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Zhang Y, Ruff SE, Oskolkov N, Tierney BT, Ryon K, Danko D, Mason CE, Elhaik E. The microbial biodiversity at the archeological site of Tel Megiddo (Israel). Front Microbiol 2023; 14:1253371. [PMID: 37808297 PMCID: PMC10559971 DOI: 10.3389/fmicb.2023.1253371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 08/25/2023] [Indexed: 10/10/2023] Open
Abstract
Introduction The ancient city of Tel Megiddo in the Jezreel Valley (Israel), which lasted from the Neolithic to the Iron Age, has been continuously excavated since 1903 and is now recognized as a World Heritage Site. The site features multiple ruins in various areas, including temples and stables, alongside modern constructions, and public access is allowed in designated areas. The site has been studied extensively since the last century; however, its microbiome has never been studied. We carried out the first survey of the microbiomes in Tel Megiddo. Our objectives were to study (i) the unique microbial community structure of the site, (ii) the variation in the microbial communities across areas, (iii) the similarity of the microbiomes to urban and archeological microbes, (iv) the presence and abundance of potential bio-corroding microbes, and (v) the presence and abundance of potentially pathogenic microbes. Methods We collected 40 swab samples from ten major areas and identified microbial taxa using next-generation sequencing of microbial genomes. These genomes were annotated and classified taxonomically and pathogenetically. Results We found that eight phyla, six of which exist in all ten areas, dominated the site (>99%). The relative sequence abundance of taxa varied between the ruins and the sampled materials and was assessed using all metagenomic reads mapping to a respective taxon. The site hosted unique taxa characteristic of the built environment and exhibited high similarity to the microbiome of other monuments. We identified acid-producing bacteria that may pose a risk to the site through biocorrosion and staining and thus pose a danger to the site's preservation. Differences in the microbiomes of the publicly accessible or inaccessible areas were insignificant; however, pathogens were more abundant in the former. Discussion We found that Tel Megiddo combines microbiomes of arid regions and monuments with human pathogens. The findings shed light on the microbial community structures and have relevance for bio-conservation efforts and visitor health.
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Affiliation(s)
- Yali Zhang
- Department of Biology, Lund University, Lund, Sweden
| | - S. Emil Ruff
- The Marine Biological Laboratory, Woods Hole, MA, United States
| | - Nikolay Oskolkov
- Department of Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, Lund, Sweden
| | - Braden T. Tierney
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
| | - Krista Ryon
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
| | - David Danko
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
| | - Christopher E. Mason
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, United States
- The Feil Family Brain and Mind Research Institute (BMRI), New York, NY, United States
- The Information Society Project, Yale Law School, New Haven, CT, United States
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, United States
| | - Eran Elhaik
- Department of Biology, Lund University, Lund, Sweden
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2
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Ejtahed HS, Parsa M, Larijani B. Ethical challenges in conducting and the clinical application of human microbiome research. J Med Ethics Hist Med 2023; 16:5. [PMID: 37753524 PMCID: PMC10518636 DOI: 10.18502/jmehm.v16i5.13313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 04/19/2023] [Indexed: 09/28/2023] Open
Abstract
The Article Abstract is not available.
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Affiliation(s)
- Hanieh Sadat Ejtahed
- AssistantProfessor, Obesity and Eating Habits Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran;Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
| | - Mojtaba Parsa
- AssistantProfessor, Medical Ethics and History of Medicine Research Center, Tehran University of Medical Sciences, Tehran, Iran; Research Center for War-affected People, Tehran University of Medical Sciences, Tehran, Iran.
| | - Bagher Larijani
- Professor, Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran;Medical Ethics and History of Medicine Research Center, Tehran University of Medical Sciences, Tehran, Iran.
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3
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Tomofuji Y, Sonehara K, Kishikawa T, Maeda Y, Ogawa K, Kawabata S, Nii T, Okuno T, Oguro-Igashira E, Kinoshita M, Takagaki M, Yamamoto K, Kurakawa T, Yagita-Sakamaki M, Hosokawa A, Motooka D, Matsumoto Y, Matsuoka H, Yoshimura M, Ohshima S, Nakamura S, Inohara H, Kishima H, Mochizuki H, Takeda K, Kumanogoh A, Okada Y. Reconstruction of the personal information from human genome reads in gut metagenome sequencing data. Nat Microbiol 2023:10.1038/s41564-023-01381-3. [PMID: 37188815 DOI: 10.1038/s41564-023-01381-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 04/12/2023] [Indexed: 05/17/2023]
Abstract
Human DNA present in faecal samples can result in a small number of human reads in gut shotgun metagenomic sequencing data. However, it is presently unclear how much personal information can be reconstructed from such reads, and this has not been quantitatively evaluated. Such a quantitative evaluation is necessary to clarify the ethical concerns related to data sharing and to enable efficient use of human genetic information in stool samples, such as for research and forensics. Here we used genomic approaches to reconstruct personal information from the faecal metagenomes of 343 Japanese individuals with associated human genotype data. Genetic sex could be accurately predicted based on the sequencing depth of sex chromosomes for 97.3% of the samples. Individuals could be re-identified from the matched genotype data based on human reads recovered from the faecal metagenomic data with 93.3% sensitivity using a likelihood score-based method. This method also enabled us to predict the ancestries of 98.3% of the samples. Finally, we performed ultra-deep shotgun metagenomic sequencing of five faecal samples as well as whole-genome sequencing of blood samples. Using genotype-calling approaches, we demonstrated that the genotypes of both common and rare variants could be reconstructed from faecal samples. This included clinically relevant variants. Our approach can be used to quantify personal information contained within gut metagenome data.
