Walls talk: Microbial biogeography of homes spanning urbanization

Urbanization of traditional villages—the villages developing in more urban form, and historical villagers migrating to towns and cities—is occurring concurrently with a global convergence toward a more Westernized urban plan and life-style (1). This process occurs as human societies integrate from hunter-gatherers into first rural and then urban life-styles. Urbanization also involves more people spending most of their lives in indoor built environments (2, 3).

A large proportion of the microbes found in the built environment are shed by humans (4–7) or animals (8), and with natural ventilation, microbes can also be transported from outdoors (5, 6, 9). Understanding the consequences of architectural changes on environmental exposures, including microbial exposures, is therefore important in improving home design and ultimately human health. Here, we determine the changes in architectural design and the resulting microbial communities of houses spanning a range of modernization within the Amazon River basin. We measured community demographics and architectural parameters, and characterized the microbial communities of 10 houses and their inhabitants from each of four locations: a traditional jungle village of hunter-gatherers near the border between Peru and Ecuador, a rural village further east along a similar latitude, the large Peruvian town of Iquitos, and, finally, the modern Brazilian city of Manaus (Fig. 1A).

The jungle village of Checherta is a 21-house Achuar community of hunter-gatherers (tables S1 and S2, and fig. S1, A and B). Homes are organized around a central area, including a communal building. This community design is retained in the 25-house rural village of Puerto Almendras, with the homes surrounding a soccer field (fig. S1C and table S1). Iquitos has 0.4 million inhabitants and is the largest urban population in the world not accessible by roads (fig. S1C and tables S1 and S2). Manaus, the capital of Amazonas State in Brazil, is a contemporary Western city with 1.8 million inhabitants (fig. S1D and tables S1 and S2).

Although no significant environmental differences were found across the urbanization gradient, large architectural changes were observed (Fig. 1). No significant differences were found across the studied locations in outdoor temperature (mean variation, <2°C; table S3) or relative humidity, and all locations had high ventilation rates (air exchange rates of 25 to 100 h⁻¹ in the jungle village, 7 to 20 h⁻¹ in the rural village, 4 to 17 h⁻¹ in the town, and 0.8 to 15 h⁻¹ in the city). The jungle village homes of Checherta are open huts made of wood and reeds, and are generally single open-plan spaces composed of two functional areas (Fig. 1, A and B, and fig. S2): a dormitory containing one platform bed per family, and a fire area for cooking and socializing. Up to six core families, among extended family members, share a home. As urbanization increases, a progressive separation of the indoor environment from the outdoor occurs first, followed by internal division of home spaces and the use of a wider variety of building materials (table S4). In the rural village, a toilet appears as an external latrine, which in the town and city becomes a piped indoor bathroom. Town and city houses typically have additional spaces differentiated by functional purpose (living room, kitchen, and bathroom) and segregated by walls (Fig. 1B).

Houses in the most urbanized conditions are more variable in design, but in general, there is an urbanization-associated increase in the number of rooms per person (privacy index) (Fig. 1C, fig. S3, and table S4), house area, and its variance (P < 0.005; Fig. 1C and table S4). The average house occupancy (persons per square meter) decreases with urbanization (P < 0.005; Fig. 1C and table S4), which is consistent with higher area and smaller families.

Remarkably, classification of house functional spaces using microbes was possible (Fig. 1D and fig. S4), and the probability of correct assignment given the wall bacterial composition increased with urbanization (Fig. 1E). We tested for differences in the types and diversity of household bacteria across locations. Microbial richness (α diversity) did not change with urbanization (Fig. 2 and figs. S5 and S6), but bacterial composition was markedly different (Fig. 2, A and B, and figs. S7 and S8) with houses becoming more microbially distinct along the gradient. Bacterial community structure in samples from floor and walls converged with urbanization (Fig. 2B). At the jungle end of the gradient, floors were made of dirt and people walked barefoot, and walls were wood columns; at the city end, floors and walls were made of synthetic materials, and people walked with shoes (in all but one house). Moreover, wall microbes better differentiated the kitchen and bathroom functional spaces in urban than in rural houses (Fig. 1D and fig. S9). The 10 most important operational taxonomic units (OTUs) that help discriminate among rooms in Manaus comprise several taxa normally associated with the human oral cavity, including Streptococcus, Neisseria, Actinomyces, and Veillonella dispar, as well as taxa normally associated with the human gut such as Enterobacteriaceae.

