Skip to content

Category: human microbiome

Published on

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.

SOME STEPS TO FEED AND NURTURE YOUR GUT MICROBES:

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.

Published on

The science world has recently been abuzz with the results finding that an isolated American Indian group (the Yanomami) in the Venezuelan  Amazon have the most diverse microbiome (microbial community) ever discovered in humans.About double those found in humans living in the U.S. The scientists suggest that our Western lifestyle with processed foods, antibiotic use, sanitation, use of antibacterials, Cesarean sections, bottle-feeding (instead of breastfeeding) all have reduced microbial diversity in humans living in developed countries such as the United States. It is currently thought that reduced diversity is linked to some chronic diseases and even some cancers.From Nature:

Bacteria bonanza found in remote Amazon village

An isolated American Indian group in the Venezuelan Amazon hosts the most-diverse constellation of microbes ever discovered in humans, researchers reported on 17 April in Science Advances1.Surprisingly, the group's microbiome includes bacteria with genes that confer antibiotic resistance — even though its members, part of the Yanomami tribe, are not thought to have been exposed to the drugs.

But scientists still do not understand all the factors that determine the make-up of a person's microbiome. “We do know that food, environment and chemicals play the big roles,” says Sarkis Mazmanian, a microbiologist at the California Institute of Technology in Pasadena. The wide adoption of antibiotics, rigorous hygiene and processed diets is thought to have have cut down the genetic diversity of microbiomes in the developed world.

This makes the microbiomes of individual Yanomami particularly interesting, Dominguez-Bello says. The researchers took oral, faecal and skin samples from 34 people in a small Yanomami community that was unknown to the Western world until 2008, when it was spotted by helicopter....When researchers analysed the microbial DNA in those samples, they found that the average Yanomami's microbiota had twice as many genes as that of the average US person. More surprisingly, the Yanomami microbiome was even more diverse than those reported for other indigenous groups in South America and in Africa.

From New Scientist: Is super-diverse Amazon microbiome something to strive for?

The Yanomami people in the Venezuelan rainforest have the most diverse population of gut microbes ever seen, far more varied than Western guts. Does it matter?

Hunter-gathering in the rainforests and mountains of northern Brazil and southern Venezuela, the Yanomami eat a high-fibre diet based largely on cassava. For thousands of years, some groups have lived without contact with the rest of the world and are thought to be some of the few remaining communities never to have been exposed to antibiotics, which can wipe out the microbes in your gut.Sequencing the genes in the faecal samples revealed that the Yanomami carried nearly double the diversity of microbial species in their intestines compared with people living in the US. They also had about 30 to 40 per cent more diversity than a less isolated group of Venezuelan hunter-gatherers that has largely maintained its traditional lifestyle but has occasionally used antibiotics and eaten processed foods.

"Our results suggest that Westernisation leads to the reduction of diversity, to different microbiota compositions," Maria Dominguez-Bello of the New York University School of Medicine, who led the research, told a teleconference on Wednesday. Her colleague Jose Clemente of the Icahn School of Medicine at Mount Sinai in New York, said the results suggest that even minimal exposure to modern lifestyle practices such as using antibacterial soaps and cleansers, taking antibiotics and having Caesarean sections, which mean babies don't pass through their mother's birth canal and pick up her microbes, can result in a dramatic loss of microbial biodiversity.

So does a more diverse microbiome make for a healthier person? Possibly. Healthier people do seem to host a more diverse array of microbes but it's hard to know whether one causes the other. There is some evidence that losing certain microbial species is linked to some cancers, plus giving mice antibiotics can make them gain weight, so perhaps a good mix of microbes in your gut can keep you from piling on the pounds.

Walter doesn't recommend striving drastically to make the paltry Western gut look more Yanomamian. Poor sanitation is probably one factor contributing to the Papua New Guinean's high microbial diversity, but they have high levels of infectious diarrhoea as a result – not a situation that Western urbanised nations would want to return to.

Published on

This research found that the beneficial gut bacteria Lactobacillus rhamnosus GG (LGG) interacts and facilitates (modifies the activity) of other gut bacteria. This isn't surprising. All our microbiomes are communities or ecosystems of microbes. But the really important bacteria have been called keystone species by other researchers. From Medical Xpress:

New research sheds light on how popular probiotic benefits the gut

In recent years, research into the benefits of gut bacteria has exploded. Scientists across the globe are examining how these microbes can help improve health and prevent disease. One of the most well-known of these is Lactobacillus rhamnosus GG (LGG). This strain of bacteria, which is part of many popular probiotic products, has a reputation as a helpful microbe. Researchers have found evidence that it can help with intestinal problems, respiratory infections and some skin disorders. Some research suggests that it may even help with weight loss. But a key question has remained unanswered: How does LGG actually produce benefits?

