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Microorganisms
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Dietary and Animal Gut Microbiota
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Dietary and Animal Gut Microbiota

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

Deadline for manuscript submissions: 31 July 2025 | Viewed by 6865

Special Issue Editor

Dr. Yu Pi

E-Mail Website
Guest Editor
Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Interests: animal nutrition; gut microbiota; microbial metabolism; gut health; pigs
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The gut microbiota is crucial in animal health and performance, interacting closely with dietary components. Recent research has highlighted how one’s diet shapes the gut microbiota, affecting immune function, nutrient absorption, and overall health. However, the complex interactions between diet and the gut microbiota remain poorly understood, especially across animal species and production systems.

This Special Issue focuses on the relationship between diet and the gut microbiota in animals (e.g., pigs, ruminants, poultry, or pets), examining how these interactions influence health, growth, and disease resistance. The scope of this Special Issue includes, but is not limited to, the following topics: (1) Dietary modulation of the gut microbiota; (2) The role of the gut microbiota in nutrient metabolism; (3) The gut microbiota and immune function; (4) Comparative studies across species; and (5) Technological innovations in microbiota analysis.

Dr. Yu Pi
Guest Editor

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Keywords

  • dietary
  • animal nutrition
  • gut microbiota
  • microbial metabolism
  • gut health

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Published Papers (7 papers)

