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 People have asked me if eating sweet desserts or hamburgers is bad for the health if the rest of their diet is good - with lots of fruits, vegetables, whole grains, legumes (beans), and nuts (much like the Mediterranean diet). My sense over the past few years of looking at the research is that one should look at the overall diet, and that a "perfect diet" all the time is pretty darn hard to achieve, if not impossible, for most of us. So this new research looking at gut bacteria and "chemical fingerprints of cellular processes" (by looking at stool and urine samples) of people eating different diets (vegan, vegetarian, omnivore) was reassuring.  The findings suggest: make sure to feed your beneficial bacteria with a healthy diet like the Mediterranean diet (lots of plant-based foods), and then some deviation (cookies! steak!) is OK.

The researchers found that while the kind of gut bacteria dominating were different among the groups (vegan, vegetarian, omnivores), they also found that eating a lot of fiber-rich foods, such as fruit, vegetables, and legumes (typical of a Mediterranean diet) is linked to a rise in health promoting short chain fatty acids (SCFA). Yes, levels of trimethylamine oxide (TMAO) (which is linked to cardiovascular disease) were significantly lower in vegetarians and vegans than they were in those of the omnivores. But the more omnivores closely followed a Mediterranean diet, the lower were their TMAO levels.(Which is great!). As the researchers said: "Western omnivore diets are not necessarily detrimental when a certain consumption level of plant foods is included. From Science Daily:

High dietary fiber intake linked to health promoting short chain fatty acids

Eating a lot of fibre-rich foods, such as fruit, vegetables, and legumes--typical of a Mediterranean diet--is linked to a rise in health promoting short chain fatty acids, finds research published online in the journal Gut. And you don't have to be a vegetarian or a vegan to reap the benefits, the findings suggest.

Short chain fatty acids (SCFAs), which include acetate, propionate, and butyrate, are produced by bacteria in the gut during fermentation of insoluble fibre from dietary plant matter. SCFAs have been linked to health promoting effects, including a reduced risk of inflammatory diseases, diabetes, and cardiovascular disease.

The researchers gathered a week's information on the typical daily diet of 153 adults who either ate everything (omnivores, 51), or were vegetarians (51), or vegans (51), and living in four geographically distant cities in Italy....The Mediterranean diet is characterised by high intake of fruit, vegetables, legumes, nuts and cereals; moderately high intake of fish; regular but moderate alcohol consumption; and low intake of saturated fat, red meat, and dairy products. Most (88%) of the vegans, almost two thirds of the vegetarians (65%), and around a third (30%) of the omnivores consistently ate a predominantly Mediterranean diet.

The investigation showed distinct patterns of microbial colonisation according to usual dietary intake. Bacteroidetes were more abundant in the stool samples of those who ate a predominantly plant based diet, while Firmicutes were more abundant in those who ate a predominantly animal products diet. Both these categories of organisms (phyla) contain microbial species that can break down complex carbohydrates, resulting in the production of SCFAs.

Specifically, Prevotella and Lachnospira were more common among the vegetarians and vegans while Streptococcus was more common among the omnivores. And higher levels of SCFA were found in vegans, vegetarians, and those who consistently followed a Mediterranean dietLevels of SCFAs were also strongly associated with the quantity of fruit, vegetables, legumes, and fibre habitually consumed, irrespective of the type of diet normally eaten.

On the other hand, levels of trimethylamine oxide (TMAO)--a compound that has been linked to cardiovascular disease--were significantly lower in the urine samples of vegetarians and vegans than they were in those of the omnivores. But the more omnivores closely followed a Mediterranean diet, the lower were their TMAO levels, the analysis showed.

TMAO levels were linked to the prevalence of microbes associated with the intake of animal proteins and fat, including L-Ruminococcus (from the Lachnospiraceae family). Eggs, beef, pork and fish are the primary sources of carnitine and choline--compounds that are converted by gut microbes into trimethylamine, which is then processed by the liver and released into the circulation as TMAO.

The researchers point out that SCFA levels can naturally vary as a result of age and gender, and their study did not set out to establish any causal links. But they nevertheless suggest that the Mediterranean diet does seem to be associated with the production of health promoting SCFAs. They conclude: "We provide here tangible evidence of the impact of a healthy diet and a Mediterranean dietary pattern on gut microbiota and on the beneficial regulation of microbial metabolism towards health maintenance in the host." And they add: "Western omnivore diets are not necessarily detrimental when a certain consumption level of [plant] foods is included."

