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Venkatasubramanian S, Plumlee CR, Dill-McFarland KA, Cohen SB, Gern BH, Rane DA, Meyer MK, Saha A, Hinderstein SA, Pearson GL, Lietzke AC, Pacheco A, Chow YH, Hung CF, Soleimanpour SA, Altman M, Urdahl KB, Shah JA. TOLLIP inhibits lipid accumulation and the integrated stress response in alveolar macrophages to control Mycobacterium tuberculosis infection. Nat Microbiol 2024; 9:949-963. [PMID: 38528148 PMCID: PMC11034867 DOI: 10.1038/s41564-024-01641-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 02/16/2024] [Indexed: 03/27/2024]
Abstract
A polymorphism causing deficiencies in Toll-interacting protein (TOLLIP), an inhibitory adaptor protein affecting endosomal trafficking, is associated with increased tuberculosis (TB) risk. It is, however, unclear how TOLLIP affects TB pathogenesis. Here we show that TB severity is increased in Tollip-/- mice, characterized by macrophage- and T cell-driven inflammation, foam cell formation and lipid accumulation. Tollip-/- alveolar macrophages (AM) specifically accumulated lipid and underwent necrosis. Transcriptional and protein analyses of Mycobacterium tuberculosis (Mtb)-infected, Tollip-/- AM revealed increased EIF2 signalling and downstream upregulation of the integrated stress response (ISR). These phenotypes were linked, as incubation of the Mtb lipid mycolic acid with Mtb-infected Tollip-/- AM activated the ISR and increased Mtb replication. Correspondingly, the ISR inhibitor, ISRIB, reduced Mtb numbers in AM and improved Mtb control, overcoming the inflammatory phenotype. In conclusion, targeting the ISR offers a promising target for host-directed anti-TB therapy towards improved Mtb control and reduced immunopathology.
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Affiliation(s)
| | | | | | - Sara B Cohen
- Seattle Children's Research Institute, Seattle, WA, USA
| | - Benjamin H Gern
- Seattle Children's Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Divya A Rane
- Department of Medicine, University of Washington, Seattle, WA, USA
| | | | - Aparajita Saha
- Department of Medicine, University of Washington, Seattle, WA, USA
| | | | - Gemma L Pearson
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Anne C Lietzke
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Amanda Pacheco
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Yu-Hua Chow
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Chi F Hung
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Scott A Soleimanpour
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- VA Ann Arbor Healthcare System, Ann Arbor, MI, USA
| | - Matthew Altman
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Kevin B Urdahl
- Seattle Children's Research Institute, Seattle, WA, USA
- Departments of Pediatrics and Immunology, University of Washington, Seattle, WA, USA
| | - Javeed A Shah
- Department of Medicine, University of Washington, Seattle, WA, USA.
- VA Puget Sound Healthcare System, Seattle, WA, USA.
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2
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Hong H, Dill-McFarland KA, Simmons JD, Peterson GJ, Benchek P, Mayanja-Kizza H, Boom WH, Stein CM, Hawn TR. Mycobacterium tuberculosis-dependent monocyte expression quantitative trait loci, cytokine production, and TB pathogenesis. Front Immunol 2024; 15:1359178. [PMID: 38515745 PMCID: PMC10954790 DOI: 10.3389/fimmu.2024.1359178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/05/2024] [Indexed: 03/23/2024] Open
Abstract
Introduction The heterogeneity of outcomes after Mycobacterium tuberculosis (Mtb) exposure is a conundrum associated with millennia of host-pathogen co-evolution. We hypothesized that human myeloid cells contain genetically encoded, Mtb-specific responses that regulate critical steps in tuberculosis (TB) pathogenesis. Methods We mapped genome-wide expression quantitative trait loci (eQTLs) in Mtb-infected monocytes with RNAseq from 80 Ugandan household contacts of pulmonary TB cases to identify monocyte-specific, Mtb-dependent eQTLs and their association with cytokine expression and clinical resistance to tuberculin skin test (TST) and interferon-γ release assay (IGRA) conversion. Results cis-eQTLs (n=1,567) were identified in Mtb-infected monocytes (FDR<0.01), including 29 eQTLs in 16 genes which were Mtb-dependent (significant for Mtb:genotype interaction [FDR<0.1], but not classified as eQTL in uninfected condition [FDR≥0.01]). A subset of eQTLs were associated with Mtb-induced cytokine expression (n=8) and/or clinical resistance to TST/IGRA conversion (n=1). Expression of BMP6, an Mtb-dependent eQTL gene, was associated with IFNB1 induction in Mtb-infected and DNA ligand-induced cells. Network and enrichment analyses identified fatty acid metabolism as a pathway associated with eQTL genes. Discussion These findings suggest that monocyte genes contain Mtb-dependent eQTLs, including a subset associated with cytokine expression and/or clinical resistance to TST/IGRA conversion, providing insight into immunogenetic pathways regulating susceptibility to Mtb infection and TB pathogenesis.
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Affiliation(s)
- Hyejeong Hong
- Department of Biobehavioral Health Sciences, School of Nursing, University of Pennsylvania, Philadelphia, PA, United States
| | | | - Jason D. Simmons
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Glenna J. Peterson
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Penelope Benchek
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, United States
| | | | - W. Henry Boom
- Department of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Catherine M. Stein
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, United States
- Department of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Thomas R. Hawn
- Department of Medicine, University of Washington, Seattle, WA, United States
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3
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Dill-McFarland KA, Simmons JD, Peterson GJ, Nguyen FK, Campo M, Benchek P, Stein CM, Vaisar T, Mayanja-Kizza H, Boom WH, Hawn TR. Epigenetic programming of host lipid metabolism associates with resistance to TST/IGRA conversion after exposure to Mycobacterium tuberculosis. bioRxiv 2024:2024.02.27.582348. [PMID: 38464296 PMCID: PMC10925331 DOI: 10.1101/2024.02.27.582348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Mycobacterium tuberculosis (Mtb) exposure leads to a range of outcomes including clearance, latent TB infection (LTBI), and pulmonary tuberculosis (TB). Some heavily exposed individuals resist tuberculin skin test (TST) and interferon gamma release assay (IGRA) conversion (RSTR), which suggests that they employ IFNγ-independent mechanisms of Mtb control. Here, we compare monocyte epigenetic profiles of RSTR and LTBI from a Ugandan household contact cohort. Chromatin accessibility did not differ between uninfected RSTR and LTBI monocytes. In contrast, methylation significantly differed at 174 CpG sites and across 63 genomic regions. Consistent with previous transcriptional findings in this cohort, differential methylation was enriched in lipid and cholesterol associated pathways including in the genes APOC3, KCNQ1, and PLA2G3. In addition, methylation was enriched in Hippo signaling, which is associated with cholesterol homeostasis and includes CIT and SHANK2. Lipid export and Hippo signaling pathways were also associated with gene expression in response to Mtb in RSTR as well as IFN stimulation in monocyte-derived macrophages (MDMs) from an independent healthy donor cohort. Moreover, serum-derived HDL from RSTR had elevated ABCA1-mediated cholesterol efflux capacity (CEC) compared to LTBI. Our findings suggest that resistance to TST/IGRA conversion is linked to regulation of lipid accumulation in monocytes, which could facilitate early Mtb clearance among RSTR subjects through IFNγ-independent mechanisms.
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Affiliation(s)
| | - Jason D Simmons
- Department of Medicine, University of Washington, Seattle, WA, USA
| | | | - Felicia K Nguyen
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Monica Campo
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Penelope Benchek
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Catherine M Stein
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Tomas Vaisar
- Department of Medicine, University of Washington, Seattle, WA, USA
| | | | - W Henry Boom
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Thomas R Hawn
- Department of Medicine, University of Washington, Seattle, WA, USA
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4
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Dill-McFarland KA, Altman MC, Esnault S, Jarjour NN, Busse WW, Rosenkranz MA. Molecular pathways underlying lung-brain axis signaling in asthma: Relevance for psychopathology and neuroinflammation. J Allergy Clin Immunol 2024; 153:111-121. [PMID: 37730134 PMCID: PMC10841090 DOI: 10.1016/j.jaci.2023.07.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 07/12/2023] [Accepted: 07/20/2023] [Indexed: 09/22/2023]
Abstract
BACKGROUND Accumulating evidence indicates that asthma has systemic effects and affects brain function. Although airway inflammation is proposed to initiate afferent communications with the brain, the signaling pathways have not been established. OBJECTIVE We sought to identify the cellular and molecular pathways involved in afferent lung-brain communication during airway inflammation in asthma. METHODS In 23 adults with mild asthma, segmental bronchial provocation with allergen (SBP-Ag) was used to provoke airway inflammation and retrieve bronchoalveolar lavage fluid for targeted protein analysis and RNA sequencing to determine gene expression profiles. Neural responses to emotional cues in nodes of the salience network were assessed with functional magnetic resonance imaging at baseline and 48 hours after SBP-Ag. RESULTS Cell deconvolution and gene coexpression network analysis identified 11 cell-associated gene modules that changed in response to SBP-Ag. SBP-Ag increased bronchoalveolar lavage eosinophils and expression of an eosinophil-associated module enriched for genes related to TH17-type inflammation (eg, IL17A), as well as cell proliferation in lung and brain (eg, NOTCH1, VEGFA, and LIF). Increased expression of genes in this module, as well as several TH17-type inflammation-related proteins, was associated with an increase from baseline in salience network reactivity. CONCLUSIONS Our results identify a specific inflammatory pathway linking asthma-related airway inflammation and emotion-related neural function. Systemically, TH17-type inflammation has been implicated in both depression and neuroinflammation, with impacts on long-term brain health. Thus, our data emphasize that inflammation in the lung in asthma may have profound effects outside of the lung that may be targetable with novel therapeutic approaches.
