Paired analysis report for Fermented Dairy Product Intervention Study

Report summary

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

Created18/08/2017
Updated29/05/2018
TypePaired analysis report
ProjectFermented Dairy Product Intervention Study
Uploaded samples297

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. Distance metric: weighted Unifrac. List of outliers:

287, 23, 14, 265, 281, 115, 276, 196, 103, 141

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

Alpha-diversity does not vary significantly in the groups(p= 0.6260569952200887)

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).

Members of the cooperatives

Relative abundance of each cooperative in the samples.

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 128
number of permutations 20000
significance level 0.05
group variations equal (p = 0.605)
R-squared 0.008
p-value 0.239

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.

The sample size is too small (< 10) to evaluate the test.

Feature comparison between two groups

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

MaAsLin comparison

Method: MaAsLin. 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%), arcsin(sqrt) transformation of abundance values, removal of outliers according to Grubbs' test, multiple linear regression with group and subject ID as covariates applied to each taxon to detect the taxa differentially abundant between the groups. Multiple testing adjustment is performed using Benjamini–Hochberg procedure only for group coefficient p-values. Contribution of each taxon to the inter-group difference is estimated using LDA method.

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

phylum

k__Bacteria;p__Cyanobacteria, k__Bacteria;p__Synergistetes

class

k__Bacteria;p__Cyanobacteria;c__4C0d-2, k__Bacteria;p__Cyanobacteria;c__Chloroplast, k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria, k__Bacteria;p__Synergistetes;c__Synergistia, k__Bacteria;p__Proteobacteria;c__Betaproteobacteria

order

k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pasteurellales, k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales, k__Bacteria;p__Cyanobacteria;c__Chloroplast;o__Streptophyta, k__Bacteria;p__Cyanobacteria;c__4C0d-2;o__YS2, k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales, k__Bacteria;p__Synergistetes;c__Synergistia;o__Synergistales, k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32, k__Bacteria;p__Firmicutes;c__Bacilli;o__Turicibacterales, k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales, k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales

family

k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Alcaligenaceae, k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__[Odoribacteraceae], k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__[Tissierellaceae], k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae, k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pasteurellales;f__Pasteurellaceae, k__Bacteria;p__Firmicutes;c__Bacilli;o__Turicibacterales;f__Turicibacteraceae, k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae, k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Leuconostocaceae, k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Corynebacteriaceae, k__Bacteria;p__Cyanobacteria;c__Chloroplast;o__Streptophyta;f__, k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Oxalobacteraceae, k__Bacteria;p__Cyanobacteria;c__4C0d-2;o__YS2;f__, k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__, k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__, k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Peptostreptococcaceae, k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae

genus

k__Bacteria;p__Firmicutes;c__Bacilli;o__Turicibacterales;f__Turicibacteraceae;g__Turicibacter, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__[Mogibacteriaceae];g__Mogibacterium, k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Oxalobacteraceae;g__Oxalobacter, k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__[Odoribacteraceae];g__Odoribacter, k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__;g__, k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Alcaligenaceae;g__Sutterella, k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas, k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Staphylococcaceae;g__Staphylococcus, k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteriales;f__Enterobacteriaceae;g__Klebsiella, k__Bacteria;p__Cyanobacteria;c__Chloroplast;o__Streptophyta;f__;g__, k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Bilophila, k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemania, k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Corynebacteriaceae;g__Corynebacterium, k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__[Paraprevotellaceae];g__, k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Coprobacillus, k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__;g__, k__Bacteria;p__Actinobacteria;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Slackia, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Roseburia, k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__[Odoribacteraceae];g__Butyricimonas, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Sarcina, k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__;g__, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Veillonellaceae;g__Mitsuokella, k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus, k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pasteurellales;f__Pasteurellaceae;g__Haemophilus, k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanosphaera, k__Bacteria;p__Cyanobacteria;c__4C0d-2;o__YS2;f__;g__, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Veillonellaceae;g__Acidaminococcus, k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Leuconostocaceae;g__Leuconostoc, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Peptostreptococcaceae;g__, k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Veillonellaceae;g__, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Peptococcaceae;g__Peptococcus, k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__[Paraprevotellaceae];g__[Prevotella]

