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The British Gut Project

snowathlete

Senior Member
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Did you? I couldn't fathom my uBiome results.
Richard Sprague's tool is useful. It helps you compare two samples, so you can see which bacteria became extinct between the two samples ('are absent' would probably be more accurate). And which are new (unique in each sample).

One of the issues with the uBiome and American Gut labs is that their results can vary significantly if you take two fecal samples from different parts of the same stool. See the following article, where the author sent away three different samples from the same piece of stool, to be analyzed by uBiome and American Gut:

Which bacteria are in my poop? It depends where you look

This variation probably occurs because the food you eat makes a great deal of difference as to which bacteria grow on that day, and presumably one stool could comprise the food from more than one meal, or could comprise different parts of the same meal (main course versus dessert).

The good news, though, was that uBiome and American Gut produced similar results from a piece of feces taken from exactly the same spot on the stool.



Perhaps the only thing of reliable scientific value in these high-throughput sequencing microbiome analyses is the actual species of bacteria you have present; the relative population sizes of these species, which can vary from day to day, and vary even within the same stool, probably has little meaning.

The tests have limitations, certainly, but I still think they are very useful, and for the cost are well worth it. There can be variation but I suspect there is more variation if you have slow digestion and varied diet, than if you have high transit time and less variation in diet (personally, this probably works in my favour).
You may be able to minimize the variability by homogonizing the stool you take your sample from.

I haven't used American Gut, but from a few results I've seen posted on the net, I wonder if they are not as good as uBiome.

Some bacteria have had a lot of research, others practically none. But there is a lot of research out there on certain bacteria which are considered to be key to gut health, that appear in a high proportion of healthy guts, but are absent or low in diseased individuals. There is a lot more strength of data from IBD research for instance than there is for ME/CFS.

There are conflicting papers out there about gut bacteria and what is healthy though, so you have to be careful what you believe, and this extends to what people say on blogs and so on with suggestions about which supplements to take and so on. My approach is to read a lot of research and try things, but slowly; I don't think there are any quick fixes, but I think you can improve your gut health gradually. I'd be wary about making any major decisions based on a single sample, overal trends seen across multiple samples likely paint a more accurate picture.

Because of the scarcity of genera/species available as probiotic, prebiotics and diet are my main tool for trying to control what is in my gut.
 
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Sasha

Fine, thank you
Messages
17,863
Location
UK
Richard Sprague's tool is useful. It helps you compare two samples, so you can see which bacteria became extinct between the two samples ('are absent' would probably be more accurate). And which are new (unique in each sample).

I only did one sample and then when I got the results back, I simply didn't know if anything was low/missing that should be there, or was high/present that shouldn't. So I didn't know what to do.

Not quite sure why I did the test! :cool:
 

snowathlete

Senior Member
Messages
5,374
Location
UK
I only did one sample and then when I got the results back, I simply didn't know if anything was low/missing that should be there, or was high/present that shouldn't. So I didn't know what to do.

Not quite sure why I did the test! :cool:

Happy to look at your results for you if you like.
 

Hip

Senior Member
Messages
17,824
The tests have limitations, certainly, but I still think they are very useful, and for the cost are well worth it. There can be variation but I suspect there is more variation if you have slow digestion and varied diet, than if you have high transit time and less variation in diet (personally, this probably works in my favour).

You may be able to minimize the variability by homogonizing the stool you take your sample from.

The homogenizing might be a very good idea. I would have thought, though, that this should really be done by uBiome and American Gut themselves, perhaps by providing multiple sample bottles that you fill over several successive days, so that you get an average.

uBiome and American Gut must be aware of this significant variation in results, so it's not clear why are they not using an averaging process.

When had a Genova Diagnostics Comprehensive Digestive Stool Analysis test done several years ago, this required three stool samples to be taken over three successive days.



By the way, does anyone know much about the strengths and weaknesses of these high-throughput sequencing microbiome analyses, versus the traditional stool analyses, such as the one I had from Genova Diagnostics?