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Research

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19 pages, 3218 KiB  
Article
Multi-Omics Integration Reveals the Impact of Gastrointestinal Microbiota on Feed Efficiency in Tan Sheep
by Guohan Sun, Xiaohong Han, Tonggao Liu, Xinrui Zhang, An Shi, Chong Yang and Jinzhong Tao
Microorganisms 2025, 13(7), 1608; https://doi.org/10.3390/microorganisms13071608 - 8 Jul 2025
Viewed by 289
Abstract
The rumen and intestinal microbiota play a pivotal role in the digestion and absorption processes of ruminants. Elucidating the mechanisms by which gastrointestinal microbiota influence the feed conversion ratio (FCR) in ruminants is significantly important for enhancing feed utilization efficiency in these animals. [...] Read more.
The rumen and intestinal microbiota play a pivotal role in the digestion and absorption processes of ruminants. Elucidating the mechanisms by which gastrointestinal microbiota influence the feed conversion ratio (FCR) in ruminants is significantly important for enhancing feed utilization efficiency in these animals. In this study, RT-qPCR, 16S rRNA sequencing, and metabolomic techniques were systematically employed to compare the microbial community structures in the rumen, cecum, and rectum, as well as the differences in rumen metabolites between high- and low-FCR Tan sheep. The results showed that, compared to the HFCR group of Tan sheep, the LFCR group exhibited a significant reduction in unclassified_f__Selenomonadaceae, Blvii28_wastewater-sludge_group, and Papillibacter in the rumen; a significant increase in Lachnospiraceae_AC2044_group and Sanguibacteroides; a significant reduction in unclassified_f__Peptostreptococcaceae, Clostridium_sensu_stricto_1, and Parasutterella in the cecum; a significant increase in norank_f__Bacteroidales_UCG-001; and a significant reduction in norank_f__Muribaculaceae, Blautia, and Turicibacter in the rectum. There is a significant positive correlation between Parasutterella in the cecum and three microorganisms, including unclassified_f__Selenomonadaceae, in the rumen. Additionally, Blvii28_wastewater-sludge_group was positively correlated with Lactobacillus. Furthermore, unclassified_f__Selenomonadaceae in the rumen was positively correlated with Turicibacter, unclassified_f__Peptostreptococcaceae, and Breznakia in the rectum. Blvii28_wastewater-sludge_group also showed positive correlations with Blautia, norank_f__Muribaculaceae, and Clostridium_sensu_stricto_1, while Papillibacter was positively correlated with Faecalitalea. The metabolomic results indicated that, compared to the HFCR group, 261 differential metabolites, including Phenylacetylglutamine and Populin, in the rumen of Tan sheep in the LFCR group were significantly downregulated, whereas 36 differential metabolites, including Glycyl-L-tyrosine, were significantly upregulated. Furthermore, the rumen microbe unclassified_f__Selenomonadaceae exhibited positive correlations with significantly differential metabolites such as L-tryptophan, Etiocholanolone glucuronide, N-acetyl-O-demethylpuromycin, and 6-deoxyerythronolide B. Blvii28_wastewater-sludge_group and Papillibacter also exhibited positive correlations with Icilin. High and low FCRs in the rumen of Tan sheep were investigated, especially in relation to unclassified_f__Selenomonadaceae, Blvii28_wastewater-sludge_group, and Papillibacter. Correlations can be seen with microorganisms such as Parasutatella and Lactobacillus in the cecum; Turicibacter, norank_f__Bacteroideales_UCG-001, and Blautia in the rectum; and metabolites such as L-tryptophan, Etiocholanolone glucuronide, and N-acetyl-O-demethylpuromycin. This reveals the role of microorganisms in the digestion and absorption of Tan sheep feed, thus providing a preliminary basis for further research on the microbial regulation of ruminant animal feed utilization and a theoretical basis for improving Tan sheep feed utilization efficiency. Full article
(This article belongs to the Special Issue Dietary and Animal Gut Microbiota)
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20 pages, 2308 KiB  
Article
Effect of Two Selected Levels of Padina gymnospora Biowaste and Enteric Methane Emission, Nutrient Digestibility, and Rumen Metagenome in Growing Sheep
by Archit Mohapatra, Shraddha Trivedi, Chaluvanahalli S. Tejpal, Manojkumar Janardhan Aware, Shalini Vaswani, Vedant Jayeshkumar Prajapati, Atul Purshottam Kolte, Pradeep Kumar Malik, Artabandhu Sahoo, Chandragiri Nagarajarao Ravishankar and Raghavendra Bhatta
Microorganisms 2025, 13(4), 780; https://doi.org/10.3390/microorganisms13040780 - 28 Mar 2025
Cited by 1 | Viewed by 485
Abstract
A study was conducted on growing sheep to investigate the effect of two selected levels of biowaste of Padina gymnospora on feed intake, digestibility, daily enteric methane (CH4) emission, growth performance, and rumen metagenome. We randomly divided the 18 growing male [...] Read more.
