 As you know, I’m always looking for practical uses of microbes. One that I stumbled upon a long while back was “transfaunation”, or, seeding one person’s gut with microbes from another’s. Yes, transfering poop microbes from one to another.
Be an adult. Don’t get grossed out. I’ve read some great papers on the process how our guts get colonized after birth. Also, there are some really interesting papers on how our gut microbes (or lack thereof) are involved in various intestinal disorders. And there are some promising papers on how diet affect the bacterial ecology in the gut. [Sorry, I'll link to the papers in a larger gut related set of posts at some point in the future - you can also just search for gut and microbes in my posts.]
Here’s the basic idea. People suffering from the hardy C. diff bacteria are generally prescribed a powerful antibiotic. Problem is, the drugs don’t just kill the invaders; they also wipe out much of the beneficial bacteria in the gut. With these “good” microorganisms out of the way, any C. diff stragglers have a much easier time regrouping for a second bout of illness. If there were some way to respawn the beneficial bacteria in the intestines, such re-infections could be warded off. Some people, like Ruth, turn to expensive probiotic supplements. (At one point she was spending $350 on them every week.) But in certain cases, a patient who has lost nearly all of her good bacteria will find it nearly impossible to get them back. A fecal transplant seems to work as a sort of mega-probiotic, allowing doctors to repopulate a patient’s intestines with the appropriate microorganisms by placing a robust sample directly into her gut.
Slate had a nice article on the subject (quoted above). It’s a serious subject and for many, the only hope to get a better and healthier bacterial gut fauna (hence the term, transfaunation).
My wife’s a vet and she’s not only heard of this procedure, but performed it on animals. It’s not uncommon to jumpstart an animal’s ability to digest grass by grabbing bugs from one animal and putting it in the right place. And, did you know, some animals eat poop on purpose for this very reason – rabbits, capibaras, hamsters, elephants, termites, pandas, koalas, and hippos – to colonize their gut?
And really, folks eat yogurt to populate their gut with good bacteria. Why not poo bacteria as probiotics? I actually think, as we learn more about our gut fauna, this will be come a more accepted course of action for folks with nasty bowel infections, colitis, or inflammatory bowel diseases.
What do you think?
Image of Kristen Paulson’s Anatomy and Guts Embroidery Hoop Art on Etsy (get your own!)
“But what happens next? Can Janelia Farm do ‘great science’ during the next 5 to 10 years? Will it pass Rubin’s deletion test? Can it rewrite the introductory biology texts (Cech’s favourite definition of great science), or foster “a couple of programmes that create a whole new direction” (Tjian’s favourite)? That is the great unanswerable question. As Simpson says, “you can’t engineer great science. You just have to create the conditions that make it possible, and see what happens.””
Great overview of the current state of HHMI’s experiment in cross-disciplinary collaboration. I say, step back and let it happen. Heck, it’s only been five years.
But also, 1) don’t measure it against traditional measures; 2) serve a an inspiration, if not model, for other privately (foundation) funded institutes. The government is at its limit and we’re all fretting. We need new funding models. The HHMI and Jenelia is one.
Read this article…
 I am still a novice when it comes to the technical underpinnings of databases and Hadoop. So, I thought it might be useful if I just asked if my thought on the future of databases is correct.
Basically, “Does Hadoop signal the end of the database as we know it?’
Here’s where this question comes from:
I work for Netezza, who make blazingly fast data warehouse appliances. At the heart of the appliance is a Postgres database. But due to the appliance architecture (and I think the fast speed) you don’t have to do the usual things you have to do to make databases work, such as tuning, indexing, and so forth (indeed, we have a long list of “no”s that set database folks crazy, as in “How can you not do that?”).
That got me thinking. Our appliance has changed the need for coddling databases. Indeed, weren’t databases created to make it easier for (what back then were) slow computers to handle large amounts of data, and all the coddling is to compensate for weak hardware? Would we need databases if it didn’t matter how the data was structured, as long as we had a fast search and processing of the data?
Segue to Hadoop
Lately, at work we’ve been taking about Hadoop, hearing folks actually NOT wanting to have a structured database. And, we see folks with large amounts of data with Hadoop, just throwing more processing power at the data when needed.
Following that thread, I started wondering if the evolution of tools like Hadoop might make structure databases obsolete*, that it really doesn’t matter how the data is structured, just so long as we can find it. And the processing issues are obviated by just throwing more processing nodes at it.**
So, teach me:
Where am I wrong in this thought thread? Will data always need to be structured somehow for computing purposes? How much of the structured data world can Hadoop gobble up (though the unstructured data world must be larger than the structured data world, right?)?
What do you think?
*Of course, just like folks are still using VAX, databases will really never disappear. When a technology is displaced, it usually doesn’t disappear, just gets relegated to a different niche.
