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Zhou ZZ, Zhu J, Yin Y, Ding LJ. Seasonal variations of profiles of antibiotic resistance genes and virulence factor genes in household dust from Beijing, China revealed by the metagenomics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 928:172542. [PMID: 38636860 DOI: 10.1016/j.scitotenv.2024.172542] [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: 01/10/2024] [Revised: 04/09/2024] [Accepted: 04/15/2024] [Indexed: 04/20/2024]
Abstract
Household-related microbiome is closely related with human health. However, the knowledge about profiles of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) which are carried by microbes inside homes and their temporal dynamics are rather limited. Here we monitored the seasonal changes of bacterial community (especially pathogenic bacteria), ARGs, and VFGs in household dust samples during two years. Based on metagenomic sequencing, the dust-related bacterial pathogenic community, ARGs, and VFGs all harbored the lowest richness in spring among four seasons. Their structure (except that of VFGs) also exhibited remarkable differences among the seasons. The structural variations of ARGs and VFGs were almost explained by mobile genetic elements (MGEs), bacterial pathogens, and particulate matter-related factors, with MGEs explaining the most. Moreover, the total normalized abundance of ARGs or VFGs showed no significant change across the seasons. Results of metagenomic binning and microbial network both showed that several pathogenic taxa (e.g., Ralstonia pickettii) were strongly linked with numerous ARGs (mainly resistant to multidrug) and VFGs (mainly encoding motility) simultaneously. Overall, these findings underline the significance of MGEs in structuring ARGs and VFGs inside homes along with seasonal variations, suggesting that household dust is a neglected reservoir for ARGs and VFGs.
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Affiliation(s)
- Zhi-Zi Zhou
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Jasmine Zhu
- School of Journalism and Communication, Tsinghua University, Beijing 100084, China
| | - Yue Yin
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Long-Jun Ding
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.
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2
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Ma L, Zhang H, Jia Q, Bai T, Yang S, Wang M, Li Y, Shao L. Facial Physiological Characteristics and Skin Microbiomes Changes are Associated with Body Mass Index (BMI). Clin Cosmet Investig Dermatol 2024; 17:513-528. [PMID: 38463558 PMCID: PMC10921894 DOI: 10.2147/ccid.s447412] [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: 10/31/2023] [Accepted: 02/22/2024] [Indexed: 03/12/2024]
Abstract
Background Overweight and obesity have become public health problems worldwide. An increasing number of research works are focusing on skin physiology and the manifestations of obesity-associated skin diseases, but little is known about the correlations between body mass index (BMI), facial skin physiological parameters, and the facial skin microbiome in healthy women. Objective To investigate the correlations between BMI, facial skin physiological parameters and facial bacteria and fungi in 198 women aged 18 to 35 years in Shanghai. Methods According to the international BMI standard and Chinese reference standard, subjects were divided into three groups, "lean" B1, "normal" B2 and "overweight" B3, and the physiological parameters of facial skin were measured by non-invasive instrumental methods, and the skin microbiota was analyzed by 16S rRNA and ITS high-throughput sequencing. Results Compared with the skin physiological parameters of the normal group, those of the overweight group exhibited a significant increase in trans-epidermal water loss (TEWL), which indicated that the skin barrier was impaired. The skin haemoglobin content was significantly increased, and skin surface pH was significant decreased in those with a high BMI. Furthermore, α-diversity, analysed using the Shannon, Chao, Sobs, and Ace indexes, was increased in the overweight group, suggesting that the diversity and species abundance of facial bacterial and fungal microbiota were also increased. Moreover, the overweight group had higher abundances of Streptococcus, Corynebacterium, Malassezia, and Candida. Notably, skin surface pH was significantly and negatively correlated with the relative abundances of Malassezia, Candida, and Cladosporium. Besides, the abundance of Malassezia was positively associated with the abundances of Staphylococcus and Corynebacterium. Conclusion These results indicate that BMI is associated with differences in the biophysical properties and microbiome of the facial skin. A high BMI affects the integrity of skin barrier and changes the skin flora diversity and species composition.
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Affiliation(s)
- Laiji Ma
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, People's Republic of China
| | - Huan Zhang
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, People's Republic of China
| | - Qingwen Jia
- R&D Innovation Center, Shandong Freda Biotech Co., Ltd., Jinan, Shandong, People's Republic of China
| | - Tianming Bai
- R&D Innovation Center, Shandong Freda Biotech Co., Ltd., Jinan, Shandong, People's Republic of China
| | - Suzhen Yang
- R&D Innovation Center, Shandong Freda Biotech Co., Ltd., Jinan, Shandong, People's Republic of China
| | - Man Wang
- Department of Nutrition, Shanghai Jiao Tong University Affiliated Sixth People's Hospital South Campus, Shanghai, People's Republic of China
| | - Yan Li
- R&D Innovation Center, Shandong Freda Biotech Co., Ltd., Jinan, Shandong, People's Republic of China
| | - Li Shao
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, People's Republic of China
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3
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Ghosh A, Panda S. Cutaneous Dysbiosis and Dermatophytosis: The Unexplored Link. Indian J Dermatol 2023; 68:508-514. [PMID: 38099124 PMCID: PMC10718259 DOI: 10.4103/ijd.ijd_828_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023] Open
Abstract
The skin, besides being the largest interface between the body and the external environment, also forms an ecological niche which is populated by almost a trillion microorganisms. These, collectively known as the cutaneous microbiome, form a dynamic yet well-controlled system that resists invasion by pathogenic microorganisms, functioning as the so-called 'microbiological barrier', modulating the body's immune response, indirectly playing a crucial role in the pathogenesis of several inflammatory diseases. The composition and complexity of the microbiome are yet to be fully understood. The term 'dysbiosis' originally was coined in 1908 for a change in the gut microbiome. The potential role of 'cutaneous dysbiosis' in human dermatophytic infections, especially in the backdrop of the current epidemic of chronic, recurrent and treatment-resistant dermatophytosis, is understandably a topic of interest. The purpose of this review was to assess all studies using culture-independent methods for analysing the skin microbiome in various dermatophyte infections. The PubMed and Google Scholar databases were searched using the terms 'microbiome', 'dysbiosis', 'dermatophytes', 'dermatophytosis' and 'tinea'. All studies involving the use of standard sequencing methods for the study of the microbiome in various dermatophytoses were included. A total of four studies assessing the local skin microbiome associated with dermatophytic infections were found-one for tinea capitis, one for onychomycosis (in both psoriatic and nonpsoriatic nails) and two studying patients of tinea pedis. The studies determined the microbiological patterns in patients and compared them with healthy individuals using sequencing methods. Significant differences in the species diversity and counts of the various microorganisms between patient and control groups were demonstrated in all. However, cross-sectional design and the absence of pre- and post-treatment data along with a limited sample size were the major limitations in all of them. No data regarding other forms of tinea, most importantly, tinea cruris, corporis, faciei, etc. were found. The existing studies demonstrate a change in the microbiome or dysbiosis associated with cases of dermatophytosis, but are inadequate to determine a causal association. The changes may also be wholly or partly attributed to the effect of the infection. Further longitudinal studies from different regions of the world, also involving other forms of dermatophytosis, are required to provide a clearer insight and a more representative picture.
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Affiliation(s)
- Aparajita Ghosh
- From the Department of Dermatology, K.P.C Medical College and Hospital, Kolkata, West Bengal, India
| | - Saumya Panda
- Department of Dermatology, JIMS Hospital and Medical College, Kolkata, West Bengal, India
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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.
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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
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Shen K, Din AU, Sinha B, Zhou Y, Qian F, Shen B. Translational informatics for human microbiota: data resources, models and applications. Brief Bioinform 2023; 24:7152256. [PMID: 37141135 DOI: 10.1093/bib/bbad168] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 04/07/2023] [Accepted: 04/11/2023] [Indexed: 05/05/2023] Open
Abstract
With the rapid development of human intestinal microbiology and diverse microbiome-related studies and investigations, a large amount of data have been generated and accumulated. Meanwhile, different computational and bioinformatics models have been developed for pattern recognition and knowledge discovery using these data. Given the heterogeneity of these resources and models, we aimed to provide a landscape of the data resources, a comparison of the computational models and a summary of the translational informatics applied to microbiota data. We first review the existing databases, knowledge bases, knowledge graphs and standardizations of microbiome data. Then, the high-throughput sequencing techniques for the microbiome and the informatics tools for their analyses are compared. Finally, translational informatics for the microbiome, including biomarker discovery, personalized treatment and smart healthcare for complex diseases, are discussed.
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Affiliation(s)
- Ke Shen
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, China
| | - Ahmad Ud Din
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, China
| | - Baivab Sinha
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, China
| | - Yi Zhou
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, China
| | - Fuliang Qian
- Center for Systems Biology, Suzhou Medical College of Soochow University, Suzhou 215123, China
- Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Suzhou 215123, China
| | - Bairong Shen
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, China
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6
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Hoisington AJ, Stamper CE, Bates KL, Stanislawski MA, Flux MC, Postolache TT, Lowry CA, Brenner LA. Human microbiome transfer in the built environment differs based on occupants, objects, and buildings. Sci Rep 2023; 13:6446. [PMID: 37081054 PMCID: PMC10116103 DOI: 10.1038/s41598-023-33719-6] [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: 01/20/2023] [Accepted: 04/18/2023] [Indexed: 04/22/2023] Open
Abstract
Compared to microbiomes on other skin sites, the bacterial microbiome of the human hand has been found to have greater variability across time. To increase understanding regarding the longitudinal transfer of the hand microbiome to objects in the built environment, and vice versa, 22 participants provided skin microbiome samples from their dominant hands, as well as from frequently and infrequently touched objects in their office environments. Additional longitudinal samples from home environments were obtained from a subset of 11 participants. We observed stability of the microbiomes of both the hand and built environments within the office and home settings; however, differences in the microbial communities were detected across the two built environments. Occupants' frequency of touching an object correlated to that object having a higher relative abundance of human microbes, yet the percent of shared microbes was variable by participants. Finally, objects that were horizontal surfaces in the built environment had higher microbial diversity as compared to objects and the occupants' hands. This study adds to the existing knowledge of microbiomes of the built environment, enables more detailed studies of indoor microbial transfer, and contributes to future models and building interventions to reduce negative outcomes and improve health and well-being.
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Affiliation(s)
- Andrew J Hoisington
- Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Rocky Mountain Regional Veterans Affairs Medical Center (RMRVAMC), VISN 19, Aurora, CO, 80045, USA.
- Department of Physical Medicine and Rehabilitation, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
- Military and Veteran Microbiome Consortium for Research and Education (MVM-CoRE), Aurora, CO, 80045, USA.
