Friday, January 16, 2015

uBiome 2-for-1 until Feb 1st!

$89 for a kit and get a second kit free.  If anyone is wanting to do any before-after's or test two people, here is a great chance!

Go here to purchase a kit.

This is not an affiliate link.  Just passing this on.  I'm always happy to help folks read their results, too. 

From uBiome:

Here at uBiome, we want to help you get to know your bacteria a little better.

With that in mind, we asked some of our bacteria what their New Year's resolutions are for 2015!

More Exercise
Bear in mind, this is typically difficult for bacteria such as Staphylococcus Cohnii, who are not motile. We like to support their efforts though.

A Healthier Diet
Just look back through your holiday photos to see what your bacteria have been snacking on since December. We know your Bacteroides thought the roast ham was particularly delicious.

Volunteering to help others
Bacteria are, by nature, remarkably gregarious microbes. They're all about personal growth and giving of themselves. This year, they would just like to be able to do it outside the agar broth.
We know you undoubtedly have resolutions of your own this New Year. With that in mind, we're offering a two for one sale on gut kits between now and 1st February 2015.

Track how big an impact your resolutions are having on your microbiome.

Thinking of switching to a paleo diet? Introducing more vegetables to your meals? Learn about the changes to your microbiome over two time periods. You can also compare your bacterial balance to other participants.
To receive your second gut kit for free, enter
on checkout.


  1. It worked. Thanks!

  2. I just sent off for my kit(s), too! So excited. Do you charge to look at them?

  3. Charge? lol, no. Email me when you get your results. I can answer any questions you have, or better, give me your user name and password and let me snoop around and I'll be able to give you my interpretation. I wish they had a better way to share the data, but there's not.

    Basically, if you go to the 'Dashboard' and click 'Compare' then choose 'Genus,' you will see the most useful information. I like to look for listing that appear to deviate substantially from the norm. For instance, you may see the normal level of E. coli is 1%, but you have 25%...that would be of interest. But mostly what I've seen is that everyone just kind of looks 'normal'.

    I don't think we are to the point of looking at a gut report and being able to make precision changes. If someone had serious health issues, and their doctor is lost, a uBiome test showing high levels of pathogens would be a good discussion starting point.

    Also, I think that a well-fed gut shows low levels of proteobacteria and high levels of proteobacteria. This should be indicative of a gut with an optimal pH and butyrate production.

    But, yeah, if anyone wants help with a uBiome (or AmGut) report, just email me and we'll figure out something (for free!).

    1. Are you saying both low and high levels of proteobacteria are a sign of good gut health?

    2. Tim says "But mostly what I've seen is that everyone just kind of looks 'normal'. "

      Tim, does this surprise you?

    3. I just wanted to comment on everyone having normal patterns. My impression is that the rampant horizontal gene transfer just shambles the metabolic genes with the species marking rRNA genes. The result is that what you see is not what you are getting and the species profiles don't mean the same thing in different people. E. coli is not always E. coli. The pattern of genes present is more important that the species markers present.

      In a related way, knowing one's genome, will provide little predictability with respect to disease risk, because it doesn't matter if your gut flora is healthy.

    4. Bless you, Dr. Art Ayers, that went WHOOSH, right over my head. Are you saying that's because the results are only down to genus and not species?

    5. what is species, genes, genus?

    6. @Dr. Ayers,

      Yes. Plus bacteria sampled may not be representative of the population anyway. Catch is, many use these genome test results to measure "if your gut is healthy". Are secondary markers (like SCFA, etc) a better way to measure health? Are there objective ways to measure gut health? How does one evaluate the pattern of genes?


    7. Anonymous, studies on the incidence of colorectal cancer and fecal pH indicate that lower pH is associated with a much lower incidence of colorectal cancer.

      However, and I think this is also important: the people who have been sampled have a lower life expectancy due to poverty, parasitic and other diseases than the people who were weathier, had better medical 'care' available and generally have a longer life expectancy. There is a South African study of diet (mealie mealie multiple times per day) and CRC.

      I don't know because I haven't checked, if 7th Day Adventists have been surveyed for CRC. They have been for other health problems. Most are vegetarian, some are lacto-ovo vegetarian and some have fallen off the wagon entirely and eat meat.

      All in all though, most likely the ambient poop pH is probably the best indicator of colon health. Lower pH discourages the growth of some of the nasties.

    8. Thanks Gabrielle. I think you are might be right on target. I had been wavering on this measurement when I learned about how PH varies throughout the GIT and maybe the end measurement was not that important. I reviewed my recent results from the newly designed Genova test and although the microbiome section is enhanced, they might not report fecal PH anymore.


