1
|
Gu X, Li Z, Su J. Air pollution and skin diseases: A comprehensive evaluation of the associated mechanism. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 278:116429. [PMID: 38718731 DOI: 10.1016/j.ecoenv.2024.116429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/28/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024]
Abstract
Air pollutants deteriorate the survival environment and endanger human health around the world. A large number of studies have confirmed that air pollution jeopardizes multiple organs, such as the cardiovascular, respiratory, and central nervous systems. Skin is the largest organ and the first barrier that protects us from the outside world. Air pollutants such as particulate matter (PM), polycyclic aromatic hydrocarbons (PAHs), volatile organic compounds (VOCs) will affect the structure and function of the skin and bring about the development of inflammatory skin diseases (atopic dermatitis (AD), psoriasis), skin accessory diseases (acne, alopecia), auto-immune skin diseases (cutaneous lupus erythematosus(CLE) scleroderma), and even skin tumors (melanoma, basal cell carcinoma (BCC), squamous-cell carcinoma (SCC)). Oxidative stress, skin barrier damage, microbiome dysbiosis, and skin inflammation are the pathogenesis of air pollution stimulation. In this review, we summarize the current evidence on the effects of air pollution on skin diseases and possible mechanisms to provide strategies for future research.
Collapse
Affiliation(s)
- Xiaoyu Gu
- Department of Dermatology | Hunan Engineering Research Center of Skin Health and Disease | Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha 410008, China; National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha 410008, China; National Clinical Research Center for Geriatric Disorders (Xiangya Hospital), Changsha 410008, China; Furong Laboratory, Changsha, Hunan 410008, China
| | - Zhengrui Li
- XiangYa School of Medicine, Central South University, Changsha 410008, China
| | - Juan Su
- Department of Dermatology | Hunan Engineering Research Center of Skin Health and Disease | Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha 410008, China; National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha 410008, China; National Clinical Research Center for Geriatric Disorders (Xiangya Hospital), Changsha 410008, China; Furong Laboratory, Changsha, Hunan 410008, China.
| |
Collapse
|
2
|
Bhatt S, Patel A, Kesselman MM, Demory ML. Hand Sanitizer: Stopping the Spread of Infection at a Cost. Cureus 2024; 16:e61846. [PMID: 38975405 PMCID: PMC11227450 DOI: 10.7759/cureus.61846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 06/06/2024] [Indexed: 07/09/2024] Open
Abstract
The recent rise in hand sanitizer use due to the COVID-19 pandemic has had a beneficial impact on stopping the spread of disease, but the potential negative implications of its overuse on the body and the microbiome have yet to be thoroughly reviewed. Epidermal layers absorb hand sanitizer from direct application to the skin, making them some of the most susceptible cells to the adverse effects of overuse. The increased usage of hand sanitizer can affect the variation, quantity, and diversity of the skin microflora, leading to conditions such as eczema, atopic dermatitis, and even systemic toxicity due to colonization of the skin with pathogenic bacteria. Due to the close-knit relationship between the skin and gut, the gastrointestinal system can also incur disruptions due to the negative effects on the skin as a result of excessive hand sanitizer use, leading to gut dysbiosis. Additionally, the accidental ingestion of hand sanitizer, and its abuse or misuse, can be toxic and lead to alcohol poisoning, which is an issue most commonly seen not only in the pediatric population but also in adolescents and adults due to aberrant recreational exposure. As a vulnerable body system, the eyes can also be negatively impacted by hand sanitizer misuse leading to chemical injury, visual impairment, and even blindness. In this review, we aim to highlight the variations in hand sanitizer formulation, the benefits, and how misuse or overuse may lead to adverse effects on the skin, gut, and eyes. In particular, we review the advantages and disadvantages of alcohol-based hand sanitizers (ABHSs) and non-alcohol-based hand sanitizers (NABHSs) and how the components and chemicals used in each can contribute to organ dysbiosis and systemic damage.
Collapse
Affiliation(s)
- Shreya Bhatt
- Medicine, Dr. Kiran C. Patel College of Osteopathic Medicine, Nova Southeastern University, Davie, USA
| | - Aasha Patel
- Dentistry, Roseman University College of Dental Medicine, South Jordan, USA
| | - Marc M Kesselman
- Rheumatology, Dr. Kiran C. Patel College of Osteopathic Medicine, Nova Southeastern University, Davie, USA
| | - Michelle L Demory
- Microbiology and Immunology, Dr. Kiran C. Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, USA
| |
Collapse
|
3
|
Rook GAW. Evolution and the critical role of the microbiota in the reduced mental and physical health associated with low socioeconomic status (SES). Neurosci Biobehav Rev 2024; 161:105653. [PMID: 38582194 DOI: 10.1016/j.neubiorev.2024.105653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/03/2024] [Indexed: 04/08/2024]
Abstract
The evolution of the gut-microbiota-brain axis in animals reveals that microbial inputs influence metabolism, the regulation of inflammation and the development of organs, including the brain. Inflammatory, neurodegenerative and psychiatric disorders are more prevalent in people of low socioeconomic status (SES). Many aspects of low SES reduce exposure to the microbial inputs on which we are in a state of evolved dependence, whereas the lifestyle of wealthy citizens maintains these exposures. This partially explains the health deficit of low SES, so focussing on our evolutionary history and on environmental and lifestyle factors that distort microbial exposures might help to mitigate that deficit. But the human microbiota is complex and we have poor understanding of its functions at the microbial and mechanistic levels, and in the brain. Perhaps its composition is more flexible than the microbiota of animals that have restricted habitats and less diverse diets? These uncertainties are discussed in relation to the encouraging but frustrating results of attempts to treat psychiatric disorders by modulating the microbiota.
Collapse
Affiliation(s)
- Graham A W Rook
- Centre for Clinical Microbiology, Department of infection, UCL (University College London), London, UK.
| |
Collapse
|
4
|
Guerrieri F, Libert C. The invisible life. Front Microbiol 2024; 15:1401487. [PMID: 38832115 PMCID: PMC11144902 DOI: 10.3389/fmicb.2024.1401487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 04/29/2024] [Indexed: 06/05/2024] Open
Affiliation(s)
- Francesca Guerrieri
- Cancer Research Center of Lyon (CRCL), UMR Inserm 1052 - CNRS 5286, Lyon, France
| | - Cédric Libert
- Ecole Nationale Superieure d'Architecture de Saint-Etienne, Saint-Etienne, France
| |
Collapse
|
5
|
Bosch TCG, Wigley M, Colomina B, Bohannan B, Meggers F, Amato KR, Azad MB, Blaser MJ, Brown K, Dominguez-Bello MG, Ehrlich SD, Elinav E, Finlay BB, Geddie K, Geva-Zatorsky N, Giles-Vernick T, Gros P, Guillemin K, Haraoui LP, Johnson E, Keck F, Lorimer J, McFall-Ngai MJ, Nichter M, Pettersson S, Poinar H, Rees T, Tropini C, Undurraga EA, Zhao L, Melby MK. The potential importance of the built-environment microbiome and its impact on human health. Proc Natl Acad Sci U S A 2024; 121:e2313971121. [PMID: 38662573 PMCID: PMC11098107 DOI: 10.1073/pnas.2313971121] [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] [Indexed: 05/18/2024] Open
Abstract
There is increasing evidence that interactions between microbes and their hosts not only play a role in determining health and disease but also in emotions, thought, and behavior. Built environments greatly influence microbiome exposures because of their built-in highly specific microbiomes coproduced with myriad metaorganisms including humans, pets, plants, rodents, and insects. Seemingly static built structures host complex ecologies of microorganisms that are only starting to be mapped. These microbial ecologies of built environments are directly and interdependently affected by social, spatial, and technological norms. Advances in technology have made these organisms visible and forced the scientific community and architects to rethink gene-environment and microbe interactions respectively. Thus, built environment design must consider the microbiome, and research involving host-microbiome interaction must consider the built-environment. This paradigm shift becomes increasingly important as evidence grows that contemporary built environments are steadily reducing the microbial diversity essential for human health, well-being, and resilience while accelerating the symptoms of human chronic diseases including environmental allergies, and other more life-altering diseases. New models of design are required to balance maximizing exposure to microbial diversity while minimizing exposure to human-associated diseases. Sustained trans-disciplinary research across time (evolutionary, historical, and generational) and space (cultural and geographical) is needed to develop experimental design protocols that address multigenerational multispecies health and health equity in built environments.
Collapse
Affiliation(s)
- Thomas C. G. Bosch
- Zoological Institute, University of Kiel, Kiel24118, Germany
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
| | - Mark Wigley
- Graduate School of Architecture, Planning and Preservation, Columbia University, New York, NY10027
| | - Beatriz Colomina
- School of Architecture, Princeton University, Princeton, NJ08544
| | - Brendan Bohannan
- The Institute of Ecology and Evolution, University of Oregon, Eugene, OR97403-5289
| | - Forrest Meggers
- Princeton University School of Architecture & Andlinger Center for Energy and the Environment, Princeton, NJ08540
| | - Katherine R. Amato
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Department of Anthropology, Northwestern University, Evanston, IL60208
| | - Meghan B. Azad
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB R3E 0Z3, Canada
- Department of Community Health Sciences, University of Manitoba, Winnipeg, MB R3E 3P5, Canada
| | - Martin J. Blaser
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Children’s Hospital Research Institute of Manitoba, Winnipeg, MBR3E 3P4, Canada
- Center for Advanced Biotechnology and Medicine at Rutgers Biomedical and Health Sciences, Rutgers University, Piscataway, NJ08854-8021
| | - Kate Brown
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Program in Science, Technology and Society, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Maria Gloria Dominguez-Bello
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ08901
- Department of Anthropology, Rutgers University, New Brunswick, NJ08901
| | - Stanislav Dusko Ehrlich
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Institute of Neurology, University College London, LondonWC1N 3RX, United Kingdom
| | - Eran Elinav
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Systems Immunology Department, Weizmann Institute of Science, Rehovot761000, Israel
- Division of Microbiome & Cancer, Deutsches Krebsforschungszentrum, 69120Heidelberg, Germany
| | - B. Brett Finlay
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
| | - Kate Geddie
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Medical and Related Sciences Centre, The Canadian Institute for Advanced Research, Toronto, ONM5G 1L7, Canada
| | - Naama Geva-Zatorsky
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Technion Integrated Cancer Center, Technion-Israel Institute of Technology, Haifa3525433, Israel
- Department of Cell Biology and Cancer Science, Technion-Israel Institute of Technology, Haifa3525433, Israel
| | - Tamara Giles-Vernick
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Anthropology & Ecology of Disease Emergence, Institut Pasteur, Université Paris Cité, Paris75015, France
| | - Philippe Gros
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Department of Biochemistry, McGill University, Montreal, QCH3G 1Y6, Canada
| | - Karen Guillemin
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Institute of Molecular Biology, University of Oregon, Eugene, OR97403
| | - Louis-Patrick Haraoui
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, CanadaJ1E 4K8
| | - Elizabeth Johnson
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- College of Human Ecology, Cornell University, IthakaNY14853
| | - Frédéric Keck
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Laboratoire d’Anthropologie Sociale, Collège de France, Paris75005, France
| | - Jamie Lorimer
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- School of Geography and the Environment, University of Oxford, OX1 3QY, United Kingdom
| | - Margaret J. McFall-Ngai
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Division of Biology and Biological Engineering, Caltech, Pasadena, CA91125
| | - Mark Nichter
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- School of Anthropology, University of Arizona, Tucson, AZ85721
| | - Sven Pettersson
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Nanyang Technological University, Singapore637715, Singapore
| | - Hendrik Poinar
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Department of Anthropology, McMaster University, Hamilton, ONL8S 4M4, Canada
| | - Tobias Rees
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- LIMN, Berkeley, CA94708
| | - Carolina Tropini
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Department of Microbiology and Immunology and School of Biomedical Engineering, University of British Columbia, Vancouver, BCV6T 1Z3, Canada
| | - Eduardo A. Undurraga
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Escuela de Gobierno, Pontificia Universidad Católica de Chile, Santiago7820436, Chile
| | - Liping Zhao
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ08901
| | - Melissa K. Melby
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Department of Anthropology, University of Delaware, Newark, DE19716
| |
Collapse
|
6
|
Nguyen Y, Rudd Zhong Manis J, Ronczkowski NM, Bui T, Oxenrider A, Jadeja RN, Thounaojam MC. Unveiling the gut-eye axis: how microbial metabolites influence ocular health and disease. Front Med (Lausanne) 2024; 11:1377186. [PMID: 38799150 PMCID: PMC11122920 DOI: 10.3389/fmed.2024.1377186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 04/19/2024] [Indexed: 05/29/2024] Open
Abstract
The intricate interplay between the gut microbiota and ocular health has surpassed conventional medical beliefs, fundamentally reshaping our understanding of organ interconnectivity. This review investigates into the intricate relationship between gut microbiota-derived metabolites and their consequential impact on ocular health and disease pathogenesis. By examining the role of specific metabolites, such as short-chain fatty acids (SCFAs) like butyrate and bile acids (BAs), herein we elucidate their significant contributions to ocular pathologies, thought-provoking the traditional belief of organ sterility, particularly in the field of ophthalmology. Highlighting the dynamic nature of the gut microbiota and its profound influence on ocular health, this review underlines the necessity of comprehending the complex workings of the gut-eye axis, an emerging field of science ready for further exploration and scrutiny. While acknowledging the therapeutic promise in manipulating the gut microbiome and its metabolites, the available literature advocates for a targeted, precise approach. Instead of broad interventions, it emphasizes the potential of exploiting specific microbiome-related metabolites as a focused strategy. This targeted approach compared to a precision tool rather than a broad-spectrum solution, aims to explore the therapeutic applications of microbiome-related metabolites in the context of various retinal diseases. By proposing a nuanced strategy targeted at specific microbial metabolites, this review suggests that addressing specific deficiencies or imbalances through microbiome-related metabolites might yield expedited and pronounced outcomes in systemic health, extending to the eye. This focused strategy holds the potential in bypassing the irregularity associated with manipulating microbes themselves, paving a more efficient pathway toward desired outcomes in optimizing gut health and its implications for retinal diseases.
Collapse
Affiliation(s)
- Yvonne Nguyen
- Mercer University School of Medicine, Macon, GA, United States
| | | | | | - Tommy Bui
- Departments of Cellular Biology and Anatomy, Augusta University, Augusta, GA, United States
| | - Allston Oxenrider
- Departments of Cellular Biology and Anatomy, Augusta University, Augusta, GA, United States
| | - Ravirajsinh N. Jadeja
- Biochemistry and Molecular Biology, Medical College of Georgia at Augusta University, Augusta, GA, United States
| | - Menaka C. Thounaojam
- Departments of Cellular Biology and Anatomy, Augusta University, Augusta, GA, United States
| |
Collapse
|
7
|
Sargsian S, Mondragón-Palomino O, Lejeune A, Ercelen D, Jin WB, Varghese A, Lim YAL, Guo CJ, Loke P, Cadwell K. Functional characterization of helminth-associated Clostridiales reveals covariates of Treg differentiation. MICROBIOME 2024; 12:86. [PMID: 38730492 PMCID: PMC11084060 DOI: 10.1186/s40168-024-01793-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 03/10/2024] [Indexed: 05/13/2024]
Abstract
BACKGROUND Parasitic helminths influence the composition of the gut microbiome. However, the microbiomes of individuals living in helminth-endemic regions are understudied. The Orang Asli, an indigenous population in Malaysia with high burdens of the helminth Trichuris trichiura, display microbiotas enriched in Clostridiales, an order of spore-forming obligate anaerobes with immunogenic properties. We previously isolated novel Clostridiales that were enriched in these individuals and found that a subset promoted the Trichuris life cycle. In this study, we aimed to further characterize the functional properties of these bacteria. RESULTS Clostridiales isolates were profiled for their ability to perform 57 enzymatic reactions and produce short-chain fatty acids (SCFAs) and hydrogen sulfide, revealing that these bacteria were capable of a range of activities associated with metabolism and host response. Consistent with this finding, monocolonization of mice with individual isolates identified bacteria that were potent inducers of regulatory T-cell (Treg) differentiation in the colon. Comparisons between variables revealed by these studies identified enzymatic properties correlated with Treg induction and Trichuris egg hatching. CONCLUSION We identified Clostridiales species that are sufficient to induce high levels of Tregs. We also identified a set of metabolic activities linked with Treg differentiation and Trichuris egg hatching mediated by these newly isolated bacteria. Altogether, this study provides functional insights into the microbiotas of individuals residing in a helminth-endemic region. Video Abstract.
