Suggestions on best tests for checking gut health

I just had a look, and I don't think it does the kind of thing that would help me. I am convinced that surgery with a good colo-rectal surgeon is probably my only hope, either to cut out infected tissue if there is any, and/or to divide adhesions from previous surgeries. I do think that reducing my carbs and sugar intake would be helpful though.

 

Unfortunately there is no single ideal test for checking gut health.

I agree that hydrogen and methane breath tests can be useful for detecting SIBO, though be aware that there is disputation about what means what.

This however is concerned only with the small intestine, not the colon where the vast bulk of the gut microbiota live.

There are two types of test looking at colonic microbial content, the older complete digestive stool analysis (CDSA) based on culture of microorganisms, and the newer DNA based analysis.

A CDSA is not what you want. There are some parameters in the test which are useful - eg analysis of SCFAs, pancreatic enzyme production, fat and fibre content of stool etc, but the microbial analysis by culture which is the bulk of the test is useless. The cost is too great to justify the useful info.

There are two types of DNA based tests. One has specific targets - ie it detects only the organisms specified, while the other attempts to sequence all DNA present and so identify all organisms.

Here and here are posts which talks more about these issues.

As for which tests to order - well of course it depends what you most want to know and how much money you have to spend. The Diagnostic Solutions GI MAP test looks like a sensitive and fairly comprehensive test if you want to focus on parasites and problematic bacterial species, but it doesn't give the full gut picture.

I've not had this test so am not sure if you can order it yourself.

The uBiome Explorer test is a fairly inexpensive way (about USD 100) to get a comprehensive picture of gut bacteria, which are far and away the most dominant gut inhabitants. It can also detect archaea those these are very minor in comparison with bacteria. American Gut and RedLabs Belgium offer similar tests though the RedLabs test must be ordered by a doctor and is considerably more expensive.

This is a citizen science project so you order the test yourself, you get the results and it is up to you to interpret them.

Very recently they have offered Explorer Plus - the same test plus eukaryotes (fungi, parasites etc). This is considerably more expensive and they haven't actually sent out the first kits yet. American Gut has offered such a test for some time but it is extraordinarily expensive.

 

@Arnie Pye Have you been checked for acid reflux? As @andypants mentioned, it could be that you have an inflammed esophagus and/or stomach.

 

The fact that erythromycin helps you, two things are likely in my opinion: The antibiotics help against a particular bacterial overgrowth you have in your bowel.
The other option is that it's the prokinetic effect of erythromycin that works for you. If you read the work of Dr. Pimentel (in my opinion one of the leading people in IBS/microbiome work) he gives everyone a prokinetic for SIBO.

My doctor works mostly on the gut (in ME) and he prescribes prokinetics too.

 

A GI consultant I was seeing came to the same conclusion and prescribed a different prokinetic drug after the erythromycin was so successful. It was a dopamine antagonist. I developed personality changes within the first day (my driving became totally reckless and even my non-observant husband noticed the change in my personality), and developed severe akathisia after just 5 tablets. I was so severely affected that I had to be prescribed an emergency antidote. The consultant said that she thought many of the best or most popular drugs of the prokinetic type were likely to cause these effects in someone susceptible, and that I should avoid them.

I think this is the most likely cause of my pain. When I take erythromycin it has good affects throughout my gut from one end to the other, including improving my mouth ulcers (I have one or more of these most of the time - a day without ulcers is a very rare red-letter day for me). I think I probably have a significant overgrowth of something. If I could identify it then I might be able to find an antibiotic that would eliminate it more effectively than the erythromycin does.

 

If your symtoms are clearing up with erythromycin, than maybe that ís the right antibiotic. In my experience it takes a really long time to get a lasting change in your microbiome. My GI symptoms clear up from certain antibiotics as well, but it's very difficult to get it to last. That's already true when you only have SIBO/IBS, but it probably gets complicated by ME big time because there's more problems than only the overgrowth.

I read somewhere that erythromycin can be given without problem as a prokinetic, because it's in a dosis that doesn't lead to significant antibiotic-resistance.

 

@alicec Thank you for all that information. I'll follow up the links you've given. One thing I'm concerned about with any test is that I should understand the results I'm going to be provided with. I have looked at sample reports for some stool tests and haven't understood them very well. Or alternatively, I know what the results are saying, but don't necessarily understand how to improve a dodgy result.

You referred to the American Gut project. Well, there is a sister project - a British equivalent called (drum roll) British Gut ( http://britishgut.org/ ). I have thought of paying for this but results take 3 - 6 months. Nevertheless I may do it anyway.

 

I've been given about 4 courses of erythromycin. My doctor won't prescribe more than the minimum dose described in the British National Formulary (a total of 1g per day in divided doses). I've done some comparison with the drugs.com site (which is US-based) and the lowest dose in the US for different conditions is usually higher then the lowest dose in the UK. The same is true of the highest possible dose - the US maximum dose is higher than the UK maximum dose.

The last time I was given a prescription for erythromycin I was given four weeks worth of 1g per day. After 6 days I had had no improvement whatsoever, so I doubled my dose from that point on, and had 11 days of 2g per day (still comfortably within the maximum suggested in both the UK and the US) and at that dose I got a lot of relief. I thought the relief I got lasted longer with the higher dose than it had with the lower doses I had had previously.

Since the first tablet of erythromycin I ever took gave me noticeable pain relief, but now that no longer happens, and I have had to increase dose to get some benefit, I think the chances are good that I will eventually end up getting no relief at all if I continue to take low doses because antibiotic-resistance is already in evidence.

I did discuss taking erythromycin full time with my doctor. But she would only allow me a total daily dose of either 250mg or 500 mg, I forget which. On the assumption that this would just allow my bad bugs to get used to erythromycin I refused her offer.

I'm considering buying erythromycin online. Then I can determine my own dose and length of course.

 

If only a higher dose works, than I presume that it is the antibiotic effect that is helping you and not the prokinetic effect.

I have experience with changing my microbiome with pulsed antibiotica and probiotics (and getting rid of SIBO and leaky gut). You will need to test constantly and change the antibiotics accordingly, and you need to know what is normal and what is not.

Personally, I wouldn’t test it on my own, wouldn’t know where to start.

 

I take probiotics. I try to stick to good quality ones and vary the brand I take, just to get some variety.

I've never understood the logic of pulse-dosing antibiotics. I would have thought it just increases the risk of the bad bugs becoming resistant.

 

uBiome turn-around can often be 2-3 weeks - certainly quicker than that.

 

I get the antibiotics in a normal dose (to kill the bacteria), but then take probiotics for two weeks and then have another course of AB.
I think when it comes to the microbiome, it's just not as simple to kill the bugs. You have to change an entire ecosystem and a lot of the bacteria that you want to kill are just normal bugs, but you just have too many of them or in the wrong place or the balance between some of the bugs isn't right. Plus you need the good ones to grow back, plus there is a whole biofilm in place in the gut so that the AB does not have the impact that you would want.