- Department of Systems Engineering and Management, US Air Force Institute of Technology, Wright-Patterson Air Force Base, OH, 45433, USA.
| | - Christopher E Stamper
- Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Rocky Mountain Regional Veterans Affairs Medical Center (RMRVAMC), VISN 19, Aurora, CO, 80045, USA
- Department of Physical Medicine and Rehabilitation, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
- Military and Veteran Microbiome Consortium for Research and Education (MVM-CoRE), Aurora, CO, 80045, USA
| | - Katherine L Bates
- Department of Biology, US Air Force Academy, USAF Academy, CO, 80840, USA
| | - Maggie A Stanislawski
- Department of Biomedical Informatics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
- Eastern Colorado Health Care System, Veterans Affairs, Denver, CO, 80220, USA
| | - Michael C Flux
- Department of Psychology and Center for Neuroscience, University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Teodor T Postolache
- Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Rocky Mountain Regional Veterans Affairs Medical Center (RMRVAMC), VISN 19, Aurora, CO, 80045, USA
- Military and Veteran Microbiome Consortium for Research and Education (MVM-CoRE), Aurora, CO, 80045, USA
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Veterans Health Administration, Mental Illness Research Education and Clinical Center (MIRECC), Baltimore VA Annex, VISN 5, Baltimore, MD, 21201, USA
| | - Christopher A Lowry
- Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Rocky Mountain Regional Veterans Affairs Medical Center (RMRVAMC), VISN 19, Aurora, CO, 80045, USA
- Department of Physical Medicine and Rehabilitation, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
- Military and Veteran Microbiome Consortium for Research and Education (MVM-CoRE), Aurora, CO, 80045, USA
- Department of Integrative Physiology and Center for Neuroscience, University of Colorado Boulder, Boulder, CO, 80309, USA
- Center for Microbial Exploration, University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Lisa A Brenner
- Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Rocky Mountain Regional Veterans Affairs Medical Center (RMRVAMC), VISN 19, Aurora, CO, 80045, USA
- Department of Physical Medicine and Rehabilitation, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
- Military and Veteran Microbiome Consortium for Research and Education (MVM-CoRE), Aurora, CO, 80045, USA
- Departments of Psychiatry and Neurology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
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The dynamic balance of the skin microbiome across the lifespan. Biochem Soc Trans 2023; 51:71-86. [PMID: 36606709 PMCID: PMC9988004 DOI: 10.1042/bst20220216] [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: 08/05/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 01/07/2023]
Abstract
For decades research has centered on identifying the ideal balanced skin microbiome that prevents disease and on developing therapeutics to foster this balance. However, this single idealized balance may not exist. The skin microbiome changes across the lifespan. This is reflected in the dynamic shifts of the skin microbiome's diverse, inter-connected community of microorganisms with age. While there are core skin microbial taxa, the precise community composition for any individual person is determined by local skin physiology, genetics, microbe-host interactions, and microbe-microbe interactions. As a key interface with the environment, the skin surface and its appendages are also constantly exchanging microbes with close personal contacts and the environment. Hormone fluctuations and immune system maturation also drive age-dependent changes in skin physiology that support different microbial community structures over time. Here, we review recent insights into the factors that shape the skin microbiome throughout life. Collectively, the works summarized within this review highlight how, depending on where we are in lifespan, our skin supports robust microbial communities, while still maintaining microbial features unique to us. This review will also highlight how disruptions to this dynamic microbial balance can influence risk for dermatological diseases as well as impact lifelong health.
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8
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Abstract
Shopping malls offer various niches for microbial populations, potentially serving as sources and reservoirs for the spread of microorganisms of public health concern. However, knowledge about the microbiome and the distribution of human pathogens in malls is largely unknown. Here, we examine the microbial community dynamics and genotypes of potential pathogens from floor and escalator surfaces in shopping malls and adjacent road dusts and greenbelt soils. The distribution pattern of microbial communities is driven primarily by habitats and seasons. A significant enrichment of human-associated microbiota in the indoor environment indicates that human interactions with surfaces might be another strong driver for mall microbiomes. Neutral community models suggest that the microbial community assembly is strongly driven by stochastic processes. Distinct performances of microbial taxonomic signatures for environmental classifications indicate the consistent differences of microbial communities of different seasons/habitats and the strong anthropogenic effect on homogenizing microbial communities of shopping malls. Indoor environments harbored higher concentrations of human pathogens than outdoor samples, also carrying a high proportion of antimicrobial resistance-associated multidrug efflux genes and virulence genes. These findings enhanced the understanding of the microbiome in the built environment and the interactions between humans and the built environment, providing a basis for tracking biothreats and communicable diseases and developing sophisticated early warning systems. IMPORTANCE Shopping malls are distinct microbial environments which can facilitate a constant transmission of microorganisms of public health concern between humans and the built environment or between human and human. Despite extensive investigation of the natural environmental microbiome, no comprehensive profile of microbial ecology has been reported in malls. Characterizing microbial distribution, potential pathogens, and antimicrobial resistance will enhance our understanding of how these microbial communities are formed, maintained, and transferred and help establish a baseline for biosurveillance of potential public health threats in malls.
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Fei N, Miyoshi S, Hermanson JB, Miyoshi J, Xie B, DeLeon O, Hawkins M, Charlton W, D’Souza M, Hart J, Sulakhe D, Martinez-Guryn KB, Chang EB, Charlton MR, Leone VA. Imbalanced gut microbiota predicts and drives the progression of nonalcoholic fatty liver disease and nonalcoholic steatohepatitis in a fast-food diet mouse model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.09.523249. [PMID: 36712061 PMCID: PMC9882021 DOI: 10.1101/2023.01.09.523249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Nonalcoholic fatty liver disease (NAFLD) is multifactorial in nature, affecting over a billion people worldwide. The gut microbiome has emerged as an associative factor in NAFLD, yet mechanistic contributions are unclear. Here, we show fast food (FF) diets containing high fat, added cholesterol, and fructose/glucose drinking water differentially impact short- vs. long-term NAFLD severity and progression in conventionally-raised, but not germ-free mice. Correlation and machine learning analyses independently demonstrate FF diets induce early and specific gut microbiota changes that are predictive of NAFLD indicators, with corresponding microbial community instability relative to control-fed mice. Shotgun metagenomics showed FF diets containing high cholesterol elevate fecal pro-inflammatory effectors over time, relating to a reshaping of host hepatic metabolic and inflammatory transcriptomes. FF diet-induced gut dysbiosis precedes onset and is highly predictive of NAFLD outcomes, providing potential insights into microbially-based pathogenesis and therapeutics.
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Affiliation(s)
- Na Fei
- Department of Medicine, University of Chicago Medical Center, University of Chicago, Chicago, IL, 60637, USA
| | - Sawako Miyoshi
- Department of General Medicine, Kyorin University School of Medicine, Tokyo 1818611, Japan
| | - Jake B. Hermanson
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jun Miyoshi
- Department of Gastroenterology and Hepatology, Kyorin University School of Medicine, Tokyo 1818611, Japan
| | - Bingqing Xie
- Department of Medicine, University of Chicago Medical Center, University of Chicago, Chicago, IL, 60637, USA
| | - Orlando DeLeon
- Department of Medicine, University of Chicago Medical Center, University of Chicago, Chicago, IL, 60637, USA
| | - Maximilian Hawkins
- Department of Medicine, University of Chicago Medical Center, University of Chicago, Chicago, IL, 60637, USA
| | - William Charlton
- Department of Medicine, University of Chicago Medical Center, University of Chicago, Chicago, IL, 60637, USA
| | - Mark D’Souza
- Duchossois Family Institute, University of Chicago, Chicago, IL, 60637, USA
| | - John Hart
- Department of Medicine, University of Chicago Medical Center, University of Chicago, Chicago, IL, 60637, USA
| | - Dinanath Sulakhe
- Duchossois Family Institute, University of Chicago, Chicago, IL, 60637, USA
| | | | - Eugene B. Chang
- Department of Medicine, University of Chicago Medical Center, University of Chicago, Chicago, IL, 60637, USA
| | - Michael R. Charlton
- Department of Medicine, University of Chicago Medical Center, University of Chicago, Chicago, IL, 60637, USA
| | - Vanessa A. Leone
- Department of Animal & Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
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10
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Ullmann T, Peschel S, Finger P, Müller CL, Boulesteix AL. Over-optimism in unsupervised microbiome analysis: Insights from network learning and clustering. PLoS Comput Biol 2023; 19:e1010820. [PMID: 36608142 PMCID: PMC9873197 DOI: 10.1371/journal.pcbi.1010820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 01/24/2023] [Accepted: 12/15/2022] [Indexed: 01/07/2023] Open
Abstract
In recent years, unsupervised analysis of microbiome data, such as microbial network analysis and clustering, has increased in popularity. Many new statistical and computational methods have been proposed for these tasks. This multiplicity of analysis strategies poses a challenge for researchers, who are often unsure which method(s) to use and might be tempted to try different methods on their dataset to look for the "best" ones. However, if only the best results are selectively reported, this may cause over-optimism: the "best" method is overly fitted to the specific dataset, and the results might be non-replicable on validation data. Such effects will ultimately hinder research progress. Yet so far, these topics have been given little attention in the context of unsupervised microbiome analysis. In our illustrative study, we aim to quantify over-optimism effects in this context. We model the approach of a hypothetical microbiome researcher who undertakes four unsupervised research tasks: clustering of bacterial genera, hub detection in microbial networks, differential microbial network analysis, and clustering of samples. While these tasks are unsupervised, the researcher might still have certain expectations as to what constitutes interesting results. We translate these expectations into concrete evaluation criteria that the hypothetical researcher might want to optimize. We then randomly split an exemplary dataset from the American Gut Project into discovery and validation sets multiple times. For each research task, multiple method combinations (e.g., methods for data normalization, network generation, and/or clustering) are tried on the discovery data, and the combination that yields the best result according to the evaluation criterion is chosen. While the hypothetical researcher might only report this result, we also apply the "best" method combination to the validation dataset. The results are then compared between discovery and validation data. In all four research tasks, there are notable over-optimism effects; the results on the validation data set are worse compared to the discovery data, averaged over multiple random splits into discovery/validation data. Our study thus highlights the importance of validation and replication in microbiome analysis to obtain reliable results and demonstrates that the issue of over-optimism goes beyond the context of statistical testing and fishing for significance.
