Report summary
Compare user data with the volume of curated published metagenomes (without analysis of factors).
| Created | 25/04/2019 |
|---|---|
| Updated | 09/10/2019 |
| Type | External comparison report |
| Project | Gut microbiome of Yakuts without Viliuisk encephalomyelitis compared to other cohorts |
| Uploaded samples | 11 |
External data info
Below is the description of external datasets (PMID or PMC and title of the article).
userdata637
Girard, C., Tromas, N., Amyot, M., & Shapiro, B. J. (2017). Gut microbiome of the canadian arctic Inuit. mSphere, 2(1), e00297-16.
Taxonomic composition
Heatmap of taxonomic composition
Interactive heatmap represents relative abundance of major microbial taxa (columns) in the samples (rows), for each taxonomic level. The last row represent mean values for external data. White colour corresponds to absent taxa. Using the drop-down list “Heatmap settings” on the right of the heatmap, users can select taxonomic level 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 and factors value of corresponding sample (click again or on the cross near sample name to “unfreeze”).
Major taxa
The boxplots represent distribution of relative abundance for 25 most abundant taxa across all samples (for each taxonomic rank). For proper display on log scale, zero values were replaced with a pseudocount not higher than minimum value of relative abundance of major taxa.
phylum
class
order
family
genus
species
Taxonomic core
The plot represents the proportion of OTUs shared across the varying proportion of samples.
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 (users and external data):
pmiduserdata637_R20, pmiduserdata637_R7, pmiduserdata637_R13
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.
alpha_div_plot_int
Сomparison
Wilcoxon rank-sum test is applied to compare the alpha-diversity between the two groups.
Alpha-diversity is significantly different in the groups(p= 0.0)
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).
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 | 34 |
| number of permutations | 20000 |
| significance level | 0.05 |
| group variations | equal (p = 0.099) |
| R-squared | 0.316 |
| p-value | 0.0 |
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 | 34 |
| number of permutations | 20000 |
| significance level | 0.05 |
| group variations | equal (p = 0.086) |
| R-squared | 0.137 |
| p-value | 0.008 |
Taxonomic composition
Individual microbial taxa for which relative abundance is significantly different between user and external datasets are identified.
Wilcoxon test comparison
Method: Wilcoxon rank-sum 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 rank-sum test applied to each taxon to detect the taxa differentially abundant between the user and external data. 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 were excluded from this analysis.
Differentially abundant taxa
Tables of differentially abundant taxa overpresented in the groups
Overpresented in group: external_data
| taxon | taxa level | user_data median, % | external_data median, % | p-value | adjusted p-value | lda score |
|---|---|---|---|---|---|---|
| p__Proteobacteria | phylum | 1.56 | 4.540 | 0.016 | 0.022 | 5.369 |
| p__Bacteroidetes | phylum | 2.60 | 38.043 | 0.000 | 0.001 | 5.233 |
| c__Bacteroidia | class | 2.58 | 38.043 | 0.000 | 0.001 | 5.191 |
| c__Betaproteobacteria | class | 0.10 | 1.122 | 0.002 | 0.004 | 4.430 |
| c__Deltaproteobacteria | class | 0.06 | 0.640 | 0.018 | 0.026 | 4.390 |
| o__Bacteroidales | order | 2.58 | 38.096 | 0.000 | 0.001 | 5.221 |
| o__Desulfovibrionales | order | 0.06 | 0.641 | 0.018 | 0.027 | 4.402 |
| o__Burkholderiales | order | 0.10 | 1.122 | 0.001 | 0.003 | 4.320 |
| f__Bacteroidaceae | family | 0.60 | 25.190 | 0.000 | 0.000 | 5.108 |
| f__Desulfovibrionaceae | family | 0.06 | 0.641 | 0.018 | 0.034 | 4.336 |
| f__[Odoribacteraceae] | family | 0.00 | 0.261 | 0.003 | 0.008 | 4.177 |
| f__Porphyromonadaceae | family | 0.18 | 1.981 | 0.000 | 0.001 | 4.093 |
| f__Alcaligenaceae | family | 0.00 | 1.103 | 0.000 | 0.000 | 4.086 |
| f__Rikenellaceae | family | 0.12 | 1.121 | 0.007 | 0.016 | 3.943 |
| f__[Barnesiellaceae] | family | 0.00 | 0.040 | 0.029 | 0.045 | 3.835 |
| g__Bacteroides | genus | 0.60 | 25.773 | 0.000 | 0.000 | 5.096 |
| g__Bilophila | genus | 0.00 | 0.361 | 0.000 | 0.001 | 4.328 |
| g__Odoribacter | genus | 0.00 | 0.060 | 0.005 | 0.012 | 4.149 |
| g__Parabacteroides | genus | 0.18 | 1.962 | 0.000 | 0.001 | 4.064 |
| g__Sutterella | genus | 0.00 | 1.109 | 0.000 | 0.000 | 4.044 |
| g__Phascolarctobacterium | genus | 0.00 | 0.761 | 0.000 | 0.002 | 3.869 |
| g__u(f__[Barnesiellaceae]) | genus | 0.00 | 0.042 | 0.029 | 0.048 | 3.819 |
| g__u(f__Rikenellaceae) | genus | 0.12 | 1.141 | 0.007 | 0.015 | 3.813 |
| g__Bacteroides s__fragilis | species | 0.00 | 0.154 | 0.011 | 0.021 | 4.991 |
| g__Parabacteroides s__distasonis | species | 0.02 | 0.614 | 0.002 | 0.005 | 4.425 |
| s__u(g__Odoribacter) | species | 0.00 | 0.066 | 0.005 | 0.011 | 4.214 |
| s__u(g__Bilophila) | species | 0.00 | 0.362 | 0.000 | 0.001 | 4.204 |
| g__Bacteroides s__ovatus | species | 0.00 | 1.589 | 0.000 | 0.000 | 3.835 |
| s__u(g__Sutterella) | species | 0.00 | 1.109 | 0.000 | 0.000 | 3.801 |
| s__u(f__Rikenellaceae) | species | 0.12 | 1.141 | 0.006 | 0.012 | 3.788 |
| s__u(g__Bacteroides) | species | 0.20 | 19.823 | 0.000 | 0.000 | 3.773 |
| s__u(g__Parabacteroides) | species | 0.14 | 0.882 | 0.001 | 0.003 | 3.712 |
| g__Blautia s__obeum | species | 0.04 | 0.160 | 0.012 | 0.022 | 3.580 |
| s__u(f__[Barnesiellaceae]) | species | 0.00 | 0.042 | 0.029 | 0.047 | 3.529 |
| g__Roseburia s__faecis | species | 0.00 | 0.060 | 0.003 | 0.008 | 3.425 |
| g__Bacteroides s__uniformis | species | 0.04 | 1.812 | 0.001 | 0.002 | 3.415 |
| s__u(g__Phascolarctobacterium) | species | 0.00 | 0.761 | 0.000 | 0.002 | 3.392 |
Overpresented in group: user_data
| taxon | taxa level | user_data median, % | external_data median, % | p-value | adjusted p-value | lda score |
|---|---|---|---|---|---|---|
| p__Actinobacteria | phylum | 5.86 | 1.221 | 0.000 | 0.001 | 5.035 |
| p__Tenericutes | phylum | 0.16 | 0.000 | 0.014 | 0.022 | 5.001 |
| p__Firmicutes | phylum | 83.44 | 40.000 | 0.000 | 0.000 | 4.770 |
| c__Clostridia | class | 69.24 | 38.360 | 0.000 | 0.001 | 5.201 |
| c__Erysipelotrichi | class | 7.06 | 0.820 | 0.001 | 0.004 | 4.667 |
| c__Mollicutes | class | 0.16 | 0.000 | 0.016 | 0.026 | 4.472 |
| c__Actinobacteria | class | 2.04 | 0.140 | 0.001 | 0.002 | 4.466 |
| c__Bacilli | class | 1.50 | 0.180 | 0.002 | 0.004 | 4.447 |
| c__Coriobacteriia | class | 3.58 | 0.520 | 0.000 | 0.002 | 4.437 |
| o__Clostridiales | order | 69.24 | 38.391 | 0.000 | 0.001 | 5.186 |
| o__Erysipelotrichales | order | 7.06 | 0.822 | 0.001 | 0.003 | 4.622 |
| o__Bacillales | order | 0.08 | 0.000 | 0.000 | 0.002 | 4.553 |
| o__RF39 | order | 0.16 | 0.000 | 0.018 | 0.027 | 4.482 |
| o__Coriobacteriales | order | 3.58 | 0.520 | 0.000 | 0.002 | 4.456 |
| o__Lactobacillales | order | 1.38 | 0.060 | 0.001 | 0.002 | 4.415 |
| o__Bifidobacteriales | order | 1.98 | 0.140 | 0.002 | 0.003 | 4.375 |
| f__Ruminococcaceae | family | 31.24 | 13.879 | 0.000 | 0.001 | 4.941 |
| f__Lachnospiraceae | family | 21.38 | 11.747 | 0.000 | 0.002 | 4.704 |
| f__Erysipelotrichaceae | family | 7.06 | 0.822 | 0.001 | 0.005 | 4.534 |
| f__[Mogibacteriaceae] | family | 0.22 | 0.040 | 0.001 | 0.005 | 4.281 |
| f__Coriobacteriaceae | family | 3.58 | 0.520 | 0.000 | 0.002 | 4.246 |
| f__Bifidobacteriaceae | family | 1.98 | 0.140 | 0.002 | 0.005 | 4.228 |
| f__Lactobacillaceae | family | 0.26 | 0.000 | 0.001 | 0.005 | 4.213 |
| f__u(o__RF39) | family | 0.16 | 0.000 | 0.018 | 0.034 | 4.182 |
| f__Veillonellaceae | family | 3.56 | 1.922 | 0.020 | 0.034 | 4.148 |