Collapse
Affiliation(s)
- Shushan Sargsian
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Octavio Mondragón-Palomino
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Alannah Lejeune
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Defne Ercelen
- Department of Medicine, Division of Gastroenterology and Hepatology, New York University Langone Health, New York, NY, 10016, USA
| | - Wen-Bing Jin
- Weill Cornell Medicine, Jill Roberts Institute for Research in Inflammatory Bowel Disease, Cornell University, New York, NY, 10021, USA
| | - Alan Varghese
- Department of Cell Biology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Yvonne A L Lim
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, 50603, Malaysia
| | - Chun-Jun Guo
- Weill Cornell Medicine, Jill Roberts Institute for Research in Inflammatory Bowel Disease, Cornell University, New York, NY, 10021, USA
| | - P'ng Loke
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Ken Cadwell
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
| |
Collapse
|
8
|
Hao Y, Lu C, Xiang Q, Sun A, Su JQ, Chen QL. Unveiling the overlooked microbial niches thriving on building exteriors. ENVIRONMENT INTERNATIONAL 2024; 187:108649. [PMID: 38642506 DOI: 10.1016/j.envint.2024.108649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/07/2024] [Accepted: 04/09/2024] [Indexed: 04/22/2024]
Abstract
Rapid urbanization in the Asia-Pacific region is expected to place two-thirds of its population in concrete-dominated urban landscapes by 2050. While diverse architectural facades define the unique appearance of these urban systems. There remains a significant gap in our understanding of the composition, assembly, and ecological potential of microbial communities on building exteriors. Here, we examined bacterial and protistan communities on building surfaces along an urbanization gradient (urban, suburban and rural regions), investigating their spatial patterns and the driving factors behind their presence. A total of 55 bacterial and protist phyla were identified. The bacterial community was predominantly composed of Proteobacteria (33.7% to 67.5%). The protistan community exhibited a prevalence of Opisthokonta and Archaeplastida (17.5% to 82.1% and 1.8% to 61.2%, respectively). The composition and functionality of bacterial communities exhibited spatial patterns correlated with urbanization. In urban buildings, factors such as facade type, light exposure, and building height had comparatively less impact on bacterial composition compared to suburban and rural areas. The highest bacterial diversity and lowest Weighted Average Community Identity (WACI) were observed on suburban buildings, followed by rural buildings. In contrast, protists did not show spatial distribution characteristics related to facade type, light exposure, building height and urbanization level. The distinct spatial patterns of protists were primarily shaped by community diffusion and the bottom-up regulation exerted by bacterial communities. Together, our findings suggest that building exteriors serve as attachment points for local microbial metacommunities, offering unique habitats where bacteria and protists exhibit independent adaptive strategies closely tied to the overall ecological potential of the community.
Collapse
Affiliation(s)
- Yilong Hao
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Changyi Lu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Qian Xiang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Anqi Sun
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Qing-Lin Chen
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China.
| |
Collapse
|
9
|
Li J, Chen C, Ji L, Wen S, Peng J, Yang L, He G. Urbanization-driven forest soil greenhouse gas emissions: Insights from the role of soil bacteria in carbon and nitrogen cycling using a metagenomic approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 923:171364. [PMID: 38438026 DOI: 10.1016/j.scitotenv.2024.171364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 02/07/2024] [Accepted: 02/27/2024] [Indexed: 03/06/2024]
Abstract
Increasing population densities and urban sprawl have induced greenhouse gas (GHG) emissions from the soil, and the soil microbiota of urban forests play a critical role in the production and consumption of GHGs, supporting green development. However, the function and potential mechanism of soil bacteria in GHG emissions from forests during urbanization processes need to be better understood. Here, we measured the fluxes of carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) in Cinnamomum camphora forest soils along an urbanization gradient. 16S amplicon and metagenomic sequencing approaches were employed to examine the structure and potential functions of the soil bacterial community involved in carbon (C) and nitrogen (N) cycling. In this study, the CH4 and CO2 emissions from urban forest soils (sites U and G) were significantly greater than those from suburban soils (sites S and M). The N2O emissions in the urban center (site U) were 24.0 % (G), 13.8 % (S), and 13.5 % (M) greater than those at the other three sites. These results were related to the increasing bacterial alpha diversity, interactions, and C and N cycling gene abundances (especially those involved in denitrification) in urban forest soils. Additionally, the soil pH and metal contents (K, Ca, Mg) affected key bacterial populations (such as Methylomirabilota, Acidobacteriota, and Proteobacteria) and indicators (napA, nosZ, nrfA, nifH) involved in reducing N2O emissions. The soil heavy metal contents (Fe, Cr, Pb) were the main contributors to CH4 emissions, possibly by affecting methanogens (Desulfobacterota) and methanotrophic bacteria (Proteobacteria, Actinobacteriota, and Patescibacteria). Our study provides new insights into the benefits of conservation-minded urban planning and close-to-nature urban forest management and construction, which are conducive to mitigating GHG emissions and supporting urban sustainable development by mediating the core bacterial population.
Collapse
Affiliation(s)
- Jing Li
- School of Forestry, Central South University of Forestry and Technology, 498 Shaoshan South Road, 410004 Changsha, PR China
| | - Chuxiang Chen
- School of Forestry, Central South University of Forestry and Technology, 498 Shaoshan South Road, 410004 Changsha, PR China
| | - Li Ji
- School of Forestry, Central South University of Forestry and Technology, 498 Shaoshan South Road, 410004 Changsha, PR China.
| | - Shizhi Wen
- School of Forestry, Central South University of Forestry and Technology, 498 Shaoshan South Road, 410004 Changsha, PR China
| | - Jun Peng
- Hunan Geological Experiment and Testing Center, Changsha, 290 Middle Chengnan Road, 410007, PR China
| | - Lili Yang
- School of Forestry, Central South University of Forestry and Technology, 498 Shaoshan South Road, 410004 Changsha, PR China
| | - Gongxiu He
- School of Forestry, Central South University of Forestry and Technology, 498 Shaoshan South Road, 410004 Changsha, PR China.
| |
Collapse
|
10
|
Ramaboli MC, Ocvirk S, Khan Mirzaei M, Eberhart BL, Valdivia-Garcia M, Metwaly A, Neuhaus K, Barker G, Ru J, Nesengani LT, Mahdi-Joest D, Wilson AS, Joni SK, Layman DC, Zheng J, Mandal R, Chen Q, Perez MR, Fortuin S, Gaunt B, Wishart D, Methé B, Haller D, Li JV, Deng L, Swart R, O'Keefe SJD. Diet changes due to urbanization in South Africa are linked to microbiome and metabolome signatures of Westernization and colorectal cancer. Nat Commun 2024; 15:3379. [PMID: 38643180 PMCID: PMC11032404 DOI: 10.1038/s41467-024-46265-0] [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: 07/13/2023] [Accepted: 02/15/2024] [Indexed: 04/22/2024] Open
Abstract
Transition from traditional high-fiber to Western diets in urbanizing communities of Sub-Saharan Africa is associated with increased risk of non-communicable diseases (NCD), exemplified by colorectal cancer (CRC) risk. To investigate how urbanization gives rise to microbial patterns that may be amenable by dietary intervention, we analyzed diet intake, fecal 16 S bacteriome, virome, and metabolome in a cross-sectional study in healthy rural and urban Xhosa people (South Africa). Urban Xhosa individuals had higher intakes of energy (urban: 3,578 ± 455; rural: 2,185 ± 179 kcal/d), fat and animal protein. This was associated with lower fecal bacteriome diversity and a shift from genera favoring degradation of complex carbohydrates (e.g., Prevotella) to taxa previously shown to be associated with bile acid metabolism and CRC. Urban Xhosa individuals had higher fecal levels of deoxycholic acid, shown to be associated with higher CRC risk, but similar short-chain fatty acid concentrations compared with rural individuals. Fecal virome composition was associated with distinct gut bacterial communities across urbanization, characterized by different dominant host bacteria (urban: Bacteriodota; rural: unassigned taxa) and variable correlation with fecal metabolites and dietary nutrients. Food and skin microbiota samples showed compositional differences along the urbanization gradient. Rural-urban dietary transition in South Africa is linked to major changes in the gut microbiome and metabolome. Further studies are needed to prove cause and identify whether restoration of specific components of the traditional diet will arrest the accelerating rise in NCDs in Sub-Saharan Africa.
Collapse
Affiliation(s)
- M C Ramaboli
- African Microbiome Institute, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - S Ocvirk
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Intestinal Microbiology Research Group, German Institute of Human Nutrition, Potsdam, Germany
- ZIEL - Institute for Food and Health, Technical University of Munich, Freising, Germany
| | - M Khan Mirzaei
- Institute of Virology, Helmholtz Centre Munich - German Research Centre for Environmental Health, Neuherberg, Germany
- Chair of Microbial Disease Prevention, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - B L Eberhart
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - M Valdivia-Garcia
- Section of Nutrition, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - A Metwaly
- Chair of Nutrition and Immunology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - K Neuhaus
- Core Facility Microbiome, ZIEL - Institute for Food and Health, Technical University of Munich, Freising, Germany
| | - G Barker
- Section of Nutrition, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - J Ru
- Institute of Virology, Helmholtz Centre Munich - German Research Centre for Environmental Health, Neuherberg, Germany
- Chair of Microbial Disease Prevention, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - L T Nesengani
- Department of Agriculture and Animal Health, University of South Africa, Pretoria, South Africa
| | - D Mahdi-Joest
- Intestinal Microbiology Research Group, German Institute of Human Nutrition, Potsdam, Germany
| | - A S Wilson
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - S K Joni
- Department of Nutrition and Dietetics, School of Public Health, University of the Western Cape, Cape Town, South Africa
| | - D C Layman
- Department of Nutrition and Dietetics, School of Public Health, University of the Western Cape, Cape Town, South Africa
| | - J Zheng
- The Metabolomics Innovation Centre & Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - R Mandal
- The Metabolomics Innovation Centre & Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Q Chen
- Section of Nutrition, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - M R Perez
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - S Fortuin
- African Microbiome Institute, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - B Gaunt
- Zithulele Hospital, Mqanduli District, Mqanduli, Eastern Cape Province, South Africa
| | - D Wishart
- The Metabolomics Innovation Centre & Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - B Methé
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - D Haller
- ZIEL - Institute for Food and Health, Technical University of Munich, Freising, Germany
- Chair of Nutrition and Immunology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - J V Li
- Section of Nutrition, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - L Deng
- Institute of Virology, Helmholtz Centre Munich - German Research Centre for Environmental Health, Neuherberg, Germany
- Chair of Microbial Disease Prevention, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - R Swart
- Department of Nutrition and Dietetics, School of Public Health, University of the Western Cape, Cape Town, South Africa
| | - S J D O'Keefe
- African Microbiome Institute, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
| |
Collapse
|
11
|
Robinson JM, Breed AC, Camargo A, Redvers N, Breed MF. Biodiversity and human health: A scoping review and examples of underrepresented linkages. ENVIRONMENTAL RESEARCH 2024; 246:118115. [PMID: 38199470 DOI: 10.1016/j.envres.2024.118115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/09/2023] [Accepted: 01/04/2024] [Indexed: 01/12/2024]
Abstract
Mounting evidence supports the connections between exposure to environmental typologies(such as green and blue spaces)and human health. However, the mechanistic links that connect biodiversity (the variety of life) and human health, and the extent of supporting evidence remain less clear. Here, we undertook a scoping review to map the links between biodiversity and human health and summarise the levels of associated evidence using an established weight of evidence framework. Distinct from other reviews, we provide additional context regarding the environment-microbiome-health axis, evaluate the environmental buffering pathway (e.g., biodiversity impacts on air pollution), and provide examples of three under- or minimally-represented linkages. The examples are (1) biodiversity and Indigenous Peoples' health, (2) biodiversity and urban social equity, and (3) biodiversity and COVID-19. We observed a moderate level of evidence to support the environmental microbiota-human health pathway and a moderate-high level of evidence to support broader nature pathways (e.g., greenspace) to various health outcomes, from stress reduction to enhanced wellbeing and improved social cohesion. However, studies of broader nature pathways did not typically include specific biodiversity metrics, indicating clear research gaps. Further research is required to understand the connections and causative pathways between biodiversity (e.g., using metrics such as taxonomy, diversity/richness, structure, and function) and health outcomes. There are well-established frameworks to assess the effects of broad classifications of nature on human health. These can assist future research in linking biodiversity metrics to human health outcomes. Our examples of underrepresented linkages highlight the roles of biodiversity and its loss on urban lived experiences, infectious diseases, and Indigenous Peoples' sovereignty and livelihoods. More research and awareness of these socioecological interconnections are needed.
Collapse
Affiliation(s)
- Jake M Robinson
- College of Science and Engineering, Flinders University, Bedford Park, SA, Australia.
| | - Andrew C Breed
- Epidemiology and One Health Section, Department of Agriculture, Water, and the Environment, Canberra, ACT, Australia; School of Veterinary Science, University of Queensland, Gatton, Qld, Australia
| | | | - Nicole Redvers
- Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Martin F Breed
- College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
| |
Collapse
|
12
|
Hernandez-Nicols BF, Robledo-Pulido JJ, Alvarado-Navarro A. Etiopathogenesis of Psoriasis: Integration of Proposed Theories. Immunol Invest 2024; 53:348-415. [PMID: 38240030 DOI: 10.1080/08820139.2024.2302823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
Psoriasis is a chronic inflammatory disease characterized by squamous and erythematous plaques on the skin and the involvement of the immune system. Global prevalence for psoriasis has been reported around 1-3% with a higher incidence in adults and similar proportions between men and women. The risk factors associated with psoriasis are both extrinsic and intrinsic, out of which a polygenic predisposition is a highlight out of the latter. Psoriasis etiology is not yet fully described, but several hypothesis have been proposed: 1) the autoimmunity hypothesis is based on the over-expression of antimicrobial peptides such as LL-37, the proteins ADAMTSL5, K17, and hsp27, or lipids synthesized by the PLA2G4D enzyme, all of which may serve as autoantigens to promote the differentiation of autoreactive lymphocytes T and unleash a chronic inflammatory response; 2) dysbiosis of skin microbiota hypothesis in psoriasis has gained relevance due to the observations of a loss of diversity and the participation of pathogenic bacteria such as Streptococcus spp. or Staphylococcus spp. the fungi Malassezia spp. or Candida spp. and the virus HPV, HCV, or HIV in psoriatic plaques; 3) the oxidative stress hypothesis, the most recent one, describes that the cell injury and the release of proinflammatory mediators and antimicrobial peptides that leads to activate of the Th1/Th17 axis observed in psoriasis is caused by a higher release of reactive oxygen species and the imbalance between oxidant and antioxidant mechanisms. This review aims to describe the mechanisms involved in the three hypotheses on the etiopathogeneses of psoriasis.
