Understanding Microbiome Communities in Human Health

Fruit- and vegetable-associated microbes may have probiotic [and not just prebiotic] effects that contribute positively to bacterial diversity in the human gut. Bacterial diversity plays an important role in human health. During early life, several key periods/time points influence the maturation of the gut microbiome. These include the event of birth itself, feeding via breast milk, and the transition from breast milk to the introduction of solid foods [among other things]. Among solid foods, fruits, and vegetables are known to influence the gut through the delivery of key micronutrients as well as other nutrient (e.g., fiber) and non-nutrient compounds (e.g., polyphenols, etc.). Recently, a research team succeeded in showing that plant microorganisms from fruits and vegetables may also contribute to the human microbiome. Published in the journal Gut Microbes, a research team from the Institute of Environmental Biotechnology at TU Graz created a catalog of microbiome data from fruits and vegetables which enabled them to assign their bacteria. They compared these with publicly available data from two studies on intestinal flora in humans (one study looking at the microbiome of infants and one looking at adults). By analyzing data from roughly 2,500 stool samples, they demonstrated the presence of plant-associated bacteria in the human gut. Interestingly, the study demonstrated that host age, vegetable consumption frequency, and the diversity of plants consumed were positively associated with the amount of plant-associated bacteria found in human samples. This data suggests that foodborne microbes can survive in the digestive tract (two previous Nature publications have also suggested as much - PMID: 24336217; PMID: 30894548). This study also shows us that the intake of fruits and vegetables is one of the main connections between the human microbiome and the environmental microbiome. https://lnkd.in/gu6UbsBn

“The microbiome” isn't just one thing. It's lots of things and each habitat has its own.  To say the human microbiome is complicated is an understatement.  It's generally agreed that a microbiome is the community of organisms (bacteria, fungi, viruses, archaea) that live and interact in a particular habitat inclusive of the environmental, physical and chemical properties of that habitat. This means that we're surrounded by microbiomes and if we're talking about them from the human perspective, there are at least 6 that we need to discuss: Respiratory tract - The upper airway, your nose and the cavity behind it are colonized by specific microbes that thrive in the mucosa that helps to warm, humidify and filter the air that we breathe. Similarly, the lower respiratory tract and lungs host their own crew of microbes. The microbiomes in these regions change significantly during respiratory infections or after the development of respiratory diseases like asthma. Eye - Anyone who has ever suffered from conjunctivitis (infection of the eye) understands the importance of having a healthy eye microbiome. But the eye has three distinct habitats which include the outer eye, the conjunctiva (the membrane that covers the eye), and the meibum (the fatty, slippery, liquid that lubricates our eyes!). Each of these are inhabited by specific microbes that thrive in these ocular environments! Oral - Our mouth is one of the microbiomes we’re most conscious of. Dental hygiene is extremely important for human health, and a dysfunctional oral microbiome is typified by unpleasant odors as a result of infections of our gums and teeth. Skin - This is one of the more complicated microbiomes to classify since “skin” is present on every outer surface of our body. The skin microbiome can differ significantly depending on whether we’re talking about our armpit, scalp, or face! But be aware, this surface that you scrub clean every day is host to trillions of microbes! Urogenital - This primarily refers to the vaginal microbiome which changes throughout a woman’s cycle and during pregnancy. The microbial community here is sensitive to changes in pH (and can cause changes in pH!). Dysfunction can lead to infertility or even miscarriages. Digestive - The “gut” microbiome is probably the one that we’ve heard the most about. But the digestive tract is made up of the stomach, small intestine, large intestine, and colon. Each of these has a distinct physical and chemical environment, and you guessed it, each supports its own unique microbial community! While we contain multitudes of microbes that form communities on and in various parts of our body, we’re still at the earliest stages of trying to tease out the cause and effect relationships here that impact human health. While it’s pretty easy to define an unhealthy microbiome when we have an infection, identifying the factors that create and maintain a healthy one is still a huge work in progress!

