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Category: microbes

Published on Leave a comment on Common Foods Contain Hundreds Of Diverse Bacterial Species

Whoa.... a recent study examined food microbiomes (community of microbes) of some foods and found that the foods contained many species of microbes - hundreds of species! The foods examined were a variety of masala spice mixes, cilantro, smoked salmon, cucumbers, and mung bean sprouts.

Other studies have also found large numbers of bacterial species in all sorts of foods, including raw fruits and vegetables, cheeses, and fermented foods, such as kimchi. There are also bacterial differences between conventional and organic foods. No wonder it's good to eat a diverse diet - all those microbes that you're ingesting! A diverse gut microbial community in humans is considered healthy by researchers.

The researchers (all associated with the US FDA - Food and Drug Administration) looked at the bacterial "species richness" (number of different bacterial species) normally found on the 5 types of foods. They used modern genetic sequencing methods to analyze the food microbiomes and found a LOT of bacterial species ("high bacterial diversity"), as well as species unique to the different foods sampled - whether animal or plant based foods.

They found not only beneficial species, but also species associated with food spoilage. Every food had some bacteria that could eventually lead to food spoilage (which makes sense - eventually all foods can spoil). Also, how the food was handled and packaged, as well as moisture levels, influenced the bacterial species found in the foods.

The masala spice mixes were especially rich in bacterial species (from from 968 to 1097) and in unique species (19), but the mixes also contained as many as 17 ingredients. Cucumbers had between 227 and 423 bacterial species, and 216 to 573 species for cilantro. Smoked salmon samples had fewer species - ranging from 89 to 181 species. An example of the diversity is that the cucumber microbiome is comprised of species within Proteobacteria (45 to 85%), Firmicutes (2 to 40%), Actinobacteria (8 to 31%), and Bacteroidetes (0 to 2%).

I don't know if one can ever replenish all the bacteria lost from years of antibiotics (e.g. for sinus infections - both chronic and acute sinusitis), but this is a good reason to eat a variety of foods - for all the species of bacteria. These bacterial species are not found in general probiotic pills - one must eat the foods to ingest the variety and richness of microbes.

The researchers wrote: "Once established, the most likely source of new microbes joining our GI microbiome is the food we eat: each food stuff and commodity we consume likely contains a microbiome that passes through our bodies while nutritional ingredients and components are digested."

It is unknown how many of these microbes stick around in our body, but lots of research finds that a diet rich in fruits, vegetables, whole grains, seeds, nuts, legumes, some fish and meat (including poultry), some dairy - are beneficial to our gut microbiome, along with numerous health benefits. The fiber in these foods is also beneficial in that it feeds beneficial microbes. [see category NUTRITION for research, also Feeding Your Gut Microbes page.]

Excerpts from research by Karen G. jarvis et al in Frontiers In Microbiology:

Microbiomes Associated With Foods From Plant and Animal Sources

...continue reading "Common Foods Contain Hundreds Of Diverse Bacterial Species"

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Published on 31 Comments on The Best Probiotic For Sinus Infections

Probiotics are the future of sinusitis treatment. Research found that a probiotic (beneficial bacteria) that is lacking in those with chronic sinusitis, and which can successfully treat sinusitis is Lactobacillus sakei.

[See June 2022 updated version of this post.] This article is the summary of what has been learned over the past 7 years: the best L. sakei  products (such as kimchi and Lanto Sinus - which can treat even the worst recurring sinus infections, frequently within days), results of people trying various L. sakei products, and other possibilities for sinus health.

Back in 2012, a study by Abreu et al suggested Lactobacillus sakei as a possible treatment for sinusitis. In the past 6 years those conclusions have been supported by the experiences of hundreds of people contacting me, and my family's experiences with L. sakei products. It really is the best sinusitis treatment for most people!

When Lactobacillus sakei works as a treatment - it can seem miraculous as sinusitis symptoms gradually disappear or greatly improve. Many times within a few days! Unfortunately it doesn't work for everyone - for a minority there seems to be no effect, and it is not clear why. It also doesn't treat seasonal allergies or allergy symptoms.

Lactobacillus sakei works best when it is used only when needed, when there are sinus symptoms. No boosters needed when feeling well! (See Treatment Summary page for different ways to use products.)

