Gut Biome Book Update: Intestinal Fortitude

Intestinal Fortitude is the working title. Credit: Mark Sisson for the idea. I like it.

I feel compelled to give an update about the progress of the book originally launched by Tim “Tatertot” Steele and I last December, incorporating Grace Liu as Science Editor in February. The reason is simply that I keep getting emails and comments various places, asking for updates—and everyone is still under the impression that we’re all three still collaborating on it. Nope, not since mid-June.

Well, just like rock bands had and have conflicts, so did we. I won’t get into details. Irreconcilable differences. All anyone will ever know from me, besides close confidants I trust. I believe Tim and Grace will handle it similarly. There’s always fault to go around, chez moi too.

Such is life. Fortunately, everyone gets to do what they want and that’s what the three of us have done.

Basically, Grace’s contributions have been redacted and Tim and I have come to an agreement regarding his massive contributions. I’m working solo, now; vigorously, of late.

When the book is done and published, the acknowledgements will credit Grace for much inspiration and Tim: for writing 90% of the rough draft during the cold, dark Alaska winter…while I was busy putting together post after post in general promotion—now over 100 posts—on resistant starch, incorporating many more aspects of the gut biome in general. There’s only a single chapter in the book on RS, specifically.

It stands at about 350-400 pages.

Yesterday, as I was working on the editing and wordcrafting of some of Tim’s draft, I put up some updates on Facebook. So, here’s a taste:

  1. On the gut biome and Autism
  2. On the gut biome and Alzheimer’s
  3. On the gut biome and Autoimmunity in general
  4. On the gut biome and Rheumatoid Arthritis and Ankylosing Spondylitis

About half of the book is manuscript ready at this point. Another month or two, and it’ll be done. No idea when actual publishing will happen, but I guarantee it will happen.

Grace and Tim are engaged separately in their own endeavors and I wish them both the best of success. Grace blogs at AnimalPharm (link removed) and Tim has dipped his toe into blogging waters at VegetablePharm—and he’s also engaged in a graduate program in biological sciences he’ll perhaps blog about. Additionally, Grace did a presentation at the Ancestral Health Symposium 2014 and her presentation is now up and I highly recommend it.

Onward. As always, every time, no exceptions ever.


  1. tatertot on August 18, 2014 at 14:47

    I’m sure it will turn out great…I know how it ends: The gut bugs did it!

    Good luck, it was fun,

  2. Kyle on August 18, 2014 at 17:52


    Here’s one I thought you might miss: primary sclerosing cholangitis. Since you included cirrhosis here,, I thought you would have an interest. It’s been discussed quite a bit on the Crohns forums.

    Please see for a discussion.

    Note that the biofilm growth of the small intestine doesn’t stop there. It will grow up the bile ducts and may possibly affect the whole bile duct system including into the pancreas, gall bladder and liver. I have physical proof of the bile duct involvement.

    Dr. BG and Dr. Ayers seem to think that biofilm development in the SI is normal, I don’t.

    Hope you can use this.


  3. Gassman on August 19, 2014 at 05:16

    I’m looking forward to purchasing and reading the book as soon as it is available. Good luck. In the meantime, I’d lke some advice. I’m having the standard 50 year old’s routine colonoscopy on Friday and will start the cleanout process tomorrow, bacially washing out the gut biome I’ve been cultivating since I’ve been followint is blog.

    I’ve got potato and tapioca starch and banana flour, as well as FOS and probiotics. I have primal defense ultra, AOR3, and prescript assist. I plan on doing smoothies and trying to stay with a real food fresh diet afterwords.

    I have thoughts that this is really unnecessary and when its over, I can tell my wife “see, my colon is in great shape!” But I am looking forward to the cleanout to see if it clears my head of some occasional brain fog.

    I thought of making my own fecal transplant, but dismissed it as too risky. I’m pretty sure my appendix stores microbes and will assist in repopulation. I suppose I should seek out fermented foods. What other tweeks might I incorporate?

    • Richard Nikoley on August 19, 2014 at 09:02

      I don’t know what to tell you, Gassman. I’f be very loath to get a colonoscopy unless a stool sample turned up something to be highly concerned about.

      But, otherwise, I’d probably do what you’ve been doing. And, check out what Karen Pendergrass did after her DIY FT. Perhaps something along those lines. Massive, various fibers from fruit, veggies, starchy veggies, along with the probiotics and supplemental RS and maybe a few of the others that have been mentioned.

