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.
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.
"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.