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Category: human microbiome

Published on Leave a comment on Millions of Bacteria In Our Water and Water Pipes

Interesting, but in some ways horrifying - the hidden world of microbes teeming around us. With new techniques such as genetic sequencing we now know that at least a couple of thousand different species live in our water pipes in biofilms (concentrated microbial communities) that coat our water pipes. About eighty thousand bacteria per milliliter are in our drinking water, with one glass of clean drinking water containing ten million bacteria! And same as with microbes in human bodies, researchers think that a number of these bacteria and other microbes are beneficial and actually help purify the water. From Science Daily:

Our water pipes crawl with millions of bacteria

Researchers from Lund University in Sweden have discovered that our drinking water is to a large extent purified by millions of "good bacteria" found in water pipes and purification plants. So far, the knowledge about them has been practically non-existent, but this new research is about to change that.

A glass of clean drinking water actually contains ten million bacteria! But that is as it should be -- clean tap water always contains harmless bacteria. These bacteria and other microbes grow in the drinking water treatment plant and on the inside of our water pipes, which can be seen in the form of a thin, sticky coating -- a so-called biofilm. All surfaces from the raw water intake to the tap are covered in this biofilm.

Findings by researchers in Applied Microbiology and Water Resources Engineering show that the diversity of species of bacteria in water pipes is huge, and that bacteria may play a larger role than previously thought. Among other things, the researchers suspect that a large part of water purification takes place in the pipes and not only in water purification plants.

"A previously completely unknown ecosystem has revealed itself to us. Formerly, you could hardly see any bacteria at all and now, thanks to techniques such as massive DNA sequencing and flow cytometry, we suddenly see eighty thousand bacteria per millilitre in drinking water," says researcher Catherine Paul enthusiastically.

At least a couple of thousand different species live in the water pipes. According to the researchers there is a connection between the composition of bacteria and water quality."We suspect there are 'good' bacteria that help purify the water and keep it safe -- similar to what happens in our bodies. Our intestines are full of bacteria, and most the time when we are healthy, they help us digest our food and fight illness, says Catherine Paul.

Although the research was conducted in southern Sweden, bacteria and biofilms are found all over the world, in plumbing, taps and water pipes. This knowledge will be very useful for countries when updating and improving their water pipe systems."The hope is that we eventually may be able to control the composition and quality of water in the water supply to steer the growth of 'good' bacteria that can help purify the water even more efficiently than today," says Catherine Paul.

Published on Leave a comment on Amazing Paper Sculptures of Microbes

Just saw some of  Rogan Brown's amazing paper sculptures of microbes. He designs, then cuts by hand or laser thousands of paper microorganisms, including tree moss, cell structures, bacteria, coral, and diatoms. Absolutely gorgeous! From :

Paper Life – The artist Rogan Brown cuts thousands of microorganisms in paper

The following article was from April 2015, and it described the work of various artists contributing to a permanent exhibit of the human microbiome. Go to the article and check out the various fascinating artworks. From Wired (UK edition): Eden Project's 'Human Biome' is a gross, musical microbe showcase

The great domed biomes of the Eden Project are to play host to a new permanent exhibition that will focus on one of nature's most important and complex ecosystems: the human body. Invisible You: The Human Biome will explore the community of microbes that live in and on each and every one of us. Artistic and interactive displays will show bacteria, fungi and viruses, with 11 artists commissioned to create works for the exhibition.

"These trillions of microbes outnumber our cells ten to one and, in the main, work together to keep us healthy -- whether it’s the bacteria in the gut helping to digest our food or the microbes on our skin working to keep it soft. This fascinating new exhibition is one of the most compelling and important we have ever staged," said Jo Elsworthy, the Eden Project's interpretation director. Among the artists commissioned to create work for the exhibition is Rogan Brown, who creates beautifully intricate, hand-cut paper artworks, including microbes. 

Published on Leave a comment on What is “Seeding” the Microbiomes of Babies Born By C-section?

