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Ni Y, Li R, Shen X, Yi D, Ren Y, Wang F, Geng Y, You Q. Diaphorobacter nitroreducens synergize with oxaliplatin to reduce tumor burden in mice with lung adenocarcinoma. mSystems 2024; 9:e0132323. [PMID: 38483163 PMCID: PMC11019951 DOI: 10.1128/msystems.01323-23] [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: 12/07/2023] [Accepted: 02/29/2024] [Indexed: 04/17/2024] Open
Abstract
Lung adenocarcinoma (LADC) is the most common lung cancer and the leading cause of cancer-related deaths globally. Accumulating evidence suggests that the gut microbiota regulates the host response to chemotherapeutic drugs and can be targeted to reduce the toxicity of current chemotherapeutic agents. However, the effect of Diaphorobacter nitroreducens synergized with oxaliplatin on the gut microbiota and their impact on LADC have never been explored. This study aimed to evaluate the anti-cancer effects of D. nitroreducens, oxaliplatin, and their combined treatment on tumor growth in tumor-bearing mice. The composition of gut microbiota and the immune infiltration of tumors were evaluated by using 16S rRNA gene high-throughput sequencing and immunofluorescence, respectively. The inhibitory effect of the combination treatment with D. nitroreducens and oxaliplatin was significantly stronger than that of oxaliplatin alone in tumor-bearing mice. Furthermore, we observed that the combination treatment significantly increased the relative abundance of Lactobacillus and Akkermansia in the gut microbiota. Meanwhile, the combination treatment significantly increased the proportions of macrophage but decreased the proportion of regulatory T cells in the LADC tumor tissues of mice. These findings underscored the relationship between D. nitroreducens and the gut microbiota-immune cell-LADC axis, highlighting potential therapeutic avenues for LADC treatment. IMPORTANCE Oxaliplatin is widely used as an effective chemotherapeutic agent in cancer treatment, but its side effects and response rate still need to be improved. Conventional probiotics potentially benefit cancer chemotherapy by regulating gut microbiota and tumor immune infiltration. This study was novel in reporting a more significant inhibitory effect of Diaphorobacter nitroreducens on lung adenocarcinoma (LADC) cells compared with common traditional probiotics and validating its potential as an adjuvant therapy for LADC chemotherapy in mice. This study investigated the impact of D. nitroreducens combined with oxaliplatin on the gut microbiota and immune infiltration of tumors as a potential mechanism to improve anticancer effects.
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Affiliation(s)
- Yalan Ni
- Department of Oncology, Affiliated Children’s Hospital of Jiangnan University, Wuxi, Jiangsu, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Rui Li
- Department of Oncology, Affiliated Children’s Hospital of Jiangnan University, Wuxi, Jiangsu, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Xiaoyu Shen
- Department of Oncology, Affiliated Children’s Hospital of Jiangnan University, Wuxi, Jiangsu, China
- Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Deli Yi
- Department of Oncology, Affiliated Children’s Hospital of Jiangnan University, Wuxi, Jiangsu, China
- Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Yilin Ren
- Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Fudong Wang
- Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Yan Geng
- School of Life Science and Health Engineering, Jiangnan University, Wuxi, China
| | - Qingjun You
- Department of Oncology, Affiliated Children’s Hospital of Jiangnan University, Wuxi, Jiangsu, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
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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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Pant A, Das B, Arimbasseri GA. Host microbiome in tuberculosis: disease, treatment, and immunity perspectives. Front Microbiol 2023; 14:1236348. [PMID: 37808315 PMCID: PMC10559974 DOI: 10.3389/fmicb.2023.1236348] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/29/2023] [Indexed: 10/10/2023] Open
Abstract
Tuberculosis (TB), an airborne pulmonary disease caused by Mycobacterium tuberculosis (M. tb), poses an unprecedented health and economic burden to most of the developing countries. Treatment of TB requires prolonged use of a cocktail of antibiotics, which often manifest several side effects, including stomach upset, nausea, and loss of appetite spurring on treatment non-compliance and the emergence of antibiotic resistant M. tb. The anti-TB treatment regimen causes imbalances in the composition of autochthonous microbiota associated with the human body, which also contributes to major side effects. The microbiota residing in the gastrointestinal tract play an important role in various physiological processes, including resistance against colonization by pathogens, boosting host immunity, and providing key metabolic functions. In TB patients, due to prolonged exposure to anti-tuberculosis drugs, the gut microbiota significantly loses its diversity and several keystone bacterial taxa. This loss may result in a significant reduction in the functional potency of the microbiota, which is a probable reason for poor treatment outcomes. In this review, we discuss the structural and functional changes of the gut microbiota during TB and its treatment. A major focus of the review is oriented to the gut microbial association with micronutrient profiles and immune cell dynamics during TB infection. Furthermore, we summarize the acquisition of anti-microbial resistance in M. tb along with the microbiome-based therapeutics to cure the infections. Understanding the relationship between these components and host susceptibility to TB disease is important to finding potential targets that may be used in TB prevention, progression, and cure.
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Affiliation(s)
- Archana Pant
- Molecular Genetics Lab, National Institute of Immunology, New Delhi, India
| | - Bhabatosh Das
- Functional Genomics Laboratory, Infection and Immunology Division, Translational Health Science and Technology Institute, Faridabad, India
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Tejeda-Garibay S, Hoyer KK. Coccidioidomycosis and Host Microbiome Interactions: What We Know and What We Can Infer from Other Respiratory Infections. J Fungi (Basel) 2023; 9:586. [PMID: 37233297 PMCID: PMC10219296 DOI: 10.3390/jof9050586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/25/2023] [Accepted: 05/10/2023] [Indexed: 05/27/2023] Open
Abstract
Between 70 and 80% of Valley fever patients receive one or more rounds of antibiotic treatment prior to accurate diagnosis with coccidioidomycosis. Antibiotic treatment and infection (bacterial, viral, fungal, parasitic) often have negative implications on host microbial dysbiosis, immunological responses, and disease outcome. These perturbations have focused on the impact of gut dysbiosis on pulmonary disease instead of the implications of direct lung dysbiosis. However, recent work highlights a need to establish the direct effects of the lung microbiota on infection outcome. Cystic fibrosis, chronic obstructive pulmonary disease, COVID-19, and M. tuberculosis studies suggest that surveying the lung microbiota composition can serve as a predictive factor of disease severity and could inform treatment options. In addition to traditional treatment options, probiotics can reverse perturbation-induced repercussions on disease outcomes. The purpose of this review is to speculate on the effects perturbations of the host microbiome can have on coccidioidomycosis progression. To do this, parallels are drawn to aa compilation of other host microbiome infection studies.
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Affiliation(s)
- Susana Tejeda-Garibay
- Quantitative and Systems Biology, Graduate Program, University of California Merced, Merced, CA 95343, USA
| | - Katrina K. Hoyer
- Department of Molecular and Cell Biology, University California Merced, Merced, CA 95343, USA
- Health Sciences Research Institute, University of California Merced, Merced, CA 95343, USA
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Ruiz-Tagle C, Ugalde JA, Naves R, Araos R, García P, Balcells ME. Reduced microbial diversity of the nasopharyngeal microbiome in household contacts with latent tuberculosis infection. Sci Rep 2023; 13:7301. [PMID: 37147354 PMCID: PMC10160714 DOI: 10.1038/s41598-023-34052-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 04/24/2023] [Indexed: 05/07/2023] Open
Abstract
The upper respiratory tract is an obliged pathway for respiratory pathogens and a healthy microbiota may support the host's mucosal immunity preventing infection. We analyzed the nasopharyngeal microbiome in tuberculosis household contacts (HHCs) and its association with latent tuberculosis infection (TBI). A prospective cohort of HHCs was established and latent TBI status was assessed by serial interferon-γ release assay (IGRA). Nasopharyngeal swabs collected at baseline were processed for 16S rRNA gene sequencing. The 82 participants included in the analysis were classified as: (a) non-TBI [IGRA negative at baseline and follow-up, no active TB (n = 31)], (b) pre-TBI [IGRA negative at baseline but converted to IGRA positive or developed active TB at follow-up (n = 16)], and (c) TBI [IGRA positive at enrollment (n = 35)]. Predominant phyla were Actinobacteriota, Proteobacteria, Firmicutes and Bacteroidota. TBI group had a lower alpha diversity compared to non-TBI (padj = 0.04) and pre-TBI (padj = 0.04). Only TBI and non-TBI had beta diversity differences (padj = 0.035). Core microbiomes' had unique genera, and genus showed differential abundance among groups. HHCs with established latent TBI showed reduced nasopharyngeal microbial diversity with distinctive taxonomical composition. Whether a pre-existing microbiome feature favors, are a consequence, or protects against Mycobacterium tuberculosis needs further investigation.
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Affiliation(s)
- Cinthya Ruiz-Tagle
- Departamento de Enfermedades Infecciosas del Adulto, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Juan A Ugalde
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de La Vida, Universidad Andrés Bello, Republica 330, Santiago, Chile
| | - Rodrigo Naves
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Rafael Araos
- Instituto de Ciencias E Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
- Advanced Center for Chronic Diseases (ACCDiS), Santiago, Chile
| | - Patricia García
- Laboratorio de Microbiología, Departamento de Laboratorios Clínicos, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - María Elvira Balcells
- Departamento de Enfermedades Infecciosas del Adulto, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile.
