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Hernandez-Leyva AJ, Rosen AL, Tomera CP, Lin EE, Akaho EH, Blatz AM, Otto WR, Logan J, Young LR, Harris RM, Kau AL, John ARO. Developmental progression of the nasopharyngeal microbiome during childhood and association with the lower airway microbiome. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.18.23295747. [PMID: 37790477 PMCID: PMC10543049 DOI: 10.1101/2023.09.18.23295747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Background The upper (URT) and lower (LRT) respiratory tract feature distinct environments and responses affecting microbial colonization but investigating the relationship between them is technically challenging. We aimed to identify relationships between taxa colonizing the URT and LRT and explore their relationship with development during childhood. Methods We employed V4 16S rDNA sequencing to profile nasopharyngeal swabs and tracheal aspirates collected from 183 subjects between 20 weeks and 18 years of age. These samples were collected prior to elective procedures at the Children's Hospital of Philadelphia over the course of 20 weeks in 2020, from otherwise healthy subjects enrolled in a study investigating potential reservoirs of SARS-CoV-2. Findings After extraction, sequencing, and quality control, we studied the remaining 124 nasopharyngeal swabs and 98 tracheal aspirates, including 85 subject-matched pairs of samples. V4 16S rDNA sequencing revealed that the nasopharynx is colonized by few, highly-abundant taxa, while the tracheal aspirates feature a diverse assembly of microbes. While no taxa co-occur in the URT and LRT of the same subject, clusters of microbiomes in the URT correlate with clusters of microbiomes in the LRT. The clusters identified in the URT correlate with subject age across childhood development. Interpretations The correlation between clusters of taxa across sites may suggest a mutual influence from either a third site, such as the oropharynx, or host-extrinsic, environmental features. The identification of a pattern of upper respiratory microbiota development across the first 18 years of life suggests that the patterns observed in early childhood may extend beyond the early life window.
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Affiliation(s)
- Ariel J Hernandez-Leyva
- Division of Allergy and Immunology, Department of Medicine and Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Anne L Rosen
- Division of Allergy and Immunology, Department of Medicine and Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Christopher P Tomera
- Division of Allergy and Immunology, Department of Medicine and Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Elaina E Lin
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Anesthesiology and Critical Care Medicine, Children's Hospital of Philadelphia, Philadelphia PA
| | - Elikplim H Akaho
- Division of Infectious Diseases, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia PA
- Department of Medicine, John H. Stroger, Jr. Hospital of Cook County
| | - Allison M Blatz
- Division of Infectious Diseases, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia PA
- Division of Critical Care Medicine, Department of Pediatrics, Nemours Children's Hospital, Wilmington DE
| | - William R Otto
- Division of Infectious Diseases, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia PA
- Division of Infectious Disease, Cincinnati Children's Hospital Medical Center; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Joey Logan
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia PA
| | - Lisa R Young
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Pulmonary and Sleep Medicine, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia PA
| | - Rebecca M Harris
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia PA
| | - Andrew L Kau
- Division of Allergy and Immunology, Department of Medicine and Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Audrey R Odom John
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Infectious Diseases, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia PA
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Zhou Y, Liu M, Liu K, Wu G, Tan Y. Lung microbiota and potential treatment of respiratory diseases. Microb Pathog 2023:106197. [PMID: 37321423 DOI: 10.1016/j.micpath.2023.106197] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 05/21/2023] [Accepted: 06/06/2023] [Indexed: 06/17/2023]
Abstract
The unique microbiome found in the lungs has been studied and shown to be associated with both pulmonary homeostasis and lung diseases. The lung microbiome has the potential to produce metabolites that modulate host-microbe interactions. Specifically, short-chain fatty acids (SCFAs) produced by certain strains of the lung microbiota have been shown to regulate immune function and maintain gut mucosal health. In response, this review described the distribution and composition of the microbiota in lung diseases and discussed the impact of the lung microbiota on health and lung disease. In addition, the review further elaborated on the mechanism of microbial metabolites in microbial-host interaction and their application in the treatment of lung diseases. A better understanding of the interaction between the microbiota, metabolites, and host will provide potential strategies for the development of novel methods for the treatment of pulmonary microbial induced lung diseases.