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Affiliation(s)
| | - Matthew C Altman
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, Wash; Systems Immunology Program, Benaroya Research Institute, Seattle, Wash
| | - Stephane Esnault
- Division of Allergy, Pulmonary and Critical Care Medicine, University of Wisconsin-Madison, Madison, Wis
| | - Nizar N Jarjour
- Division of Allergy, Pulmonary and Critical Care Medicine, University of Wisconsin-Madison, Madison, Wis
| | - William W Busse
- Division of Allergy, Pulmonary and Critical Care Medicine, University of Wisconsin-Madison, Madison, Wis
| | - Melissa A Rosenkranz
- Center for Healthy Minds, University of Wisconsin-Madison, Madison, Wis; Department of Psychiatry, University of Wisconsin-Madison, Madison, Wis.
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5
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Hong H, Dill-McFarland KA, Simmons JD, Peterson GJ, Benchek P, Mayanja-Kizza H, Boom WH, Stein CM, Hawn TR. Mycobacterium tuberculosis-dependent Monocyte Expression Quantitative Trait Loci and Tuberculosis Pathogenesis. medRxiv 2023:2023.08.28.23294698. [PMID: 37693490 PMCID: PMC10491362 DOI: 10.1101/2023.08.28.23294698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
The heterogeneity of outcomes after Mycobacterium tuberculosis (Mtb) exposure is a conundrum associated with millennia of host-pathogen co-evolution. We hypothesized that human myeloid cells contain genetically encoded, Mtb-specific responses that regulate critical steps in tuberculosis (TB) pathogenesis. We mapped genome-wide expression quantitative trait loci (eQTLs) in Mtb-infected monocytes with RNAseq from 80 Ugandan household contacts of pulmonary TB cases to identify monocyte-specific, Mtb-dependent eQTLs and their association with cytokine expression and clinical resistance to tuberculin skin test (TST) and interferon-γ release assay (IGRA) conversion. cis-eQTLs (n=1,567) were identified in Mtb-infected monocytes (FDR<0.01), including 29 eQTLs in 16 genes which were Mtb-dependent (significant for Mtb:genotype interaction [FDR<0.1], but not classified as eQTL in media condition [FDR≥0.01]). A subset of eQTLs were associated with Mtb-induced cytokine expression (n=8) and/or clinical resistance to TST/IGRA conversion (n=1). Expression of BMP6, an Mtb-dependent eQTL gene, was associated with IFNB1 induction in Mtb-infected and DNA ligand-induced cells. Network and enrichment analyses identified fatty acid metabolism as a pathway associated with eQTL genes. These findings suggest that monocyte genes contain Mtb-dependent eQTLs, including a subset associated with cytokine expression and/or clinical resistance to TST/IGRA conversion, providing insight into immunogenetic pathways regulating susceptibility to Mtb infection and TB pathogenesis.
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Affiliation(s)
- Hyejeong Hong
- Department of Biobehavioral Health Sciences, School of Nursing, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Jason D. Simmons
- Department of Medicine, University of Washington, Seattle, WA, USA
| | | | - Penelope Benchek
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | | | - W. Henry Boom
- Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Catherine M. Stein
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
- Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Thomas R. Hawn
- Department of Medicine, University of Washington, Seattle, WA, USA
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6
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Phelan KJ, Dill-McFarland KA, Kothari A, Segnitz RM, Burkle J, Grashel B, Jenkins S, Spagna D, Martin LJ, Haslam DB, Biagini JM, Kalra M, McCoy KS, Ross KR, Jackson DJ, Mersha TB, Altman MC, Khurana Hershey GK. Airway transcriptome networks identify susceptibility to frequent asthma exacerbations in children. J Allergy Clin Immunol 2023; 152:73-83. [PMID: 36918038 PMCID: PMC10395049 DOI: 10.1016/j.jaci.2023.02.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 01/11/2023] [Accepted: 02/01/2023] [Indexed: 03/14/2023]
Abstract
BACKGROUND Frequent asthma exacerbators, defined as those experiencing more than 1 hospitalization in a year for an asthma exacerbation, represent an important subgroup of individuals with asthma. However, this group remains poorly defined and understudied in children. OBJECTIVE Our aim was to determine the molecular mechanisms underlying asthma pathogenesis and exacerbation frequency. METHODS We performed RNA sequencing of upper airway cells from both frequent and nonfrequent exacerbators enrolled in the Ohio Pediatric Asthma Repository. RESULTS Through molecular network analysis, we found that nonfrequent exacerbators display an increase in modules enriched for immune system processes, including type 2 inflammation and response to infection. In contrast, frequent exacerbators showed expression of modules enriched for nervous system processes, such as synaptic formation and axonal outgrowth. CONCLUSION These data suggest that the upper airway of frequent exacerbators undergoes peripheral nervous system remodeling, representing a novel mechanism underlying pediatric asthma exacerbation.
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Affiliation(s)
- Kieran J Phelan
- Divison of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Medical Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | | | - Arjun Kothari
- Divison of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - R Max Segnitz
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, Wash
| | - Jeff Burkle
- Divison of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Brittany Grashel
- Divison of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Seth Jenkins
- Divison of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Daniel Spagna
- Divison of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Lisa J Martin
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - David B Haslam
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio; Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Jocelyn M Biagini
- Divison of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Maninder Kalra
- Department of Pediatrics, Dayton Children's Hospital, Dayton, Ohio
| | - Karen S McCoy
- Division of Pediatric Pulmonology, Nationwide Children's Hospital, Columbus; Ohio
| | - Kristie R Ross
- Department of Pediatrics-Pulmonary, Rainbow Babies and Children's Hospital, Cleveland, Ohio
| | - Daniel J Jackson
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - Tesfaye B Mersha
- Divison of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Matthew C Altman
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, Wash; Systems Immunology Program, Benaroya Research Institute, Seattle, Wash
| | - Gurjit K Khurana Hershey
- Divison of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio.
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7
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Murphy RC, Lai Y, Altman MC, Barrow KA, Dill-McFarland KA, Liu M, Hamerman JA, Lacy-Hulbert A, Piliponsky AM, Ziegler SF, Altemeier WA, Debley JS, Gharib SA, Hallstrand TS. Rhinovirus infection of the airway epithelium enhances mast cell immune responses via epithelial-derived interferons. J Allergy Clin Immunol 2023; 151:1484-1493. [PMID: 36708815 PMCID: PMC10257743 DOI: 10.1016/j.jaci.2022.12.825] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 12/15/2022] [Accepted: 12/22/2022] [Indexed: 01/27/2023]
Abstract
BACKGROUND Mast cells (MCs) within the airway epithelium in asthma are closely related to airway dysfunction, but cross talk between airway epithelial cells (AECs) and MCs in asthma remains incompletely understood. Human rhinovirus (RV) infections are key triggers for asthma progression, and AECs from individuals with asthma may have dysregulated antiviral responses. OBJECTIVE We utilized primary AECs in an ex vivo coculture model system to examine cross talk between AECs and MCs after epithelial rhinovirus infection. METHODS Primary AECs were obtained from 11 children with asthma and 10 healthy children, differentiated at air-liquid interface, and cultured in the presence of laboratory of allergic diseases 2 (LAD2) MCs. AECs were infected with rhinovirus serogroup A 16 (RV16) for 48 hours. RNA isolated from both AECs and MCs underwent RNA sequencing. Direct effects of epithelial-derived interferons on LAD2 MCs were examined by real-time quantitative PCR. RESULTS MCs increased expression of proinflammatory and antiviral genes in AECs. AECs demonstrated a robust antiviral response after RV16 infection that resulted in significant changes in MC gene expression, including upregulation of genes involved in antiviral responses, leukocyte activation, and type 2 inflammation. Subsequent ex vivo modeling demonstrated that IFN-β induces MC type 2 gene expression. The effects of AEC donor phenotype were small relative to the effects of viral infection and the presence of MCs. CONCLUSIONS There is significant cross talk between AECs and MCs, which are present in the epithelium in asthma. Epithelial-derived interferons not only play a role in viral suppression but also further alter MC immune responses including specific type 2 genes.