species

k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae;g__Prevotella;s__, k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__eggerthii, k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Coprobacillus;s__, k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__;g__;s__, k__Bacteria;p__Firmicutes;c__Bacilli;o__Turicibacterales;f__Turicibacteraceae;g__Turicibacter;s__, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__[Mogibacteriaceae];g__Mogibacterium;s__, k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Bifidobacteriales;f__Bifidobacteriaceae;g__Bifidobacterium;s__animalis, k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Bifidobacteriales;f__Bifidobacteriaceae;g__Bifidobacterium;s__, k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Leuconostocaceae;g__Leuconostoc;s__, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Veillonellaceae;g__Mitsuokella;s__, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Veillonellaceae;g__Veillonella;s__dispar, k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio;s__, k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae;g__Prevotella;s__stercorea, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Faecalibacterium;s__, k__Bacteria;p__Cyanobacteria;c__Chloroplast;o__Streptophyta;f__;g__;s__, k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Oxalobacteraceae;g__Oxalobacter;s__formigenes, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Veillonellaceae;g__Acidaminococcus;s__, k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Staphylococcaceae;g__Staphylococcus;s__sciuri, k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__;g__;s__, k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter;s__, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Ruminococcus;s__flavefaciens, k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas;s__, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Sarcina;s__, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Veillonellaceae;g__Veillonella;s__parvula, k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__[Paraprevotellaceae];g__;s__, k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__[Odoribacteraceae];g__Odoribacter;s__, k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pasteurellales;f__Pasteurellaceae;g__Haemophilus;s__parainfluenzae, k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__[Odoribacteraceae];g__Butyricimonas;s__, k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__caccae, k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__, k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__anginosus, k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemania;s__, k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanosphaera;s__, k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Alcaligenaceae;g__Sutterella;s__, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Veillonellaceae;g__Mitsuokella;s__multacida, k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__[Eubacterium];s__cylindroides, k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__;g__;s__, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Peptostreptococcaceae;g__;s__, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Roseburia;s__, k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__[Eubacterium];s__dolichum, k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Bifidobacteriales;f__Bifidobacteriaceae;g__Bifidobacterium;s__pseudolongum, k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus;s__, k__Bacteria;p__Actinobacteria;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Slackia;s__, k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Bilophila;s__, k__Bacteria;p__Cyanobacteria;c__4C0d-2;o__YS2;f__;g__;s__, k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Coprobacillus;s__cateniformis, k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteriales;f__Enterobacteriaceae;g__Klebsiella;s__, k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__Parabacteroides;s__distasonis, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Veillonellaceae;g__;s__, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Peptococcaceae;g__Peptococcus;s__, k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__[Paraprevotellaceae];g__[Prevotella];s__, k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__ruminis, k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__plebeius

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

phylum

k__Bacteria;p__Cyanobacteria, k__Bacteria;p__Synergistetes

class

k__Bacteria;p__Cyanobacteria;c__4C0d-2, k__Bacteria;p__Cyanobacteria;c__Chloroplast, k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria, k__Bacteria;p__Synergistetes;c__Synergistia

order

k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pasteurellales, k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales, k__Bacteria;p__Cyanobacteria;c__Chloroplast;o__Streptophyta, k__Bacteria;p__Cyanobacteria;c__4C0d-2;o__YS2, k__Bacteria;p__Synergistetes;c__Synergistia;o__Synergistales, k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32, k__Bacteria;p__Firmicutes;c__Bacilli;o__Turicibacterales, k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales, k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales

family

k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__[Odoribacteraceae], k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__[Tissierellaceae], k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae, k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pasteurellales;f__Pasteurellaceae, k__Bacteria;p__Firmicutes;c__Bacilli;o__Turicibacterales;f__Turicibacteraceae, k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae, k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Leuconostocaceae, k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Corynebacteriaceae, k__Bacteria;p__Cyanobacteria;c__Chloroplast;o__Streptophyta;f__, k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Oxalobacteraceae, k__Bacteria;p__Cyanobacteria;c__4C0d-2;o__YS2;f__, k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__, k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__, k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Peptostreptococcaceae, k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae

genus

k__Bacteria;p__Firmicutes;c__Bacilli;o__Turicibacterales;f__Turicibacteraceae;g__Turicibacter, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__[Mogibacteriaceae];g__Mogibacterium, k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Oxalobacteraceae;g__Oxalobacter, k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__[Odoribacteraceae];g__Odoribacter, k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__;g__, k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas, k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Staphylococcaceae;g__Staphylococcus, k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteriales;f__Enterobacteriaceae;g__Klebsiella, k__Bacteria;p__Cyanobacteria;c__Chloroplast;o__Streptophyta;f__;g__, k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Bilophila, k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemania, k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Corynebacteriaceae;g__Corynebacterium, k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__[Paraprevotellaceae];g__, k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Coprobacillus, k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__;g__, k__Bacteria;p__Actinobacteria;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Slackia, k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__[Odoribacteraceae];g__Butyricimonas, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Sarcina, k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__;g__, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Veillonellaceae;g__Mitsuokella, k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus, k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pasteurellales;f__Pasteurellaceae;g__Haemophilus, k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanosphaera, k__Bacteria;p__Cyanobacteria;c__4C0d-2;o__YS2;f__;g__, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Veillonellaceae;g__Acidaminococcus, k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Leuconostocaceae;g__Leuconostoc, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Peptostreptococcaceae;g__, k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Veillonellaceae;g__

