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Microorganisms
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Interplays Between Gut Microbiome and Animal Health, Disease and Production...
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Interplays Between Gut Microbiome and Animal Health, Disease and Production Performance

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

Deadline for manuscript submissions: 30 June 2025 | Viewed by 311

Special Issue Editor

Dr. Shi-Yi Chen

E-Mail Website
Guest Editor
College of Animal Science and Technology, Sichuan Agricultural University, Yaan 625014, China
Interests: gut microbiota; domestic animals

Special Issue Information

Dear Colleagues,

Gut microbial communities have been comprehensively involved in regulating host nutrient utilization, immune homeostasis, and production performance in all kinds of domestic animals. Conversely, both host genetic and non-genetic aspects, such as the genomic architecture, living conditions, health status, and production performance, may have significant impacts on the composition, relative abundances, and dynamic changes in gut microbial species. In this context, we are particularly interested in exploring the interplays between gut microbial communities and animal health and disease, as well as the important production traits in farm animals. The rapid advances in collecting and analyzing multi-omics data have largely facilitated studies in this field. Thus, in this Special Issue, we aim to publish original research, reviews, mini-reviews, and perspectives exploring the mutual influences between gut microbiome and diverse aspects of the host in all kinds of domestic animals.

Dr. Shi-Yi Chen
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • gut microbiota
  • host health and disease
  • production traits
  • domestic animals
  • microbiability
  • microbial heritability

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Published Papers (1 paper)

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Research

22 pages, 5183 KiB  
Article
Gut Microbiome—Brain Crosstalk in the Early Life of Chicken Reveals the Circadian Regulation of Key Metabolic and Immune Signaling Processes
by Mridula Gupta, Mustafa Cilkiz, Mohamed M. A. Ibrahim and Giridhar Athrey
Microorganisms 2025, 13(4), 789; https://doi.org/10.3390/microorganisms13040789 - 30 Mar 2025
Viewed by 206
Abstract
Circadian rhythms are innate biological systems that control everyday behavior and physiology. Furthermore, bilateral interaction between the host’s circadian rhythm and the gut microbes influences a variety of health ramifications, including metabolic diseases, obesity, and mental health including GALT physiology and the microbiome [...] Read more.
Circadian rhythms are innate biological systems that control everyday behavior and physiology. Furthermore, bilateral interaction between the host’s circadian rhythm and the gut microbes influences a variety of health ramifications, including metabolic diseases, obesity, and mental health including GALT physiology and the microbiome population. Therefore, we are studying the correlation between differential gene expression in the chicken brain and microbiota abundance during circadian rhythms. To understand this, we raised freshly hatched chicks under two photoperiod treatments: normal photoperiod (NP = 12/12 LD) and extended photoperiod (EP 23/1 LD). The chicks were randomly assigned to one of two treatments. After 21 days of circadian entrainment, the chicks were euthanized at nine time points spaced six hours apart over 48 h to characterize the brain transcriptomes. Each sample’s RNA was extracted, and 36 mRNA libraries were generated and sequenced using Illumina technology, followed by data processing, count data generation, and differential gene expression analysis. We generated an average of 17.5 million reads per library for 237.9 M reads. When aligned to the Galgal6 reference genome, 11,867 genes had detectable expression levels, with a common dispersion value of 0.105. To identify the genes that follow 24 h rhythms, counts per million data were performed in DiscoRhythm. We discovered 577 genes with Cosinor and 417 with the JTK cycle algorithm that exhibit substantial rhythms. We used weighted gene co-expression network analysis (WGCNA) to analyze the correlation between differentially expressed genes and microbiota abundance. The most enriched pathways included aldosterone-regulated sodium reabsorption, endocrine and other factor-regulated calcium reabsorption, GABAergic synapse, oxidative phosphorylation, serotonergic synapse, dopaminergic synapse and circadian entrainment. This study builds on our previous study, and adds new findings about the specific interactions and co-regulation of the brain transcriptome and the gut microbiota. The interaction between gut microbiota and host gene expression highlights the potential benefits of microbiome-modulation approaches to improve gut health and performance in poultry. Full article
(This article belongs to the Special Issue Interplays Between Gut Microbiome and Animal Health, Disease and Production Performance)
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