Microba Research Discovery Report

Taxonomic Profiles (Species)

The charts below show the taxonomic composition of the analysed samples using different quantitative visualization techniques. Only the top most abundant species are shown.

Areachart

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Barchart clustered within each group

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All features barchart clustered within each group

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Scaled heatmap of most abundant features ordered by study group

Features were filtered by mean abundance. Samples were first ordered by study group and then clustered within each study group. Abundances were scaled to a max value of 1. Color scale shows not-detected (white), and abundance ranging from low (blue) to high (yellow).

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Heatmap of most abundant features ordered by study group

Features were filtered by mean abundance. Samples were first ordered by study group and then clustered within each study group. Color scale shows not-detected (white), and abundance ranging from low (blue) to high (yellow).

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Scaled heatmap of all features

Profiles were clustered by hierarchical clustering. Abundances were scaled to a max value of 1. Color scale shows not-detected (white), and abundance ranging from low (blue) to high (yellow).

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Heatmap of all features

Profiles were clustered by hierarchical clustering. Color scale shows not-detected (white), and abundance ranging from low (blue) to high (yellow).

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Scaled heatmap of top most abundant features filtered by mean abundance

Profiles were clustered by hierarchical clustering. Abundances were scaled to a max value of 1. Color scale shows not-detected (white), and abundance ranging from low (blue) to high (yellow).

Click here to open full-sized image in new window.

Heatmap of top most abundant features filtered by mean abundance

Profiles were clustered by hierarchical clustering. Color scale shows not-detected (white), and abundance ranging from low (blue) to high (yellow).

Click here to open full-sized image in new window.

Scaled heatmap of top most abundant features filtered by max abundance

Profiles were clustered by hierarchical clustering. Abundances were scaled to a max value of 1. Color scale shows not-detected (white), and abundance ranging from low (blue) to high (yellow).

Click here to open full-sized image in new window.

Heatmap of top most abundant features filtered by max abundance

Profiles were clustered by hierarchical clustering. Color scale shows not-detected (white), and abundance ranging from low (blue) to high (yellow).

Click here to open full-sized image in new window.

Scaled heatmap of top most variable features

Profiles were clustered by hierarchical clustering. Abundances were scaled to a max value of 1. Color scale shows not-detected (white), and abundance ranging from low (blue) to high (yellow).

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Hierarchically clustered barchart

Profiles were clustered by hierarchical clustering.

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Interactive Barchart

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Microbial alpha diversity (species)

This page provides an overview of the microbial alpha diversity of the analysed samples. Alpha diversity is measured by the Shannon index and species richnes. Richness simply quantifies the total number of species present in each sample. Shannon index additionally accounts for relative abundance and evenness of the species present and quantifies the entropy of microbial communties. Barcharts and boxplots present the mean diversity in each study group.

Methods:

Shannon diversity was compared using a standard t-test. Richness was compared using a standard t-test. Data was rarefied to 702268 reads.

Index: Richness

Index: Shannon index

Summary Table

Index	rarefiedTo	P Welch's t-test	Mean Pos	Mean Abundance	Median Abundance	Mean Post_Treatment_Fibre_Intakehigh	Median Post_Treatment_Fibre_Intakehigh	SD Post_Treatment_Fibre_Intakehigh	Mean Post_Treatment_Fibre_Intakelow	Median Post_Treatment_Fibre_Intakelow	SD Post_Treatment_Fibre_Intakelow	Fold Change Log2(Post_Treatment_Fibre_Intakelow/Post_Treatment_Fibre_Intakehigh)	Positive samples	Positive Post_Treatment_Fibre_Intakehigh	Positive Post_Treatment_Fibre_Intakelow	Positive_Post_Treatment_Fibre_Intakehigh_percent	Positive_Post_Treatment_Fibre_Intakelow_percent
Shannon	702268	0.44	3	3	3	3	3	0.2	2.9	2.8	0.51	-0.049	18 / 18 (100%)	11 / 11 (100%)	7 / 7 (100%)	1	1
Richness	702268	0.85	41	41	36	41	41	10	43	34	25	0.069	18 / 18 (100%)	11 / 11 (100%)	7 / 7 (100%)	1	1

Download diversity values in csv format . On some platforms (including Windows) you may need to change the suffix from .txt or .html to .csv before opening the file in a spreadsheet program, like Excel.

Clustering and ordination (species)

Taxonomic profiles were analyzed using supervised and unsupervised multivariate methods. Profiles were ordinated using the unsupervised methods Principal Coordinates Analysis (PCoA), Non-Metric Multidimensional Scaling (NMDS) and Principal Component Analysis (PCA). PCoA and NMDS are related to PCA, but take dissimlarity matrices as input. PCoA and NMDS both attempt to represent the pairwise dissimlarities between samples in low dimensional space as close as possible. NMDS is a rank-based approach and therefore less effected by outliers.

The supervised methods Adonis and Redundancy analysis (RDA) were used to assess if variance in microbial community composition can be attributed to the study condition. NMDS, PCoA and Adonis were run on Bray-Curtis dissimilarities. A short introduction of the used methods can be found at the GUide to STatistical Analysis in Microbial Ecology (GUSTA ME). Sparse Partial Least Square Discriminant Analysis (sPLS-DA) from the MixMc package was additionaly used to extract features associated with the study condition.

Unsupervised ordination

Interactive PCA (clr transformed)

Please click here to view an interactive 3D PCoA.

