Interstitial cystitis and the Microbiome

According to the wonderful article, The DIPP Mystery – Why are IC patients deficient in some good bacteria?:

IC Patients Found Deficient in Gut Bacteria

While they have NOT found bacteria in the urinary tract and urine distinctive to IC (i.e. such as an elusive infection), they have found significant differences in the gut. They isolated bacteria from the stool of women with interstitial cystitis as well as normal controls. IC patients had significantly lower levels of five species of bacteria – O. splanchnicus, F. prausnitzii, C. aerofaciens, E. sinensis, and L. longoviformis. They’ve dubbed this group as “deficient in interstitial cystitis pelvic pain (DIPP).”

They also found higher than normal levels of other bacteria that could, perhaps, increase pelvic pain. Researchers have labelled this population of bacteria as “increased in IC pelvic pain (IIPP).” One bacterial species, E. lenta, as well as several bacterial families were found to be elevated in the IC patient.

A closer look at these bacteria reveal new, potential insights into IC and its related conditions:

  • L. longoviformis –  metabolizes phytoestrogens, perhaps contributing to the higher number of women with IC.
  • E. sinensis – may contribute to alterations in the gut-brain axis or pelvic organ crosstalk.
  • F. prausnitzii – is highly abundant in the human GI tract and produces critical fatty acids.
  • C. aerofaciens –  is significantly associated with symptoms in IBS patients.
  • O. splanchnicus – a bacterial mystery, very little is known about it.
  • E. lenta – associated with the bacteria in the blood stream

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PPIs Diminish Gut Microbiome Diversity

“PPIs may limit the gut’s diversity by reducing its acidity and thus creating an environment that is more or less amenable to certain microbes. And that imbalance could then lead to infection, says Rinse Weersma, a gastroenterologist at the University of Groningen. The drugs may induce “a change in the microbiome that creates a niche where Salmonella or C. difficile can grow,” he explains.”

From Heartburn Meds Alter the Gut: Acid blockers reduce the diversity of bacteria in the intestines—and that could lead to trouble, published in Scientific American.

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Gut Bacteria and Nerve Myelination

Gut bacteria regulate nerve fibre insulation: Research suggests that gut bacteria may directly affect brain structure and function, offering new ways to treat multiple sclerosis and psychiatric conditions

Fascinating article – highly recommended.

Perhaps a causal link between antibiotic use and MS, psychiatric conditions, and neurodegenerative conditions, should be examined.

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Mind-Gut Connection

The article, When Gut Bacteria Changes Brain Function: Some researchers believe that the microbiome may play a role in regulating how people think and feel. published in The Atlantic, is fascinating! I highly recommend it.

It’s not yet clear how the microbiome alters the brain. Most researchers agree that microbes probably influence the brain via multiple mechanisms. Scientists have found that gut bacteria produce neurotransmitters such as serotonin, dopamine and GABA, all of which play a key role in mood (many antidepressants increase levels of these same compounds). Certain organisms also affect how people metabolize these compounds, effectively regulating the amount that circulates in the blood and brain. Gut bacteria may also generate other neuroactive chemicals, including one called butyrate, that have been linked to reduced anxiety and depression. Cryan and others have also shown that some microbes can activate the vagus nerve, the main line of communication between the gut and the brain. In addition, the microbiome is intertwined with the immune system, which itself influences mood and behavior.

This interconnection of bugs and brain seems credible, too, from an evolutionary perspective. After all, bacteria have lived inside humans for millions of years. Cryan suggests that over time, at least a few microbes have developed ways to shape their hosts’ behavior for their own ends. Modifying mood is a plausible microbial survival strategy, he argues that “happy people tend to be more social. And the more social we are, the more chances the microbes have to exchange and spread.”

As scientists learn more about how the gut-brain microbial network operates, Cryan thinks it could be hacked to treat psychiatric disorders. “These bacteria could eventually be used the way we now use Prozac or Valium,” he says. And because these microbes have eons of experience modifying our brains, they are likely to be more precise and subtle than current pharmacological approaches, which could mean fewer side effects. “I think these microbes will have a real effect on how we treat these disorders,” Cryan says. “This is a whole new way to modulate brain function.”