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6
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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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7
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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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The Microbiota of Human Lung of Pulmonary Tuberculosis and the Alteration Caused by Anti-tuberculosis Drugs. Curr Microbiol 2022; 79:321. [PMID: 36121489 DOI: 10.1007/s00284-022-03019-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 08/30/2022] [Indexed: 11/03/2022]
Abstract
An in-depth understanding of the lung microbiota in tuberculosis (TB) infection could provide optimal strategies for the prophylaxis, diagnosis, and treatment of the disease. Only a few studies have investigated the impact of Mycobacterium tuberculosis (Mtb) infection and anti-TB treatment on the lung microbiota. Bronchoalveolar lavage fluid and blood samples were collected from 23 active TB patients (TBZ), 17 latent tuberculosis infection patients (LTBI), 13 healthy controls (HC), and 14 active TB patients with 1-month anti-TB therapy (TBM) for 16S RNA sequencing and serological indexes, respectively. Low body mass index, albumin, and total triglyceride levels were detected in TBZ. Pulmonary Mtb infection led to a minor decrease in the alpha diversity of the lung microbiota in TBZ than HC, but a significant difference was noted in beta diversity. Subsequently, anti-TB therapy caused a rapid alteration in the lung community structure due to reduced alpha and beta diversity. Proteobacteria were abundant in TBZ samples, while Firmicutes was predominant in the LITB and HC samples. Lactobacillus and Subdoligranulum (genera) were the most unique in the LTBI and HC group, respectively. The TBM group showed the most predominant abundance of Bacteroides, Oscillospira, and Ruminococcus (genera). Functional pathways, such as indole alkaloid biosynthesis, Wnt signaling pathway, endocytosis, and metabolism of xenobiotics by cytochrome P450, significantly decreased in the TBM group compared with TBZ group. Pulmonary TB and anti-TB treatment caused a distinct dysbiosis of the lung microbiome. The current findings suggested potential links between the lung microbiota and TB onset, progression, and treatment.
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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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Mouse Subcutaneous BCG Vaccination and Mycobacterium tuberculosis Infection Alter the Lung and Gut Microbiota. Microbiol Spectr 2022; 10:e0169321. [PMID: 35652642 PMCID: PMC9241886 DOI: 10.1128/spectrum.01693-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The objective of this study was to characterize the effect of Bacillus Calmette-Guérin (BCG) vaccination and M. tuberculosis infection on gut and lung microbiota of C57BL/6 mice, a well-characterized mouse model of tuberculosis. BCG vaccination and infection with M. tuberculosis altered the relative abundance of Firmicutes and Bacteroidetes phyla in the lung compared with control group. Vaccination and infection changed the alpha- and beta-diversity in both the gut and the lung. However, lung diversity was the most affected organ after BCG vaccination and M. tuberculosis infection. Focusing on the gut-lung axis, a multivariate regression approach was used to compare profile evolution of gut and lung microbiota. More genera have modified relative abundances associated with BCG vaccination status at gut level compared with lung. Conversely, genera with modified relative abundances associated with M. tuberculosis infection were numerous at lung level. These results indicated that the host local response against infection impacted the whole microbial flora, while the immune response after vaccination modified mainly the gut microbiota. This study showed that a subcutaneous vaccination with a live attenuated microorganism induced both gut and lung dysbiosis that may play a key role in the immunopathogenesis of tuberculosis. IMPORTANCE The microbial communities in gut and lung are important players that may modulate the immunity against tuberculosis or other infections as well as impact the vaccine efficacy. We discovered that vaccination through the subcutaneous route affect the composition of gut and lung bacteria, and this might influence susceptibility and defense mechanisms against tuberculosis. Through these studies, we can identify microbial communities that can be manipulated to improve vaccine response and develop treatment adjuvants.
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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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Barbosa-Amezcua M, Galeana-Cadena D, Alvarado-Peña N, Silva-Herzog E. The Microbiome as Part of the Contemporary View of Tuberculosis Disease. Pathogens 2022; 11:pathogens11050584. [PMID: 35631105 PMCID: PMC9147979 DOI: 10.3390/pathogens11050584] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/03/2022] [Accepted: 05/07/2022] [Indexed: 11/28/2022] Open
Abstract
The study of the microbiome has changed our overall perspective on health and disease. Although studies of the lung microbiome have lagged behind those on the gastrointestinal microbiome, there is now evidence that the lung microbiome is a rich, dynamic ecosystem. Tuberculosis is one of the oldest human diseases, it is primarily a respiratory infectious disease caused by strains from the Mycobacterium tuberculosis Complex. Even today, during the COVID-19 pandemic, it remains one of the principal causes of morbidity and mortality worldwide. Tuberculosis disease manifests itself as a dynamic spectrum that ranges from asymptomatic latent infection to life-threatening active disease. The review aims to provide an overview of the microbiome in the tuberculosis setting, both in patients’ and animal models. We discuss the relevance of the microbiome and its dysbiosis, and how, probably through its interaction with the immune system, it is a significant factor in tuberculosis’s susceptibility, establishment, and severity.
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Affiliation(s)
- Martín Barbosa-Amezcua
- Laboratorio de Farmacogenómica, Instituto Nacional de Medicina Genomica (INMEGEN), Mexico City 14610, Mexico;
| | - David Galeana-Cadena
- Laboratorio de Inmunobiología y Genética, Instituto Nacional de Enfermedades Respiratorias (INER), Mexico City 14080, Mexico;
| | - Néstor Alvarado-Peña
- Coordinación de Infectología y Microbiología, Instituto Nacional de Enfermedades Respiratorias (INER), Mexico City 14080, Mexico;
| | - Eugenia Silva-Herzog
- Coordinación de Infectología y Microbiología, Instituto Nacional de Enfermedades Respiratorias (INER), Mexico City 14080, Mexico;
- Laboratorio de Vinculación Científica, Facultad de Medicina-Universidad Nacional Autonoma de Mexico-Instituto Nacional de Medicina Genomica (UNAM-INMEGEN), Mexico City 14610, Mexico
- Correspondence:
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13
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Dookie N, Khan A, Padayatchi N, Naidoo K. Application of Next Generation Sequencing for Diagnosis and Clinical Management of Drug-Resistant Tuberculosis: Updates on Recent Developments in the Field. Front Microbiol 2022; 13:775030. [PMID: 35401475 PMCID: PMC8988194 DOI: 10.3389/fmicb.2022.775030] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 02/17/2022] [Indexed: 11/30/2022] Open
Abstract
The World Health Organization’s End TB Strategy prioritizes universal access to an early diagnosis and comprehensive drug susceptibility testing (DST) for all individuals with tuberculosis (TB) as a key component of integrated, patient-centered TB care. Next generation whole genome sequencing (WGS) and its associated technology has demonstrated exceptional potential for reliable and comprehensive resistance prediction for Mycobacterium tuberculosis isolates, allowing for accurate clinical decisions. This review presents a descriptive analysis of research describing the potential of WGS to accelerate delivery of individualized care, recent advances in sputum-based WGS technology and the role of targeted sequencing for resistance detection. We provide an update on recent research describing the mechanisms of resistance to new and repurposed drugs and the dynamics of mixed infections and its potential implication on TB diagnosis and treatment. Whilst the studies reviewed here have greatly improved our understanding of recent advances in this arena, it highlights significant challenges that remain. The wide-spread introduction of new drugs in the absence of standardized DST has led to rapid emergence of drug resistance. This review highlights apparent gaps in our knowledge of the mechanisms contributing to resistance for these new drugs and challenges that limit the clinical utility of next generation sequencing techniques. It is recommended that a combination of genotypic and phenotypic techniques is warranted to monitor treatment response, curb emerging resistance and further dissemination of drug resistance.
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Affiliation(s)
- Navisha Dookie
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- *Correspondence: Navisha Dookie,
| | - Azraa Khan
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Nesri Padayatchi
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council (SAMRC), CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council (SAMRC), CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
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14
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Insights into the Unique Lung Microbiota Profile of Pulmonary Tuberculosis Patients Using Metagenomic Next-Generation Sequencing. Microbiol Spectr 2022; 10:e0190121. [PMID: 35196800 PMCID: PMC8865484 DOI: 10.1128/spectrum.01901-21] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The microbiota plays an important role in human health and disease development. The lung microbiota profile in pulmonary tuberculosis (TB) patients and the effects of anti-TB treatment on the profile need to be determined thoroughly and comprehensively. This study primarily aimed to determine the lung microbiota profile associated with pulmonary TB and characterize the longitudinal changes during anti-TB treatment. A total of 53 participants, comprising 8 healthy individuals, 12 untreated pulmonary TB patients, 15 treated pulmonary TB patients, 11 cured pulmonary TB patients, and 7 lung cancer patients, were recruited in the present study. Bronchioalveolar lavage fluid (BALF) samples were collected from the above participants, and throat swabs were taken from healthy individuals. Microbiomes in the samples were examined using metagenomic next-generation sequencing (mNGS). Differences in microbiota profiles were determined through a comparison of the indicated groups. Our findings indicated that the BALF samples displayed decreased richness and diversity of the microbiota compared to those of the throat swab samples, and these two kinds of samples exhibited obvious separation on principal-coordinate analysis (PCoA) plots. Untreated pulmonary TB patients displayed a unique lung microbiota signature distinct from that of healthy individuals and lung cancer patients. Our data first demonstrated that anti-TB treatment with first-line drugs increases alpha diversity and significantly affects the beta diversity of the lung microbiota, while it also induces antibiotic resistance genes (ARGs). IMPORTANCE Characterization of the lung microbiota could lead to a better understanding of the pathogenesis of pulmonary TB. Here, we applied the metagenomic shotgun sequencing instead of 16S rRNA sequencing method to characterize the lung microbiota using the BALF samples instead of sputum. We found that alterations in the lung microbiota are associated with TB infection and that anti-TB treatment significantly affects the alpha and beta diversity of the lung microbiota in pulmonary TB patients. These findings could help us better understand TB pathogenesis.
