Tag: gut microbiome

Categories : Antibiotics GastrointestinalTags :

Special Lactic Acids Reduce Antibiotic Resistance in Infants

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Photo by William Fortunato on Pexels

Infants with high levels of antibiotic-resistant bacteria face a greater risk to their health if they need to be treated with antibiotics when they contract infectious diseases during their first year of life. Now, researchers at the Technical University of Denmark have discovered a way to combat antibiotic-resistant bacteria by nourishing a special subgroup of bifidobacteria found in the gut.

The research project, recently published in the renowned journal Nature Communications, points to a new, natural strategy for combating antibiotic resistance: supporting the good bacteria in the gut from the very first months of life.

“We document that special lactic acids produced by bifidobacteria play a key role in keeping antibiotic-resistant bacteria at bay, which is important for reducing the risk of resistance genes being transferred to other bacteria in the gut. Resistance genes can jump from one type of bacteria to another, and the more bacteria with resistance that are present in the gut, the greater the chance that they will encounter other bacteria and transfer resistance genes to them,” says postdoc Ioanna Chatzigiannidou from DTU Bioengineering, who participated in the research project.

The study of gut bacteria is based on 547 stool samples from 56 children and their mothers, who were followed over a five-year period.

A matter of life and death for infants

Professor Susanne Brix Pedersen from DTU Bioengineering is the head of the research project and explains that the new knowledge about bifidobacteria can be better utilized in society when researchers have developed a rapid test for use in the first weeks of a child’s life, so that parents can check whether their child already has these bifidobacteria naturally or would benefit from receiving a supplement containing them.

“It will be very important if we can strengthen their ability to handle antibiotic-resistant bacteria from the first weeks of a child’s life. This is especially true in the first year of life where infants are exposed to many infectious diseases due to an immature immune system, and when it is a matter of life and death if they have many antibiotic-resistant bacteria, for instance the pneumonia bacteria Klebsiella pneumoniae, making it difficult to treat pneumonia with certain antibiotics,” says Susanne Brix Pedersen.

There is a lot of research into antibiotic resistance, and Susanne Brix Pedersen is also involved in another study, BEGIN, which is based in the paediatric department at Aarhus University Hospital, where researchers are investigating whether a dietary supplement containing beneficial bifidobacteria can strengthen the immune system of newborn babies. So far, the trial has involved 300 women and their newborn babies, who are given either a placebo or a dietary supplement containing the special bifidobacteria.

Source: Technical University of Denmark

Categories : Diet and Nutrition GastrointestinalTags :

Red Meat Aggravates IBD by Altering the Gut Microbiome

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Photo by Jose Ignacio Pompe on Unsplash

Epidemiological studies have revealed a strong correlation between red meat consumption and the development of inflammatory bowel disease. In a new study published in Molecular Nutrition and Food Research that was conducted in mice, red meat consumption caused an imbalance of bacteria in the intestinal microbiota. 

Investigators fed mice various kinds of red meat, including pork, beef, and mutton, for two weeks, and then they induced colitis with 2.5% dextran sulfate sodium. Intake of these three red meat diets exacerbated colonic inflammation. Analyses revealed an overproduction of pro-inflammatory cytokines and infiltration of immune cells in the colon of mice fed red meat diets. 

These diets led to a marked decrease in the relative abundance of Streptococcus, Akkermansia, Faecalibacterium, and Lactococcus bacterial strains, coupled with an increase in Clostridium and Mucispirillum.  

“This study contributes to improving food innervation approaches for inflammatory bowel disease treatment and indicates a close crosstalk among diet, gut microbiota, and intestinal immunity,” said co–corresponding author Dan Tian, MD, PhD, of Capital Medical University, in China. 

