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Kayongo A, Ntayi ML, Olweny G, Kyalo E, Ndawula J, Ssengooba W, Kigozi E, Kalyesubula R, Munana R, Namaganda J, Caroline M, Sekibira R, Bagaya BS, Kateete DP, Joloba ML, Jjingo D, Sande OJ, Mayanja-Kizza H. Airway microbiome signature accurately discriminates Mycobacterium tuberculosis infection status. iScience 2024; 27:110142. [PMID: 38904070 PMCID: PMC11187240 DOI: 10.1016/j.isci.2024.110142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/05/2024] [Accepted: 05/27/2024] [Indexed: 06/22/2024] Open
Abstract
Mycobacterium tuberculosis remains one of the deadliest infectious agents globally. Amidst efforts to control TB, long treatment duration, drug toxicity, and resistance underscore the need for novel therapeutic strategies. Despite advances in understanding the interplay between microbiome and disease in humans, the specific role of the microbiome in predicting disease susceptibility and discriminating infection status in tuberculosis still needs to be fully investigated. We investigated the impact of M.tb infection and M.tb-specific IFNγ immune responses on airway microbiome diversity by performing TB GeneXpert and QuantiFERON-GOLD assays during the follow-up phase of a longitudinal HIV-Lung Microbiome cohort of individuals recruited from two large independent cohorts in rural Uganda. M.tb rather than IFNγ immune response mainly drove a significant reduction in airway microbiome diversity. A microbiome signature comprising Streptococcus, Neisseria, Fusobacterium, Prevotella, Schaalia, Actinomyces, Cutibacterium, Brevibacillus, Microbacterium, and Beijerinckiacea accurately discriminated active TB from Latent TB and M.tb-uninfected individuals.
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Affiliation(s)
- Alex Kayongo
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
- Lung Institute, Makerere University College of Health Sciences, Kampala 256, Uganda
| | - Moses Levi Ntayi
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
- Lung Institute, Makerere University College of Health Sciences, Kampala 256, Uganda
| | - Geoffrey Olweny
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
| | - Edward Kyalo
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
- Lung Institute, Makerere University College of Health Sciences, Kampala 256, Uganda
| | - Josephine Ndawula
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
- Lung Institute, Makerere University College of Health Sciences, Kampala 256, Uganda
| | - Willy Ssengooba
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
- Lung Institute, Makerere University College of Health Sciences, Kampala 256, Uganda
| | - Edgar Kigozi
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
| | - Robert Kalyesubula
- Department of Research, African Community Center for Social Sustainability (ACCESS), Nakaseke 256, Uganda
- Department of Medicine, Makerere University, College of Health Sciences, Kampala 256, Uganda
| | - Richard Munana
- Department of Research, African Community Center for Social Sustainability (ACCESS), Nakaseke 256, Uganda
| | - Jesca Namaganda
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
- Lung Institute, Makerere University College of Health Sciences, Kampala 256, Uganda
| | - Musiime Caroline
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
| | - Rogers Sekibira
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
| | - Bernard Sentalo Bagaya
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
| | - David Patrick Kateete
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
| | - Moses Lutaakome Joloba
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
| | - Daudi Jjingo
- College of Computing and Information Sciences, Computer Science, Makerere University, Kampala 256, Uganda
- African Center of Excellence in Bioinformatics and Data Science, Infectious Diseases Institute, Kampala 256, Uganda
| | - Obondo James Sande
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
| | - Harriet Mayanja-Kizza
- Department of Medicine, Makerere University, College of Health Sciences, Kampala 256, Uganda
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Wang L, Campino S, Phelan J, Clark TG. Mixed infections in genotypic drug-resistant Mycobacterium tuberculosis. Sci Rep 2023; 13:17100. [PMID: 37816829 PMCID: PMC10564873 DOI: 10.1038/s41598-023-44341-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/06/2023] [Indexed: 10/12/2023] Open
Abstract
