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Runtuwene LR, Parbie PK, Mizutani T, Ishizaka A, Matsuoka S, Abana CZY, Kushitor D, Bonney EY, Ofori SB, Kiyono H, Ishikawa K, Ampofo WK, Matano T. Longitudinal analysis of microbiome composition in Ghanaians living with HIV-1. Front Microbiol 2024; 15:1359402. [PMID: 38426062 PMCID: PMC10902004 DOI: 10.3389/fmicb.2024.1359402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 01/18/2024] [Indexed: 03/02/2024] Open
Abstract
Human immunodeficiency virus (HIV) 1 infection is known to cause gut microbiota dysbiosis. Among the causes is the direct infection of HIV-1 in gut-resident CD4+ T cells, causing a cascade of phenomena resulting in the instability of the gut mucosa. The effect of HIV infection on gut microbiome dysbiosis remains unresolved despite antiretroviral therapy. Here, we show the results of a longitudinal study of microbiome analysis of people living with HIV (PLWH). We contrasted the diversity and composition of the microbiome of patients with HIV at the first and second time points (baseline_case and six months later follow-up_case, respectively) with those of healthy individuals (baseline_control). We found that despite low diversity indices in the follow-up_case, the abundance of some genera was recovered but not completely, similar to baseline_control. Some genera were consistently in high abundance in PLWH. Furthermore, we found that the CD4+ T-cell count and soluble CD14 level were significantly related to high and low diversity indices, respectively. We also found that the abundance of some genera was highly correlated with clinical features, especially with antiretroviral duration. This includes genera known to be correlated with worse HIV-1 progression (Achromobacter and Stenotrophomonas) and a genus associated with gut protection (Akkermansia). The fact that a protector of the gut and genera linked to a worse progression of HIV-1 are both enriched may signify that despite the improvement of clinical features, the gut mucosa remains compromised.
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Affiliation(s)
- Lucky Ronald Runtuwene
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Prince Kofi Parbie
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | - Taketoshi Mizutani
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Aya Ishizaka
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Saori Matsuoka
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Christopher Zaab-Yen Abana
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Dennis Kushitor
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Evelyn Yayra Bonney
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Sampson Badu Ofori
- Department of Internal Medicine, Eastern Regional Hospital Koforidua, Ghana Health Service, Koforidua, Ghana
| | - Hiroshi Kiyono
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Institute for Global Prominent Research, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Medicine, Chiba University-University of California San Diego Center for Mucosal Immunology, Allergy and Vaccines (cMAV), University of California San Diego, San Diego, CA, United States
| | - Koichi Ishikawa
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - William Kwabena Ampofo
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Tetsuro Matano
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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Patra PK, Banday AZ, Sadanand R, Sharma B, Angrup A, Vignesh P, Rawat A. Achromobacter xylosoxidans Pneumonia in a Young Child with Chronic Granulomatous Disease-a Case-Based Review. J Clin Immunol 2021; 41:1686-1692. [PMID: 34263392 DOI: 10.1007/s10875-021-01079-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 05/25/2021] [Indexed: 10/20/2022]
Affiliation(s)
- Pratap Kumar Patra
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India
| | - Aaqib Zaffar Banday
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India
| | - Rohit Sadanand
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India
| | - Bhawna Sharma
- Department of Microbiology, PGIMER, Chandigarh, India
| | | | - Pandiarajan Vignesh
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India.
| | - Amit Rawat
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India
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Fung TC, Artis D, Sonnenberg GF. Anatomical localization of commensal bacteria in immune cell homeostasis and disease. Immunol Rev 2015; 260:35-49. [PMID: 24942680 DOI: 10.1111/imr.12186] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The mammalian gastrointestinal (GI) tract is colonized by trillions of beneficial commensal bacteria that are essential for promoting normal intestinal physiology. While the majority of commensal bacteria are found in the intestinal lumen, many species have also adapted to colonize different anatomical locations in the intestine, including the surface of intestinal epithelial cells (IECs) and the interior of gut-associated lymphoid tissues. These distinct tissue localization patterns permit unique interactions with the mammalian immune system and collectively influence intestinal immune cell homeostasis. Conversely, dysregulated localization of commensal bacteria can lead to inappropriate activation of the immune system and is associated with numerous chronic infectious, inflammatory, and metabolic diseases. Therefore, regulatory mechanisms that control proper anatomical containment of commensal bacteria are essential to maintain tissue homeostasis and limit pathology. In this review, we propose that commensal bacteria associated with the mammalian GI tract can be anatomically defined as (i) luminal, (ii) epithelial-associated, or (iii) lymphoid tissue-resident, and we discuss the role and regulation of these microbial populations in health and disease.
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Affiliation(s)
- Thomas C Fung
- Division of Gastroenterology, Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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