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Affiliation(s)
- Yoshihiko Tomofuji
- Department of Statistical Genetics, Graduate School of Medicine, Osaka University, Suita, Japan.
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan.
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
| | - Kyuto Sonehara
- Department of Statistical Genetics, Graduate School of Medicine, Osaka University, Suita, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Toshihiro Kishikawa
- Department of Statistical Genetics, Graduate School of Medicine, Osaka University, Suita, Japan
- Department of Otorhinolaryngology-Head and Neck Surgery, Graduate School of Medicine, Osaka University, Suita, Japan
- Department of Head and Neck Surgery, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Yuichi Maeda
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Kotaro Ogawa
- Department of Neurology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Shuhei Kawabata
- Department of Neurosurgery, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Takuro Nii
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Tatsusada Okuno
- Department of Neurology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Eri Oguro-Igashira
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Makoto Kinoshita
- Department of Neurology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Masatoshi Takagaki
- Department of Neurosurgery, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Kenichi Yamamoto
- Department of Statistical Genetics, Graduate School of Medicine, Osaka University, Suita, Japan
- Department of Pediatrics, Graduate School of Medicine, Osaka University, Suita, Japan
- Laboratory of Statistical Immunology, WPI Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Takashi Kurakawa
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Mayu Yagita-Sakamaki
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Akiko Hosokawa
- Department of Neurology, Graduate School of Medicine, Osaka University, Suita, Japan
- Department of Neurology, Suita Municipal Hospital, Suita, Japan
| | - Daisuke Motooka
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Yuki Matsumoto
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Hidetoshi Matsuoka
- Department of Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano, Japan
| | - Maiko Yoshimura
- Department of Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano, Japan
| | - Shiro Ohshima
- Department of Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano, Japan
| | - Shota Nakamura
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Japan
| | - Hidenori Inohara
- Department of Otorhinolaryngology-Head and Neck Surgery, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Haruhiko Kishima
- Department of Neurosurgery, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Hideki Mochizuki
- Department of Neurology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Kiyoshi Takeda
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Japan
- WPI Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Atsushi Kumanogoh
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
- Department of Immunopathology, Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Graduate School of Medicine, Osaka University, Suita, Japan.
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan.
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
- Laboratory of Statistical Immunology, WPI Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan.
- Center for Infectious Disease Education and Research, Osaka University, Suita, Japan.
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Ryon KA, Tierney BT, Frolova A, Kahles A, Desnues C, Ouzounis C, Gibas C, Bezdan D, Deng Y, He D, Dias-Neto E, Elhaik E, Afshin E, Grills G, Iraola G, Suzuki H, Werner J, Udekwu K, Schriml L, Bhattacharyya M, Oliveira M, Zambrano MM, Hazrin-Chong NH, Osuolale O, Łabaj PP, Tiasse P, Rapuri S, Borras S, Pozdniakova S, Shi T, Sezerman U, Rodo X, Sezer ZH, Mason CE. A history of the MetaSUB consortium: Tracking urban microbes around the globe. iScience 2022; 25:104993. [PMID: 36299999 PMCID: PMC9589169 DOI: 10.1016/j.isci.2022.104993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The MetaSUB Consortium, founded in 2015, is a global consortium with an interdisciplinary team of clinicians, scientists, bioinformaticians, engineers, and designers, with members from more than 100 countries across the globe. This network has continually collected samples from urban and rural sites including subways and transit systems, sewage systems, hospitals, and other environmental sampling. These collections have been ongoing since 2015 and have continued when possible, even throughout the COVID-19 pandemic. The consortium has optimized their workflow for the collection, isolation, and sequencing of DNA and RNA collected from these various sites and processing them for metagenomics analysis, including the identification of SARS-CoV-2 and its variants. Here, the Consortium describes its foundations, and its ongoing work to expand on this network and to focus its scope on the mapping, annotation, and prediction of emerging pathogens, mapping microbial evolution and antibiotic resistance, and the discovery of novel organisms and biosynthetic gene clusters.
