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Category: microbes

Published on Leave a comment on House Dust Contains a Microhistory of Our Life

Nice update from a large crowd sourced study I posted about September 1, 2015. Main finding: all our homes are teaming with microorganisms, which vary according to sex of occupants, pets, geographical location and humidity. In total, the indoor dust contained more than sixty-three thousand species of fungi and a hundred and sixteen thousand species of bacteria. The scientists have posted it all online and members of the public can download the complete data set and hunt for new correlations and patterns. Just remember that all these microbes in our lives is completely normal, and many species are important partners in maintaining our health. Excerpts from Emily Anthes's article in the New Yorker:

Our Dust, Ourselves

Dust talks. That clump of gray fuzz hiding under the couch may look dull, but it contains multitudes: tiny errant crumbs of toast, microscopic fibres from a winter coat, fragments of dead leaves, dog dander, sidewalk grit, sloughed-off skin cells, grime-loving bacteria. “Each bit of dust is a microhistory of your life,” Rob Dunn, a biologist at North Carolina State University, told me recently. For the past four years, Dunn and two of his colleagues—Noah Fierer, a microbial ecologist at the University of Colorado Boulder, and Holly Menninger, the director of public science at N.C. State—have been deciphering these histories, investigating the microorganisms in our dust and how their lives are intertwined with our own.  ...continue reading "House Dust Contains a Microhistory of Our Life"

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Could this be? Fungal infection being the cause of Alzheimer's disease? Noteworthy from a recent study conducted in Spain: all the Alzheimer's disease (AD) patients had evidence of fungal infections in their brains, central nervous systems, and vascular systems, but none were found in the control subjects (those without Alzheimer's disease). Many of the symptoms of AD (such as inflammation of the central nervous system and activation of the immune system) match those with long-lasting fungal infections. A "microbial cause" has long been suggested as a cause of AD, and interestingly other studies have also found fungal infections in AD patients. The research so far has found several fungal species in AD patients (including Candida albicans). The researchers mention that in one study anti-fungal treatment reversed clinical symptoms of AD in 2 patients (but it was written off  as misdiagnosis).

Another possibility that immediately occurs to  explain the findings is that perhaps Alzheimer's disease somehow results in fungal infections - that the AD makes them more prone to fungal infection. In case you're wondering - all the AD patients and control patients studied had died - this is why their brain tissue could be studied so thoroughly. Excerpts from a research article by D. Pisa et al in Nature:

Different Brain Regions are Infected with Fungi in Alzheimer’s Disease

The possibility that Alzheimer’s disease (AD) has a microbial aetiology has been proposed by several researchers. Here, we provide evidence that tissue from the central nervous system (CNS) of AD patients contain fungal cells and hyphae. Fungal material can be detected both intra- and extracellularly using specific antibodies against several fungi. Different brain regions including external frontal cortex, cerebellar hemisphere, entorhinal cortex/hippocampus and choroid plexus contain fungal material, which is absent in brain tissue from control individuals. Analysis of brain sections from ten additional AD patients reveals that all are infected with fungi. Fungal infection is also observed in blood vessels, which may explain the vascular pathology frequently detected in AD patients. Sequencing of fungal DNA extracted from frozen CNS samples identifies several fungal species. Collectively, our findings provide compelling evidence for the existence of fungal infection in the CNS from AD patients, but not in control individuals.  ...continue reading "Fungal Infections Involved in Alzheimer’s Disease?"

Published on Leave a comment on Little Is Known About the Viruses Living On Healthy Skin

The microbes living on healthy human skin include bacteria, fungi, and viruses...but 90% of the viruses found on healthy skin in this study are unknown to researchers - thus "viral "dark matter". The skin virome  is the population of viruses on the skin. It turns out that most of the viruses on healthy skin are phage viruses. called bacteriophages.They infect bacteria and may take up residence within bacteria. From Science Daily:

90 percent of skin-based viruses represent viral 'dark matter,' scientists reveal

Scientists in recent years have made great progress in characterizing the bacterial population that normally lives on human skin and contributes to health and disease. Now researchers from the Perelman School of Medicine at the University of Pennsylvania have used state-of-the-art techniques to survey the skin's virus population, or "virome." The study, published in the online journal mBio last month, reveals that most DNA viruses on healthy human skin are viral "dark matter" that have never been described before. The research also includes the development of a set of virome analysis tools that are now available to researchers for further investigations.

