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Microorganisms
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Rumen Microorganisms
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Rumen Microorganisms

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

Deadline for manuscript submissions: 31 August 2026 | Viewed by 5506

Special Issue Editors

Dr. Lizhuang Hao

E-Mail Website
Guest Editor
Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, Qinghai Academy of Science and Veterinary Medicine of Qinghai University, Xining 810016, China
Interests: ruminant nutrition; animal feed and feeding; nutritional balance of plateau herbivorous livestock system; biomass and feed utilization
Special Issues, Collections and Topics in MDPI journals
Dr. Jianbo Zhang

E-Mail Website
Guest Editor Assistant
Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining 810016, China
Interests: rumen microbial ecology; rumen microbial interactions; rumen microbial metabolism; rumen microbial function; bioinformatics and omics

Special Issue Information

Dear Colleagues,

The rumen of ruminants—nature's most efficient bioreactor—harbors a complex ecosystem composed of trillions of bacteria, archaea, protozoa, and fungi. This unique microbial fermentation system transforms low-quality plant fibrous materials—inedible by humans—into high-quality animal protein for human consumption, while its reservoir of natural enzyme resources provides disruptive solutions for bioenergy and green industry. Furthermore, methanogenic archaea in the rumen contribute to 30% of global agricultural greenhouse gas emissions; their hydrogenotrophic metabolic pathways represent key targets for emission reduction efforts. Therefore, through systematic research on the rumen and its microbial ecosystem, we can provide support for ensuring food security and environmental sustainability.

This Special Issue aims to gather cutting-edge research and delve into the latest breakthroughs regarding the rumen microbiome in enhancing animal production efficiency, exploring natural enzyme resources, ensuring host health, revealing the mechanisms of methane generation and reduction, and developing novel regulatory technologies. The goal is to provide innovative solutions for improving the quality and efficiency of ruminant production and for global sustainable development.

This Special Issue focuses on the following cutting-edge directions:

  1. Dynamics of Microbial Communities: Composition and functional evolution of rumen and intestinal bacteria, archaea, fungi, and protozoa under dietary interventions and environmental stresses.
  2. Host–Microbe Interactions: Genetic background–microbiome synergistic regulatory mechanisms.
  3. Methane Emission Reduction Innovations: Inhibitor development and microbial targeted regulation.
  4. Resource Exploration and Transformation: Isolation and functional characterization of uncultivated microorganisms; application of extremophilic enzymes in feed/biomanufacturing.
  5. Multi-scale Ecological Analysis: Microbial interaction networks and metabolic flux in the rumen microenvironment.

We invite original research and review papers to jointly promote the groundbreaking applications of the rumen microbiome in enhancing animal health, resource conversion efficiency, and achieving carbon neutrality goals.

Dr. Lizhuang Hao
Guest Editor

Dr. Jianbo Zhang
Guest Editor Assistant

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. Microorganisms is an international peer-reviewed open access monthly 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 2700 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

  • rumen microbiota
  • rumen microbial ecology
  • rumen microbial interactions
  • rumen microbial metabolism, absorption, and function
  • bioinformatics and omics
  • feed conversion efficiency (FCE)
  • methane emission

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Published Papers (6 papers)