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Affiliation(s)
- Krista A. Ryon
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY USA
- Weill Cornell Medicine, New York, NY, USA
| | - Braden T. Tierney
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY USA
- Weill Cornell Medicine, New York, NY, USA
| | - Alina Frolova
- Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
- Kyiv Academic University, Kyiv, Ukraine
| | - Andre Kahles
- ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Christelle Desnues
- Mediterranean Institute of Oceanography, 163 Avenue de Luminy Bâtiment Méditerranée, 13288, Marseille Cedex 9, France
| | | | | | - Daniela Bezdan
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- GermanyNGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany
- yuri GmbH, Meckenbeuren, Germany
| | - Youping Deng
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Ding He
- University of Copenhagen, Copenhagen, Denmark
| | | | | | - Evan Afshin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | | | - Gregorio Iraola
- Institut Pasteur de Montevideo, Mataojo 2020, Montevideo, 11400, Uruguay
| | | | - Johannes Werner
- High Performance and Cloud Computing Group, Zentrum für Datenverarbeitung (ZDV), Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Klas Udekwu
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Lynn Schriml
- University of Maryland School of Medicine, University of Maryland, Baltimore, MD, USA
| | | | | | | | | | | | | | | | - Sampath Rapuri
- The Community Lab; Los Alamos Makers, Los Alamos, NM 87544, USA
| | - Silvia Borras
- Barcelona Institute for Global Health, Rosselló, 132, 708036 Barcelona, Spain
| | - Sofya Pozdniakova
- Barcelona Institute for Global Health, Rosselló, 132, 708036 Barcelona, Spain
| | - Tieliu Shi
- East China Normal University, Zhongshan Rd (N), 3663, 200050 Shanghai, Putuo, China
| | - Ugur Sezerman
- Department of Biostatistics, Acibadem University, Istanbul, Turkey
| | - Xavier Rodo
- Barcelona Institute for Global Health, Rosselló, 132, 708036 Barcelona, Spain
| | | | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- WorldQuant Initiative for Quantitative Prediction, New York, NY, USA
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5
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Lange L, Berg G, Cernava T, Champomier-Vergès MC, Charles T, Cocolin L, Cotter P, D’Hondt K, Kostic T, Maguin E, Makhalanyane T, Meisner A, Ryan M, Kiran GS, de Souza RS, Sanz Y, Schloter M, Smidt H, Wakelin S, Sessitsch A. Microbiome ethics, guiding principles for microbiome research, use and knowledge management. ENVIRONMENTAL MICROBIOME 2022; 17:50. [PMID: 36180931 PMCID: PMC9526347 DOI: 10.1186/s40793-022-00444-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 09/14/2022] [Indexed: 06/16/2023]
Abstract
The overarching biological impact of microbiomes on their hosts, and more generally their environment, reflects the co-evolution of a mutualistic symbiosis, generating fitness for both. Knowledge of microbiomes, their systemic role, interactions, and impact grows exponentially. When a research field of importance for planetary health evolves so rapidly, it is essential to consider it from an ethical holistic perspective. However, to date, the topic of microbiome ethics has received relatively little attention considering its importance. Here, ethical analysis of microbiome research, innovation, use, and potential impact is structured around the four cornerstone principles of ethics: Do Good; Don't Harm; Respect; Act Justly. This simple, but not simplistic approach allows ethical issues to be communicative and operational. The essence of the paper is captured in a set of eleven microbiome ethics recommendations, e.g., proposing gut microbiome status as common global heritage, similar to the internationally agreed status of major food crops.
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Affiliation(s)
- Lene Lange
- LL-BioEconomy, Valby, Copenhagen, Denmark
| | | | | | | | | | | | - Paul Cotter
- Teagasc Food Research Centre, Moorepark, APC Microbiome Ireland and VistaMilk, Cork, Ireland
| | - Kathleen D’Hondt
- Department of Economy, Science and Innovation, Flemish Government, Brussels, Belgium
| | - Tanja Kostic
- AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Emmanuelle Maguin
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, Jouy-en-Josas, France
| | | | - Annelein Meisner
- Wageningen Research, Wageningen University & Research, Wageningen, The Netherlands
| | | | | | | | - Yolanda Sanz
- Institute of Agrochemistry and Food Technology- Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | | | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
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Shin A, Xu H. Privacy Risks in Microbiome Research: Public Perspectives before and during a Global Pandemic. Ethics Hum Res 2022; 44:2-13. [PMID: 35802792 DOI: 10.1002/eahr.500132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We assessed public perspectives of microbiome research privacy risks before and after a nationwide emergency was declared in the United States regarding the Covid-19 pandemic. From January to July of 2020, we conducted an online survey of perceived privacy risks of microbiome research among U.S. adults. Among 3,106 participants (the preemergency group), most expressed that the microbiome posed privacy risks similar to those associated with DNA (60.3%) or medical records (50.6%) and that they would prefer detailed explanations (70.2%) of risk in consent materials. Only 8.9% reported moderate to high familiarity with microbiome privacy risks. In adjusted analyses, individuals who participated in the study after the Covid-19 emergency was declared (the Covid-19 emergency group) were less likely to express that microbiome privacy risks were similar to those of DNA or medical records and more likely to report familiarity with the privacy risks of microbiomes. There was a trend toward increased concern after the Covid-19 emergency was declared (p = 0.053). Overall, the study revealed that many U.S. adults believe that microbiome privacy risks are similar to those associated with DNA or medical records, and they prefer detailed explanations in consent documents. Individuals who participated after the Covid-19 emergency was declared reported greater knowledge of microbiome privacy risks but had more concern.
