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Oxygen therapy harms lung microbiome in mice: Study could have implications for treatment of reduced oxygen levels in critically ill patients -- ScienceDaily

"When we gave high concentrations of oxygen to healthy mice, their lung communities changed quickly, and just like we predicted," said Ashley. "The oxygen-intolerant bacteria went down, and the oxygen-tolerant bacteria went up." After three days of oxygen therapy, oxygen-tolerant Staphylococcus was by far the most commonly detected bacteria in mouse lungs. The team next designed experiments to answer a key "chicken or the egg" question: do these altered bacterial communities contribute to lung injury? Or are bacterial communities altered because the lung is injured? They first addressed this by comparing the relative timing of changes in lung bacteria as compared to the onset of lung injury. Using mice, they were able to demonstrate that while the lung microbiome was changed by high oxygen concentrations after only a day, lung injury wasn't detectable until after 3 days, proving that damage to the lung followed the disruption of the microbiome, and not the other way around. Furthermore, they showed that natural variation in lung bacteria was strongly correlated with variation in the severity of inflammation in oxygen-exposed mice.

Unparalleled inventory of the human gut ecosystem -- ScienceDaily

"Last year, three independent teams, including ours, reconstructed thousands of gut microbiome genomes. The big questions were whether these teams had comparable results, and whether we could pool them into a comprehensive inventory," says Rob Finn, Team Leader at EMBL-EBI. The scientists have now compiled 200,000 genomes and 170 million protein sequences from more than 4 600 bacterial species in the human gut. Their new databases, the Unified Human Gastrointestinal Genome collection and the Unified Gastrointestinal Protein catalogue, reveal the tremendous diversity in our guts and pave the way for further microbiome research. "This immense catalogue is a landmark in microbiome research, and will be an invaluable resource for scientists to start studying and hopefully understanding the role of each bacterial species in the human gut ecosystem," explains Nicola Segata, Principal Investigator at the University of Trento. The project revealed that more than 70% of the detected bacterial species had never been cultured in the lab -- their activity in the body remains unknown. The largest group of bacteria that falls into that category is the Comantemales, an order of gut bacteria first described in 2019 in a study led by the Bork Group at EMBL Heidelberg. "It was a real surprise to see how widespread the Comantemales are. This highlights how little we know about the bacteria in our gut," explains Alexandre Almeida, EMBL-EBI/Sanger Postdoctoral Fellow in the Finn Team. "We hope our catalogue will help bioinformaticians and microbiologists bridge that knowledge gap in the coming years." A freely accessible data resource All the data collected in the Unified Human Gastrointestinal Genome collection and the Unified Human Gastrointestinal Protein catalogue are freely available in MGnify, an EMBL-EBI online resource that allows scientists to analyse their microbial genomic data and make comparisons with existing datasets.

Microbes might manage your cholesterol: Researchers discover mysterious bacteria that break down cholesterol in the gut -- ScienceDaily

Then Kenny narrowed their search further. In the lab, he inserted each potential gene into bacteria and tested which made enzymes to break down cholesterol into coprostanol. Eventually, he found the best candidate, which the team named the Intestinal Steroid Metabolism A (IsmA) gene. "We could now correlate the presence or absence of potential bacteria that have these enzymes with blood cholesterol levels collected from the same individuals," said Xavier. Using human microbiome data sets from China, Netherlands and the United States, they discovered that people who carry the IsmA gene in their microbiome had 55 to 75 percent less cholesterol in their stool than those without. "Those who have this enzyme activity basically have lower cholesterol," Xavier said.

Your microbiome may change how drugs affect you, research confirms

For the Cell study, the researchers grew the microbes from a patient’s fecal matter in test tubes. They added one of 575 drugs in separate tubes and waited to see if the microbiome had an effect — and in particular, whether it rendered the drug inactive or even changed it into a more toxic substance, which could trigger side effects in a patient. The gut microbes broke down capecitabine very differently from the way it is processed by the liver, for example. While scientists had already observed that capecitabine often affects patients differently, how and if it was broken down by the microbiome was unknown before this study, and the new findings could shed light on those variations. The authors used 20 more patient fecal samples to test differences between how individual patients’ gut microbes break down the same drug, examining 23 drugs from the first experiment. There were huge differences between patients — some drugs were only broken down by one patient. Only three patients broke down digoxin, a drug used to treat arrhythmia, for example — suggesting that the other patients might not see the same benefit or side effects from the drug.

