Sunday, May 25, 2014

Give Us This Day Our Daily Germs

Mud and Manure
Source: PDF
Rook is a Rogue

I've been reading a lot of Graham Rook lately.

He wrote the below in 1998 in a comment in Immunology Today:
Modern vaccinations, fear of germs and obsession with hygiene are depriving the immune system of the information input upon which it is dependent. This fails to maintain the correct cytokine balance and fine-tune T-cell regulation, and may lead to increased incidences of allergies and autoimmune diseases. If humans continue to deprive their immune systems of the input to which evolution has adapted it, it may be necessary to devise ways of replacing it artificially.
Like a colonoscopy of donor poop (FMT)?

Antibiotics are Really Really REALLY Messing Us Up

We already were aware for many years that breastmilk isn't sterile.

Here's a new science flash fresh off the press: babies aren't sterile (The Maternal Microbiome: Moms bombard their babies with bugs both before and after they’re born.)  And antibiotics are wrecking both breastmilk microbiomes and those of unborn children.
The lack of Lactobacillus levels in the milk that Rodríguez observed offered him an opportunity to test whether bacteria in breast milk originate in the gut. He designed a study in which women took supplements containing the missing bacteria, and found that, sure enough, the same strains of Lactobacillus showed up in their breast milk. Unexpectedly, after about three weeks on the supplements, the women reported that their mastitis had cleared up. “For the first time we said, Maybe this is important for the treatment of mastitis or painful breastfeeding,” said Rodríguez, whose team is now wrapping up subsequent trials to treat mastitis during breastfeeding with bacteria, rather than antibiotics.

Graham Rook writes about how our lack of exposures to 'Old Friends' is leaving us susceptible to disease, inflammation, major depression and a host modern maladies with no cure or truly effective medications. He supports that these microbes, helminths, and saprophytes originate from mud, manure and farm animals. The lack of the them may cause a disturbance in the gut microbiota known as dysbiosis where pathogens can overwhelm and the symbionts, commensals and mutualists are nowhere to be found. Microbial metabolites and inputs no longer 'micromanage' LOL. Diversity plummets and disease can ensue. Obtaining these enteric Old Friends from green and natural environments, pets and farm animals might be key.

Defining Dysbiosis and
Its Influence on Host Immunity and Disease
Round, Petersen, Cell Microbio May 2014
Some Old Friends (such as helminths and infections picked up at birth that established carrier states) are almost eliminated from the urban environment. This increases our dependence on Old Friends derived from our mothers, other people, animals, and theenvironment. It is suggested that the requirement for microbial input from the environment to drive immunoregulation is a major component of the beneficial effect of green space, and a neglected ecosystem service that is essential for our well-being. This insight will allow green spaces to be designed to optimize health benefits and will provide impetus from health systems for the preservation of ecosystem biodiversity. (PNAS, 2013)

Where do you get your Old Friends?
From a bottle of SBO probiotics (like me lol)?

Farm-acology by Daphne Miller, MD

I love this book. I'm reading it so slowly so I can never finish it... Dr Miller interviewed a bunch of old school and new school farmers. As a result she uses a farm-based approach to her clinic patients, encouraging gardening and working the dirt at a local CSA instead of pharmaceuticals. Apparently she is seeing wonderful results. Here's some of her dirrrrty thoughts... How dirt heals us (YES magazine).


Holly said...

Had a cat that appeared to have asthma. Finally found a vet that correctly diagnosed him (at age 9) as having PIE - pulmonary interstial something. This same vet has a long history of medical missonary work. PIE was the bodies natural response to the worms normally acquired through fleas. Treatment rx: get him infected with fleas (the one yr he didn't have breathing problems - he had worms and I stupidly wormed him!)

Had an interesting conversation on how the parasites that we so fear can and do provide natural benefit to all of us. And this fear and subsequent treatments are resulting in increased autoimmunity.

Same doc also told me a funny story of a famous french clinic in the 60's I believe, that treated obese people with tape worms. No one discovered this until a patient did not follow instructions and take the "second pill" as instructed.

aerobic1 said...