Tuberculosis disease (TB), caused by Mycobacterium tuberculosis, is a major global public health problem, resulting in more than 1 million deaths each year. Drug resistance (DR), including multi-drug (MDR-TB), is making TB control difficult and accounts for 16% of new and 48% of previously treated cases. To further complicate treatment decision-making, many clinical studies have reported patients harbouring multiple distinct strains of M. tuberculosis across the main lineages (L1 to L4). The extent to which drug-resistant strains can be deconvoluted within mixed strain infection samples is understudied. Here, we analysed M. tuberculosis isolates with whole genome sequencing data (n = 50,723), which covered the main lineages (L1 9.1%, L2 27.6%, L3 11.8%, L4 48.3%), with genotypic resistance to isoniazid (HR-TB; n = 9546 (29.2%)), rifampicin (RR-TB; n = 7974 (24.4%)), and at least MDR-TB (n = 5385 (16.5%)). TB-Profiler software revealed 531 (1.0%) isolates with potential mixed sub-lineage infections, including some with DR mutations (RR-TB 21/531; HR-TB 59/531; at least MDR-TB 173/531). To assist with the deconvolution of such mixtures, we adopted and evaluated a statistical Gaussian Mixture model (GMM) approach. By simulating 240 artificial mixtures of different ratios from empirical data across L1 to L4, a GMM approach was able to accurately estimate the DR profile of each lineage, with a low error rate for the estimated mixing proportions (mean squared error 0.012) and high accuracy for the DR predictions (93.5%). Application of the GMM model to the clinical mixtures (n = 531), found that 33.3% (188/531) of samples consisted of DR and sensitive lineages, 20.2% (114/531) consisted of lineages with only DR mutations, and 40.6% (229/531) consisted of lineages with genotypic pan-susceptibility. Overall, our work demonstrates the utility of combined whole genome sequencing data and GMM statistical analysis approaches for providing insights into mono and mixed M. tuberculosis infections, thereby potentially assisting diagnosis, treatment decision-making, drug resistance and transmission mapping for infection control.
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Affiliation(s)
- Linfeng Wang
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel St, London, WC1E 7HT, UK
| | - Susana Campino
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel St, London, WC1E 7HT, UK
| | - Jody Phelan
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel St, London, WC1E 7HT, UK.
| | - Taane G Clark
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel St, London, WC1E 7HT, UK.
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel St, London, WC1E 7HT, UK.
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Nyawo GR, Naidoo CC, Wu B, Sulaiman I, Clemente JC, Li Y, Minnies S, Reeve BWP, Moodley S, Rautenbach C, Wright C, Singh S, Whitelaw A, Schubert P, Warren R, Segal L, Theron G. More than Mycobacterium tuberculosis: site-of-disease microbial communities, and their functional and clinical profiles in tuberculous lymphadenitis. Thorax 2023; 78:297-308. [PMID: 36598079 PMCID: PMC9957952 DOI: 10.1136/thorax-2022-219103] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 10/31/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND Lymphadenitis is the most common extrapulmonary tuberculosis (EPTB) manifestation. The microbiome is important to human health but uninvestigated in EPTB. We profiled the site-of-disease lymph node microbiome in tuberculosis lymphadenitis (TBL). METHODS Fine-needle aspiration biopsies were collected from 158 pretreatment presumptive TBL patients in Cape Town, South Africa. 16S Illumina MiSeq rRNA gene sequencing was done. RESULTS We analysed 89 definite TBLs (dTBLs) and 61 non-TBLs (nTBLs), which had similar α- but different β-diversities (p=0.001). Clustering identified five lymphotypes prior to TB status stratification: Mycobacterium-dominant, Prevotella-dominant and Streptococcus-dominant lymphotypes were more frequent in dTBLs whereas a Corynebacterium-dominant lymphotype and a fifth lymphotype (no dominant taxon) were more frequent in nTBLs. When restricted to dTBLs, clustering identified a Mycobacterium-dominant lymphotype with low α-diversity and non-Mycobacterium-dominated lymphotypes (termed Prevotella-Corynebacterium, Prevotella-Streptococcus). The Mycobacterium dTBL lymphotype was associated with HIV-positivity and features characteristic of severe lymphadenitis (eg, larger nodes). dTBL microbial communities were enriched with potentially proinflammatory microbial short-chain fatty acid metabolic pathways (propanoate, butanoate) vs nTBLs. 11% (7/61) of nTBLs had Mycobacterium reads BLAST-confirmed as Mycobacterium tuberculosis complex. CONCLUSIONS TBL at the site-of-disease is not microbially homogeneous. Distinct microbial community clusters exist that, in our setting, are associated with different clinical characteristics, and immunomodulatory potentials. Non-Mycobacterium-dominated dTBL lymphotypes, which contain taxa potentially targeted by TB treatment, were associated with milder, potentially earlier stage disease. These investigations lay foundations for studying the microbiome's role in lymphatic TB. The long-term clinical significance of these lymphotypes requires prospective validation.
