Gene Map of Body's Microbes Is New Health Tool
June 13, 2012 8:49 PM Subscribe
The Nature editorial on this is also very good, if a bit more technical. It seems like important work although, like the human genome project, I suspect that it will take years of analysis and further experimentation before we start to see hints of very useful results from it.
From the editorial and a couple of newspaper articles it sounds like they've just looked at the species of the organisms that were present. An awful lot of bacteria's abilities (antibiotic resistance, some instances of motility, some unusual metabolic pathways, etc) are not encoded by their genomes. Instead they're encoded by free-floating circles of DNA called "plasmids", which can be passed between bacteria of different species and radically change the behaviour and abilities of the bacteria that they get into. So drawing up a list of the species present is a big and important step forward, but without information on what plasmids they're carrying we can't easily know the fine detail of what ecological niches they're occupying and what effects they'll have on competitors or on the host.
posted by metaBugs at 5:22 AM on June 14, 2012 [2 favorites]
From the editorial and a couple of newspaper articles it sounds like they've just looked at the species of the organisms that were present. An awful lot of bacteria's abilities (antibiotic resistance, some instances of motility, some unusual metabolic pathways, etc) are not encoded by their genomes. Instead they're encoded by free-floating circles of DNA called "plasmids", which can be passed between bacteria of different species and radically change the behaviour and abilities of the bacteria that they get into. So drawing up a list of the species present is a big and important step forward, but without information on what plasmids they're carrying we can't easily know the fine detail of what ecological niches they're occupying and what effects they'll have on competitors or on the host.
For instance, learning which microbes in the gut regulate functions such as the digestion of fat or proteins could help in the fight against obesity, researchers said.I hope that when they were taking those swabs they also got the volunteers to fill out a loooong survey about their lifestyle and general health. For example, given the studies in mice showing that altering the gut flora can make dramatic changes to calorie uptake, obesity and insulin resistance, it'd be fascinating to see whether we could spot correlations between gut bacteria and health in humans. I suspect that this sample is too small to pull a signal out of such a noisy data set (way too many variables like widely varied diets, exercise patterns and accuracy when filling out the form) and of course it couldn't establish a causal realtionship. But it could point researchers in the right direction for a study that *could* do these things. Likewise for all sorts of other associations.
posted by metaBugs at 5:22 AM on June 14, 2012 [2 favorites]
This is so cool! Definitely the largest survey of human gut microbes I've seen - it's amazing how much more sequencing we can do, it's like every year there's something bigger and better and faster.
I hope that when they were taking those swabs they also got the volunteers to fill out a loooong survey about their lifestyle and general health. They screened for "healthy" individuals, which is definitely the best first step (and opens up the door to potentially compare individuals with conditions like IBD with this group). Though the definition of healthy is only "submitted" not published, so I'm not sure what that means yet. I'm hoping for a long survey too!
In the Nature article "Structure, function and diversity of the healthy human microbiome" they go more into functional categories of genes represented in different tissue sites - different functional groups of genes seem more common in different tissue sites, which makes sense but there is so much data here! I actually think that the sequencing technique that they used would also sequence any plasmids present, but don't quote me on that.
I love this kind of stuff!
posted by fermezporte at 6:14 AM on June 14, 2012
I hope that when they were taking those swabs they also got the volunteers to fill out a loooong survey about their lifestyle and general health. They screened for "healthy" individuals, which is definitely the best first step (and opens up the door to potentially compare individuals with conditions like IBD with this group). Though the definition of healthy is only "submitted" not published, so I'm not sure what that means yet. I'm hoping for a long survey too!
In the Nature article "Structure, function and diversity of the healthy human microbiome" they go more into functional categories of genes represented in different tissue sites - different functional groups of genes seem more common in different tissue sites, which makes sense but there is so much data here! I actually think that the sequencing technique that they used would also sequence any plasmids present, but don't quote me on that.
I love this kind of stuff!
posted by fermezporte at 6:14 AM on June 14, 2012
It's fascinating that there was no one microbial taxa that was common among the 242 individuals sampled, despite the fact that they were all people from the Baylor College of Medicine. Given that they're at least from the same geographic area, I'm surprised by the diversity. Okay, so some clades of microbes were common, but there's an incredible amount of personalization to the microbiological entourage you carry around.
I hope that when they were taking those swabs they also got the volunteers to fill out a loooong survey about their lifestyle and general health
The screening criteria are published, actually. A very long list of exclusion criteria are part of the project protocol. These are mostly about medical procedures and health, less about lifestyle. Not sure if they took more information beyond that.
The original Nature papers are available online. Both of them. (Both links from metaBugs' editorial link)
The NIH research group has also created a fantastic website to provide public access to the data as well as experimental technique.
posted by Mercaptan at 7:14 AM on June 14, 2012 [1 favorite]
I hope that when they were taking those swabs they also got the volunteers to fill out a loooong survey about their lifestyle and general health
The screening criteria are published, actually. A very long list of exclusion criteria are part of the project protocol. These are mostly about medical procedures and health, less about lifestyle. Not sure if they took more information beyond that.
The original Nature papers are available online. Both of them. (Both links from metaBugs' editorial link)
The NIH research group has also created a fantastic website to provide public access to the data as well as experimental technique.
posted by Mercaptan at 7:14 AM on June 14, 2012 [1 favorite]
Science has a special issue on the gut microbiome. It's free to the public (with registration) until June 28. Metagenomics rocks!
posted by bluefly at 7:24 AM on June 14, 2012 [1 favorite]
posted by bluefly at 7:24 AM on June 14, 2012 [1 favorite]
An
awful lot of bacteria's abilities
(antibiotic resistance, some instances
of motility, some unusual metabolic
pathways, etc) are not encoded by
their genomes. Instead they're
encoded by free-floating circles of
DNA called "plasmids", which can be
passed between bacteria of different
species and radically change the
behaviour and abilities of the bacteria
that they get into.
Huh. I did not know about plasmids, and now I can't stop reading about them. The theoretical gene therapy applications, using plasmids instead of viruses, are crazy fascinating.
posted by jason_steakums at 8:44 AM on June 14, 2012 [2 favorites]
awful lot of bacteria's abilities
(antibiotic resistance, some instances
of motility, some unusual metabolic
pathways, etc) are not encoded by
their genomes. Instead they're
encoded by free-floating circles of
DNA called "plasmids", which can be
passed between bacteria of different
species and radically change the
behaviour and abilities of the bacteria
that they get into.
Huh. I did not know about plasmids, and now I can't stop reading about them. The theoretical gene therapy applications, using plasmids instead of viruses, are crazy fascinating.
posted by jason_steakums at 8:44 AM on June 14, 2012 [2 favorites]
It amazed me to learn that all of us have a pound or so of microbes all over our bodies! So weird to think of it.
posted by Katjusa Roquette at 11:32 PM on June 14, 2012
posted by Katjusa Roquette at 11:32 PM on June 14, 2012
In fact, Katjusa, if you were to count the number of cells in your body that are human and the number that are not, you would be majority "not human"! (I think the ratio is 10:1 bacteria: human). My boss always says that we come into the world 100% human, but we do not go out that way!
posted by bluefly at 5:48 AM on June 15, 2012
posted by bluefly at 5:48 AM on June 15, 2012
Heh. Looking at it on my laptop now, I see that Opera Mini on my phone likes to turn a pasted quote into free verse poetry.
posted by jason_steakums at 9:11 AM on June 15, 2012
posted by jason_steakums at 9:11 AM on June 15, 2012
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