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Bacteroides fragilis

Bacteroides fragilis:

“The California Institute of Technology microbiologist Sarkis Mazmanian has focused on a common species called Bacteroides fragilis, which is seen in smaller quantities in some children with autism. In a paper published two years ago in the journal Cell, Mazmanian and several colleagues fed B. fragilis from humans to mice with symptoms similar to autism. The treatment altered the makeup of the animals’ microbiome, and more importantly, improved their behavior: They became less anxious, communicated more with other mice, and showed less repetitive behavior.” (source)

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Fusobacterium

Fusobacterium:

Although part of normal human gut flora, species of Fusobacterium strongly associated with numerous diseases, including colorectal cancer (CRC), appendicitis, dental plaque/ periodontal disease, hepatic cirrhosis, and inflammatory bowel disease • Fusobacterium correlates positively with TNF-alpha, suggesting involvement of mucosal inflammation • Obese, older subjects with metabolic syndrome demonstrated increased Fusobacterium as compared to younger subjects.

Source: https://www.gdx.net/core/interpretive-guides/GI-Effects-IG.pdf

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Methanobrevibacter smithii

Methanobrevibacter smithii:

• Abundance associated with higher bacterial gene richness in the gut • Lower counts of Methanobrevibacter species reported in human obesity; higher amounts reported in anorexia; in contrast, one study confirmed a positive association with increased BMI and body fat in methanogen-colonized populations • Higher levels linked to IBS-C; reduced levels linked with IBS-D • Methanogens found higher in people with colon cancer, colonic polyposis, ulcerative colitis, and diverticular disease (sigmoidoscopy enema samples) • Some studies have reported lower counts in IBD; conversely, other have reported Increased abundance.

Source: https://www.gdx.net/core/interpretive-guides/GI-Effects-IG.pdf

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Escherichia coli

Escherichia coli:

• Increased counts reported in inflammatory bowel disease; • Increased levels found in diarrhea-predominant IBS • Higher in overweight pregnant women compared to normal weight pregnant women and in women with excessive weight gain during pregnancy • Reported to increase with weight loss after gastric bypass, correlating negatively with leptin levels.

Source: https://www.gdx.net/core/interpretive-guides/GI-Effects-IG.pdf

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Collinsella aerofaciens

Collinsella aerofaciens:

Lower counts reported in IBS; lower levels may correlate with greater severity of IBS symptoms • Higher concentrations reported in IBD; thought to be result of abnormal host responses to the bacteria • Collinsella spp. reported higher in type 2 diabetes

Source: https://www.gdx.net/core/interpretive-guides/GI-Effects-IG.pdf

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Veillonella

Veillonella:

• Abundance associated with higher bacterial gene richness in the gut • Imbalances noted in IBS, although findings are mixed: some studies reported higher concentrations in IBS, in IBS-C, IBS-D; others have reported lower counts or lower counts weakly correlating with greater symptom severity • Found less abundant in autistic children compared to neurotypical children

Source: https://www.gdx.net/core/interpretive-guides/GI-Effects-IG.pdf

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Ruminococcus

Ruminococcus:

• Abundance associated with low bacterial gene richness in the gut • Human studies have reported that Ruminococcus spp. tend to be more abundant in IBD; active UC, active CD, and ileal CD • Levels are variable in IBS, depending on IBS subtype, with some researchers reporting increased concentrations and some finding decreased amounts • May be more prevalent in autism

Source: https://www.gdx.net/core/interpretive-guides/GI-Effects-IG.pdf

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Lactobacillus spp.

Lactobacillus spp.:

• Abundance associated with higher bacterial gene richness in the gut • Studies have reported altered levels in IBS, with some finding higher concentrations and others finding lower concentrations • Lower levels reported to correlate with symptom severity in IBS • Increased levels seen in obese patients compared to lean controls

Source: https://www.gdx.net/core/interpretive-guides/GI-Effects-IG.pdf

“Overall, both of these microbes seem to be major players in the gut-brain axis. John Cryan, a neuroscientist at the University College of Cork in Ireland, has examined the effects of both of them on depression in animals. In a 2010 paper published in Neuroscience, he gave mice either bifidobacterium or the antidepressant Lexapro; he then subjected them to a series of stressful situations, including a test which measured how long they continued to swim in a tank of water with no way out. (They were pulled out after a short period of time, before they drowned.) The microbe and the drug were both effective at increasing the animals’ perseverance, and reducing levels of hormones linked to stress. Another experiment, this time using lactobacillus, had similar results. Cryan is launching a study with humans (using measurements other than the forced swim test to gauge subjects’ response).” (source)

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Coprococcus eutactus

Coprococcus eutactus:

• Abundance associated with greater bacterial gene richness in the gut • Coprococcus may be less prevalent in autistic children compared to neurotypical children; may be result of intestinal disaccharidase deficiencies common in autism • In IBS, reduced abundance reported (in association with elevated Ruminococcus spp.)

