A city-scale molecular profile of DNA collected from NYC's subway system [pdf](cell.com)
cell.com
A city-scale molecular profile of DNA collected from NYC's subway system [pdf]
http://www.cell.com/pb/assets/raw/journals/research/cell-systems/do-not-delete/CELS1_FINAL.pdf
38 comments
This is the result what one would expect. Scientists (until recently) have only been able to sequence species which can be cultured in the laboratory (you need massive amounts of DNA for sequencing). But in fact, more than 90 percent of all microbial species cannot be cultured in the lab and hence (until recently) could not be sequenced and stayed unknown. However, in the past few years, "Next next generation sequencing" (that's how I like to call it) techniques emerged and we are now able to sequence nearly everything. The umbrella terms "metagenomics" and "single-cell sequencing" are often used for such new methods and have huuuge potential in many, many fields. Basically, the new methods eliminate the culturing step and instead have novel techniques for amplifying DNA from only a single strand.
If not sequenced, would we not know many of them by traditional identification methods (e.g. staining) ? I'm guessing their sequencing process prevents the concurrent use of these methods, so we can't match up DNA to known bacteria.
As for unculturability, the recent antibiotic discovery that made the news came from learning how to culture soil bacteria. No, we didn't learn what it needs. We just grew it in it's natural environment: dirt. https://news.ycombinator.com/item?id=8852487
Revolutionary. (seriously).
As for unculturability, the recent antibiotic discovery that made the news came from learning how to culture soil bacteria. No, we didn't learn what it needs. We just grew it in it's natural environment: dirt. https://news.ycombinator.com/item?id=8852487
Revolutionary. (seriously).
> If not sequenced, would we not know many of them by traditional identification methods (e.g. staining) ?
Yes, and no. Many "traditional" staining methods dont really offer up much information, like a gram-stain (common when learning microbiology, not so common in research) can only divide bacteria into two groups: gram-positive and gram-negative. More to the point, if these bacteria have no known methods of culturing (which was correctly noted at 90%+), you can not get them in a pure culture and can only stain them in mixed groups, which isnt that useful.
That being said, there are some staining-like methods you can use to identify what taxonomic group a given bacteria is from. You can use a fluorescent DNA probe that binds to a specific target region of DNA that is highly conserved in groups of bacteria (the 16S rRNA). It is not 100% accurate, and it requires reference data from known organisms, but it can be a good tool for initial surveys of mixed samples. You can also get some cool looking pictures from it.
>I'm guessing their sequencing process prevents the concurrent use of these methods, so we can't match up DNA to known bacteria.
Nope! The above method is actually used in some single-cell sequencing techniques. The cell is florescently tagged, then you can use a microfluidic device (or other methods) to isolate the cell, extract its DNA, and sequence. It is however difficult to assemble a complete genome from a single cell's DNA.
Yes, and no. Many "traditional" staining methods dont really offer up much information, like a gram-stain (common when learning microbiology, not so common in research) can only divide bacteria into two groups: gram-positive and gram-negative. More to the point, if these bacteria have no known methods of culturing (which was correctly noted at 90%+), you can not get them in a pure culture and can only stain them in mixed groups, which isnt that useful.
That being said, there are some staining-like methods you can use to identify what taxonomic group a given bacteria is from. You can use a fluorescent DNA probe that binds to a specific target region of DNA that is highly conserved in groups of bacteria (the 16S rRNA). It is not 100% accurate, and it requires reference data from known organisms, but it can be a good tool for initial surveys of mixed samples. You can also get some cool looking pictures from it.
>I'm guessing their sequencing process prevents the concurrent use of these methods, so we can't match up DNA to known bacteria.
Nope! The above method is actually used in some single-cell sequencing techniques. The cell is florescently tagged, then you can use a microfluidic device (or other methods) to isolate the cell, extract its DNA, and sequence. It is however difficult to assemble a complete genome from a single cell's DNA.
This assessment strikes me as precisely correct. This article gets dangerously close to click-bait academia, since while it (presumably) does good science, the abstract highlights this sensational-sounding result, that the authors must know will get picked up by the public.
That 1/2 of the DNA is of unknown origin does not mean it is somehow really weird or alien (as the public will imagine), rather, it just means we don't know all that much about extant DNA.
That 1/2 of the DNA is of unknown origin does not mean it is somehow really weird or alien (as the public will imagine), rather, it just means we don't know all that much about extant DNA.
