| Literature DB >> 26792212 |
Sushma K Cribbs1,2, Karan Uppal3, Shuzhao Li4, Dean P Jones5, Laurence Huang6, Laura Tipton7,8, Adam Fitch9, Ruth M Greenblatt10, Lawrence Kingsley11, David M Guidot12,13, Elodie Ghedin14, Alison Morris15.
Abstract
BACKGROUND: While 16S ribosomal RNA (rRNA) sequencing has been used to characterize the lung's bacterial microbiota in human immunodeficiency virus (HIV)-infected individuals, taxonomic studies provide limited information on bacterial function and impact on the host. Metabolic profiles can provide functional information on host-microbe interactions in the lungs. We investigated the relationship between the respiratory microbiota and metabolic profiles in the bronchoalveolar lavage fluid of HIV-infected and HIV-uninfected outpatients.Entities:
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Year: 2016 PMID: 26792212 PMCID: PMC4721204 DOI: 10.1186/s40168-016-0147-4
Source DB: PubMed Journal: Microbiome ISSN: 2049-2618 Impact factor: 14.650
Demographics of HIV-infected and HIV-uninfected participants
| Variables | HIV (+), | HIV (−), |
|
|---|---|---|---|
| Gender, | 31 (79.5) | 15 (75.0) | 0.69 |
| Race, | 0.51 | ||
| White | 20 (51.3) | 13 (65) | |
| Black | 18 (46.1) | 7 (35) | |
| Other | 1 (2.6) | ||
| Ever smokers, | 24 (61.5) | 10 (50.0) | 0.40 |
| Current smokers, | 10 (25.6) | 5 (25.0) | 0.82 |
| CD4 cell count, amedian cells/μl (IQR) | 600 (404–853) | 1137 (767–1272) | 0.008 |
| CD4 count ≤200, | 1 (2.6) | ||
| Currently taking antiretroviral therapy, | 34 (87.2) | ||
| Simpson’s Diversity Index, mean (SD) | 0.71 (0.26) | 0.81 (0.12) | 0.96 |
aSample size is different than above: HIV (+), n = 38 and HIV (−), n = 6
Fig. 1Principal coordinate analysis (PCoA) plot showing the clustering trend of bronchoalveolar (BAL) samples based on the weighted UniFrac distance. PCoA plot showing the clustering trend of bronchoalveolar (BAL) samples based on the weighted UniFrac distance between all OTUs identified in HIV-infected (n = 39) and HIV-uninfected (n = 20) individuals. In this cohort, the lung microbiota does not distinguish HIV status, but comparison of intra-group beta diversity showed a significant difference in UniFrac distances between the HIV-infected and HIV-uninfected subjects, suggesting a higher degree of heterogeneity among the microbial composition of the lower airways in HIV-infected subjects
Fig. 2Principal coordinate analysis (PCoA) analysis of 12 m/z features from C18 chromatography. PCoA analysis of 12 m/z features from C18 chromatography shows that the lung metabolome does distinguish HIV-status and there is decreased variability in the metabolome in HIV-infected subjects compared to HIV-uninfected subjects
Fig. 3Association of peripheral CD4 cell counts with metabolomic features using sPLS at a variable importance on projection (VIP) threshold of 2. Association of peripheral CD4 cell counts with metabolomic features shows that 231 m/z features were found to be significantly associated with CD4 count using partial least squares (PLS) regression at variable importance on projection threshold of 2. Metabolite annotation and pathway enrichment analysis using Mummichog mapped these 231 m/z features to inflammatory pathways, including fatty acid activation and arginine metabolic pathways
Metabolite annotation and pathway enrichment analysis using Mummichog for 231 m/z features associated with CD4 cell count
| Pathways | Pathway size |
|
|---|---|---|
| Vitamin E metabolism | 30 | 0.002 |
| Urea cycle/amino group metabolism | 37 | 0.004 |
| Fatty acid activation | 23 | 0.005 |
| Arginine and proline metabolism | 30 | 0.01 |
| Aspartate and asparagine metabolism | 55 | 0.02 |
| Starch and sucrose metabolism | 16 | 0.02 |
| Linoleate metabolism | 18 | 0.03 |
| Fatty acid metabolism | 22 | 0.04 |
| Butanoate metabolism | 23 | 0.04 |
Fig. 4a Three-way relationship between metabolome, HIV, and microbiota integration of HIV-specific m/z features with microbiota data at correlation of 0.3. This figure shows that of the 91 m/z features associated with HIV, 23 were also found to be associated with 29 microbial genera at a correlation of 0.30; red circles microbial families and genus, blue rectangles metabolome features. b Pathway analysis using m/z features that were associated with Staphylococcaceae in the global network. Using Mummichog, metabolite annotation and pathway enrichment analysis was done using the m/z features that were associated with Staphylococcaceae (as the representative bacteria since pathways for Caulobacteraceae and Nocardioidaceae were very similar). The y-axis represents the enrichment significance of the metabolic pathways. This analysis shows that the pathways most affected included lineolate, glycerophospholipid, and fatty acid metabolism
Fig. 5Overall schema. Overall schematic that postulates that HIV infection alters metabolomic profiles in lung (inflammatory and oxidant pathways) which causes a shift in the functional properties of the lung microbiome and/or in the host response to the lung microbiome which may lead to an increased risk of lung infection or to chronic lung disease associated with HIV
C18 Chromatography table of differentiating metabolites between HIV-infected and HIV-uninfected participants
| Input mass | Adduct | Mass | Database matcha | Formula |
|
|---|---|---|---|---|---|
| 241.0306778 | [M + H]+ | 240.0238 | Cystine | C6H12N2O4S2 | 0.001 |
| 1033.273196 | [M + H-2H2O]+ | 1068.2864 | 2-O-beta- | C36H60O36 | 0.03 |
| 1041.978368 | [M + H]+ | 1040.9711 | TG(21:0/22:1(13Z)/22:1(13Z))[iso3] | C68H128O6 | 0.0003 |
| 354.9312674 | [M + NH4]+ | 336.8949 | 3,5-Dibromo- | C9H9Br2NO3 | 0.0001 |
| 570.3873606 | [M + Na]+ | 547.4002 | PC(O-3:1(1E)/O-18:1(9Z))[S] | C29H58NO6P | 0.0007 |
| 1189.600044 | [M + H]+ | 1188.5928 | Camelliasaponin A1 | C58H92O25 | 0.0009 |
| 1203.845241 | [M + H]+ | 1202.8380 | GalNAcbeta1-4Galbeta1-4Glcbeta-Cer(d18:1/26:1(17Z)) | C64H118N2O18 | 2.77*10−5 |
| 481.2527897 | [M + Na]+ | 458.2603 | N-(4-benzenesulfonamide) arachidonoyl amine | C26H38N2O3S | 0.0026 |
| 541.8433866 | No match | 0.0025 | |||
| 393.2172688 | [M + H]+ | 392.2100 | Indacaterol | C24H28N2O3 | 0.0022 |
| 529.8652782 | No match | 9.96*10−7 | |||
| 272.1645049 | [M + H]+ | 271.1572 | Apoatropine | C17H21NO2 | 0.0023 |
aMatched in Metin at 10 ppm