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If taking Clostridia as a probiotic for food allergies works, it would be amazing for food allergy sufferers. Very exciting research. From Time:

The Bacteria That May One Day Cure Food Allergies

Every round of antibiotics a person takes will wipe out strains of bacteria inside the body, some of which are eliminated forever. Considering how early and how often antibiotics are administered to kids—coupled with our increasingly antimicrobial lifestyles—we’ve become more prone to allergies and other ailments, the hygiene hypothesis goes. There’s no cure for food allergies, just lifestyle adjustments and abstention. But Nagler and her team may have the germ of an idea for treatment using gut bacteria, according to a new mice study published in the Proceedings of the National Academy of Sciences.

The team dosed two groups of mice with peanut allergens. One group of mice had been bred to be entirely without gut germs; the other group had sparsely populated gut bacteria due to treatment with antibiotics. Both groups of mice had higher levels of the allergen in their bloodstream compared to mice with healthy gut-bacteria populations.

After giving those same mice a mix that contained the bacteria strain Clostridia, their allergen levels plummeted. Infusing the mice with another group of intestinal bacteria, Bacteroides, didn’t help—so the researchers think the effect is special to Clostridia. “These bacteria are very abundant and they reside very close to the epithelial lining, so they’re in intimate contact with the immune system,” Nagler says.

Next, they’ll transfer gut bacteria from food-allergic infants and healthy infants into germ-free mice, Nagler says. “If we give back Clostridia to a mouse that has the bacteria of an allergic child, can we now reverse susceptibility in that mouse?”

This is a more in-depth article of the research. From Science Daily:

Gut bacteria that protect against food allergies identified

The presence of Clostridia, a common class of gut bacteria, protects against food allergies, a new study in mice finds. The discovery points toward probiotic therapies for this so-far untreatable condition. Food allergies affect 15 million Americans, including one in 13 children, who live with this potentially life-threatening disease that currently has no cure, researchers note.

Although the causes of food allergy -- a sometimes deadly immune response to certain foods -- are unknown, studies have hinted that modern hygienic or dietary practices may play a role by disturbing the body's natural bacterial composition. In recent years, food allergy rates among children have risen sharply -- increasing approximately 50 percent between 1997 and 2011 -- and studies have shown a correlation to antibiotic and antimicrobial use.

"Environmental stimuli such as antibiotic overuse, high fat diets, caesarean birth, removal of common pathogens and even formula feeding have affected the microbiota with which we've co-evolved," said study senior author Cathryn Nagler, PhD, Bunning Food Allergy Professor at the University of Chicago. "Our results suggest this could contribute to the increasing susceptibility to food allergies."

To test how gut bacteria affect food allergies, Nagler and her team investigated the response to food allergens in mice. ...This sensitization to food allergens could be reversed, however, by reintroducing a mix of Clostridia bacteria back into the mice. Reintroduction of another major group of intestinal bacteria, Bacteroides, failed to alleviate sensitization, indicating that Clostridia have a unique, protective role against food allergens.

To identify this protective mechanism, Nagler and her team studied cellular and molecular immune responses to bacteria in the gut. Genetic analysis revealed that Clostridia caused innate immune cells to produce high levels of interleukin-22 (IL-22), a signaling molecule known to decrease the permeability of the intestinal lining.

While complex and largely undetermined factors such as genetics greatly affect whether individuals develop food allergies and how they manifest, the identification of a bacteria-induced barrier-protective response represents a new paradigm for preventing sensitization to food. Clostridia bacteria are common in humans and represent a clear target for potential therapeutics that prevent or treat food allergies. 

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An interesting small study of the human armpit bacterial community. From Real Clear Science:

Antiperspirants Alter Your Armpit Bacteria and Could Actually Make You Smell Worse

In modern society, antiperspirants are widely hailed as a godsend, dispelling the inconvenient odors wafting from armpits everywhere. But a new study casts doubts on their vaunted position. As it turns out, antiperspirants may actually make you smell worse in the long run.

