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Ghielmetti G, Kerr TJ, Bernitz N, Mhlophe SK, Streicher E, Loxton AG, Warren RM, Miller MA, Goosen WJ. Insights into mycobacteriome composition in Mycobacterium bovis-infected African buffalo (Syncerus caffer) tissue samples. Sci Rep 2024; 14:17537. [PMID: 39080347 PMCID: PMC11289279 DOI: 10.1038/s41598-024-68189-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 07/22/2024] [Indexed: 08/02/2024] Open
Abstract
Animal tuberculosis significantly challenges global health, agriculture, and wildlife conservation efforts. Mycobacterial cultures are resource-intensive, time-consuming, and challenged by heterogeneous populations. In this study, we employed a culture-independent approach, using targeted long-read-based next-generation sequencing (tNGS), to investigate the mycobacterial composition in 60 DNA samples extracted from Mycobacterium bovis infected culture-confirmed African buffalo tissue. We detected mycobacterial DNA in 93.3% of the samples and the sensitivity for detecting Mycobacterium tuberculosis complex (MTBC) was 91.7%, demonstrating a high concordance of our culture-independent tNGS approach with mycobacterial culture results. In five samples, we identified heterogenous mycobacterial populations with various non-tuberculous mycobacteria, including members of the Mycobacterium avium complex (MAC), M. smegmatis, and M. komaniense. The latter Mycobacterium species was described in South Africa from bovine nasal swabs and environmental samples from the Hluhluwe-iMfolozi Park, which was the origin of the buffalo samples in the present study. This finding suggests that exposure to environmental mycobacteria may confound detection of MTBC in wildlife. In conclusion, our approach represents a promising alternative to conventional methods for detecting mycobacterial DNA. This high-throughput technique enables rapid differentiation of heterogeneous mycobacterial populations, which will contribute valuable insights into the epidemiology, pathogenesis, and microbial synergy during mycobacterial infections.
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Affiliation(s)
- Giovanni Ghielmetti
- South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa
- Section of Veterinary Bacteriology, Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 270, 8057, Zurich, Switzerland
| | - Tanya J Kerr
- South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa
| | - Netanya Bernitz
- Cryptosporidiosis Lab, The Francis Crick Institute, London, UK
| | - Sinegugu K Mhlophe
- South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa
| | - Elizma Streicher
- South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa
| | - Andre G Loxton
- South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa
| | - Robin M Warren
- South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa
| | - Michele A Miller
- South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa
| | - Wynand J Goosen
- South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa.
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Ghielmetti G, Loubser J, Kerr TJ, Stuber T, Thacker T, Martin LC, O'Hare MA, Mhlophe SK, Okunola A, Loxton AG, Warren RM, Moseley MH, Miller MA, Goosen WJ. Advancing animal tuberculosis surveillance using culture-independent long-read whole-genome sequencing. Front Microbiol 2023; 14:1307440. [PMID: 38075895 PMCID: PMC10699144 DOI: 10.3389/fmicb.2023.1307440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 10/23/2023] [Indexed: 02/12/2024] Open
Abstract
Animal tuberculosis is a significant infectious disease affecting both livestock and wildlife populations worldwide. Effective disease surveillance and characterization of Mycobacterium bovis (M. bovis) strains are essential for understanding transmission dynamics and implementing control measures. Currently, sequencing of genomic information has relied on culture-based methods, which are time-consuming, resource-demanding, and concerning in terms of biosafety. This study explores the use of culture-independent long-read whole-genome sequencing (WGS) for a better understanding of M. bovis epidemiology in African buffaloes (Syncerus caffer). By comparing two sequencing approaches, we evaluated the efficacy of Illumina WGS performed on culture extracts and culture-independent Oxford Nanopore adaptive sampling (NAS). Our objective was to assess the potential of NAS to detect genomic variants without sample culture. In addition, culture-independent amplicon sequencing, targeting mycobacterial-specific housekeeping and full-length 16S rRNA genes, was applied to investigate the presence of microorganisms, including nontuberculous mycobacteria. The sequencing quality obtained from DNA extracted directly from tissues using NAS is comparable to the sequencing quality of reads generated from culture-derived DNA using both NAS and Illumina technologies. We present a new approach that provides complete and accurate genome sequence reconstruction, culture independently, and using an economically affordable technique.
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Affiliation(s)
- Giovanni Ghielmetti
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Section of Veterinary Bacteriology, Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Johannes Loubser
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Tanya J. Kerr
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Tod Stuber
- National Veterinary Services Laboratories, Veterinary Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA, United States
| | - Tyler Thacker
- National Veterinary Services Laboratories, Veterinary Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA, United States
| | - Lauren C. Martin
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Michaela A. O'Hare
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Sinegugu K. Mhlophe
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Abisola Okunola
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Andre G. Loxton
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Robin M. Warren
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Mark H. Moseley
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Michele A. Miller
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Wynand J. Goosen
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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3
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Klever AM, Alexander KA, Almeida D, Anderson MZ, Ball RL, Beamer G, Boggiatto P, Buikstra JE, Chandler B, Claeys TA, Concha AE, Converse PJ, Derbyshire KM, Dobos KM, Dupnik KM, Endsley JJ, Endsley MA, Fennelly K, Franco-Paredes C, Hagge DA, Hall-Stoodley L, Hayes D, Hirschfeld K, Hofman CA, Honda JR, Hull NM, Kramnik I, Lacourciere K, Lahiri R, Lamont EA, Larsen MH, Lemaire T, Lesellier S, Lee NR, Lowry CA, Mahfooz NS, McMichael TM, Merling MR, Miller MA, Nagajyothi JF, Nelson E, Nuermberger EL, Pena MT, Perea C, Podell BK, Pyle CJ, Quinn FD, Rajaram MVS, Mejia OR, Rothoff M, Sago SA, Salvador LCM, Simonson AW, Spencer JS, Sreevatsan S, Subbian S, Sunstrum J, Tobin DM, Vijayan KKV, Wright CTO, Robinson RT. The Many Hosts of Mycobacteria 9 (MHM9): A conference report. Tuberculosis (Edinb) 2023; 142:102377. [PMID: 37531864 PMCID: PMC10529179 DOI: 10.1016/j.tube.2023.102377] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/10/2023] [Accepted: 07/17/2023] [Indexed: 08/04/2023]
Abstract
The Many Hosts of Mycobacteria (MHM) meeting series brings together basic scientists, clinicians and veterinarians to promote robust discussion and dissemination of recent advances in our knowledge of numerous mycobacterial diseases, including human and bovine tuberculosis (TB), nontuberculous mycobacteria (NTM) infection, Hansen's disease (leprosy), Buruli ulcer and Johne's disease. The 9th MHM conference (MHM9) was held in July 2022 at The Ohio State University (OSU) and centered around the theme of "Confounders of Mycobacterial Disease." Confounders can and often do drive the transmission of mycobacterial diseases, as well as impact surveillance and treatment outcomes. Various confounders were presented and discussed at MHM9 including those that originate from the host (comorbidities and coinfections) as well as those arising from the environment (e.g., zoonotic exposures), economic inequality (e.g. healthcare disparities), stigma (a confounder of leprosy and TB for millennia), and historical neglect (a confounder in Native American Nations). This conference report summarizes select talks given at MHM9 highlighting recent research advances, as well as talks regarding the historic and ongoing impact of TB and other infectious diseases on Native American Nations, including those in Southwestern Alaska where the regional TB incidence rate is among the highest in the Western hemisphere.
