Microbes mirrow our social networks

The beginning of this story is probably familiar to most people. A little child rides the subway, accompanied by its mom or dad, and the little children’s hands run over basically anything they can get hold of: Windowpanes, handles, surfaces on seats and floors, and then finally and impartially come to a halt in the child’s mouth. The father of this story’s kid is the microbiologist Chris Mason and this subway ride drove him to a study on the microbiome of cities. Lo and behold, he was able to prove that cities have their own distinct microbial fingerprint (1).

Basics of the colonization of our microbiome

In the course of the study, probes from hubs and other frequently touched surfaces throughout New York City in the first run, and another 60 cities worldwide in a second run were taken and analysed regarding their composition. Handles, especially in public, are real treasure chests of microbes: starting with skin microbes, over lung microbes coughed in the hand palms, to gut microbes that are in actual fact also found on our hands. The result of the study was accordingly rich (2).

The extensive data collection was conducted over a time span of three years in 60 bigger cities from Baltimore to Bogotá, on all five continents. An interactive map documents the impressive outcome (3). The samples contain 11.000 viruses and 1.302 bacteria, along with 838.532 DNA-arrays (CRISPR) that science had not previously aligned to any living organism, so far (4). Sounds like a good plot for an alien movie – and once more proves that we are still at the very beginning of research on microbiology.

Influences on the city’s microbiome

It is common sense that microbes are exchanged between people of a household or workgroup. Over aerosols or via surfaces, microbes find their way from one host to the other. This is especially relevant with illnesses. In the New York subway, for instance, scientists were able to identify the bacterium Bacillus anthracis, the anthrax pathogen. During the relevant time frame, no cases were reported to the local authorities, therefore the scientists assumed that an average urban microbiome always contains a certain number of pathogens (which proves parents’ instinct right that licking subway handles is disgusting).

The permanent main composition of a microbiome is linked to other factors. The way of birth, to begin with, decides over the dominant bacteria on our skins (5). The colonization of our gut is influenced by our nutrition and the intake of antibiotics (6). And the microbes in our house dust are quite different depending on the location in the city or in the country (7). The composition mirrors the presence of nearby factories or the filtering effect of surrounding forests or parks. The microbiome is impacted by general climatic conditions like frequent rain or drops in temperature or – like in the mentioned case of New York City – the proximity of the subway to the ocean. All these factors foster some microbes and inhibit others.

Hit rate surprisingly high

The scientists involved in the studies were able to identify 31 species prevalent in almost all (97%) probes. They called that the urban “core” microbiome. Another 1,145 species were detected in as many as 70% of the probes. And still, the remaining differences allow to align probes with a certainty of 88% to the right city. New York City as starting point for the studies appeared to show an increased prevalence in Carnobacterium inhibens that is very tolerant against low temperatures.

Significance of the study

Of course, these outcomes are not completely unexpected and new, but a profound basis for further use. The hit rate is remarkably high considering that cities are no homogenous, self-contained units, but subject to influences by tourists or extreme weather conditions. The authors of the studies suggest the use of the outcomes in forensics or bioterrorism threat mitigation. Chris Mason, the initiator the study, stresses that a continuous surveillance of cities regarding pathogens might have been able to put a halt on or at least weaken the outbreak of the corona pandemic.

Links to sources:

(1) O’Grady C, Cities have their own distinct microbial fingerprints, Science (2021), https://www.science.org/news/2021/05/cities-have-their-own-distinct-microbial-fingerprints

(2) Afshinnekoo E, Meydan C, et al Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics, Cell Syst (2015), https://pubmed.ncbi.nlm.nih.gov/26594662/

(3) http://metasub.org/map/

(4) Danko D, Bezdan D, et al A global metagenomic map of urban microbiomes and antimicrobial resistance, Cell (2021), https://www.cell.com/cell/fulltext/S0092-8674(21)00585-7

(5) Knight R, Delivery Method Influences Microbial Communities in Newborns, HHMI (2010), https://www.hhmi.org/news/delivery-method-influences-microbial-communities-newborns

(6) Mantegazza C, Molinari P et al. Probiotics and antibiotic-associated diarrhea in children: A review and new evidence on Lactobacillus rhamnosus GG during and after antibiotic treatment (2018), https://www.sciencedirect.com/science/article/abs/pii/S1043661817309234

(7) Hanski I, von Hertzen L, Fyhrquist N, Koskinen K, Torppa K, Laatikainen T, et al. Environmental biodiversity, human microbiota, and allergy are interrelated. Proc Natl Acad Sci USA (2012), https://pubmed.ncbi.nlm.nih.gov/22566627/