#microbiome research

[equinesandeducation]

Another day of thesis work down, three more days until the deadline. Still spent my evening on the running track because I needed the mental break. In the trenches now baybyyyy!!

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How Microbiome Research Is Transforming Modern Medicine

The human body is home to trillions of microbes that quietly influence how we live, eat, and heal. Collectively known as the human microbiome, these microorganisms outnumber our own cells and play an essential role in maintaining balance within the body. In recent years, microbiome research has started to redefine the boundaries of modern medicine—transforming how we understand health and disease.

For decades, medicine has focused on treating symptoms and targeting individual organs. But as research evolves, scientists have discovered that the gut microbiome—the diverse community of microbes in our digestive tract—affects nearly every system in the body. From supporting metabolism and immune defense to influencing mood and cognition, these tiny organisms are proving to be powerful allies in human health.

Researchers now know that an imbalance in gut bacteria, called dysbiosis, can contribute to conditions like obesity, diabetes, inflammatory bowel disease, and even depression. Through microbiome studies, scientists are uncovering how bacterial metabolites—small molecules produced by microbes—communicate with human cells. This growing understanding is paving the way for new treatments that focus on restoring microbial balance rather than just managing symptoms.

Microbiome research is also reshaping the field of personalized medicine. Instead of offering the same treatment to everyone, doctors can now consider an individual’s unique microbial composition to predict how their body will respond to certain therapies. This approach is already showing promise in cancer treatment, autoimmune disorders, and gut-related illnesses.

Across the United States, top microbiome research centers are leading groundbreaking studies on how microbial chemistry influences overall well-being. One such effort is led by the Chaudhari Lab at the University of Wisconsin–Madison, where researchers are exploring how gut microbes and their metabolites impact metabolism, inflammation, and disease progression. Their work highlights how understanding the microbiome at a molecular level can inspire smarter, more targeted approaches to healthcare.

As science continues to reveal the incredible complexity of the microbiome, it’s clear that modern medicine is entering a new era—one where healing may begin not just with the human body, but with the microscopic life within it.

To learn more about ongoing microbiome research and its real-world health applications, explore the work of the Chaudhari Lab at the University of Wisconsin–Madison.

[cdifffoundation]

Noninvasive Imaging and Quantification of Bile Salt Hydrolase Activity: Abstract

Noninvasive Imaging and Quantification of Bile Salt Hydrolase Activity: Abstract

Abstract The microbiome-produced enzyme bile salt hydrolase (BSH) plays a central role in human health, but its function remains unclear due to the lack of suitable methods for measuring its activity. Here, we have developed a novel optical tool based on ultrasensitive bioluminescent imaging and demonstrated that this assay can be used for quick and cost-effective quantification of BSH activity…

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World Microbiome Day 2020 Information

World Microbiome Day 2020 Information

Microbiome research impacts many facets of life on Earth (and beyond). In a dedicated page for World Microbiome Day 2020, Microbiome, Animal Microbiome and Environmental Microbiome have highlighted some of the many ways microbiome research has benefited us.

      Click on the graphic above to access the World Microbiome 2020 Page

World Microbiome Daywas founded by APC Microbiome Ireland in 2019.…

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[thinkbiome]

The Biggest Microbiome Breakthroughs of 2019

Microbiome research continues to grow at a rapid pace, and in 2019 some amazing advances were made.

The contributions of specific species of bacteria to dysbiosis are being unraveled, prebiotics targeting specific types of bacteria are being developed, and postbiotics are moving to the forefront of research.

Here are some of the top discoveries of 2019:

Specific bacteria linked to depression

One of the most exciting and least understood areas of gut microbiome research is the link between gut bacteria and mental health with a growing body of evidence revealing how the bacteria in the gut can influence the brain through the gut-brain axis.

A large-scale analysis of the association between fecal microbiome data and diagnosed clinical depression in 1,054 individuals enrolled in the ongoing Flemish Gut Flora Project revealed that two species of gut bacteria, Coprococcus and Dialister, are consistently absent or seen at lower levels than normal in study participants suffering from depression, regardless of antidepressant treatment.

Although solidifying the depression-microbiome connection will take many more studies, these new findings are a notable signal to the clinical community that microbiome profiling should be considered for mental health patients. 

Gut bacteria protect against food allergies

There has been a startling rise in potentially life-threatening food allergies, which has been linked to a range of potential culprits, including the misuse of antibiotics and changes in dietary habits.

Differences in gut microbiome populations have been observed between infants allergic to cow’s milk and infants without allergies, and taking Lactobacilli and Bifidobacterium supplements during pregnancy has been shown to prevent atopic sensitization to food allergens among infants predisposed to food allergies.

In a particularly interesting study, scientists from the University of Chicago discovered that a particular bacterium, called Anaerostipes caccae, seems to prevent allergic reactions to food. Interestingly, this bacterium has also been shown to protect against nut allergies. 

The gut microbiome plays a protective role during aging

Studies of the links between the gut microbiome and aging have provided some surprising insights.

One study revealed that a metabolite produced by gut microbes can increase neuron production in the brain, improve intestinal function, and ultimately slow the aging process. Across several compelling mouse experiments, researchers found the negative effects of aging could be counteracted by enhanced microbial production of the short chain fatty acid butyrate. Furthermore, the administration of butyrate alone had protective effects similar to those of butyrate-producing bacteria.

Another study revealed that the decline in gut microbiome diversity that occurs as we age is associated with cardiovascular disease. The reason for the link seems to be the production of the microbial metabolite trimethylamine N-oxide (TMAO), which is produced at increased levels by the elderly microbiome.