For 90% of all Americans, slathering on deodorants and antiperspirants is a daily occurrence, a precautionary measure against foul odors and unsightly sweat stains. The odors arise when bacteria living in our armpits break down lipids and amino acids excreted in sweat into more smelly substances. Deodorants employ antimicrobial agents that kill off bacteria, as well as chemicals that replace noxious odors with pleasant aromas. Deodorants that double as antiperspirants, like Degree, Old Spice, and Dove, take the process one step further by physically plugging sweat glands with aluminum-based compounds.

While most of us might only concern ourselves with the dry, aromatic benefits of antiperspirants and deodorants, researchers at the Laboratory of Microbial Ecology and Technology at the University of Ghent in Belgium are more interested in the effects on bacteria. Billions of bacteria dwell in the "rain forests" under our arms, and the substances we don are mucking with their habitats!

To uncover how deodorants and antiperspirants affect armpit bacteria, Chris Callewaert, a Ph.D student specializing in microbial ecology, and a team of researchers recruited eight subjects for a task a great many people (and especially their friends) might deem unbearable: Six males and two females pledged not to use deodorant or antiperspirant for an entire month. Specifically, four subjects stopped using their deodorants and another four stopped using their antiperspirant deodorant. (Most antiperspirants are also deodorants. See image below for an example.) Another control subject who did not regularly use either was asked to use deodorant for a month. The duration was chosen because it takes approximately 28 days for a new layer of skin cells to form.

The researchers analyzed the diversity and abundance of subjects' armpit bacteria at various timepoints before they stopped using antiperspirant, during the period of abstaining from antiperspirant, and for a few weeks after resuming the use of antiperspirant. Switching hygiene habits plainly altered the armpit bacterial communities of every subject. Since no two armpits and their resident bacteria are identical, it was difficult to pinpoint precise changes brought about by deodorants or antiperspirants, but one clear trend did materialize: antiperspirants resulted in a clear increase of Actinobacteria.

You might not recognize the name of Actinobacteria, but chances are, you've smelled them. Dominated by Corynebacterium, they are the major instigators of noxious armpit odor. Other microbes that inhabit the armpit, like Firmicutes and Staphylococcus, don't produce odors as quickly, nor are those odors nearly as pungent.

Callewaert believes the aluminum compounds in antiperspirants may be to blame, killing off "good," less smelly bacteria and allowing "bad" bacteria to dominate. His study found that deodorants which lack these sweat-blocking antiperspirant compounds are actually linked to a slight decrease of stinky Actinobacteria.

Though antiperspirants and deodorants are widely used, they are only a temporary fix."The measures we utilize today do not take away the initial source: the odor causing bacteria," Callewaert told RealClearScience. "Deodorants only mask unpleasant odors. We can do better than that. The follow up of this research is finding better solutions."

And Callewaert is already working on one: "armpit bacterial transplantation"."We take away the bad bacteria from the armpit of somebody with a body odor, and replace it with the good bacteria of a relative who doesn't have a body odor," he explained."So far we have helped over 15 people. For most subjects it brings immediate improvements. Most of them on a permanent time scale, although there are also people who suffer again from a body odor after some months."

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The bottom line is to read the ingredients list on products, and avoid all products labeled "antimicrobial" or "antibacterial" (because those are the ones typically containing triclosan and triclorocarban). Over 2000 products contain antibacterial compounds. I've even seen them in pillows, pillow protectors, mattress pads, dish racks, toys, and blankets! As we know from the latest microbiology research, we need to cultivate a healthy microbiome, and not throw it out of whack by continuously trying to kill off all bacteria. From The Atlantic:

It's Probably Best to Avoid Antibacterial Soaps

Antimicrobial chemicals are so ubiquitous that a recent study found them in pregnant mothers' urine and newborns' cord blood. Research shows that their risks may outweigh their benefits.

Antimicrobial chemicals, intended to kill bacteria and other microorganisms, are commonly found in not just soaps, but all kinds of products—toothpaste, cosmetics, and plastics among them. There is evidence that the chemicals aren’t always effective, and may even be harmful, and their ubiquity means people are often continually exposed to them. One such chemical, triclosan, has previously been found in many human bodily fluids. New research found traces of triclosan, triclocarban, and butyl paraben in the urine of pregnant women, and the cord blood of newborn infants. 