| f__Clostridiaceae | family | 2.28 | 1.102 | 0.020 | 0.034 | 4.038 |
| f__Streptococcaceae | family | 0.50 | 0.060 | 0.002 | 0.005 | 3.916 |
| f__[Paraprevotellaceae] | family | 0.12 | 0.000 | 0.018 | 0.034 | 3.665 |
| g__u(f__Ruminococcaceae) | genus | 14.98 | 5.695 | 0.000 | 0.001 | 4.696 |
| g__Faecalibacterium | genus | 9.38 | 3.077 | 0.003 | 0.007 | 4.514 |
| g__Catenibacterium | genus | 2.16 | 0.000 | 0.000 | 0.001 | 4.496 |
| g__Blautia | genus | 6.64 | 1.445 | 0.000 | 0.002 | 4.309 |
| g__Bifidobacterium | genus | 1.98 | 0.141 | 0.002 | 0.005 | 4.225 |
| g__u(f__Lachnospiraceae) | genus | 6.74 | 4.647 | 0.025 | 0.043 | 4.211 |
| g__u(f__[Mogibacteriaceae]) | genus | 0.22 | 0.040 | 0.003 | 0.007 | 4.183 |
| g__Lactobacillus | genus | 0.26 | 0.000 | 0.001 | 0.003 | 4.144 |
| g__Dialister | genus | 1.96 | 0.000 | 0.002 | 0.006 | 4.078 |
| g__Dorea | genus | 2.58 | 0.220 | 0.000 | 0.000 | 4.068 |
| g__[Eubacterium] | genus | 1.52 | 0.020 | 0.008 | 0.017 | 3.998 |
| g__Collinsella | genus | 1.62 | 0.253 | 0.000 | 0.002 | 3.988 |
| g__[Ruminococcus] | genus | 1.86 | 0.100 | 0.000 | 0.000 | 3.958 |
| g__u(f__Coriobacteriaceae) | genus | 1.62 | 0.221 | 0.003 | 0.008 | 3.913 |
| g__Coprococcus | genus | 1.00 | 0.420 | 0.000 | 0.001 | 3.886 |
| g__Megasphaera | genus | 0.48 | 0.000 | 0.000 | 0.000 | 3.859 |
| g__Slackia | genus | 0.06 | 0.000 | 0.007 | 0.015 | 3.855 |
| g__Desulfovibrio | genus | 0.06 | 0.000 | 0.021 | 0.040 | 3.725 |
| g__u(o__RF39) | genus | 0.16 | 0.000 | 0.018 | 0.035 | 3.689 |
| g__SMB53 | genus | 0.74 | 0.000 | 0.008 | 0.017 | 3.679 |
| g__Streptococcus | genus | 0.50 | 0.040 | 0.001 | 0.002 | 3.673 |
| g__Clostridium | genus | 0.92 | 0.461 | 0.022 | 0.042 | 3.664 |
| g__u(f__Clostridiaceae) | genus | 0.82 | 0.120 | 0.025 | 0.043 | 3.585 |
| g__[Prevotella] | genus | 0.06 | 0.000 | 0.001 | 0.002 | 3.584 |
| s__u(f__Clostridiaceae) | species | 0.82 | 0.120 | 0.025 | 0.041 | 4.698 |
| s__u(o__RF39) | species | 0.16 | 0.000 | 0.018 | 0.031 | 4.441 |
| s__u(g__SMB53) | species | 0.74 | 0.000 | 0.008 | 0.016 | 4.217 |
| g__[Eubacterium] s__cylindroides | species | 0.38 | 0.000 | 0.000 | 0.001 | 4.214 |
| s__u(g__Coprococcus) | species | 0.90 | 0.321 | 0.000 | 0.000 | 4.191 |
| g__Bifidobacterium s__longum | species | 0.20 | 0.000 | 0.001 | 0.003 | 4.181 |
| s__u(f__Lachnospiraceae) | species | 6.74 | 4.650 | 0.025 | 0.041 | 4.143 |
| s__u(f__Ruminococcaceae) | species | 14.98 | 5.696 | 0.000 | 0.001 | 4.098 |
| g__Prevotella s__copri | species | 0.32 | 0.000 | 0.005 | 0.010 | 4.074 |
| s__u(g__[Prevotella]) | species | 0.06 | 0.000 | 0.001 | 0.002 | 4.013 |
| g__Clostridium s__perfringens | species | 0.68 | 0.000 | 0.000 | 0.000 | 3.899 |
| s__u(g__Megasphaera) | species | 0.48 | 0.000 | 0.000 | 0.000 | 3.896 |
| s__u(g__Streptococcus) | species | 0.48 | 0.040 | 0.000 | 0.002 | 3.877 |
| s__u(g__Slackia) | species | 0.06 | 0.000 | 0.007 | 0.013 | 3.849 |
| s__u(g__Blautia) | species | 5.38 | 1.141 | 0.001 | 0.002 | 3.848 |
| s__u(g__Catenibacterium) | species | 2.16 | 0.000 | 0.000 | 0.001 | 3.801 |
| g__[Ruminococcus] s__gnavus | species | 0.26 | 0.060 | 0.001 | 0.003 | 3.780 |
| g__Faecalibacterium s__prausnitzii | species | 9.38 | 3.077 | 0.003 | 0.007 | 3.773 |
| s__u(g__Dialister) | species | 1.96 | 0.000 | 0.002 | 0.006 | 3.707 |
| g__Lactobacillus s__ruminis | species | 0.26 | 0.000 | 0.000 | 0.000 | 3.698 |
| s__u(f__[Mogibacteriaceae]) | species | 0.22 | 0.040 | 0.003 | 0.007 | 3.684 |
| s__u(g__Dorea) | species | 1.66 | 0.160 | 0.000 | 0.000 | 3.665 |
| g__Bifidobacterium s__adolescentis | species | 1.84 | 0.121 | 0.001 | 0.003 | 3.665 |
| g__Blautia s__producta | species | 1.12 | 0.000 | 0.000 | 0.000 | 3.660 |
| s__u(g__[Ruminococcus]) | species | 1.48 | 0.022 | 0.000 | 0.000 | 3.630 |
| g__Dorea s__formicigenerans | species | 0.50 | 0.061 | 0.000 | 0.000 | 3.549 |
| s__u(f__Coriobacteriaceae) | species | 1.62 | 0.221 | 0.003 | 0.007 | 3.542 |
| g__[Eubacterium] s__biforme | species | 0.52 | 0.000 | 0.012 | 0.022 | 3.475 |
| g__Collinsella s__aerofaciens | species | 1.48 | 0.181 | 0.000 | 0.001 | 3.388 |
Cladogram of differences
Tree-like summary of the taxa differentially abundant in two groups constructed using LefSe.
Cladogram
List of differentially abundant taxa
increased in user_data
| denotation | feature |
|---|---|
| a | g__Bifidobacterium |
| b | f__Bifidobacteriaceae |
| c | o__Bifidobacteriales |
| d | c__Actinobacteria |
| e | g__Collinsella |
| f | g__Slackia |
| g | g__u(f__Coriobacteriaceae) |
| h | f__Coriobacteriaceae |
| i | o__Coriobacteriales |
| j | c__Coriobacteriia |
| u | g__[Prevotella] |
| v | f__[Paraprevotellaceae] |
| y | o__Bacillales |
| z | g__Lactobacillus |
| a0 | f__Lactobacillaceae |
| a1 | g__Streptococcus |
| a2 | f__Streptococcaceae |
| a3 | o__Lactobacillales |
| a4 | c__Bacilli |
| a5 | g__Clostridium |
| a6 | g__SMB53 |
| a7 | g__u(f__Clostridiaceae) |
| a8 | f__Clostridiaceae |
| a9 | g__Blautia |
| b0 | g__Coprococcus |
| b1 | g__Dorea |
| b2 | g__[Ruminococcus] |
| b3 | g__u(f__Lachnospiraceae) |
| b4 | f__Lachnospiraceae |
| b5 | g__Faecalibacterium |
| b6 | g__u(f__Ruminococcaceae) |
| b7 | f__Ruminococcaceae |
| b8 | g__Dialister |
| b9 | g__Megasphaera |
| c1 | f__Veillonellaceae |
| c2 | g__u(f__[Mogibacteriaceae]) |
| c3 | f__[Mogibacteriaceae] |
| c4 | o__Clostridiales |
| c5 | c__Clostridia |
| c6 | g__Catenibacterium |
| c7 | g__[Eubacterium] |
| c8 | f__Erysipelotrichaceae |
| c9 | o__Erysipelotrichales |
| d0 | c__Erysipelotrichi |
| d6 | g__Desulfovibrio |
| e0 | g__u(o__RF39) |
| e1 | f__u(o__RF39) |
| e2 | o__RF39 |
| e3 | c__Mollicutes |
increased in external_data
| denotation | feature |
|---|---|
| k | g__Bacteroides |
| l | f__Bacteroidaceae |
| m | g__Parabacteroides |
| n | f__Porphyromonadaceae |
| o | g__u(f__Rikenellaceae) |
| p | f__Rikenellaceae |
| q | g__u(f__[Barnesiellaceae]) |
| r | f__[Barnesiellaceae] |
| s | g__Odoribacter |
| t | f__[Odoribacteraceae] |
| w | o__Bacteroidales |
| x | c__Bacteroidia |
| c0 | g__Phascolarctobacterium |
| d1 | g__Sutterella |
| d2 | f__Alcaligenaceae |
| d3 | o__Burkholderiales |
| d4 | c__Betaproteobacteria |
| d5 | g__Bilophila |
| d7 | f__Desulfovibrionaceae |
| d8 | o__Desulfovibrionales |
| d9 | c__Deltaproteobacteria |
Excluded features
phylum
p__Euryarchaeota, p__Fusobacteria, p__Synergistetes, p__TM7, p__[Thermi]
class
c__Methanobacteria, c__Flavobacteriia, c__Chloroplast, c__Fusobacteriia, c__Synergistia, c__TM7-3, c__RF3, c__Verruco-5, c__Deinococci
order
o__Methanobacteriales, o__Actinomycetales, o__Flavobacteriales, o__Stramenopiles, o__Streptophyta, o__Gemellales, o__u(c__Clostridia), o__SHA-98, o__Fusobacteriales, o__Caulobacterales, o__Rhizobiales, o__Sphingomonadales, o__Aeromonadales, o__Alteromonadales, o__Chromatiales, o__Oceanospirillales, o__Pasteurellales, o__Pseudomonadales, o__Xanthomonadales, o__Synergistales, o__u(c__TM7-3), o__ML615J-28, o__WCHB1-41, o__Thermales
family
f__Methanobacteriaceae, f__Actinomycetaceae, f__Corynebacteriaceae, f__Intrasporangiaceae, f__Microbacteriaceae, f__Micrococcaceae, f__Propionibacteriaceae, f__Streptomycetaceae, f__u(o__Bacteroidales), f__RF16, f__[Weeksellaceae], f__u(o__Stramenopiles), f__u(o__Streptophyta), f__u(o__Bacillales), f__Bacillaceae, f__Planococcaceae, f__Staphylococcaceae, f__[Exiguobacteraceae], f__Gemellaceae, f__Aerococcaceae, f__Carnobacteriaceae, f__Enterococcaceae, f__Leuconostocaceae, f__u(c__Clostridia), f__Dehalobacteriaceae, f__Eubacteriaceae, f__[Tissierellaceae], f__u(o__SHA-98), f__Fusobacteriaceae, f__Caulobacteraceae, f__Beijerinckiaceae, f__Bradyrhizobiaceae, f__Brucellaceae, f__Methylobacteriaceae, f__Rhizobiaceae, f__Sphingomonadaceae, f__Comamonadaceae, f__Oxalobacteraceae, f__Succinivibrionaceae, f__Alteromonadaceae, f__Idiomarinaceae, f__[Chromatiaceae], f__Ectothiorhodospiraceae, f__Halomonadaceae, f__Pasteurellaceae, f__Moraxellaceae, f__Pseudomonadaceae, f__Xanthomonadaceae, f__Dethiosulfovibrionaceae, f__u(c__TM7-3), f__u(o__ML615J-28), f__RFP12, f__Thermaceae