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Research

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17 pages, 1263 KB  
Article
Meat Quality Differences Between Ganan Tibetan Sheep and Tianzhu Tibetan Sheep Using Metabolomics and Rumen Microbiota Analyses
by Yayuan Yang, Xindong Luo, Di Lu, Pengcheng Du, Sanye Jier, Xiaohu Wu, Yanan Lv, Pengcheng Dong and Xuezhi Ding
Microorganisms 2026, 14(3), 575; https://doi.org/10.3390/microorganisms14030575 - 3 Mar 2026
Viewed by 487
Abstract
The objective of this study was to investigate the relationships between ruminal microbial communities and carcass traits associated with adipose accumulation in two Tibetan sheep breeds—Gannan and Tianzhu. A total of twenty Tibetan sheep (ten from each breed) were slaughtered, and samples of [...] Read more.
The objective of this study was to investigate the relationships between ruminal microbial communities and carcass traits associated with adipose accumulation in two Tibetan sheep breeds—Gannan and Tianzhu. A total of twenty Tibetan sheep (ten from each breed) were slaughtered, and samples of ruminal contents along with carcass trait data were collected for analysis. Ruminal microbial DNA was analyzed by 16S rRNA gene sequencing, and correlations between microbial composition and carcass traits were examined using correlation analysis and one-way ANOVA. The results showed that marbling score (p = 0.001) and longissimus lipid content (p = 0.007) were positively correlated with the Chao1 richness index, indicating that individuals with higher intramuscular fat content had greater ruminal microbial species richness. At the phylum level, Rikenellaceae RC9 gut group, Ruminococcaceae NK4A214 group were negatively correlated (p ≤ 0.05) with the above fat traits, whereas the abundance of the bacterial family Ruminococcus 1 was positively correlated with marbling score (p = 0.002). Stratified analysis by marbling grade further revealed associations with microbial richness (p ≤ 0.063), diversity (p = 0.044), and Ruminococcus 1 abundance (p < 0.001). However, microbial metabolic pathway prediction showed no significant differences (p ≥ 0.05) between the high- and low-marbling groups. In addition, several microbial taxa were positively correlated (p ≤ 0.05) with rib fat thickness and yield grade. In summary, ruminal microbial composition was closely associated with variations in carcass fat traits. Notably, most of the bacterial taxa associated with intramuscular and subcutaneous fat deposition did not overlap, suggesting that microbial metabolites may regulate fat deposition by influencing distinct adipogenic pathways in the host. Full article
(This article belongs to the Special Issue Rumen Microorganisms)
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22 pages, 6177 KB  
Article
Effects of Different Feeding Methods on Growth Performance, Enzyme Activity, Rumen Microbial Diversity and Metabolomic Profiles in Yak Calves
by Hongli Wang, Wanhao Ma, Muhammad Irfan Malik, Ali Mujtaba Shah, Aixin Liu, Guangwei Hu, Jianwu Jing, Hongkang Li, Yayu Huang, Qunying Zhang, Jianwei Zhou, Binqiang Bai, Yingkui Yang, Zhenqun Wang, Jianbo Zhang and Lizhuang Hao
Microorganisms 2026, 14(1), 81; https://doi.org/10.3390/microorganisms14010081 - 30 Dec 2025
Cited by 2 | Viewed by 777
Abstract
Yaks are important for the ecology and economy of the Qinghai-Tibetan Plateau. The growth of the yak industry depends on sustainable and accelerated growth of calves, sustaining herd reproduction and production systems. Yak calves born in the summer months of June and July [...] Read more.
Yaks are important for the ecology and economy of the Qinghai-Tibetan Plateau. The growth of the yak industry depends on sustainable and accelerated growth of calves, sustaining herd reproduction and production systems. Yak calves born in the summer months of June and July are faced with a heightened risk of winter mortality. Exclusive traditional, natural feeding prolongs the suckling period, and this leads to a series of problems due to the harsh high-altitude environment, such as inadequate nutrition leading to retarded growth and an imbalanced herd structure. To enhance growth performance and breeding efficiency, 12 male calves of similar weights (68.53 ± 6.41 kg) were randomly assigned to a control group (suckle the dam (SU)) or an experimental group (early weaning with full feeding, concentrate and oat hay at a 7:3 ratio (CO)). The results showed that compared with suckling, early weaning with full feeding significantly improved the growth performance, volatile fatty acids and digestive enzyme activity. The abundance of the Firmicutes was reduced, but there was an increased abundance of Bacteroidetes, which affected the rumen metabolome. In conclusion, early weaning with full feeding improves growth performance, promotes rumen fermentation and carbohydrate degradation, reduces the diversity and richness of rumen microbial flora and alters the content and pathways of metabolites in yak calves. These factors contribute to the growth and market readiness of yak calves born in June and July, accelerate herd turnover and enhance the production efficiency of grazing yaks. Full article
(This article belongs to the Special Issue Rumen Microorganisms)
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24 pages, 6447 KB  
Article
Metabolome Combined with 16S rDNA Sequencing Reveals a Novel Mechanistic Insight into the Collaboration of Resveratrol and β-Hydroxy-β-Methylbutyric Acid in Regulating the Meat Quality of Tibetan Sheep Through Altering Rumen Microbiota
by Jiacheng Gan, Qiurong Ji, Kaina Zhu, Zhenling Wu, Xuan Chen, Shengzhen Hou, Linsheng Gui and Chao Yang
Microorganisms 2025, 13(12), 2845; https://doi.org/10.3390/microorganisms13122845 - 15 Dec 2025
Viewed by 681
Abstract
Resveratrol (RES), a natural polyphenol, and β-hydroxy-β-methylbutyric acid (HMB), a key metabolite of leucine, are emerging as potent feed additives in animal production. This study investigated the individual and combined effects of dietary RES and HMB on gut microbiota, metabolic profiles, and meat [...] Read more.
