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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.

High-fat diet and gut bacteria linked to insulin resistance -- ScienceDaily

Overall, the research highlights a robust connection between high fat diets, obesity and the lack of gut IgA in promoting inflammation and insulin resistance. The knowledge that this class of antibodies regulate pathogenic bacteria, and protects against a "leaky gut," and additional complications of obesity, is a powerful tool in the fight against diabetes.

Rye is healthy, thanks to an interplay of microbes -- ScienceDaily

Many of the compounds found in rye are processed by gut bacteria before getting absorbed into the body. The study found that gut microbes and microbes found in sourdough produce compounds that are partially the same. However, gut microbes also produce derivatives of trimethylglycine, also known as betaine, contained in rye. An earlier study by the research group has shown that at least one of these derivatives reduces the need for oxygen in heart muscle cells, which may protect the heart from ischemia or possibly even enhance its performance. The findings can explain some of the health benefits of rye, including better blood sugar levels and a lower risk of cardiovascular diseases.

Bread Affects Clinical Parameters and Induces Gut Microbiome-Associated Personal Glycemic Responses: Cell Metabolism

numerous individuals exhibit opposite PPGRs to white and sourdough bread (Figure 4A). This result is further supported by previous evidence regarding the high interpersonal variability in PPGRs to real-life meals (Zeevi et al., 2015).

Bread Affects Clinical Parameters and Induces Gut Microbiome-Associated Personal Glycemic Responses: Cell Metabolism

Several studies indicated that even short-term dietary interventions, whether animal-based, plant-based (David et al., 2014), or involving barley bread consumption (Kovatcheva-Datchary et al., 2015), result in significant, rapid, and reproducible alterations to the gut microbiome.

Diet rapidly and reproducibly alters the human gut microbiome | Nature

Here we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression. The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila and Bacteroides) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium rectale and Ruminococcus bromii). Microbial activity mirrored differences between herbivorous and carnivorous mammals2, reflecting trade-offs between carbohydrate and protein fermentation.

Antibiotics Resistance: Scientists Develop Algorithm-Based Technique To Personalize Antibiotic Treatments

“It is now possible to computationally predict the level of bacterial resistance for infection-causing bacteria. This is done by weighing of demographic data, including age, gender, pregnancy … together with levels of resistance [which are] measured in the patient’s previous urine cultures as well as their drug purchase history,” Israel Hayom quoted Yelin. For the research, the scientists analyzed over 700,000 urine cultures. Then they focussed on urine tract infections that involve various types of bacteria, including E. coli, Klebsiella pneumonia and Proteus mirabilis. The researchers then developed an algorithm, which was based on antibiotic purchases made in the past 10 years for over five million cases. The algorithm provided treatment recommendations based on the infection’s antibiotics resistance.

Link found between gut bacteria, successful joint replacement -- ScienceDaily

In normal mice, immune system markers in the bloodstream rise during an infection, as the body responds. But in the study, these markers did not rise in mice with unhealthy microbiomes that also developed infections. The results suggest that mice with unhealthy microbiomes may have compromised immune systems.

Computational tool predicts how gut microbiome changes over time: New insights into gut microbiome dynamics could lead to better diagnosis, treatment of disease -- ScienceDaily

The researchers then used MTV-LMM to surface new insights into microbiome dynamics. For instance, they demonstrated that, in both infants and adults, gut microbiome community composition can indeed be accurately predicted based on earlier observations of the community. They also applied the model to data from 39 infants and revealed a key shift around the age of 9 months in how the gut microbiome changes over time.

Performance-enhancing bacteria found in the microbiomes of elite athletes: Introducing this bacteria to sedentary individuals improves exercise capacity -- ScienceDaily

Colonies of bacteria residing in our guts have a powerful impact on our health. Exercise is an important component of a healthy lifestyle meant to ward off diseases such as type 2 diabetes. Many people with metabolic disorders are not able to exercise at the level needed to see such benefits. Supplementing their microbiome using a probiotic capsule containing Veillonella could give them the boost they need for effective exercise. (Direct dosing with propionate pill would not work, as the short chain fatty acid would be broken down by digestive juices before it could take effect.) Dr. Scheiman has since spun this idea off into a company targeted at athletes. "The microbiome is such a powerful metabolic engine," says Dr. Kostic. This is one of the first studies to directly show a strong example of symbiosis between microbes and their human host. "It's very clear. It creates this positive feedback loop. The host is producing something that this particular microbe favors. Then in return, the microbe is creating something that benefits the host," he says. "This is a really important example of how the microbiome has evolved ways to become this symbiotic presence in the human host."

New therapy targets gut bacteria to prevent and reverse food allergies -- ScienceDaily

Recent insights about the microbiome -- the complex ecosystem of microorganisms that live in the gut and other body sites -- have suggested that an altered gut microbiome may play a pivotal role in the development of food allergies. A new study, led by investigators from Brigham and Women's Hospital and Boston Children's Hospital, identifies the species of bacteria in the human infant gut that protect against food allergies, finding changes associated with the development of food allergies and an altered immune response. In preclinical studies in a mouse model of food allergy, the team found that giving an enriched oral formulation of five or six species of bacteria found in the human gut protected against food allergies and reversed established disease by reinforcing tolerance of food allergens. The team's results are published in Nature Medicine.

A one-size-fits-all approach to nutrition doesn't work, even for twins, gene study finds - ABC News

“Genetics may not explain most nutritional differences among people,” said Spector. “Most of this variation that affects our weight, risk of diabetes and heart problems is potentially modifiable for an individual.” The researchers also analyzed how a person's metabolism may influence food choices, such as if it drives them to prefer savory or sweet foods or vice versa. However, Spector said that it was still unknown "how food preferences relate to food responses, but we do have the data.” Spector’s study also found that microbiomes differ between identical twins, who shared only about 37% of their gut microbes with each other. By comparison, the study found that unrelated people share about 35% of the same gut microbiota.

The FBI searched the offices of microbiome startup uBiome | TechCrunch

“Regrettably… we are terminating our consumer program. Our decision to do so is attributable to the simple fact that the cost of providing the service exceeds what our customers can pay for it,” the company wrote on its website. “We believe the costs of collecting the genetic, blood and microbiome assays that form the foundation of the program will eventually decline to a point where the program can be delivered to consumers cost-effectively. However, we are unable to continue to operate at a loss until that time arrives.”

Investors have been snubbing the microbiome. That may be changing

The field needed to find some basic tools before it had a chance of developing a drug successfully, she said, like better biomarkers to determine how and where a drug was working. For example, in one paper, Synlogic scientists showed that their drug was working by tracking an isotope markers through the bacteria’s metabolic pathway and by measuring levels of a chemical produced by their bacterial “drug,” SYNB1618. “One of the challenges that microbiome companies face is that you can tell what goes in the top end, you can tell what comes out the bottom end, but you can’t tell what happens in the middle,” Brennan said during a presentation earlier this month. “There’s a lot of groundwork that’s required. Papers don’t make good drugs,” she said in an interview afterward.