The impact of yogurt, probiotics and the gut microbiome has exceeded expectations and been tied to brain, digestive and immune function. 

Consumer interest in fermented foods, immune health and gut health has soared, alongside interest in the connection between gut health and the immune system.

Ingredients that affect gut health are characterized as prebiotics, probiotics, synbiotics, and newly defined “postbiotics.” Ongoing research is elucidating the mechanisms by which these ingredients confer health benefits, demonstrating how trending ingredients such as fiber affect the gut microbiome on a molecular level, by interaction with microorganisms either directly or within intestinal cells. 

Mounting research into causes of dementia and cognitive decline have produced the recognition that two of the potentially modifiable risk factors into these conditions are diet and exercise. In a recent study at King’s College, London 418 adults age 65 and up were tested every two to three years over a 12-year period. Results revealed that cognitive decline and Alzheimer’s Disease were linked to levels of neural stem cell death. Importantly, underlying which was low levels of vitamin D, carotenoids, and lipids

Danone North America honored a commitment to science and education through the ninth annual Gut Microbiome, Yogurt and Probiotics Fellowship Grant Program. This year's honorees, selected by a committee of nutrition scientists, are Catherine Shelton of Vanderbilt University and Alice Solomon of the University of Arizona. Winners were chosen based on the quality of their proposals, faculty recommendations and each of their studies' value to human health and wellness.

The impact of yogurt, probiotics and the gut microbiome can be linked to several health benefits including those relating to brain, digestive and immune function.

New Report Outlines Research Agenda to Better Understand the Relationship Among Microbiomes, Indoor Environments, and Human Health

There are the telltale signs of aging — a few more wrinkles, graying hair, and changes in posture. Other changes are less obvious. Aging-related changes also occur within the gut microbiome — a collection of bacteria, viruses, and fungi that live in your digestive tract.

Microorganisms are everywhere, even inside of our guts. The microbes we interact with can sometimes have a huge influence on our bodies...

Microorganisms are everywhere, even inside of our guts. The microbes we interact with can sometimes have a huge influence on our bodies...

It’s probably best to enjoy your Halloween spoils in moderation.

Despite its major importance in human health, the metabolic potential of the human gut microbiota is still poorly understood. We have recently shown that biosynthesis of Ruminococcin C (RumC), a novel ribosomally synthesized and posttranslationally modified peptide (RiPP) produced by the commensal bacterium Ruminococcus gnavus, requires two radical SAM enzymes (RumMC1 and RumMC2) catalyzing the formation of four Cα-thioether bridges. These bridges, which are essential for RumC's antibiotic properties against human pathogens such as Clostridium perfringens, define two hairpin domains giving this sactipeptide (sulfur-to-α-carbon thioether–containing peptide) an unusual architecture among natural products. We report here the biochemical and spectroscopic characterizations of RumMC2. EPR spectroscopy and mutagenesis data support that RumMC2 is a member of the large family of SPASM domain radical SAM enzymes characterized by the presence of three [4Fe-4S] clusters. We also demonstrate that this enzyme initiates its reaction by Cα H-atom abstraction and is able to catalyze the formation of nonnatural thioether bonds in engineered peptide substrates. Unexpectedly, our data support the formation of a ketoimine rather than an α,β-dehydro-amino acid intermediate during Cα-thioether bridge LC–MS/MS fragmentation. Finally, we explored the roles of the leader peptide and of the RiPP precursor peptide recognition element, present in myriad RiPP-modifying enzymes. Collectively, our data support a more complex role for the peptide recognition element and the core peptide for the installation of posttranslational modifications in RiPPs than previously anticipated and suggest a possible reaction intermediate for thioether bond formation.