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Affiliation(s)
- Andrea Shin
- Assistant professor in the Division of Gastroenterology and Hepatology in the Department of Medicine and at the Indiana University Center for Bioethics at the Indiana University School of Medicine
| | - Huiping Xu
- Associate professor in the Department of Biostatistics and Health Data Science at the Indiana University School of Medicine
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Bruno A, Agostinetto G, Fumagalli S, Ghisleni G, Sandionigi A. It’s a Long Way to the Tap: Microbiome and DNA-Based Omics at the Core of Drinking Water Quality. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19137940. [PMID: 35805598 PMCID: PMC9266242 DOI: 10.3390/ijerph19137940] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/17/2022] [Accepted: 06/24/2022] [Indexed: 11/16/2022]
Abstract
Microbial communities interact with us and affect our health in ways that are only beginning to be understood. Microorganisms have been detected in every ecosystem on Earth, as well as in any built environment that has been investigated. Drinking water sources, drinking water treatment plants and distribution systems provide peculiar microbial ecological niches, dismantling the belief of the “biological simplicity” of drinking water. Nevertheless, drinking water microbiomes are understudied compared to other microbiomes. Recent DNA sequencing and meta-omics advancements allow a deeper understanding of drinking water microbiota. Thus, moving beyond the limits of day-to-day testing for specific pathogenic microbes, new approaches aim at predicting microbiome changes driven by disturbances at the macro-scale and overtime. This will foster an effective and proactive management of water sources, improving the drinking water supply system and the monitoring activities to lower public health risk. Here, we want to give a new angle on drinking water microbiome research. Starting from a selection of 231 scientific publications on this topic, we emphasize the value of biodiversity in drinking water ecosystems and how it can be related with industrialization. We then discuss how microbiome research can support sustainable drinking water management, encouraging collaborations across sectors and involving the society through responsible research and innovation.
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Affiliation(s)
- Antonia Bruno
- Biotechnology and Biosciences Department, University of Milano-Bicocca, 20126 Milan, Italy; (G.A.); (S.F.); (G.G.)
- Correspondence:
| | - Giulia Agostinetto
- Biotechnology and Biosciences Department, University of Milano-Bicocca, 20126 Milan, Italy; (G.A.); (S.F.); (G.G.)
| | - Sara Fumagalli
- Biotechnology and Biosciences Department, University of Milano-Bicocca, 20126 Milan, Italy; (G.A.); (S.F.); (G.G.)
| | - Giulia Ghisleni
- Biotechnology and Biosciences Department, University of Milano-Bicocca, 20126 Milan, Italy; (G.A.); (S.F.); (G.G.)
- Institut Jacques Monod, Université Paris Cité, CNRS, 75013 Paris, France
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Abstract
In this article, we argue that a careful examination of human microbiome science's relationship with race and racism is necessary to foster equitable social and ecological relations in the field. We point to the origins and evolution of the problematic use of race in microbiome literature by demonstrating the increased usage of race both explicitly and implicitly in and beyond the human microbiome sciences. We demonstrate how these uses limit the future of rigorous and just microbiome research. We conclude with an outline of alternative actionable ways to build a more effective, antiracist microbiome science.
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9
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Meisner A, Wepner B, Kostic T, van Overbeek LS, Bunthof CJ, de Souza RSC, Olivares M, Sanz Y, Lange L, Fischer D, Sessitsch A, Smidt H. Calling for a systems approach in microbiome research and innovation. Curr Opin Biotechnol 2021; 73:171-178. [PMID: 34479027 DOI: 10.1016/j.copbio.2021.08.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 07/27/2021] [Accepted: 08/05/2021] [Indexed: 12/23/2022]
Abstract
Microbiomes are all around us in natural and cultivated ecosystems, for example, soils, plants, animals and our own body. Microbiomes are essential players of biotechnological applications, and their functions drive human, animal, plant and environmental health. The rapidly developing microbiome research landscape was studied by a global mapping excercise and bibliometric analysis. Although microbiome research is performed in many different science fields, using similar concepts within and across fields, microbiomes are mostly investigated one ecosystem at-a-time. In order to fully understand microbiome impacts and leverage microbial functions, research needs to adopt a systems approach connecting microbiomes and research initiatives in divergent fields to create understanding on how microbiomes can be modulated for desirable functions as a basis of sustainable, circular bioeconomy.
