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Animals
Special Issues
Microbiome, Immune and Intestinal Health in Animals
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Microbiome, Immune and Intestinal Health in Animals

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

Deadline for manuscript submissions: 20 July 2025 | Viewed by 9674

Special Issue Editor

Dr. Robert W. Li

E-Mail Website
Guest Editor
USDA, Agricultural Research Service, Animal Parasitic Diseases Laboratory, Beltsville, MD 20705, USA
Interests: animal; livestock; parasite; helminth; drug resistance; climate change; ruminants; therapeutics; vaccines; alternative parasite control
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The intricate interplay between gut microbiota, immune responses, and intestinal health is a critical aspect of animal well-being. In this Special Issue titled “Microbiome, Immune, and Intestinal Health in Animals”, we aim to explore these relationships, with a special emphasis on the control of intestinal parasites. The role of the gut microbiota in shaping immune function, maintaining gut integrity, and its potential in parasite control strategies is of growing interest in the field of animal health.

Intestinal parasites, including helminths and protozoa, pose significant challenges to the health of livestock, companion animals, and wildlife. These parasites can cause a range of health issues, from mild gastrointestinal disturbances to severe systemic diseases. The control of these parasites is essential for the health and productivity of animals, especially in agricultural settings.

In this issue, we invite contributions that shed light on various aspects of microbiome, immune, and intestinal health in animals, including but not limited to:

  • The role of gut microbiota in modulating immune responses to intestinal parasites.
  • The impact of intestinal parasites on the composition and function of the gut microbiota.
  • Novel approaches to controlling intestinal parasites through manipulation of the gut microbiota.
  • The interplay between diet, gut microbiota, and parasite control.

The use of probiotics, prebiotics, and other microbiome-targeted interventions in the management of intestinal parasites. 

We welcome submissions in the form of original research articles, reviews, brief communications, and case reports. Manuscripts can be submitted until the deadline and will undergo peer review upon receipt.

We look forward to your contributions to this important and evolving field of research.

Dr. Robert W. Li
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

  • microbiome
  • immune
  • intestinal health

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Published Papers (5 papers)