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Affiliation(s)
- Theresa Ullmann
- Institute for Medical Information Processing, Biometry, and Epidemiology, Ludwig-Maximilians-Universität München, München, Germany
- Munich Center for Machine Learning (MCML), München, Germany
- * E-mail:
| | - Stefanie Peschel
- Institute for Asthma and Allergy Prevention, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Statistics, Ludwig-Maximilians-Universität München, München, Germany
| | - Philipp Finger
- Institute for Medical Information Processing, Biometry, and Epidemiology, Ludwig-Maximilians-Universität München, München, Germany
| | - Christian L. Müller
- Department of Statistics, Ludwig-Maximilians-Universität München, München, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Center for Computational Mathematics, Flatiron Institute, New York, New York, United States of America
| | - Anne-Laure Boulesteix
- Institute for Medical Information Processing, Biometry, and Epidemiology, Ludwig-Maximilians-Universität München, München, Germany
- Munich Center for Machine Learning (MCML), München, Germany
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11
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Robert C, Cascella F, Mellai M, Barizzone N, Mignone F, Massa N, Nobile V, Bona E. Influence of Sex on the Microbiota of the Human Face. Microorganisms 2022; 10:microorganisms10122470. [PMID: 36557723 PMCID: PMC9786802 DOI: 10.3390/microorganisms10122470] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/24/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
The role of the microbiota in health and disease has long been recognized and, so far, the cutaneous microbiota in humans has been widely investigated. The research regarded mainly the microbiota variations between body districts and disease skin states (i.e., atopic dermatitis, psoriasis, acne). In fact, relatively little information is available about the composition of the healthy skin microbiota. The cosmetic industry is especially interested in developing products that maintain and/or improve a healthy skin microbiota. Therefore, in the present work, the authors chose to investigate in detail the structure and composition of the basal bacterial community of the face. Ninety-six cheek samples (48 women and 48 men) were collected in the same season and the same location in central northern Italy. Bacterial DNA was extracted, the 16S rDNA gene was amplified by PCR, the obtained amplicons were subjected to next generation sequencing. The principal members of the community were identified at the genus level, and statistical analyses showed significant variations between the two sexes. This study identified abundant members of the facial skin microbiota that were rarely reported before in the literature and demonstrated the differences between male and female microbiota in terms of both community structure and composition.
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Affiliation(s)
- Clémence Robert
- R&D Department, Complife Italia c/a Centre for Autoimmune and Allergic Diseases (CAAD), 22100 Novara, Italy
- Centre for Autoimmune and Allergic Diseases (CAAD), University of Eastern Piedmont, 28100 Novara, Italy
- Correspondence: (C.R.); (E.B.)
| | - Federica Cascella
- R&D Department, Complife Italia c/a Centre for Autoimmune and Allergic Diseases (CAAD), 22100 Novara, Italy
- Centre for Autoimmune and Allergic Diseases (CAAD), University of Eastern Piedmont, 28100 Novara, Italy
| | - Marta Mellai
- Centre for Autoimmune and Allergic Diseases (CAAD), University of Eastern Piedmont, 28100 Novara, Italy
- Department of Health Sciences, University of Eastern Piedmont, 28100 Novara, Italy
| | - Nadia Barizzone
- Department of Health Sciences, University of Eastern Piedmont, 28100 Novara, Italy
| | - Flavio Mignone
- Department of Science and Technologic Innovation, University of Eastern Piedmont, 15121 Alessandria, Italy
- SmartSeq s.r.l., 28100 Novara, Italy
| | - Nadia Massa
- Department of Science and Technologic Innovation, University of Eastern Piedmont, 15121 Alessandria, Italy
| | - Vincenzo Nobile
- R&D Department, Complife Italia c/a Centre for Autoimmune and Allergic Diseases (CAAD), 22100 Novara, Italy
| | - Elisa Bona
- Centre for Autoimmune and Allergic Diseases (CAAD), University of Eastern Piedmont, 28100 Novara, Italy
- Department for Sustainable Development and Ecological Transition, University of Eastern Piedmont, 13100 Vercelli, Italy
- Correspondence: (C.R.); (E.B.)
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12
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Lawrence G, Midtervoll I, Samuelsen SO, Kristoffersen AK, Enersen M, Håheim LL. The blood microbiome and its association to cardiovascular disease mortality: case-cohort study. BMC Cardiovasc Disord 2022; 22:344. [PMID: 35909117 PMCID: PMC9339179 DOI: 10.1186/s12872-022-02791-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 07/26/2022] [Indexed: 01/29/2023] Open
Abstract
Background Little is known about the association between bacterial DNA in human blood and the risk of cardiovascular disease (CVD) mortality. Methods A case-cohort study was performed based on a 9 ½ year follow-up of the Oslo II study from 2000. Eligible for this analysis were men born in 1923 and from 1926 to 1932. The cases were men (n = 227) who had died from CVD, and the controls were randomly selected participants from the same cohort (n = 178). Analysis of the bacterial microbiome was performed on stored frozen blood samples for both cases and controls. Association analyses for CVD mortality were performed by Cox proportional hazard regression adapted to the case-cohort design. We used the Bonferroni correction due to the many bacterial genera that were identified. Results Bacterial DNA was identified in 372 (82%) of the blood samples and included 78 bacterial genera from six phyla. Three genera were significantly associated with CVD mortality. The genera Kocuria (adjusted hazard ratio (HR) 8.50, 95% confidence interval (CI) (4.05, 17.84)) and Enhydrobacter (HR 3.30 (2.01, 5.57)) indicate an association with CVD mortality with increasing levels. The genera Paracoccus (HR 0.29 (0.15, 0.57)) was inversely related. Significant predictors of CVD mortality were: the feeling of bad health; and the consumption of more than three cups of coffee per day. The following registered factors were borderline significant, namely: a history of heart failure; increased systolic blood pressure; and currently taking antihypertensive drugs now, versus previously. Conclusions The increasing levels of two bacterial genera Kocuria (skin and oral) and Enhydrobacter (skin) and low levels of Paracoccus (soil) were associated with CVD mortality independent of known risk factors for CVD. Supplementary Information The online version contains supplementary material available at 10.1186/s12872-022-02791-7.
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13
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Li Z, Zheng N, An Q, Li X, Sun S, Zhang W, Ji Y, Wang S, Li P. Impact of environmental factors and bacterial interactions on dust mite allergens in different indoor dust. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 844:157177. [PMID: 35803427 DOI: 10.1016/j.scitotenv.2022.157177] [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: 03/07/2022] [Revised: 06/11/2022] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
Indoor dust is the main carrier of indoor pollutants, especially dust mite allergens and bacteria, they can trigger asthma, rhinitis, eczema and other allergic diseases. However, the interactions between dust mite allergens and bacterial communities in different types of indoor dust are not clear. The study focused on particulate and flocculent fibrous dust, explored the concentrations of Der p 1 (Dermatophagoides pteronyssinus) and Der f 1 (D. farinae) in 46 households in Changchun and their environmental influences, characterized the bacterial communities by high-throughput sequencing, and the interactions between Der p 1, Der f 1 and bacterial communities were explored. The results showed that Der p 1 and Der f 1 tended to accumulate more in flocculent fibrous dust, and Der p 1 predominated in the indoor dust samples. The floor height, years of housing occupancy and the living areas all affected the concentrations of dust mite allergens. In bacterial community, Proteobacteria, Firmicutes and Actinobacteria were leading phyla in the two types of dust. Kocuria, Blastococcus and Massilia were dominating genera in particulate dust and Acinetobacter, Lactobacillus, Corynebacterium_1 were dominating genera in flocculent fibrous dust. The overall diversity and species richness of bacteria in particulate dust were significantly higher than those in flocculent dust (p < 0.001). The living area was an important environmental factor affecting the bacterial community in flocculent fibrous dust (p < 0.01). The interaction between the relative abundance of Proteobacteria, Firmicutes and Actinobacteria and dust mite allergen concentrations significantly differed between the two dust types, indicating that bacteria could be used both as food and to establish symbiotic relationships with household dust mites (HDMs) hosts and provide nutrition.
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Affiliation(s)
- Zimeng Li
- College of New Energy and Environment, Jilin University, Changchun, 130012, China
| | - Na Zheng
- College of New Energy and Environment, Jilin University, Changchun, 130012, China; Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130012, China.
| | - Qirui An
- College of New Energy and Environment, Jilin University, Changchun, 130012, China
| | - Xiaoqian Li
- College of New Energy and Environment, Jilin University, Changchun, 130012, China
| | - Siyu Sun
- College of New Energy and Environment, Jilin University, Changchun, 130012, China
| | - Wenhui Zhang
- College of New Energy and Environment, Jilin University, Changchun, 130012, China
| | - Yining Ji
- College of New Energy and Environment, Jilin University, Changchun, 130012, China
| | - Sujing Wang
- College of New Energy and Environment, Jilin University, Changchun, 130012, China
| | - Pengyang Li
- College of New Energy and Environment, Jilin University, Changchun, 130012, China
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14
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Effect of Solar Radiation on Skin Microbiome: Study of Two Populations. Microorganisms 2022; 10:microorganisms10081523. [PMID: 36013941 PMCID: PMC9415396 DOI: 10.3390/microorganisms10081523] [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: 06/25/2022] [Revised: 07/18/2022] [Accepted: 07/22/2022] [Indexed: 12/01/2022] Open
Abstract
Here, we examined the skin microbiome of two groups of healthy volunteers living on the Mediterranean coast with different exposures to sun radiation. One group, exposed to the sun in the summer, was compared with a group covered with clothing throughout the year. The seasonal effects on the skin microbiome of three body sites were determined before and after summer. Surprisingly, at the phyla level, there were no significant differences in microbiome diversity between the groups. Furthermore, within each group, there were no significant seasonal differences in high-abundance species at any of the sampling sites. These results suggest that the skin microbiome, developed over years, remains stable even after several months of exposure to summer weather, direct sunlight and humidity. However, in the group exposed to the sun during the summer months, there were significant differences in low-abundance species in sun-exposed areas of the skin (the inner and outer arm). These subtle changes in low-abundance species are interesting, and their effect on skin physiology should be studied further.
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15
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Shao L, Jiang S, Li Y, Shi Y, Wang M, Liu T, Yang S, Ma L. Regular Late Bedtime Significantly Affects the Skin Physiological Characteristics and Skin Bacterial Microbiome. Clin Cosmet Investig Dermatol 2022; 15:1051-1063. [PMID: 35698548 PMCID: PMC9188400 DOI: 10.2147/ccid.s364542] [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: 03/01/2022] [Accepted: 06/01/2022] [Indexed: 11/23/2022]
Abstract
Background Late bedtime is a common form of unhealthy sleep pattern in adulthood, which influences circadian rhythm, and negatively affects health. However, little is known about the effect of regular late bedtime on skin characteristics, particularly on skin microbiome. Objective To investigate the changes and effects of the regular late bedtime on skin physiological parameters and facial bacterial microbiome of 219 cases of Chinese women aged 18-38 years living in Shanghai. Methods Based on the Self-Evaluation Questionnaire, bedtime was categorized as 11:00 PM; thus, the volunteers were divided into early bedtime group (S0) and late bedtime group (S1). The physiological parameters of facial skin were measured by non-invasive instrumental methods, and the skin microbiome was analyzed by 16S rRNA high-throughput sequencing. Results The skin physiological parameters of the late bedtime group exhibited significant decrease in skin hydration content, skin firmness (F4) and elasticity (R2), while TEWL, sebum and wrinkle significantly increased. The result indicated that late bedtime significantly impaired the integrity of skin barrier, damaged skin structure, and disrupted water-oil balance. Furthermore, the analysis of α-diversity, Sobs, Ace and Chao index were found to significantly decrease (P < 0.05) in the late bedtime group, suggesting that late bedtime reduced both the abundance and the diversity of facial bacterial microbiota. Moreover, the abundance of Pseudomonas increased significantly, while Streptococcus, Stenotrophomonas, Acinetobacter, Haemophilus, Actinomyces and Neisseria decreased significantly. In addition, Spearman correlation analysis revealed strong correlations between the microbiota and the physiological parameters. Notably, the abundance of Pseudomonas significantly positively correlated with skin firmness and elasticity, but significantly negatively correlated with skin hemoglobin content, melanin content and skin hydration. Conclusion Bedtime is an important factor in maintaining skin health. Regular late bedtime not only damages the skin barrier and skin structure but also reduces the diversity and composition of facial bacterial microbiome.