Please click here to view an interactive 3D PCA.

Supervised Analysis

sPLS-DA

Univariate analysis of species abundance

Differentially abundant species were identified by ANOVA or LMER (linear mixed effect regression) of clr transformed relative abudances, Fisher's exact test and/or ALDEx2 (on species read counts). Fisher's exact test is used to test for differences in the detection rate, i.e. number of samples in which each species has been detected.

LMER is used for repeated measures data, using random effects to control for correlation between samples from the same subject. Fixed effects are included for treatment groups, time, and treatment over time, where appropriate. The LMER P values correspond to a nested model test of the significance of including the corresponding fixed effect.

ALDEx2 uses subsampling (Bayesian sampling) to estimate the underlying technical variation. For each subsample instance, center log-ratio transformed data is statistically compared across study groups and computed P values are corrected for multiple testing using the Benjamini–Hochberg procedure. The expected P value (mean P value) is reported, which are those that would likely have been observed if the same samples had been run multiple times. The expected values are reported for both the distribution of P values and for the distribution of Benjamini–Hochberg corrected values.

Taxon	GTDB taxonomy	P Welch's t-test (sqrt)	FDR Welch's t-test (sqrt)	Pbonf Welch's t-test (sqrt)	Cohen's d Welch's t-test (sqrt)	P Welch's t-test (clr)	FDR Welch's t-test (clr)	Pbonf Welch's t-test (clr)	Cohen's d Welch's t-test (clr)	P Fisher's exact test	FDR Fisher's exact test	Pbonf Fisher's exact test	P Welch's t-test (ALDEx2)	FDR Welch's t-test (ALDEx2)	P Wilcoxon rank test (ALDEx2)	FDR Wilcoxon rank test (ALDEx2)	Mean Pos	Mean Abundance	Median Abundance	Mean Post_Treatment_Fibre_Intakehigh	Median Post_Treatment_Fibre_Intakehigh	SD Post_Treatment_Fibre_Intakehigh	Mean Post_Treatment_Fibre_Intakelow	Median Post_Treatment_Fibre_Intakelow	SD Post_Treatment_Fibre_Intakelow	Fold Change Log2(Post_Treatment_Fibre_Intakelow/Post_Treatment_Fibre_Intakehigh)	Positive samples	Positive Post_Treatment_Fibre_Intakehigh	Positive Post_Treatment_Fibre_Intakelow	Positive_Post_Treatment_Fibre_Intakehigh_percent	Positive_Post_Treatment_Fibre_Intakelow_percent
s__Acetatifactor sp900066565	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Lachnospirales; f__Lachnospiraceae; g__Acetatifactor	0.091	0.72	1	-1.2	0.086	0.45	1	-1.3	0.043	0.44	1	0.086	0.55	0.15	0.59	0.98	0.16	0	0	0	0	0.42	0	0.64	Inf	3 / 18 (17%)	0 / 11 (0%)	3 / 7 (43%)	0	0.429
s__Agathobacter faecis	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Lachnospirales; f__Lachnospiraceae; g__Agathobacter	0.072	0.72	1	0.9	0.021	0.45	1	1.2	0.05	0.44	1	0.027	0.5	0.08	0.57	2.4	1.2	0.26	1.6	0.67	2	0.51	0	1.4	-1.6	9 / 18 (50%)	8 / 11 (73%)	1 / 7 (14%)	0.727	0.143
s__Agathobacter rectale	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Lachnospirales; f__Lachnospiraceae; g__Agathobacter	0.16	0.75	1	0.86	0.077	0.45	1	1.3	0.043	0.44	1	0.088	0.55	0.27	0.71	10	8.4	6.2	9.9	8.7	6.8	6.2	3.8	8	-0.68	15 / 18 (83%)	11 / 11 (100%)	4 / 7 (57%)	1	0.571
s__Agathobaculum butyriciproducens	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Oscillospirales; f__Butyricicoccaceae; g__Agathobaculum	0.041	0.72	1	0.94	0.051	0.45	1	0.92	0.15	0.89	1	0.1	0.56	0.17	0.64	0.64	0.25	0	0.38	0.36	0.44	0.051	0	0.13	-2.9	7 / 18 (39%)	6 / 11 (55%)	1 / 7 (14%)	0.545	0.143
s__Akkermansia muciniphila	d__Bacteria; p__Verrucomicrobiota; c__Verrucomicrobiae; o__Verrucomicrobiales; f__Akkermansiaceae; g__Akkermansia	0.75	0.98	1	-0.17	0.98	1	1	0.01	1	1	1	0.79	0.93	0.68	0.89	1.2	0.21	0	0.13	0	0.37	0.33	0	0.88	1.3	3 / 18 (17%)	2 / 11 (18%)	1 / 7 (14%)	0.182	0.143