A study was conducted on growing sheep to investigate the effect of two selected levels of biowaste of Padina gymnospora on feed intake, digestibility, daily enteric methane (CH4) emission, growth performance, and rumen metagenome. We randomly divided the 18 growing male sheep into three groups of six animals each. The animals were fed on a basal diet comprising finger millet straw (Eleusine coracana) and a concentrate mixture in a 35:65 ratio. The sheep in the control group (C) were offered a concentrate mixture without waste, whereas the wheat bran in the concentrate mixture in test group I (A2) and test group II (A5) was replaced (w/w) with the biowaste of Padina gymnospora at a level of 3.07 and 7.69%, respectively. The biowaste of Padina gymnospora at the above levels in concentrate constituted 2 and 5% of the diet. A significant decrease of 28.4% in daily enteric CH4 emission (g/d) was reported in the A5 group, whereas the difference in daily enteric CH4 emission between the C and A2 & A2 and A5 groups did not prove significant. The inclusion of Padina gymnospora biowaste did not affect the nutrient intake and digestibility among the groups. The inclusion of Padina gymnospora biowaste in the A5 group resulted in a significant reduction (p = 0.0012) in daily CH4 emissions compared with group C; however, no significant differences were observed in daily CH4 emissions between groups C–A2 (p = 0.0793) and A2–A5 (p = 0.3269). Likewise, the adjustment of data to CH4 emissions per 100 g of organic matter intake indicated a substantial decrease in the A5 group relative to C. The energy loss in CH4 as a percentage of GE relative to group C decreased significantly (−23.4%) in the A5 group; however, this reduction was not associated with an increase in productivity, as almost similar average daily gain (p = 0.827) was observed in the groups. The replacement of wheat bran with the biowaste of Padina gymnospora significantly decreased the numbers of total protozoa and holotrichs in the A5 group. Irrespective of the group, the Bacteroidota was the single largest phylum in the rumen metagenome, representing >60% of the microbiota. However, the abundance of Bacteroidota was similar among the groups. The methanogenic phyla Euryarchaeota was the 5th most abundant; however, it constituted only 3.14% of the metagenome. The abundance of Desulfovibrio was significantly higher in the A5 group as compared with the control. In conclusion, the significant increase in the abundance of sulfate-reducing bacteria and reduction in protozoal numbers led to a significant reduction in CH4 emissions with the incorporation of biowaste of Padina gymnospora at a 5% level of the diet. Full article
(This article belongs to the Special Issue Dietary and Animal Gut Microbiota)
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26 pages, 5013 KiB  
Article
Anti-Methanogenic Potential of Seaweeds and Impact on Feed Fermentation and Rumen Microbiome In Vitro
by Pradeep Kumar Malik, Atul Purshottam Kolte, Shraddha Trivedi, Govindan Tamilmani, Archit Mohapatra, Shalini Vaswani, Johnson Belevendran, Artabandhu Sahoo, Achamveetil Gopalakrishnan and Raghavendra Bhatta
Microorganisms 2025, 13(1), 123; https://doi.org/10.3390/microorganisms13010123 - 9 Jan 2025
Cited by 1 | Viewed by 1244
Abstract
A series of in vitro studies were conducted to explore the anti-methanogenic potential of five seaweeds collected from the Indian sea and to optimize the level(s) of incorporation of the most promising seaweed(s) into a straw and concentrate diet to achieve a significant [...] Read more.
A series of in vitro studies were conducted to explore the anti-methanogenic potential of five seaweeds collected from the Indian sea and to optimize the level(s) of incorporation of the most promising seaweed(s) into a straw and concentrate diet to achieve a significant reduction in methane (CH4) production without disturbing rumen fermentation characteristics. A chemical composition analysis revealed a notable ash content varying between 55 and 70% in seaweeds. The crude protein content was highly variable and ranged between 3.25 and 15.3% of dry matter. Seaweeds contained appreciable concentrations of tannins and saponins. Among the seaweeds, Spyridia filamentosa exhibited significantly higher CH4 production, whereas the percentage of CH4 in total gas was significantly lower in the cases of Kappaphycus alvarezii and Sargassum wightii. The ranking of seaweeds in terms of CH4 production (mL/g OM) is as follows: Sargassum wightii < Kappaphycus alvarezii < Acanthophora specifera < Padina gymnospora < Spyridia filamentosa. A remarkable decrease of 31–42% in CH4 production was recorded with the incremental inclusion of Kappaphycus alvarezii at levels of 3–5% of the dry matter in the diet. The addition of Sargassum wightii led to a significant decrease of 36–48% in CH4 emissions when incorporated at levels of 4–5% of dry matter, respectively. The findings of this study revealed a significant decrease in the numbers of total protozoa and Entodinomorphs, coupled with increasing abundances of sulfate-reducing microbes and minor methanogens. Metagenome data revealed that irrespective of the seaweed and treatment, the predominant microbial phyla included Bacteroidota, Bacillota, Pseudomonadota, Actinomycetota, Fibrobacterota, and Euryarchaeota. The prevalence of Methanobrevibacter was similar across treatments, constituting the majority (~79%) of the archaeal community. The results also demonstrated that the supplementation of Kappaphycus alvarezii and Sargassum wightii did not alter the feed fermentation pattern, and therefore, the reduction in CH4 production in the present study could not be attributed to it. Animal studies are warranted to validate the extent of reduction in CH4 production and the key processes involved by supplementation with Kappaphycus alvarezii and Sargassum wightii at the recommended levels. Full article
(This article belongs to the Special Issue Dietary and Animal Gut Microbiota)
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12 pages, 537 KiB  
Article
Impacts of Nano-Composite of Copper and Carbon on Intestinal Luminal Micro-Ecosystem and Mucosal Homeostasis of Yellow-Feather Broilers
by Xianglin Wang, Chunlong Xiao, Shuqing Wu, Qingjie Lin, Shiying Lin, Jing Liu, Dingcheng Ye, Changkang Wang and Pingting Guo