Source: https://www.gdx.net/core/interpretive-guides/GI-Effects-IG.pdf

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Mind-Gut Connection and Mindfulness

What is the connection between the mind and the gut? Can gut health be improved through mindfulness and meditation?

“Mindfulness can boost immunity via the gut microbiota. As per a previous article I wrote here on Mindful, the human body is comprised of trillions of micro-organisms, most of which reside in the gut, which are called the gut microbiota. It turns out that the gut microbiota are key players in the development and maintenance of the immune system; the bacteria in the body that helps distinguish between intruder/foreign microbes vs. those that are endogenous. Studies have shown that stress tips our microbial balance, putting us at risk for dysbiosis, (a shift away from “normal” gut microbiota diversity), stripping us of one of our prime defenses against infectious disease, not to mention the cascade of reactions that ensue, which potentially wreak havoc on the central nervous system (CNS). Mindfulness-based stress reduction impacts our immune system by helping to maintain healthy gut microbiota diversity that is often upset by stress.”

Yup.

From Train Your Brain to Boost Your Immune System.

The connections are fascinating!

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B. vulgatus

B. vulgatus is associated with:

• Bacteroides spp. associated with lower bacterial gene richness in the gut• Lower levels of B. vulgatus have been seen in IBS patients in comparison to healthy controls • Low relative proportions of B. vulgatus, along with high concentrations of Lactobacillus spp. observed in the microbiota of obese children when compared to lean; B. vulgatus also found under-represented in microbiota of type-2 diabetics • B. vulgatus found to be present in significantly higher numbers in stools of severely autistic children when compared to controls • While increased B. vulgatus prevalence was associated with the genotype of infants at high risk of celiac disease development, another study found that B. vulgatus was more frequently detected in controls than in patients with treated celiac disease (p<0.01)

Source – https://www.gdx.net/core/interpretive-guides/GI-Effects-IG.pdf

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Bacteroides-Prevotella

Features of Bacteroides-Prevotella include:

• Abundance associated with lower bacterial gene richness in the gut • Reduced patterns of Bacteroides reported in IBS and ulcerative colitis; conversely, other researchers found increased levels in IBD • When compared with fibromyalgia patients, early RA patients showed less Bacteroides-Prevotella-Porphyromonas • Higher levels associated with excessive weight gain in pregnancy and in obesity • Other researchers reported lower Bacteroides (as part of Bacteroides-Prevotella group) in obese subjects compared to lean • Ratio of Bacteroides-Prevotella group to other gut bacteria correlated positively and significantly with plasma glucose; • In contrast, some have reported half the Bacteroides abundance in T2DM compared to those with normal glucose tolerance or those with pre-diabetes

Source – https://www.gdx.net/core/interpretive-guides/GI-Effects-IG.pdf

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Oxalobacter formigenes

Oxalobacter formigenes metabolizes oxalates in the gut and therefore colonization with this organism may reduce the risk of calcium oxalate kidney stones with healthy levels associated with a 70% reduced risk of being a recurrent calcium-oxalate stone former.

Kidney stones aren’t the only problems that oxalates cause though. Oxalates cause methylation problems that inhibit detoxification. According to Dr. Rostenberg’s article, OXALATES AND MTHFR: UNDERSTANDING THE GUT-KIDNEY AXIS:

“oxalates create biochemical problems that make methylation issues worse. Since oxalate problems cause sulfate problems, the genes most effected will be the SULT and other phase II related pathways. The sulfate molecule is key in order for the liver to perform the daily task of detoxification. If sulfate levels drop, then the body cannot use the SULT pathway to detoxify. Instead it will be forced to use other Phase II pathways which can put greater demand on pathways that are also genetically slowed down. When we consider other slowed Phase II detoxification gene SNPs such as NAT2, ALDH, COMT, GSH, GSS, UGT, and SOUX we can begin to see that a lack of sulfate molecules can have a broad negative impact on all of our detoxification pathways.”

