Microbiome testing and foods to promote gut microbiome balance


As we learn more about this disease, it seems to be directly related to the imbalance of the microbiome in our gut. It may look like a fools errand to influence the interplay between different types of gut bacteria but has anyone tested microbiome and attempted to influence it with food?

We have done the microbiome testing for our son and came to know which ones are low compared to other healthy individuals. Using western science based articles and ancient ayurvedic science, we are planning to do a little bit to try influence the gut imbalance with normal foods along with continuing the western medicine.

Below list shows some of the gut bacteria that’s low for him and one on the higher side. Note that gut bacteria changes many times in a day, based on what we eat, how we feel and a snapshot at a certain time can’t represent the whole picture unless we trace it over time.

Akkermansia muciniphila
Anaerotruncus colihominis
Butyrivibrio crossotus 
Collinsella aerofaciens 
Dialister invisus 
Methanobrevibacter smithii 
Ruminococcus flavefaciens 
Fusobacterium - high

There are many articles like below and its impossible to list all of them but you get the basic idea.



I’ve tested my microbiome, though only after being treated with oral vancomycin. My gut closely mirrors the vanco guts found in studies online and is dominated by Enterobacteriaceae and other potentially scary things.

We actually have a half dozen studies looking into the PSC gut, so we have many points of comparison between healthy controls, PSC patients, and those taking oral vanco. The main commonality between the PSC studies is that the PSC gut lacks diversity compared to healthy controls. I’m not sure how relevant this is as vancomycin significantly reduces richness and evenness even further (with the assumption that vanco works as a treatment for PSC). The vanco gut lacks SCFA producing bacteria and other good bacteria that internet articles would have you believe we can’t live without. The point is that us vanco users tend to thrive despite or perhaps because of gut dysbiosis.

It is also interesting that while we have many studies looking into the bacterial component of the gut microbiota, we have never bothered to look at the other components such as the mycobiota (yeast). We frequently see C. albicans in the liver in cases of cholangitis yet we’ve never bothered to look at GI composition.

I can post up links to these PSC studies if anyone is interested.

Thanks jtb for the feedback. Please do post the links to these PSC studies as we continue to learn more details.

PSC gut studies:

  1. Primary sclerosing cholangitis is characterised by intestinal dysbiosis independent from IBD (Sabino, 2016)
    -HC vs IBD vs PSC/IBD

  2. Characterisation of the faecal microbiota in Japanese patients with paediatric-onset primary sclerosing cholangitis (Iwasawa, 2017)
    -HC vs IBD vs PSC/IBD

  3. The gut microbial profile in patients with primary sclerosing cholangitis is distinct from patients with ulcerative colitis without biliary disease and healthy controls (Kummen, 2017)
    -HC vs UC vs PSC/IBD

  4. Integrated collaboration of intestinal microbiota induces bacterial translocation and Th17 immune response in primary sclerosing cholangitis (Nakamoto, 2017, abstract 832)
    -HC vs UC vs PSC/IBD

  5. The gut microbiota, bile acids and their correlation in primary sclerosing cholangitis associated with inflammatory bowel disease (Torres, 2018)
    -IBD vs PSC/IBD
    (Previous abstract: https://www.ecco-ibd.eu/publications/congress-abstract-s/abstracts-2016/item/p741-the-gut-microbiota-in-primary-sclerosing-cholangitis-and-inflammatory-bowel-disease-correlations-with-disease-andx00a0diet.html)

  6. A pilot study of fecal bile acid and microbiota profiles in inflammatory bowel disease and primary sclerosing cholangitis (Vaughn, 2019)
    -HC vs. IBD vs PSC/IBD

I have small duct psc for a few years now. I saw an Ayurvedic practitioner who prescribed me a pitta reducing diet and some gentle herbal remedies. The diet was super strict and basically cut out red meats, potatoes, tomatoes, dairy, yeasts, wheat, sugar, reduced salt. I ate a whole load of veggies, white meat, fish, some fruits. Also I had to watch how I combined foods in one meal, so no fruit within an hour of eating other foods for example. The result after a few months of this was normalised lft’s on my blood test. All lft readings far below the upper range. It sounds strange but this diet was so strict, even though I got good results on the blood tests, I found it almost impossibly hard to stick to and with not having the same disabling symptoms that large psc’ers have perhaps my motivation was lacking to stick to it. Whilst I eat better now than I ever did, I have never managed to return to the strictness of the diet I was on, therefore my lfts have crept back up - at least that’s why I think they have. Hope this helps.

hi Rick,

that’s good to know & understand this diet restrictions from ayurveda can he hard. If you don’t mind me asking can you share if the herbs are bilva, triphala or something else? We have started seeing a functional medicine doctor as well who is a physician from harvard but also trained in ayurvedic practices specializing in autoimmune + gastro issues. No medicines prescribed yet and testing for few things that might be contributing to my son’s issues like leaky gut and some metals. We will see how this side of testing goes.

