3/3/2020 Microbiome Influences on Asthma: From the Environment to Clinical Phenotype Yvonne Huang MD Division of Pulmonary and Critical Care Medicine Department of Medicine University of Michigan, Ann Arbor Masoli et al. Allergy 2004; Science 2011 “Wherefore is this disease different from all other diseases?” M. Pappworth, A primer of medicine, 1984 Pavord et al. Lancet 2018 ... 1 3/3/2020 Objectives 1. Explain how microbiome research methods have been applied to understand microbial influences on asthma 2. Articulate key findings from studies of the airway and gut microbiome and their associations with asthma risk or clinical phenotype Multiple Factors Shape Asthma Risk and Phenotype Huang and Boushey. J Allergy Clin Immunol. 2015 Jan;135(1):25-30. Kozik and Huang, Annals Allerg Asth Immunol 2019 2 3/3/2020 Asthma Susceptibility Genes Epithelial cells: Chemokines, Microbial recognition, antimicrobial Immunoregulation peptides Type 2 effector functions Vercelli D. Nature Rev Immunol 2008 Human Microbiological History adapted from Rook, Dig. Dis. 2011 Human Microbiological History Dramatic changes in: Home environments Living standards Dietary consumption “Hygiene hypothesis” (Strachan,1989) Exposures “Old friends hypothesis” (Rook, 2010) “Biodiversity hypothesis” (von Hertzen, 2011) “Biome depletion” (Parker, 2014) • Decrease infectious diseases • Rise in allergic and autoimmune diseases adapted from Rook, Dig. Dis. 2011 3 3/3/2020 Single microbial species Microbial “communities” (Microbiota) “Microbiome” vs. “Microbiota” “Microbiome” vs. “Microbiota” “the entire habitat, including the microorganisms, their genes and Bacteria surrounding environmental Fungi Archaea conditions and interactions”. Viruses Helminths • Marchesi and Ravel, Microbiome 2015 • Environmental Chemicals, the Human Microbiome, and Health Risk: A Research Strategy. National Academies of Sciences, Engineering, and Medicine. 2017. (Committee Report) 4 3/3/2020 Childhood Asthma Risk Microbes and Asthma Risk: Childhood – Environment Microbes and Asthma Risk: Childhood – Environment ① Perinatal, early life exposure to a diverse repertoire of microbes is associated with decreased risk of allergic disease, including asthma. Examples: Growing up in small farm environment, Early life pet exposure 5 3/3/2020 Richness of bacteria or fungi found in mattress dust negatively associated with asthma Ege MJ et al. NEJM 2011 Similar relationships between microbial exposures and asthma risk in studies of Amish vs. Hutterite children Peripheral blood gene expression Increased in Amish Increased in Hutterite Stein et al. NEJM 2016 Microbes and Asthma Risk: Childhood – Gut Microbiome 6 3/3/2020 Microbes and Asthma Risk: Childhood – Gut Microbiome ② Differences in gut microbiome composition and functions in early life are linked to risk for childhood- onset allergy or asthma • Clinical studies • Mechanistic studies Penders, Gut 2007.; Vael BMC Microb 2011 Abrahamsson, Clin Exp Allergy 2014 Arrieta, Science Transl Med 2015 Van Nimwegen, J Allerg Clin Immunol 2011 Trompette, Nature Med 2014 Specific intestinal bacteria and risk of allergic asthma Culture or Molecular high-throughput species-specific PCR vs. approaches examples: • Clostridia (C. difficile) • Bacteroides fragilis • E. coli • Bifidobacteria • Lactobacillus Arrieta et al. Science Transl Med 2015 Canadian Longitudinal Birth Cohort study (CHILD) Atopic + wheezy children: Had at age 3 months, decreased Faecalibacterium, Lachnospira, Veillonella, Rothia (FLVR) AW children: Lower fecal short- chain fatty acids Arrieta et al. Science Transl Med 2015 7 3/3/2020 Germ-free mice inoculated with stool from an atopic wheezy 3-mo infant, +/– FLVR bacteria Altered gut microbiota composition in pups of mothers who received AW infant stool + FLVR Decrease in allergic airway inflammation Arrieta et al. Science Transl Med 2015 Bacteria and Asthma Risk: Childhood – Respiratory Bacteria and Asthma Risk: Childhood – Respiratory ③ Differences in upper respiratory (nasopharyngeal) microbiota also linked to risk for childhood asthma * Copenhagen birth cohort * Child Asthma Study (Australia) Bisgaard et al. NEJM 2007; Gollweitzer et al. Nature Med 2014; Teo et al. Cell Host Microb 2015, 2018 8 3/3/2020 Copenhagen Birth Cohort study Pharyngeal colonization at age 1 month with S. pneumoniae, M. catarrhalis, or H. influenzae, associated with increased risk of persistent wheeze or asthma by age 5 Bisgaard H et al. NEJM 2007 Childhood Asthma Study (Australia) The risk for asthma linked to nasal presence of potentially pathogenic bacteria may depend on underlying atopy Teo SM et al. Cell Host Microb 2015 & 2018 Nasal microbiota and loss of asthma control in U.S. school-age children (STICS trial; NHLBI AsthmaNet) Zhou et al. Nat Comm 