Unraveling host regulation of gut microbiota through the epigenome–microbiome axis

Trends in Microbiology, Год журнала: 2024, Номер 32(12), С. 1229 - 1240

Опубликована: Июнь 5, 2024

Recent studies of dynamic interactions between epigenetic modifications a host organism and the composition or activity its associated gut microbiota suggest an opportunity for to shape microbiome through alterations that lead changes in gene expression noncoding RNA activity. We use insights from microbiota-induced review potential epigenetically regulate microbiome, which bidirectional 'epigenome–microbiome axis' emerges. This axis embeds environmentally induced variation, may influence adaptive evolution host–microbe interactions. furthermore present our perspective on how epigenome–microbiome can be understood investigated within holo-omic framework with applications applied health food sciences.

Язык: Английский

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The Genetic Architecture of Adaptation to Leaf and Root Bacterial Microbiota inArabidopsis thaliana

Molecular Biology and Evolution, Год журнала: 2023, Номер 40(5)

Опубликована: Апрель 18, 2023

Understanding the role of host genome in modulating microbiota variation is a need to shed light on holobiont theory and overcome current limits description host-microbiota interactions at genomic molecular levels. However, genetic architecture structuring only partly described plants. In addition, most association studies are often carried out outside native habitats where evolves identification signatures local adaptation candidate genes has been overlooked. To fill these gaps dissect driving adaptive plant-microbiota interactions, we adopted genome-environment (GEA) analysis 141 whole-genome sequenced natural populations Arabidopsis thaliana characterized situ for their leaf root bacterial communities fall spring, large range nonmicrobial ecological factors (i.e., climate, soil, plant communities). A much higher fraction among-population variance was explained by genetics than factors. Importantly, relative importance explaining presence particular operational taxonomic units (OTUs) differs between families genera. polygenic highly flexible compartments seasons. Relatedly, were stronger quantitative trait loci (QTLs) spring. Finally, immunity appears as major source assemblages A. thaliana.

Язык: Английский

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Hierarchical eco-evo dynamics mediated by the gut microbiome

Trends in Ecology & Evolution, Год журнала: 2023, Номер 39(2), С. 165 - 174

Опубликована: Окт. 18, 2023

The concept of eco-evolutionary (eco-evo) dynamics, stating that ecological and evolutionary processes occur at similar time scales influence each other, has contributed to our understanding responses populations, communities, ecosystems environmental change. Phenotypes, central these eco-evo processes, can be strongly impacted by the gut microbiome. microbiome shapes dynamics in host community through its effects on phenotype. Complex feedback loops between communities might thus common. Bottom-up when interactions shaping affect phenotypes with consequences population, community, ecosystem levels. Top-down structure

Язык: Английский

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Host genetics drives differences in cecal microbiota composition and immune traits of laying hens raised in the same environment

Poultry Science, Год журнала: 2024, Номер 103(5), С. 103609 - 103609

Опубликована: Март 6, 2024

Vaccination is one of the most effective strategies for preventing infectious diseases but individual vaccine responses are highly heterogeneous. Host genetics and gut microbiota composition two likely drivers this heterogeneity. We studied 94 animals belonging to 4 lines laying hens: a White Leghorn experimental line genetically selected high antibody response against Newcastle Disease Virus (NDV) (ND3) its unselected control (CTR), 2 commercial (White (LEG) Rhode Island Red (RIR)). Animals were reared in same conditions from hatching 42 days age, different genetic mixed. vaccinated at 22 age their humoral NDV was assessed by hemagglutination inhibition assay ELISA blood samples collected 15, 19, 21 after vaccination. The immune parameters three immunoglobulins subtypes A, M, Y cell flow cytometry. caecal end experiment analyzing amplified 16S rRNA gene sequences obtain amplicon sequence variants (ASV). four showed significantly levels measured points, with, logically, higher ND3 line, intermediate low CTR lines, respectively. displayed also proportion (IgA, IgM, IgY). RIR composition. characteristics: composition, abundances all taxonomic levels, correlations between genera response. tested differ functions. These phenotypic differences can be attributed lines. Causal relationships both types discussed will investigated further studies.