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Affiliation(s)
- Annelein Meisner
- Wageningen University & Research,Wageningen Research, Droevendaalsesteeg 4, Wageningen, 6708 PB, The Netherlands
| | - Beatrix Wepner
- AIT Austrian Institute of Technology, Center for Innovation Systems & Policy, Giefinggasse 4, Vienna, 1210, Austria
| | - Tanja Kostic
- AIT Austrian Institute of Technology, Center for Health & Bioresources, Bioresources Unit, Konrad Lorenz Strasse 24, Tulln, 3430, Austria
| | - Leo S van Overbeek
- Wageningen University & Research,Wageningen Research, Droevendaalsesteeg 4, Wageningen, 6708 PB, The Netherlands
| | - Christine J Bunthof
- Wageningen University & Research,Wageningen Research, Droevendaalsesteeg 4, Wageningen, 6708 PB, The Netherlands
| | - Rafael Soares Correa de Souza
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas (UNICAMP), Campinas, SP, 13083-875, Brazil
| | - Marta Olivares
- Institute of Agrochemistry and Food Technology, National Research Council (IATA-CSIC), Paterna-Valencia, 46980, Spain
| | - Yolanda Sanz
- Institute of Agrochemistry and Food Technology, National Research Council (IATA-CSIC), Paterna-Valencia, 46980, Spain
| | - Lene Lange
- BioEconomy, Research & Advisory, Karensgade 5, Valby, 2500, Denmark
| | - Doreen Fischer
- Helmholtz Zentrum München, National Research Center for Environmental Health, Research Unit for Comparative Microbiome Analysis, Ingolstaedter Landstr. 1, Neuherberg, Munich, D-85764, Germany
| | - Angela Sessitsch
- AIT Austrian Institute of Technology, Center for Health & Bioresources, Bioresources Unit, Konrad Lorenz Strasse 24, Tulln, 3430, Austria
| | - Hauke Smidt
- Wageningen University & Research, Laboratory of Microbiology, Stippeneng 4, Wageningen, 6708 WE, The Netherlands.
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10
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Elhaik E, Ahsanuddin S, Robinson JM, Foster EM, Mason CE. The impact of cross-kingdom molecular forensics on genetic privacy. MICROBIOME 2021; 9:114. [PMID: 34016161 PMCID: PMC8138925 DOI: 10.1186/s40168-021-01076-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 04/07/2021] [Indexed: 05/21/2023]
Abstract
Recent advances in metagenomic technology and computational prediction may inadvertently weaken an individual's reasonable expectation of privacy. Through cross-kingdom genetic and metagenomic forensics, we can already predict at least a dozen human phenotypes with varying degrees of accuracy. There is also growing potential to detect a "molecular echo" of an individual's microbiome from cells deposited on public surfaces. At present, host genetic data from somatic or germ cells provide more reliable information than microbiome samples. However, the emerging ability to infer personal details from different microscopic biological materials left behind on surfaces requires in-depth ethical and legal scrutiny. There is potential to identify and track individuals, along with new, surreptitious means of genetic discrimination. This commentary underscores the need to update legal and policy frameworks for genetic privacy with additional considerations for the information that could be acquired from microbiome-derived data. The article also aims to stimulate ubiquitous discourse to ensure the protection of genetic rights and liberties in the post-genomic era. Video abstract.
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Affiliation(s)
- Eran Elhaik
- Department of Biology, Lund University, 22362, Lund, Sweden.
| | - Sofia Ahsanuddin
- Department of Medical Education, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Jake M Robinson
- The Department of Landscape Architecture, University of Sheffield, Sheffield, S10 2TN, UK
- The Healthy Urban Microbiome Initiative (HUMI), Adelaide, 5005, South Australia
| | | | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10021, USA.
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, 10021, USA.
- The Feil Family Brain and Mind Research Institute (BMRI), New York, NY, 10021, USA.
- The Information Society Project, Yale Law School, New Haven, CT, 06511, USA.
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11
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Li D, Gao C, Zhang F, Yang R, Lan C, Ma Y, Wang J. Seven facts and five initiatives for gut microbiome research. Protein Cell 2021; 11:391-400. [PMID: 32172500 PMCID: PMC7251010 DOI: 10.1007/s13238-020-00697-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Danyi Li
- Beijing Rexinchang Biotechnology Research Institute Co. Ltd, Beijing, 100011, China
| | - Chunhui Gao
- Beijing Rexinchang Biotechnology Research Institute Co. Ltd, Beijing, 100011, China
| | - Faming Zhang
- Medical Center for Digestive Diseases, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210011, China
- Key Lab of Holistic Integrative Enterology, Nanjing Medical University, Nanjing, 210011, China
- Division of Microbiotherapy, Sir Run Run Shaw Hospital, Nanjing Medical University, Nanjing, 211166, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Canhui Lan
- Beijing Rexinchang Biotechnology Research Institute Co. Ltd, Beijing, 100011, China
| | - Yonghui Ma
- Centre for Bioethics, Medical College, Xiamen University, Xiamen, 361102, China.
| | - Jun Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science, Beijing, 100101, China.
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12
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Robinson JM, Pasternak Z, Mason CE, Elhaik E. Forensic Applications of Microbiomics: A Review. Front Microbiol 2021; 11:608101. [PMID: 33519756 PMCID: PMC7838326 DOI: 10.3389/fmicb.2020.608101] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/14/2020] [Indexed: 01/04/2023] Open
Abstract
The rise of microbiomics and metagenomics has been driven by advances in genomic sequencing technology, improved microbial sampling methods, and fast-evolving approaches in bioinformatics. Humans are a host to diverse microbial communities in and on their bodies, which continuously interact with and alter the surrounding environments. Since information relating to these interactions can be extracted by analyzing human and environmental microbial profiles, they have the potential to be relevant to forensics. In this review, we analyzed over 100 papers describing forensic microbiome applications with emphasis on geolocation, personal identification, trace evidence, manner and cause of death, and inference of the postmortem interval (PMI). We found that although the field is in its infancy, utilizing microbiome and metagenome signatures has the potential to enhance the forensic toolkit. However, many of the studies suffer from limited sample sizes and model accuracies, and unrealistic environmental settings, leaving the full potential of microbiomics to forensics unexplored. It is unlikely that the information that can currently be elucidated from microbiomics can be used by law enforcement. Nonetheless, the research to overcome these challenges is ongoing, and it is foreseeable that microbiome-based evidence could contribute to forensic investigations in the future.