There is no question that we live in a too clean of a world. Ultra-pasteurized and irradiated foods; antiseptic soaps, toothpastes and mouthwashes, indiscriminant use of antibiotics, all aimed at killing off "harmful bacteria" and pathogens which in most cases turn out to be our friends and stimulate our immune systems if we just leave things alone.

I just finished 6-months of treatments for chronic Lyme, parasites, heavy metals and leaky gut. The upside is that I'm better. The downside was that the treatments which made be better also killed off just the majority of my protective bacteria. Time to repopulate the little buggers and strengthen my immune response.

Mike Sheldrick said...

I would highly recommend another book, which covers Rook's work extensively, as well as the revolution in immunology, and even parasitology.

It's called "Epidemic of Absence." Published in late 2012, it's almost up-to-date. Rook himself highly praised the book in a frontispiece blurb. "Groundbreaking and ambitious....should be compulsory reading for all medical students."

The author, Moises Velasquez-Manoff (a journalist, BTW) suffered from an autoimmune disease, alapecia, and set out on a quest for a cure, which led him to an almost exhaustive effort to understand the hygiene hypothesis. The book is the distillation of that effort.

A must read for Animal Pharm devotees.

Finally, there was an excellent review at the time of publication in the NYT:


Unknown said...

Hi Max,

One of our cats also suffers from asthma-like symptoms and we've tried everything. Well, everything short of encouraging her to become infested with fleas! The wife and I just aren't too keen on our house, carpets, bed, and three other kitties being loaded with fleas.

Is your cat still flea-ridden or have you treated him? What's the protocol?



Unknown said...

The opposite way of viewing the Old Friends Hypothesis is more accurate and less considered: it's not that our environment is too clean, hence we're not being exposed to Friends. The real problem is we've polluted our environment, a toxic mess allowing tolerant microbes such as gram-negative bacteria, clostridium spores and protozoal cysts the upper hand. With vulnerable gram-positive bacteria on the run, opportunistic fungi run the show (and they are, just ask the suffering bees, frogs, snakes and decimated bats).

Hygiene Hypothesis promoters like Moises Velasquez-Manoff (and possibly Rook) haven't done their due diligence in understanding how pollution shatters microbiomes. They blindly promote poor sanitation. Most people have never heard air pollution causes diabetes, leave alone the the underlying mechanism (flora shift). And there still isn't ONE study about how any of the childhood vaccines affect the microbiome. Can you say vaccine injury?

Unknown said...

Rook's 2012 chart kicking-off this blog should be considered obsolete. Here's an article published earlier this month about antibiotic resistance in the developing world associated with antibiotic abuse. Meanwhile over a billion people in the developing world still practice open defecation.

Most people would be surprised that obesity in the developing world surpasses the developed world. The reason is a toxic environment, not about poor diet and sedentary lifestyle as commonly believed.

Anonymous said...

Keith, I'd love to hear more about this line of reverse thinking. It seems a both-and. I get how to incorporate exposure to healthy dirt and natural environments (and of course SBO's), but what is the thinking re: toxicity? There are the obvious micro responses like cleaning products, dental fillings, living outside major cities, but is there more? Do we need to engage in regular detoxification? If so, how? Thanks! Lauren

Unknown said...

Lauren, somehow I sense I'm preaching to the choir, or readers may think I'm conversing with myself using different accounts (not a bad idea!). "Is there more?"

I like to use China, where this wonderful blog originates, as example because of some of the horrifically absurd levels of pollution, though things are just as bad or worse in the USA. China leads the world in diabetes along with a fierce obesity epidemic they still believe about diet and exercise, while air and soil are badly damaged, skewing intestinal microbial balance:

Do you actually trust municipal drinking water? EPA laws guiding wastewater treatment are an obsolete joke from the early 1990s. We defecate in water, then use barbaric technology in attempt to clean it, altering microbial balance akin to deforestation, i.e., increasing protozoans to lower bacteria. Then we pour effluent and sludge back into our environment, a coprophagous society (we consume our own waste like mice). Did you know chlorine raises cholesterol while some probiotics lower it and triglycerides?

Favorite examples of water mismanagement in China:

With all the endocrine-disrupting pesticides and chemicals used, we don't know who's in our cabbage willing to make sauerkraut. And radiation's effect on intestinal health is notorious as the main way people die in nuclear holocaust is sepsis due to translocation of microbes.

