Microbiome testing reports discussion

I wouldn't waste my time with those species. They are not very important in the big picture. It's mostly hyped up yogurt marketing.

 

When it's not listed in the report, does that mean it's non-existent? And if that is the case, perhaps FMT could be of some use, for both of us?

 

I can't afford testing. However, I am convinced by some of the recent research around how the microbiome affects depression and other things (I know there are 'other things' but can't remember what (brain fog). I have also read that the best thing for the microbiome is to eat as diverse a healthy diet as possible.

Before I became ill I had quite a limited diet, with little variation in what I ate. I've been vegetarian for many years but never used to think about what I might be lacking nutrition wise. I wonder whether this was a contributing factor to becoming ill due to the microbiome becoming a bit rubbish- excuse my limited understanding of the science here. I was low in iron, b12, folate and vit d when I was tested in the early days of becoming ill. I know that isn't to do with the microbiome but if the vitamin deficiencies were caused by poor diet, that poor diet could also have affected the microbiome.

I'd like to start taking a probiotic, or a prebiotic, with no idea what the difference is. BUT I have no idea where to start. Can anyone recommend anything which isn't a specific treatment for anything, but will help with general diversity of bacteria, which is what I understand to be a good thing, in the absence of specific testing?

 

It isn't as simple as that. You need a range of different fibers to support your microbiome. So the best overall advice is to include a diversity of fiber sources in your diet.

 

Yes if not listed it's not there or present at such a low level that it was missed in sampling.

I used to be very keen on FMT, now that I've seen what is actually in my gut I am not so sure. I don't think my gut is so bad (your's has a lot of similarities to mine) and while it could do with improvement, FMT seems very drastic and at least as it's currently practiced, there's no guarantee that the replacement will be any better.

Maybe I would consider FMT if I first knew the full microbial composition of the donor and could choose one that was tailored to my own deficiencies.

What we need of course is more targetted probiotics but these don't even seem to be on the horizon.

I just keep trying to eat well, keep up a range of prebiotics and test every now and then to see if things are improving.

 

Probiotics are live bacteria which do seem to have various beneficial effects as they transit through the gut, though for the most part they don't actually colonise the gut.

Prebiotics are food for colonic bacteria, components of food we eat which we can't digest but our gut bacteria can.

Probiotics can be very useful but prebiotics provide the foundation for a healthy gut microbiota.

Here is a series of articles on prebiotics which gather together a lot of valuable info in one place 1,2,3,4,5.

Note this was written for essentially healthy people. A lot of us have found that we are very sensitive to pre and probiotics so the usual cautions apply. Start low and go slow when experimenting with any of these.

The place to start is diet, ensuring you include as wide a range of prebiotic rich foods as possible. There is discussion of this in the articles. You could then consider boosting this with some concentrated fibre sources. Look for a range of different types but start with just one at a time in very small amounts to gauge your own reaction. Again the articles canvass some of these.

I try to take several different types daily, varying these from day to day. I think it is better to take smaller amounts of several different types rather than a large amount of one or two, more like what happens when we eat a varied diet. I also favour relatively unprocessed products rather than some of the artificial laboratory creations (though I do take a little of one of these, benefibre, as a starch substitute since I don't eat much in my diet), again more like normal eating.

Here are a few notes I made on the prebiotics which I most often take. They are by no means complete but give an idea of range of types.

aloe vera inner leaf predominantly acetylated glucomannan
benefibre is hydrolysed wheat dextrin (RS4)
acacia gum is predominantly arabinogalactan
baobab powder is a source of pectin, polyglucuronic-galacturonic, polyphenols and other fibres
larch is a source of arabinogalactans - good for bifido - reduces NH3
psyllium is a source of arabinoxylans
raw potato starch is a source of RS2 - increases butyrate, acetate, propionate production in vivo
Artinia is a source of insoluble β1-4 N-acetyl D-glucosamine chitin-glucan - liked by Roseburia and other cluster XIVa
PGX is a source of glucomannan, glucomannan/glucuronate; mannuronic/guluronic acids
Fucoidin is predominantly sulfated polyfucose
Mushrooms are a source of polymers of N-acetylglucosmine (chitin), βglucans and mannans
fructans (inulin/FOS) enhance Ca uptake in gut; feed bifido
Pectins increase acetate production in vivo; apple pectin good for Faecalibacterium

 

Wow @alicec that is really helpful and really useful information- thank you!