Presumably the main advantage is that high-throughput sequencing will cover a greatly increased range of bacteria. My own Genova Diagnostics test only detailed 8 bacterial organisms (my Genova Diagnostics gut bacteria results are shown below). Are uBiome and American Gut also able to detect particular strains of a given bacteria species?

I'd also like to know whether uBiome and American Gut also cover other non-bacterial organisms like fungi, parasites and helminths? For example, one of the most difficult organisms to detect in the gut is the parasite Blastocystis hominis. If you have a pathogenic strain of BH, it is linked to IBS, and also some nasty mental symptoms. Is Blastocystis hominis and other parasites picked up by the high-throughput sequencing analysis provided by uBiome and American Gut?


Genova Diagnostics test.png
 
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alicec

Senior Member
Messages
1,572
Location
Australia
The homogenizing might be a very good idea. I would have thought, though, that this should really be done by uBiome and American Gut themselves, perhaps by providing multiple sample bottles that you fill over several successive days, so that you get an average.

uBiome and American Gut must be aware of this significant variation in results, so it's not clear why are they not using an averaging process.

When had a Genova Diagnostics Comprehensive Digestive Stool Analysis test done several years ago, this required three stool samples to be taken over three successive days.



By the way, does anyone know much about the strengths and weaknesses of these high-throughput sequencing microbiome analyses, versus the traditional stool analyses, such as the one I had from Genova Diagnostics?

Presumably the main advantage is that high-throughput sequencing will cover a greatly increased range of bacteria. My own Genova Diagnostics test only detailed 8 bacterial organisms (my Genova Diagnostics gut bacteria results are shown below). Are uBiome and American Gut also able to detect particular strains of a given bacteria species?

I'd also like to know whether uBiome and American Gut also cover other non-bacterial organisms like fungi, parasites and helminths? For example, one of the most difficult organisms to detect in the gut is the parasite Blastocystis hominis. If you have a pathogenic strain of BH, it is linked to IBS, and also some nasty mental symptoms. Is Blastocystis hominis and other parasites picked up by the high-throughput sequencing analysis provided by uBiome and American Gut?


View attachment 11023

I am familiar with uBiome and have only read about the American Gut sampling procedure. Both of course are well aware of the possibility of differences in sampling resulting in different results (as are the older traditional CSDA tests) and have taken various approaches to this. None are completely ideal and of course it would be better to collect the entire stool sample, homogenise thoroughly and sample the puree. Quite rightly they believe that most people could not overcome the uck factor and simply wouldn't do it.

uBiome decided to keep it really simple by asking people to swab their toilet paper. This means that the sample will always be coming from pretty much the same part of the stool. Also the tiny amount of faeces involved means that the sample can be sent in the regular post - no special requirements, minimum cost.

The most important difference between these newer DNA sequencing tests and the older culture based tests is that the former is trying to get a total picture of the bacterial population while the latter are looking only at cultivable species. CSDA tests miss all of the strict anaerobes, which outnumber aerotolerant organisms maybe by 10 to 1, and pick up only a small number of aerotolerant organisms which adapt well to laboratory culture conditions. Thus they have given a very distorted picture of the composition of the gut flora which is only now being reversed by genetic analysis.

Genova has tried to update its stool analysis by grafting a small amount of PCR based analysis onto a traditional stool test. 24 analytes are included, some at the species level, some at the genus level. It is difficult to understand why at least some of these were chosen since nothing is known about function. I suspect because they can!

American Gut and uBiome look only at bacteria, no archaea, no eukaryotes. They analyse down to the genus level.

No time now to comment on what to do with the genetic analysis - will leave for another time.

Alice
 

snowathlete

Senior Member
Messages
5,374
Location
UK
The homogenizing might be a very good idea. I would have thought, though, that this should really be done by uBiome and American Gut themselves, perhaps by providing multiple sample bottles that you fill over several successive days, so that you get an average.

uBiome and American Gut must be aware of this significant variation in results, so it's not clear why are they not using an averaging process.