Viruses from feces can help combat obesity and diabetes -- ScienceDaily

In recent years, faecal transplants from healthy donors to sick patients have become a popular way of treating a serious type of diarrhea caused by the bacterium Clostridioides difficile in humans. Recent trials in mice suggest that a similar treatment, in which only the virus in stool is transplanted, may help people suffering from obesity and type 2 diabetes. The majority of virus particles transmitted are so-called bacteriophages -- viruses that specifically attack other bacteria and not humans. "When we transmit virus particles from the faeces of lean mice to obese ones, the obese mice put on significantly less weight compared to those that do not receive transplanted faeces," says Professor with Special Responsibilities (MSO) and senior author of the study, Dennis Sandris Nielsen of the University of Copenhagen's Department of Food Science.

Gut communicates with the entire brain through cross-talking neurons -- ScienceDaily

"We saw a lot of connections in the brainstem and hindbrain regions. We knew these regions are involved in sensing and controlling the organs of the body, so there weren't any big surprises there. But things got more interesting as the viruses moved farther up into parts of the brain that are usually considered emotional centers or learning centers, cognitive places. They have all these multifaceted functions. So thinking about how information from the small intestine might be nudging those processes a little bit is really cool," says Coltan Parker, doctoral student in the Neuroscience Program at Illinois and lead author on a study published in Autonomic Neuroscience: Basic and Clinical.

Diet, nutrition have profound effects on gut microbiome -- ScienceDaily

The authors found that research has mostly focused on the benefits of dietary fiber, which serves as fuel for gut microbiota, and also found that, in contrast, protein promotes microbial protein metabolism and potentially harmful byproducts that may sit in the gut, increasing the risk of negative health outcomes.

More than just a carnival trick: Researchers can guess your age based on your microbes -- ScienceDaily

Given a microbiome sample (skin, mouth or fecal swab), researchers have demonstrated they can now use machine learning to predict a person's chronological age, with a varying degree of accuracy. Skin samples provided the most accurate prediction, estimating correctly to within approximately 3.8 years, compared to 4.5 years with an oral sample and 11.5 years with a fecal sample. The types of microbes living in the oral cavity or within the gut of young people (age 18 to 30 years old) tended to be more diverse and abundant than in comparative microbiomes of older adults (age 60 years and older).[…]

How Mucus Tames Microbes – NIH Director's Blog

The researchers found that in the presence of glycans, P. aeruginosa was rendered less harmful and infectious. The bacteria also produced fewer toxins. The findings show that it isn’t just that microbes get trapped in a tangled web within mucus, but rather that glycans have a special ability to moderate the bugs’ behavior. The researchers also have evidence of similar interactions between mucus and other microorganisms, such as those responsible for yeast infections.

Fatty meal interrupts gut's communication with the body, but why? If that second helping of prime rib stuns your gut into silence, is that good or bad? -- ScienceDaily

These cells produce at least 15 different hormones to send signals to the rest of the body about gut movement, feelings of fullness, digestion, nutrient absorption, insulin sensitivity and energy storage. "But they fall asleep on the job for a few hours after a high-fat meal, and we don't yet know if that's good or bad," said John Rawls, an associate professor of molecular genetics and microbiology in the Duke School of Medicine. Since enteroendocrine cells are key players in digestion, the feeling of being full and subsequent feeding behavior, this silencing may be a mechanism that somehow causes people eating a high-fat diet to eat even more. "This is a previously unappreciated part of the postprandial (after-meal) cycle," Rawls said. "If this happens every time we eat an unhealthy, high-fat meal, it might cause a change in insulin signaling, which could in turn contribute to the development of insulin resistance and Type 2 diabetes."

Asthma severity linked to microbiome of upper airway - ScienceBlog.com

The researchers found that children who experienced early warning signs that their asthma was going to flare up were more likely to have bacteria associated with disease — including Staphylococcus, Streptococcus and Moraxella bacterial groups — living in their upper airways. In contrast, airway microbes dominated by Corynebacterium and Dolosigranulum bacteria were associated with periods of good health, when asthma was well-controlled.

