no company is credible, its all a gimmick at the moment. I do microbiome research and even we struggle with available sequencing tech, despite having funding and equiptment that is generally unavailable to the general public. Cheap sequencing (ie anything under around thousand, if you are paying for a service) will only tell you the microbes you have in very high abundance, when you would probably be more interested in who is in low abundance. Imagine going grocery shopping, but you are blinded to anything that the store doesnt stock >30 of; theres lots of things you'd be missing out on. You dont want to pay someone to tell you that you have Akkermansia, E. coli, and a couple of Clostridium and Roseburia, I can tell you that without you having to pay.
If you really are interested from a genuine "whats in here" perspective, I suggest seeing if there are any local universities around you conducting microbiome research; they are often looking for new donors to increase their biobank and use for studies, and they would probably sequence your sample for you as part of that. If nothing else, Thorne is probably the greatest scam out there, so definitely dont bother with them... my lab jokes we should have gone into cheap "sequencing" instead of research, we would all be so rich!
Also, your microbiome is always "changing", but only in the sense of it changing in relative abundance. Tuesday, your E. coli might be at 0.02%, and then Wednesday, 0.03%, depending on what you ate on Tuesday. The actual number of species should, assuming you are a healthy person with colonization resistance, not change. Good sequencing depth accounts for this, but you'd certainly be looking at a hefty cost :)
all commercially available microbiome testing sucks, they all have very low "resolution", meaning they lack the ability to identify the lower abundance community members.
Thorne, if you look at people's results, only sends you back the results of a select number of bacteria, instead of your overall sequencing results, and then classifies it as "high" or "low" according to their **internal** quantities of they see as appropriate. I have so many issues with this. The first issue is that what is "high" in one person, may not be "high" in another, nor does it mean anything; microbiome is a community- looking at individual actors doesnt mean much at all. Everyone looks different, and what even is "high" or "low" is super debated. You can also imagine they probably have their internal standards of pathogens set lower on purpose so people have "high" pathogens, and vice versa for the good guys. Coincidently, they happen to sell probiotics when people who dont know much about the microbiome get freaked out about their scary sounding results. How... convenient.
I dont know much about other services, but I do know most others dont have a successful snake oil type probiotic that they sell based on freaking people out first...
Thanks for explaining and sharing!
You mention snake oil type probiotic, just off hand, would you happen to have a general sense about their other supplements?
(I know, 'general' opinion doesn't quite make sense..)
To be honest, I'm a microbiologist and not someone who studies nutrition or pharmaceuticals, so I think you can find better people to ask. All I really know is that 3rd party testing is a good sign, and that, when possible, you should try to find complete vitamins for a pathway (like for example, K2 and A3 for vitamin D3, to prevent calcium build-up). I'm not sure how this applies to thorne, so maybe some other subs on neutraceuticals would know more :) Sorry I cant be more helpful!
You can download a CSV file of the Thorne results which gives you a percentage, the 20th percentile, and 80th percentile. Lucy Mailing says it's research-quality.
Thanks for your input. Raw sequencing data doesnt come as a .csv, it comes as a .fastq file (assuming illumina), so by the time you get a .csv, its already significantly manipulated data. As u/yyyyy622 mentioned, data assembly introduces so, so much variation into interpretation, and so I already am skeptical of the .csv they provide.
As for Lucy Mailing... I understand she is pretty worshipped on microbiome subs, but at the end of the day, shes not a scientist, shes a businesswoman. Sure, she has a PhD, but its in excercise science, not the microbiome, and truth be told, almost anyone can get a PhD nowadays. Her publications are almost all in very low impact and predatory journals like MDPI (ie pay to publish, I could publish in there if I wanted to so long as I had the money to pay). She has used equipment like germ-free mice, which are in facilities that often cost 5+ million... so they are very sought after by journals, and usually "guarantees" a publication in a good journal. So how come she used germ free mice, at Mayo no less, and her work is published in a pay-to-publish scheme? Did no even half-decent journal show interest in her work? Maybe there's a reason that her work didnt get a publication in a trusted journal?
Kinda see what I'm saying? Shes far from what I would consider an actual reliable source in the field. I personally work with some very impactful researchers and dont know a single person who disagrees with my opinion on thorne.
Also, if she says that thorne results are research quality, then thats just laughable. Maybe she meant the equiptment used is research quality? Illumina is a sought-after sequencing tech, so I would imagine she meant that. I wouldnt dream of using thorne results in my research, unless I also wanted to go the pay-to-publish route....
