Resident Humans and microbes adapt with each other inside homes

The presence of humans interacts with their microbial roommates, changing the home’s biology and chemistry.


Modern humans spend almost 70% of their time in their home environment. Certainly, they can reshape microbiomes around them with inputs from their bodies.

Many studies of the indoor environment have revealed that human activity inside buildings leads to potentially higher particle, pollutant, and toxin exposures than typically observed in the outdoor environment, but all these studies were focused on one or a few molecular species. Entire molecular composition throughout the home may also be influenced by human interference.

In a recent study in Science Advances, scientists at the University of California San Diego School of Medicine and elsewhere report on the molecular impact of life indoors, describing how the presence of humans interacts with their microbial roommates, changing the home’s biology and chemistry.

This is the first survey that observed the adaptation of a whole set of microbes around humans inside homes.

“Our indoor habitat appears to be not just a reflection of human activities but rather is in a mutualistic relationship with its inhabitants. Such household-microbial chemistry, its potential impact on health and well-being of the house inhabitants, and possible ways to control and how to optimize such chemistries to promote beneficial effects are factors that should be considered in the engineering of indoor environments.” Study mentions.

An Experiment

This was accomplished by using an experimental test home in Austin, Texas, during the summer of 2018 that was sampled at two-time points with 28 days apart, time points T1 and T2, to detect the distribution of molecules and microbes throughout the living spaces simulating normal activity and occupancy.

Experimental conditions

4 weeks of use that included cooking, cleaning, and human occupancy.

The house experienced normal daytime human use (e.g., using one of the bathrooms, sitting on chairs, cleaning, eating and using computers on the tables, and cooking in the kitchen).

Overnight stays were not permitted, but some people occupied this home for 6 ± 4 hours per day for 26 days and performed scripted activities.

In total, ~45 different people visited the home in those 30 days, which included an open house for the media and the local community.

The home was sampled to inventory the detectable molecules and microbes that were present at T1 and T2 by swabbing surfaces throughout the occupied areas of the house.

Microbiomes remained persistent along with humans.

Researchers found molecules associated with skin care products, skin cells, drugs (such as antidepressants and anabolic steroids), food-derived molecules (such as terpenes and flavonoids), human or animal metabolites (molecules generated during the process of metabolisms, such as bile and fatty acids), amino acids, sugars and microbial metabolites.

Most of the indoor surface molecules were natural products (biologically produced molecules rather than synthetic compounds), food, molecules associated with the outdoors, personal care products, and human-derived metabolites, often traced to fecal matter.

Food, human-associated microbes, feces, building materials, and the microbes that grow upon them and building materials in humid conditions were deemed the likely primary sources.

The kitchen and toilet were hotspots of molecular and microbial diversity, though numbers fluctuated with surface cleaning and sanitation. “It appears that, even when a subset of chemistry is removed because of the cleaning, it is only temporary and/or partial, as the sum total of cleaning and human activities overall results in an increase in accumulation of richer chemistry,” the authors wrote.

Surfaces routinely touched by people, such as tables, light switches, and knobs, were more abundant in molecular and microbial chemistry. Floors showed less molecular diversity, perhaps because they were cleaned more often. Windows, chairs, and doors not routinely touched by human occupants displayed the least change in chemical diversity between T1 and T2.

Researchers found indoor surfaces covered with bacteria, fungi and other microbes, plus their metabolites. Regular cleaning altered these microbial populations and diversity over time, allowing different species to recolonize cleaned spaces.

“We don’t know exactly how the human-related microbes squeezed out the environmental microbes because there are many ways this could happen, but it’s clear that they do,” said Rob Knight, Ph.D., one of the study’s principal investigators and director of the Center for Microbiome Innovation at UC San Diego. “Understanding this phenomenon will be a key goal of future research on the microbiology of the built environment.”

The authors noted that at least 1 percent of the detected indoor molecules might pose an outsized health effect.

“As an example, Paenibacillus sp. was associated with molecules from coffee, one of the dominant sources of food-derived indoor molecules (e.g., caffeine, trigonelline, and chlorogenic acid). In the home, especially at T2, Paenibacillus was observed in and around the area where coffee was prepared, and this genus has been found to grow in coffee machines. We observed that Paenibacillus cultures transformed coffee-derived molecules into the molecules that we detected inside the house; chlorogenic acid was detected in the culture of these strains when grown on spent coffee grounds, and its metabolized versions were also found in the house, supporting this causal hypothesis about its origin.” Researchers mentioned.

Futuristic view of study

“Understanding specifically how our observations that both human and microbial occupants change the chemical make-up of a home should influence building material design to improve human health will require additional studies,” said co-principle investigator Pieter Dorrestein, Ph.D., director of the Collaborative Mass Spectrometry Innovation Center at Skaggs School of Pharmacy and Pharmaceutical Sciences at UC San Diego.

The awareness of and the ability to observe the molecular changes introduced by people should influence future building designs.

“We hope that this work will stimulate interest in future studies.” Researchers quote.

Journal Reference

  1. Alexander A. Aksenov, Rodolfo A. Salido, Alexey V. Melnik, Caitriona Brennan, Asker Brejnrod, Andrés Mauricio Caraballo-Rodríguez, Julia M. Gauglitz, Franck Lejzerowicz, Delphine K. Farmer, Marina E. Vance, Rob Knight, and Pieter C. Dorrestein. The molecular impact of life in an indoor environment. Science Advances, 24 Jun 2022, Vol 8, Issue 25, DOI: 10.1126/sciadv.abn8016
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