Dr. Rostenberg goes on to say:

“As you will soon see, when oxalate levels are high, sulfate levels drop slowing down detoxification. Low sulfate levels put extra stress into the methylation cycle to provide the body with sulfate molecules. In individuals with an impaired methylation cycle this can provoke methylation issues such as high homocysteine, developmental disorders, gallbladder dysfunction, hormone imbalances, excess inflammation, poor growth and to name but a few. So with oxalate issues and the biochemical chaos it creates, a great deal of stress is placed on the methylation cycle.”

More information about oxalates can be found through the following links:

Trying Low Oxalates Facebook Group – https://www.facebook.com/groups/TryingLowOxalates/

http://www.lowoxalate.info/

Information about a low-oxalate diet can be found on Low Oxalate Info: Hope and Healing on the Low Oxalate Diet.

Dr. Rostenberg’s protocol for reducing oxalates can also be found here –http://www.beyondmthfr.com/high-oxalates/. Additional information from Dr. Rostenberg can be found through the Contact page on http://www.beyondmthfr.com/.

Additional information about MTHFR and other gene mutations, and how they affect health, can be found on https://mthfrsupport.com/.

Fluoroquinolone Antibiotics and Oxalate Overload

Normally present in 46–77% of healthy adults • Unique ability to metabolize oxalates in the gut • Dietary oxalate consumption generally increases O. formigenes abundance in controls, but not stone formers • Colonization with this bacteria may reduce risk of oxalate stone formation, with healthy levels associated with 70% reduced risk of being recurrent calcium-oxalate stone-former. (source)

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Verrucomicrobia

Verrucomicrobia are abundant in aquatic and soil environments, and also found in the human gut. This is a recently discovered phylum, with a wart-like cell shape. Interestingly, Verrucomicrobia have been found to be elevated in hibernating squirrels and in some people after antibiotic treatment. There are no known pathogens in this group. (source: uBiome)

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Exercise Impacts Gut Microbial Diversity

The article, The Irish rugby team has exceptional guts: Exercise and diet impact gut microbial diversity, notes that:

“Exercise and diet impact gut microbial diversity, according to recent research. The gut microbiota of athletes is more diverse than that of controls and this diversity is linked to exercise and protein consumption in athletes. Athletes also have lower inflammatory and improved metabolic markers relative to controls.”

Fascinating! Exercise can increase the diversity of microbes in one’s gut, and more diverse microbes decrease inflammation. Wonderful!

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Clostridium clostridioforme

“High Clostridium clostridioforme which is associated with diabetes, low gut diversity, inflammatory conditions and human invasive and severe infections like bacteremia. Often it produces alcohol and other toxins, which are associated with inflammation, artery hardening, and histamine responses. Alcohol from microbial fermentation results in blockages of multiple enzyme pathways in the host including the degradation of histamine. When more histamine accumulates, subsequently, the host has more allergic reactions, congestion, rash, headaches or other manifestations of high histamine. These are all secondary to a dysbiotic and imbalanced gut.” (source)

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Clostridium baratii

Clostridium baratii is an anaerobic, motile, gram-positive bacterium. It is a rare cause of infant botulism, in which newborns or infants lose their muscle tone, and develop trouble feeding due to a difficulty in breathing, which can be fatal. Newborns can recover spontaneously or as in two known cases improve with injected botulism antitoxin. As of 2015, the environmental source of this bacterium is unknown, despite extensive investigations when cases have occurred. (source)

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Clostridium botulinum

The Wikipedia entry for Clostridium botulinum notes that:

Clostridium botulinum is a Gram-positive, rod-shaped, anaerobic, spore-forming, motile bacterium with the ability to produce the neurotoxinbotulinum.[1][2] The botulinum toxin can cause a severe flaccid paralytic disease in humans and other animals[2] and is the most potent toxin known to humankind, natural or synthetic, with a lethal dose of 1.3–2.1 ng/kg in humans.[3]

