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Browne HP, Neville BA, Forster SC, Lawley TD. Transmission of the gut microbiota: spreading of health. Nat Rev Microbiol 2017; 15:531-543. [PMID: 28603278 PMCID: PMC5837012 DOI: 10.1038/nrmicro.2017.50] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Transmission of commensal intestinal bacteria between humans could promote health by establishing, maintaining and replenishing microbial diversity in the microbiota of an individual. Unlike pathogens, the routes of transmission for commensal bacteria remain unappreciated and poorly understood, despite the likely commonalities between both. Consequently, broad infection control measures that are designed to prevent pathogen transmission and infection, such as oversanitation and the overuse of antibiotics, may inadvertently affect human health by altering normal commensal transmission. In this Review, we discuss the mechanisms and factors that influence host-to-host transmission of the intestinal microbiota and examine how a better understanding of these processes will identify new approaches to nurture and restore transmission routes that are used by beneficial bacteria.
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Affiliation(s)
- Hilary P Browne
- Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - B Anne Neville
- Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Samuel C Forster
- Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
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52
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Maritz JM, Sullivan SA, Prill RJ, Aksoy E, Scheid P, Carlton JM. Filthy lucre: A metagenomic pilot study of microbes found on circulating currency in New York City. PLoS One 2017; 12:e0175527. [PMID: 28384336 PMCID: PMC5383295 DOI: 10.1371/journal.pone.0175527] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 03/27/2017] [Indexed: 12/25/2022] Open
Abstract
Background Paper currency by its very nature is frequently transferred from one person to another and represents an important medium for human contact with—and potential exchange of—microbes. In this pilot study, we swabbed circulating $1 bills obtained from a New York City bank in February (Winter) and June (Summer) 2013 and used shotgun metagenomic sequencing to profile the communities found on their surface. Using basic culture conditions, we also tested whether viable microbes could be recovered from bills. Results Shotgun metagenomics identified eukaryotes as the most abundant sequences on money, followed by bacteria, viruses and archaea. Eukaryotic assemblages were dominated by human, other metazoan and fungal taxa. The currency investigated harbored a diverse microbial population that was dominated by human skin and oral commensals, including Propionibacterium acnes, Staphylococcus epidermidis and Micrococcus luteus. Other taxa detected not associated with humans included Lactococcus lactis and Streptococcus thermophilus, microbes typically associated with dairy production and fermentation. Culturing results indicated that viable microbes can be isolated from paper currency. Conclusions We conducted the first metagenomic characterization of the surface of paper money in the United States, establishing a baseline for microbes found on $1 bills circulating in New York City. Our results suggest that money amalgamates DNA from sources inhabiting the human microbiome, food, and other environmental inputs, some of which can be recovered as viable organisms. These monetary communities may be maintained through contact with human skin, and DNA obtained from money may provide a record of human behavior and health. Understanding these microbial profiles is especially relevant to public health as money could potentially mediate interpersonal transfer of microbes.
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Affiliation(s)
- Julia M. Maritz
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States of America
| | - Steven A. Sullivan
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States of America
| | - Robert J. Prill
- Accelerated Discovery Lab, IBM Almaden Research Center, San Jose, California, United States of America
| | - Emre Aksoy
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States of America
| | - Paul Scheid
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States of America
| | - Jane M. Carlton
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States of America
- * E-mail:
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Casterline BW, Hecht AL, Choi VM, Bubeck Wardenburg J. The Bacteroides fragilis pathogenicity island links virulence and strain competition. Gut Microbes 2017; 8. [PMID: 28632016 PMCID: PMC5570422 DOI: 10.1080/19490976.2017.1290758] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The mature microbiome is a stable ecosystem that resists perturbation despite constant host exposure to exogenous microbes. However, the microbial mechanisms determining microbiome development and composition are poorly understood. We recently demonstrated that a non-toxigenic B. fragilis (NTBF) strain restricts enteric colonization by an enterotoxigenic (ETBF) strain dependent on a type VI secretion system (T6SS). We show here that a second enterotoxigenic strain is competent to colonize, dependent on the Bacteroides fragilis pathogenicity island (BFPAI). Additional data showing complex environmental regulation of the Bacteroides fragilis toxin (BFT) suggest that virulence factors may be adapted to modify the colonic niche to provide a strain-specific colonization advantage. We conclude that more complex models of host-microbe-microbiome interactions are needed to investigate this hypothesis.
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Affiliation(s)
- Benjamin W. Casterline
- Department of Microbiology, University of Chicago, Chicago, IL, USA,Interdisciplinary Scientist Training Program, University of Chicago, Chicago, IL, USA
| | - Aaron L. Hecht
- Department of Microbiology, University of Chicago, Chicago, IL, USA,Interdisciplinary Scientist Training Program, University of Chicago, Chicago, IL, USA
| | - Vivian M. Choi
- Department of Microbiology, University of Chicago, Chicago, IL, USA,Interdisciplinary Scientist Training Program, University of Chicago, Chicago, IL, USA
| | - Juliane Bubeck Wardenburg
- Department of Microbiology, University of Chicago, Chicago, IL, USA,Department of Pediatrics, University of Chicago, Chicago, IL, USA,CONTACT Juliane Bubeck Wardenburg Department of Pediatrics, Washington University, 4938 Parkview Place Rm 6107, St. Louis, MO 63110
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Wilkins D, Leung MHY, Lee PKH. Microbiota fingerprints lose individually identifying features over time. MICROBIOME 2017; 5:1. [PMID: 28086968 PMCID: PMC5234115 DOI: 10.1186/s40168-016-0209-7] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 11/22/2016] [Indexed: 05/19/2023]
Abstract
BACKGROUND Humans host individually unique skin microbiota, suggesting that microbiota traces transferred from skin to surfaces could serve as forensic markers analogous to fingerprints. While it is known that individuals leave identifiable microbiota traces on surfaces, it is not clear for how long these traces persist. Moreover, as skin and surface microbiota change with time, even persistent traces may lose their forensic potential as they would cease to resemble the microbiota of the person who left them. We followed skin and surface microbiota within households for four seasons to determine whether accurate microbiota-based matching of individuals to their households could be achieved across long time delays. RESULTS While household surface microbiota traces could be matched to the correct occupant or occupants with 67% accuracy, accuracy decreased substantially when skin and surface samples were collected in different seasons, and particularly when surface samples were collected long after skin samples. Most OTUs persisted on skin or surfaces for less than one season, indicating that OTU loss was the major cause of decreased matching accuracy. OTUs that were more useful for individual identification persisted for less time and were less likely to be deposited from skin to surface, suggesting a trade-off between the longevity and identifying value of microbiota traces. CONCLUSIONS While microbiota traces have potential forensic value, unlike fingerprints they are not static and may degrade in a way that preferentially erases features useful in identifying individuals.