Microorganisms 2024, 12(11), 2247; https://doi.org/10.3390/microorganisms12112247 - 6 Nov 2024
Viewed by 1172
Abstract
The present study was undertaken to evaluate the impacts of nano-composites of copper and carbon (NCCC) on the intestinal luminal micro-ecosystem and mucosal homeostasis of yellow-feather broilers. A total of two-hundred and forty 1-day-old male yellow-feather broilers were randomly allocated into four groups, [...] Read more.
The present study was undertaken to evaluate the impacts of nano-composites of copper and carbon (NCCC) on the intestinal luminal micro-ecosystem and mucosal homeostasis of yellow-feather broilers. A total of two-hundred and forty 1-day-old male yellow-feather broilers were randomly allocated into four groups, each with five replications of twelve birds. The control (CON) group received a corn-soybean basal diet, while the N50, N100, and N200 groups were supplemented with 50, 100, and 200 mg/kg of NCCC in basal diets, respectively. The trial duration was 63 days. The findings demonstrated that there were slight impacts of NCCC addition on the intestinal luminal micro-ecosystem of broilers, with the fecal moisture content in the N100 group being slightly higher on Day 3 in the starter phase (p < 0.05). The cecal microbiota structure also did not obviously change (p > 0.05), in spite of the fall in the relative abundance of the Ruminococcus torques group in the N50 group and norank Clostridia UCG-014 in N200 group (p < 0.05). But for intestinal mucosal homeostasis, NCCC played a crucial part in jejunal morphology, tight junction, immunologic status, and antioxidant capacity. There was linear growth in villus height and a quadratic increase in villus height, crypt depth and their ratio with the increase in NCCC dosage (p < 0.05), and 100 mg/kg NCCC supplementation could intensify the expression of CLDN-3 genes (p < 0.05). In addition, IL-4 and IL-10 linearly increased after NCCC treatment (p < 0.05), along with some irregular changes in sIgA (p < 0.05). In addition, higher jejunal mucosal total antioxidant capacities in N50 and N200 groups were also observed (p < 0.05). Overall, NCCC treatment optimized the intestinal mucosa function of broilers in terms of physical barrier and immune and antioxidant capacities, but exerted subtle influence in the luminal environment of yellow-feather broilers. More precisely, dietary supplementation with 50 mg/kg NCCC is recommended for intestinal homeostasis of broilers. Full article
(This article belongs to the Special Issue Dietary and Animal Gut Microbiota)
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20 pages, 8457 KiB  
Article
Prickly Ash Seeds Improve the Ruminal Epithelial Development and Growth Performance of Hu Sheep by Modulating the Rumen Microbiota and Metabolome
by Qiao Li, Yi Wu, Xingcai Qi, Zilong Liu, Chunhui Wang, Xueyi Ma and Youji Ma
Microorganisms 2024, 12(11), 2242; https://doi.org/10.3390/microorganisms12112242 - 6 Nov 2024
Cited by 3 | Viewed by 1068
Abstract
It is known that the addition of feed rich in bioactive components to animal diets will affect rumen fermentation parameters and flora structure. However, research on the regulatory effects of prickly ash seeds (PASs) during rumen development or on the rumen microbiome and [...] Read more.
It is known that the addition of feed rich in bioactive components to animal diets will affect rumen fermentation parameters and flora structure. However, research on the regulatory effects of prickly ash seeds (PASs) during rumen development or on the rumen microbiome and its metabolites in sheep is limited. The current study was designed to explore the effects of PASs on sheep rumen development and growth performance using metagenomics and metabolomics. Eighteen 3-month-old Hu lambs were randomly allotted to three different dietary treatment groups: 0% (basal diet, CK), 3% (CK with 3% PAS, low-dose PAS, LPS), and 6% (CK with 6% PAS, high-dose PAS, HPS) PASs. The lambs were slaughtered to evaluate production performance. Our results showed that dietary PAS addition improved the average daily gain and reduced the F/G ratio of the experimental animals. Additionally, the height and width of the rumen papilla in the treatment groups were significantly higher than those in the CK group. The fermentation parameters showed that the levels of acetate and butyrate were significantly higher in the LPS group than in the CK and HPS groups. The propionate levels in the HPS group were significantly higher than those in the CK and LPS groups. Metagenomics analysis revealed that PAS dietary supplementation improved the abundance of Clostridiales and Bacteroidales and reduced the abundance of Prevotella, Butyrivibrio, and Methanococcus. Metabolomic analyses revealed that increased metabolite levels, such as those of serotonin, L-isoleucine, and L-valine, were closely related to growth-related metabolic pathways. The correlations analyzed showed that papilla height and muscular thickness were positively and negatively correlated with serotonin and L-valine, respectively. Average daily gain (ADG) was positively and negatively correlated with L-valine and several Prevotella, respectively. In addition, muscular thickness was positively correlated with Sodaliphilus pleomorphus, four Prevotella strains, Sarcina_sp_DSM_11001, and Methanobrevibacter_thaueri. Overall, PAS addition improved sheep growth performance by regulating beneficial microorganism and metabolite abundances, facilitating bacterial and viral invasion resistance. Full article
(This article belongs to the Special Issue Dietary and Animal Gut Microbiota)
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Review

