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1. The nexus of gut microbiota, diet, and health

   https://doi.org/10.31989/ffs.v2i2.885  

   Bhattarai, Sajal; Janaswamy, Srinivas (February 2022, Functional Food Science)

   The gut microbiome incorporates the ecological niche specific to the totality of the microorganisms in the human gut. Unique to every individual, the blueprint of the microbiome sets up at birth and functions as a human organ and plays a significant role in digestion, detoxification, fighting pathogens, modulating the immune system, and improving health. The gut microbiota and associated health implications are influenced by factors such as birth and age, diseases, use of antibiotics and food components (e.g., complex carbohydrates and dietary fibers, plant proteins, unsaturated fatty acids, and functional compounds of natural origin such as flavones, flavonoids, polyphenols, and antioxidants). Toward this end, diet and the gut microbiome interact and govern each other’s fate. Herein, gut dysbiosis, the alteration of natural state and composition of the gut microbiome, and the gut microflora diversity modulated by food constituents and associated health effects have been discussed. The gut microbiota composition and related metabolites are influenced by the diet which in turn modulates human health. The outcome is deemed to aid in developing personalized diet recommendations (based on the unique gut microbiome) toward improving human health. Keywords: gut microbiome, gut microbiota, gut dysbiosis, short-chain fatty acids, metabolites, health modulation 

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2. Interactions between dietary flavonoids and the gut microbiome: a comprehensive review

   https://doi.org/10.1017/S0007114521003627  

   Baky, Mostafa Hassan; Elshahed, Mostafa; Wessjohann, Ludger; Farag, Mohamed A. (August 2022, British Journal of Nutrition)

   Abstract Flavonoids are natural polyphenol secondary metabolites that are widely produced in planta . Flavonoids are ubiquities in human dietary intake and exhibit a myriad of health benefits. Flavonoids-induced biological activities are strongly influenced by their in situ availability in the human GI tract, as well as the levels of which are modulated by interaction with the gut bacteria. As such, assessing flavonoids–microbiome interactions is considered a key to understand their physiological activities. Here, we review the interaction between the various classes of dietary flavonoids (flavonols, flavones, flavanones, isoflavones, flavan-3-ols and anthocyanins) and gut microbiota. We aim to provide a holistic overview of the nature and identity of flavonoids on diet and highlight how flavonoids chemical structure, metabolism and impact on humans and their microbiomes are interconnected. Emphasis is placed on how flavonoids and their biotransformation products affect gut microbiota population, influence gut homoeostasis and induce measurable physiological changes and biological benefits. 

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3. Decrypting bacterial polyphenol metabolism in an anoxic wetland soil

   https://doi.org/10.1038/s41467-021-22765-1  

   McGivern, Bridget B.; Tfaily, Malak M.; Borton, Mikayla A.; Kosina, Suzanne M.; Daly, Rebecca A.; Nicora, Carrie D.; Purvine, Samuel O.; Wong, Allison R.; Lipton, Mary S.; Hoyt, David W.; et al (April 2021, Nature Communications)

   Abstract Microorganisms play vital roles in modulating organic matter decomposition and nutrient cycling in soil ecosystems. The enzyme latch paradigm posits microbial degradation of polyphenols is hindered in anoxic peat leading to polyphenol accumulation, and consequently diminished microbial activity. This model assumes that polyphenols are microbially unavailable under anoxia, a supposition that has not been thoroughly investigated in any soil type. Here, we use anoxic soil reactors amended with and without a chemically defined polyphenol to test this hypothesis, employing metabolomics and genome-resolved metaproteomics to interrogate soil microbial polyphenol metabolism. Challenging the idea that polyphenols are not bioavailable under anoxia, we provide metabolite evidence that polyphenols are depolymerized, resulting in monomer accumulation, followed by the generation of small phenolic degradation products. Further, we show that soil microbiome function is maintained, and possibly enhanced, with polyphenol addition. In summary, this study provides chemical and enzymatic evidence that some soil microbiota can degrade polyphenols under anoxia and subvert the assumed polyphenol lock on soil microbial metabolism. 

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4. Characterization and Spatial Mapping of the Human Gut Metasecretome

   https://doi.org/10.1128/msystems.00717-22  

   Velez-Cortes, Florencia; Wang, Harris (December 2022, mSystems)

   Sangwan, Naseer (Ed.)

   ABSTRACT Bacterially secreted proteins play an important role in microbial physiology and ecology in many environments, including the mammalian gut. While gut microbes have been extensively studied over the past decades, little is known about the proteins that they secrete into the gastrointestinal tract. In this study, we developed and applied a computational pipeline to a comprehensive catalog of human-associated metagenome-assembled genomes in order to predict and analyze the bacterial metasecretome of the human gut, i.e., the collection of proteins secreted out of the cytoplasm by human gut bacteria. We identified the presence of large and diverse families of secreted carbohydrate-active enzymes and assessed their phylogenetic distributions across different taxonomic groups, which revealed an enrichment in Bacteroidetes and Verrucomicrobia . By mapping secreted proteins to available metagenomic data from endoscopic sampling of the human gastrointestinal tract, we specifically pinpointed regions in the upper and lower intestinal tract along the lumen and mucosa where specific glycosidases are secreted by resident microbes. The metasecretome analyzed in this study constitutes the most comprehensive list of secreted proteins produced by human gut bacteria reported to date and serves as a useful resource for the microbiome research community. IMPORTANCE Bacterially secreted proteins are necessary for the proper functioning of bacterial cells and communities. Secreted proteins provide bacterial cells with the ability to harvest resources from the exterior, import these resources into the cell, and signal to other bacteria. In the human gut microbiome, these actions impact host health and allow the maintenance of a healthy gut bacterial community. We utilized computational tools to identify the major components of human gut bacterially secreted proteins and determined their spatial distribution in the gastrointestinal tract. Our analysis of human gut bacterial secreted proteins will allow a better understanding of the impact of gut bacteria on human health and represents a step toward identifying new protein functions with interesting applications in biomedicine and industry. 

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5. Gut Microbiome: Profound Implications for Diet and Disease

   https://doi.org/10.3390/nu11071613  

   Hills, Ronald D.; Pontefract, Benjamin A.; Mishcon, Hillary R.; Black, Cody A.; Sutton, Steven C.; Theberge, Cory R. (July 2019, Nutrients)

   The gut microbiome plays an important role in human health and influences the development of chronic diseases ranging from metabolic disease to gastrointestinal disorders and colorectal cancer. Of increasing prevalence in Western societies, these conditions carry a high burden of care. Dietary patterns and environmental factors have a profound effect on shaping gut microbiota in real time. Diverse populations of intestinal bacteria mediate their beneficial effects through the fermentation of dietary fiber to produce short-chain fatty acids, endogenous signals with important roles in lipid homeostasis and reducing inflammation. Recent progress shows that an individual’s starting microbial profile is a key determinant in predicting their response to intervention with live probiotics. The gut microbiota is complex and challenging to characterize. Enterotypes have been proposed using metrics such as alpha species diversity, the ratio of Firmicutes to Bacteroidetes phyla, and the relative abundance of beneficial genera (e.g., Bifidobacterium, Akkermansia) versus facultative anaerobes (E. coli), pro-inflammatory Ruminococcus, or nonbacterial microbes. Microbiota composition and relative populations of bacterial species are linked to physiologic health along different axes. We review the role of diet quality, carbohydrate intake, fermentable FODMAPs, and prebiotic fiber in maintaining healthy gut flora. The implications are discussed for various conditions including obesity, diabetes, irritable bowel syndrome, inflammatory bowel disease, depression, and cardiovascular disease. 

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