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Animals
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Avian Gut Microbiomes
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Avian Gut Microbiomes

A special issue of Animals (ISSN 2076-2615). This special issue belongs to the section "Birds".

Deadline for manuscript submissions: 31 October 2026 | Viewed by 263

Editor

Dr. Jing Liu

E-Mail Website
Guest Editor
Institute of Environmental Health Laboratory and Consulting Group, 15300 Bothell Way NE, Lake Forest Park, WA 98155, USA
Interests: gut microbiota; animal health and disease; NGS; bioinformatics

Special Issue Information

Dear Colleagues,

The poultry industry plays a critical role in meeting the global demand for affordable and high-quality protein. As the sector continues to expand, maintaining poultry health while reducing dependence on antibiotics has become a major challenge. In this context, the gut microbiota has emerged as a key modulator of host health, nutrition, immunity, and disease resistance. Recent advances in microbiome research, next-generation sequencing, and bioinformatics have enabled deeper insights into the complex interactions between gut microbial communities and their avian hosts. This Special Issue aims to highlight the latest findings on the role of gut microbiota in poultry health and disease, including coccidiosis, necrotic enteritis, and other gastrointestinal disorders. We welcome interdisciplinary studies that explore microbiome-based strategies such as probiotics, prebiotics, fecal microbiota transplantation, and precision nutrition to enhance poultry productivity and welfare. Contributions involving host–microbe interactions, functional microbiome analysis, metagenomics, metabolomics, and mechanisms of microbial modulation are particularly encouraged. This Special Issue is open to original research articles and comprehensive reviews that contribute to advancing our understanding of gut microbiota in poultry systems. We invite researchers from microbiology, immunology, animal science, and veterinary medicine to submit their work and help shape the future of sustainable poultry production.

Dr. Jing Liu
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 250 words) can be sent to the Editorial Office for assessment.

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-anonymized peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Animals is an international peer-reviewed open access semimonthly 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 2400 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
  • poultry health
  • coccidiosis
  • necrotic enteritis
  • antibiotic alternatives
  • host–microbe interactions
  • probiotics and prebiotics
  • metagenomics
  • poultry nutrition
  • gut immunity

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Published Papers (1 paper)

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Research

22 pages, 8881 KB  
Article
The Artificial-Feeding System with a Lactic Acid Bacteria-Fermented Diet, Compared with Parent Feeding, Is Associated with Tract-Wide Microbiota Shifts and Coordinated Developmental Indices in Squabs
by Qijun Liang, Jinquan Xi, Shihong Liu, Tieshan Xu, Xinli Zheng, Li Zhang, Shudai Lin, Lizhi Lu, Zongxi Cao, Asmaa Taha Yaseen Kishawy and Lihong Gu
Animals 2026, 16(14), 2145; https://doi.org/10.3390/ani16142145 - 10 Jul 2026
Abstract
Early-life dietary transition is a critical window for gut microbiota assembly and intestinal maturation in squabs. This study compared the overall artificial-feeding system using a lactic acid bacteria-fermented diet (AF) with a parent-feeding system (PF) during 18–25 days of age. Because AF differed [...] Read more.
Early-life dietary transition is a critical window for gut microbiota assembly and intestinal maturation in squabs. This study compared the overall artificial-feeding system using a lactic acid bacteria-fermented diet (AF) with a parent-feeding system (PF) during 18–25 days of age. Because AF differed from PF in both diet exposure and feeding ecology, including manual feeding, absence of parental feeding and crop milk, altered feeding rhythm, and potential loss of parental microbial transmission, the objective was to characterize associations between the two systems rather than to isolate the effect of fermentation alone. Squabs were assigned to AF or PF for 7 days. Microbial communities in the duodenum, jejunum, ileum, and rectum were profiled by 16S rRNA sequencing, and body size traits, organ indices, jejunal morphology, muscle histology, serum biochemical indicators, and muscle composition were assessed. The AF system, characterized by lower pH, a higher acid value, and detectable lactic acid bacteria in the feed, was associated with higher alpha diversity in multiple segments and distinct beta-diversity profiles relative to PF. Across intestinal regions, lactobacilli-related genera were enriched, with Limosilactobacillus consistently identified as the most discriminant genus and, together with Lactobacillus, occupying central positions in exploratory co-occurrence networks. AF was also associated with a greater jejunal villus height and villus height-to-crypt depth ratio, larger muscle fiber dimensions, higher intramuscular fat content with increased levels of selected polyunsaturated fatty acids, altered lipid-related serum indicators, and higher organ indices, including the bursa of Fabricius. PICRUSt2 further suggested differences in predicted functional potential related to carbohydrate, amino acid, lipid, and cofactor/vitamin metabolism, although these outputs represent inference from 16S data rather than directly measured functions. Collectively, the AF system was associated with a lactobacilli-centered, tract-wide microbial signature and coordinated intestinal, muscular, and lipid-related phenotypes in squabs, but the findings should not be interpreted as evidence for fermentation alone. Full article
(This article belongs to the Special Issue Avian Gut Microbiomes)
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