s__Alistipes putredinis	d__Bacteria; p__Bacteroidota; c__Bacteroidia; o__Bacteroidales; f__Rikenellaceae; g__Alistipes	0.89	1	1	-0.06	0.45	0.82	1	-0.39	0.53	1	1	0.36	0.72	0.35	0.72	2.2	0.37	0	0.46	0	1.5	0.23	0	0.51	-1	3 / 18 (17%)	1 / 11 (9.1%)	2 / 7 (29%)	0.0909	0.286
s__Anaerostipes hadrus	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Lachnospirales; f__Lachnospiraceae; g__Anaerostipes	0.47	0.86	1	0.43	0.11	0.51	1	1.1	0.043	0.44	1	0.11	0.55	0.27	0.71	4.6	3.9	3.4	3.8	4	2.2	4	1.4	5.6	0.074	15 / 18 (83%)	11 / 11 (100%)	4 / 7 (57%)	1	0.571
s__Anaerostipes hadrus_A	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Lachnospirales; f__Lachnospiraceae; g__Anaerostipes	1	1	1	0.0014	0.66	0.92	1	0.21	1	1	1	0.75	0.9	0.68	0.89	2.8	0.63	0	0.5	0	1.1	0.82	0	2.2	0.71	4 / 18 (22%)	3 / 11 (27%)	1 / 7 (14%)	0.273	0.143
s__Bacteroides ovatus	d__Bacteria; p__Bacteroidota; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides	0.13	0.74	1	0.63	0.079	0.45	1	0.75	0.25	0.97	1	0.2	0.62	0.51	0.81	1.4	0.24	0	0.39	0	1	0	0	0	-Inf	3 / 18 (17%)	3 / 11 (27%)	0 / 7 (0%)	0.273	0
s__Bacteroides stercoris	d__Bacteria; p__Bacteroidota; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides	0.93	1	1	-0.041	0.75	0.92	1	-0.16	1	1	1	0.63	0.86	0.57	0.85	1.7	0.38	0	0.4	0	0.89	0.35	0	0.77	-0.19	4 / 18 (22%)	2 / 11 (18%)	2 / 7 (29%)	0.182	0.286
s__Bacteroides uniformis	d__Bacteria; p__Bacteroidota; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides	0.13	0.74	1	-1	0.037	0.45	1	-1.2	0.049	0.44	1	0.031	0.49	0.055	0.54	5.7	2.2	0	0.33	0	0.74	5.2	0.81	10	4	7 / 18 (39%)	2 / 11 (18%)	5 / 7 (71%)	0.182	0.714
s__Bacteroides_B vulgatus	d__Bacteria; p__Bacteroidota; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides_B	0.76	0.98	1	0.13	0.81	0.92	1	-0.11	1	1	1	0.54	0.82	0.39	0.76	3.3	0.73	0	0.98	0	2.8	0.33	0	0.79	-1.6	4 / 18 (22%)	2 / 11 (18%)	2 / 7 (29%)	0.182	0.286
s__Bifidobacterium adolescentis	d__Bacteria; p__Actinobacteriota; c__Actinobacteria; o__Actinomycetales; f__Bifidobacteriaceae; g__Bifidobacterium	0.019	0.72	1	1.1	0.03	0.45	1	1.2	0.049	0.44	1	0.044	0.53	0.046	0.54	6	3.7	1.1	5.6	2.8	6.7	0.74	0	1.5	-2.9	11 / 18 (61%)	9 / 11 (82%)	2 / 7 (29%)	0.818	0.286
s__Bifidobacterium bifidum	d__Bacteria; p__Actinobacteriota; c__Actinobacteria; o__Actinomycetales; f__Bifidobacteriaceae; g__Bifidobacterium	0.7	0.98	1	0.18	0.78	0.92	1	0.13	1	1	1	0.74	0.91	0.64	0.88	0.4	0.067	0	0.082	0	0.18	0.042	0	0.11	-0.97	3 / 18 (17%)	2 / 11 (18%)	1 / 7 (14%)	0.182	0.143
s__Bifidobacterium longum	d__Bacteria; p__Actinobacteriota; c__Actinobacteria; o__Actinomycetales; f__Bifidobacteriaceae; g__Bifidobacterium	0.4	0.86	1	0.47	0.23	0.79	1	0.7	0.25	0.97	1	0.27	0.7	0.74	0.93	3.3	2.6	2.6	2.8	2.8	1.9	2.2	2.3	2.5	-0.35	14 / 18 (78%)	10 / 11 (91%)	4 / 7 (57%)	0.909	0.571
s__Bifidobacterium pseudocatenulatum	d__Bacteria; p__Actinobacteriota; c__Actinobacteria; o__Actinomycetales; f__Bifidobacteriaceae; g__Bifidobacterium	0.99	1	1	-0.009	0.63	0.91	1	0.24	0.64	1	1	0.63	0.87	0.75	0.92	1.9	0.74	0	0.58	0	0.8	0.99	0	2	0.77	7 / 18 (39%)	5 / 11 (45%)	2 / 7 (29%)	0.455	0.286
s__Blautia sp000436935	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Lachnospirales; f__Lachnospiraceae; g__Blautia	0.37	0.86	1	-0.56	0.38	0.79	1	-0.5	0.53	1	1	0.37	0.73	0.48	0.8	2.2	0.37	0	0.1	0	0.33	0.8	0	1.9	3	3 / 18 (17%)	1 / 11 (9.1%)	2 / 7 (29%)	0.0909	0.286
s__Blautia_A MIC8050	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Lachnospirales; f__Lachnospiraceae; g__Blautia_A	0.92	1	1	-0.055	0.9	0.95	1	0.062	1	1	1	0.71	0.89	0.55	0.84	0.88	0.15	0	0.12	0	0.27	0.19	0	0.51	0.66	3 / 18 (17%)	2 / 11 (18%)	1 / 7 (14%)	0.182	0.143
s__Blautia_A massiliensis	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Lachnospirales; f__Lachnospiraceae; g__Blautia_A	0.41	0.86	1	0.38	0.69	0.92	1	0.2	1	1	1	0.8	0.93	0.82	0.95	1.7	1.1	0.64	1.3	0.84	1.6	0.63	0.5	0.78	-1	11 / 18 (61%)	7 / 11 (64%)	4 / 7 (57%)	0.636	0.571
