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

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

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