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Zhang L, Liu X, Fan B, Chen J, Chen J, Li Q, Wu X. Microbiome features in bronchoalveolar lavage fluid of patients with idiopathic inflammatory myopathy-related interstitial lung disease. Front Med (Lausanne) 2024; 11:1338947. [PMID: 38633306 PMCID: PMC11021725 DOI: 10.3389/fmed.2024.1338947] [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: 11/15/2023] [Accepted: 03/08/2024] [Indexed: 04/19/2024] Open
Abstract
Background Interstitial lung disease (ILD) is a common complication of idiopathic inflammatory myopathy (IIM), which is one of the connective tissue diseases (CTD). It can lead to poor prognosis and increased mortality. However, the distribution and role of the lower respiratory tract (LRT) microbiome in patients with IIM-ILD remains unclear. This study aimed to investigate the microbial diversity and community differences in bronchoalveolar lavage fluid (BALF) in patients with IIM-ILD. Methods From 28 June 2021 to 26 December 2023, 51 individual BALF samples were enrolled, consisting of 20 patients with IIM-ILD, 16 patients with other CTD-ILD (including 8 patients with SLE and 8 with RA) and 15 patients with CAP. The structure and function of microbiota in BALF were identified by metagenomic next-generation sequencing (mNGS). Results The community evenness of LRT microbiota within the IIM-ILD group was marginally lower compared to the other CTD-ILD and CAP groups. Nonetheless, there were no noticeable differences. The species community structure was similar among the three groups, based on the Bray-Curtis distance between the samples. At the level of genus, the IIM-ILD group displayed a considerably higher abundance of Pseudomonas and Corynebacterium in comparison to the CAP group (p < 0.01, p < 0.05). At the species level, we found that the relative abundance of Pseudomonas aeruginosa increased significantly in the IIM-ILD group compared to the CAP group (p < 0.05). Additionally, the relative abundance of Prevotella pallens was significantly higher in other CTD-ILD groups compared to that in the IIM-ILD group (p < 0.05). Of all the clinical indicators examined in the correlation analysis, ferritin level demonstrated the strongest association with LRT flora, followed by Serum interleukin-6 level (p < 0.05). Conclusion Our research has identified particular LRT microorganisms that were found to be altered in the IIM-ILD group and were significantly associated with immune function and inflammatory markers in patients. The lower respiratory tract microbiota has potential in the diagnosis and treatment of IIM-ILD.
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Affiliation(s)
- Liyan Zhang
- Department of Respiratory and Critical Care Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xueqing Liu
- Department of Respiratory and Critical Care Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bijun Fan
- Department of Respiratory and Critical Care Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiajun Chen
- Department of Respiratory and Critical Care Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie Chen
- Department of Rheumatology Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qiuhong Li
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xueling Wu
- Department of Respiratory and Critical Care Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Drigot ZG, Clark SE. Insights into the role of the respiratory tract microbiome in defense against bacterial pneumonia. Curr Opin Microbiol 2024; 77:102428. [PMID: 38277901 PMCID: PMC10922932 DOI: 10.1016/j.mib.2024.102428] [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: 09/26/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 01/28/2024]
Abstract
The respiratory tract microbiome (RTM) is a microbial ecosystem inhabiting different niches throughout the airway. A critical role for the RTM in dictating lung infection outcomes is underlined by recent efforts to identify community members benefiting respiratory tract health. Obligate anaerobes common in the oropharynx and lung such as Prevotella and Veillonella are associated with improved pneumonia outcomes and activate several immune defense pathways in the lower airway. Colonizers of the nasal cavity, including Corynebacterium and Dolosigranulum, directly impact the growth and virulence of lung pathogens, aligning with robust clinical correlations between their upper airway abundance and reduced respiratory tract infection risk. Here, we highlight recent work identifying respiratory tract bacteria that promote airway health and resilience against disease, with a focus on lung infections and the underlying mechanisms driving RTM-protective benefits.
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Affiliation(s)
- Zoe G Drigot
- University of Colorado School of Medicine, Department of Otolaryngology, Aurora, CO 80045, USA
| | - Sarah E Clark
- University of Colorado School of Medicine, Department of Otolaryngology, Aurora, CO 80045, USA.
