide products, ko03015 : mRNA surveillance pathway, ko03050 : Proteasome, ko03450 : Non-homologous end-joining

KEGG modules

M00001 : Glycolysis (Embden-Meyerhof pathway), glucose => pyruvate, M00002 : Glycolysis, core module involving three-carbon compounds, M00006 : Pentose phosphate pathway, oxidative phase, glucose 6P => ribulose 5P, M00008 : Entner-Doudoroff pathway, glucose-6P => glyceraldehyde-3P + pyruvate, M00010 : Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate, M00011 : Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate, M00012 : Glyoxylate cycle, M00013 : Malonate semialdehyde pathway, propanoyl-CoA => acetyl-CoA, M00024 : Phenylalanine biosynthesis, chorismate => phenylalanine, M00027 : GABA (gamma-Aminobutyrate) shunt, M00031 : Lysine biosynthesis, mediated by LysW, 2-aminoadipate => lysine, M00032 : Lysine degradation, lysine => saccharopine => acetoacetyl-CoA, M00033 : Ectoine biosynthesis, aspartate => ectoine, M00034 : Methionine salvage pathway, M00036 : Leucine degradation, leucine => acetoacetate + acetyl-CoA, M00037 : Melatonin biosynthesis, tryptophan => serotonin => melatonin, M00038 : Tryptophan metabolism, tryptophan => kynurenine => 2-aminomuconate, M00040 : Tyrosine biosynthesis, prephanate => pretyrosine => tyrosine, M00042 : Catecholamine biosynthesis, tyrosine => dopamine => noradrenaline => adrenaline, M00044 : Tyrosine degradation, tyrosine => homogentisate, M00045 : Histidine degradation, histidine => N-formiminoglutamate => glutamate, M00046 : Pyrimidine degradation, uracil => beta-alanine, thymine => 3-aminoisobutanoate, M00047 : Creatine pathway, M00055 : N-glycan precursor biosynthesis, M00057 : Glycosaminoglycan biosynthesis, linkage tetrasaccharide, M00061 : D-Glucuronate degradation, D-glucuronate => pyruvate + D-glyceraldehyde 3P, M00064 : ADP-L-glycero-D-manno-heptose biosynthesis, M00065 : GPI-anchor biosynthesis, core oligosaccharide, M00066 : Lactosylceramide biosynthesis, M00072 : N-glycosylation by oligosaccharyltransferase, M00074 : N-glycan biosynthesis, high-mannose type, M00075 : N-glycan biosynthesis, complex type, M00077 : Chondroitin sulfate degradation, M00078 : Heparan sulfate degradation, M00079 : Keratan sulfate degradation, M00080 : , M00081 : Pectin degradation, M00082 : Fatty acid biosynthesis, initiation, M00085 : Fatty acid biosynthesis, elongation, mitochondria, M00087 : beta-Oxidation, M00088 : Ketone body biosynthesis, acetyl-CoA => acetoacetate/3-hydroxybutyrate/acetone, M00090 : Phosphatidylcholine (PC) biosynthesis, choline => PC, M00091 : Phosphatidylcholine (PC) biosynthesis, PE => PC, M00095 : C5 isoprenoid biosynthesis, mevalonate pathway, M00097 : beta-Carotene biosynthesis, GGAP => beta-carotene, M00098 : Acylglycerol degradation, M00099 : Sphingosine biosynthesis, M00100 : Sphingosine degradation, M00101 : Cholesterol biosynthesis, squalene 2,3-epoxide => cholesterol, M00102 : Ergocalciferol biosynthesis, M00104 : Bile acid biosynthesis, cholesterol => cholate/chenodeoxycholate, M00109 : C21-Steroid hormone biosynthesis, progesterone => cortisol/cortisone, M00110 : C19/C18-Steroid hormone biosynthesis, pregnenolone => androstenedione => estrone, M00112 : Tocopherol/tocotorienol biosynthesis, M00113 : Jasmonic acid biosynthesis, M00117 : Ubiquinone biosynthesis, prokaryotes, chorismate => ubiquinone, M00118 : Glutathione biosynthesis, glutamate => glutathione, M00128 : Ubiquinone biosynthesis, eukaryotes, 4-hydroxybenzoate => ubiquinone, M00129 : Ascorbate biosynthesis, animals, glucose-1P => ascorbate, M00131 : Inositol phosphate metabolism, Ins(1,3,4,5)P4 => Ins(1,3,4)P3 => myo-inositol, M00134 : Polyamine biosynthesis, arginine => ornithine => putrescine, M00135 : GABA biosynthesis, eukaryotes, putrescine => GABA, M00136 : GABA biosynthesis, prokaryotes, putrescine => GABA, M00137 : Flavanone biosynthesis, phenylalanine => naringenin, M00141 : C1-unit interconversion, eukaryotes, M00142 : NADH:ubiquinone oxidoreductase, mitochondria, M00143 : NADH dehydrogenase (ubiquinone) Fe-S protein/flavoprotein complex, mitochondria, M00145 : NAD(P)H:quinone oxidoreductase, chloroplasts and cyanobacteria, M00146 : NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, M00148 : Succinate dehydrogenase (ubiquinone), M00151 : Cytochrome bc1 complex respiratory unit, M00152 : Cytochrome bc1 complex, M00153 : Cytochrome bd ubiquinol oxidase, M00154 : Cytochrome c oxidase, M00155 : Cytochrome c oxidase, prokaryotes, M00156 : Cytochrome c oxidase, cbb3-type, M00158 : F-type ATPase, eukaryotes, M00161 : Photosystem II, M00162 : Cytochrome b6f complex, M00163 : Photosystem I, M00166 : Reductive pentose phosphate cycle, ribulose-5P => glyceraldehyde-3P, M00170 : C4-dicarboxylic acid cycle, phosphoenolpyruvate carboxykinase type, M00171 : C4-dicarboxylic acid cycle, NAD - malic enzyme type, M00172 : C4-dicarboxylic acid cycle, NADP - malic enzyme type, M00174 : Methane oxidation, methanotroph, methane => formaldehyde, M00175 : Nitrogen fixation, nitrogen => ammonia, M00176 : Assimilatory sulfate reduction, sulfate => H2S, M00177 : Ribosome, eukaryotes, M00182 : RNA polymerase I, eukaryotes, M00184 : RNA polymerase, archaea, M00186 : Tungstate transport system, M00191 : Thiamine transport system, M00192 : Putative thiamine transport system, M00193 : Putative spermidine/putrescine transport system, M00197 : Putative fructooligosaccharide transport system, M00198 : Putative sn-glycerol-phosphate transport system, M00200 : Putative sorbitol/mannitol transport system, M00201 : alpha-Glucoside transport system, M00202 : Oligogalacturonide transport system, M00203 : Glucose/arabinose transport system, M00204 : Trehalose/maltose transport system, M00206 : Cellobiose transport system, M00208 : Glycine betaine/proline transport system, M00209 : Osmoprotectant transport system, M00210 : Phospholipid transport system, M00211 : Putative ABC transport system, M00213 : L-Arabinose transport system, M00215 : D-Xylose transport system, M00217 : D-Allose transport system, M00218 : Fructose transport system, M00219 : AI-2 transport system, M00220 : Rhamnose transport system, M00223 : Phosphonate transport system, M00225 : Lysine/arginine/ornithine transport system, M00226 : Histidine transport system, M00227 : Glutamine transport system, M00229 : Arginine transport system, M00230 : Glutamate/aspartate transport system, M00231 : Octopine/nopaline transport system, M00232 : General L-amino acid transport system, M00233 : Glutamate transport system, M00234 : L-Cystine transport system, M00235 : Arginine/ornithine transport system, M00241 : Vitamin B12 transport system, M00243 : Manganese/iron transport system, M00244 : Putative zinc/manganese transport system, M00249 : Capsular polysaccharide transport system, M00251 : Teichoic acid transport system, M00252 : Lipooligosaccharide transport system, M00253 : Sodium transport system, M00255 : Lipoprotein-releasing system, M00257 : Hemin transport system, M00259 : Heme transport system, M00261 : DNA polymerase alpha / primase complex, M00264 : DNA polymerase II complex, archaea, M00265 : PTS system, glucose-specific II component, M00266 : PTS system, maltose/glucose-specific II component, M00267 : PTS system, N-acetylglucosamine-specific II component, M00268 : PTS system, alpha-glucoside-specific II component, M00269 : PTS system, sucrose-specific II component, M00270 : PTS system, trehalose-specific II component, M00272 : PTS system, beta-glucoside (arbutin/salicin/cellobiose)-specific II component, M00273 : PTS system, fructose-specific II component, M00274 : PTS system, mannitol-specific II component, M00277 : PTS system, N-acetylgalactosamine-specific II component, M00278 : PTS system, sorbose-specific II component, M00279 : PTS system, galactitol-specific II component, M00280 : PTS system, glucitol/sorbitol-specific II component, M00281 : PTS system, lactose-specific II component, M00282 : PTS system, D-glucosamine-specific II component, M00287 : PTS system, galactosamine-specific II component, M00288 : RPA complex, M00290 : Holo-TFIIH complex, M00295 : BRCA1-associated genome surveillance complex (BASC), M00296 : BER complex, M00298 : Multidrug/hemolysin transport system, M00300 : Putrescine transport system, M00301 : Mannopine transport system, M00302 : 2-Aminoethylphosphonate transport system, M00303 : PTS system, N-acetylmuramic acid-specific II component, M00304 : PTS system, fructose-specific II component, M00305 : PTS system, 2-O-A-mannosyl-D-glycerate-specific II component, M00306 : PTS system, fructose-specific II-like component, M00309 : Non-phosphorylative Entner-Doudoroff pathway, gluconate/galactonate => glycerate, M00315 : Uncharacterized ABC transport system, M00316 : Manganese transport system, M00317 : Manganese/iron transport system, M00318 : Iron/zinc/manganese/copper transport system, M00319 : Manganese/zinc/iron transport system, M00320 : Lipopolysaccharide export system, M00321 : Bicarbonate transport system, M00322 : Neutral amino acid transport system, M00323 : Urea transport system, M00324 : Dipeptide transport system, M00326 : RTX toxin transport system, M00327 : S-Layer protein transport system, M00328 : Hemophore/metalloprotease transport system, M00329 : Multiple protein transport system, M00330 : Adhesin protein transport system, M00332 : Type III secretion system, M00334 : Type VI secretion system, M00336 : Twin-arginine translocation (Tat) system, M00338 : Cysteine biosynthesis, homocysteine + serine => cysteine, M00339 : RaxAB-RaxC type I secretion system, M00341 : Proteasome, 19S regulatory particle (PA700), M00342 : Bacterial proteasome, M00343 : Archaeal proteasome, M00344 : Formaldehyde assimilation, xylulose monophosphate pathway, M00346 : Formaldehyde assimilation, serine pathway, M00348 : Glutathione transport system, M00349 : Microcin C transport system, M00350 : , M00354 : Spliceosome, U4/U6.U5 tri-snRNP, M00355 : Spliceosome, 35S U5-snRNP, M00356 : Methanogenesis, methanol => methane, M00357 : Methanogenesis, acetate => methane, M00358 : Coenzyme M biosynthesis, M00363 : EHEC pathogenicity signature, Shiga toxin, M00364 : C10-C20 isoprenoid biosynthesis, bacteria, M00365 : C10-C20 isoprenoid biosynthesis, archaea, M00367 : C10-C20 isoprenoid biosynthesis, non-plant eukaryotes, M00368 : Ethylene biosynthesis, methionine => ethylene, M00371 : Castasterone biosynthesis, campesterol => castasterone, M00372 : Abscisic acid biosynthesis, beta-carotene => abscisic acid, M00373 : Ethylmalonyl pathway, M00374 : Dicarboxylate-hydroxybutyrate cycle, M00375 : Hydroxypropionate-hydroxybutylate cycle, M00378 : F420 biosynthesis, M00391 : Exosome, eukaryotes, M00392 : Ski complex, M00401 : Sec61 complex, M00403 : HRD1/SEL1 ERAD complex, M00413 : FA core complex, M00414 : Bloom's syndrome complex, M00415 : Fatty acid biosynthesis, elongation, endoplasmic reticulum, M00416 : Cytochrome aa3-600 menaquinol oxidase, M00417 : Cytochrome o ubiquinol oxidase, M00418 : Toluene degradation, anaerobic, toluene => benzoyl-CoA, M00419 : Cymene degradation, p-cymene => p-cumate, M00422 : Acetyl-CoA pathway, CO2 => acetyl-CoA, M00433 : Lysine biosynthesis, 2-oxoglutarate => 2-oxoadipate, M00439 : Oligopeptide transport system, M00443 : SenX3-RegX3 (phosphate starvation response) two-component regulatory system, M00446 : RstB-RstA two-component regulatory system, M00448 : CssS-CssR (secretion stress response) two-component regulatory system, M00449 : CreC-CreB (phosphate regulation) two-component regulatory system, M00453 : QseC-QseB (quorum sensing) two-component regulatory system, M00455 : TorS-TorR (TMAO respiration) two-component regulatory system, M00456 : ArcB-ArcA (anoxic redox control) two-component regulatory system, M00457 : TctE-TctD (tricarboxylic acid transport) two-component regulatory system, M00458 : ResE-ResD (aerobic and anaerobic respiration) two-component regulatory system, M00459 : VicK-VicR (cell wall metabolism) two-component regulatory system, M00460 : MprB-MprA (maintenance of persistent infection) two-component regulatory system, M00461 : MtrB-MtrA (osmotic stress response) two-component regulatory system, M00462 : PrrB-PrrA (intracellular multiplication) two-component regulatory system, M00463 : TrcS-TrcR two-component regulatory system, M00464 : NrsS-NrsR (nickel tolerance) two-component regulatory system, M00465 : ManS-ManR (manganese homeostasis) two-component regulatory system, M00466 : NblS-NblR (photosynthesis) two-component regulatory system, M00467 : SasA-RpaAB (circadian timing mediating) two-component regulatory system, M00468 : SaeS-SaeR (staphylococcal virulence regulation) two-component regulatory system, M00470 : YxdK-YxdJ (antimicrobial peptide response) two-component regulatory system, M00471 : NarX-NarL (nitrate respiration) two-component regulatory system, M00472 : NarQ-NarP (nitrate respiration) two-component regulatory system, M00473 : UhpB-UhpA (hexose phosphates uptake) two-component regulatory system, M00474 : RcsC-RcsD-RcsB (capsule synthesis) two-component regulatory system, M00475 : BarA-UvrY (central carbon metabolism) two-component regulatory system, M00476 : ComP-ComA (competence) two-component regulatory system, M00477 : EvgS-EvgA (acid and drug tolerance) two-component regulatory system, M00478 : DegS-DegU (multicellular behavior control) two-component regulatory system, M00479 : DesK-DesR (membrane lipid fluidity regulation) two-component regulatory system, M00480 : VraS-VraR (cell-wall peptidoglycan synthesis) two-component regulatory system, M00482 : DevS-DevR (redox response) two-component regulatory system, M00483 : NreB-NreC (dissimilatory nitrate/nitrite reduction) two-component regulatory system, M00484 : YdfH-YdfI two-component regulatory system, M00485 : KinABCDE-Spo0FA (sporulation control) two-component regulatory system, M00486 : CitA-CitB (citrate fermentation) two-component regulatory system, M00487 : CitS-CitT (magnesium-citrate transport) two-component regulatory system, M00488 : DcuS-DcuR (C4-dicarboxylate metabolism) two-component regulatory system, M00490 : MalK-MalR (malate transport) two-component regulatory system, M00491 : arabinogalactan oligomer/maltooligosaccharide transport system, M00492 : LytS-LytR two-component regulatory system, M00493 : AlgZ-AlgR (alginate production) two-component regulatory system, M00494 : NatK-NatR (sodium extrusion) two-component regulatory system, M00495 : AgrC-AgrA (exoprotein synthesis) two-component regulatory system, M00496 : ComD-ComE (competence) two-component regulatory system, M00497 : GlnL-GlnG (nitrogen regulation) two-component regulatory system, M00498 : NtrY-NtrX (nitrogen regulation) two-component regulatory system, M00499 : HydH-HydG (metal tolerance) two-component regulatory system, M00500 : AtoS-AtoC (cPHB biosynthesis) two-component regulatory system, M00501 : PilS-PilR (type 4 fimbriae synthesis) two-component regulatory system, M00502 : GlrK-GlrR (amino sugar metabolism) two-component regulatory system, M00503 : PgtB-PgtA (phosphoglycerate transport) two-component regulatory system, M00504 : DctB-DctD (C4-dicarboxylate transport) two-component regulatory system, M00505 : KinB-AlgB (alginate production) two-component regulatory system, M00507 : ChpA-ChpB/PilGH (chemosensory) two-component regulatory system, M00508 : PixL-PixGH (positive phototaxis) two-component regulatory system, M00509 : WspE-WspRF (chemosensory) two-component regulatory system, M00510 : Cph1-Rcp1 (light response) two-component regulatory system, M00511 : PleC-PleD (cell fate control) two-component regulatory system, M00512 : CckA-CtrA/CpdR (cell cycle control) two-component regulatory system, M00513 : LuxQN/CqsS-LuxU-LuxO (quorum sensing) two-component regulatory system, M00514 : TtrS-TtrR (tetrathionate respiration) two-component regulatory system, M00515 : FlrB-FlrC (polar flagellar synthesis) two-component regulatory system, M00517 : RpfC-RpfG (cell-to-cell signaling) two-component regulatory system, M00518 : GlnK-GlnL (glutamine utilization) two-component regulatory system, M00525 : Lysine biosynthesis, acetyl-DAP pathway, aspartate => lysine, M00526 : Lysine biosynthesis, DAP dehydrogenase pathway, aspartate => lysine, M00529 : Denitrification, nitrate => nitrogen, M00530 : Dissimilatory nitrate reduction, nitrate => ammonia, M00531 : Assimilatory nitrate reduction, nitrate => ammonia, M00533 : Homoprotocatechuate degradation, homoprotocatechuate => 2-oxohept-3-enedioate, M00534 : Naphthalene degradation, naphthalene => salicylate, M00538 : Toluene degradation, toluene => benzoate, M00539 : Cumate degradation, p-cumate => 2-oxopent-4-enoate + 2-methylpropanoate, M00540 : Benzoate degradation, cyclohexanecarboxylic acid =>pimeloyl-CoA, M00541 : Benzoyl-CoA degradation, benzoyl-CoA => 3-hydroxypimeloyl-CoA, M00542 : EHEC/EPEC pathogenicity signature, T3SS and effectors, M00543 : Biphenyl degradation, biphenyl => 2-oxopent-4-enoate + benzoate, M00545 : Trans-cinnamate degradation, trans-cinnamate => acetyl-CoA, M00546 : Purine degradation, xanthine => urea, M00547 : Benzene/toluene degradation, benzene => catechol / toluene => 3-methylcatechol, M00550 : Ascorbate degradation, ascorbate => D-xylulose-5P, M00551 : Benzoate degradation, benzoate => catechol / methylbenzoate => methylcatechol, M00555 : Betaine biosynthesis, choline => betaine, M00563 : Methanogenesis, methylamine/dimethylamine/trimethylamine => methane, M00564 : Helicobacter pylori pathogenicity signature, cagA pathogenicity island, M00568 : Catechol ortho-cleavage, catechol => 3-oxoadipate, M00569 : Catechol meta-cleavage, catechol => acetyl-CoA / 4-methylcatechol => propanoyl-CoA, M00574 : Pertussis pathogenicity signature, pertussis toxin, M00575 : Pertussis pathogenicity signature, T1SS, M00580 : Pentose phosphate pathway, archaea, fructose 6P => ribose 5P, M00595 : Thiosulfate oxidation by SOX complex, thiosulfate => sulfate, M00597 : Anoxygenic photosystem II, M00598 : Anoxygenic photosystem I, M00606 : N,N'-Diacetylchitobiose transport system, M00608 : 2-Oxocarboxylic acid chain extension, 2-oxoglutarate => 2-oxoadipate => 2-oxopimelate => 2-oxosuberate, M00615 : Nitrate assimilation, M00622 : Nicotinate degradation, nicotinate => fumarate, M00623 : Phthalate degradation, phthalate => protocatechuate, M00625 : Methicillin resistance, M00627 : beta-Lactam resistance, Bla system, M00633 : Semi-phosphorylative Entner-Doudoroff pathway, gluconate/galactonate => glycerate-3P, M00637 : Anthranilate degradation, anthranilate => catechol, M00638 : Salicylate degradation, salicylate => gentisate, M00639 : Multidrug resistance, efflux pump MexCD-OprJ, M00647 : Multidrug resistance, efflux pump AcrAB-TolC/SmeDEF, M00648 : Multidrug resistance, efflux pump MdtABC, M00651 : Vancomycin resistance, D-Ala-D-Lac type, M00660 : Xanthomonas spp. pathogenicity signature, T3SS and effectors, M00662 : Hk1-Rrp1 (glycerol uptake and utilization) two-component regulatory system, M00664 : Nodulation, M00668 : Tetracycline resistance, TetA transporter, M00670 : Mce transport system, M00672 : Penicillin biosynthesis, aminoadipate + cycteine + valine => penicillin, M00673 : Cephamycin C biosynthesis, aminoadipate + cycteine + valine => cephamycin C, M00674 : Clavaminate biosynthesis, arginine + glyceraldehyde-3P => clavaminate, M00695 : cAMP signaling, M00697 : Multidrug resistance, efflux pump MdtEF-TolC, M00701 : Multidrug resistance, efflux pump EmrAB, M00702 : Multidrug resistance, efflux pump NorB, M00704 : Tetracycline resistance, efflux pump Tet38, M00709 : Macrolide resistance, MacAB-TolC transporter, M00710 : Multidrug resistance, efflux pump EbrAB, M00711 : Multidrug resistance, efflux pump MdtIJ, M00714 : Multidrug resistance, efflux pump QacA, M00717 : Multidrug resistance, efflux pump NorA, M00718 : Multidrug resistance, efflux pump MexAB-OprM, M00720 : Multidrug resistance, efflux pump VexEF-TolC, M00721 : Cationic antimicrobial peptide (CAMP) resistance, arnBCADTEF operon, M00722 : Cationic antimicrobial peptide (CAMP) resistance, ethanolaminephosphotransferase EptA, M00723 : Cationic antimicrobial peptide (CAMP) resistance, ethanolaminephosphotransferase EptB, M00724 : Cationic antimicrobial peptide (CAMP) resistance, palmitoyl transferase PagP, M00725 : Cationic antimicrobial peptide (CAMP) resistance, dltABCD operon, M00726 : Cationic antimicrobial peptide (CAMP) resistance, lysyl-phosphatidylglycerol (L-PG) synthase MprF, M00728 : Cationic antimicrobial peptide (CAMP) resistance, envelope protein folding and degrading factors DegP and DsbA, M00736 : Nocardicin A biosynthesis, L-pHPG + arginine + serine => nocardicin A, M00738 : Bacitracin resistance, BceAB transporter, M00741 : Propanoyl-CoA metabolism, propanoyl-CoA => succinyl-CoA, M00743 : Aminoglycoside resistance, protease HtpX, M00744 : Cationic antimicrobial peptide (CAMP) resistance, protease PgtE, M00745 : Imipenem resistance, repression of porin OprD, M00746 : Multidrug resistance, repression of porin OmpF, M00754 : Nisin resistance, phage shock protein homolog LiaH, M00760 : Erythromycin resistance, macrolide 2'-phosphotransferase I MphA, M00761 : Undecaprenylphosphate alpha-L-Ara4N biosynthesis, UDP-GlcA => undecaprenyl phosphate alpha-L-Ara4N, M00763 : Ornithine biosynthesis, mediated by LysW, glutamate => ornithine, M00766 : Streptomycin resistance, deactivating enzyme StrAB, M00767 : Multidrug resistance, efflux pump OqxAB, M00774 : Erythromycin biosynthesis, propanoyl-CoA + methylmalonyl-CoA => deoxyerythronolide B => erythromycin A/B, M00777 : Avermectin biosynthesis, 2-methylbutanoyl-CoA/isobutyryl-CoA => 6,8a-Seco-6,8a-deoxy-5-oxoavermectin 1a/1b aglycone => avermectin A1a/B1a/A1b/B1b, M00778 : Type II polyketide backbone biosynthesis, acyl-CoA + malonyl-CoA => polyketide, M00779 : Dihydrokalafungin biosynthesis, octaketide => dihydrokalafungin, M00790 : Pyrrolnitrin biosynthesis, tryptophan => pyrrolnitrin, M00798 : dTDP-L-mycarose biosynthesis, M00804 : Complete nitrification, comammox, ammonia => nitrite => nitrate, M00806 : PTS system, maltose-specific II component, M00819 : Pentalenolactone biosynthesis, farnesyl-PP => pentalenolactone

