Cities Have Their Own Distinct Microbial Fingerprints (sciencemag.org) 26
sciencehabit shares a report from Science Magazine: When Chris Mason's daughter was a toddler, he watched, intrigued, as she touched surfaces on the New York City subway. Then, one day, she licked a pole. "There was a clear microbial exchange," says Mason, a geneticist at Weill Cornell Medicine. "I desperately wanted to know what had happened." So he started swabbing the subway, sampling the microbial world that coexists with people in our transit systems. After his 2015 study revealed a wealth of previously unknown species in New York City, other researchers contacted him to contribute. Now, Mason and dozens of collaborators have released their study of subways, buses, elevated trains, and trams in 60 cities worldwide, from Baltimore to Bogota, Colombia, to Seoul, South Korea. They identified thousands of new viruses and bacteria, and found that each city has a unique microbial "fingerprint."
They found that about 45% didn't match any known species: Nearly 11,000 viruses and 1,302 bacteria were new to science. The researchers also found a set of 31 species present in 97% of the samples; these formed what they called a "core" urban microbiome. A further 1145 species were present in more than 70% of samples. Samples taken from surfaces that people touch -- like railings -- were more likely to have bacteria associated with human skin, compared with surfaces like windows. Other common species in the mix were bacteria often found in soil, water, air, and dust. But the researchers also found species that were less widespread. Those gave each city a unique microbiomeâ"and helped the researchers predict, with 88% accuracy, which city random samples came from, they report today in Cell.
The study's main value isn't in its findings (which are mapped here) so much as its open data, available at metagraph.ethz.ch, says Noah Fierer, a microbiologist at the University of Colorado, Boulder, who was not involved with the research. That will give other researchers the chance to delve into new questions. "Different cities have different microbial communities," Fierer says. "That's not super surprising. The question for me is, why?" Mason sees an opportunity for "awe and excitement about mass transit systems as a source of unexplored and phenomenal biodiversity." Newly discovered species have potential for drug research, he says, and wide-scale mapping and monitoring of urban microbiomes would be a boon for public health, helping researchers spot emerging pathogens early.
They found that about 45% didn't match any known species: Nearly 11,000 viruses and 1,302 bacteria were new to science. The researchers also found a set of 31 species present in 97% of the samples; these formed what they called a "core" urban microbiome. A further 1145 species were present in more than 70% of samples. Samples taken from surfaces that people touch -- like railings -- were more likely to have bacteria associated with human skin, compared with surfaces like windows. Other common species in the mix were bacteria often found in soil, water, air, and dust. But the researchers also found species that were less widespread. Those gave each city a unique microbiomeâ"and helped the researchers predict, with 88% accuracy, which city random samples came from, they report today in Cell.
The study's main value isn't in its findings (which are mapped here) so much as its open data, available at metagraph.ethz.ch, says Noah Fierer, a microbiologist at the University of Colorado, Boulder, who was not involved with the research. That will give other researchers the chance to delve into new questions. "Different cities have different microbial communities," Fierer says. "That's not super surprising. The question for me is, why?" Mason sees an opportunity for "awe and excitement about mass transit systems as a source of unexplored and phenomenal biodiversity." Newly discovered species have potential for drug research, he says, and wide-scale mapping and monitoring of urban microbiomes would be a boon for public health, helping researchers spot emerging pathogens early.
Interesting For Old Insight (Score:3)
Died where? (Score:4, Insightful)
This could come in handy when doing forensics.
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Probably not.
When someone dies their microbiome goes for a free for all. As the body is no longer living, A lot of the microbes die soon later, while some flourish for a while, because they were being in check with other microbes, and the body And those often will interact oddly with other microbes.
So while checking a metal poll, or a brick, you probably can figure out what city it is from. From a dead persons body not so much.
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Probably not because it requires cities/towns to keep a microbial record (presumably the fingerprint changes over time) and share that info. This might be feasible if it were highly useful in forensics but not a lot of bodies are getting dumped in another city. There is also the question if this microbial state is preserved in death or if the body has to be found immediately. However, this might be useful for objects... but probably only for a short period before everything on it dies.
There seem to be ma
From the Obvious Department .. (Score:3, Funny)
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My personal experience of this (Score:2, Interesting)
I don't know if it was microbes, or pollen, or both; but when I moved from the east coast of the USA to the west I got sick on the regular. I acclimated quickly to my apartment. For about a year, trips to the beach or San Francisco were a coin toss on some kind of illness. One trip to San Francisco was particularly bad, causing me to vomit and have diarrhea at the same time before I even left the city. Somebody attributed this to walking up and down the hills, but that didn't seem to jibe. I've walked
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Drug research? (Score:3, Interesting)
Newly discovered species have potential for drug research
Considering the samples come from the subway system, they're probably genetically related to drugs.
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If you are talking about narcotics, probably not.
It's okay to lick the subway. (Score:5, Interesting)
Last sentence of the post:
"... wide-scale mapping and monitoring of urban microbiomes would be a boon for public health, helping researchers spot emerging pathogens early."