I thought the same, that they should do that. My guess is that they decided not to because from a business point of view it puts focus on the test's limitations and creates a requirement on the customer to remember and be willing to collect multiple samples, and that might be a turn-off? The samples would all need to end up in one place - one pot somehow as well, else it creates a manual stage for the company, and they probably want to keep the poo handling (and spillage!) to a minimum. They use a robot to do much of the actual test procedure I imagine.

When had a Genova Diagnostics Comprehensive Digestive Stool Analysis test done several years ago, this required three stool samples to be taken over three successive days.



By the way, does anyone know much about the strengths and weaknesses of these high-throughput sequencing microbiome analyses, versus the traditional stool analyses, such as the one I had from Genova Diagnostics?

Presumably the main advantage is that high-throughput sequencing will cover a greatly increased range of bacteria. My own Genova Diagnostics test only detailed 8 bacterial organisms (my Genova Diagnostics gut bacteria results are shown below). Are uBiome and American Gut also able to detect particular strains of a given bacteria species?

I'd also like to know whether uBiome and American Gut also cover other non-bacterial organisms like fungi, parasites and helminths? For example, one of the most difficult organisms to detect in the gut is the parasite Blastocystis hominis. If you have a pathogenic strain of BH, it is linked to IBS, and also some nasty mental symptoms. Is Blastocystis hominis and other parasites picked up by the high-throughput sequencing analysis provided by uBiome and American Gut?


View attachment 11023

That's interesting about the Geneva test. I am thinking about doing one as it provides more data about SCFAs and yeasts perhaps?

The uBiome test presents data at five levels between phylum and genus. But the raw data file also has some other levels including species. The species data only reaches ~80% maximum, likely much less in most cases. It is only as good as their database and many species haven't even been discovered yet. Some species probably look very similar to somethign in their database, but arent an exact match. What do they do then? My guess is that they dont classify it in such cases, but I don't know for sure.

But the species data often has a species and strain name/number, and when you look it up on the net you find the paper where it was originally isolated, from sewerage or somewhere in the environment, a pigs gut, or whatever, and there will be nothing else known about it. Obviously, knowing you have this thing but knowing nothing about it is pretty useless. But, other species there is a lot known about (the species that make up a greater proportion of most people's gut, common pathogens, those researched in agriculture, and probiotics). As an example, I know that I have around a dozen different species of bifidobacterium in my gut, and that includes the ones that I was taking as a supplement last year. but B. longum which is usually dominant is only third. So I have just ordered some single strain B. longum, and I am going to take that and see if I can make B. longum dominant. We'll see if it works. In theory it shoud, but in reality, who knows?

And no, uBiome (and I think AmGut) only look at Bacteria. But I suspect that will chage in a few year's time. I hope so. At the moment its bacteria because 16S rRNA technology is common, affordable, reliable, and I assume there is not anything equivelant for the rest of the gut biome. I know nothing about the fungi in my gut for instance but would love to take a peek!
 

Hip

Senior Member
Messages
17,824
American Gut and uBiome look only at bacteria, no archaea, no eukaryotes. They analyse down to the genus level.

That is a great shame, because knowing whether you have gut parasites like Blastocystis hominis or Giardia lamblia would be useful. I am not sure why they cannot test for these, because presumably these organisms are also detectable by their genetic fingerprints.


No time now to comment on what to do with the genetic analysis - will leave for another time.

I look forward to reading it.


That's interesting about the Geneva test. I am thinking about doing one as it provides more data about SCFAs and yeasts perhaps?

Yes, it seems to cover yeasts, and if you do the CDSA 2.0 + Parasitology they will check for parasites too.

There is a sample CDSA report here that gives you an idea of what Genova test for. They have quite a few different variations of their stool tests, though, and it's not always clear in each what they test for and what they don't.


The uBiome test presents data at five levels between phylum and genus. But the raw data file also has some other levels including species.