Язык: Английский

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Oral Fusobacterium nucleatum resists the acidic pH of the stomach due to membrane erucic acid synthesized via enoyl-CoA hydratase-related protein FnFabM

Journal of Oral Microbiology, Год журнала: 2025, Номер 17(1)

Опубликована: Янв. 21, 2025

Background and Objective Oral bacteria can translocate to the intestine, their colonization efficiency is influenced by gastrointestinal tract pH. Understanding how oral resist acidic environments crucial for elucidating role in gut health disease.

Язык: Английский

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Reviving diversity: cryoprotectants and culturing methods enhance recovery of mammalian gut microbes from field samples

Journal of Mammalogy, Год журнала: 2025, Номер unknown

Опубликована: Янв. 21, 2025

Abstract The field of microbial ecology is increasingly recognizing the need for methods to isolate and culture gut microbes better understand how these microorganisms impact animal physiology, especially in mammalian hosts. Currently, there a lack clear store samples cultivability, when are collected from field, transported laboratory, preserved under long-term storage weeks months compared mere days biomedical field. Here, cecal contents groundhogs (Marmota monax) were processed stored with or without various preservation solutions at −80 °C least 2 months. All then grown distinct nutrient media liquid plate conditions incubated anaerobic aerobic environments. Treatment comparisons revealed that containing 1 more cryoprotectants provided greatest most consistent bacterial densities. To test efficacy solutions, we inventoried taxonomic identities abundances cultures using 16S rRNA amplicon sequencing. Our findings highlight that: (1) exhibited highest richness diversity resembled original conditions; (2) effect individual identity was detectable membership cultured communities, irrespective solutions. study first demonstrate importance multiple further culturing novel isolation. Understanding improving preserve physiology conserve their compositional essential field-collected useful microbiome culturomics studies, promoting comprehension function wild host-associated microbiomes.

Язык: Английский

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Identification of intestinal mediators of Caenorhabditis elegans DBL-1/BMP immune signaling shaping gut microbiome composition

mBio, Год журнала: 2025, Номер unknown

Опубликована: Янв. 29, 2025

ABSTRACT The composition of the gut microbiome is determined by a complex interplay diet, host genetics, microbe-microbe interactions, abiotic factors, and stochasticity. Previous studies have demonstrated importance genetics in community assembly Caenorhabditis elegans identified central role for DBL-1/BMP immune signaling determining abundance Enterobacteriaceae . However, effects DBL-1 on bacteria were found to depend its activation extra-intestinal tissues, highlighting gap our understanding proximal factors that determine composition. In present study, we used RNA-seq gene expression analysis wildtype, dbl-1 sma-3 mutants, over-expressors identify candidate targets may mediate pathway’s commensals. Bacterial colonization experiments or following RNAi-mediated knock-down genes specifically intestine, their local contribution intestinal control abundance. Furthermore, epistasis suggested these contributions downstream pathway, together suggesting examined candidates effectors mediators signaling, contributing shaping IMPORTANCE Compared roles environmental availability, lifestyle composition, genetic least understood often underestimated. identification distinct molecular functions enteric offers glimpse into logic as well list future exploration this logic.

