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Category: human microbiome

Published on Leave a comment on Meat is OK If You Also Eat Lots of Plant-Based Foods

 People have asked me if eating sweet desserts or hamburgers is bad for the health if the rest of their diet is good - with lots of fruits, vegetables, whole grains, legumes (beans), and nuts (much like the Mediterranean diet). My sense over the past few years of looking at the research is that one should look at the overall diet, and that a "perfect diet" all the time is pretty darn hard to achieve, if not impossible, for most of us. So this new research looking at gut bacteria and "chemical fingerprints of cellular processes" (by looking at stool and urine samples) of people eating different diets (vegan, vegetarian, omnivore) was reassuring.  The findings suggest: make sure to feed your beneficial bacteria with a healthy diet like the Mediterranean diet (lots of plant-based foods), and then some deviation (cookies! steak!) is OK.

The researchers found that while the kind of gut bacteria dominating were different among the groups (vegan, vegetarian, omnivores), they also found that eating a lot of fiber-rich foods, such as fruit, vegetables, and legumes (typical of a Mediterranean diet) is linked to a rise in health promoting short chain fatty acids (SCFA). Yes, levels of trimethylamine oxide (TMAO) (which is linked to cardiovascular disease) were significantly lower in vegetarians and vegans than they were in those of the omnivores. But the more omnivores closely followed a Mediterranean diet, the lower were their TMAO levels.(Which is great!). As the researchers said: "Western omnivore diets are not necessarily detrimental when a certain consumption level of plant foods is included. From Science Daily:

High dietary fiber intake linked to health promoting short chain fatty acids

Eating a lot of fibre-rich foods, such as fruit, vegetables, and legumes--typical of a Mediterranean diet--is linked to a rise in health promoting short chain fatty acids, finds research published online in the journal Gut. And you don't have to be a vegetarian or a vegan to reap the benefits, the findings suggest.

Short chain fatty acids (SCFAs), which include acetate, propionate, and butyrate, are produced by bacteria in the gut during fermentation of insoluble fibre from dietary plant matter. SCFAs have been linked to health promoting effects, including a reduced risk of inflammatory diseases, diabetes, and cardiovascular disease.

The researchers gathered a week's information on the typical daily diet of 153 adults who either ate everything (omnivores, 51), or were vegetarians (51), or vegans (51), and living in four geographically distant cities in Italy....The Mediterranean diet is characterised by high intake of fruit, vegetables, legumes, nuts and cereals; moderately high intake of fish; regular but moderate alcohol consumption; and low intake of saturated fat, red meat, and dairy products. Most (88%) of the vegans, almost two thirds of the vegetarians (65%), and around a third (30%) of the omnivores consistently ate a predominantly Mediterranean diet.

The investigation showed distinct patterns of microbial colonisation according to usual dietary intake. Bacteroidetes were more abundant in the stool samples of those who ate a predominantly plant based diet, while Firmicutes were more abundant in those who ate a predominantly animal products diet. Both these categories of organisms (phyla) contain microbial species that can break down complex carbohydrates, resulting in the production of SCFAs.

Specifically, Prevotella and Lachnospira were more common among the vegetarians and vegans while Streptococcus was more common among the omnivores. And higher levels of SCFA were found in vegans, vegetarians, and those who consistently followed a Mediterranean diet. Levels of SCFAs were also strongly associated with the quantity of fruit, vegetables, legumes, and fibre habitually consumed, irrespective of the type of diet normally eaten.

On the other hand, levels of trimethylamine oxide (TMAO)--a compound that has been linked to cardiovascular disease--were significantly lower in the urine samples of vegetarians and vegans than they were in those of the omnivores. But the more omnivores closely followed a Mediterranean diet, the lower were their TMAO levels, the analysis showed.

TMAO levels were linked to the prevalence of microbes associated with the intake of animal proteins and fat, including L-Ruminococcus (from the Lachnospiraceae family). Eggs, beef, pork and fish are the primary sources of carnitine and choline--compounds that are converted by gut microbes into trimethylamine, which is then processed by the liver and released into the circulation as TMAO.