genus
g__Methanobrevibacter, g__u(f__Actinomycetaceae), g__Actinomyces, g__Corynebacterium, g__u(f__Intrasporangiaceae), g__u(f__Microbacteriaceae), g__Mycetocola, g__u(f__Micrococcaceae), g__Nesterenkonia, g__Rothia, g__Propionibacterium, g__u(f__Streptomycetaceae), g__Streptomyces, g__Gardnerella, g__Adlercreutzia, g__Atopobium, g__u(o__Bacteroidales), g__Porphyromonas, g__u(f__Prevotellaceae), g__u(f__RF16), g__u(f__[Paraprevotellaceae]), g__Chryseobacterium, g__u(o__Stramenopiles), g__u(o__Streptophyta), g__u(o__Bacillales), g__u(f__Bacillaceae), g__Bacillus, g__u(f__Planococcaceae), g__Staphylococcus, g__Exiguobacterium, g__u(f__Gemellaceae), g__u(f__Aerococcaceae), g__Granulicatella, g__u(f__Enterococcaceae), g__Enterococcus, g__Vagococcus, g__u(f__Lactobacillaceae), g__u(f__Leuconostocaceae), g__Leuconostoc, g__u(f__Streptococcaceae), g__Lactococcus, g__u(c__Clostridia), g__Christensenella, g__02d06, g__Sarcina, g__Dehalobacterium, g__Pseudoramibacter_Eubacterium, g__Butyrivibrio, g__Epulopiscium, g__Pseudobutyrivibrio, g__Shuttleworthia, g__u(f__Peptococcaceae), g__rc4-4, g__Peptostreptococcus, g__Anaerotruncus, g__Acidaminococcus, g__Megamonas, g__Mitsuokella, g__Veillonella, g__Mogibacterium, g__Anaerococcus, g__Parvimonas, g__Peptoniphilus, g__WAL_1855D, g__ph2, g__u(o__SHA-98), g__Bulleidia, g__Coprobacillus, g__Holdemania, g__cc_115, g__p-75-a5, g__Fusobacterium, g__u(f__Caulobacteraceae), g__Brevundimonas, g__u(f__Beijerinckiaceae), g__Bradyrhizobium, g__Ochrobactrum, g__Methylobacterium, g__Shinella, g__u(f__Sphingomonadaceae), g__Blastomonas, g__Kaistobacter, g__u(f__Comamonadaceae), g__Comamonas, g__Delftia, g__u(f__Oxalobacteraceae), g__Ralstonia, g__Succinivibrio, g__Marinobacter, g__u(f__Idiomarinaceae), g__Idiomarina, g__Rheinheimera, g__u(f__Ectothiorhodospiraceae), g__Serratia, g__Halomonas, g__Haemophilus, g__Acinetobacter, g__u(f__Pseudomonadaceae), g__Pseudomonas, g__Stenotrophomonas, g__Pyramidobacter, g__u(c__TM7-3), g__u(o__ML615J-28), g__u(f__RFP12), g__Thermus
species
s__u(g__Methanobrevibacter), s__u(f__Actinomycetaceae), s__u(g__Actinomyces), s__u(g__Corynebacterium), s__u(f__Intrasporangiaceae), s__u(f__Microbacteriaceae), s__u(g__Mycetocola), s__u(f__Micrococcaceae), s__u(g__Nesterenkonia), g__Rothia s__aeria, g__Rothia s__mucilaginosa, g__Propionibacterium s__acnes, s__u(f__Streptomycetaceae), s__u(g__Streptomyces), g__Bifidobacterium s__bifidum, g__Bifidobacterium s__pseudolongum, s__u(g__Gardnerella), s__u(g__Adlercreutzia), s__u(g__Atopobium), s__u(g__Collinsella), s__u(o__Bacteroidales), g__Bacteroides s__caccae, g__Bacteroides s__plebeius, s__u(g__Porphyromonas), s__u(f__Prevotellaceae), g__Prevotella s__stercorea, s__u(f__RF16), s__u(f__[Paraprevotellaceae]), s__u(g__Chryseobacterium), s__u(o__Stramenopiles), s__u(o__Streptophyta), s__u(o__Bacillales), s__u(f__Bacillaceae), s__u(g__Bacillus), s__u(f__Planococcaceae), s__u(g__Staphylococcus), g__Staphylococcus s__aureus, s__u(g__Exiguobacterium), s__u(f__Gemellaceae), s__u(f__Aerococcaceae), s__u(g__Granulicatella), s__u(f__Enterococcaceae), s__u(g__Enterococcus), s__u(g__Vagococcus), s__u(f__Lactobacillaceae), s__u(g__Lactobacillus), g__Lactobacillus s__mucosae, g__Lactobacillus s__reuteri, g__Lactobacillus s__vaginalis, g__Lactobacillus s__zeae, s__u(f__Leuconostocaceae), s__u(g__Leuconostoc), s__u(f__Streptococcaceae), s__u(g__Lactococcus), g__Lactococcus s__garvieae, g__Streptococcus s__anginosus, g__Streptococcus s__minor, g__Streptococcus s__sobrinus, s__u(c__Clostridia), s__u(g__Christensenella), s__u(g__02d06), g__Clostridium s__hiranonis, s__u(g__Sarcina), s__u(g__Dehalobacterium), s__u(g__Pseudoramibacter_Eubacterium), s__u(g__Butyrivibrio), s__u(g__Epulopiscium), s__u(g__Pseudobutyrivibrio), s__u(g__Shuttleworthia), g__[Ruminococcus] s__torques, s__u(f__Peptococcaceae), s__u(g__rc4-4), g__Peptostreptococcus s__anaerobius, s__u(g__Anaerotruncus), s__u(g__Faecalibacterium), g__Ruminococcus s__bromii, g__Ruminococcus s__flavefaciens, s__u(g__Acidaminococcus), s__u(g__Megamonas), s__u(g__Mitsuokella), g__Mitsuokella s__multacida, s__u(g__Veillonella), g__Veillonella s__dispar, g__Veillonella s__parvula, s__u(g__Mogibacterium), s__u(g__Anaerococcus), s__u(g__Parvimonas), s__u(g__Peptoniphilus), s__u(g__WAL_1855D), s__u(g__ph2), s__u(o__SHA-98), s__u(g__Bulleidia), g__Bulleidia s__moorei, g__Bulleidia s__p-1630-c5, s__u(g__Coprobacillus), g__Coprobacillus s__cateniformis, s__u(g__Holdemania), g__[Eubacterium] s__dolichum, s__u(g__cc_115), s__u(g__p-75-a5), s__u(g__Fusobacterium), s__u(f__Caulobacteraceae), g__Brevundimonas s__diminuta, s__u(f__Beijerinckiaceae), s__u(g__Bradyrhizobium), s__u(g__Ochrobactrum), s__u(g__Methylobacterium), s__u(g__Shinella), s__u(f__Sphingomonadaceae), s__u(g__Blastomonas), s__u(g__Kaistobacter), s__u(f__Comamonadaceae), s__u(g__Comamonas), s__u(g__Delftia), s__u(f__Oxalobacteraceae), s__u(g__Ralstonia), g__Desulfovibrio s__D168, s__u(g__Succinivibrio), s__u(g__Marinobacter), s__u(f__Idiomarinaceae), s__u(g__Idiomarina), s__u(g__Rheinheimera), s__u(f__Ectothiorhodospiraceae), g__Erwinia s__dispersa, s__u(g__Serratia), s__u(g__Halomonas), g__Halomonas s__nitritophilus, s__u(g__Haemophilus), g__Haemophilus s__parainfluenzae, s__u(g__Acinetobacter), g__Acinetobacter s__guillouiae, g__Acinetobacter s__lwoffii, s__u(f__Pseudomonadaceae), s__u(g__Pseudomonas), g__Pseudomonas s__stutzeri, g__Stenotrophomonas s__geniculata, g__Pyramidobacter s__piscolens, s__u(c__TM7-3), s__u(o__ML615J-28), s__u(f__RFP12), s__u(g__Thermus)
All results of the test
Generalized linear mixed effect model
A generalized linear model is fitted for each taxon to identify if it is differentially abundant between the user and context data. 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: external_data
| taxon | taxa level | user_data mean, % | user_data sd, % | external_data mean, % | external_data sd, % | p-value | adjusted p-value | lda score | sample size |
|---|---|---|---|---|---|---|---|---|---|
| p__Bacteroidetes | phylum | 8.429 | 11.976 | 39.840 | 17.003 | 0.000 | 0.000 | 5.209 | 34 |
| p__Cyanobacteria | phylum | 0.013 | 0.034 | 0.306 | 0.814 | 0.006 | 0.008 | 4.583 | 34 |
| p__Proteobacteria | phylum | 3.996 | 5.758 | 18.839 | 28.265 | 0.001 | 0.002 | 4.396 | 34 |
| c__Bacteroidia | class | 8.427 | 11.977 | 39.843 | 17.005 | 0.000 | 0.000 | 5.161 | 34 |
| c__Betaproteobacteria | class | 0.429 | 0.949 | 1.886 | 1.799 | 0.001 | 0.004 | 4.689 | 34 |
| c__4C0d-2 | class | 0.002 | 0.006 | 0.303 | 0.816 | 0.002 | 0.004 | 4.501 | 34 |
| c__Deltaproteobacteria | class | 0.175 | 0.218 | 3.825 | 7.635 | 0.000 | 0.000 | 4.497 | 34 |
| o__Bacteroidales | order | 8.427 | 11.977 | 39.915 | 16.970 | 0.000 | 0.000 | 5.221 | 34 |
| o__YS2 | order | 0.002 | 0.006 | 0.303 | 0.816 | 0.002 | 0.005 | 4.742 | 34 |
| o__Desulfovibrionales | order | 0.175 | 0.218 | 3.876 | 7.753 | 0.000 | 0.000 | 4.479 | 34 |
| o__Burkholderiales | order | 0.429 | 0.949 | 1.886 | 1.799 | 0.001 | 0.004 | 4.472 | 34 |
| f__Bacteroidaceae | family | 1.645 | 3.409 | 26.937 | 16.689 | 0.000 | 0.000 | 5.105 | 34 |
| f__Desulfovibrionaceae | family | 0.175 | 0.218 | 3.901 | 7.816 | 0.000 | 0.000 | 4.234 | 34 |
| f__Porphyromonadaceae | family | 0.269 | 0.389 | 2.543 | 2.486 | 0.000 | 0.000 | 4.068 | 34 |
| f__Alcaligenaceae | family | 0.065 | 0.144 | 1.883 | 1.800 | 0.000 | 0.000 | 3.996 | 34 |
| f__[Odoribacteraceae] | family | 0.045 | 0.078 | 0.344 | 0.326 | 0.000 | 0.001 | 3.789 | 34 |
| f__Rikenellaceae | family | 0.387 | 0.846 | 1.553 | 1.847 | 0.008 | 0.021 | 3.788 | 34 |
