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Category: human microbiome

Published on Leave a comment on There Are Thousands of Human Gut Bacteria Strains

We have trillions of bacterial cells from thousands of different strains of bacteria living in our gut! Researchers at MIT (Massachusetts Institute of Technology) collected stool samples from 90 people living in the Boston area (some for as long as 2 years), did modern genetic sequencing, and in this way isolated nearly 8000 strains of bacteria.  These bacterial strains were from the six major phyla of bacteria (e.g. Bacteroidetes and Firmicutes) that dominate the human gastrointestinal tract. Just remember that the human gut also has fungi, archaea, and viruses living there. Yes, it is crowded in the gut!

The researchers took repeated stool samples from about a dozen of the volunteers and so were able to study bacterial changes within individuals over time. They are making all the data about the gut bacterial strains available to other researchers, with the hope that this will help scientists develop new treatments for a variety of diseases. This data set is called the Broad Institute-OpenBiome Microbiome Library (BIO-ML). This is important information to have because study after study is finding that there are gut microbial differences in people with a number of diseases as compared to healthy individuals.

BOTTOM LINE: The goal should be to feed and nurture beneficial gut microbes, ones that are associated with health. The best way to feed your beneficial gut microbes is to have a diet with lots of whole, real foods and fiber - which means a diet rich in fruits, vegetables, whole grains, nuts, legumes (beans), and seeds. (Think Mediterranean style dietary pattern.) And to eat less (a lot less) highly processed, low fiber, refined grains, and sugary foods. In other words, you don't want to feed microbes linked to chronic inflammation and diseases, but instead want to feed beneficial microbes linked to health (and not chronic inflammation). For example, choose the apple and not the candy bar. Your gut microbes will thank you.

From MIT News Office: A comprehensive catalogue of human digestive tract bacteria   ...continue reading "There Are Thousands of Human Gut Bacteria Strains"

Published on Leave a comment on Antibiotics, Flu Vaccines, and Gut Bacteria

A really interesting study found that in humans, taking antibiotics (which reduces the gut bacteria) may result in the flu vaccine not being as effective as in people who did not take antibiotics. An earlier similar study had found that this was true for mice, which is why the researchers did the study on humans.

The Stanford University and Emory University researchers studied healthy people who had recent (in last few years) flu vaccinations and those who hadn't had a flu vaccine for several years prior to the study. Some individuals took 5 days of broad spectrum antibiotics, and on day 4 received a flu vaccine, while others did not take antibiotics, but did receive the flu vaccine on day 4.

Not surprisingly: The antibiotics lowered the gut-bacterial population by 10,000-fold. While month by month there was increasing recovery, the resulting loss of overall diversity was detectable for up to one year after the antibiotics were taken. Keep in mind that they found that: "Notably, species richness and biodiversity were not fully recovered at 6 months, indicating long-lasting loss of unique bacterial species, consistent with previous studies." [BOTTOM LINE: Only take antibiotics when necessary.]

Interestingly, after antibiotic use, the researchers found other changes besides an alteration in gut bacteria populations. They also found changes within the immune system which resulted in an inflammatory state, which was due to "impairments in bile acid metabolism by the gut flora". In other words, taking antibiotics has a number of effects beyond treating an infection (the reason they were taken).

By the way, those who had taken flu vaccines in prior years had much better responses to the vaccines - they only had a minimal impact on vaccine response, even though they took antibiotics, than those who had not. Those who had not received flu vaccines or the flu in recent years had "low preexisting immunity", and taking the antibiotics (which resulted in loss of gut bacterial species) impaired their antibody response to the flu  vaccine. The researchers said: "The results of this study are consistent with the concept of immune responses in adults being largely determined by immune history and resilient to transient changes in the microbiome."

From Medical Xpress: Individual response to flu vaccine influenced by gut microbes   ...continue reading "Antibiotics, Flu Vaccines, and Gut Bacteria"

Published on Leave a comment on Children, Animals, and Gut Microbes

The evidence is growing. Another recent study found that exposure to dirt and animals in the first year of life is beneficial for development of a a rich and diverse gut microbiome - that is, for greater species "richness" as well as more beneficial microbes. This is linked to lower levels of allergies and asthma in children.