The mother is an important source of the first microbiome for infants by "seeding" the baby's microbiome - from the vaginal birth and then breastfeeding. However, research finds that infants born by C-section acquire bacteria commonly found on skin (Staphylococcus, Corynebacterium, and Propionibacterium) rather than the bacteria acquired during a vaginal birth.

This study examined the source of the skin-type bacteria found on C-section babies. The researchers analyzed the dust from operating rooms (which they collected right after C-sections) and found that it contains deposits of human skin bacteria and human skin flakes. The researchers point out that "Humans shed up to 37 million bacterial genomes into the environment per hour." Operating rooms are occupied by humans, lack natural ventilation, and even though they are regularly cleaned, the humans using the operating rooms shed bacteria and skin flakes. From Microbiome:

The first microbial environment of infants born by C-section: the operating room microbes

Newborns delivered by C-section acquire human skin microbes just after birth, but the sources remain unknown. We hypothesized that the operating room (OR) environment contains human skin bacteria that could be seeding C-section born infants. To test this hypothesis, we sampled 11 sites in four operating rooms from three hospitals in two cities. Following a C-section procedure, we swabbed OR floors, walls, ventilation grids, armrests, and lamps....The bacterial content of OR (operating room) dust corresponded to human skin bacteria, with dominance of Staphylococcus and Corynebacterium. Diversity of bacteria was the highest in the ventilation grids and walls but was also present on top of the surgery lamps. 

We conclude that the dust from ORs, collected right after a C-section procedure, contains deposits of human skin bacteria. The OR microbiota is the first environment for C-section newborns, and OR microbes might be seeding the microbiome in these babies. 

In the present study, we used 16S rRNA gene sequencing to show that OR dust, collected right after a C-section procedure, contains bacteria similar to human skin microbiota. Previous studies using culture-dependent methods also showed that over 85 % of air samples from ORs had skin-like bacteria which were mostly coagulase-negative staphylococci and Corynebacterium. These airborne skin-bacteria could be from individuals present during C-section but could also be shed by cleaning personnel between operations.

In our study, 30 % of samples failed to yield sufficient DNA sequences to be analyzed. While there are no published data on the microbiota in operating rooms using 16S rRNA gene sequencing, very few bacteria (average 3.3–3.5 CFU/10 cm2) were detected in ORs after regular decontamination using standard culturing methods, consistent with the low sequence numbers in our study.

In addition, we found that the microbiota of OR samples was more similar to human skin microbiota than oral microbiota and that OR dust contains deposits of human skin flakes. These results reveal that while the use of surgical masks has limited effectiveness at curtailing oral microbial shedding, skin flakes from individuals present during C-section and/or from cleaning personnel between operations could be a more influential factor contributing to the structure of OR microbiota.

Our SourceTracker analysis results suggest that the OR microbes could play a role in seeding infants born by C-section. C-section born infants, in particular, may be solely receiving this inoculum, while vaginally born infants have exposure to vaginal bacteria. The results of these further studies could be relevant to the possible effects on the priming of the immune system by skin bacteria from environmental sources as the primordial inoculum seeding the infant microbiome. This might be relevant to the increased risk of immune diseases observed in C-section born infants.

Published on Leave a comment on The Appendix Has A Purpose

This new study gives further support for the role of the appendix as a "natural reservoir for 'good' bacteria". The researchers found that a network of immune cells (innate lymphoid cells or ILCs)  safeguard the appendix during a bacterial attack and help the appendix "reseed" the gut microbiome. They also said that a person's diet, such as the proteins in leafy green vegetables, could help produce ILCs. Note that while it is thought that this applies to humans, the research was done on mice. From Medical Xpress:

Immune cells make appendix 'silent hero' of digestive health

New research shows a network of immune cells helps the appendix to play a pivotal role in maintaining the health of the digestive system, supporting the theory that the appendix isn't a vestigial—or redundant—organ.

