The New Astronomy of the Human Gut: Mapping the signature constellations of our microbiome


Constellations: inside & outside~

The Autoimmune Protocol is founded on evidence that gut health is the key to reversing systemic inflammation and autoimmune symptoms.

According to recent research, it turns out that particular microbiome ‘signatures’ in the human gut can be linked to specific autoimmune conditions.

Stick with me: this stuff is important. And medically, it’s paradigm-altering.

What follows are selected quotes from a paper that was published in the January 2015 issue of Arthitis & Rheumatology, called Decreased Bacterial Diversity Characterizes the Altered Gut Microbiota in Patients with Psoriatic Arthritis, Resembling Dysbiosis in Inflammatory Bowel Disease by Dr Jose Scher and 13 other researchers.

This study adds additional scientific research to the mounting anecdotal evidence that Autoimmune Protocol pioneers have been amassing, regarding the connection between gut health and autoimmune. It begins to explore the unique constellations of intestinal bacteria that are associated with different forms of autoimmune disease.

This particular paper focuses on Psoriatic Arthritis (PsA) and Psoriasis, two of the interrelated autoimmune conditions that Matthew lives with.

In our ongoing quest to hack Matthew’s health, we constantly seek new information to inform, confirm or disconfirm our observations, hunches & hypotheses. This paper confirms everything we’ve learned through our biohacking to date. It has raised some new research questions for us & could potentially revolutionize standard medical practice for treating autoimmune.

The Findings

In summary:

  • People with Psoriatic Arthritis (PsA) have less diversity in the population of organisms in their gut than healthy people, and they lack particular types of of bacteria:  specifically, Akkermansia and Ruminococcus.
  • People with psoriasis also have reduced diversity in their intestinal microbiome, and the reduction follows a pattern, with maximum variety in healthy people, reduced flora in people with psoriasis alone, and even further reduced diversity in people who, like Matthew, have psoriasis and Psoriatic Arthritis.

In the words of Dr Scher et al:

“In this study…we have shown, for the first time, that patients with PsA and patients with psoriasis of the skin have decreased diversity in their gut microbiota, mainly due to the lower relative abundance of several taxa.”

Internal constellations~

Internal constellations~

In addition to less diverse intestinal flora, researchers have identified a “common gut microbiota signature in patients with psoriasis and patients with PsA.”

“Our studies constitute a novel and comprehensive approach to investigate the symbiotic relationship between gut microbiota and PsA. We have identified several organisms that are virtually absent from PsA patients (i.e., Akkermansia and Ruminococcus).”

“The gut microbiota profile in patients with psoriasis appears to be intermediate, between that of PsA patients and that of healthy subjects, suggesting that there exists a possible continuum in disappearing intestinal taxa through the natural history of the disease.”

A “key question left unanswered by our study is whether patients with current psoriasis of the skin alone will lose certain potentially protective taxa, such as Akkermansia and Ruminococcus, at the time of, or prior to, transition into PsA. This is crucial because, although it is established that 25-30% of patients with psoriasis will develop arthritis over time, there is currently no possible way to predict progression.”

Similar research has previously focused on the constellations of gut flora in people with rheumatoid arthritis. A comparable lack of diversity was found, but with a different signature. “We have previously utilized this same approach to examine the intestinal microbiome in treatment-naive patients with new-onset rheumatoid arthritis (RA) and found that expansion of Prevotella copri was associated with enhanced susceptibility  to as yet untreated human RA. This is contrast with our present findings in PsA patients and suggests that there is a distinctive pattern associated with each condition.”

Potential Treatment & Further Study

“These investigations may ultimately lead to novel diagnostic tests and interventions, in the form of probiotics, prebiotics, specific microbiome-derived metabolites or molecular targets, and even bacterial transplant techniques.”

“The role of the gut microbiome in the continuum of psoriasis-PsA parthenogenesis and the associated immune response merits further study.”

We agree~!

What if replacing the missing Akkermansia and Ruminococcus could assist in reversing Psoriatic Arthritis? This would likely not be as simple as repopulating the gut with these bacteria. Favorable gut conditions would probably need to be cultivated to allow these extinct organisms to thrive. And re-population might need to be done through ‘bacterial transplant techniques’ including, perhaps, fecal transplants.

We think these findings could revolutionize medical treatment for autoimmune arthritis (and autoimmune conditions generally).

Find the full Decreased Bacterial Diversity Characterizes the Altered Gut Microbiota in Patients with Psoriatic Arthritis paper here.


27 thoughts on “The New Astronomy of the Human Gut: Mapping the signature constellations of our microbiome

  1. Excellent review. Do have a suggestion regarding repopulating these flora using diet? Which foods contain the target microflora? Thank you.

    • That’s what we’re trying to figure out next. Diet can improve overall gut health but I don’t know if it can assist in repopulating specific flora. I’m guessing a combined approach: improving gut health through diet to provide a flora-friendly environment & then medical intervention might be required to repopulate the required flora.

      • As listed in the article, it might not be as simple as taking probiotics to repopulate the gut with missing flora. But I was unable to find any products containing either Akkermansia or Ruminococcus. Anyone else have better luck? Thank you.

      • Thank you for your reply, Petra. And, yes, I understand that fecal implant might be ultimately recommended if this avenue of study/treatment is pursued. I was just looking for a pro/prebiotic that might contain the missing flora. Thought it might make an interesting personal experiment to add back the (possibly) missing flora interim to more study findings.