    9. @Gabriella, I apologize for spelling your name incorrectly.


    10. just don't call me 'late for dinner'.....:)

  4. Thanks for the heads up and the offer to help with the test results. I plan to order mine and will be seeking your expertise when I get the results.

  5. I have a Doctors Data Comprehensive Stool Analysis/Parasitology x3 report that I would love to have analyzed. There is no link, but I could type it out in email form if you are familiar with it or just willing to have a look.

  6. Hi Tim, I'm hoping you can help me hone in on an ingredient that sends me into heavy flares(ankylosing spondylitis). Sprouted and well cooked mung beans put me out of commission for days. Also, boiled and thoroughly cooked rolled oats have recently crushed my soul! I tried a pre mix of uncooked oats and nuts which didn't effect me as much. I felt that all my years of dietary efforts, exercising, de-stressing, gut healing, expensive probiotics, time consuming home made ferments were all for naught. I went on tilt and devoured a couple donuts and some mcdonalds fries and a flurry with no immediate(1-3 days) issues. I thought oats and beans would be good for me and didn't anticipate any issues. I expected issues with Mcd's and donuts, of course, but experienced none. I think it's safe to say that placebo is not a factor. I have a milder reaction to white rice. I tolerate sweet potatoes, psyllium, inulin, and I haven't noticed any issues with most resistant starches and fibres in supplement form. In short, I'm hoping you can help me find THEE common "ingredient" in mung beans and rolled oats that might be causing my problems so that I can temporarily avoid them and other similar foods.
    I'll be getting two biome reports thanks to your link. I've been taking strong pharma anti-bx, followed by strong natural anti-bx and followed by more mild natural anti-bx. About 5 months altogether. I'm interested to know if all of my pro-bx supplementation throughout was just a waste of money but mostly I'm interested as one will be pre-FMT and the other is for after. I'm really excited to see the results and would appreciate you allowing me to share them with you as well?

    1. @G.R.

      My very wild guess is interaction with High-Mobility Group Box Protein (HMGB1).
      Good or bad in your condition? I do not know.

    2. @G.R.
      It will be interesting seeing your results, pre- and post- FMT.

      I have been on low dose pulsing antibiotics (Doxycycline 200 mg MWF) since 2008 for Rheumatoid Arthritis. I wish I could explain how it works.

      There are a lot of patients at that have successfully used the protocol for a wide range of connective tissue diseases.

      I'm recently off antibiotics, hoping to stay in remission with supplemental fibers, fermented foods, and sticking with real food.

      I just had a uBiome test done, and was surprised the results weren't "worse"---whatever that means at this stage of the game.


    3. @ Michelle,
      Did you have any Prevotella Copri in your uBiome test? I read an article that discussed RA and a high concentration of PC. I used the antibiotic protocol but have since dropped it. It will be 2 years. I do have some flares from time to time. I have not had a uBiome test and am on the fence about it.

    4. @ Olaf,

      Prevotella (genus) showed up at 0.004% for me, with 7.63% being the average. I'm taking the test results with a grain of salt. I did the uBiome test out of curiosity, with an understanding of its limitations.

      I did some reading at Roadback. In one article, the late Dr. Thomas McPherson Brown describes the affinity that mycoplasma and other L forms of bacteria have for the joint tissue & produce arthritis. The body reacts, in a hypersensitive state, to the organisms' antigens. The antibiotics "work" by suppressing the antigen via inhibiting mycoplasma growth, and reducing the reactive state.

      With my health history, I doubt I've ever had a healthy gut. So, maybe no surprise that I've developed an autoimmune disease in mid-life. I try to avoid getting sucked into stories where people make diet changes and experience a miraculous cure. It's probably just me feeling discouraged because I feel like I'm already doing a lot of the "right" things.

      I suspect the body is complicated. You think?


  7. Hey, guys - sorry I've been slow to respond. I'm in Mexico for the week stocking up on Vitamin D and some new gut microbes. I was ordered to stay off the computer! I'll get back on next week.

    Hasta la vista!

  8. Thanks Gemma. I'll look into that and see if I can put some more pieces of the puzzle together.
    Enjoy, Tim. See if you can one up you own sunset feet shot from your last holiday.

    1. @G.R.

      Here some hints to save you the googling. Though they are just pieces of the puzzle, nothing more. There must be more to the story, I think. The dual role of HMGB1 is confusing.

      It Is Not Just Folklore: The Aqueous Extract of Mung Bean Coat Is Protective against Sepsis

      Recent Developments in the Role of High-Mobility Group Box 1 in Systemic Lupus Erythematosus

  9. Hi GR - Have you ever done any food sensitivity testing? I know it is not cheap but while you are healing your gut it may help you avoid foods that are triggering your flare ups.