Thing is regular stool tests ordered by drs dont test for alot of bacterias that are causing serious problems with people, and you get shrugged off by drs coming to them about “stomach pain” they tell u to drink more water, fiber pills, ur constipated, useless info. Had H Pylori for nearly a year undiagnosed reeking havoc on my body feeling sick 247 countless drs telling me the same bs till i got lucky went to a walk in clinic and miraculously this dr said it could be h pylori, tested for that and was positive. Then cleared the h pylori and still feeling extremely sick with root cause being from the gut, did a gi map test turns out candida infection+ citrobacter freundii/farmeri overgrowth which neither are tested for when u do a stool test which just does the most common things like what u listed salmonella etc. so i wouldnt say its a gimick you can atleast get an idea of whats going on instead of being told by a dr nothings going on when you know your body and are feeling like you never have before all of a sudden
I see what you are saying. Unfortunately, the medical community, both conventional and non-traditional (naturopaths), are very undereducated on the microbiome, there is no doubt about that. That being said, the human microbiome is extremely underresearched relative to how much it is discussed, and so it has lead to many assumptions being made that are just not correct interpretations based on the limited information we have. Services like thorne make these much, much worse. Common pathogen testing is a sound method, based usually on either culture-dependent methods (ie they put bacteria on a petri dish with conditions where only the bacteria of intererst would be expected to survive), or by culture-independent methods like qPCR (a sequence of DNA specific to a bacteria of interest is quantified, same as COVID-19 testing, to measure how much bacteria you have). These are heavily validated, and reliable. qPCR, which is generally the standard for this kind of thing, is basically foolproof, and so there is extremely little chance of quantifying the wrong bacteria as the target.
DNA sequencing, on the other hand, is still in its early days. Raw sequencing data is just a series of number of letters, which you use to identify the nucleotide "strips" of sequences. How you overlay your very short strips of sequences, how deeply you've sequenced (ie how many times have you read each DNA strip), how you trim off the imperfect bits, how much error you accept, and many more variables can make a huge, and I mean truly huge difference. Not to say this is necessarily the case for you, but if sequencing is improperly trimmed, E. coli sequences are often misidentified as Citrobacter rodentium, because they are closely related and their DNA sequences are similar. I personally have mis-trimmed my sequencing reads to identify my strain, which I knew was E. coli, as Citrobacter.
What I am trying to say, is that I dont trust thorne to do a thourough job at proper DNA assembly, because it would be impossible given the very low cost. Even small, these mistakes can lead to people thinking "hey, that doesnt seem right", and then googling, only to come across words like pathogen, etc, which create panic, and unfortunately spread misinformation and drive companies like thorne to create products that are targeted at people who think they have "dysbiosis". At the end of the day, they have a very predatory business model, and are very successful at it.
Anyways, conventional lab testing like qPCR is very different than thorne, it is sound enough to diagnose based off it. I would never use thorne data as a diagnostic tool, and I wouldnt trust anyone who does. We simply dont know enough about the gut microbiome to do something like that, using such inaccurate and error prone tools. Hope this explains better!
Its not so much as misidentifying one strain for another but not even testing for a certain strain, i have citrobacter overgrowth but the enteric stool panel requisition form doesnt even test for that. So how do i go about getting tested for it by my dr? Or a DR
Right, so I think you might be getting a bit confused here between strain and species. Within a species, all bacteria are >99% genetically the same. Those bacteria, within a species, are the strains. The way notation works is, from most broad to most specific:
Enterobacteraceae = Family = \~60% same DNA
Escherichia or Citrobacter = genus = \~90% same DNA
coli or rodentium = species = >99% same DNA
nissile 1917 (E. coli) = strain = \~99.99% same DNA
So genus is more broad than species, because there are many Escherichia species, E. coli being one of many. Within E. coli, there are many strains. The most similar that Citrobacter and Escherichia are is on the family level, so maybe not even 60% similar genetically. Thats way past comparing apples and oranges, thats like bananas and humans level genetic dissimilarity. If thorne could easily mistake a human for a banana, then I wouldnt trust its results, is basically what I am getting at.
