Tag Archives: bacteria

Image result for bdellovibrio bacteriovorus Great idea and one that this blog has been pushing for a long time - the use of beneficial bacteria to get rid of other harmful bacteria. Some researchers refer to the bacteria acting as "living antibiotics" when they overpower harmful bacteria.

Researchers such as Daniel Kadouri, a micro-biologist at Rutgers School of Dental Medicine in Newark, are studying bacteria that aggressively attack harmful  bacteria, and calling them "predator bacteria". They are focusing on one specific bacteria - Bdellovibrio bacteriovorus, a gram-negative bacteria that dines on other gram-negative bacteria. They hope to eventually be able to give this bacteria as a medicine to humans , and then this predator bacteria would overpower and destroy "superbugs" (pathogenic bacteria that are resistant to many antibiotics). A great idea, but unfortunately the researchers think that it'll take about 10 more years of testing and development before it's ready for use in humans. From Science News:

Live antibiotics use bacteria to kill bacteria

The woman in her 70s was in trouble. What started as a broken leg led to an infection in her hip that hung on for two years and several hospital stays. At a Nevada hospital, doctors gave the woman seven different antibiotics, one after the other. The drugs did little to help her. Lab results showed that none of the 14 antibiotics available at the hospital could fight the infection, caused by the bacterium Klebsiella pneumoniae.... The CDC’s final report revealed startling news: The bacteria raging in the woman’s body were resistant to all 26 antibiotics available in the United States. She died from septic shock; the infection shut down her organs.

Kallen estimates that there have been fewer than 10 cases of completely resistant bacterial infections in the United States. Such absolute resistance to all available drugs, though incredibly rare, was a “nightmare scenario,” says Daniel Kadouri, a micro-biologist at Rutgers School of Dental Medicine in Newark, N.J. Antibiotic-resistant bacteria infect more than 2 million people in the United States every year, and at least 23,000 die, according to 2013 data, the most recent available from the CDC.

It’s time to flip the nightmare scenario and send a killer after the killer bacteria, say a handful of scientists with a new approach for fighting infection. The strategy, referred to as a “living antibiotic,” would pit one group of bacteria — given as a drug and dubbed “the predators” — against the bacteria that are wreaking havoc among humans.

The notion of predatory bacteria sounds a bit scary, especially when Kadouri likens the most thoroughly studied of the predators, Bdellovibrio bacteriovorus, to the vicious space creatures in the Alien movies. B. bacteriovorus, called gram-negative because of how they are stained for microscope viewing, dine on other gram-negative bacteria. All gram-negative bacteria have an inner membrane and outer cell wall. The predators don’t go after the other main type of bacteria, gram-positives, which have just one membrane.

“It’s a very efficient killing machine,” Kadouri says. That’s good news because many of the most dangerous pathogens that are resistant to antibiotics are gram-negative (SN: 6/10/17, p. 8), according to a list released by the WHO in February. It’s the predator’s hunger for the bad-guy bacteria, the ones that current drugs have become useless against, that Kadouri and other researchers hope to harness.  Pitting predatory against pathogenic bacteria sounds risky. But, from what researchers can tell, these killer bacteria appear safe. “We know that [B. bacteriovorus] doesn’t target mammalian cells,” Kadouri says.

Predatory bacteria can efficiently eat other gram-negative bacteria, munch through biofilms and even save zebrafish from the jaws of an infectious death. But are they safe? Kadouri and the other researchers have done many studies, though none in humans yet, to try to answer that question.... Other studies looking for potential toxic effects of B. bacteriovorus have so far found none. Both Mitchell and Kadouri tested B. bacteriovoruson human cells and found that the predatory bacteria didn’t harm the cells or prompt an immune response. The researchers separately reported their findings in late 2016 in Scientific Reports and PLOS ONE.