  4. McSack on August 19, 2014 at 05:48

    Despite the schism on the book, I hope that it was amicable enough that we’ll continue to see Tim and Grace commenting on the blog. There seems to be good energy between all of you and I would be disappointed to see that interaction missing here.

    • Gemma on August 19, 2014 at 06:38


      From the AUTOIMMUNE DISEASES chapter, as linked above:

      “Here’s a partial list of autoimmune conditions that have been linked to disruptions in gut microbes.”

      …a very, very long list follows…

      I hope you do work hard on the editing and get it out soon, as there are many people that might benefit reading the book, even though these conditions are not addressed in detail.

  5. JakeS on August 19, 2014 at 09:06

    Looking forward to the book.

    Just a question on the autism snippet: how do we get bacteroides fragilis into our gut? I can’t find it in probiotic supplements and I found a site in the UK, drmyhill, that says: “There is no probiotic which contains bacteroides simply because bacteroides cannot exist outside the human gut – oxygen kills it quickly. We just have to feed the gut with the right food (prebiotics) found in pulses, nuts, seeds and vegetables.”
    So how did they give it to the mice in the Hsiao study?

    • Richard Nikoley on August 20, 2014 at 10:15


      I assume they get it there using whatever techniques used to do a fecal transplant and avoid contact with oxygen (why there exists a lot of skepticism in terms of DIY transplants.

      However, near as I can tell, Bacteroides fragilis is a gram-negative anaerobe that is a double-edged sword. Kept in check at 1-2% of the gut biome, it’s actually beneficial because it competes with others for food. So, I don’t think you’d want to be taking it as a probiotic. Also, it’s not a spore former so no way to get it under normal circumstances.

      “Although Bacteroides fragilis makes up from 1-2% of the normal flora in our body [4], they are responsible for 80% of anaerobic infections [16]. As an anaerobic pathogen, Bacteroides fragilis also competes with other organisms inside the colon/intestinal lumen for nutrients and food [16]. This can be of great benefit to our body because when organisms compete, it decreases the availability of nutrients for other dangerous pathogens to grow, harming our body [16].”

    • JakeS on August 21, 2014 at 02:08

      That’s very interesting. Well, it seems that the beneficial effects of B Fragilis derive mostly from a sugar Polysaccharide A that is expressed on it’s outside:
      “… once B. fragilis expressing the polysaccharide A (PSA) is added to the gut, dendritic cells take up and present the PSA molecule on their surface, activating CD4 T cells and regulatory T cells(Tregs). The Tregs release IL-10 which suppresses the inflammatory action of IL-17, in effect alleviating IBD in mice. ”
      So, maybe we don’t need to take any risks with the microbe itself and can just take PSA (if it ever becomes available as a supplement)?

    • Saraswati on August 21, 2014 at 04:07

      What about the Russian Rhamnosus lysate. Could it work because of PSA?

    • JakeS on August 21, 2014 at 13:34

      I’d never heard of the Russian rhamnosus lysate – thanks for bringing it to my attention.
      A very quick scan of a few online articles seems to indicate that rhamnosus lysate enhances TH1 cytokine production, as does B fragilis. But I can’t find any references to rhamnosus lysate and PSA. That doesn’t mean it’s not involved, though.

    • JakeS on August 25, 2014 at 04:00

      Here’s B. fragilis again, this time increasing exercise endurance in mice (thanks to Marius for the link):
      “What they found was an increased time to exhaustion for the previously germ-free (GF) mice after they’d been colonized with B. fragilis (BF). Similar results were observed for the specific pathogen-free and Bacteroides fragilis gnotobiotic mice, who were also more enduring than the obesity resistant (Bäckhed. 2007) germ-free mice.”

  6. anderson on August 20, 2014 at 02:39

    I recommend you to take a look at Artour Rakhimov’s book Perfect Digestion (available at least on his site, on Smashwords, and on Barnes&Noble). It’s not only about gut health, but I’m sure you could pick up some great ideas for your book.

  7. Ian on August 20, 2014 at 16:47

    Thought your readers would find this interesting.

    A quick talk about how parasites can interface with their hosts and control their behaviour.

Leave a Comment

You must be logged in to post a comment.