Now, researchers at the University of Maryland School of Medicine (UM SOM) have come up with an explanation. It appears that LGG may act as a facilitator, modifying the activity of other gut bacteria....Claire M. Fraser, PhD, professor of medicine at the UM SOM, as well as director of the Institute for Genome Sciences, studied the effect of LGG on a group of elderly subjects.

She and her collaborator, Dr. Patricia Hibberd at Massachusetts General Hospital, tested 12 subjects, who ingested LGG twice a day for 28 days. She analyzed gut bacteria before and after this regimen, and found that ingesting LGG led to increases in several genes that foster several species of gut bacteria, including Bacteroides, Eubacterium, Faecalibacterium, Bifidobacterium and Streptococcus. These microbes have been shown to have a range of benefits in humans, including the promotion of a healthy immune system. (Fraser notes that LGG may also have direct effects, in addition to its ability to modify the overall ecosystem.)

"This is a new idea, that some probiotics may work by affecting the overall ecosystem of the gut," said Prof. Fraser. "Previously we tended to think that LGG and other probiotics worked directly on the host. I think this finding has many exciting implications." For one, Fraser says, it lends support to the idea that we need to look at the microbes in the gut as an interconnected ecosystem rather than a series of solitary bacteria. Modifying the behavior of microbes already in the gut may be just as important as adding any single species to this population.

Published on

The American diet with its emphasis on highly processed foods is linked to chronic diseases. It's also not healthy when you look at the microbiome (community of microbes living in your body). With all the health research out there showing health benefits of real whole foods (especially fruits, vegetables, whole grains, seeds, legumes), then the finding that highly processed foods dominate U.S. food purchases are just plain sad. But I'm not surprised. From Science Daily:

Highly processed foods dominate U. S. grocery purchases

A nation-wide analysis of U.S. grocery purchases reveals that highly processed foods make up more than 60 percent of the calories in food we buy, and these items tend to have more fat, sugar and salt than less-processed foods.

From 2000 to 2012, the researchers asked 157,142 households to use UPC barcode scanners to record all foods and beverages they purchased from grocery stores for at least 1 year. Although items without barcodes were not included, Poti points out that packaged produce such bagged lettuce or pints of berries can be scanned. Households participated in the study for an average of four years and collectively purchased 1.2 million items. The research team then linked each item to its nutrition information, product description and ingredient list, allowing them to rank each product's degree of food processing.

The researchers classified products as highly processed if they contained multi-ingredient, industrially formulated mixtures. They labeled foods such as soda, cookies, chips, white bread, candy and prepared meals as highly processed foods and categorized fresh or frozen fruits and vegetables, milk, eggs, dried beans and fresh meat as unprocessed or minimally processed. The investigators also examined convenience, distinguishing between foods that are ready to eat, ready to heat or require cooking and/or preparation. Candy and chips are examples of ready-to-eat foods, and frozen meals are a ready-to-heat food.

"Overall, we found that not only are highly processed foods a dominant, stable part of U.S. purchasing patterns, but also that the highly-processed foods that households are purchasing are higher in fat, sugar, and salt, on average, compared to the less-processed foods that they buy," said Poti, who will present these findings at the American Society for Nutrition (ASN) Annual Meeting during Experimental Biology 2015."

The analysis revealed that from 2000 to 2012, the proportion of calories in highly processed food and beverage purchases by U.S. households remained stable at 61.0 to 62.5 percent. The researchers noted a significant increase in the proportion of calories purchased in ready-to-heat foods, which reached 15.2 percent in 2012. More than 80 percent of calories were purchased in ready-to-eat or ready-to-heat form in 2012, and these tended to be higher in fat, sugar and salt than food purchases that required preparation.