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15
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Kateete DP, Mbabazi MM, Nakazzi F, Katabazi FA, Kigozi E, Ssengooba W, Nakiyingi L, Namiiro S, Okwera A, Joloba ML, Muwonge A. Sputum microbiota profiles of treatment-naïve TB patients in Uganda before and during first-line therapy. Sci Rep 2021; 11:24486. [PMID: 34966183 PMCID: PMC8716532 DOI: 10.1038/s41598-021-04271-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 12/14/2021] [Indexed: 11/23/2022] Open
Abstract
Information on microbiota dynamics in pulmonary tuberculosis (TB) in Africa is scarce. Here, we sequenced sputa from 120 treatment-naïve TB patients in Uganda, and investigated changes in microbiota of 30 patients with treatment-response follow-up samples. Overall, HIV-status and anti-TB treatment were associated with microbial structural and abundance changes. The predominant phyla were Bacteroidetes, Firmicutes, Proteobacteria, Fusobacteria and Actinobacteria, accounting for nearly 95% of the sputum microbiota composition; the predominant genera across time were Prevotella, Streptococcus, Veillonella, Haemophilus, Neisseria, Alloprevotella, Porphyromonas, Fusobacterium, Gemella, and Rothia. Treatment-response follow-up at month 2 was characterized by a reduction in abundance of Mycobacterium and Fretibacterium, and an increase in Ruminococcus and Peptococcus; month 5 was characterized by a reduction in Tannerella and Fusobacterium, and an increase in members of the family Neisseriaceae. The microbiota core comprised of 44 genera that were stable during treatment. Hierarchical clustering of this core's abundance distinctly separated baseline (month 0) samples from treatment follow-up samples (months 2/5). We also observed a reduction in microbial diversity with 9.1% (CI 6-14%) of the structural variation attributed to HIV-status and anti-TB treatment. Our findings show discernible microbiota signals associated with treatment with potential to inform anti-TB treatment response monitoring.
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Affiliation(s)
- David Patrick Kateete
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda.
| | - Monica M Mbabazi
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Faith Nakazzi
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Fred A Katabazi
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Edgar Kigozi
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Willy Ssengooba
- BSL-3 Mycobacteriology Laboratory, Department of Medical Microbiology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Lydia Nakiyingi
- Department of Medicine, School of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
- Infectious Diseases Institute, Makerere University College of Health Sciences, Mulago Hospital Complex, Kampala, Uganda
| | - Sharon Namiiro
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Alphonse Okwera
- TB Clinics, Mulago National Referral Hospital, Kampala, Uganda
| | - Moses L Joloba
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Adrian Muwonge
- Division of Genetics and Genomics, The Roslin Institute, University of Edinburgh, Edinburg, UK.
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Edinburg, UK.
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16
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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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17
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Cho SY, Choi JH, Lee SH, Choi YS, Hwang SW, Kim YJ. Metataxonomic investigation of the microbial community in the trachea and oropharynx of healthy controls and diabetic patients using endotracheal tubes. PLoS One 2021; 16:e0259596. [PMID: 34739518 PMCID: PMC8570478 DOI: 10.1371/journal.pone.0259596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 10/21/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Although the study of respiratory microbiota has been an active field of research, obtaining the appropriate respiratory samples for healthy controls remains to be a challenge. As such, this study aims to evaluate the use of endotracheal tube washing as a viable control for sputum samples. METHODS A total of 14 subjects, including 8 healthy respiratory controls and 6 diabetic patients without any respiratory disease, were enrolled in this study, during which the endotracheal tubes used in their scheduled routine surgery were collected. Pre-operative oral gargles were also collected from non-diabetic subjects. RESULTS 16S amplicon sequencing revealed similar taxa composition in endotracheal tube washings and oral gargles in the healthy control subjects, although the relative abundance of 11 genus level operational taxonomic units was significantly different between the two sample sources. The diabetic subjects showed relatively lower diversity than those of non-diabetic subjects. The proportion range of the most abundant taxa detected in each endotracheal tube washings were 10.1-33.2%. CONCLUSION Endotracheal tube washing fluid may provide healthy control samples for upper respiratory investigations without incurring any additional risk to the subject.
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Affiliation(s)
- Sun Young Cho
- Department of Laboratory Medicine, Kyung Hee University Hospital, Kyung Hee University School of Medicine, Seoul, Republic of Korea
| | - Jeong-Hyun Choi
- Department of Anesthesiology, Kyung Hee University Hospital, Kyung Hee University School of Medicine, Seoul, Republic of Korea
| | - Seung Hyeun Lee
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Kyung Hee University Hospital, Kyung Hee University School of Medicine, Seoul, Republic of Korea
| | - Yong-Sung Choi
- Department of Pediatrics, Kyung Hee University Hospital, Kyung Hee University School of Medicine, Seoul, Republic of Korea
| | - Sung Wook Hwang
- Department of Anesthesiology and Pain Medicine, Kyung Hee University Hospital, Seoul, Republic of Korea
| | - Young Jin Kim
- Department of Laboratory Medicine, Kyung Hee University Hospital, Kyung Hee University School of Medicine, Seoul, Republic of Korea
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18
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Xiang L, Meng X. Emerging cellular and molecular interactions between the lung microbiota and lung diseases. Crit Rev Microbiol 2021; 48:577-610. [PMID: 34693852 DOI: 10.1080/1040841x.2021.1992345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
With the discovery of the lung microbiota, its study in both pulmonary health and disease has become a vibrant area of emerging research interest. Thus far, most studies have described the lung microbiota composition in lung disease quite well, and some of these studies indicated alterations in lung microbial communities related to the onset and development of lung disease and vice versa. However, the underlying mechanisms, particularly the cellular and molecular links, are still largely unknown. In this review, we highlight the current progress in the complex cellular and molecular mechanisms by which the lung microbiome interacts with immune homeostasis and pulmonary disease pathogenesis to advance our understanding of the elaborate function of the lung microbiota in lung disease. We hope that this work can attract more attention to this still-young yet very promising field to facilitate the identification of new therapeutic targets and provide more innovative therapies. Additional accurate standard-based methodologies and technological breakthroughs are critical to propel the field forward to ultimately achieve the goal of maintaining respiratory health.
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Affiliation(s)
- Li Xiang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China.,Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xianli Meng
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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19
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Khan AA, Singh H, Bilal M, Ashraf MT. Microbiota, probiotics and respiratory infections: the three musketeers can tip off potential management of COVID-19. Am J Transl Res 2021; 13:10977-10993. [PMID: 34786037 PMCID: PMC8581851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/15/2021] [Indexed: 06/13/2023]
Abstract
Rapid infectivity of SARS-CoV2 with recent viral variants is posing a challenge in the development of robust therapeutic strategies. On the other hand, microbiota is debated for its involvement in SARS-CoV2 infection with varied opinions. Although ample data about the role of microbiota and probiotics in respiratory viral infections are available, their role in COVID-19 is limited albeit emerging rapidly. The utilization of probiotics for the management of COVID-19 is still under investigation in many clinical trials. Existing information coupled with recent COVID-19 related studies can suggest various ways to use microbiota modulation and probiotics for managing this pandemic. Present article indicates the role of microbiota modulation and probiotics in respiratory infections. In addition, scattered evidence was gathered to understand the potential of microbiota and probiotics in the management of SARS-CoV2. Gut-airway microbiota connection is already apparent in respiratory tract viral infections, including SARS-CoV2. Though few clinical trials are evaluating microbiota and probiotics for COVID-19 management, the safety evaluation must be given more serious consideration because of the possibility of opportunistic infections among COVID-19 patients. Nevertheless, the information about microbiota modulation using probiotics and prebiotics can be helpful to manage this outbreak and this review presents different aspects of this idea.
