Ubiome results for 2.5 yo with ASD and gut issues

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  • #396

    Any idea about the high concentration of thalassospira? I don’t see some of the ‘typical’ markers for ASD, aside from alistipes (and general dysbiosis)…but I am new to all of this, and welcome any insights!

    We will be participating in a microbiome research trial starting next week, and then I will be looking into FMT to hopefully relieve abdominal pain.

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  • #406

    Keith Bell

    Thanks so much for posting. Very interesting about the microbiome research trial. Where is this being done?

    The reports you’ve provided are full taxonomy, so it’s hard to see the bigger picture. Please try to generate reports at these levels:

    This way we see the relative ratios of microbiota, i.e., high Clostridia and low Lactobacillus, and hopefully get a better understanding of the dysbiosis.

  • #407

    Hi Keith,
    Thanks for your response, and for creating this site!

    There are actually several research studies right now related to ASD and the microbiome…so exciting that funds are starting to trickle into this area!

    Stanford has this ongoing study:


    And, ASU just finished an FMT for autism trial (results not yet published)

    We will participating in this one:


    I’ll try to post his results…

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  • #421

    Keith Bell

    Great job posting, thank you.

    What’s pretty obvious is a massive Proteobacteria overgrowth. What should be seen is a much smaller amount of Proteobacteria and the first two on the Phylum list would normally be Firmicutes and Bacteroidetes.

    Did you order this test through a doctor or through The Gut Club site or elsewhere? Are you working with a doctor to interpret these results?

    This gram-negative bacteria overgrowth produces toxins like LPS wreaking havoc on brain and gut. You’ve already noticed the “high concentration of thalassospira,” so I may not be telling you anything new. How have you been attempting to balance flora?

    Inhibition of nitric oxide production may affect neurotransmitter balance resulting in glutamate excitotoxicity in my view:

  • #422

    Keith Bell

    Would you mind if I post this thread on The Gut Club page on Facebook? We may receive additional input there . . .

  • #428

    Thank you for the link and info about proteobacteria! I just got these results back a couple of days ago, and have been scrambling to make sense of them. My son has been seeing a few doctors, who have helped us with some testing and diet/supplement recommendations, but I’m kind of on my own with the bacteria part. He just got his confirmed ASD diagnosis in July, so I’m getting a crash course on the gut-brain connection.

    His integrative medicine doctor suggested that I read Brain Maker, and that led me to reading Bugs, Bowels, and Behavior, and now I am reading/listening to anything I can get my hands on. I’m excited about the research study, because I’ll actually have some microbiologists looking at my son’s data so his future isn’t left in my novice hands!

    We consulted with a wonderful GI doctor who, though he can’t treat my son’s condition, was willing to advise us on how to find a healthy donor for FMT. We plan to move ahead as soon as the study finishes…if he finds relief through this method, I hope something can be learned from it all.

    Anyway, I hadn’t been able to find anything about thalassospira, other than that is can apparently be reduced by vancomycin (which we plan to do prior to FMT). I sincerely thank you for the information about nitric oxide reduction…I’m oddly relieved to know that the thalassospira could be a bad guy, and the mechanism by which it could be wreaking havoc.

    Please feel free to share this with anyone who might have interest or insight! I just found this website yesterday, and didn’t even know about the FB page. Will go there now!

    Thanks again!!!

  • #429

    Oh, and to answer your question about balancing flora, we have been GF/CF for 6 months, and SCD for 1.5 months. I’ve been experimenting with fermented foods, and have also given OTC probiotics. I think we’re just scratching the surface of the problem, though, and that is why I feel it is crucial to reset with FMT (even more so after seeing these results!).

  • #430

    p.s. I had never read about LPS before your post. While waiting for these results, I was fully expecting to see more clostridium, and was focusing on PPA.

    Thanks to you, I’m now reading here:


    I can’t thank you enough for explaining what might be going on…this makes so much sense with many of his symptoms!

    What are your thoughts on FMT for this type of condition?