I agree. The whole "NYC Subway" could be replaced with any transit vehicle in any town/city and you would get the same results. Nothing special about NYC subway.
The article in question used the Illumina HiSeq 2500 for sequencing. Which would normally be described as a "next-generation" or "2nd generation" sequencer.
I would guess that the rapid reduction in sequencing cost, has in part allowed novel sample preps to be developed which have reduced the amount of material required for a sequencing project (such that even single cell sequencing projects are now feasible).
I would guess that the rapid reduction in sequencing cost, has in part allowed novel sample preps to be developed which have reduced the amount of material required for a sequencing project (such that even single cell sequencing projects are now feasible).
Not to mention that petri dishes were broken! [1]
[1] http://schaechter.asmblog.org/schaechter/2014/12/the-great-p...
[1] http://schaechter.asmblog.org/schaechter/2014/12/the-great-p...
The title is definitely linkbait!
Abstract for no-PDFers:
The panoply of microorganisms and other species present in our environment influence human health and disease, especially in cities, but have not been profiled with metagenomics at a city-wide scale. We sequenced DNA from surfaces across the entire New York City (NYC) subway system, the Gowanus Canal, and public parks. Nearly half of the DNA (48%) does not match any known organism; identified organisms spanned 1,688 bacterial, viral, archaeal, and eukaryotic taxa, which were enriched for harmless genera associated with skin (e.g.,Acinetobacter). Predicted ancestry of human DNA left on subway surfaces can recapitulate U.S. Census demographic data, and bacterial signatures can reveal a station’s history, such as marine-associated bacteria in a hurricane-flooded station. Some evidence of pathogens was found (Bacillus anthracis), but a lack of reported cases in NYC suggests that the pathogens represent a normal, urban microbiome. This baseline metagenomic map of NYC could help long-term disease surveillance, bioterrorism threat mitigation, and health management in the built environment of cities.
The panoply of microorganisms and other species present in our environment influence human health and disease, especially in cities, but have not been profiled with metagenomics at a city-wide scale. We sequenced DNA from surfaces across the entire New York City (NYC) subway system, the Gowanus Canal, and public parks. Nearly half of the DNA (48%) does not match any known organism; identified organisms spanned 1,688 bacterial, viral, archaeal, and eukaryotic taxa, which were enriched for harmless genera associated with skin (e.g.,Acinetobacter). Predicted ancestry of human DNA left on subway surfaces can recapitulate U.S. Census demographic data, and bacterial signatures can reveal a station’s history, such as marine-associated bacteria in a hurricane-flooded station. Some evidence of pathogens was found (Bacillus anthracis), but a lack of reported cases in NYC suggests that the pathogens represent a normal, urban microbiome. This baseline metagenomic map of NYC could help long-term disease surveillance, bioterrorism threat mitigation, and health management in the built environment of cities.
I've heard similar things said for dirt, and even the human gut. The big story is that we have this incredible ability to isolate insanely tiny fragments of DNA, but there are a lot of organisms all around us we can't yet identify, because scientists have been able to isolate the organisms themselves, intact, and grow them.
Although there was an article on here not too long ago about how a guy discovered that autoclaving standard growth media was found to be producing tiny amounts of unwanted chemicals that had been inhibiting the growth of many types of bacteria thought to be unculturable.
Although there was an article on here not too long ago about how a guy discovered that autoclaving standard growth media was found to be producing tiny amounts of unwanted chemicals that had been inhibiting the growth of many types of bacteria thought to be unculturable.
Spot on. Sometimes switching from agar agar to a different hydrocolloidal grown medium like gellan gum can enable the culture of bacteria that would be otherwise difficult to culture. (And in food science, different guns are used for different purposes as well—gellan, agar, xanthan, guar, etc.)
And then you have the fun media like Blood Agar (https://en.wikipedia.org/wiki/Agar_plate#Blood_agar).
But it's not just finding the right media, many microbes are obligate symbionts meaning that we'll never be able to culture them in isolation. I vaguely recall a spc. of Mycoplasma that would only grow in the presence of a peptidoglycan matrix containing E. coli (though it's been a while, so I could be misremembering). For situations like this, having the ability to do raw analysis on environmental DNA is hugely beneficial.
But it's not just finding the right media, many microbes are obligate symbionts meaning that we'll never be able to culture them in isolation. I vaguely recall a spc. of Mycoplasma that would only grow in the presence of a peptidoglycan matrix containing E. coli (though it's been a while, so I could be misremembering). For situations like this, having the ability to do raw analysis on environmental DNA is hugely beneficial.