The sinus microbiome is the community of microbes (bacteria, viruses, fungi) that live in the sinuses. This community can become disrupted and imbalanced (dysbiosis) from illnesses, allergies, or antibiotics and cause a sinus infection or sinusitis.

Research in the last decade has found that not only do sinusitis sufferers lack L. sakei, they have too much of some other bacteria, and they don't have the bacteria diversity in their sinuses that healthy people without sinusitis have. There is a depletion of some bacterial species, and an increase in "abundance" of other species.

Luckily Lactobacillus sakei is found in some foods (such as some brands of live fermented kimchi), some sausage starter cultures (such as B-2), and recently in some probiotic supplements (e.g. Lanto Sinus). One reason it is used in sausage starter cultures is because L. sakei dominates over and inhibits growth of pathogenic bacteria, including Staphylococcus aureus.

BACKGROUND STORY: Seven years ago there were no probiotics containing L. sakei. None. So instead members of my family experimented using a very easy kimchi sinusitis treatment (basically dabbing and smearing kimchi at certain stages of fermentation into the nostrils like a very messy eater) and found that it cured  chronic sinusitis of many years within several weeks. Obviously it contained L. sakei. It felt miraculous, especially because it was so easy to do.

After 7 years we still feel great! Because we no longer have chronic sinusitis and can easily treat sinusitis if it occurs with L. sakei, we have NOT taken antibiotics or any other bacteria killing spray or product (such as xylitol) for over 6 years. We do not use cortisone or antihistamine nasal sprays either.

WHEN A TREATMENT WORKS: Many of you have contacted me to report your own progress with various sinusitis treatments. People used terms such as "miraculous", "transformative", and "fabulous" when they had positive results with a product containing L. sakei.

When a treatment works, then all sinusitis symptoms go away  or there is major improvement - frequently within a few days. Symptoms that go away include post nasal drip, sinus headaches, "clogged ears", bad breath, and sinusitis-related coughs. Even tonsil stones! (Please note: trying products to treat sinusitis is self-experimentation - effects can be positive or negative. Always be cautious. Best results are to use L. sakei only when needed.)

OVERALL RESULTS: The majority of people contacting me with results reported positive results (chronic sinusitis greatly improved or totally gone) from some form of L. sakei treatment. Successes have been from the USA, Canada, Europe, Australia, New Zealand, Japan, and Africa. Since it's from self-experimentation and not a clinical trial, I don't know the actual percentage of positive results.

Some of the people reporting success have had multiple operations, some currently have deviated septums, some with nasal polyps, and all have had long-standing chronic sinusitis, some for decades.

Chronic sinusitis sufferers also reported that the same treatments also worked to treat acute sinusitis. It seems that after colds, etc. many develop acute sinusitis again and need re-treatment (the L. sakei frequently doesn't stay in the sinuses from earlier treatments). However, the sinuses do continue improving over time, so fewer and more minimal treatments (perhaps only a few days) are needed over time.

Another very small group reported that other probiotic strains helped (but it is not always clear whether they also tried a L. sakei product), and a minority of people reported that nothing has helped and there could be a variety of reasons for this (see below). Some people reported that one product helped, but not another - whether kimchi or a L. sakei product.

THREE MAIN PRODUCT CATEGORIES: Products containing live Lactobacillus sakei which people have reported success in treating sinusitis: kimchi (and some sauerkraut), refrigerated products (e.g. Lanto Sinus), and frozen products. Note that currently the FDA does not allow any probiotics to be sold as a medical treatment – they can only be sold as a supplement.

Using the following products to treat sinusitis is self-experimentation (results are unknown and can vary). Always be cautious. (See Sinusitis Treament Summary page for methods.)

KIMCHI - Many people report that kimchi helped them. And one person reported a homemade kimchi worked great (he was finally symptom free after many years). A few have even mentioned that kimchi has helped sinusitis with fungal problems.

Kimchi brands that people reported helping their chronic sinusitis: Sunja's Kimchi (medium spicy cucumber kimchi and mild white kimchi), Sinto Gourmet brand kimchi, Mama-O's Premium Kimchi, the white Napa kimchi and cabbage kimchi made by Choi's Kimchi Company, Farmhouse Culture Kimchi, Mother-in-law's Kimchi, Ozuke Kimchi, in the United Kingdom the brand Mr Kimchi, and in Australia Kehoe's Kitchen white kimchi.