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Affiliation(s)
- David Wilkins
- School of Energy and Environment, City University of Hong Kong, B5423-AC1, Tat Chee Avenue, Kowloon, Hong Kong, Special Administrative Region of China
| | - Marcus H. Y. Leung
- School of Energy and Environment, City University of Hong Kong, B5423-AC1, Tat Chee Avenue, Kowloon, Hong Kong, Special Administrative Region of China
| | - Patrick K. H. Lee
- School of Energy and Environment, City University of Hong Kong, B5423-AC1, Tat Chee Avenue, Kowloon, Hong Kong, Special Administrative Region of China
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55
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Fouquier J, Schwartz T, Kelley ST. Rapid assemblage of diverse environmental fungal communities on public restroom floors. INDOOR AIR 2016; 26:869-879. [PMID: 26717555 DOI: 10.1111/ina.12279] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 12/23/2015] [Indexed: 05/25/2023]
Abstract
An increasing proportion of humanity lives in urban environments where they spend most of their lives indoors. Recent molecular studies have shown that bacterial assemblages in built environments (BEs) are extremely diverse, but BE fungal diversity remains poorly understood. We applied culture-independent methods based on next-generation sequencing (NGS) of the fungal internal transcribed spacer to investigate the diversity and temporal dynamics of fungi in restrooms. Swab samples were collected weekly from three different surfaces in two public restrooms (male and female) in San Diego, CA, USA, over an 8-week period. DNA amplification and culturing methods both found that the floor samples had significantly higher fungal loads than other surfaces. NGS sequencing of floor fungal assemblages identified a total of 2550 unique phylotypes (~800 per sample), less than half of which were identifiable. Of the known fungi, the majority came from environmental sources and we found little evidence of known human skin fungi. Fungal assemblages reformed rapidly in a highly consistent manner, and the variance in the species diversity among samples was low. Overall, our study contributes to a better understanding of public restroom floor fungal communities.
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Affiliation(s)
- J Fouquier
- Graduate Program in Bioinformatics and Medical Informatics, San Diego State University, San Diego, CA, USA
| | - T Schwartz
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - S T Kelley
- Graduate Program in Bioinformatics and Medical Informatics, San Diego State University, San Diego, CA, USA
- Department of Biology, San Diego State University, San Diego, CA, USA
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56
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Leung MHY, Chan KCK, Lee PKH. Skin fungal community and its correlation with bacterial community of urban Chinese individuals. MICROBIOME 2016; 4:46. [PMID: 27558504 PMCID: PMC4997687 DOI: 10.1186/s40168-016-0192-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 08/17/2016] [Indexed: 05/17/2023]
Abstract
BACKGROUND High-throughput sequencing has led to increased insights into the human skin microbiome. Currently, the majority of skin microbiome investigations are limited to characterizing prokaryotic communities, and our understanding of the skin fungal community (mycobiome) is limited, more so for cohorts outside of the western hemisphere. Here, the skin mycobiome across healthy Chinese individuals in Hong Kong are characterized. RESULTS Based on a curated fungal reference database designed for skin mycobiome analyses, previously documented common skin colonizers are also abundant and prevalent in this cohort. However, genera associated with local terrains, food, and medicine are also detected. Fungal community composition shows interpersonal (Bray-Curtis ANOSIM = 0.398) and household (Bray-Curtis ANOSIM = 0.134) clustering. Roles of gender and age on diversity analyses are test- and site-specific, and, contrary to bacteria, the effect of household on fungal community composition dissimilarity between samples is insignificant. Site-specific, cross-domain positive and negative correlations at both community and operational taxonomic unit levels may uncover potential relationships between fungi and bacteria on skin. CONCLUSIONS The studied Chinese population presents similar major fungal skin colonizers that are also common in western populations, but local outdoor environments and lifestyles may also contribute to mycobiomes of specific cohorts. Cohabitation plays an insignificant role in shaping mycobiome differences between individuals in this cohort. Increased understanding of fungal communities of non-western cohorts will contribute to understanding the size of the global skin pan-mycobiome, which will ultimately help understand relationships between environmental exposures, microbial populations, and the health of global humans.
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Affiliation(s)
- Marcus H. Y. Leung
- B5423-AC1, School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | | | - Patrick K. H. Lee
- B5423-AC1, School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
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Gilbert JA, Quinn RA, Debelius J, Xu ZZ, Morton J, Garg N, Jansson JK, Dorrestein PC, Knight R. Microbiome-wide association studies link dynamic microbial consortia to disease. Nature 2016; 535:94-103. [PMID: 27383984 DOI: 10.1038/nature18850] [Citation(s) in RCA: 428] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 05/06/2016] [Indexed: 12/16/2022]
Abstract
Rapid advances in DNA sequencing, metabolomics, proteomics and computational tools are dramatically increasing access to the microbiome and identification of its links with disease. In particular, time-series studies and multiple molecular perspectives are facilitating microbiome-wide association studies, which are analogous to genome-wide association studies. Early findings point to actionable outcomes of microbiome-wide association studies, although their clinical application has yet to be approved. An appreciation of the complexity of interactions among the microbiome and the host's diet, chemistry and health, as well as determining the frequency of observations that are needed to capture and integrate this dynamic interface, is paramount for developing precision diagnostics and therapies that are based on the microbiome.