The research looked at the same population of 180 expectant mothers living in Brooklyn, New York, most of Puerto Rican descent. In a study published last week in Environmental Science and Technology, researchers from Arizona State University and State University of New York’s Downstate School of Public Health found triclosan in 100 percent of the women’s urine samples, and triclocarban in 87 percent of the samples. Of the 33 cord blood samples they looked at, 46 percent contained triclosan and 23 percent contained triclocarban.

In another, still-unpublished study, the researchers found that all of the cord blood samples contained “at least one paraben,” according to Dr. Rolf Halden, director of ASU’s Center for Environmental Security. 

Triclosan and triclocarban are endocrine disruptors, Halden explains. The risk there is that the chemicals can mimic thyroid hormones, potentially disrupting the metabolism and causing weight gain or weight loss. Previous research has also shown a connection between higher levels of triclosan in urine, and allergy diagnoses in children.

In the study looking at butyl paraben, the researchers found an association between higher exposure to the chemical, and a smaller head circumference and length of babies after they were born. Butyl paraben is used as a preservative, so it’s found in a wider breadth of products, according to Halden.

From Science News: Pregnant women, fetuses exposed to antibacterial compounds face potential health risks 


As the Food and Drug Administration mulls over whether to rein in the use of common antibacterial compounds that are causing growing concern among environmental health experts, scientists are reporting that many pregnant women and their fetuses are being exposed to these substances. The compounds are used in more than 2,000 everyday products marketed as antimicrobial, including toothpastes, soaps, detergents, carpets, paints, school supplies and toys, the researchers say.

The problem with this, explains Pycke, a research scientist at Arizona State University (ASU), is that there is a growing body of evidence showing that the compounds can lead to developmental and reproductive problems in animals and potentially in humans. Also, some research suggests that the additives could contribute to antibiotic resistance, a growing public health problem.

Although the human body is efficient at flushing out triclosan and triclocarban, a person's exposure to them can potentially be constant. "If you cut off the source of exposure, eventually triclosan and triclocarban would quickly be diluted out, but the truth is that we have universal use of these chemicals, and therefore also universal exposure," says Rolf Halden, Ph.D., the lead investigator of the study at ASU.

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Treating tumors with bacteria is very exciting and new.From Medical Express:

Injected bacteria shrink tumors in rats, dogs and humans

A modified version of the Clostridium novyi (C. noyvi-NT) bacterium can produce a strong and precisely targeted anti-tumor response in rats, dogs and now humans, according to a new report from Johns Hopkins Kimmel Cancer Center researchers.

In its natural form, C. novyi is found in the soil and, in certain cases, can cause tissue-damaging infection in cattle, sheep and humans. The microbe thrives only in oxygen-poor environments, which makes it a targeted means of destroying oxygen-starved cells in tumors that are difficult to treat with chemotherapy and radiation. The Johns Hopkins team removed one of the bacteria's toxin-producing genes to make it safer for therapeutic use.

For the study, the researchers tested direct-tumor injection of the C. noyvi-NT spores in 16 pet dogs that were being treated for naturally occurring tumors. Six of the dogs had an anti-tumor response 21 days after their first treatment. Three of the six showed complete eradication of their tumors, and the length of the longest diameter of the tumor shrunk by at least 30 percent in the three other dogs.

In a Phase I clinical trial of C. noyvi-NT spores conducted at MD Anderson Cancer Center, a patient with an advanced soft tissue tumor in the abdomen received the spore injection directly into a metastatic tumor in her arm. The treatment significantly reduced the tumor in and around the bone. "She had a very vigorous inflammatory response and abscess formation," according to Nicholas Roberts, Vet.M.B., Ph.D. "But at the moment, we haven't treated enough people to be sure if the spectrum of responses that we see in dogs will truly recapitulate what we see in people."