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Affiliation(s)
- Jake M Robinson
- Department of Landscape, University of Sheffield, Sheffield, United Kingdom.,Healthy Urban Microbiome Initiative (HUMI), Adelaide, SA, Australia
| | - Zohar Pasternak
- Quality Assurance and Evidence Unit, Division of Identification and Forensic Science (DIFS), National Headquarters of the Israel Police, Jerusalem, Israel
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States.,The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, United States
| | - Eran Elhaik
- Department of Biology, Lund University, Lund, Sweden
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13
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Butler ÉM, Reynolds AJ, Derraik JGB, Wilson BC, Cutfield WS, Grigg CP. The views of pregnant women in New Zealand on vaginal seeding: a mixed-methods study. BMC Pregnancy Childbirth 2021; 21:49. [PMID: 33435920 PMCID: PMC7802193 DOI: 10.1186/s12884-020-03500-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 12/16/2020] [Indexed: 12/03/2022] Open
Abstract
Background Vaginal seeding is the administration of maternal vaginal bacteria to babies following birth by caesarean section (CS), intended to mimic the microbial exposure that occurs during vaginal birth. Appropriate development of the infant gut microbiome assists early immune development and might help reduce the risk of certain health conditions later in life, such as obesity and asthma. We aimed to explore the views of pregnant women on this practice. Methods We conducted a sequential mixed-methods study on the views of pregnant women in New Zealand (NZ) on vaginal seeding. Phase one: brief semi-structured interviews with pregnant women participating in a clinical trial of vaginal seeding (n = 15); and phase two: online questionnaire of pregnant women throughout NZ (not in the trial) (n = 264). Reflexive thematic analysis was applied to interview and open-ended questionnaire data. Closed-ended questionnaire responses were analysed using descriptive statistics. Results Six themes were produced through analysis of the open-ended data: “seeding replicates a natural process”, “microbiome is in the media”, “seeding may have potential benefits”, “seeking validation by a maternity caregiver”, “seeding could help reduce CS guilt”, and “the unknowns of seeding”. The idea that vaginal seeding replicates a natural process was suggested by some as an explanation to help overcome any initial negative perceptions of it. Many considered vaginal seeding to have potential benefit for the gut microbiome, while comparatively fewer considered it to be potentially beneficial for specific conditions such as obesity. Just under 30% of questionnaire respondents (n = 78; 29.5%) had prior knowledge of vaginal seeding, while most (n = 133; 82.6%) had an initially positive or neutral reaction to it. Few respondents changed their initial views on the practice after reading provided evidence-based information (n = 60; 22.7%), but of those who did, most became more positive (n = 51; 86.4%). Conclusions Given its apparent acceptability, and if shown to be safe and effective for the prevention of early childhood obesity, vaginal seeding could be a non-stigmatising approach to prevention of this condition among children born by CS. Our findings also highlight the importance of lead maternity carers in NZ remaining current in their knowledge of vaginal seeding research. Supplementary Information The online version contains supplementary material available at 10.1186/s12884-020-03500-y.
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Affiliation(s)
- Éadaoin M Butler
- A Better Start - National Science Challenge, Auckland, New Zealand.,Liggins Institute, University of Auckland, Private Bag, Auckland, 92019, New Zealand
| | - Abigail J Reynolds
- Liggins Institute, University of Auckland, Private Bag, Auckland, 92019, New Zealand.,Dartmouth College, Hanover, NH, USA
| | - José G B Derraik
- A Better Start - National Science Challenge, Auckland, New Zealand.,Liggins Institute, University of Auckland, Private Bag, Auckland, 92019, New Zealand.,Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden.,Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Brooke C Wilson
- Liggins Institute, University of Auckland, Private Bag, Auckland, 92019, New Zealand
| | - Wayne S Cutfield
- A Better Start - National Science Challenge, Auckland, New Zealand. .,Liggins Institute, University of Auckland, Private Bag, Auckland, 92019, New Zealand.
| | - Celia P Grigg
- Liggins Institute, University of Auckland, Private Bag, Auckland, 92019, New Zealand
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14
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Clarke LJ, Jones PJ, Ammitzboll H, Barmuta LA, Breed MF, Chariton A, Charleston M, Dakwa V, Dewi F, Eri R, Fountain-Jones NM, Freeman J, Kendal D, McDougal R, Raes EJ, Sow SLS, Staples T, Sutcliffe B, Vemuri R, Weyrich LS, Flies EJ. Mainstreaming Microbes across Biomes. Bioscience 2020. [DOI: 10.1093/biosci/biaa057] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Abstract
Bacteria, fungi, and other microorganisms in the environment (i.e., environmental microbiomes) provide vital ecosystem services and affect human health. Despite their importance, public awareness of environmental microbiomes has lagged behind that of human microbiomes. A key problem has been a scarcity of research demonstrating the microbial connections across environmental biomes (e.g., marine, soil) and between environmental and human microbiomes. We show in the present article, through analyses of almost 10,000 microbiome papers and three global data sets, that there are significant taxonomic similarities in microbial communities across biomes, but very little cross-biome research exists. This disconnect may be hindering advances in microbiome knowledge and translation. In this article, we highlight current and potential applications of environmental microbiome research and the benefits of an interdisciplinary, cross-biome approach. Microbiome scientists need to engage with each other, government, industry, and the public to ensure that research and applications proceed ethically, maximizing the potential benefits to society.