The researchers point out that SCFA levels can naturally vary as a result of age and gender, and their study did not set out to establish any causal links. But they nevertheless suggest that the Mediterranean diet does seem to be associated with the production of health promoting SCFAs. They conclude: "We provide here tangible evidence of the impact of a healthy diet and a Mediterranean dietary pattern on gut microbiota and on the beneficial regulation of microbial metabolism towards health maintenance in the host." And they add: "Western omnivore diets are not necessarily detrimental when a certain consumption level of [plant] foods is included."

Published on Leave a comment on Missing Microbes in Infancy and Asthma

An interesting Canadian study that followed young children for 3 years found that young infants may be more likely to develop allergic asthma if they lack four beneficial bacteria in their gut. Children with low levels of Lachnospira, Veillonella, Faecalibacterium, and Rothia bacteria in their gut in their first 3 months were at higher risk for asthma and tended to receive more antibiotics than healthier children before they turned 1 year old.

Other studies have shown that the risk of developing asthma and allergies has been linked with such things as taking antibiotics, cesarean birth, bottle fed with formula, not living on a farm, and not having furry pets in the first year of life.

The researchers wrote: "Our findings indicate that in humans, the first 100 days of life represent an early-life critical window in which gut microbial dysbiosis {the microbial community being out of whack} is linked to the risk of asthma and allergic disease." How do the infants get these microbes? It is thought that infants get exposed to the mother's microbiome (microbial community) via vaginal birth, breast-milk, and mouth contact with the mother's skin.  From NPR News:

Missing Microbes Provide Clues About Asthma Risk

The composition of the microbes living in babies' guts appears to play a role in whether the children develop asthma later on, researchers reported Wednesday. The researchers sampled the microbes living in the digestive tracts of 319 babies, and followed up on the children to see if there was a relationship between their microbes and their risk for the breathing disorder. In the journal Science Translational Medicine, the researchers report Wednesday that those who had low levels of four bacteria were more likely to develop asthma by the time they were 3-years-old.

Specifically, the researchers focused on 22 children who showed early signs of asthma, such as wheezing, when they were 1-year-old. They were much more likely than the other children to have had low levels of the four bacteria when they were 3-months-old. By the time they turned 3, most had developed full-blown asthma."The bottom line is that if you have these four microbes in high levels you have a very low risk of getting asthma," says Brett Finlay, a microbiologist at the University of British Columbia who helped conduct the research. "If you don't have these four microbes or low levels of these microbes you have a much greater chance of asthma."

Asthma is a common and growing problem among children. Evidence has been accumulating that one reason may be a disruption in the healthful microbes children get early in life, Finlay says."There's all these smoking guns like, for example, if you breast-feed versus bottle feed you have less asthma," he says. "If you're born by C-section instead of vaginal birth you have a 20 percent higher rate of asthma. If you get antibiotics in the first year of life you have more asthma." The microbiomes of kids who aren't breast-fed and are born by Caesarean section may miss out on getting helpful bugs. Antibiotics can kill off the good bacteria that seem important for the development of healthy immune systems.

"What's become clear recently is that microbes play a major role in shaping how the immune system develops. And asthma is really an immune allergic-type reaction in the lungs," Finlay says. "And so our best guess is the way these microbes are working is they are influencing how our immune system is shaped really early in life."

To further test their theory, the researchers gave laboratory mice bred to have a condition resembling asthma in humans the four missing microbes. The intervention reduced the signs of levels of inflammation in their lungs, which is a risk factor for developing asthma.

The bacteria are from four genuses: Lachnospira, Veillonella, Faecalibacterium and Rothia. The researchers aren't exactly sure how the microbes may protect against asthma. But babies with few or none of them had low levels of a substance known as acetate, which is believed to be involved with regulating the immune system.

Published on Leave a comment on A Viral Cause of Some Breast Cancers?