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Affiliation(s)
- Li Shao
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, People's Republic of China
| | - Sujing Jiang
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, People's Republic of China
| | - Yan Li
- R&D Innovation Center, Shandong Freda Biotech Co., Ltd, Jinan, Shandong, People's Republic of China
| | - Yanqin Shi
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, People's Republic of China.,The Oriental Beauty Valley Research Institute, Shanghai Institute of Technology, Shanghai, People's Republic of China
| | - Man Wang
- Department of Nutrition, Shanghai Jiao Tong University Affiliated Sixth People's Hospital South Campus, Shanghai, People's Republic of China
| | - Ting Liu
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, People's Republic of China
| | - Suzhen Yang
- R&D Innovation Center, Shandong Freda Biotech Co., Ltd, Jinan, Shandong, People's Republic of China
| | - Laiji Ma
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, People's Republic of China.,The Oriental Beauty Valley Research Institute, Shanghai Institute of Technology, Shanghai, People's Republic of China
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16
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Mills JG, Selway CA, Thomas T, Weyrich LS, Lowe AJ. Schoolyard Biodiversity Determines Short-Term Recovery of Disturbed Skin Microbiota in Children. MICROBIAL ECOLOGY 2022:1-12. [PMID: 35689685 PMCID: PMC9188306 DOI: 10.1007/s00248-022-02052-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
Creating biodiverse urban habitat has been proposed, with growing empirical support, as an intervention for increasing human microbial diversity and reducing associated diseases. However, ecological understanding of urban biodiversity interventions on human skin microbiota remains limited. Here, we experimentally test the hypotheses that disturbed skin microbiota recover better in outdoor schoolyard environments and that greater biodiversity provides a greater response. Repeating the experiment three times, we disturbed skin microbiota of fifty-seven healthy 10-to-11-year-old students with a skin swab (i.e., cleaning), then exposed them to one school environment-either a 'classroom' (n = 20), 'sports field' (n = 14), or biodiverse 'forest' (n = 23)-for 45 min. Another skin swab followed the exposure to compare 'before' and 'after' microbial communities. After 45 min, the disturbance immediately followed by outdoor exposure, especially the 'forest', had an enriching and diversifying effect on skin microbiota, while 'classroom' exposure homogenised inter-personal variability. Each effect compounded over consecutive days indicating longer-term exposure outcomes. The experimental disturbance also reduced the core skin microbiota, and only outdoor environments were able to replenish lost species richness to core membership (n species > 50% prevalent). Overall, we find that environmental setting, especially including biodiversity, is important in human microbiota recovery periods and that the outdoors provide resilience to skin communities. This work also has implications for the inclusion of short periods of outside or forest exposure in school scheduling. Future investigations of the health impacts of permanent urban biodiversity interventions are needed.
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Affiliation(s)
- Jacob G Mills
- School of Biological Sciences, The University of Adelaide, Kaurna Country, Adelaide, South Australia, Australia.
| | - Caitlin A Selway
- School of Biological Sciences, The University of Adelaide, Kaurna Country, Adelaide, South Australia, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Environmental and Earth Sciences, University of New South Wales, Bidjigal Country, Sydney, Australia
| | - Laura S Weyrich
- School of Biological Sciences, The University of Adelaide, Kaurna Country, Adelaide, South Australia, Australia
- Department of Anthropology, The Pennsylvania State University, University Park, State College, PA, USA
| | - Andrew J Lowe
- School of Biological Sciences, The University of Adelaide, Kaurna Country, Adelaide, South Australia, Australia
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17
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Zhang Y, Shen F, Yang Y, Niu M, Chen D, Chen L, Wang S, Zheng Y, Sun Y, Zhou F, Qian H, Wu Y, Zhu T. Insights into the Profile of the Human Expiratory Microbiota and Its Associations with Indoor Microbiotas. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:6282-6293. [PMID: 35512288 PMCID: PMC9113006 DOI: 10.1021/acs.est.2c00688] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/19/2022] [Accepted: 04/22/2022] [Indexed: 05/04/2023]
Abstract
Microorganisms residing in the human respiratory tract can be exhaled, and they constitute a part of environmental microbiotas. However, the expiratory microbiota community and its associations with environmental microbiotas remain poorly understood. Here, expiratory bacteria and fungi and the corresponding microbiotas from the living environments were characterized by DNA amplicon sequencing of residents' exhaled breath condensate (EBC) and environmental samples collected from 14 residences in Nanjing, China. The microbiotas of EBC samples, with a substantial heterogeneity, were found to be as diverse as those of skin, floor dust, and airborne microbiotas. Model fitting results demonstrated the role of stochastic processes in the assembly of the expiratory microbiota. Using a fast expectation-maximization algorithm, microbial community analysis revealed that expiratory microbiotas were differentially associated with other types of microbiotas in a type-dependent and residence-specific manner. Importantly, the expiratory bacteria showed a composition similarity with airborne bacteria in the bathroom and kitchen environments with an average of 12.60%, while the expiratory fungi showed a 53.99% composition similarity with the floor dust fungi. These differential patterns indicate different relationships between expiratory microbiotas and the airborne microbiotas and floor dust microbiotas. The results here illustrated for the first time the associations between expiratory microbiotas and indoor microbiotas, showing a potential microbial exchange between the respiratory tract and indoor environment. Thus, improved hygiene and ventilation practices can be implemented to optimize the indoor microbial exposome, especially in indoor bathrooms and kitchens.
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Affiliation(s)
- Yin Zhang
- School
of Space and Environment, Beihang University, Beijing 100191, China
| | - Fangxia Shen
- School
of Space and Environment, Beihang University, Beijing 100191, China
| | - Yi Yang
- School
of Space and Environment, Beihang University, Beijing 100191, China
| | - Mutong Niu
- School
of Space and Environment, Beihang University, Beijing 100191, China
| | - Da Chen
- School
of Environment and Guangdong Key Laboratory of Environmental Pollution
and Health, Jinan University, Guangzhou 510632, China
| | - Longfei Chen
- School
of Energy and Power Engineering, Beihang
University, Beijing 100191, China
| | - Shengqi Wang
- School
of Energy and Environment, Southeast University, Nanjing 210096, China
| | - Yunhao Zheng
- Institute
of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ye Sun
- School
of Space and Environment, Beihang University, Beijing 100191, China
| | - Feng Zhou
- School
of Space and Environment, Beihang University, Beijing 100191, China
| | - Hua Qian
- School
of Energy and Environment, Southeast University, Nanjing 210096, China
| | - Yan Wu
- School of
Environmental Science and Engineering, Shandong
University, Jinan 250100, China
| | - Tianle Zhu
- School
of Space and Environment, Beihang University, Beijing 100191, China
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18
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Fomite Transmission Follows Invasion Ecology Principles. mSystems 2022; 7:e0021122. [PMID: 35502902 PMCID: PMC9238404 DOI: 10.1128/msystems.00211-22] [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] [Indexed: 12/02/2022] Open
Abstract
The invasion ecology principles illustrated in many ecosystems have not yet been explored in the context of fomite transmission. We hypothesized that invaders in fomite transmission are trackable, are neutrally distributed between hands and environmental surfaces, and exhibit a proximity effect. To test this hypothesis, a surrogate invader, Lactobacillus delbrueckii subsp. bulgaricus, was spread by a root carrier in an office housing more than 20 participants undertaking normal activities, and the microbiotas on skin and environmental surfaces were analyzed before and after invasion. First, we found that the invader was trackable. Its identity and emission source could be determined using microbial-interaction networks, and the root carrier could be identified using a rank analysis. Without prior information, L. bulgaricus could be identified as the invader emitted from a source that exclusively contained the invader, and the probable root carrier could be located. In addition to the single-taxon invasion by L. bulgaricus, multiple-taxon invasion was observed, as genera from sputum/saliva exhibited co-occurrence relationships on skin and environmental surfaces. Second, the invader had a below-neutral distribution in a neutral community model, suggesting that hands accrued heavier invader contamination than environmental surfaces. Third, a proximity effect was observed on a surface touch network. Invader contamination on surfaces decreased with increasing geodesic distance from the hands of the carrier, indicating that the carrier’s touching behaviors were the main driver of fomite transmission. Taken together, these results demonstrate the invasion ecology principles in fomite transmission and provide a general basis for the management of ecological fomite transmission. IMPORTANCE Fomite transmission contributes to the spread of many infectious diseases. However, pathogens in fomite transmission typically are either investigated individually without considering the context of native microbiotas or investigated in a nondiscriminatory way from the dispersal of microbiotas. In this study, we adopted an invasion ecology framework in which we considered pathogens as invaders, the surface environment as an ecosystem, and human behaviors as the driver of microbial dispersal. With this approach, we assessed the ability of quantitative ecological theories to track and forecast pathogen movements in fomite transmission. By uncovering the relationships between the invader and native microbiotas and between human behaviors and invader/microbiota dispersal, we demonstrated that fomite transmission follows idiosyncratic invasion ecology principles. Our findings suggest that attempts to manage fomite transmission for public health purposes should focus on the microbial communities and anthropogenic factors involved, in addition to the pathogens.
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Wang L, Yu T, Zhu Y, Luo Y, Dong F, Lin X, Zhao W, He Z, Hu S, Dong Z. Amplicon-based sequencing and co-occurence network analysis reveals notable differences of microbial community structure in healthy and dandruff scalps. BMC Genomics 2022; 23:312. [PMID: 35439925 PMCID: PMC9017024 DOI: 10.1186/s12864-022-08534-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 03/30/2022] [Indexed: 12/27/2022] Open
Abstract
Background Dandruff is a chronic, recurring, and common scalp problem that is caused by several etiopathogeneses with complex mechanisms. Management of this condition is typically achieved via antifungal therapies. However, the precise roles played by microbiota in the development of the condition have not been elucidated. Despite their omnipresence on human scalp little is known about the co-occurrence/co-exclusion network of cutaneous microbiota. Results We characterized the scalp and hair surface bacterial and fungal communities of 95 dandruff-afflicted and healthy individuals residing in China. The degree distributions of co-occurrence/co-exclusion network in fungi-bacteria and bacteria-bacteria were higher in the healthy group (P < 0.0001), whereas the betweenness values are higher in the dandruff group (P < 0.01). Meanwhile, the co-occurrence/co-exclusion network among fungi-fungi and fungi-bacteria showed that compared to the healthy group, the dandruff group had more positive links (P < 0.0001). In addition, we observed that Malassezia slooffiae, Malassezia japonica and Malassezia furfur, were more abundant in the dandruff group than in the healthy group. These microbiota were co-exclusion by either multiple bacterial genera or Malassezia sp. in healthy group. The lactic acid bacteria on the scalp and hair surface, especially the genera Lactobacillus and Lactococcus, exhibit a negative correlation with multiple bacterial genera on the scalp and hair surface. Lactobacillus plantarum and Pediococcus lactis isolated on the healthy human scalp can inhibit the growth of Staphylococcus epidermidis in vitro. Conclusions We showed that microbial networks on scalp and hair surface with dandruff were less integrated than their healthy counterparts, with lower node degree and more positive and stronger links which were deemed to be unstable and may be more susceptible to environmental fluctuations. Lactobacillus bacteria have extensive interactions with other bacteria or fungi in the scalp and hair surface micro-ecological network and can be used as targets for improving scalp health. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08534-4.