OK that's good. So the uBiome test should be able to cover the function of the Genova CDSA test in identifying the species you have.


the species data often has a species and strain name/number, and when you look it up on the net you find the paper where it was originally isolated, from sewerage or somewhere in the environment, a pigs gut, or whatever, and there will be nothing else known about it. Obviously, knowing you have this thing but knowing nothing about it is pretty useless. But, other species there is a lot known about (the species that make up a greater proportion of most people's gut, common pathogens, those researched in agriculture, and probiotics).

That species and strain data could be useful to determine whether you have pathogenic strains of common gut bacteria.

For example, Genova found Staphylococcus aureus in my gut. I wanted to know whether this might be methicillin-resistant Staphylococcus aureus (MRSA), because this was not stated in my Genova test report. I found out that Genova only perform a MRSA test for those who have Staphylococcus aureus growth at level 4+ (and my Staphylococcus growth was only at level 2+).
 

alicec

Senior Member
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1,572
Location
Australia
The homogenizing might be a very good idea. I would have thought, though, that this should really be done by uBiome and American Gut themselves, perhaps by providing multiple sample bottles that you fill over several successive days, so that you get an average.

Sorry had to rush my previous reply when I realised the time.

There are two aspects to sampling problems. One is differences produced by sampling from different parts of the stool, the other is prevention of breakdown or other change to the contents from the time of collection to receipt by the lab.

CSDA tests try to overcome the first by recommending taking a number of small samples from different parts of the stool. This is a partial solution at best and open to much variability. With the second they are pretty useless - plain faeces sitting in tubes for days, or in culture medium which supposedly preserves anaerobes but which doesn't. Collecting samples over several days only compounds the problem.

To overcome these difficulties, the entire stool would need to be homogenised by the individual providing the sample, as quickly as possible after passing it. A tiny sample of the puree would then be mixed with the appropriate buffer/preservative provided by the company, or alternatively it might be better to homogenise the stool with the buffer, in which case the company would need to provide a significant volume. I really don't think many customers would be prepared to do this.

uBiome's solution is neat and simple. There may be some differences with other tests because of sampling variability but at least within uBiome tests there should be a lot of consistency.

Of course each test is only a snapshot in time and trying to average over a few days wouldn't add anything I believe. Studies so far show that the microbiome is remarkably resistant to perturbation. If you are trying to follow what is happening in your gut as a result of deliberate attempts to influence it by diet, I think a test every few months would be more than sufficient.
 

alicec

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Australia
I suppose my question would be what are you going to do with the results? It's not like you would be doing anything different than you are right now seeing as no one has any idea what the results mean, how to interpret them or how to act on them. Seems like money spent for no actionable information.

There might not be immediate actionable information, but that's not the only reason for doing the test.

The scientist in me just wants to know. The information might only be partial and poorly understood but it is more than I had before and who knows where it might take me in future.

Many of us on the resistant starch thread have enjoyed the posts by @Vegas who, based on his symptoms and reactions to various things, has hypothesised that he is missing certain key gut bacterial populations and proposed that certain prebiotics which stimulate these populations might therefore be valuable supplements. He has then put these to the test and reported on his response. By extension, others with similar sets of problems have maybe applied his analysis to themselves.

Well a microbiome analysis is one way of putting some flesh on these kinds of bones. We don't have to guess about whether certain keystone populations are missing, we can find out. We can see whether over time the interventions we are undertaking are making any difference and try a different approach if they are not. Maybe we might have some peculiarity which warrants further research.

Of course the ultimate test of any intervention is the response of our symptoms and in that respect a microbiome analysis might be unnecessary. I, however, like to have some understanding of why something has been helpful or unhelpful. Maybe by extension I might be able to come up with something that would be even more helpful, or know what to avoid, based on that knowledge. So I have every intention of monitoring the progress of my gut intervention program via both symptom response and any relevant test I can find, no matter how imperfect.

Finally I think most people on PR see themselves as pioneers and here is a great opportunity to maybe make a contribution in this new and fascinating field.

With best wishes
Alice
 

Hip

Senior Member
Messages
17,824
Thanks very much for that explanation @alicec.