  This study found something surprising in many samples of human breast tissue - bovine leukemia virus (BLV). Specifically, 59 percent of breast cancer tissue samples had evidence of exposure to BLV (as determined by the presence of viral DNA using modern genetic tests). In contrast, 29 percent of the tissue samples from women who did not have breast cancer (the controls) showed exposure to BLV. Also, BLV was found in 38% of women with premalignant breast tissue changes. The big question: is the bovine leukemia virus somehow leading to breast cancer? That would mean that some breast cancers have a viral origin (and a vaccine can be developed). No one knows this answer, and now more studies need to be done. But....the odds of having breast cancer if BLV was present was 3.1 times greater than if BLV was absent. It also raises the question of whether those women showing exposure with BLV, but currently no breast cancer, are at higher risk for later breast cancer. Stay tuned...  From Medical Xpress:

Virus in cattle linked to human breast cancer

A new study by University of California, Berkeley, researchers establishes for the first time a link between infection with the bovine leukemia virus and human breast cancer. In the study, published this month in the journal PLOS ONE and available online, researchers analyzed breast tissue from 239 women, comparing samples from women who had breast cancer with women who had no history of the disease for the presence of bovine leukemia virus (BLV). They found that 59 percent of breast cancer samples had evidence of exposure to BLV, as determined by the presence of viral DNA. By contrast, 29 percent of the tissue samples from women who never had breast cancer showed exposure to BLV.

"The association between BLV infection and breast cancer was surprising to many previous reviewers of the study, but it's important to note that our results do not prove that the virus causes cancer," said study lead author Gertrude Buehring, a professor of virology in the Division of Infectious Diseases and Vaccinology at UC Berkeley's School of Public Health. "However, this is the most important first step. We still need to confirm that the infection with the virus happened before, not after, breast cancer developed, and if so, how."

Bovine leukemia virus infects dairy and beef cattle's blood cells and mammary tissue. The retrovirus is easily transmitted among cattle primarily through infected blood and milk, but it only causes disease in fewer than 5 percent of infected animals.   A 2007 U.S. Department of Agriculture survey of bulk milk tanks found that 100 percent of dairy operations with large herds of 500 or more cows tested positive for BLV antibodies. This may not be surprising since milk from one infected cow is mixed in with others. Even dairy operations with small herds of fewer than 100 cows tested positive for BLV 83 percent of the time.

What had been unclear until recently is whether the virus could be found in humans, something that was confirmed in a study led by Buehring and published last year in Emerging Infectious Diseases. That paper overturned a long-held belief that the virus could not be transmitted to humans."Studies done in the 1970s failed to detect evidence of human infection with BLV," said Buehring. "The tests we have now are more sensitive, but it was still hard to overturn the established dogma that BLV was not transmissible to humans. As a result, there has been little incentive for the cattle industry to set up procedures to contain the spread of the virus."

The new paper takes the earlier findings a step further by showing a higher likelihood of the presence of BLV in breast cancer tissue. When the data was analyzed statistically, the odds of having breast cancer if BLV were present was 3.1 times greater than if BLV was absent. "This odds ratio is higher than any of the frequently publicized risk factors for breast cancer, such as obesity, alcohol consumption and use of post-menopausal hormones," said Buehring.

There is precedence for viral origins of cancer. Hepatitis B virus is known to cause liver cancer, and the human papillomavirus can lead to cervical and anal cancers. Notably, vaccines have been developed for both those viruses and are routinely used to prevent the cancers associated with them. "If BLV were proven to be a cause of breast cancer, it could change the way we currently look at breast cancer control," said Buehring. "It could shift the emphasis to prevention of breast cancer, rather than trying to cure or control it after it has already occurred."

Buehring emphasized that this study does not identify how the virus infected the breast tissue samples in their study. The virus could have come through the consumption of unpasteurized milk or undercooked meat, or it could have been transmitted by other humans.

Published on Leave a comment on We Each Give Off a Personal Microbial Cloud

Amazing! We each release a "personal microbial cloud" with its own "microbial cloud signature" every day. The unique combination of millions of bacteria (from our microbiome or community of microbes - including bacteria, viruses, fungi -  that live within and on us) can identify us. Not only do we each give off a unique combination, but we each give off different amounts of microbes - some more, some less. Some very common bacteria: Streptococcus, Propionobacterium, Corynebacterium, and Lactobacillus (among women).The microbes are given off with every movement, every exhalation, every scratching of the head, every burp and fart, etc. - and they go in the air around the person and settle around the person (they researchers even collected bacteria from dishes set on the ground around the person). From Science Daily:

The 'Pig-Pen' in each of us: People emit their own personal microbial cloud

We each give off millions of bacteria from our human microbiome to the air around us every day, and that cloud of bacteria can be traced back to an individual. New research focused on the personal microbial cloud -- the airborne microbes we emit into the air -- examined the microbial connection we have with the air around us. The findings demonstrate the extent to which humans possess a unique 'microbial cloud signature'.