Image result for bdellovibrio bacteriovorus Bdellovibrio bacteriovorus  Credit: BBC

Bdellovibrio bacteriaBACTERIAL COMBATANTS Bdellovibrio bacteria (yellow) attack larger bacteria (blue), using the prey’s remains to replicate. Bdellovibrio microbes are a kind of living antibiotic (predator bacteria). Credit: Science News

Image result for permafrost  There are many posts on this site about the microbes within us (the microbiome) or around us, but the following article may be a real eye opener. Due to the permafrost melting (as in Alaska, northern Canada, Siberia, etc) from global warming, old infectious viruses and bacteria might be released from the thawing permafrost. This is what recently happened in Siberia, where melting permafrost released anthrax spores which killed 2300 reindeer and a 12 year old boy, and sickened at least 20 other people. From Scientific American:

As Earth Warms, the Diseases That May Lie Within Permafrost Become a Bigger Worry

This past summer anthrax killed a 12-year-old boy in a remote part of Siberia. At least 20 other people, also from the Yamal Peninsula, were diagnosed with the potentially deadly disease after approximately 100 suspected cases were hospitalized. Additionally, more than 2,300 reindeer in the area died from the infection. The likely cause? Thawing permafrost. According to Russian officials, thawed permafrost—a permanently frozen layer of soil—released previously immobile spores of Bacillus anthracis into nearby water and soil and then into the food supply. The outbreak was the region's first in 75 years.

Researchers have predicted for years that one of the effects of global warming could be that whatever is frozen in permafrost—such as ancient bacteria—might be released as temperatures climb. This could include infectious agents humans might not be prepared for, or have immunity to, the scientists said. Now they are witnessing the theoretical turning into reality: infectious microorganisms emerging from a deep freeze....In a 2011 paper published in Global Health Action, co-authors Boris A. Revich and Marina A. Podolnaya wrote of their predictions: “As a consequence of permafrost melting, the vectors of deadly infections of the 18th and 19th centuries may come back, especially near the cemeteries where the victims of these infections were buried.”

And permafrost is indeed thawing—at higher latitudes and to greater depths than ever before....What thawing permafrost could unleash depends on the heartiness of the infectious agent involved. A lot of microorganisms cannot survive in extreme cold, but some can withstand it for many years. “B. anthracis are special because they are sporulating bacteria,” says Jean-Michel Claverie, head of the Mediterranean Institute of Microbiology and a professor at Aix-Marseille University in France. “Spores are extremely resistant and, like seeds, can survive for longer than a century.”

Viruses could also survive for lengthy periods. In 2014 and 2015 Claverie and his colleague Chantal Abergel published their findings on two still infectious viruses from a chunk of 30,000-year-old Siberian permafrost. Although Pithovirus sibericum and Mollivirus sibericum can infect only amoebas, the discovery is an indication that viruses that infect humans—such as smallpox and the Spanish flu—could potentially be preserved in permafrost.

Human viruses from even further back could also make a showing. For instance, the microorganisms living on and within the early humans who populated the Arctic could still be frozen in the soil. “There are hints that Neandertals and Denisovans could have settled in northern Siberia [and] were plagued by various viral diseases, some of which we know, like smallpox, and some others that might have disappeared,” Claverie says....Janet Jansson, who studies permafrost at the Pacific Northwest National Laboratory in Washington State, is not worried about ancient viruses. Several attempts to discover these infectious agents in corpses have come up empty, she notes. 

In effect, infectious agents buried in the permafrost are unknowable and unpredictable in their timing and ferocity. Thus, researchers say thawing permafrost is not our biggest worry when it comes to infectious diseases and global warming. The more immediate, and certain, threat to humans is the widening geographical ranges of modern infectious diseases (and their carriers, such as mosquitoes) as the earth warms. “We now have dengue in southern parts of Texas,” says George C. Stewart, McKee Professor of Microbial Pathogenesis and chair of the department of veterinary pathobiology at the University of Missouri. “Malaria is seen at higher elevations and latitudes as temperatures climb. And the cholera agent, Vibrio cholerae, replicates better at higher temperatures.”

 Bacillus anthracis - Anthrax bacteria  Credit:Wikipedia

Image result for anthrax disease, wiki Skin anthrax lesion on the neck  Credit:Wikipedia

Beautiful photos of the microbes within and on us by the British scientific photographer Steve Gschmeisser. Check out his site (http://www.theworldcloseup.com/) to see photos of microbes and other images made with the very expensive SEM - a scanning electron microscope. All the photos are by Steve Gschmeisser.

 gingivitis causing bacteria in the gums of the mouth

 E. coli bacteria in urine sample

 breast cancer cells

 prostate cancer cell

Microvilli Photograph - Large Intestine by Steve Gschmeissner large intestine

 In 1837, Charles Darwin sketched a simple tree of life (shown left) to illustrate the idea that all living things share a common ancestor. Ever since then, scientists have been adding names to the tree of life, including a massive effort of 2.3 million named species of animals, plants, fungi and microbes in 2015. A tree of life is a visual hypothesis of how scientists think species are related to one another, so it has been evolving over the years as more information is learned and species discovered.