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Affiliation(s)
- Yaxuan Zhou
- Department of Psychiatry, Department of Medicine, Xiangya School of Medical, Central South University, Changsha, 410083, Hunan, China
| | - Mengjun Liu
- Department of Clinical Medicine, Xiangya School of Medicine, Central South University, Changsha, 410083, Hunan, China
| | - Kaixuan Liu
- Department of Excellent Doctor Training, Xiangya School of Medicine, Central South University, Changsha, 410083, Hunan, China
| | - Guojun Wu
- Department of Medical Microbiology, School of Basic Medicine, Central South University, Changsha, 410083, Hunan, China.
| | - Yurong Tan
- Department of Medical Microbiology, School of Basic Medicine, Central South University, Changsha, 410083, Hunan, China.
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Editorial overview of Pearls Microbiome Series: E pluribus unum. PLoS Pathog 2021; 17:e1009912. [PMID: 34464427 PMCID: PMC8407538 DOI: 10.1371/journal.ppat.1009912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Hsieh CS, Rengarajan S, Kau A, Tarazona-Meza C, Nicholson A, Checkley W, Romero K, Hansel NN. Altered IgA Response to Gut Bacteria Is Associated with Childhood Asthma in Peru. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2021; 207:398-407. [PMID: 34193598 PMCID: PMC8516662 DOI: 10.4049/jimmunol.2001296] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 04/28/2021] [Indexed: 12/24/2022]
Abstract
Alterations in gut microbiota in early life have been associated with the development of asthma; however, the role of gut bacteria or the IgA response to gut bacteria in school-aged children with asthma is unclear. To address this question, we profiled the microbial populations in fecal and nasal swab samples by 16S rRNA sequencing from 40 asthma and 40 control children aged 9-17 y from Peru. Clinical history and laboratory evaluation of asthma and allergy were obtained. Fecal samples were analyzed by flow cytometry and sorted into IgA+ and IgA- subsets for 16S rRNA sequencing. We found that the fecal or nasal microbial 16S rRNA diversity and frequency of IgA+ fecal bacteria did not differ between children with or without asthma. However, the α diversity of fecal IgA+ bacteria was decreased in asthma compared with control. Machine learning analysis of fecal bacterial IgA-enrichment data revealed loss of IgA binding to the Blautia, Ruminococcus, and Lachnospiraceae taxa in children with asthma compared with controls. In addition, this loss of IgA binding was associated with worse asthma control (Asthma Control Test) and increased odds of severe as opposed to mild to moderate asthma. Thus, despite little to no change in the microbiota, children with asthma exhibit an altered host IgA response to gut bacteria compared with control participants. Notably, the signature of altered IgA responses is loss of IgA binding, in particular to members of Clostridia spp., which is associated with greater severity of asthma.
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Affiliation(s)
- Chyi-Song Hsieh
- Division of Rheumatology, John T. Milliken Department of Internal Medicine, Washington University School of Medicine, Saint Louis, MO;
| | - Sunaina Rengarajan
- Division of Rheumatology, John T. Milliken Department of Internal Medicine, Washington University School of Medicine, Saint Louis, MO
| | - Andrew Kau
- Division of Allergy and Immunology, John T. Milliken Department of Internal Medicine, Washington University School of Medicine, Saint Louis, MO
| | - Carla Tarazona-Meza
- Asociacion Benefica Prisma, PRISMA, Lima, Peru
- Center for Global Non-Communicable Disease Research and Training, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Andrew Nicholson
- Program in Global Disease Epidemiology and Control, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD; and
| | - William Checkley
- Center for Global Non-Communicable Disease Research and Training, Johns Hopkins University School of Medicine, Baltimore, MD
- Program in Global Disease Epidemiology and Control, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD; and
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Karina Romero
- Asociacion Benefica Prisma, PRISMA, Lima, Peru
- Center for Global Non-Communicable Disease Research and Training, Johns Hopkins University School of Medicine, Baltimore, MD
- Program in Global Disease Epidemiology and Control, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD; and
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Nadia N Hansel
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
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Abstract
The global COVID-19 pandemic has brought respiratory disease to the forefront of public health, but asthma prevalence has been rising globally for decades. Asthma is mediated by errant immune activation and airway remodeling, but the influences of environment, nutrition, and comorbidities (e.g., asthma-chronic obstructive pulmonary disorder-overlap [ACO]) are still poorly understood. Even as a new generation of biologic-based treatments offer better airway control and reductions in mortality, a lack of prophylactic treatments and mechanistic understanding complicates efforts to prevent pathogenesis. This review will explicate and synthesize current knowledge on the effect of ACO and biologics (omalizumab, mepolizumab, reslizumab, benralizumab, and dupilumab) on pathogenesis, treatment, and prognosis.
