Friday, June 6, 2014

AHS 2014: August 7-9th U.C.Berkeley... GET YOUR ANCESTRAL ON

Only two months away~!!

The venue has returned to my old haunting grounds, UCB campus, where I did my undergrad in Nutrition and Food Science and worked for two years in Plant Biology as a lab technician. Hope to see and meet many ancestral health fans! My family and I are re-patriating back to California from Shanghai, so it is a homecoming on many fronts.

AHS 2014: Aug 7-9th

Location: U. C. Berkeley Campus
Theme: WOODSTOCK lol

Registration is open

AHS11 Rockstar edition ~ AHS11 was the inaugural Woodstock. Nothing is like the first time but hopefully some of magic and mystery will be re-created this year with an amazing collection of events, topics, speakers, and eye-opening panels this year. I hope for lots of casual hanging out as well.

Ode to Seth Roberts ~ We will be missing and honoring our friend and AHS co-founder. His contributions to our community, his fairness and attention to science will never be forgotten.


Topics I'm Attending For Certain

Since this blog is called Animal Pharm, the opening speaker has got my undivided attention.

Zoobiquity: Species-Spanning Medicine
Speaker: Barbara Natterson-Horowitz, M.D., M.A., B.A.
Scheduled at: August 7, 2014, 10:10 am
Animals and humans get the same diseases, yet physicians and veterinarians do not often consult one another. Spontaneously-occurring diseases such as cancer, heart disease, obesity, and infection as well as psychiatric conditions including self-injury, compulsive grooming, sexual dysfunction and substance-seeking affect not only people but a broad range of animal species. An integrated, interdisciplinary approach using the latest in medical and veterinary science to understand physical and behavioral health can lead to novel insights, hypotheses, and innovative therapies. This species-spanning approach challenges academic institutions, clinical practitioners, pharmaceutical companies, and biotech firms to recognize comparative medicine as a translational science, bringing knowledge from the veterinary medicine to the human hospital bedside.

My talk is @11:50

Re-Savaging the Gut: Solution to the Identity Crisis of the Ancestral Gut
Scheduled at: August 7, 2014, 11:50 am
The gut microbiota has undergone radical changes. Human gut anatomy are unaltered but the microbial ecosystems have degraded. Health may mirror these changes and how we acquire our microbiota including the ways we procure our food -- shifting at the neolithic from tedious hand foraging to village crops to (now) massive, post-industrial farming operations and livestock production. Our distance from the dirt is immeasurable. New technology allows characterization of the ancestral gut. Comparatively, species in ancestral and non-industrialized guts are robust in diversity and less fragile in balance. Ways to resolve this 'gut identity' crisis involve re-wilding and revisiting the ancestral, soil-connected gut.

My brilliant co-speaker from AHS11. Ancestral genetic polymorphisms determine many things. My family and I did 23andme (fyi, they're still open and analyzing ancestry). We don't have the main MTHFR SNP but we own one of the COMT variants that affect carbon methylation; it explains why the ancestral diet suits us and our DNA very well. We have also 2 of the main FUT2 variants for non-secretors in the Asian population which might explain a few of our gut vulnerabilities to MTHFR, COMT and the gut toxins which are related to methylation. FUT2 secretion is related to the capacity the mucosa membranes to secrete fucose on the surface, which feeds the grazing beneficial gut symbionts like a grassy lawn. The absence of fucose affects both pathogen adherence (non-secretion confers protection against norovirus, HIV and campylobacter infections) and susceptibilities to gut conditions (T1D, celiac, ulcerative colitis, Crohn's, autoimmunity, etc). Lack of beneficial gut flora when fiber/fuel is missing or due to antibiotics are strong factors affecting gut health depending on individuality. Check out Tim's solutions.

It's Your Parents Fault! Methylation: How 1 Carbon Affects Your Brain, Your DNA and Everything in Between
Speaker: Tim Gerstmar, N.D.
Scheduled at: August 9, 2014, 3:35 pm
Why is it that some people don't get better in spite of a good diet and lifestyle? One recently identified issue is defects in methylation, the epigenetic process by which the body turns on and off almost every process in the body. While normally methylation works seamlessly and without any need for conscious control, mutations in the methylation genes can 'gum up the works' and lead to chronic health issues. Our ability to identify genes has recently allowed us to peer inside this process, identify dysfunctional methylation genes, and provide help for suffering people.