The research team....found that innate lymphoid cells (ILCs) are crucial for protecting against bacterial infection in people with compromised immune systems. By preventing significant damage and inflammation of the appendix during a bacterial attack, ILCs safeguard the organ and help it to perform an important function in the body, as a natural reservoir for 'good' bacteria.

"Popular belief tells us the appendix is a liability," she said. "Its removal is one of the most common surgical procedures in Australia, with more than 70,000 operations each year. However, we may wish to rethink whether the appendix is so irrelevant for our health. "We've found that ILCs may help the appendix to potentially reseed 'good' bacteria within the microbiome—or community of bacteria—in the body. A balanced microbiome is essential for recovery from bacterial threats to gut health, such as food poisoning."

Professor Belz said having a healthy appendix might even save people from having to stomach more extreme options for repopulating—or 'balancing out'—their microbiomes. "In certain cases, people require reseeding of their intestines with healthy bacteria by faecal transplant—a process where intestinal bacteria is transplanted to a sick person from a healthy individual," Professor Belz said. "Our research suggests ILCs may be able to play this important part in maintaining the integrity of the appendix.

"We found ILCs are part of a multi-layered protective armoury of immune cells that exist in healthy individuals. So even when one layer is depleted, the body has 'back ups' that can fight the infection. "In people who have compromised immune systems—such as people undergoing cancer treatment—these cells are vital for fighting bacterial infections in the gastrointestinal system. This is particularly important because ILCs are able to survive in the gut even during these treatments, which typically wipe out other immune cells."

Professor Belz has previously shown that diet, such as the proteins in leafy green vegetables, could help produce ILCs."ILCs are also known to play a role in allergic diseases, such as asthma; inflammatory bowel disease; and psoriasis," she said. "So it is vital that we better understand their role in the intestine and how we might manipulate this population to treat disease, or promote better health."

Drawing of colon seen from front (appendix is colored red). From Wikipedia.

Published on Leave a comment on One Course of Antibiotics And Your Microbes

New research found that one course of antibiotics (ciprofloxacin, clindamycin, amoxicillin or minocycline) had varying effects on the gut and saliva microbes, with ciprofloxacin having a negative and disruptive effect on gut microbiome diversity up to 12 months. While the microscopic communities living in the mouth rebound quickly, just one course of antibiotics can disrupt the gut microbiome for months - with amoxicillin the least and ciprofloxacin the most (up to a year).The researchers stressed that for these reasons "antibiotics should only be used when really, really necessary. Even a single antibiotic treatment in healthy individuals contributes to the risk of resistance development and leads to long-lasting detrimental shifts in the gut microbiome."

The scary part is that Americans typically take many courses of antibiotics throughout life. And people with conditions such as chronic sinusitis typically take many more than average. From Medical Xpress:

One course of antibiotics can affect diversity of microorganisms in the gut

A single course of antibiotics has enough strength to disrupt the normal makeup of microorganisms in the gut for as long as a year, potentially leading to antibiotic resistance, European researchers reported this week in mBio, an online open-access journal of the American Society for Microbiology. In a study of 66 healthy adults prescribed different antibiotics, the drugs were found to enrich genes associated with antibiotic resistance and to severely affect microbial diversity in the gut for months after exposure. By contrast, microorganisms in the saliva showed signs of recovery in as little as few weeks.

The microorganisms in study participants' feces were severely affected by most antibiotics for months, said lead study author Egija Zaura, PhD, an associate professor in oral microbial ecology at the Academic Centre for Dentistry in Amsterdam, the Netherlands. In particular, researchers saw a decline in the abundance of health-associated species that produce butyrate, a substance that inhibits inflammation, cancer formation and stress in the gut.

"My message would be that antibiotics should only be used when really, really necessary," Zaura said. "Even a single antibiotic treatment in healthy individuals contributes to the risk of resistance development and leads to long-lasting detrimental shifts in the gut microbiome."