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Affiliation(s)
- Jack A Gilbert
- Department of Surgery, University of Chicago, Chicago, Illinois 60637, USA
| | - Robert A Quinn
- Department of Pharmacology, University of California San Diego, La Jolla, California 92093, USA.,Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, USA.,Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Justine Debelius
- Department of Pediatrics, University of California, San Diego School of Medicine, La Jolla, California 92093, USA
| | - Zhenjiang Z Xu
- Department of Pediatrics, University of California, San Diego School of Medicine, La Jolla, California 92093, USA
| | - James Morton
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, California 92093, USA
| | - Neha Garg
- Department of Pharmacology, University of California San Diego, La Jolla, California 92093, USA.,Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Pieter C Dorrestein
- Department of Pharmacology, University of California San Diego, La Jolla, California 92093, USA.,Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, USA.,Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, La Jolla, California 92093, USA.,Department of Pediatrics, University of California, San Diego School of Medicine, La Jolla, California 92093, USA
| | - Rob Knight
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, La Jolla, California 92093, USA.,Department of Pediatrics, University of California, San Diego School of Medicine, La Jolla, California 92093, USA.,Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, California 92093, USA
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Abstract
The advent and application of high-throughput molecular techniques for analyzing microbial communities in the indoor environment have led to illuminating findings and are beginning to change the way we think about human health in relation to the built environment. Here I review recent studies on the microbiology of the built environment, organize their findings into 12 major thematic categories, and comment on how these studies have or have not advanced knowledge in each area beyond what we already knew from over 100 years of applying culture-based methods to building samples. The advent and application of high-throughput molecular techniques for analyzing microbial communities in the indoor environment have led to illuminating findings and are beginning to change the way we think about human health in relation to the built environment. Here I review recent studies on the microbiology of the built environment, organize their findings into 12 major thematic categories, and comment on how these studies have or have not advanced knowledge in each area beyond what we already knew from over 100 years of applying culture-based methods to building samples. I propose that while we have added tremendous complexity to the rich existing knowledge base, the practical implications of this added complexity remain somewhat elusive. It remains to be seen how this new knowledge base will change how we design, build, and operate buildings. Much more research is needed to better understand the complexity with which indoor microbiomes may affect human health in both positive and negative ways.
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59
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Stephens B. What Have We Learned about the Microbiomes of Indoor Environments? mSystems 2016. [PMID: 27822547 DOI: 10.1128/msystems.00083-16.editor] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
The advent and application of high-throughput molecular techniques for analyzing microbial communities in the indoor environment have led to illuminating findings and are beginning to change the way we think about human health in relation to the built environment. Here I review recent studies on the microbiology of the built environment, organize their findings into 12 major thematic categories, and comment on how these studies have or have not advanced knowledge in each area beyond what we already knew from over 100 years of applying culture-based methods to building samples. I propose that while we have added tremendous complexity to the rich existing knowledge base, the practical implications of this added complexity remain somewhat elusive. It remains to be seen how this new knowledge base will change how we design, build, and operate buildings. Much more research is needed to better understand the complexity with which indoor microbiomes may affect human health in both positive and negative ways.
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Affiliation(s)
- Brent Stephens
- Department of Civil, Architectural and Environmental Engineering, Illinois Institute of Technology, Chicago, Illinois, USA
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Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment. mSystems 2016; 1:mSystems00018-16. [PMID: 27822528 PMCID: PMC5069760 DOI: 10.1128/msystems.00018-16] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 03/28/2016] [Indexed: 01/01/2023] Open
Abstract
Public transit systems are ideal for studying the urban microbiome and interindividual community transfer. In this study, we used 16S amplicon and shotgun metagenomic sequencing to profile microbial communities on multiple transit surfaces across train lines and stations in the Boston metropolitan transit system. The greatest determinant of microbial community structure was the transit surface type. In contrast, little variation was observed between geographically distinct train lines and stations serving different demographics. All surfaces were dominated by human skin and oral commensals such as Propionibacterium, Corynebacterium, Staphylococcus, and Streptococcus. The detected taxa not associated with humans included generalists from alphaproteobacteria, which were especially abundant on outdoor touchscreens. Shotgun metagenomics further identified viral and eukaryotic microbes, including Propionibacterium phage and Malassezia globosa. Functional profiling showed that Propionibacterium acnes pathways such as propionate production and porphyrin synthesis were enriched on train holding surfaces (holds), while electron transport chain components for aerobic respiration were enriched on touchscreens and seats. Lastly, the transit environment was not found to be a reservoir of antimicrobial resistance and virulence genes. Our results suggest that microbial communities on transit surfaces are maintained from a metapopulation of human skin commensals and environmental generalists, with enrichments corresponding to local interactions with the human body and environmental exposures. IMPORTANCE Mass transit environments, specifically, urban subways, are distinct microbial environments with high occupant densities, diversities, and turnovers, and they are thus especially relevant to public health. Despite this, only three culture-independent subway studies have been performed, all since 2013 and all with widely differing designs and conclusions. In this study, we profiled the Boston subway system, which provides 238 million trips per year overseen by the Massachusetts Bay Transportation Authority (MBTA). This yielded the first high-precision microbial survey of a variety of surfaces, ridership environments, and microbiological functions (including tests for potential pathogenicity) in a mass transit environment. Characterizing microbial profiles for multiple transit systems will become increasingly important for biosurveillance of antibiotic resistance genes or pathogens, which can be early indicators for outbreak or sanitation events. Understanding how human contact, materials, and the environment affect microbial profiles may eventually allow us to rationally design public spaces to sustain our health in the presence of microbial reservoirs. Author Video: An author video summary of this article is available.
