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Nutritional Modulation in Ruminants: Integrated Transcripts and Microbiome Analyses

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A special issue of Animals (ISSN 2076-2615).

Deadline for manuscript submissions: closed (30 November 2021) | Viewed by 9187

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Special Issue Editors

Dr. Francesca Bennato

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Guest Editor

Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, 64100 Teramo, TE, Italy
Interests: animal nutrition; animal product quality; sustainable animal production; rumen microbiota
Special Issues, Collections and Topics in MDPI journals

Dr. Camillo Martino

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Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise “G. Caporale”, Via Campo Boario 37, 64100 Teramo, Italy
Interests: animal nutrition; animal product quality; animal transcriptomics; animal health and welfare; microbiota

Dr. Cesare Cammà

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Department of Molecular Biology and Omics Technologies, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", 64100 Teramo (TE), Italy
Interests: genomics; microbiology; metagenomics; next-generation sequencing

Special Issue Information

Dear Colleagues,

Recently, the development of ‘omics’ technologies such as metagenomics, transcriptomics, proteomics, and metabolomics has opened up new avenues regarding our understanding of interactions between biological and molecular processes and animal nutrition. The different components of diet and metabolites, the lack or excess of nutrients, and the use of supplements can interfere with gene expression and cellular functions. In addition, animal nutrition is the principal factor in maintaining the balance of gut microbiota, which in turn influences the health of the gastrointestinal epithelium. The gastrointestinal tract plays a crucial role in feed digestion, nutrient absorption, and immune and endocrine functions and is the basis for nutrient deposition and healthy growth.

The aim of this Special Issue, entitled “Nutritional Modulation in Ruminants: Integrated Transcripts and Microbiome Analyses” is to collect studies concerning the relationship among ruminant nutrition, gene expression, and microbiome. Applications of new, high-throughput techniques based on the multi-omics approach combining metagenomics (amplicon-based metagenomic, shotgun metagenomics) and transcriptomics (microarrays, RNA seq) are welcome.

Dr. Francesca Bennato
Dr. Camillo Martino
Dr. Cesare Cammà
Guest Editors

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Keywords

Ruminant
Nutrition
Gene expression
Microbiome
‘Omics’ technologies
Animal health and welfare
Metagenomics

Published Papers (3 papers)

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Research

23 pages, 2957 KiB

Open AccessArticle

Diet Transition from High-Forage to High-Concentrate Alters Rumen Bacterial Community Composition, Epithelial Transcriptomes and Ruminal Fermentation Parameters in Dairy Cows

by Sonny C. Ramos, Chang Dae Jeong, Lovelia L. Mamuad, Seon Ho Kim, Seung Ha Kang, Eun Tae Kim, Yong Il Cho, Sung Sill Lee and Sang Suk Lee

Animals 2021, 11(3), 838; https://doi.org/10.3390/ani11030838 - 16 Mar 2021

Cited by 36 | Viewed by 3734

Abstract

Effects of changing diet on rumen fermentation parameters, bacterial community composition, and transcriptome profiles were determined in three rumen-cannulated Holstein Friesian cows using a 3 × 4 cross-over design. Treatments include HF-1 (first high-forage diet), HC-1 (first high-concentrate diet), HC-2 (succeeding high-concentrate diet), and HF-2 (second high-forage diet as a recovery period). Animal diets contained Klein grass and concentrate at ratios of 8:2, 2:8, 2:8, and 8:2 (two weeks each), respectively. Ammonia-nitrogen and individual and total volatile fatty acid concentrations were increased significantly during HC-1 and HC-2. Rumen species richness significantly increased for HF-1 and HF-2. Bacteroidetes were dominant for all treatments, while phylum Firmicutes significantly increased during the HC period. Prevotella, Erysipelothrix, and Galbibacter significantly differed between HF and HC diet periods. Ruminococcus abundance was lower during HF feeding and tended to increase during successive HC feeding periods. Prevotellaruminicola was the predominant species for all diets. The RNA sequence analysis revealed the keratin gene as differentially expressed during the HF diet, while carbonic-anhydrase I and S100 calcium-binding protein were expressed in the HC diet. Most of these genes were highly expressed for HC-1 and HC-2. These results suggested that ruminal bacterial community composition, transcriptome profile, and rumen fermentation characteristics were altered by the diet transitions in dairy cows. Full article

(This article belongs to the Special Issue Nutritional Modulation in Ruminants: Integrated Transcripts and Microbiome Analyses)

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13 pages, 2139 KiB

Open AccessArticle

Effects of Multi-Species Direct-Fed Microbial Products on Ruminal Metatranscriptome and Carboxyl-Metabolome of Beef Steers

by Megan McCoun, Adeoye Oyebade, Zaira M. Estrada-Reyes, Andres A. Pech-Cervantes and Ibukun M. Ogunade