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Affiliation(s)
- Georgina R Nyawo
- 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, Western Cape, South Africa
- African Microbiome Institute, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, Western Cape, South Africa
| | - Charissa C Naidoo
- 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, Western Cape, South Africa
- African Microbiome Institute, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, Western Cape, South Africa
| | - Benjamin Wu
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Imran Sulaiman
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Jose C Clemente
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yonghua Li
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Stephanie Minnies
- 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, Western Cape, South Africa
| | - Byron W P Reeve
- 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, Western Cape, South Africa
| | - Suventha Moodley
- 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, Western Cape, South Africa
- African Microbiome Institute, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, Western Cape, South Africa
| | - Cornelia Rautenbach
- National Health Laboratory Service, Tygerberg Hospital, Cape Town, Western Cape, South Africa
- Division of Medical Microbiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, Western Cape, South Africa
| | - Colleen Wright
- Division Anatomical Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, Western Cape, South Africa
| | - Shivani Singh
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Andrew Whitelaw
- National Health Laboratory Service, Tygerberg Hospital, Cape Town, Western Cape, South Africa
- Division of Medical Microbiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, Western Cape, South Africa
| | - Pawel Schubert
- National Health Laboratory Service, Tygerberg Hospital, Cape Town, Western Cape, South Africa
- Division Anatomical Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, Western Cape, South Africa
| | - Robin Warren
- 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, Western Cape, South Africa
| | - Leopoldo Segal
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Grant Theron
- 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, Western Cape, South Africa
- African Microbiome Institute, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, Western Cape, South Africa
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Kayongo A, Bartolomaeus TUP, Birkner T, Markó L, Löber U, Kigozi E, Atugonza C, Munana R, Mawanda D, Sekibira R, Uwimaana E, Alupo P, Kalyesubula R, Knauf F, Siddharthan T, Bagaya BS, Kateete DP, Joloba ML, Sewankambo NK, Jjingo D, Kirenga B, Checkley W, Forslund SK. Sputum Microbiome and Chronic Obstructive Pulmonary Disease in a Rural Ugandan Cohort of Well-Controlled HIV Infection. Microbiol Spectr 2023; 11:e0213921. [PMID: 36790203 PMCID: PMC10100697 DOI: 10.1128/spectrum.02139-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/23/2023] [Indexed: 02/16/2023] Open
Abstract
Sub-Saharan Africa has increased morbidity and mortality related to chronic obstructive pulmonary disease (COPD). COPD among people living with HIV (PLWH) has not been well studied in this region, where HIV/AIDS is endemic. Increasing evidence suggests that respiratory microbial composition plays a role in COPD severity. Therefore, we aimed to investigate microbiome patterns and associations among PLWH with COPD in Sub-Saharan Africa. We conducted a cross-sectional study of 200 adults stratified by HIV and COPD in rural Uganda. Induced sputum samples were collected as an easy-to-obtain proxy for the lower respiratory tract microbiota. We performed 16S rRNA gene sequencing and used PICRUSt2 (version 2.2.3) to infer the functional profiles of the microbial community. We used a statistical tool to detect changes in specific taxa that searches and adjusts for confounding factors such as antiretroviral therapy (ART), age, sex, and other participant characteristics. We could cluster the microbial community into three community types whose distribution was shown to be significantly impacted by HIV. Some genera, e.g., Veillonella, Actinomyces, Atopobium, and Filifactor, were significantly enriched in HIV-infected individuals, while the COPD status was significantly associated with Gammaproteobacteria and Selenomonas abundance. Furthermore, reduced bacterial richness and significant enrichment in Campylobacter were associated with HIV-COPD comorbidity. Functional prediction using PICRUSt2 revealed a significant depletion in glutamate degradation capacity pathways in HIV-positive patients. A comparison of our findings with an HIV cohort from the United Kingdom revealed significant differences in the sputum microbiome composition, irrespective of viral suppression. IMPORTANCE Even with ART available, HIV-infected individuals are at high risk of suffering comorbidities, as shown by the high prevalence of noninfectious lung diseases in the HIV population. Recent studies have suggested a role for the respiratory microbiota in driving chronic lung inflammation. The respiratory microbiota was significantly altered among PLWH, with disease persisting up to 3 years post-ART initiation and HIV suppression. The community structure and diversity of the sputum microbiota in COPD are associated with disease severity and clinical outcomes, both in stable COPD and during exacerbations. Therefore, a better understanding of the sputum microbiome among PLWH could improve COPD prognostic and risk stratification strategies. In this study, we observed that in a virologically suppressed HIV cohort in rural Uganda, we could show differences in sputum microbiota stratified by HIV and COPD, reduced bacterial richness, and significant enrichment in Campylobacter associated with HIV-COPD comorbidity.