| f__[Barnesiellaceae] | family | 0.082 | 0.252 | 0.931 | 1.617 | 0.021 | 0.041 | 3.714 | 34 |
| f__u(o__YS2) | family | 0.002 | 0.006 | 0.303 | 0.816 | 0.002 | 0.007 | 3.534 | 34 |
| g__Bacteroides | genus | 1.645 | 3.409 | 27.055 | 16.723 | 0.000 | 0.000 | 5.122 | 34 |
| g__Bilophila | genus | 0.013 | 0.040 | 3.764 | 7.959 | 0.000 | 0.000 | 4.321 | 34 |
| g__Parabacteroides | genus | 0.258 | 0.389 | 2.560 | 2.515 | 0.000 | 0.000 | 4.078 | 34 |
| g__Erwinia | genus | 0.004 | 0.011 | 2.328 | 5.373 | 0.000 | 0.001 | 4.070 | 34 |
| g__Odoribacter | genus | 0.018 | 0.040 | 0.123 | 0.124 | 0.001 | 0.003 | 4.053 | 34 |
| g__Sutterella | genus | 0.065 | 0.144 | 1.889 | 1.804 | 0.000 | 0.000 | 4.050 | 34 |
| g__Butyricimonas | genus | 0.027 | 0.047 | 0.222 | 0.296 | 0.010 | 0.026 | 3.892 | 34 |
| g__u(o__YS2) | genus | 0.002 | 0.006 | 0.308 | 0.836 | 0.002 | 0.008 | 3.834 | 34 |
| g__u(f__[Barnesiellaceae]) | genus | 0.082 | 0.252 | 0.937 | 1.630 | 0.021 | 0.046 | 3.828 | 34 |
| g__Phascolarctobacterium | genus | 0.058 | 0.178 | 1.170 | 1.164 | 0.000 | 0.000 | 3.823 | 34 |
| g__Oscillospira | genus | 0.527 | 0.204 | 1.208 | 1.132 | 0.019 | 0.044 | 3.817 | 34 |
| g__u(f__Rikenellaceae) | genus | 0.387 | 0.846 | 1.561 | 1.852 | 0.008 | 0.022 | 3.809 | 34 |
| g__Paraprevotella | genus | 0.027 | 0.043 | 0.494 | 0.972 | 0.014 | 0.035 | 3.745 | 34 |
| s__u(g__Bacteroides) | species | 1.295 | 3.028 | 19.742 | 10.914 | 0.000 | 0.000 | 4.952 | 34 |
| s__u(g__Bilophila) | species | 0.013 | 0.040 | 3.764 | 7.959 | 0.000 | 0.000 | 4.292 | 34 |
| g__Bacteroides s__ovatus | species | 0.029 | 0.038 | 2.959 | 3.232 | 0.000 | 0.000 | 4.168 | 34 |
| g__Bacteroides s__uniformis | species | 0.129 | 0.225 | 3.323 | 3.414 | 0.000 | 0.000 | 4.146 | 34 |
| s__u(g__Erwinia) | species | 0.002 | 0.006 | 2.328 | 5.373 | 0.000 | 0.000 | 4.118 | 34 |
| s__u(g__Sutterella) | species | 0.065 | 0.144 | 1.914 | 1.860 | 0.000 | 0.000 | 3.970 | 34 |
| g__Parabacteroides s__distasonis | species | 0.124 | 0.322 | 1.297 | 2.218 | 0.000 | 0.001 | 3.850 | 34 |
| s__u(f__Rikenellaceae) | species | 0.387 | 0.846 | 1.564 | 1.852 | 0.007 | 0.019 | 3.806 | 34 |
| s__u(g__Parabacteroides) | species | 0.135 | 0.106 | 1.269 | 1.385 | 0.000 | 0.000 | 3.767 | 34 |
| s__u(g__Phascolarctobacterium) | species | 0.058 | 0.178 | 1.175 | 1.165 | 0.000 | 0.000 | 3.764 | 34 |
| s__u(f__[Barnesiellaceae]) | species | 0.082 | 0.252 | 0.939 | 1.633 | 0.020 | 0.045 | 3.595 | 34 |
| s__u(g__Oscillospira) | species | 0.527 | 0.204 | 1.211 | 1.132 | 0.018 | 0.041 | 3.555 | 34 |
| s__u(g__Paraprevotella) | species | 0.027 | 0.043 | 0.501 | 0.978 | 0.014 | 0.033 | 3.541 | 34 |
| g__Roseburia s__faecis | species | 0.007 | 0.013 | 0.109 | 0.126 | 0.000 | 0.000 | 3.501 | 34 |
| s__u(g__Odoribacter) | species | 0.018 | 0.040 | 0.123 | 0.124 | 0.001 | 0.003 | 3.408 | 34 |
| g__Blautia s__obeum | species | 0.029 | 0.027 | 0.233 | 0.268 | 0.000 | 0.000 | 3.376 | 34 |
| s__u(o__YS2) | species | 0.002 | 0.006 | 0.308 | 0.836 | 0.002 | 0.006 | 3.360 | 34 |
| s__u(g__Butyricimonas) | species | 0.027 | 0.047 | 0.223 | 0.297 | 0.010 | 0.024 | 3.346 | 34 |
Overpresented in group: user_data
| taxon | taxa level | user_data mean, % | user_data sd, % | external_data mean, % | external_data sd, % | p-value | adjusted p-value | lda score | sample size |
|---|---|---|---|---|---|---|---|---|---|
| p__Actinobacteria | phylum | 7.824 | 6.401 | 1.574 | 1.775 | 0.000 | 0.001 | 5.334 | 34 |
| p__Firmicutes | phylum | 78.916 | 12.284 | 38.246 | 19.008 | 0.001 | 0.002 | 4.935 | 34 |
| c__Clostridia | class | 65.387 | 11.444 | 35.373 | 17.951 | 0.006 | 0.009 | 5.216 | 34 |
| c__Erysipelotrichi | class | 9.098 | 7.731 | 2.029 | 2.246 | 0.002 | 0.004 | 4.657 | 34 |
| c__Actinobacteria | class | 4.067 | 4.749 | 0.790 | 1.402 | 0.003 | 0.005 | 4.505 | 34 |
| c__Coriobacteriia | class | 3.756 | 2.529 | 0.783 | 0.770 | 0.000 | 0.001 | 4.472 | 34 |
| c__Bacilli | class | 4.431 | 5.921 | 0.848 | 1.838 | 0.002 | 0.004 | 4.424 | 34 |
| o__Clostridiales | order | 65.378 | 11.441 | 35.400 | 17.944 | 0.006 | 0.010 | 5.226 | 34 |
| o__Coriobacteriales | order | 3.756 | 2.529 | 0.783 | 0.770 | 0.000 | 0.001 | 4.661 | 34 |
| o__Erysipelotrichales | order | 9.098 | 7.731 | 2.030 | 2.248 | 0.002 | 0.005 | 4.625 | 34 |
| o__Bifidobacteriales | order | 3.927 | 4.620 | 0.777 | 1.404 | 0.005 | 0.009 | 4.561 | 34 |
| o__Lactobacillales | order | 4.036 | 5.825 | 0.688 | 1.855 | 0.005 | 0.009 | 4.472 | 34 |
| f__Ruminococcaceae | family | 29.862 | 7.161 | 13.399 | 8.348 | 0.013 | 0.027 | 4.940 | 34 |
| f__Erysipelotrichaceae | family | 9.098 | 7.731 | 2.031 | 2.248 | 0.002 | 0.006 | 4.505 | 34 |
| f__Lactobacillaceae | family | 3.013 | 5.801 | 0.035 | 0.114 | 0.000 | 0.000 | 4.194 | 34 |
| f__Coriobacteriaceae | family | 3.756 | 2.529 | 0.783 | 0.770 | 0.000 | 0.001 | 4.151 | 34 |
| f__Bifidobacteriaceae | family | 3.927 | 4.620 | 0.777 | 1.404 | 0.005 | 0.015 | 4.144 | 34 |
| f__Veillonellaceae | family | 4.318 | 2.894 | 2.160 | 1.740 | 0.025 | 0.047 | 4.008 | 34 |
| f__Christensenellaceae | family | 0.625 | 0.820 | 0.134 | 0.266 | 0.010 | 0.022 | 3.719 | 34 |
| f__[Mogibacteriaceae] | family | 0.256 | 0.139 | 0.091 | 0.116 | 0.009 | 0.022 | 3.653 | 34 |
| g__u(f__Ruminococcaceae) | genus | 16.622 | 6.831 | 6.297 | 4.452 | 0.002 | 0.007 | 4.726 | 34 |
| g__Catenibacterium | genus | 5.987 | 6.993 | 0.265 | 0.577 | 0.003 | 0.010 | 4.467 | 34 |
| g__Blautia | genus | 5.855 | 3.338 | 1.574 | 1.179 | 0.000 | 0.002 | 4.342 | 34 |
| g__Bifidobacterium | genus | 3.925 | 4.615 | 0.779 | 1.408 | 0.005 | 0.015 | 4.222 | 34 |
| g__[Ruminococcus] | genus | 1.727 | 0.793 | 0.222 | 0.333 | 0.000 | 0.000 | 4.210 | 34 |
| g__Dorea | genus | 2.273 | 0.804 | 0.403 | 0.400 | 0.000 | 0.000 | 4.173 | 34 |
| g__Lactobacillus | genus | 3.011 | 5.801 | 0.035 | 0.118 | 0.000 | 0.000 | 4.150 | 34 |
| g__Collinsella | genus | 1.702 | 1.249 | 0.349 | 0.432 | 0.000 | 0.001 | 3.992 | 34 |
| g__u(f__Coriobacteriaceae) | genus | 1.836 | 1.435 | 0.372 | 0.441 | 0.003 | 0.009 | 3.975 | 34 |
| g__Coprococcus | genus | 1.425 | 0.769 | 0.453 | 0.380 | 0.000 | 0.001 | 3.906 | 34 |
| g__u(f__Christensenellaceae) | genus | 0.622 | 0.820 | 0.132 | 0.266 | 0.010 | 0.026 | 3.881 | 34 |
| s__u(f__Ruminococcaceae) | species | 16.622 | 6.831 | 6.332 | 4.464 | 0.002 | 0.006 | 4.723 | 34 |
| s__u(g__Catenibacterium) | species | 5.987 | 6.993 | 0.265 | 0.577 | 0.003 | 0.009 | 4.495 | 34 |
| s__u(g__Blautia) | species | 4.544 | 2.823 | 1.317 | 1.074 | 0.001 | 0.005 | 4.218 | 34 |
| g__Bifidobacterium s__adolescentis | species | 2.869 | 2.844 | 0.391 | 0.511 | 0.001 | 0.004 | 4.125 | 34 |
| s__u(g__Dorea) | species | 1.558 | 0.571 | 0.239 | 0.263 | 0.000 | 0.000 | 3.937 | 34 |
| s__u(f__Coriobacteriaceae) | species | 1.836 | 1.435 | 0.373 | 0.441 | 0.003 | 0.008 | 3.928 | 34 |
| s__u(g__[Ruminococcus]) | species | 1.402 | 0.680 | 0.066 | 0.098 | 0.000 | 0.000 | 3.915 | 34 |
| g__Blautia s__producta | species | 1.282 | 0.810 | 0.034 | 0.069 | 0.000 | 0.000 | 3.879 | 34 |
| g__Collinsella s__aerofaciens | species | 1.647 | 1.210 | 0.331 | 0.440 | 0.001 | 0.004 | 3.856 | 34 |
| s__u(g__Coprococcus) | species | 1.240 | 0.635 | 0.295 | 0.197 | 0.000 | 0.000 | 3.827 | 34 |
| g__Bifidobacterium s__longum | species | 0.645 | 1.168 | 0.007 | 0.014 | 0.000 | 0.000 | 3.663 | 34 |
| g__Dorea s__formicigenerans | species | 0.715 | 0.446 | 0.166 | 0.321 | 0.001 | 0.004 | 3.559 | 34 |
| s__u(f__Christensenellaceae) | species | 0.622 | 0.820 | 0.132 | 0.266 | 0.010 | 0.024 | 3.534 | 34 |
| g__[Ruminococcus] s__gnavus | species | 0.316 | 0.185 | 0.096 | 0.134 | 0.003 | 0.009 | 3.421 | 34 |
Cladogram of differences
Tree-like summary of the taxa differentially abundant in two groups constructed using LefSe.