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Affiliation(s)
- Ryan C Murphy
- Division of Pulmonary, Critical Care, and Sleep Medicine, Seattle, Wash; Center for Lung Biology, University of Washington, Seattle, Wash.
| | - Ying Lai
- Division of Pulmonary, Critical Care, and Sleep Medicine, Seattle, Wash; Center for Lung Biology, University of Washington, Seattle, Wash
| | - Matthew C Altman
- Division of Allergy and Infectious Disease, Department of Medicine, Seattle, Wash; Immunology Program, Benaroya Research Institute, Seattle, Wash
| | - Kaitlyn A Barrow
- Division of Pulmonary and Sleep Medicine, Seattle Children's Hospital, Department of Pediatrics, Seattle, Wash; Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Wash
| | | | - Matthew Liu
- Division of Pulmonary, Critical Care, and Sleep Medicine, Seattle, Wash; Center for Lung Biology, University of Washington, Seattle, Wash
| | | | | | - Adrian M Piliponsky
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Wash
| | | | - William A Altemeier
- Division of Pulmonary, Critical Care, and Sleep Medicine, Seattle, Wash; Center for Lung Biology, University of Washington, Seattle, Wash
| | - Jason S Debley
- Division of Pulmonary and Sleep Medicine, Seattle Children's Hospital, Department of Pediatrics, Seattle, Wash; Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Wash
| | - Sina A Gharib
- Division of Pulmonary, Critical Care, and Sleep Medicine, Seattle, Wash; Center for Lung Biology, University of Washington, Seattle, Wash
| | - Teal S Hallstrand
- Division of Pulmonary, Critical Care, and Sleep Medicine, Seattle, Wash; Center for Lung Biology, University of Washington, Seattle, Wash
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8
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Dill-McFarland KA, Mitchell K, Batchu S, Segnitz RM, Benson B, Janczyk T, Cox MS, Mayanja-Kizza H, Boom WH, Benchek P, Stein CM, Hawn TR, Altman MC. Kimma: flexible linear mixed effects modeling with kinship covariance for RNA-seq data. Bioinformatics 2023; 39:btad279. [PMID: 37140544 PMCID: PMC10182851 DOI: 10.1093/bioinformatics/btad279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 05/05/2023] Open
Abstract
MOTIVATION The identification of differentially expressed genes (DEGs) from transcriptomic datasets is a major avenue of research across diverse disciplines. However, current bioinformatic tools do not support covariance matrices in DEG modeling. Here, we introduce kimma (Kinship In Mixed Model Analysis), an open-source R package for flexible linear mixed effects modeling including covariates, weights, random effects, covariance matrices, and fit metrics. RESULTS In simulated datasets, kimma detects DEGs with similar specificity, sensitivity, and computational time as limma unpaired and dream paired models. Unlike other software, kimma supports covariance matrices as well as fit metrics like Akaike information criterion (AIC). Utilizing genetic kinship covariance, kimma revealed that kinship impacts model fit and DEG detection in a related cohort. Thus, kimma equals or outcompetes current DEG pipelines in sensitivity, computational time, and model complexity. AVAILABILITY AND IMPLEMENTATION Kimma is freely available on GitHub https://github.com/BIGslu/kimma with an instructional vignette at https://bigslu.github.io/kimma_vignette/kimma_vignette.html.
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Affiliation(s)
- Kimberly A Dill-McFarland
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, 750 Republican St, Seattle, WA 98109, United States
| | - Kiana Mitchell
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, 750 Republican St, Seattle, WA 98109, United States
- Department of Biology, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, United States
| | - Sashank Batchu
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, 750 Republican St, Seattle, WA 98109, United States
| | - Richard Max Segnitz
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, 750 Republican St, Seattle, WA 98109, United States
| | - Basilin Benson
- Systems Immunology Division, Benaroya Research Institute, 1201 Ninth Avenue, Seattle, CA 98101, United States
| | - Tomasz Janczyk
- Systems Immunology Division, Benaroya Research Institute, 1201 Ninth Avenue, Seattle, CA 98101, United States
| | - Madison S Cox
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, 750 Republican St, Seattle, WA 98109, United States
| | - Harriet Mayanja-Kizza
- Department of Medicine, School of Medicine, Makerere University, PO Box 7072, Kampala, Uganda
| | - William Henry Boom
- Department of Medicine, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106, United States
| | - Penelope Benchek
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106, United States
| | - Catherine M Stein
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106, United States
| | - Thomas R Hawn
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, 750 Republican St, Seattle, WA 98109, United States
| | - Matthew C Altman
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, 750 Republican St, Seattle, WA 98109, United States
- Systems Immunology Division, Benaroya Research Institute, 1201 Ninth Avenue, Seattle, CA 98101, United States
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9
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Simmons JD, Segnitz RM, Dill-McFarland KA, Stein CM, Peterson GJ, Mayanja-Kizza H, Boom WH, Hawn TR. Differentially expressed transcript isoforms associate with resistance to tuberculin skin test and interferon gamma release assay conversion. PLoS One 2023; 18:e0284498. [PMID: 37058459 PMCID: PMC10104279 DOI: 10.1371/journal.pone.0284498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 04/02/2023] [Indexed: 04/15/2023] Open
Abstract
BACKGROUND A mechanistic understanding of uncommon immune outcomes such as resistance to infection has led to the development of novel therapies. Using gene level analytic methods, we previously found distinct monocyte transcriptional responses associated with resistance to Mycobacterium tuberculosis (Mtb) infection defined as persistently negative tuberculin skin test (TST) and interferon gamma release assay (IGRA) reactivity among highly exposed contacts (RSTR phenotype). OBJECTIVE Using transcript isoform analyses, we aimed to identify novel RSTR-associated genes hypothesizing that previous gene-level differential expression analysis obscures isoform-specific differences that contribute to phenotype. MATERIALS AND METHODS Monocytes from 49 RSTR versus 52 subjects with latent Mtb infection (LTBI) were infected with M. tuberculosis (H37Rv) or left unstimulated (media) prior to RNA isolation and sequencing. RSTR-associated gene expression was then identified using differential transcript isoform analysis. RESULTS We identified 81 differentially expressed transcripts (DETs) in 70 genes (FDR <0.05) comparing RSTR and LTBI phenotypes with the majority (n = 79 DETs) identified under Mtb-stimulated conditions. Seventeen of these genes were previously identified with gene-level bulk RNAseq analyses including genes in the IFNγ response that had increased expression among LTBI subjects, findings consistent with a clinical phenotype based on IGRA reactivity. Among the subset of 23 genes with positive differential expression among Mtb-infected RSTR monocytes, 13 were not previously identified. These novel DET genes included PDE4A and ZEB2, which each had multiple DETs with higher expression among RSTR subjects, and ACSL4 and GAPDH that each had a single transcript isoform associated with RSTR. CONCLUSION AND LIMITATIONS Transcript isoform-specific analyses identify transcriptional associations, such as those associated with resistance to TST/IGRA conversion, that are obscured when using gene-level approaches. These findings should be validated with additional RSTR cohorts and whether the newly identified candidate resistance genes directly influence the monocyte Mtb response requires functional study.
