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Mapping Rumen Microbial Complexity through '-Omics'

Kulkarni Aarohi
2019 Archives of Animal & Poultry Sciences  
The rumen is a highly complex and dynamic ecosystem where, the microbiome displays symbiotic interactions and provides energy to ruminants through breakdown of plant fibers.  ...  It has raised the interest in fundamental understanding of the rumen microbiome to develop novel approaches for improving the livestock production.  ...  Metagenomics: Metagenomics conquered the necessity of microbial culturing and thus became a critical approach towards exploration of full genomic potential residing inside the rumen microbiome.  ... 
doi:10.19080/aaps.2019.01.555557 fatcat:b3kc5hzbwbgi5copfdcbjqb7eu

Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases

Jennifer M. Brulc, Dionysios A. Antonopoulos, Margret E. Berg Miller, Melissa K. Wilson, Anthony C. Yannarell, Elizabeth A. Dinsdale, Robert E. Edwards, Edward D. Frank, Joanne B. Emerson, Pirjo Wacklin, Pedro M. Coutinho, Bernard Henrissat (+2 others)
2009 Proceedings of the National Academy of Sciences of the United States of America  
In contrast, metagenomic analysis of a bovine rumen expression library (17) identified 22 glycoside hydrolase (GH) clones of which 4 potentially represent undescribed families of GHs.  ...  The use of small subunit (SSU) rRNA sequence analysis has allowed for a more complete description of the rumen microbiome and these inventories have demonstrated that a large microbial component remains  ...  Presented in this study is a comparative metagenome analysis of a gastrointestinal microbiome from a foregut-fermenting mammal by using the inexpensive, massively parallel, and rapid method of pyrosequencing  ... 
doi:10.1073/pnas.0806191105 pmid:19181843 pmcid:PMC2633212 fatcat:y6afjnn7ofgkrpsu3kifoleroa

High Potential Source for Biomass Degradation Enzyme Discovery and Environmental Aspects Revealed through Metagenomics of Indian Buffalo Rumen

K. M. Singh, Bhaskar Reddy, Dishita Patel, A. K. Patel, Nidhi Parmar, Anand Patel, J. B. Patel, C. G. Joshi
2014 BioMed Research International  
The complex microbiomes of the rumen functions as an effective system for plant cell wall degradation, and biomass utilization provide genetic resource for degrading microbial enzymes that could be used  ...  This metagenomic sequencing generated 3.9 GB of sequences and data were assembled into 137270 contiguous sequences (contigs).  ...  Acknowledgments The work was supported by the Niche Area of Excellence Project funded by Indian Council of Agricultural Research, New Delhi.  ... 
doi:10.1155/2014/267189 pmid:25136572 pmcid:PMC4124647 fatcat:c765ygcobzgfzljeprpjbjejme

CowPI: A Rumen Microbiome Focussed Version of the PICRUSt Functional Inference Software

Toby J. Wilkinson, Sharon A. Huws, Joan E. Edwards, Alison H. Kingston-Smith, Karen Siu-Ting, Martin Hughes, Francesco Rubino, Maximillian Friedersdorff, Christopher J. Creevey
2018 Frontiers in Microbiology  
Metataxonomic 16S rDNA based studies are a commonplace and useful tool in the research of the microbiome, but they do not provide the full investigative power of metagenomics and metatranscriptomics for  ...  Using this information, we have developed "CowPI," a focused version of the PICRUSt tool provided for use by the wider scientific community in the study of the rumen microbiome.  ...  Metagenomic investigation of microbiomes currently represents a complex and involved process.  ... 
doi:10.3389/fmicb.2018.01095 pmid:29887853 pmcid:PMC5981159 fatcat:7x7nq4l5dzclfo2ghb4ob5byne

Comparative metagenomic and metatranscriptomic analyses reveal the breed effect on the rumen microbiome and its associations with feed efficiency in beef cattle

Fuyong Li, Thomas C. A. Hitch, Yanhong Chen, Christopher J. Creevey, Le Luo Guan
2019 Microbiome  
Here, rumen microbiomes of beef cattle (n = 48) from three breeds (Angus, Charolais, Kinsella composite hybrid) with high and low feed efficiency were explored using metagenomics and metatranscriptomics  ...  , aiming to identify differences between functional potentials and activities of same rumen microbiomes and to evaluate the effects of host breed and feed efficiency on the rumen microbiome.  ...  Fitzsimmons for providing all phenotypic records of beef steers. Many thanks to X. Sun and F. Cox for their assistance on the DNA/RNA isolation and sequencing library  ... 
doi:10.1186/s40168-019-0618-5 pmid:30642389 pmcid:PMC6332916 fatcat:7pcutndilnfwpjawf3t3xauqry