Cladogram
List of differentially abundant taxa
increased in user_data
| denotation | feature |
|---|---|
| a | g__Bifidobacterium |
| b | f__Bifidobacteriaceae |
| c | o__Bifidobacteriales |
| d | c__Actinobacteria |
| e | g__Collinsella |
| f | g__u(f__Coriobacteriaceae) |
| g | f__Coriobacteriaceae |
| h | o__Coriobacteriales |
| i | c__Coriobacteriia |
| a1 | g__Lactobacillus |
| a2 | f__Lactobacillaceae |
| a3 | o__Lactobacillales |
| a4 | c__Bacilli |
| a5 | g__u(f__Christensenellaceae) |
| a6 | f__Christensenellaceae |
| a7 | g__Blautia |
| a8 | g__Coprococcus |
| a9 | g__Dorea |
| b0 | g__[Ruminococcus] |
| b2 | g__u(f__Ruminococcaceae) |
| b3 | f__Ruminococcaceae |
| b5 | f__Veillonellaceae |
| b6 | f__[Mogibacteriaceae] |
| b7 | o__Clostridiales |
| b8 | c__Clostridia |
| b9 | g__Catenibacterium |
| c0 | f__Erysipelotrichaceae |
| c1 | o__Erysipelotrichales |
| c2 | c__Erysipelotrichi |
increased in external_data
| denotation | feature |
|---|---|
| j | g__Bacteroides |
| k | f__Bacteroidaceae |
| l | g__Parabacteroides |
| m | f__Porphyromonadaceae |
| n | g__u(f__Rikenellaceae) |
| o | f__Rikenellaceae |
| p | g__u(f__[Barnesiellaceae]) |
| q | f__[Barnesiellaceae] |
| r | g__Butyricimonas |
| s | g__Odoribacter |
| t | f__[Odoribacteraceae] |
| u | g__Paraprevotella |
| v | o__Bacteroidales |
| w | c__Bacteroidia |
| x | g__u(o__YS2) |
| y | f__u(o__YS2) |
| z | o__YS2 |
| a0 | c__4C0d-2 |
| b1 | g__Oscillospira |
| b4 | g__Phascolarctobacterium |
| c3 | g__Sutterella |
| c4 | f__Alcaligenaceae |
| c5 | o__Burkholderiales |
| c6 | c__Betaproteobacteria |
| c7 | g__Bilophila |
| c8 | f__Desulfovibrionaceae |
| c9 | o__Desulfovibrionales |
| d0 | c__Deltaproteobacteria |
| d1 | g__Erwinia |
Excluded features
phylum
p__Fusobacteria, p__Synergistetes, p__TM7, p__[Thermi], p__Euryarchaeota
class
c__RF3, c__Chloroplast, c__Verruco-5, c__Fusobacteriia, c__Deinococci, c__Flavobacteriia, c__Methanobacteria, c__TM7-3, c__Synergistia
order
o__Streptophyta, o__Pasteurellales, o__Xanthomonadales, o__Actinomycetales, o__Chromatiales, o__Fusobacteriales, o__ML615J-28, o__Sphingomonadales, o__Methanobacteriales, o__u(c__Clostridia), o__Aeromonadales, o__SHA-98, o__Thermales, o__WCHB1-41, o__Stramenopiles, o__Gemellales, o__Synergistales, o__Caulobacterales, o__Alteromonadales, o__Pseudomonadales, o__u(c__TM7-3), o__Oceanospirillales, o__Flavobacteriales, o__Rhizobiales
family
f__Methanobacteriaceae, f__Fusobacteriaceae, f__Brucellaceae, f__u(o__Stramenopiles), f__Alteromonadaceae, f__Actinomycetaceae, f__[Exiguobacteraceae], f__Methylobacteriaceae, f__Bacillaceae, f__u(c__TM7-3), f__RF16, f__[Chromatiaceae], f__Enterococcaceae, f__Idiomarinaceae, f__Thermaceae, f__Moraxellaceae, f__Xanthomonadaceae, f__Ectothiorhodospiraceae, f__u(o__SHA-98), f__Dethiosulfovibrionaceae, f__Gemellaceae, f__u(o__ML615J-28), f__Microbacteriaceae, f__u(o__Streptophyta), f__Halomonadaceae, f__Aerococcaceae, f__Pasteurellaceae, f__RFP12, f__Intrasporangiaceae, f__Streptomycetaceae, f__[Tissierellaceae], f__Propionibacteriaceae, f__u(o__Bacillales), f__Succinivibrionaceae, f__Leuconostocaceae, f__Beijerinckiaceae, f__Planococcaceae, f__Micrococcaceae, f__Comamonadaceae, f__Corynebacteriaceae, f__Dehalobacteriaceae, f__Rhizobiaceae, f__[Weeksellaceae], f__u(o__Bacteroidales), f__u(c__Clostridia), f__Carnobacteriaceae, f__Caulobacteraceae, f__Pseudomonadaceae, f__Sphingomonadaceae, f__Oxalobacteraceae, f__Staphylococcaceae, f__Eubacteriaceae, f__Bradyrhizobiaceae
genus
g__Actinomyces, g__Propionibacterium, g__u(o__ML615J-28), g__Lactococcus, g__u(o__Bacteroidales), g__Serratia, g__u(f__Idiomarinaceae), g__Blastomonas, g__u(f__Beijerinckiaceae), g__u(f__Planococcaceae), g__Gardnerella, g__u(f__Streptomycetaceae), g__Acidaminococcus, g__Anaerococcus, g__Halomonas, g__u(f__RF16), g__Epulopiscium, g__Leuconostoc, g__Adlercreutzia, g__u(f__Oxalobacteraceae), g__Corynebacterium, g__ph2, g__Shuttleworthia, g__u(c__TM7-3), g__u(f__Comamonadaceae), g__u(o__SHA-98), g__Nesterenkonia, g__Megamonas, g__Stenotrophomonas, g__u(f__Microbacteriaceae), g__Holdemania, g__cc_115, g__Sarcina, g__u(f__Pseudomonadaceae), g__Succinivibrio, g__Porphyromonas, g__Enterococcus, g__Kaistobacter, g__u(f__Gemellaceae), g__u(o__Streptophyta), g__u(f__Ectothiorhodospiraceae), g__Delftia, g__Haemophilus, g__Methanobrevibacter, g__Marinobacter, g__WAL_1855D, g__Pseudomonas, g__Ochrobactrum, g__p-75-a5, g__Mycetocola, g__u(o__Stramenopiles), g__Brevundimonas, g__Veillonella, g__Thermus, g__u(o__Bacillales), g__u(f__Streptococcaceae), g__Granulicatella, g__u(f__[Paraprevotellaceae]), g__u(f__Intrasporangiaceae), g__Mitsuokella, g__Coprobacillus, g__Ralstonia, g__Rheinheimera, g__u(f__Aerococcaceae), g__Chryseobacterium, g__Dehalobacterium, g__u(f__Micrococcaceae), g__Bulleidia, g__Comamonas, g__u(f__Bacillaceae), g__Idiomarina, g__Parvimonas, g__Butyrivibrio, g__Exiguobacterium, g__Streptomyces, g__02d06, g__Acinetobacter, g__u(f__Sphingomonadaceae), g__Fusobacterium, g__Pseudobutyrivibrio, g__Anaerotruncus, g__Mogibacterium, g__Shinella, g__u(f__Enterococcaceae), g__Pyramidobacter, g__Vagococcus, g__u(f__Lactobacillaceae), g__Peptostreptococcus, g__Methylobacterium, g__Christensenella, g__u(f__Actinomycetaceae), g__Atopobium, g__Rothia, g__Bacillus, g__u(f__Caulobacteraceae), g__Staphylococcus, g__Peptoniphilus, g__u(f__Prevotellaceae), g__Pseudoramibacter_Eubacterium, g__u(c__Clostridia), g__rc4-4, g__u(f__Peptococcaceae), g__Bradyrhizobium, g__u(f__Leuconostocaceae), g__u(f__RFP12)
species
s__u(g__Staphylococcus), s__u(g__Epulopiscium), s__u(g__Bulleidia), g__Lactococcus s__garvieae, g__Pseudomonas s__stutzeri, s__u(f__Leuconostocaceae), s__u(g__Megamonas), s__u(g__Veillonella), g__Staphylococcus s__aureus, g__Bacteroides s__caccae, s__u(f__RF16), s__u(g__Atopobium), g__Bulleidia s__p-1630-c5, s__u(g__Corynebacterium), g__Prevotella s__stercorea, s__u(g__Acidaminococcus), s__u(f__Pseudomonadaceae), g__Mitsuokella s__multacida, s__u(o__Bacillales), s__u(g__Bradyrhizobium), s__u(g__Methanobrevibacter), g__Streptococcus s__sobrinus, s__u(g__Delftia), g__Erwinia s__dispersa, s__u(g__Collinsella), s__u(f__Micrococcaceae), s__u(g__Chryseobacterium), s__u(g__Marinobacter), s__u(f__Ectothiorhodospiraceae), g__Bulleidia s__moorei, s__u(g__Granulicatella), s__u(f__Bacillaceae), s__u(g__Succinivibrio), s__u(g__Nesterenkonia), s__u(g__ph2), s__u(f__Aerococcaceae), g__Bacteroides s__plebeius, s__u(g__Pseudoramibacter_Eubacterium), s__u(g__Serratia), s__u(g__p-75-a5), s__u(g__Leuconostoc), s__u(g__Coprobacillus), s__u(f__[Paraprevotellaceae]), s__u(g__WAL_1855D), g__Bifidobacterium s__bifidum, s__u(f__Gemellaceae), s__u(g__Haemophilus), g__Propionibacterium s__acnes, g__Brevundimonas s__diminuta, s__u(g__Comamonas), g__Veillonella s__parvula, s__u(g__Mitsuokella), s__u(f__Actinomycetaceae), s__u(g__Blastomonas), s__u(f__Streptomycetaceae), s__u(g__Mogibacterium), g__[Ruminococcus] s__torques, g__Ruminococcus s__flavefaciens, s__u(f__RFP12), g__Peptostreptococcus s__anaerobius, s__u(g__Methylobacterium), s__u(g__Adlercreutzia), s__u(f__Comamonadaceae), g__Rothia s__aeria, s__u(g__Peptoniphilus), s__u(g__Vagococcus), s__u(g__Ochrobactrum), s__u(g__Lactobacillus), g__Lactobacillus s__zeae, s__u(f__Prevotellaceae), s__u(g__Acinetobacter), s__u(g__Rheinheimera), s__u(o__Bacteroidales), s__u(g__cc_115), g__Streptococcus s__minor, s__u(g__Sarcina), s__u(g__Pseudomonas), s__u(g__rc4-4), s__u(f__Oxalobacteraceae), g__Stenotrophomonas s__geniculata, s__u(c__Clostridia), g__Clostridium s__hiranonis, s__u(g__Bacillus), s__u(g__Mycetocola), s__u(g__Shuttleworthia), g__Lactobacillus