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Belizário J, Garay-Malpartida M, Faintuch J. Lung microbiome and origins of the respiratory diseases. CURRENT RESEARCH IN IMMUNOLOGY 2023; 4:100065. [PMID: 37456520 PMCID: PMC10339129 DOI: 10.1016/j.crimmu.2023.100065] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 05/08/2023] [Accepted: 06/13/2023] [Indexed: 07/18/2023] Open
Abstract
The studies on the composition of the human microbiomes in healthy individuals, its variability in the course of inflammation, infection, antibiotic therapy, diets and different pathological conditions have revealed their intra and inter-kingdom relationships. The lung microbiome comprises of major species members of the phylum Bacteroidetes, Firmicutes, Actinobacteria, Fusobacteria and Proteobacteria, which are distributed in ecological niches along nasal cavity, nasopharynx, oropharynx, trachea and in the lungs. Commensal and pathogenic species are maintained in equilibrium as they have strong relationships. Bacterial overgrowth after dysbiosis and/or imbalanced of CD4+ helper T cells, CD8+ cytotoxic T cells and regulatory T cells (Treg) populations can promote lung inflammatory reactions and distress, and consequently acute and chronic respiratory diseases. This review is aimed to summarize the latest advances in resident lung microbiome and its participation in most common pulmonary infections and pneumonia, community-acquired pneumonia (CAP), ventilator-associated pneumonia (VAP), immunodeficiency associated pneumonia, SARS-CoV-2-associated pneumonia, acute respiratory distress syndrome (ARDS) and chronic obstructive pulmonary disease (COPD). We briefly describe physiological and immunological mechanisms that selectively create advantages or disadvantages for relative growth of pathogenic bacterial species in the respiratory tract. At the end, we propose some directions and analytical methods that may facilitate the identification of key genera and species of resident and transient microbes involved in the respiratory diseases' initiation and progression.
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Affiliation(s)
- José Belizário
- School of Arts, Sciences and Humanities of the University of Sao Paulo, Rua Arlindo Bettio, 1000, São Paulo, CEP 03828-000, Brazil
| | - Miguel Garay-Malpartida
- School of Arts, Sciences and Humanities of the University of Sao Paulo, Rua Arlindo Bettio, 1000, São Paulo, CEP 03828-000, Brazil
| | - Joel Faintuch
- Department of Gastroenterology of the Clinics Hospital of the University of São Paulo, Av. Dr. Enéas de Carvalho Aguiar, 255, São Paulo, CEP 05403-000, Brazil
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He Y, Li J, Yu W, Zheng Y, Yang D, Xu Y, Zhao L, Ma X, Gong P, Gao Z. Characteristics of lower respiratory tract microbiota in the patients with post-hematopoietic stem cell transplantation pneumonia. Front Cell Infect Microbiol 2022; 12:943317. [PMID: 36176576 PMCID: PMC9513191 DOI: 10.3389/fcimb.2022.943317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/23/2022] [Indexed: 11/25/2022] Open
Abstract
Background Pneumonia is a leading cause of non-relapse mortality after hematopoietic stem cell transplantation (HSCT), and the lower respiratory tract (LRT) microbiome has been proven to be associated with various respiratory diseases. However, little is known about the characteristics of the LRT microbiome in patients with post-HSCT compared to healthy controls (HC) and community-acquired pneumonia (CAP). Methods Bronchoalveolar lavage samples from 55 patients with post-HSCT pneumonia, 44 patients with CAP, and 30 healthy volunteers were used to detect microbiota using 16S rRNA gene sequencing. Results The diversity of the LRT microbiome significantly decreased in patients with post-HSCT pneumonia, and the overall community was different from the CAP and HC groups. At the phylum level, post-HSCT pneumonia samples had a high abundance of Actinobacteria and a relatively low abundance of Bacteroidetes. The same is true for non-survivors compared with survivors in patients with post-HSCT pneumonia. At the genus level, the abundances of Pseudomonas, Acinetobacter, Burkholderia, and Mycobacterium were prominent in the pneumonia group after HSCT. On the other hand, gut-associated bacteria, Enterococcus were more abundant in the non-survivors. Some pathways concerning amino acid and lipid metabolism were predicted to be altered in patients with post-HSCT pneumonia. Conclusions Our results reveal that the LRT microbiome in patients with post-HSCT pneumonia differs from CAP patients and healthy controls, which could be associated with the outcome. The LRT microbiota could be a target for intervention during post-HSCT pneumonia.