Published on

The researchers think that repeated courses of antibiotics destroy the gut bacteria resulting in gut bacteria imbalance. From Red Orbit:

Antibiotic overuse could up diabetes risk, study says

Repeated use of some antibiotics could increase a person’s risk of developing type 2 diabetes, according to research published online Tuesday in the European Journal of Endocrinology. In the study, scientists from the University of Pennsylvania found that men and women who had ever been prescribed with at least two courses of specific types of antibiotics were more likely to eventually be diagnosed with type 2 diabetes than those who had taken no more than one.

The antibiotics used in the research came from one of four categories, according to LiveScience: penicillins, cephalosporins, quinolones and macrolides. The authors reviewed a database of UK patients, looking at the number of antibiotic prescriptions given to over 200,000 diabetic patients at least one year before those individuals were diagnosed with the condition...They found that the more courses of antibiotics that were prescribed to a person, the greater the risk that he or she would go on to develop the disease.

Patients who had been prescribed between two and five courses of penicillin increased their risk of diabetes by 8 percent, according to the Daily Mail, and the risk increased by 23 percent for those receiving more than five courses of the frequently used antibiotic versus the one- or no-course group.

Those who were given between two and five courses of quinolones, which are used to treat respiratory and urinary tract infections, had an increased diabetes risk of 15 percent, and those receiving more than five courses saw that risk shoot up by 37 percent. 

Those who were given just one course of antibiotics showed no such increase in diabetes risk, the researchers reported. Nor was there any link found between exposure to anti-virals and anti-fungals and diabetes risk. The reason for the association between frequent antibiotic use and the risk of diabetes is not clear, but may be related to a gut bacteria imbalance, they wrote.“Gut bacteria have been suggested to influence the mechanisms behind obesity, insulin resistance and diabetes in both animal and human models. Previous studies have shown that antibiotics can alter the digestive ecosystem,” added lead author Dr. Ben Boursi.

Published on

Discussions of the benefits of dietary fiber seem to be everywhere this week.

From Forbes: Eat Whole Grains For A Long Life, New Study Says

Eating lots of whole grains – especially those high in cereal fiber – may help people live longer, according to new research. The study out in BMC Medicine this week suggests that eating hefty amounts of cereal fibers can help reduce the risk of death from a number of causes, including cancer and diabetes, by almost 20%. Previous research has certainly linked whole grains to the reduction of certain chronic diseases and to reduced mortality, but this one is the largest of its kind to show a reduction in death from a number of different causes. So if you want to live longer, grab a bowl of cereal. The less refined, the better.

Whole grains are grains in their most unadulterated form, still containing the endosperm, bran, and germ – most of the plant’s nutritional value lies in the bran and germ. When grains go through milling to become processed or refined, they’re typically stripped of the bran and germ parts, along with a number of B vitamins, fiber, and iron.

In the new study, the Harvard Medical School team tracked over 367,000 healthy people who were taking part in the NIH-AARP Diet and Health Study, for an average of 14 years. ..It turned out that people who ate more whole grains – 1.2 ounces of per day, on average – had a 17% reduced risk of death, compared to those who ate much less, around 0.13 ounces per day. And when it came to the cereal fiber itself, people who ate the most had a 19% reduced risk of death from any cause, compared to those who ate the least.

The researchers even broke it down by disease: People who ate the highest amounts of whole grains had a 48% reduced risk of death from diabetes, and an 11% reduced risk of dying from respiratory diseases. And people who ate the most cereal fiber had 15% and 34% reduced risk of death from cancer and diabetes, respectively. 

The study cannot of course determine causation, since it’s just observational...Still, a number of studies have pointed to a strong connection between whole grains and improved health and longevity in recent years. It may be the anti-inflammatory properties of fiber per se – and its effect of reducing c-reactive protein (CRP) and tumor necrosis factor – that are responsible for their health benefits. If you’re going to up your grain intake, make sure to choose whole ones, like steel cut oats, quinoa, or even whole grain bread, over refined ones like cereal flakes or white bread. 

From Scientific American: Fiber-Famished Gut Microbes Linked to Poor Health

Your gut is the site of constant turf wars. Hundreds of bacterial species—along with fungi, archaea and viruses—do battle daily, competing for resources. Some companies advocate for consuming more probiotics, live beneficial bacteria, to improve microbial communities in our gut, but more and more research supports the idea that the most powerful approach might be to better feed the good bacteria we already harbor. Their meal of choice? Fiber.  

