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 New research found that one course of antibiotics (ciprofloxacin, clindamycin, amoxicillin or minocycline) had varying effects on the gut and saliva microbes, with ciprofloxacin having a negative and disruptive effect on gut microbiome diversity up to 12 months. While the microscopic communities living in the mouth rebound quickly, just one course of antibiotics can disrupt the gut microbiome for months - with amoxicillin the least and ciprofloxacin the most (up to a year).The researchers stressed that for these reasons "antibiotics should only be used when really, really necessary. Even a single antibiotic treatment in healthy individuals contributes to the risk of resistance development and leads to long-lasting detrimental shifts in the gut microbiome."

The scary part is that Americans typically take many courses of antibiotics throughout life. And people with conditions such as chronic sinusitis typically take many more than average. From Medical Xpress:

One course of antibiotics can affect diversity of microorganisms in the gut

A single course of antibiotics has enough strength to disrupt the normal makeup of microorganisms in the gut for as long as a year, potentially leading to antibiotic resistance, European researchers reported this week in mBio, an online open-access journal of the American Society for Microbiology. In a study of 66 healthy adults prescribed different antibiotics, the drugs were found to enrich genes associated with antibiotic resistance and to severely affect microbial diversity in the gut for months after exposure. By contrast, microorganisms in the saliva showed signs of recovery in as little as few weeks.

The microorganisms in study participants' feces were severely affected by most antibiotics for months, said lead study author Egija Zaura, PhD, an associate professor in oral microbial ecology at the Academic Centre for Dentistry in Amsterdam, the Netherlands. In particular, researchers saw a decline in the abundance of health-associated species that produce butyrate, a substance that inhibits inflammation, cancer formation and stress in the gut.

"My message would be that antibiotics should only be used when really, really necessary," Zaura said. "Even a single antibiotic treatment in healthy individuals contributes to the risk of resistance development and leads to long-lasting detrimental shifts in the gut microbiome."

It's not clear why the oral cavity returns to normal sooner than the gut, Zaura said, but it could be because the gut is exposed to a longer period of antibiotics. Another possibility, she said, is that the oral cavity is intrinsically more resilient toward stress because it is exposed to different stressors every day.

The investigators enrolled healthy adult volunteers from the United Kingdom and Sweden. Participants were randomly assigned to receive a full course of one of four antibiotics (ciprofloxacin, clindamycin, amoxicillin or minocycline) or a placebo. The researchers, who did not know which medication participants took, collected fecal and saliva samples from the participants at the start of the study; immediately after taking the study drugs; and one, two, four and 12 months after finishing the medications....

Researchers found that participants from the United Kingdom started the study with more antibiotic resistance than did the participants from Sweden, which could result from cultural differences. There has been a significant decline in antibiotic use in Sweden over the last two decades, Zaura said.

In addition, fecal microbiome diversity was significantly reduced for up to four months in participants taking clindamycin and up to 12 months in those taking ciprofloxacin, though those drugs only altered the oral cavity microbiome up to one week after drug exposure. Exposure to amoxicillin had no significant effect on microbiome diversity in either the gut or oral cavity but was associated with the greatest number of antibiotic-resistant genes.

1412 Gut bacteria. Credit: Med. Mic. Sciences Cardiff Uni, Wellcome Images

This study confirms all my recent posts on the importance of fiber, fruits, vegetables, whole grains, seeds, nuts, and legumes for beneficial gut bacteria health (have to feed them!). This study found dramatic changes in the colon (specifically in the colonic mucosa) from dietary changes in as little as 2 weeks. In the study the Americans ate the typical low-fat, high fiber diet of South Africa which included foods such as hi-maize corn fritters, beans, salmon croquettes, spinach, red pepper and onions, homemade tater tots, mango slices,okra, tomatoes, corn muffins, black-eyed peas, and pineapple. Meanwhile, people in South Africa ate an “American” high-fat, low-fiber diet: Foods included beef sausage links and pancakes for breakfast; hamburger and French fries for lunch; and meatloaf and rice for dinner. From Science Daily:

Diet swap has dramatic effects on colon cancer risk for Americans and Africans

Scientists have found dramatic effects on risk factors for colon cancer when American and African volunteers swapped diets for just two weeks. Western diets, high in protein and fat but low in fibre, are thought to raise colon cancer risk compared with African diets high in fibre and low in fat and protein.The new study, published in Nature Communications today, confirms that a high fibre diet can substantially reduce risk, and shows that bacteria living in the gut play an important role in this effect.

Colon cancer is the fourth commonest cause of death from cancer worldwide, accounting for over 600,000 deaths per year. Colon cancer rates are much higher in the western world than in Africa or the Far East, yet in the United States, African Americans shoulder the greatest burden of the disease.