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Affiliation(s)
- Li Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing, 100101, China.,Department of Microbiology, College of Life Science, State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, 36 Lushan Rd., Yuelu District, Changsha, Hunan, 410081, China
| | - Tao Yu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing, 100101, China.,University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, 100049, Beijing, China
| | - Yaxin Zhu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Yingfeng Luo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Fan Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Xuemei Lin
- Lafang China Co.. Ltd., LAF Building, Wanji Industrial Park, Shantou, Guangdong, 515041, China
| | - Wenzhong Zhao
- Lafang China Co.. Ltd., LAF Building, Wanji Industrial Park, Shantou, Guangdong, 515041, China
| | - Zilong He
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Interdisciplinary Innovation Institute of Medicine and Engineering, Beihang University , No. 37 Xueyuan Road, Haidian District, Beijing, 100191, China.
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing, 100101, China. .,University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, 100049, Beijing, China.
| | - Zhiyang Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing, 100101, China. .,University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, 100049, Beijing, China.
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20
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Chia M, Naim AN, Tay AS, Lim K, Lee CK, Yow SJ, Chen J, Common JE, Nagarajan N, Tham EH. Shared signatures and divergence in skin microbiomes of children with atopic dermatitis and their caregivers. J Allergy Clin Immunol 2022; 150:894-908. [DOI: 10.1016/j.jaci.2022.01.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 01/17/2022] [Accepted: 01/25/2022] [Indexed: 10/18/2022]
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21
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Ogai K, Nana BC, Lloyd YM, Arios JP, Jiyarom B, Awanakam H, Esemu LF, Hori A, Matsuoka A, Nainu F, Megnekou R, Leke RGF, Ekali GL, Okamoto S, Kuraishi T. Skin microbiome profile of healthy Cameroonians and Japanese. Sci Rep 2022; 12:1364. [PMID: 35079063 PMCID: PMC8789912 DOI: 10.1038/s41598-022-05244-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 01/10/2022] [Indexed: 12/20/2022] Open
Abstract
The commensal microbes of the skin have a significant impact on dermal physiology and pathophysiology. Racial and geographical differences in the skin microbiome are suggested and may play a role in the sensitivity to dermatological disorders, including infectious diseases. However, little is known about the skin microbiome profiles of people living in Central Africa, where severe tropical infectious diseases impose a burden on the inhabitants. This study provided the skin profiles of healthy Cameroonians in different body sites and compared them to healthy Japanese participants. The skin microbiome of Cameroonians was distinguishable from that of Japanese in all skin sites examined in this study. For example, Micrococcus was predominantly found in skin samples of Cameroonians but mostly absent in Japanese skin samples. Instead, the relative abundance of Cutibacterium species was significantly higher in healthy Japanese. Principal coordinate analysis of beta diversity showed that the skin microbiome of Cameroonians formed different clusters from Japanese, suggesting a substantial difference in the microbiome profiles between participants of both countries. In addition, the alpha diversity in skin microbes was higher in Cameroonians than Japanese participants. These data may offer insights into the determinant factors responsible for the distinctness of the skin microbiome of people living in Central Africa and Asia.
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Affiliation(s)
- Kazuhiro Ogai
- AI Hospital/Macro Signal Dynamics Research and Development Center (ai@ku), Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Benderli Christine Nana
- Biotechnology Center, University of Yaoundé I, Yaoundé, Cameroon
- Department of Animal Biology and Physiology of the Faculty of Science, University of Yaoundé I, Yaoundé, Cameroon
| | - Yukie Michelle Lloyd
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Hawaii, USA
| | - John Paul Arios
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Hawaii, USA
| | - Boonyanudh Jiyarom
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Hawaii, USA
| | - Honore Awanakam
- Biotechnology Center, University of Yaoundé I, Yaoundé, Cameroon
| | - Livo Forgu Esemu
- Biotechnology Center, University of Yaoundé I, Yaoundé, Cameroon
- Institute of Medical Research and Medicinal Plant Studies, Ministry of Scientific Research and Innovation, Yaoundé, Cameroon
| | - Aki Hori
- Laboratory of Host Defense and Responses, Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Ayaka Matsuoka
- Faculty of Health Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Firzan Nainu
- Laboratory of Host Defense and Responses, Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
- Department of Pharmacy, Faculty of Pharmacy, Hasanuddin University, Makassar, Indonesia
| | - Rosette Megnekou
- Biotechnology Center, University of Yaoundé I, Yaoundé, Cameroon
- Department of Animal Biology and Physiology of the Faculty of Science, University of Yaoundé I, Yaoundé, Cameroon
| | - Rose Gana Fomban Leke
- Biotechnology Center, University of Yaoundé I, Yaoundé, Cameroon
- Institute of Medical Research and Medicinal Plant Studies, Ministry of Scientific Research and Innovation, Yaoundé, Cameroon
| | | | - Shigefumi Okamoto
- Faculty of Health Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan.
- Advanced Health Care Science Research Unit, Institute for Frontier Science Initiative, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa, Ishikawa, 920-0942, Japan.
| | - Takayuki Kuraishi
- Laboratory of Host Defense and Responses, Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan.
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22
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Fei N, Choo-Kang C, Reutrakul S, Crowley SJ, Rae D, Bedu-Addo K, Plange-Rhule J, Forrester TE, Lambert EV, Bovet P, Riesen W, Korte W, Luke A, Layden BT, Gilbert JA, Dugas LR. Gut microbiota alterations in response to sleep length among African-origin adults. PLoS One 2021; 16:e0255323. [PMID: 34495955 PMCID: PMC8425534 DOI: 10.1371/journal.pone.0255323] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 07/14/2021] [Indexed: 12/15/2022] Open
Abstract
Sleep disorders are increasingly being characterized in modern society as contributing to a host of serious medical problems, including obesity and metabolic syndrome. Changes to the microbial community in the human gut have been reportedly associated with many of these cardiometabolic outcomes. In this study, we investigated the impact of sleep length on the gut microbiota in a large cohort of 655 participants of African descent, aged 25-45, from Ghana, South Africa (SA), Jamaica, and the United States (US). The sleep duration was self-reported via a questionnaire. Participants were classified into 3 sleep groups: short (<7hrs), normal (7-<9hrs), and long (≥9hrs). Forty-seven percent of US participants were classified as short sleepers and 88% of SA participants as long sleepers. Gut microbial composition analysis (16S rRNA gene sequencing) revealed that bacterial alpha diversity negatively correlated with sleep length (p<0.05). Furthermore, sleep length significantly contributed to the inter-individual beta diversity dissimilarity in gut microbial composition (p<0.01). Participants with both short and long-sleep durations exhibited significantly higher abundances of several taxonomic features, compared to normal sleep duration participants. The predicted relative proportion of two genes involved in the butyrate synthesis via lysine pathway were enriched in short sleep duration participants. Finally, co-occurrence relationships revealed by network analysis showed unique interactions among the short, normal and long duration sleepers. These results suggest that sleep length in humans may alter gut microbiota by driving population shifts of the whole microbiota and also specific changes in Exact Sequence Variants abundance, which may have implications for chronic inflammation associated diseases. The current findings suggest a possible relationship between disrupted sleep patterns and the composition of the gut microbiota. Prospective investigations in larger and more prolonged sleep researches and causally experimental studies are needed to confirm these findings, investigate the underlying mechanism and determine whether improving microbial homeostasis may buffer against sleep-related health decline in humans.
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Affiliation(s)
- Na Fei
- Microbiome Center, Department of Surgery, University of Chicago, Chicago, IL, United States of America
| | - Candice Choo-Kang
- Public Health Sciences, Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, IL, United States of America
| | - Sirimon Reutrakul
- Department of Psychiatry & Behavioral Sciences, Biological Rhythms Research Laboratory, Rush University Medical Center, Chicago, IL, United States of America
| | - Stephanie J. Crowley
- Department of Psychiatry & Behavioral Sciences, Biological Rhythms Research Laboratory, Rush University Medical Center, Chicago, IL, United States of America
| | - Dale Rae
- Research Unit for Exercise Science and Sports Medicine, University of Cape Town, Cape Town, South Africa
| | - Kweku Bedu-Addo
- Research Unit for Exercise Science and Sports Medicine, University of Cape Town, Cape Town, South Africa
| | - Jacob Plange-Rhule
- Research Unit for Exercise Science and Sports Medicine, University of Cape Town, Cape Town, South Africa
| | - Terrence E. Forrester
- Solutions for Developing Countries, University of the West Indies, Mona, Kingston, Jamaica
| | - Estelle V. Lambert
- Department of Physiology, School of Medical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Pascal Bovet
- University Center for Primary Care and Public Health (Unisanté), Lausanne, Switzerland
- Ministry of Health, Victoria, Republic of Seychelles
| | - Walter Riesen
- University Center for Primary Care and Public Health (Unisanté), Lausanne, Switzerland
- Ministry of Health, Victoria, Republic of Seychelles
| | - Wolfgang Korte
- Center for Laboratory Medicine, Canton Hospital, St. Gallen, Switzerland
| | - Amy Luke
- Public Health Sciences, Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, IL, United States of America
| | - Brian T. Layden
- Department of Psychiatry & Behavioral Sciences, Biological Rhythms Research Laboratory, Rush University Medical Center, Chicago, IL, United States of America
- Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois, United States of America
| | - Jack A. Gilbert
- University of California San Diego, San Diego, California, United States of America
| | - Lara R. Dugas
- Public Health Sciences, Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, IL, United States of America
- Division of Epidemiology & Biostatistics, School of Public Health & Family Medicine, University of Cape Town, Cape Town, South Africa
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23
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Mills S, Ross RP. Colliding and interacting microbiomes and microbial communities - consequences for human health. Environ Microbiol 2021; 23:7341-7354. [PMID: 34390616 DOI: 10.1111/1462-2920.15722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 08/09/2021] [Accepted: 08/12/2021] [Indexed: 11/26/2022]
Abstract
Living 'things' coexist with microorganisms, known as the microbiota/microbiome that provides essential physiological functions to its host. Despite this reliance, the microbiome is malleable and can be altered by several factors including birth-mode, age, antibiotics, nutrition, and disease. In this minireview, we consider how other microbiomes and microbial communities impact the host microbiome and the host through the concept of microbiome collisions (initial exposures) and interactions. Interactions include changes in host microbiome composition and functionality and/or host responses. Understanding the impact of other microbiomes and microbial communities on the microbiome and host are important considering the decline in human microbiota diversity in the developed world - paralleled by the surge of non-communicable, inflammatory-based diseases. Thus, surrounding ourselves with rich and diverse beneficial microbiomes and microbial communities to collide and interact with should help to diminish the loss in microbial diversity and protect from certain diseases. In the same vein, our microbiomes not only influence our health but potentially the health of those close to us. We also consider strategies for enhanced host microbiome collisions and interactions through the surrounding environment that ensure increased microbiome diversity and functionality contributing to enhanced symbiotic return to the host in terms of health benefit.