s__Blautia_A obeum	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Lachnospirales; f__Lachnospiraceae; g__Blautia_A	0.25	0.8	1	0.54	0.33	0.79	1	0.48	0.63	1	1	0.48	0.8	0.45	0.81	2.3	1.3	0.46	1.6	0.58	1.9	0.69	0	1.3	-1.2	10 / 18 (56%)	7 / 11 (64%)	3 / 7 (43%)	0.636	0.429
s__Blautia_A sp000285855	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Lachnospirales; f__Lachnospiraceae; g__Blautia_A	0.89	1	1	0.069	0.83	0.92	1	0.099	1	1	1	0.7	0.89	0.59	0.85	0.34	0.056	0	0.058	0	0.13	0.053	0	0.14	-0.13	3 / 18 (17%)	2 / 11 (18%)	1 / 7 (14%)	0.182	0.143
s__Blautia_A sp000436615	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Lachnospirales; f__Lachnospiraceae; g__Blautia_A	0.29	0.8	1	-0.65	0.28	0.79	1	-0.62	0.53	1	1	0.24	0.65	0.24	0.65	0.91	0.15	0	0.048	0	0.16	0.32	0	0.54	2.7	3 / 18 (17%)	1 / 11 (9.1%)	2 / 7 (29%)	0.0909	0.286
s__Blautia_A sp900066165	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Lachnospirales; f__Lachnospiraceae; g__Blautia_A	0.99	1	1	0.0037	0.83	0.92	1	0.1	1	1	1	0.87	0.95	0.85	0.96	1.8	1.1	0.64	1	0.7	1.1	1.2	0.49	1.4	0.26	11 / 18 (61%)	7 / 11 (64%)	4 / 7 (57%)	0.636	0.571
s__Blautia_A wexlerae	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Lachnospirales; f__Lachnospiraceae; g__Blautia_A	0.057	0.72	1	-1.1	0.13	0.54	1	-0.78	NA	NA	NA	0.1	0.55	0.052	0.55	9.9	9.9	7.7	6.6	4	5.4	15	13	10	1.2	18 / 18 (100%)	11 / 11 (100%)	7 / 7 (100%)	1	1
s__CAG-103 sp000432375	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Oscillospirales; f__Oscillospiraceae; g__CAG-103	0.51	0.87	1	-0.34	0.43	0.82	1	-0.44	0.53	1	1	0.42	0.76	0.5	0.81	0.84	0.14	0	0.11	0	0.38	0.18	0	0.32	0.71	3 / 18 (17%)	1 / 11 (9.1%)	2 / 7 (29%)	0.0909	0.286
s__CAG-177 sp003514385	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Oscillospirales; f__Acutalibacteraceae; g__CAG-177	0.083	0.72	1	0.74	0.094	0.45	1	0.71	0.25	0.97	1	0.26	0.66	0.63	0.86	1	0.17	0	0.28	0	0.49	0	0	0	-Inf	3 / 18 (17%)	3 / 11 (27%)	0 / 7 (0%)	0.273	0
s__CAG-217 sp000436335	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Oscillospirales; f__Acutalibacteraceae; g__CAG-217	0.26	0.8	1	-0.65	0.31	0.79	1	-0.57	0.33	1	1	0.3	0.69	0.33	0.72	1.3	0.36	0	0.16	0	0.36	0.67	0	1	2.1	5 / 18 (28%)	2 / 11 (18%)	3 / 7 (43%)	0.182	0.429
s__CAG-274 sp000432155	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Lachnospirales; f__CAG-274; g__CAG-274	0.84	1	1	-0.11	0.95	0.98	1	0.029	1	1	1	0.77	0.92	0.66	0.88	0.73	0.12	0	0.088	0	0.24	0.17	0	0.46	0.95	3 / 18 (17%)	2 / 11 (18%)	1 / 7 (14%)	0.182	0.143
s__CAG-41 sp900066215	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Monoglobales; f__UBA1381; g__CAG-41	0.73	0.98	1	0.2	0.35	0.79	1	0.5	0.33	1	1	0.39	0.75	0.69	0.91	0.81	0.5	0.42	0.44	0.48	0.35	0.58	0	1.1	0.4	11 / 18 (61%)	8 / 11 (73%)	3 / 7 (43%)	0.727	0.429
s__CAG-56 sp900066615	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Lachnospirales; f__Lachnospiraceae; g__CAG-56	0.32	0.83	1	0.57	0.084	0.45	1	1	0.049	0.44	1	0.084	0.55	0.31	0.73	0.88	0.54	0.38	0.56	0.48	0.44	0.5	0	0.91	-0.16	11 / 18 (61%)	9 / 11 (82%)	2 / 7 (29%)	0.818	0.286
s__Clostridium MIC8163	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Clostridiales; f__Clostridiaceae; g__Clostridium	0.24	0.8	1	0.5	0.34	0.79	1	0.41	1	1	1	0.64	0.85	0.67	0.89	0.28	0.063	0	0.095	0	0.18	0.012	0	0.032	-3	4 / 18 (22%)	3 / 11 (27%)	1 / 7 (14%)	0.273	0.143
s__Coprococcus eutactus_A	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Lachnospirales; f__Lachnospiraceae; g__Coprococcus	0.97	1	1	-0.018	0.76	0.92	1	-0.15	1	1	1	0.51	0.8	0.41	0.77	2.3	0.52	0	0.54	0	1.2	0.49	0	1.2	-0.14	4 / 18 (22%)	2 / 11 (18%)	2 / 7 (29%)	0.182	0.286
