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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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Isaiah S, Loots DT, van Furth AMT, Davoren E, van Elsland S, Solomons R, van der Kuip M, Mason S. Urinary markers of Mycobacterium tuberculosis and dysbiosis in paediatric tuberculous meningitis cases undergoing treatment. Gut Pathog 2024; 16:14. [PMID: 38475868 DOI: 10.1186/s13099-024-00609-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/29/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND The pathogenesis of tuberculous meningitis (TBM) involves infection by Mycobacterium tuberculosis in the meninges and brain. However, recent studies have shown that the immune response and inflammatory processes triggered by TBM can have significant effects on gut microbiota. Disruptions in the gut microbiome have been linked to various systemic consequences, including altered immunity and metabolic dysregulation. Inflammation caused by TBM, antibiotic treatment, and changes in host immunity can all influence the composition of gut microbes. This complex relationship between TBM and the gut microbiome is of great importance in clinical settings. To gain a deeper understanding of the intricate interactions between TBM and the gut microbiome, we report innovative insights into the development of the disease in response to treatment. Ultimately, this could lead to improved outcomes, management strategies and quality of life for individuals affected by TBM. METHOD We used a targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) approach to investigate metabolites associated with gut metabolism in paediatric participants by analysing the urine samples collected from a control group (n = 40), and an experimental group (n = 35) with confirmed TBM, which were subdivided into TBM stage 1 (n = 8), stage 2 (n = 11) and stage 3 (n = 16). FINDINGS Our metabolomics investigation showed that, of the 78 initially selected compounds of microbiome origin, eight unique urinary metabolites were identified: 2-methylbutyrlglycine, 3-hydroxypropionic acid, 3-methylcrotonylglycine, 4-hydroxyhippuric acid, 5-hydroxyindoleacetic acid, 5-hydroxyhexanoic acid, isobutyrylglycine, and phenylacetylglutamine as urinary markers of dysbiosis in TBM. CONCLUSION These results - which are supported by previous urinary studies of tuberculosis - highlight the importance of gut metabolism and of identifying corresponding microbial metabolites as novel points for the foundation of improved management of TBM patients.
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Affiliation(s)
- Simon Isaiah
- Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom, South Africa
| | - Du Toit Loots
- Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom, South Africa
| | - A Marceline Tutu van Furth
- Vrije Universiteit, Pediatric Infectious Diseases and Immunology, Amsterdam University Medical Centers, Emma Children's Hospital, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Elmarie Davoren
- Centre for Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Sabine van Elsland
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Regan Solomons
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Martijn van der Kuip
- Vrije Universiteit, Pediatric Infectious Diseases and Immunology, Amsterdam University Medical Centers, Emma Children's Hospital, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Shayne Mason
- Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom, South Africa.
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Nguyen M, Ahn P, Dawi J, Gargaloyan A, Kiriaki A, Shou T, Wu K, Yazdan K, Venketaraman V. The Interplay between Mycobacterium tuberculosis and Human Microbiome. Clin Pract 2024; 14:198-213. [PMID: 38391403 PMCID: PMC10887847 DOI: 10.3390/clinpract14010017] [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: 12/27/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 02/24/2024] Open
Abstract
Tuberculosis (TB), a respiratory disease caused by Mycobacterium tuberculosis (Mtb), is a significant cause of mortality worldwide. The lung, a breeding ground for Mtb, was once thought to be a sterile environment, but has now been found to host its own profile of microbes. These microbes are critical in the development of the host immune system and can produce metabolites that aid in host defense against various pathogens. Mtb infection as well as antibiotics can shift the microbial profile, causing dysbiosis and dampening the host immune response. Additionally, increasing cases of drug resistant TB have impacted the success rates of the traditional therapies of isoniazid, rifampin, pyrazinamide, and ethambutol. Recent years have produced tremendous research into the human microbiome and its role in contributing to or attenuating disease processes. Potential treatments aimed at altering the gut-lung bacterial axis may offer promising results against drug resistant TB and help mitigate the effects of TB.
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Affiliation(s)
- Michelle Nguyen
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Phillip Ahn
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA
| | - John Dawi
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Areg Gargaloyan
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Anthony Kiriaki
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Tiffany Shou
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Kevin Wu
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Kian Yazdan
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Vishwanath Venketaraman
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA
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Ghoshal A, Verma A, Bhaskar A, Dwivedi VP. The uncharted territory of host-pathogen interaction in tuberculosis. Front Immunol 2024; 15:1339467. [PMID: 38312835 PMCID: PMC10834760 DOI: 10.3389/fimmu.2024.1339467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/03/2024] [Indexed: 02/06/2024] Open
Abstract
Mycobacterium tuberculosis (M.tb) effectively manipulates the host processes to establish the deadly respiratory disease, Tuberculosis (TB). M.tb has developed key mechanisms to disrupt the host cell health to combat immune responses and replicate efficaciously. M.tb antigens such as ESAT-6, 19kDa lipoprotein, Hip1, and Hsp70 destroy the integrity of cell organelles (Mitochondria, Endoplasmic Reticulum, Nucleus, Phagosomes) or delay innate/adaptive cell responses. This is followed by the induction of cellular stress responses in the host. Such cells can either undergo various cell death processes such as apoptosis or necrosis, or mount effective immune responses to clear the invading pathogen. Further, to combat the infection progression, the host secretes extracellular vesicles such as exosomes to initiate immune signaling. The exosomes can contain M.tb as well as host cell-derived peptides that can act as a double-edged sword in the immune signaling event. The host-symbiont microbiota produces various metabolites that are beneficial for maintaining healthy tissue microenvironment. In juxtaposition to the above-mentioned mechanisms, M.tb dysregulates the gut and respiratory microbiome to support its replication and dissemination process. The above-mentioned interconnected host cellular processes of Immunometabolism, Cellular stress, Host Microbiome, and Extracellular vesicles are less explored in the realm of exploration of novel Host-directed therapies for TB. Therefore, this review highlights the intertwined host cellular processes to control M.tb survival and showcases the important factors that can be targeted for designing efficacious therapy.
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Affiliation(s)
| | | | | | - Ved Prakash Dwivedi
- Immunobiology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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Liu Y, Zhang J, Leng G, Hu J, Wang W, Deng G, Ma Y, Sha S. Mycobacterium tuberculosis Rv1987 protein attenuates inflammatory response and consequently alters microbiota in mouse lung. Front Cell Infect Microbiol 2023; 13:1256866. [PMID: 38029253 PMCID: PMC10646435 DOI: 10.3389/fcimb.2023.1256866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Healthy lung microbiota plays an important role in preventing Mycobacterium tuberculosis (Mtb) infections by activating immune cells and stimulating production of T-helper cell type 1 cytokines. The dynamic stability of lung microbiota relies mostly on lung homeostasis. In our previous studies, we found that Mtb virulence factor, Rv1987 protein, can mediate host immune response and enhance mycobacterial survival in host lung. However, the alteration of lung microbiota and the contribution of lung microbiota dysbiosis to mycobacterial evasion in this process are not clear so far. Methods M. smegmatis which does not contain the ortholog of Rv1987 protein was selected as a model strain to study the effects of Rv1987 on host lung microbiota. The lung microbiota, immune state and metabolites of mice infected by M. smegmatis overexpressing Rv1987 protein (MS1987) were detected and analyzed. Results The results showed that Rv1987 inhibited inflammatory response in mouse lung and anaerobic bacteria and Proteobacteria, Bacteroidota, Actinobacteriota and Acidobacteriota bacteria were enriched in the lung tissues correspondingly. The immune alterations and microbiota dysbiosis affected host metabolic profiles, and some of significantly altered bacteria in MS1987-infected mouse lung, such as Delftia acidovorans, Ralstonia pickettii and Escherichia coli, led to anti-inflammatory responses in mouse lung. The secretory metabolites of these altered bacteria also influenced mycobacterial growth and biofilm formation directly. Conclusion All these results suggested that Rv1987 can attenuate inflammatory response and alter microbiota in the lung, which in turn facilitates mycobacterial survival in the host.
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Affiliation(s)
- Yingying Liu
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian, Liaoning, China
| | - Jiaqi Zhang
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian, Liaoning, China
| | - Guangxian Leng
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian, Liaoning, China
| | - Junxing Hu
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian, Liaoning, China
| | - Wenzhen Wang
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian, Liaoning, China
| | - Guoying Deng
- Department of Microbiology, Dalian Medical University, Dalian, Liaoning, China
| | - Yufang Ma
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian, Liaoning, China
- Department of Microbiology, Dalian Medical University, Dalian, Liaoning, China
| | - Shanshan Sha
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian, Liaoning, China
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Qiu Q, Li S, Chen Y, Yan X, Yang S, Qiu S, Peng A, Chen Y. Development, assessment and validation of a novel prediction nomogram model for risk identification of tracheobronchial tuberculosis in patients with pulmonary tuberculosis. BMJ Open Respir Res 2023; 10:e001781. [PMID: 37931979 PMCID: PMC10632898 DOI: 10.1136/bmjresp-2023-001781] [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: 04/21/2023] [Accepted: 10/20/2023] [Indexed: 11/08/2023] Open
Abstract
OBJECTIVE Tracheobronchial tuberculosis (TBTB), a specific subtype of pulmonary tuberculosis (PTB), can lead to bronchial stenosis or bronchial occlusion if not identified early. However, there is currently no available means for predicting the risk of associated TBTB in PTB patients. The objective of this study was to establish a risk prediction nomogram model for estimating the associated TBTB risk in every PTB patient. METHODS A retrospective cohort study was conducted with 2153 PTB patients. Optimised characteristics were selected using least absolute shrinkage and selection operator regression. Multivariate logistic regression was applied to build a predictive nomogram model. Discrimination, calibration and clinical usefulness of the prediction model were assessed using C-statistics, receiver operator characteristic curves, calibration plots and decision analysis. The developed model was validated both internally and externally. RESULTS Among all PTB patients who underwent bronchoscopies (n=2153), 40.36% (n=869) were diagnosed with TBTB. A nomogram model incorporating 11 predictors was developed and displayed good discrimination with a C-statistics of 0.782, a sensitivity of 0.661 and a specificity of 0.762 and good calibration with a calibration-in-the-large of 0.052 and a calibration slope of 0.957. Model's discrimination was favourable in both internal (C-statistics, 0.782) and external (C-statistics, 0.806) validation. External validation showed satisfactory accuracy (sensitivity, 0.690; specificity, 0.804) in independent cohort. Decision curve analysis showed that the model was clinically useful when intervention was decided on at the exacerbation possibility threshold of 2.3%-99.2%. A clinical impact curve demonstrated that our model predicted high-risk estimates and true positives. CONCLUSION We developed a novel and convenient risk prediction nomogram model that enhances the risk assessment of associated TBTB in PTB patients. This nomogram can help identify high-risk PTB patients who may benefit from early bronchoscopy and aggressive treatment to prevent disease progression.