Source: Wiley

Categories : Cancer GastrointestinalTags :

Scientists Find Few Links Between Cancer and Microbiome

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Gut Microbiome. Credit Darryl Leja National Human Genome Research Institute National Institutes Of Health

About a dozen studies in the past five years have made claims linking nearly every type of human cancer with the presence of microbiomes, “communities” of bacteria, viruses and fungi that live in or on peoples’ bodies. Now, scientists at Johns Hopkins Medicine say a study that sequenced human cancers found far less microbial DNA sequences than earlier studies reported in the same cancer tissue samples.

“It’s the nature of science to validate, confirm and reproduce findings,” says Steven Salzberg, PhD, Professor of Biomedical Engineering, Computer Science, and Biostatistics at The Johns Hopkins University. “Over time, we see a more complete picture of new research, and in this case, we did not find any associations between microbiomes and many types of cancer.”

Salzberg says details of the new study, published Sept. 3 in Science Translational Medicine, surveyed the whole genome sequences generated from 5734 tissue samples collected from 25 cancer types and stored in a large National Cancer Institute-funded database, The Cancer Genome Atlas (TCGA). About half of the samples are from normal tissues and blood, the other half from solid tumours and blood-based cancers.

The TCGA’s whole genome sequencing data contains millions of chopped up pieces of DNA molecules, known as reads, from each tissue sample. The original goal of the TCGA studies was to identify mutations in the DNA sequence of genes that might be associated with various cancer types. Sometimes, though, the original tumors might have microbes in them, and the reads could be used to identify those microbes.

Because reads often contain contaminants from bits of DNA left behind in sequencing machinery or picked up from the air or surfaces, samples can acquire DNA from those sources, as well as from the original tumour tissues. Salzberg says extraordinary efforts were made to identify such contaminants, preventing their study from displaying false results.

To rule out contaminants, Salzberg and his team relied on extensive experience with genomic sequencing and careful analysis of control samples to identify reads belonging to sequences known or highly likely to have contaminated samples.  

For the current study, a continuation of one that the Johns Hopkins team published in 2023, Salzberg and first author Yuchen “Peter” Ge, a graduate student in biomedical engineering at Johns Hopkins, removed human DNA sequences from the TCGA data sets by mapping each read against two human reference genomes – one from the Telomere-to-Telomere (T2T) project and another from the Genome Reference Consortium.

After removing human DNA, the research team was left with, on average, 2.4 million reads per sample, or about 0.35% of the total 6.5 billion tumour sample reads. Of these, the research team found 323 million human DNA reads that weren’t eliminated in the first pass and 986 million reads they classified as contaminants.

They next compared the remaining sequencing reads against a database containing 50 651 genomes representing 30,355 species of bacteria, viruses, fungi and archaea (single-celled organisms that aren’t bacteria or viruses).

After removing human DNA sequences and contaminants, the average proportion of microbial DNA reads in solid tumour samples was 0.57% and 0.73% in blood cancers.

The Johns Hopkins researchers then compared their new results to a study published five years ago in the journal Nature [since retracted, because of concerns about contaminants in the microbial data], and found the previous study identified 56 times as many microbial reads as the new study for half of the total microbial reads. And 5% of the time, the previous study found 9,000 times the number of microbial reads as the current Johns Hopkins study. Salzberg says the microbial reads in the retracted study were highly likely to be contaminants.

“This disparity in the number of microbial reads didn’t occur in just a few samples,” says Salzberg. “Over the whole study, the previous researchers found far more microbial reads than we did.”

In another comparison of a study published in Cell in 2022 and the current Johns Hopkins work, the 2022 study reported fungal DNA amounts that were hundreds of times more than what was found in the current Johns Hopkins study, largely due to contaminants.

Among the DNA samples in the current Johns Hopkins study, in which they did find microbiome DNA, the researchers found microbes that have long been linked with human cancer, such as HPV (linked with cervical and some head and neck cancers), Helicobacter pylori (linked to stomach cancer), and Fusobacterium nucleatum and Bacteroides fragilis (linked with GI cancers).

