“The Earth Microbiome Project (EMP) is the most ambitious attempt to provide a systematic characterization of the microbial world that dominates this planet. The ecosystem services provided by microbes in every environment (including the human body) are fundamental to the survival of life on this planet and the continued economic and physical health of the human race. The pilot study of the EMP started in March 2011 and is now reaching its zenith.”
This session has four interesting talks on handling the data deluge, a field guide, why we should care, and mathematical modeling. Cool. Can’t wait for the speaker notes and the like.
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“A mouthwash that kills S. mutans and leaves the rest of the bacteria to take over S. mutans‘s real estate could spell the end of cavities. In a small clinical study last year, one team found that one application of the mouthwash knocked down S. mutans levels, and that harmless bacteria grew back in its place. If the mouthwash pans out, it could join the ranks of an emerging new type of treatment: better living through hacking the microbiome.”
This is really cool. And this article get extra points for the endnotes on probiotics and fecal transplants.
I totally believe we are entering an age where we are going to manipulate our microbiome for health and medicine.
[via @edyong209]
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An Analysis of the Existing Regulatory Framework and Recommendations for Alternative Frameworks
A team of researchers at the University of Maryland Baltimore is studying federal regulation of probiotics under a grant from NIH’s Human Microbiome Project (HMP). A portion of HMP funds were set aside to study the Ethical, Legal, and Social Implications (often referred to as the ELSI issues) of the Project’s scientific goals. The probiotics project is an interdisciplinary collaboration between faculty members from the University of Maryland Schools of Law, Pharmacy and Medicine.
This site is chock-full of info on probiotics policy, regulations, and science. Really good stuff.
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“Now, a new study by Eric Martens, David Bolam, and colleagues has looked into how a pair of the most common species of gut bacteria metabolize polysaccharides, showing that each bacterium is highly specialized. Using a high-throughput system for feeding the bacteria dozens of kinds of carbohydrates, one at a time, and tracking the bacteria’s gene expression, they were able to see how these microbes have tailored themselves to fill specific niches in the gut.”
This is a really good study. For me, a better understanding of the gut metabolic ecology will allow for the development of better probiotics. One interesting finding in this study is that some bug don’t grow well on simple sugar because their sensors are built for complex sugars. Made me think of folks in developed world and what effect eating more simple sugars (high-fructose corn syrup) has on gut flora and any consequential obesity.
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“Many yoghurts are loaded with live bacteria, and labelled with claims that consuming these microorganisms can be good for your health. But a study published today shows that such yoghurts have only subtle effects on the bacteria already in the gut and do not replace them.”
Yes, but the paper goes to point out that both in humans and mice, there was an upregulation of polysaccharide metabolism genes in the existing gut microbes. Hm, there are some serious implications there.
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“This study has identified the first bacterial genes required for induction of settlement and metamorphosis of a marine invertebrate animal.”
This is an interesting genetic study as to what in the bacteria cause the induction of settlement and metamorphosis. Hooray for Nature for making this paper open so that I could read it. Though the paper focused on the genetic aspects and didn’t speculate (unless I missed it) how this connection arose evolutionarily. My speculation is that the bacteria is an environmental marker, telling the worm where to settle and grow.
Cool, huh?
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“Supplements containing a combination of Lactobacillus salivarius and fructo-oligosaccharide for eight weeks were associated with significant reductions in measures of the severity of eczema, compared with a control group receiving only prebiotics, according to findings published in the British Journal of Dermatology.”
In addition to the usual yogurt bugs, I am starting to see salivarius popping up more frequently. It’s from the mouth, by the way.
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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.
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!)
 I stumbled upon domestic-use in-vessel composters (on a lead from @harvestpower, of course).
I had heard of in-vessel composting, but never realized that at least two companies created machines that you plug in, feed with your organic waste (with addition of saw dust), and out comes compost.
As far as I can tell, the process is very fast, so it’s immature compost (composting has a final curing step). But I’m sure the raw stuff that comes out of these machines is pretty good. And to me, one could use this machine for the first step and have a larger separate bin for the curing step.
The two are:
- NatureMill Automatic Compost Bin is from San Francisco (it’s the silver box in the pic on right*)
- And GreenGood are the North American distributors of the Oklin (Korea) in-vessel composter. The interesting thing about the Oklin composters is that they use a special thermophile (called “acidulo” bacteria).
I am so tempted to buy one. Maybe the manufacturers could “lend” me a machine for review and comparisons (hint hint)?
Alas, my wife suggested I build one myself. Gah. Not happening soon.
Image from Nature Mill
*The picture cracks me up. It’s such a Euro-couple. And she’s smiling at him as he dumps an almost full plate of food in the bin. Perhaps it was some bad cooking? Only, whose – his or hers? Sheesh.
“Health claims for probiotics are evaluated by the Panel on Dietetic Products, Nutrition and Allergies of the European Food Safety Authority. Despite a substantial amount of basic and clinical research on the beneficial effects of probiotics, all of the evaluated claim applications thus far have received a negative opinion. With the restrictions on the use of clinical endpoints, validated biomarkers for gut health and immune health in relation to reduction in disease risk are needed. Clear-cut criteria for design as well as evaluation of future studies are needed. An open dialogue between basic and clinical scientists, regulatory authorities, food and nutrition industry, and consumers could bridge the gap between science and marketing of probiotics.”
Not sure what to make of this other than the comment that ‘clear-cut criteria’ will be needed to actually turn claims into science.
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