"One advantage of using bacteria to treat cancer is that you can modify these bacteria relatively easily, to equip them with other therapeutic agents, or make them less toxic as we have done here, " said Shibin Zhou, M.D., Ph.D., associate professor of oncology at the Cancer Center.  He and colleagues at Johns Hopkins began exploring C. novyi's cancer-fighting potential more than a decade ago after studying hundred-year old accounts of an early immunotherapy called Coley toxins, which grew out of the observation that some cancer patients who contracted serious bacterial infections showed cancer remission.

The researchers focused on soft tissue tumors because "these tumors are often locally advanced, and they have spread into normal tissue," said Roberts, a Ludwig Center and Department of Pathology researcher. The bacteria cannot germinate in normal tissues and will only attack the oxygen-starved or hypoxic cells in the tumor and spare healthy tissue around the cancer.

Verena Staedtke, M.D., Ph.D., a Johns Hopkins neuro-oncology fellow, first tested the spore injection in rats with implanted brain tumors called gliomas. Microscopic evaluation of the tumors showed that the treatment killed tumor cells but spared healthy cells just a few micrometers away. The treatment also prolonged the rats' survival, with treated rats surviving an average of 33 days after the tumor was implanted, compared with an average of 18 days in rats that did not receive the C. noyvi-NT spore injection.

Zhou said that study of the C. noyvi-NT spore injection in humans is ongoing, but the final results of their treatment are not yet available. "We expect that some patients will have a stronger response than others, but that's true of other therapies as well. Now, we want to know how well the patients can tolerate this kind of therapy."

It may be possible to combine traditional treatments like chemotherapy with the C. noyvi-NT therapy, said Zhou, who added that the researchers have already studied these combinations in mice. "Another good thing about using bacteria as a therapeutic agent is that once they're infecting the tumor, they can induce a strong immune response against tumor cells themselves," Zhou said.

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I've posted on whether probiotics can be used to treat mental disorders (see Probiotics and Psychobiotics- Part 1 and 2). But this article poses the interesting reverse question of whether the microbes are engaging in "microbial manipulations"? From NY Times:

Our Microbiome May Be Looking Out for Itself

Your body is home to about 100 trillion bacteria and other microbes, collectively known as your microbiome. We’ve come to appreciate how beneficial our microbes are — breaking down our food, fighting off infections and nurturing our immune system. 

But in the journal Bioessays, a team of scientists has raised a creepier possibility. Perhaps our menagerie of germs is also influencing our behavior in order to advance its own evolutionary success — giving us cravings for certain foods, for example. Maybe the microbiome is our puppet master.

The idea that a simple organism could control a complex animal may sound like science fiction. In fact, there are many well-documented examples of parasites controlling their hosts. How parasites control their hosts remains mysterious. But it looks as if they release molecules that directly or indirectly can influence their brains.

Our microbiome has the biochemical potential to do the same thing. In our guts, bacteria make some of the same chemicals that our neurons use to communicate with one another, such as dopamine and serotonin. And the microbes can deliver these neurological molecules to the dense web of nerve endings that line the gastrointestinal tract.

A number of recent studies have shown that gut bacteria can use these signals to alter the biochemistry of the brain.Compared with ordinary mice, those raised free of germs behave differently in a number of ways. They are more anxious, for example, and have impaired memory.Adding certain species of bacteria to a normal mouse’s microbiome can reveal other ways in which they can influence behavior. Some bacteria lower stress levels in the mouse. When scientists sever the nerve relaying signals from the gut to the brain, this stress-reducing effect disappears.

Some experiments suggest that bacteria also can influence the way their hosts eat. Germ-free mice develop more receptors for sweet flavors in their intestines, for example. They also prefer to drink sweeter drinks than normal mice do. Scientists have also found that bacteria can alter levels of hormones that govern appetite in mice.

Different species of microbes thrive on different kinds of food. If they can prompt us to eat more of the food they depend on, they can multiply. Microbial manipulations might fill in some of the puzzling holes in our understandings about food cravings, Dr. Maley said. Scientists have tried to explain food cravings as the body’s way to build up a supply of nutrients after deprivation, or as addictions, much like those for drugs like tobacco and cocaine. But both explanations fall short.