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Differential Functional Constraints Cause Strain-Level Endemism in Polynucleobacter Populations. mSystems 2016; 1:mSystems00003-16. [PMID: 27822527 PMCID: PMC5069759 DOI: 10.1128/msystems.00003-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 04/27/2016] [Indexed: 11/20/2022] Open
Abstract
Understanding the biological factors influencing habitat-wide genetic endemism is important for explaining observed biogeographic patterns. Polynucleobacter is a genus of bacteria that seems to have found a way to colonize myriad freshwater ecosystems and by doing so has become one of the most abundant bacteria in these environments. We sequenced metagenomes from locations across the Chicago River system and assembled Polynucleobacter genomes from different sites and compared how the nucleotide composition, gene codon usage, and the ratio of synonymous (codes for the same amino acid) to nonsynonymous (codes for a different amino acid) mutations varied across these population genomes at each site. The environmental pressures at each site drove purifying selection for functional traits that maintained a streamlined core genome across the Chicago River Polynucleobacter population while allowing for site-specific genomic adaptation. These adaptations enable Polynucleobacter to become dominant across different riverine environmental gradients. The adaptation of bacterial lineages to local environmental conditions creates the potential for broader genotypic diversity within a species, which can enable a species to dominate across ecological gradients because of niche flexibility. The genus Polynucleobacter maintains both free-living and symbiotic ecotypes and maintains an apparently ubiquitous distribution in freshwater ecosystems. Subspecies-level resolution supplemented with metagenome-derived genotype analysis revealed that differential functional constraints, not geographic distance, produce and maintain strain-level genetic conservation in Polynucleobacter populations across three geographically proximal riverine environments. Genes associated with cofactor biosynthesis and one-carbon metabolism showed habitat specificity, and protein-coding genes of unknown function and membrane transport proteins were under positive selection across each habitat. Characterized by different median ratios of nonsynonymous to synonymous evolutionary changes (dN/dS ratios) and a limited but statistically significant negative correlation between the dN/dS ratio and codon usage bias between habitats, the free-living and core genotypes were observed to be evolving under strong purifying selection pressure. Highlighting the potential role of genetic adaptation to the local environment, the two-component system protein-coding genes were highly stable (dN/dS ratio, < 0.03). These results suggest that despite the impact of the habitat on genetic diversity, and hence niche partition, strong environmental selection pressure maintains a conserved core genome for Polynucleobacter populations. IMPORTANCE Understanding the biological factors influencing habitat-wide genetic endemism is important for explaining observed biogeographic patterns. Polynucleobacter is a genus of bacteria that seems to have found a way to colonize myriad freshwater ecosystems and by doing so has become one of the most abundant bacteria in these environments. We sequenced metagenomes from locations across the Chicago River system and assembled Polynucleobacter genomes from different sites and compared how the nucleotide composition, gene codon usage, and the ratio of synonymous (codes for the same amino acid) to nonsynonymous (codes for a different amino acid) mutations varied across these population genomes at each site. The environmental pressures at each site drove purifying selection for functional traits that maintained a streamlined core genome across the Chicago River Polynucleobacter population while allowing for site-specific genomic adaptation. These adaptations enable Polynucleobacter to become dominant across different riverine environmental gradients.
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Leung MHY, Lee PKH. The roles of the outdoors and occupants in contributing to a potential pan-microbiome of the built environment: a review. MICROBIOME 2016; 4:21. [PMID: 27216717 PMCID: PMC4877933 DOI: 10.1186/s40168-016-0165-2] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 04/11/2016] [Indexed: 05/10/2023]
Abstract
Recent high-throughput sequencing technology has led to an expansion of knowledge regarding the microbial communities (microbiome) across various built environments (BEs). The microbiome of the BE is dependent upon building factors and conditions that govern how outdoor microbes enter and persist in the BE. Additionally, occupants are crucial in shaping the microbiome of the BE by releasing human-associated microorganisms and resuspending microbes on floors and surfaces. Therefore, both the outdoors and occupants act as major sources of microorganisms found in the BE. However, most characterizations of the microbiome of the BE have been conducted in the Western world. Notably, outdoor locations and population groups present geographical variations in outdoor and human microbiomes, respectively. Given the influences of the outdoor and human microbiomes on BE microbiology, and the geographical variations in outdoor and human microbiomes, it is likely that the microbiomes of BEs also vary by location. The summation of microbiomes between BEs contribute to a potential BE pan-microbiome, which will both consist of microbes that are ubiquitous in indoor environments around the world, and microbes that appear to be endemic to particular geographical locations. Importantly, the BE pan-microbiome can potentially question the global application of our current views on indoor microbiology. In this review, we first provide an assessment on the roles of building and occupant properties on shaping the microbiome of the BE. This is then followed by a description of geographical variations in the microbiomes of the outdoors and humans, the two main sources of microbes in BEs. We present evidence of differences in microbiomes of BEs around the world, demonstrating the existence of a global pan-microbiome of the BE that is larger than the microbiome of any single indoor environment. Finally, we discuss the significance of understanding the BE pan-microbiome and identifying universal and location-specific relationships between building and occupant characteristics and indoor microbiology. This review highlights the much needed efforts towards determining the pan-microbiome of the BE, thereby identifying general and location-specific links between the microbial communities of the outdoors, human, and BE ecosystems, ultimately improving the health, comfort, and productivity of occupants around the world.
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Affiliation(s)
- Marcus H. Y. Leung
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, B5423-AC1 Hong Kong
| | - Patrick K. H. Lee
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, B5423-AC1 Hong Kong
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Using MALDI-TOF Mass Spectrometry to Identify Drug Resistant Staphylococcal Isolates from Nonhospital Environments in Brunei Darussalam. Interdiscip Perspect Infect Dis 2016; 2016:8685602. [PMID: 27127505 PMCID: PMC4834169 DOI: 10.1155/2016/8685602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 03/07/2016] [Indexed: 11/30/2022] Open
Abstract
Drug resistant bacteria have been a growing threat to the community and hospitals due to the misuse of antibiotics by humans, industrialization, and lack of novel antimicrobials currently available. Little is known about the prevalence of drug resistant bacteria in nonhealthcare environments in Brunei Darussalam and about how antibiotic resistant genes are transferred within these environments. Human contact points from different types of environments in Brunei Darussalam, varying from urban to jungle settings, were swabbed and cultured onto selective media to isolate staphylococci bacteria before performing antimicrobial susceptibility testing on the isolates. The identity of the isolates was determined using MALDI-TOF mass spectrometry (MS). Staphylococci isolates resistant to oxacillin were further tested for their minimum inhibitory concentration (MIC). PCR analysis of the mecA gene, a gene that confers resistance to oxacillin, is done to determine the level of resistance to oxacillin. Ten different staphylococcal species were identified by MALDI-TOF-MS analysis. Out of the 36 staphylococci isolates, 24 were resistant to multiple antibiotics including two isolates which were oxacillin resistant. Some staphylococci isolates had similar antibiotic resistance profiles to other staphylococci isolates of different species in the same location. This work provides the first-ever evidence of drug resistant staphylococci in the nonhospital environment in Brunei Darussalam.
