midsummer bug hunt |  The Economist

Drspinning around Long live, June 21 is either summer or winter solstice. For some, this is a moment of celebration accompanied by strange rituals. Among the revelers are members of the Metagenomics and Metadesign of Subways and Urban Biomes Consortium (Meta).Sub). If in Bogotá, or Doha, or Kuala Lumpur, or London, or Minneapolis, or any other of about 60 cities around the world, on that day I saw someone invisibly sweeping a ticket counter, a handrail, a turnstile, or a seat at a station Local subway, so don’t be afraid. It’s just one of the MetaSubSociety volunteers collect samples of local microbes.

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deadSubThe purpose is to understand the invisible complexes of bacteria, archaea, fungi and viruses that are the smallest representatives of life. Every year, on the twenty-first of June, she coordinates an army of small game hunters who have the task of sampling public transportation in their city. The swabs are then labeled with collection time, local temperature, humidity, and the nature of the sample surface and sent for genetic sequencing and statistical analysis.

The consortium’s latest results, recently published in cell, based on 4,728 samples collected in 2015, 2016 and 2017. These samples show that each city has a microbial ecosystem distinct enough (see chart) to act as a fingerprint. An algorithm trained on the data can determine the origin of a randomly selected sample 88% of the time. There are a few species everywhere. Thirty-one (all bacteria) were found in nearly every swab, and 1145 (also Bar-Yeast and Bacteria) were found in more than 70% of the samples. However, the vast majority of the 4,246 identifiable species were much narrower distributed.

On top of these identifiable objects are the unknown. Nearly half of the sequenced creatures have no equivalent in the world’s public genetic data banks, says Daniela Bezdan, a former CEO of Meta.Sub who was one of the leaders of the study. It is estimated that more than 1,000 bacteria collected, and 10,000 viruses, remain unidentified.

I’ll meet the moonlight…

Unidentified organisms are common in such microbiological fishing expeditions, for a proper understanding of microbial biodiversity remains elusive. But, as intriguing as they are, these hiding neighbors are unlikely to be dangerous. “We know there are no pathogens because people don’t get ridiculously sick,” says David Danko, one of the authors of the paper.

The identities of the members of this dark microbiome are just one of the mysteries that remain to be resolved. The last thing that regulates the microbial ecology of the city. Remarkably, the observed pattern reflects the more common environment for plants and animals in that tropical cities have richer ecosystems than those near the poles (microbial diversity decreases by an average of seven species for each degree of latitude). No one knows for sure why this pattern is associated with macroscopic creatures. This may also be true for microbes may add insight.

On top of differing latitudes, three other patterns emerged. Coastal cities share characteristics that inland cities lack. So do those at higher altitudes, compared to those at lower altitudes. The same is true of cities with high population density.

For now, deadSub It’s still on the site of early botanists and zoologists, gathering information about exactly what was out there. As the underlying patterns become clear, such surveys can have practical benefits. They should, for example, enable public health agencies to monitor and map the spread of diseases, and to identify harmful new species. They can also allow monitoring of the genes carrying bacteria that confer antibiotic resistance. deadSub He found that such genes are widely distributed, but not evenly distributed. It was less common in Oceania and the Middle East. Why, so far it is impossible to say.

The current paper is only looking at DNA From the samples, but deadSub Scanning starts now RNA As well. This is particularly relevant for viruses, many of which, like the coronavirus currently sweeping the world, store their genes as RNA, Not DNA. As the team prepares for the next collection day, it hopes the data it collects will give a more accurate picture of the role of viruses in cities, and provide insights into the spread of the coronavirus.

This article appeared in the Science and Technology section of the print edition under the headline “Midsummer Bug Hunting”

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