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The intersect of genetics, environment, and microbiota in asthma-perspectives and challenges. J Allergy Clin Immunol 2021; 147:781-793. [PMID: 33678251 DOI: 10.1016/j.jaci.2020.08.026] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/07/2020] [Accepted: 08/05/2020] [Indexed: 02/07/2023]
Abstract
In asthma, a significant portion of the interaction between genetics and environment occurs through microbiota. The proposed mechanisms behind this interaction are complex and at times contradictory. This review covers recent developments in our understanding of this interaction: the "microbial hypothesis" and the "farm effect"; the role of endotoxin and genetic variation in pattern recognition systems; the interaction with allergen exposure; the additional involvement of host gut and airway microbiota; the role of viral respiratory infections in interaction with the 17q21 and CDHR3 genetic loci; and the importance of in utero and early-life timing of exposures. We propose a unified framework for understanding how all these phenomena interact to drive asthma pathogenesis. Finally, we point out some future challenges for continued research in this field, in particular the need for multiomic integration, as well as the potential utility of asthma endotyping.
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Rich HE, Antos D, Melton NR, Alcorn JF, Manni ML. Insights Into Type I and III Interferons in Asthma and Exacerbations. Front Immunol 2020; 11:574027. [PMID: 33101299 PMCID: PMC7546400 DOI: 10.3389/fimmu.2020.574027] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/25/2020] [Indexed: 01/16/2023] Open
Abstract
Asthma is a highly prevalent, chronic respiratory disease that impacts millions of people worldwide and causes thousands of deaths every year. Asthmatics display different phenotypes with distinct genetic components, environmental causes, and immunopathologic signatures, and are broadly characterized into type 2-high or type 2-low (non-type 2) endotypes by linking clinical characteristics, steroid responsiveness, and molecular pathways. Regardless of asthma severity and adequate disease management, patients may experience acute exacerbations of symptoms and a loss of disease control, often triggered by respiratory infections. The interferon (IFN) family represents a group of cytokines that play a central role in the protection against and exacerbation of various infections and pathologies, including asthma. Type I and III IFNs in particular play an indispensable role in the host immune system to fight off pathogens, which seems to be altered in both pediatric and adult asthmatics. Impaired IFN production leaves asthmatics susceptible to infection and with uncontrolled type 2 immunity, promotes airway hyperresponsiveness (AHR), and inflammation which can lead to asthma exacerbations. However, IFN deficiency is not observed in all asthmatics, and alterations in IFN expression may be independent of type 2 immunity. In this review, we discuss the link between type I and III IFNs and asthma both in general and in specific contexts, including during viral infection, co-infection, and bacterial/fungal infection. We also highlight several studies which examine the potential role for type I and III IFNs as asthma-related therapies.