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Affiliation(s)
- Qian Qiu
- Post-Doctoral Research Center, Chongqing Public Health Medical Center, Chongqing, China
| | - Siju Li
- Emergency Department, Chongqing Public Health Medical Center, Chongqing, China
| | - Yong Chen
- Department of Endocrinology, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xiaofeng Yan
- Division of Tuberculosis, Chongqing Public Health Medical Center, Chongqing, China
| | - Song Yang
- Division of Tuberculosis, Chongqing Public Health Medical Center, Chongqing, China
| | - Shi Qiu
- Department of Nutrition, The Seventh Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Anzhou Peng
- Division of Tuberculosis, Chongqing Public Health Medical Center, Chongqing, China
| | - Yaokai Chen
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
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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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Cai X, Luo Y, Zhang Y, Lin Y, Wu B, Cao Z, Hu Z, Wu X, Tan S. Airway microecology in rifampicin-resistant and rifampicin-sensitive pulmonary tuberculosis patients. BMC Microbiol 2022; 22:286. [PMID: 36447140 PMCID: PMC9706898 DOI: 10.1186/s12866-022-02705-9] [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: 05/21/2022] [Accepted: 11/11/2022] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Pulmonary tuberculosis is a chronic infectious disease of the respiratory system. It is still one of the leading causes of death from a single infectious disease, but it has been stuck in the study of a single pathogen. Recent studies have shown that many diseases are associated with disruption of the native microbiota. In this study we investigated the occurrence of tuberculosis and the correlation between drug resistance and respiratory flora. High-throughput 16 S rRNA gene sequencing was used to characterize the respiratory microbiota composition of 30 tuberculosis (TB) affected patients and compared with 30 healthy (H) controls. According to their Gene Xpert results, 30 pulmonary tuberculosis patients were divided into 12 persons in the drug-sensitive group (DS0) and 18 persons in the drug-resistant group (DR0). The microbial flora of the two were compared with the H group. RESULTS The data generated by sequencing showed that Firmicutes, Proteus, Bacteroides, Actinomyces and Fusobacterium were the five main bacterial phyla detected, and they constituted more than 96% of the microbial community. The relative abundances of Fusobacterium, Haemophilus, Porphyromonas, Neisseria, TM7, Spirochetes, SR1, and Tenericutes in the TB group was lower than that of the H group, and Granulicatella was higher than the H group. The PcoA diagrams of the two groups had obvious clustering differences. The Alpha diversity of the TB group was lower than that of the H group, and the Beta diversity was higher than that of the H group (P < 0.05). The relative abundance of Streptococcus in the DS0 group was significantly higher than that in the DR0 group (P < 0.05). CONCLUSION Pulmonary tuberculosis can cause disorders of the respiratory tract microbial flora, in which the relative abundance of Streptococcus was significantly different between rifampicin-sensitive and rifampicin-resistant patients.
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Affiliation(s)
- Xingshan Cai
- grid.413422.20000 0004 1773 0966Department of Medical Laboratory, Guangzhou Chest Hospital, Guangzhou, 510095 P. R. China
| | - Yang Luo
- grid.413422.20000 0004 1773 0966Department of Medical Laboratory, Guangzhou Chest Hospital, Guangzhou, 510095 P. R. China
| | - Yuanliang Zhang
- grid.413422.20000 0004 1773 0966Department of Medical Laboratory, Guangzhou Chest Hospital, Guangzhou, 510095 P. R. China
| | - Yuan Lin
- grid.413422.20000 0004 1773 0966Department of Tuberculosis Internal Medicine, Guangzhou Chest Hospital, Guangzhou, 510095 P. R. China
| | - Bitong Wu
- grid.413422.20000 0004 1773 0966Department of Tuberculosis Internal Medicine, Guangzhou Chest Hospital, Guangzhou, 510095 P. R. China
| | - Zhizhong Cao
- grid.413422.20000 0004 1773 0966Department of Medical Laboratory, Guangzhou Chest Hospital, Guangzhou, 510095 P. R. China
| | - Zuqiong Hu
- grid.413422.20000 0004 1773 0966Department of Medical Laboratory, Guangzhou Chest Hospital, Guangzhou, 510095 P. R. China
| | - Xingyi Wu
- grid.413422.20000 0004 1773 0966Department of Medical Laboratory, Guangzhou Chest Hospital, Guangzhou, 510095 P. R. China
| | - Shouyong Tan
- grid.413422.20000 0004 1773 0966Department of Tuberculosis Internal Medicine, Guangzhou Chest Hospital, Guangzhou, 510095 P. R. China
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9
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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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10
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Xia X, Chen J, Cheng Y, Chen F, Lu H, Liu J, Wang L, Pu F, Wang Y, Liu H, Cao D, Zhang Z, Xia Z, Fan M, Ling Z, Zhao L. Comparative analysis of the lung microbiota in patients with respiratory infections, tuberculosis, and lung cancer: A preliminary study. Front Cell Infect Microbiol 2022; 12:1024867. [PMID: 36389135 PMCID: PMC9663837 DOI: 10.3389/fcimb.2022.1024867] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 10/06/2022] [Indexed: 11/29/2022] Open
Abstract
Recent evidence suggests that lung microbiota can be recognized as one of the ecological determinants of various respiratory diseases. However, alterations in the lung microbiota and associated lung immunity in these respiratory diseases remain unclear. To compare the lung microbiota and lung immune profiles in common respiratory diseases, a total of 78 patients were enrolled in the present study, including 21 patients with primary pulmonary tuberculosis (PTB), eight patients with newly diagnosed lung cancer (LC), and 49 patients with community-acquired pneumonia (CAP). Bronchoalveolar lavage fluid (BALF) was collected for microbiota and cytokine analyses. With MiSeq sequencing system, increased bacterial alpha-diversity and richness were observed in patients with LC than in those with PTB and CAP. Linear discriminant analysis effect size revealed that CAP-associated pulmonary microbiota were significantly different between the PTB and LC groups. More key functionally different genera were found in the PTB and LC groups than in the CAP group. The interaction network revealed stronger positive and negative correlations among these genera in the LC group than in the other two groups. However, increased BALF cytokine profiles were observed in the PTB group than in the other two groups, while BALF cytokines were correlated with key functional bacteria. This comparative study provides evidence for the associations among altered lung microbiota, BALF inflammation, and different respiratory disorders, which provides insight into the possible roles and mechanisms of pulmonary microbiota in the progression of respiratory disorders.
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Affiliation(s)
- Xiaoxue Xia
- Department of Infectious Diseases, Changxing People’s Hospital, Huzhou, China
| | - Jiang Chen
- Department of Neurosurgery, Changxing People’s Hospital, Huzhou, China
| | - Yiwen Cheng
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China,Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Feng Chen
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Huoquan Lu
- Department of Respiratory, Changxing People’s Hospital, Huzhou, China
| | - Jianfeng Liu
- Department of Respiratory, Changxing People’s Hospital, Huzhou, China
| | - Ling Wang
- Department of Laboratory Medicine, Lishui Second People’s Hospital, Lishui, China
| | - Fengxia Pu
- Department of Infectious Diseases, Changxing People’s Hospital, Huzhou, China
| | - Ying Wang
- Department of Infectious Diseases, Changxing People’s Hospital, Huzhou, China
| | - Hua Liu
- Department of Infectious Diseases, Changxing People’s Hospital, Huzhou, China
| | - Daxing Cao
- Department of Infectious Diseases, Changxing People’s Hospital, Huzhou, China
| | - Zhengye Zhang
- Department of Infectious Diseases, Changxing People’s Hospital, Huzhou, China
| | - Zeping Xia
- Department of Infectious Diseases, Changxing People’s Hospital, Huzhou, China
| | - Meili Fan
- Department of Infectious Diseases, Changxing People’s Hospital, Huzhou, China
| | - Zongxin Ling
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China,Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China,*Correspondence: Zongxin Ling, ; Longyou Zhao,
| | - Longyou Zhao
- Department of Laboratory Medicine, Lishui Second People’s Hospital, Lishui, China,*Correspondence: Zongxin Ling, ; Longyou Zhao,
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11
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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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12
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Fu M, Cao LJ, Xia HL, Ji ZM, Hu NN, Leng ZJ, Xie W, Fang Y, Zhang JQ, Xia DQ. The performance of detecting Mycobacterium tuberculosis complex in lung biopsy tissue by metagenomic next-generation sequencing. BMC Pulm Med 2022; 22:288. [PMID: 35902819 PMCID: PMC9330940 DOI: 10.1186/s12890-022-02079-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 07/18/2022] [Indexed: 11/16/2022] Open
Abstract
Background Tuberculosis (TB) is a chronic infectious disease caused by the Mycobacterium tuberculosis complex (MTBC), which is the leading cause of death from infectious diseases. The rapid and accurate microbiological detection of the MTBC is crucial for the diagnosis and treatment of TB. Metagenomic next-generation sequencing (mNGS) has been shown to be a promising and satisfying application of detection in infectious diseases. However, relevant research about the difference in MTBC detection by mNGS between bronchoalveolar lavage fluid (BALF) and lung biopsy tissue specimens remains scarce. Methods We used mNGS to detect pathogens in BALF and lung biopsy tissue obtained by CT-guide percutaneous lung puncture (CPLP) or radial endobronchial ultrasound transbronchial lung biopsy (R-EBUS-TBLB) from 443 hospitalized patients in mainland China suspected of pulmonary infections between May 1, 2019 and October 31, 2021. Aim to evaluate the diagnostic performance of mNGS for detecting MTBC and explore differences in the microbial composition in the 2 specimen types. Results Among the 443 patients, 46 patients finally were diagnosed with TB, of which 36 patients were detected as MTBC positive by mNGS (8.93%). Striking differences were noticed in the higher detection efficiency of lung biopsy tissue compared with BALF (P = 0.004). There were no significant differences between the 2 specimen types in the relative abundance among the 27 pathogens detected by mNGS from the 36 patients. Conclusions This study demonstrates that mNGS could offer an effective detection method of MTBC in BALF or lung tissue biopsy samples in patients suspected of TB infections. When it comes to the situations that BALF samples have limited value to catch pathogens for special lesion sites or the patients have contraindications to bronchoalveolar lavage (BAL) procedures, lung biopsy tissue is an optional specimen for MTBC detection by mNGS. However, whether lung tissue-mNGS is superior to BALF-mNGS in patients with MTBC infection requires further prospective multicenter randomized controlled studies with more cases.