C. botulinum is a diverse group of pathogenic bacteria initially grouped together by their ability to produce botulinum toxin and now known as four distinct groups, C. botulinum groups I-IV. C. botulinum groups I-IV, as well as some strains of Clostridium butyricum and Clostridium baratii, are the bacteria responsible for producing botulinum toxin.[1]

C. botulinum is responsible for foodborne botulism (ingestion of preformed toxin), infant botulism (intestinal infection with toxin-forming C. botulinum), and wound botulism (infection of a wound with C. botulinum). C. botulinum produces heat-resistant endospores that are commonly found in soil and are able to survive under adverse conditions.[1]

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Bifidobacterium

Bifidobacterium is a genus of gram-positive, nonmotile, often branched anaerobic bacteria. They are ubiquitous inhabitants of the gastrointestinal tract, vagina and mouth (B. dentium) of mammals, including humans. Bifidobacteria are one of the major genera of bacteria that make up the colon flora in mammals. Some bifidobacteria are used as probiotics. (source)

According to a Bangladeshi microbiota study published last month, poor vaccine efficacy is associated with systemic inflammation due to gut dysbiosis. Bifidobacteria were found a key factor in improving vaccine responsiveness. There are many known strains of bifidobacteria, some considered better than others. Bifidobacteria levels in the USA vary widely among individuals. Studies report much lower levels of bifidobacteria in children with autism. (source)

• Abundance associated with higher bacterial gene richness in the gut • Modulates local and systemic immune responses • Abundance lower in IBD • Abundance lower in IBS; low levels also correlate with symptom severity in IBS • Lower levels seen in type 2 diabetes, pediatric allergy, and autism • Increased levels in obese subjects compared to lean/overweight; infants with lower Bifidobacterium may have increased risk for weight gain in childhood • Abundance decreases after weight loss and gastric-bypass surgery (source)

“Overall, both of these microbes seem to be major players in the gut-brain axis. John Cryan, a neuroscientist at the University College of Cork in Ireland, has examined the effects of both of them on depression in animals. In a 2010 paper published in Neuroscience, he gave mice either bifidobacterium or the antidepressant Lexapro; he then subjected them to a series of stressful situations, including a test which measured how long they continued to swim in a tank of water with no way out. (They were pulled out after a short period of time, before they drowned.) The microbe and the drug were both effective at increasing the animals’ perseverance, and reducing levels of hormones linked to stress. Another experiment, this time using lactobacillus, had similar results. Cryan is launching a study with humans (using measurements other than the forced swim test to gauge subjects’ response).” (source)

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Akkermansia muciniphila

Akkermansia muciniphila, the only currently known species within genus Akkermansia, can reside in the human intestinal tract and is currently being studied for its effects on human metabolism. Recently performed studies in rodents have indicated that Akkermansia muciniphila in the intestinal tract may mediate obesity, diabetes, and inflammation. (source)

Akkermansia muciniphila:

Dominant mucus-layer species; may represent 3-5% of microbial community in healthy adults • Abundance associated with higher bacterial gene richness in the gut • Plays role glucose homeostasis • Abundance inversely correlated with IBD (both Crohn’s and UC) and appendicitis • Abundance inversely correlates with body weight in pregnant women and children • Some have reported decreased A. muciniphila in pre-diabetes and decreased Verrocomicrobiae abundance in T2D and pre-diabetes • Lower in autism (source)

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Christensenella minuta

Christensenella minuta is a heritable firmicute that is linked to leanness.

From The Most Heritable Gut Bacterium is… Wait, What is That?:

By studying 416 pairs of British twins, Julia Goodrich and colleagues from Cornell University have identified the gut microbes whose presence is most strongly affected by our genes. And chief among them was a mysterious bacterium called Christensenella minuta, the one and only member of a family that was discovered just three years ago.

Genetically and physically, it’s rather mundane. It’s yet another rod-shaped, oxygen-hating, nutrient-fermenting bacterium from the Firmicute dynasty—one of the two major groups in our guts. And yet, more than any other microbe, its presence in our body is strongly influenced by our genes. Christensenella also seems to sit at the centre of a large network of microbes; if it’s there, these others are likely to show up too. And it influences our weight: it’s more common in lean people, and it can reduce weight gain in mice.

