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Microbiome

Human Microbiome Project (Wikipedia). Was launched by the NIH in 2008 and closed in 2012. Results can be found on the website: NIH Human Microbiome Project. In 2016 the estimate of ratio between human cells and microbial cells is roughly 1:1. The estimate number of human cells is around 37 trillion cells in an average 70 kg male.

Notes

  • Gut Bugs: The Microbiome and IBD. Published 2/12/2017. Duration 37:18. The first few minutes introduction is very good. It gets technical after that.
  • Introducing the Human Gut Microbiota. Published 12/13/2016. Presented by Karen Madsen PhD. Good set of slides in the presentation. ILSI NA: Fiber Symposium 2017: Gut Permeability and..(Karen Madsen Ph.D - University of Alberta). Published 10/27/2017. Better presentation and set of slides.
  • Microbiome: Gut Bugs and You | Warren Peters | TEDxLaSierraUniversity. Good material. 72% of our foods (U.S.) have added sugar. 70% of all antibiotics used in the U.S. are given to animals that provide us with food. Overuse of antibiotics for children and adults. Gut bugs need their sleep (circadian rhythmns).
  • The gut flora: You and your 100 trillion friends: Jeroen Raes at TEDxBrussels. Bacteria are all over you. You are a walking bacterial colony. You are outnumbered 10 to 1. Benefits: food digestion, protection against pathogens, provides essential nutrients (e.g. vitamins like K2), trains your immune system. ... Different gut (enterotypes) compositions if your diet is primarily fat, or protein or carbohydrates. ... Antibiotics will destroy gut flora that can take a fews days to many months to recover. Some may not recover a normal gut flora at all.
  • Biohacking the microbiome: Dee Eggars at TEDxUNCAsheville. EM (Effective Microorganisms).
  • Mind-altering microbes: how the microbiome affects brain and behavior: Elaine Hsiao at TEDxCaltech. Published 2/8/2013. Good summary of how the gut affects the brain.
  • Fecal transplants & why you should give a crap | Mark Davis | TEDxSalem. Published 11/3/2015. Dr. Mark Davis is a Portland-based naturopath who specializes in stomach and intestinal health. He is an expert in fecal transplantation, having successfully administered it for patients of many conditions. Davis cofounded Microbiomes, LLC, which was the first group in the U.S. to offer a fecal transplant capsule, which is taken orally. He hopes that the U.S. Food and Drug Administration will eventually allow more patients to benefit from fecal transplantation.
  • Ibid. (from comments section). I'm heading to the UK in a couple of days, to the Taymount Clinic, for my third round of FMT (fecal matter transplant) treatment. I was diagnosed with CFS and IBS-C after years of antibiotics and accutane, for acne, tonsillitis, and recurrent chest infections. So far it has almost cured my fatigue, and my IBS is greatly improved, but I will continue the treatment until I am fully cured, and I have total faith that it will do the job.
  • Clostridium Difficile and the Microbiome. Clostridium Difficile, AKA C. Diff is one of the most prevalent and contagious healthcare associated infections along with methicillin resistant staphylococcus aureus (MRSA). According to the CDC, people at the most risk are those who are taking antibiotics, get medical care, and many times are older adults.
  • Dirt is Good with Rob Knight -- An Author Talk on The Library Channel. Duration 49:58. Gives a lot of information about the Human Microbiome Project sponsored by NIH. Talks about C. Diff and how FMT cures it (hear at around duration 15:00).
  • The Enormous Impact of Tiny Microbes with Rob Knight -- Sages and Scientists 2016. Published 11/21/2016. You can make a mouse obese by simply implanting the microbes of an obese person in its gut.
  • Glyphosate Dissolving Tight Junctions. Duration 1:45. The use of Restore on tight junctions of the small intestine. This video shows glyphosate placed on small intestine cells in the lab at 10 parts per million (ppm) degrading the tight junctions cells of the gut barrier over a 16 minute period. When RESTORE is placed on the same tight junction cells along with glyphosate, the tight junction barrier remains strong.
  • Cooling Inflammation from the Inside-Out: Sources of Microbiome Disruption. IHS 2016. Published 3/2/2016. Duration 52:09. Up to date and informative.
  • Contributions of Intestinal Bacteria to Nutrition and Metabolism in the Critically Ill. Published 8/1/2011. Utilization of complex polysaccharides via fermentation by anaerobic bacteria in the large intestine results in the accumulation of short chain fatty acids (SCFA). The principal SCFAs seen in the colon, acetate, propionate, and butyrate, have inherent nutritional value, but also impact gut epithelial physiology in other ways. ...Interestingly, the colonic epithelium derives up to 70% of its energy needs directly from butyrate. ...A series of experiments involving labeled inorganic nitrogen suggests that up to 20% of circulating lysine and threonine in nonruminant mammals, including adult humans, is synthesized by gut microbes. Similarly, Raj, et al. demonstrated that gut microbial synthesis of leucine in adult men was approximately 20% of the dietary amount. ...The intestinal microbiota also contributes to nitrogen balance by participating in urea nitrogen salvaging (UNS). ...Other experiments that analyzed the lipids present in the serum and adipose tissue of WT (Wild-Type) and GF (Germ-Free) mice show that WT animals had elevated levels of 18 phosphatidylcholine species and decreased levels of nine triglyceride species relative to GF animals. ...Several bacterial genera that are common in the distal intestine (e.g., Bacteroides, Bifidobacterium, and Enterococcus) are known to synthesize vitamins. Thiamine, folate, biotin, riboflavin, and panthothenic acid are water-soluble vitamins that are plentiful in the diet, but that are also synthesized by gut bacteria. Likewise, it has been estimated that up to half of the daily Vitamin K requirement is provided by gut bacteria.
  • Ibid. The administration of probiotics and prebiotics represents an increasingly popular alternative to gut decontamination protocols. Probiotics are defined as live microorganisms that confer health benefits upon humans and animals that ingest them in adequate amounts; prebiotics are nondigestible food ingredients that confer health benefits by selectively inducing the growth of probiotic species. The most commonly used probiotic species are nonpathogenic yeasts and organisms from the genera Lactobacillus and Bifidobacterium. The most commonly used prebiotics are the naturally occurring oligosaccharides known as fructans that are normally found in foods such as garlic, artichokes, and bananas. Another well-studied class of prebiotics is resistant starches, such as those found in unripe bananas and raw potatoes.
  • Amino acid metabolism in intestinal bacteria and its potential implications for mammalian reproduction. Published 1/20/2015.