Teams of Microbes Are at Work in Our Bodies. Researchers Have Figured Out What They’re up to. - ScienceBlog.com

“We call this method ‘themetagenomics,’ because we are looking for recurring themes in microbiomes that are indicators of co-occurring groups of microbes,” Rosen said. “There are thousands of species of microbes living in the body, so if you think about all the permutations of groupings that could exist you can imagine what a daunting task it is to determine which of them are living in community with each other. Our method puts a pattern-spotting algorithm to work on the task, which saves a tremendous amount of time and eliminates some guesswork.”

Association of Dietary Fiber and Yogurt Consumption With Lung Cancer Risk: A Pooled Analysis | Lifestyle Behaviors | JAMA Oncology | JAMA Network

The analytic sample included 627 988 men, with a mean (SD) age of 57.9 (9.0) years, and 817 862 women, with a mean (SD) age of 54.8 (9.7) years. During a median follow-up of 8.6 years, 18 822 incident lung cancer cases were documented. Both fiber and yogurt intakes were inversely associated with lung cancer risk after adjustment for status and pack-years of smoking and other lung cancer risk factors: hazard ratio, 0.83 (95% CI, 0.76-0.91) for the highest vs lowest quintile of fiber intake; and hazard ratio, 0.81 (95% CI, 0.76-0.87) for high vs no yogurt consumption. The fiber or yogurt associations with lung cancer were significant in never smokers and were consistently observed across sex, race/ethnicity, and tumor histologic type. When considered jointly, high yogurt consumption with the highest quintile of fiber intake showed more than 30% reduced risk of lung cancer than nonyogurt consumption with the lowest quintile of fiber intake (hazard ratio, 0.67 [95% CI, 0.61-0.73] in total study populations; hazard ratio 0.69 [95% CI, 0.54-0.89] in never smokers), suggesting potential synergism.

Transient and long-term disruption of gut microbes after antibiotics - ScienceBlog.com

In contrast, the triple-antibiotics individuals showed a significant increase of new strains that persisted as long as six months after treatment, as compared to the single antibiotic and the control individuals. Furthermore, the fraction of transient strains was also significantly higher in the multiple antibiotics individuals. This suggested a long-term change to an alternative stable microbiome state, Morrow says. These changes were not due to a difference in growth rates. “Given the importance of the microbiome in human health, we think our results with these data sets can be used to help evaluate microbiome stability under different conditions,” Morrow said. “For example, we can now provide guidance to clinical investigators to judge the impact of certain treatments for diseases, such as cancer or diabetes, on the gut microbial community that could be significant for evaluation of outcomes. Furthermore, this approach could be applied to a patient’s pre- and post-hospitalization to identify individuals who may need further management of their microbiomes.”

A reliable clock for your microbiome: Genetic oscillator records changes in microbiome growth patterns in vivo -- ScienceDaily

The system uses an oscillating gene circuit, called a repressilator, as a kind of genetic clock to measure bacterial growth. The repressilator consists of three bacterial genes that code for three proteins (tetR, cl, and lacI), each of which blocks the expression of one of the other proteins. The genes are linked into a negative feedback loop, so that when the concentration of one of the repressor proteins falls below a certain level, the protein it had been repressing is expressed, which blocks the expression of the third protein, and the process repeats in a cyclical fashion. When all three genes are inserted into a plasmid and introduced into bacteria, the number of negative feedback loop cycles completed can serve as a record of how many cell divisions the bacteria have undergone. Every time the bacteria divide, any repressor proteins present in their cytoplasm are diluted, so their concentration gradually falls and triggers the expression of the next protein in the repressilator cycle. Crucially, the repressilator cycle repeats after 15.5 bacterial generations regardless of how quickly or slowly the bacteria are growing. This allows it to act as an objective measurement of time, much like a clock or a watch.