Coincidentally I switched on radio 4 this afternoon and caught the end of somebody discussing ‘the British Gut Project’ which offers testing as part of a research project. I’m thinking about it, but having read a bit about it this subject a bit more this afternoon, I think it’s possible my gut is doing quite well from a much improved diet over the last year or two.

 

I'm amazed at how little changes in my diet affect my illness. I have made major modifications of late, cut out all flour and sugar products. Effect on my symptoms: zero.

I suspect if my microbiome had anything to do with my illness, then it should be possible to influence my symptoms at least a bit by altering diet (even if only for the worse).

This is one of those things that makes me think ME is more than one single unitary disease. There appear to be the food-sensitive and the food-insensitive subtypes, and this would seem to me to suggest a major source of variability.

 

Not necessarily. It's possible that a particular bacteria(s) got completely wiped out or a bad bacteria became over populated that has nothing to do with the food you eat.

 

That's a fair point, but then the whole thing becomes sort of unfalisifiable. Not to mention unmodifiable.

I'm just wary of hopping on the microbiome bandwagon here. Think it might be relevant to those who have dietary sensitivities, but maybe not for the rest of us.

 

At first i thought you said compared to genius level

 

I don't think those categories are fixed - I used to fit in the former but am now in the latter.

Improvements in digestion and in microbiota composition (which I have followed with uBiome tests) haven't affected my illness either.

This doesn't mean there is no influence of the microbiome but it's more complex than just the presence or absence of some species.

 

Gut bacteria has many more sources than food alone. You take in bacteria through breathing, your skin, and through your mouth. Gardening is a great way to get good bacteria. And then you have antibiotics that are notorious for wiping out good bacteria. In some cases there will be enough left for the body to repopulate, however, Cipro is one antibiotic for instance that the second time used can completely eliminate some beneficial bacterias. I definitely believe that for some of us with ME, that our gut bacteria definitely plays a role in our illness.

 

Not to forget the amount of stomach acid and bile, that also affect the microbiome. (Beware, people with hypothyroidism)

According to a Lyme doctor, Bifidus bacterias are low in infected patients.

A diet high in omega 3 and fish has been recommended by a group researching the microbiome; Backhed et.al.

Exercise changes the microbiome positively. Sigh...

There are so many factors that affect the microbiome. Sorry, I should have linked to the sources. Hopefully I´ll have the energy another day. Just wanted to add some factors that I find important to the discussion.

 

I totally forgot about exercise when I was listing different sources.

 

My husband was prescribed a round of antibiotics for a puncture wound last month and it caused him to suddenly develop horrible halitosis (wicked bad breath). He and I both were freaked out at the prospect of his breath staying like that forever. We decided to start by seeing what would happen if he drank 1/4 cup of store bought Kefir once a day for a week. By day 6 of the daily Kefir the halitosis was GONE completely and his breath was back to it's normal state. We were sooooo happy and it only cost a few dollars. I was kinda shocked it was all it took to get his gut flora back in check.

 

I'm very intrigued by the Fusicatenibacter in your sample, something I don't see often. Do you drink kefir, by chance? It's one of a very few clear signals I've seen in thousands of uBiome samples I've studied. https://www.biorxiv.org/content/early/2017/11/15/218313

 

No, I don't drink kefir, never have. What's so interesting about this bacteria?

 

I've had a bottle of Miyarisan in my cupboard for 8 months, maybe longer. Was about to take it when I read quite a few reports of worsened constipation, which is already a problem w/me during the last 2 years or so. I'm guessing you didn't have that issue @adreno?

 

No, I didn't.