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26 pages, 1156 KiB  
Review
The Biological Functions of Yeast and Yeast Derivatives and Their Application in Swine Production: A Review
by Yuyang Fan, Chenggang Yin, Lei Xu, Rong Bai, Zixi Wei, Ge Gao, Yanpin Li, Wenjuan Sun, Xilong Li and Yu Pi
Microorganisms 2025, 13(7), 1669; https://doi.org/10.3390/microorganisms13071669 - 16 Jul 2025
Viewed by 377
Abstract
Yeast and its derivatives, including yeast extract and yeast cell wall, are well established as safe and environmentally sustainable feed additives that significantly improve animal production performance and health. Their incorporation into swine production serves as an innovative nutritional strategy aimed at improving [...] Read more.
Yeast and its derivatives, including yeast extract and yeast cell wall, are well established as safe and environmentally sustainable feed additives that significantly improve animal production performance and health. Their incorporation into swine production serves as an innovative nutritional strategy aimed at improving growth performance, bolstering health status, and enhancing immune function in pigs. As a versatile microorganism, yeast generates a variety of bioactive compounds through fermentation, such as amino acids, vitamins, enzymes, and growth factors, which collectively contribute to improved growth and overall health in pigs. This review consolidates current research on the utilization of yeast and yeast derivatives in swine production, highlighting their biological functions and practical implications within the industry. Full article
(This article belongs to the Special Issue Dietary and Animal Gut Microbiota)
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14 pages, 934 KiB  
Review
The Influence of Microbiota on Wild Birds’ Parental Coprophagy Behavior: Current Advances and Future Research Directions
by Saba Gul, Yurou Shi, Jie Hu and Sen Song
Microorganisms 2024, 12(12), 2468; https://doi.org/10.3390/microorganisms12122468 - 30 Nov 2024
Cited by 1 | Viewed by 1353
Abstract
This comprehensive review provides an in-depth exploration of the intriguing phenomenon of parental coprophagy in wild birds and its profound implications on the influence of adult avian parents’ health. This review investigates the composition and dynamics of avian feces’ microbiota, casting light on [...] Read more.
This comprehensive review provides an in-depth exploration of the intriguing phenomenon of parental coprophagy in wild birds and its profound implications on the influence of adult avian parents’ health. This review investigates the composition and dynamics of avian feces’ microbiota, casting light on the various dietary, environmental, and genetic factors that influence its diversity. Furthermore, it emphasizes parental coprophagy, a behavior observed in numerous bird species, particularly among herbivorous and passerine birds. The review investigates multiple hypotheses proposed to explain the occurrence of coprophagy. It delves into its function as a potential mechanism for transmitting microorganisms, particularly feces bacteria, from nestlings to their parents. This microbial transfer may affect the health and well-being of adult avian parents. In addition, the review highlights the current research deficits and debates surrounding coprophagy. These gaps include crucial aspects such as the onset of coprophagy, its long-term effects on both parents and offspring, the nutritional implications of consuming nestling feces, the potential risks of pathogen transmission, and the ecological and evolutionary factors that drive this behavior. As the review synthesizes existing knowledge and identifies areas requiring additional research, it emphasizes the significance of future studies that comprehensively address these gaps. By doing so, we can understand coprophagy’s ecological and evolutionary significance in wild birds, advancing our knowledge on avian biology. This information can improve conservation efforts to protect migratory bird populations and their complex ecosystems. Full article
(This article belongs to the Special Issue Dietary and Animal Gut Microbiota)
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