The British Gut Project

[adreno]

When comparing ourselves, we like to compare a microbiome template from a disease population with a normal western population. But who says that what is normal in western populations is also optimal? How healthy are "healthy" western populations, really? Many likely suffer from subclinical illnesses. So I would be more interested in finding an "optimal" microbiome template, rather than a "normal" one.

 

[Hip]

Regarding soil from the earth being part of the diet: don't forget about pica.

Pica is a behavioral response which involves eating non-food substances such as soil, sand, clay, cigarette ashes, burnt matches, coffee grounds, chalk, plaster, etc. Pica most commonly appears in young children and pregnant women. It is also found in animals.

Pica is considered an eating disorder, but may in fact be a natural instinct that kicks in when mineral levels are low, or for other reasons. Very little research has be done on it. In this article it says:

Many young kids put nonfood items in their mouths at one time or another. They're naturally curious about their environment and might, for instance, eat some dirt out of the sandbox.

Kids with pica, however, go beyond this innocent exploration of their surroundings. Between 10% and 30% of kids ages of 1 to 6 years have the eating disorder pica, which is characterized by persistent and compulsive cravings (lasting 1 month or longer) to eat nonfood items.

The word pica comes from the Latin word for magpie, a bird known for its large and indiscriminate appetite.

Pica is most common in people with developmental disabilities, including autism and mental retardation, and in children between the ages of 2 and 3. Pica also may surface in children who've had a brain injury affecting their development. It can also be a problem for some pregnant women, as well as people with epilepsy.

As well as replenishing minerals, it's conceivable that pica might be a build-in instinct that helps populate the gut with a wide variety of bacteria from the soil at an early age.

I find it interesting that children with pica eat cigarette ashes, burnt matches and coffee grounds, as these have the approximate appearance of soil, and so it could be that this primitive pica instinct just mistakes these items for soil. One might speculate that the pica instinct may be keyed on substances that have the general visual appearance of substances that look like soil.



Another similar instinct in appears in dogs, where they start sniffing and may eat feces that they come across on the ground. Owners often try to discourage this behavior, but I have often thought that this feces eating instinct may exist in part to help populate the dog's gut with a healthy microbiome. It may be a dog's DIY bacteriotherapy.

 

[snowathlete]

I'll upload the summary that I did of my own results. In it I included what information I could find about the role of the various genera. I regarded this as a baseline against which I can compare future analyses, given that it was done before significant changes to pre and probiotic use. I am waiting for results of the next analysis and for that the Richard Sprague tool should be very helpful for doing the comparison. I wasn't looking forward to manually going through the long list of genera off the uBiome website and painfully entering them into a spreadsheet.

To briefly summarise what I gleaned from my reading, there is considerable redundancy in the microbiome - ie many species can perform the same function, so there is no "right" pattern for everyone. At the same time there is not an infinite number of possible patterns either. There does seem to be some sort of ancestral core, key species which make substrate available to much broader populations and without which there is widespread collapse of many populations. I have made a note of at least some of those thought to fulfil this keystone role.

The other key concept is diversity. There seems to be a great loss of diversity among people eating a western diet compared with traditional hunter-gatherer type diets, and within the western group, there seems to be an even great loss of diversity among those with the so-called modern illnesses - diabetes, IBD, celiac, autism, to name just a few.

So it is patterns rather than individual elements that are very important, although some elements do seem to be much more critical than others.

With best wishes
Alice

Thanks for posting your analysis. Interesting!
It is actually really helpful for me to see your results because as my gut is recovering from antibiotics, I have a lot missing. You mention this on your report too, that the uBiome test currently does not tell you what you don't have - only what you do have.
Cyanobacteria for instance...I have none, so it doesn't show on my report. I'm blind to that sort of thing currently, as are you, but when you have more missing than present, it is even more of a problem.
I wish they would include some data on what is missing but which is commonly found in most samples. I am going to give them some feedback along those lines as well as some feedback on their new dashboard. If enough people ask for it they might start providing it.
Where did you get the #50 MOST COMMON GENERA IN AVERAGE OF ALL SAMPLES list from?

