Microbiomes of the built environment: Difference between revisions
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== Components of the Built Environment that Impact Microbiomes == |
== Components of the Built Environment that Impact Microbiomes == |
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A major component of studies of Microbiomes of the Built Environment involves determining how components of the built environment impact these microbes and microbial communities. Factors that are thought to be important include humidity, pH, chemical exposures, temperature, filtration, surface materials, and air flow.<ref>http://nas-sites.org/builtmicrobiome/about-the-study-2/</ref> |
A major component of studies of Microbiomes of the Built Environment involves determining how components of the built environment impact these microbes and microbial communities. Factors that are thought to be important include humidity, pH, chemical exposures, temperature, filtration, surface materials, and air flow.<ref>http://nas-sites.org/builtmicrobiome/about-the-study-2/</ref> There has been an effort to develop standards for what built environment "metadata" to collect associated with studies of the microbial communities in the built environment. <ref>{{Cite journal|last=Glass|first=Elizabeth M.|last2=Dribinsky|first2=Yekaterina|last3=Yilmaz|first3=Pelin|last4=Levin|first4=Hal|last5=Van Pelt|first5=Robert|last6=Wendel|first6=Doug|last7=Wilke|first7=Andreas|last8=Eisen|first8=Jonathan A.|last9=Huse|first9=Sue|date=2014-01-01|title=MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment|url=http://www.nature.com/ismej/journal/v8/n1/full/ismej2013176a.html|journal=The ISME Journal|language=en|volume=8|issue=1|pages=1–3|doi=10.1038/ismej.2013.176|issn=1751-7362|pmc=3869023|pmid=24152717}}</ref> In addition many tools are available to improve the built environment data that is collected associated with such studies. <ref>{{Cite journal|last=Ramos|first=Tiffanie|last2=Stephens|first2=Brent|date=2014-11-01|title=Tools to improve built environment data collection for indoor microbial ecology investigations|url=http://www.sciencedirect.com/science/article/pii/S0360132314002200|journal=Building and Environment|volume=81|pages=243–257|doi=10.1016/j.buildenv.2014.07.004}}</ref> |
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== Methods Used == |
== Methods Used == |
Revision as of 16:22, 20 August 2016
Microbiomes of the built environment [1][2] is a field of inquiry focusing on the study of the communities of microorganisms found in human constructed environments (i.e., the built environment). It is also sometimes referred to as "microbiology of the built environment".
This field encompasses studies of any kind of microorganism (e.g. bacteria, archaea, viruses, various microbial eukaryotes including yeasts, and others sometimes generally referred to as protists) and studies of any kind of built environment such as buildings, vehicles, and water systems.
Some key highlights emphasizing the growing importance of the field include:
- The field has accelerated somewhat in recent years, with significant funding from the Alfred P. Sloan Foundation.[3] and with the increase attention being given to microbiomes and communities of microbes generally.
- The National Academies of Sciences, Engineering, and Medicine of the USA is conducting a study of the this field with the study entitled "Microbiomes of the Built Environment: From Research to Application".
- The American Association for the Advancement of Science ran a symposium on the topic in 2014.[4]
- The American Academy of Microbiology had a colloquium on this topic in September 2015 and published a report "Microbiology of Built Environments".[5]
A 2016 paper by Brent Stephens [6] highlights some of the key findings of studies of "microbiomes of the indoor environment". These key findings include those listed below:
- "Culture-independent methods reveal vastly greater microbial diversity compared to culture-based methods"
- "Indoor spaces often harbor unique microbial communities"
- "Indoor bacterial communities often originate from indoor sources."
- "Humans are also major sources of bacteria to indoor air"
- "Building design and operation can influence indoor microbial communities."
The microbiomes of the built environment are being studied for multiple reasons including how they may impact the health of humans and other organisms occupying the built environment but also some non health reasons such as as diagnostics of building properties, for forensic application, impact on food production, impact on built environment function, and more.
