Unique Community of Gut Bacterial Microbiome as Indicator for HIV Infection and Progression
International Journal of TROPICAL DISEASE & Health, Volume 44, Issue 9,
The human digestive tract harbors complex microbial communities within its epithelial cell lining. Disruption in enteric immunity will promote gut dysbiosis, which can successively induce chronic inflammation within the mucous membrane and periphery. Interpretation of the specific gut microbiome changes observed during HIV infection is warranted in populations most affected.This was a case-control and comparative study design carried out between June 2018 to September 2019. A total of 40 volunteer adult participants were recruited (15 HIV-negative and 25 HIV-positive) at the Buea Regional Hospital. Blood analysis was done for CD4+ T cell count and HIV viral load. Fecal samples from all participants were analyzed using the 16S rRNA gene sequencing on the next-generation Illumina® MiSeq™ sequencer.
Biomarker Linear Discriminant Analysis (LDA) score from LEfSe analysis indicated that the specific gut microbiome, Lachnoclostridium sp32343-sp32393-sp32423 communities could serve as an indicator for HIV infection. Findings also showed that Bacteroides vulgatus (seq 11 & seq 42), Megamonas funiformis (seq 63), unclassified members of Prevotallaceae family sp14289 (seq 51), sp13942 (seq 4), and Prevotella copri-sp13942 (seq 5) could be used as gut microbiome biomarkers for increased HIV viral load and decreased CD4+ T cell count. Meanwhile gut microbiome biomarkers for decreased HIV viral load and increased CD4+ T cell count were identified as Succinivibrionaceae sp56244 (seq 47), Eubacterium rectale (seq 8), Megamonas funiformis (seq 1 and seq 14), Prevotella copri (seq 29, seq 34, and seq 12) and unclassified Prevotellaceae sp13927 (seq 17), sp13942 (seq 5). Specific gut microbiome communities of Lachnoclostridium sp32343-sp32393-sp32423 could be used as an indicator of HIV presence. Some gut bacteria microbiome can be utilized in the management of HIV disease progression.
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Tobias R, Thomas R, Angela ED. How the microbiome challenges our concept of self. PLoS Biol. 2018;16 (2):e2005358.
Sunil T, Jacques I, Emily W, Kristen B, Pakawat C, Gerard C, David AS, et al. The host microbiome regulates and maintains human health:a primer and perspective for non-microbiologists. Cancer Res. 2017;77(8):1783–1812.
Kumar A, Chordia N. Role of microbes in human health. Applied Microbiology. 2016;3(2):1-3.
Iacob S, Iacob DG, Luminos LM. Intestinal microbiota as a host defense mechanism to infectious threats. Front. Microbiol. 2019;9:3328.
5.Cani PD, Hul MV, Lefort C, Depommier C, Rastelli M, Everard. Microbial regulation of organismal energy homeostasis. Nature Metabolism. 2019;1:34 – 46.
Simon C, Daniel T, Bernard M, Lauren JO. Dysbiosis of the gut microbiota in disease. Microbial Ecology in Health & Disease. 2015;26:26191
Food Institutional Research Measure Food For Health Research Initiative (FHRI), 2013.ELDERMET:[internet]. Gut Microbiota as an indicator and agent of nutritional health in elderly Irish subjects. DAFM Project Ref No:07/FHRI/UCC/3. [Internet.]. Available:http://eldermet.ucc.ie/elderfood-2/ pg 1 – 30.
UNAIDS/Global AIDS Monitoring 2018. Indicators for monitoring the 2016 United Nations Political Declaration on ending AIDS-UNAIDS. [Internet]. Available:https://www.unaids.org/sites/default/files/media_asset/2017-Global-AIDS-Monitoring.
Cameroon/UNAIDS 2018. [Internet] Available:https://www.unaids.org/en/regionscountries/cameroon.
Abi-Rached L, Jobin MJ, Kulkarni S, McWhinnie A, Dalva K, Gragert L, et al. The shaping of modern human immune systems by multiregional admixture with archaic humans. Science. 2011;7:334(6052):89–94.
Alcaide ML, Parmigiani A, Pallikkuth S, Roach M, Freguja R, Della Negra M, Bolivar H, Fischl MA, Pahwa S. Immune activation in HIV-infected aging women on antiretrovirals—implications for age-associated comorbidities: a cross-sectional pilot study. PLoS One. 2013;8:e63804.