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Affiliation(s)
- Susan Mills
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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24
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Boxberger M, Cenizo V, Cassir N, La Scola B. Challenges in exploring and manipulating the human skin microbiome. MICROBIOME 2021; 9:125. [PMID: 34053468 PMCID: PMC8166136 DOI: 10.1186/s40168-021-01062-5] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 03/25/2021] [Indexed: 05/08/2023]
Abstract
The skin is the exterior interface of the human body with the environment. Despite its harsh physical landscape, the skin is colonized by diverse commensal microbes. In this review, we discuss recent insights into skin microbial populations, including their composition and role in health and disease and their modulation by intrinsic and extrinsic factors, with a focus on the pathobiological basis of skin aging. We also describe the most recent tools for investigating the skin microbiota composition and microbe-skin relationships and perspectives regarding the challenges of skin microbiome manipulation. Video abstract.
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Affiliation(s)
- Manon Boxberger
- IRD, AP-HM, MEPHI, Aix Marseille Université, Marseille, France
- IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385 Marseille Cedex 05, France
| | - Valérie Cenizo
- Groupe L’Occitane, R&D Department, Zone Industrielle Saint Maurice, 4100 Manosque, Alpes-de Haute-Provence France
| | - Nadim Cassir
- IRD, AP-HM, MEPHI, Aix Marseille Université, Marseille, France
- IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385 Marseille Cedex 05, France
| | - Bernard La Scola
- IRD, AP-HM, MEPHI, Aix Marseille Université, Marseille, France
- IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385 Marseille Cedex 05, France
- IRD, AP-HM, SSA, VITROME, Aix Marseille Université, Marseille, France
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25
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Yu J, Tang SN, Lee PKH. Microbial Communities in Full-Scale Wastewater Treatment Systems Exhibit Deterministic Assembly Processes and Functional Dependency over Time. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:5312-5323. [PMID: 33784458 DOI: 10.1021/acs.est.0c06732] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Microbial communities constitute the core component of biological wastewater treatment processes. We conducted a meta-analysis based on the 16S rRNA gene of temporal samples obtained from diverse full-scale activated sludge and anaerobic digestion systems treating municipal and industrial wastewater (collected in this study and published previously) to investigate their community assembly mechanism and functional traits over time, which are not currently well understood. The influent composition was found to be the main driver of the microbial community's composition, and relatively large proportions of specialist (26.1% and 18.6%) and transient taxa (67.2% and 68.1%) were estimated in both systems. Deterministic processes, especially homogeneous selection events (accounting for >53.8% of assembly events), were consistently identified as the dominant microbial community assembly mechanisms in both systems over time. Significant and strong correlations (Pearson's r = 0.51-0.92) were detected between the dynamics of the temporal community and the functional compositions in both systems, which suggests functional dependency. In contrast, the occurrence of sludge bulking and foaming in the activated sludge system led to an increase in stochastic assembly processes (i.e., limited dispersal and undominated events), a shift toward functional redundancy and less community diversity, a decreased community niche breadth index, and a more compact co-association network. This study illustrates that the mechanism of microbial community assembly and functional traits over time can be used to diagnose system performance and provide information on potential system malfunction.
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Affiliation(s)
- Jinjin Yu
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Siang Nee Tang
- Facility Management and Environmental Engineering, TAL Group, Hong Kong SAR, China
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China
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26
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Cao Y, Liu Y, Dong Q, Wang T, Niu C. Alterations in the gut microbiome and metabolic profile in rats acclimated to high environmental temperature. Microb Biotechnol 2021; 15:276-288. [PMID: 33620148 PMCID: PMC8719808 DOI: 10.1111/1751-7915.13772] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 01/26/2021] [Accepted: 01/30/2021] [Indexed: 12/29/2022] Open
Abstract
Heat acclimation (HA) is the best strategy to improve heat stress tolerance by inducing positive physiological adaptations. Evidence indicates that the gut microbiome plays a fundamental role in the development of HA, and modulation of gut microbiota can improve tolerance to heat exposure and decrease the risks of heat illness. In this study, for the first time, we applied 16S rRNA gene sequencing and untargeted liquid chromatography–mass spectrometry (LC‐MS) metabolomics to explore variations in the gut microbiome and faecal metabolic profiles in rats after HA. The gut microbiota of HA subjects exhibited higher diversity and richer microbes. HA altered the gut microbiota composition with significant increases in the genera Lactobacillus (a major probiotic) and Oscillospira alongside significant decreases in the genera Blautia and Allobaculum. The faecal metabolome was also significantly changed after HA, and among the 13 perturbed metabolites, (S)‐AL 8810 and celastrol were increased. Moreover, the two increased genera were positively correlated with the two upregulated metabolites and negatively correlated with the other 11 downregulated metabolites, while the correlations between the two decreased genera and the upregulated/downregulated metabolites were completely contrary. In summary, both the structure of the gut microbiome community and the faecal metabolome were improved after 28 days of HA. These findings provide novel insights regarding the improvement of the gut microbiome and its functions as a potential mechanism by which HA confers protection against heat stress.
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Affiliation(s)
- Yang Cao
- Department of Environmental Medicine, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Ying Liu
- Department of Environmental Medicine, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Qingyang Dong
- Department of Environmental Medicine, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Tao Wang
- Department of Environmental Medicine, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Chao Niu
- Department of Environmental Medicine, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
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27
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Mahnert A, Verseux C, Schwendner P, Koskinen K, Kumpitsch C, Blohs M, Wink L, Brunner D, Goessler T, Billi D, Moissl-Eichinger C. Microbiome dynamics during the HI-SEAS IV mission, and implications for future crewed missions beyond Earth. MICROBIOME 2021; 9:27. [PMID: 33487169 PMCID: PMC7831191 DOI: 10.1186/s40168-020-00959-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/06/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND Human health is closely interconnected with its microbiome. Resilient microbiomes in, on, and around the human body will be key for safe and successful long-term space travel. However, longitudinal dynamics of microbiomes inside confined built environments are still poorly understood. Herein, we used the Hawaii Space Exploration Analog and Simulation IV (HI-SEAS IV) mission, a 1 year-long isolation study, to investigate microbial transfer between crew and habitat, in order to understand adverse developments which may occur in a future outpost on the Moon or Mars. RESULTS Longitudinal 16S rRNA gene profiles, as well as quantitative observations, revealed significant differences in microbial diversity, abundance, and composition between samples of the built environment and its crew. The microbiome composition and diversity associated with abiotic surfaces was found to be rather stable, whereas the microbial skin profiles of individual crew members were highly dynamic, resulting in an increased microbiome diversity at the end of the isolation period. The skin microbiome dynamics were especially pronounced by a regular transfer of the indicator species Methanobrevibacter between crew members within the first 200 days. Quantitative information was used to track the propagation of antimicrobial resistance in the habitat. Together with functional and phenotypic predictions, quantitative and qualitative data supported the observation of a delayed longitudinal microbial homogenization between crew and habitat surfaces which was mainly caused by a malfunctioning sanitary facility. CONCLUSIONS This study highlights main routes of microbial transfer, interaction of the crew, and origins of microbial dynamics in an isolated environment. We identify key targets of microbial monitoring, and emphasize the need for defined baselines of microbiome diversity and abundance on surfaces and crew skin. Targeted manipulation to counteract adverse developments of the microbiome could be a highly important strategy to ensure safety during future space endeavors. Video abstract.
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Affiliation(s)
- Alexander Mahnert
- Interactive Microbiome Research, Diagnostic & Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Cyprien Verseux
- Laboratory of Applied Space Microbiology, Center of Applied Space Technology and Microgravity (ZARM), University of Bremen, Am Fallturm 2, 28359 Bremen, Germany
| | - Petra Schwendner
- University of Florida, Space Life Sciences Lab, 505 Odyssey Way, Exploration Park, N. Merritt Island, FL 32953 USA
| | - Kaisa Koskinen
- Interactive Microbiome Research, Diagnostic & Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Christina Kumpitsch
- Interactive Microbiome Research, Diagnostic & Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Marcus Blohs
- Interactive Microbiome Research, Diagnostic & Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Lisa Wink
- Interactive Microbiome Research, Diagnostic & Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Daniela Brunner
- Interactive Microbiome Research, Diagnostic & Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Theodora Goessler
- Interactive Microbiome Research, Diagnostic & Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Daniela Billi
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica s.n.c, 00133 Rome, Italy
| | - Christine Moissl-Eichinger
- Interactive Microbiome Research, Diagnostic & Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
- BioTechMed-Graz, Graz, Austria
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28
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Zhou Y, Leung MHY, Tong X, Lai Y, Tong JCK, Ridley IA, Lee PKH. Profiling Airborne Microbiota in Mechanically Ventilated Buildings Across Seasons in Hong Kong Reveals Higher Metabolic Activity in Low-Abundance Bacteria. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:249-259. [PMID: 33346641 DOI: 10.1021/acs.est.0c06201] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Metabolically active bacteria within built environments are poorly understood. This study aims to investigate the active airborne bacterial microbiota and compare the total and active microbiota in eight mechanically ventilated buildings over four consecutive seasons using the 16S rRNA gene (rDNA) and the 16S rRNA (rRNA), respectively. The relative abundances of the taxa of presumptive occupants and environmental origins were significantly different between the active and total microbiota. The Sloan neutral model suggested that ecological drift and random dispersal played a smaller role in the assembly of the active microbiota than the total microbiota. The seasonal nature of the active microbiota was consistent with that of the total microbiota in both indoor and outdoor environments, while only the indoor environment was significantly affected by geography. The relative abundances of the active and total taxa were positively correlated, suggesting that the high-abundance members were also the greatest contributors to the community-level metabolic activity. Based on the rRNA/rDNA ratio, the low-abundance members consistently had a higher taxon-level metabolic activity than the high-abundance members over seasons, suggesting that the low-abundance members may have the ability to survive and thrive in the indoor environment and their impact on the health of occupants cannot be overlooked.