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Abstract
Humanity’s transition from the outdoor environment to the built environment (BE) has reduced our exposure to microbial diversity. The relative importance of factors that contribute to the composition of human-dominated BE microbial communities remains largely unknown. Humanity’s transition from the outdoor environment to the built environment (BE) has reduced our exposure to microbial diversity. The relative importance of factors that contribute to the composition of human-dominated BE microbial communities remains largely unknown. In their article in this issue, Chase and colleagues (J. Chase, J. Fouquier, M. Zare, D. L. Sonderegger, R. Knight, S. T. Kelley, J. Siegel, and J. G. Caporaso, mSystems 1(2):e00022-16, 2016, http://dx.doi.org/10.1128/mSystems.00022-16) present an office building study in which they controlled for environmental factors, geography, surface material, sampling location, and human interaction type. They found that surface location and geography were the strongest factors contributing to microbial community structure, while surface material had little effect. Even in the absence of direct human interaction, BE surfaces were composed of 25 to 30% human skin-associated taxa. The authors demonstrate how technical variation across sequencing runs is a major issue, especially in BE work, where the biomass is often low and the potential for PCR contaminants is high. Overall, the authors conclude that BE surfaces are desert-like environments where microbes passively accumulate.
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Sangwan N, Xia F, Gilbert JA. Recovering complete and draft population genomes from metagenome datasets. MICROBIOME 2016; 4:8. [PMID: 26951112 PMCID: PMC4782286 DOI: 10.1186/s40168-016-0154-5] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 02/05/2016] [Indexed: 05/03/2023]
Abstract
Assembly of metagenomic sequence data into microbial genomes is of fundamental value to improving our understanding of microbial ecology and metabolism by elucidating the functional potential of hard-to-culture microorganisms. Here, we provide a synthesis of available methods to bin metagenomic contigs into species-level groups and highlight how genetic diversity, sequencing depth, and coverage influence binning success. Despite the computational cost on application to deeply sequenced complex metagenomes (e.g., soil), covarying patterns of contig coverage across multiple datasets significantly improves the binning process. We also discuss and compare current genome validation methods and reveal how these methods tackle the problem of chimeric genome bins i.e., sequences from multiple species. Finally, we explore how population genome assembly can be used to uncover biogeographic trends and to characterize the effect of in situ functional constraints on the genome-wide evolution.
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Affiliation(s)
- Naseer Sangwan
- Biosciences Division (BIO), Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA.
- Department of Surgery, University of Chicago, 5841 South Maryland Avenue, MC 5029, Chicago, IL, 60637, USA.
| | - Fangfang Xia
- Computing, Environment and Life Sciences, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA.
| | - Jack A Gilbert
- Biosciences Division (BIO), Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA.
- Department of Ecology and Evolution, University of Chicago, 1101 E 57th Street, Chicago, IL, 60637, USA.
- Department of Surgery, University of Chicago, 5841 South Maryland Avenue, MC 5029, Chicago, IL, 60637, USA.
- Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, 02543, USA.
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66
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Fouquier J, Rideout JR, Bolyen E, Chase J, Shiffer A, McDonald D, Knight R, Caporaso JG, Kelley ST. Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses. MICROBIOME 2016; 4:11. [PMID: 26905735 PMCID: PMC4765138 DOI: 10.1186/s40168-016-0153-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 02/05/2016] [Indexed: 05/11/2023]
Abstract
BACKGROUND Fungi play critical roles in many ecosystems, cause serious diseases in plants and animals, and pose significant threats to human health and structural integrity problems in built environments. While most fungal diversity remains unknown, the development of PCR primers for the internal transcribed spacer (ITS) combined with next-generation sequencing has substantially improved our ability to profile fungal microbial diversity. Although the high sequence variability in the ITS region facilitates more accurate species identification, it also makes multiple sequence alignment and phylogenetic analysis unreliable across evolutionarily distant fungi because the sequences are hard to align accurately. To address this issue, we created ghost-tree, a bioinformatics tool that integrates sequence data from two genetic markers into a single phylogenetic tree that can be used for diversity analyses. Our approach starts with a "foundation" phylogeny based on one genetic marker whose sequences can be aligned across organisms spanning divergent taxonomic groups (e.g., fungal families). Then, "extension" phylogenies are built for more closely related organisms (e.g., fungal species or strains) using a second more rapidly evolving genetic marker. These smaller phylogenies are then grafted onto the foundation tree by mapping taxonomic names such that each corresponding foundation-tree tip would branch into its new "extension tree" child. RESULTS We applied ghost-tree to graft fungal extension phylogenies derived from ITS sequences onto a foundation phylogeny derived from fungal 18S sequences. Our analysis of simulated and real fungal ITS data sets found that phylogenetic distances between fungal communities computed using ghost-tree phylogenies explained significantly more variance than non-phylogenetic distances. The phylogenetic metrics also improved our ability to distinguish small differences (effect sizes) between microbial communities, though results were similar to non-phylogenetic methods for larger effect sizes. CONCLUSIONS The Silva/UNITE-based ghost tree presented here can be easily integrated into existing fungal analysis pipelines to enhance the resolution of fungal community differences and improve understanding of these communities in built environments. The ghost-tree software package can also be used to develop phylogenetic trees for other marker gene sets that afford different taxonomic resolution, or for bridging genome trees with amplicon trees. AVAILABILITY ghost-tree is pip-installable. All source code, documentation, and test code are available under the BSD license at https://github.com/JTFouquier/ghost-tree .
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Affiliation(s)
- Jennifer Fouquier
- Graduate Program in Bioinformatics and Medical Informatics, San Diego State University, San Diego, CA, USA.
| | - Jai Ram Rideout
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA.
| | - Evan Bolyen
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA.
| | - John Chase
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA.
| | - Arron Shiffer
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA.
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
| | | | - Rob Knight
- Department of Pediatrics, and Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA.
| | - J Gregory Caporaso
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA.
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
| | - Scott T Kelley
- Graduate Program in Bioinformatics and Medical Informatics, San Diego State University, San Diego, CA, USA.
- Department of Biology, San Diego State University, San Diego, CA, USA.
- San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182-4614, USA.