Animals 2021, 11(1), 72; https://doi.org/10.3390/ani11010072 - 2 Jan 2021

Cited by 2 | Viewed by 2086

Abstract

We examined the effects of two direct-fed microbial (DFM) products containing multiple microbial species and their fermentation products on ruminal metatranscriptome and carboxyl-metabolome of beef steers. Nine ruminally-cannulated Holstein steers were assigned to 3 treatments arranged in a 3 × 3 Latin square design with three 21-d periods. Dietary treatments were (1) Control (CON; basal diet without additive), (2) Commence (PROB; basal diet plus 19 g/d of Commence), and (3) RX3 (SYNB; basal diet plus 28 g/d of RX3). Commence and RX3 are both S. cerevisiae-based DFM products containing several microbial species and their fermentation products. Mixed ruminal contents collected multiple times after feeding on day 21 were used for metatranscriptome and carboxyl-metabolome analysis. Partial least squares discriminant analysis revealed a distinct transcriptionally active taxonomy profiles between CON and each of the PROB and SYNB samples. Compared to CON, the steers fed supplemental PROB had 3 differential (LDA ≥ 2.0; p ≤ 0.05) transcriptionally active taxa, none of which were at the species level, and those fed SYNB had eight differential (LDA > 2.0, p ≤ 0.05) transcriptionally active taxa, but there was no difference (p > 0.05) between PROB and SYNB. No functional microbial genes were differentially expressed among the treatments. Compared with CON, 3 metabolites (hydroxylpropionic acid and 2 isomers of propionic acid) were increased (FC ≥ 1.2, FDR ≤ 0.05), whereas 15 metabolites, including succinic acid and fatty acid peroxidation and amino acid degradation products were reduced (FC ≤ 0.83, FDR ≤ 0.05) by supplemental PROB. Compared with CON, 2 metabolites (2 isomers of propionic acid) were increased (FC ≥ 1.2, FDR ≤ 0.05), whereas 2 metabolites (succinic acid and pimelate) were reduced (FC ≤ 0.83, FDR ≤ 0.05) by supplemental SYNB. Compared to SYNB, supplemental PROB reduced (FC ≤ 0.83, FDR ≤ 0.05) the relative abundance of four fatty acid peroxidation products in the rumen. This study demonstrated that dietary supplementation with either PROB or SYNB altered the ruminal fermentation pattern. In addition, supplemental PROB reduced concentrations of metabolic products of fatty acid peroxidation and amino acid degradation. Future studies are needed to evaluate the significance of these alterations to ruminal fatty acid and amino acid metabolisms, and their influence on beef cattle performance. Full article

(This article belongs to the Special Issue Nutritional Modulation in Ruminants: Integrated Transcripts and Microbiome Analyses)

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Figure 1

16 pages, 2374 KiB

Open AccessArticle

Dietary Energy Levels Affect Rumen Bacterial Populations that Influence the Intramuscular Fat Fatty Acids of Fattening Yaks (Bos grunniens)

by Rui Hu, Huawei Zou, Hongze Wang, Zhisheng Wang, Xueying Wang, Jian Ma, Ali Mujtaba Shah, Quanhui Peng, Bai Xue, Lizhi Wang, Suonan Zhao and Xiangying Kong

Animals 2020, 10(9), 1474; https://doi.org/10.3390/ani10091474 - 22 Aug 2020

Cited by 25 | Viewed by 2634

Abstract

The yak rumen microflora has more efficient fiber-degrading and energy-harvesting abilities than that of low-altitude cattle; however, few studies have investigated the effects of dietary energy levels on the rumen bacterial populations and the relationship between rumen bacteria and the intramuscular fatty acid profile of fattening yaks. In this study, thirty yaks were randomly assigned to three groups. Each group received one of the three isonitrogenous diets with low (3.72 MJ/kg), medium (4.52 MJ/kg), and high (5.32 MJ/kg) levels of net energy for maintenance and fattening. After 120 days of feeding, results showed that increasing dietary energy significantly increased ruminal propionate fermentation and reduced ammonia concentration. The 16S rDNA sequencing results showed that increasing dietary energy significantly increased the ratio of Firmicutes to Bacteroidetes and stimulated the relative abundance of Succiniclasticum, Saccharofermentans, Ruminococcus, and Blautia populations. The quantitative real-time PCR analysis showed that high dietary energy increased the abundances of Streptococcus bovis, Prevotella ruminicola, and Ruminobacter amylophilus at the species level. Association analysis showed that ruminal acetate was positively related to some intramuscular saturated fatty acid (SFA) contents, and Prevotella was significantly positively related to intramuscular total polyunsaturated fatty acid content and negatively related to intramuscular total SFA content. This study showed that high dietary energy mainly increased ruminal amylolytic and propionate-producing bacteria populations, which gave insights into how the effects of dietary energy on rumen bacteria are related to intramuscular fat fatty acids of fattening yaks. Full article

(This article belongs to the Special Issue Nutritional Modulation in Ruminants: Integrated Transcripts and Microbiome Analyses)

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