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Affiliation(s)
- Jason D. Simmons
- TB Research & Training Center, Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - R. Max Segnitz
- TB Research & Training Center, Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Kimberly A. Dill-McFarland
- TB Research & Training Center, Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Catherine M. Stein
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Glenna J. Peterson
- TB Research & Training Center, Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | | | - W. Henry Boom
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Thomas R. Hawn
- TB Research & Training Center, Department of Medicine, University of Washington, Seattle, Washington, United States of America
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10
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Lindestam Arlehamn CS, Benson B, Kuan R, Dill-McFarland KA, Peterson GJ, Paul S, Nguyen FK, Gilman RH, Saito M, Taplitz R, Arentz M, Goss CH, Aitken ML, Horne DJ, Shah JA, Sette A, Hawn TR. T-cell deficiency and hyperinflammatory monocyte responses associate with Mycobacterium avium complex lung disease. Front Immunol 2022; 13:1016038. [PMID: 36263044 PMCID: PMC9574438 DOI: 10.3389/fimmu.2022.1016038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/16/2022] [Indexed: 11/13/2022] Open
Abstract
Immunological mechanisms of susceptibility to nontuberculous mycobacterial (NTM) disease are poorly understood. To understand NTM pathogenesis, we evaluated innate and antigen-specific adaptive immune responses to Mycobacterium avium complex (MAC) in asymptomatic individuals with a previous history of MAC lung disease (MACDZ). We hypothesized that Mav-specific immune responses are associated with susceptibility to MAC lung disease. We measured MAC-, NTM-, or MAC/Mtb-specific T-cell responses by cytokine production, expression of surface markers, and analysis of global gene expression in 27 MACDZ individuals and 32 healthy controls. We also analyzed global gene expression in Mycobacterium avium-infected and uninfected peripheral blood monocytes from 17 MACDZ and 17 healthy controls. We were unable to detect increased T-cell responses against MAC-specific reagents in MACDZ compared to controls, while the responses to non-mycobacteria derived antigens were preserved. MACDZ individuals had a lower frequency of Th1 and Th1* T-cell populations. In addition, MACDZ subjects had lower transcriptional responses in PBMCs stimulated with a mycobacterial peptide pool (MTB300). By contrast, global gene expression analysis demonstrated upregulation of proinflammatory pathways in uninfected and M. avium-infected monocytes, i.e. a hyperinflammatory in vitro response, derived from MACDZ subjects compared to controls. Together, these data suggest a novel immunologic defect which underlies MAC pathogenesis and includes concurrent innate and adaptive dysregulation which persists years after completion of treatment.
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Affiliation(s)
- Cecilia S. Lindestam Arlehamn
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
- *Correspondence: Cecilia S. Lindestam Arlehamn,
| | - Basilin Benson
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Rebecca Kuan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
| | | | - Glenna J. Peterson
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Sinu Paul
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Felicia K. Nguyen
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Robert H. Gilman
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, United States
- Department of Microbiology, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Randy Taplitz
- Department of Medicine, City of Hope National Medical Center, Duarte, CA, United States
| | - Matthew Arentz
- Department of Global Health, University of Washington, Seattle, WA, United States
- FIND, the global alliance for diagnostics, Geneva, Switzerland
| | - Christopher H. Goss
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Moira L. Aitken
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - David J. Horne
- Department of Medicine, University of Washington, Seattle, WA, United States
- Department of Global Health, University of Washington, Seattle, WA, United States
| | - Javeed A. Shah
- Department of Medicine, University of Washington, Seattle, WA, United States
- VA Puget Sound Healthcare System, Seattle, WA, United States
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
- Department of Medicine, University of California San Diego, La Jolla, CA, United States
| | - Thomas R. Hawn
- Department of Medicine, University of Washington, Seattle, WA, United States
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11
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Jackson DJ, Bacharier LB, Gergen PJ, Gagalis L, Calatroni A, Wellford S, Gill MA, Stokes J, Liu AH, Gruchalla RS, Cohen RT, Makhija M, Khurana Hershey GK, O'Connor GT, Pongracic JA, Sherenian MG, Rivera-Spoljaric K, Zoratti EM, Teach SJ, Kattan M, Dutmer CM, Kim H, Lamm C, Sheehan WJ, Segnitz RM, Dill-McFarland KA, Visness CM, Becker PM, Gern JE, Sorkness CA, Busse WW, Altman MC. Mepolizumab for urban children with exacerbation-prone eosinophilic asthma in the USA (MUPPITS-2): a randomised, double-blind, placebo-controlled, parallel-group trial. Lancet 2022; 400:502-511. [PMID: 35964610 PMCID: PMC9623810 DOI: 10.1016/s0140-6736(22)01198-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/07/2022] [Accepted: 06/14/2022] [Indexed: 01/13/2023]
Abstract
BACKGROUND Black and Hispanic children living in urban environments in the USA have an excess burden of morbidity and mortality from asthma. Therapies directed at the eosinophilic phenotype reduce asthma exacerbations in adults, but few data are available in children and diverse populations. Furthermore, the molecular mechanisms that underlie exacerbations either being prevented by, or persisting despite, immune-based therapies are not well understood. We aimed to determine whether mepolizumab, added to guidelines-based care, reduced the number of asthma exacerbations during a 52-week period compared with guidelines-based care alone. METHODS This is a randomised, double-blind, placebo-controlled, parallel-group trial done at nine urban medical centres in the USA. Children and adolescents aged 6-17 years, who lived in socioeconomically disadvantaged neighbourhoods and had exacerbation-prone asthma (defined as ≥two exacerbations in the previous year) and blood eosinophils of at least 150 cells per μL were randomly assigned 1:1 to mepolizumab (6-11 years: 40 mg; 12-17 years: 100 mg) or placebo injections once every 4 weeks, plus guideline-based care, for 52 weeks. Randomisation was done using a validated automated system. Participants, investigators, and the research staff who collected outcome measures remained masked to group assignments. The primary outcome was the number of asthma exacerbations that were treated with systemic corticosteroids during 52 weeks in the intention-to-treat population. The mechanisms of treatment response were assessed by study investigators using nasal transcriptomic modular analysis. Safety was assessed in the intention-to-treat population. This trial is registered with ClinicalTrials.gov, NCT03292588. FINDINGS Between Nov 1, 2017, and Mar 12, 2020, we recruited 585 children and adolescents. We screened 390 individuals, of whom 335 met the inclusion criteria and were enrolled. 290 met the randomisation criteria, were randomly assigned to mepolizumab (n=146) or placebo (n=144), and were included in the intention-to-treat analysis. 248 completed the study. The mean number of asthma exacerbations within the 52-week study period was 0·96 (95% CI 0·78-1·17) with mepolizumab and 1·30 (1·08-1·57) with placebo (rate ratio 0·73; 0·56-0·96; p=0·027). Treatment-emergent adverse events occurred in 42 (29%) of 146 participants in the mepolizumab group versus 16 (11%) of 144 participants in the placebo group. No deaths were attributed to mepolizumab. INTERPRETATION Phenotype-directed therapy with mepolizumab in urban children with exacerbation-prone eosinophilic asthma reduced the number of exacerbations. FUNDING US National Institute of Allergy and Infectious Diseases and GlaxoSmithKline.
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Affiliation(s)
- Daniel J Jackson
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA; Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
| | - Leonard B Bacharier
- Department of Pediatrics, Monroe Carell Jr Children's Hospital at Vanderbilt, Nashville, TN, USA
| | - Peter J Gergen
- National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Lisa Gagalis
- National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | | | | | - Michelle A Gill
- Department of Pediatrics, Washington University, St Louis, MO, USA
| | - Jeffrey Stokes
- Department of Pediatrics, Washington University, St Louis, MO, USA
| | - Andrew H Liu
- Pediatric Pulmonary and Sleep Medicine, Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, CO, USA
| | - Rebecca S Gruchalla
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Robyn T Cohen
- Department of Pediatrics, Boston University School of Medicine, Boston, MA, USA
| | - Melanie Makhija
- Division of Allergy and Immunology, Ann and Robert H Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | | | - George T O'Connor
- Department of Pediatrics, Boston University School of Medicine, Boston, MA, USA
| | - Jacqueline A Pongracic
- Division of Allergy and Immunology, Ann and Robert H Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Michael G Sherenian
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Katherine Rivera-Spoljaric
- Department of Pediatrics, Washington University, St Louis, MO, USA; St Louis Children's Hospital, St Louis, MO, USA
| | - Edward M Zoratti
- Department of Medicine, Henry Ford Health System, Detroit, MI, USA
| | - Stephen J Teach
- Children's National Hospital, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Meyer Kattan
- Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Cullen M Dutmer
- Pediatrics-Allergy and Immunology, Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, CO, USA
| | - Haejin Kim
- Department of Medicine, Henry Ford Health System, Detroit, MI, USA
| | - Carin Lamm
- Department of Pediatrics, New York Columbia University Medical Center, New York, NY, USA
| | - William J Sheehan
- Children's National Hospital, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - R Max Segnitz
- Department of Medicine, University of Washington, Seattle, WA, USA
| | | | | | - Patrice M Becker
- National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - James E Gern
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA; Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Christine A Sorkness
- School of Pharmacy, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - William W Busse
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Matthew C Altman
- Department of Medicine, University of Washington, Seattle, WA, USA; Benaroya Research Institute, Seattle, WA, USA
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12
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Dill-McFarland KA, Schwartz JT, Zhao H, Shao B, Fulkerson PC, Altman MC, Gill MA. Eosinophil-mediated suppression and Anti-IL-5 enhancement of plasmacytoid dendritic cell interferon responses in asthma. J Allergy Clin Immunol 2022; 150:666-675. [DOI: 10.1016/j.jaci.2022.03.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 02/25/2022] [Accepted: 03/03/2022] [Indexed: 10/18/2022]
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Abstract
We live in an increasingly data-driven world, where high-throughput sequencing and mass spectrometry platforms are transforming biology into an information science. This has shifted major challenges in biological research from data generation and processing to interpretation and knowledge translation. However, postsecondary training in bioinformatics, or more generally data science for life scientists, lags behind current demand. In particular, development of accessible, undergraduate data science curricula has the potential to improve research and learning outcomes as well as better prepare students in the life sciences to thrive in public and private sector careers. Here, we describe the Experiential Data science for Undergraduate Cross-Disciplinary Education (EDUCE) initiative, which aims to progressively build data science competency across several years of integrated practice. Through EDUCE, students complete data science modules integrated into required and elective courses augmented with coordinated cocurricular activities. The EDUCE initiative draws on a community of practice consisting of teaching assistants (TAs), postdocs, instructors, and research faculty from multiple disciplines to overcome several reported barriers to data science for life scientists, including instructor capacity, student prior knowledge, and relevance to discipline-specific problems. Preliminary survey results indicate that even a single module improves student self-reported interest and/or experience in bioinformatics and computer science. Thus, EDUCE provides a flexible and extensible active learning framework for integration of data science curriculum into undergraduate courses and programs across the life sciences.