s__reuteri, s__u(o__Stramenopiles), s__u(g__Gardnerella), s__u(g__Thermus), g__Haemophilus s__parainfluenzae, g__Ruminococcus s__bromii, s__u(g__Anaerotruncus), s__u(g__Ralstonia), s__u(f__Enterococcaceae), s__u(g__Actinomyces), s__u(g__Kaistobacter), g__Coprobacillus s__cateniformis, g__[Eubacterium] s__dolichum, s__u(f__Streptococcaceae), s__u(g__Exiguobacterium), s__u(f__Peptococcaceae), s__u(f__Lactobacillaceae), s__u(g__Lactococcus), s__u(g__Christensenella), s__u(g__Butyrivibrio), g__Acinetobacter s__guillouiae, s__u(g__Streptomyces), s__u(g__Parvimonas), g__Desulfovibrio s__D168, s__u(g__Dehalobacterium), s__u(o__Streptophyta), s__u(g__Fusobacterium), s__u(c__TM7-3), g__Streptococcus s__anginosus, g__Rothia s__mucilaginosa, s__u(g__Enterococcus), g__Lactobacillus s__mucosae, s__u(g__Pseudobutyrivibrio), s__u(f__Planococcaceae), s__u(f__Sphingomonadaceae), s__u(f__Intrasporangiaceae), s__u(g__02d06), s__u(o__SHA-98), s__u(g__Idiomarina), s__u(o__ML615J-28), s__u(f__Idiomarinaceae), s__u(f__Caulobacteraceae), s__u(f__Beijerinckiaceae), s__u(f__Microbacteriaceae), s__u(g__Halomonas), g__Acinetobacter s__lwoffii, s__u(g__Porphyromonas), s__u(g__Faecalibacterium), s__u(g__Anaerococcus), g__Lactobacillus s__vaginalis, s__u(g__Holdemania), g__Bifidobacterium s__pseudolongum, g__Veillonella s__dispar, g__Pyramidobacter s__piscolens, s__u(g__Shinella), g__Halomonas s__nitritophilus
All results of the test
Model details
| trait | state |
|---|---|
| distribution | negative binomial |
| formula | feature_abundance ~ case_control |
| link function | log |
| number of samples | 34 |
Functional composition
Individual pathways and reactions for which relative abundance is significantly different between user and external data are identified.
Wilcoxon test comparison
Method: Wilcoxon rank-sum 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 rank-sum test applied to each taxon to detect the taxa differentially abundant between the user and external data. 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 were excluded from this analysis.
Differentially abundant taxa
Tables of differentially abundant taxa overpresented in the groups
Overpresented in group: external_data
| pathway | metabolic level | user_data median, % | external_data median, % | p-value | adjusted p-value | lda score |
|---|---|---|---|---|---|---|
| ko00540 : Lipopolysaccharide biosynthesis | KEGG pathways | 0.258 | 0.679 | 0.000 | 0.001 | 3.514 |
| ko03070 : Bacterial secretion system | KEGG pathways | 1.590 | 1.685 | 0.014 | 0.028 | 3.290 |
| ko00130 : Ubiquinone and other terpenoid-quinone biosynthesis | KEGG pathways | 0.180 | 0.477 | 0.000 | 0.001 | 3.235 |
| ko00910 : Nitrogen metabolism | KEGG pathways | 1.484 | 1.644 | 0.000 | 0.002 | 3.128 |
| ko00600 : Sphingolipid metabolism | KEGG pathways | 0.331 | 0.579 | 0.000 | 0.002 | 3.113 |
| ko00720 : Carbon fixation pathways in prokaryotes | KEGG pathways | 2.161 | 2.447 | 0.000 | 0.002 | 3.099 |
| ko00190 : Oxidative phosphorylation | KEGG pathways | 1.969 | 2.173 | 0.005 | 0.012 | 2.974 |
| ko00604 : Glycosphingolipid biosynthesis - ganglio series | KEGG pathways | 0.037 | 0.187 | 0.000 | 0.001 | 2.929 |
| ko00620 : Pyruvate metabolism | KEGG pathways | 0.809 | 0.981 | 0.001 | 0.003 | 2.893 |
| ko00920 : Sulfur metabolism | KEGG pathways | 0.732 | 0.878 | 0.000 | 0.001 | 2.812 |
| ko00480 : Glutathione metabolism | KEGG pathways | 0.278 | 0.357 | 0.000 | 0.002 | 2.791 |
| ko00520 : Amino sugar and nucleotide sugar metabolism | KEGG pathways | 3.043 | 3.229 | 0.030 | 0.049 | 2.789 |
| ko03020 : RNA polymerase | KEGG pathways | 2.117 | 2.400 | 0.020 | 0.039 | 2.773 |
| ko00511 : Other glycan degradation | KEGG pathways | 0.220 | 0.350 | 0.006 | 0.013 | 2.765 |
| ko00940 : Phenylpropanoid biosynthesis | KEGG pathways | 0.438 | 0.576 | 0.025 | 0.042 | 2.732 |
| ko00633 : Nitrotoluene degradation | KEGG pathways | 0.009 | 0.035 | 0.001 | 0.004 | 2.712 |
| ko00790 : Folate biosynthesis | KEGG pathways | 0.811 | 0.875 | 0.003 | 0.008 | 2.703 |
| ko00740 : Riboflavin metabolism | KEGG pathways | 0.608 | 0.691 | 0.001 | 0.004 | 2.702 |
| ko00785 : Lipoic acid metabolism | KEGG pathways | 0.030 | 0.106 | 0.000 | 0.001 | 2.690 |
| ko00780 : Biotin metabolism | KEGG pathways | 0.403 | 0.484 | 0.000 | 0.001 | 2.670 |
| ko00061 : Fatty acid biosynthesis | KEGG pathways | 0.617 | 0.704 | 0.000 | 0.001 | 2.646 |
| ko00750 : Vitamin B6 metabolism | KEGG pathways | 0.521 | 0.601 | 0.000 | 0.002 | 2.632 |
| ko00360 : Phenylalanine metabolism | KEGG pathways | 0.134 | 0.194 | 0.001 | 0.004 | 2.527 |
| ko00071 : Fatty acid degradation | KEGG pathways | 0.151 | 0.212 | 0.001 | 0.004 | 2.519 |
| ko03018 : RNA degradation | KEGG pathways | 1.297 | 1.393 | 0.018 | 0.036 | 2.519 |
| ko00440 : Phosphonate and phosphinate metabolism | KEGG pathways | 0.144 | 0.176 | 0.007 | 0.016 | 2.482 |
| ko00960 : Tropane, piperidine and pyridine alkaloid biosynthesis | KEGG pathways | 0.320 | 0.354 | 0.000 | 0.002 | 2.435 |
| ko01055 : Biosynthesis of vancomycin group antibiotics | KEGG pathways | 0.163 | 0.195 | 0.025 | 0.042 | 2.231 |
Overpresented in group: user_data
| pathway | metabolic level | user_data median, % | external_data median, % | p-value | adjusted p-value | lda score |
|---|---|---|---|---|---|---|
| ko02010 : ABC transporters | KEGG pathways | 10.095 | 8.617 | 0.025 | 0.042 | 3.652 |
| ko03010 : Ribosome | KEGG pathways | 7.039 | 6.719 | 0.027 | 0.045 | 3.482 |
| ko02060 : Phosphotransferase system (PTS) | KEGG pathways | 1.550 | 0.951 | 0.002 | 0.007 | 3.380 |
| ko00970 : Aminoacyl-tRNA biosynthesis | KEGG pathways | 3.641 | 3.345 | 0.000 | 0.002 | 3.354 |
| ko00860 : Porphyrin and chlorophyll metabolism | KEGG pathways | 2.909 | 2.473 | 0.001 | 0.004 | 3.274 |
| ko00550 : Peptidoglycan biosynthesis | KEGG pathways | 2.499 | 2.348 | 0.002 | 0.007 | 3.028 |
| ko00240 : Pyrimidine metabolism | KEGG pathways | 2.377 | 2.294 | 0.001 | 0.005 | 2.976 |
| ko00300 : Lysine biosynthesis | KEGG pathways | 1.565 | 1.420 | 0.000 | 0.001 | 2.942 |
| ko00230 : Purine metabolism | KEGG pathways | 2.396 | 2.198 | 0.000 | 0.001 | 2.940 |
| ko00730 : Thiamine metabolism | KEGG pathways | 1.559 | 1.511 | 0.004 | 0.011 | 2.790 |
| ko00564 : Glycerophospholipid metabolism | KEGG pathways | 1.538 | 1.469 | 0.003 | 0.007 | 2.703 |
| ko00630 : Glyoxylate and dicarboxylate metabolism | KEGG pathways | 1.012 | 0.910 | 0.001 | 0.004 | 2.658 |
| ko01051 : Biosynthesis of ansamycins | KEGG pathways | 0.394 | 0.333 | 0.000 | 0.002 | 2.626 |
| ko00660 : C5-Branched dibasic acid metabolism | KEGG pathways | 0.590 | 0.557 | 0.014 | 0.028 | 2.617 |
| ko00710 : Carbon fixation in photosynthetic organisms | KEGG pathways | 1.412 | 1.361 | 0.005 | 0.011 | 2.601 |
| ko03060 : Protein export | KEGG pathways | 0.486 | 0.468 | 0.008 | 0.018 | 2.557 |
| ko00270 : Cysteine and methionine metabolism | KEGG pathways | 0.968 | 0.921 | 0.004 | 0.011 | 2.542 |
| ko00640 : Propanoate metabolism | KEGG pathways | 0.281 | 0.194 | 0.002 | 0.006 | 2.540 |
| ko00624 : Polycyclic aromatic hydrocarbon degradation | KEGG pathways | 0.350 | 0.334 | 0.022 | 0.041 | 2.508 |
| ko00561 : Glycerolipid metabolism | KEGG pathways | 0.347 | 0.282 | 0.005 | 0.011 | 2.507 |
| ko03030 : DNA replication | KEGG pathways | 0.563 | 0.532 | 0.004 | 0.011 | 2.396 |
| ko03410 : Base excision repair | KEGG pathways | 0.863 | 0.817 | 0.011 | 0.024 | 2.354 |
| ko00450 : Selenocompound metabolism | KEGG pathways | 0.262 | 0.240 | 0.022 | 0.041 | 2.323 |
| ko00052 : Galactose metabolism | KEGG pathways | 0.240 | 0.206 | 0.017 | 0.033 | 2.295 |
Cladogram of differences
Tree-like summary of the taxa differentially abundant in two groups constructed using LefSe.
