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Ruminal Fermentation

A special issue of Fermentation (ISSN 2311-5637). This special issue belongs to the section "Microbial Metabolism, Physiology & Genetics".

Deadline for manuscript submissions: 31 March 2025 | Viewed by 4979

Special Issue Editor


E-Mail Website
Guest Editor
Department of Animal Science, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Unaí, Brazil
Interests: alternative additives; antimicrobials; beef and dairy cattle; composition of ruminal microbiota; deamination; nitrogen metabolism

Special Issue Information

Dear Colleagues,

The success of ruminant animals is associated with their ability to digest fiber-rich plant material. Although ruminants do not secrete digestive enzymes in the rumen, a number of various microorganisms, including bacteria, methanogenic archaea, anaerobic fungi, and protozoa, which live in symbiosis with the host, are capable of performing ruminal fermentation and hydrolyzing soluble and insoluble carbohydrates, proteins, and lipids from the diet.

Ruminal fermentation is the result of the balance of interactions among the different species of microorganisms present in the rumen. It is the outcome of microbiological activities responsible for converting food components (carbohydrates and nitrogen) into products used in animal metabolism, such as volatile organic acids (VOAs), microbial proteins, and B vitamins. This process also produces substances not utilized by the animal (CH4 and CO2), which are physiologically eliminated and represent energy losses.

The proportion and quantity of by-products resulting from the ruminal fermentation process depend on various factors, such as the type of feed, the manner in which the feed is offered, balanced diets, the use of feed additives, as well as physiological factors related to the ruminal environment, such as temperature, pH, and redox potential.

The aim of this Special Issue is to publish both recent innovative research results and review papers that assess ruminal fermentation both in vitro and in vivo using different strategies aimed not only at improving the health and performance of ruminants but also at playing a role in mitigating climate change by reducing ammonia production and greenhouse gas emissions, such as methane. If you would like to contribute a review paper, please contact one of the editors to discuss the topic's relevance before submitting the manuscript.

Prof. Dr. Cláudia Braga Pereira Bento
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. Fermentation 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 2100 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

  • ammoniacal nitrogen
  • animal nutrition
  • antimicrobials
  • enteric methane
  • environmental impact
  • feed additives
  • feed efficiency
  • next-generation sequencing
  • rumen parameters
  • ruminal microbiota
  • ruminants

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Published Papers (5 papers)

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Research

Jump to: Review, Other

17 pages, 923 KiB  
Article
Preliminary Study on the Impact of Ruminal Ciliate Inoculation in Fauna-Free Conditions on the Ruminal Fermentation and Ciliate–Prokaryote Association In Vitro
by Geonwoo Kim, Woohyung Lee and Tansol Park
Fermentation 2025, 11(1), 28; https://doi.org/10.3390/fermentation11010028 - 11 Jan 2025
Viewed by 340
Abstract
Ruminants rely on the rumen for the anaerobic fermentation of fibrous plant materials, facilitated by a complex microbial community of bacteria, archaea, fungi, and ciliates. Among them, ruminal ciliates significantly influence ruminal fermentation, methane production, nitrogen utilization efficiency, and microbial interactions. This study [...] Read more.
Ruminants rely on the rumen for the anaerobic fermentation of fibrous plant materials, facilitated by a complex microbial community of bacteria, archaea, fungi, and ciliates. Among them, ruminal ciliates significantly influence ruminal fermentation, methane production, nitrogen utilization efficiency, and microbial interactions. This study examined the impact of ciliate inoculation on ruminal fermentation, microbial composition, and functional profiles in fauna-free conditions. Six treatments were tested: control (no ciliates), small entodinia, Epidinium spp., isotrichids, Ophryoscolex spp., and a mixed inoculum. Using QIIME2 to analyze 16S rRNA gene sequences, the study revealed group-specific effects on methane production, volatile fatty acids (VFAs), and microbial diversity. Small entodinia inoculation increased Streptococcus abundance, while isotrichids enriched Megasphaera, enhancing butyrate production. Alpha diversity indices indicated reduced richness in the ciliate-inoculated groups, reflecting predation on prokaryotes. Beta diversity showed distinct microbial and functional profiles among the treatments. Functional analysis highlighted elevated glycerolipid metabolism in isotrichid groups, associated with Bacteroides and Megasphaera, suggesting roles in lipid metabolism and oxidative stress resistance. Despite limited ciliate cell counts, the study emphasizes ciliate-specific interactions and the role of lactic acid-associated bacteria in shaping ruminal fermentation. Full article
(This article belongs to the Special Issue Ruminal Fermentation)
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Figure 1