To investigate the possible roles of diet and gut bacteria, an international team including scientists from the University of Pittsburgh and Imperial College London carried out a study with a group of 20 African American volunteers and another group of 20 participants from rural South Africa. The two groups swapped diets under tightly controlled conditions for two weeks.... At the start, when the groups had been eating their normal diets, almost half of the American subjects had polyps -- abnormal growths in the bowel lining that may be harmless but can progress to cancer. None of the Africans had these abnormalities.

After two weeks on the African diet, the American group had significantly less inflammation in the colon and reduced biomarkers of cancer risk. In the African group, measurements indicating cancer risk dramatically increased after two weeks on the western diet.

"The findings suggest that people can substantially lower their risk of colon cancer by eating more fibre. This is not new in itself but what is really surprising is how quickly and dramatically the risk markers can switch in both groups following diet change. These findings also raise serious concerns that the progressive westernization of African communities may lead to the emergence of colon cancer as a major health issue."

Professor Stephen O'Keefe at the University of Pittsburgh, who directed the study, said: "Studies on Japanese migrants to Hawaii have shown that it takes one generation of westernization to change their low incidence of colon cancer to the high rates observed in native Hawaiians. Our study suggests that westernization of the diet induces changes in biomarkers of colon cancer risk in the colonic mucosa within two weeks. Perhaps even more importantly, a change in diet from a westernized composition to a 'traditional African' high fiber low fat diet reduced these biomarkers of cancer risk within two weeks, indicating that it is likely never too late to change your diet to change your risk of colon cancer."

The study found that a major reason for the changes in cancer risk was the way in which the bacteria in the gut -- known as the microbiome -- altered their metabolism to adapt to the new diet. In the American group, the researchers found that the African diet led to an increase in the production of butyrate, a byproduct of fibre metabolism that has important anti-cancer effects.

The American subjects switched to a low-fat, high-fibre diet based on that of rural Africans in KwaZulu-Natal.Photograph: brianafrica / Alamy/Alamy

My last post A Special Gut Microbe was on the very essential and beneficial microbe Faecalibacterium prausnitzii. It is one of the most abundant  bacteria in the gut of healthy individuals, but low or depleted levels are associated with inflammation and found in a number of diseases, including intestinal bowel diseases such as Crohn's disease. It is a butyrate producing bacteria (beneficial). F. prausnitzii is viewed as so essential that it has been called a "keystone species" in the gut. Now the question I've been asked is: how can one increase the numbers of this bacteria in the gut and where can one buy some to take as a probiotic? (Probiotics are live bacteria that are beneficial to health when consumed.)

The typical bacteria added to yogurts or sold as supplements are able to survive when exposed to air (oxygen). However, F. prausnitzii are "oxygen sensitive" and they die within minutes upon exposure to air. Researchers view this beneficial bacteria as a "probiotic of the future" and currently there is research going on to figure out ways it can be easily stored and be exposed to air a few hours and not die. So currently there is NO way to take a probiotic F. prausnitzii supplement. So what else can one do?

After reviewing the scientific literature, it seems that the current ways to get F. prausnitzii into the gut or increase its numbers are: fecal microbiota transplant or FMT (currently only done with desperately ill individuals), drastically restricting calories for one week by obese individuals increases beneficial bacteria, and making changes to the diet. For example, a high animal meat, high animal fat, high sugar, highly processed foods, and low fiber diet (the typical westernized diet) lowers F. prausnitzii numbers, while a high-fiber, low meat diet increases F. prausnitzii numbers.

Repeat: the number one thing a person can do to increase numbers of F. prausnitzii is to increase fiber in the diet. By the way, increasing dietary fiber increases butyrate, and butyrate is involved with colon health, is anti-inflammatory, and anti-cancer . See, it's all related. By high fiber is meant: whole grains, vegetables, fruits, nuts, seeds, and legumes. Eat a varied plant-based diet, which means lots of plant based foods. It seems that Michael Pollan's emphasis on "Eat real foods. Mostly plants. Not too much." is just right. And variety seems important - with different types of fiber feeding different bacteria. While F. prausnitzii may be an important beneficial bacteria in the gut, it is not the only beneficial one. So a food labeled "with added fiber" may not be the right fiber for bacteria, This is even true for enteral formula supplementation, for example one formula containing fiber used pea fiber and this did not feed the F. prausnitziiAssociation between Faecalibacterium prausnitzii and dietary fibre in colonic fermentation in healthy human subjects

In the first paragraph I mentioned that research has consistently shown F. prausnitzii depletion in adults sick with IBDs such as Crohn's disease. So it was interesting to find that one recent study found that even people sick with Crohn's disease showed significant improvement and remission (92% remission at 2 years) on a semi-vegetarian diet, namely a lacto-ovo-vegetarian diet (daily 32.4 g of dietary fiber in 2000 calories). High Amount of Dietary Fiber Not Harmful But Favorable for Crohn Disease This is totally opposite from the current prevailing medical view which currently encourages people with IBD to "rest the intestine" with a fiber-restricted diet.