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Affiliation(s)
- Meng Fu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, No. 17 Lujiang Road, Hefei, 230001, Anhui, China.,Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, Anhui, China.,University of Science and Technology of China, Hefei, 230026, Anhui, China
| | - Le-Jie Cao
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, No. 17 Lujiang Road, Hefei, 230001, Anhui, China
| | - Huai-Ling Xia
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, No. 17 Lujiang Road, Hefei, 230001, Anhui, China
| | - Zi-Mei Ji
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, No. 17 Lujiang Road, Hefei, 230001, Anhui, China
| | - Na-Na Hu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, No. 17 Lujiang Road, Hefei, 230001, Anhui, China
| | - Zai-Jun Leng
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, No. 17 Lujiang Road, Hefei, 230001, Anhui, China
| | - Wang Xie
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, No. 17 Lujiang Road, Hefei, 230001, Anhui, China
| | - Yuan Fang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, No. 17 Lujiang Road, Hefei, 230001, Anhui, China
| | - Jun-Qiang Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, No. 17 Lujiang Road, Hefei, 230001, Anhui, China.
| | - Da-Qing Xia
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, No. 17 Lujiang Road, Hefei, 230001, Anhui, China.
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13
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Alterations in the nasopharyngeal microbiota associated with active and latent tuberculosis. Tuberculosis (Edinb) 2022; 136:102231. [DOI: 10.1016/j.tube.2022.102231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/24/2022] [Accepted: 07/13/2022] [Indexed: 11/20/2022]
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14
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The lung microbiome in HIV-positive patients with active pulmonary tuberculosis. Sci Rep 2022; 12:8975. [PMID: 35643931 PMCID: PMC9148312 DOI: 10.1038/s41598-022-12970-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 05/19/2022] [Indexed: 11/08/2022] Open
Abstract
Tuberculosis poses one of the greatest infectious disease threats of our time, especially when associated with human immunodeficiency virus (HIV) infection. Very little data is available on the lung microbiome in pulmonary tuberculosis (PTB) in HIV-positive patients. Three patient cohorts were studied: (i) HIV-positive with no respiratory disease (control cohort), (ii) HIV-positive with pneumonia and (iii) HIV-positive with PTB. Sputum specimens were collected in all patients and where possible a paired BALF was collected. DNA extraction was performed using the QIAamp DNA mini kit (QIAGEN, Germany) and extracted DNA specimens were sent to Inqaba Biotechnical Industries (Pty) Ltd for 16S rRNA gene sequence analysis using the Illumina platform (Illumina Inc, USA). Data analysis was performed using QIMME II and R Studio version 3.6.2 (2020). The lung microbiomes of patients with PTB, in the context of HIV co-infection, were dominated by Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Loss of biodiversity and dysbiosis was found in these patients when compared to the HIV-positive control cohort. Microbial community structure was also distinct from the control cohort, with the dominance of genera such as Achromobacter, Mycobacterium, Acinetobacter, Stenotrophomonas and Pseudomonas in those patients with PTB. This is the first study to describe the lung microbiome in patients with HIV and PTB co-infection and to compare findings with an HIV-positive control cohort. The lung microbiomes of patients with HIV and PTB were distinct from the HIV-positive control cohort without PTB, with an associated loss of microbial diversity.
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15
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Transcriptomic Characterization of Tuberculous Sputum Reveals a Host Warburg Effect and Microbial Cholesterol Catabolism. mBio 2021; 12:e0176621. [PMID: 34872348 PMCID: PMC8649757 DOI: 10.1128/mbio.01766-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The crucial transmission phase of tuberculosis (TB) relies on infectious sputum and yet cannot easily be modeled. We applied one-step RNA sequencing (RNA-Seq) to sputum from infectious TB patients to investigate the host and microbial environments underlying transmission of Mycobacterium tuberculosis. In such TB sputa, compared to non-TB controls, transcriptional upregulation of inflammatory responses, including an interferon-driven proinflammatory response and a metabolic shift toward glycolysis, was observed in the host. Among all bacterial sequences in the sputum, approximately 1.5% originated from M. tuberculosis, and its transcript abundance was lower in HIV-1-coinfected patients. Commensal bacterial abundance was reduced in the presence of M. tuberculosis infection. Direct alignment to the genomes of the predominant microbiota species also reveals differential adaptation, whereby firmicutes (e.g., streptococci) displayed a nonreplicating phenotype with reduced transcription of ribosomal proteins and reduced activities of ATP synthases, while Neisseria and Prevotella spp. were less affected. The transcriptome of sputum M. tuberculosis more closely resembled aerobic replication and shared similarity in carbon metabolism to in vitro and in vivo models with significant upregulation of genes associated with cholesterol metabolism and downstream propionate detoxification pathways. In addition, and counter to previous reports on intracellular M. tuberculosis infection in vitro, M. tuberculosis in sputum was zinc, but not iron, deprived, and the phoP loci were also significantly downregulated, suggesting that the pathogen is likely extracellular in location.
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16
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Comberiati P, Di Cicco M, Paravati F, Pelosi U, Di Gangi A, Arasi S, Barni S, Caimmi D, Mastrorilli C, Licari A, Chiera F. The Role of Gut and Lung Microbiota in Susceptibility to Tuberculosis. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph182212220. [PMID: 34831976 PMCID: PMC8623605 DOI: 10.3390/ijerph182212220] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 12/12/2022]
Abstract
Tuberculosis is one of the most common infectious diseases and infectious causes of death worldwide. Over the last decades, significant research effort has been directed towards defining the understanding of the pathogenesis of tuberculosis to improve diagnosis and therapeutic options. Emerging scientific evidence indicates a possible role of the human microbiota in the pathophysiology of tuberculosis, response to therapy, clinical outcomes, and post-treatment outcomes. Although human studies on the role of the microbiota in tuberculosis are limited, published data in recent years, both from experimental and clinical studies, suggest that a better understanding of the gut-lung microbiome axis and microbiome-immune crosstalk could shed light on the specific pathogenetic mechanisms of Mycobacterium tuberculosis infection and identify new therapeutic targets. In this review, we address the current knowledge of the host immune responses against Mycobacterium tuberculosis infection, the emerging evidence on how gut and lung microbiota can modulate susceptibility to tuberculosis, the available studies on the possible use of probiotic-antibiotic combination therapy for the treatment of tuberculosis, and the knowledge gaps and future research priorities in this field.
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Affiliation(s)
- Pasquale Comberiati
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy; (M.D.C.); (A.D.G.)
- Allergology and Pulmonology Section, Pediatrics Unit, Pisa University Hospital, 56126 Pisa, Italy
- Department of Clinical Immunology and Allergology, I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
- Correspondence:
| | - Maria Di Cicco
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy; (M.D.C.); (A.D.G.)
- Allergology and Pulmonology Section, Pediatrics Unit, Pisa University Hospital, 56126 Pisa, Italy
| | - Francesco Paravati
- Department of Pediatrics, San Giovanni di Dio Hospital, 88900 Crotone, Italy; (F.P.); (F.C.)
| | - Umberto Pelosi
- Pediatric Unit, Santa Barbara Hospital, 09016 Iglesias, Italy;
| | - Alessandro Di Gangi
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy; (M.D.C.); (A.D.G.)
- Allergology and Pulmonology Section, Pediatrics Unit, Pisa University Hospital, 56126 Pisa, Italy
| | - Stefania Arasi
- Area of Translational Research in Pediatric Specialities, Allergy Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy;
| | - Simona Barni
- Allergic Unit, Department of Pediatric, Meyer Children’s Hospital, 50139 Florence, Italy;
| | - Davide Caimmi
- Allergy Unit, CHU de Montpellier, Université de Montpellier, 34295 Montpellier, France;
- IDESP, UMR A11, Université de Montpellier, 34093 Montpellier, France
| | - Carla Mastrorilli
- Department of Pediatrics, University Hospital Consortium Corporation Polyclinic of Bari, Pediatric Hospital Giovanni XXIII, 70124 Bari, Italy;
| | - Amelia Licari
- Pediatric Clinic, Pediatrics Department, Policlinico San Matteo, University of Pavia, 27100 Pavia, Italy;
| | - Fernanda Chiera
- Department of Pediatrics, San Giovanni di Dio Hospital, 88900 Crotone, Italy; (F.P.); (F.C.)
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The role of microbiota in respiratory health and diseases, particularly in tuberculosis. Biomed Pharmacother 2021; 143:112108. [PMID: 34560539 DOI: 10.1016/j.biopha.2021.112108] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/11/2021] [Accepted: 08/23/2021] [Indexed: 12/11/2022] Open
Abstract
Trillions of beneficial and hostile microorganisms live in the human respiratory and gastrointestinal tracts, which act as gatekeepers in maintaining human health, i.e., protecting the body from pathogens by colonizing mucosal surfaces with microbiota-derived antimicrobial metabolites such as short-chain fatty acids or host-derived cytokines and chemokines. It is widely accepted that the microbiome interacts with each other and with the host in a mutually beneficial relationship. Microbiota in the respiratory tract may also play a crucial role in immune homeostasis, maturation, and maintenance of respiratory physiology. Anti-TB antibiotics may cause dysbiosis in the lung and intestinal microbiota, affecting colonization resistance and making the host more susceptible to Mycobacterium tuberculosis (M. tuberculosis) infection. This review discusses recent advances in our understanding of the lung microbiota composition, the lungs and intestinal microbiota related to respiratory health and diseases, microbiome sequencing and analysis, the bloodstream, and the lymphatic system that underpin the gut-lung axis in M. tuberculosis-infected humans and animals. We also discuss the gut-lung axis interactions with the immune system, the role of the microbiome in TB pathogenesis, and the impact of anti-TB antibiotic therapy on the microbiota in animals, humans, and drug-resistant TB individuals.