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Affiliation(s)
- You Zhou
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Marcus H Y Leung
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Yonghang Lai
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Jimmy C K Tong
- Building Sustainability Group, Arup, Hong Kong SAR, China
| | - Ian A Ridley
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
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29
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Combs MP, Dickson RP. Turning the Lungs Inside Out: The Intersecting Microbiomes of the Lungs and the Built Environment. Am J Respir Crit Care Med 2020; 202:1618-1620. [PMID: 32822203 PMCID: PMC7737593 DOI: 10.1164/rccm.202007-2973ed] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Michael P Combs
- Department of Internal Medicine University of Michigan Medical School Ann Arbor, Michigan
| | - Robert P Dickson
- Department of Internal Medicine
- Department of Microbiology and Immunology University of Michigan Medical School Ann Arbor, Michigan and
- Michigan Center for Integrative Research in Critical Care Ann Arbor, Michigan
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30
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Liu HY, Li CX, Liang ZY, Zhang SY, Yang WY, Ye YM, Lin YX, Chen RC, Zhou HW, Su J. The Interactions of Airway Bacterial and Fungal Communities in Clinically Stable Asthma. Front Microbiol 2020; 11:1647. [PMID: 32849339 PMCID: PMC7396634 DOI: 10.3389/fmicb.2020.01647] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 06/24/2020] [Indexed: 12/31/2022] Open
Abstract
Dysbiotic airway microbiota play important roles in the inflammatory progression of asthma, and exploration of airway microbial interactions further elucidates asthma pathogenesis. However, little is known regarding the airway bacterial-fungal interactions in asthma patients. We conducted a cross-sectional survey of the sputum bacterial and fungal microbiota from 116 clinically stable asthma patients and 29 healthy controls using 16S rRNA gene and ITS1 sequencing. Compared with healthy individuals, asthma patients exhibited a significantly altered microbiota and increased bacterial and fungal alpha diversities in the airway. Microbial genera Moraxella, Capnocytophaga, and Ralstonia (bacteria) and Schizophyllum, Candida, and Phialemoniopsis (fungi) were more abundant in the asthma airways, while Rothia, Veillonella and Leptotrichia (bacteria) and Meyerozyma (fungus) were increased in healthy controls. The Moraxellaceae family and their genus Moraxella were significantly enriched in asthma patients compared with healthy controls (80.5-fold, P = 0.007 and 314.7-fold, P = 0.027, respectively). Moreover, Moraxellaceae, along with Schizophyllum, Candida, and Aspergillus (fungal genera), were positively associated with fungal alpha diversity. Correlation networks revealed 3 fungal genera (Schizophyllum, Candida, and Aspergillus) as important airway microbes in asthma that showed positive correlations with each other and multiple co-exclusions with other common microbiota. Moraxellaceae members were positively associated with asthma-enriched fungal taxa but negatively related to several healthy-enriched bacterial taxa. Collectively, our findings revealed an altered microbiota and complex microbial interactions in the airways of asthma patients. The Moraxellaceae family and their genus Moraxella, along with 3 important fungal taxa, showed significant interactions with the airway microbiota, providing potential insights into the novel pathogenic mechanisms of asthma.
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Affiliation(s)
- Hai-Yue Liu
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China.,State Key Laboratory of Organ Failure Research, Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Chun-Xi Li
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zhen-Yu Liang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shi-Yu Zhang
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Wan-Ying Yang
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yan-Mei Ye
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yan-Xia Lin
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Rong-Chang Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Hong-Wei Zhou
- State Key Laboratory of Organ Failure Research, Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jin Su
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
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Leung MHY, Tong X, Bastien P, Guinot F, Tenenhaus A, Appenzeller BMR, Betts RJ, Mezzache S, Li J, Bourokba N, Breton L, Clavaud C, Lee PKH. Changes of the human skin microbiota upon chronic exposure to polycyclic aromatic hydrocarbon pollutants. MICROBIOME 2020; 8:100. [PMID: 32591010 PMCID: PMC7320578 DOI: 10.1186/s40168-020-00874-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 05/20/2020] [Indexed: 05/25/2023]
Abstract
BACKGROUND Polycyclic aromatic hydrocarbons (PAHs) are of environmental and public health concerns and contribute to adverse skin attributes such as premature skin aging and pigmentary disorder. However, little information is available on the potential roles of chronic urban PAH pollutant exposure on the cutaneous microbiota. Given the roles of the skin microbiota have on healthy and undesirable skin phenotypes and the relationships between PAHs and skin properties, we hypothesize that exposure of PAHs may be associated with changes in the cutaneous microbiota. In this study, the skin microbiota of over two hundred Chinese individuals from two cities in China with varying exposure levels of PAHs were characterized by bacterial and fungal amplicon and shotgun metagenomics sequencing. RESULTS Skin site and city were strong parameters in changing microbial communities and their assembly processes. Reductions of bacterial-fungal microbial network structural integrity and stability were associated with skin conditions (acne and dandruff). Multivariate analysis revealed associations between abundances of Propionibacterium and Malassezia with host properties and pollutant exposure levels. Shannon diversity increase was correlated to exposure levels of PAHs in a dose-dependent manner. Shotgun metagenomics analysis of samples (n = 32) from individuals of the lowest and highest exposure levels of PAHs further highlighted associations between the PAHs quantified and decrease in abundances of skin commensals and increase in oral bacteria. Functional analysis identified associations between levels of PAHs and abundance of microbial genes of metabolic and other pathways with potential importance in host-microbe interactions as well as degradation of aromatic compounds. CONCLUSIONS The results in this study demonstrated the changes in composition and functional capacities of the cutaneous microbiota associated with chronic exposure levels of PAHs. Findings from this study will aid the development of strategies to harness the microbiota in protecting the skin against pollutants. Video Abstract.
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Affiliation(s)
- Marcus H. Y. Leung
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | | | - Florent Guinot
- L’Oréal Research and Innovation, Aulnay-sous-Bois, France
| | - Arthur Tenenhaus
- CentraleSupelec-L2S-Laboratoire des signaux et systèmes, Brain and Spine Institute, Université Paris-Sud, Orsay, France
| | | | | | | | - Jing Li
- L’Oréal Research and Innovation, Pudong, China
| | | | - Lionel Breton
- L’Oréal Research and Innovation, Aulnay-sous-Bois, France
| | - Cécile Clavaud
- L’Oréal Research and Innovation, Aulnay-sous-Bois, France
| | - Patrick K. H. Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
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Zhang N, Jia W, Wang P, King MF, Chan PT, Li Y. Most self-touches are with the nondominant hand. Sci Rep 2020; 10:10457. [PMID: 32591572 PMCID: PMC7320184 DOI: 10.1038/s41598-020-67521-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 05/22/2020] [Indexed: 02/08/2023] Open
Abstract
Self-touch may promote the transfer of microorganisms between body parts or surfaces to mucosa. In overt videography of a post-graduate office, students spent 9% of their time touching their own hair, face, neck, and shoulders (HFNS). These data were collected from 274,000 s of surveillance video in a Chinese graduate student office. The non-dominant hand contributed to 66.1% of HFNS-touches. Most importantly, mucous membranes were touched, on average, 34.3 (SE = 2.4) times per hour, which the non-dominant hand contributed to 240% more than the dominant hand. Gender had no significant effect on touch frequency, but a significant effect on duration per touch. The duration per touch on the HFNS was fitted with a log–log linear distribution. Touch behaviour analysis included surface combinations and a probability matrix for sequential touches of 20 sub-surfaces. These findings may partly explain the observed variation in the literature regarding the microbiome community distribution on human skin, supporting the importance of indirect contact transmission route in some respiratory disease transmission and providing data for risk analysis of infection spread and control.
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Affiliation(s)
- Nan Zhang
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, People's Republic of China
| | - Wei Jia
- Zhejiang Institute of Research and Innovation, The University of Hong Kong, Lin An, Zhejiang, People's Republic of China
| | - Peihua Wang
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, People's Republic of China
| | | | - Pak-To Chan
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, People's Republic of China
| | - Yuguo Li
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, People's Republic of China. .,School of Public Health, The University of Hong Kong, 7 Sassoon Road, Pokfulam, Hong Kong, People's Republic of China.
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33
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Ding LJ, Zhou XY, Zhu YG. Microbiome and antibiotic resistome in household dust from Beijing, China. ENVIRONMENT INTERNATIONAL 2020; 139:105702. [PMID: 32248025 DOI: 10.1016/j.envint.2020.105702] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/26/2020] [Accepted: 03/28/2020] [Indexed: 06/11/2023]
Abstract
We spend ever-increasing time indoors along with urbanization; however, the geographical distribution patterns of microbiome and antibiotic resistome, and their driving forces in household environment remains poorly characterized. Here, we surveyed the bacterial and fungal communities, and the resistome in settled dust gathered from 82 homes located across Beijing, China, employing Illumina sequencing and high-throughput quantitative PCR techniques. There was no clear geographical distribution pattern in dust-related bacterial communities although a slight but significant (P < 0.05) distance-decay relationship occurred in its community similarity; by contrast, a relatively distinct geographical clustering and a stronger distance-decay relationship were observed in fungal communities at the local scale. The cross-domain (bacteria versus fungi) relationships in the microbiome of the dust samples were mostly observed as robust co-occurrence correlations. The bacterial communities were dominated by Proteobacteria and Actinobacteria phyla, with human skin, soil and plants being potential major sources. The fungal communities largely comprised potential allergens (a median 61% of the fungal sequences), with Alternaria genus within Ascomycota phylum being the most predominant taxa. The profile of dust-related bacterial communities was mainly affected by housing factors related to occupants and houseplants, while that of fungal communities was determined by georeferenced environmental factors, particularly vascular plant diversity. Additionally, a great diversity (1.96 on average for Shannon index) and normalized abundance (2.22 copies per bacterial cell on average) of antibiotic resistance genes were detected across the dust samples, with the dominance of genes resistant to vancomycin and Macrolide-Lincosamide-Streptogramin B. The resistome profile exhibited no distinct geographical pattern, and was primarily driven by certain bacterial phyla and occupancy-related factors. Overall, we underline the significance of anthropogenic impacts and house location in structuring bacterial and fungal communities inside homes, respectively, and suggest that household dust is an overlooked reservoir for antibiotic resistance.
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Affiliation(s)
- Long-Jun Ding
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Xin-Yuan Zhou
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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Impact of the early-life skin microbiota on the development of canine atopic dermatitis in a high-risk breed birth cohort. Sci Rep 2020; 10:1044. [PMID: 31974513 PMCID: PMC6978374 DOI: 10.1038/s41598-020-57798-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 01/08/2020] [Indexed: 01/10/2023] Open
Abstract
Canine atopic dermatitis (CAD) is a prevalent inflammatory skin disease of dogs worldwide. Certain breeds such as the West Highland White Terriers (WHWT) are predisposed to suffer from CAD. Microbial dysbiosis is known to play a significant role in the pathogenesis of the disease, which is similar to its human counterpart, atopic dermatitis (AD). To date, no large cohort-study has been conducted in a predisposed dog breed to study the impact of the early-life microbiota on the development of CAD, as well as the possible implication of factors such as hygiene and access to the outdoors. In this study skin samples of 143 WHWT, including 109 puppies up to three weeks old and 34 parent dogs, from 17 breeders, were subjected to 16S rRNA gene and ITS2 amplicon sequencing to disclose the bacterial and fungal oral and skin microbiota, respectively. The oral samples served as a control group to confirm differences between haired and mucosal surfaces. The cutaneous microbiota differed between sample sites and age of the dogs. The season of sampling, geographical origin as well as hygiene status of the household and the access to the outdoors shaped the skin microbiota of the puppies significantly. However, we found that the individual early-life microbiota did not predispose for the later development of CAD.