— Invited Review — Metagenomic investigation of gastrointestinal microbiome in cattle

Minseok Kim, Tansol Park, Zhongtang Yu
2017 Asian-Australasian Journal of Animal Sciences  
By now, hundreds of metagenomic studies have been reported to address different aspects of the rumen microbiome, such as the effect of feed additive or diets on the rumen microbiome, early patterns of  ...  view of the diversity of the rumen and intestinal microbiome of cattle.  ...  Therefore, metatranscriptomics is better suited than shotgun metagenomic sequencing in functional analysis of rumen microbiome.  ... 
doi:10.5713/ajas.17.0544 pmid:28830126 pmcid:PMC5666186 fatcat:ms2fictx3jfhtj5tqusjwevtti

Multi-omics reveals that the rumen microbiome and its metabolome together with the host metabolome contribute to individualized dairy cow performance

Ming-Yuan Xue, Hui-Zeng Sun, Xue-Hui Wu, Jian-Xin Liu, Le Luo Guan
2020 Microbiome  
Here, analysis of rumen metagenomics and metabolomics, together with serum metabolomics was performed to identify potential regulatory mechanisms of MPY at both the rumen microbiome and host levels.  ...  Metagenomics analysis revealed that several Prevotella species were significantly more abundant in the rumen of high-MPY cows, contributing to improved functions related to branched-chain amino acid biosynthesis  ...  Acknowledgements We acknowledge the members in the Institute of Dairy Science of Zhejiang University (Hangzhou, China) for their assistance in the field sampling and data analysis.  ... 
doi:10.1186/s40168-020-00819-8 pmid:32398126 fatcat:vunw5zw6lvfrrdil4oibnhi6ua

The potential for mitigation of methane emissions in ruminants through the application of metagenomics, metabolomics, and other -OMICS technologies

Victoria Asselstine, Stephanie Lam, Filippo Miglior, Luiz F Brito, Hannah Sweett, Leluo Guan, Sinead M Waters, Graham Plastow, Angela Cánovas
2021 Journal of Animal Science  
The advancement of "-omics" technologies, such as metabolomics and metagenomics, may provide valuable information in this regard.  ...  Improved understanding of genetic mechanisms associated with CH4 production and the interaction between the microbiome profile and host genetics will increase the rate of genetic progress for reduced CH4  ...  Acknowledgments This research was supported by the Ontario Ministry of Agriculture, Food, and Rural Affairs (OMAFRA)  ... 
doi:10.1093/jas/skab193 pmid:34586400 fatcat:xik6bk3airawfklj5wi554ucp4

Metagenomic Insights into the Fibrolytic Microbiome in Yak Rumen

Xin Dai, Yaxin Zhu, Yingfeng Luo, Lei Song, Di Liu, Li Liu, Furong Chen, Min Wang, Jiabao Li, Xiaowei Zeng, Zhiyang Dong, Songnian Hu (+5 others)
2012 PLoS ONE  
Here we investigated the cellulolytic microbiome of the yak rumen by using a combination of metagenome-based and bacterial artificial chromosome (BAC)-based functional screening approaches.  ...  Genes encoding an endoglucanase of a novel GH5 subfamily occurred frequently in the metagenome, and the recombinant proteins encoded by the genes displayed moderate Avicelase in addition to endoglucanase  ...  Metagenomic approaches permit analysis of the rumen microbiome at a level of complexity that has never been Table 1 .  ... 
doi:10.1371/journal.pone.0040430 pmid:22808161 pmcid:PMC3396655 fatcat:rhediz334jftbosmur5fqxvycq

Metagenome Sequencing of the Greater Kudu ( Tragelaphus strepsiceros ) Rumen Microbiome

Anita N. Dube, Freeman Moyo, Zephaniah Dhlamini
2015 Genome Announcements  
Metagenome sequencing of the greater kudu (Tragelaphus strepsiceros) rumen microbiome. Genome Announc 3(4):e00897-15.  ...  We report the metagenome sequences of the greater kudu (Tragelaphus strepsiceros) rumen digesta, revealing a diverse community of microbes and some novel hydrolytic enzymes.  ...  ACKNOWLEDGMENT This work has been supported by a grant from the Research Board of the National University of Science and Technology.  ... 
doi:10.1128/genomea.00897-15 pmid:26272573 pmcid:PMC4536684 fatcat:7ht6jgyr65fd7ay5um3gh4ocai