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Affiliation(s)
- Abigail Marie Klever
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, OH, USA
| | - Kathleen A Alexander
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, VA, USA; CARACAL/Chobe Research Institute Kasane, Botswana
| | - Deepak Almeida
- Center for Tuberculosis Research, Johns Hopkins University, Baltimore, MD, USA
| | - Matthew Z Anderson
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, OH, USA; Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | | | - Gillian Beamer
- Host Pathogen Interactions and Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Paola Boggiatto
- Agricultural Research Service, United States Department of Agriculture, Ames, IA, USA
| | - Jane E Buikstra
- Center for Bioarchaeological Research, Arizona State University, Tempe, AZ, USA
| | - Bruce Chandler
- Division of Public Health, Alaska Department of Health, AK, USA
| | - Tiffany A Claeys
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, OH, USA
| | - Aislinn E Concha
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Paul J Converse
- Center for Tuberculosis Research, Johns Hopkins University, Baltimore, MD, USA
| | - Keith M Derbyshire
- Division of Genetics, The Wadsworth Center, New York State Department of Health, Albany, NY, USA; Department of Biomedical Sciences, University at Albany, Albany, NY, USA
| | - Karen M Dobos
- Department of Microbiology, Immunology, and Pathology, Mycobacteria Research Laboratories, Colorado State University, Fort Collins, CO, USA
| | - Kathryn M Dupnik
- Center for Global Health, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Janice J Endsley
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Mark A Endsley
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Kevin Fennelly
- Pulmonary Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, MD, USA
| | - Carlos Franco-Paredes
- Department of Microbiology, Immunology, and Pathology, Mycobacteria Research Laboratories, Colorado State University, Fort Collins, CO, USA; Hospital Infantil de México Federico Gómez, México, USA
| | | | - Luanne Hall-Stoodley
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, OH, USA
| | - Don Hayes
- Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | | | - Courtney A Hofman
- Department of Anthropology, University of Oklahoma, Norman, OK, USA; Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK, USA
| | - Jennifer R Honda
- Department of Cellular and Molecular Biology, University of Texas Health Science Center at Tyler, Tyler, TX, USA
| | - Natalie M Hull
- Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, Columbus, OH, USA
| | - Igor Kramnik
- Pulmonary Center, The Department of Medicine, Boston University Chobanian & Aveedisian School of Medicine, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Karen Lacourciere
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Ramanuj Lahiri
- United States Department of Health and Human Services, Health Resources and Services Administration, Health Systems Bureau, National Hansen's Disease Program, Baton Rouge, LA, USA
| | - Elise A Lamont
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Michelle H Larsen
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Sandrine Lesellier
- French Agency for Food, Environmental & Occupational Health & Safety (ANSES), Laboratory for Rabies and Wildlife,Nancy, France
| | - Naomi R Lee
- Department of Chemistry and Biochemistry, Northern Arizona University, Flagstaff, AZ, USA
| | - Christopher A Lowry
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Najmus S Mahfooz
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, OH, USA
| | - Temet M McMichael
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, OH, USA
| | - Marlena R Merling
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, OH, USA
| | - Michele A Miller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Jyothi F Nagajyothi
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Elizabeth Nelson
- Microbial Paleogenomics Unit, Dept of Genomes and Genetics, Institut Pasteur, Paris, France
| | - Eric L Nuermberger
- Center for Tuberculosis Research, Johns Hopkins University, Baltimore, MD, USA
| | - Maria T Pena
- United States Department of Health and Human Services, Health Resources and Services Administration, Health Systems Bureau, National Hansen's Disease Program, Baton Rouge, LA, USA
| | - Claudia Perea
- Animal & Plant Health Inspection Service, United States Department of Agriculture, Ames, IA, USA
| | - Brendan K Podell
- Department of Microbiology, Immunology, and Pathology, Mycobacteria Research Laboratories, Colorado State University, Fort Collins, CO, USA
| | - Charlie J Pyle
- Department of Molecular Genetics & Microbiology, Duke University School of Medicine, Durham, NC, USA; Department of Immunology, Duke University School of Medicine, Durham, NC, USA
| | - Fred D Quinn
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Murugesan V S Rajaram
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, OH, USA
| | - Oscar Rosas Mejia
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, OH, USA
| | | | - Saydie A Sago
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Liliana C M Salvador
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USA
| | - Andrew W Simonson
- Department of Microbiology and Molecular Genetics and the Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - John S Spencer
- Department of Microbiology, Immunology, and Pathology, Mycobacteria Research Laboratories, Colorado State University, Fort Collins, CO, USA
| | - Srinand Sreevatsan
- Pathobiology & Diagnostic Investigation Department, College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Selvakumar Subbian
- Public Health Research Institute (PHRI), New Jersey Medical School, Rutgers University, Newark, NJ, USA
| | | | - David M Tobin
- Department of Molecular Genetics & Microbiology, Duke University School of Medicine, Durham, NC, USA; Department of Immunology, Duke University School of Medicine, Durham, NC, USA
| | - K K Vidya Vijayan
- Department of Microbiology and Immunology, Center for AIDS Research, and Children's Research Institute, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Caelan T O Wright
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Richard T Robinson
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, OH, USA.
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Kim BG, Kang N, Kim SY, Kim DH, Kim H, Kwon OJ, Huh HJ, Lee NY, Jhun BW. The lung microbiota in nontuberculous mycobacterial pulmonary disease. PLoS One 2023; 18:e0285143. [PMID: 37235629 DOI: 10.1371/journal.pone.0285143] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/14/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND The role of bacterial microbiota in the pathogenesis of nontuberculous mycobacterial pulmonary disease (NTM-PD) is unclear. We aimed to compare the bacterial microbiome of disease-invaded lesions and non-invaded lung tissue from NTM-PD patients. METHODS We analyzed lung tissues from 23 NTM-PD patients who underwent surgical lung resection. Lung tissues were collected in pairs from each patient, with one sample from a disease-involved site and the other from a non-involved site. Lung tissue microbiome libraries were constructed using 16S rRNA gene sequences (V3-V4 regions). RESULTS Sixteen (70%) patients had Mycobacterium avium complex (MAC)-PD, and the remaining seven (30%) had Mycobacterium abscessus-PD. Compared to non-involved sites, involved sites showed greater species richness (ACE, Chao1, and Jackknife analyses, all p = 0.001); greater diversity on the Shannon index (p = 0.007); and genus-level differences (Jensen-Shannon, PERMANOVA p = 0.001). Analysis of taxonomic biomarkers using linear discriminant analysis (LDA) effect sizes (LEfSe) demonstrated that several genera, including Limnohabitans, Rahnella, Lachnospira, Flavobacterium, Megamonas, Gaiella, Subdoligranulum, Rheinheimera, Dorea, Collinsella, and Phascolarctobacterium, had significantly greater abundance in involved sites (LDA >3.00, p <0.05, and q <0.05). In contrast, Acinetobacter had significantly greater abundance at non-involved sites (LDA = 4.27, p<0.001, and q = 0.002). Several genera were differentially distributed between lung tissues from MAC-PD (n = 16) and M. abscessus-PD (n = 7), and between nodular bronchiectatic form (n = 12) and fibrocavitary form (n = 11) patients. However, there was no genus with a significant q-value. CONCLUSIONS We identified differential microbial distributions between disease-invaded and normal lung tissues from NTM-PD patients, and microbial diversity was significantly higher in disease-invaded tissues. TRIAL REGISTRATION Clinical Trial registration number: NCT00970801.
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Affiliation(s)
- Bo-Guen Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Noeul Kang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Su-Young Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Dae Hun Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Hojoong Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - O Jung Kwon
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Byung Woo Jhun
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
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Matsuyama M, Matsumura S, Nonaka M, Nakajima M, Sakai C, Arai N, Ueda K, Hizawa N. Pathophysiology of pulmonary nontuberculous mycobacterial (NTM) disease. Respir Investig 2023; 61:135-148. [PMID: 36640546 DOI: 10.1016/j.resinv.2022.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/25/2022] [Accepted: 12/08/2022] [Indexed: 01/15/2023]
Abstract
In recent years, the incidence and prevalence of pulmonary nontuberculous mycobacterial (NTM) disease have increased worldwide. Although the reasons for this increase are unclear, dealing with this disease is essential. Pulmonary NTM disease is a chronic pulmonary infection caused by NTM bacteria, which are ubiquitous in various environments. In Japan, Mycobacterium avium-intracellulare complex (MAC) accounts for approximately 90% of the causative organisms of pulmonary NTM disease, which is also called pulmonary MAC disease or pulmonary MAI disease. It is important to elucidate the pathophysiology of this disease, which occurs frequently in postmenopausal women despite the absence of obvious immunodeficiency. The pathophysiology of this disease has not been fully elucidated; however, it can largely be divided into bacterial (environmental) and host-side problems. The host factors can be further divided into immune and airway problems. The authors suggest that the triangular relationship between bacteria, immunity, and the airway is important in the pathophysiology of this disease. The latest findings on the pathophysiology of pulmonary NTM disease are reviewed.
