Table 1.

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

Category	Factor	PERMANOVAa
		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 speciesb	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 sampled	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