Generalized linear mixed effect model

A generalized mixed effects linear model is fitted for each taxon to identify if it is differentially abundant between the groups. "Subject_id", is treated as a random effect. The specific probability distribution is selected heuristically depending on the number of samples. For >100 samples, a zero-inflated negative binomial regression is fitted; in other cases - a negative binomial model. 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. Contribution of each taxon to the inter-group difference is estimated using LDA method. The information about distribution family, terms of the model and sample size is displayed in "Model details" section.

Differentially abundant taxa

Tables of differentially abundant taxa overpresented in the groups

Overpresented in group: 2_opisth

pathway metabolic level 3_treat mean, % 3_treat sd, % 2_opisth mean, % 2_opisth sd, % p-value adjusted p-value lda score sample size
ko00130 : Ubiquinone and other terpenoid-quinone biosynthesis KEGG pathways 0.205 0.076 0.284 0.176 0.007 0.047 3.534 94
ko00480 : Glutathione metabolism KEGG pathways 0.293 0.039 0.346 0.110 0.003 0.047 3.337 94
ko00260 : Glycine, serine and threonine metabolism KEGG pathways 0.218 0.031 0.251 0.070 0.003 0.047 3.279 94
ko00010 : KEGG pathways 0.435 0.021 0.451 0.040 0.007 0.047 3.027 94
ko00270 : Cysteine and methionine metabolism KEGG pathways 0.939 0.037 0.960 0.044 0.004 0.047 2.875 94

Overpresented in group: 3_treat

pathway metabolic level 3_treat mean, % 3_treat sd, % 2_opisth mean, % 2_opisth sd, % p-value adjusted p-value lda score sample size
ko00051 : Fructose and mannose metabolism KEGG pathways 0.766 0.131 0.679 0.101 0.001 0.020 3.418 94
ko00680 : Methane metabolism KEGG pathways 2.961 0.289 2.796 0.291 0.008 0.047 3.383 94
ko00500 : Starch and sucrose metabolism KEGG pathways 1.705 0.119 1.625 0.141 0.004 0.047 3.323 94
ko00511 : Other glycan degradation KEGG pathways 0.268 0.050 0.236 0.062 0.005 0.047 3.274 94
ko03410 : Base excision repair KEGG pathways 0.878 0.034 0.850 0.037 0.000 0.010 3.247 94
ko00660 : C5-Branched dibasic acid metabolism KEGG pathways 0.650 0.067 0.610 0.071 0.008 0.047 3.211 94
ko00523 : Polyketide sugar unit biosynthesis KEGG pathways 0.468 0.045 0.436 0.061 0.005 0.047 3.194 94
ko00603 : Glycosphingolipid biosynthesis - globo and isoglobo series KEGG pathways 0.204 0.021 0.191 0.025 0.007 0.047 3.004 94

Cladogram of differences

Tree-like summary of the taxa differentially abundant in two groups constructed using LefSe.

List of differentially abundant taxa

increased in 3_treat

denotation feature
b ko00051
g ko00500
h ko00511
i ko00523
j ko00603
k ko00660
l ko00680
m ko03410