As to engaging in regular detoxification, it should be a way of life and would a great subject for Dr. BG to blog on, if she hasn't already. I like to view treatment and prevention as basically the same thing and commonly supplement things like boron, zinc, magnesium, selenium, sulfur, niacinamide . . . I think Dr. BG is a fan of activated charcoal and clays are probably a great thing. Once I tested the herb, chanca piedra as proactive liver detox; maybe too powerful.

Unknown said...

And what about Celiac disease, once thought low in China, but now "rampant"? China still believes its microbiome-shattering heavy-metal-laced soils and absurd levels of air pollution (video-broadcasted sunsets) have nothing to do with their leading the world in diabetes along with a fierce obesity epidemic. They think it's about diet and sedentary lifestyle where wheat becomes a scapegoat:

Anonymous said...

Thanks, Keith. I may be a member of the Grace & Keith choir, but I can assure folks I'm not your alter-ego. I really appreciate the links and the information. I'm raising young children and this has far-reaching implications regarding long term health and well being. A huge thank you to you and Grace for your contributions. Lauren

Anonymous said...


why shitting into water is not good: on keystone species in the alascan ecosystem

Thanks for your inputs here


Tim Steele said...

Gemma - Great article you linked. Loved the pictures of my backyard. You can read the history of past salmon populations by looking that the rings in the trees. Nothing makes the hair on your neck stand up like a still-steaming pile of bear poop!

Keith - What do you consider the worst aspects of poor sanitation? There's not a lot of difference between people pooping in the water in 3rd World countries and using the antibiotic-filled poop of factory-farmed animals to fertilize food crops.

Unknown said...

Hey Tim, quite a lot of difference between the two when you look at the bigger picture. When mixing waste with water, we're changing entire ecosystems outside our own gut, global challenges such as algae blooms including in Alaska. We're over-feeding our rivers lakes and oceans a poor diet of nitrogen and phosphorus-laden waste leading to microbial explosion, dead zones. This toxic algae threatens already endangered species and comes back to haunt humans, i.e., toxins associated with Parkinson's which begins in the gut.

Check out this recent documentary about poor sanitation in Alaska and an article about Alaskan algae blooms:

Maybe the worst aspect of poor sanitation and toxic pollution is how it affects the brain, beginning in the womb, perhaps often indirectly through the gut; things like lead and mercury toxicity. We still don't really understand the mechanism behind lead toxicity and brain damage. A recent study found lead affects BDNF levels, brain-derived neurotrophic factor which regulates how the brain grows and regulates synaptic transmission and plasticity. What's really interesting is BDNF levels were found regulated by intestinal microbiota. I've been theorizing lactic acid bacteria (LAB) and fungi may play this crucial role in regulating BDNF via lactate (also how exercise raises BDNF). Lactate is brain fuel.

Unknown said...
This comment has been removed by the author.
Unknown said...

Note: like butyrate, you can have too much of a good thing where high levels of BDNF (and lactobacillus bacteria!) are found in autism.

Tim Steele said...

Keith - Thanks. I see what you are saying. Just imagine what the Mississippi River is pumping into the Gulf of Mexico every second of every day. No wonder the big underwater oil spill was no big deal. Kind of makes me appreciate where I live even more, although I am reliant on shipped-in fruit and veggies most of the year. Planning on freezing even more this summer, I figure frozen veggies from my garden are better than the 'fresh' irradiated, sprayed, and treated veggies that look so wonderful in the store.

I knew that about LAB and BDNF. L. plantarum, specifically, has been shown to raise BDNF. Chalk another one up for sauerkraut, eh?

Unknown said...

Yesterday the UN launched a global campaign to end open defecation:

If you believe our sanitation systems are much better in the developed world, think again.

By the way, my civil comments have been blocked by Moises Velasquez-Manoff on two of his Facebook pages for fear of causing problems with his publisher. In private communication, his citations and thought process were backward in my view. He's got the longest bibliography in town, but didn't think enough to investigate sanitation issues. He's famous for recklessly swallowing worm ova in attempt to cure alopecia. Meanwhile, worms consume up to 20% of a child's daily nutritional intake in millions of children throughout the developing world. Worm ova are legally disposed of in Class B biosolids guided by obsolete EPA law; that's about 90% of the sludge we produce in the developed world.