The current Johns Hopkins study and the previous ones published in Cell and Nature reported microbiomes of Saccharomyces cerevisiae, commonly known as baker’s yeast. “It’s one of the most common contaminants in sequencing labs,” says Salzberg. They also found a virus that infects plant fungi, Rosellinia necatrix partitivirus 8, which has no known link to human disease.

Salzberg said the need to carefully document claims about the links between cancer and microbiomes is “especially important” as efforts ramp up to diagnose cancers early using microbiome information.

The Johns Hopkins researchers have made their sequencing analysis data available online to other scientists in the supplementary materials in Science Translational Medicine and online.

Source: Johns Hopkins Medicine

Categories : Antibiotics PaediatricsTags :

Probiotics for Preterm Babies Lowered Antibiotic-resistant Bacteria in the Gut

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Photo by Hush Naidoo on Unsplash

Preterm babies with very low birth weight who received a probiotic alongside antibiotics had fewer multidrug resistant bacteria and a more typical gut microbiome, a new study shows.

The paper published in Nature Communications is the result of a trial testing probiotics among a group of 34 pre-term babies born with a very low birth weight, under 1500g representing around 1-1.5% of babies born around the world. The study sequenced gut bacteria from the babies during the first three weeks after birth.

The collaborative study led by Professor Lindsay Hall and Dr Raymond Kiu from the University of Birmingham found that among babies who received a probiotic treatment of a certain strain including Bifidobacterium alongside antibiotics, levels of typical bacterial strains associated with early-life gut microbiota were at levels typical among full-term babies, reducing both the abundance of antibiotic resistance genes and the number of multi-drug resistant bacteria in the gut.

In the context of the global AMR crisis, this is a major finding, especially for NICUs where preterm infants are especially vulnerable. Probiotics are now used in many neonatal ICUs around the UK, and the WHO have recommended probiotic supplementation in preterm babies. Our paper shows how beneficial this intervention can be for babies born prematurely to help them give their gut a kickstart, and reduce the impact of concerning pathogens taking hold.Professor Lindsay Hall – University of Birmingham

There were lower levels of drug-resistant pathogens including Enterococcus associated with risks of infections and longer hospital stays. Babies who received probiotics also saw higher levels of certain positive bacteria found naturally in the gut.

Among babies who didn’t receive probiotics, analysis of the gut bacteria found that while some differences occurred between those receiving antibiotics or not, both groups saw a dominant microbiome develop that included key bacteria (pathobionts) that can cause health problems including life-threatening infections during the crucial period after birth, as well as in later life.

Professor Lindsay Hall from the University of Birmingham and a group leader at Quadram Institute Bioscience, and senior corresponding author of the study said: “We have already shown that probiotics are highly effective in protecting vulnerable preterm babies from serious infections, and this study now reveals that these probiotics also significantly reduce the presence of antibiotic resistance genes and multidrug-resistant bacteria in the infant gut. Crucially, they seem to do so selectively – targeting resistant strains without disrupting non-resistant strains that might be beneficial.

“In the context of the global AMR crisis, this is a major finding, especially for NICUs where preterm infants are especially vulnerable. Probiotics are now used in many neonatal ICUs around the UK, and the WHO have recommended probiotic supplementation in preterm babies.

“Our paper shows how beneficial this intervention can be for babies born prematurely to help them give their gut a kickstart, and reduce the impact of concerning pathogens taking hold.”

Dr Raymond Kiu from the University of Birmingham, first and co-corresponding author of the paper said: “Sequencing technology has now confirmed that probiotic Bifidobacterium rapidly replicates in the preterm gut during the first three weeks of life. Importantly, this successful colonisation drives the maturation of the gut microbiota and is linked to a noticeable reduction in multi-drug-resistant pathogens – pointing to its pivotal role in improving neonatal health. Our findings also shed light on the complex interactions between antibiotics, probiotics, and horizontal gene transfer (HGT) in shaping the early-life microbiome.