Collapse
Affiliation(s)
- Brenda Fernanda Hernandez-Nicols
- Centro de Investigación en Inmunología y Dermatología, Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Juan José Robledo-Pulido
- Centro de Investigación en Inmunología y Dermatología, Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Anabell Alvarado-Navarro
- Centro de Investigación en Inmunología y Dermatología, Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| |
Collapse
|
13
|
Rühlemann MC, Bang C, Gogarten JF, Hermes BM, Groussin M, Waschina S, Poyet M, Ulrich M, Akoua-Koffi C, Deschner T, Muyembe-Tamfum JJ, Robbins MM, Surbeck M, Wittig RM, Zuberbühler K, Baines JF, Leendertz FH, Franke A. Functional host-specific adaptation of the intestinal microbiome in hominids. Nat Commun 2024; 15:326. [PMID: 38182626 PMCID: PMC10770139 DOI: 10.1038/s41467-023-44636-7] [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: 04/05/2023] [Accepted: 12/20/2023] [Indexed: 01/07/2024] Open
Abstract
Fine-scale knowledge of the changes in composition and function of the human gut microbiome compared that of our closest relatives is critical for understanding the evolutionary processes underlying its developmental trajectory. To infer taxonomic and functional changes in the gut microbiome across hominids at different timescales, we perform high-resolution metagenomic-based analyzes of the fecal microbiome from over two hundred samples including diverse human populations, as well as wild-living chimpanzees, bonobos, and gorillas. We find human-associated taxa depleted within non-human apes and patterns of host-specific gut microbiota, suggesting the widespread acquisition of novel microbial clades along the evolutionary divergence of hosts. In contrast, we reveal multiple lines of evidence for a pervasive loss of diversity in human populations in correlation with a high Human Development Index, including evolutionarily conserved clades. Similarly, patterns of co-phylogeny between microbes and hosts are found to be disrupted in humans. Together with identifying individual microbial taxa and functional adaptations that correlate to host phylogeny, these findings offer insights into specific candidates playing a role in the diverging trajectories of the gut microbiome of hominids. We find that repeated horizontal gene transfer and gene loss, as well as the adaptation to transient microaerobic conditions appear to have played a role in the evolution of the human gut microbiome.
Collapse
Affiliation(s)
- M C Rühlemann
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany.
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany.
| | - C Bang
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - J F Gogarten
- Applied Zoology and Nature Conservation, University of Greifswald, Greifswald, Germany
- Helmholtz Institute for One Health, Helmholtz-Centre for Infection Research (HZI), Greifswald, Germany
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
- Viral Evolution, Robert Koch Institute, Berlin, Germany
| | - B M Hermes
- Evolutionary Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Institute of Experimental Medicine, Kiel University, Kiel, Germany
| | - M Groussin
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - S Waschina
- Nutriinformatics Research Group, Institute for Human Nutrition and Food Science, Kiel University, Kiel, Germany
| | - M Poyet
- Institute of Experimental Medicine, Kiel University, Kiel, Germany
| | - M Ulrich
- Helmholtz Institute for One Health, Helmholtz-Centre for Infection Research (HZI), Greifswald, Germany
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
| | - C Akoua-Koffi
- Training and Research Unit for in Medical Sciences, Alassane Ouattara University / University Teaching Hospital of Bouaké, Bouaké, Côte d'Ivoire
| | - T Deschner
- Comparative BioCognition, Institute of Cognitive Science, University of Osnabrück, Osnabrück, Germany
| | - J J Muyembe-Tamfum
- National Institute for Biomedical Research, National Laboratory of Public Health, Kinshasa, Democratic Republic of the Congo
| | - M M Robbins
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - M Surbeck
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - R M Wittig
- Institute of Cognitive Sciences, CNRS UMR5229 University Lyon 1, Bron Cedex, France
- Taï Chimpanzee Project, CSRS, Abidjan, Côte d'Ivoire
| | - K Zuberbühler
- Institute of Biology, University of Neuchatel, Neuchatel, Switzerland
- School of Psychology & Neuroscience, University of St Andrews, St Andrews, Scotland, UK
| | - J F Baines
- Evolutionary Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Institute of Experimental Medicine, Kiel University, Kiel, Germany
| | - F H Leendertz
- Helmholtz Institute for One Health, Helmholtz-Centre for Infection Research (HZI), Greifswald, Germany
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
| | - A Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany.
| |
Collapse
|
14
|
Wang N, Wang T, Ning K. Refining biome labeling for large-scale microbial community samples: Leveraging neural networks and transfer learning. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2024; 17:100304. [PMID: 37635952 PMCID: PMC10457426 DOI: 10.1016/j.ese.2023.100304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 07/09/2023] [Accepted: 07/22/2023] [Indexed: 08/29/2023]
Abstract
Microbiome research has generated an extensive amount of data, resulting in a wealth of publicly accessible samples. Accurate annotation of these samples is crucial for effectively utilizing microbiome data across scientific disciplines. However, a notable challenge arises from the lack of essential annotations, particularly regarding collection location and sample biome information, which significantly hinders environmental microbiome research. In this study, we introduce Meta-Sorter, a novel approach utilizing neural networks and transfer learning, to enhance biome labeling for thousands of microbiome samples in the MGnify database that have incomplete information. Our findings demonstrate that Meta-Sorter achieved a remarkable accuracy rate of 96.7% in classifying samples among the 16,507 lacking detailed biome annotations. Notably, Meta-Sorter provides precise classifications for representative environmental samples that were previously ambiguously labeled as "Marine" in MGnify, thereby elucidating their specific origins in benthic and water column environments. Moreover, Meta-Sorter effectively distinguishes samples derived from human-environment interactions, enabling clear differentiation between environmental and human-related studies. By improving the completeness of biome label information for numerous microbial community samples, our research facilitates more accurate knowledge discovery across diverse disciplines, with particular implications for environmental research.
Collapse
Affiliation(s)
| | | | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| |
Collapse
|
15
|
Hill MS, Gilbert JA. Microbiology of the built environment: harnessing human-associated built environment research to inform the study and design of animal nests and enclosures. Microbiol Mol Biol Rev 2023; 87:e0012121. [PMID: 38047636 PMCID: PMC10732082 DOI: 10.1128/mmbr.00121-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023] Open
Abstract
SUMMARYOver the past decade, hundreds of studies have characterized the microbial communities found in human-associated built environments (BEs). These have focused primarily on how the design and use of our built spaces have shaped human-microbe interactions and how the differential selection of certain taxa or genetic traits has influenced health outcomes. It is now known that the more removed humans are from the natural environment, the greater the risk for the development of autoimmune and allergic diseases, and that indoor spaces can be harsh, selective environments that can increase the emergence of antimicrobial-resistant and virulent phenotypes in surface-bound communities. However, despite the abundance of research that now points to the importance of BEs in determining human-microbe interactions, only a fraction of non-human animal structures have been comparatively explored. It is here, in the context of human-associated BE research, that we consider the microbial ecology of animal-built natural nests and burrows, as well as artificial enclosures, and point to areas of primary interest for future research.
Collapse
Affiliation(s)
- Megan S. Hill
- Department of Pediatrics, University of California San Diego School of Medicine, San Diego, California, USA
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Jack A. Gilbert
- Department of Pediatrics, University of California San Diego School of Medicine, San Diego, California, USA
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
| |
Collapse
|
16
|
Le MM, Zhong LW, Ren ZW, An MQ, Long YH, Ling TJ. Dynamic Changes in the Microbial Community and Metabolite Profile during the Pile Fermentation Process of Fuzhuan Brick Tea. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:19142-19153. [PMID: 37827989 DOI: 10.1021/acs.jafc.3c04459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
The pile fermentation process of Fuzhuan brick tea is unique in that it involves preheating without the use of starter cultures. The detailed metabolite changes and their drivers during this procedure are not known. Characterizing these unknown changes that occur in the metabolites and microbes during pile fermentation of Fuzhuan brick tea is important for industrial modernization of this traditional fermented food. Using microbial DNA amplicon sequencing, mass spectrometry-based untargeted metabolomics, and feature-based molecular networking, we herein reveal that significant changes in the microbial community occur before changes in the metabolite profile. These changes were characterized by a decrease in Klebsiella and Aspergillus, alongside an increase in Bacillus and Eurotium. The decrease in lysophosphatidylcholines, unsaturated fatty acids, and some astringent flavan-3-ols and bitter amino acids, as well as the increase in some less astringent flavan-3-ols and sweet or umami amino acids, contributed importantly to the overall changes observed in the metabolite profile. The majority of these changes was caused by bacterial metabolism and the corresponding heat generated by it.
Collapse
Affiliation(s)
- Miao-Miao Le
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, Anhui, P. R. China
- Xianyang Jingwei Fu Tea Co. Ltd., Xianyang 712044, Shaanxi, China
| | - Li-Wen Zhong
- School of Tea and Food Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, Anhui, P. R. China
| | - Zhi-Wei Ren
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, Anhui, P. R. China
| | - Mao-Qiang An
- Yiyang Fu Cha Industry Development Co. Ltd., 690 North Datao Road, Yiyang 413000, Hunan, P. R. China
| | - Yan-Hua Long
- School of Life Sciences, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, Anhui, P. R. China
| | - Tie-Jun Ling
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, Anhui, P. R. China
| |
Collapse
|
17
|
Moody M, Sawyer R. Is There a Community Microbial Community? A Comparison of Pathogens Between Two Hospital Surgical Intensive Care Units in a Single City. Surg Infect (Larchmt) 2023; 24:897-902. [PMID: 38011708 DOI: 10.1089/sur.2023.069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023] Open
Abstract
Background: Nosocomial and health-care-associated infections drive increased healthcare costs and negatively affect patient outcomes. The human microbiome has been heavily explored in recent years with incomplete data regarding hospital-specific and community-specific microbial communities. Although bacterial species differ between intensive care units in the same hospital, it is unclear if they differ between similar units in similar hospitals in the same community. Our hypothesis is that pathogens in surgical intensive care units (SICUs) are distinct between hospitals, even in the same community. Methods: From 2017 to 2021, data were collected prospectively from the SICUs of two 400-bed hospitals located three miles apart in the same city (Hospital A and Hospital B). Infections defined using U.S. Centers for Disease Control and Prevention (CDC) criteria were recorded for trauma and general surgery patients, as well as patient demographics, Acute Physiology and Chronic Health Evaluation (APACHE) II score, and causative organism. Results: Overall, Escherichia coli was the most commonly isolated pathogen in Hospital A, whereas Staphylococcus aureus was most commonly isolated at Hospital B. Enterococci were more common in Hospital A, and Haemophilus influenzae and Enterobacter spp. were more common in Hospital B. After stratification between trauma and non-trauma patients, however, these differences disappeared, with the exception of more overall gram-positive organisms and fewer gram-negative organisms among Hospital A trauma patients compared to Hospital B. There were no differences in rates of isolation of either fungi or resistant bacteria between hospitals. Conclusions: At a species level, admission diagnosis appears to be a greater determinant of pathogen isolation than hospital when comparing similar intensive care units (ICUs) in the same geographic area, but a larger body of data is needed to flesh out a distinct microbial map of the organisms occupying a certain geographic region. Further areas for investigation include comparison between hospital units, specific anatomic sites, and ICU versus floor patients.
Collapse
Affiliation(s)
- Mikayla Moody
- Western Michigan University, Kalamazoo, Michigan, USA
| | - Robert Sawyer
- Western Michigan University, Kalamazoo, Michigan, USA
| |
Collapse
|
18
|
Fang H, Li J, Ren L, Liu E. Age-related differences in IgE between childhood and adulthood allergic asthma: Analysis of NHANES 2005-2006. World Allergy Organ J 2023; 16:100842. [PMID: 38213391 PMCID: PMC10782400 DOI: 10.1016/j.waojou.2023.100842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/03/2023] [Accepted: 10/24/2023] [Indexed: 01/13/2024] Open
Abstract
Background Asthma exhibits varying clinical features in children and adults. However, previous studies have mainly focused on the clinical significance of immunoglobulin E (IgE) in the diagnosis and treatment of asthma, disregarding the characteristics of IgE and its relevant factors. Objective This study aimed to gain a better understanding of the differences in the characteristics of IgE between childhood and adulthood allergic asthma (AA). Methods Patients with AA from the 2005 to 2006 National Health and Nutrition Examination Survey (NHANES) were divided into 3 groups based on their current age and onset age of AA: childhood AA (Group 1), childhood-onset adult AA (Group 2), and adulthood-onset AA (Group 3). Intragroup analysis and intergroup comparison were carried out, focusing on the characteristics and relevant factors of IgE, as well as the clinical relevance of total IgE (total IgE, tIgE) and allergen-specific IgE (allergen-specific IgE, sIgE). Results A total of 424 patients were analyzed, including 187 with childhood AA, 132 with childhood-onset adult AA, and 105 with adulthood-onset AA. The concentration of tIgE was found to be higher in Group 1 (268.0, 118.0-686.0 kU/L) than in Group 2 (224.0, 78.0-494.0 kU/L) and Group 3 (165.0, 74.4-350.5 kU/L). The sensitization rates did not differ between Group 1 and Group 2 but were higher compared with Group 3, particularly for Alternaria-sIgE (50.3% and 46.2% vs 15.2%) and Aspergillus-sIgE (43.9% and 37.1% vs 16.2%). In Group 1, there was a negative correlation between pollen-sIgEs and indoor allergens, but this correlation was not commonly observed in Group 2 and Group 3. On the other hand, in Group 1, environmental chemicals such as phthalates, polyaromatic hydrocarbons, trihalomethanes, and phenols showed a positive correlation with IgE. However, a greater number of chemicals was observed in Group 2 and Group 3, including cotinine, metals, trihalomethanes, phthalates, phenols, and other volatile organic compounds (VOCs). Furthermore, in Group 1, IgE was positively correlated with asthma-related issues such as emergency visits, absenteeism, limited activities, and medication needs. These correlations were less common in Group 2 and Group 3, particularly in Group 3. Conclusions There are notable differences in the characteristics and environmental factors of IgE among childhood AA, childhood-onset adult AA, and adulthood-onset AA. Additionally, IgE plays a more significant role in childhood AA due to its higher concentration, fewer relevant environmental chemicals and greater clinical relevance. This may partially explain the age-related features of asthma.