Despite lower occupant density in urban houses, “humanization” of the houses occurred with increased urbanization (Fig. 2D), associated with home enclosure—isolation from the outdoor environment—especially in dwellings sealed for air conditioning. Human bacteria were enriched in the town and city houses, with Prevotella, Verrucomicrobia, and Serratia on the walls (figs. S7 and S10), and skin taxa on the floors, consistent with human shedding (7, 10–12) and with the isolation of homes from bacterial sources from outdoor environments. Environmental bacteria were proportionally higher in the jungle and rural village house floors and included soil bacteria [for example, Mesorhizobium and Luteimonas from water sources and Rickettsiella from arthropods (figs. S7 and S10)]. The environmental bacterium found in walls included Acidobacteriales, Bradyrhizobium, Dactylosporangium, Actinomycetospora, Actinoalloteichus, Saccharopolyspora, Pedomicrobium, and Rickettsiella (figs. S7 and S10). As we move from the rural to the urban locations, there is a shift within Actinobacteria, from Brachybacterium and Brevibacterium commonly found in the environment to Corynebacterium, common in human skin (Fig. 2B).

A Bayesian approach called SourceTracker allowed the estimation of proportion of each community (that is, sample) that are likely to originate from each of a specified set of source environments (9). This analysis further confirmed the presence of a partially oral-like community on the urban bathroom walls (Fig. 3); these traces of human oral microbes from bathrooms and traces of water-associated microbes on kitchen countertops and walls likely contribute to the increased ability to identify both the houses and the indoor functional spaces.

We found no systematic association between the bacterial communities and many other parameters measured in the study including the structural materials in the households, number of people living in the house, number of pets (Fig. 2C), temperature variations, light incidence, frequency of cleaning, number of outsiders at sampling time, date of last rain, and time of day samples were collected (P > 0.05 in all cases). In particular, consistent with recent studies (11, 13), we find that samples within a house with different materials are more similar to one another than samples from the same material across different houses and that, in all communities, the inhabitants of each house are a major source of bacteria (Fig. 3).

Our findings indicate that the bacteria from the surfaces of house walls are informative of level of urbanization based on architectural design. Floors are the most informative of the commonalities found in individual houses across urbanization levels, whereas walls, less perturbed reservoirs of microbes accumulated through room usage, provide an indicator of room function.

Ventilation, described as a key factor for microbial community composition in urban settings (14–16), was very high in all of the houses of our study and does not explain differences in home microbial composition with urbanization. Instead, we propose that the presence of walls dividing functional spaces acquires function-dependent microbes, mostly of human origin.

The current study is limited to one geographical region of the world and is a small pilot study, and thus, results may not be generalizable. Further research should identify mechanistic explanations for these phenomena. Insights into the chemical signals that bacteria provide in different sites within the home are also needed. These remarkable changes in house microbial content across urbanization might translate into differences in microbial exposure that may have developmental health implications for humans (17), according to several related hypotheses [the “hygiene” hypothesis (18), the “Old Friends” hypothesis (19), and the “Disappearing microbiota” hypothesis (20)], suggesting that the reduced pattern of microbial exposure leads to immune and metabolic disorders that have become the new disease paradigm in the industrialized world.

We acknowledge the collaborators in Peru, the interpreter J. J. Semu, and the late Father Luigi for being a source of information and inspiration. In Manaus, we had the valuable help of A. Vasconcelos and J. Machado with the fieldwork. Funding: This work was supported by the Sloan Foundation, the C&D Fund, and the Emch Fund for Microbial Diversity (to M.G.D.-B.). Partial support was also provided by the NIH Research Initiative for Scientific Enhancement Program 2R25GM061151-13 (to J.F.R.-C.). Author contributions: M.G.D.-B. and R.K. designed the study. J.F.R.-C., H.C., A.N., J.N.H., R.R., O.H.B., H.P., L.C.P., M.J.B., and M.G.D.-B. collected the data and processed the specimens. J.F.R.-C., S.J.S., R.K., H.C., L.R.P., and M.G.D.-B. analyzed the data. M.G.D.B., J.F.R.-C., H.C., S.J.S., and R.K. drafted the manuscript. All authors reviewed the final manuscript. Competing interests: The authors declare that they have no competing interests. Data and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. Additional data related to this paper may be requested from the authors and/or http://qiita.ucsd.edu/study/description/10333.