“We believe this research lays the groundwork for future studies exploring the role of probiotics in antimicrobial stewardship and infection control among preterm populations.”

Source: University of Birmingham

Categories : Diet and Nutrition Metabolic DisordersTags :

A Nighttime Pistachio Snack May Reshape Gut Microbiome in Prediabetes

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Eating pistachios every night for 12 weeks altered gut bacteria, according to new study

Photo by Brenan Greene on Unsplash

Prediabetes affects a third of people in the United States and most of them will develop Type 2 diabetes, yet effective dietary intervention strategies remain limited. Pistachios have shown promise in improving markers of diet quality, yet little is known about how they influence the gut microbiome – a key player in glucose regulation and inflammation.

A new study led by Kristina Petersen, associate professor of nutritional sciences at Penn State, determined that nighttime pistachio consumption affects gut bacteria in adults with prediabetes. Though the potential therapeutic implications of the findings remain unclear, according to Petersen, they may prove significant for people who are working to improve their metabolic health.

The findings, published in the journal Current Developments in Nutrition, suggested that replacing a traditional carbohydrate-based bedtime snack with pistachios may reshape the gut microbiome. A previous study by these researchers demonstrated that pistachios have a similar effect on blood glucose as 15 to 30 grams of carbohydrates.

“Pistachios seem to be able to meaningfully shift the gut microbial landscape in adults with prediabetes especially when consumed as a nighttime snack.”

Kristina Petersen, associate professor of nutritional sciences at Penn State

“A common dietary recommendation for individuals with prediabetes is to consume a nighttime snack consisting of 15 to 30 grams of carbohydrates to help regulate overnight and morning blood glucose levels,” said Terrence Riley, lead author of this research who earned his doctorate in nutritional sciences at Penn State and currently works as a postdoctoral research fellow at Louisiana State University. “As an example, you could eat one or two slices of whole grain bread.”

Researchers observed that consuming about two ounces of pistachios each night for 12 weeks resulted in significantly different stool microbial community profiles compared to those who consumed the recommended 15 to 30 grams of a carbohydrate snack. Specific bacterial groups, including Roseburia and members of the Lachnospiraceae family – known as “good” bacteria that produces beneficial short-chain fatty acids like butyrate – were more abundant following the pistachio condition.

According to Petersen, butyrate serves as a primary energy source for colon cells, helps maintain the gut barrier and supports anti-inflammatory processes.  

“Pistachios seem to be able to meaningfully shift the gut microbial landscape in adults with prediabetes especially when consumed as a nighttime snack,” Petersen said. “These microbiome changes may offer other long-term health benefits – potentially helping to slow the development of Type 2 diabetes or to reduce systemic inflammation – which we hope to explore in future research.”

The study involved 51 adults with prediabetes and was conducted over two 12-week periods separated by a break, so the effects of the first part of the trial would not affect the second part. By the end of the study, all participants received both treatments. Stool samples were collected and analysed using 16S rRNA gene sequencing, a technique that can help classify bacteria based on their genetic makeup.

Petersen noted that participants who ate pistachios also experienced reductions in several bacterial groups that have been linked to less favorable metabolic outcomes.

“Levels of Blautia hydrogenotrophica – a bacterium that helps produce compounds that can build up in the blood and harm kidney and heart health – were lower after pistachio consumption,” Petersen said. “Levels of Eubacterium flavonifractor, which breaks down beneficial antioxidant compounds from foods like pistachios, also decreased.”

Petersen added that the strength of this study is the design used – a randomised crossover clinical trial, in which all participants receive both treatments in a randomised order. By including all participants in the pistachio group and the standard care group, the study helped the researchers better understand how specific foods like pistachios can influence the gut microbiome.

While the study demonstrated shifts in gut bacteria, it remains unclear whether these changes directly translate to improvements in health – a question that requires further research, Petersen said.

Source: Pennsylvania State University