{ "abstract": "Understanding the association of HIV exposure, antiretroviral therapy (ART) prophylaxis and human milk oligosaccharides (HMOs) on the gut microbiota of breastfed infants is crucial for developing strategies to promote infant health. Our study explored gut microbiota diversity and development in breastfed infants, analysing the influence of nevirapine (NVP) in HIV Exposed infants and HMOs in HIV Unexposed infants. Infants delivered vaginally and exclusively breastfed were recruited from City Council Clinics in Harare, Zimbabwe, at six weeks postpartum. A total of 110 infants were enrolled, and stool samples were collected for shotgun metagenomic sequencing. Dried blood spots from HIV-exposed infants were analyzed for nevirapine using HPLC-MS/MS, and breast milk from HIV-uninfected mothers was analyzed for human milk oligosaccharides using UPLC-MS. Of the collected samples, 93 stool specimens passed all bioinformatics quality filters. Alpha diversity and beta diversity were assessed, and associations between microbial diversity and HIV exposure, nevirapine levels, and HMO concentrations were evaluated using MaAsLin2. Our analysis showed no significant differences in microbial diversity across various NVP concentrations in HE infants or in 3'SL and 6'SL in the HU infants group (p ≥ 0.05). HIV exposure was associated with higher levels of Stenotrophomonas maltophilia and Mediterraneibacter faecis (corrected p-values 2.08×10-5 and 0.00246), respectively. Moreover, HIV exposure was linked to changes in specific metabolic pathways. Although overall diversity remained stable across NVP concentrations in HE infants and HMO levels in HU infants, specific taxa and functional pathways differed by HIV exposure, highlighting that compositional and functional changes can occur independently of global diversity metrics. Therefore, HIV exposure itself may influence gut microbiota composition and metabolic functions at species level, particularly with an increased abundance of specific bacteria and altered metabolic pathways leading to disturbances in vitamin metabolism.", "abstract_shown": true, "affiliations": [ "Department of Laboratory Investigative and Diagnostic Sciences, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe.", "Department of Biochemistry, Faculty of Medicine and Health Sciences, Midlands State University, Gweru, Zimbabwe.", "Department of Biomedical Sciences, African Microbiome Institute, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.", "Intestinal Microbiome Department, ZIEL - Institute for Food & Health, Technical University of Munich, Freising, Germany.", "Department of Microbes, Infection and Microbiomes, School of Infection, Inflammation and Immunology, College of Medicine and Health, University of Birmingham, Birmingham, UK.", "Department of Maternal and Child Health, Paediatrics Division, Faculty of Health Sciences and Veterinary Medicine, School of Medicine, University of Namibia, Windhoek, Namibia.", "DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.", "Department of Maternal and Child Health, Paediatrics Unit, University of Zimbabwe, Harare, Zimbabwe.", "Food, Microbiome and Health, Quadram Institute Bioscience, Norwich, UK.", "Norwich Medical School, University of East Anglia, Norwich, UK." ], "article_type": "research article", "arxiv": null, "author_total": 11, "authors": [ { "affs": [ 0, 1 ], "name": "Taona Emmah Mudhluli", "orcid": "0000-0002-9743-2023" }, { "affs": [ 2 ], "name": "Kristien Nel Van Zyl", "orcid": "0000-0001-5529-4526" }, { "affs": [ 3, 4 ], "name": "Magdalena Kujawska", "orcid": "0000-0002-8842-3512" }, { "affs": [ 5 ], "name": "Runyararo Mashingaidze-Mano", "orcid": "0000-0002-2089-182X" }, { "affs": [ 2, 6 ], "name": "Charissa C Marsh", "orcid": "0000-0003-0822-3180" }, { "affs": [ 7 ], "name": "Inam Chitsike" }, { "affs": [ 0 ], "name": "Nikhat Zia" }, { "affs": [ 0 ], "name": "Justen Manasa", "orcid": "0000-0002-8874-907X" }, { "affs": [ 4, 8, 9 ], "name": "Lindsay J Hall", "orcid": "0000-0001-8938-5709" }, { "affs": [ 0 ], "name": "Exnevia Gomo", "orcid": "0000-0003-0891-6251" }, { "affs": [ 0 ], "name": "Danai Tavonga Zhou", "orcid": "0000-0001-7907-2442" } ], "bibtex": "https://research.draconitic.com/paper/bbvdapyehhenh.bib", "cited_by": 0, "doi": "10.2147/phmt.s596049", "fulltext_url": "https://europepmc.org/articles/PMC13744174", "id": "bbvdapyehhenh", "issns": [ "1179-9927" ], "landing_url": "https://europepmc.org/article/MED/42999625", "language": "eng", "licence": "CC-BY-NC", "licence_label": "CC BY-NC", "licence_source": "article", "licence_url": "https://creativecommons.org/licenses/by-nc/4.0/", "metadata_licence": null, "native_subjects": [ [ "openalex", "2916|Infant Nutrition and Health" ] ], "openalex": "W7225137910", "pdf_url": "https://europepmc.org/articles/PMC13744174?pdf=render", "pmcid": "PMC13744174", "pmid": "42999625", "published": "2026-11-03", "publisher": null, "ris": "https://research.draconitic.com/paper/bbvdapyehhenh.ris", "sources": [ { "first_seen": "2026-11-09T15:20:34Z", "native_id": "MED:42999625", "source": "europepmc", "url": "https://europepmc.org/article/MED/42999625" } ], "subjects": [ { "field": "medicine", "origin": "journal-openalex:F27", "subfield": "general" } ], "title": "Changes in the Gut Microbiota Composition and Metabolic Pathways in Six-Week-Old HIV Exposed Breastfed Infants Receiving Antiretroviral Prophylaxis.", "title_text": "Changes in the Gut Microbiota Composition and Metabolic Pathways in Six-Week-Old HIV Exposed Breastfed Infants Receiving Antiretroviral Prophylaxis.", "type": "peer-reviewed", "updated_at": "2026-11-10T03:20:49Z", "url": "https://research.draconitic.com/paper/bbvdapyehhenh", "venue": "Pediatric health, medicine and therapeutics", "versions": [] }