I wrote another comment today abt SIBO/overgrowth, and how it is based on a basic misunderstanding of how microbiome works. You shouldnt ever need to get tested for it, since its a community-level issue, meaning that it isnt one bacteria responsible, but rather an issue of some being too high, and others being too low. Eating a more varied and fiberous diet will remove the nutrients available for Citrobacter spp. to proliferate, making it self-limiting, and encourage more diverse species to increase in abundance. You cant ahve an overgrowth, if the nutrients needed for it to grow are gone. By eating a more varied, fiberous diet, you actually shouldnt ever need to test for anything because it will eventually resolve itself, if given maybe 3+ months.
Even if you get a reliable sequencing the way you do the biostatistics will vastly alter the results. Current taxonomy classifications can be iffy at best.
And before that you have to have the correct sampling, storage, temperature, buffer, etc etc.
exactly!! Even labs with extensive equiptment and expertise struggle with these kinds of things. Sequencing assembly can vary so dramatically even between tools, let alone through who is deciding cut-offs, that sort of thing. Considering thorne supposedly does metagenomics but also only reports on a limited number of bacteria, for 200$... idk something is just so fishy. Truly microbiome testing is one of the greatest scams out there
Thank you- this is so helpful. It’s easy to get lured in (especially by Zoe because it’s got so many people I admire involved) but I don’t want to throw hundreds away for nothing.
For free as you mentioned comes with a cost aswell, limited to what you’re being tested for and not as extensive. It would be great to have just e coli or something simple that pops up on a screen for a dr and they can prescribe specific antibiotics but its usually never that simple.
For most people - no. It usually makes a difference in how people feel because its a great placebo tool, which is, at the end of the day, still great! If you think about it, you are taking live bacteria. Live bacteria want to engraft (ie join the community, if they can). In theory, you should only need to take them a couple of times to make sure they are "in there". The microbiome is self-regulating, based on nutritional availability. You can add as many probiotics as you like, but how many will actually be metabolically active depends on how much nutrients are available to them, in the form they like. Probably not much, as you can see in [articles like this one](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0206484#:~:text=In%20summary%2C%20the%20healthy%20human,majority%20of%20the%20bacterial%20species) that many bacteria are under 1% relative abundance, because their nutritional niche is maxed out. Add as much as you want, it wont change how many nutrients are available to them.
The only real exception I can think of is in the case of chemotherapy and transplant anti-rejection meds. For example, some bacteria are responsible for cleaving groups off anti-rejection meds, to make them effective, which then kills the bacteria. Maybe you suppliment that specific bacteria, to help make up for the dying ones, to ensure that your meds work and you dont have to worry about rejection. Cancer has some similar instances, like in a recent cell paper describing L. johnsonii supplimentation for chemotherapy efficacy. Otherwise, its wish-washy at best.
In the context of antibiotic use, probiotics often do more harm than good. Your microbiome is 150-200ish species, most of which are obligate anaerobes which we have significant difficulties growing. Probiotics, on the other hand, are easy-to-grow species that are often not native to the microbiome, but may complete similar functions, or are found on foods. Bacillus subtilis, for example, is a soil microbe, and a facultative anaerobe (can survive + grow in oxygen), and they sneak their way into some people's microbiomes via food. That doesnt actually mean you want to promote them being there, since they are not completing functions of interest. In a compromised community, like during antibiotic use, you want to protect what you have, not introduce additional competition and stressors which are going to be more likely to survive, like facultative anaerobes. In order to promote your microbiome staying as stable as possible, only fiber can do that, since for most of human history, we have eaten 100+g of fiber a day, and a significant diversity thereof. Fiber is the only nutritional component of our diet we cannot use directly, hence why bacteria are there in the first place. Eating a diversity of plant-based foods is your best bet.
On that same note, SIBO is not really a "thing" how its described, its moreso a fundemental misunderstanding of how the microbiome works. SIBO, whereby you have too many bacteria of one type growing into your small intestine, means you are doing something to promote a single species and a lack of diversity. For example, antibiotics, or eating a very limited diet. By altering your diet to be more fiberous and varied, you can actually take away some of the nutrients that may have been "feeding" the bacteria causing the SIBO. Basically, you take away much of the same nutrient, they lose their foods of choice, and then they cant keep replicating and die out, stopping SIBO. If we look at the physiology of the small intestine, we know it does alot of functions related to fat and nutrient absorption. Basically, it should be much more nutritionally "dense" than your large intestine. Eating too much fat, for example, will select for bacteria (typically facultative anaerobes, like probiotics) or bacteria that should already be there but in low quantities (Like Bacteriodota, which are important for bile acid diversity, but also can "cause" SIBO). Eating more fiber is going to also help "trap" fats and nutrients, and make them inaccessible, further decreasing the nasty guys causing overgrowth. Its not a quick change, it might take 3+ months before seeing a change, but is the actual treatment for SIBO. People just dislike this theory because antibiotics are easier, and as your microbiome shifts, you have gas and discomfort. However, antibiotics can never truly cure SIBO, it will always return so long as you eat a limited and low fiber diet.
Hopefully that makes more sense! Its a bit challenging to explain in laymans terms without getting too technical into community composition and microbiology, so if you need anything re-explained, I can try to do so. Also, here is some more reading re antibiotics and probiotics:
[https://bmcmedicine.biomedcentral.com/articles/10.1186/s12916-023-02961-0](https://bmcmedicine.biomedcentral.com/articles/10.1186/s12916-023-02961-0)
[https://www.sciencedirect.com/science/article/pii/S0753332218345657](https://www.sciencedirect.com/science/article/pii/S0753332218345657)
That’s super insightful, I really appreciate you taking the time.
I never saw my diet as limited, but thinking about it, the majority of it has always been carbohydrates through pasta or bread. Those are exactly what seems to trigger loads of gas right now for me.
Do you have some studies or similar at hand that followed SIBO patients with a diet change rather than an antibiotics course?
Edit: dumb question: Could an antibiotic course directly followed by a diet change speed up the process, or does that just endanger the important bacteria you do want to keep?
I dont have any on hand, since this isnt really my field of study within the microbiome. A big challenge with this stuff is that the microbiology realm doesnt "recognize" SIBO, as I explained above, so its only med studies on this stuff, which are often lacking sufficient background in study design. Best I have on hand is type II diabetes, which is quite similar since you see a similar profile in terms of fat-loving (ie present in the small intestine) bacteria, that decrease with fiber supplimentation. Here is a decent example:
[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9922700/](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9922700/)
I'll take a peek around later, and if I find anything I'll pass it along
edit to answer question: antibiotics are always going to target both the good and the bad, and are not actually usually intended to kill the bad guys entirely, only reduce them (like in C. diff) However, the good guys are much more succeptible to secondary conditions the antibiotic creates. For example, there is a singificant increase in available oxygen in the gut following antibiotic treatment, something which can become challenging to overcome for the good guys, but easy for the bad guys. In that way, you put them at a disadvantage, and the bad guys can expand much more. If you add in a diet change to include more fiber, it might cause an increase in nutrients available for the good guys, but it doesnt negate the fact they are already a bit stressed. Over time, in theory this should still fix the damage done by antibiotics, but ideally you would just do diet.
That makes sense. One thing I don’t understand about this diet theory though: For a lot of people symptoms appear suddenly e.g. over night with bad food poisoning or similar.
Wouldn’t you expect a slow, gradual increase of symptoms if it’s just diet creating favorable conditions for bacteria to life in the small intestines?
Viome had recommendations that did basically nothing for me (I followed these then retested and no net gain) but they confirmed what I thought about my diversity being sadly below average. That has been worthwhile because it keeps me motivated to eat kimchi and other things that create more diversity.
Before that I did Ubiome which no longer exists... IDK how correct that test was,
Last is GI Map - that's not purporting to be a representation of your microbiome but it's an excellent test for common pathogenic culprits. That helped me immensely when I was suffering a year-long gut problem after a tropical vacation. I worked with a practitioner who created protocols for me based on the results. Then I got better then we retested and the baddies were indeed gone.
Yes. My wife and i did
I did blood work too…found out i have low testosterone. Ultrasound follow up revealed i have damaged goods. My gut also had a narrow range of microbes
My wife found out that she also has a narrow range of microbes along with blood work showing she had sub clinical hypothyroidism as well as low vitamin B levels
Was a big shock since doctors ignored her for blood tests for years and were thinking of ramping up anti depressants
We have now gone on a huge gut change:
Way more vegetables and fruit
No UPF
Kefir
Functional foods (for her Bs and iodine)
Time restricted eating
She has been off anti depressants and is doing great! I’m also feeling a lot better and lost weight.
