Our skin is not only our largest organ, and the surface through which we experience the world, it is also a complex ecosystem in its own right. Grice et al (2008)1 estimated that more than a million micro-organisms of more than a hundred distinct species reside on a square centimeter of skin. The recent research into the microbiome of the skin shows that we have not only a great diversity of microorganisms in our skin microbiome, but also a high degree of variation from individual to individual. And although research into the interactions between the skin microbiome and dermal and other disorders is fairly new, it has become clear that the more diverse the microbiome, the healthier the skin.
The literature on the interaction between the skin microbiome and disorders such as psoriatic arthritis is growing rapidly. Another potential area for microbiome-related research is not from the skin in, but from the skin out.
As humans, we spend the majority of our time indoors, and thus interact extensively with the microbiome of our man-made environment rather than in the natural world. Humans contribute 106 microbial cells to their indoor environment every hour; the interaction between microorganisms from the built environment and the various occupants’ cutaneous and mucosal membranes play a subtle role in immunoregulatory, inflammatory, and/or many other processes.2
Research into the microbiome of built environments (MoBE) has only just begun. However, studies to date have confirmed that, like the microbiome of our skin, the more diverse the microbiome in the built environment, the better for our health—mental as well as physical.
The Microbiome of Built Environments (MoBE)
Most of the cells shed into the environment rapidly degrade, and the extent to which the MoBE serves as a reservoir for the human microbiome as a whole is unknown. Substantial research has been done on the transmission of airborne pathogens in building ventilation systems and effects of water damage (as in the devastating effects of Legionella and presence of molds). However, the transmission of other elements of the microbiome is not yet clearly defined.
One study showed that humans (and pets) moving between residences rapidly colonize their new home, maintaining an identical microbial signature between dwelling places. Other research has shown that the microorganisms comprising the MoBE do not have to be viable or even intact to have an influence on our health.2
The skin microbiome and the MoBE share a number of characteristics. Both show a high diversity in microbiota composition that varies from location to location on the body (inner elbow, scalp, hand, etc.) and surface (kitchen floor, doorknobs, sink, etc.). There is also a large variation in microbiome composition between different individuals as well as different equivalent environments (kitchen vs. kitchen, etc.). However, the microbiome of individuals and their environments are remarkably consistent over time.
The study of the MoBE, like that of the skin microbiome, has been hindered by lack of established techniques for sampling and analysis. However, practices that originated with the Occupational Safety and Health Administration (OSHA) for the study of toxins are evolving for use in analysis of the microbiome, and somewhat parallel sample collections for studying the skin microbiome:
- Swabbing (rubbing a sterile swab, either dry or dipped in a solution, over the area and then sealing it in a test tube for the trip to the laboratory)
- Bulk Sampling (directly removing a chunk of the surface to be analyzed, similar to a skin punch)
- Tape or Imprint (adhesive tape or culture medium is directly applied to the surface )
- "Carpet Stamp” technique (a small piece of sterilized wool is rubbed against the skin or other surface and placed on a culture medium, useful for isolation of fungi)
- Vacuum Sock (a surface is vacuumed to collect the spores and other particulates present onto a filter sock)
These sample collection methods are acceptable for immediate testing, but we do not have data on how freezing and long term storage of these samples may alter their composition, or how to process and preserve these samples for downstream research.
Hoisington, et al.2 notes that much MoBE research uses sequencing techniques that do not distinguish between living, dead but intact, and non-intact organisms. Application of more specialized and targeted sequencing will be useful for distinguishing between residue and living microorganisms and in determining their influence. In addition, PCR –based applications are used to determine the portfolio of microbial (fungal and bacterial) populations with respect to their relative numbers, types and proportions of each type.
Criteria for sample collection, storage, and analysis are emerging. Like other biospecimens, it is assumed that freezing at either ultra-low temperatures (-80°C) or in liquid nitrogen will preserve samples for microbiome-related research at an acceptable level of stability. Analyses must be performed immediately on thawing, so collecting multiple generous samples (if possible) and aliquoting (if applicable) before freezing is strongly recommended. It is also recommended that a pilot study, including neutrality tests (if chemical stabilization is used) as well as stability tests be performed to verify that sample handling practices will not skew results.
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1. Grice. E. A.; Kong, H. H.; Renaud, G. et al. (2008). A diversity profile of the human skin microbiota. Genome Research, 18: 1043–1050
2. Hoisington, A. J.; Brenner, L. A.; Kinney, K. A.; Pastolache, T. T. & Lwory, C. A. (2015). The microbiome of the built environment and mental health. Microbiome, 3:60, DOI 10.1186/s40168-015-0127-0.