Fiber has long been linked to better health, but new research shows how the gut microbiota might play a role in this pattern. One investigation discovered that adding more fiber to the diet can trigger a shift from a microbial profile linked to obesity to one correlated with a leaner physique. Another recent study shows that when microbes are starved of fiber, they can start to feed on the protective mucus lining of the gut, possibly triggering inflammation and disease.

"Diet is one of the most powerful tools we have for changing the microbiota," Justin Sonnenburg, a biologist at Stanford University, said earlier this month at a Keystone Symposia conference on the gut microbiome. "Dietary fiber and diversity of the microbiota complement each other for better health outcomes." In particular, beneficial microbes feast on fermentable fibers—which can come from various vegetables, whole grains and other foods—that resist digestion by human-made enzymes as they travel down the digestive tract. These fibers arrive in the large intestine relatively intact, ready to be devoured by our microbial multitudes. Microbes can extract the fiber's extra energy, nutrients, vitamins and other compounds for us. Short-chain fatty acids obtained from fiber are of particular interest, as they have been linked to improved immune function, decreased inflammation and protection against obesity.

Today's Western diet, however, is exceedingly fiber-poor by historical standards. It contains roughly 15 grams of fiber daily, Sonnenburg noted. For most of our early history as hunter-gatherers, we were likely eating close to 10 times that amount of fiber each day. "Imagine the effect that has on our microbiota over the course of our evolution," he said.

Not all helpful fiber, however, needs to come from the roots and roughage for which our ancestors foraged, new research suggests. Kelly Swanson, a professor of comparative nutrition at the University of Illinois at Urbana-Champaign, and his team found that simply adding a fiber-enriched snack bar to subjects' daily diets could swing microbial profiles in a matter of weeks... The findings were published in the January issue of the American Journal of Clinical Nutrition.

As gut microbes are starved of fermentable fiber, some do die off. Others, however, are able to switch to another food source in the gut: the mucus lining that helps keep the gut wall intact and free from infection. In a recent study presented at the Keystone meeting, Eric Martens of the University of Michigan Medical School, postdoctoral researcher Mahesh Desai and their colleagues found that this fuel switch had striking consequences in rodents. A group of mice fed a high-fiber diet had healthy gut lining, but for mice on a fiber-free diet, "the mucus layer becomes dramatically diminished," he explained at the meeting. This shift might sometimes have severe health consequences. Research by a Swedish team, published last year in the journal Gut, showed a link between bacteria penetrating the mucus layer and ulcerative colitis, a painful chronic bowel disease.

A third group of mice received high-fiber chow and fiber-free chow on alternating days—"like what we would do if we were being bad and eating McDonald's one day and eating our whole grains the next," Martens joked. Even the part-time high-fiber diet was not enough to keep guts healthy: these mice had a mucus layer about half the thickness of mice on the consistently high-fiber diet. If we can extend these results to humans, he said, it "tells us that even eating your whole fiber foods every other day is still not enough to protect you. You need to eat a high-fiber diet every day to keep a healthy gut." Along the same lines, Swanson's group found that the gut microbiomes of his adult subjects reverted back to initial profiles as soon as the high-fiber bars were discontinued.

Published on

How much fiber is there in the different foods we eat? And how much should we eat? Recent posts (Where Do I Get That Beneficial Gut Bacteria? and A Special Gut Microbe) stressed the importance of eating dietary fiber for various health benefits and to feed the beneficial bacteria (such as Faecalibacterium prausnitzii) in our gut. Are there different types of fiber and does it matter?

Currently the average American adult eats about 12 to 18 grams of dietary fiber daily. But the latest advice (from both National Academy of Sciences and Academy of Nutrition and Dietetics) is to eat over 20 grams of dietary fiber daily to about 35 grams daily, depending on weight. So a person eating a 2000 calorie daily diet should have about 25 grams of fiber daily. Their recommendation for children is that intake should equal age in years plus 5 g/day (e.g., a 4 year old should consume 9 g/day). 

Good fiber foods are: fruits, vegetables, whole grains, legumes (beans), nuts, and seeds. But people eating a typical westernized diet are instead eating a high fat, high meat, highly processed food diet which neglects plant-based foods. Go look at the ingredient labels of favorite American foods and see that many don't have fiber or are low in dietary fiber (e.g., hot dogs, salami, candy, cookies, potato chips).

Dietary fiber or roughage is the indigestible portion of food derived from plants. There are two types of fiber: soluble and insoluble, and both should be eaten for good health because they benefit health in a number of ways.