Take chocolate: Many people crave it fiercely, but it isn’t an essential nutrient. And chocolate doesn’t drive people to increase their dose to get the same high. Perhaps, he suggests, the certain kinds of bacteria that thrive on chocolate are coaxing us to feed them.

John F. Cryan, a neuroscientist at University College Cork in Ireland who was not involved in the new study, suggested that microbes might also manipulate us in ways that benefited both them and us. “It’s probably not a simple parasitic scenario,” he said.

Research by Dr. Cryan and others suggests that a healthy microbiome helps mammals develop socially. Germ-free mice, for example, tend to avoid contact with other mice. That social bonding is good for the mammals. But it may also be good for the bacteria. “When mammals are in social groups, they’re more likely to pass on microbes from one to the other,” Dr. Cryan said.

If microbes do in fact manipulate us, Dr. Knight said, we might be able to manipulate them for our own benefit — for example, by eating yogurt laced with bacteria that would make use crave healthy foods. The most important thing to do now, Dr. Knight and other scientists said, was to run experiments to see if microbes really are manipulating us.

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The following is from a presentation from The American Association of Diabetes Educators Annual Meeting August 6-9, 2014 by M.Jardin and C.Kafity. But the coffee and tea statement is different from what I've read elsewhere, specifically that coffee is beneficial, is a source of soluble fiber, and may keep pathogenic bacteria in check. From Endocrinology Today:

Plant-based diet helps grow healthy microbiota, halt diabetes disease process

With research mounting on the onslaught the body’s microbiota take from human eating patterns and the environment, making choices to maintain inner ecosystem health is essential, according to presenters at the American Association of Diabetes Educators Annual Meeting. Choosing a plant-based diet is one way people can increase the diversity of bacteria in their biome, reduce inflammation and begin to reverse the diseases processes involved in obesity and diabetes — often in just a few days.

“We know obesity and diabetes have increased tremendously in the last 20 years and we know that our genes haven’t changed, so that can’t account for the change,” Meghan Jardine, MS, MBA, RD, LD, CDE, RDN, of Parkland Health and Hospital System, said during a presentation. “Many scientists believe the changes in our diet and physical activity can’t really account for the change either, that there’s something else at work here.”

Weighing at least two kilograms in all and accounting for more than 3 times the amount of the body’s human cells, gut bacteria is colonized after birth, stabilized by age 3 years but influenced by a number of external factors, Jardine explained. Areas of influence include nutrition and immune function, both priorities in treating obesity and diabetes.

“Microbiota releases enzymes that digest food so we can absorb nutrients, produces vitamins, combats opportunistic infections and works with the immune system,” Jardine said. “About 70% of our immune systems are in our gut.”

People who consume plant-based diets have “healthy” gut microbiota in terms of global parameters and functional and compositional features, Christina Kafity, RN, BSN,CHC... “Children and elderly individuals who consumed more plant carbohydrates versus the typical standard American diet had rapid, reproducible alterations of the gut microbiota for the better, and this happened within 24 hours to a week,” Kafity said.

Growing good bacteria depends on creating an environment in which they can thrive, Kafity explained, including choosing foods that contain certain fibers intact in plants and probiotics; among them are soluble, insoluble and functional fibers as well as psyllium and inulin.

Intake of cruciferous vegetables including Brussels sprouts, kale and cabbage can help boost healthy microbes and, further, provide glucosinolates to help to reduce inflammation, Kafity said. Yogurt, kefir and probiotics also promote the growth of good bacteria, Kafity noted, while some popular beverages may not be much help. “We’re considering that coffee and teas may actually sterilize the bacteria.”

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I'm glad that there is interest in therapeutic possibilities of bacteria, but I'm worried (a lot) about the possibility of companies claiming rights to naturally occurring bacteria. The article simply said: "...intellectual-property rights for naturally occurring bacteria, may complicate the path of products to market."  From Scientific American:

Drugs to Be Derived from Insights into Body-Dwelling Bacteria

The human body teems with trillions of microorganisms — a microbial landscape that has attracted roughly $500 million in research spending since 2008. Yet with a few exceptions, such as the use of fecal transplants for treating life- threatening gut infections or inflammatory bowel disease, research on the human microbiome has produced few therapies.