Figure 1
<p>NMDS plots for overall microbiota at different taxonomic levels (phyla, (<b>A</b>); genera, (<b>B</b>), respectively), and prokaryotic functional profile (KEGG orthologs, (<b>C</b>); KEGG pathways, (<b>D</b>), respectively) based on the Bray–Curtis dissimilarity. Red font indicates statistically significant differences (<span class="html-italic">p</span> ≤ 0.05). CON, control group without ciliate added; ENTO, small entodinia inoculated; EPI, <span class="html-italic">Epidinium</span> spp. inoculated; ISO, isotrichids inoculated; OPH, <span class="html-italic">Ophryoscolex</span> spp. inoculated; MIX, mixed group with small entodinia, <span class="html-italic">Epidinium</span> spp., isotrichids, and <span class="html-italic">Ophryoscolex</span> spp. inoculated; <span class="html-italic">NS</span>, no significant difference between treatment groups.</p>
Full article ">Figure 1 Cont.
<p>NMDS plots for overall microbiota at different taxonomic levels (phyla, (<b>A</b>); genera, (<b>B</b>), respectively), and prokaryotic functional profile (KEGG orthologs, (<b>C</b>); KEGG pathways, (<b>D</b>), respectively) based on the Bray–Curtis dissimilarity. Red font indicates statistically significant differences (<span class="html-italic">p</span> ≤ 0.05). CON, control group without ciliate added; ENTO, small entodinia inoculated; EPI, <span class="html-italic">Epidinium</span> spp. inoculated; ISO, isotrichids inoculated; OPH, <span class="html-italic">Ophryoscolex</span> spp. inoculated; MIX, mixed group with small entodinia, <span class="html-italic">Epidinium</span> spp., isotrichids, and <span class="html-italic">Ophryoscolex</span> spp. inoculated; <span class="html-italic">NS</span>, no significant difference between treatment groups.</p>
Full article ">Figure 2
<p>Heatmap of Spearman’s correlation coefficients between the in vitro rumen fermentation parameters and relative abundance of differentially abundant bacterial genera, as well as log copy number total methanogen, total ciliates, and total bacteria after 24 h of incubation (|<span class="html-italic">r</span>| ≥ 0.4, *, <span class="html-italic">p</span> ≤ 0.05; **, <span class="html-italic">p</span> &lt; 0.01; ***, <span class="html-italic">p</span> &lt; 0.001). NH<sub>3</sub>-N, ammonia nitrogen; A:P ratio, acetate-to-propionate ratio.</p>
Full article ">
12 pages, 630 KiB  
Article
Ferulic Acid and Clinoptilolite Affect In Vitro Rumen Fermentation Characteristics and Bacterial Abundance
by Ana Tánori-Lozano, M. Ángeles López-Baca, Adriana Muhlia-Almazán, Maricela Montalvo-Corral, Araceli Pinelli-Saavedra, Thalia Y. Islava-Lagarda, José Luis Dávila-Ramírez, Martín Valenzuela-Melendres and Humberto González-Rios
Fermentation 2024, 10(11), 549; https://doi.org/10.3390/fermentation10110549 - 26 Oct 2024
Viewed by 913
Abstract
This study evaluated the effects of clinoptilolite (CTL) and ferulic acid (FA) supplementation on in vitro ruminal fermentation characteristics, gas production, and bacterial abundance. Treatments were arranged in a 2 × 2 factorial design (FA: 0 or 300 ppm; CTL: 0 or 1%) [...] Read more.
This study evaluated the effects of clinoptilolite (CTL) and ferulic acid (FA) supplementation on in vitro ruminal fermentation characteristics, gas production, and bacterial abundance. Treatments were arranged in a 2 × 2 factorial design (FA: 0 or 300 ppm; CTL: 0 or 1%) with repeated measures over time (2, 4, 8, 12, 24, 36, 48, and 72 h). Throughout the incubation period, the CTL and FAZ treatments recorded the highest pH values (p ≤ 0.05), maintaining levels closest to neutrality after 72 h. After 48 and 72 h, FA and CTL decreased (p ≤ 0.05) the ammonia concentrations while increasing (p ≤ 0.05) acetate and propionate. The methane, butyrate, and iso-VFA concentrations were unaffected (p > 0.05) by any treatment. FA increased the total gas production throughout the experimental period (p ≤ 0.05). Additionally, FA and CTL significantly reduced the relative abundance of Ruminococcus albus and Streptococcus bovis (p ≤ 0.05), while no significant effects were observed for Selenomonas ruminantium (p > 0.05). These findings suggest that both additives can positively modify the rumen fermentation characteristics and microbial composition, which could significantly contribute to animal nutrition by providing a promising strategy for enhancing rumen fermentation. Full article
(This article belongs to the Special Issue Ruminal Fermentation)
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Figure 1