  • #431

    Keith Bell

    My heart goes out to you and your young child. WIth persistence and the right plan, there is hope to reverse this ASD diagnosis. Be sure to use the best probiotics possible. There are also probiotic enemas, perhaps the next best thing to FMT. But the battleground may be in the small intestine, so oral probiotics high in Bifidobacteria and Lactobacillus are probably warranted. Many OTC probiotics are inferior, so choose wisely. Organism count in the hundreds of billions makes a big difference, but begin slowly to avoid adverse reaction.

    Also, learn about prebiotics to grow the protective microbes. And a low carb diet, especially low sugar will, hopefully, starve Proteobacteria. You may be on the right track with SCD. Please look into the GAPS diet.

  • #432

    Keith Bell

    Also, be careful with some prebiotics as they may also feed the bad guys.

    Vancomycin appears contraindicated with this dysbiosis as it’s effective with gram-positive organisms like Clostridia and would lead to growth in Proteobacteria. Look into Rifaximin if you want to use an antibiotic.

  • #433

    Keith Bell

    And you’re going to want to learn about biofilm to be able to balance flora. Things known to disrupt biofilm are essential oils, phage therapy, digestive enzymes, soil-based probiotics . . . perhaps the right phage therapy would be a better choice than antibiotics.

    Also, natural ways to inhibit adhesion such as bee propolis and things high in proanthocyanidins and anthocyanins like cranberry and tart cherry, though I’m not sure if these things apply to alphaproteobacteria as they do other Proteobacteria like E. coli.

    Lots to consider.

  • #434

    Wow it is a lot to consider…but it will all be worth it if it brings him relief!

    Thanks for the advice about vancomycin – I will discuss this with the doctor who has agreed to write an antibiotic for this purpose. He is very supportive and open minded, but has not encountered this particular issue before.

    I had briefly considered GAPS before starting SCD, but it seemed more difficult logistically…easier to get a 2yo to eat coconut yogurt than to drink broth! I’ll give it another look though!

    We have a couple of weeks to figure our plan out, as I want to wait until the study is over. I’ll look into your recommendations for the biofilm & keep you posted!

    Thanks again!!!

  • #541

    Quick update – just received post-FMT ubiome results!

    Huge jump in bacterial diversity, which goes along with recent improvement in sleep, speech, and other ASD behaviors. Still a long way to go, but he is much more happy, engaged, and responsive to therapy now.

    Happy mama!

  • #544

    Coincidentally, this was just published:

    Wednesday, January 18, 2017
    Study finds alterations in both blood-brain barrier and intestinal permeability in individuals with autism


  • #757

    Hello Just Keep Swimming!

    My son is 2.5 years old and was diagnosed autistic as well. I have believed in the gut brain thing for a while but didn’t know what the heck I was doing (tried out a lot of things). He just okay until antibiotics for “Whooping Cough” I don’t think he had it, at 7 months old. We did a Ubiome test in November and then in December we did an organic acids test that showed not only did he have yeast but also C.Difficile that was then confirmed with a fecal. Not sure why it didn’t show up on the ubiome test. Though later when it was “active” I noticed a distinctive smell that wasn’t there when I did the sample. So maybe when it was mostly dormant it didn’t show in the poo???

    I’d love to get some advice from you! Considering FMT as well! Is there a way I could contact you?

    And thank you Keith Bell! Your info was so helpful for understanding my own results!

  • #758

    Yes, Keith is amazing.
    Are you in the FB Gut Club Stool Discussion group?

    I’d be happy to chat about FMT, etc. I think it can really help a lot of our kids.

    I have actually wondered why c.diff doesn’t seem to show on ubiome very often, even though we all supposedly have at least a little. I don’t think I’ve ever seen someone confirm c.diff infection with ubiome…Keith, do you have thoughts on this?

  • #824

    Keith Bell

    Swimming, great question. My understanding is some pathogens like C. diff aren’t included in some of the tests to avoid issues with the FDA. Such is regulated medicine in the age of citizen science; they don’t want these tests to replace medical diagnostics. But C. diff is included in uBiome’s SmartGut test which requires a medical professional to order. Still learning!

    Hope things have continued to improve post-FMT.

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