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Outstanding Overview of the Gut Microbiota – Gut Bacteria 101

Adam-Scheuer iHaveUC founderThere is a fascinating scientific study I think you’ll enjoy. 

WAY MORE interesting than Kate and Will’s new royal baby, the Kardashians(when are they going to be over with), President Morsi’s troubles, and all of the other news that’s out there.

The news makes you dumber, this will make you smarter, for sure!

You don’t need to be treating your UC with diet, you don’t need to be medication free, and you sure don’t need to be in remission for this to be interesting (in my opinion which I’m sure as hell hoping you’ll agree with too)

A group of doctors and scientists have put together a fantastic resource that explains some of the most important things about the insides of our colons.


If you’ve read some of my previous stories over the past several years, you’re probably sick of me going on and on about gut bacteria, doodie hole bacteria, the microbiome, mirobiota, crap colony, or whatever fancy word means the same thing to you.

But I’m guessing that you may still have some questions about gut bacteria that you would like answered.  So here goes:

5 of the world’s leading researchers put together a study titled:

“Diversity, Stability and Resilience

of the Human Gut Microbiota”




JUST A FEW of the Topics Covered:

  • Antibiotic use and the effects on our gut bacteria
  • Breastfeeding and gut bacteria
  • the incidence of IBD and allergy is greater in industrialized Western societies than in traditional agrarian cultures
  • Resilience to dietary changes
  • Individuals with a ‘degraded’ microbiota from long-term consumption of a high-fat/high-sugar Western diet may need long-term dietary changes to restore their microbiota to a healthy state.
  • fecal microbial community diversity, composition and function have also been correlated with IBD (Crohn’s disease and ulcerative colitis)
  • Resilience to antibiotic administration

Here’s a great direct quote:

“The landscape of stable states of the microbiota and its implications for resilience is an important research direction. Current evidence suggests that small perturbations, such as short-term dietary changes, may allow a return to the same state, but larger perturbations, such as antibiotic administration, may cause movement to a different state. The long-term implications for such changes for health are not yet well understood. Furthermore, perturbation of the landscape of stable equilibrium states of the gut microbiota through long-term changes, such as inflammation, diet, or repeated antibiotic administration, might make new states reachable even with smaller perturbations. Factors such as host genetics, the process of development, diet, and long-term drug administration might all contribute to differences in the landscape among individuals. Consequently, both the general landscape and the current community state may be important for determining individual responses to a given intervention.”

gut bacteria community


There are more diagrams and pictures within the study like the one above.

Enjoy the reading, there’s lots of great info to get through.


here’s the link one more time:

Side note:

If you read the study carefully, there’s a direct reference made to the exact study from the Stanford Scientist I interviewed and recorded in the original Gut Bacteria Videos.

If you’re on the newsletter you already know all about this, but pretty cool eitherr way.

13 thoughts on “Outstanding Overview of the Gut Microbiota – Gut Bacteria 101”

  1. Great link and writeup, Adam. Thanks. Some of us might also be interested in knowing about American Gut Project. You send a stool sample and they send back details about the bacteria that populate your gut. It’s not free to participate, but also not too expensive, and a pretty cool concept and program:
    Unfortunately it was open to anyone worldwide but is currently limited to US residents.

  2. Adam,
    So cool, so much info. Feels like progress and steps to finally seeing a bigger and very complex human body system with so many individual puzzle pieces. Wow and awesome.
    Thanks, Shelly

    1. Glad you enjoyed Shelly, its a pretty loaded study, but compared to most scientific ones, I think its “somewhat easy” to comprehend without getting our PhD in microbiology and immunology:) take care,


  3. Adam,

    Good read. Funny how papers written from various different countries all seem to point to the same facts, its like a stampede waiting to occur, the time is now for a solution!!

    I enjoyed the bit about rainforests when explaining how we have a shared functional core microbiome, but not a core microbiota; ‘rainforests in different parts of the world, for example, are highly simialar visually and in many functional aspects, yet are composed of different species that have independently evolved’.

    Just to add to this, just like species in forests, (they communicate verbally to understand numbers) bacteria via qaudrum sensing communicate by sending out ‘messages’ which is recieved by fellow bacteria to understand numbers, which seem to play a big part in ‘attack’ and immune response in IBD. Whilst in the USA they are developing medication to intercept the signals (still not solving the underlining problem), main line established healthcare feel the T-Cells are just not responding to Dendritic cells when they present antigen material and hence ‘there is no solution to IBD, its forever, it is an out of wack immune system’.

    In reality, IBD patients do have a disposition allowing us to be prone to a number of problems (remember no one has prefect genes though) and allowing an overgrowth of harmful bacteria (antibiotic use, diet, major imbalance microbiota through birth)and at which point (when rising in numbers via qaudrum sensing) the T-Cell response is overwhelmed and…this is my theory so forgive me if its a bit out there; if the Dendritic sample the lumen to present a antigen, is it presenting one from a particular bacteria? If so, we know there is an overwhelming gut imbalance so maybe when one antigen is presenting, the continued ‘attack’ could be caused by also another bacteria, meaning the response is not quick enough to the threat. Therefore there is not a defect T-Cell, it is just presented with one antigen when several antigen is required to be presented and equally quickly responsed to.

    A Gene disposition might be unable to efficiantly deal with an imbalance or even help in the development of it, but fundamentally a developing imbalance is what needs to be addressed. Everything seems to point to FMT and the treatment (diet, supplement…)thereafter

    Sorry for the blabbering. Good article, nice post

  4. Don

    I joined the study this morning for my wife and myself. I think this is a great project and look forward to seeing the results of the gut bacteria testing. This should be really interesting. I will post results when I have them. Thanks Adam!

  5. Michael Hurst

    Good stuff and those topics are being covered in even greater depth right now at the Human Microbiome Science Conference in Bethesda this week. which includes a live video stream of the conference from 8 am to 5 pm Eastern time.

    They covered the different kinds of bacteria for Crohn’s Disease and Ulcerative Colitis and also discussed the mouse experiments and obesity today. Fascinating stuff!

  6. Joan H

    This is great stuff! I’ve been seeing more and more about repopulation of intestinal flora and and so happy to see it’s becoming more and more main stream and the info available. Thank God for progress! There was a FB chat today live on CCFA FB site with a research MD from Virginia too – talking about pre and probiotics, FMT, and all kinds of other topics related to UC. Fantastic – thanks for posting Adam and also the link from MichaelKHurst!

  7. Great information. Thank you for sharing. Looking for FMT in Toronto. My goal is to recolonize good bacteria to proliferate in my colon forest where it has somehow been obliterated. I am currently suffering alot with severe colitis. Thank u Adam for this place to exchange info. Eternally grateful. Wishing everyone good health.

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