Gut bacteria 'fingerprint' predicts radiotherapy side effects: First clinical study to show link between types of gut bacteria and radiotherapy-induced gut damage -- ScienceDaily

The researchers found that patients who had a high risk of gut damage had 30-50 per cent higher levels of three bacteria types, and lower overall diversity in their gut microbiome, than patients who had not undergone any radiotherapy. This suggests that patients with less diverse gut microbiomes and high levels of the bacteria -- Clostridium IV, Roseburia and Phascolarctobacterium -- are more susceptible to gut damage. The researchers also believe these patients may require more 'good bacteria' to maintain a healthy gut -- and so may be more susceptible to side effects when these bacteria are killed by radiation.

Molecule links weight gain to gut bacteria -- ScienceDaily

The study also found that microbes program these so-called circadian rhythms by activating a protein named histone deacetylase 3 (HDAC3), which is made by cells that line the gut. Those cells act as intermediaries between bacteria that aid in digestion of food and proteins that enable absorption of nutrients. The study, done in mice, revealed that HDAC3 turns on genes involved in the absorption of fat. They found that HDAC3 interacts with the biological clock machinery within the gut to refine the rhythmic ebb and flow of proteins that enhance absorption of fat. This regulation occurs in the daytime in humans, who eat during the day, and at night in mice, which eat at night. "The microbiome actually communicates with our metabolic machinery to make fat absorption more efficient. But when fat is overabundant, this communication can result in obesity. Whether the same thing is going on in other mammals, including humans, is the subject of future studies," added lead author Dr. Zheng Kuang, a postdoctoral fellow in the Hooper laboratory.

Researchers alter mouse gut microbiomes by feeding good bacteria their preferred fibers -- ScienceDaily

"Fiber is understood to be beneficial. But fiber is actually a very complicated mixture of many different components," says senior author Jeffrey Gordon, a microbiologist at the Washington University School of Medicine in St. Louis. "Moreover, fibers from different plant sources that are processed in different ways during food manufacturing have different constituents. Unfortunately, we lack detailed knowledge of these differences and their biological significance. We do know that modern Western diets have low levels of fiber; this lack of fiber has been linked to loss of important members of the gut community and deleterious health effects." The researchers started by testing 34 food-grade fiber preparations, many purified from byproducts of food manufacturing such as peels from fruits and vegetables that are thrown out during production of processed foods and drinks. They used mice initially raised under sterile conditions and then colonized with human gut microbes. The animals were fed a high-fat, low-fiber diet representative of diets typically consumed in the United States, with or without different types of supplemental fibers. The goal was to identify those fibers that were best at boosting the levels of key fiber-degrading bacterial species and promoting the expression of beneficial metabolic enzymes in the microbiome.

Microbiome may be involved in mechanisms related to muscle strength in older adults -- ScienceDaily

To gain insight into this population, the researchers compared bacteria from the gut microbiomes of 18 older adults with high-physical function and a favorable body composition (higher percentage of lean mass, lower percentage of fat mass) with 11 older adults with low-physical function and a less favorable body composition. The small study identified differences in the bacterial profiles between the two groups. Similar bacterial differences were present when mice were colonized with fecal samples from the two human groups, and grip strength was increased in mice colonized with samples from the high-functioning older adults, suggesting a role for the gut microbiome in mechanisms related to muscle strength in older adults. Specifically, when compared to the low-functioning older adult group, the researchers found higher levels of Prevotellaceae, Prevotella, Barnesiella, and Barnesiella intestinihominis -- all potentially good bacteria -- in the high-functioning older adults and in the mice that were colonized with fecal samples from the high-functioning older adults.

Short-term study suggests vegan diet can boost gut microbes related to body weight, body composition and blood sugar control -- ScienceDaily

The study included 147 participants (86% women and 14% men; mean age was 55.6±11.3 years), who were randomised to follow a low-fat vegan diet (n=73) or to make no changes to their diet (n=74) for 16 weeks. At baseline and 16 weeks, gut microbiota composition was assessed, using uBiome kits. Dual energy X-ray absorptiometry was used to measure body composition. A standard method called the PREDIM index was used to assess insulin sensitivity. Following the 16-week study, body weight was reduced significantly in the vegan group (treatment effect average -5.8 kg), particularly due to a reduction in fat mass (average -3.9 kg) and in visceral fat. Insulin sensitivity also increased significantly in the vegan group. The relative abundance of Faecalibacterium prausnitzii increased in the vegan group (treatment effect +4.8%). Relative changes in Faecalibacterium prausnitzii were associated with decreases in body weight, fat mass and visceral fat. The relative abundance of Bacteoides fragilis also increased in the vegan group (treatment effect +19.5%). Relative changes in Bacteroides fragilis were associated with decreases in body weight, fat mass and visceral fat, and increases in insulin sensitivity.