To test the individualized nature of the personal microbial cloud, University of Oregon researchers sequenced microbes from the air surrounding 11 different people in a sanitized experimental chamber. The study found that most of the occupants sitting alone in the chamber could be identified within 4 hours just by the unique combinations of bacteria in the surrounding air. The findings appear in the September 22 issue of the open-access, peer-reviewed journal PeerJ.

The striking results were driven by several groups of bacteria that are ubiquitous on and in humans, such as Streptococcus, which is commonly found in the mouth, and Propionibacterium and Corynebacterium, both common skin residents. While these common human-associated microbes were detected in the air around all people in the study, the authors found that the different combinations of those bacteria were the key to distinguishing among individual people.

The analyses, utilizing analysis of suspended particulate matter and short-read 16S sequencing, focused on categorizing whole microbial communities rather than identifying pathogens. The findings emerged from two different studies and more than 14 million sequences representing thousands of different types of bacteria found in the 312 samples from air and dust from the experimental chamber.

"We expected that we would be able to detect the human microbiome in the air around a person, but we were surprised to find that we could identify most of the occupants just by sampling their microbial cloud," said lead author James F. Meadow, a postdoctoral researcher formerly from the Biology and the Built Environment Center at the University of Oregon."Our results confirm that an occupied space is microbially distinct from an unoccupied one, and and demonstrate for the first time that individuals release their own personalized microbial cloud," the authors concluded.

Image result for personal microbial cloud wikipediaSneeze. Credit: Wikipedia and CDC

Published on Leave a comment on Early Childhood Experiences Key to Preventing Allergies

It's official - the medical community has accepted that a key element in preventing allergies and asthma is early childhood exposure to allergens - whether peanuts, dust, or pets. Instead of avoiding the allergens (which was the medical advice for decades) - getting early exposure to them is key to preventing allergies. Apparently growing up on a farm is best (with exposure to farm dirt and dust), especially a dairy farm with animals and raw milk (a number of studies have found that unprocessed raw milk and its microbes also helps health). But if one doesn't live on a farm, then having furry pets in early childhood is also beneficial in reducing the incidence of allergies. The following study shows that microbes are involved - pet microbes were found in the guts of many of those children who did not develop early allergies! From Medscape:

Furry Pets 'Enrich' Gut Bacteria of Infants at Risk for Allergies

In a small, preliminary study, infants in households with furry pets were found to share some of the animals' gut bacteria - possibly explaining why early animal exposure may protect against some allergies, researchers say. The infants' mothers had a history of allergy, so the babies were at increased risk. It was once thought that pets might be a trigger for allergies in such children, the authors pointed out online September 3 in the Journal of Allergy and Clinical Immunology.

"Earlier it was thought that exposure to pets early in childhood was a risk factor for developing allergic disease," coauthor Dr. Merja Nermes, of the University of Turku in Finland, told Reuters Health by email. "Later epidemiologic studies have given contradictory results and even suggested that early exposure to pets may be protective against allergies, though the mechanisms of this protective effect have remained elusive."Adding pet microbes to the infant intestinal biome may strengthen the immune system, she said.  ...continue reading "Early Childhood Experiences Key to Preventing Allergies"

Published on Leave a comment on Viruses Live in The Guts of Healthy Babies

Yes, even healthy newborns have a diversity of viruses in the gut - this is their virome (community of viruses), and it undergoes changes over time. In fact, the entire infant microbiome (community of microbes) is highly dynamic and the composition of bacteria, viruses and bacteriophages changes with age. One interesting finding is that initially newborn babies have a lot of bacteriophages (viruses that infect bacteria), but that these decline over the first two years of age. From Medical Xpress:

Viruses flourish in guts of healthy babies

Bacteria aren't the only nonhuman invaders to colonize the gut shortly after a baby's birth. Viruses also set up house there, according to new research at Washington University School of Medicine in St. Louis. All together, these invisible residents are thought to play important roles in human health.The study, published online Sept. 14 in Nature Medicine, reports data from eight healthy infants and is one of the first surveys of viruses that reside in the intestine. The investigators analyzed stool samples to track how the babies' bacterial gut microbiomes and viromes changed over the first two years of life.