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Biteen JS, Blainey PC, Cardon ZG, Chun M, Church GM, Dorrestein PC, Fraser SE, Gilbert JA, Jansson JK, Knight R, Miller JF, Ozcan A, Prather KA, Quake SR, Ruby EG, Silver PA, Taha S, van den Engh G, Weiss PS, Wong GCL, Wright AT, Young TD. Tools for the Microbiome: Nano and Beyond. ACS NANO 2016; 10:6-37. [PMID: 26695070 DOI: 10.1021/acsnano.5b07826] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The microbiome presents great opportunities for understanding and improving the world around us and elucidating the interactions that compose it. The microbiome also poses tremendous challenges for mapping and manipulating the entangled networks of interactions among myriad diverse organisms. Here, we describe the opportunities, technical needs, and potential approaches to address these challenges, based on recent and upcoming advances in measurement and control at the nanoscale and beyond. These technical needs will provide the basis for advancing the largely descriptive studies of the microbiome to the theoretical and mechanistic understandings that will underpin the discipline of microbiome engineering. We anticipate that the new tools and methods developed will also be more broadly useful in environmental monitoring, medicine, forensics, and other areas.
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Affiliation(s)
- Julie S Biteen
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Paul C Blainey
- Department of Biological Engineering, Massachusetts Institute of Technology , and Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02138, United States
| | - Zoe G Cardon
- The Ecosystems Center, Marine Biological Laboratory , Woods Hole, Massachusetts 02543-1015, United States
| | - Miyoung Chun
- The Kavli Foundation , Oxnard, California 93030, United States
| | - George M Church
- Wyss Institute for Biologically Inspired Engineering and Biophysics Program, Harvard University , Boston, Massachusetts 02115, United States
| | | | - Scott E Fraser
- Translational Imaging Center, University of Southern California , Molecular and Computational Biology, Los Angeles, California 90089, United States
| | - Jack A Gilbert
- Institute for Genomic and Systems Biology, Argonne National Laboratory , Argonne, Illinois 60439, United States
- Department of Ecology and Evolution and Department of Surgery, University of Chicago , Chicago, Illinois 60637, United States
| | - Janet K Jansson
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | | | | | | | | | | | - Edward G Ruby
- Kewalo Marine Laboratory, University of Hawaii-Manoa , Honolulu, Hawaii 96813, United States
| | - Pamela A Silver
- Wyss Institute for Biologically Inspired Engineering and Biophysics Program, Harvard University , Boston, Massachusetts 02115, United States
| | - Sharif Taha
- The Kavli Foundation , Oxnard, California 93030, United States
| | - Ger van den Engh
- Center for Marine Cytometry , Concrete, Washington 98237, United States
- Instituto Milenio de Oceanografía, Universidad de Concepción , Concepción, Chile
| | | | | | - Aaron T Wright
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
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Miletto M, Lindow SE. Relative and contextual contribution of different sources to the composition and abundance of indoor air bacteria in residences. MICROBIOME 2015; 3:61. [PMID: 26653310 PMCID: PMC4674937 DOI: 10.1186/s40168-015-0128-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 10/29/2015] [Indexed: 05/10/2023]
Abstract
BACKGROUND The study of the microbial communities in the built environment is of critical importance as humans spend the majority of their time indoors. While the microorganisms in living spaces, especially those in the air, can impact health and well-being, little is known of their identity and the processes that determine their assembly. We investigated the source-sink relationships of airborne bacteria in 29 homes in the San Francisco Bay Area. Samples taken in the sites expected to be source habitats for indoor air microbes were analyzed by 16S rRNA-based pyrosequencing and quantitative PCR. The community composition was related to the characteristics of the household collected at the time of sampling, including the number of residents and pets, activity levels, frequency of cooking and vacuum cleaning, extent of natural ventilation, and abundance and type of vegetation surrounding the building. RESULTS Indoor air harbored a diverse bacterial community dominated by Diaphorobacter sp., Propionibacterium sp., Sphingomonas sp., and Alicyclobacillus sp. Source-sink analysis suggested that outdoor air was the primary source of indoor air microbes in most homes. Bacterial phylogenetic diversity and relative abundance in indoor air did not differ statistically from that in outdoor air. Moreover, the abundance of bacteria in outdoor air was positively correlated with that in indoor air, as would be expected if outdoor air was the main contributor to the bacterial community in indoor bioaerosols. The number of residents, presence of pets, and local tap water also influenced the diversity and size of indoor air microbes. The bacterial load in air increased with the number of residents, activity, and frequency of natural ventilation, and the proportion of bacteria putatively derived from skin increased with the number of residents. Vacuum cleaning increased the signature of pet- and floor-derived bacteria in indoor air, while the frequency of natural ventilation decreased the relative abundance of tap water-derived microorganisms in air. CONCLUSIONS Indoor air in residences harbors a diverse bacterial community originating from both outdoor and indoor sources and is strongly influenced by household characteristics.
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Affiliation(s)
- Marzia Miletto
- Plant & Microbial Biology, University of California Berkeley, 331 Koshland Hall, Berkeley, CA, 94720, USA.
| | - Steven E Lindow
- Plant & Microbial Biology, University of California Berkeley, 331 Koshland Hall, Berkeley, CA, 94720, USA.
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69
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Gibbons SM, Gilbert JA. Microbial diversity--exploration of natural ecosystems and microbiomes. Curr Opin Genet Dev 2015; 35:66-72. [PMID: 26598941 DOI: 10.1016/j.gde.2015.10.003] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 10/09/2015] [Accepted: 10/22/2015] [Indexed: 12/24/2022]
Abstract
Microorganisms are the pillars of life on Earth. Over billions of years, they have evolved into every conceivable niche on the planet. Microbes reshaped the oceans and atmosphere and gave rise to conditions conducive to multicellular organisms. Only in the past decade have we started to peer deeply into the microbial cosmos, and what we have found is amazing. Microbial ecosystems behave, in many ways, like large-scale ecosystems, although there are important exceptions. We review recent advances in our understanding of how microbial diversity is distributed across environments, how microbes influence the ecosystems in which they live, and how these nano-machines might be harnessed to advance our understanding of the natural world.
