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Dietary Regulation of the Rumen Microbiome and Fermentation

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

Deadline for manuscript submissions: 30 November 2026 | Viewed by 3208

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Dr. Li Min

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Guest Editor

Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
Interests: rumen microbiome; rumen fermentation; dietary intervention; feed additives; methane mitigation
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Special Issue Information

Dear Colleagues,

The rumen microbiome drives ruminant nutrient utilization by orchestrating fermentation pathways that determine energy supply (VFA), microbial protein yield, and greenhouse gas emissions. With increasing pressure to enhance feed efficiency while reducing environmental footprints, “diet–microbiome–fermentation” regulation has become a central theme in ruminant science. Advances in sequencing, metabolomics, and fermentation phenotyping now enable us to move beyond descriptive associations toward testable mechanisms and actionable dietary solutions. We invite you to contribute to the Special Issue of Animals entitled “Dietary Regulation of the Rumen Microbiome and Fermentation.”

This Special Issue will compile mechanistic and applied studies showing how diets and feed additives modulate rumen microbial communities, fermentation patterns, and animal-level outcomes (performance, health, and emissions). The topic aligns with the scope of Animals by covering in animal nutrition and feeding, physiology, microbiology, production, and sustainable livestock systems.

In this Special Issue, original research articles and reviews are welcome. Research areas may include (but are not limited to) the following:

Dietary drivers of rumen community structure and function (forage–concentrate ratio, starch/fiber/protein/lipid profiles);
Feed additives and functional ingredients (e.g., seaweeds, tannins, probiotics/yeasts, essential oils, organic acids, nitrates, 3-NOP);
Microbial cross-feeding, hydrogen sinks, and methanogenesis regulation;
Fermentation outcomes: VFA shifts, ammonia-N utilization, microbial protein synthesis, lactate dynamics, pH stability, and gas kinetics;
Multi-omics and integrative approaches (16S/shotgun, metatranscriptomics, metabolomics, SIP/isotope tracing, network analysis);
Translational studies from in vitro systems to in vivo validation, including dose–response and safety assessments;
Modeling and precision feeding tools linking microbiome changes to fermentation and emissions;
Diet × stress interactions (heat stress, transition period, acidosis risk) and rumen resilience.

I look forward to receiving your contributions.

Dr. Li Min
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 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-anonymized 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

rumen microbiome
rumen fermentation
dietary intervention
feed additives
methane mitigation
hydrogen metabolism
multi-omics
metabolomics
isotope tracing
precision feeding

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Published Papers (4 papers)

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Research

17 pages, 2743 KB

Open AccessArticle

Effects of Replacing Whole-Crop Maize Silage with Pennisetum giganteum Silage on the Rumen Microbial Community in Beef Cattle

by Shuai Fang, Junyu Zhang, Xubiao Han, Mirizhati Aireti, Yong Tuo, Bayin Bate, Meiling Yan, Kailibinuer Abudukaiyoumu and Tongjun Guo

Animals 2026, 16(10), 1535; https://doi.org/10.3390/ani16101535 - 17 May 2026

Viewed by 842

Abstract

This study evaluated the effects of replacing whole-crop maize silage with varying proportions of Pennisetum giganteum silage on rumen fermentation, microbial composition, and metabolic function in beef cattle. A single-factor completely randomized design was employed using 50 healthy crossbred Simmental cattle aged 11–12 months (average body weight: 251.08 ± 51.54 kg). Animals were randomly assigned to five groups, with 10 replicates per group and one animal per replicate. Diets contained 0% (Group A), 25% (Group B), 50% (Group C), 75% (Group D), or 100% (Group E) Pennisetum giganteum silage replacing whole-crop maize silage over a 67-day feeding period, including a 7-day adaptation phase. Rumen fluid samples were collected via rumen catheter at the end of the trial to assess bacterial diversity and functional characteristics. Increasing the proportion of Pennisetum giganteum silage resulted in quadratic changes in volatile fatty acids (VFAs) and propionate (PA) concentrations (p < 0.05), while ammonia nitrogen (NH₃-N) increased linearly (p < 0.05). No significant differences were observed in α- or β-diversity among groups (p > 0.05). Group C exhibited significantly higher relative abundances of Verrucomicrobiota and Prevotellaceae_UCG_003 compared with the other groups (p < 0.05). At the phylum level, Proteobacteria increased linearly, whereas Spirochaetota decreased linearly; at the genus level, Treponema decreased linearly (p < 0.05). LEfSe analysis indicated enrichment of g__Prevotellaceae_UCG_003 and o__WCHB1_41 in Group C, while the relative abundances of f__Enterobacteriaceae and g__Citrobacter were elevated in Group E. Under the conditions of this study, replacing 50% of whole-crop maize silage with Pennisetum giganteum silage enhanced rumen fermentation efficiency and modulated key microbial populations in beef cattle. Full article