species

k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae;g__Prevotella;s__, k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__eggerthii, k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Coprobacillus;s__, k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__;g__;s__, k__Bacteria;p__Firmicutes;c__Bacilli;o__Turicibacterales;f__Turicibacteraceae;g__Turicibacter;s__, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__[Mogibacteriaceae];g__Mogibacterium;s__, k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Bifidobacteriales;f__Bifidobacteriaceae;g__Bifidobacterium;s__animalis, k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Bifidobacteriales;f__Bifidobacteriaceae;g__Bifidobacterium;s__, k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Leuconostocaceae;g__Leuconostoc;s__, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Veillonellaceae;g__Mitsuokella;s__, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Veillonellaceae;g__Veillonella;s__dispar, k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio;s__, k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae;g__Prevotella;s__stercorea, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Faecalibacterium;s__, k__Bacteria;p__Cyanobacteria;c__Chloroplast;o__Streptophyta;f__;g__;s__, k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Oxalobacteraceae;g__Oxalobacter;s__formigenes, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Veillonellaceae;g__Acidaminococcus;s__, k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Staphylococcaceae;g__Staphylococcus;s__sciuri, k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__;g__;s__, k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter;s__, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Ruminococcus;s__flavefaciens, k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas;s__, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Sarcina;s__, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Veillonellaceae;g__Veillonella;s__parvula, k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__[Paraprevotellaceae];g__;s__, k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__[Odoribacteraceae];g__Odoribacter;s__, k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pasteurellales;f__Pasteurellaceae;g__Haemophilus;s__parainfluenzae, k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__[Odoribacteraceae];g__Butyricimonas;s__, k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__caccae, k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__, k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__anginosus, k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemania;s__, k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanosphaera;s__, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Veillonellaceae;g__Mitsuokella;s__multacida, k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__[Eubacterium];s__cylindroides, k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__;g__;s__, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Peptostreptococcaceae;g__;s__, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Roseburia;s__, k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__[Eubacterium];s__dolichum, k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Bifidobacteriales;f__Bifidobacteriaceae;g__Bifidobacterium;s__pseudolongum, k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus;s__, k__Bacteria;p__Actinobacteria;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Slackia;s__, k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Bilophila;s__, k__Bacteria;p__Cyanobacteria;c__4C0d-2;o__YS2;f__;g__;s__, k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Coprobacillus;s__cateniformis, k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteriales;f__Enterobacteriaceae;g__Klebsiella;s__, k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__Parabacteroides;s__distasonis, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Veillonellaceae;g__;s__

Comparison of pathways and reactions abundances in two groups

Individual pathways and reactions for which relative abundance is significantly different between two groups are identified.

MaAsLin comparison

Method: MaAsLin. The analysis includes the following steps: filtration of rare pathways and reactions (pathway or reaction must be present in at least 10% of the samples at the level of >0.2%), arcsin(sqrt) transformation of abundance values, removal of outliers according to Grubbs' test, multiple linear regression with group and subject ID as covariates applied to each taxon to detect the taxa differentially abundant between the groups. Multiple testing adjustment is performed using Benjamini–Hochberg procedure only for group coefficient p-values. Contribution of each pathway or reaction to the inter-group difference is estimated using LDA method.

Differentially abundant pathways

Tables of differentially abundant pathways and reactions 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

PICRUSt

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

MaAsLin comparison of specific functions

Method: MaAsLin. The analysis includes the following steps: filtration of rare pathways and reactions (pathway or reaction must be present in at least 10% of the samples at the level of >0.2%), arcsin(sqrt) transformation of abundance values, removal of outliers according to Grubbs' test, multiple linear regression with group and subject ID as covariates applied to each taxon to detect the taxa differentially abundant between the groups. Multiple testing adjustment is performed using Benjamini–Hochberg procedure only for group coefficient p-values. Contribution of each pathway or reaction to the inter-group difference is estimated using LDA method.

Differentially abundant pathways

Tables of differentially abundant pathways and reactions 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

propionate

Succinate_a, Succinate_b, acrylate_a, propanediol_a

vitamin

B6_a, B6_b

Wilcoxon test comparison

Method: Wilcoxon signed rank test. The analysis includes the following steps: filtration of rare pathways and reactions (pathway or reaction must be present in at least 10% of the samples at the level of >0.2%), Wilcoxon signed rank test applied to each pathway and reaction to detect the ones differentially abundant between the groups. Multiple testing adjustment is performed using Benjamini–Hochberg procedure. Contribution of each pathway and reaction 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 pathways

Tables of differentially abundant pathways and reactions 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

PICRUSt

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

datalab: 3.7.0
knb_lib: 4.6.2
knb_interactive: 2.0.2