Collapse
Affiliation(s)
| | | | - Luo Ren
- Corresponding author. Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Road, Yuzhong District, Chongqing 400014, China.
| | - Enmei Liu
- Corresponding author. Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Road, Yuzhong District, Chongqing 400014, China.
| |
Collapse
|
19
|
Wallen-Russell C, Pearlman N, Wallen-Russell S, Cretoiu D, Thompson DC, Voinea SC. A Catastrophic Biodiversity Loss in the Environment Is Being Replicated on the Skin Microbiome: Is This a Major Contributor to the Chronic Disease Epidemic? Microorganisms 2023; 11:2784. [PMID: 38004795 PMCID: PMC10672968 DOI: 10.3390/microorganisms11112784] [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: 08/30/2023] [Revised: 10/16/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
There has been a catastrophic loss of biodiversity in ecosystems across the world. A similar crisis has been observed in the human gut microbiome, which has been linked to "all human diseases affecting westernized countries". This is of great importance because chronic diseases are the leading cause of death worldwide and make up 90% of America's healthcare costs. Disease development is complex and multifactorial, but there is one part of the body's interlinked ecosystem that is often overlooked in discussions about whole-body health, and that is the skin microbiome. This is despite it being a crucial part of the immune, endocrine, and nervous systems and being continuously exposed to environmental stressors. Here we show that a parallel biodiversity loss of 30-84% has occurred on the skin of people in the developed world compared to our ancestors. Research has shown that dysbiosis of the skin microbiome has been linked to many common skin diseases and, more recently, that it could even play an active role in the development of a growing number of whole-body health problems, such as food allergies, asthma, cardiovascular diseases, and Parkinson's, traditionally thought unrelated to the skin. Damaged skin is now known to induce systemic inflammation, which is involved in many chronic diseases. We highlight that biodiversity loss is not only a common finding in dysbiotic ecosystems but also a type of dysbiosis. As a result, we make the case that biodiversity loss in the skin microbiome is a major contributor to the chronic disease epidemic. The link between biodiversity loss and dysbiosis forms the basis of this paper's focus on the subject. The key to understanding why biodiversity loss creates an unhealthy system could be highlighted by complex physics. We introduce entropy to help understand why biodiversity has been linked with ecosystem health and stability. Meanwhile, we also introduce ecosystems as being governed by "non-linear physics" principles-including chaos theory-which suggests that every individual part of any system is intrinsically linked and implies any disruption to a small part of the system (skin) could have a significant and unknown effect on overall system health (whole-body health). Recognizing the link between ecosystem health and human health allows us to understand how crucial it could be to maintain biodiversity across systems everywhere, from the macro-environment we inhabit right down to our body's microbiome. Further, in-depth research is needed so we can aid in the treatment of chronic diseases and potentially change how we think about our health. With millions of people currently suffering, research to help mitigate the crisis is of vital importance.
Collapse
Affiliation(s)
| | - Nancy Pearlman
- Ecology Center of Southern California, Los Angeles, CA 90035, USA;
| | | | - Dragos Cretoiu
- Department of Medical Genetics, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania
- Fetal Medicine Excellence Research Center, Alessandrescu-Rusescu National Institute for Mother and Child Health, 011062 Bucharest, Romania
| | - Dana Claudia Thompson
- Fetal Medicine Excellence Research Center, Alessandrescu-Rusescu National Institute for Mother and Child Health, 011062 Bucharest, Romania
| | - Silviu Cristian Voinea
- Department of Surgical Oncology, Prof. Dr. Al. Trestioreanu Oncology Institute, Carol Davila University of Medicine and Pharmacy, 022328 Bucharest, Romania
| |
Collapse
|
20
|
Donald K, Finlay BB. Early-life interactions between the microbiota and immune system: impact on immune system development and atopic disease. Nat Rev Immunol 2023; 23:735-748. [PMID: 37138015 DOI: 10.1038/s41577-023-00874-w] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/28/2023] [Indexed: 05/05/2023]
Abstract
Prenatal and early postnatal life represent key periods of immune system development. In addition to genetics and host biology, environment has a large and irreversible role in the immune maturation and health of an infant. One key player in this process is the gut microbiota, a diverse community of microorganisms that colonizes the human intestine. The diet, environment and medical interventions experienced by an infant determine the establishment and progression of the intestinal microbiota, which interacts with and trains the developing immune system. Several chronic immune-mediated diseases have been linked to an altered gut microbiota during early infancy. The recent rise in allergic disease incidence has been explained by the 'hygiene hypothesis', which states that societal changes in developed countries have led to reduced early-life microbial exposures, negatively impacting immunity. Although human cohort studies across the globe have established a correlation between early-life microbiota composition and atopy, mechanistic links and specific host-microorganism interactions are still being uncovered. Here, we detail the progression of immune system and microbiota maturation in early life, highlight the mechanistic links between microbes and the immune system, and summarize the role of early-life host-microorganism interactions in allergic disease development.
Collapse
Affiliation(s)
- Katherine Donald
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - B Brett Finlay
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada.
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada.
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada.
| |
Collapse
|
21
|
Rook GAW. The old friends hypothesis: evolution, immunoregulation and essential microbial inputs. FRONTIERS IN ALLERGY 2023; 4:1220481. [PMID: 37772259 PMCID: PMC10524266 DOI: 10.3389/falgy.2023.1220481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/18/2023] [Indexed: 09/30/2023] Open
Abstract
In wealthy urbanised societies there have been striking increases in chronic inflammatory disorders such as allergies, autoimmunity and inflammatory bowel diseases. There has also been an increase in the prevalence of individuals with systemically raised levels of inflammatory biomarkers correlating with increased risk of metabolic, cardiovascular and psychiatric problems. These changing disease patterns indicate a broad failure of the mechanisms that should stop the immune system from attacking harmless allergens, components of self or gut contents, and that should terminate inappropriate inflammation. The Old Friends Hypothesis postulates that this broad failure of immunoregulation is due to inadequate exposures to the microorganisms that drive development of the immune system, and drive the expansion of components such as regulatory T cells (Treg) that mediate immunoregulatory mechanisms. An evolutionary approach helps us to identify the organisms on which we are in a state of evolved dependence for this function (Old Friends). The bottom line is that most of the organisms that drive the regulatory arm of the immune system come from our mothers and family and from the natural environment (including animals) and many of these organisms are symbiotic components of a healthy microbiota. Lifestyle changes that are interrupting our exposure to these organisms can now be identified, and many are closely associated with low socioeconomic status (SES) in wealthy countries. These insights will facilitate the development of education, diets and urban planning that can correct the immunoregulatory deficit, while simultaneously reducing other contributory factors such as epithelial damage.
Collapse
Affiliation(s)
- Graham A. W. Rook
- Centre for Clinical Microbiology, Department of Infection, UCL (University College London), London, United Kingdom
| |
Collapse
|
22
|
Zhang YD, Fan SJ, Zhang Z, Li JX, Liu XX, Hu LX, Knibbs LD, Dadvand P, Jalaludin B, Browning MH, Zhao T, Heinrich J, He Z, Chen CZ, Zhou Y, Dong GH, Yang BY. Association between Residential Greenness and Human Microbiota: Evidence from Multiple Countries. ENVIRONMENTAL HEALTH PERSPECTIVES 2023; 131:87010. [PMID: 37585351 PMCID: PMC10431502 DOI: 10.1289/ehp12186] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 07/06/2023] [Accepted: 07/17/2023] [Indexed: 08/18/2023]
Abstract
BACKGROUND Greenness, referring to a measurement of the density of vegetated land (e.g., gardens, parks, grasslands), has been linked with many human health outcomes. However, the evidence on greenness exposure and human microbiota remains limited, inconclusive, drawn from specific regions, and based on only modest sample size. OBJECTIVES We aimed to study the association between greenness exposure and human microbial diversity and composition in a large sample across 34 countries and regions. METHODS We explored associations between residential greenness and human microbial alpha-diversity, composition, and genus abundance using data from 34 countries. Greenness exposure was assessed using the normalized difference vegetation index and the enhanced vegetation index mean values in the month before sampling. We used linear regression models to estimate the association between greenness and microbial alpha-diversity and tested the effect modification of age, sex, climate zone, and pet ownership of participants. Differences in microbial composition were tested by permutational multivariate analysis of variance based on Bray-Curtis distance and differential taxa were detected using the DESeq2 R package between two greenness exposure groups split by median values of greenness. RESULTS We found that higher greenness was significantly associated with greater richness levels in the palm and gut microbiota but decreased evenness in the gut microbiota. Pet ownership and climate zone modified some associations between greenness and alpha-diversity. Palm and gut microbial composition at the genus level also varied by greenness. Higher abundances of the genera Lactobacillus and Bifidobacterium, and lower abundances of the genera Anaerotruncus and Streptococcus, were observed in people with higher greenness levels. DISCUSSION These findings suggest that residential greenness was associated with microbial richness and composition in the human skin and gut samples, collected across different geographic contexts. Future studies may validate the observed associations and determine whether they correspond to improvements in human health. https://doi.org/10.1289/EHP12186.
Collapse
Affiliation(s)
- Yi-Dan Zhang
- Guangdong Provincial Engineering Technology Research Center of Environmental Pollution and Health Risk Assessment, Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Shu-Jun Fan
- Department of Environmental Health, Guangzhou Center for Disease Control and Prevention, Guangzhou, China
- Institute of Public Health, Guangzhou Medical University and Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Zheng Zhang
- Department of Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Jia-Xin Li
- Guangdong Provincial Engineering Technology Research Center of Environmental Pollution and Health Risk Assessment, Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Xiao-Xuan Liu
- Guangdong Provincial Engineering Technology Research Center of Environmental Pollution and Health Risk Assessment, Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Li-Xin Hu
- Department of Maternal and Child Health, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Luke D. Knibbs
- School of Public Health, University of Sydney, Camperdown, New South Wales, Australia
| | - Payam Dadvand
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
| | - Bin Jalaludin
- School of Population Health, University of New South Wales, Kensington, New South Wales, Australia
| | - Matthew H.E.M. Browning
- Department of Park, Recreation, and Tourism Management, Clemson University, Clemson, South Carolina, USA
| | - Tianyu Zhao
- Institute and Clinic for Occupational, Social and Environmental Medicine, Hospital of the Ludwig-Maximilians-Universität München (LMU Munich), Munich, Germany
- Comprehensive Pneumology Center Munich, LMU Munich, Munich, Germany
- German Center for Lung Research, Justus Liebig University Giessen, Giessen, Germany
- Institute of Epidemiology, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
| | - Joachim Heinrich
- Institute and Clinic for Occupational, Social and Environmental Medicine, LMU Munich, Munich, Germany
- Allergy and Lung Health Unit, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Zhini He
- Food Safety and Health Research Center, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Cheng-Zhi Chen
- School of Public Health and Management, Research Center for Medicine and Social Development, Innovation Center for Social Risk Governance in Health, Chongqing Medical University, Chongqing, China
| | - Yuanzhong Zhou
- Department of Epidemiology, School of Public Health, Zunyi Medical University, Zunyi, China
| | - Guang-Hui Dong
- Guangdong Provincial Engineering Technology Research Center of Environmental Pollution and Health Risk Assessment, Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Bo-Yi Yang
- Guangdong Provincial Engineering Technology Research Center of Environmental Pollution and Health Risk Assessment, Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou, China
| |
Collapse
|
23
|
Yan D, Li M, Si W, Ni S, Liu X, Chang Y, Guo X, Wang J, Bai J, Chen Y, Jia H, Zhang T, Wu M, Song X, Tian Z, Yu L. Haze Exposure Changes the Skin Fungal Community and Promotes the Growth of Talaromyces Strains. Microbiol Spectr 2023; 11:e0118822. [PMID: 36507683 PMCID: PMC10269824 DOI: 10.1128/spectrum.01188-22] [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: 04/01/2022] [Accepted: 11/18/2022] [Indexed: 12/15/2022] Open
Abstract
Haze pollution has been a public health issue. The skin microbiota, as a component of the first line of defense, is disturbed by environmental pollutants, which may have an impact on human health. A total of 74 skin samples from healthy students were collected during haze and nonhaze days in spring and winter. Significant differences of skin fungal community composition between haze and nonhaze days were observed in female and male samples in spring and male samples in winter based on unweighted UniFrac distance analysis. Phylogenetic diversity whole-tree indices and observed features were significantly increased during haze days in male samples in winter compared to nonhaze days, but no significant difference was observed in other groups. Dothideomycetes, Capnodiales, Mycosphaerellaceae, etc. were significantly enriched during nonhaze days, whereas Trichocomaceae, Talaromyces, and Pezizaceae were significantly enriched during haze days. Thus, five Talaromyces strains were isolated, and an in vitro culture experiment revealed that the growth of representative Talaromyces strains was increased at high concentrations of particulate matter, confirming the sequencing results. Furthermore, during haze days, the fungal community assembly was better fitted to a niche-based assembly model than during nonhaze days. Talaromyces enriched during haze days deviated from the neutral assembly process. Our findings provided a comprehensive characterization of the skin fungal community during haze and nonhaze days and elucidated novel insights into how haze exposure influences the skin fungal community. IMPORTANCE Skin fungi play an important role in human health. Particulate matter (PM), the main haze pollutant, has been a public environmental threat. However, few studies have assessed the effects of air pollutants on skin fungi. Here, haze exposure influenced the diversity and composition of the skin fungal community. In an in vitro experiment, a high concentration of PM promoted the growth of Talaromyces strains. The fungal community assembly is better fitted to a niche-based assembly model during haze days. We anticipate that this study may provide new insights on the role of haze exposure disturbing the skin fungal community. It lays the groundwork for further clarifying the association between the changes of the skin fungal community and adverse health outcomes. Our study is the first to report the changes in the skin fungal community during haze and nonhaze days, which expands the understanding of the relationship between haze and skin fungi.
Collapse
Affiliation(s)
- Dong Yan
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan, China
| | - Min Li
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan, China
| | - Wenhao Si
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan, China
- Department of Dermatology, the First Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
| | - Shijun Ni
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan, China
| | - Xin Liu
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan, China
| | - Yahan Chang
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan, China
| | - Xiaochan Guo
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan, China
| | - Jingjing Wang
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan, China
| | - Jie Bai
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan, China
| | - Yuanhang Chen
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan, China
| | - Haoyue Jia
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan, China
| | - Tao Zhang
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Minna Wu
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan, China
| | - Xiangfeng Song
- Department of Immunology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan, China
| | - Zhongwei Tian
- Department of Dermatology, the First Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
| | - Liyan Yu
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| |
Collapse
|
24
|
Fu X, Du B, Meng Y, Li Y, Zhu X, Ou Z, Zhang M, Wen H, Ma'pol A, Hashim JH, Hashim Z, Wieslander G, Chen Q, Jiang J, Wang J, Norbäck D, Xia Y, Chen Q, Sun Y. Associations between environmental characteristics, high-resolution indoor microbiome, metabolome and allergic and non-allergic rhinitis symptoms for junior high school students. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2023; 25:791-804. [PMID: 36883483 DOI: 10.1039/d2em00480a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Rhinitis is one of the most prevalent chronic diseases globally. Microbiome exposure affects the occurrence of rhinitis. However, previous studies did not differentiate allergic rhinitis (AR) and non-allergic rhinitis (NAR) in the microbial association analysis. In this study, we investigate 347 students in 8 junior high schools, Terengganu, Malaysia, who were categorized as healthy (70.9%), AR (13.8%) and NAR (15.3%) based on a self-administered questionnaire and skin prick tests of pollen, pet, mould and house dust mite allergens. Classroom microbial and metabolite exposure in vacuumed dust was characterized by PacBio long-read amplicon sequencing, quantitative PCR and LC-MS-based untargeted metabolomics. Our findings indicate a similar microbial association pattern between AR and NAR. The richness in Gammaproteobacteria was negatively associated with AR and NAR symptoms, whereas total fungal richness was positively associated with AR and NAR symptoms (p < 0.05). Brasilonema bromeliae and Aeromonas enteropelogenes were negatively associated with AR and NAR, and Deinococcus was positively associated with AR and NAR (p < 0.01). Pipecolic acid was protectively associated with AR and NAR symptoms (OR = 0.06 and 0.13, p = 0.009 and 0.045). A neural network analysis showed that B. bromeliae was co-occurring with pipecolic acid, suggesting that the protective role of this species may be mediated by releasing pipecolic acid. Indoor relative humidity and the weight of vacuum dust were associated with AR and NAR, respectively (p < 0.05), but the health effects were mediated by two protective bacterial species, Aliinostoc morphoplasticum and Ilumatobacter fluminis. Overall, our study reported a similar microbial association pattern between AR and NAR and also revealed the complex interactions between microbial species, environmental characteristics, and rhinitis symptoms.