Now a group of 17 researchers have sketched out a radically different tree of life. It has two main trunks—one full of bacteria and another comprised of archaea, a group of single-celled microbes that run on very different biochemistry. The eukaryotes—the domain that includes all animals, fungi, and plants—are crowded on a thin branch coming off the archaeal trunk. About half of these bacterial branches belong to a supergroup, which was discovered very recently and is currently known as the candidate phyla radiation. Within these branches are numerous species that we’re almost completely ignorant about, and they’ve never been isolated or grown in a lab (with one exception called TM7). In fact, this supergroup of bacteria and “other lineages that lack isolated representatives clearly comprise the majority of life’s current diversity,” write researchers Hug and Banfield. Wow. From Science Daily:

Wealth of unsuspected new microbes expands tree of life

Scientists have dramatically expanded the tree of life, which depicts the variety and evolution of life on Earth, to account for over a thousand new microscopic life forms discovered over the past 15 years. The expanded view finally gives bacteria and Archaea their due, showing that about two-thirds of all diversity on Earth is bacterial -- half bacteria that cannot be isolated and grown in the lab -- while nearly one-third is Archaeal.

Much of this microbial diversity remained hidden until the genome revolution allowed researchers like Banfield to search directly for their genomes in the environment, rather than trying to culture them in a lab dish. Many of the microbes cannot be isolated and cultured because they cannot live on their own: they must beg, borrow or steal stuff from other animals or microbes, either as parasites, symbiotic organisms or scavengers.

The new tree, to be published online April 11 in the new journal Nature Microbiology, reinforces once again that the life we see around us -- plants, animals, humans and other so-called eukaryotes -- represent a tiny percentage of the world's biodiversity.

"Bacteria and Archaea from major lineages completely lacking isolated representatives comprise the majority of life's diversity," said Banfield.....According to first author Laura Hug,... the more than 1,000 newly reported organisms appearing on the revised tree are from a range of environments, including a hot spring in Yellowstone National Park, a salt flat in Chile's Atacama desert, terrestrial and wetland sediments, a sparkling water geyser, meadow soil and the inside of a dolphin's mouth. All of these newly recognized organisms are known only from their genomes.

One striking aspect of the new tree of life is that a group of bacteria described as the "candidate phyla radiation" forms a very major branch. Only recognized recently, and seemingly comprised only of bacteria with symbiotic lifestyles, the candidate phyla radiation now appears to contain around half of all bacterial evolutionary diversity.

Charles Darwin first sketched a tree of life in 1837 as he sought ways of showing how plants, animals and bacteria are related to one another. The idea took root in the 19th century, with the tips of the twigs representing life on Earth today, while the branches connecting them to the trunk implied evolutionary relationships among these creatures.....Archaea were first added in 1977 after work showing that they are distinctly different from bacteria, though they are single-celled like bacteria. A tree published in 1990 by microbiologist Carl Woese was "a transformative visualization of the tree," Banfield said. With its three domains, it remains the most recognizable today.

With the increasing ease of DNA sequencing in the 2000s, Banfield and others began sequencing whole communities of organisms at once and picking out the individual groups based on their genes alone. This metagenomic sequencing revealed whole new groups of bacteria and Archaea, many of them from extreme environments, such as the toxic puddles in abandoned mines, the dirt under toxic waste sites and the human gut. Some of these had been detected before, but nothing was known about them because they wouldn't survive when isolated in a lab dish.

For the new paper, Banfield and Hug teamed up with more than a dozen other researchers who have sequenced new microbial species, gathering 1,011 previously unpublished genomes to add to already known genome sequences of organisms representing the major families of life on Earth.....The analysis, representing the total diversity among all sequenced genomes, produced a tree with branches dominated by bacteria, especially by uncultivated bacteria. A second view of the tree grouped organisms by their evolutionary distance from one another rather than current taxonomic definitions, making clear that about one-third of all biodiversity comes from bacteria, one-third from uncultivable bacteria and a bit less than one-third from Archaea and eukaryotes. (Original article and diagrams.)