Resveratrol (RES), a natural polyphenol, and β-hydroxy-β-methylbutyric acid (HMB), a key metabolite of leucine, are emerging as potent feed additives in animal production. This study investigated the individual and combined effects of dietary RES and HMB on gut microbiota, metabolic profiles, and meat quality in Tibetan sheep. A total of 120 two-month-old male lambs were randomly assigned to four experimental groups: control (C, basal diet, n = 6), RES (basal diet + 1.5 g/d RES, n = 6), HMB (basal diet + 1.25 g/d HMB, n = 6), and RES-HMB (basal diet + 1.5 g/d RES + 1.25 g/d HMB, n = 6), with 16S rDNA sequencing and LC-MS/MS analyses performed on rumen fluid and longissimus lumborum (LL). Meat quality improved significantly in all supplemented groups, the RES-HMB co-administration exhibited the most pronounced effects, suggesting a synergistic interaction. These improvements were linked to the activation of amino acid (AA) and unsaturated fatty acid biosynthesis pathways, leading to increased levels of AAs and polyunsaturated fatty acids (PUFAs). Concurrently, dietary RES and HMB supplementation enriched the relative abundance of beneficial gut microbiota, notably Christensenellaceae_R-7_group and Solibacillus, which further promoted the production of short-chain fatty acids, AAs, and PUFAs. The study highlights the role of rumen microbiota in regulating muscle metabolism and meat quality, offering a new scientific basis of strategies for using green feed additives in Tibetan sheep. Full article
(This article belongs to the Special Issue Rumen Microorganisms)
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36 pages, 8096 KB  
Article
Enhancing Sheep Rumen Function, and Growth Performance Through Yeast Culture and Oxalic Acid Supplementation in a Hemicellulose-Based Diet
by Natnael D. Aschalew, Jialei Liu, Yuetong Liu, Wuwen Sun, Guopei Yin, Long Cheng, He Wang, Wanzhu Zhao, Longyu Zhang, Ziyuan Wang, Huaizhi Jiang, Tao Wang, Guixin Qin, Yuguo Zhen and Zhe Sun
Microorganisms 2025, 13(12), 2834; https://doi.org/10.3390/microorganisms13122834 - 12 Dec 2025
Cited by 1 | Viewed by 1013
Abstract
Yeast culture (YC) is a microbial product that enhances ruminal fiber breakdown and improves nutrient digestion and utilization. Our previous research showed that oxalic acid (OA) is a crucial metabolite in YC that enhances rumen function. This study aimed to investigate the effects [...] Read more.
Yeast culture (YC) is a microbial product that enhances ruminal fiber breakdown and improves nutrient digestion and utilization. Our previous research showed that oxalic acid (OA) is a crucial metabolite in YC that enhances rumen function. This study aimed to investigate the effects of YC, OA, and their combination (YO) on rumen function, growth, and fattening in sheep. Twenty lambs were divided into 4 groups (ctrl, YC, OA, and YO; n = 5 each) and fed a diet supplemented with 2 levels of YC and 2 doses of OA for 60 days in a 2 × 2 factorial design. Growth and fattening performance, rumen microbiome analysis, serum indices and anti-oxidant levels, and metabolomic profiling were performed. Individual supplementation with YC and OA significantly increased the digestibility of dry matter (DM), organic matter (OM), and crude protein (CP) (p < 0.001); neutral detergent fiber (NDF) (p < 0.05); and acid detergent fiber (ADF) (p < 0.001) and their interaction significantly increased dry matter intake (DMI) (p = 0.05). Serum IgA and IgM levels were higher in the supplemented groups (p < 0.05). Serum calcium levels were higher in the OA and YO groups (p < 0.001). The supplemented groups showed significantly higher growth hormone and superoxide dismutase levels (p < 0.05). The longissimus dorsi muscle had higher levels of iron in the OA and YO groups; zinc in the OA, YO, and YC groups (p < 0.01); and selenium in the YC group (p < 0.05). The OA group had a higher total antioxidant capacity. All supplemented groups showed higher bacterial richness and diversity. Ruminococcus, Succinivibrio, and Fibrobacter were positively correlated with the fermentation and digestibility parameters. The supplementation also altered metabolite levels and types in key physiological pathways. In conclusion, this supplementation improved bacterial composition, nutrient digestibility, weight gain, carcass weight and quality, serum indices, antioxidant levels and metabolomic profiles. This suggests potential for the development of dietary supplements for ruminants. Full article
(This article belongs to the Special Issue Rumen Microorganisms)
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17 pages, 1860 KB  
Article
Effects of Sea Buckthorn Polysaccharides on Rumen In Vitro Fermentation Characteristics and Microbial Composition of Hu Sheep
by Junlin Lan, Zhenzi Xu, Jiahao Li, Xin Li, Yuanyuan Li and Wenju Zhang
Microorganisms 2025, 13(11), 2639; https://doi.org/10.3390/microorganisms13112639 - 20 Nov 2025
Cited by 1 | Viewed by 671
Abstract
This study evaluated the effects of sea buckthorn polysaccharides (SBP) on rumen fermentation in Hu sheep through in vitro fermentation. A single-factor randomized design was employed with four treatment groups in which SBP was added to a basal diet at 0, 1%, 2% [...] Read more.
This study evaluated the effects of sea buckthorn polysaccharides (SBP) on rumen fermentation in Hu sheep through in vitro fermentation. A single-factor randomized design was employed with four treatment groups in which SBP was added to a basal diet at 0, 1%, 2% and 3% of the total ration dry matter (DM). Based on gas production, degradation rates, and fermentation parameters, the control group and the 2% group were selected for 16S rDNA sequencing. The results showed that compared with the control group, the 2% SBP treatment significantly increased gas production rate (p < 0.05). Addition of 2% and 3% SBP significantly increased DM degradability (p < 0.05). SBP supplementation significantly increased fermentation fluid pH (p < 0.05) and altered volatile fatty acid profiles, increasing the acetate/propionate ratio as well as the concentrations of butyrate, isobutyrate and valerate. Compared with the control group, the addition of 2% SBP led to significant changes in the microbial composition of the in vitro rumen fermentation fluid. It significantly increased beneficial bacterial phyla and genera, such as Bacteroidetes, Rikenellaceae_RC9_gut_group and others, while reducing pathogenic bacteria (p < 0.05). Additionally, functional prediction revealed that the SBP group was significantly enriched in pathways related to carbohydrate metabolism, biosynthesis of amino acid, and biosynthesis of secondary metabolites (p < 0.05). In summary, adding 2% SBP to Hu sheep feed can improve the Rumen fermentation and microbial communities. However, higher doses did not yield additional benefits in these measured indicators. Full article
(This article belongs to the Special Issue Rumen Microorganisms)
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Review