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Affiliation(s)
- Laurence J Clarke
- Institute for Marine and Antarctic Studies, and LJC is also affiliated with the Antarctic Climate and Ecosystems Cooperative Research Centre, University of Tasmania, in Hobart, Australia
| | - Penelope J Jones
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia
| | - Hans Ammitzboll
- School of Natural Sciences, University of Tasmania, Hobart, Australia
- ARC Training Centre for Forest Value, University of Tasmania, Hobart, Australia
| | - Leon A Barmuta
- School of Natural Sciences, University of Tasmania, Hobart, Australia
| | - Martin F Breed
- College of Scienceand Engineering, Flinders University, Adelaide, Australia, and with the Healthy Urban Microbiome Initiative (www.HUMIglobal.org) in the United Kingdom
| | - Anthony Chariton
- Department of Biological Sciences, Macquarie University, Sydney, Australia
| | | | - Vongai Dakwa
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Australia
| | - Fera Dewi
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Australia
| | - Rajaraman Eri
- School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston, Australia
| | | | - Jules Freeman
- Scion, part of the New Zealand Forest Research Institute Ltd., Rotorua, New Zealand
| | - Dave Kendal
- Research Centre for Marine and Fisheries Product Processing and Biotechnology, Ministry of Marine Affairs and Fisheries, Jakarta, Indonesia
- School of Technology, Environments, and Design, University of Tasmania, Hobart, Australia
| | - Rebecca McDougal
- Scion, part of the New Zealand Forest Research Institute Ltd., Rotorua, New Zealand
| | - Eric J Raes
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Australia
| | - Swan Li San Sow
- Institute for Marine and Antarctic Studies, and LJC is also affiliated with the Antarctic Climate and Ecosystems Cooperative Research Centre, University of Tasmania, in Hobart, Australia
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Australia
| | - Timothy Staples
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Australia, and with the School of Biological Sciences, University of Queensland, Brisbane, Australia. RV is also affiliated with the Department of Comparative Medicine, in the School of Medicine, at Wake Forest Baptist Medical Center, in Winston-Salem, North Carolina
| | - Brodie Sutcliffe
- Department of Biological Sciences, Macquarie University, Sydney, Australia
| | - Ravichandra Vemuri
- School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston, Australia
| | - Laura S Weyrich
- School of Biological Sciences, University of Adelaide, Adelaide, Australia, and with the Department of Anthropology at The Pennsylvania State University, in University Park, Pennsylvania
| | - Emily J Flies
- School of Natural Sciences, University of Tasmania, Hobart, Australia
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15
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Advances in Understanding the Human Urinary Microbiome and Its Potential Role in Urinary Tract Infection. mBio 2020; 11:mBio.00218-20. [PMID: 32345639 PMCID: PMC7188990 DOI: 10.1128/mbio.00218-20] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Recent advances in the analysis of microbial communities colonizing the human body have identified a resident microbial community in the human urinary tract (UT). Compared to many other microbial niches, the human UT harbors a relatively low biomass. Studies have identified many genera and species that may constitute a core urinary microbiome. However, the contribution of the UT microbiome to urinary tract infection (UTI) and recurrent UTI (rUTI) pathobiology is not yet clearly understood. Evidence suggests that commensal species within the UT and urogenital tract (UGT) microbiomes, such as Lactobacillus crispatus, may act to protect against colonization with uropathogens. However, the mechanisms and fundamental biology of the urinary microbiome-host relationship are not understood. The ability to measure and characterize the urinary microbiome has been enabled through the development of next-generation sequencing and bioinformatic platforms that allow for the unbiased detection of resident microbial DNA. Translating technological advances into clinical insight will require further study of the microbial and genomic ecology of the urinary microbiome in both health and disease. Future diagnostic, prognostic, and therapeutic options for the management of UTI may soon incorporate efforts to measure, restore, and/or preserve the native, healthy ecology of the urinary microbiomes.