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Affiliation(s)
- Alex Kayongo
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda
- Makerere University, College of Health Sciences, Department of Immunology and Molecular Biology, Kampala, Uganda
| | - Theda Ulrike Patricia Bartolomaeus
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Experimental and Clinical Research Center, A Cooperation of Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- German Centre for Cardiovascular Research, Berlin, Germany
| | - Till Birkner
- Experimental and Clinical Research Center, A Cooperation of Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- German Centre for Cardiovascular Research, Berlin, Germany
| | - Lajos Markó
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Experimental and Clinical Research Center, A Cooperation of Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- German Centre for Cardiovascular Research, Berlin, Germany
| | - Ulrike Löber
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Experimental and Clinical Research Center, A Cooperation of Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- German Centre for Cardiovascular Research, Berlin, Germany
| | - Edgar Kigozi
- Makerere University, College of Health Sciences, Department of Immunology and Molecular Biology, Kampala, Uganda
| | - Carolyne Atugonza
- Makerere University, College of Health Sciences, Department of Immunology and Molecular Biology, Kampala, Uganda
| | - Richard Munana
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Denis Mawanda
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Rogers Sekibira
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Esther Uwimaana
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda
- Makerere University, College of Health Sciences, Department of Immunology and Molecular Biology, Kampala, Uganda
| | - Patricia Alupo
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Robert Kalyesubula
- African Community Center for Social Sustainability (ACCESS), Department of Research, Nakaseke, Uganda
- Makerere University, College of Health Sciences, Department of Medicine, Kampala, Uganda
| | - Felix Knauf
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Trishul Siddharthan
- University of Miami, School of Medicine, Division of pulmonary and critical care medicine, Miami, Florida, USA
| | - Bernard S. Bagaya
- Makerere University, College of Health Sciences, Department of Immunology and Molecular Biology, Kampala, Uganda
| | - David P. Kateete
- Makerere University, College of Health Sciences, Department of Immunology and Molecular Biology, Kampala, Uganda
| | - Moses L. Joloba
- Makerere University, College of Health Sciences, Department of Immunology and Molecular Biology, Kampala, Uganda
| | - Nelson K. Sewankambo
- Makerere University, College of Health Sciences, Department of Medicine, Kampala, Uganda
| | - Daudi Jjingo
- Makerere University, College of Computing and Information Sciences, Department of Computer Science, Kampala, Uganda
- African Center of Excellence in Bioinformatics and Data Science, Infectious Diseases Institute, Kampala, Uganda
| | - Bruce Kirenga
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda
- Makerere University, College of Health Sciences, Department of Medicine, Kampala, Uganda
| | - William Checkley
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University, Baltimore, Maryland, USA
- Center for Global Non-Communicable Disease Research and Training, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Sofia K. Forslund
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Experimental and Clinical Research Center, A Cooperation of Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- German Centre for Cardiovascular Research, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
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Bacteriomes in lesions of pulmonary tuberculosis and its association with status of Mycobacterium tuberculosis excretion. BMC Microbiol 2022; 22:280. [PMID: 36418957 PMCID: PMC9686068 DOI: 10.1186/s12866-022-02698-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 11/09/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Bacteria in lung play an important role in sustaining lung health. Understanding the characteristics of bacteriomes in lesions of pulmonary tuberculosis (TB) patients, who excrete Mycobacterium tuberculosis (MTB), is important for TB prevention and effective treatment. METHODS: In this study, bacteriomes in lesions from TB patients excreting bacteria (TB-E) and those from TB patients not excreting bacteria (TB-NE) with matched normal lung tissues (NT) were compared by 16S rRNA sequencing. Bacterial MetaCyc functions in TB lesions were also predicted by PICRUSt2 tool. RESULTS Alpha diversity of bacteria, including Chao 1 and Shannon indexes, for TB-E was significantly higher than those in TB-NE and NT; while for TB-NE group, Chao 1 index was higher than that in NT group. Predominant phyla in TB lesions and NT were Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes, but analysis of similarity (ANOSIM, p < 0.001) revealed significantly different bacterial compositions among TB-E, TB-NE and NT samples. As for bacteriomes in TB lesions, a strong association (ANOSIM, p < 0.001) was observed with the status of MTB excretion. Indicator genera identified in TB-E and TB-NE demonstrated distinctive micro-ecological environments of TB lesions from patients with different clinical manifestations. Co-occurrence analysis revealed a densely-linked bacterial community in TB-NE compared to that in TB-E. MetaCyc functions responsible for menaquinone synthesis and chorismate metabolism that could potentially impact the persistent-state and nutrient metabolism of MTB were enriched in TB-E samples. While in TB-NE samples, enrichment of bacterial MetaCyc function responsible for heme b synthesis might contribute to TB pathology through ferroptosis. CONCLUSION Bacteriomes and their MetaCyc functions in TB lesions are elucidated, and they are associated with status of MTB excretion among pulmonary TB patients. These results serve as a basis for designing novel strategies for preventing and treating pulmonary TB disease.