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Affiliation(s)
- Masashi Matsuyama
- Department of Respiratory Medicine, Institute of Medicine, University of Tsukuba, Japan.
| | - Sosuke Matsumura
- Department of Respiratory Medicine, Institute of Medicine, University of Tsukuba, Japan
| | - Mizu Nonaka
- Department of Respiratory Medicine, Institute of Medicine, University of Tsukuba, Japan
| | - Masayuki Nakajima
- Department of Respiratory Medicine, Institute of Medicine, University of Tsukuba, Japan
| | - Chio Sakai
- Department of Respiratory Medicine, Institute of Medicine, University of Tsukuba, Japan
| | - Naoki Arai
- Department of Respiratory Medicine, Institute of Medicine, University of Tsukuba, Japan
| | - Kodai Ueda
- Department of Respiratory Medicine, Institute of Medicine, University of Tsukuba, Japan
| | - Nobuyuki Hizawa
- Department of Respiratory Medicine, Institute of Medicine, University of Tsukuba, Japan
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6
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Dawud LM, Holbrook EM, Lowry CA. Evolutionary Aspects of Diverse Microbial Exposures and Mental Health: Focus on "Old Friends" and Stress Resilience. Curr Top Behav Neurosci 2023; 61:93-117. [PMID: 35947354 PMCID: PMC9918614 DOI: 10.1007/7854_2022_385] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The prevalence of inflammatory disease conditions, including allergies, asthma, and autoimmune disorders, increased during the latter half of the twentieth century, as societies transitioned from rural to urban lifestyles. A number of hypotheses have been put forward to explain the increasing prevalence of inflammatory disease in modern urban societies, including the hygiene hypothesis and the "Old Friends" hypothesis. In 2008, Rook and Lowry proposed, based on the evidence that increased inflammation was a risk factor for stress-related psychiatric disorders, that the hygiene hypothesis or "Old Friends" hypothesis may be relevant to psychiatric disorders. Since then, it has become more clear that chronic low-grade inflammation is a risk factor for stress-related psychiatric disorders, including anxiety disorders, mood disorders, and trauma- and stressor-related disorders, such as posttraumatic stress disorder (PTSD). Evidence now indicates that persons raised in modern urban environments without daily contact with pets, relative to persons raised in rural environments in proximity to farm animals, respond with greater systemic inflammation to psychosocial stress. Here we consider the possibility that increased inflammation in persons living in modern urban environments is due to a failure of immunoregulation, i.e., a balanced expression of regulatory and effector T cells, which is known to be dependent on microbial signals. We highlight evidence that microbial signals that can drive immunoregulation arise from phylogenetically diverse taxa but are strain specific. Finally, we highlight Mycobacterium vaccae NCTC 11659, a soil-derived bacterium with anti-inflammatory and immunoregulatory properties, as a case study of how single strains of bacteria might be used in a psychoneuroimmunologic approach for prevention and treatment of stress-related psychiatric disorders.
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Affiliation(s)
- Lamya'a M Dawud
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Evan M Holbrook
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Christopher A Lowry
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA.
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA.
- Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Rocky Mountain Regional VA Medical Center (RMRVAMC), Aurora, CO, USA.
- Department of Physical Medicine and Rehabilitation, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
- Military and Veteran Microbiome: Consortium for Research and Education (MVM-CoRE), Aurora, CO, USA.
- Center for Neuroscience, University of Colorado Boulder, Boulder, CO, USA.
- Center for Microbial Exploration, University of Colorado Boulder, Boulder, CO, USA.
- inVIVO Planetary Health, Worldwide Universities Network (WUN), West New York, NJ, USA.
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7
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Mycobacterium avium complex infected cells promote growth of the pathogen Pseudomonas aeruginosa. Microb Pathog 2022; 166:105549. [DOI: 10.1016/j.micpath.2022.105549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 04/11/2022] [Accepted: 04/19/2022] [Indexed: 11/19/2022]
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8
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Fisher BS, Fancher KA, Gustin AT, Fisher C, Wood MP, Gale M, Burwitz BJ, Smedley J, Klatt NR, Derby N, Sodora DL. Liver Bacterial Dysbiosis With Non-Tuberculosis Mycobacteria Occurs in SIV-Infected Macaques and Persists During Antiretroviral Therapy. Front Immunol 2022; 12:793842. [PMID: 35082782 PMCID: PMC8784802 DOI: 10.3389/fimmu.2021.793842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/16/2021] [Indexed: 01/26/2023] Open
Abstract
Liver disease is a significant contributor to morbidity and mortality in HIV-infected individuals, even during successful viral suppression with combination antiretroviral therapy (cART). Similar to HIV infection, SIV infection of rhesus macaques is associated with gut microbiome dysbiosis and microbial translocation that can be detected systemically in the blood. As microbes leaving the intestines must first pass through the liver via the portal vein, we evaluated the livers of both SIV-infected (SIV+) and SIV-infected cART treated (SIV+cART) rhesus macaques for evidence of microbial changes compared to uninfected macaques. Dysbiosis was observed in both the SIV+ and SIV+cART macaques, encompassing changes in the relative abundance of several genera, including a reduction in the levels of Lactobacillus and Staphylococcus. Most strikingly, we found an increase in the relative abundance and absolute quantity of bacteria within the Mycobacterium genus in both SIV+ and SIV+cART macaques. Multi-gene sequencing identified a species of atypical mycobacteria similar to the opportunistic pathogen M. smegmatis. Phosphatidyl inositol lipoarabinomannan (PILAM) (a glycolipid cell wall component found in atypical mycobacteria) stimulation in primary human hepatocytes resulted in an upregulation of inflammatory transcriptional responses, including an increase in the chemokines associated with neutrophil recruitment (CXCL1, CXCL5, and CXCL6). These studies provide key insights into SIV associated changes in hepatic microbial composition and indicate a link between microbial components and immune cell recruitment in SIV+ and SIV+cART treated macaques.
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Affiliation(s)
- Bridget S. Fisher
- Seattle Children’s Research Institute, Center for Global Infectious Disease Research, Seattle, WA, United States
| | - Katherine A. Fancher
- Seattle Children’s Research Institute, Center for Global Infectious Disease Research, Seattle, WA, United States
| | - Andrew T. Gustin
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, WA, United States
| | - Cole Fisher
- Seattle Children’s Research Institute, Center for Global Infectious Disease Research, Seattle, WA, United States
| | - Matthew P. Wood
- Seattle Children’s Research Institute, Center for Global Infectious Disease Research, Seattle, WA, United States
| | - Michael Gale
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, WA, United States
| | - Benjamin J. Burwitz
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, United States
| | - Jeremy Smedley
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, United States
| | - Nichole R. Klatt
- Department of Surgery, University of Minnesota, Minneapolis, MN, United States
| | - Nina Derby
- Seattle Children’s Research Institute, Center for Global Infectious Disease Research, Seattle, WA, United States
| | - Donald L. Sodora
- Seattle Children’s Research Institute, Center for Global Infectious Disease Research, Seattle, WA, United States
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9
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Amoroso M, Langgartner D, Lowry CA, Reber SO. Rapidly Growing Mycobacterium Species: The Long and Winding Road from Tuberculosis Vaccines to Potent Stress-Resilience Agents. Int J Mol Sci 2021; 22:ijms222312938. [PMID: 34884743 PMCID: PMC8657684 DOI: 10.3390/ijms222312938] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/22/2021] [Accepted: 11/26/2021] [Indexed: 02/06/2023] Open
Abstract
Inflammatory diseases and stressor-related psychiatric disorders, for which inflammation is a risk factor, are increasing in modern Western societies. Recent studies suggest that immunoregulatory approaches are a promising tool in reducing the risk of suffering from such disorders. Specifically, the environmental saprophyte Mycobacterium vaccae National Collection of Type Cultures (NCTC) 11659 has recently gained attention for the prevention and treatment of stress-related psychiatric disorders. However, effective use requires a sophisticated understanding of the effects of M. vaccae NCTC 11659 and related rapidly growing mycobacteria (RGMs) on microbiome–gut–immune–brain interactions. This historical narrative review is intended as a first step in exploring these mechanisms and provides an overview of preclinical and clinical studies on M. vaccae NCTC 11659 and related RGMs. The overall objective of this review article is to increase the comprehension of, and interest in, the mechanisms through which M. vaccae NCTC 11659 and related RGMs promote stress resilience, with the intention of fostering novel clinical strategies for the prevention and treatment of stressor-related disorders.