increased in 2_opisth

denotation feature
a ko00010
c ko00130
d ko00260
e ko00270
f ko00480

Excluded features

KEGG pathways

ko00312 : , ko00980 : Metabolism of xenobiotics by cytochrome P450, ko00053 : Ascorbate and aldarate metabolism, ko00563 : Glycosylphosphatidylinositol (GPI)-anchor biosynthesis, ko00643 : Styrene degradation, ko00100 : Steroid biosynthesis, ko00943 : Isoflavonoid biosynthesis, ko00941 : Flavonoid biosynthesis, ko00311 : Penicillin and cephalosporin biosynthesis, ko00410 : beta-Alanine metabolism, ko00331 : Clavulanic acid biosynthesis, ko00642 : Ethylbenzene degradation, ko00633 : Nitrotoluene degradation, ko00908 : Zeatin biosynthesis, ko00590 : Arachidonic acid metabolism, ko00140 : Steroid hormone biosynthesis, ko01053 : Biosynthesis of siderophore group nonribosomal peptides, ko00623 : Toluene degradation, ko00565 : Ether lipid metabolism, ko00791 : Atrazine degradation, ko03015 : mRNA surveillance pathway, ko00785 : Lipoic acid metabolism, ko00361 : Chlorocyclohexane and chlorobenzene degradation, ko00625 : Chloroalkane and chloroalkene degradation, ko00513 : Various types of N-glycan biosynthesis, ko00930 : Caprolactam degradation, ko01057 : Biosynthesis of type II polyketide products, ko00362 : Benzoate degradation, ko03450 : Non-homologous end-joining, ko00363 : Bisphenol degradation, ko00471 : D-Glutamine and D-glutamate metabolism, ko00310 : Lysine degradation, ko00622 : Xylene degradation, ko00196 : Photosynthesis - antenna proteins, ko00020 : Citrate cycle (TCA cycle), ko00521 : Streptomycin biosynthesis, ko00945 : Stilbenoid, diarylheptanoid and gingerol biosynthesis, ko00460 : Cyanoamino acid metabolism, ko00965 : Betalain biosynthesis, ko00592 : alpha-Linolenic acid metabolism, ko00253 : Tetracycline biosynthesis, ko00627 : Aminobenzoate degradation, ko00621 : Dioxin degradation, ko00472 : D-Arginine and D-ornithine metabolism, ko00510 : N-Glycan biosynthesis, ko00906 : Carotenoid biosynthesis, ko00601 : Glycosphingolipid biosynthesis - lacto and neolacto series, ko00473 : D-Alanine metabolism, ko00364 : Fluorobenzoate degradation, ko00062 : Fatty acid elongation, ko00232 : Caffeine metabolism, ko00350 : Tyrosine metabolism, ko00514 : Other types of O-glycan biosynthesis, ko01056 : Biosynthesis of type II polyketide backbone, ko00360 : Phenylalanine metabolism, ko00909 : Sesquiterpenoid and triterpenoid biosynthesis, ko00626 : Naphthalene degradation, ko00380 : Tryptophan metabolism, ko01055 : Biosynthesis of vancomycin group antibiotics, ko00830 : Retinol metabolism, ko00604 : Glycosphingolipid biosynthesis - ganglio series, ko00982 : Drug metabolism - cytochrome P450, ko00430 : Taurine and hypotaurine metabolism, ko00440 : Phosphonate and phosphinate metabolism, ko00522 : Biosynthesis of 12-, 14- and 16-membered macrolides, ko00591 : Linoleic acid metabolism, ko03050 : Proteasome, ko00280 : Valine, leucine and isoleucine degradation, ko00281 : Geraniol degradation, ko00531 : Glycosaminoglycan degradation, ko00534 : Glycosaminoglycan biosynthesis - heparan sulfate / heparin, ko00905 : Brassinosteroid biosynthesis, ko00562 : Inositol phosphate metabolism, ko00120 : Primary bile acid biosynthesis, ko00901 : Indole alkaloid biosynthesis, ko00532 : Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate, ko00950 : Isoquinoline alkaloid biosynthesis, ko00401 : Novobiocin biosynthesis, ko00121 : Secondary bile acid biosynthesis

