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Category: human microbiome

Published on Leave a comment on The Effects of Low Fiber Diet Over Generations

A recent study using mice, and following them for 4 generations, has implications for Americans who typically eat a low-fiber diet (average of 15 grams daily). Note that current dietary guidelines recommend that women should eat around 25 grams and men 38 grams daily of fiber. The researchers found that low-fiber diets not only deplete the complex microbial ecosystems residing in the gut, but can cause an irreversible loss of diversity within those ecosystems in as few as three or four generations.

This is because fiber feeds the millions of microbes in the gut - and so a fiber-rich diet can nourish a wide variety of gut microbes, but a low-fiber diet can only sustain a narrower community. As the generations went by, the rodents’ guts became progressively less diverse, as more and more species were extinguished. If the fourth-generation mice switched to high-fiber meals, some of the missing microbes rebounded, but most did not. It took a fecal transplant (mice style) to get back the missing microbes. From Science Daily:

Low-fiber diet may cause irreversible depletion of gut bacteria over generations

A study by Stanford University School of Medicine investigators raises concerns that the lower-fiber diets typical in industrialized societies may produce internal deficiencies that get passed along to future generations. The study, conducted in mice, indicates that low-fiber diets not only deplete the complex microbial ecosystems residing in every mammalian gut, but can cause an irreversible loss of diversity within those ecosystems in as few as three or four generations.

Once an entire population has experienced the extinction of key bacterial species, simply "eating right" may no longer be enough to restore these lost species to the guts of individuals in that population, the study suggests. Those of us who live in advanced industrial societies may already be heading down that path.

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 Bacterial Communities Vary Between the Sinuses In People With Chronic Sinusitis

New research that found that microbial communities vary between the sinuses in a person with chronic sinusitis. This is a result that many sinusitis sufferers already suspect based on their sinusitis symptoms. The researchers also found that bacterial communities in the sinuses vary between people with chronic sinusitis. It is frustrating though for me to read study after study where the researchers focus on describing the types of bacteria found in chronic sinusitis sufferers (and then just saying that the sinus microbiomes or community of microbes vary from person to person) rather than studies comparing the sinus microbiomes (bacteria and other microbes, such as fungi) between healthy individuals and sinusitis sufferers.

Since research finds that sinusitis sufferers have altered sinus microbiomes, then what would be really helpful now is finding more beneficial or keystone species (besides Lactobacillus sakei) that are needed for healthy sinus microbiomes. This would be an important step towards then adding (perhaps using a nasal spray) these missing microbes to the sinus microbiome. From Frontiers in Microbiology:

Bacterial communities vary between sinuses in chronic rhinosinusitis patients

ABSTRACT: Chronic rhinosinusitis (CRS) is a common and potentially debilitating disease characterized by inflammation of the sinus mucosa for longer than 12 weeks. Bacterial colonization of the sinuses and its role in the pathogenesis of this disease is an ongoing area of research. Recent advances in culture-independent molecular techniques for bacterial identification have the potential to provide a more accurate and complete assessment of the sinus microbiome, however there is little concordance in results between studies, possibly due to differences in the sampling location and techniques. This study aimed to determine whether the microbial communities from one sinus could be considered representative of all sinuses, and examine differences between two commonly used methods for sample collection, swabs and tissue biopsies. High-throughput DNA sequencing of the bacterial 16S rRNA gene was applied to both swab and tissue samples from multiple sinuses of 19 patients undergoing surgery for treatment of CRS. Results from swabs and tissue biopsies showed a high degree of similarity, indicating that swabbing is sufficient to recover the microbial community from the sinuses. Microbial communities from different sinuses within individual patients differed to varying degrees, demonstrating that it is possible for distinct microbiomes to exist simultaneously in different sinuses of the same patient. The sequencing results correlated well with culture-based pathogen identification conducted in parallel, although the culturing missed many species detected by sequencing. This finding has implications for future research into the sinus microbiome, which should take this heterogeneity into account by sampling patients from more than one sinus. It may also be of clinical importance, as determination of antibiotic sensitivities using culture of a swab from a single sinus could miss relevant pathogens that are localized to another sinus.

CRS can be a debilitating condition that is recalcitrant to treatment. Bacterial colonization of the sinuses is likely to play an important role in the pathogenesis and perpetuation of the disease; however different studies have yielded contrasting results with respect to which bacterial taxa are characteristic of the disease (ref). We observed bacterial communities dominated by different taxa in CRS patients; for example some have sinuses colonized primarily with Haemophilus, while others are dominated by Corynebacterium and Staphylococcus, or Pseudomonas. Some patients’ sinuses contain anaerobic bacteria such as Anaerococcus, Finegoldia, and Peptoniphilus, while these were absent from others. Indeed, our results have shown, for the first time, that it is possible for a patient to simultaneously have different bacterial communities in different sinuses, pointing to distinct, localized microbiomes within the same patient. Understanding this variation in the sinus microbiome could prove critical to the appropriate selection of treatments for CRS in the future.

The weighted unifrac distances between samples within patients (Figure 1) demonstrate that at least some CRS patients have substantial variation of bacterial communities between sinuses, although it is significantly smaller than the variation observed between different individuals. While this variation was related to abundance rather than the presence or absence of dominant community members, some of these variations were large: for example Corynebacterium sequences dominating the right sinuses of patient 003 (60.7 and 41.7% of all sequences), while the left sinuses had much smaller abundances (9.8 and 6.2%) and were dominated by the anaerobic bacteria Anaerococcus, Finegoldia  and Peptinophillus.