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Affiliation(s)
- Mattia Amoroso
- Laboratory for Molecular Psychosomatics, Department of Psychosomatic Medicine and Psychotherapy, University of Ulm, 89081 Ulm, Germany; (M.A.); (D.L.)
| | - Dominik Langgartner
- Laboratory for Molecular Psychosomatics, Department of Psychosomatic Medicine and Psychotherapy, University of Ulm, 89081 Ulm, Germany; (M.A.); (D.L.)
| | - Christopher A. Lowry
- Department of Integrative Physiology, Center for Neuroscience and Center for Microbial Exploration, University of Colorado Boulder, Boulder, CO 80309, USA;
- Department of Physical Medicine and Rehabilitation and Center for Neuroscience, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), The Rocky Mountain Regional Veterans Affairs Medical Center (RMRVAMC), Aurora, CO 80045, USA
- Military and Veteran Microbiome: Consortium for Research and Education (MVM-CoRE), Aurora, CO 80045, USA
- Senior Fellow, inVIVO Planetary Health, of the Worldwide Universities Network (WUN), West New York, NJ 07093, USA
| | - Stefan O. Reber
- Laboratory for Molecular Psychosomatics, Department of Psychosomatic Medicine and Psychotherapy, University of Ulm, 89081 Ulm, Germany; (M.A.); (D.L.)
- Correspondence:
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10
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Nouioui I, Dye T. Heat-killed Mycolicibacterium aurum Aogashima: An environmental nonpathogenic actinobacteria under development as a safe novel food ingredient. Food Sci Nutr 2021; 9:4839-4854. [PMID: 34531996 PMCID: PMC8441333 DOI: 10.1002/fsn3.2413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 05/25/2021] [Accepted: 05/29/2021] [Indexed: 12/17/2022] Open
Abstract
Over the last few decades, a wealth of evidence has formed the basis for "the Old Friends hypothesis" suggesting that, in contrast to the past, increasingly people are living in environments with limited and less diverse microbial exposure, with potential consequences for their health. Hence, including safe live or heat-killed microbes in the diet may be beneficial in promoting and maintaining human health. In order to assess the safety of microbes beyond the current use of standardized cultures and probiotic supplements, new approaches are being developed. Here, we present evidence for the safety of heat-killed Mycolicibacterium aurum Aogashima as a novel food, utilizing the decision tree approach developed by Pariza and colleagues (2015). We provide evidence that the genome of M. aurum Aogashima is free of (1) genetic elements associated with pathogenicity or toxigenicity, (2) transferable antibiotic resistance gene DNA, and (3) genes coding for antibiotics used in human or veterinary medicine. Moreover, a 90-day oral toxicity study in rats showed that (4) the no observed adverse effect level (NOAEL) was the highest concentration tested, namely 2000 μg/kg BW/day. We conclude that oral consumption of heat-killed M. aurum Aogashima is safe and warrants further evaluation as a novel food ingredient.
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Affiliation(s)
- Imen Nouioui
- Devonshire BuildingNewcastle University School of Natural and Environmental SciencesNewcastle Upon TyneUnited Kingdom of Great Britain and Northern Ireland
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11
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Thornton CS, Mellett M, Jarand J, Barss L, Field SK, Fisher DA. The respiratory microbiome and nontuberculous mycobacteria: an emerging concern in human health. Eur Respir Rev 2021; 30:30/160/200299. [PMID: 34039671 DOI: 10.1183/16000617.0299-2020] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 03/09/2021] [Indexed: 12/24/2022] Open
Abstract
Nontuberculous mycobacteria (NTM) are diverse microbial species encompassing commensals and pathogens with the ability to cause pulmonary disease in both immunocompetent and immunocompromised individuals. In contrast to Mycobacterium tuberculosis, which has seen a reduction in disease rates in developed countries, the incidence and prevalence of NTM disease is increasing. NTM are difficult to treat with standard antimicrobial regimens and may contain both virulence and antibiotic-resistance genes with potential for pathogenicity. With the advent of molecular techniques, it has been elucidated that these organisms do not reside in isolation and are rather part of a complex milieu of microorganisms within the host lung microbiome. Over the last decade, studies have highlighted the impact of the microbiome on host immunity, metabolism and cell-cell communication. This recognition of a broader community raises the possibility that the microbiome may disrupt the balance between infection and disease. Additionally, NTM disease progression and antimicrobial therapy may affect the healthy steady state of the host and function of the microbiome, contributing to further dysbiosis and clinical deterioration. There have been limited studies assessing how NTM may influence the relationship between microbiome and host. In this review, we highlight available studies about NTM and the microbiome, postulate on virulence mechanisms by which these microorganisms communicate and discuss implications for treatment.
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Affiliation(s)
- Christina S Thornton
- Division of Respirology, University of Calgary, Calgary, Canada .,Dept of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Canada.,Joint first authors
| | - Madeline Mellett
- Dept of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Canada.,Joint first authors
| | - Julie Jarand
- Division of Respirology, University of Calgary, Calgary, Canada.,Dept of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Canada.,TB Services, University of Calgary, Calgary, Canada
| | - Leila Barss
- Division of Respirology, University of Calgary, Calgary, Canada.,Dept of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Canada.,TB Services, University of Calgary, Calgary, Canada
| | - Stephen K Field
- Division of Respirology, University of Calgary, Calgary, Canada.,Dept of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Canada.,TB Services, University of Calgary, Calgary, Canada
| | - Dina A Fisher
- Division of Respirology, University of Calgary, Calgary, Canada.,Dept of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Canada.,TB Services, University of Calgary, Calgary, Canada.,Dept of Community Health Sciences, University of Calgary, Calgary, Canada
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12
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Izawa K, Okamoto-Shibayama K, Kita D, Tomita S, Saito A, Ishida T, Ohue M, Akiyama Y, Ishihara K. Taxonomic and Gene Category Analyses of Subgingival Plaques from a Group of Japanese Individuals with and without Periodontitis. Int J Mol Sci 2021; 22:ijms22105298. [PMID: 34069916 PMCID: PMC8157553 DOI: 10.3390/ijms22105298] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/12/2021] [Accepted: 05/15/2021] [Indexed: 12/11/2022] Open
Abstract
Periodontitis is an inflammation of tooth-supporting tissues, which is caused by bacteria in the subgingival plaque (biofilm) and the host immune response. Traditionally, subgingival pathogens have been investigated using methods such as culturing, DNA probes, or PCR. The development of next-generation sequencing made it possible to investigate the whole microbiome in the subgingival plaque. Previous studies have implicated dysbiosis of the subgingival microbiome in the etiology of periodontitis. However, details are still lacking. In this study, we conducted a metagenomic analysis of subgingival plaque samples from a group of Japanese individuals with and without periodontitis. In the taxonomic composition analysis, genus Bacteroides and Mycobacterium demonstrated significantly different compositions between healthy sites and sites with periodontal pockets. The results from the relative abundance of functional gene categories, carbohydrate metabolism, glycan biosynthesis and metabolism, amino acid metabolism, replication and repair showed significant differences between healthy sites and sites with periodontal pockets. These results provide important insights into the shift in the taxonomic and functional gene category abundance caused by dysbiosis, which occurs during the progression of periodontal disease.
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Affiliation(s)
- Kazuki Izawa
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan; (K.I.); (T.I.); (M.O.); (Y.A.)
| | | | - Daichi Kita
- Department of Periodontology, Tokyo Dental College, Chiyoda-ku, Tokyo 101-0061, Japan; (D.K.); (S.T.); (A.S.)
- Oral Health Science Center, Tokyo Dental College, Chiyoda-ku, Tokyo 101-0061, Japan
| | - Sachiyo Tomita
- Department of Periodontology, Tokyo Dental College, Chiyoda-ku, Tokyo 101-0061, Japan; (D.K.); (S.T.); (A.S.)
| | - Atsushi Saito
- Department of Periodontology, Tokyo Dental College, Chiyoda-ku, Tokyo 101-0061, Japan; (D.K.); (S.T.); (A.S.)
- Oral Health Science Center, Tokyo Dental College, Chiyoda-ku, Tokyo 101-0061, Japan
| | - Takashi Ishida
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan; (K.I.); (T.I.); (M.O.); (Y.A.)
| | - Masahito Ohue
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan; (K.I.); (T.I.); (M.O.); (Y.A.)
| | - Yutaka Akiyama
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan; (K.I.); (T.I.); (M.O.); (Y.A.)
| | - Kazuyuki Ishihara
- Department of Microbiology, Tokyo Dental College, Chiyoda-ku, Tokyo 101-0061, Japan;
- Oral Health Science Center, Tokyo Dental College, Chiyoda-ku, Tokyo 101-0061, Japan
- Correspondence: ; Tel.: +81–3-6380−9558
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13
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Nutritional immunity: the impact of metals on lung immune cells and the airway microbiome during chronic respiratory disease. Respir Res 2021; 22:133. [PMID: 33926483 PMCID: PMC8082489 DOI: 10.1186/s12931-021-01722-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/15/2021] [Indexed: 12/15/2022] Open
Abstract
Nutritional immunity is the sequestration of bioavailable trace metals such as iron, zinc and copper by the host to limit pathogenicity by invading microorganisms. As one of the most conserved activities of the innate immune system, limiting the availability of free trace metals by cells of the immune system serves not only to conceal these vital nutrients from invading bacteria but also operates to tightly regulate host immune cell responses and function. In the setting of chronic lung disease, the regulation of trace metals by the host is often disrupted, leading to the altered availability of these nutrients to commensal and invading opportunistic pathogenic microbes. Similarly, alterations in the uptake, secretion, turnover and redox activity of these vitally important metals has significant repercussions for immune cell function including the response to and resolution of infection. This review will discuss the intricate role of nutritional immunity in host immune cells of the lung and how changes in this fundamental process as a result of chronic lung disease may alter the airway microbiome, disease progression and the response to infection.