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18
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Ding L, Liu Y, Wu X, Wu M, Luo X, Ouyang H, Xia J, Liu X, Ding T. Pathogen Metagenomics Reveals Distinct Lung Microbiota Signatures Between Bacteriologically Confirmed and Negative Tuberculosis Patients. Front Cell Infect Microbiol 2021; 11:708827. [PMID: 34589441 PMCID: PMC8475726 DOI: 10.3389/fcimb.2021.708827] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/20/2021] [Indexed: 11/13/2022] Open
Abstract
Understanding the dynamics of lung microbiota in tuberculosis patients, especially those who cannot be confirmed bacteriologically in clinical practice, is imperative for accurate diagnosis and effective treatment. This study aims to characterize the distinct lung microbial features between bacteriologically confirmed and negative tuberculosis patients to understand the influence of microbiota on tuberculosis patients. We collected specimens of bronchoalveolar lavage fluid from 123 tuberculosis patients. Samples were subjected to metagenomic next-generation sequencing to reveal the lung microbial signatures. By combining conventional bacterial detection and metagenomic sequencing, 101/123 (82%) tuberculosis patients were bacteriologically confirmed. In addition to Mycobacterium tuberculosis, Staphylococcus aureus, Kluyveromyces lactis, and Pyricularia pennisetigena were also enriched in the bacteriological confirmation group. In contrast, Haemophilus parainfluenzae was enriched in the bacteriologically negative group. Besides, microbial interaction exhibits a different state between bacteriologically confirmed and negative tuberculosis patients. Mycobacterium tuberculosis was confirmed correlated with clinical characteristics such as albumin and chest cavities. Our study comprehensively demonstrates the correlation between unique features of lung microbial dynamics and the clinical characteristics of tuberculosis patients, suggesting the importance of studying the pulmonary microbiome in tuberculosis disease and providing new insights for future precision diagnosis and treatment.
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Affiliation(s)
- Li Ding
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Yanmin Liu
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xiaorong Wu
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Minhao Wu
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xiaoqing Luo
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Hui Ouyang
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Jinyu Xia
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Xi Liu
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Tao Ding
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
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19
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Ticlla MR, Hella J, Hiza H, Sasamalo M, Mhimbira F, Rutaihwa LK, Droz S, Schaller S, Reither K, Hilty M, Comas I, Beisel C, Schmid CD, Fenner L, Gagneux S. The Sputum Microbiome in Pulmonary Tuberculosis and Its Association With Disease Manifestations: A Cross-Sectional Study. Front Microbiol 2021; 12:633396. [PMID: 34489876 PMCID: PMC8417804 DOI: 10.3389/fmicb.2021.633396] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 07/09/2021] [Indexed: 12/31/2022] Open
Abstract
Each day, approximately 27,000 people become ill with tuberculosis (TB), and 4,000 die from this disease. Pulmonary TB is the main clinical form of TB, and affects the lungs with a considerably heterogeneous manifestation among patients. Immunomodulation by an interplay of host-, environment-, and pathogen-associated factors partially explains such heterogeneity. Microbial communities residing in the host's airways have immunomodulatory effects, but it is unclear if the inter-individual variability of these microbial communities is associated with the heterogeneity of pulmonary TB. Here, we investigated this possibility by characterizing the microbial composition in the sputum of 334 TB patients from Tanzania, and by assessing its association with three aspects of disease manifestations: sputum mycobacterial load, severe clinical findings, and chest x-ray (CXR) findings. Compositional data analysis of taxonomic profiles based on 16S-rRNA gene amplicon sequencing and on whole metagenome shotgun sequencing, and graph-based inference of microbial associations revealed that the airway microbiome of TB patients was shaped by inverse relationships between Streptococcus and two anaerobes: Selenomonas and Fusobacterium. Specifically, the strength of these microbial associations was negatively correlated with Faith's phylogenetic diversity (PD) and with the accumulation of transient genera. Furthermore, low body mass index (BMI) determined the association between abnormal CXRs and community diversity and composition. These associations were mediated by increased abundance of Selenomonas and Fusobacterium, relative to the abundance of Streptococcus, in underweight patients with lung parenchymal infiltrates and in comparison to those with normal chest x-rays. And last, the detection of herpesviruses and anelloviruses in sputum microbial assemblage was linked to co-infection with HIV. Given the anaerobic metabolism of Selenomonas and Fusobacterium, and the hypoxic environment of lung infiltrates, our results suggest that in underweight TB patients, lung tissue remodeling toward anaerobic conditions favors the growth of Selenomonas and Fusobacterium at the expense of Streptococcus. These new insights into the interplay among particular members of the airway microbiome, BMI, and lung parenchymal lesions in TB patients, add a new dimension to the long-known association between low BMI and pulmonary TB. Our results also drive attention to the airways virome in the context of HIV-TB coinfection.
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Affiliation(s)
- Monica R Ticlla
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jerry Hella
- University of Basel, Basel, Switzerland.,Ifakara Health Institute, Dar es Salaam, Tanzania
| | - Hellen Hiza
- Ifakara Health Institute, Dar es Salaam, Tanzania
| | | | | | - Liliana K Rutaihwa
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Ifakara Health Institute, Dar es Salaam, Tanzania
| | - Sara Droz
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Sarah Schaller
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Klaus Reither
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Markus Hilty
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Inaki Comas
- Tuberculosis Genomics Unit, Biomedicine Institute of Valencia, Valencia, Spain
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Christoph D Schmid
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Lukas Fenner
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
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20
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Valdez-Palomares F, Muñoz Torrico M, Palacios-González B, Soberón X, Silva-Herzog E. Altered Microbial Composition of Drug-Sensitive and Drug-Resistant TB Patients Compared with Healthy Volunteers. Microorganisms 2021; 9:1762. [PMID: 34442841 PMCID: PMC8398572 DOI: 10.3390/microorganisms9081762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/07/2021] [Accepted: 08/11/2021] [Indexed: 01/09/2023] Open
Abstract
Mycobacterium tuberculosis infection has three discernible outcomes: active tuberculosis, latent tuberculosis, or clearance of the bacterium. The outcome of the infection depends on the interaction of the bacterium, the immune system, and the microbiome of the host. The current study uses 16S rRNA sequencing to determine the diversity and composition of the respiratory microbiome of drug-resistant and drug-sensitive tuberculosis patients as well as healthy volunteers. Tuberculosis patients exhibited increased microbial diversity and differentially abundant bacteria than healthy volunteers. Compositional differences were also observed when comparing drug-sensitive or -resistant tuberculosis patients. Finally, we defined and assessed the differences in the core sputum microbiota between tuberculosis patients and healthy volunteers. Our observations collectively suggest that in sputum, Mycobacterium tuberculosis infection is related to altered bacterial diversity and compositional differences of core members of the microbiome, with potential implications for the bacterial pulmonary ecosystem's stability and function.
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Affiliation(s)
- Fernanda Valdez-Palomares
- Laboratorio de Vinculación Científica, Facultad de Medicina-UNAM en INMEGEN, Mexico City 14610, Mexico; (F.V.-P.); (B.P.-G.)
| | | | - Berenice Palacios-González
- Laboratorio de Vinculación Científica, Facultad de Medicina-UNAM en INMEGEN, Mexico City 14610, Mexico; (F.V.-P.); (B.P.-G.)
| | - Xavier Soberón
- Departamento de Ingeniería Celular y Biocatálisis, Universidad Nacional Autónoma de México (UNAM), Cuernavaca 62210, Mexico;
| | - Eugenia Silva-Herzog
- Laboratorio de Vinculación Científica, Facultad de Medicina-UNAM en INMEGEN, Mexico City 14610, Mexico; (F.V.-P.); (B.P.-G.)
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21
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Pfeiffer S, Herzmann C, Gaede KI, Kovacevic D, Krauss-Etschmann S, Schloter M. Different responses of the oral, nasal and lung microbiomes to cigarette smoke. Thorax 2021; 77:191-195. [PMID: 34389656 PMCID: PMC8762037 DOI: 10.1136/thoraxjnl-2020-216153] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 05/19/2021] [Indexed: 11/17/2022]
Abstract
To examine the role of smoking on the bacterial community composition of the upper and the lower respiratory tract, a monocentric, controlled prospective study was performed, including healthy smokers, ex-smokers and never-smokers. Smokers were further grouped according to their smoking history. Bacterial diversity was analysed using a molecular barcoding approach based on directly extracted DNA. Our study shows for the first time distinct bacterial response patterns in the upper and lower respiratory tract to cigarette smoking leading to a higher abundance of opportunistic pathogens. The clinical significance of these dysbioses for health needs to be further explored.
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Affiliation(s)
- Stefan Pfeiffer
- Technical University of Munich ZIEL - Institute for Food and Health, Freising, Germany.,Research Unit of Comparative Microbiome Analysis, Helmholtz Center Munich German Research Center for Environmental Health, Neuherberg, Germany
| | - Christian Herzmann
- Center for Clinical Studies, Research Center Borstel - Leibniz Lung Center, Borstel, Germany.,Clinical Trials Unit, German Center for Infection Research (DZIF), Borstel, Germany
| | - Karoline I Gaede
- BioMaterialBank North, Research Center Borstel - Leibniz Lung Center, Borstel, Germany.,German Center for Lung Research (DZL), Airway Research Center North (ARCN), Borstel, Germany
| | - Draginja Kovacevic
- German Center for Lung Research (DZL), Airway Research Center North (ARCN), Borstel, Germany.,Early Life Origins of Chronic Lung Disease, Research Center Borstel - Leibniz Lung Center, Borstel, Germany
| | - Susanne Krauss-Etschmann
- German Center for Lung Research (DZL), Airway Research Center North (ARCN), Borstel, Germany .,Early Life Origins of Chronic Lung Disease, Research Center Borstel - Leibniz Lung Center, Borstel, Germany.,Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Michael Schloter
- Technical University of Munich ZIEL - Institute for Food and Health, Freising, Germany.,Research Unit of Comparative Microbiome Analysis, Helmholtz Center Munich German Research Center for Environmental Health, Neuherberg, Germany
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22
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Nutritional immunity: the impact of metals on lung immune cells and the airway microbiome during chronic respiratory disease. Respir Res 2021; 22:133. [PMID: 33926483 PMCID: PMC8082489 DOI: 10.1186/s12931-021-01722-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/15/2021] [Indexed: 12/15/2022] Open
Abstract
Nutritional immunity is the sequestration of bioavailable trace metals such as iron, zinc and copper by the host to limit pathogenicity by invading microorganisms. As one of the most conserved activities of the innate immune system, limiting the availability of free trace metals by cells of the immune system serves not only to conceal these vital nutrients from invading bacteria but also operates to tightly regulate host immune cell responses and function. In the setting of chronic lung disease, the regulation of trace metals by the host is often disrupted, leading to the altered availability of these nutrients to commensal and invading opportunistic pathogenic microbes. Similarly, alterations in the uptake, secretion, turnover and redox activity of these vitally important metals has significant repercussions for immune cell function including the response to and resolution of infection. This review will discuss the intricate role of nutritional immunity in host immune cells of the lung and how changes in this fundamental process as a result of chronic lung disease may alter the airway microbiome, disease progression and the response to infection.