[Finding a kimchi brand with L. sakei is due to self-experimentation. The kimchi must be live, and not pasteurized. We found that kimchi may contain L. sakei from about day 14 (or earlier) to about 2 to 2 1/2 months (from the day it's made.]

When the kimchi contained L. sakei we felt the same or started feeling better within one or 2 days. If we felt more mucusy over the next 2 days, or the acute sinusitis kept getting worse, than it did not contain L. sakei. Researchers feel that it's the garlic in kimchi that encourages L. sakei growth.

SAUERKRAUT - Sauerkraut has worked for some people if it is a sauerkraut made with garlic, such as some varieties of Cleveland Kraut. Researchers feel that it's the garlic in kimchi that encourages L. sakei growth, and traditional sauerkraut typically doesn't contain garlic.

REFRIGERATED LACTOBACILLUS SAKEI PRODUCTS  – A high-quality refrigerated L. sakei product specifically meant for the sinuses and treatment of sinusitis is sold by Lanto Health. The kimchi derived Lactobacillus sakei product called Lanto Sinus is meant to be used when needed. Lanto Sinus  holds up well in the refrigerator, is effective, reliable, and easy to use. This product ships well because it holds up for a while (days) without refrigeration.

People have reported success using it mixed with bottled water (dabbing, smearing, spooning a little in nostrils), or swishing it dry in the mouth. I’ve been a consultant with Lanto Health on this product and have been testing and using this product successfully for over 2 years (self-experimentation!).    ...continue reading "The Best Probiotic For Sinus Infections"

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Published on 6 Comments on Another Probiotic That Treats Infections?

I'm always on the lookout for probiotics (beneficial bacteria) that can somehow  suppress or dominate Staphylococcus aureus  - because that bacteria is implicated in many illnesses, including sinusitis. Some strains of S. aureus are antibiotic resistant and the cause of serious illnesses, such as MRSA  (Methicillin-resistant Staphylococcus aureus). However, S. aureus is also found in the microbiomes (microbial communities) of healthy people - including on the skin, nose, and gut - but it appears to reside there harmlessly in healthy people.

So finding species of bacteria that suppress or controls S. aureus is noteworthy. Researchers (from National Institute of Health and Thailand) found that in both humans and mice strains of Bacillus, especially B. subtilis, which is already added to many probiotic products, suppressed all strains of S. aureus. Interestingly, the researchers found no S. aureus in any of the gut and nasal samples from humans where Bacillus species were present.The researchers think that the Bacillus species eradicate S. aureus - in both the gut and nasal passages. So the researchers tested further using mice - they gave B. subtilis to the mice every 2 days, and it eliminated S. aureus in the guts of the mice.

But why did I title this post '"another probiotic" ? Because from research and personal experiences told to me - Lactobacillus sakei seems to have the same effect against S. aureus (a frequent problem in sinusitis). Studies find some strains of L. sakei (such as Lactobacillus sakei proBio65 - found in Lanto Sinus) to be especially effective against Staphylococcus aureus.

Stay tuned for more research with B. subtilis and other probiotics versus S. aureus. [UPDATE: Since I posted this, I've read some concerns over B.subtilis. Be careful.]  From Science Daily:

Probiotic bacillus eliminates staphylococcus bacteria  ...continue reading "Another Probiotic That Treats Infections?"

Published on Leave a comment on Research Suggests Not Taking Probiotics After Antibiotics

Many people take probiotics in the belief that the probiotics will help their gut microbiome (microbial community) recover after taking antibiotics. This is because antibiotics kill both beneficial and pathogenic bacteria, and research shows it may take months for the gut to recover (it depends on the antibiotics taken). However, 2 studies (in both mice and healthy humans) conducted by a group of researchers at the Weizmann Institute of Science in Israel challenge that belief. The researchers used both mice and healthy humans in both well-done studies. They found that taking probiotics after a week of antibiotics actually delayed recovery of the gut microbial community in humans - months longer!