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14
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Kang SY, Kim H, Jung S, Lee SM, Lee SP. The lung microbiota in Korean patients with non-tuberculous mycobacterial pulmonary disease. BMC Microbiol 2021; 21:84. [PMID: 33736609 PMCID: PMC7977250 DOI: 10.1186/s12866-021-02141-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 03/01/2021] [Indexed: 12/21/2022] Open
Abstract
Background The microbiota of the lower respiratory tract in patients with non-tuberculous mycobacterial pulmonary disease (NTM-PD) has not been fully evaluated. We explored the role of the lung microbiota in NTM-PD by analyzing protected specimen brushing (PSB) and bronchial washing samples from patients with NTM-PD obtained using a flexible bronchoscope. Results Bronchial washing and PSB samples from the NTM-PD group tended to have fewer OTUs and lower Chao1 richness values compared with those from the control group. In both bronchial washing and PSB samples, beta diversity was significantly lower in the NTM-PD group than in the control group (P = 2.25E-6 and P = 4.13E-4, respectively). Principal component analysis showed that the PSBs and bronchial washings exhibited similar patterns within each group but differed between the two groups. The volcano plots indicated differences in several phyla and genera between the two groups. Conclusions The lower respiratory tract of patients with NTM-PD has a unique microbiota distribution that is low in richness/diversity. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02141-1.
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Affiliation(s)
- Sung-Yoon Kang
- Division of Pulmonology and Allergy, Department of Internal Medicine, Gil Medical Center, Gachon University College of Medicine, 21, Namdong-daero 774 beon-gil, Namdong-gu, Incheon, 21565, Republic of Korea
| | - Hyojung Kim
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon, Republic of Korea
| | - Sungwon Jung
- Department of Genome Medicine and Science, Gachon University College of Medicine, Incheon, Republic of Korea. .,Gachon Institute of Genome Medicine and Science, Gil Medical Center, Gachon University College of Medicine, 38-13 Dokjeom-ro 3 beon-gil, Namdong-gu, Incheon, 21565, Republic of Korea.
| | - Sang Min Lee
- Division of Pulmonology and Allergy, Department of Internal Medicine, Gil Medical Center, Gachon University College of Medicine, 21, Namdong-daero 774 beon-gil, Namdong-gu, Incheon, 21565, Republic of Korea.
| | - Sang Pyo Lee
- Division of Pulmonology and Allergy, Department of Internal Medicine, Gil Medical Center, Gachon University College of Medicine, 21, Namdong-daero 774 beon-gil, Namdong-gu, Incheon, 21565, Republic of Korea
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15
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Pawlaczyk-Kamieńska T, Borysewicz-Lewicka M. Dental bacterial biofilm and gingival status
in cystic fibrosis adult patients. POSTEP HIG MED DOSW 2021. [DOI: 10.5604/01.3001.0014.7699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Introduction: The purpose of the study conducted on cystic fibrosis (CF) patients was the bacterial plaque
accumulation and the gingival condition assessment, and microbial analysis of the subgingival
biofilm.
Materials/Methods: The study included 22 CF adult patients and 22 healthy controls, sex and age compatible with
the CF patients. The dental plaque was assessed using plaque index (PLI), and the gingival
status using gingival index (GI). Analyses of the subgingival biofilm were performed by the
real-time polymerase chain reaction (PCR) test.
Results: The mean value of GI in CF patients was 0.39 ±0.36 and was significantly lower comparing
to the healthy controls (1.02 ±0.63), PLI was similar in both the groups (1.31 ±0.69) for the
study group and 1.04 ±0.62 for controls). In CF patients there was no correlation between PLI
and GI, which was observed in the control group. In both the groups there was a correlation
between PLI and the total number of periopathogens. Furthermore, in the control group, there
was a correlation between GI and the number of periopathogens. Such a correlation was not
observed in the CF patients.
Conclusions: In patients with CF, the lack of correlation between the amount of tooth deposits and the
gingival condition may indicate a stable, most likely pharmacologically conditioned oral biofilm
ecology. Among the aetiological factors of gingivitis and periodontitis in patients with CF, the
bacterial activity does not seem to be modified. However, the unsatisfactory oral hygiene found
in the study participants does not exclude the possibility of disease development in the future.
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Affiliation(s)
- Tamara Pawlaczyk-Kamieńska
- Department of Risk Group Dentistry, Chair of Pediatric Dentistry, Poznan University of Medical Sciences, Poznań, Poland
| | - Maria Borysewicz-Lewicka
- Department of Risk Group Dentistry, Chair of Pediatric Dentistry, Poznan University of Medical Sciences, Poznań, Poland
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16
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Acosta A, Fonte L, Sarmiento ME, Norazmi MN. Does our Mycobacteriome Influence COVID-19 Morbidity and Lethality? Front Microbiol 2021; 12:589165. [PMID: 33613475 PMCID: PMC7890112 DOI: 10.3389/fmicb.2021.589165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 01/14/2021] [Indexed: 12/23/2022] Open
Affiliation(s)
- Armando Acosta
- School of Health Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Luis Fonte
- Department of Parasitology, Institute of Tropical Medicine "Pedro Kourí", Havana, Cuba
| | - Maria E Sarmiento
- School of Health Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Mohd Nor Norazmi
- School of Health Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
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17
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Kursa O, Tomczyk G, Sawicka-Durkalec A, Giza A, Słomiany-Szwarc M. Bacterial communities of the upper respiratory tract of turkeys. Sci Rep 2021; 11:2544. [PMID: 33510238 PMCID: PMC7843632 DOI: 10.1038/s41598-021-81984-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 01/13/2021] [Indexed: 02/02/2023] Open
Abstract
The respiratory tracts of turkeys play important roles in the overall health and performance of the birds. Understanding the bacterial communities present in the respiratory tracts of turkeys can be helpful to better understand the interactions between commensal or symbiotic microorganisms and other pathogenic bacteria or viral infections. The aim of this study was the characterization of the bacterial communities of upper respiratory tracks in commercial turkeys using NGS sequencing by the amplification of 16S rRNA gene with primers designed for hypervariable regions V3 and V4 (MiSeq, Illumina). From 10 phyla identified in upper respiratory tract in turkeys, the most dominated phyla were Firmicutes and Proteobacteria. Differences in composition of bacterial diversity were found at the family and genus level. At the genus level, the turkey sequences present in respiratory tract represent 144 established bacteria. Several respiratory pathogens that contribute to the development of infections in the respiratory system of birds were identified, including the presence of Ornithobacterium and Mycoplasma OTUs. These results obtained in this study supply information about bacterial composition and diversity of the turkey upper respiratory tract. Knowledge about bacteria present in the respiratory tract and the roles they can play in infections can be useful in controlling, diagnosing and treating commercial turkey flocks.