I wonder when someone will set up an inexpensive commercial high-throughput sequencing service for viruses. High-throughput sequencing is regularly used by researchers to determine the full set of viruses present in a patient's blood or tissues.

If uBiome can offer high-throughput sequencing service for gut bacteria for $90, then perhaps viral high-throughput sequencing might be similarly priced. It would be great to be tested for all possible viruses using just one blood test for ~$90.
 

alicec

Senior Member
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Location
Australia
That is a great shame, because knowing whether you have gut parasites like Blastocystis hominis or Giardia lamblia would be useful. I am not sure why they cannot test for these, because presumably these organisms are also detectable by their genetic fingerprints.

I guess we have to get our heads around the vast differences in scale between microbiome analyses which is trying to detect everything and pathology tests looking at a relative handful of organisms. We have certainly come a long way since the years it took to bring the human genome to fruition, but still the DNA sequencing of the entire bacterial population associated with us humans is not a trivial undertaking. The first papers had a huge consortium of authors who, backed by many more technicians, no doubt worked for several years assembling and analysing the information. Even when it was realised that sequencing of a single gene, viz that of 16S RNA, would suffice to give a complete picture, an enormous amount of work had to be done to validate the procedure, and this relied on a huge background of bacterial information that had accumulated over many years.

It was only after all of this that it became possible for groups like American Gut and uBiome to offer microbiome sequencing to the public but there is just not nearly as much known about our arcaheon and eukaryote friends/foes. Undoubtedly people are working away on this right now and as @snowathlete says, such a test will undoubtedly become available in the near future. Then we will begin to learn about all the species in these groups that coexist with us rather than just the few which can be cultured or remain stable enough to be seen under a microscope.

There are pathology tests which reliably detect certain parasites such as those you mention, but the range is limited. Old fashioned microscope based tests are fine as long as the faeces is collected into a preservative. There are some PCR based parasite tests also though I don't have any specific information about them. These are likely to be more sensitive.

I'm no expert but I believe yeast detection is more problematic, ie a negative on a culture based test doesn't necessarily mean yeast is not an issue. At the same time there is an enormous amount of speculative nonsense written about yeast overgrowth so it is hard to know what to think. Hopefully once someone cracks the problem of sequencing the entirety of the microbiome, not just the bacterial part, we may begin to get a much clearer picture.

With best wishes
Alice
 

alicec

Senior Member
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Location
Australia
I only did one sample and then when I got the results back, I simply didn't know if anything was low/missing that should be there, or was high/present that shouldn't. So I didn't know what to do.

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
 

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adreno

PR activist
Messages
4,841
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.
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?
 

Sasha

Fine, thank you
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17,863
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UK
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?

Isn't it because they're exposed to a bigger range of bacteria (lack of Western-style hygiene) and no anti-biotics?
 

adreno

PR activist
Messages
4,841
Isn't it because they're exposed to a bigger range of bacteria (lack of Western-style hygiene) and no anti-biotics?
That's what I'm thinking, but @alicec specifically wrote diet, and that's why I'm bringing it up. Also, it seems to be a common recommendation that a more diverse diet gives a more diverse microbiome, but perhaps other factors are more important?
 

Sasha

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That's what I'm thinking, but @alicec specifically wrote diet, and that's why I'm bringing it up. Also, it seems to be a common recommendation that a more diverse diet gives a more diverse microbiome, but perhaps other factors are more important?

Sorry - wasn't following the thread properly!
 

Sidereal

Senior Member
Messages
4,856
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?

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

adreno

PR activist
Messages
4,841
Eating dirt? :D Folks like the Hadza do very well eating just baobab, tubers, honey and meat.
I agree, but dirt is not part of a diet, per se. So again, other factors (hygiene) seems more important than diet.

Or could it be that certain foods are special prebiotic superfoods that support the microbiome better than eating a variety of others?

Perhaps it is actually better to eat only those superfoods that support key species, rather than eating a diet that supports a whole lot of "useless" species?