Язык: Английский

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Recent Issues in the Development and Application of Targeted Therapies with Respect to Individual Animal Variability

Animals, Год журнала: 2025, Номер 15(3), С. 444 - 444

Опубликована: Фев. 6, 2025

This literature review explores the impact of molecular, genetic, and environmental factors on efficacy targeted therapies in veterinary medicine. Relevant studies were identified through systematic searches PubMed, Web Science, Scopus, ScienceDirect using keywords such as “species-specific treatment strategies”, “signalling pathways”, “epigenetic paragenetic influences”, “targeted therapies”, “veterinary medicine”, “genetic variation”, “free radicals oxidative stress”. Inclusion criteria included focusing species-specific therapeutic responses, genetic influences, stress. To ensure that only most recent relevant evidence was included, peer-reviewed publications from last two decades considered. Each study selected for analysis critically appraised, with a particular emphasis methodological quality, experimental design, scientific contribution to understanding how biological influence outcomes. A special placed used comparative, cross-species approach assess variability responses potential adverse effects. The synthesises role epigenetic highlights importance understand By highlighting variation, stress, individual species differences, argues personalised approaches. emphasises an would improve care inform future research aimed at optimising therapies, ultimately leading better animal health efficacy. key is its need more protocols take into account profiles factors; it also calls greater integration studies.

Язык: Английский

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Metabolic pathways associated with Firmicutes prevalence in the gut of multiple livestock animals and humans

Animal Microbiome, Год журнала: 2025, Номер 7(1)

Опубликована: Март 3, 2025

Dynamic interspecific interactions and environmental factors deeply impact the composition of microbiotic communities in gut. These intertwined with host's genetic background social habits cooperate synergistically as a hidden force modulating physiological health determinants, certain bacterial species being maintained from generation to generation. Firmicutes, one dominant phyla present across vertebrate classes, exhibits wide range functional capabilities colonization strategies. While ecological scenarios involving microbial specialization metabolic functions have been hypothesized, specific mechanisms that sustain persistence its taxa high diversity hosts remain elusive. This study fills this gap by investigating Firmicutes contributing their prevalence heritability host gut on metagenomes-assembled genomes collected 351 samples, covering 18 food-producing animals humans, breeds closely-related species. We observed belonging Acetivibrionaceae, Clostridiaceae, Lachnospiraceae, Ruminococcaceae, not well understood CAG-74 family were evolutionarily shared all hosts. prevalent exhibit pathways significantly correlated extra-host survival mechanisms, cell adhesion, transmission, highlighted sporulation, glycan biosynthesis, bile acid metabolism, short-chain fatty encoded genes. Our findings provide deeper understanding foundations governing distinct transmission modes, effective establishment, maintenance offering new perspectives both well-known poorly characterized

Язык: Английский

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Herbal extract fermented with inherent microbiota improves intestinal health by exerting antioxidant and anti-inflammatory effects in vitro and in vivo

Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology, Год журнала: 2025, Номер 16(1)

Опубликована: Апрель 5, 2025

Abstract Background Maintaining intestinal health is crucial for the overall well-being and productivity of livestock, as it impacts nutrient absorption, immune function, disease resistance. Oxidative stress inflammation are key threats to integrity. This study explored antioxidant, anti-inflammatory, barrier-strengthening properties a fermented plant macerate (FPM) derived from 45 local herbs, using specifically developed fermentation process utilizing plants’ inherent microbiota enhance bioactivity sustainability. Results In vitro experiments with IPEC-J2 cells showed that FPM significantly reduced intracellular reactive oxygen species (ROS) levels, improved barrier integrity, enhanced cell migration under stress. Similar antioxidant effects were observed in THP-1 macrophages, where ROS production modulated inflammatory responses by decreasing pro-inflammatory cytokines [tumor necrosis factor alpha (TNF-α), monokine induced gamma interferon (MIG), interferon-inducible T chemoattractant (I-TAC), macrophage proteins (MIP)-1α -1β] increasing anti-inflammatory interleukin (IL)-10 levels. Mechanistic studies HEK-Blue reporter lines revealed inhibited nuclear kappa B (NF-κB) activation via toll-like receptor (TLR)4-independent pathway. vivo, levels Drosophila melanogaster activity LT 50 values Caenorhabditis elegans oxidative stress, although did not affect integrity these models. Conclusion The findings indicate shows promising application functional feed supplement improving livestock mitigating inflammation. Further studies, including feeding trials, recommended validate results.

Язык: Английский

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