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Affiliation(s)
- Olimpia Kursa
- Department of Poultry Diseases, National Veterinary Research Institute, Al. Partyzantów 57, 24-100, Pulawy, Poland.
| | - Grzegorz Tomczyk
- Department of Poultry Diseases, National Veterinary Research Institute, Al. Partyzantów 57, 24-100, Pulawy, Poland
| | - Anna Sawicka-Durkalec
- Department of Poultry Diseases, National Veterinary Research Institute, Al. Partyzantów 57, 24-100, Pulawy, Poland
| | - Aleksandra Giza
- Department of Omics Analyses, National Veterinary Research Institute, Al. Partyzantów 57, 24-100, Pulawy, Poland
| | - Magdalena Słomiany-Szwarc
- Department of Omics Analyses, National Veterinary Research Institute, Al. Partyzantów 57, 24-100, Pulawy, Poland
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18
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Ji L, Jiang Y, Li G, Zhao X, Wan K. A real-time PCR assay based on a specific mutation of PstS1 gene for detection of M. bovis strains. Biologicals 2020; 64:23-27. [PMID: 31980349 DOI: 10.1016/j.biologicals.2020.01.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 01/07/2020] [Accepted: 01/16/2020] [Indexed: 11/25/2022] Open
Abstract
The Mycobacterium tuberculosis complex (MTBC) is composed of several genetically related and pathogenic mycobacterial species, including M. tuberculosis, M. bovis and M.africanum et al. In our previous study, we found that M. bovis strains had a unique SNP located in position 1055 in the sequence of the pstS1 gene in which a T was substituted by a C. In this study, specific primers and MGB probes were designed according to the mutation in PstS1 gene, and a sensitive, specific and rapid real-time PCR assay for M. bovis was established. Then the assay was used to detect M. bovis in simulation samples. The minimum detectable concentration is 101 copies for M. bovis DNA. The standard curve showed correlation coefficient between threshold cycle and PstS1 gene fragment copy number was 0.997 and slope is -3.144. The minimum detectable concentration is 101 cells/ml for simulation sample. In addition, M.bovis strain 93006, 14 clinical BCG stains and 7 clinical M.bovis strain showed positive while the other strains showed negative results, which proved good specificity. This assay had high sensitivity and specificity for identification of M. bovis from the simulation specimens. The assay can be applied for epidemiological and ecological surveillance of M. bovis strains.
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Affiliation(s)
- Lingyun Ji
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, PR China; Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200123, PR China
| | - Yi Jiang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, PR China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, PR China.
| | - Guilian Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, PR China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, PR China
| | - Xiuqin Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, PR China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, PR China
| | - Kanglin Wan
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, PR China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, PR China
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19
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Intranasal Mycobacterium vaccae administration prevents stress-induced aggravation of dextran sulfate sodium (DSS) colitis. Brain Behav Immun 2019; 80:595-604. [PMID: 31059809 DOI: 10.1016/j.bbi.2019.05.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 04/02/2019] [Accepted: 05/02/2019] [Indexed: 12/30/2022] Open
Abstract
An increasing body of evidence indicates that immunodysregulation and subsequent chronic low-grade inflammation can promote the development of stress-related somatic and psychiatric pathologies, including inflammatory bowel disease (IBD) and posttraumatic stress disorder (PTSD). Thus, immunoregulatory approaches counterbalancing basal and/or stress-induced immune activation should have stress-protective potential. In support of this hypothesis, we recently demonstrated that repeated s.c. preimmunization with a heat-killed preparation of the immunoregulatory bacterium Mycobacterium vaccae (M. vaccae; National Collection of Type Culture (NCTC) 11659), protects mice against stress-induced general anxiety, spontaneous colitis, and aggravation of dextran sulfate sodium (DSS)-induced colitis in the chronic subordinate colony housing (CSC) paradigm, a validated model for PTSD in male mice. In the current study, we repeatedly administered M. vaccae via the non-invasive intranasal (i.n.; 0.1 mg/mouse/administration) route, prior to or during CSC exposure or single housed control (SHC) conditions, and assessed the effects on general and social anxiety, and on parameters related to the severity of DSS-induced colitis. While administration of M. vaccae prior to the onset of CSC exposure only had minor stress-protective effects, administration of M. vaccae during CSC completely prevented CSC-induced aggravation of DSS colitis. As CSC in the current experimental setting did not reliably increase general anxiety-related behavior, potential stress-protective effects of M.vaccae are difficult to interpret. Taken together, these data broaden the framework for developing bioimmunoregulatory approaches, based on the administration of microorganisms with anti-inflammatory and immunoregulatory properties, for the prevention of stress-related disorders.
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Identification and characterization of a novel anti-inflammatory lipid isolated from Mycobacterium vaccae, a soil-derived bacterium with immunoregulatory and stress resilience properties. Psychopharmacology (Berl) 2019; 236:1653-1670. [PMID: 31119329 PMCID: PMC6626661 DOI: 10.1007/s00213-019-05253-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 04/22/2019] [Indexed: 12/14/2022]
Abstract
RATIONALE Mycobacterium vaccae (NCTC 11659) is an environmental saprophytic bacterium with anti-inflammatory, immunoregulatory, and stress resilience properties. Previous studies have shown that whole, heat-killed preparations of M. vaccae prevent allergic airway inflammation in a murine model of allergic asthma. Recent studies also demonstrate that immunization with M. vaccae prevents stress-induced exaggeration of proinflammatory cytokine secretion from mesenteric lymph node cells stimulated ex vivo, prevents stress-induced exaggeration of chemically induced colitis in a model of inflammatory bowel disease, and prevents stress-induced anxiety-like defensive behavioral responses. Furthermore, immunization with M. vaccae induces anti-inflammatory responses in the brain and prevents stress-induced exaggeration of microglial priming. However, the molecular mechanisms underlying anti-inflammatory effects of M. vaccae are not known. OBJECTIVES Our objective was to identify and characterize novel anti-inflammatory molecules from M. vaccae NCTC 11659. METHODS We have purified and identified a unique anti-inflammatory triglyceride, 1,2,3-tri [Z-10-hexadecenoyl] glycerol, from M. vaccae and evaluated its effects in freshly isolated murine peritoneal macrophages. RESULTS The free fatty acid form of 1,2,3-tri [Z-10-hexadecenoyl] glycerol, 10(Z)-hexadecenoic acid, decreased lipopolysaccharide-stimulated secretion of the proinflammatory cytokine IL-6 ex vivo. Meanwhile, next-generation RNA sequencing revealed that pretreatment with 10(Z)-hexadecenoic acid upregulated genes associated with peroxisome proliferator-activated receptor alpha (PPARα) signaling in lipopolysaccharide-stimulated macrophages, in association with a broad transcriptional repression of inflammatory markers. We confirmed using luciferase-based transfection assays that 10(Z)-hexadecenoic acid activated PPARα signaling, but not PPARγ, PPARδ, or retinoic acid receptor (RAR) α signaling. The effects of 10(Z)-hexadecenoic acid on lipopolysaccharide-stimulated secretion of IL-6 were prevented by PPARα antagonists and absent in PPARα-deficient mice. CONCLUSION Future studies should evaluate the effects of 10(Z)-hexadecenoic acid on stress-induced exaggeration of peripheral inflammatory signaling, central neuroinflammatory signaling, and anxiety- and fear-related defensive behavioral responses.
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Cowman SA, James P, Wilson R, Cookson WOC, Moffatt MF, Loebinger MR. Profiling mycobacterial communities in pulmonary nontuberculous mycobacterial disease. PLoS One 2018; 13:e0208018. [PMID: 30533049 PMCID: PMC6289444 DOI: 10.1371/journal.pone.0208018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 11/10/2018] [Indexed: 01/05/2023] Open
Abstract
The diagnosis of pulmonary non-tuberculous mycobacterial disease (pNTM) is dependent on the isolation of NTM in culture, which is prone to overgrowth and contamination and may not capture the diversity of mycobacteria present, including rare or unidentified species. This study aimed to develop a culture independent method of detecting and identifying mycobacteria from sputum samples using partial sequencing of the hsp65 gene. DNA was extracted from sputum samples from subjects with pNTM and disease controls. Multiplexed partial sequencing of the hsp65 gene was performed using the Illumina MiSeq and custom primers. A reference database of hsp65 sequences was created for taxonomy assignment. Sequencing results were obtained from 42 subjects (31 cases, 11 controls). Mycobacterial sequences were identified in all subjects. In 90.5% of samples more than one species was found (median 5.5). The species isolated in culture was detected by sequencing in 81% of subjects and was the most abundant species in 62%. The sequencing of NTM from clinical samples reveals a far greater diversity than conventional culture and suggests NTM are present as communities rather than a single species. NTM were found to be present even in the absence of isolation in culture or clinical disease.