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Affiliation(s)
- Abdul Arif Khan
- Division of Microbiology, Indian Council of Medical Research-National AIDS Research InstitutePune, Maharashtra 411026, India
| | - HariOm Singh
- Division of Molecular Biology, Indian Council of Medical Research-National AIDS Research InstitutePune, Maharashtra 411026, India
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of TechnologyHuaian 223003, China
| | - Mohd Tashfeen Ashraf
- School of Biotechnology, Gautam Buddha UniversityGautam Budh Nagar, Greater Noida (UP), India
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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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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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22
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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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23
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Lin D, Wang X, Li Y, Wang W, Li Y, Yu X, Lin B, Chen Y, Lei C, Zhang X, Zhang X, Huang J, Lin B, Yang W, Zhou J, Zeng J, Liu X. Sputum microbiota as a potential diagnostic marker for multidrug-resistant tuberculosis. Int J Med Sci 2021; 18:1935-1945. [PMID: 33850462 PMCID: PMC8040397 DOI: 10.7150/ijms.53492] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 11/23/2020] [Indexed: 11/19/2022] Open
Abstract
The prevalence of drug-resistant Mycobacterium tuberculosis (Mtb) strains makes disease control more complicated, which is the main cause of death in tuberculosis (TB) patients. Early detection and timely standard treatment are the key to current prevention and control of drug-resistant TB. In recent years, despite the continuous advancement in drug-resistant TB diagnostic technology, the needs for clinical rapid and accurate diagnosis are still not fully met. With the development of sequencing technology, the research of human microecology has been intensified. This study aims to use 16 rRNA sequencing technology to detect and analyze upper respiratory flora of TB patients with anti-TB drug sensitivity (DS, n = 55), monoresistance isoniazide (MR-INH, n = 33), monoresistance rifampin (MR-RFP, n = 12), multidrug resistance (MDR, n = 26) and polyresistance (PR, n = 39) in southern China. Potential microbial diagnostic markers for different types of TB drug resistance are searched by screening differential flora, which provides certain guiding significance for drug resistance diagnosis and clinical drug use of TB. The results showed that the pulmonary microenvironment of TB patients was more susceptible to infection by external pathogens, and the infection of different drug-resistant Mtb leads to changes in different flora. Importantly, seven novel microorganisms (Leptotrichia, Granulicatella, Campylobacter, Delfitia, Kingella, Chlamydophila, Bordetella) were identified by 16S rRNA sequencing as diagnostic markers for different drug resistance types of TB. Leptotrichia, Granulicatella, Campylobacter were potential diagnostic marker for TB patients with INH single-resistance. Delftia was a potential diagnostic marker for TB patients with RFP single drug-resistance. Kingella and Chlamydophila can be used as diagnostic markers for TB patients with PR. Bordetella can be used as a potential diagnostic marker for identification of TB patients with MDR.
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Affiliation(s)
- Dongzi Lin
- Dongguan Key Laboratory of Medical Bioactive Molecular Developmental and Translational Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, China.,Department of Laboratory Medicine, Foshan Fourth People's Hospital, Foshan, Guangdong, 528041, China
| | - Xuezhi Wang
- Department of Laboratory Medicine, Foshan Fourth People's Hospital, Foshan, Guangdong, 528041, China
| | - Yanyun Li
- Dongguan Key Laboratory of Medical Bioactive Molecular Developmental and Translational Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, China
| | - Wei Wang
- Department of Laboratory Medicine, Foshan Fourth People's Hospital, Foshan, Guangdong, 528041, China
| | - Yumei Li
- Department of Laboratory Medicine, Dongguan Sixth People's Hospital, Dongguan, Guangdong, 523008, China
| | - Xiaolin Yu
- Department of Laboratory Medicine, Dongguan Sixth People's Hospital, Dongguan, Guangdong, 523008, China
| | - Bingyao Lin
- Department of Laboratory Medicine, Foshan Fourth People's Hospital, Foshan, Guangdong, 528041, China
| | - Yinwen Chen
- Department of Laboratory Medicine, Dongguan Sixth People's Hospital, Dongguan, Guangdong, 523008, China
| | - Chunyan Lei
- Department of Laboratory Medicine, Foshan Fourth People's Hospital, Foshan, Guangdong, 528041, China
| | - Xueying Zhang
- Dongguan Key Laboratory of Medical Bioactive Molecular Developmental and Translational Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, China
| | - Xilin Zhang
- Department of Laboratory Medicine, Foshan Fourth People's Hospital, Foshan, Guangdong, 528041, China
| | - Juan Huang
- Dongguan Key Laboratory of Medical Bioactive Molecular Developmental and Translational Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, China
| | - Bihua Lin
- Dongguan Key Laboratory of Medical Bioactive Molecular Developmental and Translational Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, China
| | - Weiqing Yang
- Dongguan Key Laboratory of Medical Bioactive Molecular Developmental and Translational Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, China
| | - Jie Zhou
- Department of Laboratory Medicine, Foshan Fourth People's Hospital, Foshan, Guangdong, 528041, China
| | - Jincheng Zeng
- Dongguan Key Laboratory of Medical Bioactive Molecular Developmental and Translational Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, China
| | - Xinguang Liu
- Dongguan Key Laboratory of Medical Bioactive Molecular Developmental and Translational Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, China
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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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Microbial biodiversity in the throats of pulmonary tuberculosis patients and tuberculin skin test (TST) positive and negative healthy individuals in Malaysia. Tuberculosis (Edinb) 2020; 124:101965. [PMID: 32692651 DOI: 10.1016/j.tube.2020.101965] [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: 02/19/2020] [Revised: 06/18/2020] [Accepted: 06/26/2020] [Indexed: 11/22/2022]
Abstract
The purpose of this study was to investigate the composition of throat microbiota in pulmonary tuberculosis patients (PTB) in comparison to healthy tuberculin skin test positive (TSTp) and negative (TSTn) individuals. Throat swabs samples were collected, and the microbiota was characterized. Richer operational taxonomic units (OTUs) were present in PTB group, compared to TSTp and TSTn. Regarding alpha diversity analysis there was a higher community diversity in TSTn compared to TSTp. Beta diversity analysis showed different species composition in TSTp compared to TSTn and PTB. There was higher presence of Firmicutes in PTB and TSTn compared to TSTp group at phylum level. At the genus level, Leuconostoc and Enterococcus were higher in TSTn compared to TSTp and Pediococcus, Chryseobacterium, Bifidobacterium, Butyrivibrio, and Bulleidia were higher in PTB compared to TSTn. Streptococcus was higher in TSTn compared to PTB and Lactobacillus in PTB compared to TSTp. At species level, Streptococcus sobrinus and Bulleidia moorei were higher in PTB compared to TSTn individuals, while Lactobacillus salivarius was higher in PTB compared to TSTp. The differences in the microbiome composition could influence the resistance/susceptibility to Mtb infection.
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The Echo of Pulmonary Tuberculosis: Mechanisms of Clinical Symptoms and Other Disease-Induced Systemic Complications. Clin Microbiol Rev 2020; 33:33/4/e00036-20. [PMID: 32611585 DOI: 10.1128/cmr.00036-20] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Clinical symptoms of active tuberculosis (TB) can range from a simple cough to more severe reactions, such as irreversible lung damage and, eventually, death, depending on disease progression. In addition to its clinical presentation, TB has been associated with several other disease-induced systemic complications, such as hyponatremia and glucose intolerance. Here, we provide an overview of the known, although ill-described, underlying biochemical mechanisms responsible for the clinical and systemic presentations associated with this disease and discuss novel hypotheses recently generated by various omics technologies. This summative update can assist clinicians to improve the tentative diagnosis of TB based on a patient's clinical presentation and aid in the development of improved treatment protocols specifically aimed at restoring the disease-induced imbalance for overall homeostasis while simultaneously eradicating the pathogen. Furthermore, future applications of this knowledge could be applied to personalized diagnostic and therapeutic options, bettering the treatment outcome and quality of life of TB patients.
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Kim SB, Lee WY, Lee JH, Lee SJ, Lee MK, Kim SH, Uh Y, Jung SH, Shin B. A variety of bacterial aetiologies in the lower respiratory tract at patients with endobronchial tuberculosis. PLoS One 2020; 15:e0234558. [PMID: 32584852 PMCID: PMC7316277 DOI: 10.1371/journal.pone.0234558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 05/27/2020] [Indexed: 12/31/2022] Open
Abstract
Recently, our understanding of the elusive bacterial communities in the lower respiratory tract and their role in chronic lung disease has increased significantly. However, little is known about the respiratory microorganisms in patients with endobronchial tuberculosis (EBTB), which is a chronic inflammatory disease characterized by destruction of the tracheobronchial tree due to Mycobacterium tuberculosis (MTB) infection. We retrospectively reviewed data for histopathologically and microbiologically confirmed EBTB patients diagnosed at a tertiary referral hospital in South Korea between January 2013 and January 2019. Bacterial cultures were performed on bronchial washing from these patients at the time of EBTB diagnosis. A total of 216 patients with EBTB were included in the study. The median age was 73 years and 142 (65.7%) patients were female. Bacteria were detected in 42 (19.4%) patients. Additionally, bacterial co-infection was present in 6 (2.8%) patients. Apart from MTB, the most common microorganisms identified were Staphylococcus aureus (n = 14, 33.3%) followed by Klebsiella species (n = 12, 28.6%; 10 Klebsiella pneumoniae, 2 Klebsiella oxytoca), Streptococcus species (n = 5, 11.9%), Enterobacter species (n = 4, 9.5%), and Pseudomonas aeruginosa (n = 3, 7.1%). A variety of microorganisms were isolated from the bronchial washing indicating that changes in microorganism composition occur in the airways of patients with EBTB. Further studies are needed to investigate the clinical significance of this finding.