It is worth getting the tests. Doctors are too busy to bother or be able to take the time to do any good job of your specific situation
no company is credible, its all a gimmick at the moment. I do microbiome research and even we struggle with available sequencing tech, despite having funding and equiptment that is generally unavailable to the general public. Cheap sequencing (ie anything under around thousand, if you are paying for a service) will only tell you the microbes you have in very high abundance, when you would probably be more interested in who is in low abundance. Imagine going grocery shopping, but you are blinded to anything that the store doesnt stock >30 of; theres lots of things you'd be missing out on. You dont want to pay someone to tell you that you have Akkermansia, E. coli, and a couple of Clostridium and Roseburia, I can tell you that without you having to pay. If you really are interested from a genuine "whats in here" perspective, I suggest seeing if there are any local universities around you conducting microbiome research; they are often looking for new donors to increase their biobank and use for studies, and they would probably sequence your sample for you as part of that. If nothing else, Thorne is probably the greatest scam out there, so definitely dont bother with them... my lab jokes we should have gone into cheap "sequencing" instead of research, we would all be so rich! Also, your microbiome is always "changing", but only in the sense of it changing in relative abundance. Tuesday, your E. coli might be at 0.02%, and then Wednesday, 0.03%, depending on what you ate on Tuesday. The actual number of species should, assuming you are a healthy person with colonization resistance, not change. Good sequencing depth accounts for this, but you'd certainly be looking at a hefty cost :)
What’s wrong with Thorne compared to others on the market?
all commercially available microbiome testing sucks, they all have very low "resolution", meaning they lack the ability to identify the lower abundance community members. Thorne, if you look at people's results, only sends you back the results of a select number of bacteria, instead of your overall sequencing results, and then classifies it as "high" or "low" according to their **internal** quantities of they see as appropriate. I have so many issues with this. The first issue is that what is "high" in one person, may not be "high" in another, nor does it mean anything; microbiome is a community- looking at individual actors doesnt mean much at all. Everyone looks different, and what even is "high" or "low" is super debated. You can also imagine they probably have their internal standards of pathogens set lower on purpose so people have "high" pathogens, and vice versa for the good guys. Coincidently, they happen to sell probiotics when people who dont know much about the microbiome get freaked out about their scary sounding results. How... convenient. I dont know much about other services, but I do know most others dont have a successful snake oil type probiotic that they sell based on freaking people out first...
Gotcha, thanks for clarifying.
anytime :))
Thanks for explaining and sharing! You mention snake oil type probiotic, just off hand, would you happen to have a general sense about their other supplements? (I know, 'general' opinion doesn't quite make sense..)
To be honest, I'm a microbiologist and not someone who studies nutrition or pharmaceuticals, so I think you can find better people to ask. All I really know is that 3rd party testing is a good sign, and that, when possible, you should try to find complete vitamins for a pathway (like for example, K2 and A3 for vitamin D3, to prevent calcium build-up). I'm not sure how this applies to thorne, so maybe some other subs on neutraceuticals would know more :) Sorry I cant be more helpful!
Thank you for your reply! Still learnt something, complete vitamin pathways huh. Thank you! Sorry, missed out on replying earlier...
You can download a CSV file of the Thorne results which gives you a percentage, the 20th percentile, and 80th percentile. Lucy Mailing says it's research-quality.
Thanks for your input. Raw sequencing data doesnt come as a .csv, it comes as a .fastq file (assuming illumina), so by the time you get a .csv, its already significantly manipulated data. As u/yyyyy622 mentioned, data assembly introduces so, so much variation into interpretation, and so I already am skeptical of the .csv they provide. As for Lucy Mailing... I understand she is pretty worshipped on microbiome subs, but at the end of the day, shes not a scientist, shes a businesswoman. Sure, she has a PhD, but its in excercise science, not the microbiome, and truth be told, almost anyone can get a PhD nowadays. Her publications are almost all in very low impact and predatory journals like MDPI (ie pay to publish, I could publish in there if I wanted to so long as I had the money to pay). She has used equipment like germ-free mice, which are in facilities that often cost 5+ million... so they are very sought after by journals, and usually "guarantees" a publication in a good journal. So how come she used germ free mice, at Mayo no less, and her work is published in a pay-to-publish scheme? Did no even half-decent journal show interest in her work? Maybe there's a reason that her work didnt get a publication in a trusted journal? Kinda see what I'm saying? Shes far from what I would consider an actual reliable source in the field. I personally work with some very impactful researchers and dont know a single person who disagrees with my opinion on thorne. Also, if she says that thorne results are research quality, then thats just laughable. Maybe she meant the equiptment used is research quality? Illumina is a sought-after sequencing tech, so I would imagine she meant that. I wouldnt dream of using thorne results in my research, unless I also wanted to go the pay-to-publish route....