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Research

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24 pages, 9916 KiB  
Article
16S rRNA Sequencing Analysis Uncovers Dose-Dependent Cupric Chloride Effects on Silkworm Gut Microbiome Composition and Diversity
by Wantao Rong, Yanqi Wei, Yazhen Chen, Lida Huang, Shuiwang Huang, Yiwei Lv, Delong Guan and Xiaodong Li
Animals 2024, 14(24), 3634; https://doi.org/10.3390/ani14243634 - 17 Dec 2024
Viewed by 1054
Abstract
Copper-based pesticides are extensively used in agriculture, yet their impacts on beneficial insects remain poorly understood. Here, we investigate how cupric chloride exposure affects the gut microbiome of Bombyx mori, a model organism crucial for silk production. Using 16S rRNA sequencing, we analyzed [...] Read more.
Copper-based pesticides are extensively used in agriculture, yet their impacts on beneficial insects remain poorly understood. Here, we investigate how cupric chloride exposure affects the gut microbiome of Bombyx mori, a model organism crucial for silk production. Using 16S rRNA sequencing, we analyzed the gut bacterial communities of fifth-instar silkworm larvae exposed to different concentrations of cupric chloride (0, 4, and 8 g/kg) in an artificial diet. The high-dose exposure dramatically altered the microbial diversity and community structure, where the Bacteroidota abundance decreased from 50.43% to 23.50%, while Firmicutes increased from 0.93% to 18.92%. A network analysis revealed complex interactions between the bacterial genera, with Proteobacteria and Firmicutes emerging as key players in the community response to copper stress. The functional prediction indicated significant shifts in metabolic pathways and genetic information processing in the high-dose group. Notably, the low-dose treatment induced minimal changes in both the taxonomic composition and predicted functions, suggesting a threshold effect in the microbiome response to copper exposure. Our findings provide novel insights into how agricultural chemicals influence insect gut microbiota and highlight potential implications for silkworm health and silk production. This work contributes to understanding the ecological impacts of copper-based pesticides and may inform evidence-based policies for their use in sericulture regions. Full article
(This article belongs to the Special Issue Microbiome, Immune and Intestinal Health in Animals)
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21 pages, 6247 KiB  
Article
The Interactive Effects of Nutrient Density and Breed on Growth Performance and Gut Microbiota in Broilers
by Meiting Jia, Jiaqi Lei, Yuanyang Dong, Yuming Guo and Bingkun Zhang
Animals 2024, 14(23), 3528; https://doi.org/10.3390/ani14233528 - 6 Dec 2024
Cited by 1 | Viewed by 1301
Abstract
This study investigated whether variations in growth response to low nutrient density across breeds are linked to microbiota regulation. Arbor Acres (AA) and Beijing-You (BY) were fed high- (HN) and low-nutrient (LN) diets from day [...] Read more.
This study investigated whether variations in growth response to low nutrient density across breeds are linked to microbiota regulation. Arbor Acres (AA) and Beijing-You (BY) were fed high- (HN) and low-nutrient (LN) diets from day (d) 0 to d42. Body weight, feed intake, and intestinal measurements were recorded, and microbiota from the ileum and cecum were analyzed on d7, d21, and d42. Results showed that AA broilers had greater growth performance with a lower feed conversion ratio (FCR) and greater average daily gain (ADG) than BY chickens. The LN diet negatively affected AA broiler growth due to impaired intestinal development, while BY chickens compensated by increasing feed intake. Microbiota composition was primarily affected by breed than by nutrient density, with AA broilers having more beneficial bacteria and BY chickens having more short-chain fatty acid (SCFA)-producing bacteria. The LN diets reduced anti-inflammatory bacteria such as Shuttleworthia and Eisenbergiella in the cecum on d7. By d21, LN diets decreased Lactobacillus and increased proinflammatory Marvinbryantia, potentially impairing growth. However, LN diets enriched SCFA-producing bacteria like Ruminococcaceae_UCG.013, Eisenbergiella, and Tyzzerella in BY chickens and Faecalitalea in AA broilers by d21, which may benefit gut health. By d42, LN diets reduced genera linked to intestinal permeability and fat deposition, including Ruminococcus_torques_group, Romboutsia, Erysipelatoclostridium, and Oscillibacter. Additionally, LN diets enriched Christensenellaceae_R-7_group in AA broilers, associated with intestinal barrier integrity, and increased anti-inflammatory bacteria Alistipes and Barnesiella in AA broilers and BY chickens, respectively, by d42. Overall, AA broilers were more susceptible to reduced nutrient density due to impaired intestinal development, while BY chickens adapted better by increasing feed intake. The microbiota responses to low nutrient density varied over time, potentially negatively affecting gut health in the early stage and growth in the middle stage but possibly improving lipid deposition and gut health in the middle and late stages. Full article
(This article belongs to the Special Issue Microbiome, Immune and Intestinal Health in Animals)
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18 pages, 3891 KiB  
Article
Altered Gut Microbiome Composition in Dogs with Hyperadrenocorticism: Key Bacterial Genera Analysis
by Hee-Jun Kang, Sang-Won Kim, Seon-Myung Kim, Tae-Min La, Jae-Eun Hyun, Sang-Won Lee and Jung-Hyun Kim
Animals 2024, 14(19), 2883; https://doi.org/10.3390/ani14192883 - 7 Oct 2024
Viewed by 2057
Abstract
Hyperadrenocorticism (HAC) is a common endocrine disorder in dogs, which is associated with diverse metabolic abnormalities. We hypothesized that elevated cortisol levels in dogs with HAC disrupt the gut microbiome (GM), and this disruption persists even after trilostane treatment. This study explored GM [...] Read more.
Hyperadrenocorticism (HAC) is a common endocrine disorder in dogs, which is associated with diverse metabolic abnormalities. We hypothesized that elevated cortisol levels in dogs with HAC disrupt the gut microbiome (GM), and this disruption persists even after trilostane treatment. This study explored GM composition in dogs with HAC. We included 24 dogs, 15 with HAC and 9 healthy controls, and followed up with 5 dogs with HAC who received trilostane treatment. The GM analysis revealed significant compositional changes in dogs with HAC, including reduced microbiome diversity compared to healthy controls, particularly in rare taxa, as indicated by the Shannon index (p = 0.0148). Beta diversity analysis further showed a distinct clustering of microbiomes in dogs with HAC, separating them from healthy dogs (p < 0.003). Specifically, an overrepresentation of Proteobacteria (Pseudomonadota), Actinobacteria, Bacteroides, Enterococcus, Corynebacterium, Escherichia, and Proteus populations occurred alongside a decreased Firmicutes (Bacillota) population. Despite trilostane treatment, gut dysbiosis persisted in dogs with HAC at a median of 41 d post treatment, suggesting its potential role in ongoing metabolic issues. We identified GM dysbiosis in dogs with HAC by examining key bacterial genera, offering insights into potential interventions like probiotics or fecal microbiota transplants for better HAC management. Full article
(This article belongs to the Special Issue Microbiome, Immune and Intestinal Health in Animals)
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14 pages, 3299 KiB  
Article
Integration of Gut Microbiota with Transcriptomic and Metabolomic Profiling Reveals Growth Differences in Male Giant River Prawns (Macrobrachium rosenbergii)
by Quanxin Gao, Hao Huang, Peimin Liu, Xiuxin Zhao, Qiongying Tang, Zhenglong Xia, Miuying Cai, Rui Wang, Guanghua Huang and Shaokui Yi
Animals 2024, 14(17), 2539; https://doi.org/10.3390/ani14172539 - 31 Aug 2024
Viewed by 1638
Abstract
The giant freshwater prawn (GFP; Macrobrachium rosenbergii), a tropical species cultured worldwide, has high market demand and economic value. Male GFP growth varies considerably; however, the mechanisms underlying these growth differences remain unclear. In this study, we collected gut and hemolymphatic samples [...] Read more.
The giant freshwater prawn (GFP; Macrobrachium rosenbergii), a tropical species cultured worldwide, has high market demand and economic value. Male GFP growth varies considerably; however, the mechanisms underlying these growth differences remain unclear. In this study, we collected gut and hemolymphatic samples of large (ML), medium (MM), and small (MS) male GFPs and used the 16S rRNA sequencing and liquid chromatography–mass spectrometry-based metabolomic methods to explore gut microbiota and metabolites associated with GFP growth. The dominant bacteria were Firmicutes and Proteobacteria; higher growth rates correlated with a higher Firmicutes/Bacteroides ratio. Serum metabolite levels significantly differed between the ML and MS groups. We also combined transcriptomics with integrative multiomic techniques to further elucidate systematic molecular mechanisms in the GFPs. The results revealed that Faecalibacterium and Roseburia may improve gut health in GFP through butyrate release, affecting physiological homeostasis and leading to metabolic variations related to GFP growth differences. Notably, our results provide novel, fundamental insights into the molecular networks connecting various genes, metabolites, microbes, and phenotypes in GFPs, facilitating the elucidation of differential growth mechanisms in GFPs. Full article
(This article belongs to the Special Issue Microbiome, Immune and Intestinal Health in Animals)
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Review