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Affiliation(s)
- Yukun He
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Jia Li
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Wenyi Yu
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Yali Zheng
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
- Department of Respiratory, Critical Care, and Sleep Medicine, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Donghong Yang
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Yu Xu
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Lili Zhao
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Xinqian Ma
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Pihua Gong
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
- *Correspondence: Pihua Gong, ; Zhancheng Gao,
| | - Zhancheng Gao
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
- *Correspondence: Pihua Gong, ; Zhancheng Gao,
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Yang X, Chang T, Yuan Q, Wei W, Wang P, Song X, Yuan H. Changes in the composition of gut and vaginal microbiota in patients with postmenopausal osteoporosis. Front Immunol 2022; 13:930244. [PMID: 36032115 PMCID: PMC9411790 DOI: 10.3389/fimmu.2022.930244] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
Background Postmenopausal osteoporosis (PMO) is influenced by estrogen metabolism and immune response, which are modulated by several factors including the microbiome and inflammation. Therefore, there is increasing interest in understanding the role of microbiota in PMO. Objectives To investigate variations in gut microbiota (GM) and vaginal microbiota (VM) in postmenopausal women with osteoporosis. Methods A total of 132 postmenopausal women were recruited for the study and divided into osteoporosis (n = 34), osteopenia (n = 47), and control (n = 51) groups based on their T score. The serum levels of interleukin (IL)-10, tumor necrosis factor (TNF)-α, and lipopolysaccharide-binding protein were determined via enzyme-linked immunosorbent assay. Additionally, 16S rRNA gene V3-V4 region sequencing was performed to investigate the GM and VM of the participants. Results Significant differences were observed in the microbial compositions of fecal and vaginal samples between groups (p < 0.05). It was noted that for GM, Romboutsia, unclassified_Mollicutes, and Weissella spp. were enriched in the control group, whereas the abundances of Fusicatenibacter, Lachnoclostridium, and Megamonas spp. were higher in the osteoporosis group than in the other groups. Additionally, for VM, Lactobacillus was enriched in the control group, whereas the abundances of Peptoniphilus, Propionimicrobium, and Gallicola spp. were higher in the osteoporosis group than in the other groups. The predicted functional capacities of GM and VM were different in the various groups. We also found that the serum level of IL-10 in the osteoporosis group was significantly lower than that in the control group and osteopenia group, while TNF-α was significantly higher in the osteoporosis group than that in the control group (p < 0.05). Conclusion The results show that changes in BMD in postmenopausal women are associated with the changes in GM and VM; however, changes in GM are more closely correlated with PMO than VM.
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Affiliation(s)
- Xueli Yang
- Department of Endocrinology of Henan Provincial People’s Hospital, Henan Provincial Key Laboratory of Intestinal Microecology and Diabetes Control, People’s Hospital of Zhengzhou University, Henan Provincial People’s Hospital of Henan University, Zhengzhou, China
| | - Tian Chang
- Department of Endocrinology of Henan Provincial People’s Hospital, Henan Provincial Key Laboratory of Intestinal Microecology and Diabetes Control, People’s Hospital of Zhengzhou University, Henan Provincial People’s Hospital of Henan University, Zhengzhou, China
- Department of Medical and Health, Zhengzhou University Press, Zhengzhou, China
| | - Qian Yuan
- Department of Endocrinology of Henan Provincial People’s Hospital, Henan Provincial Key Laboratory of Intestinal Microecology and Diabetes Control, People’s Hospital of Zhengzhou University, Henan Provincial People’s Hospital of Henan University, Zhengzhou, China
| | - Wei Wei
- Department of Endocrinology of Henan Provincial People’s Hospital, Henan Provincial Key Laboratory of Intestinal Microecology and Diabetes Control, People’s Hospital of Zhengzhou University, Henan Provincial People’s Hospital of Henan University, Zhengzhou, China
| | - Pingping Wang
- Department of Endocrinology of Henan Provincial People’s Hospital, Henan Provincial Key Laboratory of Intestinal Microecology and Diabetes Control, People’s Hospital of Zhengzhou University, Henan Provincial People’s Hospital of Henan University, Zhengzhou, China
| | - Xiaojian Song
- Department of Endocrinology of Henan Provincial People’s Hospital, Henan Provincial Key Laboratory of Intestinal Microecology and Diabetes Control, People’s Hospital of Zhengzhou University, Henan Provincial People’s Hospital of Henan University, Zhengzhou, China
| | - Huijuan Yuan