"We are just beginning to understand the interplay between all the different types of life within our gut," said senior author Lori R. Holtz, MD, assistant professor of pediatrics. "They are not stand-alone communities. We also are seeing that the environment of the infant gut is extremely dynamic, which differs from the relative stability that has been shown in adults."The earliest stool samples were taken at 1-4 days of life, and even at this early time point, Holtz noted, viruses were present.  ...continue reading "Viruses Live in The Guts of Healthy Babies"

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Published on 6 Comments on Update on Sinusitis Treatment

[UPDATE:  I added an Oct. 2018 update to the post The One Probiotic That Treats Sinusitis, which was originally posted in January 2015.]  Updates incorporate the latest information about treatments and products with Lactobacillus sakei  (kimchi brands, the probiotic Lacto Sinus , the sausage starter culture Bactoferm F-RM-52, etc.). According to research by Abreu et al (2012), Lactobacillus sakei is a bacteria or probiotic (beneficial bacteria) that chronic sinusitis sufferers lack and which treats chronic sinusitis. Chronic sinusitis sufferers also don't have the bacteria diversity in the sinuses that healthy people have.

Many thanks to those who have written to me about their experiences with L. sakei products and sinusitis treatment.  Please keep the updates, results, and progress reports coming. If you have had success with other kimchi brands, please let me know so that I can add it to the list. And I also want to hear if other probiotics work or don't work, or if you have found other sources of Lactobacillus sakei or new ways to use L. sakei. It all adds to the knowledge base which I will continue to update.  You can Comment after posts, the Sinus Treatment Summary page, on the CONTACT page, or write me privately (see CONTACT page).

It is now over 2 1/2 years since my family (4 people) successfully treated ourselves with Lactobacillu sakei for chronic sinusitis and acute sinusitis. We feel great! With each passing year we can tell that our sinus microbial community is bettter, and levels of inflammation are down. As a consequence, we are getting fewer colds or viruses than ever. And best of all - no antibiotics taken in over 2 1/2 years! Yes, Lactobacillus sakei absolutely works as a treatment for sinusitis.

[Read the updated post: The One Probiotic That Treats Sinusitis - with Oct. 2018 update]

Published on Leave a comment on Fungi and Bacteria in Household Dust

Another article from results of the crowdsourced study in which household dust samples were sent to researchers at the University of Colorado from approximately 1200 homes across the United States. Some findings after the dust was analyzed: differences were found in the dust of households that were occupied by more males than females and vice versa, indoor fungi mainly comes from the outside and varies with the geographical location of the house, bacteria is determined by the house's inhabitants (people, pets, and insects), clothes do not prevent the spread of bacteria from our bodies, and dogs and cats had a dramatic influence on bacteria in the home. In other words: where you live determines the fungi in the house and who you live with determines the bacteria in the house. From Discovery News:

Household Dust Packed With Thousands of Microbes

Household dust is full of living organisms that are determined, in large part, by where the home is located and who is living in it, finds a new study that includes some surprising revelations. Homes with a greater ratio of male occupants, for example, were found to contain large amounts of skin and fecal-associated bacteria, while women-dominated households contained an abundance of vaginally shed bacteria that somehow wound up in dust.

He and his colleagues used DNA sequencing and high tech imaging to analyze dust samples from approximately 1,200 homes across the United States. They used volunteers to help collect the material. They discovered that indoor fungi mostly originates outside of the home, such that the geographical location of any home strongly predicts the types of fungi existing within dust.“If you want to change the types of fungi you are exposed to in your home, then it is best to move to a different home, preferably one far away,” Fierer and his team said.