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Affiliation(s)
- Sae Byol Kim
- Department of Internal Medicine, Yonsei University Wonju College of Medicine, Wonju, Republic of Korea
| | - Won-Yeon Lee
- Department of Internal Medicine, Yonsei University Wonju College of Medicine, Wonju, Republic of Korea
| | - Ji-Ho Lee
- Department of Internal Medicine, Yonsei University Wonju College of Medicine, Wonju, Republic of Korea
| | - Seok Jeong Lee
- Department of Internal Medicine, Yonsei University Wonju College of Medicine, Wonju, Republic of Korea
| | - Myoung Kyu Lee
- Department of Internal Medicine, Yonsei University Wonju College of Medicine, Wonju, Republic of Korea
| | - Sang-Ha Kim
- Department of Internal Medicine, Yonsei University Wonju College of Medicine, Wonju, Republic of Korea
| | - Young Uh
- Department of Laboratory Medicine, Yonsei University Wonju College of Medicine, Wonju, Republic of Korea
| | - Soon-Hee Jung
- Department of Pathology, Yonsei University Wonju College of Medicine, Wonju, Republic of Korea
| | - Beomsu Shin
- Department of Internal Medicine, Yonsei University Wonju College of Medicine, Wonju, Republic of Korea
- * E-mail:
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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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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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Singhvi N, Gupta V, Gaur M, Sharma V, Puri A, Singh Y, Dubey GP, Lal R. Interplay of Human Gut Microbiome in Health and Wellness. Indian J Microbiol 2020; 60:26-36. [PMID: 32089571 PMCID: PMC7000599 DOI: 10.1007/s12088-019-00825-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 08/30/2019] [Indexed: 12/19/2022] Open
Abstract
The gut microbiome analysis, with specific interest on their direct impact towards the human health, is currently revolutionizing the unexplored frontiers of the pathogenesis and wellness. Although in-depth investigations of gut microbiome, 'the Black Boxes', complexities and functionalities are yet at its infancy, profound evidences are being reported for their concurrent involvement in disease etiology and its treatment. Interestingly, studies from the 'minimal murine' (Oligo-MM12), 'humanized' microbiota gnotobiotic mice models and patient samples, combined with multi-omics and cell biology approaches, have been revealing the implications of these findings in the treatment of gut dysbiosis associated diseases. Nonetheless, due to the inherent heterogeneity of the gut commensals and their unified co-existence with opportunistic pathobionts, it is utmost essential to highlight their functionalities in 'good or bad' gut in human wellness. We have specifically reviewed dietary lifestyle and infectious diseases linked with the gut bacterial consortia to delineate the ecobiotic approaches towards their treatment. This notably includes gut mucosal immunity mediated diseases such as Tuberculosis, IBD, CDI, Type 2 Diabetes, etc. Alongside of each dysbiosis, we have described the current therapeutic advancements of the pre- and probiotics derived from human microbiome studies to restore gut microbial homeostasis. With a continuous running debate on the role of microbiota in above mentioned diseases, we have collected numerous scientific evidences highlighting a previously unanticipated complex involvement of gut microbiome in the potential of human health.
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Affiliation(s)
- Nirjara Singhvi
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Vipin Gupta
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Mohita Gaur
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Vishal Sharma
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Akshita Puri
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Yogendra Singh
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Gyanendra P. Dubey
- Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, 75015 Paris, France
| | - Rup Lal
- The Energy and Resources Institute, Darbari Seth Block, IHC Complex, Lodhi Road, New Delhi, 110003 India
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Vázquez-Pérez JA, Carrillo CO, Iñiguez-García MA, Romero-Espinoza I, Márquez-García JE, Falcón LI, Torres M, Herrera MT. Alveolar microbiota profile in patients with human pulmonary tuberculosis and interstitial pneumonia. Microb Pathog 2019; 139:103851. [PMID: 31715320 DOI: 10.1016/j.micpath.2019.103851] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 09/19/2019] [Accepted: 11/05/2019] [Indexed: 01/10/2023]
Abstract
BACKGROUND The presence of the human lung microbiota has been demonstrated in patients with different lung diseases, mainly in sputum samples. However, for study of the alveolar microbiota, a bronchoalveolar lavage (BAL) sample represents the lower respiratory tract (LRT) environment. It is currently unknown whether there is a specific alveolar microbiota profile in human lung diseases, such as pulmonary tuberculosis (TB) and interstitial pneumonia (IP). METHODS BAL samples from six active TB patients, six IP patients and ten healthy volunteers were used for DNA extraction followed by amplification of the complete bacterial 16S ribosomal RNA gene (16S rDNA). The 16S rDNA was sequenced with a MiSeq Desktop Sequencer, and the data were analysed by QIIME software for taxonomic assignment. RESULTS The alveolar microbiota in TB and IP patients and healthy volunteers was characterized by six dominant phyla, Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Fusobacteria and Cyanobacteria. A significant reduction in the abundance of Firmicutes was observed in IP patients. In TB and IP patients, the diversity of the alveolar microbiota was diminished, characterized by a significant reduction in the abundance of the Streptococcus genus and associated with increased Mycobacterium abundance in TB patients and diminished Acinetobacter abundance in IP patients with respect to their abundances in healthy volunteers. However, an important difference was observed between TB and IP patients: the Fusobacterium abundance was significantly reduced in TB patients. Exclusive genera that were less abundant in patients than in healthy volunteers were characterized for each study group. CONCLUSIONS This study shows that the alveolar microbiota profile in BAL samples from TB and IP patients, representing infectious and non-infectious lung diseases, respectively, is characterized by decreased diversity.
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Affiliation(s)
- Joel Armando Vázquez-Pérez
- Departamento de Investigación en Tabaquismo y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico
| | - Concepción Ortega Carrillo
- Servicio de Broncoscopía, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico
| | | | - Ivan Romero-Espinoza
- Departamento de Investigación en Tabaquismo y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico
| | - José Eduardo Márquez-García
- Subdirección de Investigación Biomédica, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico
| | - Luisa I Falcón
- Laboratorio de Ecología Bacteriana, Instituto de Ecología, Universidad Nacional Autónoma de México, PCTY Yucatán, Mexico
| | - Martha Torres
- Subdirección de Investigación Biomédica, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico; Departamento de Investigación en Microbiología, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico
| | - María Teresa Herrera
- Departamento de Investigación en Microbiología, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico.
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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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Pinna NK, Dutta A, Monzoorul Haque M, Mande SS. Can Targeting Non-Contiguous V-Regions With Paired-End Sequencing Improve 16S rRNA-Based Taxonomic Resolution of Microbiomes?: An In Silico Evaluation. Front Genet 2019; 10:653. [PMID: 31354793 PMCID: PMC6640118 DOI: 10.3389/fgene.2019.00653] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 06/20/2019] [Indexed: 12/14/2022] Open
Abstract
Background: Next-generation sequencing (NGS) technologies have enabled probing of microbial diversity in different environmental niches with unprecedented sequencing depth. However, due to read-length limitations of popular NGS technologies, 16S amplicon sequencing-based microbiome studies rely on targeting short stretches of the 16S rRNA gene encompassing a selection of variable (V) regions. In most cases, such a short stretch constitutes a single V-region or a couple of V-regions placed adjacent to each other on the 16S rRNA gene. Given that different V-regions have different resolving ability with respect to various taxonomic groups, selecting the optimal V-region (or a combination thereof) remains a challenge. Methods: The accuracy of taxonomic profiles generated from sequences encompassing 1) individual V-regions, 2) adjacent V-regions, and 3) pairs of non-contiguous V-regions were assessed and compared. Subsequently, the discriminating capability of different V-regions with respect to different taxonomic lineages was assessed. The possibility of using paired-end sequencing protocols to target combinations of non-adjacent V-regions was finally evaluated with respect to the utility of such an experimental design in providing improved taxonomic resolution. Results: Extensive validation with simulated microbiome datasets mimicking different environmental and host-associated microbiome samples suggest that targeting certain combinations of non-contiguously placed V-regions might yield better taxonomic classification accuracy compared to conventional 16S amplicon sequencing targets. This work also puts forward a novel in silico combinatorial strategy that enables creation of consensus taxonomic profiles from experiments targeting multiple pair-wise combinations of V-regions to improve accuracy in taxonomic classification. Conclusion: The study suggests that targeting non-contiguous V-regions with paired-end sequencing can improve 16S rRNA–based taxonomic resolution of microbiomes. Furthermore, employing the novel in silico combinatorial strategy can improve taxonomic classification without any significant additional experimental costs and/or efforts. The empirical observations obtained can potentially serve as a guideline for future 16S microbiome studies, and facilitate researchers in choosing the optimal combination of V-regions for a specific experiment/sampled environment.
