
A city-scale molecular profile of DNA collected from NYC's subway system [pdf] - wallflower
http://www.cell.com/pb/assets/raw/journals/research/cell-systems/do-not-delete/CELS1_FINAL.pdf
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mlu
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.

~~~
abandonliberty
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](https://news.ycombinator.com/item?id=8852487)

Revolutionary. (seriously).

~~~
ac29
> 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.

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comboy
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.

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acjohnson55
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.

~~~
tomkinstinch
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.)

~~~
jballanc
And then you have the fun media like Blood Agar
([https://en.wikipedia.org/wiki/Agar_plate#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.

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acomjean
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.

~~~
hibikir
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.

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JonnieCache
This reminds me of the
[https://en.wikipedia.org/wiki/London_Underground_mosquito](https://en.wikipedia.org/wiki/London_Underground_mosquito)

------
daemonk
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.

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dang
NYT and WSJ articles on this:

[https://news.ycombinator.com/item?id=9007702](https://news.ycombinator.com/item?id=9007702)

[https://news.ycombinator.com/item?id=9006315](https://news.ycombinator.com/item?id=9006315)

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coryfklein
> 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.

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bitL
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?

~~~
gnrlbzik
Thats an interesting idea. Any help looking up that article would be
appreciated.

~~~
bitL
It's difficult to find anything relevant on Google nowadays :-( If I manage to
find it, I will post a link

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kingkawn
no genetically sequenced organism.

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dekhn
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).

~~~
zoltz
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)

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arno_v
Looking at the url, it seems they don't want someone to accidentely delete the
article!

~~~
gnrlbzik
i was wondering about that my self. do not delete folder but ok to delete
contents?

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danielmorrison
That URL is fantastic. The article may be too, but I'm in love with the URL.

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gm3dmo
NYC is full of mutants. Who knew?

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whatsgood
"Half the Rain Drops in NYC Have No Known Origin"

~~~
whatsgood
I'm assuming I'm being down-voted by folks that have not spent any appreciable
amount of time walking around Manhattan and have no clue to what I was
referring to.

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Shivetya
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

~~~
jamesrcole
> _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?