That is poised to change as large pharmaceutical companies eye the medical potential of manipulating interactions between humans and the bacteria that live in or on the body.

On 2 May, drug giant Pfizer announced plans to partner with Second Genome, a biotechnology firm in South San Francisco, California, to study the microbiomes of around 900 people, including those with metabolic disorders and a control group.A day earlier, Paris-based Enterome revealed that it had raised €10 million ($13.8 million) in venture capital to develop tests that use the composition of gut bacteria to diagnose inflammatory and liver diseases.

Experts predict that the next few months will see a boom in such partnerships and investments, and that new microbiome-derived drugs and therapies will come to market within a few years.

Probiotics, or beneficial gut bacteria, have become a popular therapy in recent years. Television advertisements feature celebrities touting Bifidobacterium-laced yogurt, and consumers flock to buy pills that contain Lactobacillus to quell their gut disturbances and other ailments. But many physicians and scientists doubt the effectiveness of such remedies. 

But as scientists come to understand the mechanisms by which specific bacteria affect the body, many think that they can pinpoint the right combination of microbes to treat different conditions. Others aim to develop molecules that mimic a beneficial bacterium–host interaction, or block a harmful one. “Undoubtedly, the microbiome is a  little drug factory in our intestine,” says Justin Sonnenburg, a microbiologist at Stanford University in Palo Alto, California.

Changing the balance of ‘good’ and ‘bad’ bacteria in the gut microbiome can also influence health — inflammation, for example, or even depression and anxiety. 

Getting microbiome-inspired therapies to market presents a number of challenges, however. Small molecules such as those developed by Microbiome Therapeutics may be able to go through the normal drug regulatory pathway. But there may be a different or new set of regulatory hurdles for genetically modified bacteria — for example, those in development by Ghent-based ActoGeniX in Belgium and ViThera Pharmaceuticals in Cambridge, Massachusetts — that deliver anti-inflammatory agents to the gut. Other issues, including intellectual-property rights for naturally occurring bacteria, may complicate the path of products to market.

Pierre Belichard, Enterome’s chief executive, says that such investment has been a long time coming — but companies are now flocking to microbiome research.

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This was done in mice, so much more needs to be done. But...if it holds true for humans, probiotics (with IPA-producing bacteria) can be used as therapies for all sorts of diseases. From Medical Xpress:

'Normal' bacteria vital for keeping intestinal lining intact

Scientists at Albert Einstein College of Medicine of Yeshiva University have found that bacteria that aid in digestion help keep the intestinal lining intact. The findings, reported online in the journal Immunity, could yield new therapies for inflammatory bowel disease (IBD) and a wide range of other disorders.

The research involved the intestinal microbiome, which contains some 100 trillion . The role of these microorganisms in promoting or preventing disease is a major emerging field of study. Einstein scientists found that absorption of a specific bacterial byproduct is crucial for maintaining the integrity of the intestinal epithelium —the single-cell layer responsible for keeping intestinal bacteria  and their toxins inside the gut and away from the rest of the body. Breaching of the intact intestinal epithelium is associated with a number of diseases.

"Intestinal bacteria secrete a wide variety of chemicals known as metabolites," said Sridhar Mani, M.D., co-corresponding author of the paper. Dr. Mani and his colleagues suspected that bacterial metabolites exert their influence by binding to and activating a protein in the nuclei of intestinal epithelial cells called the pregnane X receptor (PXR). PXR was known to be activated by chemicals within the body (such as bile acids) as well as by drugs including steroids and antibiotics.

In a series of mouse studies, the researchers found that a metabolite called indole 3-propionicacid (IPA)—produced exclusively by so-called commensal bacteria, which aid in digestion—both strengthens the intestinal epithelium's barrier function and prevents its inflammation by activating PXR. More specifically, PXR activation suppresses production of an inflammatory protein called tumor necrosis factor alpha (TNF-α) while increasing levels of a protein that strengthens the junctions between adjacent intestinal epithelial cells. 