KEGG modules

M00476 : ComP-ComA (competence) two-component regulatory system, M00492 : LytS-LytR two-component regulatory system, M00295 : BRCA1-associated genome surveillance complex (BASC), M00088 : Ketone body biosynthesis, acetyl-CoA => acetoacetate/3-hydroxybutyrate/acetone, M00391 : Exosome, eukaryotes, M00151 : Cytochrome bc1 complex respiratory unit, M00608 : 2-Oxocarboxylic acid chain extension, 2-oxoglutarate => 2-oxoadipate => 2-oxopimelate => 2-oxosuberate, M00718 : Multidrug resistance, efflux pump MexAB-OprM, M00176 : Assimilatory sulfate reduction, sulfate => H2S, M00184 : RNA polymerase, archaea, M00475 : BarA-UvrY (central carbon metabolism) two-component regulatory system, M00326 : RTX toxin transport system, M00413 : FA core complex, M00206 : Cellobiose transport system, M00209 : Osmoprotectant transport system, M00033 : Ectoine biosynthesis, aspartate => ectoine, M00319 : Manganese/zinc/iron transport system, M00763 : Ornithine biosynthesis, mediated by LysW, glutamate => ornithine, M00218 : Fructose transport system, M00171 : C4-dicarboxylic acid cycle, NAD - malic enzyme type, M00257 : Hemin transport system, M00080 : , M00346 : Formaldehyde assimilation, serine pathway, M00529 : Denitrification, nitrate => nitrogen, M00595 : Thiosulfate oxidation by SOX complex, thiosulfate => sulfate, M00002 : Glycolysis, core module involving three-carbon compounds, M00743 : Aminoglycoside resistance, protease HtpX, M00449 : CreC-CreB (phosphate regulation) two-component regulatory system, M00518 : GlnK-GlnL (glutamine utilization) two-component regulatory system, M00110 : C19/C18-Steroid hormone biosynthesis, pregnenolone => androstenedione => estrone, M00495 : AgrC-AgrA (exoprotein synthesis) two-component regulatory system, M00701 : Multidrug resistance, efflux pump EmrAB, M00118 : Glutathione biosynthesis, glutamate => glutathione, M00102 : Ergocalciferol biosynthesis, M00098 : Acylglycerol degradation, M00055 : N-glycan precursor biosynthesis, M00210 : Phospholipid transport system, M00211 : Putative ABC transport system, M00711 : Multidrug resistance, efflux pump MdtIJ, M00231 : Octopine/nopaline transport system, M00697 : Multidrug resistance, efflux pump MdtEF-TolC, M00203 : Glucose/arabinose transport system, M00280 : PTS system, glucitol/sorbitol-specific II component, M00223 : Phosphonate transport system, M00627 : beta-Lactam resistance, Bla system, M00012 : Glyoxylate cycle, M00509 : WspE-WspRF (chemosensory) two-component regulatory system, M00668 : Tetracycline resistance, TetA transporter, M00343 : Archaeal proteasome, M00074 : N-glycan biosynthesis, high-mannose type, M00267 : PTS system, N-acetylglucosamine-specific II component, M00129 : Ascorbate biosynthesis, animals, glucose-1P => ascorbate, M00364 : C10-C20 isoprenoid biosynthesis, bacteria, M00474 : RcsC-RcsD-RcsB (capsule synthesis) two-component regulatory system, M00538 : Toluene degradation, toluene => benzoate, M00128 : Ubiquinone biosynthesis, eukaryotes, 4-hydroxybenzoate => ubiquinone, M00233 : Glutamate transport system, M00368 : Ethylene biosynthesis, methionine => ethylene, M00334 : Type VI secretion system, M00546 : Purine degradation, xanthine => urea, M00564 : Helicobacter pylori pathogenicity signature, cagA pathogenicity island, M00087 : beta-Oxidation, M00766 : Streptomycin resistance, deactivating enzyme StrAB, M00574 : Pertussis pathogenicity signature, pertussis toxin, M00419 : Cymene degradation, p-cymene => p-cumate, M00161 : Photosystem II, M00720 : Multidrug resistance, efflux pump VexEF-TolC, M00459 : VicK-VicR (cell wall metabolism) two-component regulatory system, M00433 : Lysine biosynthesis, 2-oxoglutarate => 2-oxoadipate, M00482 : DevS-DevR (redox response) two-component regulatory system, M00371 : Castasterone biosynthesis, campesterol => castasterone, M00235 : Arginine/ornithine transport system, M00191 : Thiamine transport system, M00494 : NatK-NatR (sodium extrusion) two-component regulatory system, M00497 : GlnL-GlnG (nitrogen regulation) two-component regulatory system, M00471 : NarX-NarL (nitrate respiration) two-component regulatory system, M00541 : Benzoyl-CoA degradation, benzoyl-CoA => 3-hydroxypimeloyl-CoA, M00287 : PTS system, galactosamine-specific II component, M00443 : SenX3-RegX3 (phosphate starvation response) two-component regulatory system, M00044 : Tyrosine degradation, tyrosine => homogentisate, M00213 : L-Arabinose transport system, M00651 : Vancomycin resistance, D-Ala-D-Lac type, M00468 : SaeS-SaeR (staphylococcal virulence regulation) two-component regulatory system, M00721 : Cationic antimicrobial peptide (CAMP) resistance, arnBCADTEF operon, M00673 : Cephamycin C biosynthesis, aminoadipate + cycteine + valine => cephamycin C, M00439 : Oligopeptide transport system, M00234 : L-Cystine transport system, M00415 : Fatty acid biosynthesis, elongation, endoplasmic reticulum, M00177 : Ribosome, eukaryotes, M00467 : SasA-RpaAB (circadian timing mediating) two-component regulatory system, M00633 : Semi-phosphorylative Entner-Doudoroff pathway, gluconate/galactonate => glycerate-3P, M00342 : Bacterial proteasome, M00104 : Bile acid biosynthesis, cholesterol => cholate/chenodeoxycholate, M00298 : Multidrug/hemolysin transport system, M00306 : PTS system, fructose-specific II-like component, M00798 : dTDP-L-mycarose biosynthesis, M00463 : TrcS-TrcR two-component regulatory system, M00480 : VraS-VraR (cell-wall peptidoglycan synthesis) two-component regulatory system, M00790 : Pyrrolnitrin biosynthesis, tryptophan => pyrrolnitrin, M00637 : Anthranilate degradation, anthranilate => catechol, M00327 : S-Layer protein transport system, M00539 : Cumate degradation, p-cumate => 2-oxopent-4-enoate + 2-methylpropanoate, M00363 : EHEC pathogenicity signature, Shiga toxin, M00378 : F420 biosynthesis, M00741 : Propanoyl-CoA metabolism, propanoyl-CoA => succinyl-CoA, M00252 : Lipooligosaccharide transport system, M00456 : ArcB-ArcA (anoxic redox control) two-component regulatory system, M00249 : Capsular polysaccharide transport system, M00744 : Cationic antimicrobial peptide (CAMP) resistance, protease PgtE, M00702 : Multidrug resistance, efflux pump NorB, M00606 : N,N'-Diacetylchitobiose transport system, M00510 : Cph1-Rcp1 (light response) two-component regulatory system, M00081 : Pectin degradation, M00075 : N-glycan biosynthesis, complex type, M00373 : Ethylmalonyl pathway, M00414 : Bloom's syndrome complex, M00338 : Cysteine biosynthesis, homocysteine + serine => cysteine, M00142 : NADH:ubiquinone oxidoreductase, mitochondria, M00153 : Cytochrome bd ubiquinol oxidase, M00777 : Avermectin biosynthesis, 2-methylbutanoyl-CoA/isobutyryl-CoA => 6,8a-Seco-6,8a-deoxy-5-oxoavermectin 1a/1b aglycone => avermectin A1a/B1a/A1b/B1b, M00226 : Histidine transport system, M00498 : NtrY-NtrX (nitrogen regulation) two-component regulatory system, M00344 : Formaldehyde assimilation, xylulose monophosphate pathway, M00525 : Lysine biosynthesis, acetyl-DAP pathway, aspartate => lysine, M00416 : Cytochrome aa3-600 menaquinol oxidase, M00550 : Ascorbate degradation, ascorbate => D-xylulose-5P, M00738 : Bacitracin resistance, BceAB transporter, M00091 : Phosphatidylcholine (PC) biosynthesis, PE => PC, M00695 : cAMP signaling, M00355 : Spliceosome, 35S U5-snRNP, M00496 : ComD-ComE (competence) two-component regulatory system, M00201 : alpha-Glucoside transport system, M00027 : GABA (gamma-Aminobutyrate) shunt, M00046 : Pyrimidine degradation, uracil => beta-alanine, thymine => 3-aminoisobutanoate, M00066 : Lactosylceramide biosynthesis, M00100 : Sphingosine degradation, M00545 : Trans-cinnamate degradation, trans-cinnamate => acetyl-CoA, M00341 : Proteasome, 19S regulatory particle (PA700), M00061 : D-Glucuronate degradation, D-glucuronate => pyruvate + D-glyceraldehyde 3P, M00175 : Nitrogen fixation, nitrogen => ammonia, M00170 : C4-dicarboxylic acid cycle, phosphoenolpyruvate carboxykinase type, M00329 : Multiple protein transport system, M00531 : Assimilatory nitrate reduction, nitrate => ammonia, M00251 : Teichoic acid transport system, M00804 : Complete nitrification, comammox, ammonia => nitrite => nitrate, M00317 : Manganese/iron transport system, M00575 : Pertussis pathogenicity signature, T1SS, M00186 : Tungstate transport system, M00277 : PTS system, N-acetylgalactosamine-specific II component, M00154 : Cytochrome c oxidase, M00305 : PTS system, 2-O-A-mannosyl-D-glycerate-specific II component, M00670 : Mce transport system, M00806 : PTS system, maltose-specific II component, M00301 : Mannopine transport system, M00225 : Lysine/arginine/ornithine transport system, M00010 : Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate, M00473 : UhpB-UhpA (hexose phosphates uptake) two-component regulatory system, M00422 : Acetyl-CoA pathway, CO2 => acetyl-CoA, M00724 : Cationic antimicrobial peptide (CAMP) resistance, palmitoyl transferase PagP, M00077 : Chondroitin sulfate degradation, M00339 : RaxAB-RaxC type I secretion system, M00269 : PTS system, sucrose-specific II component, M00350 : , M00356 : Methanogenesis, methanol => methane, M00290 : Holo-TFIIH complex, M00131 : Inositol phosphate metabolism, Ins(1,3,4,5)P4 => Ins(1,3,4)P3 => myo-inositol, M00493 : AlgZ-AlgR (alginate production) two-component regulatory system, M00136 : GABA biosynthesis, prokaryotes, putrescine => GABA, M00155 : Cytochrome c oxidase, prokaryotes, M00045 : Histidine degradation, histidine => N-formiminoglutamate => glutamate, M00704 : Tetracycline resistance, efflux pump Tet38, M00660 : Xanthomonas spp. pathogenicity signature, T3SS and effectors, M00526 : Lysine biosynthesis, DAP dehydrogenase pathway, aspartate => lysine, M00513 : LuxQN/CqsS-LuxU-LuxO (quorum sensing) two-component regulatory system, M00774 : Erythromycin biosynthesis, propanoyl-CoA + methylmalonyl-CoA => deoxyerythronolide B => erythromycin A/B, M00082 : Fatty acid biosynthesis, initiation, M00736 : Nocardicin A biosynthesis, L-pHPG + arginine + serine => nocardicin A, M00725 : Cationic antimicrobial peptide (CAMP) resistance, dltABCD operon, M00514 : TtrS-TtrR (tetrathionate respiration) two-component regulatory system, M00453 : QseC-QseB (quorum sensing) two-component regulatory system, M00512 : CckA-CtrA/CpdR (cell cycle control) two-component regulatory system, M00542 : EHEC/EPEC pathogenicity signature, T3SS and effectors, M00555 : Betaine biosynthesis, choline => betaine, M00166 : Reductive pentose phosphate cycle, ribulose-5P => glyceraldehyde-3P, M00208 : Glycine betaine/proline transport system, M00259 : Heme transport system, M00315 : Uncharacterized ABC transport system, M00229 : Arginine transport system, M00597 : Anoxygenic photosystem II, M00200 : Putative sorbitol/mannitol transport system, M00182 : RNA polymerase I, eukaryotes, M00485 : KinABCDE-Spo0FA (sporulation control) two-component regulatory system, M00268 : PTS system, alpha-glucoside-specific II component, M00460 : MprB-MprA (maintenance of persistent infection) two-component regulatory system, M00723 : Cationic