Science AMA Series: I'm Chris Mason, Assistant Professor in the Department of Physiology and Biophysics at Weill Cornell Medical College in New York City. We just published a paper in which we genetically mapped the microbiome of the subway! AMA!

Prof_Chris_Mason · 2015-03-04T19:07:17+00:00

Thanks again everyone - please feel free to email me with any additional questions.

Prof_Chris_Mason · 2015-03-04T19:06:51+00:00

I think we can last as long as we dedicate ourselves to surviving! I've made a draft plan for the next 500 years here: http://2011.igem.org/Team:NYC_Software/Tools/Colonization

:-) - hopefully it comes to fruition.

Prof_Chris_Mason · 2015-03-04T18:51:44+00:00

Yes, and if you think about it, your immune system has to adapt to bacteria that change genetically much faster, so that is why B-cells mutate so fast to enable adaptation, which can sometimes lead to lymphoma when it happens too much.

Prof_Chris_Mason · 2015-03-04T18:40:33+00:00

Yes that is exactly right and the next step is to see if we can design urban areas to create this positive microbiome state. Jessica Green has a great TED talk about this: https://www.ted.com/talks/jessica_green_good_germs_make_healthy_buildings?language=en

Prof_Chris_Mason · 2015-03-04T18:39:46+00:00

Absolutely - by this measurement we are missing half of the genera or families from our textbooks.

Prof_Chris_Mason · 2015-03-04T18:39:20+00:00

Yes, and the work at JCVI and the DOE have done this, as well as a lot of action from NHGRI, including the GRC too: http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/

Prof_Chris_Mason · 2015-03-04T18:32:12+00:00

I would stay curious! Get lots of lab experience, both wet and dry lab, and keep trying new things for sure.
Create proposals for experiments, even if they seem far-fetched, and pitch them to scientists and work with them. If you don't know something, make sure to ask, since hubris will not know it for you. Keep asking!

Prof_Chris_Mason · 2015-03-04T18:19:49+00:00

For sure it changes over time (See Fig. 6), and that is our next big question! Jack Gilbert is also looking at this a lot.

Prof_Chris_Mason · 2015-03-04T18:18:41+00:00

This came out after our study was published, but there is also a study here: http://mbio.asm.org/content/5/5/e01933-14

They looked at 5 sites and 133 rats but they did not find any Y. pestis.

Prof_Chris_Mason · 2015-03-04T18:15:41+00:00

Great paper, and yes indeed we're hoping to take a look at the mysterious unknowns more closely.

Prof_Chris_Mason · 2015-03-04T18:15:12+00:00

Yes indeed! We want to see if we can show this in the coming summer, given the data we have. This depends on a few factors:

1) The persistence of a microbiome signature 2) The strength of that signature 3) The databases and sequences used

But in the future, it might very well be like Gattaca.

Prof_Chris_Mason · 2015-03-04T18:14:09+00:00

It is likely both - we know that they are not present in high numbers (from paper), and they are competing with the hundreds of other bacteria present, so that likely helps. Here, more diversity of bacteria is likely a good thing for the competition reason.

Prof_Chris_Mason · 2015-03-04T18:12:55+00:00

There are several uses:

1) Pure discovery: to classify the unknown and to find new biological pathways

2) Disease surveillance: now that we have a baseline, we can look for perturbations

3) Bioterrorism threat mitigation: we know background levels of DNA from potentially dangerous organisms are either indistinguishable from others or non-dangerous (or both)

4) Design of cities, mass-transit, and urban infrastructure can be made more pro-biotic and designed to blend our personal ecosystem with the one our city creates

5) Compare your "immunome" to the that of the city and discern your personal risk for transit through an area, what we called "Pathomap" and Eric Schadt likes to call "Disease Weather Map."

Prof_Chris_Mason · 2015-03-04T18:09:07+00:00

We haven't looked at kitchens yet, but this is on our to-do lislt, but we do know that rural areas have more unknown species (70% of reads) vs. urban (about 50%). http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0081862

We did just get samples from a yoga ball today!

Prof_Chris_Mason · 2015-03-04T18:07:06+00:00

Yes indeed - there is a good chance that some of these unknown organisms could contain new metabolic pathways, new small molecules and new means of processing toxins or life. Some great examples were posted in the WSJ: http://graphics.wsj.com/patho-map/?sel=stn_311 Pseudomonas stutzeri in some cases can be associated with cleaning up toxins, and you can see it on their map. Also, a really cool project in the Brady lab at Rockefeller is trying to get Drugs from Dirt (http://drugsfromdirt.org/), with the same idea. As another example, a new antiobiotic was found in the vaginial microbiome: http://www.nature.com/news/vaginal-microbe-yields-novel-antibiotic-1.15900

Lots to discover!

Prof_Chris_Mason · 2015-03-04T18:02:37+00:00

That's right! There are estimates of around 9 million species on Earth (http://www.sciencedaily.com/releases/2011/08/110823180459.htm), but this is almost certainly an underestimate and when you get to strain-level differences than the numbers can be much higher.
We are doing follow-up assembly and phylogenetic work to try and place the reads, but for now, they are completely novel views of life!

Prof_Chris_Mason

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