s__Coprococcus sp900066115	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Lachnospirales; f__Lachnospiraceae; g__Coprococcus	0.44	0.86	1	-0.42	0.38	0.79	1	-0.49	0.53	1	1	0.32	0.71	0.32	0.71	2.2	0.36	0	0.25	0	0.84	0.54	0	0.96	1.1	3 / 18 (17%)	1 / 11 (9.1%)	2 / 7 (29%)	0.0909	0.286
s__Coprococcus_A catus	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Lachnospirales; f__Lachnospiraceae; g__Coprococcus_A	0.86	1	1	-0.083	0.68	0.92	1	-0.2	1	1	1	0.49	0.79	0.4	0.76	0.39	0.086	0	0.091	0	0.22	0.078	0	0.14	-0.22	4 / 18 (22%)	2 / 11 (18%)	2 / 7 (29%)	0.182	0.286
s__Coprococcus_B comes	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Lachnospirales; f__Lachnospiraceae; g__Coprococcus_B	0.82	1	1	0.12	0.61	0.91	1	0.26	0.63	1	1	0.66	0.88	0.89	0.97	0.68	0.46	0.5	0.45	0.48	0.36	0.47	0.56	0.55	0.063	12 / 18 (67%)	8 / 11 (73%)	4 / 7 (57%)	0.727	0.571
s__Dialister invisus	d__Bacteria; p__Firmicutes_C; c__Negativicutes; o__Veillonellales; f__Dialisteraceae; g__Dialister	0.29	0.8	1	-0.58	0.22	0.79	1	-0.72	0.25	0.97	1	0.23	0.64	0.37	0.75	1.6	0.36	0	0.22	0	0.74	0.57	0	1	1.4	4 / 18 (22%)	1 / 11 (9.1%)	3 / 7 (43%)	0.0909	0.429
s__Dialister sp900343095	d__Bacteria; p__Firmicutes_C; c__Negativicutes; o__Veillonellales; f__Dialisteraceae; g__Dialister	0.097	0.72	1	0.7	0.088	0.45	1	0.72	0.25	0.97	1	0.32	0.69	0.64	0.88	0.93	0.16	0	0.25	0	0.52	0	0	0	-Inf	3 / 18 (17%)	3 / 11 (27%)	0 / 7 (0%)	0.273	0
s__Dorea formicigenerans	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Lachnospirales; f__Lachnospiraceae; g__Dorea	0.36	0.86	1	-0.5	0.53	0.84	1	-0.33	1	1	1	0.52	0.82	0.4	0.78	0.61	0.31	0.11	0.21	0	0.31	0.46	0.41	0.47	1.1	9 / 18 (50%)	5 / 11 (45%)	4 / 7 (57%)	0.455	0.571
s__Dorea longicatena	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Lachnospirales; f__Lachnospiraceae; g__Dorea	0.036	0.72	1	1	0.039	0.45	1	1	0.066	0.52	1	0.082	0.54	0.24	0.68	0.95	0.42	0	0.61	0.5	0.67	0.12	0	0.33	-2.3	8 / 18 (44%)	7 / 11 (64%)	1 / 7 (14%)	0.636	0.143
s__Dorea longicatena_B	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Lachnospirales; f__Lachnospiraceae; g__Dorea	0.23	0.8	1	-0.71	0.47	0.82	1	-0.38	1	1	1	0.49	0.8	0.32	0.74	0.89	0.45	0.14	0.21	0	0.27	0.82	0.73	0.97	2	9 / 18 (50%)	5 / 11 (45%)	4 / 7 (57%)	0.455	0.571
s__ER4 sp900317525	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Oscillospirales; f__Oscillospiraceae; g__ER4	0.47	0.86	1	-0.39	0.34	0.79	1	-0.52	0.53	1	1	0.25	0.65	0.24	0.67	0.36	0.06	0	0.044	0	0.14	0.086	0	0.16	0.97	3 / 18 (17%)	1 / 11 (9.1%)	2 / 7 (29%)	0.0909	0.286
s__Erysipelatoclostridium sp000752095	d__Bacteria; p__Firmicutes; c__Bacilli; o__Erysipelotrichales; f__Erysipelatoclostridiaceae; g__Erysipelatoclostridium	0.89	1	1	-0.076	0.87	0.95	1	0.081	1	1	1	0.84	0.95	0.77	0.93	0.92	0.56	0.35	0.48	0.46	0.49	0.69	0.25	1	0.52	11 / 18 (61%)	7 / 11 (64%)	4 / 7 (57%)	0.636	0.571
s__Eubacterium_E hallii	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Lachnospirales; f__Lachnospiraceae; g__Eubacterium_E	0.56	0.93	1	0.28	0.94	0.98	1	0.039	1	1	1	0.78	0.92	0.56	0.86	2	1.7	1.7	1.9	2.1	1.3	1.4	1.5	1	-0.44	15 / 18 (83%)	9 / 11 (82%)	6 / 7 (86%)	0.818	0.857
s__Eubacterium_E hallii_A	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Lachnospirales; f__Lachnospiraceae; g__Eubacterium_E	0.25	0.8	1	-0.68	0.28	0.79	1	-0.6	0.33	1	1	0.29	0.69	0.26	0.69	0.77	0.21	0	0.098	0	0.22	0.39	0	0.57	2	5 / 18 (28%)	2 / 11 (18%)	3 / 7 (43%)	0.182	0.429
s__Faecalibacterium MIC9210	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Oscillospirales; f__Ruminococcaceae; g__Faecalibacterium	0.49	0.86	1	-0.44	0.89	0.95	1	-0.077	1	1	1	0.79	0.93	0.71	0.91	3.1	0.51	0	0.064	0	0.15	1.2	0	3.2	4.2	3 / 18 (17%)	2 / 11 (18%)	1 / 7 (14%)	0.182	0.143
s__Faecalibacterium prausnitzii_C	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Oscillospirales; f__Ruminococcaceae; g__Faecalibacterium	0.14	0.74	1	0.74	0.061	0.45	1	0.97	0.14	0.89	1	0.12	0.56	0.19	0.66	4.9	2.7	0.55	3.5	1.4	4.1	1.5	0	3.8	-1.2	10 / 18 (56%)	8 / 11 (73%)	2 / 7 (29%)	0.727	0.286