Ding T, Schloss PD. Dynamics and associations of microbial community types across the human body. Nature. 2009;509:357–360
Marcel T, Darren PM, Lycias Z, Eitel M, Carolyn W, Wendy AB. Characterization of HIV-1 gag and nef in Cameroon:further evidence of extreme diversity at the origin of the HIV-1 group M epidemic Virol J. 2013;10:29. Published online 2013 Jan 22. DOI:10.1186/1743-422X-10-29 PMCID:PMC3560183
Simon EA, Eric AA, Céline NN, Thumamo BP, Jules CA. Fecal gram stain morphotype and their distribution patterns in a Cameroonian cohort with and without HIV Infection. Scientific African. 2020;e00376.
Respess RA, Rayfield MA, Dondero TJ. Laboratory testing and rapid HIV assays: applications for HIV surveillance in hard-to-reach populations. AIDS 15 Supplement. 2001;3:S49-S59.
Julius YF, Alfred KN, Charles K, Fang Q, Dora M, et al. Adherence to antiretroviral therapy (ART) in Yaoundé-Cameroon: Association with opportunistic infections, depression, ART regimen and side effects. PLoS One. 2017;12(1):e0170893.
Neogi U, Gupta S, Rodridges R, Sahoo PN, Rao SD, Rewari BB, Shet A. Dried blood spot HIV-1 RNA quantification:a useful tool for viral load monitoring among HIV-infected individuals in India. The Indian Journal of Medical Research. 2012;136(6):956–962.
Shantelle C, Elloise du T, Mamadou K, Clinton M, Heather JZ, Mark PN. A comparison of the efficiency of five different commercial DNA extraction kits for extraction of DNA from faecal samples. J Microbiol Methods. 2013 Aug;94(2):103–110. DOI:10.1016/j.mimet.2013.05.008
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2:High-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13(7):581-3.
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335-336.
Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C. Metagenomic biomarker discovery, and explanation. Genome Biol. 2011;12:R60.
Leandro NL, Roberta RF, Eric WT, Luiz FW. Rethinking microbial diversity analysis in the high throughput sequencing era. Journal of Microbiological Methods. 2011;86:1:42-51.
Homero S-V, Eduardo Z, Nadim JA, Christian M, Mario P, et al. A Lachnospiraceae-dominated bacterial signature in the fecal microbiota of HIV-infected individuals from Colombia, South America. Scientific Reports. 2018;8:4479
Dinh DM, Volpe GE, Duffalo C, Bhalchandra S, Tai AK, Kane AV, Wanke CA, Ward HD. Intestinal microbiota, microbial translocation, and systemic inflammation in chronic HIV infection. J. Infect. Dis. 2015;211:19–27.
Lozupone CA, Li M, Campbell TB, Flores SC, Linderman D, Gebert MJ, Knight R, Fontenot AP, Palmer BE. Alterations in the gut microbiota associated with HIV-1 infection. Cell Host Microbe. 2013;14:329– 339.
Vujkovic-Cvijin I, Dunham RM, Iwai S, Maher MC, Albright RG, Broadhurst MJ, Hernandez RD, Lederman MM, Huang Y, Somsouk M, et al. Dysbiosis of the gut microbiota is associated with HIV disease progression and tryptophan catabolism. Sci. Transl. Med. 2013;5:193ra91.
Hiippala K, Kainulainen V, Kalliomaki M, Arkkila P, Satokari R. Mucosal prevalence and interactions with the epithelium indicate commensalism of Sutterella spp. Frontiers in Microbiology. 2016;7: 1706.
Nowak P, Troseid M, Avershina E, Barqasho B, Neogi U, Holm K, Hov JR, Noyan K, Vesterbacka J, Sva¨rd J, et al. Gut microbiota diversity predicts immune status in HIV-1 infection. AIDS. 2015;29:2409–2418.
Serrano-Villar, S, et al. Gut bacteria metabolism impacts immune recovery in HIV-infected individuals. EBioMedicine. 2016;8:203–216. DOI:10.1016/j.ebiom.2016.04.033.
Danfeng Lu, Jian Bo Zhang, Yue Xin Wang et al. Association between CD4 + T cell counts and gut microbiota and serum cytokines levels in HIV-infected immunological non-responders. BMC Infect Dis. 2021;21:742.
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