The human microbiome: Me, myself, us

Thomas Page

The human microbiome: Me, myself, us | The Economist - http://www.economist.com/node...

Aug 18, 2012 from

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pstp biol Microbes maketh man People are not just people. They are an awful lot of microbes, too http://www.economist.com/node... , 8 -27 http://science.time.com/2012... , 9 -24 http://www.sciencedaily.com/news... , 11 -26 http://www.indiegogo.com/ubiome - Thomas Page

Good article. - JB

:) Motility http://en.wikipedia.org/wiki... Activia http://en.wikipedia.org/wiki... is marketed as a beneficial health product, with a focus on improved intestinal motility. Activia products contain Bifidobacterium animalis DN 173 010, a proprietary strain of Bifidobacterium, a probiotic which is marketed by Dannon under the trade names Bifidus Regularis, Bifidus Actiregularis, Bifidus Digestivum and Bifidobacterium Lactis. Activia is classified as a functional food, designed to improve digestive health. In its marketing for Activia, Danone claimed that Bifidobacterium animalis relieves irregularity. , Yakult a special strain of the bacterium Lactobacillus casei Shirota. It was created by Minoru Shirota who graduated from the Medical School of Kyoto University in 1930. In 1935, he started manufacturing and selling Yakult. Official claims state that the name is derived from jahurto, an older form of jogurto, the Esperanto word for "yoghurt".[1][2] Since then, Yakult has also introduced a line of beverages for the Japanese market that contain Bifidobacterium breve bacteria http://en.wikipedia.org/wiki... , http://en.wikipedia.org/wiki... http://emedicine.medscape.com/article... , 10 -6 Probiotics: A gut-check on bacterial health http://www.latimes.com/health... - Thomas Page

strengthening of the body's natural defences through the use of patented bacterial culture called Lactobacillus casei DN-114001, marketed as Lactobacillus casei Defensis or Immunitas(s) and more recently as L. casei Danone. Each bottle is claimed to contain 10 billion of these bacteria.[1] In addition Actimel contains the traditional yogurt cultures Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus salivarius subsp. thermophilus. http://en.wikipedia.org/wiki... , 10 -6 Probiotics: A gut-check on bacterial health http://www.latimes.com/health... - Thomas Page

Firmicutes http://en.wikipedia.org/wiki... Microbes in gut grab more fat from food http://www.futurity.org/top-sto... Infectobesity http://en.wikipedia.org/wiki... , http://en.wikipedia.org/wiki... , 10 -1 Gut Bacteria Can Affect Fat Absorption, and Act in Accordance to “Social Structures” http://articles.mercola.com/sites... , 10 -24 http://articles.mercola.com/sites... , 10 -25 http://journals.cambridge.org/action... http://en.wikipedia.org/wiki... - Thomas Page

Taxonomy of Common Probiotic Strains Recognized Probiotic Strains are CAPITALIZED. Species known to comprise the microbiome are noted with commensal [COM] tag. http://www.datapunk.net/visuali... , 11 -22 “Taste” in the gut http://www.the-scientist.com/... ( 11 -26 Lactobacillus reuteri Cardioviva™ NCIMB 30242 Cardioviva™ was selected and optimized for production of bile salt hydrolase which results in deconjugation of bile, reduced absorption of dietary cholesterol, and increased cholesterol catabolism and excretion. http://www.micropharma.net/technol... ) , 12 -17 http://microbial-earth.namesforlife.com/v2... http://www.microbial-earth.org/ http://phylogenomics.blogspot.com/2012... , 1 -21 http://articles.mercola.com/sites... 9 -25 http://en.wikipedia.org/wiki... - Thomas Page