s__Faecalibacterium prausnitzii_D	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Oscillospirales; f__Ruminococcaceae; g__Faecalibacterium	0.26	0.8	1	-0.57	0.17	0.67	1	-0.69	0.33	1	1	0.13	0.57	0.16	0.64	1.9	0.94	0.22	0.75	0	1.5	1.2	1.1	1.3	0.68	9 / 18 (50%)	4 / 11 (36%)	5 / 7 (71%)	0.364	0.714
s__Faecalibacterium prausnitzii_G	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Oscillospirales; f__Ruminococcaceae; g__Faecalibacterium	0.3	0.8	1	-0.54	0.28	0.79	1	-0.54	0.37	1	1	0.23	0.65	0.13	0.61	1.4	0.79	0.45	0.58	0	0.8	1.1	0.83	1.3	0.92	10 / 18 (56%)	5 / 11 (45%)	5 / 7 (71%)	0.455	0.714
s__Faecalibacterium prausnitzii_I	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Oscillospirales; f__Ruminococcaceae; g__Faecalibacterium	0.099	0.72	1	0.69	0.09	0.45	1	0.72	0.25	0.97	1	0.26	0.66	0.54	0.82	0.52	0.087	0	0.14	0	0.29	0	0	0	-Inf	3 / 18 (17%)	3 / 11 (27%)	0 / 7 (0%)	0.273	0
s__Faecalibacterium prausnitzii_J	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Oscillospirales; f__Ruminococcaceae; g__Faecalibacterium	0.57	0.94	1	-0.28	0.42	0.82	1	-0.44	0.53	1	1	0.35	0.72	0.35	0.74	0.85	0.14	0	0.13	0	0.44	0.16	0	0.27	0.3	3 / 18 (17%)	1 / 11 (9.1%)	2 / 7 (29%)	0.0909	0.286
s__Faecalibacterium prausnitzii_K	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Oscillospirales; f__Ruminococcaceae; g__Faecalibacterium	0.032	0.72	1	0.95	0.0069	0.45	0.5	1.3	0.038	0.44	1	0.02	0.43	0.1	0.57	2.2	0.74	0	1.2	0.29	2.6	0	0	0	-Inf	6 / 18 (33%)	6 / 11 (55%)	0 / 7 (0%)	0.545	0
s__Faecalicatena faecis	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Lachnospirales; f__Lachnospiraceae; g__Faecalicatena	0.19	0.8	1	-0.78	0.23	0.79	1	-0.64	0.33	1	1	0.19	0.62	0.16	0.63	0.96	0.37	0	0.16	0	0.3	0.7	0.21	0.97	2.1	7 / 18 (39%)	3 / 11 (27%)	4 / 7 (57%)	0.273	0.571
s__Faecalicatena lactaris	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Lachnospirales; f__Lachnospiraceae; g__Faecalicatena	0.28	0.8	1	-0.68	0.36	0.79	1	-0.54	0.53	1	1	0.39	0.74	0.49	0.8	0.85	0.14	0	0.036	0	0.12	0.31	0	0.55	3.1	3 / 18 (17%)	1 / 11 (9.1%)	2 / 7 (29%)	0.0909	0.286
s__Fusicatenibacter saccharivorans	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Lachnospirales; f__Lachnospiraceae; g__Fusicatenibacter	0.99	1	1	0.0072	0.77	0.92	1	0.16	1	1	1	0.87	0.95	0.92	0.98	4.9	4.3	3.2	4.1	3	3.2	4.7	3.8	5	0.2	16 / 18 (89%)	10 / 11 (91%)	6 / 7 (86%)	0.909	0.857
s__GCA-900066135 MIC6659	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Lachnospirales; f__Lachnospiraceae; g__GCA-900066135	0.84	1	1	0.1	0.76	0.92	1	0.15	1	1	1	0.81	0.93	0.75	0.92	0.28	0.095	0	0.097	0	0.15	0.092	0	0.18	-0.076	6 / 18 (33%)	4 / 11 (36%)	2 / 7 (29%)	0.364	0.286
s__Gemmiger formicilis	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Oscillospirales; f__Ruminococcaceae; g__Gemmiger	0.72	0.98	1	-0.21	0.53	0.84	1	0.33	0.37	1	1	0.54	0.83	0.73	0.91	2.5	1.1	0	0.58	0.33	0.79	1.9	0	3.8	1.7	8 / 18 (44%)	6 / 11 (55%)	2 / 7 (29%)	0.545	0.286
s__Gemmiger sp003476825	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Oscillospirales; f__Ruminococcaceae; g__Gemmiger	0.68	0.98	1	0.21	0.63	0.91	1	0.25	1	1	1	0.76	0.92	0.74	0.92	1.8	1.4	1	1.5	1.1	1.4	1.3	0.73	1.5	-0.21	14 / 18 (78%)	9 / 11 (82%)	5 / 7 (71%)	0.818	0.714
s__Intestinibacter bartlettii	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Peptostreptococcales; f__Peptostreptococcaceae; g__Intestinibacter	0.75	0.98	1	0.15	0.81	0.92	1	0.12	1	1	1	0.78	0.92	0.66	0.88	0.31	0.052	0	0.061	0	0.14	0.037	0	0.097	-0.72	3 / 18 (17%)	2 / 11 (18%)	1 / 7 (14%)	0.182	0.143
s__KLE1615 sp900066985	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Lachnospirales; f__Lachnospiraceae; g__KLE1615	0.18	0.8	1	0.66	0.09	0.45	1	0.82	0.15	0.89	1	0.15	0.59	0.33	0.73	1.3	0.52	0	0.67	0.22	0.81	0.28	0	0.73	-1.3	7 / 18 (39%)	6 / 11 (55%)	1 / 7 (14%)	0.545	0.143