Gut Microbiota Acts Like an Auxiliary Liver. Microbes in mammalian gut can significantly change their hosts’ amino acid and glucose metabolism, acting almost like an extra liver, according to a new preclinical study by Weill Cornell Medicine investigators. New York, New York. April 23, 2024. Excerpt: The study, published April 23 in Cell Host & Microbe, adds to the growing list of ways in which the microbiome influences physiology, and could lead to new strategies to treat conditions such as inflammatory bowel disease and diabetes. In recent years, scientists have found billions of microbes living on and in the human body profoundly influence our physiology. Senior author Dr. Chun-Jun Guo, an assistant professor of microbiology & immunology in medicine and a member of the Jill Roberts Institute for Research in Inflammatory Bowel Disease at Weill Cornell Medicine, wanted to take a deeper look at how essential microbes in the gut affect our access to the nutrients extracted from the food we ingest. “They ‘eat’ before us, taking nutrients from food we consume, and leaving us with what remains after they satisfy their own nutritional needs,” said Dr. Guo, a member of the Friedman Center for Nutrition and Inflammation at Weill Cornell Medicine. To better understand this process, first author Dr. Ting-Ting Li, a postdoctoral associate in the Guo lab, and collaborators, assessed how efficiently different bacteria that inhabit our intestines, called human gut commensals, deplete amino acids, the building blocks of proteins. Due to poorly characterized metabolic functions of many gut bacteria, the team experimented with various settings to find optimal conditions for their study. After screening more than 100 human gut microbes, investigators pinpointed several that are highly efficient at metabolizing various dietary amino acids. When these microbes colonized the gastrointestinal tracts of germ-free mice—mice without microbes-- the levels of amino acids dropped in the host's intestine and bloodstream. Note: The team identified specific bacterial metabolic genes that deplete amino acids. “We found in one single bacterium, over 20 genes encoding a similar enzymatic function,” Dr. Guo said. “And because we improved our CRISPR-Cas9 gene deletion techniques for gut bacteria, we performed a large gene deletion screen and identified metabolic genes in the bacteria responsible for depleting amino acids." The scientists took their findings from cultured cells into animals, giving germ-free mice genetically modified strains of bacteria, one at a time. “We can now precisely manipulate individual genes for depleting amino acids in the gut,” Dr. Guo said. “This allows us to assess the individual function of these genes and to see how they impact host amino acid homeostasis.” Link to April 23 published research in enclosed announcement. https://lnkd.in/egYJq5Ce

The human gut is home to hundreds of different bacterial species collectively known as the gut microbiome. A major health benefit these provide is to protect the gut against invading pathogens (disease-causing microorganisms) that could cause harmful infections. But up to now, how this protective effect comes about has been unclear, and whether certain bacterial species have a more important role than others. To investigate this, researchers at the University of Oxford tested 100 different gut bacteria strains individually and in combination for their ability to limit the growth of two harmful bacterial pathogens: Klebsiella pneumoniae and Salmonella enterica. The study "Microbiome diversity protects against pathogens by nutrient blocking" was published in Science. Individual gut bacteria showed a very poor ability to restrict the spread of either pathogen. But when communities of up to 50 species were cultured together, the pathogens grew up to 1000 times less effectively than when cultured with any individual species. https://lnkd.in/gdBSpMsp