I think you are right about some redundancy in the biome. It's possible this doesn't extend to everything though, I suspect there are some bacteria that do something pretty unique. But something I noticed from having ulcerative colitis is that not everyone fits the research on gut flora even though it is more extensive than that on ME/CFS and I suspect there are several different types of ulcerative colitis in reality. Obviously having 16S rRNA analysis available is a massive boon for IBD research, but I do look forward to the day we can easily, reliably and cheaply test all the other 'stuff' in the gut.

 

[adreno]

I wish they would include some data on what is missing but which is commonly found in most samples.

Don't uBiome have some normal populations to compare with?

I found a study comparing UC patients with controls. Note that clostridum butyricum is almost completely missing in UC (black) :

Longitudinal Analyses of Gut Mucosal Microbiotas in Ulcerative Colitis in Relation to Patient Age and Disease Severity and Duration

 

[snowathlete]

Another similar instinct in appears in dogs, where they start sniffing and may eat feces that they come across on the ground. Owners often try to discourage this behavior, but I have often thought that this feces eating instinct may exist in part to help populate the dog's gut with a healthy microbiome. It may be a dog's DIY bacteriotherapy.

The line, for me, is when the owner follows suit. Seriously though rat moles feed crap to their young.

 

[snowathlete]

Don't uBiome have some normal populations to compare with?

I found a study comparing UC patients with controls. Note that clostridum butyricum is almost completely missing in UC (black) :

Longitudinal Analyses of Gut Mucosal Microbiotas in Ulcerative Colitis in Relation to Patient Age and Disease Severity and Duration

uBiome do have normal populations to compare with, yes, but it works such that say you have Lactobaccilus in your gut, you then get to see how this compares to various grouping (diet, gender, antibiotics, etc.) but if you do not have Lactobaccilus in your gut then you can't see how much is 'normal' in the various groupings for that bacteria.

Thanks for linking the UC study. Interestingly, after antibiotics I had C. butyricum, but a year later after "improving" my gut, I have none...In this single sample at least - I will have to see if it is back or not in the next one. For this reason I probably won't take it until I send off my next sample.

Of course, that's another thing, that many studies on IBD are looking at the mucosa itself, rather than the stool, so you can't really compare. When I next have a colonscopy (hopefully a few years away yet!) I plan to ask for one of the biopsy samples so that I can scrape it and see what uBiome says about it.

 

[alicec]

That's interesting, @alicec! Did you use your results to determine which pre/probiotics to use?

Not really possible because of the time lapse in getting the results (last time 6 weeks, I suspect longer this time). I am much too impatient to wait that long before I try something.

I see the tests as being useful to monitor change in retrospect.

 

[alicec]

I find this bit interesting, as well as somewhat puzzling. It would seem logical that primitive societies do not have access to the broad variety of foods in modern supermarkets. Rather, from what I've read, tribal people often have an array of stable foods, rather than huge variety. Still, there microbiome is more diverse. Why is that?

I used diet loosely in the sense of everything that goes into the mouth, so dirt on foods would count. Also I didn't mean this exclusively rather as a short-hand way to characterise the people I am referring to. Lack of antibiotics is likely to be a big contributor also.

Still the food issue is very important - it is not so much the variety of foods eaten as what is in those foods. Western analysis of food content has concentrated on the stuff in it that we can digest. Resistant starch, cellulose and many other fibres were considered a waste of space and we have gone to a lot of trouble to breed varieties which contain lots of stuff digestible by us and as little as possible of the "useless" stuff.

In order to increase the prebiotic content of our diet, people have begun casting around for sources of prebiotic foods that could resemble the things eaten traditionally - tiger nuts, acacia gum, baobab, larch, seaweeds etc as well as attempting to increase resistant starch by eating cooked and cooled rice and potatoes - all the things talked about on the resistant starch thread.

Here is an interesting paper on the diversity of the gut microbiome in a group untouched by western influences, just to illustrate the point. http://advances.sciencemag.org/content/1/3/e1500183

What it all means is something people are still grappling with. One suggestion I like is from "The Missing Microbes" by Martin Blaser. He hypothesises that among the many minor phyla which are greatly reduced among westerners (and about which we have no clue about function) is that at least some of these are held in reserve, a small population which is kept ticking over and which can be rapidly expanded in face of unexpected events (like sudden loss of substrates for more numerous populations), ie they contribute to resilience.

