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Microbiota in the Poultry Gastrointestinal Tract: Implications for Health, Nutrition...
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Microbiota in the Poultry Gastrointestinal Tract: Implications for Health, Nutrition and Productivity

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

Deadline for manuscript submissions: 30 June 2025 | Viewed by 6011

Special Issue Editor

Dr. Yadav Sharma Bajagai

E-Mail Website
Guest Editor
School of Health, Medical and Applied Sciences, Institute for Future Farming Systems, CQUniversity Australia, Norman Gardens, Australia
Interests: microbiome; gut health; genomics

Special Issue Information

Dear Colleagues,

Recent advancements in nucleotide sequencing technologies, accompanied by a significant decrease in costs, have led to an upsurge in microbiome-related research over the past decade. This has enhanced our understanding of the role of intestinal microbiota in health, nutrition and productivity in poultry. The intestinal microbiota is instrumental in a variety of functions, including nutrient digestion, development of the immune system, synthesis of essential nutrients, metabolism regulation, modulation of the gut–brain axis, detoxification, nutrient absorption, enhancement of gut barrier function and mucosal development. These multifaceted roles of the intestinal microbiota are critical in influencing the health, feed efficiency and growth rates of poultry, which, in turn, have direct implications on birds' welfare and the economic yield from the poultry industry. Consequently, maintaining a healthy intestinal microbiota is vital in poultry production. This emerging knowledge has led to numerous studies focusing on modifying the intestinal microbiome, employing cutting-edge next-generation technologies to investigate the intricate interactions between the intestinal microbiome and hosts.

Considering the substantial progress in microbiome research and its profound impact on poultry health and production, we are excited to announce a Special Issue of Animals dedicated to this dynamic field. We cordially invite researchers, scholars and experts to contribute original research papers, reviews and insightful perspectives.

This Special Issue aims to showcase the latest findings and innovations in the role of gastrointestinal microbiota in the health, nutrition and productivity of poultry.

Dr. Yadav Sharma Bajagai
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. 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

  • microbiota
  • microbiome
  • gut health
  • poultry
  • host–microbiome interaction

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Published Papers (4 papers)