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Affiliation(s)
- Kimberly A Dill-McFarland
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
- ECOSCOPE, University of British Columbia, Vancouver, British Columbia, Canada
| | - Stephan G König
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
- ECOSCOPE, University of British Columbia, Vancouver, British Columbia, Canada
| | - Florent Mazel
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
- ECOSCOPE, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany and Biodiversity Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - David C Oliver
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lisa M McEwen
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
- ECOSCOPE, University of British Columbia, Vancouver, British Columbia, Canada
- School of Health Information Science, Faculty of Human and Social Development, University of Victoria, Victoria, British Columbia, Canada
| | - Kris Y Hong
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
- ECOSCOPE, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
- ECOSCOPE, University of British Columbia, Vancouver, British Columbia, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, Vancouver, British Columbia, Canada
- Genome Science and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada
- Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
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14
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Kehoe SI, Dill-McFarland KA, Breaker JD, Suen G. Effects of corn silage inclusion in preweaning calf diets. J Dairy Sci 2019; 102:4131-4137. [PMID: 30879818 DOI: 10.3168/jds.2018-15799] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 01/09/2019] [Indexed: 11/19/2022]
Abstract
The objective of this research was to evaluate the effects of corn silage inclusion in starter feed provided to calves after birth through weaning at 7 wk of age. Thirty-six heifer calves and 9 bull calves were individually housed in hutches. Calves in treatment groups received pasteurized milk with all calf starter, 25% calf starter and 75% corn silage, or all corn silage. Values were recorded daily for feed intake and health, which included fecal, respiratory, and attitude scores; and at wk 2, 4, and 8 for concentrations of serum protein, hematocrit, and serum β-hydroxybutyrate. Body weight, withers height, and hip height were measured at wk 2, 4, 8, and 52. Nine bull calves (3/treatment) were killed at 8 wk of age for assessment of rumen and intestinal tissue morphology. Feed intake and average daily gain were not different among treatments. Least squares means of rumen papillae lengths were significantly different and decreased as corn silage inclusion increased. Crypt depths and total thickness of epithelium were reduced for the corn silage group. Least squares means of body weight, heart girth, hip height, withers height, serum protein, hematocrit, and β-hydroxybutyrate concentrations did not differ among treatments. These data indicated that the mixture of corn silage and starter did not affect growth, feed intake, or intestinal morphology but did affect rumen wall morphology. Feeding solely corn silage as starter feed stunted the growth of rumen papillae and tended to impair intestinal morphology, indicating that only calf starter or a mixture of calf starter and corn silage is more appropriate.
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Affiliation(s)
- S I Kehoe
- Department of Animal and Food Science, University of Wisconsin-River Falls, River Falls 54022.
| | - K A Dill-McFarland
- Department of Microbiology and Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Jacob D Breaker
- Department of Bacteriology, University of Wisconsin-Madison, Madison 53715
| | - G Suen
- Department of Bacteriology, University of Wisconsin-Madison, Madison 53715
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15
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Carroll C, Olsen KD, Ricks NJ, Dill-McFarland KA, Suen G, Robinson TF, Chaston JM. Bacterial Communities in the Alpaca Gastrointestinal Tract Vary With Diet and Body Site. Front Microbiol 2019; 9:3334. [PMID: 30713530 PMCID: PMC6345687 DOI: 10.3389/fmicb.2018.03334] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 12/24/2018] [Indexed: 12/31/2022] Open
Abstract
Gut -associated microbes (‘gut microbiota’) impact the nutrition of their hosts, especially in ruminants and pseudoruminants that consume high-cellulose diets. Examples include the pseudoruminant alpaca. To better understand how body site and diet influence the alpaca microbiota, we performed three 16S rRNA gene surveys. First, we surveyed the compartment 1 (C1), duodenum, jejunum, ileum, cecum, and large intestine (LI) of alpacas fed a grass hay (GH; tall fescue) or alfalfa hay (AH) diet for 30 days. Second, we performed a C1 survey of alpacas fed a series of 2-week mixed grass hay (MGH) diets supplemented with ∼25% dry weight barley, quinoa, amaranth, or soybean meal. Third, we examined the microbial differences of alpacas with normal versus poor body condition. Samples from GH- and AH-fed alpacas grouped by diet and body site but none of the four supplements significantly altered C1 microbiota composition, relative to each other, and none of the OTUs were differentially abundant between alpacas with normal versus poor body conditions. Taken together, the findings of a diet- and body-site specific alpaca microbiota are consistent with previous findings in ruminants and other mammals, but we provide no evidence to link changes in alpaca body condition with variation in microbiota relative abundance or identity.
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Affiliation(s)
- Courtney Carroll
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, United States
| | - Kyle D Olsen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, United States
| | - Nathan J Ricks
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, United States
| | | | - Garret Suen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Todd F Robinson
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, United States
| | - John M Chaston
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, United States
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16
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Cunha CS, Marcondes MI, Veloso CM, Mantovani HC, Pereira LGR, Tomich TR, Dill-McFarland KA, Suen G. Compositional and structural dynamics of the ruminal microbiota in dairy heifers and its relationship to methane production. J Sci Food Agric 2019; 99:210-218. [PMID: 29851082 DOI: 10.1002/jsfa.9162] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 05/28/2018] [Accepted: 05/29/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Heifers emit more enteric methane (CH4 ) than adult cows and these emissions tend to decrease per unit feed intake as they age. However, common mitigation strategies like expensive high-quality feeds are not economically feasible for these pre-production animals. Given its direct role in CH4 production, altering the rumen microbiota is another potential avenue for reducing CH4 production by ruminants. However, to identify effective microbial targets, a better understanding of the rumen microbiota and its relationship to CH4 production across heifer development is needed. RESULTS Here, we investigate the relationship between rumen bacterial, archaeal, and fungal communities as well as CH4 emissions and a number of production traits in prepubertal (PP), pubertal (PB), and pregnant heifers (PG). Overall, PG heifers emitted the most CH4 , followed by PB and PP heifers. The bacterial genus Acetobacter and the archaeal genus Methanobrevibacter were positively associated, while Eubacterium and Methanosphaera were negatively associated with raw CH4 production by heifers. When corrected for dietary intake, both Eubacterium and Methanosphaera remained negatively associated with CH4 production. CONCLUSION We suggest that Eubacterium and Methanosphaera represent likely targets for CH4 mitigation efforts in heifers as they were negatively associated with CH4 production and not significantly associated with production traits. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Camila S Cunha
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Marcos I Marcondes
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Cristina M Veloso
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | | | - Thierry R Tomich
- Brazilian Agricultural Research Corporation, EMBRAPA Dairy Cattle, Juiz de Fora, Brazil
| | | | - Garret Suen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
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17
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Romano KA, Dill-McFarland KA, Kasahara K, Kerby RL, Vivas EI, Amador-Noguez D, Herd P, Rey FE. Fecal Aliquot Straw Technique (FAST) allows for easy and reproducible subsampling: assessing interpersonal variation in trimethylamine-N-oxide (TMAO) accumulation. Microbiome 2018; 6:91. [PMID: 29776435 PMCID: PMC5960144 DOI: 10.1186/s40168-018-0458-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 04/05/2018] [Indexed: 05/25/2023]
Abstract
BACKGROUND Convenient, reproducible, and rapid preservation of unique biological specimens is pivotal to their use in microbiome analyses. As an increasing number of human studies incorporate the gut microbiome in their design, there is a high demand for streamlined sample collection and storage methods that are amenable to different settings and experimental needs. While several commercial kits address collection/shipping needs for sequence-based studies, these methods do not preserve samples properly for studies that require viable microbes. RESULTS We describe the Fecal Aliquot Straw Technique (FAST) of fecal sample processing for storage and subsampling. This method uses a straw to collect fecal material from samples recently voided or preserved at low temperature but not frozen (i.e., 4 °C). Different straw aliquots collected from the same sample yielded highly reproducible communities as disclosed by 16S rRNA gene sequencing; operational taxonomic units that were lost, or gained, between the two aliquots represented very low-abundance taxa (i.e., < 0.3% of the community). FAST-processed samples inoculated into germ-free animals resulted in gut communities that retained on average ~ 80% of the donor's bacterial community. Assessment of choline metabolism and trimethylamine-N-oxide accumulation in transplanted mice suggests large interpersonal variation. CONCLUSIONS Overall, FAST allows for repetitive subsampling without thawing of the specimens and requires minimal supplies and storage space, making it convenient to utilize both in the lab and in the field. FAST has the potential to advance microbiome research through easy, reproducible sample processing.