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23
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Abstract
Tuberculosis (TB) remains an infectious disease of global significance and a
leading cause of death in low- and middle-income countries. Significant effort
has been directed towards understanding Mycobacterium
tuberculosis genomics, virulence, and pathophysiology within the
framework of Koch postulates. More recently, the advent of “-omics” approaches
has broadened our appreciation of how “commensal” microbes have coevolved with
their host and have a central role in shaping health and susceptibility to
disease. It is now clear that there is a diverse repertoire of interactions
between the microbiota and host immune responses that can either sustain or
disrupt homeostasis. In the context of the global efforts to combatting TB, such
findings and knowledge have raised important questions: Does microbiome
composition indicate or determine susceptibility or resistance to
M. tuberculosis infection? Is the
development of active disease or latent infection upon M.
tuberculosis exposure influenced by the microbiome? Does
microbiome composition influence TB therapy outcome and risk of reinfection with
M. tuberculosis? Can the microbiome be
actively managed to reduce risk of M.
tuberculosis infection or recurrence of TB? Here, we
explore these questions with a particular focus on microbiome-immune
interactions that may affect TB susceptibility, manifestation and progression,
the long-term implications of anti-TB therapy, as well as the potential of the
host microbiome as target for clinical manipulation.
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Affiliation(s)
- Giorgia Mori
- The University of Queensland Diamantina Institute, Faculty
of Medicine, The University of Queensland, Brisbane, Australia
| | - Mark Morrison
- The University of Queensland Diamantina Institute, Faculty
of Medicine, The University of Queensland, Brisbane, Australia
| | - Antje Blumenthal
- The University of Queensland Diamantina Institute, Faculty
of Medicine, The University of Queensland, Brisbane, Australia
- * E-mail:
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24
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Sala C, Benjak A, Goletti D, Banu S, Mazza-Stadler J, Jaton K, Busso P, Remm S, Leleu M, Rougemont J, Palmieri F, Cuzzi G, Butera O, Vanini V, Kabir S, Rahman SMM, Nicod L, Cole ST. Multicenter analysis of sputum microbiota in tuberculosis patients. PLoS One 2020; 15:e0240250. [PMID: 33044973 PMCID: PMC7549818 DOI: 10.1371/journal.pone.0240250] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 09/22/2020] [Indexed: 12/11/2022] Open
Abstract
The impact of tuberculosis and of anti-tuberculosis therapy on composition and modification of human lung microbiota has been the object of several investigations. However, no clear outcome has been presented so far and the relationship between M. tuberculosis pulmonary infection and the resident lung microbiota remains vague. In this work we describe the results obtained from a multicenter study of the microbiota of sputum samples from patients with tuberculosis or unrelated lung diseases and healthy donors recruited in Switzerland, Italy and Bangladesh, with the ultimate goal of discovering a microbiota-based biomarker associated with tuberculosis. Bacterial 16S rDNA amplification, high-throughput sequencing and extensive bioinformatic analyses revealed patient-specific flora and high variability in taxon abundance. No common signature could be identified among the individuals enrolled except for minor differences which were not consistent among the different geographical settings. Moreover, anti-tuberculosis therapy did not cause any important variation in microbiota diversity, thus precluding its exploitation as a biomarker for the follow up of tuberculosis patients undergoing treatment.
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Affiliation(s)
- Claudia Sala
- Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Andrej Benjak
- Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Delia Goletti
- National Institute for Infectious Diseases "L. Spallanzani"-IRCCS, Rome, Italy
| | | | | | - Katia Jaton
- Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Philippe Busso
- Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Sille Remm
- Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Marion Leleu
- Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.,BioInformatics Competence Center, UNIL-EPFL, Lausanne, Switzerland
| | - Jacques Rougemont
- Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Department of Theoretical Physics, University of Geneva, Geneva, Switzerland
| | - Fabrizio Palmieri
- National Institute for Infectious Diseases "L. Spallanzani"-IRCCS, Rome, Italy
| | - Gilda Cuzzi
- National Institute for Infectious Diseases "L. Spallanzani"-IRCCS, Rome, Italy
| | - Ornella Butera
- National Institute for Infectious Diseases "L. Spallanzani"-IRCCS, Rome, Italy
| | - Valentina Vanini
- National Institute for Infectious Diseases "L. Spallanzani"-IRCCS, Rome, Italy
| | | | | | - Laurent Nicod
- Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Stewart T Cole
- Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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25
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Liu G, Gu A, E M. [Mechanism and Research Progress of Microbiome in the Development of Lung Cancer]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2020; 23:948-953. [PMID: 32819055 PMCID: PMC7679216 DOI: 10.3779/j.issn.1009-3419.2020.101.38] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
肺癌是我国最常见的、预后较差的恶性肿瘤之一,大多数患者确诊时即为晚期。有研究表明肺癌患者的微生态特征有别于健康人群,呼吸道的微生物可以通过多种机制影响肺癌的发生发展。近年来微生物组学与疾病相关性研究已成为继人类基因组计划又一研究热点,然而目前有关肺癌与呼吸道微生物组特征的研究相对较少,因此,需要更深入地探讨肺癌与微生物菌群间的潜在联系,通过研究呼吸道微生物在肺癌发生发展中的作用机制,以期在为肺癌的临床诊治、预后评估提供更明确的科学依据。本文对目前关于微生物菌群与肺癌相关研究进行综述,并为临床上诊断与治疗肺癌提供新的思路。
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Affiliation(s)
- Guohui Liu
- Department of Radiation Oncology, Harbin Medical University Cancer Hospital, Harbin 150040, China
| | - Anxin Gu
- Department of Radiation Oncology, Harbin Medical University Cancer Hospital, Harbin 150040, China
| | - Mingyan E
- Department of Radiation Oncology, Harbin Medical University Cancer Hospital, Harbin 150040, China
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26
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Persistent Legionnaires' Disease and Associated Antibiotic Treatment Engender a Highly Disturbed Pulmonary Microbiome Enriched in Opportunistic Microorganisms. mBio 2020; 11:mBio.00889-20. [PMID: 32430469 PMCID: PMC7240155 DOI: 10.1128/mbio.00889-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Despite the importance of pneumonia to public health, little is known about the composition of the lung microbiome during infectious diseases, such as pneumonia, and how it evolves during antibiotic therapy. To study the possible relation of the pulmonary microbiome to the severity and outcome of this respiratory disease, we analyzed the dynamics of the pathogen and the human lung microbiome during persistent infections caused by the bacterium Legionella pneumophila and their evolution during antimicrobial treatment. We collected 10 bronchoalveolar lavage fluid samples from three patients during long-term hospitalization due to pneumonia and performed a unique longitudinal study of the interkingdom microbiome, analyzing the samples for presence of bacteria, archaea, fungi, and protozoa by high-throughput Illumina sequencing of marker genes. The lung microbiome of the patients was characterized by a strong predominance of the pathogen, a low diversity of the bacterial fraction, and an increased presence of opportunistic microorganisms. The fungal fraction was more stable than the bacterial fraction. During long-term treatment, no genomic changes or antibiotic resistance-associated mutations that could explain the persistent infection occurred, according to whole-genome sequencing analyses of the pathogen. After antibiotic treatment, the microbiome did not recover rapidly but was mainly constituted of antibiotic-resistant species and enriched in bacteria, archaea, fungi, or protozoa associated with pathogenicity. The lung microbiome seems to contribute to nonresolving Legionella pneumonia, as it is strongly disturbed during infection and enriched in opportunistic and/or antibiotic-resistant bacteria and microorganisms, including fungi, archaea, and protozoa that are often associated with infections.IMPORTANCE The composition and dynamics of the lung microbiome during pneumonia are not known, although the lung microbiome might influence the severity and outcome of this infectious disease, similar to what was shown for the microbiome at other body sites. Here we report the findings of a comprehensive analysis of the lung microbiome composition of three patients with long-term pneumonia due to L. pneumophila and its evolution during antibiotic treatment. This work adds to our understanding of how the microbiome changes during disease and antibiotic treatment and points to microorganisms and their interactions that might be beneficial. In addition to bacteria and fungi, our analyses included archaea and eukaryotes (protozoa), showing that both are present in the pulmonary microbiota and that they might also play a role in the response to the microbiome disturbance.
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27
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Patients infected with Mycobacterium africanum versus Mycobacterium tuberculosis possess distinct intestinal microbiota. PLoS Negl Trop Dis 2020; 14:e0008230. [PMID: 32401750 PMCID: PMC7219701 DOI: 10.1371/journal.pntd.0008230] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 03/17/2020] [Indexed: 12/15/2022] Open
Abstract
Background Mycobacterium tuberculosis complex (MTBC), the causative agent of tuberculosis (TB), is composed of eight subspecies. TB in West Africa, in contrast to other geographical regions, is caused by Mycobacterium africanum (MAF) in addition to M. tuberculosis (MTB), with both infections presenting similar symptoms. Nevertheless, MAF is considered to be hypovirulent in comparison with MTB and less likely to progress to active disease. In this study, we asked whether MAF and MTB infected patients possess distinct intestinal microbiomes and characterized how these microbiota communities are affected by anti-tuberculosis therapy (ATT). Additionally, we assessed if the changes in microbiota composition following infection correlate with pathogen induced alterations in host blood-gene expression. Methods A longitudinal, clinical study of MAF infected, MTB infected patients assessed at diagnosis and two months after start of ATT, and healthy, endemic controls was conducted to compare compositions of the fecal microbiome as determined by 16S rRNA sequencing. A blood transcriptome analysis was also performed on a subset of subjects in each group by microarray and the results cross-compared with the same individual’s microbiota composition. Findings MAF participants have distinct microbiomes compared with MTB patients, displaying decreased diversity and increases in Enterobacteriaceae with respect to healthy participants not observed in the latter patient group. Interestingly, this observed elevation in Enterobacteriaceae positively correlated with enhanced inflammatory gene expression in peripheral blood and was reversed after initiation of ATT. Interpretation Our findings indicate that MAF and MTB have distinct associations with the gut microbiome that may be reflective of the differential susceptibility of West Africans to these two co-endemic infections either as biomarkers or as a contributing determinant. Mycobacterium africanum (MAF) is a hypovirulent mycobacterium species that is co-endemic with Mycobacterium tuberculosis (MTB) in West Africa and is selectively responsible for up to half the tuberculosis cases in this region. Why some individuals become infected with MAF versus MTB is unclear but has been suggested to be determined by differential host immune competency. Since the microbiome has now been implicated in numerous studies to generally influence host resistance to disease, we investigated whether differences in the intestinal microbiota might associate with MAF as compared with MTB infection. This report presents the first analysis of the intestinal microbiome of MAF-infected subjects as well as a comparison with the microbiota of co-endemic MTB patients and reveals that the microbiota of individuals with MAF infection display both decreased diversity and distinct differences in microbial taxa when compared to both MTB-infected and healthy controls. Furthermore, our data reveal for the first time in TB patients a correlation between the abundance of certain taxa and host blood transcriptional changes related to immune function. Our study also establishes that antibiotic treatment induces parallel changes in the gut microbiota of MAF- and MTB-infected patients. Although not directly addressed in the present study, the findings presented here raise the possibility that the microbiota or other host physiologic or immune factors closely associated with it may be a factor underlying the differential susceptibility of West Africans to MAF infection. In addition, the data identify certain commensal taxa that could be tested in future studies as specific determinants of this association.