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16
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Hervé V, Lopez PJ. Analysis of interdomain taxonomic patterns in urban street mats. Environ Microbiol 2020; 22:1280-1293. [PMID: 31997567 DOI: 10.1111/1462-2920.14933] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 01/15/2020] [Accepted: 01/27/2020] [Indexed: 11/28/2022]
Abstract
Streets are constantly crossed by billions of vehicles and pedestrians. Their gutters, which convey stormwater and contribute to waste management, and are important for human health and well-being, probably play a number of ecological roles. Street surfaces may also represent an important part of city surface areas. To better characterize the ecology of this yet poorly explored compartment, we used filtration and DNA metabarcoding to address microbial community composition and assembly across the city of Paris, France. Diverse bacterial and eukaryotic taxonomic groups were identified, including members involved in key biogeochemical processes, along with a number of parasites and putative pathogens of human, animals and plants. We showed that the beta diversity patterns between bacterial and eukaryotic communities were correlated, suggesting interdomain associations. Beta diversity analyses revealed the significance of biotic factors (cohesion metrics) in shaping gutter microbial community assembly and, to a lesser extent, the contribution of abiotic factors (pH and conductivity). Co-occurrences analysis confirmed contrasting non-random patterns both within and between domains of life, specifically when comparing diatoms and fungi. Our results highlight microbial coexistence patterns in streets and reinforce the need to further explore biodiversity in urban ground transportation infrastructures.
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Affiliation(s)
- Vincent Hervé
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043, Marburg, Germany
| | - Pascal Jean Lopez
- Laboratoire Biologie des ORganismes et Ecosystèmes Aquatiques (BOREA), Muséum national d'Histoire naturelle, Centre National de la Recherche Scientifique, Sorbonne Université, Institut de Recherche pour le Développement, Université de Caen Normandie, Université des Antilles, 43 rue Cuvier, 75005, Paris, France
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17
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Abstract
More than a decade ago, the term "next-generation" sequencing was coined to describe what was, at the time, revolutionary new methods to sequence RNA and DNA at a faster pace and cheaper cost than could be performed by standard bench-top protocols. Since then, the field of DNA sequencing has evolved at a rapid pace, with new breakthroughs allowing capacity to exponentially increase and cost to dramatically decrease. As genome-scale sequencing has become routine, a paradigm shift is occurring in genomics, which uses the power of high-throughput, rapid sequencing power with large-scale studies. These new approaches to genetic discovery will provide direct impact to fields such as personalized medicine, evolution, and biodiversity. This work reviews recent technology advances and methods in next-generation sequencing and highlights current large-scale sequencing efforts driving the evolution of the genomics space.
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Affiliation(s)
- Shawn E Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806
| | - Braden E Boone
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806
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18
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Li H, Zhou XY, Yang XR, Zhu YG, Hong YW, Su JQ. Spatial and seasonal variation of the airborne microbiome in a rapidly developing city of China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 665:61-68. [PMID: 30772579 DOI: 10.1016/j.scitotenv.2019.01.367] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/21/2019] [Accepted: 01/28/2019] [Indexed: 05/04/2023]
Abstract
Exposure to airborne microbes (AM) can affect the human microbiome and has various consequences for human health. Investigating the profiles of AM and the potential bacterial pathogens within, along with the factors influencing their community, is pivotal for understanding the impact of AM on human health. In this study, we collected AM during spring and summer from 11 sites with various levels of urbanization in the city of Xiamen, China. Bacterial community compositions of the AM were determined based on 16S rRNA gene amplicon sequencing. Firmicutes and Proteobacteria were the predominating phyla in the airborne bacterial communities, and a higher (P < 0.05) diversity of AM was found during the summer as compared to the spring. Significant differences in the community structure of the AM and the potential bacterial pathogens within airborne microbes were observed among the seasons and the sites with different levels of urbanization. Increases and/or decreases in the abundance of Bacillus and Acinetobacter could explain a major part of the variations in the AM community compositions. The proportion of potential bacterial pathogens during the summer was significantly higher (P < 0.01) than in the spring, and the relative abundance of several bacterial pathogens (i.e. Burkholderia multivoran, Enterococcus faecium and Streptococcus thermophilus) related to human diseases (39.8% of total pathogens on average) increased with increasing urbanization levels, suggesting that urbanization can increase the AM-associated human health risk.
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Affiliation(s)
- Hu Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, China
| | - Xin-Yuan Zhou
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, China
| | - Xiao-Ru Yang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, China; State Key Laboratory of Urban and Regional Ecology Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - You-Wei Hong
- Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, China
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, China.
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19
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Yeo SK, Sun Y, McKasy M, Shugart EC. Disgusting microbes: The effect of disgust on perceptions of risks related to modifying microbiomes. PUBLIC UNDERSTANDING OF SCIENCE (BRISTOL, ENGLAND) 2019; 28:433-448. [PMID: 30827192 DOI: 10.1177/0963662519832200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Research on perceived risks of scientific issues has largely overlooked the influence of disgust as a predictor. Here, we examine the impact of disgust on perceived risks of modifying microbiomes using a 2 (emotion) × 2 (focus) experiment embedded in an online survey. We find evidence of moderated mediation where individuals exposed to an article about microbiome research and therapies with explicit references to disgusting stimuli perceived greater risk through a mediating variable, elicited disgust. This indirect effect is moderated by the focus of the article; those who viewed a human-focused article experienced greater disgust and reported greater perceived risks. These findings have implications for assessing and addressing lay audiences' reactions to an emerging issue that has significant societal implications.
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20
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Ma Y, Chen H, Lei R, Ren J. Biobanking for human microbiome research: promise, risks, and ethics. Asian Bioeth Rev 2017. [DOI: 10.1007/s41649-017-0033-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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