All of these traits suggest that Christensenella might (emphasis on might) be a keystone species: one that wields a disproportionate influence upon the world around it. The term was first used to describe a starfish, whose absence could entirely change the nature of a seashore. It has since been used to describe sea otters, wolves, and mistletoe. These species might be relatively rare, but they are ecologically powerful. Perhaps Christensenella is similarly important in the world of our guts. And yet, until recently, no one even knew it existed.

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Roseburia

Roseburia is a genus of butyrate-producing, Gram-positive anaerobic bacteria that inhabit the human colon. Named in honor of Theodor Rosebury, they are members of the phylum firmicutes. Increased abundance of Roseburia is associated with weight loss and reduced glucose intolerance. (source)

• Abundance associated with higher bacterial gene richness in the gut • Less abundant in individuals with IBS, particularly constipation-predominant IBS • Counts lower in type 2 diabetics; trending inversely with plasma glucose • Lower in IBD and early-onset rheumatoid arthritis (as part of decreased E. rectale-C. coccoides group) (source)

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Faecalibacterium prausnitzii

Faecalibacterium prausnitzii is very special. It is a gut barrier and immune system warrior and known as a keystone ‘Peacekeeper‘ (Nature 2015, fantastic photos).You can see above it is a red-orange and found in robustly in concentration of hundreds in 94% of tested healthy subjects. In clinical trials, it is low where diseases are present and high in disease-free people. It is a harbinger for bad health if it and several other ‘ancestral core’ species are depleted. (source)

From Among Trillions of Microbes in the Gut, a Few Are Special:

In the mid-2000s Harry Sokol, a gastroenterologist at Saint Antoine Hospital in Paris, was surprised by what he found when he ran some laboratory tests on tissue samples from his patients with Crohn’s disease, a chronic inflammatory disorder of the gut. The exact cause of inflammatory bowel disease remains a mystery. Some have argued that it results from a hidden infection; others suspect a proliferation of certain bacteria among the trillions of microbes that inhabit the human gut. But when Sokol did a comparative DNA analysis of diseased sections of intestine surgically removed from the patients, he observed a relative depletion of just one common bacterium, Faecalibacterium prausnitzii. Rather than “bad” microbes prompting disease, he wondered, could a single “good” microbe prevent disease?

Sokol transferred the bacterium to mice and found it protected them against experimentally induced intestinal inflammation. And when he subsequently mixed F. prausnitzii with human immune cells in a test tube, he noted a strong anti-inflammatory response. Sokol seemed to have identified a powerfully anti-inflammatory member of the human microbiota.

• In a healthy gut, represents more than 5% of the total bacterial population and is comprised of only one species • Abundance associated with higher bacterial gene richness in the gut • Controls inflammation through inflammatory-cytokine inhibition; lower counts reported in IBD: Crohn’s disease and ulcerative colitis (UC), although increases have been noted • Appears to protect against glucose intolerance and type 2 diabetes; possibly due to anti-inflammatory effects and/or positive effects on insulin resistance status (source)

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The Gut Brain Connection Science News Article

Microbes can play games with the mind: The bacteria in our guts may help decide who gets anxiety and depression

The 22 men took the same pill for four weeks. When interviewed, they said they felt less daily stress and their memories were sharper. The brain benefits were subtle, but the results, reported at last year’s annual meeting of the Society for Neuroscience, got attention. That’s because the pills were not a precise chemical formula synthesized by the pharmaceutical industry.

The capsules were brimming with bacteria.

In the ultimate PR turnaround, once-dreaded bacteria are being welcomed as health heroes. People gobble them up in probiotic yogurts, swallow pills packed with billions of bugs and recoil from hand sanitizers. Helping us nurture the microbial gardens in and on our bodies has become big business, judging by grocery store shelves.

These bacteria are possibly working at more than just keeping our bodies healthy: They may be changing our minds. Recent studies have begun turning up tantalizing hints about how the bacteria living in the gut can alter the way the brain works. These findings raise a question with profound implications for mental health: Can we soothe our brains by cultivating our bacteria?

The remainder of the article can be found here – https://www.sciencenews.org/article/microbes-can-play-games-mind

http://www.sciencedirect.com/science/article/pii/S0022395615000655

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Neisseriales

Neisseriales (order): are abundant commensal bacteria that frequent healthy gut, urinary, and oral microbiomes. These bacteria are more common in healthy folks digestive tracts than they are in those of Crohn€™s disease sufferers, and the microbes tend to be depleted in the mouths of patients experiencing active tooth decay. They are also found on our skin, and the longer we go between successive hand-washings, the more Neisseriales that grown on our hands (Source: Ubiome).

