Rumen metaproteomics: Closer to linking rumen microbial function to animal productivity traits

Andersen, Thea Os; Kunath, Benoît J.; Hagen, Live Heldal; Arntzen, Magnus Ø.; Pope, Phillip B.

doi:10.1016/j.ymeth.2020.07.011

Cited by 26 publications

(16 citation statements)

References 98 publications

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“…Rumen and its microbial abundance are closely related to the growth traits of ruminants ( Andersen et al, 2021 ). Large amounts of VFAs and microbial proteins were produced in rumen with the assistance of rumen microbes ( Krause et al, 2020 ; Newbold and Ramos-Morales 2020 ; Chai et al, 2021 ), which are important sources of energy, fatty acids, and amino acids for ruminants ( Bergman 1990 ; Pathak 2008 ; Li et al, 2013 ; Liu et al, 2018 ).…”

Section: Discussionmentioning

confidence: 99%

Transcriptome Analysis of Bovine Rumen Tissue in Three Developmental Stages

Zhang

Cai

et al. 2022

Front. Genet.

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Rumen development is a crucial physiological challenge for ruminants. However, the molecular mechanism regulating rumen development has not been clearly elucidated. In this study, we investigated genes involved in rumen development in 13 rumen tissues from three developmental stages (birth, youth, and adult) using RNA sequencing. We identified that 6,048 genes were differentially expressed among three developmental stages. Using weighted correlation network analysis, we found that 12 modules were significantly associated with developmental stages. Functional annotation and protein–protein interaction (PPI) network analysis revealed that CCNB1, CCNB2, IGF1, IGF2, HMGCL, BDH1, ACAT1, HMGCS2, and CREBBP involved in rumen development. Integrated transcriptome with GWAS information of carcass weight (CW), stomach weight (SW), marbling score (MS), backfat thickness (BFT), ribeye area (REA), and lean meat weight (LMW), we found that upregulated DEGs (fold change 0∼1) in birth–youth comparison were significantly enriched with GWAS signals of MS, downregulated DEGs (fold change >3) were significantly enriched with GWAS signals of SW, and fold change 0∼1 up/downregulated DEGs in birth–adult comparison were significantly enriched with GWAS signals of CW, LMW, REA, and BFT. Furthermore, we found that GWAS signals for CW, LMW, and REA were enriched in turquoise module, and GWAS signals for CW was enriched in lightgreen module. Our study provides novel insights into the molecular mechanism underlying rumen development in cattle and highlights an integrative analysis for illustrating the genetic architecture of beef complex traits.

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Section: Discussionmentioning

confidence: 99%

Transcriptome Analysis of Bovine Rumen Tissue in Three Developmental Stages

Zhang

Cai

et al. 2022

Front. Genet.

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“…In the current work, we optimize the procedure for extraction and identification of rumen proteins that, when compared to previous studies, allowed us to substantially improve the number of proteins identified [23,[46][47][48]. We investigated the rumen microbiome state through its produced proteome profile and its link to the host feed efficiency phenotype, previously Fig.…”

Section: Discussionmentioning

confidence: 99%

Metaproteome plasticity sheds light on the ecology of the rumen microbiome and its connection to host traits

et al. 2022

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The arsenal of genes that microbes express reflect the way in which they sense their environment. We have previously reported that the rumen microbiome composition and its coding capacity are different in animals having distinct feed efficiency states, even when fed an identical diet. Here, we reveal that many microbial populations belonging to the bacteria and archaea domains show divergent proteome production in function of the feed efficiency state. Thus, proteomic data serve as a strong indicator of host feed efficiency state phenotype, overpowering predictions based on genomic and taxonomic information. We highlight protein production of specific phylogenies associated with each of the feed efficiency states. We also find remarkable plasticity of the proteome both in the individual population and at the community level, driven by niche partitioning and competition. These mechanisms result in protein production patterns that exhibit functional redundancy and checkerboard distribution that are tightly linked to the host feed efficiency phenotype. By linking microbial protein production and the ecological mechanisms that act within the microbiome feed efficiency states, our present work reveals a layer of complexity that bears immense importance to the current global challenges of food security and sustainability.

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“…Probiotics for mature ruminant animals have primarily been chosen for targeting the rumen compartment, which would be the primary site of feed digestion [70]. A wide variety of strictly anaerobic bacteria, ciliate protozoa, anaerobic fungi, and archaea constitute the rumen microbial ecosystem, which is responsible for the breakdown and fermentation of 70-75% of food components [71,72]. Live yeast (Saccharomyces) formulations are by far the most commonly marketed products for ruminants [73,74].…”

Section: Application Of Probiotics In In Vivo Studies For Ruminant Pr...mentioning

confidence: 99%

Immunomodulation Potential of Probiotics: A Novel Strategy for Improving Livestock Health, Immunity, and Productivity

et al. 2022

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Over the past decade, the use of probiotics as feed supplements in animal production has increased considerably due to the ban on antibiotic growth promoters in livestock. This review provides an overview of the current situation, limitation, and prospects for probiotic formulations applied to livestock. Recently, the use of probiotics in livestock has been suggested to significantly improve their health, immunity, growth performance, nutritional digestibility, and intestinal microbial balance. Furthermore, it was reported that the use of probiotics in animals was helpful in equilibrating their beneficial microbial population and microbial turnover via stimulating the host immune response through specific secretions and competitive exclusion of potentially pathogenic bacteria in the digestive tract. Recently, there has been great interest in the understanding of probiotics targeted diet and its ability to compete with harmful microbes and acquire their niches. Therefore, the present review explores the most commonly used probiotic formulations in livestock feed and their effect on animal health. In summary, this article provides an in-depth knowledge about the formulation of probiotics as a step toward a better alternative to antibiotic healthy growth strategies.

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Rumen metaproteomics: Closer to linking rumen microbial function to animal productivity traits

Cited by 26 publications

References 98 publications

Transcriptome Analysis of Bovine Rumen Tissue in Three Developmental Stages

Transcriptome Analysis of Bovine Rumen Tissue in Three Developmental Stages

Metaproteome plasticity sheds light on the ecology of the rumen microbiome and its connection to host traits

Immunomodulation Potential of Probiotics: A Novel Strategy for Improving Livestock Health, Immunity, and Productivity

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