Not really.
That last sentence reveals a bias in microbiological science, medicine, and public health ever since Koch, Pasteur, and Lister elucidated the role of microbial species in human disease. Infectious diseases are all too real of course, but the idea has done more than almost anything else to engender fear or be used as marketing FUD. That includes fear of political regimes, terrorism, earthquakes, and asteroids. And as a marketing or mind bending tool, germs are a subtle and persuasive tool. Unlike politics, they are apolitical, everybody equally at risk (so the germ fear mongers would have you believe). And unlike the theoretical next Chixilub, the microbes are here already. Ever since the latter 19th century, fear of germs, hyped by those with something to sell, ensures a never ending reliable stream of revenue for sterility and antiseptic products.
But here is why this fear is not only not warranted, not as stated in this report, but tangibly dangerous.
There are hundreds of thousands of bacteria and other classes of non-viral microbes. Millions actually, or likely. DNA sequencing has opened up the flood gates of identifying unknown species, just as implied in this report.
Each microbe has its own requirements for life. Higher taxa, especially man, are highly adaptable to hostile environments. Most lower taxa are quite restricted in where they can live, because they have simple metabolic systems that require a narrowly defined environment, ecology, and energy substrates. Take an organism out of its home environment, and it cannot survive. We use the designation "extremophiles" for organism that live in volcanic vents or under glaciers, but for them, they are home. Your armpit or the sewer on your street would not be a tasty meal for them, indeed those environments would be their death.
Despite the 10^5 to 10^7 microbial species possibly out there, only a minute fraction cause human disease. On any given typical day in any hospital, the number of species actually causing infection and being treated is maybe 20-30. In the course of a month, maybe 30-50 species have been identified. Taking account of endemic species in different parts of the world, then in any year, maybe 200-300 species of bacteria and mycetes would have had any notable presence. If all clinical labs pooled all data on human pathogens identified in the course of 10 years, I don't think it would break the 1000 mark.
Then, there are many more species that live on our bodies that never cause disease (except perhaps in the most extreme circumstances of immunosuppression). Then again, there are hundreds of known species that actually populate our gut and skin that have never been identified as a pathogen. In fact, current research has started to emphasize the protective value that many of them have to help us, either to protect us from genuine pathogens that might "get us", or to supply micronutrients and other metabolic benefits to our systems. Indiscriminate use of antibiotics to simply kill germs on our bodies is detrimental. Perhaps the most common clinical problem that has become prevalent in hospitals is Clostridium difficile necrotizing enterocolitis, an often fatal disease that occurs solely from antibiotics eliminating protective species.
And how do we treat C. difficle? In part by eating certain other bacteria. We eat yogurt, cheeses, sausages, all which use friendly microbes to spoil our food in tasty healthy ways. If the microbial fear mongers knew that, you would be persuaded never to eat cheese. Imagine streptomycin yogurt, with pills instead of strawberries at the bottom of the cup.
We indiscriminately try to kill germs, in our kitchens and bathrooms, and in our hospitals, because companies with products to sell, playing on our own innate primal fears and susceptibility to FUD, ha
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Ah, the joys of being a parent (Score:1)
Then, one day, she licked a pole.
wonderful
We're new here. (Score:2)
(Viral researcher) "Whew, finally almost done with this cataloging! And just in time for the holiday weekend."
They found that about 45% didn't match any known species: Nearly 11,000 viruses and 1,302 bacteria were new to science.
(Viral researcher) "It's like we just started looking yesterday.."
Hollywood (Score:1)
Re: Cities Have Their Own Microbial Fingerprint (Score:2)
Is this actually news to anyone? Granted, the article goes into more detail, but the basic premise is not anything ground breaking. Sourdough bread has different characteristics based on where it's made--and if you take a starter from, say, San Francisco, to somewhere else, you will not have the same results--because over a fairly short period of time, the bacteria in the starter is replaced by the local bugs who are better adapted to the environment.
Subway poles? (Score:2)
...And that's the story... (Score:3)
When Chris Mason's daughter was a toddler, he watched, intrigued, as she touched surfaces on the New York City subway. Then, one day, she licked a pole. "There was a clear microbial exchange," says Mason, a geneticist at Weill Cornell Medicine. "I desperately wanted to know what had happened."
...And that's the story of how this guy's daughter got herpes.
Isn't public transportation wonderful? (Score:1)
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Several cities had trolley systems before companies like Ford came in and bought them out and shut them down to get us all to buy private vehicles.
Chicago's style of rail would be greatly welcome in most cities, and you're a fool thinking it wouldn't be.
A way for people to avoid getting a DUI? Sold.
A way to not need to buy gas? Sold.
t. midwesterner in city that has trolley car rails all over, but no rail ca
surprising? (Score:2)
"The most exciting phrase to hear in science, the one that heralds new discoveries, is not “Eureka!” (I found it!) but 'That’s funny '”
— Isaac Asimov (an earlier version is attributed to Alexander Fleming)