Cladogram
List of differentially abundant taxa
increased in user_data
| denotation | feature |
|---|---|
| a | ko00052 |
| f | ko00230 |
| g | ko00240 |
| h | ko00270 |
| i | ko00300 |
| l | ko00450 |
| q | ko00550 |
| r | ko00561 |
| s | ko00564 |
| w | ko00624 |
| x | ko00630 |
| z | ko00640 |
| a0 | ko00660 |
| a1 | ko00710 |
| a3 | ko00730 |
| a9 | ko00860 |
| b4 | ko00970 |
| b5 | ko01051 |
| b7 | ko02010 |
| b8 | ko02060 |
| b9 | ko03010 |
| c2 | ko03030 |
| c3 | ko03060 |
| c5 | ko03410 |
increased in external_data
| denotation | feature |
|---|---|
| b | ko00061 |
| c | ko00071 |
| d | ko00130 |
| e | ko00190 |
| j | ko00360 |
| k | ko00440 |
| m | ko00480 |
| n | ko00511 |
| o | ko00520 |
| p | ko00540 |
| t | ko00600 |
| u | ko00604 |
| v | ko00620 |
| y | ko00633 |
| a2 | ko00720 |
| a4 | ko00740 |
| a5 | ko00750 |
| a6 | ko00780 |
| a7 | ko00785 |
| a8 | ko00790 |
| b0 | ko00910 |
| b1 | ko00920 |
| b2 | ko00940 |
| b3 | ko00960 |
| b6 | ko01055 |
| c0 | ko03018 |
| c1 | ko03020 |
| c4 | ko03070 |
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, 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, 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, ko00621 : Dioxin degradation, ko00622 : Xylene degradation, ko00623 : Toluene degradation, ko00625 : Chloroalkane and chloroalkene degradation, ko00626 : Naphthalene degradation, ko00627 : Aminobenzoate degradation, ko00642 : Ethylbenzene degradation, ko00643 : Styrene degradation, 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, 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
All results of the test
Generalized linear mixed effect model
A generalized linear model is fitted for each taxon to identify if it is differentially abundant between the user and context data. 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: external_data
| pathway | metabolic level | user_data mean, % | user_data sd, % | external_data mean, % | external_data sd, % | p-value | adjusted p-value | lda score | sample size |
|---|---|---|---|---|---|---|---|---|---|
| ko00540 : Lipopolysaccharide biosynthesis | KEGG pathways | 0.248 | 0.178 | 0.893 | 0.424 | 0.000 | 0.001 | 4.380 | 34 |
| ko00130 : Ubiquinone and other terpenoid-quinone biosynthesis | KEGG pathways | 0.234 | 0.095 | 0.565 | 0.264 | 0.000 | 0.003 | 4.127 | 34 |
| ko00604 : Glycosphingolipid biosynthesis - ganglio series | KEGG pathways | 0.049 | 0.031 | 0.219 | 0.092 | 0.000 | 0.000 | 4.106 | 34 |
| ko00600 : Sphingolipid metabolism | KEGG pathways | 0.339 | 0.060 | 0.615 | 0.256 | 0.002 | 0.007 | 3.973 | 34 |
| ko00785 : Lipoic acid metabolism | KEGG pathways | 0.040 | 0.021 | 0.129 | 0.065 | 0.000 | 0.001 | 3.893 | 34 |
| ko00511 : Other glycan degradation | KEGG pathways | 0.215 | 0.030 | 0.330 | 0.111 | 0.003 | 0.009 | 3.726 | 34 |
| ko00910 : Nitrogen metabolism | KEGG pathways | 1.490 | 0.081 | 1.737 | 0.207 | 0.001 | 0.004 | 3.690 | 34 |
| ko00720 : Carbon fixation pathways in prokaryotes | KEGG pathways | 2.189 | 0.132 | 2.443 | 0.171 | 0.000 | 0.001 | 3.683 | 34 |
| ko00480 : Glutathione metabolism | KEGG pathways | 0.296 | 0.052 | 0.408 | 0.126 | 0.010 | 0.025 | 3.665 | 34 |
| ko00620 : Pyruvate metabolism | KEGG pathways | 0.829 | 0.057 | 0.987 | 0.116 | 0.000 | 0.002 | 3.641 | 34 |
| ko00920 : Sulfur metabolism | KEGG pathways | 0.739 | 0.044 | 0.871 | 0.076 | 0.000 | 0.000 | 3.601 | 34 |
| ko00071 : Fatty acid degradation | KEGG pathways | 0.168 | 0.036 | 0.222 | 0.045 | 0.002 | 0.007 | 3.584 | 34 |
| ko00190 : Oxidative phosphorylation | KEGG pathways | 2.000 | 0.145 | 2.181 | 0.157 | 0.004 | 0.012 | 3.569 | 34 |
| ko00360 : Phenylalanine metabolism | KEGG pathways | 0.149 | 0.031 | 0.205 | 0.046 | 0.001 | 0.005 | 3.557 | 34 |
| ko00740 : Riboflavin metabolism | KEGG pathways | 0.601 | 0.077 | 0.694 | 0.057 | 0.001 | 0.003 | 3.555 | 34 |
| ko00750 : Vitamin B6 metabolism | KEGG pathways | 0.533 | 0.046 | 0.609 | 0.028 | 0.000 | 0.000 | 3.540 | 34 |
| ko00061 : Fatty acid biosynthesis | KEGG pathways | 0.619 | 0.044 | 0.703 | 0.034 | 0.000 | 0.000 | 3.537 | 34 |
| ko00780 : Biotin metabolism | KEGG pathways | 0.410 | 0.023 | 0.486 | 0.045 | 0.000 | 0.000 | 3.523 | 34 |
| ko00790 : Folate biosynthesis | KEGG pathways | 0.817 | 0.080 | 0.907 | 0.077 | 0.004 | 0.013 | 3.508 | 34 |
| ko00440 : Phosphonate and phosphinate metabolism | KEGG pathways | 0.143 | 0.021 | 0.174 | 0.031 | 0.006 | 0.018 | 3.421 | 34 |
| ko00960 : Tropane, piperidine and pyridine alkaloid biosynthesis | KEGG pathways | 0.327 | 0.017 | 0.371 | 0.036 | 0.001 | 0.005 | 3.399 | 34 |
| ko04070 : Phosphatidylinositol signaling system | KEGG pathways | 0.248 | 0.017 | 0.273 | 0.030 | 0.016 | 0.034 | 3.284 | 34 |
Overpresented in group: user_data
| pathway | metabolic level | user_data mean, % | user_data sd, % | external_data mean, % | external_data sd, % | p-value | adjusted p-value | lda score | sample size |
|---|---|---|---|---|---|---|---|---|---|
| ko02060 : Phosphotransferase system (PTS) | KEGG pathways | 1.725 | 0.490 | 1.148 | 0.542 | 0.007 | 0.018 | 4.128 | 34 |
| ko00860 : Porphyrin and chlorophyll metabolism | KEGG pathways | 2.858 | 0.303 | 2.478 | 0.229 | 0.000 | 0.003 | 3.812 | 34 |
| ko00970 : Aminoacyl-tRNA biosynthesis | KEGG pathways | 3.641 | 0.080 | 3.213 | 0.403 | 0.002 | 0.007 | 3.779 | 34 |
| ko00300 : Lysine biosynthesis | KEGG pathways | 1.561 | 0.063 | 1.390 | 0.111 | 0.000 | 0.001 | 3.613 | 34 |
| ko00640 : Propanoate metabolism | KEGG pathways | 0.269 | 0.051 | 0.202 | 0.054 | 0.002 | 0.008 | 3.593 | 34 |
| ko00230 : Purine metabolism | KEGG pathways | 2.389 | 0.067 | 2.214 | 0.076 | 0.000 | 0.000 | 3.589 | 34 |
| ko00550 : Peptidoglycan biosynthesis | KEGG pathways | 2.509 | 0.069 | 2.303 | 0.230 | 0.008 | 0.021 | 3.536 | 34 |
| ko00561 : Glycerolipid metabolism | KEGG pathways | 0.340 | 0.036 | 0.280 | 0.062 | 0.008 | 0.020 | 3.532 | 34 |
| ko01051 : Biosynthesis of ansamycins | KEGG pathways | 0.396 | 0.032 | 0.327 | 0.045 | 0.000 | 0.001 | 3.530 | 34 |
| ko00240 : Pyrimidine metabolism | KEGG pathways | 2.379 | 0.059 | 2.198 | 0.213 | 0.012 | 0.028 | 3.483 | 34 |
| ko00660 : C5-Branched dibasic acid metabolism | KEGG pathways | 0.591 | 0.041 | 0.515 | 0.087 | 0.013 | 0.029 | 3.474 | 34 |
| ko00630 : Glyoxylate and dicarboxylate metabolism | KEGG pathways | 1.002 | 0.053 | 0.920 | 0.060 | 0.001 | 0.004 | 3.461 | 34 |
| ko00564 : Glycerophospholipid metabolism | KEGG pathways | 1.538 | 0.068 | 1.459 | 0.060 | 0.002 | 0.008 | 3.442 | 34 |
| ko00730 : Thiamine metabolism | KEGG pathways | 1.560 | 0.051 | 1.451 | 0.132 | 0.015 | 0.033 | 3.411 | 34 |
| ko00270 : Cysteine and methionine metabolism | KEGG pathways | 0.966 | 0.023 | 0.925 | 0.038 | 0.003 | 0.010 | 3.348 | 34 |
| ko00710 : Carbon fixation in photosynthetic organisms | KEGG pathways | 1.407 | 0.043 | 1.344 | 0.072 | 0.014 | 0.031 | 3.298 | 34 |
| ko03030 : DNA replication | KEGG pathways | 0.559 | 0.017 | 0.520 | 0.043 | 0.009 | 0.022 | 3.275 | 34 |
| ko03410 : Base excision repair | KEGG pathways | 0.860 | 0.032 | 0.826 | 0.030 | 0.006 | 0.016 | 3.247 | 34 |
| ko00450 : Selenocompound metabolism | KEGG pathways | 0.260 | 0.016 | 0.241 | 0.023 | 0.023 | 0.047 | 3.200 | 34 |
Cladogram of differences
Tree-like summary of the taxa differentially abundant in two groups constructed using LefSe.