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19 pages, 698 KiB  
Review
Black Soldier Fly (Hermetia illucens) Microbiome and Microbe Interactions: A Scoping Review
by Shu-Wei Lin and Matan Shelomi
Animals 2024, 14(22), 3183; https://doi.org/10.3390/ani14223183 - 6 Nov 2024
Cited by 1 | Viewed by 3004
Abstract
Black soldier fly (Hermetia illucens, BSF) is farmed worldwide to convert organic waste into usable biomaterials. Studies on the larval microbiome have been carried out to check for symbiotic or pathogenic microbes and their respective functions and fates. Some studies tested [...] Read more.
Black soldier fly (Hermetia illucens, BSF) is farmed worldwide to convert organic waste into usable biomaterials. Studies on the larval microbiome have been carried out to check for symbiotic or pathogenic microbes and their respective functions and fates. Some studies tested these microbes for industrial applications, while others tested the effects of exogenous microbes as probiotics or for substrate pre-processing to improve larval fitness, bioconversion rates, or nutritional qualities. This review examined all peer-reviewed literature on these topics to consolidate many disparate findings together. It followed the PRISMA guidelines for scoping reviews. The results found no evidence of globally conserved core microbes, as diet strongly correlated with gut microbiome, but some genera appeared most frequently in BSF larval guts worldwide regardless of diet. The gut microbes undoubtably assist in digestion, including pathogen suppression, and so microbial probiotics show promise for future investigations. However, the common gut microbes have not been explored as probiotics themselves, which would be a promising direction for future work. The impacts of BSF bioconversion on pathogens varied, so each rearing facility should investigate and manage their pathogen risks independently. The data summarized in this study provide useful reference points for future investigations into BSF–microbe interactions. Full article
(This article belongs to the Special Issue Microbiome, Immune and Intestinal Health in Animals)
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