In summary: As expected, taking antibiotics had a big effect on the gut microbiome - the researchers wrote "a dramatic impact"  and "profound microbial depletion" (after taking one week of standard doses of "broad-spectrum antibiotics").  However, they found large differences among the 3 groups in gut microbial recovery after antibiotics. The spontaneous recovery group (they did not take probiotics after antibiotics) showed recovery of gut microbes within 3 weeks. The fecal transplant group (of their own fecal microbes which was collected before they took antibiotics) showed gut microbial recovery within 1 day of the fecal microbial transplant. In contrast, the group taking daily  probiotics for 28 days did not show full recovery (to where they were before antibiotics) by day 28, and the gut microbial community was still out of whack (dysbiosis) even 5 months after stopping probiotics (actually even at 180 days when the study ended).

What species were in the probiotics? Eleven species commonly found in ordinary probiotics: Lactobacillus acidophilus, L. casei, L. casei subsp. paracasei, L. plantarum, L. rhamnosus, Bifidobacterium longum, B. bifidum, B. breve, B. longum sbsp. infantism, Lactococcus lactis, and Streptococcus thermophilus.  These are all considered beneficial species. But keep in mind that the human gut has hundreds of microbial species - not just the few found in probiotics.

Bottom line: Eat well after taking a course of antibiotics so as to feed beneficial microbes, and do not routinely take probiotics thinking it will help the microbes in the gut.

What was also interesting was that in the first study where healthy individuals took the probiotics (and no antibiotics), they found that the probiotic species did not colonize the gut in everyone - only some species and in some people. It's as if there is a "resistance to colonization". This resistance is perhaps what other studies show - that within one week of discontinuing probiotics, they are gone from the gut.

From Science Daily - Human gut study questions probiotic health benefits  ...continue reading "Research Suggests Not Taking Probiotics After Antibiotics"

Published on Leave a comment on Diet And The Breast Microbiome

Is the Mediterranean style diet the future in breast cancer prevention? The following study was done in primates, but it makes sense that the results would also be true for humans: that the type of diet eaten influences the breast microbiome. This means the community of microbes that live in the breast. Yes, it's true - studies show that there is a breast microbiome and it varies between those who have breast cancer and those who don't (healthy breasts).

The study looked at macaque monkeys who were fed either a Mediterranean style diet or a Western style diet for 31 months, and then their breast tissue was examined. They found microbial differences in the breast tissue among the 2 groups, including  greater numbers (abundance) of Lactobacillus species in the primates that had been eating the Mediterranean diet.

Lactobacillus species are generally considered beneficial to humans (which is why they are added to many foods and supplements) and studies suggest they may have anti-tumor effects. Some research has found microbial differences between healthy and malignant (cancerous) human  breast tissue  - including lower Lactobacillus numbers or "abundance" in the malignant breast tissue (compared to those with benign breast lesions). Researchers say it suggests that microbial imbalances (dysbiosis) of breast tissue could be a possible driver of breast cancer .

Studies already show that a person's diet influences the gut microbiome. This study shows diet directly influences microbial communities far away from the gut - in the breasts. Unfortunately it is not stated in the study what Lactobacillus species increased in the breast tissue of primates fed a Mediterranean diet. There are many Lactobacillus species, and they are not equal in their effects (as our experiences with Lactobacillus sakei and sinusitis has shown).

Of course more studies are needed, but in the meantime - eat a diet rich in fruits, vegetables, whole grains, legumes (beans), nuts, and seeds. There are many other documented health benefits from a diet rich in those foods (frequently referred to as a Mediterranean diet). The diet is low in processed foods and high in fiber, and rich in "real foods". From Science Daily:

Diet affects the breast microbiome in mammals

Diet influences the composition of microbial populations in the mammary glands of nonhuman primates, researchers report October 2 in the journal Cell Reports. Specifically, a Mediterranean diet increased the abundance of probiotic bacteria previously shown to inhibit tumor growth in animals.  ...continue reading "Diet And The Breast Microbiome"

Published on Leave a comment on There Is A Personal Cloud Around Each Person

There's a microbial, particulate, and chemical cloud surrounding each one of us that is like the one around Pig Pen in the Peanuts comics. It's called the exposome. Researchers from the Stanford University of Medicine found that we each have our own distinct  personal cloud - which is everything we're exposed to both indoors and outdoors (pets, rain, household chemicals, air pollution, pesticides, etc.), and what we use on our bodies. It is influenced by geographical regions of where a person lives, works, and travels, as well as a person's lifestyle.