Cladogram
List of differentially abundant taxa
increased in user_data
| denotation | feature |
|---|---|
| e | ko00230 |
| f | ko00240 |
| g | ko00270 |
| h | ko00300 |
| k | ko00450 |
| o | ko00550 |
| p | ko00561 |
| q | ko00564 |
| u | ko00630 |
| v | ko00640 |
| w | ko00660 |
| x | ko00710 |
| z | ko00730 |
| a5 | ko00860 |
| a9 | ko00970 |
| b0 | ko01051 |
| b1 | ko02060 |
| b2 | ko03030 |
| b3 | ko03410 |
increased in external_data
| denotation | feature |
|---|---|
| a | ko00061 |
| b | ko00071 |
| c | ko00130 |
| d | ko00190 |
| i | ko00360 |
| j | ko00440 |
| l | ko00480 |
| m | ko00511 |
| n | ko00540 |
| r | ko00600 |
| s | ko00604 |
| t | ko00620 |
| y | ko00720 |
| a0 | ko00740 |
| a1 | ko00750 |
| a2 | ko00780 |
| a3 | ko00785 |
| a4 | ko00790 |
| a6 | ko00910 |
| a7 | ko00920 |
| a8 | ko00960 |
| b4 | ko04070 |
Excluded features
KEGG pathways
ko00430 : Taurine and hypotaurine metabolism, ko00531 : Glycosaminoglycan degradation, ko00830 : Retinol metabolism, ko01056 : Biosynthesis of type II polyketide backbone, ko00311 : Penicillin and cephalosporin biosynthesis, ko00100 : Steroid biosynthesis, ko00472 : D-Arginine and D-ornithine metabolism, ko00909 : Sesquiterpenoid and triterpenoid biosynthesis, ko00363 : Bisphenol degradation, ko00361 : Chlorocyclohexane and chlorobenzene degradation, ko00020 : Citrate cycle (TCA cycle), ko00364 : Fluorobenzoate degradation, ko00945 : Stilbenoid, diarylheptanoid and gingerol biosynthesis, ko01057 : Biosynthesis of type II polyketide products, ko00253 : Tetracycline biosynthesis, ko00943 : Isoflavonoid biosynthesis, ko00120 : Primary bile acid biosynthesis, ko00626 : Naphthalene degradation, ko00905 : Brassinosteroid biosynthesis, ko00965 : Betalain biosynthesis, ko00460 : Cyanoamino acid metabolism, ko00140 : Steroid hormone biosynthesis, ko00950 : Isoquinoline alkaloid biosynthesis, ko00513 : Various types of N-glycan biosynthesis, ko00941 : Flavonoid biosynthesis, ko00563 : Glycosylphosphatidylinositol (GPI)-anchor biosynthesis, ko00901 : Indole alkaloid biosynthesis, ko00312 : , ko00562 : Inositol phosphate metabolism, ko00534 : Glycosaminoglycan biosynthesis - heparan sulfate / heparin, ko00622 : Xylene degradation, ko00591 : Linoleic acid metabolism, ko00510 : N-Glycan biosynthesis, ko00627 : Aminobenzoate degradation, ko00521 : Streptomycin biosynthesis, ko00410 : beta-Alanine metabolism, ko00232 : Caffeine metabolism, ko00565 : Ether lipid metabolism, ko00643 : Styrene degradation, ko00980 : Metabolism of xenobiotics by cytochrome P450, ko00514 : Other types of O-glycan biosynthesis, ko00473 : D-Alanine metabolism, ko00310 : Lysine degradation, ko00522 : Biosynthesis of 12-, 14- and 16-membered macrolides, ko00625 : Chloroalkane and chloroalkene degradation, ko00401 : Novobiocin biosynthesis, ko03450 : Non-homologous end-joining, ko00621 : Dioxin degradation, ko00590 : Arachidonic acid metabolism, ko00281 : Geraniol degradation, ko00908 : Zeatin biosynthesis, ko03015 : mRNA surveillance pathway, ko00380 : Tryptophan metabolism, ko00642 : Ethylbenzene degradation, ko00532 : Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate, ko00362 : Benzoate degradation, ko00471 : D-Glutamine and D-glutamate metabolism, ko00791 : Atrazine degradation, ko03050 : Proteasome, ko00930 : Caprolactam degradation, ko00121 : Secondary bile acid biosynthesis, ko00906 : Carotenoid biosynthesis, ko00601 : Glycosphingolipid biosynthesis - lacto and neolacto series, ko00331 : Clavulanic acid biosynthesis, ko00623 : Toluene degradation, ko00280 : Valine, leucine and isoleucine degradation, ko00053 : Ascorbate and aldarate metabolism, ko00592 : alpha-Linolenic acid metabolism, ko00062 : Fatty acid elongation, ko00196 : Photosynthesis - antenna proteins
All results of the test
Model details
| trait | state |
|---|---|
| distribution | gaussian |
| formula | feature_abundance ~ case_control |
| number of samples | 34 |
| transform | arcsin(sqrt) |
Specific pathways
Individual pathways and reactions for which relative abundance is significantly different between user and external data are identified.
Wilcoxon test comparison
Method: Wilcoxon rank-sum 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 rank-sum test applied to each taxon to detect the taxa differentially abundant between the user and external data. 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 were excluded from this analysis.
Differentially abundant taxa
Tables of differentially abundant taxa overpresented in the groups
Overpresented in group: external_data
| pathway | metabolic level | user_data median, % | external_data median, % | p-value | adjusted p-value | lda score |
|---|---|---|---|---|---|---|
| B1_b | vitamin | 0.431 | 0.480 | 0.017 | 0.030 | 3.232 |
| K_a | vitamin | 0.094 | 0.403 | 0.000 | 0.000 | 3.182 |
| B1_a | vitamin | 0.570 | 0.628 | 0.006 | 0.015 | 3.131 |
| B7_a | vitamin | 0.224 | 0.264 | 0.006 | 0.015 | 2.952 |
| Succinate_b | propionate | 0.062 | 0.172 | 0.000 | 0.000 | 2.844 |
| Succinate_a | propionate | 0.071 | 0.134 | 0.000 | 0.000 | 2.711 |
| 4-aminobutyrate/Succinate | butyrate | 0.181 | 0.295 | 0.000 | 0.000 | 3.160 |
| Acetyl-CoA | butyrate | 0.436 | 0.480 | 0.036 | 0.036 | 3.088 |
| Glutarate | butyrate | 0.201 | 0.272 | 0.001 | 0.002 | 2.800 |
Overpresented in group: user_data
| pathway | metabolic level | user_data median, % | external_data median, % | p-value | adjusted p-value | lda score |
|---|---|---|---|---|---|---|
| B12_a | vitamin | 1.098 | 0.8 | 0.0 | 0.001 | 2.596 |
Cladogram of differences
Tree-like summary of the taxa differentially abundant in two groups constructed using LefSe.
Cladogram
List of differentially abundant taxa
increased in user_data
| denotation | feature |
|---|---|
| c | B12_a |
increased in external_data
| denotation | feature |
|---|---|
| a | 4-aminobutyrate/Succinate |
| b | Acetyl-CoA |
| d | B1_a |
| e | B1_b |
| f | B7_a |
| g | Glutarate |
| h | K_a |
| i | Succinate_a |
| j | Succinate_b |
Excluded features
vitamin
B6_a, B6_b
propionate
acrylate_a, propanediol_a
All results of the test
Generalized linear mixed effect model
A generalized linear model is fitted for each taxon to identify if it is differentially abundant between the user and context data. 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: external_data
| pathway | metabolic level | user_data mean, % | user_data sd, % | external_data mean, % | external_data sd, % | p-value | adjusted p-value | lda score | sample size |
|---|---|---|---|---|---|---|---|---|---|
| K_a | vitamin | 0.133 | 0.084 | 0.432 | 0.151 | 0.000 | 0.000 | 4.218 | 34 |
| B1_b | vitamin | 0.434 | 0.022 | 0.487 | 0.062 | 0.012 | 0.021 | 3.920 | 34 |
| B1_a | vitamin | 0.570 | 0.034 | 0.631 | 0.058 | 0.004 | 0.008 | 3.736 | 34 |
| B2_a | vitamin | 0.844 | 0.179 | 0.964 | 0.120 | 0.031 | 0.047 | 3.593 | 34 |
| B7_a | vitamin | 0.229 | 0.027 | 0.266 | 0.033 | 0.003 | 0.008 | 3.539 | 34 |
| Succinate_b | propionate | 0.080 | 0.046 | 0.202 | 0.076 | 0.000 | 0.000 | 4.008 | 34 |
| Succinate_a | propionate | 0.075 | 0.029 | 0.157 | 0.064 | 0.000 | 0.000 | 3.851 | 34 |
| 4-aminobutyrate/Succinate | butyrate | 0.189 | 0.027 | 0.288 | 0.043 | 0.000 | 0.000 | 3.811 | 34 |
| Glutarate | butyrate | 0.196 | 0.032 | 0.261 | 0.045 | 0.000 | 0.000 | 3.605 | 34 |
Overpresented in group: user_data
| pathway | metabolic level | user_data mean, % | user_data sd, % | external_data mean, % | external_data sd, % | p-value | adjusted p-value | lda score | sample size |
|---|---|---|---|---|---|---|---|---|---|
| B12_a | vitamin | 1.055 | 0.154 | 0.774 | 0.141 | 0.0 | 0.0 | 3.912 | 34 |
Cladogram of differences
Tree-like summary of the taxa differentially abundant in two groups constructed using LefSe.
Cladogram
List of differentially abundant taxa
increased in user_data
| denotation | feature |
|---|---|
| b | B12_a |
increased in external_data
| denotation | feature |
|---|---|
| a | 4-aminobutyrate/Succinate |
| c | B1_a |
| d | B1_b |
| e | B2_a |
| f | B7_a |
| g | Glutarate |
| h | K_a |
| i | Succinate_a |
| j | Succinate_b |
Excluded features
vitamin
B6_b, B6_a
propionate
propanediol_a, acrylate_a
All results of the test
Model details
| trait | state |
|---|---|
| distribution | gaussian |
| formula | feature_abundance ~ case_control |
| number of samples | 34 |
| transform | arcsin(sqrt) |
Reconstruction of metabolic potential
Predicted functional composition of microbiota.
Vitamins synthesis
Gut microbes are known to produce a number of vitamins. The boxplots represent median, standard deviation and quartiles of the vitamin biosynthesis pathways in the samples.
Plots
Total relative abundance of the genes involved in vitamins biosynthesis summed across the respective pathways.
Nothing to show
Description of pathways
Nothing to show
Synthesis of short-chain fatty acids (SCFAs)
Gut microbes are known to produce SCFAs. The boxplots represent median, standard deviation and quartiles of the SCFAs biosynthesis pathways in the samples.
Synthesis of butyrate
Plots
Total relative abundance of the genes involved in butyrate synthesis summed across the respective pathways.
Nothing to show
Description of pathways
Nothing to show
Synthesis of propionate
Plots
Total relative abundance of the genes involved in propionate synthesis summed across the respective pathways.
Nothing to show
Description of pathways
Nothing to show
datalab:
3.10.0
knb_lib:
4.8.40
knb_interactive:
2.0.2