It's not clear why the oral cavity returns to normal sooner than the gut, Zaura said, but it could be because the gut is exposed to a longer period of antibiotics. Another possibility, she said, is that the oral cavity is intrinsically more resilient toward stress because it is exposed to different stressors every day.

The investigators enrolled healthy adult volunteers from the United Kingdom and Sweden. Participants were randomly assigned to receive a full course of one of four antibiotics (ciprofloxacin, clindamycin, amoxicillin or minocycline) or a placebo. The researchers, who did not know which medication participants took, collected fecal and saliva samples from the participants at the start of the study; immediately after taking the study drugs; and one, two, four and 12 months after finishing the medications....

Researchers found that participants from the United Kingdom started the study with more antibiotic resistance than did the participants from Sweden, which could result from cultural differences. There has been a significant decline in antibiotic use in Sweden over the last two decades, Zaura said.

In addition, fecal microbiome diversity was significantly reduced for up to four months in participants taking clindamycin and up to 12 months in those taking ciprofloxacin, though those drugs only altered the oral cavity microbiome up to one week after drug exposure. Exposure to amoxicillin had no significant effect on microbiome diversity in either the gut or oral cavity but was associated with the greatest number of antibiotic-resistant genes.

Gut bacteria. Credit: Med. Mic. Sciences Cardiff Univ, Wellcome Images

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 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.

Published on

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 Could a Big Weight Loss Prevent Some Cancers?

 The important thing learned from this study is that 10% of the obese women had precancerous uterine growths (remember that obesity results in inflammation which can lead to cancer) that regressed and disappeared after the weight loss. Along with weight loss (mean loss was over 100 pounds), there was an alteration of the their gut bacteria. It was a small group of women, but very, very interesting that precancerous growths could disappear simply with reducing weight. From Medical Xpress:

Preventing cancer: Study finds dramatic benefits of weight-loss surgery

A study evaluating the effects of bariatric surgery on obese women most at risk for cancer has found that the weight-loss surgery slashed participants' weight by a third and eliminated precancerous uterine growths in those that had them. Other effects included improving patients' physical quality of life, improving their insulin levels and ability to use glucose - which may reduce their risk for diabetes - and even altering the composition of their gut bacteria.

The study speaks both to the benefits of bariatric surgery and to the tremendous toll obesity takes on health. "If you look at cancers in women, about a fifth of all cancer deaths would be prevented if we had women at normal body weight in the U.S.," said Susan C. Modesitt, MD, of the University of Virginia Cancer Center. "When you're looking at obesity-related cancers, the biggest one is endometrial cancer, but also colon cancer, breast cancer, renal cancer and gall bladder cancer. We think about 40 [percent] to 50 percent of all endometrial cancer, which is in the lining of the uterus, is caused by obesity."

The study looked at 71 women with a mean age of 44.2 years and a mean body mass index (BMI) of 50.9. Women are considered obese at a BMI of 30 and morbidly obese at 40 (which is typically about 100 pounds over a woman's ideal body weight). The study looked at the effects of bariatric surgery in a relatively short time frame, one to three years after surgery. A total of 68 participants underwent the procedure; two opted out of the surgery, and another died of a heart condition prior to surgery. The effects of surgery on body weight were dramatic: Mean weight loss was more than 100 pounds.

Ten percent of study participants who had not had a hysterectomy showed precancerous changes in the lining of the uterus, and all of those resolved with weight loss. "We're talking about small numbers, really tiny numbers" of study participants, Modesitt said, noting one limitation of the study. "So I could never say that effect is definitive, but it is suggestive, given that we know already the incredibly strong link between endometrial cancer and obesity."

Modesitt, of the UVA's Division of Gynecologic Oncology in the Department of Obstetrics and Gynecology, was most surprised by the dramatic changes seen in the patients' metabolic profiles derived from the gut microbiome, the population of microorganisms living inside us. "The study results demonstrate that there is a huge alteration, but I don't even know what to say about that, except it is really new and intriguing area to look at in the link between obesity and cancer.

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.