Researcher and professor, Blaisdell bridges technical brain science and research for advocating the role of play. Only the smartest animals evolved to 'play'. My playground is this blog, lol. Often I try tell my kids don't fear screwing up because it's an awesome way to explore, learn and play.

Functional Frivolity: Human Brain Evolution and Play as an Adaptation for Childhood Learning and Education
Speaker: Aaron Blaisdell, Ph.D.
Scheduled at: August 7, 2014, 11:00 am
Despite appearing frivolous, play is a special adaptation for normal human brain development. I review human brain evolution, and describe how play is an adaptation to teach children how to be a successful hunter gatherer. The modern educational system, by contrast, arose during industrial period and is maladapted for brain and cognitive development. The result is an epidemic of developmental and mood disorders. Recent movements in developmental and educational psychology advocate a return to the natural conditions that foster development of a child into an intelligent, creative, and happy individual.

Stanton is one of my favorite mountain men and authors (The Gnoll Credo). “We are born and we die.
No one cares, no one remembers, and it doesn’t matter. This is why we laugh.”

How We Got Fat (and Sick): Mitochondrial Dysfunction, Leptin Dynamics, and the Ratchet Effect
Speaker: J. Stanton, B.A.
Scheduled at: August 8, 2014, 2:45 pm
The question "Why are we gaining weight?" neglects an equally important question: "Why can't we lose the weight we gain?" The multiplicity of competing hypotheses, and the overwhelming failure rate of current interventions, suggests that current top-down paradigms, in which the brain controls fat mass, are incorrect. Based on current peer-reviewed research, a new, bottom-up paradigm is proposed, in which the energy requirements of individual cells both cause and predict fat gain, metabolic dysfunction, and the failure of fat loss. It will be shown that this bottom-up paradigm has both explanatory and predictive power lacking in current top-down models.

Keith and his gorgeous wife live and breathe health and ancestral fitness. He's the modern LaLanne minus the juicer.

From Teflon to Tang - Proposed Effective Training Methods for In-Mission Astronauts, with Take-Aways for the Earthbound Mortal
Speaker: Keith Norris, B.A.
Scheduled at: August 8, 2014, 11:00 am
Contrary to popular belief, neither Tang nor Teflon were created for or by NASA. Rather, these technologies existed previously, and were co opted by space agency to satisfy mission-specific needs. The success of Tang and Teflon's association with the space program then propelled their representative "brands" in the public's consciousness. In much the same way, the technology and know-how now exists to prevent one of the most limiting obstacles to prolonged spaceflight -- muscle-wasting and bone deterioration (sarcopenia and osteoporosis). What can be done to curtail in-flight muscle-wasting and bone loss, and how might this knowledge transform training protocols on earth?

Unfortunately HPA deficits are widespread for both men and women. Good news is that it's all fixable. Grrrrrrls, this is very important. Multitasking and being wanna-be-perfect-Martha's are just a few parts of the problem. Truly it's a cortisol conundrum. And VLC and IF just make it worse. Thank you Stacy for highlighting this at AHS. If you want long telomeres, keep the adrenals and HPA strong and resilient. Adrenals are the vital foundation of health, even bigger than the gut.

Ancestral Health for Women in the Modern World: the HPA Axis Meets the HPT and the HPG Axes
Speaker: Stacy Toth, B.A.
Scheduled at: August 8, 2014, 11:25 am
The evolutionary biology perspective has proven to be an invaluable tool in creating dietary guidelines for the optimal human diet. However, we are learning that there may be stark differences between optimal nutrition for women versus men. In particular, the female body responds differently to changes in macronutrient ratio as well as meal timing due to links between the hypothalamic-pituitary-adrenal axis and both the hypothalamic-pituitary-gonadal and the hypothalamic-pituitary-thyroid axes, in part due to the combined roles of leptin and cortisol. Women may experience adverse health effects, including hypothyroidism and hypothalamic amenorrhea, in response to low carbohydrate diets and intermittent fasting.

I can't wait to hear about why breastmilk is alive (!!probiotics!!) and secures a mammal's future.