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28
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Hu Y, Kang Y, Liu X, Cheng M, Dong J, Sun L, Zhu Y, Ren X, Yang Q, Chen X, Jin Q, Yang F. Distinct lung microbial community states in patients with pulmonary tuberculosis. SCIENCE CHINA-LIFE SCIENCES 2020; 63:1522-1533. [PMID: 32303963 DOI: 10.1007/s11427-019-1614-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/29/2019] [Indexed: 12/18/2022]
Abstract
An improved understanding of the lung microbiome may lead to better strategies to diagnose, treat, and prevent pulmonary tuberculosis (PTB). However, the characteristics of the lung microbiomes of patients with TB remain largely undefined. In this study, 163 bronchoalveolar lavage (BAL) samples were collected from 163 sputum-negative suspected PTB patients. Furthermore, 12 paired BAL samples were obtained from 12 Mycobacterium tuberculosis-positive (MTB+) patients before and after negative conversion following a two-month anti-TB treatment. The V3-V4 region of the 16S ribosomal RNA (rRNA) gene was used to characterize the microbial composition of the lungs. The results showed that the prevalence of MTB in the BAL samples was 42.9% (70/163) among the sputum-negative patients. The α-diversity of lung microbiota was significantly less diverse in MTB+ patients compared with Mycobacterium tuberculosis-negative (MTB-) patients. There was a significant difference in β-diversity between MTB+ and MTB- patients. MTB+ patients were enriched with Anoxybacillus, while MTB- patients were enriched with Prevotella, Alloprevotella, Veillonella, and Gemella. There was no significant difference between the Anoxybacillus detection rates of MTB+ and MTB- patients. The paired comparison between the BAL samples from MTB+ patients and their negative conversion showed that BAL negative-conversion microbiota had a higher α-diversity. In conclusion, distinct features of airway microbiota could be identified between samples from patients with and without MTB. Our results imply links between lung microbiota and different clinical groups of active PTB.
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Affiliation(s)
- Yongfeng Hu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Ying Kang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Xi Liu
- Department of Infectious Diseases, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China
| | - Min Cheng
- China Institute of Veterinary Drug Control, Beijing, 100081, China
| | - Jie Dong
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Lilian Sun
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Yafang Zhu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Xianwen Ren
- Biodynamic Optical Imaging Center, Beijing Advanced Innovation Center for Genomics, and School of Life Sciences, Peking University, Beijing, 100871, China
| | - Qianting Yang
- National Clinical Research Center for Infectious Diseases, Guangdong Key Lab for Diagnosis & Treatment of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518112, China
| | - Xinchun Chen
- Department of Pathogen Biology, Shenzhen University School of Medicine, Shenzhen, 518060, China.
| | - Qi Jin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China.
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University, Hangzhou, 310003, China.
| | - Fan Yang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China.
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29
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Xu X, Wu L, Sheng Y, Liu J, Xu Z, Kong W, Tang L, Chen Z. Airway microbiota in children with bronchial mucus plugs caused by Mycoplasma pneumoniae pneumonia. Respir Med 2020; 170:105902. [PMID: 32843185 DOI: 10.1016/j.rmed.2020.105902] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 01/29/2020] [Accepted: 02/14/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND There is increasing evidence for a role of lung microbiota in the pathogenesis of Mycoplasma pneumoniae pneumonia (MPP). However, the alterations of lung microbiota in MPP with bronchial mucus plugs and its role in disease pathogenesis remain poorly understood. METHODS In this prospective observational study, we performed a longitudinal 16S rRNA-based microbiome survey on bronchoalveolar lavage (BAL) samples collected from 31 MPP with bronchial mucus plugs and 52 MPP without mucus plugs. RESULTS Our study showed a clear difference in airway microbiota between MPP children with and without bronchial mucus plugs. The MPP children with mucus plugs had lower abundances of Sphingomonas and Elizabethkingia, and a high abundance of Mycoplasma compared with MPP children without mucus plugs, subsequently contributing to increased ratios of Mycoplasma to Sphingomonas and Mycoplasma to Elizabethkingia. Children's age, fever time and serum cytokine levels were associated with airway microbiota alteration. Furthermore, significant correlations between bacterial genus abundances were found in MPP children with mucus plugs. CONCLUSIONS Our results suggest an impact of airway microbiota on the clinical course of MPP in children, deserving further investigations.
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Affiliation(s)
- Xuefeng Xu
- Department of Respiratory Medicine, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, PR China; Department of Rheumatology Immunology & Allergy, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, PR China
| | - Lei Wu
- Department of Respiratory Medicine, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, PR China
| | - Yuanjian Sheng
- Department of Respiratory Medicine, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, PR China
| | - Jinling Liu
- Department of Respiratory Medicine, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, PR China
| | - Zhufei Xu
- Department of Respiratory Medicine, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, PR China
| | - Weixing Kong
- Department of Respiratory Medicine, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, PR China
| | - Lanfang Tang
- Department of Respiratory Medicine, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, PR China
| | - Zhimin Chen
- Department of Respiratory Medicine, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, PR China.
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30
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Naidoo CC, Nyawo GR, Wu BG, Walzl G, Warren RM, Segal LN, Theron G. The microbiome and tuberculosis: state of the art, potential applications, and defining the clinical research agenda. THE LANCET. RESPIRATORY MEDICINE 2019; 7:892-906. [PMID: 30910543 DOI: 10.1016/s2213-2600(18)30501-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 11/15/2018] [Accepted: 11/15/2018] [Indexed: 01/26/2023]
Abstract
The diverse microbial communities within our bodies produce metabolites that modulate host immune responses. Even the microbiome at distal sites has an important function in respiratory health. However, the clinical importance of the microbiome in tuberculosis, the biggest infectious cause of death worldwide, is only starting to be understood. Here, we critically review research on the microbiome's association with pulmonary tuberculosis. The research indicates five main points: (1) susceptibility to infection and progression to active tuberculosis is altered by gut Helicobacter co-infection, (2) aerosol Mycobacterium tuberculosis infection changes the gut microbiota, (3) oral anaerobes in the lung make metabolites that decrease pulmonary immunity and predict progression, (4) the increased susceptibility to reinfection of patients who have previously been treated for tuberculosis is likely due to the depletion of T-cell epitopes on commensal gut non-tuberculosis mycobacteria, and (5) the prolonged antibiotic treatment required for cure of tuberculosis has long-term detrimental effects on the microbiome. We highlight knowledge gaps, considerations for addressing these knowledge gaps, and describe potential targets for modifying the microbiome to control tuberculosis.
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Affiliation(s)
- Charissa C Naidoo
- Department of Science and Technology-National Research Foundation (DST-NRF) Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; African Microbiome Institute, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Georgina R Nyawo
- Department of Science and Technology-National Research Foundation (DST-NRF) Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; African Microbiome Institute, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Benjamin G Wu
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Gerhard Walzl
- Department of Science and Technology-National Research Foundation (DST-NRF) Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Robin M Warren
- Department of Science and Technology-National Research Foundation (DST-NRF) Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Leopoldo N Segal
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Grant Theron
- Department of Science and Technology-National Research Foundation (DST-NRF) Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; African Microbiome Institute, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
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31
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Balcells ME, Yokobori N, Hong BY, Corbett J, Cervantes J. The lung microbiome, vitamin D, and the tuberculous granuloma: A balance triangle. Microb Pathog 2019; 131:158-163. [PMID: 30953746 DOI: 10.1016/j.micpath.2019.03.041] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 03/28/2019] [Accepted: 03/29/2019] [Indexed: 12/16/2022]
Abstract
Mycobacterium tuberculosis (Mtb) has the extraordinary ability to persist for decades within granulomas in the human host. These histopathological structures involved in both protection and pathogenesis, are subject to various influences from the host systemically and through micro-niche environments. Despite the fact that vitamin D (VD) has a key role in macrophage activation and mycobacterial clearance in the early stages of Mtb infection, the overall role of VD in granuloma maintenance or functionality has been scarcely studied. VD deficiency has long time been known to influence on gut microbiota composition, and recent studies have shown that it can also impact on respiratory microbiome. The human microbiota plays an important role in pathogen colonization resistance, and it has been proposed to play a potential role in TB pathogenesis. In this article, we have reviewed current knowledge on the interaction between VD, the lung microbiome and TB, and propose mechanisms by which the tuberculous granuloma's outcome could be modulated by these two factors. The determinants of the final fate of lung granulomas are still unclear, and deciphering the underlying drivers of Mtb infection outcome within those structures is of critical importance.
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Affiliation(s)
- María Elvira Balcells
- Department of Infectious Diseases, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Noemí Yokobori
- Instituto de Medicina Experimental, CONICET-ANM, Buenos Aires, Argentina
| | - Bo-Young Hong
- Jackson Laboratory for Genomic Medicine, Farmington, USA
| | - John Corbett
- Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, USA
| | - Jorge Cervantes
- Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, USA.
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32
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Zhang M, Chen S, Gnegy M, Ye C, Lin W, Lin H, Yu X. Environmental strains potentially contribute to the proliferation and maintenance of antibiotic resistance in drinking water: A case study of Cupriavidus metallidurans. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 643:819-826. [PMID: 29960223 DOI: 10.1016/j.scitotenv.2018.06.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/02/2018] [Accepted: 06/02/2018] [Indexed: 06/08/2023]
Abstract
Fitness costs of antibiotic resistance detrimentally affect the fate of resistance carriers. Intriguingly, numerous antibiotic resistant bacteria (ARB) have been detected despite the low concentration of antibiotics in drinking water. To reveal the causes of this discrepancy, we investigated the fitness cost of antimicrobial resistance in strain Cupriavidus metallidurans CR2 which was isolated from a drinking water filter. Pure culture and 1:1 competitive experiments were established at different nutrient levels. The growth rates of strain C. metallidurans CR2 significantly decreased when pure cultured under poor nutrient conditions, however, the multi-resistance and the resistance megaplasmids were well maintained. Competitiveness costs were observed in C. metallidurans when separately co-cultured with environmentally-isolated Flectobacillus BS1 and Pseudomonas sp. S3, while C. metallidurans was outnumbered by the rivals with a decrease of 1-2 logs. But the majority of C. metallidurans retained the plasmids under oligotrophic conditions even after 144 h (1.99 and 0.199 mg C/L). Additionally, C. metallidurans CR2 has a higher tolerance to chlorine and chloramine, which potentially could become prevalent in the subsequent distribution systems other than drinking water treatment plant. As a potential pathogen, the prevalence of Cupriavidus metallidurans in drinking water would also pose certain threats to human health.
