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Published on Leave a comment on Microbes Are Circling the Earth in Air Currents and Winds

The following article is interesting because it describes how microbes are high up in the sky riding air currents and winds to circle the earth, and eventually drop down somewhere. This is one way diseases can be spread from one part of the world to another. And the study looking at how antibiotic resistant bacteria are spread in the air from cattle feedlots has implications for how antibiotic resistance is spread. From Smithsonian:

Living Bacteria Are Riding Earth's Air Currents

Considering the prevailing winds, David J. Smith figured the air samples collected atop a dormant volcano in Oregon would be full of DNA signatures from dead microorganisms from Asia and the Pacific Ocean. He didn’t expect anything could survive the journey through the harsh upper atmosphere to the research station at the Mount Bachelor Observatory, at an elevation of 9,000 feet.

But when his team got to the lab with the samples, taken from two large dust plumes in the spring of 2011, they discovered a thriving bunch of hitchhikers. More than 27 percent of the bacterial samples and more than 47 percent of the fungal samples were still alive. Ultimately, the team detected about 2,100 species of microbes, including a type of Archea that had only previously been isolated off the coast of Japan. “In my mind, that was the smoking gun,“ Smith says. Asia, as he likes to say, had sneezed on North America.

 Microbes have been found in the skies since Darwin collected windswept dust aboard the H.M.S. Beagle 1,000 miles west of Africa in the 1830s. But technologies for DNA analysis, high-altitude collection and atmospheric modeling are giving scientists a new look at crowded life high above Earth. For instance, recent research suggests that microbes are hidden players in the atmosphere, making clouds, causing rain, spreading diseases between continents and maybe even changing climates.

"I regard the atmosphere as a highway, in the most literal sense of the term," Smith says. "It enables the exchange of microorganisms between ecosystems thousands of miles apart, and to me that’s a more profound ecological consequence we still have not fully wrapped our heads around."

Airborne microbes potentially have huge impacts on our planet. Some scientists attribute a 2001 foot-and-mouth outbreak in Britain to a giant storm in north Africa that carried dust and possibly spores of the animal disease thousands of miles north only a week before the first reported cases. Bluetongue virus, which infects domestic and wild animals, was once present only in Africa. But it's found now in Great Britain, likely the result of the prevailing winds.

In west Texas, researchers from Texas Tech University collected air samples upwind and downwind of ten cattle feedlots. Antibiotic resistant microbes were 4,000 percent more prevalent in the downwind samples. .... What's clear is there are far more viable microbes in far more inhospitable places than scientists expected.

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"

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 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 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.

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Every time you inhale, you suck in thousands of microbes. And depending on where you live, the microbes will vary. From Wired:

An Atlas of the Bacteria and Fungi We Breathe Every Day

EVERY TIME YOU inhale, you suck in thousands of microbes. (Yes, even right then. And just then, too.) But which microbes? Scientists mostly assumed that the living components of air—at the tiniest scales, anyway—were the same no matter where you went.

And? Not true, it turns out. Thanks to a 14-month citizen-science project that sampled and analyzed airborne dust around the country, researchers have constructed the first atlas of airborne bacteria and fungi across the continental US. And airborne microscopic life is really diverse.

More than 1,400 volunteers swabbed surfaces in 1,200 houses around the country, focusing on the places people don’t usually clean. The dust there passively collects microbes. In the end those swabs revealed about 112,000 bacterial and 57,000 fungal phylotypes (i.e. familial groups).

Most of these little guys were harmless. The few pathogens and allergens ended up being location-specific. Alternaria, a fungal genus that’s also a common allergen, is ubiquitous but concentrates most in the midwest. The fungus Cladosporium has smaller hotspots scattered all over the country east of Texas, most frequently in the South and Mid-Atlantic. Meanwhile, the bacterial genus Cellulomonas, an normally harmless microbe (but an emerging pathogen according to one study), is much more common in the west.

The two biggest factors that shape this airborne environment, according to study author and University of Colorado microbial ecologist Noah Fierer, are the types of soil and plants that are located in the area (affecting the acidity in the environment), and the climate (humidity, temperature, etc.) Cities, for example, tended to be more like other cities than the rural areas nearby, which Fierer attributes to urban areas tending to plant the same types of trees and flowers and playing host to the same types of wildlife (pigeons, rats, etc).

Clasdosporium is a genus of fungi including some of the most common indoor and outdoor molds. Credit: Wikipedia.

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This nice general summary of what scientists know about the microbial community within us was just published by a division of the NIH (National Institutes of Health). Very simple and basic. From the National Institute of General Medical Sciences (NIGMS):

Facts about our microbial menagerie

Trillions of microorganisms inhabit us -- inside and out. Scientists are surveying these microbial metropolises to learn more about their role in health. Microbiologists Darren Sledjeski of the National Institutes of Health (NIH) and Andrew Goodman of Yale University share a few details of what researchers have learned so far.