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Research

19 pages, 3133 KiB  
Article
Effects of Embryonic Thermal Manipulation on Body Performance and Cecum Microbiome in Broiler Chickens Following a Post-Hatch Lipopolysaccharide Challenge
by Seif Hundam, Mohammad Borhan Al-Zghoul, Mustafa Ababneh, Lo’ai Alanagreh, Rahmeh Dahadha, Mohammad Mayyas, Daoud Alghizzawi, Minas A. Mustafa, David E. Gerrard and Rami A. Dalloul
Animals 2025, 15(8), 1149; https://doi.org/10.3390/ani15081149 - 17 Apr 2025
Viewed by 427
Abstract
Thermal manipulation (TM) during embryogenesis has emerged as a promising strategy to enhance post-hatch performance and improve resilience to environmental and bacterial stress, which offers a potential alternative to reduce the reliance on antibiotic growth promoters (AGPs) in broiler production. This study investigated [...] Read more.
Thermal manipulation (TM) during embryogenesis has emerged as a promising strategy to enhance post-hatch performance and improve resilience to environmental and bacterial stress, which offers a potential alternative to reduce the reliance on antibiotic growth promoters (AGPs) in broiler production. This study investigated TM’s ability to modulate broilers’ cecal microbiota and enhance resilience to lipopolysaccharide (LPS)-induced stress. Eggs in the control group (CON) were incubated at 37.8 °C and 56% relative humidity (RH), while TM eggs were exposed to 39 °C and 65% RH for 18 h daily from embryonic days 10–18. Post-hatch, the LPS subgroups (LPS-CON, LPS-TM) received intraperitoneal LPS injections, and body weight (BW) and temperature (BT) were monitored. Cecal samples were collected for microbiome sequencing. Alpha diversity showed no differences (p > 0.05), but beta diversity revealed differences between groups (PERMANOVA, p < 0.05). Firmicutes and Bacteroidota dominated the microbiota at the phylum level. Oscillospirales were enriched in the TM groups (p < 0.001) and Lactobacillales were increased in the LPS-CON group (p < 0.019). LPS reduced BT in the CON group (p < 0.01), but LPS-TM birds bypassed hypothermia. LPS significantly reduced BW (p < 0.001), while TM had no significant effect. These findings demonstrate TM’s enduring influence on gut microbiota and stress resilience, highlighting its potential to reduce antibiotic reliance and mitigate antimicrobial resistance (AMR) in poultry production. Full article
(This article belongs to the Special Issue Microbiota in the Poultry Gastrointestinal Tract: Implications for Health, Nutrition and Productivity)
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23 pages, 8722 KiB  
Article
16S rRNA Sequencing and Metabolomics to Analyze Correlation Between Fecal Flora and Metabolites of Squabs and Parent Pigeons
by Xiaobin Li, Shengchen Zheng, Haiying Li, Jiajia Liu, Fan Yang, Xiaoyu Zhao and Yafei Liang
Animals 2025, 15(1), 74; https://doi.org/10.3390/ani15010074 - 1 Jan 2025
Viewed by 1023
Abstract
Intestinal microorganisms are essential for maintaining homeostasis, health, and development, playing a critical role in nutrient digestion, growth, and exercise performance in pigeons. In young pigeons, the gut microbiota is primarily acquired through pigeon milk, meaning the microbial composition of parent pigeons directly [...] Read more.
Intestinal microorganisms are essential for maintaining homeostasis, health, and development, playing a critical role in nutrient digestion, growth, and exercise performance in pigeons. In young pigeons, the gut microbiota is primarily acquired through pigeon milk, meaning the microbial composition of parent pigeons directly influences microbial colonization in squabs. However, research on the correlation between the gut microbial diversity of parent pigeons and their offspring remains scarce. This study investigates the fecal microbiota and metabolites of 10 pairs of parent pigeons and 20 squabs raised under a 2 + 2 system. Fecal samples were collected at 15 days of age, and differences in the microbiota and metabolites between the two groups were analyzed using 16S rRNA sequencing and LC-MS/MS. The results showed the following: (1) Squabs exhibited significantly lower α diversity, with a reduction in their Chao1 index and observed OTUs compared to the parent pigeons. (2) Firmicutes dominated the fecal microbiota in both groups, but parent pigeon feces showed a notably higher abundance of Proteobacteria. At the family level, 10 distinct families were identified, with 9 at the genus level and 4 at the species level. (3) A LEfSe analysis identified 16 significantly different bacterial species in the parent pigeons and 7 in the squabs. Functional gene abundance was highest in the metabolism, genetic information processing, and environmental information processing pathways. (4) An LC-MS/MS analysis in cationic mode identified 218 metabolites, with 139 upregulated and 79 downregulated in the squabs relative to the parents. These metabolites were primarily concentrated in five functional categories and enriched in 33 pathways, 2 of which showed significant differences. In conclusion, significant differences in both the α and β diversity of fecal microbiota were observed between squabs and parent pigeons, with similar bacterial species but marked differences in abundance. Metabolite analysis revealed greater richness in the parent pigeon feces. These findings suggest that future gut modulation using beneficial bacteria, such as probiotics, could potentially enhance host health based on microbial and metabolite compositions. Full article