Here's a publication about that http://jb.asm.org/content/194/16/4151.full
Reading the discussion (page 10 after the pretty graphs), it seems mostly fragments of DNA that they can't source
"Most importantly, none of these data indicate that these organisms are alive, and the fragments of bacterial DNA detected in these data may have arisen from sources other than humans (insects, rats, mice, or other mammals)."
How many creatures have we sequenced vs we know about? Not surprising a lot of unkonwns. Bateria are everywhere, including millions of them inside us.
" half of our high-quality sequence reads do not match any known organism, which is similar to the range reported in other studies (Yooseph et al., 2013) and demonstrates the large, unknown catalog of life directly beneath our fingertips that remains to be discovered and characterized."
Millions ride (and complain about) the NY subway daily.
They found some intersting stuff (anthrax, plague?!) Although they point out we evolved with some nasty bacteria and we don't get sick from it often (thankfully).
"Indeed, these data indicate that the subway, in general, is primarily a safesurface. Although evidence of B.anthracis,Y.pestis, MRSA, and other CDC infectious agents was found on the subway system in multiple stations, the results do not suggest that the plague or anthrax is prevalent, nor do they suggest that NYC residents are at risk.... Approximately seven hu- man plague cases are reported a year, and none recently in NYC or anywhere near NYC,..... This finding further supports the notion that humans have interacted (and potentially evolved) with their environment in such a way that even low levels of Yersinia pestis (plague) or Bacillus anthracis (anthrax) will not necessarily confer a risk of acquiring these pathogens.
"Most importantly, none of these data indicate that these organisms are alive, and the fragments of bacterial DNA detected in these data may have arisen from sources other than humans (insects, rats, mice, or other mammals)."
How many creatures have we sequenced vs we know about? Not surprising a lot of unkonwns. Bateria are everywhere, including millions of them inside us.
" half of our high-quality sequence reads do not match any known organism, which is similar to the range reported in other studies (Yooseph et al., 2013) and demonstrates the large, unknown catalog of life directly beneath our fingertips that remains to be discovered and characterized."
Millions ride (and complain about) the NY subway daily.
They found some intersting stuff (anthrax, plague?!) Although they point out we evolved with some nasty bacteria and we don't get sick from it often (thankfully).
"Indeed, these data indicate that the subway, in general, is primarily a safesurface. Although evidence of B.anthracis,Y.pestis, MRSA, and other CDC infectious agents was found on the subway system in multiple stations, the results do not suggest that the plague or anthrax is prevalent, nor do they suggest that NYC residents are at risk.... Approximately seven hu- man plague cases are reported a year, and none recently in NYC or anywhere near NYC,..... This finding further supports the notion that humans have interacted (and potentially evolved) with their environment in such a way that even low levels of Yersinia pestis (plague) or Bacillus anthracis (anthrax) will not necessarily confer a risk of acquiring these pathogens.
That's the thing: We sequence a lot of microbials already. Some, it's actually hard NOT to sequence.
Say, for instance, that you are sequencing an insect. To do that, you need at least a part of the insect. When you sequence it, you won't just find that insect's DNA in there, but DNA from viruses and bacteria that live in that insect. The same thing will happen if you are sequencing from a plant, or a human.
Contamination from other sources is so common that after getting a bunch of reads from a large organism, it's pretty much mandatory to do comparisons with something with the same species and with a DNA database of microbials to remove the reads that hit a contaminant, so that the assembly that we produce represents the organism correctly.
Other times, we just look for said microbials specifically. Imagine I want to know the bacteria that grow in the roots of a wheat plant. I could try to culture them all in a lab, and if something doens't grow, I lose it. Or I could sequence the root, take out everything that actually looks like wheat, and try to assemble bacteria out of the rest of the DNA.
Say, for instance, that you are sequencing an insect. To do that, you need at least a part of the insect. When you sequence it, you won't just find that insect's DNA in there, but DNA from viruses and bacteria that live in that insect. The same thing will happen if you are sequencing from a plant, or a human.
Contamination from other sources is so common that after getting a bunch of reads from a large organism, it's pretty much mandatory to do comparisons with something with the same species and with a DNA database of microbials to remove the reads that hit a contaminant, so that the assembly that we produce represents the organism correctly.
Other times, we just look for said microbials specifically. Imagine I want to know the bacteria that grow in the roots of a wheat plant. I could try to culture them all in a lab, and if something doens't grow, I lose it. Or I could sequence the root, take out everything that actually looks like wheat, and try to assemble bacteria out of the rest of the DNA.