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Affiliation(s)
- Kymberleigh A. Romano
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706 USA
- Present address: Department of Cellular and Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195 USA
| | - Kimberly A. Dill-McFarland
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706 USA
- Center for the Demography of Health and Aging, University of Wisconsin-Madison, Madison, WI 53706 USA
- Present address: Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z3 Canada
| | - Kazuyuki Kasahara
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Robert L. Kerby
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Eugenio I. Vivas
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Pamela Herd
- Center for the Demography of Health and Aging, University of Wisconsin-Madison, Madison, WI 53706 USA
- Department of Sociology, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Federico E. Rey
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706 USA
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18
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Williams CL, Dill-McFarland KA, Sparks DL, Kouba AJ, Willard ST, Suen G, Brown AE. Dietary changes during weaning shape the gut microbiota of red pandas ( Ailurus fulgens). Conserv Physiol 2018; 6:cox075. [PMID: 29399361 PMCID: PMC5772406 DOI: 10.1093/conphys/cox075] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 11/10/2017] [Accepted: 12/07/2017] [Indexed: 05/30/2023]
Abstract
Mammalian herbivores have developed numerous adaptations to utilize their plant-based diets including a modified gastrointestinal tract (GIT) and symbiosis with a GIT microbiota that plays a major role in digestion and the maintenance of host health. The red panda (Ailurus fulgens) is a herbivorous carnivore that lacks the specialized GIT common to other herbivores but still relies on microorganisms for survival on its almost entirely bamboo diet. The GIT microbiota is of further importance in young red pandas, as high cub mortality is problematic and has been attributed to failure to meet nutritional requirements. To gain insight into the establishment of the GIT microbiota of red pandas, we examined microbial communities in two individuals following dietary changes associated with weaning using next-generation 16S rRNA Illumina MiSeq paired-end sequencing of faecal samples. Across all four stages (pre-weaning, during weaning, post-weaning and adult), the GIT microbial community displayed low diversity and was dominated by bacteria in the phylum Firmicutes with lesser contributions from the Proteobacteria. A core community was found consistently across all weaning stages and included species within the taxa Escherichia-Shigella, Streptococcus, Clostridium and an unclassified Clostridiaceae. Analysis of the overall community composition and structure showed that although the GIT microbiota is established early in red pandas, dietary changes during weaning further shape the community and are correlated with the presence of new bacterial species. This work is the first analysis of the GIT microbiota for red panda cubs during weaning and provides a framework for understanding how diet and host microbiota impact the development of these threatened animals.
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Affiliation(s)
- Candace L Williams
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, 32 Creelman Street, Mississippi State, MS 39762, USA
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, 2 Research Blvd, Box 9627, Mississippi State, MS 39762, USA
| | | | - Darrell L Sparks
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, 32 Creelman Street, Mississippi State, MS 39762, USA
- Mississippi State Chemical Laboratory, 1145 Hand Lab, 310 Presidents Circle, Mississippi State, MS 39762, USA
| | - Andrew J Kouba
- Department of Research and Conservation, Memphis Zoological Society, 2000 Prentiss Place, Memphis, TN 38112, USA
| | - Scott T Willard
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, 32 Creelman Street, Mississippi State, MS 39762, USA
| | - Garret Suen
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Dr, Madison, WI 53706, USA
| | - Ashli E Brown
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, 32 Creelman Street, Mississippi State, MS 39762, USA
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, 2 Research Blvd, Box 9627, Mississippi State, MS 39762, USA
- Mississippi State Chemical Laboratory, 1145 Hand Lab, 310 Presidents Circle, Mississippi State, MS 39762, USA
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19
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Dai X, Weimer PJ, Dill-McFarland KA, Brandao VLN, Suen G, Faciola AP. Camelina Seed Supplementation at Two Dietary Fat Levels Change Ruminal Bacterial Community Composition in a Dual-Flow Continuous Culture System. Front Microbiol 2017; 8:2147. [PMID: 29163431 PMCID: PMC5675879 DOI: 10.3389/fmicb.2017.02147] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/20/2017] [Indexed: 12/26/2022] Open
Abstract
This experiment aimed to determine the effects of camelina seed (CS) supplementation at different dietary fat levels on ruminal bacterial community composition and how it relates to changes in ruminal fermentation in a dual-flow continuous culture system. Diets were randomly assigned to 8 fermenters (1,200–1,250 mL) in a 2 × 2 factorial arrangement of treatments in a replicated 4 × 4 Latin square with four 10-day experimental periods that consisted of 7 days for diet adaptation and 3 days for sample collection. Treatments were: (1) no CS at 5% ether extract (EE, NCS5); (2) no CS at 8% EE (NCS8); (3) 7.7% CS at 5% EE (CS5); and (4) 17.7% CS at 8% EE (CS8). Megalac was used as a control to adjust EE levels. Diets contained 55% orchardgrass hay and 45% concentrate, and fermenters were equally fed a total of 72 g/day (DM basis) twice daily. The bacterial community was determined by sequencing the V4 region of the 16S rRNA gene using the Illumina MiSeq platform. Sequencing data were analyzed using mothur and statistical analyses were performed in R and SAS. The most abundant phyla across treatments were the Bacteroidetes and Firmicutes, accounting for 49 and 39% of the total sequences, respectively. The bacterial community composition in both liquid and solid fractions of the effluent digesta changed with CS supplementation but not by dietary EE. Including CS in the diets decreased the relative abundances of Ruminococcus spp., Fibrobacter spp., and Butyrivibrio spp. The most abundant genus across treatments, Prevotella, was reduced by high dietary EE levels, while Megasphaera and Succinivibrio were increased by CS supplementation in the liquid fraction. Correlatively, the concentration of acetate was decreased while propionate increased; C18:0 was decreased and polyunsaturated fatty acids, especially C18:2 n-6 and C18:3 n-3, were increased by CS supplementation. Based on the correlation analysis between genera and fermentation end products, this study revealed that CS supplementation could be energetically beneficial to dairy cows by increasing propionate-producing bacteria and suppressing ruminal bacteria associated with biohydrogenation. However, attention should be given to avoid the effects of CS supplementation on suppressing cellulolytic bacteria.
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Affiliation(s)
- Xiaoxia Dai
- Department of Animal Sciences, University of Florida, Gainesville, FL, United States
| | - Paul J Weimer
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States.,Agricultural Research Service, United States Department of Agriculture, Madison, WI, United States
| | | | - Virginia L N Brandao
- Department of Animal Sciences, University of Florida, Gainesville, FL, United States
| | - Garret Suen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Antonio P Faciola
- Department of Animal Sciences, University of Florida, Gainesville, FL, United States
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20
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Vogt NM, Kerby RL, Dill-McFarland KA, Harding SJ, Merluzzi AP, Johnson SC, Carlsson CM, Asthana S, Zetterberg H, Blennow K, Bendlin BB, Rey FE. Gut microbiome alterations in Alzheimer's disease. Sci Rep 2017; 7:13537. [PMID: 29051531 PMCID: PMC5648830 DOI: 10.1038/s41598-017-13601-y] [Citation(s) in RCA: 1063] [Impact Index Per Article: 151.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 09/27/2017] [Indexed: 12/22/2022] Open
Abstract
Alzheimer’s disease (AD) is the most common form of dementia. However, the etiopathogenesis of this devastating disease is not fully understood. Recent studies in rodents suggest that alterations in the gut microbiome may contribute to amyloid deposition, yet the microbial communities associated with AD have not been characterized in humans. Towards this end, we characterized the bacterial taxonomic composition of fecal samples from participants with and without a diagnosis of dementia due to AD. Our analyses revealed that the gut microbiome of AD participants has decreased microbial diversity and is compositionally distinct from control age- and sex-matched individuals. We identified phylum- through genus-wide differences in bacterial abundance including decreased Firmicutes, increased Bacteroidetes, and decreased Bifidobacterium in the microbiome of AD participants. Furthermore, we observed correlations between levels of differentially abundant genera and cerebrospinal fluid (CSF) biomarkers of AD. These findings add AD to the growing list of diseases associated with gut microbial alterations, as well as suggest that gut bacterial communities may be a target for therapeutic intervention.
