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Category: human microbiome

Published on Leave a comment on Certain Gut Bacteria Are Associated With Lower Cholesterol Levels
Intestines Credit:Wikipedia

New discoveries about our gut microbiome (the community of viruses, bacteria, fungi) keep occurring. There is growing evidence that certain bacterial species in the gut are associated with cholesterol levels and heart disease.

Adding to the evidence, a recent study found that people with higher levels of several species of Oscillibacter bacteria had lower cholesterol levels than people without or diminished levels of these bacteria. The researchers than  found (in the lab) that these species of Oscillibacter bacteria actually take up and metabolize artery-clogging cholesterol, which could explain the lower cholesterol levels.

By the way, other species (e.g., Eubacterium coprostanoligenes)  were also associated with lower cholesterol levels in the study. The same people with higher levels of beneficial bacteria also had greater diversity of gut bacteria, which is considered a sign of gut health.

Species of Oscillibacter bacteria are not available in any supplements at this time. You'll just have to eat a diet that feeds and nurtures beneficial gut microbes.

And what is a health-promoting diet? A recent study found that a diet rich in fruits, vegetables, whole grains, nuts, seeds, legumes, and olive oil promotes healthy bacteria in the gut, which are associated with good health. This also is a diet high in fiber. Think along the lines of a Mediterranean diet.

From Science Daily: Scientists link certain gut bacteria to lower heart disease risk

Changes in the gut microbiome have been implicated in a range of diseases including type 2 diabetes, obesity, and inflammatory bowel disease. Now, a team of researchers at the Broad Institute of MIT and Harvard along with Massachusetts General Hospital has found that microbes in the gut may affect cardiovascular disease as well. In a study published in Cell, the team has identified specific species of bacteria that consume cholesterol in the gut and may help lower cholesterol and heart disease risk in people. ...continue reading "Certain Gut Bacteria Are Associated With Lower Cholesterol Levels"

Published on Leave a comment on A Specific Bacteria and Colorectal Cancer
Credit: Wikipedia

Cancer tumors have a different microbiome (community of microbes) than healthy tissue. Researchers have been finding the bacteria Fusobacterium nucleatum (F. nucleatum) in a number of cancers, with high levels of its presence associated with a poorer outcome for the person (more metastases and death).

A recent study found that one strain or subtype of  F. nucleatum (called Fna C2)  is found in tumors of about 50% of aggressive colon cancers.

Interestingly, F. nucleatum is a normal oral bacteria - one found in the mouth of people, and also associated with periodontal disease. It is rarely found in the gastrointestinal (GI) tract of healthy persons.

It is thought that the bacteria somehow travels from the mouth to the stomach, where it can withstand stomach acid, and then grows there in the gastrointestinal tract. F. nucleatum is cancer promoting - for example, it has a supporting role in tumor progression. It appears to be resistant to cancer treatments.

Researchers are now wondering if certain beneficial or good bacteria ingested by the person or somehow delivered to the tumor site  can battle the F. nucleatum, perhaps as part of cancer therapy. Stay tuned....

From Science Daily: Bacteria subtype linked to growth in up to 50% of human colorectal cancers

Researchers at Fred Hutchinson Cancer Center have found that a specific subtype of a microbe commonly found in the mouth is able to travel to the gut and grow within colorectal cancer tumors. This microbe is also a culprit for driving cancer progression and leads to poorer patient outcomes after cancer treatment. ...continue reading "A Specific Bacteria and Colorectal Cancer"

Published on Leave a comment on Artificial Sweeteners Alter the Gut Microbiome
Small intestine Credit: Wikipedia

It turns out that artificial sweeteners alter the gut microbiome, specifically the duodenum (the first part of the small intestine after the stomach). And not in a good way.

The gut microbiome is the community of microbes (bacteria, fungi, viruses) that lives in the small intestine - and it looks different in persons who use artificial sweeteners compared to persons who don't.

Researchers found that artificial sweeteners lowered microbial diversity (not good), and increased numbers of harmful bacteria in the duodenum. They also alter inflammation markers that circulate in the blood in a negative way. The use of non-aspartame artificial sweeteners (sucralose, saccharin, stevia) had slightly different effects than aspartame, but both overall had negative effects (when compared to gut microbiomes of persons not ingesting artificial sweeteners in their diet).

From Medical Xpress: Could artificial sweeteners alter your microbiome?

You may think that artificial sweeteners can help you lose some weight, but a new study finds they are no good for your gut's microbiome. ...continue reading "Artificial Sweeteners Alter the Gut Microbiome"

Published on Leave a comment on How to Identify An Ultra-Processed Food

There is much concern with the amount of highly or ultra-processed foods the typical American eats - over 50% of the calories eaten daily! Ultra-processed foods are linked to all sorts of health issues (e.g., diabetes, heart disease). One reason is because these foods are not good for the gut microbiome - they feed microbes linked to poor health and not the microbes linked to good health.

So how does one know if a food is ultra-processed? An easy way is to look at the ingredients list on the package or container and look for one or more ingredients not normally found in our kitchens at home. Instead, these ingredients will have chemical sounding names.

What ingredients indicate a food is ultra-processed? Some examples indicating a food is ultra-processed: soy lecithin, carrageenan, high-fructose corn syrup,  hydrogenated oils, interesterified oils, hydrolysed proteins, invert sugar, dextrose, lactose, gluten, whey protein, nitrates, flavors, colors, titanium dioxide, caramel color, and emulsifiers. The list goes on and on. Even the innocent sounding "natural flavors" is a laboratory concoction.

These ingredients have typically been added to extend shelf-life or manipulate the taste, flavor, or appearance. Ultra-processed foods are "formulations of ingredients" that result from a series of industrial processes (thus "ultra-processed"). Researchers of the following article say that "ultra-processed foods are not real food" due to all the modifications and alterations.

Note that ultra-processed foods can be on the grocery shelf right next to similar foods with all natural ingredients. Examples are breads, cereals, and maple syrup (is it real maple syrup or an ultra-processed concoction?). This is why you should read ingredient lists.

Also, these foods are generally ultra-processed: soda, candy, margarines, cake mixes, hot dogs and processed meats (e.g., cold cuts), instant soups, mass-produced breads and cookies, frozen meals, fast food meals, energy bars and drinks, and protein bars.

By the way, most foods that we buy or cook at home are processed to some extent, for example pasteurization of milk, freezing or boiling foods, fermentation, seasoning foods, cooking food, or even baking bread. Using real foods to prepare (process) food is OK for our health. It's totally fine.

Foods can be unprocessed (e.g., raw fruits and vegetables), minimally processed, processed, and finally ultra-processed. The ingredients will tell you if it's just processed food (contains only normal foods or culinary ingredients - e.g., flour, sugar, salt, eggs) or whether it's ultra-processed (contains one or more chemical sounding ingredients).

These foods are NOT ultra-processed: pasteurized milk, raw fruits and vegetables, starchy roots and tubers (e.g., potatoes, yams), chilled meat and fish, plant oils (e.g., olive oil), sugar, oats, and salt.

A big problem is that ultra-processed foods are replacing unprocessed or minimally processed foods in our diet. This is also why we are getting less and less fiber in our diet, which is linked to health problems. Simple way to think about it: fiber from foods feeds beneficial gut microbes.

Excerpts from an April 2019 article in Public Health Nutrition: Ultra-processed foods: what they are and how to identify them

Ultra-processed foods are defined within the NOVA classification system, which groups foods according to the extent and purpose of industrial processing.

...continue reading "How to Identify An Ultra-Processed Food"

Published on Leave a comment on Kidney Stones and the Gut Microbiome
Kidney stones Credit: Wikipedia

What causes a person to develop kidney stones has long been debated. A recent study found that in persons who develop kidney stones, there are alterations in the gut, salivary, and urinary microbiomes. In other words, the community of fungi, viruses, and bacteria at each of these sites are out of whack or imbalanced.

In the study, not only were the 3 microbiomes imbalanced in the persons with kidney stones (when compared to healthy people without kidney stones), but they also had less diversity (fewer species) in their microbiomes. For example, persons with kidney stones had significantly fewer gut health associated bacteria F. prausnitzii, and significantly more inflammation associated E. lenta.

Those with kidney stones also had a history of having taken more antibiotics (antimicrobials).

The researchers conclusion: To avoid kidney stones a healthy diet is essential (for a healthy gut microbiome). One should also avoid taking antibiotics unless necessary. [BTW, the bacteria F. prausnitzii has long been viewed as a keystone microbe in a healthy gut microbiome. It can be increased by increasing fiber in the diet - e.g., fruits, vegetables, seeds, nuts, whole grains, legumes.]

From Medical Xpress: New study sheds light on the connection between the microbiome and kidney stones

A new study from Lawson Health Research Institute and Western University published in the journal Microbiome has found changes in the microbiome in multiple locations in the body are linked to the formation of kidney stones. ...continue reading "Kidney Stones and the Gut Microbiome"

Published on Leave a comment on Ear Piercing and the Skin Microbiome
Credit: Wikimedia Commons

We all have a skin microbiome - the community of millions of microbes (bacteria, fungi, viruses) that normally live on the skin. New research shows that when we get the ears pierced and start to wear earrings, it causes a disruption to the skin microbiome of the earlobes, and there is an actual shift to different microbes. A new normal develops.

The researchers found that before piercing, the earlobe skin to be pierced is disinfected (which disrupts and kills off microbes), and then after the piercing and insertion of an earring that area of the skin is permanently more moist - thus there is a shift in the community of microbes (their composition). It becomes more complex, with a greater variety of microbes, and some moisture loving species move in.

Therefore. the researchers say that ear piercing represents "ecosystem engineering on the human body". Yes. And wow.

From Science Alert: After an Ear Piercing, Your Skin Microbiome Changes in a Fundamental Way

You may not have ever realized it, but there are many trillions of microorganisms living on our skin – and puncturing the skin and inserting a metal object, also known as getting a piercing, creates a significant shift in that microbiome. ...continue reading "Ear Piercing and the Skin Microbiome"

Published on Leave a comment on Kimchi Made With Seafood and Vegan Kimchi Contain the Same Microbes

Over the years I've received many questions about vegan versus kimchi that contains seafood. Are the microbes in the kimchi the same?

One reason this is an important question is because at certain stages of kimchi fermentation the beneficial bacteria Lactobacillus sakei (which treat sinusitis in many people) appears for a time. And during that time when L.sakei is present, dabbing a little kimchi juice in the nostrils helps and treats many individuals with sinusitis. Amazing, yes?

Many people prefer to treat sinusitis with vegan kimchi - which is also my personal preference. I don't want to worry about what is in the seafood used in kimchi. Therefore, it's vegan kimchi for me.

Earlier studies have suggested that even though kimchi is made with cabbage, the L. sakei grows from the surface of raw garlic used in making  the kimchi. From the M.A. Zabat et al (2018) study:

"Because kimchi is made without the use of a starter culture, the raw ingredients play a key role in establishing the bacterial community that is responsible for fermenting kimchi (Jung et al., 2011; Lee et al., 2015)".

"Large amounts of garlic are associated with more kimchi-associated LAB [lactic acid bacteria] in the final product (Lee et al., 2015)." [Note: L. sakei is one of the lactic acid bacteria in kimchi]

This is why the 2018 study, which I just read, is so interesting. The researchers found that both vegan (no seafood)and kimchi made with seafood (e.g., fish sauce) contain the same microbes after fermentation. They may have started out with different populations of microbes, but during fermentation the microbes become similar.

"We found that, despite initial differences in microbial composition between vegan and non-vegan kimchi, there was no notable difference in the final products. Ultimately, the microbial community of both vegan and non-vegan kimchi is dominated by Lactobacillaceae and Leuconostocaceae, and lacks the Enterobacteriaceae found in the fish sauce or miso paste."

Well... that's a relief. What kimchi you choose to eat and use as a sinusitis treatment is personal preference. It's all good. And yes, fermented foods such as kimchi are great for the gut microbiome. They increase gut microbial diversity (good!) and reduce inflammation.

From Physics News: Vegan and traditional kimchi have same microbes, study finds

Good news, vegans: A new study finds that kimchi made without fish products has the same type of bacteria as more traditionally made kimchi. That finding suggests that any "probiotic" benefits associated with traditional kimchi could be present in vegan versions as well. ...continue reading "Kimchi Made With Seafood and Vegan Kimchi Contain the Same Microbes"

Published on Leave a comment on The Vaginal Microbiome

We have microbiomes all over our bodies. Millions of microbes in communities - for example, the ear, the sinuses, the skin, the gut, and on and on. Women also have a vaginal microbiome. When the microbiome of the vagina gets disrupted, health effects such as bacterial vaginosis (BV) can occur.

The Scientist recently published a good article on the vaginal microbiome, as well as the microbes in the vagina associated with health and those associated with health problems. [Note: All these microbes live together in a healthy vaginal microbiome - it's just that sometimes the balance gets disrupted.] Much has been learned since they first wrote about the microbiome of the healthy vagina in 2014 - but much is still unknown.

Some good news is that the beneficial bacteria Lactobacillus crispatus, which is very important for a healthy vagina, is now easily available as a probiotic supplement (to be taken when needed) in the US. Back in 2016 it was only available in Europe for BV and urinary tract infections (UTIs). This bacteria has been referred to as the "golden child of all the lactobacilli" in the vaginal microbiome.

Excerpts from The Scientist: The Vaginal Microbiome is Finally Getting Recognized

Vaginal dysbiosis has long been a taboo subject, but studying and optimizing the vaginal microbiome could be a game changer for women's health. ...continue reading "The Vaginal Microbiome"

Published on Leave a comment on Adding Herbs and Spices To Your Foods Improves Gut Microbiome
Thyme Credit: Wikipedia

It turns out that even making minor adjustments to your usual diet can improve the gut microbiome (the community of bacteria, fungi, viruses living in the gut) within a few weeks. Two separate studies found that eating some peanuts daily or adding some herbs or spices to the  foods you eat can improve the numbers of beneficial bacteria living in the gut.

In the peanut study - eating or not eating peanuts didn't change the diversity or main types of bacteria living in the gut. But eating peanuts did increase the numbers of several beneficial species --Roseburia and Ruminococcaceae, which are butyrate producing bacteria (good!). The peanut group ate 28 grams of peanuts (1 ounce or about 33 peanuts) as a night-time snack for 6 weeks.

In the spice and herb study, adding a combination of spices and herbs to the diet for 4 weeks increased microbial diversity in the gut (good!), and also increased beneficial Ruminococcaceae numbers (good!) in persons at risk for heart disease. Faecalibacterium and Agathobacter  numbers also increased (good!). A variety of dried spices and herbs (1/8 tsp, 3/4 tsp. or 1/1/2 tsp) were added to foods in the daily diet, and not taken as a capsule.

Dried spices added to foods in the spice and herb study included coriander, cumin, allspice, cinnamon, oregano, thyme, onion powder, garlic, ginger, rosemary, thyme, basil, black pepper, paprika, parsley, red pepper, etc. - 24 in all!

Bottom line: These studies agree with other research finding that eating peanuts (and all sorts of nuts, legumes), as well as adding spices and herbs to your foods is beneficial to the gut microbiome. They feed beneficial microbes in your gut, have all sorts of micronutrients, and they also have multitudes of microbes. A win-win.

From Science Daily: Peanuts and herbs and spices may positively impact gut microbiome

Adding a daily ounce of peanuts or about a teaspoon of herbs and spices to your diet may affect the composition of gut bacteria, an indicator of overall health, according to new research from Penn State. In two separate studies, nutritional scientists studied the effects of small changes to the average American diet and found improvements to the gut microbiome. ...continue reading "Adding Herbs and Spices To Your Foods Improves Gut Microbiome"

Published on Leave a comment on Lupus Involves Changes In Gut Microbes

Recent research found that flare-ups of the disease lupus involves microbial changes in the gut microbiome. The gut microbiome is the community of microbes (fungi, bacteria, viruses) living in the small intestine.

NYU School of Medicine researchers found in a study that about half of the individuals having flare-ups of lupus (Systemic lupus erythematosus) had an overgrowth (or "bloom") of the bacteria Ruminococcus blautia gnavus. They also found that during flare-ups the gut microbiome was out-of-whack, with an increase in some harmful (pathogenic) species.

Lupus is an autoimmune disease that occurs when the body's immune system attacks its own tissues and organs, especially kidneys, joints, skin, blood vessels, brain, heart, and lungs. A tell-tale sign of lupus that many people get is a butterfly shaped rash across the nose and cheeks.

These research results raise the possibility that future treatments for lupus may involve somehow altering gut microbes. Maybe dietary changes or certain probiotics?

From Science Daily: Lupus flare-ups strongly linked to specific bacterial growth in gut

Recurrent bouts of systemic lupus erythematosus, marked by the body's immune system attack of its own tissues, closely tracked with measureable upticks in growth in the gut of a certain species of bacteria. ...continue reading "Lupus Involves Changes In Gut Microbes"