Skip to content

Category: human microbiome

Published on Leave a comment on Farts and Good Gut Health

Those who enjoy a little "potty humor" will like the results of a recent nutrition study comparing the results of a Western style diet (high fat, low fiber) to a high fiber Mediterranean diet. The high fiber diet resulted in much larger, softer stools, and an increase in stomach noises and farting. (Yes, they weighed their stools and counted daily farts!) There was no change in the number of stools per day.

In the study 18 healthy men followed both types of diets for two week periods (first one diet, then a break, and then the other diet). The high fiber diet (54.2 grams fiber per day) resulted in numerous beneficial changes, especially nurturing healthy gut bacteria and metabolic improvements. The low fiber Western diet only had an intake of 4.7 g fiber per day. Interestingly, all participants were told to avoid fermented dairy products (e.g. yogurts) during the study.

The high fiber diet resulted in greater numbers of beneficial bacteria in the gut without any major changes in the core microbiome (microbial community). There were also numerous gut microbial metabolic improvements while on this diet. Interestingly, men who already had a more diverse gut microbiota (which is a sign of health) and routinely already ate more fiber rich plants foods, had less farting and stomach noises during the study.

Think of it this way: your diet is what feeds and nurtures the microbes living in your gut. Some microbes are associated with chronic diseases, and some with health - so you want to nurture the health-associated bacteria by eating a diet rich in plant foods (Mediterranean style diet).

By the way, a recent study found that eating fermented foods is a quick way to increase gut microbial diversity and health. It's beneficial to add some fermented foods (e.g. yogurt, kimchi, sauerkraut, kefir) to your regular diet.

From New Scientist: Men fart more when eating a plant-based diet due to good gut bacteria

Plant-based diets cause men to fart more and have larger stools, researchers have found – but that seems to be a good thing, because it means these foods are promoting healthy gut bacteria.  ...continue reading "Farts and Good Gut Health"

Published on Leave a comment on Antibiotics and Colon Cancer

Antibiotics can be life-saving, but there are also unintended consequences. One of them is that they disrupt and alter the gut microbiome (the microbial community of the millions of microbes living in the intestines). A large study found that use of antibiotics is linked to a higher risk of colon cancer 5 to 10 years later.

The researchers thought this was due to the antibiotics having negative effects on the gut microbiome. Antibiotics reduce numbers of beneficial bacteria in the intestines, while allowing bacteria linked to colorectal cancer to increase.

Researchers at Unea Univ. in Sweden compared 40,545 colon cancer cases to 202,720 controls (no cancer), and found that as antibiotic use increased, colon cancer increased in those persons during the next 10 years. It is unknown what happens after 10 years, because that is when the study ended. Interestingly, in women - increased use of antibiotics was linked to a lower incidence of rectal cancer.

The researchers analyzed the results with respect to different classes  of antibiotics, and found the strongest association with the use of quinolones, sulfonamides, and trimethoprims. These antibiotics have an effect on bacterial diversity - specifically allowing anaerobic Fusobacteria and Bacteroidetes species to live and become more abundant. Other studies also support the view that Fusobacteria (e.g., Fusobacterium nucleatum) and Bacteroidetes species contribute to colorectal cancer development.

What to do? To increase beneficial species in the gut and lower levels of inflammation in the body, studies support eating a diet rich in fruits, vegetables, whole grains, nuts, seeds, legumes, and fish - which also results in a high fiber intake (e.g., Mediterranean diet). Also, to quickly improve the diversity of microbes in the gut (a sign of health!) and to lower inflammation in the body, increase your intake of fermented foods.

Fermented foods include: yogurt, buttermilk, sour cream, cheese, kefir, fermented vegetables, kimchi, natto, miso, sauerkraut, traditional pickles, traditional sourdough bread, apple cider vinegar, and kombucha. To quickly improve the gut microbiome, try to eat six 1/2 cup servings each day for a few months.

From Science Daily: Antibiotics linked to increased risk of colon cancer

There is a clear link between taking antibiotics and an increased risk of developing colon cancer within the next five to ten years. This has been confirmed by researchers at Umeå University, Sweden, after a study of 40,000 cancer cases. The impact of antibiotics on the intestinal microbiome is thought to lie behind the increased risk of cancer.  ...continue reading "Antibiotics and Colon Cancer"

Published on Leave a comment on Fermented Foods Are Good For Your Gut Microbiome

It has been known for a while that eating fermented foods and high fiber foods is healthy for us. A recent study confirms this view. Researchers at the Stanford Univ. of Medicine found that eating fermented foods actually reduces inflammation and increases the diversity of gut microbes (gut microbiome).