s__Lachnospira sp003451515	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Lachnospirales; f__Lachnospiraceae; g__Lachnospira	0.37	0.86	1	0.39	0.46	0.82	1	0.34	1	1	1	0.66	0.87	0.67	0.89	0.87	0.19	0	0.28	0	0.61	0.066	0	0.18	-2.1	4 / 18 (22%)	3 / 11 (27%)	1 / 7 (14%)	0.273	0.143
s__Parabacteroides merdae	d__Bacteria; p__Bacteroidota; c__Bacteroidia; o__Bacteroidales; f__Tannerellaceae; g__Parabacteroides	0.68	0.98	1	-0.19	0.39	0.79	1	-0.45	0.53	1	1	0.25	0.65	0.25	0.67	0.25	0.042	0	0.045	0	0.15	0.037	0	0.062	-0.28	3 / 18 (17%)	1 / 11 (9.1%)	2 / 7 (29%)	0.0909	0.286
s__Phascolarctobacterium faecium	d__Bacteria; p__Firmicutes_C; c__Negativicutes; o__Acidaminococcales; f__Acidaminococcaceae; g__Phascolarctobacterium	0.76	0.98	1	0.13	0.79	0.92	1	-0.12	1	1	1	0.48	0.79	0.41	0.77	0.71	0.16	0	0.22	0	0.64	0.06	0	0.1	-1.9	4 / 18 (22%)	2 / 11 (18%)	2 / 7 (29%)	0.182	0.286
s__Romboutsia timonensis	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Peptostreptococcales; f__Peptostreptococcaceae; g__Romboutsia	0.43	0.86	1	0.36	0.59	0.91	1	0.24	1	1	1	0.75	0.91	0.72	0.91	0.64	0.21	0	0.28	0	0.42	0.11	0	0.21	-1.3	6 / 18 (33%)	4 / 11 (36%)	2 / 7 (29%)	0.364	0.286
s__Ruminiclostridium_C sp000435295	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Oscillospirales; f__Oscillospiraceae; g__Ruminiclostridium_C	0.43	0.86	1	-0.44	0.41	0.82	1	-0.46	0.53	1	1	0.36	0.72	0.38	0.76	0.18	0.03	0	0.018	0	0.06	0.048	0	0.1	1.4	3 / 18 (17%)	1 / 11 (9.1%)	2 / 7 (29%)	0.0909	0.286
s__Ruminococcus_A sp003011855	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Lachnospirales; f__Lachnospiraceae; g__Ruminococcus_A	0.6	0.94	1	0.23	1	1	1	0.0011	1	1	1	0.7	0.89	0.67	0.9	0.92	0.36	0	0.47	0	0.81	0.19	0	0.27	-1.3	7 / 18 (39%)	4 / 11 (36%)	3 / 7 (43%)	0.364	0.429
s__Ruminococcus_C sp000433635	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Oscillospirales; f__Ruminococcaceae; g__Ruminococcus_C	0.48	0.86	1	-0.38	0.38	0.79	1	-0.49	0.53	1	1	0.34	0.72	0.39	0.75	0.84	0.14	0	0.11	0	0.35	0.19	0	0.36	0.79	3 / 18 (17%)	1 / 11 (9.1%)	2 / 7 (29%)	0.0909	0.286
s__Ruminococcus_D bicirculans	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Oscillospirales; f__Ruminococcaceae; g__Ruminococcus_D	0.12	0.74	1	0.69	0.25	0.79	1	0.56	0.37	1	1	0.37	0.74	0.5	0.82	3.6	1.6	0	2.3	0.82	3.2	0.48	0	0.93	-2.3	8 / 18 (44%)	6 / 11 (55%)	2 / 7 (29%)	0.545	0.286
s__Ruminococcus_E bromii_B	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Oscillospirales; f__Acutalibacteraceae; g__Ruminococcus_E	0.94	1	1	0.037	0.74	0.92	1	0.16	1	1	1	0.82	0.94	0.8	0.95	4.6	2.3	0.21	2.3	0.43	3.7	2.3	0	3.5	0	9 / 18 (50%)	6 / 11 (55%)	3 / 7 (43%)	0.545	0.429
s__Streptococcus salivarius	d__Bacteria; p__Firmicutes; c__Bacilli; o__Lactobacillales; f__Streptococcaceae; g__Streptococcus	0.77	0.98	1	-0.14	0.52	0.84	1	-0.32	0.63	1	1	0.43	0.77	0.36	0.75	0.7	0.31	0	0.33	0	0.62	0.28	0.15	0.31	-0.24	8 / 18 (44%)	4 / 11 (36%)	4 / 7 (57%)	0.364	0.571
s__Streptococcus thermophilus	d__Bacteria; p__Firmicutes; c__Bacilli; o__Lactobacillales; f__Streptococcaceae; g__Streptococcus	0.46	0.86	1	-0.44	0.55	0.87	1	-0.32	1	1	1	0.45	0.77	0.38	0.75	0.68	0.15	0	0.056	0	0.16	0.3	0	0.73	2.4	4 / 18 (22%)	2 / 11 (18%)	2 / 7 (29%)	0.182	0.286
s__UBA11774 sp003507655	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Lachnospirales; f__Lachnospiraceae; g__UBA11774	0.6	0.94	1	-0.27	0.52	0.84	1	-0.33	0.63	1	1	0.36	0.73	0.31	0.73	0.96	0.32	0	0.27	0	0.6	0.4	0	0.68	0.57	6 / 18 (33%)	3 / 11 (27%)	3 / 7 (43%)	0.273	0.429
s__UBA7160 MIC6745	d__Bacteria; p__Firmicutes_A; c__Clostridia; o__Lachnospirales; f__Lachnospiraceae; g__UBA7160	0.92	1	1	-0.054	0.67	0.92	1	0.21	1	1	1	0.68	0.89	0.66	0.89	0.52	0.11	0	0.077	0	0.15	0.17	0	0.46	1.1	4 / 18 (22%)	3 / 11 (27%)	1 / 7 (14%)	0.273	0.143

