A Worldwide Microbial Atlas

By Iva Fedorka

Chris Mason, a geneticist at Weill Cornell Medicine, was inspired to survey the microbial world of various cities when he saw his daughter lick a public subway surface in New York City. His study included nearly 5,000 samples from subways, buses, and other public transportation in 60 cities and took more than three years to complete. After preliminary results were published, other researchers offered to contribute.

Sampling Techniques

Sampling was performed on three occasions:

• During a pilot study in 2015 and 2016
• On global city sampling day June 21, 2016
• On global city sampling day June 21, 2017

Samples of transit system bench, turnstile, and ticket kiosk surfaces were swabbed for three minutes, producing samples with enough DNA to test without making  bystanders uncomfortable.

The Atlas

The atlas Mason and his colleagues created contains profiles of microbial strains, characteristics, antimicrobial resistance markers, and other genetic characteristics for 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 previously undocumented CRISPR arrays. The three most common bacterial phyla across the world’s cities (by the number of species observed) were Proteobacteria, Actinobacteria, and Firmicutes.

Of those, 45% didn’t match any known species, approximately 11,000 viruses and 1,302 bacteria were new to the scientists, and 4,246 were known species. Within this group, a “core” microbiome was identified, which included 31 species that were present in 97% of the samples. Another 1,145 species were found in more than 70% of the samples.

Antimicrobial Resistance Findings

Genes for antimicrobial resistance (AMR) were much less present than those typically found in samples from hospitals or the human gut. The most common AMR genes were found for beta-lactams, glycopeptides, and fluoroquinolones.

Fewer AMR genes were found in samples from Oceania and the Middle East, perhaps due to levels of antibiotic use, urban geography differences, or as a reflection of varied microbiomes. More research may reveal effects on medical environments and phenotypes of resistance.

Other Results and Limitations

Taxonomic profiles from North America and Europe were distinct from those collected in East Asia. The researchers also found more localized species. Cities exhibited distinct microbiomes, along with climatic and geographic differences. In fact, the researchers were eventually able to accurately predict the city from which a particular sample was collected based on its microbial mix.

The anniversary sampling date in 2017 was used to assess the impact of time. The annual difference within cities was less than between cities, but time-related changes could become more significant over the long term.

Conclusions

The coronavirus pandemic of 2020 has demonstrated the need for better microbial surveillance that could help assess risk, map outbreaks, and characterize problematic species. Many environmental viruses and bacterial antimicrobial resistance genes have been identified, but just the ones that are DNA-based. Future RNA studies would help with tracking and mitigating future epidemics.

The predictability of a city’s microbiome may also be useful in forensic investigations, and new species have potential for drug research. This effort is a first critical step toward quantifying the distribution and dynamics of environmental microbiomes for tracking changes in ecology and virulence. Ongoing updates may help physicians, public health departments, government officials, and scientists assess epidemiological risks and trends and support data-driven policies and medical decisions.