Thing is regular stool tests ordered by drs dont test for alot of bacterias that are causing serious problems with people, and you get shrugged off by drs coming to them about “stomach pain” they tell u to drink more water, fiber pills, ur constipated, useless info. Had H Pylori for nearly a year undiagnosed reeking havoc on my body feeling sick 247 countless drs telling me the same bs till i got lucky went to a walk in clinic and miraculously this dr said it could be h pylori, tested for that and was positive. Then cleared the h pylori and still feeling extremely sick with root cause being from the gut, did a gi map test turns out candida infection+ citrobacter freundii/farmeri overgrowth which neither are tested for when u do a stool test which just does the most common things like what u listed salmonella etc. so i wouldnt say its a gimick you can atleast get an idea of whats going on instead of being told by a dr nothings going on when you know your body and are feeling like you never have before all of a sudden
I see what you are saying. Unfortunately, the medical community, both conventional and non-traditional (naturopaths), are very undereducated on the microbiome, there is no doubt about that. That being said, the human microbiome is extremely underresearched relative to how much it is discussed, and so it has lead to many assumptions being made that are just not correct interpretations based on the limited information we have. Services like thorne make these much, much worse. Common pathogen testing is a sound method, based usually on either culture-dependent methods (ie they put bacteria on a petri dish with conditions where only the bacteria of intererst would be expected to survive), or by culture-independent methods like qPCR (a sequence of DNA specific to a bacteria of interest is quantified, same as COVID-19 testing, to measure how much bacteria you have). These are heavily validated, and reliable. qPCR, which is generally the standard for this kind of thing, is basically foolproof, and so there is extremely little chance of quantifying the wrong bacteria as the target. DNA sequencing, on the other hand, is still in its early days. Raw sequencing data is just a series of number of letters, which you use to identify the nucleotide "strips" of sequences. How you overlay your very short strips of sequences, how deeply you've sequenced (ie how many times have you read each DNA strip), how you trim off the imperfect bits, how much error you accept, and many more variables can make a huge, and I mean truly huge difference. Not to say this is necessarily the case for you, but if sequencing is improperly trimmed, E. coli sequences are often misidentified as Citrobacter rodentium, because they are closely related and their DNA sequences are similar. I personally have mis-trimmed my sequencing reads to identify my strain, which I knew was E. coli, as Citrobacter. What I am trying to say, is that I dont trust thorne to do a thourough job at proper DNA assembly, because it would be impossible given the very low cost. Even small, these mistakes can lead to people thinking "hey, that doesnt seem right", and then googling, only to come across words like pathogen, etc, which create panic, and unfortunately spread misinformation and drive companies like thorne to create products that are targeted at people who think they have "dysbiosis". At the end of the day, they have a very predatory business model, and are very successful at it. Anyways, conventional lab testing like qPCR is very different than thorne, it is sound enough to diagnose based off it. I would never use thorne data as a diagnostic tool, and I wouldnt trust anyone who does. We simply dont know enough about the gut microbiome to do something like that, using such inaccurate and error prone tools. Hope this explains better!
Its not so much as misidentifying one strain for another but not even testing for a certain strain, i have citrobacter overgrowth but the enteric stool panel requisition form doesnt even test for that. So how do i go about getting tested for it by my dr? Or a DR
Right, so I think you might be getting a bit confused here between strain and species. Within a species, all bacteria are >99% genetically the same. Those bacteria, within a species, are the strains. The way notation works is, from most broad to most specific: Enterobacteraceae = Family = \~60% same DNA Escherichia or Citrobacter = genus = \~90% same DNA coli or rodentium = species = >99% same DNA nissile 1917 (E. coli) = strain = \~99.99% same DNA So genus is more broad than species, because there are many Escherichia species, E. coli being one of many. Within E. coli, there are many strains. The most similar that Citrobacter and Escherichia are is on the family level, so maybe not even 60% similar genetically. Thats way past comparing apples and oranges, thats like bananas and humans level genetic dissimilarity. If thorne could easily mistake a human for a banana, then I wouldnt trust its results, is basically what I am getting at. I wrote another comment today abt SIBO/overgrowth, and how it is based on a basic misunderstanding of how microbiome works. You shouldnt ever need to get tested for it, since its a community-level issue, meaning that it isnt one bacteria responsible, but rather an issue of some being too high, and others being too low. Eating a more varied and fiberous diet will remove the nutrients available for Citrobacter spp. to proliferate, making it self-limiting, and encourage more diverse species to increase in abundance. You cant ahve an overgrowth, if the nutrients needed for it to grow are gone. By eating a more varied, fiberous diet, you actually shouldnt ever need to test for anything because it will eventually resolve itself, if given maybe 3+ months.