Insoluble fiber doesn't dissolve in water and passes through the intestines (it provides bulking), while soluble fiber dissolves in water, and becomes a gel. Plant foods contain both types of fiber in varying degrees, depending on the plant's characteristics. For example, plums and prunes have a thick skin covering a juicy pulp. The skin is a source of insoluble fiber, whereas soluble fiber is in the pulp.

One can also take fiber supplements, but actual real foods have many more health benefits to them, and also provide a variety of fiber sources. Eating a variety of whole plant-based foods is beneficial in many ways, including feeding the variety of bacteria species in your gut. Remember that different bacteria need different foods, and so eating a variety of foods is best.

To increase your daily dietary fiber intake, first take a look at the amount of fiber in different foods. And then eat lots of fruits, vegetables, whole grains, legumes (beans), seeds, and nuts.

The following tables give approximate fiber amounts in some high fiber foods (NOTE: different sources give slightly different numbers):

Fresh & Dried Fruit  Serving Size Fiber (g)
 Apples with skin  1 medium 5.0
 Apricot  3 medium 1.0
 Apricots, dried  4 pieces 2.9
 Banana  1 medium 3.9
 Blueberries  1 cup 4.2
 Cantaloupe, cubes  1 cup 1.3
 Figs, dried  2 medium 3.7
 Grapefruit  1/2 medium 3.1
 Orange, navel  1 medium 3.4
 Peach  1 medium 2.0
 Peaches, dried  3 pieces 3.2
 Pear  1 medium 5.1
 Plum  1 medium 1.1
 Raisins  1.5 oz box 1.6
 Raspberries  1 cup 8.0
 Strawberries  1 cup 4.4
Grains, Beans (Legumes), Nuts, Seeds  Serving Size Fiber (g)
 Almonds  1 oz 4.2
 Black beans, cooked  1 cup 13.9
 Bran cereal  1 cup 19.9
 Bread, whole wheat  1 slice 2.0
 Brown rice, dry  1 cup 7.9
 Cashews  1 oz 1.0
 Flax seeds  3 Tbsp. 6.9
 Garbanzo beans, cooked  1 cup 5.8
 Kidney beans, cooked  1 cup 11.6
 Lentils, red cooked  1 cup 13.6
 Lima beans, cooked  1 cup 8.6
 Oats, rolled dry  1 cup 12.0
 Quinoa (seeds) dry  1/4 cup 6.2
 Quinoa, cooked  1 cup 8.4
 Pasta, whole wheat  1 cup 6.3
 Peanuts  1 oz 2.3
 Pistachio nuts  1 oz 3.1
 Pumpkin seeds  1/4 cup 4.1
 Soybeans, cooked  1 cup 8.6
 Sunflower seeds  1/4 cup 3.0
 Walnuts  1 cup 5.0
 Vegetables  Serving Size Fiber (g)
 Avocado (fruit)  1 medium 11.8
 Beets, cooked  1 cup 2.8
 Beet greens  1 cup 4.2
 Bok choy, cooked  1 cup 2.8
 Broccoli, cooked  1 cup 4.5
 Brussels sprouts, cooked  1 cup 3.6
 Cabbage, cooked  1 cup 4.2
 Carrot  1 medium 2.6
 Carrot, cooked  1 cup 5.2
 Cauliflower, cooked  1 cup 3.4
 Cole slaw  1 cup 4.0
 Collard greens, cooked  1 cup 2.6
 Corn, sweet  1 cup 4.6
 Green beans  1 cup 4.0
 Celery  1 stalk 1.1
 Kale, cooked  1 cup 7.2
 Onions, raw  1 cup 2.9
 Peas, cooked  1 cup 8.8
 Peppers, sweet  1 cup 2.6
 Pop corn, air-popped  3 cups 3.6
 Potato, baked w/ skin  1 medium 4.8
 Spinach, cooked  1 cup 4.3
 Summer squash, cooked  1 cup 2.5
 Sweet potato, cooked  1 medium 4.9
 Swiss chard, cooked  1 cup 3.7
 Tomato  1 medium 1.5
 Winter squash, cooked  1 cup 6.2
 Zucchini, cooked  1 cup 2.6

The tables were from http://commonsensehealth.com/high-fiber-foods-list-for-a-high-fiber-diet/

Published on

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. A 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. 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.

High fiber is: 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. prausnitzii.

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.