So don't worry about children being exposed to animal "germs" and getting dirty! Instead, consider the microbes as having health benefits, such as developing a "robust immune system". In summary, it now appears that in the first year of life the immune system needs lots of exposure to all sorts of microbes (e.g. from pets, animals, dirt)  to "train it" to develop normally.

The Ohio State University researchers compared 5 healthy rural Amish infants to 5 healthy non-Amish urban infants in Ohio, also found that all of the rural (Amish) children were breastfed, while 2 of the urban (non-Amish) children were only formula fed (some microbial differences there). The Amish households had farm animals (cattle, sheep, and/or horses) and pets (dogs and/or cats), while the non-Amish households had no contact with livestock, but did have a pet dog or cat. Just like in other studies, one pet doesn't seem to be enough - even more animal exposure in early childhood is best for the gut microbiome. [One study found a dose-dependent effect with exposure to 5 furry pets in early childhood was needed to prevent all allergies.]

Studies find that rural (Amish) children have a low incidence of allergies and asthma, while urban children have a high incidence of allergies and asthma. In this study, an example of microbial differences in the 2 groups of children was that Bifidobacterium bacteria were "enriched" in non-Amish (urban) infants, while Roseburia species were "enriched" in Amish (rural, farm-raised) infants. Similar gut microbe differences have been observed in other studies comparing rural and urban children, and both dietary differences (e.g. farm raised children eat lots of homegrown produce) and environmental differences (animal exposure) are thought to be responsible for the differences.

From Science Daily: Keeping livestock in the yard just might help your baby's immune system  ...continue reading "Children, Animals, and Gut Microbes"

Published on Leave a comment on Problems With Paleo Diet?

The Paleo diet has been around for years and yet it continues to be controversial. The debate is whether following the Paleo diet long-term has health benefits or not? Supporters of the Paleo (Paleolothic) diet say it promotes gut health and is good for gut microbes, but recent research findings are a strike against this claim. The Paleo diet is based on the hypothesis that humans have not adapted to eating products of agricultural farming such as grains, dairy products, or legumes (beans), as well as all processed foods, so they should be avoided. Instead it stresses eating meat, fish, eggs, nuts, (some) fruits, and vegetables.

So what were the new research findings?  Australian researchers found that people who had been on a Paleo diet for more than a year ate lower amounts of resistant starch, and so had a different bacteria profile in the gut - with lower levels of some beneficial species. They also had high levels of a biomarker in the blood (trimethylamine-n-oxide or TMAO) that is linked to heart disease.

The problem seems to be the lower intake of resistant starch - which is a carbohydrate that resists digestion in the small intestine and ferments in the large intestine. As the fibers ferment they act as a prebiotic and feed the beneficial bacteria in the gut. More than one type of resistant starch can be present in a single food. And what foods contain resistant starches? Precisely some foods avoided in the Paleo diet: grains, rice, beans, peas, lentils, plantains, and green bananas. A number of studies find health benefits (e.g. gut health) from eating foods with resistant starches.

From Medical Xpress: Heart disease biomarker linked to paleo diet

People who follow the paleo diet have twice the amount of a key blood biomarker linked closely to heart disease, the world's first major study examining the impact of the diet on gut bacteria has found.  ...continue reading "Problems With Paleo Diet?"

Published on Leave a comment on Excellent Reason To Eat Apples: The Bacteria

New research once again confirms that raw fruits and vegetables result in a person ingesting lots of microbes. Millions of bacteria. Which is considered beneficial for our gut microbiome! What's interesting in the latest study looking at bacteria in both conventionally and organically grown apples is that organic apples are a better source of bacteria - that their bacteria are more diverse, distinct, and balanced (when compared to conventionally grown apples).