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Affiliation(s)
- Menglu Zhang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China; University of Chinese Academy of Science, Beijing 100049, People's Republic of China
| | - Sheng Chen
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China; University of Chinese Academy of Science, Beijing 100049, People's Republic of China
| | - Mariah Gnegy
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24060, USA
| | - Chengsong Ye
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China
| | - Wenfang Lin
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China
| | - Huirong Lin
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China
| | - Xin Yu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China.
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Tarashi S, Ahmadi Badi S, Moshiri A, Nasehi M, Fateh A, Vaziri F, Siadat SD. The human microbiota in pulmonary tuberculosis: Not so innocent bystanders. Tuberculosis (Edinb) 2018; 113:215-221. [PMID: 30514505 DOI: 10.1016/j.tube.2018.10.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 09/22/2018] [Accepted: 10/23/2018] [Indexed: 12/12/2022]
Abstract
Mycobacterium tuberculosis (Mtb) infection is a worldwide health concern, which needs robust and efficient control strategies, and the evaluation of human microbiota can be very important in this regard. Dysbiosis of normal microbiota is an important issue in the pathogenesis of Mtb. However, only few studies demonstrated the interaction between Mtb infection and microbiota. The current study aimed at reviewing literature on gut and lung microbiota in Mtb infection. Eleven articles regarding gut and lung microbiota composition in individuals with Mtb infection were selected, and then the importance of gut-lung axis in Mtb infection was evaluated. Also the relationship between microbiota composition and Mtb infection were discussed in terms of treatment, epigenetic field, and biomarkers.
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Affiliation(s)
- Samira Tarashi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Sara Ahmadi Badi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Arfa Moshiri
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran; Gastroenterology and Liver Disease Research Center, Research Institute for Gastroenterology and Liver Disease, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Experimental Therapy Unit, Laboratory of Oncology, G.Gaslini Children's Hospital, Genoa, Italy
| | - Mahshid Nasehi
- Center for Communicable Diseases Control, Ministry of Health and Medical Education, Tehran, Iran; Department of Epidemiology and Biostatistics, School of Public Health, Iran University of Medical Sciences, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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34
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Cadena AM, Ma Y, Ding T, Bryant M, Maiello P, Geber A, Lin PL, Flynn JL, Ghedin E. Profiling the airway in the macaque model of tuberculosis reveals variable microbial dysbiosis and alteration of community structure. MICROBIOME 2018; 6:180. [PMID: 30301469 PMCID: PMC6178261 DOI: 10.1186/s40168-018-0560-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 09/20/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND The specific interactions of Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), and the lung microbiota in infection are entirely unexplored. Studies in cancer and other infectious diseases suggest that there are important exchanges occurring between host and microbiota that influence the immunological landscape. This can result in alterations in immune regulation and inflammation both locally and systemically. To assess whether Mtb infection modifies the lung microbiome, and identify changes in microbial abundance and diversity as a function of pulmonary inflammation, we compared infected and uninfected lung lobe washes collected serially from 26 macaques by bronchoalveolar lavage over the course of infection. RESULTS We found that Mtb induced an initial increase in lung microbial diversity at 1 month post infection that normalized by 5 months of infection across all macaques. Several core genera showed global shifts from baseline and throughout infection. Moreover, we identified several specific taxa normally associated with the oral microbiome that increased in relative abundance in the lung following Mtb infection, including SR1, Aggregatibacter, Leptotrichia, Prevotella, and Campylobacter. On an individual macaque level, we found significant heterogeneity in both the magnitude and duration of change within the lung microbial community that was unrelated to lung inflammation and lobe involvement as seen by positron emission tomography/computed tomography (PET/CT) imaging. By comparing microbial interaction networks pre- and post-infection using the predictive algorithm SPIEC-EASI, we observe that extra connections are gained by Actinomycetales, the order containing Mtb, in spite of an overall reduction in the number of interactions of the whole community post-infection, implicating Mtb-driven ecological reorganization within the lung. CONCLUSIONS This study is the first to probe the dynamic interplay between Mtb and host microbiota longitudinally and in the macaque lung. Our findings suggest that Mtb can alter the microbial landscape of infected lung lobes and that these interactions induce dysbiosis that can disrupt oral-airway boundaries, shift overall lung diversity, and modulate specific microbial relationships. We also provide evidence that this effect is heterogeneous across different macaques. Overall, however, the changes to the airway microbiota after Mtb infection were surprisingly modest, despite a range of Mtb-induced pulmonary inflammation in this cohort of macaques.
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Affiliation(s)
- Anthony M Cadena
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Present address: Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Yixuan Ma
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, USA
| | - Tao Ding
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, USA
| | - MacKenzie Bryant
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Present address: Department of Pediatrics, University of California, San Diego School of Medicine, La Jolla, California, USA
| | - Pauline Maiello
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Adam Geber
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, USA
| | - Philana Ling Lin
- Department of Pediatrics, Children's Hospital of Pittsburgh of University of Pittsburgh Medical Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - JoAnne L Flynn
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Elodie Ghedin
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, USA.
- College of Global Public Health, New York University, New York, NY, USA.
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35
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Abstract
Tuberculosis (TB) is an ancient infectious disease of humans that has been extensively studied both clinically and experimentally. Although susceptibility to Mycobacterium tuberculosis infection is clearly influenced by factors such as nutrition, immune status, and both mycobacterial and host genetics, the variable pathogenesis of TB in infected individuals remains poorly understood. Tuberculosis (TB) is an ancient infectious disease of humans that has been extensively studied both clinically and experimentally. Although susceptibility to Mycobacterium tuberculosis infection is clearly influenced by factors such as nutrition, immune status, and both mycobacterial and host genetics, the variable pathogenesis of TB in infected individuals remains poorly understood. During the past two decades, it has become clear that the microbiota—the trillion organisms that reside at mucosal surfaces within and on the body—can exert a major influence on disease outcome through its effects on host innate and adaptive immune function and metabolism. This new recognition of the potentially pleiotropic participation of the microbiome in immune responses has raised the possibility that the microbiota may influence M. tuberculosis infection and/or disease. Similarly, treatment of TB may alter the healthy steady-state composition and function of the microbiome, possibly affecting treatment outcome in addition to other host physiological parameters. Herein, we review emerging evidence for how the microbiota may influence the transition points in the life cycle of TB infection, including (i) resistance to initial infection, (ii) initial infection to latent tuberculosis (LTBI), (iii) LTBI to reactivated disease, and (iv) treatment to cure. A major goal of this review is to frame questions to guide future scientific and clinical studies in this largely unexplored but increasingly important area of TB research.
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36
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Lange C, Alghamdi WA, Al-Shaer MH, Brighenti S, Diacon AH, DiNardo AR, Grobbel HP, Gröschel MI, von Groote-Bidlingmaier F, Hauptmann M, Heyckendorf J, Köhler N, Kohl TA, Merker M, Niemann S, Peloquin CA, Reimann M, Schaible UE, Schaub D, Schleusener V, Thye T, Schön T. Perspectives for personalized therapy for patients with multidrug-resistant tuberculosis. J Intern Med 2018; 284:163-188. [PMID: 29806961 DOI: 10.1111/joim.12780] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
According to the World Health Organization (WHO), tuberculosis is the leading cause of death attributed to a single microbial pathogen worldwide. In addition to the large number of patients affected by tuberculosis, the emergence of Mycobacterium tuberculosis drug-resistance is complicating tuberculosis control in many high-burden countries. During the past 5 years, the global number of patients identified with multidrug-resistant tuberculosis (MDR-TB), defined as bacillary resistance at least against rifampicin and isoniazid, the two most active drugs in a treatment regimen, has increased by more than 20% annually. Today we experience a historical peak in the number of patients affected by MDR-TB. The management of MDR-TB is characterized by delayed diagnosis, uncertainty of the extent of bacillary drug-resistance, imprecise standardized drug regimens and dosages, very long duration of therapy and high frequency of adverse events which all translate into a poor prognosis for many of the affected patients. Major scientific and technological advances in recent years provide new perspectives through treatment regimens tailor-made to individual needs. Where available, such personalized treatment has major implications on the treatment outcomes of patients with MDR-TB. The challenge now is to bring these adances to those patients that need them most.
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Affiliation(s)
- C Lange
- Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- Tuberculosis Unit, German Center for Infection Research (DZIF), Borstel, Germany
- International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany
- Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - W A Alghamdi
- Department of Pharmacotherapy and Translational Research, Infectious Disease Pharmacokinetics Laboratory, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - M H Al-Shaer
- Department of Pharmacotherapy and Translational Research, Infectious Disease Pharmacokinetics Laboratory, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - S Brighenti
- Department of Medicine, Center for Infectious Medicine (CIM), Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - A H Diacon
- Task Applied Science, Bellville, South Africa
- Division of Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - A R DiNardo
- Section of Global and Immigrant Health, Baylor College of Medicine, Houston, TX, USA
| | - H P Grobbel
- Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- Tuberculosis Unit, German Center for Infection Research (DZIF), Borstel, Germany
- International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany
| | - M I Gröschel
- Department of Pumonary Diseases & Tuberculosis, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Molecular and Experimental Mycobacteriology, National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | | | - M Hauptmann
- Tuberculosis Unit, German Center for Infection Research (DZIF), Borstel, Germany
- Cellular Microbiology, Research Center Borstel, Borstel, Germany
| | - J Heyckendorf
- Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- Tuberculosis Unit, German Center for Infection Research (DZIF), Borstel, Germany
- International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany
| | - N Köhler
- Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- Tuberculosis Unit, German Center for Infection Research (DZIF), Borstel, Germany
- International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany
| | - T A Kohl
- Molecular and Experimental Mycobacteriology, National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - M Merker
- Molecular and Experimental Mycobacteriology, National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - S Niemann
- Tuberculosis Unit, German Center for Infection Research (DZIF), Borstel, Germany
- Molecular and Experimental Mycobacteriology, National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - C A Peloquin
- Department of Pharmacotherapy and Translational Research, Infectious Disease Pharmacokinetics Laboratory, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - M Reimann
- Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- Tuberculosis Unit, German Center for Infection Research (DZIF), Borstel, Germany
- International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany
| | - U E Schaible
- Tuberculosis Unit, German Center for Infection Research (DZIF), Borstel, Germany
- Cellular Microbiology, Research Center Borstel, Borstel, Germany
- Biochemical Microbiology & Immunochemistry, University of Lübeck, Lübeck, Germany
- LRA INFECTIONS'21, Borstel, Germany
| | - D Schaub
- Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- Tuberculosis Unit, German Center for Infection Research (DZIF), Borstel, Germany
- International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany
| | - V Schleusener
- Molecular and Experimental Mycobacteriology, National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - T Thye
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - T Schön
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
- Department of Clinical Microbiology and Infectious Diseases, Kalmar County Hospital, Linköping University, Linköping, Sweden
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Abstract
Protective immunity in tuberculosis (TB) is subject of debate in the TB research community, as this is key to fully understand TB pathogenesis and to develop new promising tools for TB diagnosis and prognosis as well as a more efficient TB vaccine. IFN-γ producing CD4+ T cells are key in TB control, but may not be sufficient to provide protection. Additional subsets have been identified that contribute to protection such as multifunctional and cytolytic T-cell subsets, including classical and nonclassical T cells as well as novel innate immune cell subsets resulting from trained immunity. However, to define protective immune responses against TB, the complexity of balancing TB immunity also has to be considered. In this review, insights into effector cell immunity and how this is modulated by regulatory cells, associated comorbidities and the host microbiome, is discussed. We systematically map how different suppressive immune cell subsets may affect effector cell responses at the local site of infection. We also dissect how common comorbidities such as HIV, helminths and diabetes may bias protective TB immunity towards pathogenic and regulatory responses. Finally, also the composition and diversity of the microbiome in the lung and gut could affect host TB immunity. Understanding these various aspects of the immunological balance in the human host is fundamental to prevent TB infection and disease.