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Affiliation(s)
- Nishal Kumar Pinna
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., Pune, Maharashtra, India
| | - Anirban Dutta
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., Pune, Maharashtra, India
| | - Mohammed Monzoorul Haque
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., Pune, Maharashtra, India
| | - Sharmila S Mande
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., Pune, Maharashtra, India
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Affiliation(s)
- Nicole M. Gilbert
- Department of Obstetrics and Gynecology, Center for Reproductive Health Sciences, Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Amanda L. Lewis
- Department of Obstetrics and Gynecology, Center for Reproductive Health Sciences, Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Molecular Microbiology, Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
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Eshetie S, van Soolingen D. The respiratory microbiota: new insights into pulmonary tuberculosis. BMC Infect Dis 2019; 19:92. [PMID: 30683056 PMCID: PMC6347808 DOI: 10.1186/s12879-019-3712-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 01/10/2019] [Indexed: 12/31/2022] Open
Abstract
Background Previous studies demonstrated that the diversity and composition of respiratory microbiota in TB patients were different from healthy individuals. Therefore, the aim of the present analysis was to estimate the relative proportion of respiratory microbiota at phylum and genus levels among TB cases and healthy controls. Methods The PubMed and Google Scholar online databases were searched to retrieve relevant studies for the analysis. The statistical analysis was done using STATA version 11, pooled estimates are presented using graphs. The summary of findings in included studies is also presented in Table 1. Results The phylum level analysis shows that the pooled proportions of Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Crenarchaeota were determined among tuberculosis patients and healthy controls. In brief, Firmicutes, and Proteobacteria were the most abundant bacterial phyla in both TB cases and healthy controls, composing 39.9 and 22.7% in TB cases and 39.4 and 19.5% in healthy controls, respectively. The genus level analysis noted that Streptococcus (35.01%), Neisseria (27.1%), Prevotella (9.02%) and Veillonella (7.8%) were abundant in TB patients. The Prevotella (36.9%), Gammaproteobacteria (22%), Streptococcus (19.2%) and Haemophilus (15.4%) were largely seen in healthy controls. Interestingly, Veillonella, Rothia, Leuconostoc were unique to TB cases, whereas Lactobacillus, and Gammaproteobacteria, Haemophilus, and Actinobacillus were identified only in healthy controls. Conclusion The composition of the respiratory microbiota in TB patients and healthy controls were quite different. More deep sequencing studies are needed to explore the microbial variation in the respiratory system in connection with TB.
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Affiliation(s)
- Setegn Eshetie
- Departent of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, P.O.Box: 196, Gondar, Ethiopia.
| | - Dick van Soolingen
- National Institute for Public Health and the Environment (RIVM), 3720, BA, Bilthoven, The Netherlands
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Nagpal S, Haque MM, Singh R, Mande SS. iVikodak-A Platform and Standard Workflow for Inferring, Analyzing, Comparing, and Visualizing the Functional Potential of Microbial Communities. Front Microbiol 2019; 9:3336. [PMID: 30692979 PMCID: PMC6339920 DOI: 10.3389/fmicb.2018.03336] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 12/24/2018] [Indexed: 01/19/2023] Open
Abstract
Background: The objectives of any metagenomic study typically include identification of resident microbes and their relative proportions (taxonomic analysis), profiling functional diversity (functional analysis), and comparing the identified microbes and functions with available metadata (comparative metagenomics). Given the advantage of cost-effectiveness and convenient data-size, amplicon-based sequencing has remained the technology of choice for exploring phylogenetic diversity of an environment. A recent school of thought, employing the existing genome annotation information for inferring functional capacity of an identified microbiome community, has given a promising alternative to Whole Genome Shotgun sequencing for functional analysis. Although a handful of tools are currently available for function inference, their scope, functionality and utility has essentially remained limited. Need for a comprehensive framework that expands upon the existing scope and enables a standardized workflow for function inference, analysis, and visualization, is therefore felt. Methods: We present iVikodak, a multi-modular web-platform that hosts a logically inter-connected repertoire of functional inference and analysis tools, coupled with a comprehensive visualization interface. iVikodak is equipped with microbial co-inhabitance pattern driven published algorithms along with multiple updated databases of various curated microbe-function maps. It also features an advanced task management and result sharing system through introduction of personalized and portable dashboards. Results: In addition to inferring functions from 16S rRNA gene data, iVikodak enables (a) an in-depth analysis of specific functions of interest (b) identification of microbes contributing to various functions (c) microbial interaction patterns through function-driven correlation networks, and (d) simultaneous functional comparison between multiple microbial communities. We have bench-marked iVikodak through multiple case studies and comparisons with existing state of art. We also introduce the concept of a public repository which provides a first of its kind community-driven framework for scientific data analytics, collaboration and sharing in this area of microbiome research. Conclusion: Developed using modern design and task management practices, iVikodak provides a multi-modular, yet inter-operable, one-stop framework, that intends to simplify the entire approach toward inferred function analysis. It is anticipated to serve as a significant value addition to the existing space of functional metagenomics. iVikodak web-server may be freely accessed at https://web.rniapps.net/iVikodak/.
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Affiliation(s)
- Sunil Nagpal
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services, Pune, India
| | | | - Rashmi Singh
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services, Pune, India
| | - Sharmila S Mande
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services, Pune, India
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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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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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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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40
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Costa AN, Costa FMD, Campos SV, Salles RK, Athanazio RA. The pulmonary microbiome: challenges of a new paradigm. ACTA ACUST UNITED AC 2018; 44:424-432. [PMID: 30066739 PMCID: PMC6467588 DOI: 10.1590/s1806-37562017000000209] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 07/16/2017] [Indexed: 01/06/2023]
Abstract
The study of the human microbiome-and, more recently, that of the respiratory system-by means of sophisticated molecular biology techniques, has revealed the immense diversity of microbial colonization in humans, in human health, and in various diseases. Apparently, contrary to what has been believed, there can be nonpathogenic colonization of the lungs by microorganisms such as bacteria, fungi, and viruses. Although this physiological lung microbiome presents low colony density, it presents high diversity. However, some pathological conditions lead to a loss of that diversity, with increasing concentrations of some bacterial genera, to the detriment of others. Although we possess qualitative knowledge of the bacteria present in the lungs in different states of health or disease, that knowledge has advanced to an understanding of the interaction of this microbiota with the local and systemic immune systems, through which it modulates the immune response. Given this intrinsic relationship between the microbiota and the lungs, studies have put forth new concepts about the pathophysiological mechanisms of homeostasis in the respiratory system and the potential dysbiosis in some diseases, such as cystic fibrosis, COPD, asthma, and interstitial lung disease. This departure from the paradigm regarding knowledge of the lung microbiota has made it imperative to improve understanding of the role of the microbiome, in order to identify possible therapeutic targets and to develop innovative clinical approaches. Through this new leap of knowledge, the results of preliminary studies could translate to benefits for our patients.
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Affiliation(s)
- André Nathan Costa
- . Divisão de Pneumologia, Instituto do Coração - InCor - Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo (SP) Brasil
| | - Felipe Marques da Costa
- . Divisão de Pneumologia, Instituto do Coração - InCor - Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo (SP) Brasil
| | - Silvia Vidal Campos
- . Divisão de Pneumologia, Instituto do Coração - InCor - Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo (SP) Brasil
| | - Roberta Karla Salles
- . Divisão de Pneumologia, Instituto do Coração - InCor - Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo (SP) Brasil
| | - Rodrigo Abensur Athanazio
- . Divisão de Pneumologia, Instituto do Coração - InCor - Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo (SP) Brasil
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Thakore N, Norville R, Franke M, Calderon R, Lecca L, Villanueva M, Murray MB, Cooney CG, Chandler DP, Holmberg RC. Automated TruTip nucleic acid extraction and purification from raw sputum. PLoS One 2018; 13:e0199869. [PMID: 29975759 PMCID: PMC6033430 DOI: 10.1371/journal.pone.0199869] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 05/30/2018] [Indexed: 12/12/2022] Open
Abstract
Automated nucleic acid extraction from primary (raw) sputum continues to be a significant technical challenge for molecular diagnostics. In this work, we developed a prototype open-architecture, automated nucleic acid workstation that includes a mechanical homogenization and lysis function integrated with heating and TruTip purification; optimized an extraction protocol for raw sputum; and evaluated system performance on primary clinical specimens. Eight samples could be processed within 70 min. The system efficiently homogenized primary sputa and doubled nucleic acid recovery relative to an automated protocol that did not incorporate sample homogenization. Nucleic acid recovery was at least five times higher from raw sputum as compared to that of matched sediments regardless of smear or culture grade, and the automated workstation reproducibly recovered PCR-detectable DNA to at least 80 CFU mL-1 raw sputum. M. tuberculosis DNA was recovered and detected from 122/123 (99.2%) and 124/124 (100%) primary sputum and sediment extracts, respectively. There was no detectable cross-contamination across 53 automated system runs and amplification or fluorescent inhibitors (if present) were not detectable. The open fluidic architecture of the prototype automated workstation yields purified sputum DNA that can be used for any molecular diagnostic test. The ability to transfer TruTip protocols between personalized, on-demand pipetting tools and the fully automated workstation also affords public health agencies an opportunity to standardize sputum nucleic acid sample preparation procedures, reagents, and quality control across multiple levels of the health care system.