(This article belongs to the Special Issue Microbiota in the Poultry Gastrointestinal Tract: Implications for Health, Nutrition and Productivity)
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15 pages, 2072 KiB  
Article
The Association between Broiler Litter Microbiota and the Supplementation of Bacillus Probiotics in a Leaky Gut Model
by Darwin Horyanto, Yadav S. Bajagai, Juhani von Hellens, Xiaojing Chen, Van Thi Thu Hao, Mark W. Dunlop and Dragana Stanley
Animals 2024, 14(12), 1758; https://doi.org/10.3390/ani14121758 - 11 Jun 2024
Viewed by 1502
Abstract
Probiotics provided from hatch have a major influence on microbiota development, and together with environmental and bedding microbiota, shape the microbial community of the litter. We investigated the influence of probiotic supplementation and a leaky gut challenge induced using dexamethasone (DEX) on the [...] Read more.
Probiotics provided from hatch have a major influence on microbiota development, and together with environmental and bedding microbiota, shape the microbial community of the litter. We investigated the influence of probiotic supplementation and a leaky gut challenge induced using dexamethasone (DEX) on the litter microbial community and litter parameters. The probiotic product was a mix of three Bacillus amyloliquefaciens strains. The litter microbiota were compared to the microbial communities from other gut sections. The litter samples had higher microbial diversity compared to the caecum, gizzard, jejunum, and jejunal mucosa. The high similarity between the litter phylum-level microbiota and gizzard microbiota detected in our study could be a consequence of ingested feed and litter passing through the gizzard. Moreover, the litter microbial community is fundamentally distinct from the intestinal microbiota, as evidenced by the number of genera present in the litter but absent from all the intestinal sections and vice versa. Furthermore, LEfSe analysis identified distinct microbial taxa across different groups, with specific genera associated with different treatments. In terms of litter quality, the birds in the DEX groups had a significantly higher moisture content, indicating successful leaky gut challenge, while probiotic supplementation did not significantly affect the moisture levels. These findings provide comprehensive insights into the distinct microbiota characteristics of litter. Full article
(This article belongs to the Special Issue Microbiota in the Poultry Gastrointestinal Tract: Implications for Health, Nutrition and Productivity)
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19 pages, 4621 KiB  
Article
Dynamic Changes in Intestinal Gene Expression and Microbiota across Chicken Egg-Laying Stages
by Kai Shi, Xiangping Liu, Ying Duan, Xusheng Jiang, Ni Li, Yuesong Du, Dongfeng Li and Chungang Feng
Animals 2024, 14(11), 1529; https://doi.org/10.3390/ani14111529 - 22 May 2024
Cited by 4 | Viewed by 2174
Abstract
Eggs are a vital dietary component for humans, and it is beneficial to increase egg production to support poultry farming. Initially, the egg production rate rises rapidly with young hens until it reaches its peak, and then it declines gradually. By extending the [...] Read more.
Eggs are a vital dietary component for humans, and it is beneficial to increase egg production to support poultry farming. Initially, the egg production rate rises rapidly with young hens until it reaches its peak, and then it declines gradually. By extending the duration of peak egg production, the hens’ performance can be enhanced significantly. Previous studies found dynamic changes in gut microbiota during egg-laying, and several species of microbiota isolated from the chicken gut improved egg-laying performance. However, the interaction between microbes and host gene expression is still unclear. This study provides a more comprehensive understanding of chicken egg-laying by examining dynamic alterations in the microbiota of the entire intestinal tract (i.e., duodenum, jejunum, and ileum) and gene expression. The microbial community in the intestine underwent significant changes during different egg-laying periods (i.e., pre-, peak-, and late-laying periods). Metagenomic functional analysis showed that the relative abundance of biosynthesis of amino acids, secondary metabolites, and cofactors decreased significantly in the duodenum, jejunum, and ileum of aging hens. The relative levels of aldosterone, GnRH, insulin, growth hormone, and other hormone-related pathways increased dramatically in the intestinal microbiota during egg-laying, but only in the microbiota located in the duodenum and ileum. Transcriptome analysis suggested that genes associated with various transport processes were upregulated consistently in the small intestine during egg-laying; genes involved in the development of intestinal structure were down-regulated; and genes involved in response to DNA damage and stress were consistent with changes in laying rate. The abundance of Lactobacillus was related to the expression of ANGPTRL1, ANGPTRL2, ANGPT1L, and NOXO1 in the duodenum; Muricomes was correlated significantly with NFKBIZ, LYG2, and IRG1L expression in the jejunum; and Campylobacter was correlated positively with the expression of KMT2A and USF3 in the ileum. These results indicated that the intestinal microbiota and host gene expression may influence egg production jointly. Full article
(This article belongs to the Special Issue Microbiota in the Poultry Gastrointestinal Tract: Implications for Health, Nutrition and Productivity)
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