Sequence similarity of input GreenGenes sequences to sequenced reference genomes. When
Sequence similarity of input GreenGenes sequences to sequenced reference genomes. When combined with HUMAnN, a separate bioinformatic tool that organizes metagenomic data into relative abundances of KEGG pathways per sample, the resulting data are highly comparable to sequenced metagenomic data and observed metabolomic data [26,47]. Using these bioinformatic tools, metagenomic functions were compared between cART(-), cART(+) and HC subjects. For these metagenomic analyses, the q-value threshold for correcting multiple comparisons was relaxed to include q <0.25 comparisons in agreement with previous studies using this methodology [26]. Like the analyses above, no PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/27385778 significant differences were observed between cART(+) and HC subjects or between cART(+) and cART(-) subjects after correction for multiple comparisons. However, 10 KEGG pathways were significantly different between cART(-) and HC subjects (Kruskal-Wallis, q <0.25). Plotting these pathways with respect to cART status revealed that the distribution of these pathways was similar to the distribution of enriched and depleted genera (Figure 5); While cART(-) subjects exhibited the most enrichment or depletion of each pathway, cART(+) subjects had intermediate levels of metagenomic pathwayabundance relative to HC (Figure 5). Overall, the metagenomes of cART(-) subjects tended to be depleted of amino acid production, amino acid metabolism, CoA biosynthesis, and fructose/mannose metabolism compared with HC subjects. Instead, the microbiota of cART (-) subjects were metagenomically enriched for glutathione metabolism, selenocompound metabolism, folate biosynthesis and siderophore biosynthetic genes. These results indicate that HIV infection in the absence of cART results in significant functional metagenomic differences that are not fully restored with cART. Such functional differences may reflect the functions that HIV-infected mucosa select for and could have downstream implications on vitamin and nutrient availability for the host.Discussion This PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/26240184 study represents one of the first attempts to define changes in the mucosal microbiota composition in HIV infection and revealed several HIV-dependent changes in the mucosal microbiota. HIV infection in the absence of cART was associated with significant increases in Fusobacterium, Anaerococcus, Peptostreptococcus and Porpyromonas species and significant decreases in Roseburia, Alistipes, Coprococcus, Eubacterium, Ruminococcus and Lachnospira species. Surprisingly, of the genera enriched in cART(-) subjects all are (i) commonly isolated from the oral cavity and (ii) considered opportunistic pathogens. Indeed, Anaerococcus, Porphyromonas and PeptostreptococcusMcHardy et al. Microbiome 2013, 1:26 http://www.microbiomejournal.com/content/1/1/Page 9 ofSelenocompound metabolism Glutathione metabolism* * *HC Subjects cART(+) Subects cART(-) SubjectsFructose and mannose metabolism Ala, Asp and Glu metabolism Val, Leu and Ile biosynthesis* * *Lys biosynthesis Phe, Tyr and Trp biosynthesis Pantothenate and CoA biosynthesis**Biosynthesis of siderophore peptides*Folate biosynthesis*Figure 5 Imputed metagenomic differences between subjects not on combination anti-retroviral therapy (cART(-)) and healthy AG-490MedChemExpress AG-490 control (HC) subjects. The relative abundance of metabolic pathways encoded in each imputed sample metagenome was analyzed by HIV infection status of each subject using box plots. From these box plots, clear differences are observed between the relative.