Figure 1
<p>Effects of ferulic acid (FA) and clinoptilolite (CTL) on in vitro gas production (mL/g DM). (<b>A</b>) Cumulative gas production throughout the in vitro fermentation period. (<b>B</b>) Total gas production during the fermentation period. Cumulative gas production was affected by incubation time (<span class="html-italic">p</span> ≤ 0.05). FA (<span class="html-italic">p</span> = 0.014) main effect and FA × CTL interaction (<span class="html-italic">p</span> = 0.040) on total gas production were significant. abcdef, means with different letters, are different (<span class="html-italic">p</span> ≤ 0.05).</p>
Full article ">Figure 2
<p>Effect of ferulic acid (FA) and clinoptilolite (CTL) on relative abundance (relative units) of bacterial species. Different letters denote statistical differences at <span class="html-italic">p</span> ≤ 0.05. Bars represent mean values with standard error.</p>
Full article ">

Review

Jump to: Research, Other

16 pages, 313 KiB  
Review
Ferulic Acid Esterase-Producing Lactobacilli as Silage Inoculants: A Review on the Efficacy of Improving Fiber Composition and Digestibility of Forages
by Estefanía Andrada, María Claudia Abeijón-Mukdsi, Gabriel Vinderola and Roxana Beatriz Medina
Fermentation 2024, 10(12), 614; https://doi.org/10.3390/fermentation10120614 - 30 Nov 2024
Viewed by 675
Abstract
Environmental-, animal-, and plant-associated factors are involved in the intake and digestibility of forages. Ferulated crosslinks are key targets for increasing the extent of fiber digestion in forages, for which ferulic acid esterase-producing lactic acid bacteria (FAE+ LAB) arise as silage inoculants that [...] Read more.
Environmental-, animal-, and plant-associated factors are involved in the intake and digestibility of forages. Ferulated crosslinks are key targets for increasing the extent of fiber digestion in forages, for which ferulic acid esterase-producing lactic acid bacteria (FAE+ LAB) arise as silage inoculants that could beneficially impact animal husbandry. In this review article, we analyze the published effects of these inoculants on silage fiber composition, digestibility measures, ferulic acid content, and animal performance. To date, 17 FAE+ LAB strains have been evaluated in ensiling trials, obtaining variable results. When significant effects were detected, reductions in the content of neutral or acid detergent fiber (1.3–6.6% DM, compared with uninoculated silages) and increased digestibility measures (1.4–9.6% DM) were the most frequent outcomes. FAE+ LAB increased the free FA content of silages in several reports. Factors involved in the variability of responses have been scarcely evaluated but include inoculant strain, strain–forage combination, forage characteristics, and ensiling conditions. Two studies indicate that productive and health improvements were obtained when FAE+ LAB-inoculated silages were predominant in the diet of growing steers or dairy goats. Additional research is needed to understand the factors associated with the performance of FAE+ inoculants and the extent of their potential benefits for animal nutrition. Full article
(This article belongs to the Special Issue Ruminal Fermentation)