Published on

In the past year I keep coming across one special gut microbe: Faecalibacterium prausnitzii. This bacteria is considered beneficial and is one of the most prevalent intestinal bacterial species in healthy adults. The reduction of this bacteria in the gut (as measured by analyzing bacteria in fecal samples) is seen in several diseases, including Intestinal Bowel Disease (IBD). This bacteria has also been found to be anti-inflammatory. In other words, you really, really want a healthy population in your gut.

But now the question is: how does the bacteria get there? And how can you increase it if you have a low population in your gut? It certainly isn't found in any probiotic supplement that I know of.  Part of the answer seems to be eating foods with fiber, lots of it, to feed the good microbes. Eat fruits, vegetables, whole grains, seeds, legumes, and nuts.

The following lengthy article discusses the importance of keystone species (F. prausnitzii is one). From Scientific American:

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.. 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.

Each of us harbors a teeming ecosystem of microbes that outnumbers the total number of cells in the human body by a factor of 10 to one and whose collective genome is at least 150 times larger than our own... The microbiome varies dramatically from one individual to the next and can change quickly over time in a single individual. The great majority of the microbes live in the gut, particularly the large intestine, which serves as an anaerobic digestion chamber. 

Independent researchers around the world have identified a select group of microbes that seem important for gut health and a balanced immune system. They belong to several clustered branches of the clostridial group. Dubbed “clostridial clusters,” these microbes are distantly related to Clostridium difficile, a scourge of hospitals and an all too frequent cause of death by diarrhea. But where C. difficile prompts endless inflammation, bleeding and potentially catastrophic loss of fluids, the clostridial clusters do just the opposite—they keep the gut barrier tight and healthy, and they soothe the immune system. Scientists are now exploring whether these microbes can be used to treat a bevy of the autoimmune, allergic and inflammatory disorders that have increased in recent decades, including Crohn's and maybe even obesity.

F. prausnitzii was one of the first clostridial microbes to be identified. In Sokol's patients those with higher counts of F. prausnitzii consistently fared best six months after surgery. After he published his initial findings in 2008, scientists in India and Japan also found F. prausnitzii to be depleted in patients with inflammatory bowel disease... This suggested that whereas different genetic vulnerabilities might underlie the disorder, the path to disease was similar: a loss of anti-inflammatory microbes from the gut. And although Sokol suspects that other good bacteria besides F. prausnitzii exist, this similarity hinted at a potential one-size-fits-all remedy for Crohn's and possibly other inflammatory disorders: restoration of peacekeeping microbes.

One of the questions central to microbiome research is why people in modern society, who are relatively free of infectious diseases, a major cause of inflammation, are so prone to inflammatory, autoimmune and allergic diseases. Many now suspect that society-wide shifts in our microbial communities have contributed to our seemingly hyperreactive immune systems. Drivers of these changes might include antibiotics; sanitary practices that are aimed at limiting infectious disease but that also hinder the transmission of symbiotic microbes; and, of course, our high-sugar, high-fat modern diet. Our microbes eat what we eat, after all. Moreover, our particular surroundings may seed us with unique microbes, “localizing” our microbiota.

A number of studies have found a small but significant correlation between the early-life use of antibiotics and the later development of inflammatory disorders, including asthma, inflammatory bowel disease and, more recently, colorectal cancer and childhood obesity. One explanation for this association might be that sickly people take more antibiotics. Antibiotics are not the cause, in other words, but the result of preexisting ill health. Honda's studies suggest another explanation: antibiotics may deplete the very bacteria that favorably calibrate the immune system, leaving it prone to overreaction. 

A number of studies over the years have linked having fewer sanitary amenities in childhood with a lower risk of inflammatory bowel disease in adulthood. And a 2014 study from Aarhus University in Denmark found that among northern Europeans, growing up on a farm with livestock—another microbially enriched environment—halved the risk of being stricken with inflammatory bowel disease in adulthood.

These patterns suggest that perhaps by seeding the gut microbiota early in life or by direct modification of the immune system the environment can affect our risk of inflammatory bowel disease despite the genes we carry. And they raise the question of what proactive steps those of us who do not live on farms can take to increase our chances of harboring a healthy mix of microbes.