Researchers randomly assigned volunteers to one of 2 groups for 10 weeks: the fermentation foods group, and the high fiber group. Surprisingly, the group eating the high fiber diet for 10 weeks did not have changes in microbial diversity or changes in the 19 inflammatory markers studied. Instead, the researchers reported that the high-fiber diet "changes microbiome function and elicits personalized immune responses".

The fermented foods group ate a diet rich in yogurt, kefir, fermented cottage cheese, kimchi and other fermented vegetables (e.g. sauerkraut, traditional dill pickles), vegetable brine drinks, and kombucha tea. Each day they ate 6 servings (1/2 cup = 1 serving generally). The high fiber diet was rich in legumes, seeds, whole grains, nuts, vegetables, and fruits (increased their fiber intake from about 22 grams per day to 45 grams).

The fermented foods group ate six servings daily (e.g. 1/2 cup yogurt, kefir, fermented cottage cheese, kimchi, sauerkraut, traditional dill pickles, and kombucha tea). The high fiber group increased their fiber intake from about 22 grams per day to 45 grams, by eating a diet rich in legumes, seeds, whole grains, nuts, vegetables, and fruits.

High-fiber diets are associated with numerous health benefits such as lower rates of numerous chronic diseases and mortality. The consumption of fermented foods can help with weight maintenance and may decrease the risk of diabetes, cancer, and cardiovascular disease.

From Futurity: Fermented Food Diet Boosts Microbiome and Cuts Inflammation

In a clinical trial, 36 healthy adults were randomly assigned to a 10-week diet that included either fermented or high-fiber foods. The two diets resulted in different effects on the gut microbiome and the immune system. 
...continue reading "Fermented Foods Are Good For Your Gut Microbiome"

Published on Leave a comment on Missing Birth Canal Bacteria Can Be Restored to Cesarean Birth Babies

There are microbial differences (microbiome) in babies who are born by cesarean vs vaginal deliveries. Research shows that bacterial differences can be minimized by a simple procedure - swabbing the newborn infant with the mother's vaginal fluids (using a gauze pad).

An infant normally picks up bacteria during birth as it passes through the birth canal, and these bacteria "seed" (colonize) the baby's skin and gut microbial community. On the other hand, babies born by C-section are colonized by microbes floating around in the operating room (from doctors, nurses) and these are predominantly skin bacteria. These bacterial differences between babies born by vaginal birth or C-section persist and are thought to explain some health differences between babies born vaginally or by C-section.

Dr. Dominguez-Bello has been doing a long-term study in which babies born by cesarean section are immediately swabbed with a gauze cloth soaked with the mother's vaginal fluids (which contain the mother's microbes). This resulted in the infants' skin and gut microbial community being more like vaginally born babies. These microbial changes persisted during the first year of life.

Such big changes from such a small procedure!

From The Scientist: Maternal Vaginal Fluids Mimic Microbe Transfer of Vaginal Birth

Babies born by C-section carry an increased risk of immune and metabolic disorders later in life, which studies have suggested may be associated with the communities of microbes on and in their bodies at the time of birth.  ...continue reading "Missing Birth Canal Bacteria Can Be Restored to Cesarean Birth Babies"

Published on Leave a comment on Milk Chocolate Has Health Benefits

The findings of a recent study caught my eye - that eating milk chocolate daily was beneficial for health a number of ways. Consuming a 3.5 oz bar of milk chocolate daily did not cause weight gain, that it actually resulted in reducing hunger and desiring fewer sweets the rest of the day, increased beneficial polyphenols, improved the gut microbiome, and morning consumption decreased fasting glucose (good). Overall, it was best to eat the chocolate in the morning (as compared to the evening before bedtime). Yes!!!

The researchers studied postmenopausal women (48 to 62 years old) in Murcia, Spain who ate milk chocolate daily, or no chocolate for 2 weeks while eating as usual (regular dietary pattern), and then did the opposite for 2 weeks after a one week break. (Thus everyone ate chocolate daily at some point). This meant that the chocolate eaters actually ate slightly more calories during the study than those not eating chocolate.

The researchers state that a 2018 review of chocolate studies (clinical trials) found that overall eating chocolate daily for 2 to 24 weeks (each study lasted a different length) "does not change body weight or body fat distribution". Some studies also find that eating chocolate daily slightly reduces waist size (waist circumference reduction). And this is what they also found in this study.

How much chocolate? The women in this study ate 100 grams per day (3.5 ounces) - a normal sized chocolate bar! Chocolate lovers - rejoice!

From Medical Xpress: Starting the day off with chocolate could have unexpected benefits

A new study of postmenopausal women has found that eating a concentrated amount of chocolate during a narrow window of time in the morning may help the body burn fat and decrease blood sugar levels.  ...continue reading "Milk Chocolate Has Health Benefits"

Published on Leave a comment on Bacteria Are In the Developing Baby By the Second Trimester

We've known for a while that exposure to microbes during the baby's first year is important (and good) for the developing immune system. In addition, recent research suggests that during the second trimester of pregnancy the developing fetus already has microbes in its body which help "educate" the developing immune system.

An international team of researchers found that bacterial species are present in the fetus during the second trimester. They examined and found bacteria in the  gut, lungs, skin, and placenta of the fetuses. Gardnerella, Lactobacillus, and Staphylococcus species were found in most of the fetal organs. Streptococcus, Enterococcus, and Prevotella species were also frequently found, as well as other species. The view is that the microbes came from the mother ("vertical transmission of microbes").

What the researchers found exciting was not just that there were microbes living already in the fetus in the second trimester, but that these microbes "educate" the developing immune system, especially memory T cells. This prepares the newborn with all sorts of exposures (including harmful microbes) once it is born.

The researchers used genetic sequencing (16S ribosomal RNA sequencing) on fetal and placental tissues, which were obtained from second trimester (starting with week 13) abortions.

Excerpts from The Scientist: Microbes in Human Fetuses Spur immune Development

Over the last decade, scientists have shown that the fetal immune system comes online much sooner than was initially thought, but what type of antigens train nascent immune cells and how this affects subsequent development remain open questions. In a study published June 1 in Cell, researchers determined that second-trimester human fetuses harbor live bacteria in tissues all over their bodies that can activate fetal T cells.  ...continue reading "Bacteria Are In the Developing Baby By the Second Trimester"

Published on Leave a comment on Glyphosate May Be Having a Harmful Effect On Our Gut Microbiome

Uh oh... Glyphosate is the most widely used herbicide (plant-killer) in the world, and its pervasive use may be harming our gut microbiomes. Glyphosate (which is in Roundup) is used not only as a weed-killer, but also applied to glyphosate resistant genetically engineered (GE) crops such as soy, canola, corn, and also right before harvest (preharvest) on many grain crops. Thus we find glyphosate and glyphosate residues all around us, including in the foods we eat.

Researchers at the University of Turku  in Finland developed a bioinformatics tool to examine glyphosate effects on gut bacteria. They found that glyphosate kills many bacterial species found in the human gut, including such important keystone bacteria as Faecalibacterium prausnitzii. Their words: "54% of species in the core gut microbiome are sensitive to glyphosate". (A nice way of saying it kills them.) They summarize:

"A large proportion of bacteria in the gut microbiome (Qin et al., 2010) are susceptible to glyphosate (class I); thus, the intake of glyphosate may severely affect the composition of the human gut microbiome. "

Glyphosate has already been linked to a number of health problems (e.g. cancer, endocrine disruption). The gut microbiome or microbiota is the millions of microbes living in our intestines, and they are very important to our health. Imbalance or disruptions to our gut microbiome result in inflammation, chronic conditions, and diseases.

What to do? Try to eat as many organic foods, especially grains, soy, and corn, as possible. Organic farmers are not allowed to use glyphosate. Try to avoid using glyphosate-based herbicides on your property.  Unfortunately, our government agencies are not protecting us with regards to glyphosate, and the US allows higher glyphosate residues in food than in the European Union.

From Science Daily: Glyphosate may affect human gut microbiota

Glyphosate is the most commonly used broad-spectrum herbicide. Researchers from the University of Turku in Finland have developed a new bioinformatics tool to predict if a microbe, e.g. a human gut bacterium, is sensitive to glyphosate.  ...continue reading "Glyphosate May Be Having a Harmful Effect On Our Gut Microbiome"

Published on Leave a comment on Small Skin wounds May Heal Faster Without the Use of an Antibiotic Cream

Nowadays many people apply antibiotic ointments on any and all skin wounds, no matter how minor. This is recommended by doctors in an effort to prevent the wound from becoming infected and to promote wound healing. However, surprising results from a recent small study found that applying an antibiotic ointment on skin wounds actually slows down healing.

The John Hopkins Univ. School of Medicine researchers found that our skin microbes (microbiome), including bacteria thought of as pathogenic, are involved in skin wound healing. The skin wound healing was faster in both humans and mice when antibiotic ointments were not applied.

Their recommendation: “...perhaps people may need to reconsider their use of these products (antibiotic ointments)". Of course more research needs to be done to see if the results from the small study (six adults) hold up. Perhaps a good approach would be to let small skin wounds heal on their own, and only apply an antibiotic ointment if the wound looks infected.

From Medical Xpress: Study examines why skin lacerations may be slow to heal, even with topical antibiotics

When you get a cut, scrape or other minor skin laceration, doctors recommend that you take measures to ensure that the wound doesn't get infected and heals properly. Many people opt to use over-the-counter medications, such as topical antibiotic ointments and liquids, to aid the repair process—and as commonly believed, promote healthy skin healing.  ...continue reading "Small Skin wounds May Heal Faster Without the Use of an Antibiotic Cream"

Published on Leave a comment on Fungi Are Living In Your Lungs
Human lungs Credit: Wikipedia

We have millions of all sorts of microbes living throughout our respiratory tract (nose, sinuses, mouth, lungs, etc.). A recent study looked at the microbes in the lungs and found that fungi normally live in healthy lungs, including fungi that are usually thought of as harmful. Surprisingly, the fungi found in lungs of people with COPD (chronic obstructive pulmonary disease) are basically similar to those in healthy people.

The fungi living in different parts of the body is the mycobiome. The lung (pulmonary) microbiome is unique, meaning it is different than in other parts of the respiratory tract, such as the mouth. It used to be thought that the lungs were sterile (unless there was an infection). But now we know that is not true - we normally have fungi, bacteria, and viruses living in our lungs.

University of Bergen researchers analyzed both the oral (mouth) mycobiome and lung mycobiome of 93 persons with COPD and 100 healthy persons (the control group). Surprisingly, both the oral and lung mycobiomes of both healthy and COPD groups were dominated by Candida fungi, with more Candida in the mouth, than in the lungs for both groups. Finding that Candida resides in the lungs of heathy individuals was surprising because it can be a "fungal pathogen" (thus harmful and invasive) in different parts of the body.

One piece of good news - using inhaled steroids didn't seem to affect the lung mycobiome.

Keep in mind that fungi are all around us, both indoors and outdoors, and we are constantly breathing in fungal spores. Our bodies have evolved to handle normal amounts just fine. As the researchers wrote: "Healthy airways possess effective removal of such spores". It's when a person is immunocompromised or has COPD that problems can develop.

From Medical Xpress: Fungi are present in your lungs

The lungs were for a long time considered to be sterile in health, while in diseases like chronic obstructive pulmonary disease (COPD) failure in immune mechanisms were thought to allow microorganisms to proliferate and persist. New sequencing techniques have shown that several microorganisms reside in the lungs of healthy individuals, as well. Few studies have examined the fungal community in COPD and compared it to healthy controls using such techniques. ...continue reading "Fungi Are Living In Your Lungs"

Published on Leave a comment on What You Eat Determines The Type Of Bacteria Living In Your Gut

Another study has confirmed that if a person wants to have beneficial gut microbes that are associated with lower rates of chronic inflammation and many health conditions and diseases, then you need to eat a diet that nourishes the beneficial gut microbes. And once again, research finds that it is a plant based diet that does this.

A plant based diet is one rich in fruits, vegetables, whole grains, legumes (beans), nuts, and seeds, thus containing lots of fiber - and these nourish beneficial gut microbes. In this group is also oily fish. This is an anti-inflammatory diet. It feeds short-chain fatty acid (SCFA)-producing microbes (this is good). A great example of plant foods also containing bacteria, as well as nutrients and fiber: one raw apple has about 10 million bacteria!

On the other hand, a diet rich in processed foods and lots of meat (an animal derived diet), is associated with microbes linked to intestinal inflammation - thus an inflammatory diet . Also includes foods with high amounts of sugar and alcohol. This type of diet is low fiber and considered a Western diet.

To arrive at these conclusions, researchers in the Netherlands looked at the gut microbiome of 1425 persons in 4 groups - those with Crohn's disease, ulcerative colitis, irritable bowel syndrome, and the general healthy population. They found 38 associations between dietary patterns and microbial clusters, as well as 61 individual foods and nutrients with 61 bacterial species. They found that specific foods and nutrients were associated with species known to give mucosal protection and have anti-inflammatory effects.

These beneficial bacterial species are NOT found in probiotics or supplements. You must eat the foods on a daily basis. [Another study with similar findings.] Studies show changes will occur very quickly - within two weeks, both in microbes and effects on the intestines.  Think of the saying: You are what you eat. Yes!

From Medical Xpress: Diet rich in animal foods, alcohol and sugar linked to 'inflammatory' gut microbiome

A high dietary intake of animal products, processed foods, alcohol and sugar is linked to a gut microbiome that encourages inflammation, finds research published online in the journal Gut.  ...continue reading "What You Eat Determines The Type Of Bacteria Living In Your Gut"