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Affiliation(s)
- Steven A. Cowman
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Host Defence Unit, Royal Brompton Hospital, London, United Kingdom
| | - Phillip James
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Robert Wilson
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Host Defence Unit, Royal Brompton Hospital, London, United Kingdom
| | | | - Miriam F. Moffatt
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Michael R. Loebinger
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Host Defence Unit, Royal Brompton Hospital, London, United Kingdom
- * E-mail:
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22
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Sulaiman I, Wu BG, Li Y, Scott AS, Malecha P, Scaglione B, Wang J, Basavaraj A, Chung S, Bantis K, Carpenito J, Clemente JC, Shen N, Bessich J, Rafeq S, Michaud G, Donington J, Naidoo C, Theron G, Schattner G, Garofano S, Condos R, Kamelhar D, Addrizzo-Harris D, Segal LN. Evaluation of the airway microbiome in nontuberculous mycobacteria disease. Eur Respir J 2018; 52:13993003.00810-2018. [PMID: 30093571 DOI: 10.1183/13993003.00810-2018] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 07/29/2018] [Indexed: 01/15/2023]
Abstract
Aspiration is associated with nontuberculous mycobacterial (NTM) pulmonary disease and airway dysbiosis is associated with increased inflammation. We examined whether NTM disease was associated with a distinct airway microbiota and immune profile.297 oral wash and induced sputum samples were collected from 106 participants with respiratory symptoms and imaging abnormalities compatible with NTM. Lower airway samples were obtained in 20 participants undergoing bronchoscopy. 16S rRNA gene and nested mycobacteriome sequencing approaches characterised microbiota composition. In addition, inflammatory profiles of lower airway samples were examined.The prevalence of NTM+ cultures was 58%. Few changes were noted in microbiota characteristics or composition in oral wash and sputum samples among groups. Among NTM+ samples, 27% of the lower airway samples were enriched with Mycobacterium A mycobacteriome approach identified Mycobacterium in a greater percentage of samples, including some nonpathogenic strains. In NTM+ lower airway samples, taxa identified as oral commensals were associated with increased inflammatory biomarkers.The 16S rRNA gene sequencing approach is not sensitive in identifying NTM among airway samples that are culture-positive. However, associations between lower airway inflammation and microbiota signatures suggest a potential role for these microbes in the inflammatory process in NTM disease.
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Affiliation(s)
- Imran Sulaiman
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Benjamin G Wu
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Yonghua Li
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Adrienne S Scott
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Patrick Malecha
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Benjamin Scaglione
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Jing Wang
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Ashwin Basavaraj
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Samuel Chung
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Katrina Bantis
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Joseph Carpenito
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Jose C Clemente
- Dept of Genetics and Genomic Sciences and Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nan Shen
- Dept of Genetics and Genomic Sciences and Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jamie Bessich
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Samaan Rafeq
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Gaetene Michaud
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Jessica Donington
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Charissa Naidoo
- Medicine and Health Sciences, Stellenbosch University, DST/NRF of Excellence for Biomedical Tuberculosis Research and SA MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics Tygerberg, Cape Town, South Africa
| | - Grant Theron
- Medicine and Health Sciences, Stellenbosch University, DST/NRF of Excellence for Biomedical Tuberculosis Research and SA MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics Tygerberg, Cape Town, South Africa
| | - Gail Schattner
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Suzette Garofano
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Rany Condos
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - David Kamelhar
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Doreen Addrizzo-Harris
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Leopoldo N Segal
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA.,Dept of Medicine, New York University School of Medicine, New York, NY, USA
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23
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Flandroy L, Poutahidis T, Berg G, Clarke G, Dao MC, Decaestecker E, Furman E, Haahtela T, Massart S, Plovier H, Sanz Y, Rook G. The impact of human activities and lifestyles on the interlinked microbiota and health of humans and of ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 627:1018-1038. [PMID: 29426121 DOI: 10.1016/j.scitotenv.2018.01.288] [Citation(s) in RCA: 161] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 01/28/2018] [Accepted: 01/28/2018] [Indexed: 05/03/2023]
Abstract
Plants, animals and humans, are colonized by microorganisms (microbiota) and transiently exposed to countless others. The microbiota affects the development and function of essentially all organ systems, and contributes to adaptation and evolution, while protecting against pathogenic microorganisms and toxins. Genetics and lifestyle factors, including diet, antibiotics and other drugs, and exposure to the natural environment, affect the composition of the microbiota, which influences host health through modulation of interrelated physiological systems. These include immune system development and regulation, metabolic and endocrine pathways, brain function and epigenetic modification of the genome. Importantly, parental microbiotas have transgenerational impacts on the health of progeny. Humans, animals and plants share similar relationships with microbes. Research paradigms from humans and other mammals, amphibians, insects, planktonic crustaceans and plants demonstrate the influence of environmental microbial ecosystems on the microbiota and health of organisms, and indicate links between environmental and internal microbial diversity and good health. Therefore, overlapping compositions, and interconnected roles of microbes in human, animal and plant health should be considered within the broader context of terrestrial and aquatic microbial ecosystems that are challenged by the human lifestyle and by agricultural and industrial activities. Here, we propose research priorities and organizational, educational and administrative measures that will help to identify safe microbe-associated health-promoting modalities and practices. In the spirit of an expanding version of "One health" that includes environmental health and its relation to human cultures and habits (EcoHealth), we urge that the lifestyle-microbiota-human health nexus be taken into account in societal decision making.
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Affiliation(s)
- Lucette Flandroy
- Federal Public Service Health, Food Chain Safety and Environment, Belgium
| | - Theofilos Poutahidis
- Laboratory of Pathology, Faculty of Health Sciences, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Gabriele Berg
- Environmental Biotechnology, Graz University of Technology, Petersgasse 12, A-8010 Graz, Austria
| | - Gerard Clarke
- Department of Psychiatry and Neurobehavioural Science, APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Maria-Carlota Dao
- ICAN, Institute of Cardiometabolism and Nutrition, Assistance Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Paris, France; INSERM, UMRS U1166 (Eq 6) Nutriomics, Paris 6, France; UPMC, Sorbonne University, Pierre et Marie Curie-Paris 6, France
| | - Ellen Decaestecker
- Aquatic Biology, Department Biology, Science, Engineering & Technology Group, KU Leuven, Campus Kortrijk. E. Sabbelaan 53, B-8500 Kortrijk, Belgium
| | - Eeva Furman
- Finnish Environment Institute (SYKE), Helsinki, Finland
| | - Tari Haahtela
- Skin and Allergy Hospital, Helsinki University Hospital, University of Helsinki, Finland
| | - Sébastien Massart
- Laboratory of Integrated and Urban Phytopathology, TERRA, Gembloux Agro-Bio Tech, University of Liège, Passage des deportes, 2, 5030 Gembloux, Belgium
| | - Hubert Plovier
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Yolanda Sanz
- Microbial Ecology, Nutrition & Health Research Unit, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Graham Rook
- Centre for Clinical Microbiology, Department of Infection, UCL (University College London), London, UK.
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24
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Lewinsohn DM. An Expanding Role for Environmental Microbes in Shaping the Immune Response to Infection with Mycobacterium tuberculosis. Am J Respir Crit Care Med 2017; 196:677-679. [PMID: 28841029 DOI: 10.1164/rccm.201708-1599ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- David M Lewinsohn
- 1 Pulmonary and Critical Care Medicine Oregon Health & Science University Portland, Oregon and.,2 The Portland VA Medical Center Portland, Oregon
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25
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Stamper CE, Hoisington AJ, Gomez OM, Halweg-Edwards AL, Smith DG, Bates KL, Kinney KA, Postolache TT, Brenner LA, Rook GAW, Lowry CA. The Microbiome of the Built Environment and Human Behavior: Implications for Emotional Health and Well-Being in Postmodern Western Societies. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2016; 131:289-323. [PMID: 27793224 DOI: 10.1016/bs.irn.2016.07.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
It is increasingly evident that inflammation is an important determinant of cognitive function and emotional behaviors that are dysregulated in stress-related psychiatric disorders, such as anxiety and affective disorders. Inflammatory responses to physical or psychological stressors are dependent on immunoregulation, which is indicated by a balanced expansion of effector T-cell populations and regulatory T cells. This balance is in part driven by microbial signals. The hygiene or "old friends" hypothesis posits that exposure to immunoregulation-inducing microorganisms is reduced in modern urban societies, leading to an epidemic of inflammatory disease and increased vulnerability to stress-related psychiatric disorders. With the global trend toward urbanization, humans are progressively spending more time in built environments, thereby, experiencing limited exposures to these immunoregulatory "old friends." Here, we evaluate the implications of the global trend toward urbanization, and how this transition may affect human microbial exposures and human behavior.