Types of Built Environments Being Studied
In the last few years there have been a growing number of studies of the microbiomes of built environments with an emphasis on the use of high throughout DNA sequencing to study the communities of microbes present in these systems. Major categories of built environments that have been studied in regard to their microbiomes include:
Buildings
Many categories of buildings have been under investigation for their microbiomes. Examples include those listed below.
- Homes [7][8][9]
- Dormitories [10]
- Offices[11][12]
- Hospitals [13][14][15]
- Operating rooms [16], [17], [18]
- NICUs [19]
- Classrooms [20][21]
- Transportation facilities such as train and subway stations,[22][23]
- Food production facilities like dairies, wineries [24], cheesemaking facilities [25] [26], sake breweries [27] and beer breweries [28]. Bokulich et al. in 2016 reviewed studies of the microbiome of food production facilities [29].
- Aquaria [30]
- Libraries [31]
- Cleanrooms[32] [33]
- Zoos
- Animal shelters
- Farms
- Chicken coops and housing [34]
Vehicles
- Airplanes [35]
- Ships
- Trains [23]
- Automobiles [36]
- Space vehicles including International Space Station [37], MIR [38], the Mars Odyssey [39], the Herschel Spacecraft [40].
Water systems
- Shower heads [41]
- Children's paddling pools [42]
- Municipal water systems [43]
- Drinking water and premise plumbing systems [44][45] [46] [47]. The "microbe-home" web site and blog has additional information about microbes and premise plumbing systems.
General Biogeography
Overall the many studies that have been conducted on the microbiomes of the built environment have started to identify some general patterns regarding the microbes are found in various places. For example, Adams et al, in a comparative analysis of ribosomal RNA based studies in the built environment found that geography and building type had strong associations with the types of microbes seen in the built environment.[48]. Pakpour et al in 2016 reviewed the patterns relating to the presence of archaea in indoor environments (based on analysis of rRNA gene sequence data [49].
Human Health and Microbiomes of the Built Environment
Many studies have documented possible human health implications of the microbiomes of the built environment (e.g.,[50] ). Examples include those below.
Newborn colonization
The microbes that colonize newborns come in part from the built environment (e.g., hospital rooms). This appears to be especially true for babies born by C-section (see for example Shin et al. 2016 [51]) and also babies that spend time in a NICU [52].
Risk of allergy and asthma
The risk of allergy and asthma is correlated to differences in the built environment microbiome. Some experimental tests (e.g., in mice) have suggested that these correlations may actually be causal (i.e., the differences in the microbiomes may actually lead to differences in risk of allergy or asthma). Review papers on this topic include Casas et al. 2016 [53] and Fujimura and Lynch 2015 [54]. Studies of dust in various homes has shown that the microbiome found in the dust is correlated to the risk of children in those homes developing allergy, asthma, or phenotypes connected to these ailments. [55] [56] [57]
The impact of the microbiome of the built environment on the risk of allergy and asthma and other inflammatory or immune conditions is a possible mechanism underlying what is known as the hygiene hypothesis.
Mental health
In a 2015 review Hoisington et al. discuss possible connections between the microbiology of the built environment and human health.[58] The concept presented in this paper is that more and more evidence is accumulating that the human microbiome has some impact on the brain and thus if the built environment either directly or indirectly impacts the human microbiome, this in turn could have impacts on human mental health.
Pathogen transmission
Many pathogens are transmitted in the built environment and may also reside in the built environment for some period of time [59]. Good examples include influenza, Norovirus, Legionella, and MRSA. The study of the transmission and survival of these pathogens is a component of studies of microbiomes of the built environment.
Indoor Air Quality
One aspect of the health impact of microbes in the built environment involves the microbes in air. Microbes in indoor air have been studies for many years. See for example the discussion of Legionella and bacteria on the Indoor air quality page.
Connection to Microbial Forensics
The microbiome of the built environment has some potential for being used as a feature for forensic studies. Examples are discussed below. Most of these applications are still in the early research phase.
