Diet and Gut Microbiome Interactions: Enzymes, Pathways, and Cells

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Gut Microbiota".

Deadline for manuscript submissions: closed (15 March 2022) | Viewed by 9279

Special Issue Editor


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Guest Editor
Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
Interests: "agricultural glycomics; functional genomics of carbohydrate utilization; intestinal microbiomes; carbohydrate active enzymes; enzyme discovery; alternatives to antibiotics for livestock production "

Special Issue Information

Dear Colleagues,

The study of microbiomes associated with the digestive systems of animals has emerged as a prominent area of biological science within the last two decades. The main focus of research has been on structural changes in taxonomic diversity and abundance imparted by diet, development, and disease using a spectrum of sequencing technologies, as well as animal and environmental models. Looking forward, understanding molecular interactions between the gut microbiome and dietary complex carbohydrates and other metabolites will be pivotal for unlocking the potential of functional foods, prebiotics, and probiotics; developing personalized microbiome-based therapeutics; and the sustainable production of food animals. Next-generation sequencing, multi-OMICs (e.g., metatranscriptomics, metaproteomics, metabolomics), and advances in bioinformatics and artificial intelligence have begun to illuminate the complex sequence–function relationships operating within gut microbial ecosystems. Such combinatorial approaches promise to usher in the next frontier of microbiome sciences and provide the tools researchers need to study cellular physiology at the single-cell level and to assign genotype–phenotype relationships within complex datasets.

This Special Issue is focused on understanding interactions between the gut microbiome and host diet, with a focus on enzymes, pathways, and cellular mechanisms that shape the microbial communities of the gut in humans and animals. New research articles and reviews that address these topics are invited for submission.

Dr. D. Wade Abbott
Guest Editor

Manuscript Submission Information

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Published Papers (2 papers)

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Research

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16 pages, 2955 KiB  
Article
Targeting the Gut Microbiota and Host Immunity with a Bacilli-Species Probiotic during Antibiotic Exposure in Mice
by David Shapiro, Fatemeh Ramezani Kapourchali, Anthony Santilli, Yingchun Han and Gail A. M. Cresci
Microorganisms 2022, 10(6), 1178; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10061178 - 08 Jun 2022
Cited by 2 | Viewed by 2144
Abstract
Antibiotic therapy is necessary for the treatment of bacterial infections; however, it can also disrupt the balance and function of commensal gut microbes and negatively affect the host. Probiotics have been tested as a means to counteract the negative effects of antibiotic therapy, [...] Read more.
Antibiotic therapy is necessary for the treatment of bacterial infections; however, it can also disrupt the balance and function of commensal gut microbes and negatively affect the host. Probiotics have been tested as a means to counteract the negative effects of antibiotic therapy, but many probiotics are also likely destroyed by antibiotics when taken together. Here we aimed to test the efficacy of a non-pathogenic spore-forming Bacillus-species containing a probiotic blend provided during antibiotic therapy on host immune defenses in mice. Mice were exposed to antibiotics and supplemented with or without the probiotic blend and compared to control mice. Fecal and cecal contents were analyzed for gut microbes, and intestinal tissue was tested for the expression of key enzymes involved in vitamin A metabolism, serum amyloid A, and inflammatory markers in the intestine. The probiotic blend protected against antibiotic-induced overgrowth of gram-negative bacteria and gammaproteobacteria in the cecum which correlated with host immune responses. Regional responses in mRNA expression of enzymes involved with vitamin A metabolism occurred between antibiotic groups, and intestinal inflammatory markers were mitigated with the probiotic blend. These data suggest prophylactic supplementation with a spore-forming Bacillus-containing probiotic may protect against antibiotic-induced dysregulation of host immune responses. Full article
(This article belongs to the Special Issue Diet and Gut Microbiome Interactions: Enzymes, Pathways, and Cells)
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Review

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34 pages, 4905 KiB  
Review
Effect of Gut Microbiota Biotransformation on Dietary Tannins and Human Health Implications
by Ibrahim E. Sallam, Amr Abdelwareth, Heba Attia, Ramy K. Aziz, Masun Nabhan Homsi, Martin von Bergen and Mohamed A. Farag
Microorganisms 2021, 9(5), 965; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9050965 - 29 Apr 2021
Cited by 41 | Viewed by 6342
Abstract
Tannins represent a heterogeneous group of high-molecular-weight polyphenols that are ubiquitous among plant families, especially in cereals, as well as in many fruits and vegetables. Hydrolysable and condensed tannins, in addition to phlorotannins from marine algae, are the main classes of these bioactive [...] Read more.
Tannins represent a heterogeneous group of high-molecular-weight polyphenols that are ubiquitous among plant families, especially in cereals, as well as in many fruits and vegetables. Hydrolysable and condensed tannins, in addition to phlorotannins from marine algae, are the main classes of these bioactive compounds. Despite their low bioavailability, tannins have many beneficial pharmacological effects, such as anti-inflammatory, antioxidant, antidiabetic, anticancer, and cardioprotective effects. Microbiota-mediated hydrolysis of tannins produces highly bioaccessible metabolites, which have been extensively studied and account for most of the health effects attributed to tannins. This review article summarises the effect of the human microbiota on the metabolism of different tannin groups and the expected health benefits that may be induced by such mutual interactions. Microbial metabolism of tannins yields highly bioaccessible microbial metabolites that account for most of the systemic effects of tannins. This article also uses explainable artificial intelligence to define the molecular signatures of gut-biotransformed tannin metabolites that are correlated with chemical and biological activity. An understanding of microbiota–tannin interactions, tannin metabolism-related phenotypes (metabotypes) and chemical tannin-metabolites motifs is of great importance for harnessing the biological effects of tannins for drug discovery and other health benefits. Full article
(This article belongs to the Special Issue Diet and Gut Microbiome Interactions: Enzymes, Pathways, and Cells)
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