2019, (STICS trial, Jackson et al. NEJM 2018) 9 3/3/2020 Nasal microbiota and loss of asthma control in U.S. school-age children (STICS trial; NHLBI AsthmaNet) Samples collected at: RD= randomization YZ= yellow zone Zhou et al. Nat Comm 2019, (STICS trial, Jackson et al. NEJM 2018) Asthma Phenotype Susceptibility Pathogenesis Treatment Asthma, Type 2 -“high” (established) Phenotype Treatment: Endotype - responsive Phenotype Type 2-”low” - unresponsive Endotype The Host 10 3/3/2020 Clinical and biological features of adult asthma are associated with altered airway microbiome patterns • Airway hyper-response • Asthma control • Airway immune profiles • Type 2-low • Obese asthma • Treatment response Huang & Boushey, J Allerg Clin Immunol 2015 J Allergy Clin Immunol: Huang 2011 & 2015; Denner 2016, Durack 2017, Taylor 2018, Sharma 2019 Am J Respir Crit Care Med: Goleva 2013 Nat Comm: Michalovich 2019 Severe asthma and the bronchial microbiome • Observational study (n=30) • Clinical stability during 2-3 month study period • poorly controlled despite high dose ICS • Analysis of bronchial epithelial brushings, clinical and immunologic features Huang et al. J Allergy Clin Immunol. 2015 Severe asthma: Airway gene expression patterns associated with airway enrichment in different bacteria Proteobacteria NeuSput “steroid-resistant” signature N NN F NNNNNN N NNNNNNTNNN F F NN TNTNNNNTNNTNTNTTNNTNNF N F FFF F F N NNTNNNNTNNNTTNTNTTNT F FF F FFFF TT TNTTNTTNTNNTNTTTTTT FF F F F T TTTNTTNTTNNNNTTNTTTTTT F F FF FF N TTTNTTTTTN TTNTTF F F F F FF F F TTNTT F F F (IL17-related: CXCL1, -2, -3, IL8, CSF3) T T N T F F F F TT F F F FF F FF “Th17” FF FFFFFFF F F F F FF F F F F T FKBP5 F vs. NMDS2 ActinobacteriaF “steroid-responsive” (FKBP5) F -0.25 -0.20 -0.15 -0.10 -0.05 0.00 0.05 0.10 -0.1 0.0 0.1 0.2 NMDS1 Similar bacterial enrichment Proteobacteria Worsening of asthma patterns correlated with stability of asthma control Actinobacteria Better/stable asthma Huang et al. J Allergy Clin Immunol. 2015 11 3/3/2020 Severe asthma: Less type 2 inflammation, more airway bacterial ‘burden’ Microbiome Type 2-“low” Immune Phenotype Type 2-”high” *similar relationship with % sputum eosinophils Huang et al. J Allergy Clin Immunol. 2015 Obesity in Severe Asthma 5 Bacteroidetes / Phylum (Family) 4 Bacteroidetes (Flavobacteriaceae) * • Prevotella Bacteroidetes (Prevotellaceae) * Bacteroidetes (Rikenellaceae II) Chlorobi (OPB56) 3 Firmicutes (Clostridiales Family XI. Incertae Sedis) * Firmicutes (Clostridiales Family XIII. Incertae Sedis) Firmicutes (Lachnospiraceae) * Firmicutes Fusobacteria (Fusobacteriaceae) -log10 p-value-log10 Proteobacteria (Desulfobacteraceae) 2 Proteobacteria (Helicobacteraceae) * • Clostridiales Spirochaetes (Spirochaetaceae) Tenericutes (Erysipelotrichaceae) Tenericutes (Mycoplasmataceae) • Lachnospiraceae 1 • Fusobacteria 0 -4 -2 0 2 4 Difference in taxon relative abundance (log2) obese vs. nonobese Huang et al. J Allergy Clin Immunol. 2015 Altered respiratory microbiota composition in pediatric and adult asthma studies Pediatric cohorts Adult cohorts • Nasopharyngeal • PSBs, BAL aspirate, swabs, • Induced sputum wash/lavage Haemophilus Haemophilus Streptococcus Moraxella Moraxella Streptococcus Corynebacterium Others… Staphylococcus Alloiococcus Dolosigranulum Marri 2013 Green 2014 Bisgaard, 2010 Huang 2015 severe Kloepfer, 2014 Zhang 2016 Teo et al 2015 asthma Taylor 2018 Depner, 2017 12 3/3/2020 NHLBI AsthmaNet Microbiome study: Mild Asthma and Allergic Individuals without Asthma nasal oral sputum, PSBs BAL T2- sig mean 3-gene (TGM: Expression signature of three, IL-13-inducible genes) Durack et al. J Allergy Clin Immunol. 2017 Atopic subjects without asthma displayed an altered bronchial microbiota pattern that was distinct from the asthma group. ? Microbial-immune interactions related to atopy vs. asthma Controlling for atopic status likely important Durack et al. J Allergy Clin Immunol. 2017 Looking within: nasal microbiota and lung inflammation Nasal Corynebacterium: biomarker of respiratory health in adults? Nasal oral Sputum, Brushes BAL Durack et al. Microbiome 2018 13 3/3/2020 Looking within: nasal microbiota and lung inflammation Nasal Moraxella and asthma-related lung immune responses Durack et al. Microbiome 2018 Univ. of Michigan: • CAARS (Characterization of Adults for Asthma Research Studies) • MICROMAAP (Microbiome Markers of Adult Asthma Phenotype) • Seasonal visits • Clinical events “colds” Exacerbations Med changes • Obesity, metabolic syndrome Gut • Allergies (food) Microbiome • Systemic inflammation • Susceptibility to viral infections 14 3/3/2020 • Obesity, metabolic syndrome Gut • Allergies (food) Microbiome • Systemic inflammation • Susceptibility to viral infections Begley et al. BMJ Resp Res