The Austrian researchers (Wassermann et al) wrote in the Frontiers In Microbiology: "Our results suggest that we consume about 100 million bacterial cells with one apple. Although this amount was the same, the bacterial composition was significantly different in conventionally and organically produced apples."

Interestingly, there were a lot of beneficial Lactobacillus species in the organic apples, but not conventionally grown ones. The researchers thought that the diverse microbiome of organic apples probably limits or hampers harmful microbes (human pathogens). The researchers also wrote: "The described microbial patterns in organic apples resemble the impact of apple polyphenols on human health, which have not only been shown to alleviate allergic symptoms (Zuercher et al., 2010), but also to promote growth of Lactobacillus and Bifidobacterium in the human gut and to reduce abundance of food-borne pathogens."

Another bonus of eating organic apples is that it means avoiding pesticides that are routinely sprayed on conventional fruit. So eat away! Microbes, fiber, and nutrients all in one small fruit!

Fun fact: The researchers write that apples are the most consumed fruit world-wide. Excerpts from Science Daily: An apple carries about 100 million bacteria -- good luck washing them off  ...continue reading "Excellent Reason To Eat Apples: The Bacteria"

Published on Leave a comment on Gut Bacteria Has An Effect On Some Medicines?

New research is raising questions about the role of gut bacteria in how people react to medications and whether the medicines are effective, at least some medications such as L-dopa treatment for Parkinson's disease. Why do medicines work for some people and not others? Perhaps the gut microbes are playing a part by interacting with the medicines! The gut microbes may actually be breaking down medicines and preventing them from reaching their target.

Researchers from Harvard University and University of California found that the composition of the gut microbes has an effect on whether the medicine L-dopa is effective or becomes ineffective as a Parkinson's disease treatment. They found that some bacteria can inactivate the medicine. Definitely research that needs following up on. Also, which medications is this true for?

Excerpts from Science Daily: Gut microbes eat our medication    ...continue reading "Gut Bacteria Has An Effect On Some Medicines?"

Published on Leave a comment on Do You Eat Foods With Nanoparticles In Them?

How frequently do you eat foods with nanoparticles in them? The use of nanoparticles in foods is increasing every year, with the result that people may eat foods with them daily (thus having chronic exposure). Nanoparticles in foods are ingredients so small that they are measured in nanometers or billionths of one meter.

The most common nanoparticle is the food additive titanium dioxide, which in Europe is known as E171. Titanium dioxide is added to many processed foods, candy, and even supplements  and non-prescription medicines (e.g. antihistamines) as a "coloring" to make foods whiter or brighter. Currently there are no restrictions on using titanium dioxide nanoparticles in foods.

We still know very little about whether titanium dioxide nanoparticles have health risks to humans, but studies suggest they may cause intestinal inflammation, may disrupt gut microbes, and may migrate to other parts of the body.

Now another study is raising more questions about the safety of titanium dioxide in food. It was done in mice, but the researchers feel it applies to humans. The researchers found that titanium dioxide resulted in a "pro-inflammatory environment and biofilm formation" in the intestines of the mice, and in this way could predispose humans to conditions such as inflammatory bowel disease and colorectal cancer. Bottom line: Read food ingredient lists!

From Science  Daily: Common food additive found to affect gut microbiota

...continue reading "Do You Eat Foods With Nanoparticles In Them?"

Published on Leave a comment on Reductions In Autism Symptoms Two Years After Fecal Transplants

Two years ago a study was published showing good results in 18 children with autism who received fecal transplants. Fecal transplants involves giving stool (along with all the microbes in the stool) from a healthy donor to a recipient. After getting fecal transplants, the children (ages 7 to 16) had significant improvements in their gastrointestinal symptoms (e.g. abdominal pain, indigestion, diarrhea, and constipation, and stools), autism related symptoms, and in their gut microbes.