Want to learn more about your microbiome? Read the book "I Contain Multitudes" by Ed Young. The book gives a profound glimpse into the microbial world that thrives within and around us. While Yong's narrative primarily unfolds the intricate relationships between microbes and their hosts, it inadvertently lays the groundwork for a revolution in how we approach nutrition—personalized nutrition, to be precise. The concept of personalized nutrition, which tailors dietary recommendations to individual dietary habits, lifestyle choices, genetic makeup, and, notably, the unique composition of one's microbiome, finds an indirect advocate in Yong's exploration. Through his compelling narrative, Yong elucidates several key insights: 1. The Crucial Link Between Microbial Diversity and Health: Yong's discussion reveals how a rich tapestry of microbial life in our guts correlates with a myriad of health outcomes. This diversity, sculpted by an array of factors including our diet, lifestyle, and even our birth method, suggests the inadequacy of a universal dietary guideline. 2. The Intimate Dance Between Diet and Microbiome: The book highlights the dynamic interactions between our diets and our microbiome, affecting everything from nutrient absorption to the synthesis of essential vitamins. These interactions are highly individualized, underscoring the necessity for dietary advice that is not just personalized but is also responsive to our microbial companions. 3. Adaptability of the Microbiome to Dietary Patterns: Yong presents fascinating examples, such as the microbiome's adaptation to digest seaweed in some Japanese populations, showcasing the microbiome's ability to evolve with our dietary habits. This adaptability hints at the potential of diets designed to cultivate beneficial microbial populations, offering a tailored approach to health and nutrition. 4. The Future of Probiotics and Prebiotics: While Yong approaches the topic with a measured skepticism, he acknowledges the burgeoning field of probiotics and prebiotics. This area, though still in its infancy, points towards a future where manipulating our microbiome could become integral to personalized nutrition strategies. Although Ed Yong does not explicitly map out a vision for personalized nutrition in "I Contain Multitudes," the implications of his work are clear. By understanding the pivotal role of the microbiome in our health, the path towards dietary recommendations that honor our unique microbial signature is illuminated. In a world where nutrition is increasingly recognized as a key pillar of health, Yong's insights suggest a paradigm shift—towards a future where the adage "you are what you eat" extends beyond the individual to the microscopic communities that reside within us.

Diverse microbiomes are key for robust pathogen exclusion--Just published in Science. This study explores colonization resistance, a crucial aspect of the microbiota's role in host defense against pathogens. The researchers discovered that colonization resistance is a higher-order effect of a diverse community of bacteria, with key species like Escherichia coli playing essential roles. Through in vitro and in vivo experiments, they found that a diverse microbiota, with the right composition, collectively consumes nutrients required by incoming pathogens, limiting their growth in the host. The predictability of colonization resistance arises when the symbiotic community shares similar proteins with the pathogen. The study emphasizes that microbiome diversity, community composition, and nutrient utilization profiles are critical factors in providing protection against pathogen colonization. Manuscript: https://lnkd.in/g4fApU6w #microbiome #pathogen #diversity

Evidence suggests that the gut #microbiome influences socio-affective behavior. A team from INSEAD, France; The Brain Institute of America, The University of Bonn, Germany, sought to understand how the composition of the microbiome influences social skills. They recruited 101 healthy men. "We chose only men for our study, particularly due to the hormonal factors in women that are significant in decision-making," explained Hilke Plassmann, a professor at INSEAD and coauthor of the study published in PNAS Nexus. Half of the participants received a mixture of #prebiotics and #probiotics, including Lactobacillus and Bifidobacterium, while the other half received a placebo for 7 weeks. Their microbiome composition was analyzed at the beginning and end of the experiment. "The participants continued their usual diet. The prebiotics allowed the bacteria to colonize the gut more easily," the researcher explained. Measuring Sensitivity to Injustice. Participants were invited to take part in a behavioral test called the "ultimatum game," before and after receiving the supplementation. This game experimentally measures sensitivity to injustice. The study results showed that participants who received the supplements were more likely to reject unequal offers at the end of the 7 weeks, even when the imbalance was slight. The placebo group behaved identically during the first and second test sessions. "This suggests that modifying the gut microbiome made the participants less rational and more human, more sensitive to social considerations." Role of Tyrosine. Participants who, at the beginning of the study had the greatest imbalance between the two types of bacteria dominating the gut flora (Firmicutes and Bacteroidetes) saw their microbiome composition evolve more with the supplements. These individuals showed the greatest sensitivity to injustice during the ultimatum game. Blood tests before and after supplementation revealed a decrease in tyrosine levels, a dopamine precursor, after 7 weeks of supplementation. This study needs to be complemented by further research, particularly on other social groups. "For future studies, we can try to understand why this psychological reaction is observed," she said. The importance of the microbiome's role is increasingly studied, including in psychiatric disorders. A meta-analysis 2021 in JAMA #psychiatry showed that imbalances in the microbiota can be found in patients experiencing #depression, #anxiety, #bipolardisorder, #schizophrenia. "we don't know if it's the change in the microbiota that influences the disease or vice versa. It's the chicken or the egg problem," commented Plassmann. https://lnkd.in/eWQ9uBXc #nimh #mentalhealth The National Institutes of Health Centers for Disease Control and Prevention