Functions of the gut microbiome have a growing number of implications for host metabolic health, with diet being one of the most significant influences on microbiome composition. Compelling links between diet and the gut microbiome suggest key roles for various macronutrients, including lipids, yet how individual classes of dietary lipids interact with the microbiome remains largely unknown. Sphingolipids are bioactive components of most foods and are also produced by prominent gut microbes. This makes sphingolipids intriguing candidates for shaping diet–microbiome interactions. Here, we used a click chemistry–based approach to track the incorporation of bioorthogonal dietary omega-alkynyl sphinganine (sphinganine alkyne [SAA]) into the murine gut microbial community (Bioorthogonal labeling). We identified microbial and SAA-specific metabolic products through fluorescence-based sorting of SAA-containing microbes (Sort), 16S rRNA gene sequencing to identify the sphingolipid-interacting microbes (Seq), and comparative metabolomics to identify products of SAA assimilation by the microbiome (Spec). Together, this approach, termed Bioorthogonal labeling-Sort-Seq-Spec (BOSSS), revealed that SAA assimilation is nearly exclusively performed by gut Bacteroides, indicating that sphingolipid-producing bacteria play a major role in processing dietary sphinganine. Comparative metabolomics of cecal microbiota from SAA-treated mice revealed conversion of SAA to a suite of dihydroceramides, consistent with metabolic activities of Bacteroides and Bifidobacterium. Additionally, other sphingolipid-interacting microbes were identified with a focus on an uncharacterized ability of Bacteroides and Bifidobacterium to metabolize dietary sphingolipids. We conclude that BOSSS provides a platform to study the flux of virtually any alkyne-labeled metabolite in diet–microbiome interactions.

While no candy is truly healthy, some options are better for your gut than others. And there are ways you can help wake your gut from its sugar "spell" after holiday indulgence.

Alzheimer's disease (AD) and Alzheimer's disease-related dementias (ADRDs) are broad-impact multifactorial neurodegenerative diseases. Their complexity presents unique challenges for developing effective therapies. This review highlights research presented at the 2024 Society for Neuroscience meeting which emphasized the gut microbiome's role in AD pathogenesis by influencing brain function and neurodegeneration through the microbiota–gut–brain axis. This emerging evidence underscores the potential for targeting the gut microbiota to treat AD/ADRD.

Horses that are bred to race seem to perform better on the course if they had a diverse gut microbiome as foals

Your body is home to trillions of beneficial viruses crucial for a healthy microbiome. We may one day be able to tweak this "virome" to treat obesity and anxiety

Neuroscientists have been surprised to discover that the human brain is teeming with microbes, and we are beginning to suspect they could play a role in neurodegenerative disorders like Alzheimer's

Antibiotics can reduce diversity in the gut microbiome, raising the risk of infections that cause diarrhoea - and the effects may last years

Title: Could Red Wine Boost Your 'Microbiome'?
Category: Health News
Created: 8/28/2019 12:00:00 AM
Last Editorial Review: 8/29/2019 12:00:00 AM

Neuroscientists have been surprised to discover that the human brain is teeming with microbes, and we are beginning to suspect they could play a role in neurodegenerative disorders like Alzheimer's

Antibiotics can reduce diversity in the gut microbiome, raising the risk of infections that cause diarrhoea - and the effects may last years

Antibiotics can reduce diversity in the gut microbiome, raising the risk of infections that cause diarrhoea - and the effects may last years

Disruptions to the body's internal clock can speed up the development of colorectal cancer. By influencing the gut microbiome and intestinal barrier,

In children who have received a donor medlinkstem cell transplant/medlink, having a varied range of microorganisms in their gut before the transplant

Gut indicates that patterns of an 'unhealthy' gut microbiome are linked to an increased risk of death following a solid organ transplant (!--ref1--).

You may be familiar with the gut microbiome's impact on overall health. Surprisingly, a similar principle applies to the semen microbiome, which may significantly

A new study reveals that human medlinkbreast milk/medlink plays a crucial role in shaping a baby's microbiome, the community of microbes that live in the body.

Researchers have identified changes in the gut microbiome makeup that lead to the onset of rheumatoid arthritis, providing a window of opportunity for targeted treatments.

A new study finds specific changes in gut bacteria may signal early risk for rheumatoid arthritis, offering potential for preventive treatment.

Toys inspire biology, biology inspires toys

An inhibitor of starch-digesting enzymes stunts the growth of certain gut bacteria

An inhibitor of starch-digesting enzymes stunts the growth of certain gut bacteria

Human skin and gut microbes influence processes from digestion to disease resistance. Despite the fact that tropical forests are the most biodiverse terrestrial ecosystems on […]

The post Smithsonian scientists discover tropical tree microbiome in Panama appeared first on Smithsonian Insider.

New Report Outlines Research Agenda to Better Understand the Relationship Among Microbiomes, Indoor Environments, and Human Health

Researchers at the Stowers Institute have established a definitive link between the makeup of the microbiome, the host immune response, and an organism's ability to heal itself.