This is a new and expanded view of the tree of life, with clusters of bacteria (left), uncultivable bacteria called 'candidate phyla radiation' (center, purple) and, at lower right, the Archaea and eukaryotes (green), including humans.
Credit: Graphic by Zosia Rostomian, Lawrence Berkeley National Laboratory

 A recent study has examined the issue of whether the 10 to 1 ratio of bacteria to human cells, which is widely quoted, is actually correct. Weizmann Institute of Science researchers currently feel that based on scientific evidence (which of course will change over time) and making "educated estimates", the actual ratio is closer to 1:1 (but overall there still are more bacterial than human cells). They point out that the 10:1 ratio was originally a "back of the envelope" estimate dating back to 1972.

The researchers also point out that the ratio may vary over the course of each day - as a person defecates out huge amounts of bacteria with each bowel movement. However, this study - which is not the final word - is an educated guess about bacteria only. What about the viruses, the fungi, etc that also reside on and within us? We know much less about all the other microbes. I am disturbed that article after article, and headline after headline, equates microbes and bacteria. Microbes does not mean only bacteria.  From Science Daily:

Germs, humans and numbers: New estimate revises our microbiome numbers downwards

How many microbes inhabit our body on a regular basis? For the last few decades, the most commonly accepted estimate in the scientific world puts that number at around ten times as many bacterial as human cells. In research published in the journal Cell, a recalculation of that number by Weizmann Institute of Science researchers reveals that the average adult has just under 40 trillion bacterial cells and about 30 trillion human ones, making the ratio much closer to 1:1.

The rising importance of the microbiome in current scientific research led the Weizmann Institute's Prof. Ron Milo, Dr. Shai Fuchs and research student Ron Sender to revisit the common wisdom concerning the ratio of "personal" bacteria to human cells.

The original estimate that bacterial cells outnumber human cells in the body by ten to one was based on, among other things, the assumption that the average bacterium is about 1,000 times smaller than the average human cell. The problem with this estimate is that human cells vary widely in size, as do bacteria. For example, red blood cells are at least 100 times smaller than fat or muscle cells, and the microbes in the large intestine are about four times the size of the often-used "standard" bacterial cell volume. The Weizmann Institute scientists weighted their computations by the numbers of the different-sized human cells, as well as those of the various microbiome cells. 

Some excerpts from the original journal article from Cell: Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host Cells in Humans

The human microbiome has emerged as an area of utmost interest....One of the most fundamental and commonly cited figures in this growing field is the estimate that bacteria residing in the human body outnumber human cells by a factor of 10 or more (Figure 1A). This striking statement often serves as an entry point to the field. After all, if a human being is a cell population composed of at least 90% bacteria, it is only natural to expect a major role for them in human physiology.

Both the numerator (number of microbial cells) and the denominator (human cells) of this 10:1 ratio are based on crude assessments. Most sources cite the number of human cells as 1013 or 1014.....We performed a thorough review of the literature and found a long chain of citations originating from one “back of the envelope” estimate (Figure 1). This estimate, though illuminating, was never meant as the final word on the question.

Recently, the estimate of a 10:1 bacterial to human cell ratio (B/H) ratio has received criticism (Rosner, 2014). Therefore, an alternative value and an estimate of the uncertainty range are needed. Bacteria are found in many parts of the human body primarily on the external and internal surfaces, including the gastrointestinal tracts, skin, saliva, oral mucosa, and conjunctiva. The vast majority of commensal bacteria reside in the colon, with previous estimates of about 1014 bacteria (Savage, 1977), followed by the skin, which is estimated to harbor ∼1012 bacteriaBerg, 1996). Less than 1012 bacteria populate the rest of the body.....Almost all recent papers in the field of gut microbiota directly or indirectly rely on a single paper (Savage, 1977) discussing the overall number of bacteria in the gut. Interestingly, review of the original Savage 1977 paper demonstrates that it actually cites another paper for the estimate (Luckey, 1972)....The estimate, performed by Luckey in 1972, is an illuminating example of a back-of-the-envelope estimate, which was elegantly performed, yet was probably never meant to serve as the cornerstone reference number to be cited decades later.