**Do you still keep things in folders? I only do when I don’t have a good search tool. On my Mac, I use Spotlight to find and open anything, rather than searching through folders. Indeed, everything usually goes into one folder. Unless I need to separate something for follow up on the desktop (so, OK, folder doe not go away altogether). Nonetheless, search has replaced most of what I would use folders for.
“Genomic epidemiologists say, it’s time to use the technique to track microbial movements on a global scale. By routinely sequencing bacterial samples—perhaps up to a billion a year—scientists could pinpoint the sources of new outbreaks faster, determine whether a bug is resistant to antibiotics, and investigate how public policies or the use of certain drugs change the course of microbial evolution.”
One part of my job is talking to “pharmaco”epidemiologist who take claims data and electronic health records and mine them for outcomes and drug safety and effectiveness. [Plug] Our product can take huge amounts of data and query it at blazingly fast speeds.
For sure, if we have some large pathogen vigilance data stream being added to a large data warehouse (ours), researchers can query and analyze the data and predict outbreaks before they happen.
Read this article…
“”Natural selection has favored that mix,” says Johan du Toit, an ecologist at Utah State University in Logan. Natural selection, maybe, but not people. Convinced that other grass-chomping animals will drive their herds to starvation, ranchers in Kenya and elsewhere tend to keep their cattle separate from wildlife. But a new study suggests that thinking may be wrong. Wildlife, particularly zebras, can actually help a ranch thrive.”
Another strike against mono-cultures, in this case, cattle. I think this study is a good example of why folks need to take ecological views of plant and animal farming. For example, my son has been experimenting with the old Native American technique of growing corn (tall straight stalks), beans (that climb up the corn stalk), and squash or cucumbers (which spread low below these other two plants). True, our mechanized farming isn’t set up for mixed farming techniques, but the benefits might drive the financials and the change.
Read this article…
“A large European-Asian consortium brought some order to the chaos when it reported in a Nature paper in April that humanity can be roughly divided into three “enterotypes” depending on which genus of bacteria dominates in people’s gut: Bacteroides, Ruminococcus, or Prevotella. People’s enterotype appeared to be stable over time, but it remains unclear why your gut population might be so radically different from your neighbor’s.”
Yet another report on diet and gut microbiome. If I could start all over again in grad-school, I’d study this. Human microbiological ecology is going to be big in so many areas, helping us understand the effects that our microbiome has on our health. And of course, this will go hand-in-hand with practical use of naturally occurring microbes.
Read this article…
“In Jonathan Swift’s “Gulliver’s Travels,” Gulliver encounters a small group of immortals, the struldbrugs. “Those excellent struldbrugs,” exclaims Gulliver, “who, being born exempt from that universal calamity of human nature, have their minds free and disengaged, without the weight and depression of spirits caused by the continual apprehensions of death!”
But the fate of these immortals wasn’t so simple, as Swift goes on to report. They were still subject to aging and disease, so that by 80, they were “opinionative, peevish, covetous, morose, vain, talkative,” as well as “incapable of friendship, and dead to all natural affection, which never descended below their grandchildren.” At 90, they lost their teeth and hair and couldn’t carry on conversations.”
Long life versus living long. Thinking of the ring wraiths. 
Read this article…
“A tiny spare bedroom is not an ideal space for a high tech biofabrication facility. To get to the one Josh Perfetto is putting together, visitors must walk all the way to the back of his mostly unfurnished house in Saratoga, California—through the kitchen, past some empty rooms, across a den with a lone couch—then climb a poorly lit staircase and round a corner.”
A really nice article on the state of gadgets DIYbiologists are creating on their own to do their biology. Very fun.
Read this article…
“These results add another dimension to the evolution of resistance and suggest that the low antibiotic concentrations found in many natural environments are important for enrichment and maintenance of resistance in bacterial populations.”
I get a feeling that antibiotics will soon become as archaic as blood-letting. The sooner we deal with the consequences that any amount of the current selection of antibiotics is just generating super-bugs, the sooner we can get off traditional antibiotics. I’m really hopeful of new ways to controls microorganisms that would be a healthier mix (rather than the usual single target that can be evolved around) of other microorganisms, highly specific chemicals, and targeted designed nucleic acids.
But, then again, what do I know? What do you think of the future of antibiotics?
Read this article…
“Where others see barroom taps crowded with beer options, Chris Lohring sees opportunity brewing.”
A nice article on the state of breweries in the region, the business, and the entrepreneurs. Quite exciting.
As for me, I’ll stick to small time 5-gal brewing.
Read this article…
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As you know, I’m always looking for practical uses of microbes. One that I stumbled upon a long while back was “transfaunation”, or, seeding one person’s gut with microbes from another’s. Yes, transfering poop microbes from one to another.