Tim Steele said...

Worms you say? Just got this today from a colleague:

Although I'm sure not all worms are created equal.

Anonymous said...

Dr. Liu, I wonder if your schedule has opened up enough to assist with some gut testing. May I try emailing you again?

Unknown said...

Wow, Tim, thanks so much for the L. plantarum-BDNF info. Here's a new one:

L. plantarum is also known to shift lipids in the right direction:

You think the microbial explosion/Dead Zone in the Gulf may have helped clean up the oil spill?! My hometown of Chicago is responsible for much of the Gulf Dead Zone where female fish develop testes, speaking toward dysbiosis as cause of hormonal imbalance. Chicago was sued for sending its poorly treated sewage down the Mississippi.

Tim Steele said...

"You think the microbial explosion/Dead Zone in the Gulf may have helped clean up the oil spill?!"

That is very insightful, but I just meant that compared to all the shit we are pumping into the gulf, what's a couple billion gallons of crude?

Hey, give this a think...

Feathers seem to be natural attractants of many bacteria we consider probiotic. Many Clostridium/Bacillus strains degrade the keratin in feathers. I'm thinking that if you want to attract some beneficial microbes, surround yourself with feathers. Feather pillow, blanket, write with a feather pen, and put a big pimp feather in your hat, lol. But seriously, it's another disconnect we've made over the past century.

Unknown said...

I got started learning about BDNF a couple days ago trying to learn about lead toxicity and if the mechanism is damage to microbes. This paper is about L. plantarum to alleviate lead toxicity, I surmise by raising lactate which raises BDNF:

Why is lactation called lactation?!

Thanks for the worm and feather papers; might wanna combine the two for a new supplement to be called "Worms & Feathers".

Unknown said...

Interesting insights about different lactobacillus counts in breast milk throughout the world with Japan and Korea in the lead; not a simple matter of diet, but microbial predisposition, the underlying beauty if diversity:

Tim Steele said...

I never would have thought about L. plantarum and lead reduction..amazing! I've been taking L. plantarum 2B CFU supps for almost 2 months now to see if I can get them to grow, my last couple gut tests showed low Lacto, but not sure that indicates anything bad.

My wife and my AmGut tests showed a small population of a bacteria called Desulfovibrio. It's normally found in deep subterranean environments where no bacteria was thought to live. No great surprise since we get our drinking water from a very deep well.

Delsulfovibrio, as the name implies, degrades sulfur. It also eats radioactive waste and is being used to clean up nuclear waste sites.

Prior to my RS rich diet, I used to 'emit' foul sulfur smells on a regular basis. Now, none. I like to think that cleaning up my diet and adding prebiotics made a niche for Desulfovibrio to live in...and just in time as the Fukushima Cloud is drifting over Alaska.

Unknown said...

Congrats on balancing what sounds like hydrogen sulfide gas possibly originated from that sulphate-reducing bacteria (SRB). I've read about that SRB high in autism associated with neurotoxic propionic acid, but clostridia and some bacteroides may also make propionic acid.

With all that RS you may have raised prevotella to balance the SRB. You probably also raised clostridia which feed hydrogen to archaea in competition with SRBs. The clostridia want methane made by archaea. Know of any studies about how RS affects archaea?

Take whatever I say with a grain of himalayan sea salt, I'm far from expert. But I do think you should take your expertise to the autism community.

Dr. B G said...

aerobic1 ~I'm glad you are feeling notably better. You've got some gut ecosystem re-building to do! Good thing you're brilliant

Sheldrick~ Did you see Keith's comments? I'm hesitant to read books that lack viable solutions. We know the problems already.

Tim~ Thx for your thoughts!

Keith~ You're absolutely correct. Rook told me that chart was archaic but I like it anyway. His latest thoughts revolve around some upcoming work from Knight's work and the SBOs spores in healthy green spaces and outdoors.