The study followed the personal exposomes of 15 individuals for varying times and over 66 geographical locations (one of the researchers was followed for more than 2 years, during which time he traveled extensively). This was done by having the individuals wear a sensitive air filtering device - which collected what was in the air (environmental airborne exposures). The results showed that each person is exposed to thousands of species (plant pollen, bacteria, fungi, viruses, etc.) and chemicals. From Science Daily:

We are bombarded by thousands of diverse species and chemicals

We are all exposed to a vast and dynamic cloud of microbes, chemicals and particulates that, if visible, might make us look something like Pig-Pen from Peanuts.

Using a re-engineered air-monitoring device, scientists from the Stanford University School of Medicine have peered into that plume and discovered a smorgasbord of biological and chemical minutia that swirl in, on and around us. Their findings show, in unprecedented detail, the variety of bacteria, viruses, chemicals, plant particulates, fungi, and even tiny microscopic animals that enter our personal space -- a bombardment known as the human "exposome."  ...continue reading "There Is A Personal Cloud Around Each Person"

Published on Leave a comment on Some Bacteria Evade Antibiotics By Going Into A Dormant-Like State

Many people struggle with recurring bacterial infections - taking antibiotics seems to suppress the bacterial infection (for example, in a urinary tract infection or UTI), but the infection soon comes back. And so the cycle continues - infection, then antibiotics, then infection, more antibiotics, and so on.

Thus it was with interest that I read about a recent study that found that some pathogenic bacteria grow slowly and enter a dormant-like state (hibernation) when exposed to antibiotics so the antibiotics don't affect them (they're "persisters"). This is because antibiotics typically target a bacterial cell's ability to grow (and so do not  have an effect on bacteria in a dormant phase). Then the bacteria resume normal growth and spread when the antibiotics are gone. This study was done in cell cultures in the lab using Escherichia coli bacteria from UTIs. Future research may look for drugs to target bacteria in the dormant state. From Science Daily:

Infectious bacteria hibernate to evade antibiotics

University of Copenhagen researchers have discovered a surprising tactic of pathogenic bacteria when being attacked by antibiotics: hibernation.  ...continue reading "Some Bacteria Evade Antibiotics By Going Into A Dormant-Like State"

Published on Leave a comment on What Are Household Disinfectants Doing To Our Gut Microbes?

An interesting study about exposure to household cleaning products (regular cleaning products compared to eco-friendly products) and the gut microbiomes of young children was recently published. Canadian researchers found that the use of household cleaning disinfectants in the home was associated with changes in gut microbial communities in infants (more of some bacteria and less of others) - when compared to infants living in homes where eco-friendly cleaners were used. These changes occurred in a dose dependent manner (the more they were used, the bigger the changes).

Also interesting was that the more disinfectants (which are antibacterial) were used in a home, the more Lachnospiraceae was found in the infant's gut microbiota in infancy (age 3 to 4 months), and this was associated with a higher body mass of the child at 1 and 3 years, and increased odds of being overweight or obese at age 3. Use of eco-friendly products was associated with decreased odds of the child being overweight or obese at age 3. What was heavy use of household disinfectants? Daily or weekly. Just keep in mind that these are associations - not a definite cause and effect. But animal studies find similar results. And I wonder - what is frequent use of disinfectants doing to adult gut microbiomes? From Medical Xpress:

Household cleaning products may contribute to kids' overweight by altering their gut microbiota

Commonly used household cleaners could be making children overweight by altering their gut microbiota, suggests a Canadian study published in CMAJ (Canadian Medical Association Journal). The study analyzed the gut flora of 757 infants from the general population at age 3-4 months and weight at ages 1 and 3 years, looking at exposure to disinfectants, detergents and eco-friendly products used in the home. 

...continue reading "What Are Household Disinfectants Doing To Our Gut Microbes?"

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Published on 3 Comments on Is A Tick Killing Fungus The Answer to Tick Control?

Summer is a wonderful season here in the northeast US, but there is a dark side - ticks. Tick numbers, types of ticks, and diseases (including Lyme disease) that people are getting from tick bites are all increasing. Nothing seems to stop their spread and their increasing numbers. But what if a fungus that kills ticks is the answer? The fungus is Metarhizium anisopliae, which occurs naturally in forest soils. It is sold as Met52 - a non-toxic to humans and pets product that anyone can now purchase.