- Department of Endocrinology of Henan Provincial People’s Hospital, Henan Provincial Key Laboratory of Intestinal Microecology and Diabetes Control, People’s Hospital of Zhengzhou University, Henan Provincial People’s Hospital of Henan University, Zhengzhou, China
- *Correspondence: Huijuan Yuan,
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Jiang Q, Xu Q, Kenéz Á, Chen S, Yang G. Klebsiella pneumoniae infection is associated with alterations in the gut microbiome and lung metabolome. Microbiol Res 2022; 263:127139. [PMID: 35905579 DOI: 10.1016/j.micres.2022.127139] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/06/2022] [Accepted: 07/20/2022] [Indexed: 10/17/2022]
Abstract
Gut microbiota is involved in maintaining homeostasis, and intestinal dysbiosis may lead to opportunistic infections and diseases. Pathogens can disrupt the gut homeostasis and establish colonization, but how they modulate the microbiome and metabolome along the gut-lung axis warrants further investigation. In the present study, we used a classical low virulence Klebsiella pneumoniae (cKp) strain to address this question. We assessed the gut microbiome and lung metabolome in cKp-infected mice by 16S rRNA sequencing and untargeted liquid chromatography-mass spectrometry, respectively. Our data revealed that cKp infection reduced gut microbiota diversity and altered microbiome composition. Specifically, cKp infection increased the abundance of MWH-CFBk5 and Actinomadura and reduced the abundance of Lachnospiraceae_NK4A136_group, Clostridium sensu_stricto 1, Bifidobacterium, and Intestinimonas at the genus level. Notably, caffeine and caffeine metabolism were significantly affected in the lung by cKp infection. Moreover, Spearman correlation analysis revealed remarkable correlations of specific lung metabolites and bacteria species at the genus level. These findings suggest that cKp infection is linked to gut dysbiosis and alterations in the lung metabolome. This study is of significance for developing innovative gut microbiota-directed therapy for respiratory diseases.
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Affiliation(s)
- Qianling Jiang
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon 999077, Hong Kong Special Administrative Region of China
| | - Qi Xu
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon 999077, Hong Kong Special Administrative Region of China
| | - Ákos Kenéz
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon 999077, Hong Kong Special Administrative Region of China.
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon 999077, Hong Kong Special Administrative Region of China.
| | - Guan Yang
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon 999077, Hong Kong Special Administrative Region of China.
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Horn KJ, Schopper MA, Drigot ZG, Clark SE. Airway Prevotella promote TLR2-dependent neutrophil activation and rapid clearance of Streptococcus pneumoniae from the lung. Nat Commun 2022; 13:3321. [PMID: 35680890 PMCID: PMC9184549 DOI: 10.1038/s41467-022-31074-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 05/31/2022] [Indexed: 12/13/2022] Open
Abstract
This study investigates how specific members of the lung microbiome influence the early immune response to infection. Prevotella species are a major component of the endogenous airway microbiota. Increased abundance of Prevotella melaninogenica correlates with reduced infection with the bacterial pathogen Streptococcus pneumoniae, indicating a potentially beneficial role. Here, we show that P. melaninogenica enhances protection against S. pneumoniae, resulting in rapid pathogen clearance from the lung and improved survival in a mouse lung co-infection model. This response requires recognition of P. melaninogenica lipoproteins by toll-like receptor (TLR)2, the induction of TNFα, and neutrophils, as the loss of any of these factors abrogates Prevotella-induced protection. Improved clearance of S. pneumoniae is associated with increased serine protease-mediated killing by lung neutrophils and restraint of P. melaninogenica-induced inflammation by IL-10 in co-infected mice. Together, these findings highlight innate immune priming by airway Prevotella as an important protective feature in the respiratory tract. How the airway microbiome protects against bacterial pneumonia remains unclear. Here, the authors identify airway bacterial species that activate the immune system to facilitate rapid clearance of the pathogen Streptococcus pneumoniae from the lung.
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Affiliation(s)
- Kadi J Horn
- University of Colorado School of Medicine, Department of Otolaryngology, Aurora, CO, 80045, USA
| | - Melissa A Schopper
- University of Colorado School of Medicine, Department of Otolaryngology, Aurora, CO, 80045, USA
| | - Zoe G Drigot
- University of Colorado School of Medicine, Department of Otolaryngology, Aurora, CO, 80045, USA.,University of Colorado Boulder, College of Arts and Sciences, Boulder, CO, 80309, USA
| | - Sarah E Clark
- University of Colorado School of Medicine, Department of Otolaryngology, Aurora, CO, 80045, USA.
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