Other

Jump to: Research, Review

16 pages, 2790 KiB  
Systematic Review
The Use of Mesquite Pods (Prosopis spp.) as an Alternative to Improve the Productive Performance and Methane Mitigation in Small Ruminants: A Meta-Analysis
by Juan Carlos Angeles-Hernandez, Ever del Jesús Flores Santiago, Eduardo Cardoso-Gutiérrez, Sara S. Valencia-Salazar, Oscar Enrique del Razo Rodriguez, Erwin A. Paz, Juan C. Ku-Vera, Ermias Kebreab, Mohammed Benaouda and Ángel Garduño García
Fermentation 2024, 10(12), 625; https://doi.org/10.3390/fermentation10120625 - 7 Dec 2024
Viewed by 769
Abstract
Mesquite (Prosopis spp.), a highly nutritious legume from arid regions characterized by its secondary metabolites, offers a cost-effective resource to provide energy and protein for small ruminant farmers in harsh environments. In addition, the high concentrations of secondary metabolites found in mesquite [...] Read more.
Mesquite (Prosopis spp.), a highly nutritious legume from arid regions characterized by its secondary metabolites, offers a cost-effective resource to provide energy and protein for small ruminant farmers in harsh environments. In addition, the high concentrations of secondary metabolites found in mesquite pods could be an option to mitigate methane (CH4) emissions. Thus, the aim of this study was to conduct an analytical review to assess the impact of adding mesquite pods on small ruminant productivity and enteric CH4 emissions. A comprehensive and structured search of scientific articles resulted in a database of 38 trials. The response variables were evaluated through raw mean differences (RMDs) and standardized mean differences (SMDs), followed by a meta-regression, used to investigate the heterogeneity of the explanatory variables. Supplementation with mesquite pods significantly increased the dry matter intake (DMI) and average daily gain (ADG) and reduced the feed conversion ratio (FCR), with sheep showing the highest effect. The meta-regression demonstrated that the mesquite pod effect was influenced mainly by the species, level of incorporation and processing of the pods. Studies employing in silico CH4 estimation reported increased emissions when the diets included mesquite pods. In contrast, in vivo studies demonstrated promising results, showing a significant reduction in CH4 emissions when mesquite pods were included in small ruminant diets. Therefore, future research should focus on evaluating mesquite pod supplementation using precise methods to assess CH4 emissions. Full article
(This article belongs to the Special Issue Ruminal Fermentation)
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Figure 1