Collapse
Affiliation(s)
- Xi Fu
- Guangdong Provincial Engineering Research Center of Public Health Detection and Assessment, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China.
| | - Bingqian Du
- Guangdong Provincial Engineering Research Center of Public Health Detection and Assessment, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China.
| | - Yi Meng
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China.
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Yanling Li
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China.
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Xunhua Zhu
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China.
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Zheyuan Ou
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China.
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Mei Zhang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China.
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Huarong Wen
- Baling Health Center, Dangyang, Hubei, 444100, PR China
| | - Aminnuddin Ma'pol
- Gombak District Health Office, Ministry of Health, Batu Caves, Selangor Darul Ehsan, Malaysia
| | | | - Zailina Hashim
- Department of Environmental and Occupational Health, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM, Serdang, Selangor, Malaysia
| | - Gunilla Wieslander
- Occupational and Environmental Medicine, Department of Medical Science, University Hospital, Uppsala University, 75237 Uppsala, Sweden
| | - Qingmei Chen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China.
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Jun Jiang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China.
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Juan Wang
- Occupational and Environmental Medicine, Department of Medical Science, University Hospital, Uppsala University, 75237 Uppsala, Sweden
| | - Dan Norbäck
- Occupational and Environmental Medicine, Department of Medical Science, University Hospital, Uppsala University, 75237 Uppsala, Sweden
| | - Yun Xia
- Guangdong Provincial Engineering Research Center of Public Health Detection and Assessment, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China.
| | - Qingsong Chen
- Guangdong Provincial Engineering Research Center of Public Health Detection and Assessment, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China.
| | - Yu Sun
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China.
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| |
Collapse
|
25
|
Manus MB, Watson E, Kuthyar S, Carba D, Belarmino NM, McDade TW, Kuzawa CW, Amato KR. Prenatal household size and composition are associated with infant fecal bacterial diversity in Cebu, Philippines. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 181:45-58. [PMID: 36847111 DOI: 10.1002/ajpa.24720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/02/2023] [Accepted: 02/08/2023] [Indexed: 03/01/2023]
Abstract
OBJECTIVES The gut microbiome (GM) connects physical and social environments to infant health. Since the infant GM affects immune system development, there is interest in understanding how infants acquire microbes from mothers and other household members. MATERIALS AND METHODS As a part of the Cebu Longitudinal Health and Nutrition Survey (CLHNS), we paired fecal samples (proxy for the GM) collected from infants living in Metro Cebu, Philippines at 2 weeks (N = 39) and 6 months (N = 36) with maternal interviews about prenatal household composition. We hypothesized that relationships between prenatal household size and composition and infant GM bacterial diversity (as measured in fecal samples) would vary by infant age, as well as by household member age and sex. We also hypothesized that infant GM bacterial abundances would differ by prenatal household size and composition. RESULTS Data from 16 S rRNA bacterial gene sequencing show that prenatal household size was the most precise estimator of infant GM bacterial diversity, and that the direction of the association between this variable and infant GM bacterial diversity changed between the two time points. The abundances of bacterial families in the infant GM varied by prenatal household variables. CONCLUSIONS Results highlight the contributions of various household sources to the bacterial diversity of the infant GM, and suggest that prenatal household size is a useful measure for estimating infant GM bacterial diversity in this cohort. Future research should measure the effect of specific sources of household bacterial exposures, including social interactions with caregivers, on the infant GM.
Collapse
Affiliation(s)
- Melissa B Manus
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Elijah Watson
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Sahana Kuthyar
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA.,Department of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | - Delia Carba
- Office of Population Studies, University of San Carlos, Cebu City, Philippines
| | - Nikola M Belarmino
- Office of Population Studies, University of San Carlos, Cebu City, Philippines
| | - Thomas W McDade
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA.,Institute for Policy Research, Northwestern University, Evanston, Illinois, USA
| | - Christopher W Kuzawa
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA.,Institute for Policy Research, Northwestern University, Evanston, Illinois, USA
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| |
Collapse
|
26
|
The Molecular Effect of Wearing Silver-Threaded Clothing on the Human Skin. mSystems 2023; 8:e0092222. [PMID: 36722970 PMCID: PMC9948701 DOI: 10.1128/msystems.00922-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
With growing awareness that what we put in and on our bodies affects our health and wellbeing, little is still known about the impact of textiles on the human skin. Athletic wear often uses silver threading to improve hygiene, but little is known about its effect on the body's largest organ. In this study, we investigated the impact of such clothing on the skin's chemistry and microbiome. Samples were collected from different body sites of a dozen volunteers over the course of 12 weeks. The changes induced by the antibacterial clothing were specific for individuals, but more so defined by gender and body site. Unexpectedly, the microbial biomass on skin increased in the majority of the volunteers when wearing silver-threaded T-shirts. Although the most abundant taxa remained unaffected, silver caused an increase in diversity and richness of low-abundant bacteria and a decrease in chemical diversity. Both effects were mainly observed for women. The hallmark of the induced changes was an increase in the abundance of various monounsaturated fatty acids (MUFAs), especially in the upper back. Several microbe-metabolite associations were uncovered, including Cutibacterium, detected in the upper back area, which was correlated with the distribution of MUFAs, and Anaerococcus spp. found in the underarms, which were associated with a series of different bile acids. Overall, these findings point to a notable impact of the silver-threaded material on the skin microbiome and chemistry. We observed that relatively subtle changes in the microbiome result in pronounced shifts in molecular composition. IMPORTANCE The impact of silver-threaded material on human skin chemistry and microbiome is largely unknown. Although the most abundant taxa remained unaffected, silver caused an increase in diversity and richness of low-abundant bacteria and a decrease in chemical diversity. The major change was an increase in the abundance of various monounsaturated fatty acids that were also correlated with Cutibacterium. Additionally, Anaerococcus spp., found in the underarms, were associated with different bile acids in the armpit samples. Overall, the impact of the silver-threaded clothing was gender and body site specific.
Collapse
|
27
|
Huang Z, Li Y, Park H, Ho M, Bhardwaj K, Sugimura N, Lee HW, Meng H, Ebert MP, Chao K, Burgermeister E, Bhatt AP, Shetty SA, Li K, Wen W, Zuo T. Unveiling and harnessing the human gut microbiome in the rising burden of non-communicable diseases during urbanization. Gut Microbes 2023; 15:2237645. [PMID: 37498052 PMCID: PMC10376922 DOI: 10.1080/19490976.2023.2237645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 07/28/2023] Open
Abstract
The world is witnessing a global increase in the urban population, particularly in developing Asian and African countries. Concomitantly, the global burden of non-communicable diseases (NCDs) is rising, markedly associated with the changing landscape of lifestyle and environment during urbanization. Accumulating studies have revealed the role of the gut microbiome in regulating the immune and metabolic homeostasis of the host, which potentially bridges external factors to the host (patho-)physiology. In this review, we discuss the rising incidences of NCDs during urbanization and their links to the compositional and functional dysbiosis of the gut microbiome. In particular, we elucidate the effects of urbanization-associated factors (hygiene/pollution, urbanized diet, lifestyles, the use of antibiotics, and early life exposure) on the gut microbiome underlying the pathogenesis of NCDs. We also discuss the potential and feasibility of microbiome-inspired and microbiome-targeted approaches as novel avenues to counteract NCDs, including fecal microbiota transplantation, diet modulation, probiotics, postbiotics, synbiotics, celobiotics, and precision antibiotics.
Collapse
Affiliation(s)
- Ziyu Huang
- Key Laboratory of Human Microbiome and Chronic Diseases, Sun Yat-Sen University, Ministry of Education, Guangzhou, China
- Guangdong Institute of Gastroenterology, the Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
- Biomedical Innovation Centre, the Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
- The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yue Li
- Key Laboratory of Human Microbiome and Chronic Diseases, Sun Yat-Sen University, Ministry of Education, Guangzhou, China
- Guangdong Institute of Gastroenterology, the Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
- Biomedical Innovation Centre, the Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
- The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Heekuk Park
- Department of Medicine, Division of Infectious Diseases, Columbia University Irving Medical Centre, New York, NY, USA
| | - Martin Ho
- Department of Engineering, University of Cambridge, Cambridge, UK
| | - Kanchan Bhardwaj
- Department of Biotechnology, Faculty of Engineering and Technology, Manav Rachna International Institute of Research and Studies, Haryana, India
| | - Naoki Sugimura
- Gastrointestinal Centre and Institute of Minimally-Invasive Endoscopic Care (iMEC), Sano Hospital, Kobe, Japan
| | - Hye Won Lee
- Institute of Gastroenterology and Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Huicui Meng
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, China
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Guangzhou, China
- Guangdong Province Engineering Laboratory for Nutrition Translation, Guangzhou, China
| | - Matthias P. Ebert
- Department of Medicine II, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- DKFZ-Hector Cancer Institute, Mannheim, Germany
- Mannheim Cancer Centre (MCC), University Medical Centre Mannheim, Mannheim, Germany
| | - Kang Chao
- The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
- Department of Gastroenterology, the Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Elke Burgermeister
- Department of Medicine II, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Aadra P. Bhatt
- Department of Medicine, Centre for Gastrointestinal Biology and Disease, and the Lineberger Comprehensive Cancer Centre, University of North Carolina, Chapel Hill, NC, USA
| | - Sudarshan A. Shetty
- Department of Medical Microbiology and Infection Prevention, University Medical Centre Groningen, Groningen, The Netherlands
| | - Kai Li
- Key Laboratory of Human Microbiome and Chronic Diseases, Sun Yat-Sen University, Ministry of Education, Guangzhou, China
- Guangdong Institute of Gastroenterology, the Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
- The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Weiping Wen
- Key Laboratory of Human Microbiome and Chronic Diseases, Sun Yat-Sen University, Ministry of Education, Guangzhou, China
- Biomedical Innovation Centre, the Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
- The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Tao Zuo
- Key Laboratory of Human Microbiome and Chronic Diseases, Sun Yat-Sen University, Ministry of Education, Guangzhou, China
- Guangdong Institute of Gastroenterology, the Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
- Biomedical Innovation Centre, the Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
- The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| |
Collapse
|
28
|
Bolaños-Rosero B, Hernández-González X, Cavallín-Calanche HE, Godoy-Vitorino F, Vesper S. Impact of Hurricane Maria on mold levels in the homes of Piñones, Puerto Rico. AIR QUALITY, ATMOSPHERE, & HEALTH 2022; 16:661-668. [PMID: 37312968 PMCID: PMC10259649 DOI: 10.1007/s11869-022-01297-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 12/07/2022] [Indexed: 06/15/2023]
Abstract
Hurricane Maria struck Puerto Rico on September 20, 2017, severely impacting the island. In order to quantify the impact of the hurricane on the indoor air quality, we evaluated the fungal levels in households (n = 20) of the Piñones community for the period of 2018 and 2019. For each dust sample collected, the 36 Environmental Relative Moldiness Index (ERMI) molds were quantified using qPCR assays, and then Shannon Diversity Index (SDI) values for the fungal populations were calculated. Homes were in five separate regions, regarding their proximity in the studied area. We found that for regions with reported least water damage, the SDI values were similar for both sampled years, but for regions that reported mid-to-high level of damage region, the SDI values were significantly higher. Households that reported remediation actions between the two sampled years showed similar values for the second year as those that did not report any major impact. Our preliminary data provides insights into the significant impacts of hurricanes into indoor fungal environment.
Collapse
Affiliation(s)
- B Bolaños-Rosero
- Department of Microbiology and Medical Zoology, University of Puerto Rico, San Juan, PR, USA
| | - X Hernández-González
- Department of Microbiology and Medical Zoology, University of Puerto Rico, San Juan, PR, USA
| | | | - F Godoy-Vitorino
- Department of Microbiology and Medical Zoology, University of Puerto Rico, San Juan, PR, USA
| | - S Vesper
- Center for Environmental Measurement and Modeling, United States Environmental Protection Agency, Cincinnati, OH, USA
| |
Collapse
|
29
|
Untargeted Fecal Metabolomic Analyses across an Industrialization Gradient Reveal Shared Metabolites and Impact of Industrialization on Fecal Microbiome-Metabolome Interactions. mSystems 2022; 7:e0071022. [PMID: 36416540 PMCID: PMC9765122 DOI: 10.1128/msystems.00710-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The metabolome is a central determinant of human phenotypes and includes the plethora of small molecules produced by host and microbiome or taken up from exogenous sources. However, studies of the metabolome have so far focused predominantly on urban, industrialized populations. Through an untargeted metabolomic analysis of 90 fecal samples from human individuals from Africa and the Americas-the birthplace and the last continental expansion of our species, respectively-we characterized a shared human fecal metabolome. The majority of detected metabolite features were ubiquitous across populations, despite any geographic, dietary, or behavioral differences. Such shared metabolite features included hyocholic acid and cholesterol. However, any characterization of the shared human fecal metabolome is insufficient without exploring the influence of industrialization. Here, we show chemical differences along an industrialization gradient, where the degree of industrialization correlates with metabolomic changes. We identified differential metabolite features such as amino acid-conjugated bile acids and urobilin as major metabolic correlates of these behavioral shifts. Additionally, coanalyses with over 5,000 publicly available human fecal samples and cooccurrence probability analyses with the gut microbiome highlight connections between the human fecal metabolome and gut microbiome. Our results indicate that industrialization significantly influences the human fecal metabolome, but diverse human lifestyles and behavior still maintain a shared human fecal metabolome. This study represents the first characterization of the shared human fecal metabolome through untargeted analyses of populations along an industrialization gradient. IMPORTANCE As the world becomes increasingly industrialized, understanding the biological consequences of these lifestyle shifts and what it means for past, present, and future human health is critical. Indeed, industrialization is associated with rises in allergic and autoimmune health conditions and reduced microbial diversity. Exploring these health effects on a chemical level requires consideration of human lifestyle diversity, but understanding the significance of any differences also requires knowledge of what molecular components are shared between human groups. Our study reveals the key chemistry of the human gut as defined by varied industrialization-based differences and ubiquitous shared features. Ultimately, these novel findings extend our knowledge of human molecular biology, especially as it is influenced by lifestyle and behavior, and provide steps toward understanding how human biology has changed over our species' history.