The First Paleo Food: It's Breastmilk and It's Alive!
Speaker: Philip Goscienski, M.D., F.A.A.P.
Scheduled at:
August 9, 2014, 2:40 pm
Before the Agricultural Revolution a human's first culinary experience consisted of breastmilk. A biological system that evolved from a modification of sweat glands took more than five million years to become an extremely complex form of sustenance for newborn mammals. The most obvious benefit of breastfeeding is that it provides a complete nutritional system that will sustain an individual until it can forage for food. That is only part of the story. Breastfeeding has a major influence on immunity, brain development, future chronic diseases and the health of the breastfeeding mother.

I didn't know myopia was reversible and am eager to learn some tricks and science. Obviously paleo is not enuf, both my children have this.

Myopia: A Modern Yet Reversible Disease
Speaker: Todd Becker, M.S.
Scheduled at: August 9, 2014, 10:30 am
Myopia, or near-sightedness, is generally assumed to be an irreversible, genetically determined condition that can only be ameliorated with corrective lenses or surgery. Its prevalence is 30-40% in the U.S. and Europe, and more than 50% in some Asian countries, but it is rare in Africa and in pre-industrial cultures. The incidence of myopia correlates with IQ, school achievement, and industrialization, suggesting that an environmental factor is at work—namely, near-work. This talk will review the biology and epidemiology of myopia and present experimental evidence that myopia can be reversed naturally by specific focusing techniques and practices.

The Naughty Nutritionist, I love this lady~!!

Bone Broth and Health: A Look at the Science
Speaker: Kaayla Daniel, Ph.D., CCN
Scheduled at: August 9, 2014, 1:50 pm
A South American proverb claims "Good broth will resurrect the dead." While that's clearly an exaggeration, chicken soup has enjoyed a reputation as "Jewish penicillin" and bone broths are served to convalescents all over the world. In this presentation, Dr. Daniel will review the science that supports consuming bone broth for healthy bones, joints, skin, digestion, immunity and emotional stability. She will discuss 19th and early 20th century studies on gelatin, as well as recent investigations into the "conditionally essential" amino acids proline, glycine and glutamine and "the essential sugars" N-Acetylglucosamine and N-Acetylgalactosamine. Finally, she will report on Dr. John F. Prudden's clinical trials healing osteoarthritis, rheumatoid arthritis, Crohn's, and even cancer with cartilage. In short, much science supports the ancestral wisdom of consuming bone broth.

Telomeres are amazing. I hope he bridges the latest info on the gut microbiota's influence on telomere's and longevity. The Three Genetics (Nuclear DNA, Mitochondrial DNA, and Gut Microbiome) of Longevity in Humans Considered as Metaorganisms (hat tip, Gemma).

Approaching Immortality - Maintaining Youthful Physiology as We Age
Speaker: Daniel Stickler, M.D.
Scheduled at: August 9, 2014, 11:50 am
Aging is a disease that kills over 100,000 people each day. We age because;1.) We gradually build up byproducts of metabolism in our cells that will outpace our ability to get rid of them,
2.) We have a biologic hourglass called telomeres, and3.) We accumulate toxic and damaging waste products in our extracellular compartments.
We can alter these responses through many lifestyle mechanisms; nutrition, exercise, stress, and environmental exposures and if we stave off frailty long enough, we may be alive long enough to take advantage of major life extension technology.

Wednesday, June 4, 2014

Cooked/Crystallized RS3 Trumps Raw RS2: They are Vastly Different for Our Guts

Update ~ RS2 and RS3 are Not Exactly the Same Thing

(Hat tip: M. McEwen) Feeding raw potato (RS2) in this ancestral diet study (human v. Theropithecus gelada) appeared to overfeed and increase the RS2-chomping gut populations—Bacteroides and E. rectale—in the human simulated gut. Populations that do not eat RS2 at all or proficiently—lactobacilli and bifidobacteria—were decreased with raw potato. These sub-colonies prefer dining on oligosaccharides (beans, inulin, endive, banana), RS3 and other fiber.

However, with simulated gelada baboon gut, minimal changes were observed and this is consistent with animals without salivary amylase. Only Old World primates known as ceropithecines have evolved AMY1 (salivary alpha-amylase) to consume starches from fruit seeds that they carry in their cheek pouches.