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Affiliation(s)
- Sean M Gibbons
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA; Institute for Genomics and Systems Biology, Argonne National Laboratory, Argonne, IL 60439, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Jack A Gilbert
- Institute for Genomics and Systems Biology, Argonne National Laboratory, Argonne, IL 60439, USA; Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA; Department of Surgery, University of Chicago, Chicago, IL 60637, USA; Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA; College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
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70
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Adams RI, Bateman AC, Bik HM, Meadow JF. Microbiota of the indoor environment: a meta-analysis. MICROBIOME 2015; 3:49. [PMID: 26459172 PMCID: PMC4604073 DOI: 10.1186/s40168-015-0108-3] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 09/07/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND As modern humans, we spend the majority of our time in indoor environments. Consequently, environmental exposure to microorganisms has important implications for human health, and a better understanding of the ecological drivers and processes that impact indoor microbial assemblages will be key for expanding our knowledge of the built environment. In the present investigation, we combined recent studies examining the microbiota of the built environment in order to identify unifying community patterns and the relative importance of indoor environmental factors. Ultimately, the present meta-analysis focused on studies of bacteria and archaea due to the limited number of high-throughput fungal studies from the indoor environment. We combined 16S ribosomal RNA (rRNA) gene datasets from 16 surveys of indoor environments conducted worldwide, additionally including 7 other studies representing putative environmental sources of microbial taxa (outdoor air, soil, and the human body). RESULTS Combined analysis of subsets of studies that shared specific experimental protocols or indoor habitats revealed community patterns indicative of consistent source environments and environmental filtering. Additionally, we were able to identify several consistent sources for indoor microorganisms, particularly outdoor air and skin, mirroring what has been shown in individual studies. Technical variation across studies had a strong effect on comparisons of microbial community assemblages, with differences in experimental protocols limiting our ability to extensively explore the importance of, for example, sampling locality, building function and use, or environmental substrate in structuring indoor microbial communities. CONCLUSIONS We present a snapshot of an important scientific field in its early stages, where studies have tended to focus on heavy sampling in a few geographic areas. From the practical perspective, this endeavor reinforces the importance of negative "kit" controls in microbiome studies. From the perspective of understanding mechanistic processes in the built environment, this meta-analysis confirms that broad factors, such as geography and building type, structure indoor microbes. However, this exercise suggests that individual studies with common sampling techniques may be more appropriate to explore the relative importance of subtle indoor environmental factors on the indoor microbiome.
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Affiliation(s)
- Rachel I Adams
- Plant & Microbial Biology, University of California Berkeley, Berkeley, 94720, CA, USA.
| | - Ashley C Bateman
- Biology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, 97403, OR, USA.
| | - Holly M Bik
- UC Davis Genome Center, University of California, Davis, Davis, 95616, CA, USA.
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK.
| | - James F Meadow
- Biology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, 97403, OR, USA.
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71
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Edmonds-Wilson SL, Nurinova NI, Zapka CA, Fierer N, Wilson M. Review of human hand microbiome research. J Dermatol Sci 2015; 80:3-12. [DOI: 10.1016/j.jdermsci.2015.07.006] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 07/13/2015] [Accepted: 07/16/2015] [Indexed: 01/14/2023]
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Wood M, Gibbons SM, Lax S, Eshoo-Anton TW, Owens SM, Kennedy S, Gilbert JA, Hampton-Marcell JT. Athletic equipment microbiota are shaped by interactions with human skin. MICROBIOME 2015; 3:25. [PMID: 26113975 PMCID: PMC4480904 DOI: 10.1186/s40168-015-0088-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 06/04/2015] [Indexed: 05/24/2023]
Abstract
BACKGROUND Americans spend the vast majority of their lives in built environments. Even traditionally outdoor pursuits, such as exercising, are often now performed indoors. Bacteria that colonize these indoor ecosystems are primarily derived from the human microbiome. The modes of human interaction with indoor surfaces and the physical conditions associated with each surface type determine the steady-state ecology of the microbial community. RESULTS Bacterial assemblages associated with different surfaces in three athletic facilities, including floors, mats, benches, free weights, and elliptical handles, were sampled every other hour (8 am to 6 pm) for 2 days. Surface and equipment type had a stronger influence on bacterial community composition than the facility in which they were housed. Surfaces that were primarily in contact with human skin exhibited highly dynamic bacterial community composition and non-random co-occurrence patterns, suggesting that different host microbiomes-shaped by selective forces-were being deposited on these surfaces through time. However, bacterial assemblages found on the floors and mats changed less over time, and species co-occurrence patterns appeared random, suggesting more neutral community assembly. CONCLUSIONS These longitudinal patterns highlight the dramatic turnover of microbial communities on surfaces in regular contact with human skin. By uncovering these longitudinal patterns, this study promotes a better understanding of microbe-human interactions within the built environment.
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Affiliation(s)
- Mariah Wood
- />Northwestern University, Evanston, IL USA
- />Biosciences Division, Argonne National Laboratory, Lemont, IL USA
| | - Sean M. Gibbons
- />Biosciences Division, Argonne National Laboratory, Lemont, IL USA
- />Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL USA
| | - Simon Lax
- />Department of Ecology and Evolutionary Biology, University of Chicago, Chicago, IL USA
| | | | - Sarah M. Owens
- />Biosciences Division, Argonne National Laboratory, Lemont, IL USA
- />Computation Institute, University of Chicago, Chicago, IL USA
| | | | - Jack A. Gilbert
- />Biosciences Division, Argonne National Laboratory, Lemont, IL USA
- />Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL USA
- />Department of Ecology and Evolutionary Biology, University of Chicago, Chicago, IL USA
- />Department of Surgery, University of Chicago, 5841 South Maryland Avenue, MC 5029, Chicago, IL 60637 USA
- />Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543 USA
- />College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Jarrad T. Hampton-Marcell
- />Biosciences Division, Argonne National Laboratory, Lemont, IL USA
- />Computation Institute, University of Chicago, Chicago, IL USA
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73
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Wilkins D, Leung MHY, Lee PKH. Indoor air bacterial communities in Hong Kong households assemble independently of occupant skin microbiomes. Environ Microbiol 2015; 18:1754-63. [DOI: 10.1111/1462-2920.12889] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 04/21/2015] [Indexed: 11/28/2022]
Affiliation(s)
- David Wilkins
- School of Energy and Environment; City University of Hong Kong; Tat Chee Ave Kowloon Hong Kong
| | - Marcus HY Leung
- School of Energy and Environment; City University of Hong Kong; Tat Chee Ave Kowloon Hong Kong
| | - Patrick KH Lee
- School of Energy and Environment; City University of Hong Kong; Tat Chee Ave Kowloon Hong Kong
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74
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Abstract
A recent article examines the extent of individual variation in microbial identities and how this might determine disease susceptibility, therapeutic responses and recovery from clinical interventions. Please see related article: http://dx.doi.org/10.1186/s13059-015-0646-9
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Affiliation(s)
- Jack A Gilbert
- Argonne National Laboratory, University of Chicago, South Cass Avenue, Argonne, IL, 60439, USA.