Bacteria, on the other hand, were largely predicted by the home’s possible inhabitants, including humans, pets and even insects. Fierer said, “Our bodies are clearly the source for many bacteria that end up in our homes.” The researchers suspect that body size, relative abundance, and hygiene practices are why men tend to shed more Corynebacterium and Dermabacter (the skin-associated species), as well as the poop-associated Roseburia.

The vaginal-linked bacteria Lactobacillus, discovered in homes with a larger ratio of women, provides evidence that clothes do not fully contain the spread of microorganisms produced by our bodies. Members of this genus are actually thought to protect against allergies and asthma, based on earlier research, but further studies are needed to confirm how this, and other bacteria found in dust, impact human health.

Dogs and cats had such a dramatic effect on dust bacterial communities that the researchers could predict, with around 92 percent accuracy, whether or not such animals were in the home, just based on bacteria alone....So far, the news is good for dog lovers, as he pointed out that “previous work conducted by other groups has shown that living with a dog at a young age can actually reduce allergies.”

Published on Leave a comment on The Fungi That Live On Our Skin

This article discusses the fungi living on our skin. Recent research (using state of the art genetic analysis) has found that healthy people have lots of diversity in fungi living on their skin. Certain areas seem to have the greatest populations of fungi: in between toes (average of 40 species), the heel (average of 80 species), toenails (average of 80 species), and the genitals. Currently it is thought that there are "intricate interactions between fungi and immune cells on the skin surface", and that often this mutualistic relationship is beneficial, but at other times dysbiosis (when the microbial community is unbalanced or out of whack) can lead to diseases. If the populations get too unbalanced (e.g., antibiotics can kill off bacteria, and then an increase in fungi populations take their place) then ordinarily non-harmful fungi can become pathogenic. Note that: Mutualistic relationship is a relationship between two different species of organisms in which both benefit from the association. From E-Cronicon:

From Head to Toe: Mapping Fungi across Human Skin

The human microbiota refers to the complex aggregate of fungi, bacteria and archaea, found on the surface of the skin, within saliva and oral mucosa, the conjunctiva, the gastrointestinal. When microbial genomes are accounted for, the term microbiome is deployed. In recent years the first in-depth analysis, using sophisticated DNA sequencing, of the human microbiome has taken place through the U.S. National Institutes of Health led Human Microbiome Project. 

Many of the findings have extended, or even turned upside down, what was previously known about the relationship between humans and microorganisms. One of the most interesting areas related to fungi, especially in advancing our understanding about fungal types, locations and numbers and how this affects health and disease....some parts of the body have a greater prevalence of bacteria (such as the arms) whereas fungi are found in closer association with feet.  

A variety of bacteria and fungi are found on the typical 2 square meters that represent the surface of the skin, and within the deeper layers, of a typical adult. These can be considered as ‘residential’ (that is ordinarily found) or ‘transient’ (carried for a period of time by the host.) The resident microorganism types vary in relation to skin type on the human body; between men and women; and to the geographical region in which people live.

The first observation is that many locations across the skin contain considerable populations of fungi. Prime locations, as reported by Findley and colleagues, were inside the ear canal and behind the ear, within the eyebrows, at the back of the head; with feet: on the heel, toenails, between the toes; and with the rest of the body notable locations were the forearm, back, groin, nostrils, chest, palm, and the elbow.

The second observation is that several different species are found, and these vary according to different niches. Focusing on one ecological niche, a study by Oyeka found that the region between toes, taken from a sample of 100 people, discovered 14 genera of fungi. In terms of the individual species recovered, a relatively high number were observed (an average of 40 species.)....the greatest varieties of fungi are to be found on the heel (approximately 80 different species.) The second most populous area is with the toes, where toe nails recover around 80 different species.....With the genitals, where early investigations had suggested that Candida albicans was the most commonly isolated yeasts. However, an investigation of 83 patients by Bentubo., et al.  showed more variety, with high recoveries of Candida parapsilosis, Rhodotorulamucilaginos, Rhodotorulaglutinis, Candida tropicalis and Trichosporoninkin.

The importance of the investigative work into the human skin fungi helps medical researchers understand more fully the connections between the composition of skin-fungi and certain pathologies. Here the intricate interactions between fungi and immune cells on the skin surface is of importance; often this mutualistic relationship is beneficial, at other times dysbiosis can lead to the manifestation of diseases especially when there is a breakdown of the mutualistic relationship.

Changes to fungal diversity can be associated with several health conditions, including atopic dermatitis, psoriasis, acne vulgaris and chronic wounds. Diversity can alter through the over-use of antibiotics, where a decline in bacterial numbers can lead to a rise in fungal populations occupying the same space.

Moreover, research has indicted that patients who have a primary immunodeficiency are host to more populous fungal communities than healthy people. Here it is suggested that the weaknesses in the immune system allow higher numbers of fungi to survive, and, in turn these weaknesses can lead some ordinarily non-harmful species to become pathogenic. Such opportunistic fungi include species of Aspergillus and Candida.

Published on Leave a comment on A Mix of Bacteria Protect Against Infections?

More research that supports that both more variety (diversity) of microbes and the actual mix of types of microbes are involved in a healthy gut microbiome. Healthy communities don't have just one important species of bacteria, but a mix of bacteria, and some mixes of bacteria work better than others in preventing infections. One can say that some mixes of bacteria are "protective" against infections. And once again, antibiotics screw up the microbial communities and cause imbalances. This study was done in mice looking at gut bacteria and Clostridium difficile (which kills about 14,000 Americans annually), but they are now continuing this research in humans. From Medical Xpress:

It takes a village... to ward off dangerous infections? New microbiome research suggests so

Like a collection of ragtag villagers fighting off an invading army, the mix of bacteria that live in our guts may band together to keep dangerous infections from taking hold, new research suggests. But some "villages" may succeed better than others at holding off the invasion, because of key differences in the kinds of bacteria that make up their feisty population, the team from the University of Michigan Medical School reports. The researchers even show it may be possible to predict which collections of gut bacteria will resist invasion the best—opening the door to new ways of aiding them in their fight.

Working in mice, the team studied one of the most dangerous gut infections around: Clostridium difficile, which kills more than 14,000 Americans a year. C-diff also sickens hundreds of thousands more, mostly hospital patients whose natural collection of gut bacteria—their gut microbiome—has been disturbed by antibiotics prescribed to protect them from other infections.

In a new paper published in the journal mBIO, the team reports the results from tests of seven groups of mice that were given different antibiotics, then were exposed to C-diff spores. The scientists used advanced genetic analysis to determine which bacteria survived the antibiotic challenge, and looked at what factors made it most likely that C-diff would succeed in its invasion.The team also developed a computer model that accurately predicted C-diff's success rate for other mice in the study, based solely on knowing what bacteria the mice had in their natural gut 'village'. The model succeeded 90 percent of the time.

"We know that individual humans all have different collections of gut bacteria, that your internal 'village' is different from mine. But research has mostly focused on studying one collection at a time," says Patrick D. Schloss, Ph.D., the U-M associate professor of microbiology and immunology who led the team. "By looking at many types of microbiomes at once, we were able to tease out a subset of bacterial communities that appear to resist C-diff colonization, and predict to what extent they could prevent an infection."

Schloss, who is a key member of the Medical School's Host Microbiome Initiative, notes that no one species of bacteria by itself protected against colonization. It was the mix that did it. And no one particular mix of specific bacteria was spectacularly better than others - several of the diverse "villages" resisted invasion.

Resistance was associated with members of the Porphyromonadaceae, Lachnospiraceae, Lactobacillus, Alistipes, and Turicibacter families of bacteria. Susceptibility to C. difficile, on the other hand, was associated with loss of these protective species and a rise in Escherichia or Streptococcus bacteria. "It's the community that matters, and antibiotics screw it up," Schloss explains. Being able to use advance genetic tools to detect the DNA of dozens of different bacteria species, and tell how common or rare each one is in a particular gut, made this research possible.

A Clostridium difficile cell.                                                     Credit: Centers for Disease Control and Prevention