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Affiliation(s)
- Nicholas M Vogt
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, 600 Highland Avenue J5/1 Mezzanine, Madison, WI 53792, USA
| | - Robert L Kerby
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI 53706, USA
| | - Kimberly A Dill-McFarland
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI 53706, USA
| | - Sandra J Harding
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, 600 Highland Avenue J5/1 Mezzanine, Madison, WI 53792, USA
| | - Andrew P Merluzzi
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, 600 Highland Avenue J5/1 Mezzanine, Madison, WI 53792, USA
| | - Sterling C Johnson
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, 600 Highland Avenue J5/1 Mezzanine, Madison, WI 53792, USA.,Geriatric Research Education and Clinical Center, William S. Middleton Memorial Veterans Hospital, 2500 Overlook Terrace, Madison, WI 53705, USA.,Wisconsin Alzheimer's Institute, University of Wisconsin School of Medicine and Public Health, WARF Building, 610 Walnut Street, 9th Floor, Suite 957, Madison, WI 53726, USA
| | - Cynthia M Carlsson
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, 600 Highland Avenue J5/1 Mezzanine, Madison, WI 53792, USA.,Geriatric Research Education and Clinical Center, William S. Middleton Memorial Veterans Hospital, 2500 Overlook Terrace, Madison, WI 53705, USA.,Wisconsin Alzheimer's Institute, University of Wisconsin School of Medicine and Public Health, WARF Building, 610 Walnut Street, 9th Floor, Suite 957, Madison, WI 53726, USA
| | - Sanjay Asthana
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, 600 Highland Avenue J5/1 Mezzanine, Madison, WI 53792, USA.,Geriatric Research Education and Clinical Center, William S. Middleton Memorial Veterans Hospital, 2500 Overlook Terrace, Madison, WI 53705, USA
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.,Department of Molecular Neuroscience, University College London Institute of Neurology, Queen Square, London, United Kingdom.,UK Dementia Research Institute at University College London, London, United Kingdom
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Barbara B Bendlin
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, 600 Highland Avenue J5/1 Mezzanine, Madison, WI 53792, USA. .,Wisconsin Alzheimer's Institute, University of Wisconsin School of Medicine and Public Health, WARF Building, 610 Walnut Street, 9th Floor, Suite 957, Madison, WI 53726, USA.
| | - Federico E Rey
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI 53706, USA.
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21
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Cunha CS, Veloso CM, Marcondes MI, Mantovani HC, Tomich TR, Pereira LGR, Ferreira MFL, Dill-McFarland KA, Suen G. Assessing the impact of rumen microbial communities on methane emissions and production traits in Holstein cows in a tropical climate. Syst Appl Microbiol 2017; 40:492-499. [PMID: 29113689 DOI: 10.1016/j.syapm.2017.07.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 07/27/2017] [Accepted: 07/31/2017] [Indexed: 02/09/2023]
Abstract
The evaluation of how the gut microbiota affects both methane emissions and animal production is necessary in order to achieve methane mitigation without production losses. Toward this goal, the aim of this study was to correlate the rumen microbial communities (bacteria, archaea, and fungi) of high (HP), medium (MP), and low milk producing (LP), as well as dry (DC), Holstein dairy cows in an actual tropical production system with methane emissions and animal production traits. Overall, DC cows emitted more methane, followed by MP, HP and LP cows, although HP and LP cow emissions were similar. Using next-generation sequencing, it was found that bacteria affiliated with Christensenellaceae, Mogibacteriaceae, S24-7, Butyrivibrio, Schwartzia, and Treponema were negatively correlated with methane emissions and showed positive correlations with digestible dry matter intake (dDMI) and digestible organic matter intake (dOMI). Similar findings were observed for archaea in the genus Methanosphaera. The bacterial groups Coriobacteriaceae, RFP12, and Clostridium were negatively correlated with methane, but did not correlate with dDMI and dOMI. For anaerobic fungal communities, no significant correlations with methane or animal production traits were found. Based on these findings, it is suggested that manipulation of the abundances of these microbial taxa may be useful for modulating methane emissions without negatively affecting animal production.
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Affiliation(s)
- Camila S Cunha
- Department of Animal Science, Universidade Federal de Viçosa, Peter Henry Rolfs Avenue, University Campus, Viçosa, Minas Gerais 36570-900,Brazil.
| | - Cristina M Veloso
- Department of Animal Science, Universidade Federal de Viçosa, Peter Henry Rolfs Avenue, University Campus, Viçosa, Minas Gerais 36570-900,Brazil.
| | - Marcos I Marcondes
- Department of Animal Science, Universidade Federal de Viçosa, Peter Henry Rolfs Avenue, University Campus, Viçosa, Minas Gerais 36570-900,Brazil.
| | - Hilario C Mantovani
- Department of Microbiology, Universidade Federal de Viçosa, Peter Henry Rolfs Avenue, University Campus, Viçosa, Minas Gerais 36570-900, Brazil.
| | - Thierry R Tomich
- Brazilian Agricultural Research Corporation, Embrapa Dairy Cattle, Eugênio do Nascimento Avenue, 610, Cascatinha, Juiz de Fora, Minas Gerais 36038-330, Brazil.
| | - Luiz Gustavo R Pereira
- Brazilian Agricultural Research Corporation, Embrapa Dairy Cattle, Eugênio do Nascimento Avenue, 610, Cascatinha, Juiz de Fora, Minas Gerais 36038-330, Brazil.
| | - Matheus F L Ferreira
- Department of Animal Science, Universidade Federal de Viçosa, Peter Henry Rolfs Avenue, University Campus, Viçosa, Minas Gerais 36570-900,Brazil.
| | - Kimberly A Dill-McFarland
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Dr, Madison, Wisconsin 53706, USA; Department of Microbiology & Immunology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada.
| | - Garret Suen
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Dr, Madison, Wisconsin 53706, USA.
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22
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Dias J, Marcondes MI, Noronha MF, Resende RT, Machado FS, Mantovani HC, Dill-McFarland KA, Suen G. Effect of Pre-weaning Diet on the Ruminal Archaeal, Bacterial, and Fungal Communities of Dairy Calves. Front Microbiol 2017; 8:1553. [PMID: 28861065 PMCID: PMC5559706 DOI: 10.3389/fmicb.2017.01553] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 07/31/2017] [Indexed: 01/01/2023] Open
Abstract
At birth, calves display an underdeveloped rumen that eventually matures into a fully functional rumen as a result of solid food intake and microbial activity. However, little is known regarding the gradual impact of pre-weaning diet on the establishment of the rumen microbiota. Here, we employed next-generation sequencing to investigate the effects of the inclusion of starter concentrate (M: milk-fed vs. MC: milk plus starter concentrate fed) on archaeal, bacterial and anaerobic fungal communities in the rumens of 45 crossbred dairy calves across pre-weaning development (7, 28, 49, and 63 days). Our results show that archaeal, bacterial, and fungal taxa commonly found in the mature rumen were already established in the rumens of calves at 7 days old, regardless of diet. This confirms that microbiota colonization occurs in the absence of solid substrate. However, diet did significantly impact some microbial taxa. In the bacterial community, feeding starter concentrate promoted greater diversity of bacterial taxa known to degrade readily fermentable carbohydrates in the rumen (e.g., Megasphaera, Sharpea, and Succinivribrio). Shifts in the ruminal bacterial community also correlated to changes in fermentation patterns that favored the colonization of Methanosphaera sp. A4 in the rumen of MC calves. In contrast, M calves displayed a bacterial community dominated by taxa able to utilize milk nutrients (e.g., Lactobacillus, Bacteroides, and Parabacteroides). In both diet groups, the dominance of these milk-associated taxa decreased with age, suggesting that diet and age simultaneously drive changes in the structure and abundance of bacterial communities in the developing rumen. Changes in the composition and abundance of archaeal communities were attributed exclusively to diet, with more highly abundant Methanosphaera and less abundant Methanobrevibacter in MC calves. Finally, the fungal community was dominated by members of the genus SK3 and Caecomyces. Relative anaerobic fungal abundances did not change significantly in response to diet or age, likely due to high inter-animal variation and the low fiber content of starter concentrate. This study provides new insights into the colonization of archaea, bacteria, and anaerobic fungi communities in pre-ruminant calves that may be useful in designing strategies to promote colonization of target communities to improve functional development.