Updating the ratio of bacteria to human cells from 10:1 or 100:1 to closer to 1:1 does not take away from the biological importance of the microbiota. ...Although we still appear to be outnumbered, we now know more reliably to what degree and can quantify our uncertainty about the ratios and absolute numbers. The B/H ratio is actually close enough to one, so that each defecation event, which excretes about 1/3 of the colonic bacterial content, may flip the ratio to favor human cells over bacteria. This anecdote serves to highlight that some variation in the ratio of bacterial to human cells occurs not only across individual humans but also over the course of the day.

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Once again, two opposing views about beards have been in the news - that they harbor all sorts of nasty disease-causing bacteria vs they are hygienic. An earlier May 5, 2015 post was about the question of whether bearded men have more bacteria on their faces than clean shaven ones. I cited a 2014 study found that they don't, and that we are all covered with bacteria, all sorts of bacteria, and this is normal.

Now another study has looked at the issue of hospital workers with and without beards and whether they carry infectious bacteria. Researchers swabbed the faces (center of the cheek and the skin of the upper lip under the nostrils) of both clean shaven individuals and individuals with facial hair (beards) that worked in two hospitals (they all had direct contact with patients) and looked at the bacteria present. They especially looked for the presence of the bacteria Staphylococcus aureus, which surprisingly was found more in the clean-shaven men. Also to their surprise, it was more of the clean shaven men who carried the pathogenic bacteria Methicillin-resistant Staphylococcus aureus (also known as MRSA). For those bacterial groups most closely associated with hospital acquired infections, such as Klebsiella species, Pseudomonas species, Enterobacter species., and Acinetobacter species, prevalence was low in both groups, and less than 2% for each group.

For other, less harmful bacteria, researchers found that bearded employees harbored no more bacteria than their clean-shaven colleagues. In summary: The researchers say that "results suggest that male hospital workers with facial hair do not harbour more potentially concerning bacteria than clean-shaven workers, and that in some instances, clean-shaven individuals are significantly more likely to be colonized with potential nosocomial pathogens". (NOTE: nosocomial means a disease originating or acquired in a hospital.)

And why is that? According to the study, one explanation is "microtrauma to the skin," which occurs during shaving and results in abrasions, which could support bacterial colonisation and growth of bacteria on the clean-shaven men. However, some other researchers have a different hypothesis — that beards themselves actually fight infection. This stems from an experiment carried out by Dr. Michael Mosley who recently swabbed the beards of a variety of men and sent the samples to Dr. Adam Roberts, a microbiologist at University College London. Roberts grew more than 100 different bacteria from the beard samples, but found that in a few of the petri dishes a microbe was killing the other bacteria -  a bacteria called Staphylococcus epidermidis, and which they believe has antibiotic properties.

From the Journal of Hospital Infection: Bacterial ecology of hospital workers’ facial hair: a cross-sectional study

Summary: It is unknown whether healthcare workers' facial hair harbours nosocomial pathogens. We compared facial bacterial colonization rates among 408 male healthcare workers with and without facial hair. Workers with facial hair were less likely to be colonized with Staphylococcus aureus (41.2% vs 52.6%, P = 0.02) and meticillin-resistant coagulase-negative staphylococci (2.0% vs 7.0%, P = 0.01). Colonization rates with Gram-negative organisms were low for all healthcare workers, and Gram-negative colonization rates did not differ by facial hair type. Overall, colonization is similar in male healthcare workers with and without facial hair; however, certain bacterial species were more prevalent in workers without facial hair.

[Excerpts from Discussion]:Several studies to date have demonstrated that physician white coats and neck ties can act as significant sources of nosocomial bacteria. Our study suggests that facial hair does not increase the overall risk of bacterial colonization compared to clean-shaven control subjects. Indeed, clean-shaven control subjects exhibited higher rates of colonization with certain bacterial species. This finding may be explained by microtrauma to the skin during shaving resulting in abrasions, which may support bacterial colonization and proliferation. This may be akin to the enhanced risk of surgical site infections in patients shaved with razors prior to surgery. Further, our results are consistent with prior evidence pertaining to bacterial colonization on the hands and nares of HCWs (Health care workers).

IMG_3880 Credit:Mara Silgailis at Lacto Bacto

 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.