antimicrobial peptide (CAMP) resistance, ethanolaminephosphotransferase EptB, M00622 : Nicotinate degradation, nicotinate => fumarate, M00332 : Type III secretion system, M00112 : Tocopherol/tocotorienol biosynthesis, M00778 : Type II polyketide backbone biosynthesis, acyl-CoA + malonyl-CoA => polyketide, M00085 : Fatty acid biosynthesis, elongation, mitochondria, M00141 : C1-unit interconversion, eukaryotes, M00148 : Succinate dehydrogenase (ubiquinone), M00146 : NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, M00563 : Methanogenesis, methylamine/dimethylamine/trimethylamine => methane, M00072 : N-glycosylation by oligosaccharyltransferase, M00517 : RpfC-RpfG (cell-to-cell signaling) two-component regulatory system, M00040 : Tyrosine biosynthesis, prephanate => pretyrosine => tyrosine, M00156 : Cytochrome c oxidase, cbb3-type, M00243 : Manganese/iron transport system, M00767 : Multidrug resistance, efflux pump OqxAB, M00348 : Glutathione transport system, M00533 : Homoprotocatechuate degradation, homoprotocatechuate => 2-oxohept-3-enedioate, M00709 : Macrolide resistance, MacAB-TolC transporter, M00244 : Putative zinc/manganese transport system, M00374 : Dicarboxylate-hydroxybutyrate cycle, M00065 : GPI-anchor biosynthesis, core oligosaccharide, M00215 : D-Xylose transport system, M00502 : GlrK-GlrR (amino sugar metabolism) two-component regulatory system, M00192 : Putative thiamine transport system, M00499 : HydH-HydG (metal tolerance) two-component regulatory system, M00336 : Twin-arginine translocation (Tat) system, M00754 : Nisin resistance, phage shock protein homolog LiaH, M00664 : Nodulation, M00079 : Keratan sulfate degradation, M00328 : Hemophore/metalloprotease transport system, M00746 : Multidrug resistance, repression of porin OmpF, M00008 : Entner-Doudoroff pathway, glucose-6P => glyceraldehyde-3P + pyruvate, M00515 : FlrB-FlrC (polar flagellar synthesis) two-component regulatory system, M00227 : Glutamine transport system, M00193 : Putative spermidine/putrescine transport system, M00172 : C4-dicarboxylic acid cycle, NADP - malic enzyme type, M00101 : Cholesterol biosynthesis, squalene 2,3-epoxide => cholesterol, M00266 : PTS system, maltose/glucose-specific II component, M00728 : Cationic antimicrobial peptide (CAMP) resistance, envelope protein folding and degrading factors DegP and DsbA, M00458 : ResE-ResD (aerobic and anaerobic respiration) two-component regulatory system, M00484 : YdfH-YdfI two-component regulatory system, M00486 : CitA-CitB (citrate fermentation) two-component regulatory system, M00357 : Methanogenesis, acetate => methane, M00296 : BER complex, M00726 : Cationic antimicrobial peptide (CAMP) resistance, lysyl-phosphatidylglycerol (L-PG) synthase MprF, M00505 : KinB-AlgB (alginate production) two-component regulatory system, M00217 : D-Allose transport system, M00318 : Iron/zinc/manganese/copper transport system, M00001 : Glycolysis (Embden-Meyerhof pathway), glucose => pyruvate, M00568 : Catechol ortho-cleavage, catechol => 3-oxoadipate, M00057 : Glycosaminoglycan biosynthesis, linkage tetrasaccharide, M00465 : ManS-ManR (manganese homeostasis) two-component regulatory system, M00417 : Cytochrome o ubiquinol oxidase, M00365 : C10-C20 isoprenoid biosynthesis, archaea, M00648 : Multidrug resistance, efflux pump MdtABC, M00282 : PTS system, D-glucosamine-specific II component, M00274 : PTS system, mannitol-specific II component, M00272 : PTS system, beta-glucoside (arbutin/salicin/cellobiose)-specific II component, M00745 : Imipenem resistance, repression of porin OprD, M00455 : TorS-TorR (TMAO respiration) two-component regulatory system, M00403 : HRD1/SEL1 ERAD complex, M00354 : Spliceosome, U4/U6.U5 tri-snRNP, M00464 : NrsS-NrsR (nickel tolerance) two-component regulatory system, M00241 : Vitamin B12 transport system, M00461 : MtrB-MtrA (osmotic stress response) two-component regulatory system, M00288 : RPA complex, M00109 : C21-Steroid hormone biosynthesis, progesterone => cortisol/cortisone, M00162 : Cytochrome b6f complex, M00099 : Sphingosine biosynthesis, M00037 : Melatonin biosynthesis, tryptophan => serotonin => melatonin, M00540 : Benzoate degradation, cyclohexanecarboxylic acid =>pimeloyl-CoA, M00135 : GABA biosynthesis, eukaryotes, putrescine => GABA, M00273 : PTS system, fructose-specific II component, M00255 : Lipoprotein-releasing system, M00261 : DNA polymerase alpha / primase complex, M00534 : Naphthalene degradation, naphthalene => salicylate, M00281 : PTS system, lactose-specific II component, M00198 : Putative sn-glycerol-phosphate transport system, M00300 : Putrescine transport system, M00511 : PleC-PleD (cell fate control) two-component regulatory system, M00760 : Erythromycin resistance, macrolide 2'-phosphotransferase I MphA, M00674 : Clavaminate biosynthesis, arginine + glyceraldehyde-3P => clavaminate, M00322 : Neutral amino acid transport system, M00472 : NarQ-NarP (nitrate respiration) two-component regulatory system, M00036 : Leucine degradation, leucine => acetoacetate + acetyl-CoA, M00819 : Pentalenolactone biosynthesis, farnesyl-PP => pentalenolactone, M00113 : Jasmonic acid biosynthesis, M00137 : Flavanone biosynthesis, phenylalanine => naringenin, M00372 : Abscisic acid biosynthesis, beta-carotene => abscisic acid, M00569 : Catechol meta-cleavage, catechol => acetyl-CoA / 4-methylcatechol => propanoyl-CoA, M00117 : Ubiquinone biosynthesis, prokaryotes, chorismate => ubiquinone, M00321 : Bicarbonate transport system, M00488 : DcuS-DcuR (C4-dicarboxylate metabolism) two-component regulatory system, M00543 : Biphenyl degradation, biphenyl => 2-oxopent-4-enoate + benzoate, M00204 : Trehalose/maltose transport system, M00134 : Polyamine biosynthesis, arginine => ornithine => putrescine, M00302 : 2-Aminoethylphosphonate transport system, M00330 : Adhesin protein transport system, M00761 : Undecaprenylphosphate alpha-L-Ara4N biosynthesis, UDP-GlcA => undecaprenyl phosphate alpha-L-Ara4N, M00145 : NAD(P)H:quinone oxidoreductase, chloroplasts and cyanobacteria, M00470 : YxdK-YxdJ (antimicrobial peptide response) two-component regulatory system, M00304 : PTS system, fructose-specific II component, M00457 : TctE-TctD (tricarboxylic acid transport) two-component regulatory system, M00324 : Dipeptide transport system, M00006 : Pentose phosphate pathway, oxidative phase, glucose 6P => ribulose 5P, M00462 : PrrB-PrrA (intracellular multiplication) two-component regulatory system, M00265 : PTS system, glucose-specific II component, M00264 : DNA polymerase II complex, archaea, M00220 : Rhamnose transport system, M00095 : C5 isoprenoid biosynthesis, mevalonate pathway, M00219 : AI-2 transport system, M00503 : PgtB-PgtA (phosphoglycerate transport) two-component regulatory system, M00710 : Multidrug resistance, efflux pump EbrAB, M00013 : Malonate semialdehyde pathway, propanoyl-CoA => acetyl-CoA, M00625 : Methicillin resistance, M00647 : Multidrug resistance, efflux pump AcrAB-TolC/SmeDEF, M00174 : Methane oxidation, methanotroph, methane => formaldehyde, M00547 : Benzene/toluene degradation, benzene => catechol / toluene => 3-methylcatechol, M00064 : ADP-L-glycero-D-manno-heptose biosynthesis, M00418 : Toluene degradation, anaerobic, toluene => benzoyl-CoA, M00158 : F-type ATPase, eukaryotes, M00672 : Penicillin biosynthesis, aminoadipate + cycteine + valine => penicillin, M00478 : DegS-DegU (multicellular behavior control) two-component regulatory system, M00551 : Benzoate degradation, benzoate => catechol / methylbenzoate => methylcatechol, M00638 : Salicylate degradation, salicylate => gentisate, M00490 : MalK-MalR (malate transport) two-component regulatory system, M00163 : Photosystem I, M00477 : EvgS-EvgA (acid and drug tolerance) two-component regulatory system, M00232 : General L-amino acid transport system, M00279 : PTS system, galactitol-specific II component, M00031 : Lysine biosynthesis, mediated by LysW, 2-aminoadipate => lysine, M00042 : Catecholamine biosynthesis, tyrosine => dopamine => noradrenaline => adrenaline, M00309 : Non-phosphorylative Entner-Doudoroff pathway, gluconate/galactonate => glycerate, M00197 : Putative fructooligosaccharide transport system, M00323 : Urea transport system, M00097 : beta-Carotene biosynthesis, GGAP => beta-carotene, M00580 : Pentose phosphate pathway, archaea, fructose 6P => ribose 5P, M00358 : Coenzyme M biosynthesis, M00253 : Sodium transport system, M00779 : Dihydrokalafungin biosynthesis, octaketide => dihydrokalafungin, M00615 : Nitrate assimilation, M00278 : PTS system, sorbose-specific II component, M00316 : Manganese transport system, M00303 : PTS system, N-acetylmuramic acid-specific II component, M00483 : NreB-NreC (dissimilatory nitrate/nitrite reduction) two-component regulatory system, M00230 : Glutamate/aspartate transport system, M00508 : PixL-PixGH (positive phototaxis) two-component regulatory system, M00717 : Multidrug resistance, efflux pump NorA, M00500 : AtoS-AtoC (cPHB biosynthesis) two-component regulatory system, M00047 : Creatine pathway, M00078 : Heparan sulfate degradation, M00662 : Hk1-Rrp1 (glycerol uptake and utilization) two-component regulatory system, M00349 : Microcin C transport system, M00367 : C10-C20 isoprenoid biosynthesis, non-plant eukaryotes, M00152 : Cytochrome bc1 complex, M00143 : NADH dehydrogenase (ubiquinone) Fe-S protein/flavoprotein complex, mitochondria, M00202 : Oligogalacturonide transport system, M00034 : Methionine salvage pathway, M00507 : ChpA-ChpB/PilGH (chemosensory) two-component regulatory system, M00448 : CssS-CssR (secretion stress response) two-component regulatory system, M00487 : CitS-CitT (magnesium-citrate transport) two-component regulatory system, M00392 : Ski complex, M00011 : Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate, M00598 : Anoxygenic photosystem I, M00375 : Hydroxypropionate-hydroxybutylate cycle, M00032 : Lysine degradation, lysine => saccharopine => acetoacetyl-CoA, M00270 : PTS system, trehalose-specific II component, M00090 : Phosphatidylcholine (PC) biosynthesis, choline => PC, M00320 : Lipopolysaccharide export system, M00501 : PilS-PilR (type 4 fimbriae synthesis) two-component regulatory system, M00714 : Multidrug resistance, efflux pump QacA, M00491 : arabinogalactan oligomer/maltooligosaccharide transport system, M00024 : Phenylalanine biosynthesis, chorismate => phenylalanine, M00623 : Phthalate degradation, phthalate => protocatechuate, M00479 : DesK-DesR (membrane lipid fluidity regulation) two-component regulatory system, M00504 : DctB-DctD (C4-dicarboxylate transport) two-component regulatory system, M00038 : Tryptophan metabolism, tryptophan => kynurenine => 2-aminomuconate, M00401 : Sec61 complex, M00466 : NblS-NblR (photosynthesis) two-component regulatory system, M00530 : Dissimilatory nitrate reduction, nitrate => ammonia, M00722 : Cationic antimicrobial peptide (CAMP) resistance, ethanolaminephosphotransferase EptA, M00639 : Multidrug resistance, efflux pump MexCD-OprJ, M00446 : RstB-RstA two-component regulatory system