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This year's conference will continue to focus and build on the challenges and hurdles that companies working in the microbiome industry will have to recognize and navigate in order to successfully commercialize their products.

Fisheries science with indigenous perspective, slippery surface and seasons on other planets

Some koalas may be pickier eaters than others due to the mix of microbes in their lower gastrointestinal tract, but faecal transplants could help them diversify their diet, a new study suggests.

Boyu Ren, Sergio Bacallado, Stefano Favaro, Tommi Vatanen, Curtis Huttenhower, Lorenzo Trippa.

Source: The Annals of Applied Statistics, Volume 14, Number 1, 494--517.

Abstract:
Detecting associations between microbial compositions and sample characteristics is one of the most important tasks in microbiome studies. Most of the existing methods apply univariate models to single microbial species separately, with adjustments for multiple hypothesis testing. We propose a Bayesian analysis for a generalized mixed effects linear model tailored to this application. The marginal prior on each microbial composition is a Dirichlet process, and dependence across compositions is induced through a linear combination of individual covariates, such as disease biomarkers or the subject’s age, and latent factors. The latent factors capture residual variability and their dimensionality is learned from the data in a fully Bayesian procedure. The proposed model is tested in data analyses and simulation studies with zero-inflated compositions. In these settings and within each sample, a large proportion of counts per microbial species are equal to zero. In our Bayesian model a priori the probability of compositions with absent microbial species is strictly positive. We propose an efficient algorithm to sample from the posterior and visualizations of model parameters which reveal associations between covariates and microbial compositions. We evaluate the proposed method in simulation studies, and then analyze a microbiome dataset for infants with type 1 diabetes which contains a large proportion of zeros in the sample-specific microbial compositions.

Susheela P. Singh, Ana-Maria Staicu, Robert R. Dunn, Noah Fierer, Brian J. Reich.

Source: The Annals of Applied Statistics, Volume 13, Number 4, 2341--2362.

Abstract:
The advent of high-throughput sequencing technologies has made data from DNA material readily available, leading to a surge of microbiome-related research establishing links between markers of microbiome health and specific outcomes. However, to harness the power of microbial communities we must understand not only how they affect us, but also how they can be influenced to improve outcomes. This area has been dominated by methods that reduce community composition to summary metrics, which can fail to fully exploit the complexity of community data. Recently, methods have been developed to model the abundance of taxa in a community, but they can be computationally intensive and do not account for spatial effects underlying microbial settlement. These spatial effects are particularly relevant in the microbiome setting because we expect communities that are close together to be more similar than those that are far apart. In this paper, we propose a flexible Bayesian spike-and-slab variable selection model for presence-absence indicators that accounts for spatial dependence and cross-dependence between taxa while reducing dimensionality in both directions. We show by simulation that in the presence of spatial dependence, popular distance-based hypothesis testing methods fail to preserve their advertised size, and the proposed method improves variable selection. Finally, we present an application of our method to an indoor fungal community found within homes across the contiguous United States.

Kurtis Shuler, Marilou Sison-Mangus, Juhee Lee.

Source: Bayesian Analysis, Volume 15, Number 2, 559--578.

Abstract:
We propose a Bayesian sparse multivariate regression method to model the relationship between microbe abundance and environmental factors for microbiome data. We model abundance counts of operational taxonomic units (OTUs) with a negative binomial distribution and relate covariates to the counts through regression. Extending conventional nonlocal priors, we construct asymmetric nonlocal priors for regression coefficients to efficiently identify relevant covariates and their effect directions. We build a hierarchical model to facilitate pooling of information across OTUs that produces parsimonious results with improved accuracy. We present simulation studies that compare variable selection performance under the proposed model to those under Bayesian sparse regression models with asymmetric and symmetric local priors and two frequentist models. The simulations show the proposed model identifies important covariates and yields coefficient estimates with favorable accuracy compared with the alternatives. The proposed model is applied to analyze an ocean microbiome dataset collected over time to study the association of harmful algal bloom conditions with microbial communities.

Seoul-based genome specialist, Macrogen, has agreed a A$4.1 million investment in the Queensland microbiome testing and bioinformatics company, Microba.

Days before a national lockdown in the U.S., Daniel McDonald realized his life’s work had put a unique tool in his hands to fight COVID-19. The assay kits his team was about to have made by the tens of thousands could be repurposed to help understand the novel coronavirus that causes the disease. McDonald is Read article >

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