  10. "Tim. See if you can one up you own sunset feet shot from your last holiday."


  11. Great stuff, Gemma! Yes, quite confusing but I love to learn.

    I won't embarrass myself by saying why but I feel like this discussion

    and this article
    "HMGB-1 was more strongly expressed in SF of RA patients than in that of OA patients, inducing the release of proinflammatory cytokines from SFMs. HMGB-1 plays a pivotal role in the pathogenesis of RA and may be an original target of therapy as a novel cytokine."

    along with the activity to HMGB1 from Mung Bean Coat noted in the link you provided, all tie together nicely.

    Very interesting in the link that I put up that "HMGB-1 concentrations were significantly higher in SF(synovial Fluid) of RA patients than in that of OA patients"

    An infection I picked up overseas, at the very least, was the straw that broke the camel's back and sent my circuitry haywire. That and after reading this article
    led me to believe that my whole problem was based around a lingering systemic infection. And now reading this from your first link again makes me wonder yet again but from a slightly different angle. "Although appropriate production of various cytokines/chemokines is essential for the immunity against infection (by allowing leukocyte activation and recruitment to sites of infection), exaggerated production of these cytokines or chemokines may contribute to the pathogenesis of sepsis and other inflammatory diseases."

    Anon, I'm on immunosuppressants and was told by my Doctor that a food sensitivity test might give false results. I took it at face value and at the time was just happy to keep as much $ in my pocket as possible. I don't know if it's true or not, though?

    Tim. That's a big 10-4. Roger that. Loud and clear. Awesome pic! You've successfully one up'd yourself. No more comments from you though, young man;) Get off the computer and enjoy the rest of your holiday.

    1. @G.R.

      Here another link if you need more papers.

      HMGB1 Promotes the Differentiation of Th17 via Up-Regulating TLR2 and IL-23 of CD14+ Monocytes from Patients with Rheumatoid Arthritis 2012

      Now, what is the cause here? What are the immunosuppressants good for? Probably not treating the cause...

      May I ask how you react to boswellia, turmeric, propolis, ginger, ashwagandha, fenugreek etc.?

  12. I just had a long reply disappear when I tried to post it :(

    It'll take a few more reads to fully semi-grasp that link. From what I do understand it's really interesting.

    Exactly! What is the cause? Infection? Nothing in my stool test but I think if I have an infection it's outside of my gut. My org acids test indicated a leaky gut. I've done a lot to help that. i.e. slippery elm, marshmallow root, liquorice root, l carnatine, b5, querciten, zinc, aloe vera juice(the real stuff), aloe gel capsules, yoga, fasting, breathing, walking and so on. I still have serious food intolerances.
    I really don't like being on biologics! EVERY SINGLE health blogger that I respect and follow has, in a round about way, expressed their dislike for them. Whenever I stopp taking them I go into major flares, though. I can't play sports, eat, sleep and sometimes have trouble breathing. All that gets frustrating and I'ma firm believer that stress is the main contributor to my iritis attacks. I hate iritis! My near term goals are to get off biologics and to be able to tolerate rice.
    I've tried all of those items you listed but never really noticed any positive or negative effect. Marshmallow root liquorice root and aloe etc. make me wake up drenched in sweat almost every time I take them, though.

    1. @G.R.

      And what about oil pulling (sesame)?

      Also, have you ever about cryotherapy for AS?

      And since you have mentioned chlamydia, here another paper how they play with the cell death, inflammation (and HMGB1):
      Role of high-mobility group box 1 protein and poly(ADP-ribose) polymerase 1 degradation in Chlamydia trachomatis-induced cytopathicity. 2010

    2. @GR

      You might find some interesting info over at The main page has links at top to articles about using low dose pulsing antibiotics for connective tissue disease.

      At the Discussion Board, there are people with AS successfully using the protocol.

      Other background reading on the protocol includes: The New Arthritis Breakthrough by Henry Scammell, The Infection Connection by Katherine Poehlmann, and Why Arthritis by Harold Clark.



    3. @GR,

      Just in case it has not been covered, ever researched the links between Klebsiella, starches and AS? In your case, it does seem contradictory that some starches works for you. Mung and oat could also be higher in oxalates.

  13. This may be a dumb question....I am just curious to hear from anyone who has taken soil probiotics or whatever probiotics and then been tested by UBIOME or American gut; if any of those strains were found in your results.

  14. You guys are amazing!

    I've tried oil pulling but not consistantly and only with coconut oil. I'll do it more often now that you mention it.