Collapse
|
30
|
Winnicki MH, Dunn RR, Winther-Jensen M, Jess T, Allin KH, Bruun HH. Does childhood exposure to biodiverse greenspace reduce the risk of developing asthma? THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 850:157853. [PMID: 35940273 DOI: 10.1016/j.scitotenv.2022.157853] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 07/13/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
The prevalence of inflammatory diseases is increasing in populations throughout the industrialized world. An increasing proportion of human populations grow up and live in urban areas, probably with reduced exposure to biodiversity, including diverse soil biotas. Decreased exposure to microorganisms from natural environments, in particular in early childhood, has been hypothesized to hamper development of the human immune system and lead to increasing risks of inflammatory diseases, such as asthma. We investigated 40,249 Danish individuals born 1995-2015. Percentage greenspace was assessed in a 2 km buffer around home addresses of individuals. The Danish Biodiversity Map, charting occurrence density of red-listed animals, plants and macrofungi, was used as a proxy for multi-taxon biodiversity. For asthma defined broadly, we found no evidence of decreasing risk of developing asthma with higher levels of biodiversity, while greenspace exposure was associated with higher risk of asthma. In contrast, exposure to total and biodiverse greenspace was associated with reduced risk of developing severe asthma. Exposure to farmland, which in Denmark is heavily industrialized cropland, also showed association with elevated risk of developing asthma, even at relatively low agricultural landcover. In the subset of children growing up in highly urbanized settings, we found high exposures to urban greenspace to be associated with reduced risk of developing asthma. Our results lend limited support to the hypothesis that childhood exposure to biodiverse environments reduces the risk of acquiring inflammatory diseases later in life. However, access to urban greenspace, such as parks, which typically harbour low levels of biodiversity, seems to reduce asthma risk, potentially through exposure to common soil microbiota. Our results suggest that effects of biodiversity exposure on human health is set by a balance between ecosystem services and disservices and that biodiversity conservation is best motivated with other arguments than reduction of risks from inflammatory diseases.
Collapse
Affiliation(s)
- Martin Holm Winnicki
- Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark; Section for Data, Biostatistics and Pharmacoepidemiology, Center for Clinical Research and Prevention, Bispebjerg Frederiksberg Hospital, Copenhagen, Denmark
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Matilde Winther-Jensen
- Section for Data, Biostatistics and Pharmacoepidemiology, Center for Clinical Research and Prevention, Bispebjerg Frederiksberg Hospital, Copenhagen, Denmark
| | - Tine Jess
- Center for Molecular Prediction of Inflammatory Bowel Disease, Department of Clinical Medicine, Aalborg University, A.C. Meyers Vænge 15A, 2450 Copenhagen, Denmark; Department of Gastroenterology & Hepatology, Aalborg University Hospital, 9100 Aalborg, Denmark
| | - Kristine Højgaard Allin
- Center for Molecular Prediction of Inflammatory Bowel Disease, Department of Clinical Medicine, Aalborg University, A.C. Meyers Vænge 15A, 2450 Copenhagen, Denmark; Department of Gastroenterology & Hepatology, Aalborg University Hospital, 9100 Aalborg, Denmark
| | - Hans Henrik Bruun
- Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark.
| |
Collapse
|
31
|
A Pilot Study: the Development of a Facility-Associated Microbiome and Its Association with the Presence of Listeria Spp. in One Small Meat Processing Facility. Microbiol Spectr 2022; 10:e0204522. [PMID: 35980043 PMCID: PMC9603805 DOI: 10.1128/spectrum.02045-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Microbial communities which persist in food processing facilities may have a detrimental impact on food safety and spoilage. In meat processing, Listeria monocytogenes is an organism of concern due to its ability to cause significant human illnesses and persist in refrigerated environments. The microbial ecology of Listeria spp. in small meat processing facilities has not been well characterized. Therefore, we collected samples from a newly constructed meat processing facility as an opportunity to investigate several research objectives: (i) to determine whether a stable, consistent microbiome develops in a small meat processing facility during the first 18 months of operation, (ii) to evaluate the environmental factors that drive microbial community formation, and (iii) to elucidate the relationship between microbial communities and the presence of Listeria species. We evaluated microbiomes using 16S rRNA gene sequencing and Listeria presence using quantitative PCR. We demonstrated that microbial communities differentiate by the functional room type, which is representative of several environmental differences such as temperature, sources of microbes, and activity. Temperature was an especially important factor; in rooms with low temperatures, communities were dominated by psychotrophs, especially Pseudomonas, while warmer rooms supported greater diversity. A stable core community formed in facility drains, indicating that mechanisms which cause persistence are present in the communities. The overall presence of Listeria in the facility was low but could be tied to specific organisms within a room, and the species of Listeria could be stratified by room function. IMPORTANCE This study provides critical knowledge to improve meat safety and quality from small meat processing facilities. Principally, it demonstrates the importance of facility design and room condition to the development of important microbial communities; temperature, sanitation regimen, and physical barriers all influence the ability of microorganisms to join the stable core community. It also demonstrates a relationship between the microbial community and Listeria presence in the facility, showing the importance of managing facility sanitation plans for not only pathogens, but also the general facility microbiome.
Collapse
|
32
|
Manus MB. Ecological Processes and Human Behavior Provide a Framework for Studying the Skin Microbial Metacommunity. MICROBIAL ECOLOGY 2022; 84:689-702. [PMID: 34636925 DOI: 10.1007/s00248-021-01884-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 09/24/2021] [Indexed: 06/13/2023]
Abstract
Metacommunity theory dictates that a microbial community is supported both by local ecological processes and the dispersal of microbes between neighboring communities. Studies that apply this perspective to human-associated microbial communities are thus far limited to the gut microbiome. Yet, the skin serves as the primary barrier between the body and the external environment, suggesting frequent opportunities for microbial dispersal to the variable microbial communities that are housed across skin sites. This paper applies metacommunity theory to understand the dispersal of microbes to the skin from the physical and social environment, as well as between different skin sites on an individual's body. This includes highlighting the role of human behavior in driving microbial dispersal, as well as shaping physiological properties of skin that underscore local microbial community dynamics. By leveraging data from research on the skin microbiomes of amphibians and other animals, this paper provides recommendations for future research on the skin microbial metacommunity, including generating testable predictions about the ecological underpinnings of the skin microbiome.
Collapse
Affiliation(s)
- Melissa B Manus
- Department of Anthropology, Northwestern University, Evanston, IL, USA.
| |
Collapse
|
33
|
Johnston JD, Cowger AE, Weber KS. Bioaerosol and microbial exposures from residential evaporative coolers and their potential health outcomes: A review. INDOOR AIR 2022; 32:e13082. [PMID: 36168234 PMCID: PMC9826010 DOI: 10.1111/ina.13082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 06/10/2022] [Accepted: 07/08/2022] [Indexed: 06/16/2023]
Abstract
Evaporative cooling is an energy efficient form of air conditioning in dry climates that functions by pulling hot, dry outdoor air across a wet evaporative pad. While evaporative coolers can help save energy, they also have the potential to influence human health. Studies have shown residential evaporative coolers may pull outdoor air pollutants into the home or contribute to elevated levels of indoor bioaerosols that may be harmful to health. There is also evidence that evaporative coolers can enable a diverse microbial environment that may confer early-life immunological protection against the development of allergies and asthma or exacerbate these same hypersensitivities. This review summarizes the current knowledge of bioaerosol and microbiological studies associated with evaporative coolers, focusing on harmful and potentially helpful outcomes from their use. We evaluate the effects of evaporative coolers on indoor bacterial endotoxins, fungal β-(1 → 3)-D-glucans, dust mite antigens, residential microbial communities, and Legionella pneumophila. To our knowledge, this is the first review to summarize and evaluate studies on the influence that evaporative coolers have on the bioaerosol and microbiological profile of homes. This brings to light a gap in the literature on evaporative coolers, which is the lack of data on health effects associated with their use.
Collapse
Affiliation(s)
| | | | - K. Scott Weber
- Department of Microbiology & Molecular BiologyBrigham Young UniversityProvoUtahUSA
| |
Collapse
|
34
|
Ruuskanen MO, Vats D, Potbhare R, RaviKumar A, Munukka E, Ashma R, Lahti L. Towards standardized and reproducible research in skin microbiomes. Environ Microbiol 2022; 24:3840-3860. [PMID: 35229437 PMCID: PMC9790573 DOI: 10.1111/1462-2920.15945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 12/30/2022]
Abstract
Skin is a complex organ serving a critical role as a barrier and mediator of interactions between the human body and its environment. Recent studies have uncovered how resident microbial communities play a significant role in maintaining the normal healthy function of the skin and the immune system. In turn, numerous host-associated and environmental factors influence these communities' composition and diversity across the cutaneous surface. In addition, specific compositional changes in skin microbiota have also been connected to the development of several chronic diseases. The current era of microbiome research is characterized by its reliance on large data sets of nucleotide sequences produced with high-throughput sequencing of sample-extracted DNA. These approaches have yielded new insights into many previously uncharacterized microbial communities. Application of standardized practices in the study of skin microbial communities could help us understand their complex structures, functional capacities, and health associations and increase the reproducibility of the research. Here, we overview the current research in human skin microbiomes and outline challenges specific to their study. Furthermore, we provide perspectives on recent advances in methods, analytical tools and applications of skin microbiomes in medicine and forensics.
Collapse
Affiliation(s)
- Matti O. Ruuskanen
- Department of Computing, Faculty of TechnologyUniversity of TurkuTurkuFinland
| | - Deepti Vats
- Department of Zoology, Centre of Advanced StudySavitribai Phule Pune UniversityPuneIndia
| | - Renuka Potbhare
- Department of Zoology, Centre of Advanced StudySavitribai Phule Pune UniversityPuneIndia
| | - Ameeta RaviKumar
- Institute of Bioinformatics and BiotechnologySavitribai Phule Pune UniversityPuneIndia
| | - Eveliina Munukka
- Microbiome Biobank, Institute of BiomedicineUniversity of TurkuTurkuFinland
| | - Richa Ashma
- Department of Zoology, Centre of Advanced StudySavitribai Phule Pune UniversityPuneIndia
| | - Leo Lahti
- Department of Computing, Faculty of TechnologyUniversity of TurkuTurkuFinland
| |
Collapse
|
35
|
The Skin Microbiome in Cutaneous T-Cell Lymphomas (CTCL)—A Narrative Review. Pathogens 2022; 11:pathogens11080935. [PMID: 36015055 PMCID: PMC9414712 DOI: 10.3390/pathogens11080935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/10/2022] [Accepted: 08/16/2022] [Indexed: 12/02/2022] Open
Abstract
In recent years, numerous studies have shown a significant role of the skin microbiome in the development and exacerbation of skin diseases. Cutaneous T-cell lymphomas (CTCL) are a group of malignancies primary involving skin, with unclear pathogenesis and etiology. As external triggers appear to contribute to chronic skin inflammation and the malignant transformation of T-cells, some microorganisms or dysbiosis may be involved in these processes. Recently, studies analyzing the skin microbiome composition and diversity have been willingly conducted in CTCL patients. In this review, we summarize currently available data on the skin microbiome in CTLC. We refer to a healthy skin microbiome and the contribution of microorganisms in the pathogenesis and progression of other skin diseases, focusing on atopic dermatitis and its similarities to CTCL. Moreover, we present information about the possible role of identified microorganisms in CTCL development and progression. Additionally, we summarize information about the involvement of Staphylococcus aureus in CTCL pathogenesis. This article also presents therapeutic options used in CTCL and discusses how they may influence the microbiome.
Collapse
|
36
|
Veile A, Christopher L, Azcorra H, Dickinson F, Kramer K, Varela‐Silva I. Differences in nutritional status between rural and urban Yucatec Maya children: The importance of early life conditions. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2022. [PMCID: PMC9314705 DOI: 10.1002/ajpa.24510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Early‐life conditions shape childhood growth and are affected by urbanization and the nutritional transition. To investigate how early‐life conditions (across the “first” and “second” 1000 days) are associated with rural and urban children's nutritional status, we analyzed anthropometric data from Maya children in Yucatan, Mexico. We collected weight, height and triceps skinfold measures, then computed body mass and fat mass indices (BMI/FMI), in a cross‐sectional sample of 6‐year‐olds (urban n = 72, rural n = 66). Demographic, socioeconomic and early‐life variables (birthweight/mode, rural/urban residence, household crowding) were collected by maternal interview. We statistically analyzed rural‐urban differences in demographic, socioeconomic, early‐life, and anthropometric variables, then created linear mixed models to evaluate associations between early‐life variables and child anthropometric outcomes. Two‐way interactions were tested between early‐life variables and child sex, and between early‐life variables and rural‐urban residence. Results showed that rural children were shorter‐statured, with lower overweight/obesity and cesarean delivery rates, compared to urban children. Household crowding was a negative predictor of anthropometric outcomes; the strongest effect was in boys and in urban children. Birthweight positively predicted anthropometric outcomes, especially weight/BMI. Birth mode was positively (not statistically) associated with any anthropometric outcome. Cesarean delivery was more common in boys than in girls, and predicted increased height in urban boys. In conclusion, urbanization and household crowding were the most powerful predictors of Maya 6‐year‐old anthropometry. The negative effects of crowding may disproportionately affect Maya boys versus girls and urban versus rural children. Early‐life conditions shape Maya children's nutritional status both in the “first” and “second” 1000 days.
Collapse
Affiliation(s)
- Amanda Veile
- Department of Anthropology Purdue University West Lafayette Indiana USA
| | | | - Hugo Azcorra
- Centro de Investigaciones Silvio Zavala Universidad Modelo Mérida Mexico
| | - Federico Dickinson
- Departamento de Ecología Humana Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Mérida Mexico
| | - Karen Kramer
- Department of Anthropology University of Utah Salt Lake City Utah USA
| | - Inês Varela‐Silva
- Departamento de Ecología Humana Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Mérida Mexico
- School of Sport, Exercise and Health Sciences Loughborough University Loughborough UK
| |
Collapse
|
37
|
Kong YS, Ren HY, Liu R, da Silva RR, Aksenov AA, Melnik AV, Zhao M, Le MM, Ren ZW, Xu FQ, Yan XW, Yu LJ, Zhou Y, Xie ZW, Li DX, Wan XC, Long YH, Xu ZZ, Ling TJ. Microbial and Nonvolatile Chemical Diversities of Chinese Dark Teas Are Differed by Latitude and Pile Fermentation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:5701-5714. [PMID: 35502792 DOI: 10.1021/acs.jafc.2c01005] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Understanding the microbial and chemical diversities, as well as what affects these diversities, is important for modern manufacturing of traditional fermented foods. In this work, Chinese dark teas (CDTs) that are traditional microbial fermented beverages with relatively high sample diversity were collected. Microbial DNA amplicon sequencing and mass spectrometry-based untargeted metabolomics show that the CDT microbial β diversity, as well as the nonvolatile chemical α and β diversities, is determined by the primary impact factors of geography and manufacturing procedures, in particular, latitude and pile fermentation after blending. A large number of metabolites sharing between CDTs and fungi were discovered by Feature-based Molecular Networking (FBMN) on the Global Natural Products Social Molecular Networking (GNPS) web platform. These molecules, such as prenylated cyclic dipeptides and B-vitamins, are functionally important for nutrition, biofunctions, and flavor. Molecular networking has revealed patterns in metabolite profiles on a chemical family level in addition to individual structures.