Prebiotics and Probiotics

microRNA

  • microRNA (Wikipedia). The first human disease known to be associated with miRNA deregulation was chronic lymphocytic leukemia.[47] Many other miRNAs also have links with cancer[47] and accordingly are sometimes referred to as "oncomirs".
  • Gene Silencing by microRNAs. Published 5/17/2015. Duration 4:53. Good introduction to microRNA biology.
  • David Bartel (Whitehead Institute/MIT/HHMI) Part 1: MicroRNAs: Introduction to MicroRNAs. Published 3/24/2014. Duration 42:44. See also: David Bartel (Whitehead Institute/MIT/HHMI) Part 2: MicroRNAs: Regulation by Mammalian microRNAs (Duration 30:29), and David Bartel (Whitehead Institute/MIT/HHMI) Part 3: MicroRNAs: What is a MicroRNA? (Duration 27:11).
  • Regulatory RNA's: miRNA, siRNA, snRNA, lncRNA. Published 6/29/2017. Duration 15:50.
  • Dr. Zach Bush M.D. - Gut Health and the Microbiome. Published 12/28/2017. Discussion of microRNA starts at 20 minutes. A percentage of microRNA leave the cell as exosomes (cell-derived vesicles) and circulate via the blood, etc. What is interesting is that 35% of the microRNA circulating in the body are produced by the microbiome in the gut. Meaning, that bacteria (and fungus, parasites and viruses) in the gut is influencing gene expression in the body. See trascript here: Gut Health and the Microbiome. What we’re going after is something called redox signaling. Redox is the concentration of two words. They’re reduction and oxidation. Reduction is the donation of electron. Oxidation is the absorbance of an electron. The more reductant you have in your environment, the more negative charge, the healthier you are, literally the younger you are. ... Youth is reductant. Age is oxidative, if we will. Optimal health is a balance between that reductive and oxidant environment.
  • Ibid. This high redox signal with lots of oxidative molecules coming out of this cell over here is calling for immune system and other nutrients to be brought to it. More oxygen, more nutrients, we need to repair, we need reinforcements. Like you said, all human disease can boil down to a loss of communication at the cell level. If you start to get isolated, you start to break tight junctions, you start to break gap junctions, you start to disrupt the environment with an acidic shell, you now get cancer.
  • Ibid. Cancer is a cell that’s been damaged, damaged, damaged. It’s been calling for help but is now getting so damaged that the mitochondria itself can’t even mount this reactive oxygen species response to shout help. Now the cell is just accumulating damage, accumulating damage, to the point where now it can’t even repair itself. Amazingly, and you think of this lonely damaged cell, you would think, well, it would just give up, right? We are so wired for life at the very fabric of human existence. We are wired for life, so that damaged, lonely cell, says, “I can’t repair anymore, and I’m going to die, the only hope that I have of passing life on is to procreate.” It just starts dividing, and that will become a tumor, which then can become an aggressive cancer.
  • Ibid. We’re doing studies just showing glyphosate levels. We got back some recent data showing a drop in glyphosate just after two weeks of fixing this gut environment. Get a 20 to 30 percent drop in glyphosate over a two week period [crosstalk] Daniel S: On the same diet? zach bush: Same diet, same everything. You just put the supplement into play, and you see this drop in glyphosate levels. What’s happening is, as the microbiome expands, and then starts to get rich, it will digest glyphosate. More importantly, it will actually up regulate the enzymes that chew up zonulin and other downstream peptides that create the tight junction leak that would end the glyphosate up in your bloodstream which would then hit the kidneys, et cetera.

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