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Research on Microbiome (think Antibiotic/Probiotic)

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Generally when we undergo an operation in a hospital we are treated with antibiotics to protect us from harmful bacteria present in a hospital. This kills not only the bad bacteria but also the good gut bacteria in our colons. As a result, many of us take Probiotics to reestablish the colonies of good bacteria in our gut.

I came across research of gut flora this morning that seemed interesting. Our body’s microbiome, the bacteria living in symbiotic harmony in our gut provides us with a source of wellness. Two small, exploratory studies, analyzed microblome in terms of change and resilience.

Influence of Geographical Change

In the first study, researchers looked at the diversity of our gut flora as individuals immigrated and assimilated, changing diet and geography. The inspiration may have been the finding that immigrants to the US often develop weight gain and Western diseases - obesity, hypertension, diabetes, and coronary artery disease. While refeeding of individuals who came from food challenged areas is felt to be part of the issue, changing diet has also been implicated.

The authors collected stool samples, 24-hour food recall surveys and demographics from two distinct Thai populations, the Hmong and Karen. Individuals included those still living in Thailand as well as immigrants (1st generation) and their children (2nd generation). Thai immigrants were chosen because the study was conducted in Minnesota a central site for their immigration; women formed the predominant research population because they were more frequently the immigrants. Americans of European ancestry served as the control.

* Microbiologic richness and diversity were greatest in current Thai residents.

* 30% of that diversity was lost in the first generation immigrants, and the diversity continued to decline and resemble that of the control group as time in the US increased and in the 2nd generation, American born Thai children.

* Bacteroides strains replaced Prevotella strains among immigrants, the extent of that shift again associated with length of residence in the US.

* The loss of Prevotella was felt to be the driving force behind a decreasing functional ability of the microbiome to degrade dietary fibers indigenous to the native Thai diet. Think of it as use it or lose it.

* Dietary shifts to a Western diet was felt to account for only about 16% of total variation.

* Westernization of the microbiome began within nine months of arrival.


A second, "proof of concept" like study, looked at 12 healthy men treated for four days with an antibiotic cocktail meant to mimic common first-line choices for intensive care patients. [1] The outcome was the effect on the gut microbiome over a subsequent six month period, again measured by stool cultures taken at various time intervals. It is no surprise, at least to clinicians, that the antibiotics did not sterilize the gut, but it did bring about changes.

* There was an immediate drop in the diversity and richness of the microbiologic populations, but by Day 8 diversity was returning although it never reached baseline values.

* By Day 8, the relative abundance of about 50 species changed, some increasing and others decreasing – clearly, the ecology was different. And while some bacterial species were still absent after six months, by Day 42, the ecology had, for the most part, returned to its baseline.

* Antibiotic resistance was only one of many virulence factors enhanced by the antibiotic exposure that lead to an early increase in pathologic bacteria. But over time the pathologic bacteria were again overrun by more symbiotic species. Virulence factors

* Interestingly, Clostridium species which had not been seen initially were now present – this is a species that forms spores as protection in an unhealthy environment and then returns to its other form when “the coast is clear;” it is the source of antibiotic-related hospital-acquired morbidity, C. difficile diarrhea.

Source: I Sing The Body's Microbiome

So what are some of the takeaways? First, antibiotic treatment does not sterilize the gut microbiome. But it does reduce the diversity and richness of gut bacteria. Recovery of the colonies of good gut bacteria begins about 8 days after the antibiotic treatment end. So a patient is more vulnerable to pathologic bacteria during that time. For example - it is the source of antibiotic-related hospital-acquired morbidity, C. difficile diarrhea. Therefore using probiotics after the antibiotic treatment ends and you leave the hospital is a good approach in order to quickly reestablish the diversity of good gut bacteria.

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