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Fusobacteriales

Fusobacteriales (order): are part of the standard cast of characters in the microbiomes of our mouth, lungs, gut, and urinary tract. They are found more frequently in the digestive tracts of healthy folks than those of Crohn€™s Disease sufferers and are more common in the mouths of healthy folks than in those of noma sufferers (noma is a necrotizing disease of the gums and jaws that disproportionately affects children in developing countries (source Ubiome).

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Cyanobacteria

Cyanobacteria: residing in our gut appear to help generate B and K vitamins that we depend upon for nutrition. Although it was originally believed that the cyanobacteria in our gut originate from the chloroplasts in plants we eat, research indicates that our gut cyanobacteria are different strains that evolved to specifically inhabit our digestive tracts and help us ferment sugars we digest into acids and alcohols. Despite being commonly known as blue-green algae, cyanobacteria are in fact ancient bacteria that arose over three billion years ago. More than two billion years ago, cyanobacteria living alongside early forms of plant-life were actuallyabsorbed by plant cells and became what we now know as chloroplasts (Source Ubiome).

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Actinobacteria

Actinobacteria: which are so important to a healthy microbiome that we can even take probiotic supplements of them, are the most common microbes on our skin and are commensal to our mouths and genitals too. It is in fact the suborder Propionibacteria that is the most frequent inhabitant of our skin. Some bacteria play different roles in male versus female microbiomes – and Actinobacteria happen to crop up a lot in the female camp. These microbes are major components of the female urinary microbiome and are also affected by changes caused by pregnancy. Gender differences aside, people with psoriasis have less of these bugs but people with ulcerative colitis tend to have more. Actinobacteria are also the most common bacteria in our noses. Beyond the microbiome, these microbes are found predominantly in soil and freshwater, and strains are known to produce a variety of biologically active compounds including antibiotics, antifungals, and plant and animal growth factors. The phylum Actinobacteria is made up of only one, eponymous, class (Source Ubiome).

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ProteoBacteria

ProteoBacteria: Along with Firmicutes, Proteobacteria are the most common gut microbes in Westerners. Although all of us carry these microbes, folks with inflammatory bowel disease seem to have more Proteobacteria and fewer varieties of other bacteria. Interestingly, the proportional representation of Proteobacteria increases dramatically in the digestive tracts of pregnant women in their third trimester. (Source Ubiome).

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Bacteroidetes

Bacteroidetes: are the most prominent gut microbes in much of the world. They are thought to help protect against obesity because they do not digest fat well. The first settlers of Europe needed to be able to better digest fat, so they would have enough energy to survive brutal, Ice Age winters. People who had fewer Bacteroidetes and more fat-digesting Firmicutes therefore became the dominant players. Now Bacteroidetes are underrepresented in the guts of Europeans and North Americans, but the phenomenon doesn’t appear to be genetic. African Americans’ proportions of are more similar to fellow North Americans’ than they are to native Africans’. Fortunately, this fact means that with dietary and lifestyle changes, we should be able to grow our Bacteroidetes back especially since most of us don’t need to store up for the next saber-toothed tiger hunt. (source Ubiome).

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Firmicute

Firmicute helps us to digest fat that our bodies need for energy and are among the most common microbes in our gut. Although an oversupply of firmicutes has been linked to a higher risk of obesity, historically these bacteria helped early Europeans survive harsh winters with barely a wooly mammoth in sight. Now that we inhabit less challenging environments, an imbalance of too many Firmicutes in relation to another common gut microbe, Bacteroidetes, may be associated with obesity. However, having more Firmicutes than Bacteroidetes in the vagina is correlated with decreased risk of bacterial vaginosis. Some well-known Firmicutes are the pathogens behind diseases such as botulism and anthrax, but the vast majority are both completely harmless and necessary for normal digestion. Outside the microbiome, this diverse subgroup of bacteria is involved in processes ranging from fermentation of beer and wine, breakdown of milk into yogurt, and even toxic waste clean-up (called “bioremediation”) (Source Ubiome).

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