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
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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)
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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
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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
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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
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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)
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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. N M D S 2 ActinobacteriaF
“steroid-responsive” (FKBP5) F 02 02 01 01 00 .000 0.10 0.05 0.00 -0.05 -0.10 -0.15 -0.20 -0.25
-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
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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 -log10 p-value 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
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NHLBI AsthmaNet Microbiome study: Mild Asthma and Allergic Individuals without Asthma
nasal oral sputum, PSBs BAL T2- 3-gene 3-gene meansig T2-
(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
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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
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• Obesity, metabolic syndrome Gut • Allergies (food) Microbiome • Systemic inflammation • Susceptibility to viral infections
Begley et al. BMJ Resp Res 2018 Sherry Zhou, MD
• Obesity, metabolic syndrome Gut • Allergies (food) Microbiome • Systemic inflammation • Susceptibility to viral infections
Obesity is associated with an altered airway microbial composition, irrespective of asthmatic status
OB NonOB Fusobacterium necrophorum Prevotella pleuritidis Aggregatibacter Streptococcus anginosus Lactobacillus Treponema denticola Lactobacillus vaginalis Dialister Uncultured Prevotella Lactobacillus fermentum Prevotella dentalis DSM3688 Unclassified Mycoplasmataceae Parascardovia denticolens Oceanivirga Campylobacter fetus Uncultured Prevotella Campylobacter Uncultured Bacteroides
Ariangela Kozik, PhD unpublished
15 3/3/2020
Among obese subjects, airway microbial composition further differs by asthmatic status
Haemophilus Fusobacterium Prevotella oral taxon 299 Uncultured Lachnoanaerobaculum Porphyromonas Uncultured Bergeyella Uncultured Parvimonas Uncultured Stomatobaculum Lactobacillus Rothia Prevotella denticola Dialister Veillonella
Ariangela Kozik, PhD unpublished
Airway bacterial networks differ in obese asthma
Nob Asthma Ob Asthma
Different “hubs”, more connections: Veillonella, Streptococcus, Prevotella
Michalovich, Nat Comm 2019
16 3/3/2020
Summary, Future directions
Asthma (established) Type 2 -“high” Treatment: Phenotype - responsive Type 2-”low” - unresponsive Endotype?
The Host
Summary, Future directions
Asthma Susceptibility
Asthma Asthma Pathogenesis Treatment
Asthma Phenotype, Endotype
Acknowledgements
University of Michigan UCSF Lesa Begley MS (Juliana Durack PhD) Ariangela Kozik PhD Homer Boushey MD Jane Zhao, (Molly Cook, Snehal Nariya) Susan Lynch PhD Sherry Zhou MD Alan Baptist MD Thank You! Nicole Schafer, Elaina Sekuloski, NIH/NIEHS Kelly Rysso Stavros Garantziotis MD, PhD Kristopher Opron PhD John Erb-Downward PhD NYU Michael Coffey MD Leo Segal MD Siddharth Madapoosi BS
R01AI129958, R01HL121774S1, R03HL138310
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