Gut microbiota in HIV–pneumonia patients is related to peripheral CD4 counts, lung microbiota, and in vitro macrophage dysfunction

Table 1 Clinical and microbiological features are significantly associated with variation in stool microbial composition in HIV-infected patients with bacterial pneumonia

Category	Factor	PERMANOVA^a
Category	Factor	R ²	p value
Clinical
	CD4 count (grouped quartile 1 versus 4)	0.052	0.002
	Ceftriaxone at time of sampling	0.019	0.014
	Mortality at hospital discharge	0.018	0.017
	CD4 count (cells/μl)	0.017	0.025
	Pulmonary tuberculosis	0.009	0.499
	Ceftriaxone within 3 months prior to hospitalization	0.008	0.634
Microbiological
	Dominant family	0.319	0.001
	Shannon diversity	0.145	0.001
	Paired BAL dominant family	0.122	0.033
	Total observed species^b	0.111	0.001
	Faith’s phylogenetic diversity	0.104	0.001
	Percent dominance	0.072	0.001
	Bray–Curtis distance to paired BAL sample (grouped quartile 1 versus 4)^c	0.054	0.002
	Bray–Curtis distance to paired BAL sample (continuous)	0.026	0.007
	Faith’s phylogenetic diversity of paired BAL sample^d	0.021	0.028
	Fungal percent dominance	0.022	0.1
	Fungal dominant genus	0.095	0.284
Processing
	Sequenced on NextSeq run 1	0.012	0.132
	Sequenced on NextSeq run 2	0.012	0.132
	ITS2 fungal amplicon sequenced	0.013	0.162
	16S amplification plate	0.022	0.221
	16S primer plate	0.022	0.221
	Extraction plate	0.007	0.824

^aPermutational multivariate ANOVA results for Bray–Curtis distance shown; representative of weighted and unweighted UniFrac and Canberra distances
^bSimilar results for chao1 richness estimate
^cSimilar results for weighted and unweighted UniFrac and Canberra distances
^dStool composition is not significantly related to BAL richness or Shannon diversity

ISSN: 2049-2618