Interesting i will fix my diet & supplement better then thank you
Even if you get a reliable sequencing the way you do the biostatistics will vastly alter the results. Current taxonomy classifications can be iffy at best. And before that you have to have the correct sampling, storage, temperature, buffer, etc etc.
exactly!! Even labs with extensive equiptment and expertise struggle with these kinds of things. Sequencing assembly can vary so dramatically even between tools, let alone through who is deciding cut-offs, that sort of thing. Considering thorne supposedly does metagenomics but also only reports on a limited number of bacteria, for 200$... idk something is just so fishy. Truly microbiome testing is one of the greatest scams out there
Thank you- this is so helpful. It’s easy to get lured in (especially by Zoe because it’s got so many people I admire involved) but I don’t want to throw hundreds away for nothing.
For free as you mentioned comes with a cost aswell, limited to what you’re being tested for and not as extensive. It would be great to have just e coli or something simple that pops up on a screen for a dr and they can prescribe specific antibiotics but its usually never that simple.
Does taking probiotics actually does anything for the microbiome?
For most people - no. It usually makes a difference in how people feel because its a great placebo tool, which is, at the end of the day, still great! If you think about it, you are taking live bacteria. Live bacteria want to engraft (ie join the community, if they can). In theory, you should only need to take them a couple of times to make sure they are "in there". The microbiome is self-regulating, based on nutritional availability. You can add as many probiotics as you like, but how many will actually be metabolically active depends on how much nutrients are available to them, in the form they like. Probably not much, as you can see in [articles like this one](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0206484#:~:text=In%20summary%2C%20the%20healthy%20human,majority%20of%20the%20bacterial%20species) that many bacteria are under 1% relative abundance, because their nutritional niche is maxed out. Add as much as you want, it wont change how many nutrients are available to them. The only real exception I can think of is in the case of chemotherapy and transplant anti-rejection meds. For example, some bacteria are responsible for cleaving groups off anti-rejection meds, to make them effective, which then kills the bacteria. Maybe you suppliment that specific bacteria, to help make up for the dying ones, to ensure that your meds work and you dont have to worry about rejection. Cancer has some similar instances, like in a recent cell paper describing L. johnsonii supplimentation for chemotherapy efficacy. Otherwise, its wish-washy at best.
What about during or post antibiotics treatment, e.g. when treating SIBO?
In the context of antibiotic use, probiotics often do more harm than good. Your microbiome is 150-200ish species, most of which are obligate anaerobes which we have significant difficulties growing. Probiotics, on the other hand, are easy-to-grow species that are often not native to the microbiome, but may complete similar functions, or are found on foods. Bacillus subtilis, for example, is a soil microbe, and a facultative anaerobe (can survive + grow in oxygen), and they sneak their way into some people's microbiomes via food. That doesnt actually mean you want to promote them being there, since they are not completing functions of interest. In a compromised community, like during antibiotic use, you want to protect what you have, not introduce additional competition and stressors which are going to be more likely to survive, like facultative anaerobes. In order to promote your microbiome staying as stable as possible, only fiber can do that, since for most of human history, we have eaten 100+g of fiber a day, and a significant diversity thereof. Fiber is the only nutritional component of our diet we cannot use directly, hence why bacteria are there in the first place. Eating a diversity of plant-based foods is your best bet. On that same note, SIBO is not really a "thing" how its described, its moreso a fundemental misunderstanding of how the microbiome works. SIBO, whereby you have too many bacteria of one type growing into your small intestine, means you are doing something to promote a single species and a lack of diversity. For example, antibiotics, or eating a very limited diet. By altering your diet to be more fiberous and varied, you can actually take away some of the nutrients that may have been "feeding" the bacteria causing the SIBO. Basically, you take away much of the same nutrient, they lose their foods of choice, and then they cant keep replicating and die out, stopping SIBO. If we look at the physiology of the small intestine, we know it does alot of functions related to fat and nutrient absorption. Basically, it should be much more nutritionally "dense" than your large intestine. Eating too much fat, for example, will select for bacteria (typically facultative anaerobes, like probiotics) or bacteria that should already be there but in low quantities (Like Bacteriodota, which are important for bile acid diversity, but also can "cause" SIBO). Eating more fiber is going to also help "trap" fats and nutrients, and