Dataset Information

Longitudinal analysis of microbial interaction between humans and the indoor environment.

ABSTRACT: The bacteria that colonize humans and our built environments have the potential to influence our health. Microbial communities associated with seven families and their homes over 6 weeks were assessed, including three families that moved their home. Microbial communities differed substantially among homes, and the home microbiome was largely sourced from humans. The microbiota in each home were identifiable by family. Network analysis identified humans as the primary bacterial vector, and a Bayesian method significantly matched individuals to their dwellings. Draft genomes of potential human pathogens observed on a kitchen counter could be matched to the hands of occupants. After a house move, the microbial community in the new house rapidly converged on the microbial community of the occupants' former house, suggesting rapid colonization by the family's microbiota.

SUBMITTER: Lax S

PROVIDER: S-EPMC4337996 | biostudies-literature | 2014 Aug

REPOSITORIES: biostudies-literature

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Longitudinal analysis of microbial interaction between humans and the indoor environment.

Lax Simon S Smith Daniel P DP Hampton-Marcell Jarrad J Owens Sarah M SM Handley Kim M KM Scott Nicole M NM Gibbons Sean M SM Larsen Peter P Shogan Benjamin D BD Weiss Sophie S Metcalf Jessica L JL Ursell Luke K LK Vázquez-Baeza Yoshiki Y Van Treuren Will W Hasan Nur A NA Gibson Molly K MK Colwell Rita R Dantas Gautam G Knight Rob R Gilbert Jack A JA

Science (New York, N.Y.) 20140801 6200

The bacteria that colonize humans and our built environments have the potential to influence our health. Microbial communities associated with seven families and their homes over 6 weeks were assessed, including three families that moved their home. Microbial communities differed substantially among homes, and the home microbiome was largely sourced from humans. The microbiota in each home were identifiable by family. Network analysis identified humans as the primary bacterial vector, and a Baye ...[more]

PMID: 25170151

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Project description:There is international consensus that damp buildings and indoor mould can increase the risk of asthma, rhinitis, bronchitis and respiratory tract infections but we do not know which types of microbial agents that are causing the observed adverse health effects. Microbial indoor exposure is a broader concept than microbial growth in buildings. Other sources of indoor microbial exposure include the outdoor environment, humans (crowdedness) and furry pet keeping. Microbial exposure can have different health effects depending on the dose, different exposure route, genetic disposition and the timing of exposure. Microbial stimulation linked to large microbial diversity in early life can protect against disease development, especially for allergic asthma and atopy. Protective effects are more often reported for bacterial exposure and adverse health effects are more often linked to mould exposure. There are many studies on health associations for indoor exposure to endotoxin, mainly from homes. The risk of getting atopic asthma may be less if you are exposed to endotoxin in childhood but the risk of non-atopic asthma may increase if exposed to endotoxin especially in adulthood. Moreover, genetic disposition modifies health effects of endotoxin. Epidemiological studies on muramic acid (from gram-positive bacteria) or ergosterol (from mould) are few. Studies on health effects of indoor exposure to beta-1-3-glucan (from mould) have conflicting results (positive as well as negative associations). Epidemiological studies on health effects of indoor exposure to mycotoxins are very few. Some studies have reported health associations for MVOC, but it is unclear to what extent MVOC has microbial sources in indoor environments. Many studies have reported health associations for fungal DNA, especially as a risk factor for childhood asthma at home. Since most studies on health effects of indoor exposure to mould, bacteria and microbial agents are cross-sectional, it is difficult to draw conclusions on causality. More prospective studies on indoor microbial exposure are needed and studies should include other indoor environments than homes, such as day care centers, schools, hospitals and offices.

Project description: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.

Dataset Information

Longitudinal analysis of microbial interaction between humans and the indoor environment.

Publications

Longitudinal analysis of microbial interaction between humans and the indoor environment.

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