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Kumar KV, Pal A, Bai P, Kour A, E S, P R, Kausar A, Chatterjee M, Prasad G, Balayan S, Dutta P, Wijesekera K. Co-aggregation of bacterial flora isolated from the human skin surface. Microb Pathog 2019; 135:103630. [DOI: 10.1016/j.micpath.2019.103630] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 06/27/2019] [Accepted: 07/16/2019] [Indexed: 12/21/2022]
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Sharma A, Richardson M, Cralle L, Stamper CE, Maestre JP, Stearns-Yoder KA, Postolache TT, Bates KL, Kinney KA, Brenner LA, Lowry CA, Gilbert JA, Hoisington AJ. Longitudinal homogenization of the microbiome between both occupants and the built environment in a cohort of United States Air Force Cadets. MICROBIOME 2019; 7:70. [PMID: 31046835 PMCID: PMC6498636 DOI: 10.1186/s40168-019-0686-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 04/22/2019] [Indexed: 05/10/2023]
Abstract
BACKGROUND The microbiome of the built environment has important implications for human health and wellbeing; however, bidirectional exchange of microbes between occupants and surfaces can be confounded by lifestyle, architecture, and external environmental exposures. Here, we present a longitudinal study of United States Air Force Academy cadets (n = 34), which have substantial homogeneity in lifestyle, diet, and age, all factors that influence the human microbiome. We characterized bacterial communities associated with (1) skin and gut samples from roommate pairs, (2) four built environment sample locations inside the pairs' dormitory rooms, (3) four built environment sample locations within shared spaces in the dormitory, and (4) room-matched outdoor samples from the window ledge of their rooms. RESULTS We analyzed 2,170 samples, which generated 21,866 unique amplicon sequence variants. Linear convergence of microbial composition and structure was observed between an occupants' skin and the dormitory surfaces that were only used by that occupant (i.e., desk). Conversely, bacterial community beta diversity (weighted Unifrac) convergence between the skin of both roommates and the shared dormitory floor between the two cadet's beds was not seen across the entire study population. The sampling period included two semester breaks in which the occupants vacated their rooms; upon their return, the beta diversity similarity between their skin and the surfaces had significantly decreased compared to before the break (p < 0.05). There was no apparent convergence between the gut and building microbiota, with the exception of communal bathroom door-handles, which suggests that neither co-occupancy, diet, or lifestyle homogenization had a significant impact on gut microbiome similarity between these cadets over the observed time frame. As a result, predictive classifier models were able to identify an individual more accurately based on the gut microbiota (74%) compared to skin (51%). CONCLUSIONS To the best of our knowledge, this is the first study to show an increase in skin microbial similarity of two individuals who start living together for the first time and who are not genetically related or romantically involved. Cohabitation was significantly associated with increased skin microbiota similarity but did not significantly influence the gut microbiota. Following a departure from the occupied space of several weeks, the skin microbiota, but not the gut microbiota, showed a significant reduction in similarity relative to the building. Overall, longitudinal observation of these dynamics enables us to dissect the influence of occupation, diet, and lifestyle factors on occupant and built environment microbial ecology.
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Affiliation(s)
- Anukriti Sharma
- Department of Pediatrics and Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92037, USA
| | - Miles Richardson
- Department of Pediatrics and Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92037, USA
| | - Lauren Cralle
- Department of Pediatrics and Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92037, USA
| | - Christopher E Stamper
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Juan P Maestre
- Department of Civil, Architectural and Environmental Engineering, University of Texas Austin, Austin, TX, 78712, USA
| | - Kelly A Stearns-Yoder
- Department of Physical Medicine and Rehabilitation, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
- Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Denver Veterans Affairs Medical Center (VAMC), Denver, CO, 80220, USA
- Military and Veteran Microbiome Consortium for Research and Education (MVM-CoRE), Denver, CO, 80220, USA
| | - Teodor T Postolache
- Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Denver Veterans Affairs Medical Center (VAMC), Denver, CO, 80220, USA
- Military and Veteran Microbiome Consortium for Research and Education (MVM-CoRE), Denver, CO, 80220, USA
- School of Medicine, University of Maryland Baltimore, Baltimore, MD, 21201, USA
- VISN 5 Mental Illness Research Education and Clinical Center (MIRECC), Baltimore, MD, 21201, USA
| | - Katherine L Bates
- Military and Veteran Microbiome Consortium for Research and Education (MVM-CoRE), Denver, CO, 80220, USA
- Department of Biology, United States Air Force Academy, Colorado Springs, CO, 80840, USA
| | - Kerry A Kinney
- Department of Civil, Architectural and Environmental Engineering, University of Texas Austin, Austin, TX, 78712, USA
| | - Lisa A Brenner
- Department of Physical Medicine and Rehabilitation, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
- Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Denver Veterans Affairs Medical Center (VAMC), Denver, CO, 80220, USA
- Military and Veteran Microbiome Consortium for Research and Education (MVM-CoRE), Denver, CO, 80220, USA
- Departments of Psychiatry and Neurology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Christopher A Lowry
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, 80309, USA
- Department of Physical Medicine and Rehabilitation, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
- Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Denver Veterans Affairs Medical Center (VAMC), Denver, CO, 80220, USA
- Military and Veteran Microbiome Consortium for Research and Education (MVM-CoRE), Denver, CO, 80220, USA
- Center for Neuroscience, University of Colorado Boulder, Boulder, CO, 80309, USA
- Center for Neuroscience, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Jack A Gilbert
- Department of Pediatrics and Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92037, USA
| | - Andrew J Hoisington
- Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Denver Veterans Affairs Medical Center (VAMC), Denver, CO, 80220, USA.
- Military and Veteran Microbiome Consortium for Research and Education (MVM-CoRE), Denver, CO, 80220, USA.
- Department of Systems Engineering and Management, Air Force Institute of Technology, Wright-Patterson AFB, OH, 45433, USA.
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Neutral Processes Drive Seasonal Assembly of the Skin Mycobiome. mSystems 2019; 4:mSystems00004-19. [PMID: 30944878 PMCID: PMC6435813 DOI: 10.1128/msystems.00004-19] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 03/06/2019] [Indexed: 11/20/2022] Open
Abstract
The importance of microorganisms to human skin health has led to a growing interest in the temporal stability of skin microbiota. Here we investigated the dynamics and assembly of skin fungal communities (mycobiomes) with amplicon sequencing of samples collected from multiple sites on 24 healthy Chinese individuals across four seasons (in the order of winter, spring, summer, and autumn in a calendar year). We found a significant difference in community compositions between individuals, and intrapersonal community variation increased over time at all body sites. Within each season, the frequency of occurrence of most operational taxonomic units (OTUs) was well fitted by a neutral model, highlighting the importance of stochastic forces such as passive dispersal and ecological drift in skin community assembly. Despite the significant richness contributed by neutrally distributed OTUs, skin coassociation networks were dominated by taxa well-adapted to multiple body sites (forehead, forearm, and palm), although hub species were disproportionately rare. Taken together, these results suggest that while skin mycobiome assembly is a predominantly neutral process, taxa that could be under the influence of selective forces (e.g., host selection) are potentially key to the structure of a community network. IMPORTANCE Fungi are well recognized members of the human skin microbiota and are crucial to cutaneous health. Common cutaneous diseases such as seborrheic dermatitis and dermatophytes are linked to fungal species. Most studies related to skin microbial community dynamics have focused on Western subjects, while non-Western individuals are understudied. In this study, we explore the seasonal changes of the skin mycobiome in a healthy Chinese cohort and identify ecological processes that could possibly give rise to such variations. Our work reveals the dynamic nature of host skin fungal community, highlighting the dominant roles neutral forces play in the seasonal assembly of skin mycobiome. This study provides insight into the microbial ecology of the human skin microbiome and fills a knowledge gap in the literature regarding the dynamics of skin fungal community.
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Transfer of Enteric Viruses Adenovirus and Coxsackievirus and Bacteriophage MS2 from Liquid to Human Skin. Appl Environ Microbiol 2018; 84:AEM.01809-18. [PMID: 30217840 PMCID: PMC6210118 DOI: 10.1128/aem.01809-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 09/05/2018] [Indexed: 11/23/2022] Open
Abstract
Enteric viruses (viruses that infect the gastrointestinal tract) are responsible for most water-transmitted diseases. They are shed in high concentrations in the feces of infected individuals, persist for an extended period of time in water, and are highly infective. Exposure to contaminated water directly (through ingestion) or indirectly (for example, through hand-water contacts followed by hand-to-mouth contacts) increases the risk of virus transmission. The work described herein provides a quantitative model for estimating human-pathogenic virus retention on skin following contact with contaminated water. The work will be important in refining the contribution of indirect transmission of virus to risks associated with water-related activities. Indirect exposure to waterborne viruses increases the risk of infection, especially among children with frequent hand-to-mouth contacts. Here, we quantified the transfer of one bacteriophage (MS2) and two enteric viruses (adenovirus and coxsackievirus) from liquid to skin. MS2, a commonly used enteric virus surrogate, was used to compare virus transfer rates in a volunteer trial to those obtained using human cadaver skin and synthetic skin. MS2 transfer to volunteer skin was similar to transfer to cadaver skin but significantly different from transfer to synthetic skin. The transfer of MS2, adenovirus, and coxsackievirus to cadaver skin was modeled using measurements for viruses attaching to the skin (adsorbed) and viruses in liquid residual on skin (unadsorbed). We find virus transfer per surface area is a function of the concentration of virus in the liquid and the film thickness of liquid retained on the skin and is estimable using a linear model. Notably, the amount of MS2 adsorbed on the skin was on average 5 times higher than the amount of adenovirus and 4 times higher than the amount of coxsackievirus. Quantification of pathogenic virus retention to skin would thus be overestimated using MS2 adsorption data. This study provides models of virus transfer useful for risk assessments of water-related activities, demonstrates significant differences in the transfer of pathogenic virus and MS2, and suggests cadaver skin as an alternative testing system for studying interactions between viruses and skin. IMPORTANCE Enteric viruses (viruses that infect the gastrointestinal tract) are responsible for most water-transmitted diseases. They are shed in high concentrations in the feces of infected individuals, persist for an extended period of time in water, and are highly infective. Exposure to contaminated water directly (through ingestion) or indirectly (for example, through hand-water contacts followed by hand-to-mouth contacts) increases the risk of virus transmission. The work described herein provides a quantitative model for estimating human-pathogenic virus retention on skin following contact with contaminated water. The work will be important in refining the contribution of indirect transmission of virus to risks associated with water-related activities.
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