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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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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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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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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