Researchers and the public are increasingly aware that microbes living on and inside us -- our "microbiomes" -- can be crucial in maintaining good health, or in causing disease. Skin-resident bacteria are no exception. Ideally they help ward off harmful infections, and maintain proper skin immunity and wound-healing, but under certain circumstances they can do the opposite.

"Until now, relatively little work has been done in this area, in part because of the technical challenges involved. For example, a skin swab taken for analysis will contain mostly human and bacterial DNA, and only a tiny amount of viral genetic material -- the proverbial needles in the haystack." 

Their analysis of samples from 16 healthy individuals revealed some results that were expected. The most abundant skin-cell infecting virus was human papilloma virus, which causes common warts and has been linked to skin cancers. However, most of the detected DNA from the VLPs did not match viral genes in existing databases. "More than 90 percent was what we call viral dark matter -- it had features of viral genetic material but no taxonomic classification," Grice said. That came as a surprise, although of course it highlighted the importance of mapping this unexplored territory.

The findings also clearly linked the skin virome to the skin microbiome: Most of the detected viral DNA appeared to belong to phage viruses, which infect and often take up long-term residence within bacteria. And when Grice and colleagues sequenced skin bacterial DNA from the same 16 subjects, they found that it often contained tell-tale marks -- called CRISPR spacers -- of prior invasion by the same phage viruses.

The results also showed that the skin virome varies considerably depending on the body site. Grice's team took swabs from the palm, the forehead, the armpit, the navel, and other sites, and found, for example, that the virome was most diverse in the crook of the arm, a site that is intermittently exposed and occluded.

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According to a new report, it looks like most people under the age of 50 (throughout the world) have herpes simplex virus infections - whether type 1 or type 2. (Picture is of a herpes simplex virus type 1, at www.virology.net). From Medical Xpress:

An estimated two-thirds of world's population under age of 50 are infected with herpes simplex virus type 1

More than 3.7 billion people under the age of 50 are infected with herpes simplex virus type 1 (HSV-1), which commonly causes 'cold sores' and can also cause genital herpes, according to new research by the University of Bristol and the World Health Organisation [WHO]. The findings, published in the journal PLOS ONE, reveal the first global estimates of HSV-1 infection.

Herpes simplex virus is categorised into two types: herpes simplex virus type 1 (HSV-1) and herpes simplex virus type 2 (HSV-2). Both HSV-1 and HSV-2 are highly infectious and incurable. HSV-1 is primarily transmitted by oral-oral contact and in many cases causes orolabial herpes or "cold sores" around the mouth. HSV-2 is almost entirely sexually transmitted through skin-to-skin contact, causing genital herpes. 

The new estimates highlight, however, that HSV-1 is also an important cause of genital herpes. Some 140 million people aged 15-49 years are estimated to be infected with genital HSV-1 infection, primarily in the Americas, Europe and Western Pacific. Earlier this year, WHO published estimates of herpes simplex virus type 2 (HSV-2) infection showing that an estimated 417 million people between 15-49 years of age have infection caused by HSV-2. Taken together, these estimates suggest that over half a billion people between 15-49 years of age have a genital infection due either to HSV-1 or HSV-2. This highlights the large global burden of genital herpes caused by both HSV types.

Given the lack of a permanent and curative treatment for both HSV-1 and HSV-2, WHO and partners are working to accelerate development of HSV vaccines and topical microbicides, which will have a crucial role in preventing these infections in the future. Several candidate vaccines and microbicides are currently being studied. 

Published on Leave a comment on Lots of Diverse Bacteria On Fresh Produce

 There has been tremendous concern in recent years over pathogenic bacteria (such as Salmonella and Escherichia coli) found on raw fruits and vegetables. But what about nonpathogenic bacteria? Aren't some of the benefits of eating raw fruits and vegetables the microbes found on them? What actually is on them?

The following research using modern genetic analysis (16 S rRNA gene pyrosequencing) is from 2013, but very informative and the only study that I could find of its kind. The results suggest that humans are exposed to substantially different bacteria depending on the types of fresh produce they consume, with differences between conventionally and organically farmed varieties contributing to this variation.