Figure 1
<p>PRISMA study flow diagram of the systematic review from initial search and screening to final selection of publications to be included in the meta-analysis.</p>
Full article ">Figure 2
<p>Forest plot of dry matter intake (DMI, g/d) from studies on mesquite pods used as dietary supplement in small ruminants [<a href="#B22-fermentation-10-00625" class="html-bibr">22</a>,<a href="#B23-fermentation-10-00625" class="html-bibr">23</a>,<a href="#B24-fermentation-10-00625" class="html-bibr">24</a>,<a href="#B25-fermentation-10-00625" class="html-bibr">25</a>,<a href="#B26-fermentation-10-00625" class="html-bibr">26</a>,<a href="#B27-fermentation-10-00625" class="html-bibr">27</a>,<a href="#B28-fermentation-10-00625" class="html-bibr">28</a>,<a href="#B29-fermentation-10-00625" class="html-bibr">29</a>,<a href="#B30-fermentation-10-00625" class="html-bibr">30</a>,<a href="#B31-fermentation-10-00625" class="html-bibr">31</a>,<a href="#B32-fermentation-10-00625" class="html-bibr">32</a>,<a href="#B33-fermentation-10-00625" class="html-bibr">33</a>].</p>
Full article ">Figure 3
<p>Bubble plot of raw mean difference for dry matter intake (DMI, g/d) by the level of mesquite pod inclusion and processing method.</p>
Full article ">Figure 4
<p>Forest plot of digestibility of dry matter (g/100 g) from studies on mesquite pods used as dietary supplement in small ruminants [<a href="#B23-fermentation-10-00625" class="html-bibr">23</a>,<a href="#B24-fermentation-10-00625" class="html-bibr">24</a>,<a href="#B25-fermentation-10-00625" class="html-bibr">25</a>,<a href="#B27-fermentation-10-00625" class="html-bibr">27</a>,<a href="#B30-fermentation-10-00625" class="html-bibr">30</a>,<a href="#B31-fermentation-10-00625" class="html-bibr">31</a>,<a href="#B32-fermentation-10-00625" class="html-bibr">32</a>,<a href="#B33-fermentation-10-00625" class="html-bibr">33</a>].</p>
Full article ">Figure 5
<p>Forest plot of estimated methane emissions (CH<sub>4</sub>, g/d) from studies on mesquite pods used as dietary supplement in small ruminants [<a href="#B12-fermentation-10-00625" class="html-bibr">12</a>,<a href="#B23-fermentation-10-00625" class="html-bibr">23</a>,<a href="#B24-fermentation-10-00625" class="html-bibr">24</a>,<a href="#B25-fermentation-10-00625" class="html-bibr">25</a>,<a href="#B27-fermentation-10-00625" class="html-bibr">27</a>,<a href="#B30-fermentation-10-00625" class="html-bibr">30</a>,<a href="#B31-fermentation-10-00625" class="html-bibr">31</a>,<a href="#B32-fermentation-10-00625" class="html-bibr">32</a>,<a href="#B33-fermentation-10-00625" class="html-bibr">33</a>].</p>
Full article ">
7 pages, 223 KiB  
Opinion
Impacts of Slow-Release Urea in Ruminant Diets: A Review
by Szu-Wei Ma and Antonio P. Faciola
Fermentation 2024, 10(10), 527; https://doi.org/10.3390/fermentation10100527 - 17 Oct 2024
Cited by 1 | Viewed by 1882
Abstract
The increasing costs of traditional protein sources, such as soybean meal (SBM), have prompted interest in alternative feeds for ruminants. Non-protein nitrogen (NPN) sources, like urea, offer a cost-effective alternative by enabling rumen microorganisms to convert NPN into microbial protein, which is crucial [...] Read more.
The increasing costs of traditional protein sources, such as soybean meal (SBM), have prompted interest in alternative feeds for ruminants. Non-protein nitrogen (NPN) sources, like urea, offer a cost-effective alternative by enabling rumen microorganisms to convert NPN into microbial protein, which is crucial for ruminant nutrition. However, the rapid hydrolysis of urea in the rumen can result in excessive ammonia (NH3) production and potential toxicity. Slow-release urea (SRU) has been developed to mitigate these issues by gradually releasing nitrogen, thereby improving nutrient utilization and reducing NH3 toxicity risks. This review explores SRU’s development, types, mechanisms, and benefits, highlighting its potential to enhance ruminal fermentation, microbial protein synthesis, and overall feed efficiency. SRU formulations include polymer-coated urea, lipid-coated urea, calcium-urea, starea, and zeolite-impregnated urea, each designed to control nitrogen release and minimize adverse effects. Studies have demonstrated that SRU can improve microbial nitrogen efficiency and reduce nitrogen losses, although results regarding feed intake, digestibility, and milk yield are mixed. These discrepancies indicate that factors such as SRU type, diet formulation, and animal breed may influence outcomes. Continued research is essential to optimize SRU applications, aiming to enhance ruminant production, economic viability, and environmental stewardship. Full article
(This article belongs to the Special Issue Ruminal Fermentation)
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