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75
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Hospital-associated microbiota and implications for nosocomial infections. Trends Mol Med 2015; 21:427-32. [PMID: 25907678 DOI: 10.1016/j.molmed.2015.03.005] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 03/25/2015] [Accepted: 03/27/2015] [Indexed: 12/23/2022]
Abstract
The rise of high-throughput sequencing technologies and culture-independent microbial surveys has the potential to revolutionize our understanding of how microbes colonize, move about, and evolve in hospital environments. Genome analysis of individual organisms, characterization of population dynamics, and microbial community ecology are facilitating the identification of novel pathogens, the tracking of disease outbreaks, and the study of the evolution of antibiotic resistance. Here we review the recent applications of these methods to microbial ecology studies in hospitals and discuss their potential to influence hospital management policy and practice and to reduce nosocomial infections and the spread of antibiotic resistance.
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Lax S, Hampton-Marcell JT, Gibbons SM, Colares GB, Smith D, Eisen JA, Gilbert JA. Forensic analysis of the microbiome of phones and shoes. MICROBIOME 2015; 3:21. [PMID: 25969737 PMCID: PMC4427962 DOI: 10.1186/s40168-015-0082-9] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 04/03/2015] [Indexed: 05/21/2023]
Abstract
BACKGROUND Microbial interaction between human-associated objects and the environments we inhabit may have forensic implications, and the extent to which microbes are shared between individuals inhabiting the same space may be relevant to human health and disease transmission. In this study, two participants sampled the front and back of their cell phones, four different locations on the soles of their shoes, and the floor beneath them every waking hour over a 2-day period. A further 89 participants took individual samples of their shoes and phones at three different scientific conferences. RESULTS Samples taken from different surface types maintained significantly different microbial community structures. The impact of the floor microbial community on that of the shoe environments was strong and immediate, as evidenced by Procrustes analysis of shoe replicates and significant correlation between shoe and floor samples taken at the same time point. Supervised learning was highly effective at determining which participant had taken a given shoe or phone sample, and a Bayesian method was able to determine which participant had taken each shoe sample based entirely on its similarity to the floor samples. Both shoe and phone samples taken by conference participants clustered into distinct groups based on location, though much more so when an unweighted distance metric was used, suggesting sharing of low-abundance microbial taxa between individuals inhabiting the same space. CONCLUSIONS Correlations between microbial community sources and sinks allow for inference of the interactions between humans and their environment.
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Affiliation(s)
- Simon Lax
- />Institute for Genomics and Systems Biology, Biosciences Department, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439 USA
- />Department of Ecology and Evolution, University of Chicago, 1101 E 57th Street, Chicago, IL 60637 USA
| | - Jarrad T Hampton-Marcell
- />Institute for Genomics and Systems Biology, Biosciences Department, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439 USA
| | - Sean M Gibbons
- />Institute for Genomics and Systems Biology, Biosciences Department, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439 USA
- />Graduate Program in Biophysical Sciences, University of Chicago, 5801 South Ellis Avenue, Chicago, USA
| | - Geórgia Barguil Colares
- />Departamento de Biologia, Universidade Federal do Ceará, Avenida da Universidade, 2853 - Benfica, Fortaleza, CE 60440-900 Brazil
| | - Daniel Smith
- />Institute for Genomics and Systems Biology, Biosciences Department, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439 USA
- />Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030 USA
| | - Jonathan A Eisen
- />Department of Evolution and Ecology, University of California, 1544 Newton Ct, Davis, CA USA
- />Department of Medical Microbiology and Immunology, University of California, 1544 Newton Ct, Davis, CA USA
- />UC Davis Genome Center, University of California, 1 Shields Avenue, Davis, CA USA
| | - Jack A Gilbert
- />Institute for Genomics and Systems Biology, Biosciences Department, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439 USA
- />Department of Ecology and Evolution, University of Chicago, 1101 E 57th Street, Chicago, IL 60637 USA
- />Graduate Program in Biophysical Sciences, University of Chicago, 5801 South Ellis Avenue, Chicago, USA
- />Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543 USA
- />College of Environmental and Resource Sciences, Zhejiang University, 38 Zheda Road, Hangzhou, 310058 China
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Prussin AJ, Garcia EB, Marr LC. Total Virus and Bacteria Concentrations in Indoor and Outdoor Air. ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS 2015; 2. [PMID: 26225354 PMCID: PMC4515362 DOI: 10.1021/acs.estlett.5b00050] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Viruses play important roles in microbial ecology and some infectious diseases, but relatively little is known about concentrations, sources, transformation, and fate of viruses in the atmosphere. We have measured total airborne concentrations of virus-like and bacteria-like particles (VLPs between 0.02 μm and 0.5 μm in size and BLPs between 0.5 μm and 5 μm) in nine locations: a classroom, a daycare center, a dining facility, a health center, three houses, an office, and outdoors. Indoor concentrations of both VLPs and BLPs were ~105 particles m-3, and the virus-to-bacteria ratio was 0.9 ± 0.1 (mean ± standard deviation across different locations). There were no significant differences in concentration between different indoor environments. VLP and BLP concentrations in outdoor air were 2.6 and 1.6 times higher, respectively, than in indoor air. At the single outdoor site, the virus-to-bacteria ratio was 1.4.
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Affiliation(s)
- Aaron J. Prussin
- Department of Civil and Environmental Engineering, Virginia Tech, 418 Durham Hall, Blacksburg VA 24061
| | - Ellen B. Garcia
- Department of Civil and Environmental Engineering, Virginia Tech, 418 Durham Hall, Blacksburg VA 24061
| | - Linsey C. Marr
- Department of Civil and Environmental Engineering, Virginia Tech, 418 Durham Hall, Blacksburg VA 24061
- Corresponding author phone: (540) 231-6071; fax: (540) 231-7916;
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