Published on Leave a comment on Beneficial Bacteria In the Nose

Could the bacteria described in this research be another probiotic or beneficial bacteria (besides Lactobacillus sakei) that helps protect against sinusitis? New research found that the harmless bacteria Corynebacterium accolens is "overrepresented" in children free of Streptococcus pneumoniae (pneumococcus) -  which commonly colonizes in children's noses (and that can live harmlessly as part of a healthy microbiome), but it is also an important infectious agent. Streptococcus pneumoniae is a major cause of pneumonia, septicemia, meningitis, otitis media (ear infections), and sinusitis in children and adults worldwide.

The researchers did an analysis on the microbes in the nasal passages of children and found that the nasopharyngeal (nostrils) microbiome was different in children with and without pneumococcal nasopharyngeal colonization. This revealed that Corynebacterium species and Dolosigranulum were "overrepresented" in children negative for pneumococcal colonization, whereas Streptococcus was "overrepresented" in children positive for Streptococcus  pneumoniae colonization.

The researchers found that higher numbers of  Corynebacterium accolens cells deter and limit S. pneumoniae nostril colonization, which might partly explain why children without S. pneumoniae colonization have higher levels of nasal Corynebacterium species. The researchers write that "there is direct antagonism" between Corynebacterium spp. and S. pneumoniae in the human nose. How do children get this beneficial bacteria? Interestingly, at 6 weeks of age, Corynebacterium species. and Dolosigranulum species are also "overrepresented" in the nasopharyngeal microbiota of breastfed infants compared to formula-fed infants. From Science Daily:

Good bacteria might help prevent middle ear infections, pneumonia

A new study is helping to shed more light on the important connections among the diverse bacteria in our microbiome. According to research published in mBio, scientists at Forsyth, led by Dr. Katherine P. Lemon, along with their collaborator at Vanderbilt University, have demonstrated that a harmless bacterium found in the nose and on skin may negatively impact the growth of a pathogen that commonly causes middle ear infections in children and pneumonia in children and older adults.

This study provides the first evidence that Corynebacterium accolens, a harmless bacterial species that commonly colonizes the nose, can help inhibit Streptococcus pneumoniae (S. pneumoniae) -- a major cause of pneumonia, meningitis, middle ear infection and sinusitis. According to the World Health Organization, S. pneumoniae leads to more than 1 million deaths each year, primarily in young children in developing countries. Although most people that host S. pneumoniae do not develop these infections, colonization greatly increases the risk of, and is a perquisite for, infection and transmission.

The study, titled, "Corynebacterium accolens (C. accolens) Releases Antipneumococcal Free Fatty Acids from Human Nostril and Skin Surface Triacylglycerols," is published on January 5, 2016 in mBio. In this study, first-author Dr. Lindsey Bomar and her colleagues show that C. accolens are overrepresented in the noses of children that are not colonized by S. pneumoniae, which is commonly found in children's noses and can cause infection. In laboratory research, the team further found that C. accolens modifies its local habitat in a manner that inhibits the growth of S. pneumoniae by releasing antibacterial free fatty acids from representative host skin surface triacylglycerols. The team went on to identify the C. accolens enzyme needed for this. These results pave the way for potential future research to determine whether C. accolens might have role as a beneficial bacterium that could be used to control pathogen colonization.

Published on Leave a comment on Periodontal Disease Associated With Increased Breast Cancer Risk

Image result for teeth, wikipedia Research found that postmenopausal women with periodontal disease (gum disease) were more likely to develop breast cancer than women who did not have the chronic inflammatory disease. And it's a bigger risk among those who currently smoke or quit smoking within the last 20 years. The interesting part is the fact that periodontal disease is a bacterial disease and that it results in inflammation. An earlier post discussed research that found that the human breast microbiome (microbial community) and specifically the bacteria, is different in healthy breasts (in the breast tissue) as compared to cancerous breasts. From Science Daily:

Periodontal disease associated with increased breast cancer risk in postmenopausal women

Postmenopausal women with periodontal disease were more likely to develop breast cancer than women who did not have the chronic inflammatory disease. A history of smoking significantly affected the women's risk, researchers report. Periodontal disease is a common condition that has been associated with heart disease, stroke, and diabetes. Previous research has found links between periodontal disease and oral, esophageal, head and neck, pancreatic, and lung cancers, so the researchers wanted to see if there was any relationship with breast cancer.

Jo L. Freudenheim, PhD, and colleagues monitored 73,737 postmenopausal women enrolled in the Women's Health Initiative Observational Study, none of whom had previous breast cancer. Periodontal disease was reported in 26.1 percent of the women. Because prior studies have shown that the effects of periodontal disease vary depending on whether a person smokes, researchers examined the associations stratified by smoking status.

After a mean follow-up time of 6.7 years, 2,124 women were diagnosed with breast cancer. The researchers found that among all women, the risk of breast cancer was 14 percent higher in women who had periodontal disease.

Among women who had quit smoking within the past 20 years, those with periodontal disease had a 36 percent higher risk of breast cancer. Women who were smoking at the time of this study had a 32 percent higher risk if they had periodontal disease, but the association was not statistically significant. Those who had never smoked and had quit more than 20 years ago had a 6 percent and 8 percent increased risk, respectively, if they had periodontal disease.

"We know that the bacteria in the mouths of current and former smokers who quit recently are different from those in the mouths of non-smokers," Freudenheim explained. One possible explanation for the link between periodontal disease and breast cancer is that those bacteria enter the body's circulation and ultimately affect breast tissue. However, further studies are needed to establish a causal link, Freudenheim said.

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