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Yi X, Gao J, Wang Z. The human lung microbiome-A hidden link between microbes and human health and diseases. IMETA 2022; 1:e33. [PMID: 38868714 PMCID: PMC10989958 DOI: 10.1002/imt2.33] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/10/2022] [Accepted: 05/25/2022] [Indexed: 06/14/2024]
Abstract
Once thought to be sterile, the human lung is now well recognized to harbor a consortium of microorganisms collectively known as the lung microbiome. The lung microbiome is altered in an array of lung diseases, including chronic lung diseases such as chronic obstructive pulmonary disease, asthma, and bronchiectasis, acute lung diseases caused by pneumonia, sepsis, and COVID-19, and other lung complications such as those related to lung transplantation, lung cancer, and human immunodeficiency virus. The effects of lung microbiome in modulating host immunity and inflammation in the lung and distal organs are being elucidated. However, the precise mechanism by which members of microbiota produce structural ligands that interact with host genes and pathways remains largely uncharacterized. Multiple unique challenges, both technically and biologically, exist in the field of lung microbiome, necessitating the development of tailored experimental and analytical approaches to overcome the bottlenecks. In this review, we first provide an overview of the principles and methodologies in studying the lung microbiome. We next review current knowledge of the roles of lung microbiome in human diseases, highlighting mechanistic insights. We finally discuss critical challenges in the field and share our thoughts on broad topics for future investigation.
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Affiliation(s)
- Xinzhu Yi
- Institute of Ecological Sciences, School of Life SciencesSouth China Normal UniversityGuangzhouGuangdongChina
| | - Jingyuan Gao
- Institute of Ecological Sciences, School of Life SciencesSouth China Normal UniversityGuangzhouGuangdongChina
| | - Zhang Wang
- Institute of Ecological Sciences, School of Life SciencesSouth China Normal UniversityGuangzhouGuangdongChina
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7
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Ghosh S, Nandi S, Basu T. Nano-Antibacterials Using Medicinal Plant Components: An Overview. Front Microbiol 2022; 12:768739. [PMID: 35273578 PMCID: PMC8902597 DOI: 10.3389/fmicb.2021.768739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/13/2021] [Indexed: 11/13/2022] Open
Abstract
Gradual emergence of new bacterial strains, resistant to one or more antibiotics, necessitates development of new antibacterials to prevent us from newly evolved disease-causing, drug-resistant, pathogenic bacteria. Different inorganic and organic compounds have been synthesized as antibacterials, but with the problem of toxicity. Other alternatives of using green products, i.e., the medicinal plant extracts with biocompatible and potent antibacterial characteristics, also had limitation because of their low aqueous solubility and therefore less bioavailability. Use of nanotechnological strategy appears to be a savior, where phytochemicals are nanonized through encapsulation or entrapment within inorganic or organic hydrophilic capping agents. Nanonization of such products not only makes them water soluble but also helps to attain high surface to volume ratio and therefore high reaction area of the nanonized products with better therapeutic potential, over that of the equivalent amount of raw bulk products. Medicinal plant extracts, whose prime components are flavonoids, alkaloids, terpenoids, polyphenolic compounds, and essential oils, are in one hand nanonized (capped and stabilized) by polymers, lipids, or clay materials for developing nanodrugs; on the other hand, high antioxidant activity of those plant extracts is also used to reduce various metal salts to produce metallic nanoparticles. In this review, five medicinal plants, viz., tulsi (Ocimum sanctum), turmeric (Curcuma longa), aloe vera (Aloe vera), oregano (Oregano vulgare), and eucalyptus (Eucalyptus globulus), with promising antibacterial potential and the nanoformulations associated with the plants' crude extracts and their respective major components (eugenol, curcumin, anthraquinone, carvacrol, eucalyptus oil) have been discussed with respect to their antibacterial potency.
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Affiliation(s)
| | | | - Tarakdas Basu
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, India
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