  2. Excellent read! Thank you for sharing the information in this study. I have a minor case of psoriasis, but worry that it could turn into psoriatic arthritis. Working to heal my gut!

  3. As the article suggests, repopulating one’s gut with the missing flora might not be as simple as taking a probiotic. But I was unable to find any that contain Akkermansia or Ruminococcus. Anyone else have better luck? Thank you.

  4. Great post Petra. I’m forwarding to my psoriasis-suffering Dad…

    There is no doubt in my mind that the state of my gut health (and micro biome) has been a huge factor in my autoimmune issues. Along with overhauling my diet and lifestyle, finding a forward-thinking GP who worked with me to create a gut-healing protocol was a big step in improving my gut health. And, I’m not there yet!

    I wish Matthew all the best in his gut-healing endeavours.

  5. This is INCREDIBLE information, thank you for sharing it with us. I couldn’t help but let out an audible ugh when I read that FMT might be necessary to repopulate. While I’m not naive to think that simply fine tuning my probiotics would be “the fix”, there was that part of me that was hoping… 😉

  6. Interesting great article! Recent diagnostic stool testing revealed low gut bacterial diversity and “no growth” noted for lactobacillus or bifidobacterium. Now taking pre- and probiotics. Been treated for RA for 20 years and currently on strict AIP. Hopefully, gut healing will continue to improve. Thanks for your research – I really enjoy it..

  7. I signed up for Primal90 and they recommended the “MegaSpore Biotic” which is a probiotic. Now, I’ve signed up for many online summits but have become overwhelmed by all the information and because of that, don’t know where to start. My Hashi’s doesn’t help (if you know what I mean). Primal90 seemed different so I went ahead and joined. One of their presentations discussed MegaSpore Biotic. I’ve tried MANY probiotics and really never felt a difference, but took them because I knew I needed them for my gut, and my Hashi’s. Tried 50 billion, 80 billion, thinking the more the better. Bought from the store in the refrigerated case because I thought they had to be refrigerated. WRONG! Well, please google this product. It’s UNBELIEVABLE. I actually FEEL a difference in my gut, in a good way. Michael Roesslein wrote an article about this too, on his website titled “The Evolution of Probiotics” (click on “Blog” and you’ll see the article there). I recommend everyone with autoimmune issues check out the article. I think these probiotics are a game changer for my health. It seems impossible that a product can make such a difference, but this one seems to be doing that for me. Because I signed up for the Primal90 access, I can order through them. Honestly, I don’t get any benefit from telling you this. Just wanted to share my experience.

  8. In regards to my last comment, I just saw a comment by Michael Roesslein, in response to someone’s question, under his article “The Evolution of Probiotics”. This is what he said: “It doesn’t focus on re-seeding or re-colonizing. It focuses on making the GI environment friendly for the proliferation of beneficial bacteria, hostile towards pathogenic bacteria, and lowers inflammation/balances the immune system, among other functions. It’s a completely different paradigm/approach.”

    • I also noticed Michael provides his email address regarding ordering this product so you may be able to order without joining Primal90. (If you do join they give a 20% discount on it). Check the comments under the article for his email address if you are interested in talking with him about the product or ordering. He responds quickly to email from my experience.

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  10. Missing microbiome was the interesting topic on Dr. Wahls at Palef(x) that I was watching through live YouTube stream. When she mentioned eating raw starchy veggies(most of paleo peeps roast😔 their starchy veggies, beets) to get more bacteria from the veggies.And feed them with plantain flour, green banana flour,berries polyphenols etc She even talked on lemon juice before meals. That was hooked. Have you read the Elimination Diet book!? The author is a functional M.d. And he even mentions citrus fruit and eggs are the worst for arthrits and the Studies.

  11. Hi Petra,

    First of all, thank you for your blog and for being so incredible amidst such difficult challenges. I am currently reading (actually, ‘listening to’) “Brain Maker” by Dr. David Perlmutter and am completely blown away, as you describe in this post, of the role our gut microbiome plays in our level of wellness. I hope that you write a post about this ground-breaking book, I would love to hear your opinion.

    My partner and I read your blog regularly, are inspired by you, and we get teary thinking about your journey with Matthew’s health. Thank you for all that you do 🙂

  12. I can’t remember who i heard it from but FMT is not considered necessary for many people to repopulate. I’m about to start a very specific protocol devised by Chris Kresser (I’m working with one of his docs). It includes the megasporebiotic (mentioned aboue) and Prescript assist (and maybe one more probiotic. I’m guessing that probiotics take you part of the way and then when you can tolerate prebiotic and probiotic foods that diversifies the microflora more. But the beginning protocol is low FODMAP and low FP (Fermentation potential- Noel Robilllard) and has 3 statges to strave and kill my SIFO and then repopulate and feed a more diverse ecosystem of helpful microflora.

  13. Has anyone hear of the book by the functional MD Amy Myers, “The Autoimmune Solution?” She lists a whole 30 day plan to follow with meals and other supplements in addition to probiotics. I have psoriatic arthritus and am totally discouraged by the traditional treatment of immune suppresant dugs, so I am reading up on alternative treatments.

  14. Has anyone hear of the book by the functional MD Amy Myers, “The Autoimmune Solution?” Myers includes a 30 day plan to follow with meals and other supplements in addition to probiotics. I have psoriatic arthritus and am totally discouraged by the traditional treatment of immune suppresant dugs, so I am reading up on alternative treatments.

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