But how did they do long-term? The short answer: great. In fact, the children continued to improve over the next 2 years. Most of their gut symptoms continued to improve, their autism symptoms continued to improve, and their gut microbes kept improving over time - with significant increases in bacterial diversity (considered good), and with more Bifidobacteria and Prevotella. A professional evaluator found an average 45% reduction in core autism symptoms (language, social interaction and behavior) at two years after the initial treatment (compared with before the original treatment).

It has long been known that many persons with Autism Spectrum Disorders (ASD) experience chronic gastrointestinal (GI) symptoms, and research shows that children with ASD have distinctive gut microbiomes (as compared to neurotypical children). Researchers believe there is a link between the gut and brain (the gut-brain axis), so a therapeutic approach could be to "modify" the gut microbes. Which is what the researchers did - in a 10 week process they call Microbiota Transfer Therapy (MTT). First they gave antibiotics, then a bowel cleanse, a stomach-acid suppressant, a fecal transplant (FMT) followed by many days of low purified doses taken orally.

From Science Daily: Autism symptoms reduced nearly 50 percent two years after fecal transplant

According to the Centers for Disease Control and Prevention, about one in every 59 children in the U.S. is diagnosed with autism, up from one in every 150 in 2000.  ...continue reading "Reductions In Autism Symptoms Two Years After Fecal Transplants"

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Published on 1 Comment on It Is Normal For Fungi To Be In Breast Milk

Researchers have known for a while that human breast milk contains hundreds of species of bacteria that a baby ingests while feeding. This is good! The bacteria is seeding the baby's gut microbiome (microbial community). A recent study of breast milk from different continents found that breast milk from healthy mothers also contains species of fungi - which is the breast milk mycobiome. What was noteworthy was that some  types of fungi in breast milk were found among breast milk samples from all locations (a fungi "core group"), while other types of fungi varied among breast milk from the different locations and even how the baby was delivered (vaginal or C-section birth).

After analyzing the 80 samples of breast milk (20 from each country: Spain, Finland, South Africa, China) it was found that some fungi were the same in breast milk from the different locations: Malassezia, Davidiella, Sistotrema, and Penicillium, while others were different. Fungi from the genus Cryptococcus were higher in breast milk from women who delivered vaginally (as compared to those who had a C-section).  [Note: Genus ranks above species, but below family, and the written name is capitalized.]

This study confirms the importance of breast milk as a source of microbes (along with many nutrients and protective compounds) to the infant and infant gut. From Science Daily:

Breast milk microbiome contains yeast and fungi: Do these benefit the infant?  ...continue reading "It Is Normal For Fungi To Be In Breast Milk"

Published on Leave a comment on Birth, Cord Clamping, and Some Microbial Differences

Today's topic: BIRTH. Two recent studies have results that question some current medical practices, which are when to cut the umbilical cord, and hospital vs home birth differences in the baby's gut microbes.

The first study makes a case against the current practice of cutting the umbilical cord immediately after birth. University of Rhode Island researchers found that delaying umbilical cord clamping for more than 5 minutes transfers iron rich blood from the placenta to the baby (resulting in about a 30% increase in blood volume). This resulted in babies at 4 months of age having higher iron storage (ferritin) levels and increased brain myelination. Myelin is a fatty material that wraps around nerve cell fibers - think of it as insulation of the brain's wiring.

The second study found that birth at home results in a more diverse microbiome (microbial community) in the baby at birth and one month later - when compared to babies born in hospitals. This study was conducted in the Hudson Valley region of NY state. All babies were born vaginally and were breastfed. Hospital born babies had decreased levels of some bacteria and increased levels of other bacteria (e.g. Clostridium - with other studies finding that higher levels in children is associated with an increased risk of asthma). It was suggested that certain hospital practices may be causing this (sterile drapes, antibiotics, etc.). 

From Medical Xpress: Study shows benefits of delayed cord clamping in healthy babies

A five-minute delay in the clamping of healthy infants' umbilical cords results in increased iron stores and brain myelin in areas important for early-life functional development, a new University of Rhode Island nursing study has found.  ...continue reading "Birth, Cord Clamping, and Some Microbial Differences"