Gut Viral Database

Wishful

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https://newatlas.com/science/virus-gut-virome-microbiome-unknown-species-discovered/

Just to make gut problems more complicated, you need to figure in the viral--especially bacteriophage--populations in your gut. Simply adding a dose of another bacterial species may not help, since you might have a high bacteriophage population that attacks that particular variety. Likewise, if you have a bacteria species causing problems, you might need to add the right bacteriophage.
 

Wishful

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Would explain why probiotics can make things worse...
I'm no expert, but I suspect that any artificial alteration of your microbiome could end up with negative effects. Road traffic experts sometimes put in measures that are intended to reduce traffic congestion, yet sometimes those backfire and cause worse congestion. I think gut ecology is at least as complex as road traffic, so unexpected responses are likely.

Some of us may have unusual sensitivities to byproducts of bacteria. I'm unusually sensitive to proline, so giving me a new bacterial population that produces a lot of proline would give me problems.

Some of us might have unusual demands for a bacterial byproduct, produced by a bacteria we have a high population of. A probiotic might outcompete that variety resulting in less of whatever it is we need.

Microbiome management seems like a very complex subject, and as a science, it's just in its infancy.
 

EddieB

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I should have said, maybe that’s why probiotics make things worse. But yes, this is very complicated.

Myself, I recently tried colostrum, b-infantus, and another probiotic combo that targets histamine. I was careful to avoid prebiotic/ multi strains/ fillers. Each one separately, but same results, more gas/ bloating = more reflux.

So does this support using antibiotics/ anti microbials/ bowel flush, to lower the number of bacteria first, then do fecal transplant and/ or probiotics? Might that improve the odds?
 

Wishful

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Each one separately, but same results, more gas/ bloating = more reflux.
Maybe your microbiome is lacking in bacteria that do a proper job of breaking food down, so adding new strains means they have abundant food and likely little competition, so they multiply quickly to excessive levels.

Did you try these probiotics for several weeks for each experiment? Suddenly increasing the amount of fibre in your diet can have a similar effect (excess gas), but the microbiome typically adapts to that in a week or two, I think. A similar time frame might be necessary for probiotics or prebiotics.

A major 'killing off and flushing then adding new strains' will also likely take weeks to stabilize, and probably be uncomfortable in the meantime.

I get the impression that some aspects of microbiomes, such as variety and balances, depend on genetics influencing gut properties (number of villi, etc). Maybe some people are just set up for sparse microbiomes, and FMTs will only temporarily boost variety, and then some will die off and you go back to sparse again. We encounter vast numbers of new microbes every day, yet we seem to maintain a personal 'signature'. I read that our left hand's microbiome has more in common with other people's hand microbiomes than it does with our own right hands, despite the number of times our hands touch each other. Something maintains those microbiome signatures.
 

EddieB

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Maybe your microbiome is lacking in bacteria that do a proper job of breaking food down, so adding new strains means they have abundant food and likely little competition, so they multiply quickly to excessive levels.
Agreed.


Did you try these probiotics for several weeks for each experiment?
No, just for a few days. I took the increased gas as a sign of “not good” and quit.

A major 'killing off and flushing then adding new strains' will also likely take weeks to stabilize, and probably be uncomfortable in the meantime.
I was hoping to add tiny amounts of beneficial bacteria and gently shift things, probably too optimistic.
The gastrologist is pushing xifaxan, and yeah that’s going to be rough and could make things a lot worse. But my options are few. From discussion with others here, it was a necessary step to get on track.

I wonder if xifaxan is effective on reducing these bacteriophages?

I read that our left hand's microbiome has more in common with other people's hand microbiomes than it does with our own right hands, despite the number of times our hands touch each other.
Amazing, but I believe it. Much more complex that realized.
 

Wishful

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No, just for a few days. I took the increased gas as a sign of “not good” and quit.
I think probiotics and other gut microbiome experiments have to be run longer, because transient changes are likely.

I wonder if xifaxan is effective on reducing these bacteriophages?
Nope. Antibiotics work against becteria, while bacteriophages are viruses, so they'd be unaffected, aside from having fewer hosts to multiply in.

I thought of an example of how ecosystems are not simple. Some people might picture the digestive tract as stainless steel tubing, that can be flushed, sterilized, and replanted with the desired microbes. By the same assumption, invasive weeds should take over all land. I live in the woods, with a grassy driveway and some trails through the forest. My driveway has lots of tall buttercup (invasive weed), but it never spreads further than a couple of feet from the driveway. It outcompetes native vegetation on packed soil, but fails on regular forest soil. I find a few patches on old logging roads and cutlines, but they don't spread. Plantain has a similar pattern, but survives really hard-packed soil better. Dandelions do well in mowed areas (and tilled garden soil :mad:), but not elsewhere. Thistles do well in more places, but don't survive in forest shade. Ox-eye daisies do well on dry soil along the gravel road (calcium chloride may be involved) but don't spread from there. Likewise, native species have some fairly narrow niches.

The human digestive tract may be like my forest. You can apply large amounts of bacterial strains from one end or the other, but that doesn't guaranteed that they'll find a spot where they'll survive. Some might reach a good spot for them, but they'll be out-competed by some other strain. Maybe they'll be vulnerable to bacteriophages that some other strain is hosting. Maybe a strain that does really well in someone else's gut won't survive in yours because your genetics produce a slightly different mucus layer or produce different amounts of some chemical.

So, don't think that changing your gut microbiome is as simple as flushing and replanting. It's far more complicated. I think many of the success stories are from people who simply got lucky, and we don't hear the stories of all the other people who tried the same thing and didn't get lucky. It is possible to make improvements, but think of it as a low-chance-to-win lottery that requires buying lots of tickets, rather than a straightforward 'follow these simple steps to success' method.

I'll point out that I did play the game (antibiotics, probiotics, diet change, etc) without success, and then apparently got lucky with accidental food poisoning, which seems to have cured the type IV food sensitivity I'd had. I didn't know that my microbiome was involved, and I think it's unlikely I'd have had success intentionally changing my microbiome. Thank you spoiled coconut milk! :thumbsup: