Early Retirement Extreme Forums

http://humanfoodproject.com/please-pass-microbes/

The Hygiene Hypothesis – or Old Friends Hypothesis, if you prefer – posits that a great many diseases (specifically autoimmune diseases) result from a disconnect with the natural world and its myriad of microscopic life. Microbes and other tiny things that once trained our immune system to distinguish between friend or foe and even Self. Our children are no longer born in the microbe-rich dirt, but rather hyper-sterile rooms where even the air is scrubbed with mechanical systems. Further, an increasing number of our kids are born through an incision rather than the microbial-rich birth canal and the percentage that are still consuming microbial-rich milk from mom at 2 or even 1 year of age can be counted in the low single digits depending on where you live and your lot in life. Our kids – most of them, or adults for that matter – have no interaction with extensive microbial networks that the Hadza and our ancestors once experienced. For us, the microbial super highway that once connected all humans to the larger metacommunity of microbes now dead ends at closed windows in a home at the end of the street with very few species of plants in the yard and no or few animals – save a dog or two – and a wet wipe and anti microbial something or other at every turn.

Dramatic changes in his microbial diversity after eating like an Hadza.

http://humanfoodproject.com/microbial-d ... imes-dont/

This past January I wanted to see what would happen to my gut flora if I adopted a hunter-gatherer diet for a week – eating the plants, animals and drinking the same water as the Hadza hunter-gatherers of east Africa that I was working with. Among other hypothesis I wanted to test, would immersing myself in this microbial-rich lifestyle increase the diversity of microbes in my tattered western gut? Below is a PCoA plot of what happened.

Cutting edge science.

http://mpkb.org/home/publications/proal ... icine_2014

"In conjunction with data generated by other private ini- tiatives, these projects detected and characterized so many novel microbes in Homo sapiens that at least 90% of cells in the human body are now understood to be bacterial, fungal, or otherwise non-human in origin. As of March 2014, the Genomes Online database lists 2,723 completed and published bacterial genomes detected in the human body with at least 14,867 in progress (Pagani et al., 2012).

Our knowledge of the chronic viruses that persist in Homo sapiens is also rapidly evolving. Gordon and col- leagues analyzed the fecal virome of monozygotic twins and their mothers (Reyes et al., 2010). Eighty one percent of the reads generated from this virome did not match those of any known viruses. In 2011, Pride et al. (2012) found that hundreds of previously uncharacter- ized bacteriophage species dominate the oral cavity, some of them serving as reservoirs for pathogenic gene function.

The over nine million non-human genes represented by the microbiome (Yang et al., 2009) dwarf the meager
20,500 that comprise the human genome. This knowl- edge implies a redefinition of the human/microbe rela- tionship. The human body is best understood as a super- organism whose metabolism represents a combination of microbial and human interaction."

Interesting how this is roughly analogous to modern understanding of human brain function in the meme-pool. What would you say is the new take-away for best practice based on this research? When I had babies over 20 years ago I was aware of this sort of thing to the extent that I knew it was best practice to breast-feed and let them play in the dirt with other dirty children. OTOH, daycare centers are pretty much pathological organism greenhouses. If one 2 year old vomits at 10 AM, the likelihood that no other 2 year old will vomit by 5 PM is quite low.

Much of our food has been sterilized. Our sanitation systems work well. The inmates of daycare centers and schools may trade among themselves a small number of bugs but they are not exposed to the wide variety that kids a hundred or a thousand years ago experienced. Those bugs thinned the herd but left the survivors with resilient, intelligent immune system that could discern between threats, benign invaders and human cells. Today autoimmune diseases are exploding. Our immune systems need variety to get smart. So my best practice is to give my system variety and plenty of plant fiber for them to munch on.


Michael Pollan in the NYTimes
http://michaelpollan.com/articles-archi ... are-germs/

"It is still early days in this research, as Lozupone (and everyone else I interviewed) underscored; scientists can’t even yet say with confidence exactly what a “healthy” microbiome should look like. But some broad, intriguing patterns are emerging. More diversity is probably better than less, because a diverse ecosystem is generally more resilient — and diversity in the Western gut is significantly lower than in other, less-industrialized populations. The gut microbiota of people in the West looks very different from that of a variety of other geographically dispersed peoples. So, for example, the gut community of rural people in West Africa more closely resembles that of Amerindians in Venezuela than it does an American’s or a European’s.

These rural populations not only harbor a greater diversity of microbes but also a different cast of lead characters. American and European guts contain relatively high levels of bacteroides and firmicutes and low levels of the prevotella that dominate the guts of rural Africans and Amerindians."

Right. My ex-husband and I both had severe allergies and asthma so that is why I gave more than the usual thought to immune system development in our children. Pretty much it worked. Neither of them has severe allergies and I only took them to the doctor for stuff like vaccines and broken arms. Odd thing is that I spontaneously had an immune system shift around age 35 and lost most of my allergies too.

Anyways, I adore Michael Pollan (I immediately gobbled up every title in the gardening series he edited a number of years ago) so I shall follow his advice. I was also thinking that maybe heliciculture might prove helpful.

Can the Bacteria in Your Gut Explain Your Mood?
http://www.nytimes.com/2015/06/28/magaz ... -mood.html

‘‘You wouldn’t believe what we’re extracting out of poop,’’ he told me. ‘‘We found that the guys here in the gut make neurochemicals. We didn’t know that. Now, if they make this stuff here, does it have an influence there? Guess what? We make the same stuff. Maybe all this communication has an influence on our behavior.’’

and

Micro-organisms in our gut secrete a profound number of chemicals, and researchers like Lyte have found that among those chemicals are the same substances used by our neurons to communicate and regulate mood, like dopamine, serotonin and gamma-aminobutyric acid (GABA). These, in turn, appear to play a function in intestinal disorders, which coincide with high levels of major depression and anxiety.


and

It seems plausible, if not yet proved, that we might one day use microbes to diagnose neurodevelopmental disorders, treat mental illnesses and perhaps even fix them in the brain.

Speaking of fecal transplants....

I asked him if what amounted to a personality transplant still sounded a bit far-fetched. He seemed no closer to unlocking exactly what brain functions could be traced to the same organ that produced feces. ‘‘If you transfer the microbiota from one animal to another, you can transfer the behavior,’’ Lyte said.

Huh, maybe Lucas was onto something with Midi-clorians.

I'm following all the gut biome stuff very closely. It seems like we know almost nothing for sure. I highly recommend The Art of Fermentation by Sandor Elliott Katz, not because it is the definitive source on the HOW behind food and drink fermentation (as opposed to just giving recipes, it gives you a process that is widely applicable), but because the first two chapters make an incredible case for why this stuff is important, in mostly layman's terms. It's clear that we cannot survive without bacteria. What's interesting is the idea that we have co-evolved (with humans arriving a distant second) to support one another. The extent of the relationship isn't clear, but it is clearly important.

Best practices, given a tremendous amount of "unknown":
-eat real food, some of it wild. Avoid processed and refined crap
-expose yourself to a variety of bacteria, through food and otherwise
-eat and maybe drink fermented things semi-regularly (some of it wild fermented)
-ditch the antibacterial soap and antibiotics (unless you have a very important health reason)
- try to avoid foods that have an antibacterial effect on the gut, unless you have good reasons. For example, hot peppers, oregano, etc. can help clean out things like SIBO, just know what you are doing and why
-be clean, not sterile
-pay attention to your body. It gives you constant feedback on how it's workin. Everyone is different. If you feel like shit after eating a type of food, maybe don't do that anymore. If something makes you feel great, maybe do that more often.

Do probiotics work? A new citizen-science study hops to find out. Costs $89 to find out which microbes are in the gut.



http://www.globenewswire.com/news-relea ... e-Gut.html

SAN FRANCISCO, Calif., July 9, 2015 (GLOBE NEWSWIRE) -- via PRWEB - Millions of Americans take probiotic supplements, but until now only relatively small-scale effectiveness studies have been undertaken. Biotech startup uBiome aims to change this by giving thousands of individuals the chance to have their gut bacteria analyzed before they begin taking probiotics, then again once they have done so. Participants will receive a 20% discount on two at-home, mail-in test kits so they can explore how their own microbiome changes as a result of taking probiotics. They will also gain exclusive advance access to results from the study.

How to take part in the study: http://ubiome.com/pages/probiotics

Has natural selection driven specialization?

Here are some interesting similarities between cooperative cell metabolism and economic trade.

http://journals.plos.org/plosone/articl ... ne.0132907

NIH video

"Towards Psychobiotics: The Microbiome as a Key Regulator of Brain & Behavior"

https://videocast.nih.gov/Summary.asp?File=19216&bhcp=1

At 39:00, microbes, or a lack thereof, may play a role in introversion (in mice).

The last question at about 1:03.45 where the guy asks about Roundup, tryptophan metabolism and microbes made my mind twist into knots. :shock

http://www.prevention.com/food/healthy- ... eed-killer

@Ego -

Most awesome NIH video. Thank you for posting that.

Have you looked at https://www.consumerlab.com/ for vitamin and probiotic information? It is not free but pretty interesting. I wish there were a free and open research clearing house like it available, but have not found one.

Yeah, they seem to do good work. I'd be interested but the fee is high. I wonder if any libraries have a subscription.

Site the provides testing results on various supplements, vitamins, etc. for free. They have a probiotic section.

https://labdoor.com/

https://labdoor.com/rankings/probiotics

I have used the NOW Foods Probiotic-10 and VSL3 (not ranked by the site). In my personal experience I noticed a difference with the VSL3, which is a higher grade and higher potency probiotic. This was not a scientific test. Just observational.

Researchers at Cornell took the microbiome from mice with Alzheimer's disease and transplanted it into the gut of germ-free mice. Later the germ-free mice were found to have elevated levels of the main component of the amyloid plaques found in the brains of Alzheimer patients.

http://arxiv.org/abs/1509.02273

In other words, gut microbes appear to play a role in Alzheimer's disease.

The more I learn the more adamant I am about avoiding antibiotics for anything less than life-or-death. Anyone else?

Ego wrote:The more I learn the more adamant I am about avoiding antibiotics for anything less than life-or-death. Anyone else?

In general, I agree with you. The problem is guessing which infections would heal on their own and which might become a life-or-death problem.

Eating 'real' food would help, and foregoing antibacterial everything for more natural cleansing products would probably go a long way toward addressing the issue. We're sterilizing ourselves to death.

Ego wrote: The more I learn the more adamant I am about avoiding antibiotics for anything less than life-or-death. Anyone else?

I don't know if I'm adamant, but I've never used them internally. I've never had an infection. I do use that antibiotic ointment on dirty cuts and stuff sometimes, but usually I just suck the blood off and leave it. I wash my hands a lot due to work requirements and that no doubt helps with all the cuts I get.

I had my spring water tested recently and it has some coliform bacteria in it, but no E. Coli. I think the count was about 11 but I don't know what levels are unsafe, if any. The owner of the lab said the acceptable tolerance is zero, but I've been drinking the water for 25 years with no apparent ill effects so I don't plan to try to treat the water.

Ego wrote: The more I learn the more adamant I am about avoiding antibiotics for anything less than life-or-death. Anyone else?

Very adamant about it. It appears we are just scratching the surface of the major impact the microbiome has on our health. The big problem is the lack of research around which bacteria are healthy for us and which are not. We have a few identified, but I'm sure we don't have anywhere near all of them identified.

Enigma, Mrs. Ego is like you. On hot summer days when she was a kid they would drink from the garden hose in the backyard - in Tijuana. I often comment on how her immune system in enigma-like. I wonder how long before we start selling (or prescribing) your well water or Tijuana municipal water to build a healthy immune system.

Chad, that guy in the NIH video above seems to have become the clearinghouse on twitter (‏@jfcryan) for all of the interesting developments in this area. He says the phrase, "We don't know..." an awful lot.