The product is now being tested in a multiyear study (led by R. Ostfeld & F. Keesing) in 24 neighborhoods with a high incidence of Lyme disease in New York state. Studies show that ticks die within 3 to 7 days after being exposed to Met52 (a spray made up of the fungal spores and water). Personally, I am very excited by this natural product and hope that it works well. The researchers are hoping for a 90% reduction of ticks (or more!) in areas and yards where it is applied! That is better control than the insecticides typically used. The researchers feel that if this works well, then municipalities or neighborhoods could do it on a large scale for tick control.

I first read about the study in this July 2018 article by M. Molteni in Wired: WE HAVE NO IDEA HOW BAD THE US TICK PROBLEM IS

Together, these efforts are helping to change the way people and government agencies think about ticks as a public health threat. ...The trouble is that scientists also know very little about which interventions actually reduce those risks. “There’s no shortage of products to control ticks,” says Ostfeld. “But it’s never been demonstrated that they do a good enough job, deployed in the right places, to prevent any cases of tick-borne disease.” In a double-blind trial published in 2016, CDC researchers treated some yards with insecticides and others with a placebo. The treated yards knocked back tick numbers by 63 percent, but families living in the treated homes were still just as likely to be diagnosed with Lyme.

Ostfeld and his wife and research partner Felicia Keesing are in the middle of a four-year study to evaluate the efficacy of two tick-control methods in their home territory of Dutchess County, an area with one of the country’s highest rates of Lyme disease. It’s a private-public partnership between their academic institutions, the CDC, and the Steven and Alexandra Cohen Foundation, which provided a $5 million grant.  ...continue reading "Is A Tick Killing Fungus The Answer to Tick Control?"

Published on Leave a comment on Fruits, Vegetables, and Whole Grains Lower Inflammation

Chronic low-grade inflammation in humans is drawing a lot of interest because it is linked to so many diseases (diabetes, cancer, etc). Key ways to lower this inflammation appear to be losing weight (if overweight), exercising, not smoking, and eating a healthy diet rich in fruits, vegetables, whole grains, nuts, and seeds (thus lots of fiber). Research also shows that the type of diet a person generally eats has an effect on the composition of gut microbes (you want to feed beneficial microbes!). But which is more important for health and lowering inflammation - whole grains or fruits and vegetables or neither?

A recent study attempted to answer this question. They put 49 overweight or obese individuals, who typically ate low amounts of fruits, vegetables, and whole grains (less than 1 serving per day), into 1 of the following 3 groups for 6 weeks: 1) Whole grains (WG), 2) Fruits and vegetables (FV), and 3) a Control group (who ate refined grains). All persons were given 3 servings per day of "treatment" foods to eat at home, but the rest of their Western style diets stayed the same. The individuals did not all consume the same foods, but rather consumed their choice of foods from their group's food category.

The researchers collected blood and stool samples (both at the beginning of the study and after 6 weeks) to measure inflammation levels, and types of microbes and fatty acids in the gut. Inflammatory markers that they measured were: tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), lipopolysaccharide binding protein (LBP), and high sensitivity C-reactive protein (hs-CRP).

The researchers found an increase in microbial diversity in the FV group (perhaps due to the new variety of fibers in the fruits and vegetables), but otherwise there were no significant changes in gut microbiome composition among the groups. [Note: but each group had only some dietary changes, not drastic changes]

The researchers found that whole grains and fruits and vegetables lowered markers of inflammation - but each treatment (FV or WG) lowered different types of inflammation markers. And note that for the fruit/vegetable group - the 3 servings per day, was still below government recommendations of 5 servings per day for adults. And the rest of their diet was the same Western diet that they normally ate. So the whole grains or fruits and vegetables were not major dietary changes. And yet there were positive changes - lowering of inflammation.

So the final answer is that it is best for your health  (and gut microbes) to eat a diet rich in fruits, vegetables, and also whole grains. And they didn't even mention legumes, nuts, and seeds - all high fiber foods with lots of micronutrients, and known to be good for beneficial gut microbes. So yes, eat them also. What was a serving in this study? 1 serving = 1 cup fruits or vegetables, and 1 serving = 1 oz of whole or refined grains.  ...continue reading "Fruits, Vegetables, and Whole Grains Lower Inflammation"