It'll get really interesting once we can compare more cities.
This reminds me of the https://en.wikipedia.org/wiki/London_Underground_mosquito
I attended a conference couple years ago where Oxford Nanopore gave a talk about their sequencing technology. Their sequencing machine is now available for select labs that applied for their early access program.
While there are still a lot of problems with the technology itself in terms of error rate and data handling, I am a bit wary of the potential impact on privacy. Imagine giant vacuums in public places that sucks up, samples the air, and sequence any DNA that is found. We can potentially track people this way.
But on the other hand, I can also see this technology collecting vital information in terms of spread of diseases or ecological data.
While there are still a lot of problems with the technology itself in terms of error rate and data handling, I am a bit wary of the potential impact on privacy. Imagine giant vacuums in public places that sucks up, samples the air, and sequence any DNA that is found. We can potentially track people this way.
But on the other hand, I can also see this technology collecting vital information in terms of spread of diseases or ecological data.
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NYT and WSJ articles on this:
https://news.ycombinator.com/item?id=9007702
https://news.ycombinator.com/item?id=9006315
https://news.ycombinator.com/item?id=9007702
https://news.ycombinator.com/item?id=9006315
> Half the DNA on the NYC Subway, Gowanus Canal, and Nearby Public Parks Matches No Known Organism
FTFY - It is less surprising to me to find unknown organisms when a water way and public parks are included.
FTFY - It is less surprising to me to find unknown organisms when a water way and public parks are included.
Could it be that our understanding of DNA variations is incomplete?
There was some article a few years back where a virus was observed mutating its RNA in what appeared to be some sort of algorithm, like running a virtual machine on proteins. What if DNA does the same, i.e. being not just data but also an interpreter with some changing memory?
There was some article a few years back where a virus was observed mutating its RNA in what appeared to be some sort of algorithm, like running a virtual machine on proteins. What if DNA does the same, i.e. being not just data but also an interpreter with some changing memory?
no genetically sequenced organism.
Could you change the title of the article? It's not the title of the paper, and isn't really the most significant finding. The paper itself is a wonderful initial survey of bacterial diversity which is much more important than the trivial observation that we can't identify all the organisms (although I believe that observation should be followed up with more intensive analysis).
Indeed, title needs to be changed to "Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics".
https://news.ycombinator.com/item?id=8282204
https://news.ycombinator.com/item?id=8282204
The current headline is vastly more entertaining -- and it attracts a lot of non-life-sciences readers (like me) who are willing to linger and learn a bit about bacterial diversity.
Write a narrow headline, get a narrow audience.
In this case, I'll defend the current headline as "virtuous click-bait." That's a rarity, but nice when it happens.
Write a narrow headline, get a narrow audience.
In this case, I'll defend the current headline as "virtuous click-bait." That's a rarity, but nice when it happens.
We changed the title to a phrase from the first sentence of the abstract, which seems more accessible than the paper title. We often treat the opening sentence of an article as a kind of subtitle for HN purposes.
I wouldn't call wallflower's title ("Half the DNA on the NYC Subway Matches No Known Organism") egregiously editorialized, though, since that finding was the one the article itself highlighted.
I wouldn't call wallflower's title ("Half the DNA on the NYC Subway Matches No Known Organism") egregiously editorialized, though, since that finding was the one the article itself highlighted.
This is the difference between product and marketing. Marketing is taking a product and figuring out how to position to the right audience. If that means highlighting a single feature and letting users/readers discovery the breadth, that's an acceptable tradeoff if it gets the job done.
That URL is fantastic. The article may be too, but I'm in love with the URL.
NYC is full of mutants. Who knew?
I saw MiB, it was a documentary.
do we realistically expect otherwise. Considering the amount of animal and insect life we don't have documented when you start getting down to the scale of bacteria and the like its bound to be uncharted. We spend all this time about finding life on another planet when we haven't found all ours has to offer
do we realistically expect otherwise. Considering the amount of animal and insect life we don't have documented when you start getting down to the scale of bacteria and the like its bound to be uncharted. We spend all this time about finding life on another planet when we haven't found all ours has to offer
> We spend all this time about finding life on another planet when we haven't found all ours has to offer
What? How much time do you think we spend on the former? Why do you think it's too much? And why do you think the two goals are mutually exclusive?
What? How much time do you think we spend on the former? Why do you think it's too much? And why do you think the two goals are mutually exclusive?