Functional Metagenomics from the Rumen Environment—A Review

Wondimagegne Bekele, Abiy Zegeye, Addis Simachew, Getnet Assefa
2021 Advances in Bioscience and Biotechnology  
A better understanding of rumen microbial processes and identification of which populations are responsible for specific functions within the rumen microbiome will lead to better management and sustainable  ...  There are two basic types of metagenomics studies: Sequence-based and function-based metagenomics. Sequence-based metagenomics involves sequencing and analysis of DNA from environmental samples.  ...  Methodology Rumen Functional Metagenomics Methodology The Rumen microbiome functional metagenomics protocol consists of three parts: Environment (rumen fluid) sample collection; DNA library construction  ... 
doi:10.4236/abb.2021.125009 fatcat:eabqgskzrrdmvpjx75fhywyx3u

Metagenomics of the Svalbard Reindeer Rumen Microbiome Reveals Abundance of Polysaccharide Utilization Loci

Phillip B. Pope, Alasdair K. Mackenzie, Ivan Gregor, Wendy Smith, Monica A. Sundset, Alice C. McHardy, Mark Morrison, Vincent G.H. Eijsink, Mark R. Liles
2012 PLoS ONE  
We present here a compositional and comparative analysis of metagenomic data pertaining to a natural biomass-converting ecosystem adapted to austere arctic nutritional conditions, namely the rumen microbiome  ...  Analysis of unassembled metagenomic sequence as well as metabolic reconstruction of SRM-1 revealed the presence of multiple polysaccharide utilization loci-like systems (PULs) as well as members of more  ...  Acknowledgments We are especially grateful to the support from Karl-Arne Stokkan (University of Tromsø) and Tommy Frantzen (Svalbard) who assisted in sample collection, in addition to Sebastian Konietzny  ... 
doi:10.1371/journal.pone.0038571 pmid:22701672 pmcid:PMC3368933 fatcat:5vi25siqfjfmnavqo3wqgutjoe

A metagenomic analysis of the camel rumen's microbiome identifies the major microbes responsible for lignocellulose degradation and fermentation

Javad Gharechahi, Ghasem Hosseini Salekdeh
2018 Biotechnology for Biofuels  
In this study, a shotgun metagenomic analysis of the microbes adhering to plant fiber in the camel rumen was undertaken to identify the key species contributing to lignocellulose degradation and short  ...  The diverse microbiome present in the rumen of ruminant animals facilitates the digestion of plantbased fiber.  ...  The analysis suggested that the camel rumen microbiome encoded 25.3 GHs per Mbp of assembled DNA, a density comparable to that of both the moose rumen (23.8) and in elephant feces (22.9), but rather more  ... 
doi:10.1186/s13068-018-1214-9 pmid:30083229 pmcid:PMC6071333 fatcat:pt7nfu5xhfflfpa2s3iiulhzai

Occurrence and expression of genes encoding methyl-compound production in rumen bacteria

William J. Kelly, Sinead C. Leahy, Janine Kamke, Priya Soni, Satoshi Koike, Roderick Mackie, Rekha Seshadri, Gregory M. Cook, Sergio E. Morales, Chris Greening, Graeme T. Attwood
2019 Animal Microbiome  
We also describe the enrichment of pectin-degrading and methane-forming microbes from sheep rumen contents and the analysis of their genomes via metagenomic assembly.  ...  We have screened rumen metagenomic and metatranscriptomic datasets, metagenome assembled genomes, and the Hungate1000 genomes to identify organisms capable of producing methyl-compounds.  ...  The consortium metagenome sequences assembled into 107 contigs and MetaBAT analysis grouped the 24 largest scaffolds into three bins, each of which represent uncultivated members of the rumen microbiome  ... 
doi:10.1186/s42523-019-0016-0 pmid:33499937 fatcat:5urpep7tfjfynhy4nbdtl22xbe

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

Thea Os Andersen, Benoit J. Kunath, Live H. Hagen, Magnus Ø. Arntzen, Phillip B. Pope
2020 Methods  
The rumen microbiome constitutes a dense and complex mixture of anaerobic bacteria, archaea, protozoa, virus and fungi.  ...  This review focuses on the application of rumen metaproteomics, and its potential towards understanding the complex rumen microbiome and its metabolic functions.  ...  ACKNOWLEDGEMENTS 634 We are grateful for support from The Research Council of Norway (Project no. 250479), the 635  ... 
doi:10.1016/j.ymeth.2020.07.011 pmid:32758682 fatcat:yimq4kqz6reutprbf4ampujfzu
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