There has been a lot of discussion in the last few years of our gut bacteria (hundreds of species), the microbiome (the community of microbes living within and on a person (gut, nasal cavities, mouth, sinuses, etc.), probiotics, the finding of a link between bacteria and some chronic diseases, and how the modern lifestyle and antibiotics are wiping out our beneficial gut microbes. I am frequently asked how one can improve or nurture the beneficial bacteria in our bodies.

While no one knows what exactly is the "best" or "healthiest" microbial composition of the gut, it does look like a diversity of bacteria is best (may make you healthier and more able to resist diseases). Research also suggests that the diversity and balance of bacteria living in the body can be changed and improved, and changes can occur very quickly. And that the microbial communities fluctuate for various reasons (illness, diet,etc.). Diet seems to be key to the health of your gut microbial community. Prebiotics feed the beneficial bacteria in the gut, probiotics are live beneficial bacteria, and synbiotics are a combination of prebiotics and probiotics. But don't despair - you can improve your gut microbial community starting now. The following are some practical tips, based on what scientific research currently knows.


Eat a wide variety of foods, especially whole foods that are unprocessed or as minimally processed as possible. Eat everything in moderation.

Eat a lot of plant based foods: fruits, vegetables, whole grains, seeds, nuts, and legumes. Think of Michael Pollan's advice: "Eat food. Not too much. Mostly plants."

Eat more washed and raw fruits and vegetables (lots of bacteria and fiber to feed and nurture the bacteria). Some every day would be good.

Eat more soluble and insoluble types of fiber, and increase how many servings you eat every day. A variety of  fiber foods every day, and several servings at each meal, is best. Think fruits, vegetables, whole grains, legumes, nuts, seeds. (See How Much Dietary Fiber Should We Eat? - also has a chart with high fiber foods, and Recent Studies Show Benefits of Dietary Fiber)

Eat as many organic foods as possible. There is much we don't yet know, and pesticides are like antibiotics - they kill off microbes, both good and bad. Somehow I think that lowering the levels in your body of pesticides (as measured in blood and urine) can only be beneficial. Also, organic foods don't contain added antibiotics and hormones. (Eat Organic Foods to Lower Pesticide Exposures).  But even if you can't or won't eat organic foods, it is still better to eat non-organic fruits, vegetables, and whole grains than to not eat them.

Eat some fermented foods such as kimchi and sauerkraut (they contain live bacteria), kefir, and yogurts with live bacteria. Eat other bacteria containing foods such as cheeses, and again a variety is best (different cheeses have different bacteria).

Try to avoid or eat less of mass-produced highly processed foods, fast-foods, preservatives, colors and dyes, additives, partially hydrogenated oils, and high-fructose corn syrup. Read all ingredient lists on labels, and even try to avoid as much as possible "natural flavors" (these are chemicals concocted in a lab and unnecessary). Even emulsifiers (which are very hard to avoid) are linked to inflammation and effects on gut bacteria.

Avoid the use of triclosan or other "sanitizers" in soaps and personal care products (e.g., deodorants). Triclosan promotes antibiotic resistance and also kills off beneficial bacteria. Wash with ordinary soap and water.

Avoid unnecessary antibiotics (antibiotics kill off bacteria, including beneficial bacteria).

Vaginal births are best - microbes from the birth canal populate the baby as it is being born. If one has a cesarean section, then one can immediately take a swab of microbes from the mother's vagina (e.g., using sterile gauze cloth) and swab it over the newborn baby. (See post discussing this research by Maria Gloria Dominguez Bello )

Breastfeeding is best - breastfeeding provides lots of beneficial microbes and oligosaccharides that appear to enrich good bacteria in the baby’s gut.

Live on a farm, or try to have a pet or two. Having pets, especially in the first year of life,  ups exposure to bacteria to help develop and strengthen the immune system, and prevent allergies. Pets such as dogs and cat expose humans to lots of bacteria.

Get regular exercise or physical activity. Professional athletes have more diverse gut bacterial community (considered beneficial) than sedentary people.

Can consider taking probiotics - whether in foods or supplements. They are generally considered beneficial, but not well studied, so much is unknown. The supplements are unregulated, and the ones available in stores may not be those that are most commonly found in healthy individuals. Research the specific bacteria before taking any supplements. Researchers themselves tend to stay away from probiotic supplements and focus on eating a variety of all the foods mentioned above (fruits, vegetables, whole grains, seeds, nuts, legumes, fermented foods) to feed and nurture beneficial bacteria.