- People leave behind a somewhat diagnostic microbial signature when they type on computer keyboards.[60] See also this Wired story about this work.
- People leave behind potentially diagnostic signature microbial DNA on phones when they use them [61]
- The occupants of a room leave behind microbial DNA that may be useful as a forensic tool [10]
- Microbiome analysis may be useful in analysis of cadavers to determine time of death.[62] [63] If the cadaver was found in the built environment then it likely will accumulate microbes that have a built environment connection.
Components of the Built Environment that Impact Microbiomes
A major component of studies of Microbiomes of the Built Environment involves determining how components of the built environment impact these microbes and microbial communities. Factors that are thought to be important include humidity, pH, chemical exposures, temperature, filtration, surface materials, and air flow.[64] There has been an effort to develop standards for what built environment "metadata" to collect associated with studies of the microbial communities in the built environment. [65] In addition many tools are available to improve the built environment data that is collected associated with such studies. [66]
Methods Used
Many methods are used to study microbes in built environment. A review of such methods are some of the challenges in using them was published by NIST: Challenges in Microbial Sampling in the Indoor Environment. Hoisington et al. in 2015 reviewed methods that could be used by building professionals to study the microbiology of the built environment.[67] Methods used in the study of microbes in the built environment include culturing (with subsequent studies of the cultured microbes), microscopy, air, water and surface sampling, chemical analyses, and culture independent DNA studies such as ribosomal RNA gene PCR and metagenomics.
Examples of projects
There are a growing number of research projects and groups focusing directly or indirectly on microbiomes of the built environment. Some of these are targeted towards specific environments (e.g., homes, hospitals, showerheads) and others are broader (e.g., BIMERC, the BioBE Center). More detail about some of these projects is below.
- BIMERC - the Berkeley Indoor Microbial Ecology Research Consortium. This group is focused on "understanding the microbial components of indoor air, including the identification of the source populations and illuminating the processes that suspend and disseminate microbes and microbial products in buildings."
- The BioBE Center - Biology and the Built Environment Center
- The Wildlife of Your Homes is a Citizen science project focusing on "the diversity of bacterial communities found in nine distinct locations within our homes."
- Baby Associated Built Environment Microbiome Project
- Showerhead microbiome project
- Hospital Microbiome Project
- Home Microbiome
- PRoBE – Pathogen Research in the Built Environment
News and related coverage
- Nova Next: Mapping the Microbiome
- NPR: Your Invisible Neighbors: Each City Has Unique Microbes
- The Scientists: Your Office Has a Distinct Microbiome
- The Conversation article by Erica Hartmann Scientists at work: studying indoor microbial ecology means sampling in public restrooms
- TIME Magazine Your Home is Covered in Microbes
See also
External links
- Microbiology of the Built Environment paper collection at Biomed Central
- Jessica Green TED talk Are We Filtering the Wrong Microbes
- Jessica Green TED talk We're covered in germs. Let's design for that.
- Rob Knight TED Talk How our microbes make us who we are
- ISIAQ - International Society of Indoor Air Quality and Climate
- Indoor Air Journal
References
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- ^ Corsi, Richard L.; Kinney, Kerry A.; Levin, Hal (2012). "Microbiomes of built environments: 2011 symposium highlights and workgroup recommendations". Indoor Air. 22 (3): 171–172. doi:10.1111/j.1600-0668.2012.00782.x. ISSN 0905-6947.
- ^ http://www.sloan.org/major-program-areas/basic-research/mobe/
- ^ http://www.aaas.org/event/microbiomes-built-environment
- ^ Richmod, Dylan. "FAQ: Microbiology of Built Environments". academy.asm.org. Retrieved 2016-07-27.
- ^ Stephens, Brent; Gibbons, Sean Michael (2016). "What Have We Learned about the Microbiomes of Indoor Environments?: TABLE 1". mSystems. 1 (4): e00083-16. doi:10.1128/mSystems.00083-16. ISSN 2379-5077.
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