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Affiliation(s)
- Helen E Rich
- Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, United States
| | - Danielle Antos
- Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, United States
| | - Natalie R Melton
- Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, United States
| | - John F Alcorn
- Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, United States
| | - Michelle L Manni
- Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, United States
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Impact of plant genotype and plant habitat in shaping bacterial pathobiome: a comparative study in olive tree. Sci Rep 2020; 10:3475. [PMID: 32103149 PMCID: PMC7044170 DOI: 10.1038/s41598-020-60596-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/31/2020] [Indexed: 12/02/2022] Open
Abstract
Plant-inhabiting microorganisms interact directly with each other affecting disease progression. However, the role of host plant and plant habitat in shaping pathobiome composition and their implication for host susceptibility/resistance to a particular disease are currently unknown. For the elucidation of these questions, both epiphytic and endophytic bacterial communities, present in asymptomatic and symptomatic twigs from olive cultivars displaying different susceptibilities to olive knot (OK) disease, were investigated using culturing methods. OK disease was the main driver of the bacterial community, causing changes on their diversity, abundance and composition. OK disease effect was most notorious on OK-susceptible cultivar and when considering the endophytic communities. Plant habitat (epiphytes vs. endophytes) also contributed to the bacterial community assembling, in particular on symptomatic twigs (knots) of OK-susceptible cultivar. In contrast, host cultivar had little effect on the bacterial community composition, but OK-symptomatic twigs (knots) revealed to be more affected by this driver. Overall, the pathobiome seems to result from an intricate interaction between the pathogen, the resident bacteria, and the plant host. Specific bacterial genera were associated to the presence or absence of OK disease in each cultivar. Their ability to trigger and/or suppress disease should be studied in the future.
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Schwartz DJ, Rebeck ON, Dantas G. Complex interactions between the microbiome and cancer immune therapy. Crit Rev Clin Lab Sci 2019; 56:567-585. [PMID: 31526274 DOI: 10.1080/10408363.2019.1660303] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Immuno-oncology has rapidly grown in the last thirty years, and immunotherapeutic agents are now approved to treat many disparate cancers. Immune checkpoint inhibitors (ICIs) are employed to augment cytotoxic anti-cancer activity by inhibiting negative regulatory elements of the immune system. Modulating the immune system to target neoplasms has improved survivability of numerous cancers in many individuals, but forecasting outcomes post therapy is difficult due to insufficient predictive biomarkers. Recently, the tumor and gastrointestinal microbiome and immune milieu have been investigated as predictors and influencers of cancer immune therapy. In this review, we discuss: (1) ways to measure the microbiome including relevant bioinformatic analyses, (2) recent developments in animal studies and human clinical trials utilizing gut microbial composition and function as biomarkers of cancer immune therapy response and toxicity, and (3) using prebiotics, probiotics, postbiotics, antibiotics, and fecal microbiota transplant (FMT) to modulate immune therapy. We discuss the respective benefits of 16S ribosomal RNA (rRNA) gene and shotgun metagenomic sequencing including important considerations in obtaining samples and in designing and interpreting human and animal microbiome studies. We then focus on studies discussing the differences in response to ICIs in relation to the microbiome and inflammatory mediators. ICIs cause colitis in up to 25% of individuals, and colitis is often refractory to common immunosuppressive medications. Researchers have measured microbiota composition prior to ICI therapy and correlated baseline microbiota composition with efficacy and colitis. Certain bacterial taxa that appear to enhance therapeutic benefit are also implicated in increased susceptibility to colitis, alluding to a delicate balance between pro-inflammatory tumor killing and anti-inflammatory protection from colitis. Pre-clinical and clinical models have trialed probiotic administration, e.g. Bifidobacterium spp. or FMT, to treat colitis when immune suppressive agents fail. We are excited about the future of modulating the microbiome to predict and influence cancer outcomes. Furthermore, novel therapies employed for other illnesses including bacteriophage and genetically-engineered microbes can be adapted in the future to promote increased advancements in cancer treatment and side effect management.
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Affiliation(s)
- Drew J Schwartz
- Department of Pediatrics, Division of Infectious Diseases, Washington University School of Medicine , St. Louis , MO , USA.,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine , St. Louis , MO , USA
| | - Olivia N Rebeck
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine , St. Louis , MO , USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine , St. Louis , MO , USA.,Department of Molecular Microbiology and Microbial Pathogenesis, Washington University School of Medicine in St. Louis , MO , USA.,Department of Pathology and Immunology, Washington University School of Medicine in St. Louis , MO , USA.,Department of Biomedical Engineering, Washington University in St. Louis , St. Louis , MO , USA
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