Collapse
Affiliation(s)
- Ya-Shuai Kong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, Anhui, P. R. China
- School of Tea Science, Xinyang Agriculture and Forestry University, Xinyang 464000, Henan, P. R. China
| | - Hong-Yu Ren
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, Anhui, P. R. China
| | - Rui Liu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, Anhui, P. R. China
| | - Ricardo R da Silva
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Av. do Café─Vila Monte Alegre, Ribeirão Preto, São Paulo 14040-903, Brazil
| | - Alexander A Aksenov
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Alexey V Melnik
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Ming Zhao
- College of Tea Science, Yunnan Agricultural University, Kunming 100191, Yunnan, P. R. China
| | - Miao-Miao Le
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, Anhui, P. R. China
| | - Zhi-Wei Ren
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, Anhui, P. R. China
| | - Feng-Qing Xu
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei 230038, P. R. China
| | - Xiao-Wei Yan
- Guangxi Key Laboratory of Calcium Carbonate Resources Comprehensive Utilization, Hezhou University, Hezhou 542899, P. R. China
| | - Li-Jun Yu
- Key Laboratory of Tea Science of Ministry of Education, National Research Center of Engineering Technology for Utilization of Functional Ingredients from Botanicals, College of Horticulture, Hunan Agricultural University, Changsha 410128, P. R. China
| | - Yu Zhou
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, Anhui, P. R. China
| | - Zhong-Wen Xie
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, Anhui, P. R. China
- International Joint Laboratory on Tea Chemistry and Health Effects of Ministry of Education, Anhui Agricultural University, Hefei 230036, Anhui, P. R. China
| | - Da-Xiang Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, Anhui, P. R. China
- International Joint Laboratory on Tea Chemistry and Health Effects of Ministry of Education, Anhui Agricultural University, Hefei 230036, Anhui, P. R. China
| | - Xiao-Chun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, Anhui, P. R. China
- International Joint Laboratory on Tea Chemistry and Health Effects of Ministry of Education, Anhui Agricultural University, Hefei 230036, Anhui, P. R. China
| | - Yan-Hua Long
- School of Life Sciences, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, Anhui, P. R. China
| | - Zhenjiang Zech Xu
- State Key Laboratory of Food Science and Technology, Institute of Nutrition and College of Food Science and Technology, Nanchang University, 235 Nanjing East Road, Nanchang 330047, Jiangxi, P. R. China
| | - Tie-Jun Ling
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, Anhui, P. R. China
- International Joint Laboratory on Tea Chemistry and Health Effects of Ministry of Education, Anhui Agricultural University, Hefei 230036, Anhui, P. R. China
| |
Collapse
|
38
|
Naspolini NF, Meyer A, Moreira JC, Sun H, Froes-Asmus CIR, Dominguez-Bello MG. Environmental pollutant exposure associated with altered early-life gut microbiome: Results from a birth cohort study. ENVIRONMENTAL RESEARCH 2022; 205:112545. [PMID: 34896087 DOI: 10.1016/j.envres.2021.112545] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
Emerging evidence shows that the gut microbiota interacts with environmental pollutants, but the effect of early exposure on the neonatal microbiome remains unknown. We investigated the association between maternal exposure to environmental pollutants and changes in early-life gut microbiome development. We surveyed 16S rRNA gene on meconium and fecal samples (at 1, 3, and 6 months) from the Brazilian birth cohort, and associated with levels of metals, perfluoroalkyl chemicals (PFAS), and pesticides in maternal and umbilical cord blood. The results indicate that the magnitude of the microbiome changes associated with increasing pollutant exposure was bigger in cesarean-section (CS) born and CS-born-preterm babies, in relation to vaginally (VG) delivered infants. Breastfeeding was associated with a stronger pollutant-associated effect on the infant feces, suggesting that the exposure source could be maternal milk. Differences in microbiome effects associated with maternal or cord blood pollutant concentrations suggest that fetal exposure time - intrauterine or perinatal - may matter. Finally, despite the high developmental microbiota variability, specific microbionts were consistently affected across all pollutants, with taxa clusters found in samples from infants exposed to the highest toxicant exposure. The results evidence that perinatal exposure to environmental pollutants is associated with alterations in gut microbiome development which may have health significance.
Collapse
Affiliation(s)
- Nathalia F Naspolini
- National School of Public Health Sergio Arouca, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil.
| | - Armando Meyer
- Institute of Public Health Studies, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Josino C Moreira
- Center for the Studies on Workers' Health and Human Ecology, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Haipeng Sun
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA
| | - Carmen I R Froes-Asmus
- School Maternity Hospital, School of Medicine, Federal University of Rio de Janeiro, Laranjeiras Street, 180, Rio de Janeiro, 22240-000, Brazil
| | | |
Collapse
|
39
|
Peimbert M, Alcaraz LD. Where environmental microbiome meets its host: subway and passenger microbiome relationships. Mol Ecol 2022; 32:2602-2618. [PMID: 35318755 DOI: 10.1111/mec.16440] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 03/12/2022] [Accepted: 03/16/2022] [Indexed: 12/17/2022]
Abstract
Subways are urban transport systems with high capacity. Every day around the world, there are more than 150 million subway passengers. Since 2013, thousands of microbiome samples from various subways worldwide have been sequenced. Skin bacteria and environmental organisms dominate the subway microbiomes. The literature has revealed common bacterial groups in subway systems; even so, it is possible to identify cities by their microbiome. Low-frequency bacteria are responsible for specific bacterial fingerprints of each subway system. Furthermore, daily subway commuters leave their microbial clouds and interact with other passengers. Microbial exchange is quite fast; the hand microbiome changes within minutes, and after cleaning the handrails, the bacteria are re-established within minutes. To investigate new taxa and metabolic pathways of subway microbial communities, several high-quality metagenomic-assembled genomes (MAG) have been described. Subways are harsh environments unfavorable for microorganism growth. However, recent studies have observed a wide diversity of viable and metabolically active bacteria. Understanding which bacteria are living, dormant, or dead allows us to propose realistic ecological interactions. Questions regarding the relationship between humans and the subway microbiome, particularly the microbiome effects on personal and public health, remain unanswered. This review summarizes our knowledge of subway microbiomes and their relationship with passenger microbiomes.
Collapse
Affiliation(s)
- Mariana Peimbert
- Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autónoma Metropolitana. Ciudad de México, México
| | - Luis D Alcaraz
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México
| |
Collapse
|
40
|
Potbhare R, RaviKumar A, Munukka E, Lahti L, Ashma R. Skin microbiota diversity among genetically unrelated individuals of Indian origin. PeerJ 2022; 10:e13075. [PMID: 35313523 PMCID: PMC8934042 DOI: 10.7717/peerj.13075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 02/16/2022] [Indexed: 01/12/2023] Open
Abstract
Background Human skin harbors complex transient and resident microbial communities that show intra- & inter-individual variation due to various environmental and host-associated factors such as skin site, diet, age, gender, genetics, or the type and use of cosmetics. This variation remains largely uncharacterized in the Indian population; hence, the present study aims to characterize the variation in skin microbiota among individuals of Indian origin and quantify associations with age, diet, and geography. Methods Axillary sweat samples from genetically unrelated individuals (N = 58) residing in the three geographical locations of Maharashtra, India, were collected using a sterile cotton swab. Bacterial DNA was extracted using a standard protocol and checked for quality. Variable regions (V3-V4) of the 16S rRNA gene were sequenced using the Illumina platform. We used standard methods from microbiota bioinformatics, including alpha and beta diversity, community typing, and differential abundance, to quantify the association of skin microbiota with age, diet, and geographical location. Results Our study indicated the prevalence of phyla- Firmicutes, Proteobacteria, and Actinobacteria, consistent with previous reports on skin microbiota composition of the world population level. The alpha diversity (Shannon index) was significantly associated with the age group (Kruskal-Wallis test, p = 0.02), but not with geography (p = 0.62) or diet (p = 0.74). The overall skin microbiota community composition was significantly associated with geographical location based on Community State Types (CST) analysis and PERMANOVA (R2 = 0.07, p = 0.01). Differential abundance analysis at the genus level indicated a distinctively high abundance of Staphylococcus and Corynebacterium among individuals of the Pune district. Pseudomonas and Anaerococcus were abundant in individuals from Ahmednagar whereas, Paenibacillus, Geobacillus, Virgibacillus, Jeotgalicoccus, Pullulanibacillus, Delsulfosporomusa, Citinovibrio, and Calditerricola were abundant in individuals from Nashik district. Conclusion Our work provides one of the first characterizations of skin microbiota variation in different sub-populations in India. The analysis quantifies the level of individuality, as contrasted to the other factors of age, geography, and diet, thus helping to evaluate the applicability of skin microbiota profiles as a potential biomarker to stratify individuals.
Collapse
Affiliation(s)
- Renuka Potbhare
- Department of Zoology, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Ameeta RaviKumar
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Eveliina Munukka
- Microbiome Biobank, Institute of Biomedicine, University of Turku, Turku, Finland,Biocodex Nordics, Finland
| | - Leo Lahti
- Department of Computing, Faculty of Technology, University of Turku, Turku, Finland
| | - Richa Ashma
- Department of Zoology, Savitribai Phule Pune University, Pune, Maharashtra, India
| |
Collapse
|
41
|
Abstract
Healthy development and function of essentially all physiological systems and organs, including the brain, require exposure to the microbiota of our mothers and of the natural environment, especially in early life. We also know that some infections, if we survive them, modulate the immune system in relevant ways. If we study the evolution of the immune and metabolic systems, we can understand how these requirements developed and the nature of the organisms that we need to encounter. We can then begin to identify the mechanisms of the beneficial effects of these exposures. Against this evolutionary background, we can analyze the ways in which the modern urban lifestyle, particularly for individuals experiencing low socioeconomic status (SES), results in deficient or distorted microbial exposures and microbiomes. Thus, an evolutionary approach facilitates the identification of practical solutions to the growing scandal of health disparities linked to inequality.
Collapse
|
42
|
Katemauswa M, Hossain E, Liu Z, Lesani M, Parab AR, Dean DA, McCall LI. Enabling Quantitative Analysis of Surface Small Molecules for Exposomics and Behavioral Studies. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:412-419. [PMID: 35084848 DOI: 10.1021/jasms.1c00263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Workplace chemical exposures are a major source of occupational injury. Although over half of these are skin exposures, exposomics research often focuses on chemical levels in the air or in worker biofluids such as blood and urine. Until now, one limitation has been the lack of methods to quantitatively measure surface chemical transfer. Outside the realm of harmful chemicals, the small molecules we leave behind on surfaces can also reveal important aspects of human behavior. In this study, we developed a swab-based quantitative approach to determine small molecule concentrations across common surfaces. We demonstrate its utility using one drug, cyclobenzaprine, on metal surfaces, and two human-derived metabolites, carnitine and phenylacetylglutamine, on four common surfaces: linoleum flooring, plastified laboratory workbench, metal, and Plexiglas. We observed peak areas proportional to surface analyte concentrations at 45 min and 1 week after deposition, enabling quantification of molecule abundance on workplace built environment surfaces. In contrast, this method was unsuitable for analysis of oleanolic acid, for which we did not observe a strong linear proportional relationship following swab-based recovery from surfaces. Overall, this method paves the way for future quantitative exposomics studies in analyte-specific and surface-specific frameworks.
Collapse
Affiliation(s)
- Mitchelle Katemauswa
- University of Oklahoma, Department of Chemistry and Biochemistry, Norman, Oklahoma 73019, United States
- University of Oklahoma, Laboratories of Molecular Anthropology and Microbiome Research, Norman, Oklahoma 73019, United States
| | - Ekram Hossain
- University of Oklahoma, Department of Chemistry and Biochemistry, Norman, Oklahoma 73019, United States
- University of Oklahoma, Laboratories of Molecular Anthropology and Microbiome Research, Norman, Oklahoma 73019, United States
| | - Zongyuan Liu
- University of Oklahoma, Department of Chemistry and Biochemistry, Norman, Oklahoma 73019, United States
- University of Oklahoma, Laboratories of Molecular Anthropology and Microbiome Research, Norman, Oklahoma 73019, United States
| | - Mahbobeh Lesani
- University of Oklahoma, Department of Microbiology and Plant Biology, Norman, Oklahoma 73019, United States
- University of Oklahoma, Laboratories of Molecular Anthropology and Microbiome Research, Norman, Oklahoma 73019, United States
| | - Adwaita R Parab
- University of Oklahoma, Department of Microbiology and Plant Biology, Norman, Oklahoma 73019, United States
- University of Oklahoma, Laboratories of Molecular Anthropology and Microbiome Research, Norman, Oklahoma 73019, United States
| | - Danya A Dean
- University of Oklahoma, Department of Chemistry and Biochemistry, Norman, Oklahoma 73019, United States
- University of Oklahoma, Laboratories of Molecular Anthropology and Microbiome Research, Norman, Oklahoma 73019, United States
| | - Laura-Isobel McCall
- University of Oklahoma, Department of Chemistry and Biochemistry, Norman, Oklahoma 73019, United States
- University of Oklahoma, Department of Microbiology and Plant Biology, Norman, Oklahoma 73019, United States
- University of Oklahoma, Laboratories of Molecular Anthropology and Microbiome Research, Norman, Oklahoma 73019, United States
| |
Collapse
|
43
|
Droz L, Jannel R, Rupprecht CDD. Living through multispecies societies: Approaching the microbiome with Imanishi Kinji. ENDEAVOUR 2022; 46:100814. [PMID: 35697549 DOI: 10.1016/j.endeavour.2022.100814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 09/03/2021] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
Recent research about the microbiome points to a picture in which we, humans, are 'living through' nature, and nature itself is living in us. Our bodies are hosting-and depend on-the multiple species that constitute human microbiota. This article will discuss current research on the microbiome through the ideas of Japanese ecologist Imanishi Kinji (1902-1992). First, some of Imanishi's key ideas regarding the world of living beings and multispecies societies are presented. Second, seven types of relationships concerning the human microbiome, human beings, and the environment are explored. Third, inspired by Imanishi's work, this paper develops the idea of dynamic, porous, and complex multispecies societies in which different living beings or species are codependent on others, including microbiota and human beings.
Collapse
Affiliation(s)
- Laÿna Droz
- Basque Center for Climate Change, Spain.
| | - Romaric Jannel
- Kyoto University, Institute for Research in Humanities, Japan.
| | - Christoph D D Rupprecht
- Ehime Daigaku, Faculty of Collaborative Regional Innovation, Department of Environmental Design, Matsuyama, Ehime, Japan.
| |
Collapse
|
44
|
Advances in Microbiome-Derived Solutions and Methodologies Are Founding a New Era in Skin Health and Care. Pathogens 2022; 11:pathogens11020121. [PMID: 35215065 PMCID: PMC8879973 DOI: 10.3390/pathogens11020121] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 12/04/2022] Open
Abstract
The microbiome, as a community of microorganisms and their structural elements, genomes, metabolites/signal molecules, has been shown to play an important role in human health, with significant beneficial applications for gut health. Skin microbiome has emerged as a new field with high potential to develop disruptive solutions to manage skin health and disease. Despite an incomplete toolbox for skin microbiome analyses, much progress has been made towards functional dissection of microbiomes and host-microbiome interactions. A standardized and robust investigation of the skin microbiome is necessary to provide accurate microbial information and set the base for a successful translation of innovations in the dermo-cosmetic field. This review provides an overview of how the landscape of skin microbiome research has evolved from method development (multi-omics/data-based analytical approaches) to the discovery and development of novel microbiome-derived ingredients. Moreover, it provides a summary of the latest findings on interactions between the microbiomes (gut and skin) and skin health/disease. Solutions derived from these two paths are used to develop novel microbiome-based ingredients or solutions acting on skin homeostasis are proposed. The most promising skin and gut-derived microbiome interventional strategies are presented, along with regulatory, safety, industrial, and technical challenges related to a successful translation of these microbiome-based concepts/technologies in the dermo-cosmetic industry.
