metamicrobiomeR: an R package for analysis of microbiome relative abundance data using zero-inflated beta GAMLSS and meta-analysis across studies using random effects models

Table 5 Results of GAMLSS-BEZI and LMAS: real microbiome data example 3

	GAMLSS-BEZI					LMAS
Bacterial phyla	Estimate	95% Lower limit	95% Upper limit	p-value	FDR adjusted p-value	Estimate	95% Lower limit	95% Upper limit	p-value	FDR adjusted p-value
In infants with duration of EBF ≤ 2 months (diarrhea vs. no diarrhea comparison)
Actinobacteria	−0.73	−1.12	−0.34	0.0003	0.0011	−0.12	−0.23	0.0	0.0424	0.0848
Bacteroidetes	−0.29	−0.68	0.10	0.1524	0.2032	0.06	−0.12	0.01	0.0852	0.1136
Firmicutes	0.49	0.15	0.84	0.0055	0.0109	0.11	0.01	0.2	0.0269	0.0848
Proteobacteria	−0.17	−0.54	0.20	0.3729	0.3729	0.00	−0.07	0.08	0.9060	0.9060
In infants with duration of EBF > 2 months (diarrhea vs. no diarrhea comparison)
Actinobacteria	0.02	−0.42	0.46	0.9243	0.9243	0.00	−0.10	0.10	0.9626	0.9989
Bacteroidetes	0.07	−0.41	0.56	0.7680	0.9243	0.01	−0.07	0.09	0.8101	0.9707
Firmicutes	−0.02	−0.40	0.36	0.9142	0.9243	−0.01	−0.13	0.12	0.8927	0.9707
Proteobacteria	0.12	−0.33	0.56	0.6043	0.9243	0.02	−0.06	0.11	0.5875	0.9191

Data from Bangladesh study. Comparison of longitudinal monthly gut bacterial relative abundances at phylum level in infants from 6 months to 2 years of age with diarrhea vs. no diarrhea at the time of stool sample collection stratified by duration of exclusive breastfeeding (EBF). Significant p-values (< 0.05) are in bold
EBF exclusive breastfeeding, GAMLSS-BEZI Generalized Additive Models for Location, Scale and Shape (GAMLSS) with a zero inflated beta (BEZI) family, LMAS linear model with arcsin squareroot transformation (implemented in the software MaAsLin); FDR false discovery rate

ISSN: 1471-2105