(This article belongs to the Special Issue Dietary Regulation of the Rumen Microbiome and Fermentation)

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23 pages, 336 KB

Open AccessArticle

Effects of an Essential Oil Blend on In Vitro Methane Production, In Vitro and In Vivo Nutrient Digestibility, Growth Performance, and Meat Quality in Lithuanian Blackface Lambs

by Tomas Lileikis, Violeta Razmaitė, Virginijus Uchockis and Saulius Bliznikas

Animals 2026, 16(9), 1362; https://doi.org/10.3390/ani16091362 - 29 Apr 2026

Cited by 1 | Viewed by 538

Abstract

Essential oil-based feed additives have been proposed as a practical strategy to mitigate enteric methane emissions in ruminants, but their effects are not always consistent. The objective of this study was to evaluate the effects of dietary supplementation with an essential oil blend on in vitro methane production, rumen fermentation, nutrient digestibility, growth performance, carcass traits, and meat quality in Lithuanian Blackface lambs. We hypothesized that supplementation would induce measurable changes in in vitro methane production and selected rumen fermentation variables, while growth performance and technological meat quality would remain comparable between treatments. Sixty Lithuanian Blackface lambs were allocated to control (C) and treatment (T) groups (30 lambs per group). The C group received a basal diet, and the T group received the same diet supplemented with an essential oil blend, Agolin Ruminant, at a dose rate of 0.1 g/animal/day, consisting of linalool, eugenol, geranyl acetate, and geraniol. An in vitro rumen fermentation assay was performed using rumen fluid pooled within both dietary groups from multiple lambs and incubated as a single batch with four replicate fermentation flasks per treatment (n = 4 fermenters per group) to quantify methane production and in vitro nutrient digestibility. In vivo apparent nutrient digestibility was evaluated in a dedicated sub-trial (n = 6 animals per group). Growth performance in the main trial was analyzed using the pen as the experimental unit (n = 3 pens per group), and slaughter-based measurements—including slaughter and carcass traits, rumen volatile fatty acids and protozoal counts, and Longissimus dorsi meat quality and intramuscular fatty acids—were determined in 10 lambs per treatment (n = 10 animals per group). In vitro methane production did not differ between groups (p = 0.366); in vitro crude fiber digestibility showed a tendency to increase with supplementation (p = 0.066). Fermentation end-products were largely unchanged, although propionate tended to be higher (p = 0.063), and the acetate:propionate ratio was lower (p = 0.043) in the supplemented group; protozoal counts were not different between groups. In vivo apparent nutrient digestibility was comparable between treatments. Growth performance was lower in the supplemented group, resulting in an overall mean ADG 19.0% lower. Slaughter and carcass traits were comparable between treatments. Meat proximate composition, cholesterol concentration, pH, color, water losses, and instrumental texture/shear parameters were not affected by supplementation. Intramuscular lauric (C12:0), myristic (C14:0), and pentadecanoic (C15:0) fatty acids were lower (p < 0.05), while C14:1 n-7 tended to decrease (p = 0.050); however, total saturated, monounsaturated, and polyunsaturated fatty acids and nutritional ratios were unchanged. Overall, under the study conditions and dose used, the essential oil blend did not significantly reduce in vitro methane production and elicited only limited rumen fermentation responses; ADG was 19.0% lower in the supplemented group, whereas carcass traits and technological meat quality were unaffected, and only specific intramuscular fatty acids were altered. Full article

(This article belongs to the Special Issue Dietary Regulation of the Rumen Microbiome and Fermentation)