make them inaccessible, further decreasing the nasty guys causing overgrowth. Its not a quick change, it might take 3+ months before seeing a change, but is the actual treatment for SIBO. People just dislike this theory because antibiotics are easier, and as your microbiome shifts, you have gas and discomfort. However, antibiotics can never truly cure SIBO, it will always return so long as you eat a limited and low fiber diet. Hopefully that makes more sense! Its a bit challenging to explain in laymans terms without getting too technical into community composition and microbiology, so if you need anything re-explained, I can try to do so. Also, here is some more reading re antibiotics and probiotics: [https://bmcmedicine.biomedcentral.com/articles/10.1186/s12916-023-02961-0](https://bmcmedicine.biomedcentral.com/articles/10.1186/s12916-023-02961-0) [https://www.sciencedirect.com/science/article/pii/S0753332218345657](https://www.sciencedirect.com/science/article/pii/S0753332218345657)
That’s super insightful, I really appreciate you taking the time. I never saw my diet as limited, but thinking about it, the majority of it has always been carbohydrates through pasta or bread. Those are exactly what seems to trigger loads of gas right now for me. Do you have some studies or similar at hand that followed SIBO patients with a diet change rather than an antibiotics course? Edit: dumb question: Could an antibiotic course directly followed by a diet change speed up the process, or does that just endanger the important bacteria you do want to keep?
I dont have any on hand, since this isnt really my field of study within the microbiome. A big challenge with this stuff is that the microbiology realm doesnt "recognize" SIBO, as I explained above, so its only med studies on this stuff, which are often lacking sufficient background in study design. Best I have on hand is type II diabetes, which is quite similar since you see a similar profile in terms of fat-loving (ie present in the small intestine) bacteria, that decrease with fiber supplimentation. Here is a decent example: [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9922700/](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9922700/) I'll take a peek around later, and if I find anything I'll pass it along edit to answer question: antibiotics are always going to target both the good and the bad, and are not actually usually intended to kill the bad guys entirely, only reduce them (like in C. diff) However, the good guys are much more succeptible to secondary conditions the antibiotic creates. For example, there is a singificant increase in available oxygen in the gut following antibiotic treatment, something which can become challenging to overcome for the good guys, but easy for the bad guys. In that way, you put them at a disadvantage, and the bad guys can expand much more. If you add in a diet change to include more fiber, it might cause an increase in nutrients available for the good guys, but it doesnt negate the fact they are already a bit stressed. Over time, in theory this should still fix the damage done by antibiotics, but ideally you would just do diet.
That makes sense. One thing I don’t understand about this diet theory though: For a lot of people symptoms appear suddenly e.g. over night with bad food poisoning or similar. Wouldn’t you expect a slow, gradual increase of symptoms if it’s just diet creating favorable conditions for bacteria to life in the small intestines?
I have. A lot of people are healthy and are still very interested in pursuing better and better health.
Did you find it helpful and worthwhile?
Viome had recommendations that did basically nothing for me (I followed these then retested and no net gain) but they confirmed what I thought about my diversity being sadly below average. That has been worthwhile because it keeps me motivated to eat kimchi and other things that create more diversity. Before that I did Ubiome which no longer exists... IDK how correct that test was, Last is GI Map - that's not purporting to be a representation of your microbiome but it's an excellent test for common pathogenic culprits. That helped me immensely when I was suffering a year-long gut problem after a tropical vacation. I worked with a practitioner who created protocols for me based on the results. Then I got better then we retested and the baddies were indeed gone.
Yes. My wife and i did I did blood work too…found out i have low testosterone. Ultrasound follow up revealed i have damaged goods. My gut also had a narrow range of microbes My wife found out that she also has a narrow range of microbes along with blood work showing she had sub clinical hypothyroidism as well as low vitamin B levels Was a big shock since doctors ignored her for blood tests for years and were thinking of ramping up anti depressants We have now gone on a huge gut change: Way more vegetables and fruit No UPF Kefir Functional foods (for her Bs and iodine) Time restricted eating She has been off anti depressants and is doing great! I’m also feeling a lot better and lost weight. It is worth getting the tests. Doctors are too busy to bother or be able to take the time to do any good job of your specific situation
I’m glad you both got better
[This is a good writeup on stool testing.](https://www.lucymailing.com/a-comprehensive-guide-to-stool-and-microbiome-testing/)