Detox is key as you said. Our environ. burdens of toxins in US and around the world are crazy high and they disrupt the gut. The worse of course are municipal water and vaccines. Healthcare is naturally the worse mandating yearly mercury/flu shot for all their little busy bees.

Still digesting your links. Love the lacto and breastmilk one. I appreciate all of your BDNF and other brainy insights.

The gut communities are so complex -- I can't even begin to comment on Tim's fragant poops or H2S utilizing species (SRB)! Thank you for translating

Rebecca said...

Hiya, I'm a first-time commenter here, having just recently acquired all the soil-based probiotics and things recommended across a few blogs including this one, coolinginflammation, Free the Animal, etc. I've had some kind of systemic autoimmune-type arthritis for five years now (came on strong all at once and was initially very debilitating, but improved over time as we developed a regime of mild-ish medications plus heaps upon heaps of fish oil) and was finally doing quite well, so I figured I was up for a bit of clean-up! Prescript Assist and RS went down without issue for a couple of days, but after a single Probiotic-3 I seem to be more in pain as each day passes. No fear - I jumped on Vitamin C and milk thistle and a couple of days ago a drink of charcoal, all to no avail.

I tried kefir once (maybe a year ago) for a few days - a locally-available kind known for being full of heaps of good bugs - and (re)developed similar pain, which took months to come back from, so I'm obviously a little bit saddened, but mostly at a loss as to what to do now. If my experience now is like the last one, this doesn't feel like "just die-off", or if it is, it's not the kind that people say to hang on through because it only lasts for 3-7 days because it passes and you emerge better. Last time I quit the kefir after four days; this time I dropped all probiotics immediately, recognising the same kind of reaction to the new gut bugs. It's been 6 days of getting worse and I'm coping okay so far in pretty good humour, but I know what I've got has the capacity to make it impossible for me to get out of bed, so, y'know, there's some fear there too around experimenting that makes me want to check in at this point and see if you can offer any advice given the above. I haven't been following dietary guidelines strictly at all and that's my next step but can that really make that much difference? Does this sound like die-off? Where do I go from here?

Any advice would be truly, truly appreciated.

Rebecca :)

aerobic1 said...


Your symptoms are consistent with that of a disease state emanating from the gut. If symptomatic treatments like you have been doing do not help then you should consider looking for the root cause of your problems. IMHO, find an integrative MD who specializes in gut issues or, if you are like me, just do it yourself. You might frustrate yourself to no end if you rely on mainstream medicine providers as these types of issues are typically not in their vocabulary.

Two tests to consider having done:
• Doctor’s Data Complete Stool Analysis with Parasitology x 2 or Genova Labs CDSA2.0+P
• Genova Labs Intestinal Permeability

These tests can be done in the privacy of your home and can be purchased from Follow the directions and your results will be e-mailed to you in 7 to 10 days. You will receive an interpretive guide and there is much you can do on your own for self-treatment. Depending on the type and severity of the issue(s), if there are any, you may need to resort to professional medical treatment.

Food intolerances, heavy metals and toxins can also provoke gut issues but start with the two tests mentioned.

Keep after this.

Rebecca said...

Thanks aerobic1. Given the way things flare up for me upon adding probiotics, I'm inclined to agree with you! I think the pain's getting gradually better, so I might try and recover then give the probiotic thing another shot but more gently and/or find professional advice! Cheers. :)

BC said...

Hi dr bg,

Long time reader first time poster, the information you Tim and Richard have put out there has been very informative. Not sure if you are able to comment but I wanted to seek your opinion on the following situation: patient had a bout of food poisoning leading to Post infectious ibs, ibs-c predominant. Testing done has ruled out IBD, parasites and Sibo. (Endoscopy, colonoscopy, breath test and stool test (tradition not metrametrix or dr data).
Gastroenterologist has prescribed combination rifamaxin and vancomycin for 2 weeks (with following 2 week course if responsive followed by a prokinetic agent (prucalopide). VSL 3 (probiotic) recommended after completion of antibiotics.

Gastroenterologist then states if this results in a relapse undergo FMT.

So based on the above, would you A recommend doing a metrametrix test being proceeding, B go ahead with the above without testing, C incorporate your recommendations re SBOs after completion of antibiotic? D do something's else?

Many thanks