The Microbial Earth Project http://genome.jgi.doe.gov/program... Gut-Microbe Swap Helps with Weight Loss http://www.scientificamerican.com/article... http://www.nature.com/news... http://friendfeed.com/citizen... , 3 -28 http://www.kevinmd.com/blog... , 3 -31 sort align http://www.aligngi.com/how-ali... http://en.wikipedia.org/wiki... http://www.ncbi.nlm.nih.gov/pubmed... http://en.wikipedia.org/wiki... - Thomas Page

What killed Elvis? 'Gulp' delves into mysteries that go for the gut http://cosmiclog.nbcnews.com/_news... - Thomas Page

Gulp: Adventures on the Alimentary Canal http://www.npr.org/2013... In Digestion: Mary Roach Explains What Happens To The Food We Eat , 4 -11 http://www.slate.com/article... , gut microbial composition shifters? , 4 -12 Xylitol http://en.wikipedia.org/wiki... effect on gut? oral inflammations? 4 -6 -14 4 -6 http://pubs.acs.org/doi... http://www.npr.org/blogs... http://www.scientificamerican.com/article... - Thomas Page

Probiotic Chewing Gum http://en.wikipedia.org/wiki... BLIS M18™ (S. Salivarius) 100 Million Organism , http://www.ncbi.nlm.nih.gov/pubmed... To investigate the effect of a chewing gum containing probiotic bacteria on gingival inflammation and the levels of selected inflammatory mediators in gingival crevicular fluid (GCF). MATERIAL AND METHODS: Forty-two healthy adults with moderate levels of gingival inflammation entered a double-blind placebo-controlled study design. The subjects were randomly assigned to one of three parallel arms: Group A/P was given one active and one placebo gum daily, Group A/A received two active chewing gums, and Group P/P two placebo gums. The chewing gums contained two strains of Lactobacillus reuteri: ATCC 55730 and ATCC PTA 5289 (1 x 10(8) CFU/gum, respectively). The subjects were instructed to chew the gums for 10 min over the course of 2 weeks. Bleeding on probing (BOP) and GCF sampling were conducted at baseline and after 1, 2 and 4 weeks. The levels of IL-1beta, TNF-alpha, IL-6, IL-8 and IL-10 were determined using luminex technology and multiplex immunoassay kits. RESULTS: BOP improved and GCF volume decreased in all groups during the chewing period, but the results were statistically significant (p<0.05) only in Groups A/P and A/A. The levels of TNF-alpha and IL-8 decreased significantly (p<0.05) in Group A/A compared with baseline after 1 and 2 weeks, respectively. A non-significant decreasing tendency was also observed concerning IL-1beta during the chewing period. The levels of IL-6 and IL-10 were unaffected in all groups after 1 and 2 weeks. CONCLUSIONS: The reduction of pro-inflammatory cytokines in GCF may be proof of principle for the probiotic approach combating inflammation in the oral cavity. [ Abstract The aim was to evaluate the effect of xylitol and probiotic chewing gums on salivary mutans streptococci (MS) and lactobacilli (LB). The material consisted of 80 healthy young adults (21-24 years) who volunteered after informed consent. They were assigned by random into one of four parallel study groups: A, probiotic gum group; B, xylitol gum group; C, probiotic + xylitol gum group; and D, placebo gum group. The gums were taken three times daily after meals, and the intervention period was 3 weeks. The probiotic gums contained two strains of Lactobacilli reuteri (ATCC 55730 at a dose of 1 x 10(8) CFU/gum and ATCC PTA 5289 at a dose of 1 x 10(8) CFU/gum), and each pellet of the xylitol gum contained approximately 1.0 g xylitol as single sweetener. Pretreatment and posttreatment samples of stimulated whole saliva were collected and quantified for MS and LB with chair-side kits. A statistically significant reduction (p < 0.05) of salivary MS was displayed in group A and B after the intervention when compared with baseline. A similar but nonsignificant tendency was seen in group C. No alterations of salivary LB was demonstrated in any group. In conclusion, daily chewing on gums containing probiotic bacteria or xylitol reduced the levels of salivary MS in a significant way. However, a combination of probiotic and xylitol gums did not seem to enhance this effect. http://www.ncbi.nlm.nih.gov/pubmed... http://en.wikipedia.org/wiki... http://en.wikipedia.org/wiki... http://en.wikipedia.org/wiki... < tree gums resins .. ? http://en.wikipedia.org/wiki... http://en.wikipedia.org/wiki... http://cen.acs.org/article... , [ http://en.wikipedia.org/wiki... It works on the principle of context-dependent memory http://en.wikipedia.org/wiki... and because it contains caffeine, Ginkgo biloba, Bacopa, Vinpocetine, Guarana, Peppermint and Rosemary.[2] http://thinkgum.com/researc... , [ Spruce gum is primarily used to heal deep cuts and sores in the Dene culture http://en.wikipedia.org/wiki... http://en.wikipedia.org/wiki... http://en.wikipedia.org/wiki... http://en.wikipedia.org/wiki... [ http://en.wikipedia.org/wiki... , 11 -3 http://www.rawstory.com/rs... http://friendfeed.com/citizen... , 11 -5 http://trubiotics.com/digesti... , 11 -7 sort ? You and Your Microbiome http://fora.tv/2013... http://www.npr.org/blogs... http://news.sciencemag.org/2012... http://www.drfranklipman.com/build-a... http://www.actionbioscience.org/genomic... http://www.prebiotin.com/body-mi... ? http://www.npr.org/blogs... http://science.time.com/2013... [[[[[ 12 -12 http://www.npr.org/blogs... - Thomas Page