"By adding probiotics in the form of IPA-producing bacteria to the intestine or by administering IPA directly, we may be able to prevent or treat IBD and other inflammatory disorders that occur when the intestinal epithelium has been compromised," said Dr. Mani. "Such a strategy could also be tried for other health problems that may occur when the intestinal epithelium breaks down, including certain forms of liver disease, diabetes, asthma, allergies, obesity and heart disease."

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Two related articles, the first from a month ago, but both discuss eating fresh foods of summer and the effect on the microbiota. From Gut Microbiota Worldwatch:

Seasonal diet changes affect the composition of our gut microbiota

The mix of bacteria that live in our gut changes throughout the year, to match the food we eat in every specific season. For example, bacteria that process fresh fruit and vegetables are more abundant in the summer, and those that process fats are mode abundant in winter times. A group of scientists at the University of Chicago has found evidence of this seasonal shift in the gut flora, by studying the remote Hutterite population, in North America. The traditional diet and common meals of this community have allowed researchers to study the effect of one common diet in a large population over a long period of time.

Hutterites live in communal farms (colonies) and eat meals in common dining rooms, using traditional recipes that have been relatively stable over time and between colonies. They have little contact with the world outside their colonies, which translates into a very homogeneous genetic pool. Sixty Hutterites from six colonies answered questionnaires about what they ate over the course of a year. During the same period, scientists sampled their stool periodically, to find the genetic sequences of bacteria contained in their gut.

The Hutterites’ diet is relatively stable, except that in summer they eat more fresh fruit and vegetables, and in winter they eat less, and turn to frozen or canned food. Remarkably, their gut flora responded to these changes with massive modification in the abundance of certain bacteria. For example, during summer Bacteroidetes were more abundant: this group of bacteria contain complex carbohydrate digesters, which may be at work in processing fresh fruit and vegetables.

On the other hand Actinobacteria increased in winter: these microbes are associated with processing fat, and with a decreased content of fibre in food. Researchers also found seasonal shifts in other types of bacteria, whose associations with food are still unknown. Notably, the trends were almost identical in all six colonies, possibly a result of a very homogenous lifestyle carried on in a very similar environment.

Although Hutterites live in a relatively isolated way, they use technology and medicine, which makes their lifestyle closer to the general population than that of other more traditional communities. That is why the authors believe that these results may be extended to the general population.

This healthy living article promotes eating fresh fruits and vegetables (tomatoes, blueberries, asparagus, and leeks) as good for the gut microbiome. From Huffington Post:

4 Summer Foods That Can Help Trim Your Waist

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Future microbiome research and therapy will have to take into account that diet affects the gut microbes of men and women differently. From Science Daily:

Diet affects males' and females' gut microbes differently

The microbes living in the guts of males and females react differently to diet, even when the diets are identical, according to a new study. These results suggest that therapies designed to improve human health and treat diseases through nutrition might need to be tailored for each sex.

The researchers studied the gut microbes in two species of fish and in mice, and also conducted an in-depth analysis of data that other researchers collected on humans. They found that in fish and humans diet affected the microbiota of males and females differently. In some cases, different species of microbes would dominate, while in others, the diversity of bacteria would be higher in one sex than the other.

These results suggest that any therapies designed to improve human health through diet should take into account whether the patient is male or female.

Genetics and diet can affect the variety and number of these microbes in the human gut, which can in turn have a profound influence on human health. Obesity, diabetes, and inflammatory bowel disease have all been linked to low diversity of bacteria in the human gut.

Why men and women would react differently to changes in diet is unclear, but there are a couple of possibilities. The hormones associated with each sex could potentially influence gut microbes, favoring one strain over another. Also, the sexes often differ in how their immune systems function, which could affect which microbes live and die in the microbiome.

One notable exception in Bolnick's results was in the mice. Although there was a tiny difference between male and female mice, for the most part the microbiota of each sex reacted to diet in the same manner. Because most dietary studies are conducted on mice, this result could have a huge effect on such research, and it raises questions about how well studies of gut microbes in lab mice can be generalized to other species, particularly humans.