One of the more surprising discoveries in recent years is how much the gut microbiota of people living in North America differs from those of people living in rural conditions in Africa and South America. The microbial mix in North America is geared to digesting protein, simple sugars and fats, whereas the mix in rural African and Amazonian environments is far more diverse and geared to fermenting plant fiber. Some think that our hunter-gatherer ancestors harbored even greater microbial diversity in their guts.

What troubles Sonnenburg about this shift is that the bacteria that seem most anti-inflammatory—including the clostridial clusters—often specialize in fermenting soluble fiber...Some hunter-gatherers consumed up to 10 times as much soluble fiber as modern populations, and their bodies likely were flooded with far more fermentation by-products. Our fiber-poor modern diet may have weakened that signal, producing a state of “simmering hyperreactivity,” Sonnenburg says, and predisposing us to the “plagues” of civilization. He calls this problem “starving our microbial self.” We may not be adequately feeding some of the most important members of our microbiota.

Mouse experiments support the idea. Diets high in certain fats and sugars deplete anti-inflammatory bacteria, thin the mucous layer and foster systemic inflammation. ...In rodents, adding fermentable fiber to a diet otherwise high in fat keeps the “good” microbes happy, the mucous layer healthy and the gut barrier intact, and it prevents systemic inflammation. Taken together, these studies suggest that it is not only what is in your food that matters for your health but also what is missing.

The human studies are even more intriguing... Scientists at Catholic University of Louvain in Belgium recently showed that adding inulin, a fermentable fiber, to the diet of obese women increased counts of F. prausnitzii and other clostridial bacteria and reduced that dangerous systemic inflammation...Those without the bacteria did not benefit, which suggests that once species disappear from the “microbial organ,” the associated functions might also vanish. These individuals might not require ecosystem engineering so much as an ecosystem restoration.

Published on

The researchers were interested in lifestyle factors that are associated with lower rates of allergies.  Prior research has shown that such lifestyle factors are : living on a farm, introducing fish into the child’s diet at an early age, having pets early in life, parental cleaning of the child’s pacifier by sucking it, crowded living conditions, early daycare attendance, and having siblings. This study found that in households washing dishes by hand, rather than in a dishwasher, there are lower rates of allergies and eczema in children. In addition, the study found that consuming fermented or farm-bought food could decrease the likelihood of allergies further. It is thought that early exposure to microbes stimulates the immune system in beneficial ways. Dishwashers leave fewer bacteria behind on dishes than hand washing dishes. Living in a household that hand-washes means family members are eating off of plates and cutlery that have more bacteria, and therefore they are getting more microbial exposure. There could also be more bacteria in the air when dishes are hand washed or even some other lifestyle factor that these households have in common.From NPR:

Kids, Allergies And A Possible Downside To Squeaky Clean Dishes

Could using a dishwashing machine increase the chances your child will develop allergies? That's what some provocative new research suggests — but don't tear out your machine just yet.The study involved 1,029 Swedish children (ages 7 or 8) and found that those whose parents said they mostly wash the family's dishes by hand were significantly less likely to develop eczema, and somewhat less likely to develop allergic asthma and hay fever.

The findings are the latest to support the "hygiene hypothesis," a still-evolving proposition that's been gaining momentum in recent years. The hypothesis basically suggests that people in developed countries are growing up way too clean because of a variety of trends, including the use of hand sanitizers and detergents, and spending too little time around animals.As a result, children don't tend to be exposed to as many bacteria and other microorganisms, and maybe that deprives their immune system of the chance to be trained to recognize microbial friend from foe.That may make the immune system more likely to misfire and overreact in a way that leads to allergies, eczema and asthma, Hesselmar says.

"The hypothesis was that these different dishwashing methods ... are not equally good in reducing bacteria from eating utensils and so on," Hesselmar says. "So we thought that perhaps hand dishwashing was less effective, so that you are exposed to more bacteria" in a way that's helpful.

In a study released Monday in the online version of the journal Pediatrics, the researchers report what they found: In families who said they mostly wash dishes by hand, significantly fewer children had eczema, and somewhat fewer had either asthma or hay fever, compared to kids from families who let machines wash their dishes.

Still, there are other possible explanations, Hesselmar and Mahr both caution. Though the researchers took economic status into account in the study, it could be that people who don't have dishwashers are alike in some other way that reduces their tendency to get allergies. Interestingly, for example, certain other lifestyle characteristics — eating fermented foods regularly, and tending to buy some foods straight from the farm — seemed to strengthen the "protective" effect in families without dishwashers.