With best wishes
Alice

 

[alicec]

When comparing ourselves, we like to compare a microbiome template from a disease population with a normal western population. But who says that what is normal in western populations is also optimal? How healthy are "healthy" western populations, really? Many likely suffer from subclinical illnesses. So I would be more interested in finding an "optimal" microbiome template, rather than a "normal" one.

Absolutely but we are just starting to accumulate data on what that might look like.

 

[alicec]

Where did you get the #50 MOST COMMON GENERA IN AVERAGE OF ALL SAMPLES list from?

Just off the uBiome website - use the compare function. Of course this is still only the most common of the ones they tell me about. I had long email correspondence with them about how ridiculous their method of reporting really is. By all means complain to them - maybe they'll eventually get the message.

I tabulated the genera in both ways to get better insight into what I might be badly lacking. The almost total loss of F. prusnitzii really stood out when I did this.

 

[snowathlete]

Just off the uBiome website - use the compare function. Of course this is still only the most common of the ones they tell me about. I had long email correspondence with them about how ridiculous their method of reporting really is. By all means complain to them - maybe they'll eventually get the message.

I tabulated the genera in both ways to get better insight into what I might be badly lacking. The almost total loss of F. prusnitzii really stood out when I did this.

Ah, I thought at first that it was the 50 top across all samples in their database, but is it actually just your top 50 matches?
They don't have a compare function any longer, they just updated their site which has positives and negatives.

 

[ariel]

Eating dirt? Folks like the Hadza do very well eating just baobab, tubers, honey and meat.

I dunno about eating 'just' baobab, tubers, honey and meat. Did you ever read this article?
http://ngm.nationalgeographic.com/2009/12/hadza/finkel-text/1
Baboon's brains, mud baths with cow dung, ..... Pretty easy to see how they might have a heap more gut bugs than the rest of us city folk.

 

[Sidereal]

I dunno about eating 'just' baobab, tubers, honey and meat. Did you ever read this article?
http://ngm.nationalgeographic.com/2009/12/hadza/finkel-text/1
Baboon's brains, mud baths with cow dung, ..... Pretty easy to see how they might have a heap more gut bugs than the rest of us city folk.

Yeah, their microbiome comes from things we wouldn't consider food like crap and viscera.

 

[ariel]

Yeah, their microbiome comes from things we wouldn't consider food like crap and viscera.

Yeah..... so not our thing!
I found the article is totally fascinating though. Entirely different world. Gawd knows what they'd think of people rendered immobile by little bits of RS!

 

[Sasha]

I found the article is totally fascinating though. Entirely different world. Gawd knows what they'd think of people rendered immobile by little bits of RS!

Just read it - you're right, completely fascinating...

 

[alicec]

Ah, I thought at first that it was the 50 top across all samples in their database, but is it actually just your top 50 matches?
They don't have a compare function any longer, they just updated their site which has positives and negatives.

Just received an email from uBiome telling me about their new look data presentation. I didn't even see positives and negatives, just various ways of looking at my own data, plus a timeline function so one can follow successive analysis. It seems more like the American Gut presentation and is quite helpful.

However it now seems impossible to get any sort of picture of the average gut, other than by inference from my own data (ie they report most depleted, most enriched etc). My top 50 list (which is the top fifty across all samples but minus any genera which I don't have at all) could not be compiled now.

So a mixed update in my opinion. When my next set of results arrive I'll be complaining again about their failure to show a complete average picture.

 

[alicec]

During the recent conversation about sequencing of gut parasites, yeasts etc as well as bacteria, I recalled that I had read an analysis of the relative proportions of these based on genetic analysis. I couldn't remember the detail nor where I had read it but I do now and I thought some of you might be interested.

99.1% of faecal DNA is of bacterial origin, only 0.1% is of eukaryotic or viral origin and the remainder is archaeal.

Here is the paper http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html

This is a huge study, as evidenced by the consortium of authors, which sequenced all DNA, not just 16S rRNA. This is very strong evidence for the existence of a relatively small gut microbiota core and I found it fascinating. It is easy enough to skip most of the technical detail and just follow the basic conclusions so don't be too put off by the forbidding science.

With best wishes
Alice

 

[alicec]

I've made a post here http://forums.phoenixrising.me/inde...e-been-looking-for.26976/page-165#post-601104 that may be of interest

 

[Jenny]

Has anyone had any useful results from participating in the British Gut Project?