Collapse
|
45
|
Fang H, Ma Z, Chen L, Xian R, Wang J, Chen J, Li H, Hu Y. Trends in the contributions of atopic family history to pediatric food sensitization and allergy. Front Pediatr 2022; 10:967930. [PMID: 36568419 PMCID: PMC9768553 DOI: 10.3389/fped.2022.967930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/08/2022] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE Family history of atopic diseases (FHA) contributes to food allergy (FA). But little is known whether FHA primarily increases IgE-mediated, non-IgE-mediated FA, or both. And the trends in the contributions of FHA to food sensitization (FS) and FA remain unclear. We aim to clarify the associations among FHA, FS and FA and to understand the trends in the contributions of FHA to FS and FA. METHODS We used chi-square test and mediating effect model to analyze the associations among FHA, FS and FA through comparisons between two cross-sectional investigations on FA in children under 2 years old in 2009 and 2019. RESULTS In 2009 and 2019, the positive FHA proportion tended to be increasing without significance (28.9% to 31.6%, P = 0.39). Subgroup analysis showed the FS rate in FA group decreased significantly (37/39 to 44/62, P = 0.003). In 2009, the FS rate and FA prevalence were higher in FHA (+) group than in FHA (-) group (26% vs. 14.7%, P = 0.008 and 15% vs. 7.7%, P = 0.03), and FS had a complete mediating effect on the association between FHA and FA (Z = 2.54, P = 0.011), but the results lost significance in 2019. CONCLUSIONS The association between FHA and FA was completely mediated by FS, which means FHA mainly increases IgE-mediated FA. And the contributions of FHA to FS and FA tended to be stabilized or even diminished, which means FHA alone could no longer be enough to screen high-risk children.
Collapse
Affiliation(s)
- Heping Fang
- Department of Child Health Care, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Health and Nutrition, Chongqing, China
| | - Zhuoying Ma
- Department of Child Health Care, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Health and Nutrition, Chongqing, China
| | - Lin Chen
- Department of Child Health Care, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Health and Nutrition, Chongqing, China
| | - Ruoling Xian
- Department of Child Health Care, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Health and Nutrition, Chongqing, China
| | - Juan Wang
- Department of Child Health Care, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Health and Nutrition, Chongqing, China
| | - Jing Chen
- Department of Child Health Care, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Health and Nutrition, Chongqing, China
| | - Haiqi Li
- Department of Child Health Care, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Health and Nutrition, Chongqing, China
| | - Yan Hu
- Department of Child Health Care, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Health and Nutrition, Chongqing, China
| |
Collapse
|
46
|
Jarmusch SA, van der Hooft JJJ, Dorrestein PC, Jarmusch AK. Advancements in capturing and mining mass spectrometry data are transforming natural products research. Nat Prod Rep 2021; 38:2066-2082. [PMID: 34612288 PMCID: PMC8667781 DOI: 10.1039/d1np00040c] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering: 2016 up to 2021Mass spectrometry (MS) is an essential technology in natural products research with MS fragmentation (MS/MS) approaches becoming a key tool. Recent advancements in MS yield dense metabolomics datasets which have been, conventionally, used by individual labs for individual projects; however, a shift is brewing. The movement towards open MS data (and other structural characterization data) and accessible data mining tools is emerging in natural products research. Over the past 5 years, this movement has rapidly expanded and evolved with no slowdown in sight; the capabilities of today vastly exceed those of 5 years ago. Herein, we address the analysis of individual datasets, a situation we are calling the '2021 status quo', and the emergent framework to systematically capture sample information (metadata) and perform repository-scale analyses. We evaluate public data deposition, discuss the challenges of working in the repository scale, highlight the challenges of metadata capture and provide illustrative examples of the power of utilizing repository data and the tools that enable it. We conclude that the advancements in MS data collection must be met with advancements in how we utilize data; therefore, we argue that open data and data mining is the next evolution in obtaining the maximum potential in natural products research.
Collapse
Affiliation(s)
- Scott A Jarmusch
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, DK-2800 Kongens Lyngby, Denmark.
| | | | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093-0751, USA
| | - Alan K Jarmusch
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093-0751, USA
- Immunity, Inflammation, and Disease Laboratory, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| |
Collapse
|
47
|
Foxx AJ, Franco Meléndez KP, Hariharan J, Kozik AJ, Wattenburger CJ, Godoy-Vitorino F, Rivers AR. Advancing Equity and Inclusion in Microbiome Research and Training. mSystems 2021; 6:e0115121. [PMID: 34636663 PMCID: PMC8510545 DOI: 10.1128/msystems.01151-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This article proposes ways to improve inclusion and training in microbiome science and advocates for resource expansion to improve scientific capacity across institutions and countries. Specifically, we urge mentors, collaborators, and decision-makers to commit to inclusive and accessible research and training that improves the quality of microbiome science and begins to rectify long-standing inequities imposed by wealth disparities and racism that stall scientific progress.
Collapse
Affiliation(s)
- Alicia J. Foxx
- U.S. Department of Agriculture, Agricultural Research Service, Gainesville, Florida, USA
| | | | | | | | | | | | - Adam R. Rivers
- U.S. Department of Agriculture, Agricultural Research Service, Gainesville, Florida, USA
| |
Collapse
|
48
|
Misra N, Clavaud C, Guinot F, Bourokba N, Nouveau S, Mezzache S, Palazzi P, Appenzeller BMR, Tenenhaus A, Leung MHY, Lee PKH, Bastien P, Aguilar L, Cavusoglu N. Multi-omics analysis to decipher the molecular link between chronic exposure to pollution and human skin dysfunction. Sci Rep 2021; 11:18302. [PMID: 34526566 PMCID: PMC8443591 DOI: 10.1038/s41598-021-97572-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 08/03/2021] [Indexed: 12/24/2022] Open
Abstract
Environmental pollution is composed of several factors, namely particulate matter (PM2.5, PM10), ozone and Ultra Violet (UV) rays among others and first and the most exposed tissue to these substances is the skin epidermis. It has been established that several skin disorders such as eczema, acne, lentigines and wrinkles are aggravated by exposure to atmospheric pollution. While pollutants can interact with skin surface, contamination of deep skin by ultrafine particles or Polycyclic aromatic hydrocarbons (PAH) might be explained by their presence in blood and hair cortex. Molecular mechanisms leading to skin dysfunction due to pollution exposure have been poorly explored in humans. In addition to various host skin components, cutaneous microbiome is another target of these environment aggressors and can actively contribute to visible clinical manifestation such as wrinkles and aging. The present study aimed to investigate the association between pollution exposure, skin microbiota, metabolites and skin clinical signs in women from two cities with different pollution levels. Untargeted metabolomics and targeted proteins were analyzed from D-Squame samples from healthy women (n = 67 per city), aged 25-45 years and living for at least 15 years in the Chinese cities of Baoding (used as a model of polluted area) and Dalian (control area with lower level of pollution). Additional samples by swabs were collected from the cheeks from the same population and microbiome was analysed using bacterial 16S rRNA as well as fungal ITS1 amplicon sequencing and metagenomics analysis. The level of exposure to pollution was assessed individually by the analysis of polycyclic aromatic hydrocarbons (PAH) and their metabolites in hair samples collected from each participant. All the participants of the study were assessed for the skin clinical parameters (acne, wrinkles, pigmented spots etc.). Women from the two cities (polluted and less polluted) showed distinct metabolic profiles and alterations in skin microbiome. Profiling data from 350 identified metabolites, 143 microbes and 39 PAH served to characterize biochemical events that correlate with pollution exposure. Finally, using multiblock data analysis methods, we obtained a potential molecular map consisting of multi-omics signatures that correlated with the presence of skin pigmentation dysfunction in individuals living in a polluted environment. Overall, these signatures point towards macromolecular alterations by pollution that could manifest as clinical sign of early skin pigmentation and/or other imperfections.
Collapse
Affiliation(s)
- Namita Misra
- Research and Innovation, L'Oréal SA, Aulnay Sous Bois, France.
| | - Cécile Clavaud
- Research and Innovation, L'Oréal SA, Aulnay Sous Bois, France
| | - Florent Guinot
- Research and Innovation, L'Oréal SA, Aulnay Sous Bois, France
| | | | | | - Sakina Mezzache
- Research and Innovation, L'Oréal SA, Aulnay Sous Bois, France
| | - Paul Palazzi
- Human Biomonitoring Research Unit, Luxembourg Institute of Health, Strassen, Luxemburg
| | - Brice M R Appenzeller
- Human Biomonitoring Research Unit, Luxembourg Institute of Health, Strassen, Luxemburg
| | - Arthur Tenenhaus
- CentraleSupelec Laboratoire des Signaux et Systemes, Université Paris-Saclay, CNRS, Gif-sur-Yvette, France
- Brain and Spine Institute, Paris, France
| | - Marcus H Y Leung
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | | | - Luc Aguilar
- Research and Innovation, L'Oréal SA, Aulnay Sous Bois, France
| | | |
Collapse
|
49
|
Kuthyar S, Reese AT. Variation in Microbial Exposure at the Human-Animal Interface and the Implications for Microbiome-Mediated Health Outcome. mSystems 2021; 6:e0056721. [PMID: 34342530 PMCID: PMC8407385 DOI: 10.1128/msystems.00567-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The human gut microbiome varies between populations, largely reflecting ecological differences. One ecological variable that is rarely considered but may contribute substantially to microbiome variation is the multifaceted nature of human-animal interfaces. We present the hypothesis that different interactions with animals contribute to shaping the human microbiome globally. We utilize a One Health framework to explore how changes in microbial exposure from human-animal interfaces shape the microbiome and, in turn, contribute to differential human health across populations, focusing on commensal and pathogen exposure, changes in colonization resistance and immune system training, and the potential for other functional shifts. Although human-animal interfaces are known to underlie human health and particularly infectious disease disparities, since their impact on the human microbiome remains woefully understudied, we propose foci for future research. We believe it will be crucial to understand this critical aspect of biology and its impacts on human health around the globe.
Collapse
Affiliation(s)
- Sahana Kuthyar
- Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | - Aspen T. Reese
- Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
| |
Collapse
|
50
|
Alenius H, Sinkko H, Moitinho-Silva L, Rodriguez E, Broderick C, Alexander H, Reiger M, Hjort Hjelmsø M, Fyhrquist N, Olah P, Bryce P, Smith C, Koning F, Eyerich K, Greco D, van den Bogaard EH, Neumann AU, Traidl-Hoffmann C, Homey B, Flohr C, Bønnelykke K, Stokholm J, Weidinger S. The power and potential of BIOMAP to elucidate host-microbiome interplay in skin inflammatory diseases. Exp Dermatol 2021; 30:1517-1531. [PMID: 34387406 DOI: 10.1111/exd.14446] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 07/02/2021] [Accepted: 08/02/2021] [Indexed: 11/27/2022]
Abstract
The two most common chronic inflammatory skin diseases are atopic dermatitis (AD) and psoriasis. The underpinnings of the remarkable degree of clinical heterogeneity of AD and psoriasis are poorly understood and, as a consequence, disease onset and progression are unpredictable and the optimal type and time-point for intervention are as yet unknown. The BIOMAP project is the first IMI (Innovative Medicines Initiative) project dedicated to investigating the causes and mechanisms of AD and psoriasis and to identify potential biomarkers responsible for the variation in disease outcome. The consortium includes 7 large pharmaceutical companies and 25 non-industry partners including academia. Since there is mounting evidence supporting an important role for microbial exposures and our microbiota as factors mediating immune polarization and AD and psoriasis pathogenesis, an entire work package is dedicated to the investigation of skin and gut microbiome linked to AD or psoriasis. The large collaborative BIOMAP project will enable the integration of patient cohorts, data and knowledge in unprecedented proportions. The project has a unique opportunity with a potential to bridge and fill the gaps between current problems and solutions. This review highlights the power and potential of BIOMAP project in the investigation of microbe-host interplay in AD and psoriasis.
Collapse
Affiliation(s)
- Harri Alenius
- Institute of Environmental Medicine, Karolinska Institutet, Box 210, 171 77, Stockholm, Sweden.,Human Microbiome Research Program (HUMI), Faculty of Medicine, University of Helsinki, Finland
| | - Hanna Sinkko
- Institute of Environmental Medicine, Karolinska Institutet, Box 210, 171 77, Stockholm, Sweden.,Human Microbiome Research Program (HUMI), Faculty of Medicine, University of Helsinki, Finland
| | - Lucas Moitinho-Silva
- Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany.,Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Elke Rodriguez
- Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Conor Broderick
- Unit for Population-Based Dermatology Research, St John's Institute of Dermatology, Guy's and St Thomas' NHS Foundation Trust and King's College London, London, UK
| | - Helen Alexander
- Unit for Population-Based Dermatology Research, St John's Institute of Dermatology, Guy's and St Thomas' NHS Foundation Trust and King's College London, London, UK
| | - Matthias Reiger
- Department of Environmental Medicine, Faculty of Medicine, University of Augsburg, Augsburg, Germany.,Institute of Environmental Medicine, Helmholtz Zentrum München, Augsburg, Germany.,Chair of Environmental Medicine, Technical University Munich, Munich, Germany
| | - Mathis Hjort Hjelmsø
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Nanna Fyhrquist
- Institute of Environmental Medicine, Karolinska Institutet, Box 210, 171 77, Stockholm, Sweden
| | - Peter Olah
- Department of Dermatology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany.,Department of Dermatology, Venereology and Oncodermatology, Medical Faculty, University of Pécs, Hungary
| | - Paul Bryce
- Type 2 Inflammation & Fibrosis Cluster, Immunology & Inflammation Therapeutic Area, Sanofi US, Cambridge, MA, United States of America
| | - Catherine Smith
- St John's Institute of Dermatology, Kings College London, and Guys and St Thomas' NHS Foundation Trust, 9th Floor, Tower Wing, Guy's Hospital, Great Maze Pond, London, SE1 9RT, UK
| | - Frits Koning
- Department of Immunology, Leiden University Medical Centre (LUMC), Leiden, the Netherlands
| | - Kilian Eyerich
- Department of Medicine, Karolinska Institutet, Solna, Sweden
| | - Dario Greco
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.,Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Ellen H van den Bogaard
- Department of Dermatology, Radboud university medical center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Avidan U Neumann
- Department of Environmental Medicine, Faculty of Medicine, University of Augsburg, Augsburg, Germany.,Institute of Environmental Medicine, Helmholtz Zentrum München, Augsburg, Germany
| | - Claudia Traidl-Hoffmann
- Department of Environmental Medicine, Faculty of Medicine, University of Augsburg, Augsburg, Germany.,Institute of Environmental Medicine, Helmholtz Zentrum München, Augsburg, Germany.,Chair of Environmental Medicine, Technical University Munich, Munich, Germany.,CK CARE, Christine Kühne Center for Allergy Research and Education, Davos, Switzerland.,ZIEL - Institute for Food & Health, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Bernhard Homey
- Department of Dermatology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Carsten Flohr
- Unit for Population-Based Dermatology Research, St John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, London, United Kingdom
| | - Klaus Bønnelykke
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Jakob Stokholm
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark.,Department of Food Science, University of Copenhagen, Frederiksberg, Denmark
| | - Stephan Weidinger
- Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| |
Collapse
|