Prebiotics and postbiotics

Finally, gut microbiome research has also been accompanied by an increased interest in the use of prebiotics and postbiotics to modulate the gut microbiota and host health.

Prebiotics and probiotics have been shown to improve the immune response of healthy volunteers receiving the influenza vaccine and postbiotics, such as butyrate, have been shown to enhance sleep and protect against neurodegeneration.

Given the notable microbiome breakthroughs of 2019, we’re sure that 2020 will bring even more exciting developments. Be sure to stick with us as we continue to cover how the microbiome influences health and disease and develop research-backed nutritional supplements for microbiome health.

We wish you all a happy 2020!

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Quantifying and Understanding Well-to-Well Contamination in Microbiome Research

Quantifying and Understanding Well-to-Well Contamination in Microbiome Research

When Amnon Amir, Jon Sanders, and their collogues began using positive control samples of Vibrio fischeri in plate-based extractions as a way to validate results, they unexpectedly observed that many of the surrounding samples would also show Vibrio fischeri in their composition. They set out to design an experiment to quantify this problem which led to the newly published paper “Quantifying and…

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[thinkbiome]

Bad Bugs Love Diet Soda

A new study suggests that the sweetener trehalose has fuelled the rise of Clostridium difficile.

 There are numerous reasons to avoid processed foods. They’re often packed with sugar, fat, and salt, and tend to lack nutrients critical to health, such as fiber.

 Now, a study published in the journal Nature, suggests that some of the additives that extend the shelf life and improve the texture of processed foods may have unintended side effects on our gut microbiomes.

 The evidence suggests that these additives selectively feed certain types of bad bacteria (also called pathogens) in the gut.

 You’ve probably heard of Clostridium difficile, it is often referred to as C. diff and tends to strike after you’ve taken antibiotics for something else. The antibiotics kill off the good bugs keeping C. diff out, and the more antibiotics you take, the harder it is to get rid of.

 Why?

 Because many strains of C. diff have developed antibiotic resistance, making them very difficult to treat.

 In fact, in extreme cases, a fecal microbiome transplant may be the only way to get rid of recurrent C. diff infections. 

 C. diff infections affect almost 500,00 people per year according to the CDC, and around 29,000 of them die as a result.

 Researchers at Baylor College of Medicine have been studying C. diff. Some time ago they noticed that more virulent strains were outcompeting less virulent strains in the gut.

 So they decided to figure out why.

 The scientist searched through more than 200 sugars and amino acids present in the gut to see if C. diff better utilized some food source compared to others.

 The results were quite surprising.

 Two of the worst C. diff strains have developed a unique ability to utilize a sugar called trehalose.

 Why does that matter?

Well, trehalose is a sugar (naturally found in mushrooms) that started being used in processed foods in the 1990s. Its use in foods has skyrocketed since 2001.

 The researchers believe that by adding trehalose to processed foods, we have been selectively breeding the worst strains of C. diff.   

 In support of this, the researchers point to the timing of recent C. diff epidemics. The virulent strains existed before 2000, but caused very few outbreaks. Only after large quantities of trehalose entered the food supply did they become this deadly.

 Now, correlation does not equal causation, and trehalose is unlikely to be the only factor behind the C. diff epidemic. However, when testing their hypothesis in C. diff-infected mice, researchers found that mice consuming the sugar fared much worse than mice not consuming the sugar.

 This research adds to a to a growing body of evidence suggesting that common food additives can push our gut microbiomes in unhealthy directions, not only aiding the emergence of new pathogens, but also promoting diseases such as obesity, diabetes, and inflammatory bowel disease.

  Reference:

Collins, J. et al. (2018) Dietary trehalose enhances virulence of epidemic Clostridium difficile. Nature, 553, pages 291–294 doi:10.1038/nature25178

[thinkbiome]

Thousands of New Microbial Communities Identified in Largest Microbiome Study To-Date

The more we study the role of the microbiome in disease, the more we realize that this is just the tip of the iceberg. There is so much more to learn!

 A new study published in the prominent journal Nature shows that we are actively progressing in the right direction. This new research expands our knowledge of the specific genes, microbial communities (families of bacteria, fungi, and viruses) and changes in the microbiome over time.

 The study is the expanded second phase of the National Institutes of Health (NIH) Human Microbiome Project and was a collaboration between the University of Maryland School of Medicine, Harvard T.H. Chan School of Public Health, the Broad Institute of MIT and Harvard and the University of California – San Diego. It is the largest microbiome analysis to-date.

 The research teams analyzed 1,635 samples from 265 different people over time in order to determine which bugs were present and how they changed over time. They also began to unravel the roles of different fungi and viruses in the gut – which are both proving to play important roles in health and disease.

 The samples were taken from the human gut, skin, oral and vaginal microbiomes. While the role of the gut microbiome has been firmly established in health and disease, it’s increasingly evident microbes inhabiting the other areas of our bodies (mouth, skin etc.) are crucial for preventing diseases like psoriasis, acne and rheumatoid arthritis. 

 The findings:

One of the largest profiles of non-bacterial (viruses and fungi) members of the microbiome

Identified specific types of microbes at each body site

Profiled the biochemical activity that allows microbes to maintain human health

Identified how the microbiome changes over time

 Much like sequencing the human genome, this new study shows that we still have a lot to learn, but it provides a huge new resource for scientists to help drive microbiome research.