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Affiliation(s)
- C E Stamper
- Center for Neuroscience, University of Colorado Boulder, Boulder, CO, United States
| | - A J Hoisington
- US Air Force Academy, Colorado Springs, CO, United States; Military and Veteran Microbiome Consortium for Research and Education (MVM-CoRE), Denver, CO, United States
| | - O M Gomez
- Center for Neuroscience, University of Colorado Boulder, Boulder, CO, United States
| | | | - D G Smith
- Center for Neuroscience, University of Colorado Boulder, Boulder, CO, United States
| | - K L Bates
- US Air Force Academy, Colorado Springs, CO, United States
| | - K A Kinney
- Military and Veteran Microbiome Consortium for Research and Education (MVM-CoRE), Denver, CO, United States; University of Texas Austin, Austin, TX, United States
| | - T T Postolache
- Military and Veteran Microbiome Consortium for Research and Education (MVM-CoRE), Denver, CO, United States; University of Maryland School of Medicine, Baltimore, MD, United States; VISN 5 Mental Illness Research Education and Clinical Center (MIRECC), Baltimore, MD, United States; Rocky Mountain Mental Illness Research Education and Clinical Center, Denver, CO, United States
| | - L A Brenner
- Military and Veteran Microbiome Consortium for Research and Education (MVM-CoRE), Denver, CO, United States; Rocky Mountain Mental Illness Research Education and Clinical Center, Denver, CO, United States; University of Colorado, Aurora, CO, United States
| | - G A W Rook
- Center for Clinical Microbiology, UCL (University College London), London, United Kingdom
| | - C A Lowry
- Center for Neuroscience, University of Colorado Boulder, Boulder, CO, United States; Military and Veteran Microbiome Consortium for Research and Education (MVM-CoRE), Denver, CO, United States; Rocky Mountain Mental Illness Research Education and Clinical Center, Denver, CO, United States; University of Colorado, Aurora, CO, United States.
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26
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Lowry CA, Smith DG, Siebler PH, Schmidt D, Stamper CE, Hassell JE, Yamashita PS, Fox JH, Reber SO, Brenner LA, Hoisington AJ, Postolache TT, Kinney KA, Marciani D, Hernandez M, Hemmings SMJ, Malan-Muller S, Wright KP, Knight R, Raison CL, Rook GAW. The Microbiota, Immunoregulation, and Mental Health: Implications for Public Health. Curr Environ Health Rep 2016; 3:270-86. [PMID: 27436048 PMCID: PMC5763918 DOI: 10.1007/s40572-016-0100-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The hygiene or "Old Friends" hypothesis proposes that the epidemic of inflammatory disease in modern urban societies stems at least in part from reduced exposure to microbes that normally prime mammalian immunoregulatory circuits and suppress inappropriate inflammation. Such diseases include but are not limited to allergies and asthma; we and others have proposed that the markedly reduced exposure to these Old Friends in modern urban societies may also increase vulnerability to neurodevelopmental disorders and stress-related psychiatric disorders, such as anxiety and affective disorders, where data are emerging in support of inflammation as a risk factor. Here, we review recent advances in our understanding of the potential for Old Friends, including environmental microbial inputs, to modify risk for inflammatory disease, with a focus on neurodevelopmental and psychiatric conditions. We highlight potential mechanisms, involving bacterially derived metabolites, bacterial antigens, and helminthic antigens, through which these inputs promote immunoregulation. Though findings are encouraging, significant human subjects' research is required to evaluate the potential impact of Old Friends, including environmental microbial inputs, on biological signatures and clinically meaningful mental health prevention and intervention outcomes.
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Affiliation(s)
- Christopher A Lowry
- Department of Integrative Physiology and Center for Neuroscience, University of Colorado Boulder, 1725 Pleasant Street, Boulder, CO, 80309-0354, USA.
| | - David G Smith
- Department of Integrative Physiology and Center for Neuroscience, University of Colorado Boulder, 1725 Pleasant Street, Boulder, CO, 80309-0354, USA
| | - Philip H Siebler
- Department of Integrative Physiology and Center for Neuroscience, University of Colorado Boulder, 1725 Pleasant Street, Boulder, CO, 80309-0354, USA
| | - Dominic Schmidt
- Department of Integrative Physiology and Center for Neuroscience, University of Colorado Boulder, 1725 Pleasant Street, Boulder, CO, 80309-0354, USA
| | - Christopher E Stamper
- Department of Integrative Physiology and Center for Neuroscience, University of Colorado Boulder, 1725 Pleasant Street, Boulder, CO, 80309-0354, USA
| | - James E Hassell
- Department of Integrative Physiology and Center for Neuroscience, University of Colorado Boulder, 1725 Pleasant Street, Boulder, CO, 80309-0354, USA
| | - Paula S Yamashita
- Department of Integrative Physiology and Center for Neuroscience, University of Colorado Boulder, 1725 Pleasant Street, Boulder, CO, 80309-0354, USA
| | - James H Fox
- Department of Integrative Physiology and Center for Neuroscience, University of Colorado Boulder, 1725 Pleasant Street, Boulder, CO, 80309-0354, USA
| | - Stefan O Reber
- Laboratory for Molecular Psychosomatics, Clinic for Psychosomatic Medicine and Psychotherapy, University of Ulm, D-89081, Ulm, Germany
| | - Lisa A Brenner
- Departments of Psychiatry, Physical Medicine & Rehabilitation, University of Colorado, Anschutz School of Medicine, Aurora, CO, 80045, USA
- Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Veterans Integrated Service Network (VISN) 19, Denver, CO, 80220, USA
| | - Andrew J Hoisington
- Department of Civil and Environmental Engineering, United States Air Force Academy, Colorado Springs, CO, 80840, USA
| | - Teodor T Postolache
- University of Maryland School of Medicine, Baltimore, MD, USA
- Rocky Mountain MIRECC, Denver, CO, 80220, USA
- VISN 5 MIRECC, Baltimore, MD, 21201, USA
| | - Kerry A Kinney
- Civil, Architectural and Environmental Engineering, University of Texas Austin, Austin, TX, 78712, USA
| | | | - Mark Hernandez
- Department of Civil, Environmental and Architectural Engineering, University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Sian M J Hemmings
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, 7505, South Africa
| | - Stefanie Malan-Muller
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, 7505, South Africa
| | - Kenneth P Wright
- Department of Integrative Physiology and Center for Neuroscience, University of Colorado Boulder, 1725 Pleasant Street, Boulder, CO, 80309-0354, USA
| | - Rob Knight
- Departments of Pediatrics and Computer Science and Engineering, and Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, 92093, USA
| | - Charles L Raison
- School of Human Ecology and School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Graham A W Rook
- Center for Clinical Microbiology, UCL (University College London), WC1E 6BT, London, UK
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27
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Jackson F, Jackson L, Cross C, Clarke C. What could you do with 400 years of biological history on african americans? Evaluating the potential scientific benefit of systematic studies of dental and skeletal materials on African Americans from the 17th through 20th centuries. Am J Hum Biol 2016; 28:510-3. [PMID: 26749025 PMCID: PMC5066698 DOI: 10.1002/ajhb.22821] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 11/12/2015] [Accepted: 11/28/2015] [Indexed: 12/29/2022] Open
Abstract
Objectives How important is it to be able to reconstruct the lives of a highly diverse, historically recent macroethnic group over the course of 400 years? How many insights into human evolutionary biology and disease susceptibilities could be gained, even with this relatively recent window into the past? In this article, we explore the potential ramifications of a newly constructed dataset of Four Centuries of African American Biological Variation (4Cs). Methods This article provides initial lists of digitized variables formatted as SQL tables for the 17th and 18th century samples and for the 19th and 20th century samples. Results This database is dynamic and new information is added yearly. The database provides novel opportunities for significant insights into the past biological history of this group and three case study applications are detailed for comparative computational systems biology studies of (1) hypertension, (2) the oral microbiome, and (3) mental health disorders. Conclusions The 4Cs dataset is ideal for interdisciplinary “next generation” science research and these data represent a unique step toward the accumulation of historically contextualized Big Data on an underrepresented group known to have experienced differential survival over time. Am. J. Hum. Biol. 28:510–513, 2016. © 2016 The Authors American Journal of Human Biology Published byWiley Periodicals, Inc.
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Affiliation(s)
- Fatimah Jackson
- Cobb Research Laboratory, College of Arts and Sciences, Howard University, Washington, DC.,Department of Biology, College of Arts and Sciences, Howard University, Washington, DC
| | - Latifa Jackson
- Cobb Research Laboratory, College of Arts and Sciences, Howard University, Washington, DC.,National Human Genome Center, College of Medicine, Howard University, Washington, DC
| | - Christopher Cross
- Cobb Research Laboratory, College of Arts and Sciences, Howard University, Washington, DC.,Department of Anatomy, College of Medicine, Howard University, Washington, DC
| | - Cameron Clarke
- Cobb Research Laboratory, College of Arts and Sciences, Howard University, Washington, DC.,Department of Biology, College of Arts and Sciences, Howard University, Washington, DC
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