1. The majority of the microbes that inhabit us are bacteria. The rest of the microbial menagerie is fungi and viruses, including ones that infect the bacteria! Collectively, our resident microorganisms are referred to as the human microbiota, and their genomes are called the human microbiome.

2. Our bodies harbor more bacterial cells than human ones. Even so, the microbiota accounts for less than 3 percent of a person's body mass. That's because our cells are up to 10,000 times bigger in volume than bacterial cells.

3. Your collection of bacteria has more genes than you do. Scientists estimate that the genomes of gut bacteria contain 100-fold or more genes than our own genomes. For this reason, the human microbiome is sometimes called our second genome.

4. Most of our microbes are harmless, and some are helpful. For example, harmless microbes on the skin keep infectious microbes from occupying that space. Microbes in the colon break down lactose and other complex carbohydrates that our bodies can't naturally digest.

5. Different microbes occupy different parts of the body. Some skin bacteria prefer the oily nooks near the nose, while others like the dry terrain of the forearm. Bacteria don't all fare well in the same environment and have adapted to live in certain niches.

6. Each person's microbiota is unique. The demographics of microbiota differ among individuals. Diet is one reason. Also, while a type of microbe might be part of one person's normal microbial flora, it might not be part of another's, and could potentially make that person sick.

7. Host-microbial interactions are universal. Microbial communities may vary from person to person, but everyone's got them, including other creatures. For this reason, researchers can use model organisms to tease apart the complexities of host-microbial interactions and develop broad principles for understanding them. The mouse is the most widely used animal model for microbiome studies.

8. The role of microbiota in our health isn't entirely clear. While it's now well accepted that the microbial communities that inhabit us are actively involved in a range of conditions -- from asthma to obesity -- research studies have not yet pinpointed why or how. In other words, the results may suggest that the presence of a bacterial community is associated with a disease, but they don't show cause and effect.

9. Most of our microbes have not been grown in the lab. Microbes require a certain mix of nutrients and other microbes to survive, making it challenging to replicate their natural environments in a petri dish. New culturing techniques are enabling scientists to study previously uncultivated microbes.

10. The impact of probiotic and prebiotic products isn't clear. Fundamental knowledge gaps remain regarding how these products may work and what effects they might have on host-microbial interactions. A new NIH effort to stimulate research in this area is under way.

11. There's even more we don't know! Additional areas of research include studying the functions of microbial genes and the effects of gut microbes on medicines. The more we learn from these and other studies, the more we'll understand how our normal microbiota interacts with us and how to apply that knowledge to promote our health.

Lactobacilli. Credit: Wikipedia.

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Excerpts from an interesting article about microbes and some findings from 2014. From Wired:

9 Amazing and Gross Things Scientists Discovered About Microbes This Year

We can’t see them, but they are all around us. On us. In us. Our personal microbes—not to mention those in the environment around us—have us outnumbered by orders of magnitude, but scientists are only beginning to understand how they influence our health and other aspects of our lives. It’s an increasingly hot area of science, though, and this past year saw lots of interesting developments. Here are some of the highlights.

When you move, your microbes move with you

In a study published in Science in August, scientists cataloged the microbes of seven families, swabbing the hands, feet, and noses of each family member—including pets—for six weeks. They also collected samples from doorknobs, light switches, and other household surfaces. Each home had a distinct microbial community that came mostly from its human inhabitants, and the scientists could tell which home a person lived in just by matching microbial profiles. Three of the families moved during the study period, and it only took about a day for their microbes to settle in to the new place. As the journal’s editors put it: “When families moved, their microbiological ‘aura’ followed.”

Microbes could help solve crimes

Scientists made several findings this year that could potentially show up in court one day. One study found that the microbiome of human cadavers evolves in a predictable way, hinting at a new way to determine time of death. And earlier this month, researchers suggested that bacteria on pubic hair could be used to identify the perpetrators of sex crimes—especially useful when a rapist uses a condom to avoid leaving behind DNA evidence.

Your gut bacteria may be inherited

Exactly which bacteria choose to take up residence in your gut is determined, in part, by your genes, scientists reported this year after examining more than 1,000 fecal samples from 416 pairs of twins... One of the most heritable types was a family of bacteria called Christensenellaceae, which are more abundant in lean people than in obese people. 

Forget fecal transplants, poo pills may be just as effective

Clostridium difficile (pictured) is a nasty bacteria that wreaks havoc on the guts and kills 14,000 people a year in the US alone. Normally, other intestinal bacteria keep C. diff in check, but in the worst infections it starts to dominate. One effective but off putting treatment is a fecal transplant: taking a stool sample from a healthy person and transplanting it into the patient (in through the out door, so to speak). This year researchers developed a less cringe-inducing alternative. They created odorless frozen capsules that contained bacteria isolated from healthy stool samples. The poo pills successfully treated 18 of 20 patients with antibiotic-resistant C. diff infections, the team reported in JAMA in October.