10 -6 http://en.wikipedia.org/wiki... The gastrointestinal tract is also a prominent part of the immune system.[16] The surface area of the digestive tract is estimated to be the surface area of a football field. With such a large exposure, the immune system must work hard to prevent pathogens from entering into blood and lymph.[17][WP:V] The low pH (ranging from 1 to 4) of the stomach is fatal for many microorganisms that enter it. Similarly, mucus (containing IgA antibodies) neutralizes many of these microorganisms. Other factors in the GI tract help with immune function as well, including enzymes in saliva and bile. Enzymes such as Cyp3A4, along with the antiporter activities, also are instrumental in the intestine's role of detoxification of antigens and xenobiotics, such as drugs, involved in first phase metabolism. Health-enhancing intestinal bacteria of the gut flora serve to prevent the overgrowth of potentially harmful bacteria in the gut. These two types of bacteria compete for space and "food," as there are limited resources within the intestinal tract. A ratio of 80-85% beneficial to 15-20% potentially harmful bacteria generally is considered normal within the intestines. Microorganisms also are kept at bay by an extensive immune system comprising the gut-associated lymphoid tissue (GALT). Immune system homeostasis[edit] Beneficial bacteria also can contribute to the gastrointestinal system homeostasis. A case in point is the relationship between human gut and Clostridia, one of the most predominant bacterial groups in the gastrointestinal tract. Clostridia play an important role influencing the dynamics of our immune system in the gut. [18]It has been demonstrated that the intake of a high fiber diet could be the responsible for the induction of Treg cells. This is due to the production of short-chain fatty acids during the fermentation of plant derived nutrients such as butyrate and propionate. Basically, the butyrate induces the differentiation of Treg cells by enhancing histone H3 acetylation in the promoter and conserved non-coding sequence regions of the Foxp3 locus, and thus regulating the T cells, having as a result the reduction of the inflammatory response and allergies. Intestinal flora[edit] The large intestine hosts several kinds of bacteria that deal with molecules the human body is not able to break down itself.[19] This is an example of symbiosis. These bacteria also account for the production of gases at host-pathogen interface, inside our intestine(this gas is released as flatulence when eliminated through the anus). However the large intestine is mainly concerned with the absorption of water from digested material (which is regulated by the hypothalamus) and the re absorption of sodium, as well as any nutrients that may have escaped primary digestion in the ileum.[citation needed] - Thomas Page