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Affiliation(s)
- Juliana Dias
- Department of Animal Science, Universidade Federal de ViçosaViçosa, Brazil.,Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, Ministério da EducaçãoBrasília, Brazil
| | - Marcos I Marcondes
- Department of Animal Science, Universidade Federal de ViçosaViçosa, Brazil
| | - Melline F Noronha
- Division of Microbial Resources, Research Centre for Chemistry, Biology and Agriculture, University of CampinasCampinas, Brazil
| | - Rafael T Resende
- Forestry Department, Universidade Federal de ViçosaViçosa, Brazil
| | | | | | | | - Garret Suen
- Department of Bacteriology, University of Wisconsin-MadisonMadison, WI, United States
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23
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Dill-McFarland KA, Breaker JD, Suen G. Microbial succession in the gastrointestinal tract of dairy cows from 2 weeks to first lactation. Sci Rep 2017; 7:40864. [PMID: 28098248 PMCID: PMC5241668 DOI: 10.1038/srep40864] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 12/13/2016] [Indexed: 02/07/2023] Open
Abstract
Development of the dairy calf gastrointestinal tract (GIT) and its associated microbiota are essential for survival and milk production, as this community is responsible for converting plant-based feeds into accessible nutrients. However, little is known regarding the establishment of microbes in the calf GIT. Here, we measured fecal-associated bacterial, archaeal, and fungal communities of dairy cows from 2 weeks to the middle of first lactation (>2 years) as well as rumen-associated communities from weaning (8 weeks) to first lactation. These communities were then correlated to animal growth and health. Although succession of specific operational taxonomic units (OTUs) was unique to each animal, beta-diversity decreased while alpha-diversity increased as animals aged. Calves exhibited similar microbial families and genera but different OTUs than adults, with a transition to an adult-like microbiota between weaning and 1 year of age. This suggests that alterations of the microbiota for improving downstream milk production may be most effective during, or immediately following, the weaning transition.
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Affiliation(s)
| | - Jacob D Breaker
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Garret Suen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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24
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Williams CL, Dill-McFarland KA, Vandewege MW, Sparks DL, Willard ST, Kouba AJ, Suen G, Brown AE. Dietary Shifts May Trigger Dysbiosis and Mucous Stools in Giant Pandas (Ailuropoda melanoleuca). Front Microbiol 2016; 7:661. [PMID: 27199976 PMCID: PMC4858621 DOI: 10.3389/fmicb.2016.00661] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 04/21/2016] [Indexed: 01/19/2023] Open
Abstract
Dietary shifts can result in changes to the gastrointestinal tract (GIT) microbiota, leading to negative outcomes for the host, including inflammation. Giant pandas (Ailuropoda melanoleuca) are physiologically classified as carnivores; however, they consume an herbivorous diet with dramatic seasonal dietary shifts and episodes of chronic GIT distress with symptoms including abdominal pain, loss of appetite and the excretion of mucous stools (mucoids). These episodes adversely affect the overall nutritional and health status of giant pandas. Here, we examined the fecal microbiota of two giant pandas’ non-mucoid and mucoid stools and compared these to samples from a previous winter season that had historically few mucoid episodes. To identify the microbiota present, we isolated and sequenced the 16S rRNA using next-generation sequencing. Mucoids occurred following a seasonal feeding switch from predominately bamboo culm (stalk) to leaves. All fecal samples displayed low diversity and were dominated by bacteria in the phyla Firmicutes and to a lesser extent, Proteobacteria. Fecal samples immediately prior to mucoid episodes had lower microbial diversity as compared to mucoids. Mucoids were mostly comprised of common mucosal-associated taxa including Streptococcus and Leuconostoc species, and exhibited increased abundance for bacteria in the family Pasteurellaceae. Taken together, these findings indicate that mucoids may represent an expulsion of the mucosal lining that is driven by changes in diet. We suggest that these occurrences serve to reset their GIT microbiota following changes in bamboo part preference, as giant pandas have retained a carnivorous GIT anatomy while shifting to an herbivorous diet.
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Affiliation(s)
- Candace L Williams
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State UniversityMississippi State, Mississippi, MS, USA; Institute for Genomics, Biocomputing and Biotechnology, Mississippi State UniversityMississippi State, Mississippi, MS, USA
| | | | - Michael W Vandewege
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University Mississippi State, Mississippi, MS, USA
| | - Darrell L Sparks
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State UniversityMississippi State, Mississippi, MS, USA; Mississippi State Chemical LaboratoryMississippi State, Mississippi, MS, USA
| | - Scott T Willard
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University Mississippi State, Mississippi, MS, USA
| | - Andrew J Kouba
- Department of Conservation and Research, Memphis Zoological Society Memphis, TN, USA
| | - Garret Suen
- Department of Bacteriology, University of Wisconsin-Madison Madison, WI, USA
| | - Ashli E Brown
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State UniversityMississippi State, Mississippi, MS, USA; Institute for Genomics, Biocomputing and Biotechnology, Mississippi State UniversityMississippi State, Mississippi, MS, USA; Mississippi State Chemical LaboratoryMississippi State, Mississippi, MS, USA
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25
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Dill-McFarland KA, Weimer PJ, Pauli JN, Peery MZ, Suen G. Diet specialization selects for an unusual and simplified gut microbiota in two- and three-toed sloths. Environ Microbiol 2015; 18:1391-402. [DOI: 10.1111/1462-2920.13022] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 08/12/2015] [Indexed: 01/03/2023]
Affiliation(s)
| | - Paul J. Weimer
- Department of Bacteriology; University of Wisconsin-Madison; Madison WI 53706 USA
- US Department of Agriculture; Agricultural Research Service; Madison WI 53706 USA
| | - Jonathan N. Pauli
- Department of Forest and Wildlife Ecology; University of Wisconsin-Madison; Madison WI 53706 USA
| | - M. Zachariah Peery
- Department of Forest and Wildlife Ecology; University of Wisconsin-Madison; Madison WI 53706 USA
| | - Garret Suen
- Department of Bacteriology; University of Wisconsin-Madison; Madison WI 53706 USA
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26
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Dill-McFarland KA, Neil KL, Zeng A, Sprenger RJ, Kurtz CC, Suen G, Carey HV. Hibernation alters the diversity and composition of mucosa-associated bacteria while enhancing antimicrobial defence in the gut of 13-lined ground squirrels. Mol Ecol 2014; 23:4658-69. [PMID: 25130694 DOI: 10.1111/mec.12884] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 08/05/2014] [Accepted: 08/08/2014] [Indexed: 12/15/2022]
Abstract
The gut microbiota plays important roles in animal nutrition and health. This relationship is particularly dynamic in hibernating mammals where fasting drives the gut community to rely on host-derived nutrients instead of exogenous substrates. We used 16S rRNA pyrosequencing and caecal tissue protein analysis to investigate the effects of hibernation on the mucosa-associated bacterial microbiota and host responses in 13-lined ground squirrels. The mucosal microbiota was less diverse in winter hibernators than in actively feeding spring and summer squirrels. UniFrac analysis revealed distinct summer and late winter microbiota clusters, while spring and early winter clusters overlapped slightly, consistent with their transitional structures. Communities in all seasons were dominated by Firmicutes and Bacteroidetes, with lesser contributions from Proteobacteria, Verrucomicrobia, Tenericutes and Actinobacteria. Hibernators had lower relative abundances of Firmicutes, which include genera that prefer plant polysaccharides, and higher abundances of Bacteroidetes and Verrucomicrobia, some of which can survive solely on host-derived mucins. A core mucosal assemblage of nine operational taxonomic units shared among all individuals was identified with an average total sequence abundance of 60.2%. This core community, together with moderate shifts in specific taxa, indicates that the mucosal microbiota remains relatively stable over the annual cycle yet responds to substrate changes while potentially serving as a pool for 'seeding' the microbiota once exogenous substrates return in spring. Relative to summer, hibernation reduced caecal crypt length and increased MUC2 expression in early winter and spring. Hibernation also decreased caecal TLR4 and increased TLR5 expression, suggesting a protective response that minimizes inflammation.
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