Model details

trait state
distribution gaussian
formula feature_abundance ~ group + (1|subject_id)
number of samples 94
transform arcsin(sqrt)

Specific pathways

Individual microbial taxa for which relative abundance is significantly different between two groups are identified.

Wilcoxon test comparison

Method: Wilcoxon signed rank test. The analysis includes the following steps: filtration of rare taxa (taxon must be present in at least 10% of the samples at the level of >0.2%), Wilcoxon signed rank test applied to each taxon to detect the taxa differentially abundant between the groups. Multiple testing adjustment is performed using Benjamini–Hochberg procedure. Contribution of each taxon to the inter-group difference is estimated using LDA method. Samples-outliers listed in the taxonomic composition section are excluded from this analysis.

Differentially abundant taxa

Tables of differentially abundant taxa overpresented in the groups

Overpresented in group: 2_opisth

pathway metabolic level 2_opisth median, % 3_treat median, % p-value adjusted p-value lda score
Acetyl-CoA butyrate 0.419 0.32 0.0 0.001 3.143

Cladogram of differences

Tree-like summary of the taxa differentially abundant in two groups constructed using LefSe.

List of differentially abundant taxa

increased in 2_opisth

denotation feature
a Acetyl-CoA

Excluded features

vitamin

B6_a, B6_b

propionate

Succinate_a, Succinate_b, acrylate_a, propanediol_a

Generalized linear mixed effect model

A generalized mixed effects linear model is fitted for each taxon to identify if it is differentially abundant between the groups. "Subject_id", is treated as a random effect. The specific probability distribution is selected heuristically depending on the number of samples. For >100 samples, a zero-inflated negative binomial regression is fitted; in other cases - a negative binomial model. 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. Contribution of each taxon to the inter-group difference is estimated using LDA method. The information about distribution family, terms of the model and sample size is displayed in "Model details" section.

Differentially abundant taxa

Tables of differentially abundant taxa overpresented in the groups

Overpresented in group: 2_opisth

pathway metabolic level 3_treat mean, % 3_treat sd, % 2_opisth mean, % 2_opisth sd, % p-value adjusted p-value lda score sample size
Acetyl-CoA butyrate 0.331 0.103 0.472 0.26 0.001 0.003 4.015 94

Cladogram of differences

Tree-like summary of the taxa differentially abundant in two groups constructed using LefSe.

List of differentially abundant taxa

increased in 2_opisth

denotation feature
a Acetyl-CoA

Excluded features

vitamin

B6_a, B6_b

Model details

trait state
distribution gaussian
formula feature_abundance ~ group + (1|subject_id)
number of samples 94
transform arcsin(sqrt)

knb_interactive: 2.0.2
datalab: 3.10.0
knb_lib: 4.8.45