    More GOLDEN links, Gemma! I'll need to summon my inner savant to figure out a game plan.
    The cryotherapy is a no brainer as far as I'm concerned but if you were in my shoes, what would you do to correct your c.trachomatis infected cells? Assuming that they were infected, that is.

    Anon, yes I'm familiar with theroadback and the AS protocols. I took a stab at rifampin+azithromycin but experienced no relief after 1 and a half months. Most people seem to get some relief after a short while of being on the correct abx combo which made me think I was doing the wrong thing. I'm also very leary to stay on abx for extended amounts of time. I feel like people may experience serious long term side effects that they don't understand is from carpet bombing the gut. Tooth for a tooth I suppose but at least I know that option is there if I really need it.

    I've tried no starch for 3 months and felt no benefit at all. I've taken strong herbal anti bacterials targeted towards KP and again had zero respite. Maybe I didn't go long enough with either but I've read 100's of success stories of AS'ers on a no starch diet and wondered why it never helped me. Dr. Jaminet said that getting all of our carbs from dextrose would enable us to heal and be more curative than strictly avoiding starch altogether.
    I will pay attention to flares derived from foods with oxalates.

    Thank you guys, I really appreciate your time and help!

    1. @GR
      I was on Doxy 200 mg on MWF since 2008 until November of this year. I did a UBiome test in December. It looked not bad, I guess. But yes, I understand the concern about long term abx dose. However we are talking low doses and intermittent. Who knows!

      I wish you good health!


    2. @G.R.

      "if you were in my shoes, what would you do?"

      I would probably use a very wide-combo-low dose-rotation approach, regardless the possible bad luck with my own genes. Because not everyone with the genetic susceptibility to AS has the disease, so it cannot be predetermined.

      Low dose and rotation makes sense as it might catch the microbial persisters and their random distribution in the course of chronic infection.

      Perhaps it would even include low dose mung bean :-) (see a paper on its anti-everything properties) a paper on its anti-everything properties

      And also it would be wise to make peace with the commensal fungi, there is a link to AS too.

      And a lot of movement and exercise if possible, to show them you are alive and strong.

  15. Could I ask those posting under "anonymous" put their name at the bottom of the message, so that we discern whether there is one or more anonymouses posting.
    Jo tB

  16. Did you notice relief right away when you started doxy, Michelle? Do you still have symptoms for the issue you were addressing? I hope it helped and thank you for your the warm wishes.

    I keep hearing good things about these

    Too low dose?

    I just finished a one and a half month high dose oregano oil approach but again didn't notice any difference.
    I wonder if I were to eat a tsp of mung bean every day, then titrate up to a tbs/1/4 cup etc. if the pain would eventually go away and end up just a being a herxeimer? Anti-microbial/fungal/inflammatory and helps rid the body of heavy metals and other toxins. Worth a try:)
    Sooo, by make peace with the commensal fungi, what you're really trying to say is that I should wage war by taking 2 months of nystatin, some lufenuron and caprylic acid?...Again;) Any ideas on rebalancing or harmonizing myself with fungi?

    Yes! I'm really getting a feel for how much exercise I can do each day without stepping backwards by overdoing it. Exercise really helps.

    My Wife and I got a kitten the other week. He's awesome! All black. Hasn't missed the litter yet!!! and has learned to sit on my window-side shoulder when I'm driving. Just a lil' side note FYI ;)

    1. @GR Solicit other opinions from the experts here, but investigate a biofilm protocol like Interfase.


    2. @G.R.

      A kitten on the shoulder while driving, lol. Once I was transporting my dog and her five puppies, all nicely secured in the car boot I believed, and suddenly, out of nowhere there was a cute, black puppy under the brake pedal. It was on the highway, at high speed - no fun :-)

      "wage war by taking 2 months of nystatin, some lufenuron and caprylic acid?"

      Are you American? :-) Let's be more clever than that (and the fungi).

      "I wonder if I were to eat a tsp of mung bean every day, then titrate up"

      Yes, as if that MIGHT be a way to try. It was interesting to see that you report no reaction to all those herbals and abx, and this at least did something (despite the immunosupressants?)

    3. @G.R.

      May I ask - have you ever tried drinking RAW potato juice?

    4. @GR

      No, I did not see immediate improvement in my joint pain. This did not alarm me because I had read up on the protocol in books plus at Roadback and I knew it could take 6-18 months to see significant improvements.

      I started on a low dose, 50 mg Doxy on MWF in 2008, then increased to 100, then 150, then 200 mg MWF by 2011.

      The first signs of improvement were feeling a bit less stiff in the mornings, and having small windows during the day of where I forgot about my joint pain.