Scientists examining the decline of coral reefs in near-pristine stretches of the Caribbean are pointing at dust and accompanying microbes, stirred up during African dust storms and carried west, as the culprit. A particular fungus that kills sea fans first arrived in 1983, researchers say, when a drought in the Sahara created dust clouds that floated across the Atlantic.

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. Philip Smith, an associate professor of terrestrial ecotoxicology, and Greg Mayer, an associate professor of molecular toxicology, said the work establishes a baseline for further research.  They have completed a study of viability to be released in early 2016 and want to look at the questions of how far the particles travel and whether resistance can be transmitted to native bacteria. Antibiotics, Mayer notes, existed in nature long before humans borrowed them. But what happens when they are concentrated in places, or spread on the wind? 

What's clear is there are far more viable microbes in far more inhospitable places than scientists expected. Researchers from the Georgia Institute of Technology, supported by a NASA research grant, examined air samples collected by a plane flying during hurricanes miles above Earth. They found that living cells accounted for about 20 percent of of the storm-tossed microbes. "We were not expecting to find so many intact and alive bacterial cells at 10,000 meters," says Kostas Konstantinidis, a microbiologist at the Georgia Institute of Technology.

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. From 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.

The scientists began with a small pilot study, recruiting forty families in the Raleigh-Durham area to swab nine locations in their homes. When the researchers analyzed these cotton swabs and sequenced the fragments of bacterial DNA that they contained, they found that even the most sparkling houses were teeming with microbial squatters—more than two thousand distinct types, on average. Different rooms formed distinct ecological niches: kitchens were popular among the bacteria that grow on produce, whereas bedroom and bathroom surfaces were colonized by those that typically dwell on the skin. (In a troubling discovery, Dunn and his colleagues learned that, from a microbiological perspective, toilet seats and pillowcases look strikingly similar.)

In many ways, these findings were predictable. What the researchers had some difficulty making sense of was the variation that they observed between homes. “What, really, is determining what lives in your house versus my house?” Dunn asked. To answer that question, they expanded the study to a larger, more diverse set of homes—about eleven hundred in total, from across the continental United States—and asked volunteers to swab the trim around their interior doorways. “We focussed on that because nobody ever cleans it,” Fierer told me. “Or we don’t clean it very often—maybe you’re an exception.” (I am not.) To provide a point of comparison, each volunteer also collected dust from an exterior door and then mailed the samples to Fierer’s Colorado lab.

Fierer and his team isolated, amplified, and sequenced the DNA that was present in each sample, listing the types of bacteria and fungi that they found. The list soon grew long. “The diversity was just crazy,” Dunn said. In total, the indoor dust contained more than sixty-three thousand species of fungi and a hundred and sixteen thousand species of bacteria. For the fungi, location was king. Houses in eastern states had different fungal communities than those in western ones. Ditto homes in humid climates compared with those in dry ones. In fact, the geographic correlation was so strong that Dunn and Fierer have since shown, in a separate paper, that they can use fungal DNA to determine, to within about a hundred and fifty miles, where in the United States a dust sample originated. 

Bacterial communities, on the other hand, were shaped less by a home’s location than by its occupants. “We’re really the dominant sources—us and our pets are the dominant sources—of bacteria inside homes,” Fierer said. The fur factor loomed especially large. Dogs introduced unique drool and fecal microbes into a home and tracked in soil dwellers from outside. Cats also changed a home’s microbial makeup, but more modestly, perhaps because they are smaller and venture outside less often. By analyzing the bacterial DNA in dust, the researchers were able to predict whether a home contained a dog with ninety-two-per-cent accuracy and a cat with eighty-three-per-cent accuracy.

The sex of a home’s human occupants also played a role in shaping the indoor ecosystem. Lactobacillus bacteria, which are a major component of the vaginal microbiome, were most abundant in homes in which women outnumbered men. When men were in the majority, however, different bacteria thrived: Roseburia, which normally lives in the gut, and Corynebacterium and Dermabacter, which both inhabit the skin. Corynebacterium is known to occupy the armpit and contribute to body odor. 

Most of our microscopic roommates are unlikely to present a real threat; many species of bacteria, scientists now know, are crucial partners in maintaining our health. “We’re surrounded by microbes all the time, and that’s not a bad thing,” Fierer said.

 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 (P<0.001) 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.

  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.

 Charles M. Schultz's "Pig-Pen"