We have stopped pasteurized milk, going with raw milk & ghee from raw milk. Mostly eliminated wheat & yeast although we are still using tomatoes but peeling off the skin & seeds.

The main ones I used were virechan and amrutras made ayushakti.

Thank you for sharing this and its helpful. The below session talks about the fungi dysbiosis in PSC patients and shows how Saccharomyces is decreased and exophiala is increased.

Have you dabbled into augmenting with s. boulardii supplements or you are on vanco alone? By the way, vanco is approved for us and we will be starting from next week.



FYI: If anyone wants to try Vanco and your doc is not willing then please reach out to Dr.Yinka Davies. She is open to prescribing this for anyone across the world as long as you have correct diagnosis.

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Good stuff - thanks for the link!

I don’t take a S. boulardii supplement, but I know of a few on vanco who do. I don’t have any apparent issues with my weird vanco gut so I haven’t bothered to make any changes. I just take oral vanco and vitamin D.

Congats on getting the go ahead. Be sure to let us know how things go.

Restoring Healthy Gut Microbiome After Liver Transplant?
Can anyone recommend any specific articles or other resources that address the issue of how to restore healthy gut microbiota (both bacterial & fungal) specifically as it pertains to someone who had PSC, but is now post liver transplant?

-PSC Dx. 2008;
-Liver Transplant 08/2018 (DDLT);
-Have completed the extended antibiotic & antifungals regimens I was taking pre- & post-transplant;
-But I anticipate at least a few more 5-10 day antibiotic regimens (for out-patient procedures to address minor post transplant complications) + will continue immunosuppressant meds. forever (most likely).


So far, there is no strong evidence to overcome PSC with diet changes alone. We may hear once in a while that it might have worked for 1 or 2 folks but we don’t hear from them over a course how that worked in the long term.

Given your specific background and if you are in US, I highly encourage you to talk to Dr.Yinka Davies about Vancomycin. She has several post transplant patients responding extremely well even after 10+ years taking vanco alone and no other medication(s). I know several folks across the country who travel to Sacramento to be under her care too.

Congratulations on your transplant now almost a year ago. Unless you have some sort of major UC problem, with your new liver you shouldn’t have to worry about having to restore anything that I can see. Your liver is now functioning great I trust and although the absence of a gallbladder can have it’s issues at times, your digestive system should operate just as God made you from the beginning.
Eat a healthy diet, get regular exercise and enjoy the rest of your life without having to worry about your health constantly as you did before. And yes, unless you are one of the rare patients, you’ll be on immune suppressants the rest of your life. They will over time though gradually reduce the strength of them to the absolute minimum which helps with the side effects from those medications.
One thing that I have had a struggle at times with regarding my stomach though is the side effects of having to take so much magnesium to counteract the immune suppressants leeching that out of my system. I’ve tried a number of different types and right now I’m on Magnesium Chloride which I take at bedtime and it’s doing pretty well.
Good luck on your future and I hope you have a full and long life.


I’m certainly not advocating overcoming PSC with diet. If you have had a liver transplant then you do NOT have PSC unless it recurs. Hopefully they have had you on Prednisone for a year now which helps to prevent recurrent PSC. You mentioned you had had a liver transplant so if that’s the case you don’t have PSC.


I find your findings interesting and was wondering what test did you do to find out your sons microbiome levels.
Also what are you doing to increase the levels?


We previously used ubiome services to understand the Microbiome levels as ubiome said these services are covered under insurance. Now its bankrupt unfortunately and we haven’t done any testing in the recent past for Microbiome levels.

Ours is a complicated case and working with doctors to identify the correct diagnosis. Our PSC diagnosis might be incorrect / incomplete as we are not seeing LFT improvement with Vancomycin. We are focusing on a good home cooked diet mostly vegetarian with occasional chicken/fish and a lot of research in pubmed. We have excluded all gluten and dairy products except home based curd. So far he is completely asymptomatic but the LFT’s haven’t normalized and are elevated.