      I knew improvements would come gradually and could be easy to miss, so I kept an eye on things that were difficult for me to do bc of the arthritis and looking for a change, even small, for the better.

      The other big thing was doing labs every 3 months at first, then every six, and now annually. I put the results in a spreadsheet and everything out of range I marked red. With time, the out of range numbers moved closer to normal, then went black/normal.

      I consider myself in remission, but I am not 100% pain free. If I took OTC NSAIDS I could be pain free. My joints ache, the aches migrate, sometimes hands, sometimes wrists, sometimes knees, but I don't get the debilitating burning pain like I had in my early days of flaring.

      Some people stay on the antibiotics for life, perhaps going down to a lower mainentnce dose. I have taken a break for now and I'm trying supplemental fermentable fiber in addition to regular consumption of fermented foods.

      I would not hesitate to go back on the Doxy if needed.

      One more thing, I decided to take a break because my doctor had suggested I add in Azithromycin at 250 mg Tu Sat to my Doxy protocol. Two months on Azithromyicn threw me for a loop.

      It depressed my appetite markedly because it upset my stomach/GI tract. I also became quite blue (low mood). It was much worse than my usual Fall Blues (even with light box use!).

      Did I really need the Azithromycin or was I just having a manageable mini-flare? I don't know.

      My mood is much improved since getting off the Azithromycin and starting to rebuild.



  17. Hi, thank you for this info - I just ordered two for one. I am guessing this q is answered somewhere maybe in past posts - but I am wondering, can these microbiota genome results be usefully compared to just microbiota population results? I was thinking about doing American Gut too. I am curious if two labs say the same thing (assuming I am sampling at the same time). Thank you!

    1. I wrote a blog about comparisons between AmGut and uBiome. They reports will always be slightly different just because they have different collection and testing methods, but they seem to get the major populations pretty close.

      I think there are two reasons to get a gut test like AmGut or uBiome: For fun, or to look for serious 'red flags.' You can't really use these tests to fine-tune your gut or diagnose imbalances. It's just a snap-shot of what's going on, which can be useful to you, especially if you are trying different things and do some 'before and after' tests.

    2. Thank you so much. I will look for that post. I will also think abt most useful way to use comparison and two-fer at uBiome - so snapshots are informative. :)

  18. Thank you, B. Yes, I took interfase plus and raw enzymes before during and after my 2 month nystatin party. I took s. bollardi, most of the lactos/bifidos, prescript assist, tons of others and a bunch of homemade kraut and kimchi. I feel very confident that any potential biofilms and candida should be "dealt with." That's what I like to tell myself anyways.

    Eek! Squished puppy or highway speed accident? It'd be tough to not have that split second hesitation. I've set up a barricade around my seat so I know where he is at all times.
    I'm surprised too about the bean reaction while on biologics. The oatmeal reaction was exactly as severe which is what led me to asking if there are any potential "trigger ingredient" similarities. I've since realized(from the HMGB1 papers that even the time cooking/(if)sprouting/(if)cooling? can have big changes on the outcome of the finished product. I was really hoping it could be something semi-simple like amylose starch or phytic acid.

    I haven't tried raw potato juice but nor am I scared to. I'll add it to the arsenal.

    Michelle, that's great that you got rid of most of your pain! I know that for even just the 5 months or so I was taking abx, it was a grind. Timing the antibx, the meals, the probx and the exercise etc was doing my head in. I can only imagine years of it but still way better than the constant flares you were having before!
    Thanks for posting your regimen and I'm really glad you're feeling better since off the azith.

  19. I tried to order the 2-for-1 kit, but it didn't accept the code.

  20. I had the same problem until I ordered 2 kits. Then the code will be applied.

  21. Tim,

    I just received my ubiome results. Are there any resources that will help me interpret the results? There is a lot of data and I'm not sure of the "low hanging fruit" to focus on.


  22. Hey, Ben - If you are a total nerd, go here and see if you can follow what this guy did (thanks, Barney!): Analyzing uBiome Samples

    I have not analyzed any uBiome samples that deeply, but I know a guy who might like to try.

    If you just want me to take a look at your sample, shoot me an email and we'll figure out the best way for me to look at the report. (don't worry, just a hobby, no money will be involved!)

  23. Thanks. I imported into Excel and will email you a copy. Surprised no niche services have popped up to help with this.

  24. Hello Ben,
    I received the Ubiome result, but I do not know, how to import the raw datas into Excel. Could you please give any advice? Many thanks!

  25. Thank you, Tim, for your blog, and for all your great information, you help so much people!
    Richard Sprague explains here, how to import the raw datas of Ubiome into Excel, and gives a help for analyzing: