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Category: human microbiome

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"

Published on Leave a comment on Five Year Olds Have Similar Gut Microbes, No Matter the Type of Birth

The millions of bacteria, fungi, viruses (human microbiome) that live on and within us are extremely important for our health in all sorts of ways. The birth experience (as the baby travels down the birth canal) is one way that a mother's microbes get transmitted to the baby ("seeds" the baby's microbiome). But babies born by Cesarean delivery start out picking up different species of microbes - from dust in the operating room.

Thus there has been concern with the possibility that a baby born by C-section, as compared to a vaginal delivery, will have life long microbiome differences. Swedish researchers studied this issue in 471 children and determined that by 5 years of age that the microbiome differences at birth and first year of life have generally disappeared. The differences in microbial composition had decreased to less than 2% in the 2 groups. This is good news!

Over the 5 years everyone had a great increase in the number of microbial species that live in the gut. The gut microbiome became more "adult-like", but it wasn't yet like that of adults. A conclusion was that not only does it take years to develop adult microbial complexity, but there is also individual variation in how long this takes. A person's diet, especially the introduction of solid foods, and environment all have an effect on species diversity and composition.

By the way, another way mothers transmit hundreds of species of microbes to their babies is during nursing in the breast milk (this is great!), and these species change over time. This is a good reason to breast feed - it's not just the nutrition, but also the microbes.

From Science  Daily: Gut microbiota in Cesarean-born babies catches up

Infants born by cesarean section have a relatively meager array of bacteria in the gut. But by the age of three to five years they are broadly in line with their peers. This is shown by a study that also shows that it takes a remarkably long time for the mature intestinal microbiota to get established.  ...continue reading "Five Year Olds Have Similar Gut Microbes, No Matter the Type of Birth"

Published on Leave a comment on The Bacteria In Breast Milk Change Over Time
Breastfeeding
Credit: Wikimedia Commons/ Anton Nosik

For years it has been known that breast milk transfers hundreds of microbial species to the baby -  which is very important and beneficial for the baby's microbiome (community of fungi, viruses, bacteria, and other microbes) and health. A recent study found that the bacteria in breast milk varies over time, which is a good reason to breastfeed for at least 6 months - the baby ingests all these beneficial species in the breast milk.

Breast milk samples were collected from 76 breastfeeding (lactating) mothers living in 8 villages in the remote Western Highlands of Guatemala during "early lactation" (6–46 days postpartum) or after months of breastfeeding or "late lactation" (109 to184 days postpartum). Modern technologies (genetic sequencing) were used to analyze the breast milk.

The researchers found a bacterial or microbiome shift from Staphylococcus and several Streptococcus species in early lactation to Sphingobium and Pseudomonas species in late lactation, along with other bacterial shifts. The changing bacterial species have different roles in the body. There were even species never before reported in breast milk, such as: Janthinobacterium agaricidamnosum, Novosphingobium clariflavumm, Ottowia beijingensis, and Flavobacterium cucumis.

Of course much is still unknown about the breastmilk microbiome, and even what is a "core" breast milk microbiome - that is, what species are the core species in all breast milk. But it's clear what the baby gets from the breast milk changes over time.  It's still early days in this research!

Note that all these hundreds of species are not those found in probiotic supplements or formula - a baby must breastfeed to get them. Unfortunately, it is estimated that only 26% of North American mothers breastfeed their babies for at least 6 months (Unicef data).

From Futurity: Breast Milk Offers Different Bacteria Over Time

This bacterial cocktail could act like a daily booster shot for infant immunity and metabolism. ...continue reading "The Bacteria In Breast Milk Change Over Time"

Published on Leave a comment on Microbes and Advanced Melanoma Treatment

In the future, giving specific microbes or entire microbial communities may be part of some cancer treatments! This is because the composition of a person's gut microbiome (the community of bacteria, fungi, and viruses) influences whether a person responds to immunotherapy drugs. This means that the mixture and variety of microbial species living in your intestines may determine whether you respond to cancer immunotherapy drugs. Wow!

One recent study found benefits from fecal microbial transplants (FMT) - that is, transplanting the stool (which contains an entire microbial community of bacteria, fungi, viruses) from a donor who had responded well to immunotherapy drugs to a person with advanced melanoma who had not responded to immunotherapy drugs. In total, 15 persons received stool transplants, and 6 of them had changes to the gut microbiome (becoming more like the donor's gut microbiome) so that the immunotherapy drug now worked against melanoma.

Now studies are needed to identify which specific microbes are the ones that were critical for overcoming a tumor's resistance to immunotherapy drugs.

This is very exciting research because the best treatments for advanced melanoma (metastatic melanoma) are immunotherapy drugs, but it only works for a minority of patients at this point. Microbial manipulation (in this case with fecal transplants) could be a game changer!

Excerpts from Science Daily: Fecal microbiota transplants help patients with advanced melanoma respond to immunotherapy

For patients with cancers that do not respond to immunotherapy drugs, adjusting the composition of microorganisms in the intestines -- known as the gut microbiome -- through the use of stool, or fecal, transplants may help some of these individuals respond to the immunotherapy drugs, a new study suggests. Researchers at the National Cancer Institute (NCI) Center for Cancer Research, part of the National Institutes of Health, conducted the study in collaboration with investigators from UPMC Hillman Cancer Center at the University of Pittsburgh.  ...continue reading "Microbes and Advanced Melanoma Treatment"

Published on Leave a comment on Your Diet, Your Gut Microbes, And Your Health

There is strong evidence for a link between the foods a person eats, the microbes that live in the person's gut (gut microbiome), and the person's health, according to a large international study. Yes, it's all related.

The researchers were able to find clear patterns of the types of foods eaten and the microbes in the gut. They found that the presence of 15 specific bacteria are consistently associated with good health ("good microbes") and some other bacteria ("bad microbes") are associated with poor metabolic health (including inflammation, blood sugar control).

Study researcher Tim Spector (of King's College London) said: "When you eat, you're not just nourishing your body, you're feeding the trillions of microbes that live inside your gut."

They found that a diverse diet rich in minimally processed plant-based foods (e.g. fruits, vegetables, seeds, nuts, whole grains, dietary fiber) and fish supports and feeds "good" gut microbes associated with health, with favorable blood sugar levels (glucose control), lower levels of inflammation, improved metabolism, and thus lower risk of heart disease and other chronic conditions (e.g. type 2 diabetes).

On the other hand, persons that ate more highly processed foods, added sugars (desserts!), low fiber foods, artificial sweeteners, foods with additives were more likely to have "bad" microbes linked to poor health, inflammation, unfavorable blood sugar levels, and obesity.

They were able to see that specific foods clearly had an effect on specific bacteria, for example eating tomatoes with an increase in beneficial species of Roseburia. Eating a variety of plant based foods was also associated with an increase in diversity of bacteria (this is considered good), and also with the presence of beneficial keystone bacteria such as  Faecalibacterium prausnitzii.

VERY IMPORTANT: The beneficial bacteria the researchers list are NOT in probiotic supplements. Instead, you must eat a variety of foods that feed beneficial bacteria (e.g. eating a Mediterranean style diet). In fact, some of the microbes the researchers found have not yet been named. Foods also contain bacteria, and these are ingested. For example, an apple contains about 100 million bacteria!

From Science Daily: Link between gut microbes, diet and illnesses revealed

Diets rich in healthy and plant-based foods encourages the presence of gut microbes that are linked to a lower risk of common illnesses including heart disease, research has found.  ...continue reading "Your Diet, Your Gut Microbes, And Your Health"

Published on Leave a comment on Beneficial Effect of Breast Milk On the Baby’s Immune System
Breastfeeding
Wikimedia Commons/ Anton Nosik

There are a lot of health reasons why breast milk is better for a baby then formula, and now another reason can be added to the list. A recent study found that specific immune cells (regulatory T cells) expand more in the first three weeks of life in breastfed human babies - nearly twice as abundant as in formula fed babies.

These cells control the baby's immune response against maternal cells transferred with breast milk and help reduce inflammation. In other words, breast milk is good for the baby's immune system development.

The University of Birmingham researchers also found that specific beneficial bacteria, called Veillonella and Gemella, which support the function of regulatory T cells, are more abundant in the gut of breastfed babies.

Breast milk is considered the best food for infants. It contains a range of complex nutrients, antimicrobial proteins, bacteria, human milk oligosaccharides, and hormones from the mother. Thus it isn't surprising that whether the baby receives breast milk or formula influences the gut microbiome (community of microbes in the gut).

From Science Daily: New insight into why breastfed babies have improved immune systems

Research led by the University of Birmingham and Birmingham Women's and Children's NHS Foundation Trust has revealed new insight into the biological mechanisms of the long-term positive health effects of breastfeeding in preventing disorders of the immune system in later life.  ...continue reading "Beneficial Effect of Breast Milk On the Baby’s Immune System"

Published on Leave a comment on Gut Microbiome Is Altered In Persons With Major Depression

It turns out that people experiencing a major depression have differences in their gut microbiome (community of microbes) when compared to healthy people who are not depressed. A persistent and prolonged period of extreme sadness or depression is called a major depressive disorder (MDD).

A team of researchers (in both China and the US) analyzed stool samples from 311 people  with either MDD or healthy and not-depressed (the control group). They used modern genetic sequencing to see what microbes were in the stools. They found differences in 47 bacterial species, 3 bacteriophages (a virus that infects bacteria), and 50 fecal metabolites - which suggested to the researchers that depression is characterized by gut microbiome problems (it's imbalanced or out of whack).

There actually was a "signature composition" of gut microbes in the depressed persons, all of whom were unmedicated. They found higher levels ("increased abundance") of 18 bacterial species in people with MDD (mainly belonging to the genus Bacteroides) and 29 were less common (mainly belonging to Eubacterium and Blautia), when compared to healthy persons.

The researchers point out that other studies also find the gut microbiome to be imbalanced in MDD, and there are animal experiments showing that the gut microbiome has a role in causing MDD (e.g. transplanting gut microbes from a depressed person into a rat results in the rat exhibiting depressive behaviors).

Excerpts from The Scientist: Distinct Microbiome and Metabolites Linked with Depression

The human gut microbiome is a world in miniature, populated by a chatty community of bacteria, viruses, fungi, and protozoa nestled within various gastrointestinal niches. Over the past decade, researchers have linked disturbances within this complicated microbial society to a variety of diseases. Major depressive disorder (MDD) is one such condition, but the studies have been small and the findings imprecise.   ...continue reading "Gut Microbiome Is Altered In Persons With Major Depression"