“Microbial communities drive global biogeochemical cycles and shape the health of plants and animals—including humans. Their structure and function are determined by ecological and environmental interactions that govern the assembly, stability and evolution of microbial communities. A widely held view is that antagonistic interactions such as competition predominate in microbial communities and are ecologically more important than synergistic interactions—for example, mutualism or commensalism. Over the past decade, however, a more nuanced picture has emerged, wherein bacteria, archaea and fungi exist within interactive networks in which they exchange essential and non-essential metabolites. These metabolic interactions profoundly impact not only the physiology, ecology and evolution of the strains involved, but are also central to the functioning of many, if not all, microbiomes. “ #microbiome #microbiology #health https://lnkd.in/ghtH6-4t

"Our brains may seem physically far removed from our guts, but in recent years, research has strongly suggested that the vast communities of microbes concentrated in our digestive tract open lines of communication between the two. The intestinal microbiome has been shown to influence cognition and emotion, affecting moods and the state of psychiatric disorders, and even information processing. But how it could do so has been elusive. "Until recently, studies of the gut-brain relationship have mostly shown only correlations between the state of the microbiome and operations in the brain. But new findings are digging deeper, building on research that demonstrates the microbiome’s involvement in responses to stress. Focusing on fear, and specifically on how fear fades over time, researchers in 2019 tracked how behavior differs in mice with diminished microbiomes. They identified differences in cell wiring, brain activity and gene expression, and they pinpointed a brief window after birth when restoring the microbiome could still prevent the adult behavioral deficits. They even tracked four particular compounds that may help to account for these changes. While it may be too early to predict what therapies could arise once we understand this relationship between the microbiome and the brain, these concrete differences substantiate the theory that the two systems are deeply entwined." #stressanalysis

Congrats to researchers at the University of Antwerp for publishing a "citizen-science-enabled catalog" of the vaginal microbiome this month in Nature Microbiology. This catalog is based on 16S amplicon sequencing of 3,345 vaginal samples collected at home between July and October 2020. The vaginal microbiome refers to the community of microorganisms that inhabit the vaginal tract of women. Like the gut and skin, the vagina has its own distinct microbiota, which can vary from person to person. The composition of the vaginal microbiome plays a crucial role in protection against infections, maintenance of the vaginal mucosal barrier, and further regulation of the immune system. The vaginal microbiome is predominantly composed of bacteria, with Lactobacillus species being the most common and important. These beneficial bacteria help maintain a slightly acidic pH in the vagina, typically between 3.8 and 4.5, which is crucial for preventing the overgrowth of harmful microorganisms. Lactobacilli produce lactic acid, which contributes to this acidic environment. Not surprisingly In the Antwerp study, 78% of the vaginal samples were dominated by Lactobacillus, in particular L. crispatus and L. iners species. Network correlation analysis demonstrated that specific bacterial taxa co-exist in "modules" depicted in the image below. Notably, the module comprising L. crispatus, L. jensenii, and Limosilactobacillus taxa was associated with menstrual cycle-informed estrogen levels and contraceptive use and negatively linked to childbirth. Childbirth appears to lead to the transient establishment of certain canonical gut bacteria in the vaginal tract. These data lay a strong foundation for observational studies in populations outside of Belgium, as well as case-control and case-cohort studies in populations with disease. Ultimately, some of these co-occurrence modules may one day inform future diagnostic, probiotic, and postbiotic innovations. Click here to check out the peer-reviewed catalog: https://lnkd.in/gQj975nd #microbiome #metagenomics #vaginalhealth #immunity #probiotics #postbiotics