8 -15 But in the journal Bioessays, a team of scientists has raised a creepier possibility. Perhaps our menagerie of germs is also influencing our behavior in order to advance its own evolutionary success — giving us cravings for certain foods, for example. Maybe the microbiome is our puppet master. < joke http://www.nytimes.com/2014... Botany of Desire theme - Thomas Page

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The new study detected decreased microbial diversity in the 20 autistic subjects whose fecal samples were analyzed. Specifically, three bacterial genera – Prevotella http://en.wikipedia.org/wiki... ,Coprococcus http://eol.org/pages... and Veillonellaceae http://en.wikipedia.org/wiki... – were diminished in subjects with autism when compared with samples from normal children. Surprisingly, these microbial changes did not seem directly correlated with the severity of gastrointestinal symptoms. The three genera represent important groups of carbohydrate-degrading and/or fermenting microbes. Such bacteria could be critical for healthy microbial-gut interactions or play a supportive role for a wide network of different microorganisms in the gut. The latter would explain the decreased diversity observed in autistic samples. Bacteria: in sickness and in health Among the fully classified genera in the study, Prevotella was the most conspicuously reduced in autistic subjects. Prevotella is believed to play a key role in the composition of the human gut microbiome. For this reason, the group undertook a sub-genus investigation of autistic subjects. They found that a species known as Prevotella copri occurred only in very low levels in the autistic samples. The species is a common component in normal children exhibiting more diverse and robust microbial communities. “We think of Prevotella as a healthy, good thing to have,” Krajmalnik-Brown notes. (Michael Pollan’s recent New York Times Magazine story on the microbiome points to the fact that he is proud that his gut microbiome is rich in Prevotella regarding it as a possible sign of a healthy non-Western diet. ) http://www.vox.com/2014... - Thomas Page

Bacteroides fragilis http://en.wikipedia.org/wiki... https://microbewiki.kenyon.edu/index... [ autism http://en.wikipedia.org/wiki... http://en.wikipedia.org/wiki... http://en.wikipedia.org/wiki... http://www.ozy.com/fast-fo... https://asunews.asu.edu/2013070... ] sort https://microbewiki.kenyon.edu/index... - Thomas Page

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1 -20 Immunosenescence http://en.wikipedia.org/wiki... http://phenomena.nationalgeographic.com/2015... http://www.biologydirect.com/content... http://www.huffingtonpost.ca/jason-t... [ http://www.nasa.gov/sites... - Thomas Page

https://friendfeed.com/citizen... Encephalomyelitis http://en.wikipedia.org/wiki... is a general term for inflammation of the brain and spinal cord, describing a number of disorders: - Thomas Page