While each of the 11 produce types studies harbored different microbial communities, the most common (abundant) across all samples were: Enterobacteriaceae [30% (mean)], Bacillaceae (4.6%), and Oxalobacteraceae (4.0%). Earlier studies also suggested that non-pathogenic microbes may interact with and inhibit microbial pathogens found on produce surfaces. Bottom line: eat a variety of raw fruits and vegetables to get exposed to a variety of non pathogenic microbes.

From Science Daily: Diverse bacteria on fresh fruits, vegetables vary with produce type, farming practices

Fresh fruit and vegetables carry an abundance of bacteria on their surfaces, not all of which cause disease. In the first study to assess the variety of these non-pathogenic bacteria, scientists report that these surface bacteria vary depending on the type of produce and cultivation practices. The results are published March 27 in the open access journal PLOS ONE by Jonathan Leff and Noah Fierer at the University of Colorado, Boulder.

The study focused on eleven produce types that are often consumed raw, and found that certain species like spinach, tomatoes and strawberries have similar surface bacteria, with the majority of these microbes belonging to one family. Fruit like apples, peaches and grapes have more variable surface bacterial communities from three or four different groups. The authors also found differences in surface bacteria between produce grown using different farming practices.

The authors suggest several factors that may contribute to the differences they observed, including farm locations, storage temperature or time, and transport conditions. These surface bacteria on produce can impact the rate at which food spoils, and may be the source of typical microbes on kitchen surfaces. Previous studies have shown that although such microbes don't necessarily cause disease, they may still interact with, and perhaps inhibit the growth of disease-causing microbes. The results of this new research suggest that people may be exposed to substantially different bacteria depending on the types of produce they consume.

Excerpts of the actual study from PLoS One:  Bacterial Communities Associated with the Surfaces of Fresh Fruits and Vegetables

Fresh fruits and vegetables can harbor large and diverse populations of bacteria. However, most of the work on produce-associated bacteria has focused on a relatively small number of pathogenic bacteria....Our results demonstrated that the fruits and vegetables harbored diverse bacterial communities, and the communities on each produce type were significantly distinct from one another. However, certain produce types (i.e., sprouts, spinach, lettuce, tomatoes, peppers, and strawberries) tended to share more similar communities as they all had high relative abundances of taxa belonging to the family Enterobacteriaceae when compared to the other produce types (i.e., apples, peaches, grapes, and mushrooms) which were dominated by taxa belonging to the Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria phyla. ...Taken together, our results suggest that humans are exposed to substantially different bacteria depending on the types of fresh produce they consume with differences between conventionally and organically farmed varieties contributing to this variation.

Fresh produce, including apples, grapes, lettuce, peaches, peppers, spinach, sprouts, and tomatoes, are known to harbor large bacterial populations [1]–[7], but we are only just beginning to explore the diversity of these produce-associated communities. We do know that important human pathogens can be associated with produce (e.g., L. monocytogenes, E. coli, Salmonella), and since fresh produce is often consumed raw, such pathogens can cause widespread disease outbreaks [8]–[11]. In addition to directly causing disease, those microbes found in produce may have other, less direct, impacts on human health. Exposure to non-pathogenic microbes associated with plants may influence the development of allergies [12],and the consumption of raw produce may represent an important means by which new lineages of commensal bacteria are introduced into the human gastrointestinal system. 

Although variable, taxonomic richness levels differed among the eleven produce types with richness being highest on peaches, alfalfa sprouts, apples, peppers, and mushrooms and lowest on bean sprouts and strawberries (Fig. 1). Bacterial communities were highly diverse regardless of the produce type with between 17 and 161 families being represented on the surfaces of each produce type. However, the majority of these families were rare; on average, only 3 to 13 families were represented by at least two sequences per produce type.

Furthermore, pairwise tests revealed that the community composition on the surface of each produce type differed significantly from one another. Still, certain produce types shared more similar community structure than others. On average, tree fruits (apples and peaches) tended to share communities that were more similar in composition than they were to those on other produce types, and produce typically grown closer to the soil surface (spinach, lettuce, tomatoes, and peppers) shared communities relatively similar in composition. Surface bacterial communities on grapes and mushrooms were each strongly dissimilar from the other produce types studied.

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"