21 pages, 1297 KB

Open AccessArticle

Effects of Calf Starter Neutral Detergent Fiber Levels and Weaning on Growth and Rumen Microbial Diversity of Holstein Calves

by Özge Sayın Özdemir, Umair Ahsan, Ifrah Raza and Özcan Cengiz

Animals 2026, 16(9), 1316; https://doi.org/10.3390/ani16091316 - 25 Apr 2026

Viewed by 498

Abstract

A study was conducted to evaluate the effect of neutral detergent fiber (NDF) levels of calf starter and weaning time on growth, rumen fermentation characteristics, serum metabolites, and rumen microbial diversity of Holstein calves. A total of 24 newly born male Holstein calves were randomly distributed to four groups in a completely randomized design with a 2 × 2 factorial arrangement of NDF levels (14% and 24%) and weaning time (d 44 and d 54). There was no interaction between starter NDF levels and weaning time for any trait except rumen acetic acid in the immediate post-weaning phase (p = 0.013). Starter NDF levels had no effect on growth, feed intake, and hay intake. Late-weaned calves had greater (p = 0.050) weight gain in the pre-weaning phase whereas, early-weaned calves showed greater weight gain (p = 0.004) and starter intake (p = 0.004) in the post-weaning phase although overall weight gain, and starter and hay intakes were not affected by weaning time. Rumen pH, ammonia nitrogen, and most volatile fatty acids remained unaffected by starter NDF levels and weaning except isobutyric acid which was greater in calves fed 24% NDF starter (p = 0.001) in the immediate post-weaning and isovaleric acid which was greater in early-weaned calves (p = 0.044) at the end of experiment. Serum metabolites were largely affected (p < 0.05) by starter NDF levels and weaning time in the pre-weaning phase only. Alpha diversity of rumen microbes was greater and chaotic in 14% NDF starter group (early- and late-weaned) in the pre-weaning phase which converged in the immediate post-weaning phase and diverged on starter NDF basis at the end of experiment. Microbial ecology at phylum and genus levels composition were greatly driven by starter NDF levels in the pre-weaning phase, by weaning time in the immediate post-weaning phase, and two distinct bifurcated microbial ecologies based on starter NDF levels appeared at the end of experiment. In conclusion, the comparable growth with distinct microbial diversity but largely in favor of 24% NDF starter suggests that calves can be subjected to early weaning with 24% starter NDF levels for smooth transition from liquid to solid feed in Holstein calves. Full article

(This article belongs to the Special Issue Dietary Regulation of the Rumen Microbiome and Fermentation)

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22 pages, 3376 KB

Open AccessArticle

Effects of Dietary Non-Fibrous Carbohydrate to Neutral Detergent Fiber Ratio on Apparent Digestibility, Fecal Microbiota, and Plasma Metabolomics in Yili Horses

by Mengfei Li, Zihao Xu, Long Sun, Zhiqiang Cheng, Yingying Yu, Yong Chen, Fengming Li and Changjiang Zang

Animals 2026, 16(5), 844; https://doi.org/10.3390/ani16050844 - 7 Mar 2026

Cited by 1 | Viewed by 736

Abstract

This study aimed to investigate the effects of dietary NFC/NDF ratio on nutrient apparent digestibility, fecal fermentation parameters, microbial diversity, and plasma metabolomics in Yili horses. Twenty-four healthy Yili horses with similar body weights (406 ± 22.73 kg) were divided into four groups, each with six replicates: the Control Group (CG), Low-NFC Group (LG), Medium-NFC Group (MG), and High-NFC Group (HG). The experiment lasted 52 d, comprising a 7-day adaptation period and a 45-day experimental period. Total fecal collection was conducted from days 41 to 45 to calculate nutrient apparent digestibility. On the final day, rectal fecal samples and blood samples were collected for full-length 16S rRNA gene sequencing and plasma metabolomics analysis. The results revealed the following findings: (1) The apparent digestibility of crude protein (CP) in the MG and HG groups was significantly higher than in the CG (p < 0.01), and significantly higher in the LG group compared to the CG (p < 0.05). (2) Significant differences were observed in fecal pH, propionate concentration, and the acetate-to-propionate ratio between the CG and the experimental groups (p < 0.05). (3) At the phylum level, Firmicutes, Bacteroidota, and Verrucomicrobiota were dominant in the fecal microbiota of all groups. PICRUSt2 prediction indicated that the MG and HG groups primarily enhanced energy conversion efficiency through amino acid metabolism and pantothenate and CoA biosynthesis metabolic pathways. (4) A total of 204 differential metabolites were identified between the CG and MG groups, with 98 upregulated and 106 downregulated in the MG group compared to the CG. These metabolites were mainly enriched in pantothenate and CoA biosynthesis, fructose and mannose metabolism, pyruvate metabolism, and starch and sucrose metabolism pathways. In summary, appropriately increasing NFC/NDF content influences the gut microbiota composition and energy metabolism of Yili horses, thereby effectively improving their digestion and absorption of dietary nutrients. Full article

(This article belongs to the Special Issue Dietary Regulation of the Rumen Microbiome and Fermentation)

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