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Affiliation(s)
- Susanna Brighenti
- Karolinska Institutet, Department of Medicine, Center for Infectious Medicine (CIM), Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Simone A. Joosten
- Leiden University Medical Center, Department of Infectious Diseases, Leiden, The Netherlands
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Guilloux CA, Lamoureux C, Héry-Arnaud G. [Anaerobic bacteria, the unknown members of the lung microbiota]. Med Sci (Paris) 2018; 34:253-260. [PMID: 29547112 DOI: 10.1051/medsci/20183403014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Lungs were considered as sterile for a long time. However, it is now evident that the lungs of healthy people are colonized by microorganisms. Among the bacteria present in the pulmonary microbiota, a significant proportion is anaerobic (strict or facultative). Even though interest in the pulmonary microbiota is increasing, few studies have focused on these unknowns that represent the lung resident anaerobic bacteria. This review describes the biodiversity of anaerobes in physiological conditions, and in different chronic respiratory diseases (cystic fibrosis, COPD, asthma). It also explains anaerobes' roles in the barrier flora effect, in inflammation, or as potential biomarkers in disease progression.
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Affiliation(s)
- Charles-Antoine Guilloux
- UMR1078, Génétique, Génomique Fonctionnelle et Biotechnologies, Inserm, Université de Brest, EFS, IBSAM, 22, avenue Camille Desmoulins, 29238 Brest, France
| | - Claudie Lamoureux
- UMR1078, Génétique, Génomique Fonctionnelle et Biotechnologies, Inserm, Université de Brest, EFS, IBSAM, 22, avenue Camille Desmoulins, 29238 Brest, France - Unité de Bactériologie, Pôle de Biologie-Pathologie, Hôpital La Cavale Blanche, CHRU de Brest, 29238 Brest, France
| | - Geneviève Héry-Arnaud
- UMR1078, Génétique, Génomique Fonctionnelle et Biotechnologies, Inserm, Université de Brest, EFS, IBSAM, 22, avenue Camille Desmoulins, 29238 Brest, France - Unité de Bactériologie, Pôle de Biologie-Pathologie, Hôpital La Cavale Blanche, CHRU de Brest, 29238 Brest, France
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39
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Hong BY, Paulson JN, Stine OC, Weinstock GM, Cervantes JL. Meta-analysis of the lung microbiota in pulmonary tuberculosis. Tuberculosis (Edinb) 2018; 109:102-108. [DOI: 10.1016/j.tube.2018.02.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 01/30/2018] [Accepted: 02/20/2018] [Indexed: 02/06/2023]
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40
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The lung microbiome. Emerg Top Life Sci 2017; 1:313-324. [PMID: 33525774 DOI: 10.1042/etls20170043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 08/31/2017] [Accepted: 09/29/2017] [Indexed: 12/17/2022]
Abstract
Historically, our understanding of lung microbiology has relied on insight gained through culture-based diagnostic approaches that employ selective culture conditions to isolate specific pathogens. The relatively recent development of culture-independent microbiota-profiling techniques, particularly 16S rRNA (ribosomal ribonucleic acid) gene amplicon sequencing, has enabled more comprehensive characterisation of the microbial content of respiratory samples. The widespread application of such techniques has led to a fundamental shift in our view of respiratory microbiology. Rather than a sterile lung environment that can become colonised by microbes during infection, it appears that a more nuanced balance exists between what we consider respiratory health and disease, mediated by mechanisms that influence the clearance of microbes from the lungs. Where airway defences are compromised, the ongoing transient exposure of the lower airways to microbes can lead to the establishment of complex microbial communities within the lung. Importantly, the characteristics of these communities, and the manner in which they influence lung pathogenesis, can be very different from those of their constituent members when viewed in isolation. The lung microbiome, a construct that incorporates microbes, their genetic material, and the products of microbial genes, is increasingly central to our understanding of the regulation of respiratory physiology and the processes that underlie lung pathogenesis.
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Wood MR, Yu EA, Mehta S. The Human Microbiome in the Fight Against Tuberculosis. Am J Trop Med Hyg 2017; 96:1274-1284. [PMID: 28719264 DOI: 10.4269/ajtmh.16-0581] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
AbstractThe human microbiome is an intriguing potentially modifiable risk factor in our arsenal against Mycobacterium tuberculosis, the leading infectious disease killer globally. Previous studies have shown associations between the human microbiome and pulmonary disease states; however, etiological links between the microbiome and tuberculosis (TB) infection or disease remain unclear. Immunomodulatory roles of the microbiome may prove to be a critical asset in the host response against TB, including in preventing TB infection, reducing progression from latency, mitigating disease severity, and lowering the incidence of drug resistance and coinfections. This review examined the associations between TB and the gut and lung microbiome. Eight studies were identified through a PubMed database search, including one animal study (N = 1), case report (N = 1), and case-control studies (N = 6). TB infection and disease were associated with reduced gastrointestinal microbial diversity in a murine model and human case report. Sputum microbial diversity differed by TB status in case-control studies, although some reported heterogeneous findings. Current evidence suggests that the gut and lung microbiome are associated with TB infection and disease. However, as studies are limited, etiological and longitudinal research is needed to determine clinical relevance.
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Affiliation(s)
- Madeleine R Wood
- Division of Nutritional Sciences, College of Human Ecology, Cornell University, Ithaca, New York
| | - Elaine A Yu
- Division of Nutritional Sciences, College of Human Ecology, Cornell University, Ithaca, New York
| | - Saurabh Mehta
- Division of Nutritional Sciences, College of Human Ecology, Cornell University, Ithaca, New York.,Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York
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Van Leuvenhaege C, Vandelannoote K, Affolabi D, Portaels F, Sopoh G, de Jong BC, Eddyani M, Meehan CJ. Bacterial diversity in Buruli ulcer skin lesions: Challenges in the clinical microbiome analysis of a skin disease. PLoS One 2017; 12:e0181994. [PMID: 28750103 PMCID: PMC5531519 DOI: 10.1371/journal.pone.0181994] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/06/2017] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Buruli ulcer (BU) is an infectious disease caused by Mycobacterium ulcerans and considered the third most prevalent mycobacterial disease in humans. Secondary bacterial infections in open BU lesions are the main cause of pain, delayed healing and systemic illness, resulting in prolonged hospital stay. Thus, understanding the diversity of bacteria, termed the microbiome, in these open lesions is important for proper treatment. However, adequately studying the human microbiome in a clinical setting can prove difficult when investigating a neglected tropical skin disease due to its rarity and the setting. METHODOLOGY/PRINCIPAL FINDINGS Using 16S rRNA sequencing, we determined the microbial composition of 5 BU lesions, 3 non-BU lesions and 3 healthy skin samples. Although no significant differences in diversity were found between BU and non-BU lesions, the former were characterized by an increase of Bacteroidetes compared to the non-BU wounds and the BU lesions also contained significantly more obligate anaerobes. With this molecular-based study, we were also able to detect bacteria that were missed by culture-based methods in previous BU studies. CONCLUSIONS/SIGNIFICANCE Our study suggests that BU may lead to changes in the skin bacterial community within the lesions. However, in order to determine if such changes hold true across all BU cases and are either a cause or consequence of a specific wound environment, further microbiome studies are necessary. Such skin microbiome analysis requires large sample sizes and lesions from the same body site in many patients, both of which can be difficult for a rare disease. Our study proposes a pipeline for such studies and highlights several drawbacks that must be considered if microbiome analysis is to be utilized for neglected tropical diseases.
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Affiliation(s)
- Chloé Van Leuvenhaege
- Mycobacteriology unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Koen Vandelannoote
- Mycobacteriology unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | | | - Françoise Portaels
- Mycobacteriology unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Ghislain Sopoh
- Institut Régionale de Santé Publique, CDTUB Allada, Benin
| | - Bouke C. de Jong
- Mycobacteriology unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Miriam Eddyani
- Mycobacteriology unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Conor J. Meehan
- Mycobacteriology unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- * E-mail:
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Microbiome Changes during Tuberculosis and Antituberculous Therapy. Clin Microbiol Rev 2016; 29:915-26. [PMID: 27608937 DOI: 10.1128/cmr.00096-15] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The critical role of commensal microbiota in the human body has been increasingly recognized, and our understanding of its implications in human health and disease has expanded rapidly. The lower respiratory tract contains diverse communities of microbes known as lung microbiota, which are present in healthy individuals and in individuals with respiratory diseases. The dysbiosis of the airway microbiota in pulmonary tuberculosis (TB) may play a role in the pathophysiological processes associated with TB disease. Recent studies of the lung microbiome have pointed out changes in lung microbial communities associated with TB and other lung diseases and have also begun to elucidate the profound effects that antituberculous drug therapy can have on the human lung microbiome composition. In this review, the potential role of the human microbiome in TB pathogenesis and the changes in the human microbiome with Mycobacterium tuberculosis infection and TB therapy are presented and discussed.
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