RS2 Alone Burns FAST&FURIOUSLY in Proximal Colon; But, No Change in Stool pH
RS2 is butyrogenic, (mildly) bifidogenic and burns with smoking hawwt intensity at the caecum. However, to flood the entire colon with health promoting butyrate, other plant fibers (including RS3) are needed to add bulk and carry the beneficial granules distally toward the rectum. In human RS2 alone trials, stool pH failed to improve compared with controls indicating that little fermentation occurred toward the end of the colon (here, here, here). One experiment was 4 weeks and low fiber. These experimental diets used RS2 alone + NSP ~10 g/day, similar to that typically observed in low fiber S.A.D., Paleo, VLC or Atkins induction diets (e.g. 1 fruit + 100 g/day vegetable + little legumes or whole grains). Conventional fiber is also known as NSP, non-starch polysaccharide.

Two cups of romaine lettuce is ~ 2 g NSP fiber; one 7.5 inch carrot, 2.3 g.

High stool pH indicates a lack of both colon fermentation and butyrate flooding the colon. More and more studies are showing that stool pH can be a reliable marker for colorectal cancer (Walker et al 1986; Newmark, Lupton 1990).

Granular RS2 particles are covered with a brilliant number of constellations for bacterial amylases to adhere and attack. On the other hand, crystalline RS3 matrices are gradually, slowly degraded with quite a lot of endearing and sustained fermentation to the distal colon, unlike granular RS2 starch (hat tip: Gemma).

“The starch granule size seemingly presents
a very favourable target for attack by
amylase with many potential sites for binding of the
enzyme. In spite of this apparent binding advantage, the
complete breakdown of starch within an intact granule is a
fairly slow process. Crystalline areas tend to be unfavourable
for enzyme attack and, in addition, the granules may
contain small but variable amounts of proteins and lipids
that can also hinder starch–amylase interaction. Most of
the starch consumed by humans will have been cooked
and/or subjected to various processes during food production
that disrupts the granules to a greater or lesser
extent, but raw starch is consumed in many animal feeds.
Processing that disrupts general granule integrity and
reduces the degree of crystallinity, increases the susceptibility
to amylase.”

We like RS a lot. It’s an unconventional fiber, and synergistic with other gut fuel. Together, they are bionic nourishment that our intestinal cohabitants are intimately familiar with for tens of millenia, if not hundreds.

While technically correct that raw potato starch is a valid form of RS2, using it as a sole source of RS for your gut microbes is probably not the best plan of action.  Looking back at studies that used just RS2, we see that RS2 is somewhat unique in that in ‘burns fiery hot’ once it exits the small intestines.  This means that the RS2 granules are converted to short chain fatty acids SCFA, mostly butyrate, in the cecum. SCFA and butyrate are mildly acidic and lower pH. In many ways RS2 ‘behaves’ physiologically and biologically like soluble fiber. Like pectin or gums, it does not bulk stools significantly compared with non-soluble fibers or retrograded RS3.

RS3 Burns Perfectly Prolonged All the Way to the Distal End of the Colon
Cooked-cooled, retrograded RS3 starch is a insoluble, large matrix of crystalline structures, and on the other hand, ‘burns slowly.’ It is insoluble and behaves like insoluble fiber and architecture to soft stools and providing bulk by increasing water holding capacity. I believe it provides a solid scaffolding for microbial ecosystems to colonize and flourish.

Ever notice how hardly anyone complains of flatulence when eating RS3 rich foods such as cooked and cooled potatoes and rice?  This is probably due to the fact that it is slowly fermented and the gasses produced are dealt with by gas-degrading microbes in a timely fashion. We had originally taken the lack of gas to indicate lack of performance, but this is wholly unfounded. The older ileostomy studies prove conclusively that the RS3, formed from cooked and cooled starches, arrives intact in the large intestine and modern microbe studies using 16s rRNA sampling prove that RS3 has profound effects on the gut microbiota leading to all of the positive changes we desire.

Epidemiological studies on consumption of RS3 rich foods like beans and lentils show protection against diabetes, obesity, prostate disease as well as colon cancer. In moderate fiber human studies (here, here), the combination of RS3, RS2, RS1 (total 38 g/day) + NSP 20 g/day (including raw green banana flour) was associated with significant improvements of every marker of gut health, including the largest drop in stool pH recorded in human studies. The lower and improved pH mark how microbiota fermentation and butyrate very likely and consistently flooded the entire length of the colon to the distal end. Also, dilution of ammonia and lower concentrations of fecal carcinogens (p-cresol, phenols) were noted. The authors concluded:

“In a typical Western diet (usually low in NSPs and starch) most
fermentation occurs in the proximal colon with limited effect
on the distal colonic environment (14)...

