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Active TB is associated with specific stool taxa; however, little is known about the stool microbiota and LTBI in PLHIV. We characterised the stool microbiota of PLHIV with [interferon-\u03b3 release assay (IGRA)- and tuberculin skin test (TST)-positive] or without (IGRA- and TST-negative) LTBI (n = 25 per group). The 16S rRNA DNA sequences were analysed using QIIME2, Dirichlet-Multinomial Mixtures, DESeq2, and PICRUSt2. No \u03b1- or \u03b2-diversity differences occurred by LTBI status; however, LTBI-positive people were Faecalibacterium-, Blautia-, Gemmiger-, and Bacteroides-enriched and Moryella-, Atopobium-, Corynebacterium-, and Streptococcus-depleted. Inferred metagenome data showed that LTBI-negative-enriched pathways included several metabolite degradation pathways. Stool from LTBI-positive people demonstrated differential taxa abundance based on a quantitative response to antigen stimulation. In LTBI-positive people, older people had different \u03b2-diversities than younger people, whereas in LTBI-negative people, no differences occurred across age groups. Amongst female PLHIV, those with LTBI were, vs. those without LTBI, Faecalibacterium-, Blautia-, Gemmiger-, and Bacteriodes-enriched, which are producers of short-chain fatty acids. Taxonomic differences amongst people with LTBI occurred according to quantitative response to antigen stimulation and age. These data enhance our understanding of the microbiome\u2019s potential role in LTBI.<\/jats:p>","DOI":"10.3390\/microorganisms12061048","type":"journal-article","created":{"date-parts":[[2024,5,22]],"date-time":"2024-05-22T11:03:47Z","timestamp":1716375827000},"page":"1048","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Latent Tuberculosis Infection Is Associated with an Enrichment of Short-Chain Fatty Acid-Producing Bacteria in the Stool of Women Living with HIV"],"prefix":"10.3390","volume":"12","author":[{"given":"Suventha","family":"Moodley","sequence":"first","affiliation":[{"name":"DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa"},{"name":"African Microbiome Institute, Division of Molecular 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Global Tuberculosis Report, WHO."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1056\/NEJMoa1214289","article-title":"A trial of mass isoniazid preventive therapy for tuberculosis control","volume":"370","author":"Churchyard","year":"2014","journal-title":"N. Engl. J. Med."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1038\/s41577-018-0025-3","article-title":"Immunological mechanisms of human resistance to persistent Mycobacterium tuberculosis infection","volume":"18","author":"Simmons","year":"2018","journal-title":"Nat. Rev. Immunol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"619988","DOI":"10.3389\/fimmu.2021.619988","article-title":"Phenotype definition for \u201cresisters\u201d to Mycobacterium tuberculosis infection in the literature\u2014A review and recommendations","volume":"12","author":"Gutierrez","year":"2021","journal-title":"Front. Immunol."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Zhang, M., Shen, L., Zhou, X., and Chen, H. (2022). The microbiota of human lung of pulmonary tuberculosis and the alteration caused by anti-tuberculosis drugs. Curr. Microbiol., 79.","DOI":"10.1007\/s00284-022-03019-9"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"102231","DOI":"10.1016\/j.tube.2022.102231","article-title":"Alterations in the nasopharyngeal microbiota associated with active and latent tuberculosis","volume":"136","author":"Huang","year":"2022","journal-title":"Tuberculosis"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"7301","DOI":"10.1038\/s41598-023-34052-8","article-title":"Reduced microbial diversity of the nasopharyngeal microbiome in household contacts with latent tuberculosis infection","volume":"13","author":"Ugalde","year":"2023","journal-title":"Sci. Rep."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Naidoo, C.C., Nyawo, G.R., Sulaiman, I., Wu, B.G., Turner, C.T., Bu, K., Palmer, Z., Li, Y., Reeve, B.W., and Moodley, S. (2021). Anaerobe-enriched gut microbiota predicts pro-inflammatory responses in pulmonary tuberculosis. EBioMedicine, 67.","DOI":"10.1016\/j.ebiom.2021.103374"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/s12931-023-02312-w","article-title":"Gut microbiota composition can reflect immune responses of latent tuberculosis infection in patients with poorly controlled diabetes","volume":"24","author":"Huang","year":"2023","journal-title":"Respir. Res."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1016\/j.jinf.2018.08.006","article-title":"Gut microbiota associated with pulmonary tuberculosis and dysbiosis caused by anti-tuberculosis drugs","volume":"78","author":"Hu","year":"2019","journal-title":"J. Infect."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"e13068","DOI":"10.1111\/eci.13068","article-title":"Systemic proinflammation after Mycobacterium tuberculosis infection was correlated to the gut microbiome in HIV-uninfected humans","volume":"49","author":"Huang","year":"2019","journal-title":"Eur. J. Clin. Investig."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"2409","DOI":"10.1097\/QAD.0000000000000869","article-title":"Gut microbiota diversity predicts immune status in HIV-1 infection","volume":"29","author":"Nowak","year":"2015","journal-title":"Aids"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Kroon, E.E., Kinnear, C.J., Orlova, M., Fischinger, S., Shin, S., Boolay, S., Walzl, G., Jacobs, A., Wilkinson, R.J., and Alter, G. (2020). An observational study identifying highly tuberculosis-exposed, HIV-1-positive but persistently TB, tuberculin and IGRA negative persons with M. tuberculosis specific antibodies in Cape Town, South Africa. EBioMedicine, 61.","DOI":"10.1016\/j.ebiom.2020.103053"},{"key":"ref_14","first-page":"406","article-title":"Changing prevalence of tuberculosis infection with increasing age in high-burden townships in South Africa","volume":"14","author":"Wood","year":"2010","journal-title":"Int. J. Tuberc. Lung Dis."