Yeast evolved to lure fruit flies (not to make delicious beer)

There is crazy microbial diversity in cheese rinds

A tiny crumb of cheese rind contains about 10 billion microbial cells: bacteria and fungi that turn boring milk into something funky and delicious. Although cheesemakers have been manipulating them for centuries, not much is known about these microbes. This year scientists conducted the largest study yet on the microbial diversity of cheese, examining 137 cheeses from 10 countries.They found that microbial communities vary according to the style of cheese, but not so much according to where the cheese is made.

The microbiome could be a source of novel drugs

The bacteria that live on and in our bodies make countless molecules. Some of those molecules might make good drugs. 

We may need new branches on the tree of life for all the microbes

Life on Earth has traditionally been divided into three domains: Eukaryotes (plants, animals, and all other organisms that stash their DNA in a special compartment—the nucleus—inside their cells), Bacteria (our familiar one-celled friends and foes), and Archaea (single-celled organisms that are biochemically and genetically distinct from the other two groups). But do we really know that’s all there is? We do not, two scientists argued last month in Science. There may be entire domains of life that have eluded our methods of detection.

Without microbes, life as we know it would end

In December, two scientists posed a thought question in the journal PLOS Biology: What would happen in a world without microbes? ...Without nitrogen-fixing soil bacteria, crops would begin to fail. Decomposition would stop, waste would pile up, and the nutrient recycling that supports life as we know it would grind to a halt. “We predict complete societal collapse only within a year or so, linked to catastrophic failure of the food supply chain,” the researchers write. “Annihilation of most humans and nonmicroscopic life on the planet would follow a prolonged period of starvation, disease, unrest, civil war, anarchy, and global biogeochemical asphyxiation.”

 Clostridium difficile. Credit: CDC

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Amazing persistence of the restroom microbial community.From NPR news:

What Microbes Lurked In The Last Public Restroom You Used?

The invisible world of the bathroom isn't pretty — unless you're a microbe. After scanning the microbial zoo of four public restrooms recently, a team of researchers found a diverse swarm of characters that persisted for months despite regular cleaning of the facilities. The goal of the study, published in the December issue of Applied and Environmental Microbiology, was to better understand how communities of bacteria and viruses can shift in these very public places across a couple of months.

To get their down-and-dirty readings, the researchers selected four bathrooms at San Diego State University... They checked two women's restrooms and two men's restrooms (a high-traffic and a low-traffic bathroom for each gender). The bathrooms were thoroughly cleaned at the study's start with bleach solution, which killed any existing germ communities.Then, during the following hours, days, weeks and months of human use, the researchers periodically swabbed soap dispensers, floors and toilet seats in all four restrooms for microbe samples. 

Within one hour of sterilization, the bathrooms were completely recolonized with microbes — just as plants rapidly arrive and populate a newly emerged island. Fecal bacteria dominated, including on toilet seats and on soap dispensers — about 45 percent of the bacteria there were of fecal origin.

In all, the scientists found genetic traces of more than 77,000 distinct types of bacteria and viruses. (At least some of those species were likely dead or dormant, the scientists add; genetic testing detects them all, whatever their status.)

Patterns of regrowth and succession, as some species waned and others replaced them, were surprisingly similar from bathroom to bathroom; within just five hours the population mix in each room stabilized.

When the team tried growing cultures from different surfaces in each room, they found one set of live bacteria in overwhelming abundance: Staphylococcus. Staph's persistence in these studies points to its power as a potential pathogen, Gilbert says. Various versions are common on human skin and inside the nose and other orifices; they generally cause no problems, or trigger only minor skin infections. But staph infections can be serious, or even kill, if the bacteria get into bloodstream, joints, bones, lungs or heart. 

Gilbert notes that none of the live Staph strains detected in the San Diego bathrooms showed signs of being antibiotic resistant. They were instead relatively harmless "skin bugs that happened to have lost their skin," he says. The team did find genes from MRSA hiding on the floor, as well as traces of some troublemaker viruses, including HPV and herpes virus.

Interestingly, although restrooms that were left open for use for up to two months were cleaned regularly with soap and water, the communities of microbes found there remained relatively unchanged for the full eight weeks of the study.

No need to be scared or grossed out by that finding, Gilbert says..."All human environments contain pathogens — your bedroom, the phone you're talking on, even the bugs inside of you could turn pathogenic at any time," Gilbert tells Shots. "But we desperately need them in our lives." Having a healthy community of good — or even just neutral — microbes can crowd out the bad ones. As we've learned from using broad-spectrum antibiotics in the human body, "sterilization is not necessarily good," he says. "Bacteria come back right away, and they might come back perturbed."