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1 -13 http://www.theatlantic.com/health... Doctors aren’t entirely sure what triggers rheumatoid arthritis, a disease in which the body turns on itself to attack the joints, but an emerging body of research is focusing on a potential culprit: the bacteria that live in our intestines. Several recent studies have found intriguing links between gut microbes, rheumatoid arthritis, and other diseases in which the body’s immune system goes awry and attacks its own tissue. A study published in 2013 by Jose Scher, a rheumatologist at New York University, found that people with rheumatoid arthritis were much more likely to have a bug called Prevotella copri http://en.wikipedia.org/wiki... in their intestines than people that did not have the disease. In another study published in October, Scher found that patients with psoriatic arthritis, another kind of autoimmune joint disease, had significantly lower levels of other types of intestinal bacteria. "This is frontier stuff. With the microbiome, we’ve added a new player to the game." This work is part of a growing effort by researchers around the world to understand how the microbiome—the mass of microbes that live in the gastrointestinal tract—affects our overall health. The gut contains up to a thousand different bacteria species, which together weigh between one and three pounds. This mass contains trillions of cells, more than the number of cells that make up our own bodies. Over the past several years, scientists have compiled a growing collection of evidence that many of these bugs may have a major effect on our well-being, with some triggering chronic, non-infectious ailments such as rheumatoid arthritis, and others protecting against such diseases. “It’s become more and more clear that these microbes can affect the immune system, even in diseases that are not in the gut,” says Veena Taneja, an immunologist at the Mayo Clinic in Rochester, Minnesota, who has found clear differences in the bacterial populations of mice bred to be genetically prone to rheumatoid arthritis. In those more susceptible to the disease, a species of bacteria from the Clostridium family dominates. In mice without arthritis, other strains flourish, and the Clostridium strains are scarce. “This is frontier stuff,” says Scher, the director of the NYU’s Microbiome Center for Rheumatology and Autoimmunity. “This is a shift in paradigm. By including the microbiome, we’ve added a new player to the game.” Scientists are especially intrigued by how these bacteria influence the immune system. In recent decades, the incidence of many autoimmune diseases has been increasing; many microbiome researchers argue that at least some of this rise is due to changes in our bacterial ecosystem. Altered diet, the explosion of antibiotic use, and decreasing contact with the microbe-packed natural world of animals and plants have all combined to transform the bacteria that call humans home. “Our microbiome has changed significantly over the past century, and especially over the past 50 years,” says NYU microbiologist Martin Blaser, who puts much of the blame on widespread use of antibiotics. “We’re losing microbes with each generation; they are going extinct. These changes have consequences.” "These organisms are part of our developmental choreography. They're part of who we are." Blaser points to his own research on a species of bacteria called Helicobacter pylori (so named because it looks something like a helicopter). He sampled the gut bacteria of a group of U.S. children, and found that Helicobacter pylori existed in only 6 percent of them. By comparison, other research has shown that the strain is common in the vast majority of people from many parts of the world, especially in developing countries. The decline of Helicobacter pylori in the West, which is likely related to the spread of antibiotics as well as improved sanitation, may have medical consequences: Some research indicates that the bacteria may reduce the risk of asthma, perhaps by curtailing the body’s immune response to airborne stimuli. Blaser suspects that asthma is one of the illnesses affected by our changing microbiome: Rates in the U.S. have been climbing for three decades, and grew by more than 28 percent between 2001 and 2011. Blaser argues that H. pylori and other gut microbes are so deeply involved in our bodily operations that they shouldn’t really be considered aliens. “They are part of who we are,” he says. “These organisms are part of our developmental choreography; they have an enormous amount to do with how our immune system develops.” In fact, these bacteria have a powerful vested interest in controlling how our bodies respond to interlopers. Blaser and others say that it appears that many of the bugs that live inside us have thrived by modulating the immune system to avoid being recognized—and attacked—as invaders; in essence, these organisms train immune cells not to be trigger-happy. A microbiome with the wrong sorts of bugs, or the wrong ratio of bugs—a situation known as dysbiosis—may unbalance this immune system, causing immune cells to assault not only bacteria, but also the body itself. Microbes are especially influential in the gut, which houses two-thirds of the body’s immune cells. As the pathway for digestion, the gastrointestinal tract must deal with a constant stream of food-related foreign microbes, which must be monitored and, if