},{"key":"ref_15","first-page":"952","article-title":"Impact of age and sex on mycobacterial immunity in an area of high tuberculosis incidence","volume":"14","author":"Gallant","year":"2010","journal-title":"Int. J. Tuberc. Lung Dis."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Holmes, I., Harris, K., and Quince, C. (2012). Dirichlet multinomial mixtures: Generative models for microbial metagenomics. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0030126"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1038\/s41587-020-0548-6","article-title":"PICRUSt2 for prediction of metagenome functions","volume":"38","author":"Douglas","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1136\/thorax-2022-219103","article-title":"More than Mycobacterium tuberculosis: Site-of-disease microbial communities, and their functional and clinical profiles in tuberculous lymphadenitis","volume":"78","author":"Nyawo","year":"2023","journal-title":"Thorax"},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Segata, N., Izard, J., Waldron, L., Gevers, D., Miropolsky, L., Garrett, W.S., and Huttenhower, C. (2011). Metagenomic biomarker discovery and explanation. Genome Biol., 12.","DOI":"10.1186\/gb-2011-12-s1-p47"},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Meng, X., and Shu, Q. (2024). Novel primers to identify a wider diversity of butyrate-producing bacteria. World J. Microbiol. Biotechnol., 40.","DOI":"10.1007\/s11274-023-03872-1"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"530","DOI":"10.1016\/j.chom.2017.03.003","article-title":"Anaerobic Bacterial Fermentation Products Increase Tuberculosis Risk in Antiretroviral-Drug-Treated HIV Patients","volume":"21","author":"Segal","year":"2017","journal-title":"Cell Host Microbe"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"S130","DOI":"10.1080\/10408398.2018.1542587","article-title":"Nondigestible carbohydrates, butyrate, and butyrate-producing bacteria","volume":"59","author":"Fu","year":"2019","journal-title":"Crit. Rev. Food Sci. Nutr."},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Vitetta, L., Llewellyn, H., and Oldfield, D. (2019). Gut Dysbiosis and the Intestinal Microbiome: Streptococcus thermophilus a Key Probiotic for Reducing Uremia. Microorganisms, 7.","DOI":"10.3390\/microorganisms7080228"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"18933","DOI":"10.1038\/s41598-023-44854-5","article-title":"Gut microbiota composition and diversity before, during, and two months after rifamycin-based tuberculosis preventive therapy","volume":"13","author":"Bellot","year":"2023","journal-title":"Sci. Rep."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"892","DOI":"10.1016\/S2213-2600(18)30501-0","article-title":"The microbiome and tuberculosis: State of the art, potential applications, and defining the clinical research agenda","volume":"7","author":"Naidoo","year":"2019","journal-title":"Lancet Respir. Med."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1248","DOI":"10.1128\/jb.117.3.1248-1260.1974","article-title":"Two pathways of glutamate fermentation by anaerobic bacteria","volume":"117","author":"Buckel","year":"1974","journal-title":"J. Bacteriol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"931","DOI":"10.1017\/S0007114520001853","article-title":"Dietary inflammatory potential in relation to the gut microbiome: Results from a cross-sectional study","volume":"124","author":"Zheng","year":"2020","journal-title":"Br. J. Nutr."},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Bai, J., Li, Y., Zhang, W., Fan, M., Qian, H., Zhang, H., Qi, X., and Wang, L. (2021). Source of gut microbiota determines oat \u03b2-glucan degradation and short chain fatty acid-producing pathway. Food Biosci., 41.","DOI":"10.1016\/j.fbio.2021.101010"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"101815","DOI":"10.1016\/j.eclinm.2022.101815","article-title":"Predictive performance of interferon-gamma release assays and the tuberculin skin test for incident tuberculosis: An individual participant data meta-analysis","volume":"56","author":"Hamada","year":"2023","journal-title":"EClinicalMedicine"},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Ryan, M.P., and Pembroke, J.T. (2020). The genus Ochrobactrum as major opportunistic pathogens. Microorganisms, 8.","DOI":"10.3390\/microorganisms8111797"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"2529","DOI":"10.1023\/A:1012352626117","article-title":"High prevalence of Mycoplasma pneumoniae in intestinal mucosal biopsies from patients with inflammatory bowel disease and controls","volume":"46","author":"Chen","year":"2001","journal-title":"Dig. Dis. Sci."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1784","DOI":"10.1038\/s41467-017-01973-8","article-title":"Meta-analysis of gut microbiome studies identifies disease-specific and shared responses","volume":"8","author":"Duvallet","year":"2017","journal-title":"Nat. Commun."},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Khaliq, A., Ravindran, R., Afzal, S., Jena, P.K., Akhtar, M.W., Ambreen, A., Wan, Y.-J.Y., Malik, K.A., Irfan, M., and Khan, I.H. (2021). Gut microbiome dysbiosis and correlation with blood biomarkers in active-tuberculosis in endemic setting. PLoS ONE, 16.","DOI":"10.1371\/journal.pone.0245534"},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Oliphant, K., and Allen-Vercoe, E. (2019). Macronutrient metabolism by the human gut microbiome: Major fermentation by-products and their impact on host health. Microbiome, 7.","DOI":"10.1186\/s40168-019-0704-8"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"834","DOI":"10.1111\/j.1469-0691.2012.03958.x","article-title":"The domain Archaea in human mucosal surfaces","volume":"18","author":"Matarazzo","year":"2012","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"e3852","DOI":"10.1210\/clinem\/dgab492","article-title":"The association of gut microbiota with osteoporosis is mediated by amino acid metabolism: Multiomics in a large cohort","volume":"106","author":"Ling","year":"2021","journal-title":"J. Clin. Endocrinol. 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