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Affiliation(s)
- Nitu Thakore
- Akonni Biosystems, Inc., Frederick, Maryland, United States of America
| | - Ryan Norville
- Akonni Biosystems, Inc., Frederick, Maryland, United States of America
| | - Molly Franke
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | | | - Leonid Lecca
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Socios En Salud Sucursal Perú, Carabayllo, Lima, Peru
| | | | - Megan B. Murray
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
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42
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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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44
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Chai Q, Zhang Y, Liu CH. Mycobacterium tuberculosis: An Adaptable Pathogen Associated With Multiple Human Diseases. Front Cell Infect Microbiol 2018; 8:158. [PMID: 29868514 PMCID: PMC5962710 DOI: 10.3389/fcimb.2018.00158] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 04/25/2018] [Indexed: 12/15/2022] Open
Abstract
Mycobacterium tuberculosis, the etiological agent of tuberculosis (TB), is an extremely successful pathogen that adapts to survive within the host. During the latency phase of infection, M. tuberculosis employs a range of effector proteins to be cloud the host immune system and shapes its lifestyle to reside in granulomas, sophisticated, and organized structures of immune cells that are established by the host in response to persistent infection. While normally being restrained in immunocompetent hosts, M. tuberculosis within granulomas can cause the recrudescence of TB when host immunity is compromised. Aside from causing TB, accumulating evidence suggests that M. tuberculosis is also associated with multiple other human diseases, such as pulmonary complications, autoimmune diseases, and metabolic syndromes. Furthermore, it has been recently appreciated that M. tuberculosis infection can also reciprocally interact with the human microbiome, which has a strong link to immune balance and health. In this review, we highlight the adaptive survival of M. tuberculosis within the host and provide an overview for regulatory mechanisms underlying interactions between M. tuberculosis infection and multiple important human diseases. A better understanding of how M. tuberculosis regulates the host immune system to cause TB and reciprocally regulates other human diseases is critical for developing rational treatments to better control TB and help alleviate its associated comorbidities.
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Affiliation(s)
- Qiyao Chai
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Yong Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Cui Hua Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
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45
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Gupta N, Kumar R, Agrawal B. New Players in Immunity to Tuberculosis: The Host Microbiome, Lung Epithelium, and Innate Immune Cells. Front Immunol 2018; 9:709. [PMID: 29692778 PMCID: PMC5902499 DOI: 10.3389/fimmu.2018.00709] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 03/22/2018] [Indexed: 12/31/2022] Open
Abstract
Tuberculosis (TB) is a highly contagious infection and devastating chronic disease, causing 10.4 million new infections and 1.8 million deaths every year globally. Efforts to control and eradicate TB are hampered by the rapid emergence of drug resistance and limited efficacy of the only available vaccine, BCG. Immunological events in the airways and lungs are of major importance in determining whether exposure to Mycobacterium tuberculosis (Mtb) results in successful infection or protective immunity. Several studies have demonstrated that the host microbiota is in constant contact with the immune system, and thus continually directs the nature of immune responses occurring during new infections. However, little is known about its role in the eventual outcome of the mycobacterial infection. In this review, we highlight the changes in microbial composition in the respiratory tract and gut that have been linked to the alteration of immune responses, and to the risk, prevention, and treatment of TB. In addition, we summarize our current understanding of alveolar epithelial cells and the innate immune system, and their interaction with Mtb during early infection. Extensive studies are warranted to fully understand the all-inclusive role of the lung microbiota, its interaction with epithelium and innate immune responses and resulting adaptive immune responses, and in the pathogenesis and/or protection from Mtb infection. Novel interventions aimed at influencing the microbiota, the alveolar immune system and innate immunity will shape future strategies of prevention and treatment for TB.
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Affiliation(s)
- Nancy Gupta
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Rakesh Kumar
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Babita Agrawal
- Department of Surgery, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
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46
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Mhimbira F, Hiza H, Mbuba E, Hella J, Kamwela L, Sasamalo M, Ticlla M, Said K, Mhalu G, Chiryamkubi M, Schindler C, Reither K, Gagneux S, Fenner L. Prevalence and clinical significance of respiratory viruses and bacteria detected in tuberculosis patients compared to household contact controls in Tanzania: a cohort study. Clin Microbiol Infect 2018; 25:107.e1-107.e7. [PMID: 29581053 PMCID: PMC7128396 DOI: 10.1016/j.cmi.2018.03.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 03/04/2018] [Accepted: 03/13/2018] [Indexed: 01/27/2023]
Abstract
OBJECTIVES To describe the prevalence of respiratory pathogens in tuberculosis (TB) patients and in their household contact controls, and to determine the clinical significance of respiratory pathogens in TB patients. METHODS We studied 489 smear-positive adult TB patients and 305 household contact controls without TB with nasopharyngeal swab samples within an ongoing prospective cohort study in Dar es Salaam, Tanzania, between 2013 and 2015. We used multiplex real-time PCR to detect 16 respiratory viruses and seven bacterial pathogens from nasopharyngeal swabs. RESULTS The median age of the study participants was 33 years; 61% (484/794) were men, and 21% (168/794) were HIV-positive. TB patients had a higher prevalence of HIV (28.6%; 140/489) than controls (9.2%; 28/305). Overall prevalence of respiratory viral pathogens was 20.4% (160/794; 95%CI 17.7-23.3%) and of bacterial pathogens 38.2% (303/794; 95%CI 34.9-41.6%). TB patients and controls did not differ in the prevalence of respiratory viruses (Odds Ratio [OR] 1.00, 95%CI 0.71-1.44), but respiratory bacteria were less frequently detected in TB patients (OR 0.70, 95%CI 0.53-0.94). TB patients with both respiratory viruses and respiratory bacteria were likely to have more severe disease (adjusted OR [aOR] 1.6, 95%CI 1.1-2.4; p 0.011). TB patients with respiratory viruses tended to have more frequent lung cavitations (aOR 1.6, 95%CI 0.93-2.7; p 0.089). CONCLUSIONS Respiratory viruses are common for both TB patients and household controls. TB patients may present with more severe TB disease, particularly when they are co-infected with both bacteria and viruses.
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Affiliation(s)
- F Mhimbira
- Department of Intervention and Clinical Trials, Ifakara Health Institute, Dar es Salaam, Tanzania; Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland.
| | - H Hiza
- Department of Intervention and Clinical Trials, Ifakara Health Institute, Dar es Salaam, Tanzania
| | - E Mbuba
- Department of Intervention and Clinical Trials, Ifakara Health Institute, Dar es Salaam, Tanzania
| | - J Hella
- Department of Intervention and Clinical Trials, Ifakara Health Institute, Dar es Salaam, Tanzania; Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland
| | - L Kamwela
- Department of Intervention and Clinical Trials, Ifakara Health Institute, Dar es Salaam, Tanzania
| | - M Sasamalo
- Department of Intervention and Clinical Trials, Ifakara Health Institute, Dar es Salaam, Tanzania
| | - M Ticlla
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - K Said
- Department of Intervention and Clinical Trials, Ifakara Health Institute, Dar es Salaam, Tanzania; Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland
| | - G Mhalu
- Department of Intervention and Clinical Trials, Ifakara Health Institute, Dar es Salaam, Tanzania; Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland
| | - M Chiryamkubi
- Department of Curative Services, Ministry of Health, Community Development, Gender, Elderly and Children, Dar es Salaam, Tanzania
| | - C Schindler
- University of Basel, Basel, Switzerland; Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - K Reither
- University of Basel, Basel, Switzerland; Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - S Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland
| | - L Fenner
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
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47
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Pearl JE, Das M, Cooper AM. Immunological roulette: Luck or something more? Considering the connections between host and environment in TB. Cell Mol Immunol 2018; 15:226-232. [PMID: 29375129 DOI: 10.1038/cmi.2017.145] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 10/24/2017] [Accepted: 10/29/2017] [Indexed: 02/07/2023] Open
Abstract
Accurate prediction of which patient will progress from a sub-clinical Mycobacterium tuberculosis infection to active tuberculosis represents an elusive, yet critical, clinical research objective. From the individual perspective, progression can be considered to be the product of a series of unfortunate events or even a run of bad luck. Here, we identify the subtle physiological relationships that can influence the odds of progression to active TB and how this progression may reflect directed dysbiosis in a number of interrelated systems. Most infected individuals who progress to disease have apparently good immune responses, but these responses are, at times, compromised by either local or systemic environmental factors. Obvious disease promoting processes, such as tissue-damaging granulomata, usually manifest in the lung, but illness is systemic. This apparent dichotomy between local and systemic reflects a clear need to define the factors that promote progression to active disease within the context of the body as a physiological whole. We discuss aspects of the host environment that can impact expression of immunity, including the microbiome, glucocorticoid-mediated regulation, catecholamines and interaction between the gut, liver and lung. We suggest the importance of integrating precision medicine into our analyses of experimental outcomes such that apparently conflicting results are not contentious, but rather reflect the impact of these subtle relationships with our environment and microbiota.
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Affiliation(s)
- John E Pearl
- Leicester Tuberculosis Research Group (LTBRG), Department of Infection Immunity and Inflammation, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Mrinal Das
- Leicester Tuberculosis Research Group (LTBRG), Department of Infection Immunity and Inflammation, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Andrea M Cooper
- Leicester Tuberculosis Research Group (LTBRG), Department of Infection Immunity and Inflammation, University of Leicester, University Road, Leicester LE1 7RH, UK
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48
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Maji A, Misra R, Dhakan DB, Gupta V, Mahato NK, Saxena R, Mittal P, Thukral N, Sharma E, Singh A, Virmani R, Gaur M, Singh H, Hasija Y, Arora G, Agrawal A, Chaudhry A, Khurana JP, Sharma VK, Lal R, Singh Y. Gut microbiome contributes to impairment of immunity in pulmonary tuberculosis patients by alteration of butyrate and propionate producers. Environ Microbiol 2017; 20:402-419. [PMID: 29322681 DOI: 10.1111/1462-2920.14015] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 11/30/2017] [Indexed: 12/31/2022]
Abstract
Tuberculosis (TB) is primarily associated with decline in immune health status. As gut microbiome (GM) is implicated in the regulation of host immunity and metabolism, here we investigate GM alteration in TB patients by 16S rRNA gene and whole-genome shotgun sequencing. The study group constituted of patients with pulmonary TB and their healthy household contacts as controls (HCs). Significant alteration of microbial taxonomic and functional capacity was observed in patients with active TB as compared to the HCs. We observed that Prevotella and Bifidobacterium abundance were associated with HCs, whereas butyrate and propionate-producing bacteria like Faecalibacterium, Roseburia, Eubacterium and Phascolarctobacterium were significantly enriched in TB patients. Functional analysis showed reduced biosynthesis of vitamins and amino acids in favour of enriched metabolism of butyrate and propionate in TB subjects. The TB subjects were also investigated during the course of treatment, to analyse the variation of GM. Although perturbation in microbial composition was still evident after a month's administration of anti-TB drugs, significant changes were observed in metagenome gene pool that pointed towards recovery in functional capacity. Therefore, the findings from this pilot study suggest that microbial dysbiosis may contribute to pathophysiology of TB by enhancing the anti-inflammatory milieu in the host.
