What are you missing? What's your gut missing? Show me the antibiotics you've been on, I'll show you your ABSENT ALLIES

(1) Prakash et al, 2011
The Gut Microbiota and Human Health etc

Here's your gut (see 3 diagrams) and a couple of factors that make you who you are:

• digestive capacity: 
• AMY1 (amylase in saliva)
• gastric pH
• pancreatic enzymes (elastase)
• gallbladder function
• bile
• your microbial allies (see above diagram): 
• mutualist aerobes (upper GIT) 
• mutualist anaerobes (lower GIT)
• colon fermentive capacity: 
• Bugs R US
• fuel for microbes (fiber, RS)
• mucus layer
• SCFA from fiber metabolism by Bugs R US
• luminal and fecal pH (5.8-6.5 'sweet spot')
• colon interior and epithelium association: 
• surface and mucus layer (Clostridium, Lactobacillus, Enterococcus)
• lumen (the rest)

(2) Sekirov et al, 2010
Gut Microbiota and Human Health

Absent Allies: Imbalance Leads to Health Havoc

Have you lost your friends?

When vital parts and precious pieces are missing, the gut has a difficult time doing what it's supposed to do -- protect you from infections and pathogens,keeping serotonin and melatonin in circulation,  recycling cholesterol, and energizing the brain and muscles. In ancient times, the average human likely had an enormous load of microbes from daily exposures compared to modern lifestyles. Think about it? No cold storage -- everything fermented and room temperature. No toilet paper. No C-sections (yes sadly both more moms and babies died). No pesticides or antibiotics which indiscriminately wipe out too many protective microbes. The modern gut is reeling from the deficit of these allies which touch and provide feedback to nearly every immunological, neurological and hormone pathway.

So let's say you a had a couple courses of the pink syrup growing up (Amoxicillin) then 1-2 courses of Cipro for sinus or upper respiratory infections as an adult. Not much but what does the resultant gut microbiota look like? The infertile mom? The constipated babysitter? The morbidly obese CEO? The lymphoma patient? The athletic Ironman with alcohol-dependent ADHD? The pale boy who shot up the high school? 

Petersen, Round, 2014
(Amoxicillin, Cipro and Vancomycin v. Alterations to Microbiota Ecosystem)
Defining dysbiosis and its influence on host immunity and disease

Amoxicillin will knock out beneficial Lactobacillus, Bifidobacteria, Enterococcus and Enterobacteria which may lead to overgrowths of opportunists and yeasts if the the microbiome fails to remain resilient, robust and able to recover. 

The Cipro may then annihilate to extinction anything else that Amox failed to exterminate: the ginormous Clostridiales group and the major player Faecalibacteria (aka F. prausnitzii). 

Decimating or disorienting F. prausnitzii isn't a great idea. It works in parallel with Bacteroides to build up the thick epithelial-guarding mucus layer. It's like stripping off your SKIN or scalping your gonads. Very very bad idea. F. prausnitzii is so big it is the largest, single species that composes a healthy gut: 3-6% of all fecal species.

For example in IBD (ulcerative colitis and Crohn's), a huge chunk of Clostridiales is absent whether the diseases were in remission or acute stages. Past antibiotics may or may not have played a role per studies. Where did the Clostridiales go? Were they ever transferred at birth or did mom lack them all secondary to antibiotics, lack of healthy soil exposures, stress, sugar or a high refined carb SAD?

Bacteroides and Clostridiales are typically 1:1 in balance roughly speaking. By thrashing the Clostridiales leaves the more opportunistic and hearty Bacteroides to override symmetrical ecosystem stability. In ulcerative colitis and Crohn's, what ends up occurring is Bacteroides breaching the mucus and directly attacking crypts, colonocytes and adhering like colonies of pathogenic vipers. They set up shop and don't leave (look at ugy pictures). Re-establishment of an encompassing mucus layer is as important as getting Clostridiales back in the hood and re-creating parity.

Both Bacteroides and most of Clostridiales love to ultra-fast ferment resistant starches. Feeding a sick ecosystem is probably not as critical as first bringing order by returning absent allies back to prominence. Butyrate improves mucus linings but only if bifidobacteria and other commensals are properly located.

Norm Robillard talks about the start of his health odyssey and GERD on this podcast: Paleo Mag Radio (Tony Federico) episode 38, Resistant Starch Take 2. GERD is a form of dysbiosis and broken balance in the gut with microbes lingering up in the small intestines where they do not belong. Norm has conducted research on Cipro.

Knocking out Clostridiales is one step away from inducing iatrogenic C. difficile colitis (unremitting diarrhea, weight loss, dysfunction, death), a condition which kills 14,000 people annually but affects millions. IMHO the vancomycin treatment is almost as bad as the disorder itself in terms of gut and overall health.

Clostridiales (Cipro slaughters):

  Caldicoprobacteraceae
  Christensenellaceae
  Clostridiaceae --  massively feeds butyrate/SCFA to colonocytes and immune cells
  Defluviitaleaceae
  Eubacteriaceae -- a big RS eater
  Graciibacteraceae 
  Heliobacteriaceae
  Lachnospiraceae
  Oscillospiraceae
  Peptococcaceae
  Peptostreptococcaceae
  Ruminococcaceae -- contains the keystone RS degrader
  Syntrophomonadaceae
 Veillonellaceae

(3) Marchesi, 2011
Human Distal Gut Microbiome

Microbiome Misinterpretations?

So you can see 3 views on the microbes in our gut. Unless you do functional medicine lab testing (GDX, Biohealth, Doctor's Data), all miss the same things: yeasts, parasites, pathogens, and helminth worms. All 3 views show slightly different commensals and mutualists based on slightly different testing methodologies and diverse healthy control subjects that they tested. Actually, I like them all because you can see the variance and diversity and this reflects our ancestry and genetic evolution. What is clear is that research has finally shifted to testing non-healthy subjects and the evidence reveals vast absences in different diseases. Essentially in nearly any disease, researchers find missing mutualists and commensals -- all the above.

Vast extinctions. Empty tropical rainforests. Barren tundras.

Now you are starting be aware of what is gone. What does one have to do to find and recover stolen gems and diamonds? One can't redo birth and squeeze down lactobacilli-coated slides or start licking porcelain bowls which harbor worms or parasites.