they are harmful, destroyed. To do this, our intestines have developed an extensive immune system, whose effects reach far beyond the gut. Immune cells in the gut seem to be able to activate inflammatory cells throughout the body, including in joints. But while many scientists are confident of the link between the microbiome and arthritis, they haven’t pinned down what particular role bacteria play in triggering the disease. Scher says Prevotella copri may stimulate an immune reaction that then targets joint tissue. Or it may crowd out beneficial microbes that keep immune-system attack cells being too aggressive [a theory supported by the fact that people with high levels of Prevotella copri also had reduced amounts of the bacteria Bacteroides fragilis, which seems to restrain the immune system. Scher suspects that a similar mechanism may explain the results in the psoriatic arthritis study; the missing microbe species—Akkermansia, Ruminococcus, and Pseudobutyrivibrio—may signal the immune system to ease off. Dozens of researchers are looking into a range of potential strategies to use bacteria as medicine for immune disorders. Scher thinks that eventually, it will be possible to treat arthritis by adjusting the microbiome. Dozens of researchers, including Scher and Blaser, are looking into a range of potential strategies to use bacteria as medicine for immune disorders. Already, millions of Americans ingest probiotics—cocktails of supposedly beneficial bacteria that claim to treat everything from acne to insomnia. Scher, like many microbiome scientists I spoke to, is skeptical that these products are useful. “Probiotics are generally safe and almost completely untested,” says Scher. “There’s this idea that you can simply replace certain bugs that are missing. I don’t think it’s as simple as that.” For one, he says, it’s not clear whether most microbes from probiotics can survive the digestive process. Scher puts more faith in modifying the microbiome through diet. He notes that some patients with rheumatoid arthritis have benefitted from cutting out meat, or adopting a Mediterranean diet (high in fish, olive oil, and vegetables, and low in meat and saturated fat), though scientists don’t know exactly why this helps. In a separate study, Finnish researchers found that a vegan diet changed the gut microbiome, and that this change was linked to an improvement in arthritis symptoms. Others are focusing on particular bugs over diet. At the Mayo Clinic, Taneja has found that a species of Prevotella bacteria, P. histicola, can prevent or halt the mouse versions of both rheumatoid arthritis and multiple sclerosis, an autoimmune disease of the brain and nerves. She is hoping to begin studies on humans in the next few months. And some scientists are focusing not on the microbes, but on the compounds they produce. B. Fragilis, for instance, may ease autoimmune disease by releasing a molecule called polysaccharide A, or PSA. Harvard University microbiologist Dennis Kasper, who discovered the compound, has found that when given PSA, mice are protected from certain autoimmune diseases, including MS. "I don’t see why it can’t happen. This isn’t science fiction." Kasper says PSA may be a more effective and reliable way to modify the immune system than adjusting the balance of microbes. PSA also has an advantage over medicines now used for autoimmune disease, Kasper says: It is subtle. Rather than suppressing the entire immune system—an approach that has obvious disadvantages to the patient—PSA instructs immune cells to continue to patrol without going after harmless targets. “This is a molecule that we have lived with for eons,” Kasper, who has recently begun working on ways to turn PSA into medicine for humans, told me. “We know that our bodies can live with it.” Right now, doctors aren’t using microbes or their metabolites in patients with arthritis or M.S., but Scher, like Kasper, is optimistic: “In 10 or 15 years I think the microbiome will be a key therapeutic option for some of these diseases,” he says. “There will be challenges, but I don’t see why it can’t happen. This isn’t science fiction. - Thomas Page

https://www.wikigenes.org/e... http://www.the-scientist.com/... - Thomas Page

Hydrolysis-Polysaccharides http://en.wikipedia.org/wiki... Polysaccharide http://en.wikipedia.org/wiki... [ http://www.ncbi.nlm.nih.gov/pmc... over the past several years, there have been remarkable advances in our understanding of how commensal organisms shape host immunity. Although the full cast of immunogenic bacteria and their immunomodulatory molecules remains to be elucidated, lessons learned from the interactions between bacterial zwitterionic http://en.wikipedia.org/wiki... polysaccharides (ZPSs) and the host immune system represent an integral step toward better understanding how the intestinal microbiota effect immunologic changes. Somewhat paradoxically, ZPSs, which are found in numerous commensal organisms, are able to elicit both proinflammatory and immunoregulatory responses; both of these outcomes involve fine-tuning the balance between T-helper 17 cells and interleukin-10–producing regulatory T cells. In this review, we discuss the immunomodulatory effects of the archetypal ZPS, Bacteroides fragilis PSA. In addition, we highlight some of the opportunities and challenges in applying these lessons in clinical settings. - Thomas Page

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