Microbiota-Nourishing Immunity: A Guide to Understanding Our Microbial Self - ScienceDirect

Here we discuss the concept of microbiota-nourishing immunity, a host-microbe chimera composed of the microbiota and host factors that shape the microbial ecosystem, which functions in conferring colonization resistance against pathogens. We propose that dysbiosis is a biomarker of a weakening in microbiota-nourishing immunity and that homeostasis can be defined as a state of immune competence.

Mapping human microbiome drug metabolism by gut bacteria and their genes | Nature

Individuals vary widely in their responses to medicinal drugs, which can be dangerous and expensive owing to treatment delays and adverse effects. Although increasing evidence implicates the gut microbiome in this variability, the molecular mechanisms involved remain largely unknown. Here we show, by measuring the ability of 76 human gut bacteria from diverse clades to metabolize 271 orally administered drugs, that many drugs are chemically modified by microorganisms.

The 'pathobiome' -- a new understanding of disease -- ScienceDaily

The concept acknowledges that all organisms are in fact complex communities of viruses, microbes and other small organisms (e.g. parasites) which can interact to affect health or disease status at any given time. These complex communities continually interact with their hosts, sometimes conferring benefits (e.g. "good" bacteria in the human gut microbiome), and at other times causing harm by contributing to disease. When these communities combine to cause disease they are termed "pathobiomes" -- a recognition of their collective shift away from the healthy-state "symbiome."

Study shows how serotonin and a popular anti-depressant affect the gut's microbiota -- ScienceDaily

The team -- led by senior author Elaine Hsiao and lead author Thomas Fung, a postdoctoral fellow -- identified a specific gut bacterium that can detect and transport serotonin into bacterial cells. When mice were given the antidepressant fluoxetine, or Prozac, the biologists found this reduced the transport of serotonin into their cells. This bacterium, about which little is known, is called Turicibacter sanguinis. The study is published this week in the journal Nature Microbiology. "Our previous work showed that particular gut bacteria help the gut produce serotonin. In this study, we were interested in finding out why they might do so," said Hsiao, UCLA assistant professor of integrative biology and physiology, and of microbiology, immunology and molecular genetics in the UCLA College; and of digestive diseases in the David Geffen School of Medicine at UCLA. Hsiao and her research group reported in the journal Cell in 2015 that in mice, a specific mixture of bacteria, consisting mainly of Turicibacter sanguinis and Clostridia, produces molecules that signal to gut cells to increase production of serotonin. When Hsiao's team raised mice without the bacteria, more than 50% of their gut serotonin was missing. The researchers then added the bacteria mixture of mainly Turicibacter and Clostridia, and their serotonin increased to a normal level.

Gut bacteria may be linked to high blood pressure and depression -- ScienceDaily

The researchers isolated DNA (deoxyribonucleic acid, the carrier of genetic information) from gut bacteria obtained from the stool samples of 105 volunteers. They used a new technique involving artificial-intelligence software to analyze the bacteria, which revealed four distinct types of bacterial genes and signature molecules. Surprisingly, the investigators discovered unique patterns of bacteria from people with 1) high blood pressure plus depression; 2) high blood pressure without depression; 3) depression with healthy blood pressure; or 4) healthy subjects without depression or high blood pressure.

Diet's effect on gut bacteria could play role in reducing Alzheimer's risk -- ScienceDaily

In a small pilot study, the researchers identified several distinct gut microbiome signatures -- the chemicals produced by bacteria -- in study participants with mild cognitive impairment (MCI) but not in their counterparts with normal cognition, and found that these bacterial signatures correlated with higher levels of markers of Alzheimer's disease in the cerebrospinal fluid of the participants with MCI. Through cross-group dietary intervention, the study also showed that a modified Mediterranean-ketogenic diet produced changes in the gut microbiome and its metabolites that correlated with reduced levels of Alzheimer's markers in the members of both study groups.