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Methods:

P Fisher's exact test: differences in detection rate were detected by Fisher's exact test.

P Welch's t-test (sqrt): Differentially abundant species were identified by Welch's t-test.

P Welch's t-test (clr): Differentially abundant species were identified by Welch's t-test.

Glossary:

clr: Centered log-ratio transformation. P Welch's ANOVA (sqrt): Welch's ANOVA p-values (Anova was run on sqrt transformed abundances). It is an alternative to the classic ANOVA and can be used even if the samples have unequal variances and/or unequal sample sizes. P Welch's t-test (sqrt): Welch's T-test p-values (run on sqrt transformed abundances). It is an alternative to the classic Student's t-test and is more reliable if the data violates the assumption of homogeneity of variances and/or if the study conditions have unequal sample sizes. P Welch's ANOVA (clr): Welch's ANOVA p-values (Anova was run on clr transformed abundances). It is an alternative to the classic ANOVA and can be used even if the samples have unequal variances and/or unequal sample sizes. P Welch's t-test (clr): Welch's T-test p-values (run on clr transformed abundances). It is an alternative to the classic Student's t-test and is more reliable if the data violates the assumption of homogeneity of variances and/or if the study conditions have unequal sample sizes. P lmer XXX (clr): P-value of Linear Mixed-Effects Regression on clr transformed abundances, testing significance of XXX effect. Varying intercepts per subjects are used to control for repeated measures. Pbonf: Bonferroni corrected p-value. FDR: False Discovery Rate q-value. Mean Pos: Mean abundance in positive samples. Positive samples: The number and percentage of samples in which each species has been detected. Positive XXX: The number and percentage of positive samples in study group XXX. Positive_XXX_percent: Percentage of positive samples in study group XXX. P Welch's t-test (Aldex2): Expected P value of Welch’s t-test computed by Aldex2. FDR Welch's t-test (Aldex2): Expected Benjamini-Hochberg corrected P value for Welch’s t-test. P Wilcoxon rank test (Aldex2): Expected P value of Wilcoxon rank test computed by Aldex2. FDR Wilcoxon rank test (Aldex2): Expected Benjamini-Hochberg corrected P value of Wilcoxon test. P Kruskal-Wallace test (Aldex2): Expected P value of Kruskal-Wallace test. FDR Kruskal-Wallace test (Aldex2): Expected Benjamini-Hochberg corrected P value of Kruskal-Wallace test. P GLM test (Aldex2): Expected P value of generalized linear model. FDR GLM test (Aldex2): Expected Benjamini-Hochberg corrected P value of generalized linear model.

Differentially abundant taxa (species)

The following plots present the distribution of the top most differentially abundant species across all applied statistical analysis. Plots are ordered alphabetically.

Glossary:

"Rel. Abundance": Relative abundance data; "Rel. Abundance (sqrt)": sqrt (Hellinger) transformed relative abundances; "Rel. Abundance (clr)": centered log-ratio (clr) transformed read counts.