Fecal pH can be lowered by a variety of changes in the diet
(46, 47). Acid fecal pH has been linked with protection
against bowel cancer (48, 49). Epidemiological evidence
suggests that a drop in pH by 0.5 units is associated with
reduced risk (48, 49). During this study we were able to
reduce fecal pH by 0.6 units. To our knowledge, this is one
of the largest diet-induced changes in human fecal pH
reported. Studies using lactulose (SO) and oat bran have
recorded decreases of 0.4 units. The results obtained here
are most likely due to the higher amounts of [mixed] RS used
because there was a significant inverse correlation between
RS intake and pH, and between fecal starch and pH.
In humans the majority of colon tumors occur in the distal
colon (51). Thus, the measurement of fermentation-dependent
events in feces may reflect the environment in the distal
colon (52), and provide useful predictors of the antineoplastic
properties of certain diets.”

The mix of cooked RS3 and fiber produced outcomes that vastly contrast with the human study where RS2 did not dilute ammonia, but retrograded RS3 did.

Therefore, we feel it prudent to not seek total intake of prebiotic, fermentable fiber from isolated RS2 sources.  A diet supplying very little fiber, regardless of total carb count, and supplemented only with a refined RS2 (such as Bob’s Red Mill potato starch or Hi-Maize corn starch) will not be nearly as healthful as it could be if the RS2 was augmented with an array of other fibers. 

Both insoluble fiber and RS3 are enriched in low GI starchy foods -- lentils, peas, legumes, whole GF grains. Other roots/vegs and tubers are also abundant in either RS3 (sago, cassava, taro, heirloom potatoes) or insoluble fuel (turnips, okra).

RS and Total Dietary Fiber
From the ancestral evidence and modern studies, just getting the USDA recommended 25g/day of fiber is not enough.  More likely 40-80g/day would be optimal.  “Fiber” is such a fickle word...the fiber listed on nutrition labels is considered Total Dietary Fiber which includes every type of fiber that resists digestion.  Googling for the information you can get ‘conventional fiber’ charts.

From experience, 20-30g of ‘USDA-approved’ fiber is not that hard to achieve, nor is 20-40g of RS from real foods. For example, these 3 meals provide a nice blend of RS and fiber:
  • ½ cup soaked buckwheat porridge, ham, 1 Tbs raw potato starch BRM or green banana flour (WeDo's or Mt. Uncle's)
  • 1 cup cooked broccoli, 1 cup of pre-cooked lentils, ¼ cup kraut, ½ cup walnuts
  • chicken kale salad with raw carrots and 1/2 cup wild rice, five (small) roasted red potatoes

If you are concerned about the effect on blood glucoses (BG) and the glycemic load on the above foods, be assured that all the above have low GIs (glycemic indices) of ~20-50. Each meal contains 1 to 2 servings of carbs (15 net carbs) and need to be adjusted and personalized based on individual insulin sensitivity, exercise, diet, relaxation, stress, sleep, hormone status and health goals. PHD is 150 g/day high GI ‘white’ carbs, in other words, ~10 servings carbs.

Fermenting (soaking) lentils and legumes completely changes the structure of the beans and unlocks many nutrients, cooking then enriches insoluble fiber in addition to creating more resistant starch—besides making them edible. Cooling them crystallizes further resistant starch. Expanding on raw and cooked tubers and root vegetables, consuming a diverse and variety of plant fiber (green banana/plantains, lentils, legumes, gluten-free grains, nuts) secures phytochemicals which are anti-aging and cancer-protective antioxidants.

3 Posts Written By: Tim Steele, Grace Liu

NSP = non-starch polysaccharide (conventional fiber)
RS = resistant starch
RS2 = raw RS
RS3 = cooked/crystallized/cooled RS (superfood = fuel for superhumans + super gut flora)

See prior Animal pharm:

Feeding the Microbiota: Non-Starch Polysaccharides (NSP), Resistant Starch (RS) and Mucous

Sunday, June 1, 2014

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: 
  • 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.

  Clostridiaceae --  massively feeds butyrate/SCFA to colonocytes and immune cells
  Eubacteriaceae -- a big RS eater
  Ruminococcaceae -- contains the keystone RS degrader

(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.