“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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“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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 When I lived in the US in the 90s, it was hard to find live-culture yogurt in supermarkets (you could find them in natural food stores, of course). The only one I could find was Stonyfield yogurt.
When I lived in Finland, not only were there a bunch of live-culture milk products, but there was one in particular “Valio A+” that was specifically recommended for women to balance their flora.
Now back in the US, it’s hard not to find live-culture yogurt, and some are specifically marketed, yes, for women to balance their flora. Furthermore, the use of live bacterial cultures for health purposes, called probiotics, has become mainstream enough that you can find probiotic supplements for children in the supermarket.
What does this mean?
It means that folks are becoming aware of functional foods, of the importance of microorganism in their diet, and that the feeding desire to find a short cut (a pill rather than eating wholesome yogurt) is always a good business.
I’ve been seeking out all these probiotic products to get an idea of what’s out there, what the message is, and, for me, always on the look out for practical use of microbes, I’ve been trying to understand what microorganisms are in fashion.
OK, so the science behind probiotics is still in progress, so I will not go into that right now.
But, going on the premise that yogurt is the gold standard for beneficial live (with microorganisms) food, then my standard for all probiotic products used for digestive health is Stonyfield’s yogurt. Stonyfield’s has 6 bacteria (S thermophilus, L bulgaricus, L acidophilus, Bifidus, L casei, and L rhamnosus). I’d say that most of the products I have seen have one or more of these bugs. There are some proprietary sub-species and I’ve been pleased to see a few products with S salivarius or some other bacteria.
For me, the type, variety, and number of bacteria in a probiotic food or supplement is key. And I think it’s just snake oil if the product only has one bug.
Nonetheless, I think as probiotics go mainstream, buyers will be more astute as to what they are looking for. Also, I hope that new applications show up, beyond gut and vaginal flora health (I can think of a few).
What I do know, is that doctors are starting to suggest probiotics to patients on antibiotics or with digestive issues such as colitis or C diff.*
And that’s great.
Do you eat probiotic foods or take supplements? Send me pics of the ones you see or take! I could/should create a database of products and attach reviews or commentary. Hm…. not another project….
*Ego boost: A gastroenterologist aked me recently what probiotics I recommended. Ha! My first probiotic consulting gig?
 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!)
“Horizontal gene transfer — the exchange of genetic material between different species or lineages — is an important factor in bacterial evolution. A study of human microbiome data comprising more than 2,000 full bacterial genomes shows that this environment is a hotbed of horizontal gene transfer: pairs of bacteria isolated from the human body are 25-fold more likely to share transferred DNA than pairs from other environments. Thus microbial ecology — rather than phylogeny or geography — is the most important driver of the patterns of horizontal gene exchange. Further analysis revealed 42 unique antibiotic-resistance genes that had been transferred between human and agricultural isolates, and 43 transfers across national borders.”
This paper sets me spinning due to it being about microbes, microbes on humans, human microbial ecology, and horizontal gene transfer. The other thing that is intriguing about this paper is the mention of unique antibiotic-resistance genes.
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“We normally think of the gut microbiota as the ‘friendly’ bacteria that carry out many beneficial functions, including protecting us from infection. But two studies now identify a different side to the gut microbiota, showing that it can actually facilitate viral infection and promote transmission.”
Another interesting review that is in a CLOSED ACCESS paper. The barrier to casual reading is too high.
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“During the upcoming holidays, many events will involve traditional foods, such as turkey at Thanksgiving and Christmas. That microorganisms can spoil any of these foods, and thereby the entire party, is well known, but perhaps less obvious is the fact that microbiological processes are involved in the production of nearly all types of food. … As made clear by the recent Position statement on food security and safety … microbiologists can have a pivotal role in this important field. The position statement outlines nine research themes through which microbiologists can participate in food safety and security, including the investigation of microorganisms that cause food poisoning or kill crops and livestock, as well as research into the ways in which microorganisms can improve food production.”
Interesting overview of the impact of microorganisms in food production and safety.
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