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23 pages, 370 KB  
Review
Mechanisms and Applications of Gastrointestinal Microbiota–Metabolite Interactions in Ruminants: A Review
by Urga, Xingdong Wang, Huimin Wei and Gerelt Zhao
Microorganisms 2025, 13(12), 2880; https://doi.org/10.3390/microorganisms13122880 - 18 Dec 2025
Cited by 1 | Viewed by 1411
Abstract
The gastrointestinal microbiota of ruminants constitutes a complex invisible organ, which converts plant fibers into volatile fatty acids (VFAs) and microbial protein through fermentation, serving as the primary energy and protein sources for the host. While substantial progress has been made in characterizing [...] Read more.
The gastrointestinal microbiota of ruminants constitutes a complex invisible organ, which converts plant fibers into volatile fatty acids (VFAs) and microbial protein through fermentation, serving as the primary energy and protein sources for the host. While substantial progress has been made in characterizing this system, critical gaps remain in understanding causal mechanisms and translating knowledge into scalable interventions. This review systematically synthesizes current knowledge on the composition, function, and metabolite profiles of gastrointestinal microbial communities in ruminants, with emphasis on interaction mechanisms, methodological advances, and intervention strategies. We highlight persistent challenges, including the uncultured majority of microbes, causal inference limitations, and translational bottlenecks. The review further evaluates strategies for targeted microbiome modulation aimed at improving production performance and reducing environmental emissions. Finally, we propose integrated research priorities for developing efficient, low-carbon, and sustainable ruminant production systems. Full article
(This article belongs to the Special Issue Rumen Microorganisms)
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