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Animals
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Nutritional Regulation of Gut Microbiota in Animals
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Nutritional Regulation of Gut Microbiota in Animals

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

Deadline for manuscript submissions: 25 December 2026 | Viewed by 2779

Special Issue Editors

Dr. Huazhe Si

E-Mail Website
Guest Editor
College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
Interests: gut microbiota; nutritional regulation; microbe-metabolite-host interactions
Dr. Shengru Wu

E-Mail Website
Guest Editor
College of Animal Science and Technology, Northwest A&F University, Xianyang, China
Interests: microbiome; rumen; intestinal health
Dr. Ning Liu

E-Mail Website
Guest Editor
State Key Laboratory of Animal Nutrition and Feeding, China Agricultural University, Beijing 100193, China
Interests: gut microbiota; amino acids; animal nutrition; reproduction

Special Issue Information

Dear Colleagues,

This Special Issue, titled “Nutritional Regulation of Gut Microbiota in Animals,” focuses on how diet or feed additives shape microbial communities and microbe–metabolite–host interactions that influence growth, health, welfare, and sustainability across animal species. Its scope spans domestic livestock, Cervids and other special economic animals, companion animals, experimental animals and wildlife under managed care. We welcome original research, reviews, and methodological papers discussing controlled feeding trials; multi-omics (metagenomics, metabolomics, transcriptomics), gnotobiotic or probiotic/prebiotic/postbiotic interventions; modeling of fermentation and VFA/bile-acid pathways; and translational studies linking mechanisms to performance or clinical outcomes. This Special Issue’s goal is to move beyond correlation toward causal, mechanism-based nutrition that can be implemented in practice.

This Special Issue will complement the existing literature by (i) integrating scattered findings across species and diets into a comparative framework, (ii) pairing nutritional manipulations with rigorous multi-omics to define actionable levers, and (iii) encouraging harmonized reporting, data sharing, and replication to improve reproducibility and uptake in the field.

Dr. Huazhe Si
Dr. Shengru Wu
Dr. Ning Liu
Guest Editors

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-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

  • gut microbiota
  • nutritional regulation
  • microbe–metabolite–host interactions
  • short-chain fatty acids
  • bile acids
  • probiotics/prebiotics/postbiotics
  • multi-omics

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Published Papers (3 papers)

