Analyzing microbiome data with taxonomic misclassification using a zero-inflated Dirichlet-multinomial model

Koslovsky, Matthew D.

doi:10.1186/s12859-025-06078-4

BMC Bioinformatics

Table 3 Average posterior relative abundances estimated with the proposed MicroMiss and ZIDM models for healthy and obese participants

From: Analyzing microbiome data with taxonomic misclassification using a zero-inflated Dirichlet-multinomial model

Family	Genus	MicroMiss			ZIDM
		Obese	Healthy	p value	Obese	Healthy	p value
Acidaminococcaceae	Acidaminococcus	0.0059	0.0129	0.789	0.0056	0.0122	0.103
	Succiniclasticum	0.0018	0.0106	0.012	0.0017	0.0099	0.454
Aerococcaceae	Facklamia	0.0000	0.0172	\(<0.001\)	0.0000	0.0160	\(<0.001\)
Bacteroidaceae	Bacteroides	0.2709	0.2510	0.316	0.2632	0.2447	0.019
Bifidobacteriaceae	Bifidobacterium	0.0183	0.0307	0.109	0.0178	0.0300	0.008
Campylobacteraceae	Campylobacter	0.0217	0.0006	\(<0.001\)	0.0213	0.0007	\(<0.001\)
Clostridiales Incertae Sedis XI	Anaerococcus	0.0202	0.0057	\(<0.001\)	0.0197	0.0056	\(<0.001\)
	Finegoldia	0.0271	0.0002	\(<0.001\)	0.0264	0.0004	\(<0.001\)
	Peptoniphilus	0.0426	0.0077	\(<0.001\)	0.0417	0.0077	\(<0.001\)
Incertae Sedis XI	Murdochiella	0.0034	0.0106	\(<0.001\)	0.0034	0.0101	0.003
Lachnospiraceae	Anaerostipes	0.0081	0.0230	0.030	0.0092	0.0249	\(<0.001\)
	Blautia	0.0417	0.1728	\(<0.001\)	0.0382	0.1548	\(<0.001\)
	Coprococcus	0.0047	0.0105	0.019	0.0060	0.0116	0.004
	Lachnospiracea Incertae Sedis	0.0061	0.0164	0.005	0.0099	0.0265	\(<0.001\)
	Roseburia	0.0209	0.0558	0.019	0.0210	0.0556	\(<0.001\)
	Ruminococcus	0.0079	0.0156	0.033	0.0093	0.0177	\(<0.001\)
Porphyromonadaceae	Parabacteroides	0.0192	0.0169	0.612	0.0191	0.0170	0.262
	Porphyromonas	0.0434	0.0024	\(<0.001\)	0.0423	0.0024	0.001
Prevotellaceae	Prevotella	0.2189	0.0412	0.001	0.2189	0.0412	0.001
Rikenellaceae	Alistipes	0.0080	0.0240	0.045	0.0083	0.0238	0.003
Ruminococcaceae	Clostridium IV	0.0031	0.0126	0.010	0.0038	0.0141	\(<0.001\)
	Faecalibacterium	0.0597	0.1091	0.004	0.0588	0.1057	\(<0.001\)
	Ruminococcus	0.0185	0.0219	0.250	0.0179	0.0212	0.012
Veillonellaceae	Dialister	0.020	0.013	0.310	0.020	0.013	0.621
	Megamonas	0.0003	0.0314	\(<0.001\)	0.0003	0.0295	0.128
	Megasphaera	0.0123	0.0097	0.336	0.0115	0.0092	0.209

Only genera with relative abundances above 0.01 for obese or healthy groups are presented. P-values were obtained from a rank sum test on the centered log ratio transformations of relative abundances at the genus level

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ISSN: 1471-2105

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