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Affiliation(s)
- Abhijit Maji
- Department of Microbial Pathogenesis, CSIR-Institute of Genomics & Integrative Biology (IGIB), Mall Road, Delhi, India.,Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, India
| | - Richa Misra
- Department of Microbial Pathogenesis, CSIR-Institute of Genomics & Integrative Biology (IGIB), Mall Road, Delhi, India.,Department of Zoology, University of Delhi, Delhi, India.,Department of Zoology, Sri Venkateswara College, University of Delhi, India
| | - Darshan B Dhakan
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, India
| | - Vipin Gupta
- Department of Zoology, University of Delhi, Delhi, India
| | | | - Rituja Saxena
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, India
| | - Parul Mittal
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, India
| | - Nitin Thukral
- Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Eshan Sharma
- Department of Plant Molecular Biology, University of Delhi, Delhi, India
| | - Anoop Singh
- Department of Zoology, University of Delhi, Delhi, India
| | - Richa Virmani
- Department of Microbial Pathogenesis, CSIR-Institute of Genomics & Integrative Biology (IGIB), Mall Road, Delhi, India.,Department of Plant Molecular Biology, University of Delhi, Delhi, India
| | - Mohita Gaur
- Department of Zoology, University of Delhi, Delhi, India
| | - Harshvardhan Singh
- Department of Biochemistry, Hindu Rao Hospital, Malka Ganj, Delhi, India
| | - Yasha Hasija
- Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Gunjan Arora
- Department of Microbial Pathogenesis, CSIR-Institute of Genomics & Integrative Biology (IGIB), Mall Road, Delhi, India
| | - Anurag Agrawal
- Department of Microbial Pathogenesis, CSIR-Institute of Genomics & Integrative Biology (IGIB), Mall Road, Delhi, India
| | - Anil Chaudhry
- Department of TB and Chest, Rajan Babu Institute of Pulmonary Medicine and Tuberculosis (RBIPMT), Kingsway Camp, Delhi, India
| | - Jitendra P Khurana
- Department of Plant Molecular Biology, University of Delhi, Delhi, India
| | - Vineet K Sharma
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, India
| | - Rup Lal
- Department of Zoology, University of Delhi, Delhi, India
| | - Yogendra Singh
- Department of Microbial Pathogenesis, CSIR-Institute of Genomics & Integrative Biology (IGIB), Mall Road, Delhi, India.,Department of Zoology, University of Delhi, Delhi, India
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49
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Luo M, Liu Y, Wu P, Luo DX, Sun Q, Zheng H, Hu R, Pandol SJ, Li QF, Han YP, Zeng Y. Alternation of Gut Microbiota in Patients with Pulmonary Tuberculosis. Front Physiol 2017; 8:822. [PMID: 29204120 PMCID: PMC5698276 DOI: 10.3389/fphys.2017.00822] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 10/06/2017] [Indexed: 12/11/2022] Open
Abstract
One-third of the world's population has been infected with Mycobacterium tuberculosis (M. tuberculosis), a primary pathogen of the mammalian respiratory system, while about 10% of latent infections progress to active tuberculosis (TB), indicating that host and environmental factors may determine the outcomes such as infection clearance/persistence and treatment prognosis. The gut microbiota is essential for development of host immunity, defense, nutrition and metabolic homeostasis. Thus, the pattern of gut microbiota may contribute to M. tuberculosis infection and prognosis. In current study we characterized the differences in gut bacterial communities in new tuberculosis patients (NTB), recurrent tuberculosis patients (RTB), and healthy control. The abundance-based coverage estimator (ACE) showed the diversity index of the gut microbiota in the patients with recurrent tuberculosis was increased significantly compared with healthy controls (p < 0.05). At the phyla level, Actinobacteria and Proteobacteria, which contain many pathogenic species, were significantly enriched in the feces RTB patients. Conversely, phylum Bacteroidetes, containing a variety of beneficial commensal organisms, was reduced in the patients with the recurrent tuberculosis compared to healthy controls. The Gram-negative genus Prevotella of oral origin from phylum of Bacteroidetes and genus Lachnospira from phylum of Firmicutes were significantly decreased in both the new and recurrent TB patient groups, compared with the healthy control group (p < 0.05). We also found that there was a positive correlation between the gut microbiota and peripheral CD4+ T cell counts in the patients. This study, for the first time, showed associations between gut microbiota with tuberculosis and its clinical outcomes. Maintaining eubiosis, namely homeostasis of gut microbiota, may be beneficial for host recovery and prevention of recurrence of M. tuberculosis infection.
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Affiliation(s)
- Mei Luo
- Center for Growth, Metabolism and Aging, College of Life Sciences, Sichuan University, Chengdu, China.,Public Health and Clinical Center of Chengdu, Chengdu, China
| | - Yong Liu
- Public Health and Clinical Center of Chengdu, Chengdu, China
| | - Pengfei Wu
- Center for Growth, Metabolism and Aging, College of Life Sciences, Sichuan University, Chengdu, China
| | - Dong-Xia Luo
- Public Health and Clinical Center of Chengdu, Chengdu, China
| | - Qun Sun
- Center for Growth, Metabolism and Aging, College of Life Sciences, Sichuan University, Chengdu, China
| | - Han Zheng
- Center for Growth, Metabolism and Aging, College of Life Sciences, Sichuan University, Chengdu, China
| | - Richard Hu
- Olive View-UCLA Medical Center, Los Angeles, CA, United States
| | | | - Qing-Feng Li
- Public Health and Clinical Center of Chengdu, Chengdu, China
| | - Yuan-Ping Han
- Center for Growth, Metabolism and Aging, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yilan Zeng
- Public Health and Clinical Center of Chengdu, Chengdu, China
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50
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Li N, Qiu R, Yang Z, Li J, Chung KF, Zhong N, Zhang Q. Sputum microbiota in severe asthma patients: Relationship to eosinophilic inflammation. Respir Med 2017; 131:192-198. [PMID: 28947029 DOI: 10.1016/j.rmed.2017.08.016] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 08/11/2017] [Accepted: 08/17/2017] [Indexed: 12/21/2022]
Abstract
BACKGROUND Altered composition of airway microbiota has been reported in subjects suffering from asthma but its relation to eosinophilic phenotype is unclear. OBJECTIVE To examine the relationship between sputum microbiota, asthma severity and inflammatory type in asthmatic subjects from Guangzhou, China. METHODS Induced sputum samples were obtained from 49 non-smoking asthma patients, 25 severe and 24 non-severe, and 15 healthy subjects. Total DNA was amplified using primers specific for the V3-V5 hypervariable region of bacterial 16s rRNA and sequenced using the 454 GS FLX sequencer. Sequences were assigned to bacterial taxa by comparing them with 16s rRNA sequences in the Ribosomal Database Project. RESULTS Sputum eosinophil counts were higher and FEV1 (% predicted) was lower in severe compared to non-severe asthmatics. There were no significant differences in operational taxonomic unit (OTU) numbers at the phylum level and in diversity scores between non-severe asthmatics and severe asthmatics, and healthy subjects. At the family level, Porphyromonadaceae was most abundant in healthy subjects whereas Pseudomonadaceae and Enterobacteriaceae were higher in severe asthmatics compared to non-severe asthmatics (p < 0.05). Actinomycetaceae was particularly abundant in eosinophilic asthma patients compared to non-eosinophilic asthma (p = 0.011). Bacteroidaceae was positively correlated with FEV1 in all subjects (r = 0.335, p < 0.01), whereas body mass index was negatively associated with the number of species observed (r = -0.3, p < 0.05). Principal component analysis confirmed the positive association of Actinomycetaceae and Enterobacteriaceae abundance with eosinophilic asthma. CONCLUSION Patients with asthma have an altered airway microbiota, with specific bacteria associated with severe asthma and the eosinophilic inflammatory phenotype.
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Affiliation(s)
- Naijian Li
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Rihuang Qiu
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Zhaowei Yang
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Jing Li
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Kian Fan Chung
- Airways Disease Section, National Heart & Lung Institute, Imperial College London, & Biomedical Research Unit, Royal Brompton Hospital, London, SW3, UK
| | - Nanshan Zhong
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Qingling Zhang
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.
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