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Research

20 pages, 3322 KB  
Article
Oral Administration of Lactobacillus amylovorus Alleviates Diarrhea by Restoring Gut Microbiota and SCFAs in Neonatal Goats
by Mudathir Y. Abdulrahman, Nasir A. Ibrahim, Mohamed Osman Abdalrahem Essa, Saber Y. Adam, Raza Mohai Ud Din, Rifat Ullah Jan, Nosiba S. Basher, Mokhtar Rejili, Shaaban S. Elnesr, Ahmed A. Saleh, Hosameldeen Mohamed Husien and Mengzhi Wang
Animals 2026, 16(4), 633; https://doi.org/10.3390/ani16040633 - 16 Feb 2026
Viewed by 618
Abstract
Diarrhea in kids is a significant health and economic concern for small-scale ruminant farms. This study aims to investigate the properties of Lactobacillus amylovorus as a treatment for kids with diarrhea and its effect on the composition of the gut microbiota. A total [...] Read more.
Diarrhea in kids is a significant health and economic concern for small-scale ruminant farms. This study aims to investigate the properties of Lactobacillus amylovorus as a treatment for kids with diarrhea and its effect on the composition of the gut microbiota. A total of 20 neonatal goats (approximately 2 months old) were divided into three groups: healthy control (HC, n = 4), diarrhea (D, n = 8), and diarrhea treated with probiotic (DT, n = 8). We tracked gut microbial profiles, fecal consistency, short-chain fatty acids (SCFAs), and clinical symptoms. Probiotic-treated kids recovered fully from diarrhea within two weeks, while their untreated counterparts showed signs of clinical deterioration and gradual emaciation. Kids with diarrhea had lower microbial richness, according to alpha diversity analysis, and this was only partially restored after probiotic treatment. The kids with diarrhea had the lowest Shannon, ACE, Simpson, Dominance, Pielou-e, and Chao1 indices compared to the HC group, while the administration of Lactobacillus amylovorus significantly (p < 0.05) restored their normal enrichment in the DT group compared to the D group. The healthy group had a higher abundance of Verrucomicrobiota, while Firmicutes and Bacteroidota predominated in all groups. Bacteroides and Akkermansia predominated in the healthy and treated groups. At the genus level, analysis showed elevated levels of Escherichia-Shigella and UCG-005 in kids with diarrhea. In addition, the concentration of each SCFA in the D group was significantly (p < 0.05) lower than in the HC group. This study provides novel evidence that Lactobacillus amylovorus administration not only alleviates diarrhea but also uniquely restores the production of key SCFAs—including butyrate, acetate, and propionate—in neonatal goats, a finding not previously reported in this species. The concurrent recovery of microbial diversity and SCFA profiles highlights the dual mechanistic potential of Lactobacillus amylovorus as a gut microbiota modulator and metabolic therapeutic in young ruminants. These results lend credence to its potential as a probiotic treatment for small ruminant enteric diseases. Full article
(This article belongs to the Special Issue Nutritional Regulation of Gut Microbiota in Animals)
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15 pages, 3743 KB  
Article
Dynamic Changes in Gut Microbiota Composition and Function over Time in Suckling Raccoon Dogs
by Shaochen Yu, Weixiao Nan, Zhipeng Li, Chongshan Yuan and Chao Xu
Animals 2026, 16(2), 188; https://doi.org/10.3390/ani16020188 - 8 Jan 2026
Viewed by 405
Abstract
Raccoon dog fur is a commercially valuable animal product. As the scale of raccoon dog breeding continues to expand, ensuring the health of these animals has become an urgent priority. The gut microbiota plays a central role in regulating animal health; however, current [...] Read more.
Raccoon dog fur is a commercially valuable animal product. As the scale of raccoon dog breeding continues to expand, ensuring the health of these animals has become an urgent priority. The gut microbiota plays a central role in regulating animal health; however, current research on the composition of raccoon dog gut microbiota remains limited. This study aimed to characterize changes in the gut microbiota of suckling raccoon dogs across different stages, providing a foundation for future scientific feeding practices. Fecal samples of eight lactating raccoon dogs were collected and tested for microbiota on days 14, 21, and 45. Our results showed that the richness and diversity of microbiota increased with age in suckling raccoon dogs, peaking on the 45th day. Significant separation between groups was observed in both PCoA and NMDS analyses. UPGMA analysis indicated temporal fluctuations in gut microbiota composition. At the phylum level, Firmicutes and Bacteroidetes were the dominant taxa across all stages. LEfSe analysis at the genus level showed that Bacteroides was the most enriched taxon on the 14th day, Fusobacterium on the 21st day, and Prevotella_9 on the 45th day. Tax4Fun and PICRUSt analyses identified metabolism and genetic information processing as the primary functional roles of the gut microbiota. Further investigation suggested that the microbiota may benefit raccoon dogs through membrane transport, carbohydrate metabolism, amino acid metabolism, and energy metabolism. These findings establish a theoretical basis for improving the survival rate of suckling raccoon dogs and developing scientifically informed feeding and management protocols. Full article
(This article belongs to the Special Issue Nutritional Regulation of Gut Microbiota in Animals)
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20 pages, 2073 KB  
Article
Rumen-Protected Methionine Supplementation in the Diet Improved the Production Performance of Dairy Goats by Optimizing the Amino Acid Profile and Lipid Metabolism and Modulating the Colonic Microbiome
by Xingwei Jiang, Jiarui Wang, Yuhao Zhang, Jing Li, Huifeng Liu, Shengru Wu and Junhu Yao
Animals 2025, 15(23), 3386; https://doi.org/10.3390/ani15233386 - 24 Nov 2025
Cited by 1 | Viewed by 1247
Abstract
This study aimed to investigate the effects of rumen-protected methionine (RPM) on the production performance of lactating dairy goats. Thirty first-time lactating Guanzhong dairy goats with identical kidding dates and comparable body weights (41.17 ± 3.05 kg) were randomly assigned to two groups: [...] Read more.
This study aimed to investigate the effects of rumen-protected methionine (RPM) on the production performance of lactating dairy goats. Thirty first-time lactating Guanzhong dairy goats with identical kidding dates and comparable body weights (41.17 ± 3.05 kg) were randomly assigned to two groups: (1) CON: basal diet and (2) RPM: basal diet + 7.5 g/day RPM. The duration of the experiment was 21 days. Compared with the CON group, the RPM group presented a significant increase in milk yield, 4% fat-corrected milk (FCM), and feed efficiency; however, no significant difference was observed in dry feed intake (DMI). Moreover, milk fat, protein, lactose, and SNF production was greater in the PRM group than in the CON group. Compared with the CON group, the RPM group presented higher nonesterified fatty acid (NEFA) and very-low-density lipoprotein (VLDL) levels, and no significant differences in the other metabolites were detected. The concentrations of acetate, propionate, and total volatile fatty acids (TVFAs) in the feces of the RPM group were significantly greater than those in the CON group; however, no significant differences were detected in the concentrations of isobutyrate, butyrate, and valerate. Furthermore, genera such as Muribaculaceae, Bifidobacterium, and Christensenellaceae were significantly enriched in the feces of the RPM group. Concurrently, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that the RPM group was significantly enriched in pathways associated with amino acid synthesis, the immune system, and energy metabolism. In summary, dietary supplementation with RPM improved the lipid metabolism function of the liver, increased the abundance of beneficial bacteria such as Muribaculaceae and Bifidobacterium in the colon, and enriched microbial functions related to energy and amino acid metabolism, thereby enhancing colon fermentation and host metabolic status, ultimately improving the production performance of lactating dairy goats. These findings elucidate the positive effects of RPM on the production performance and metabolic health of dairy goats, potentially offering new perspectives and strategies for optimizing dairy production. Full article
(This article belongs to the Special Issue Nutritional Regulation of Gut Microbiota in Animals)
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