REVIEW: The rumen microbiome: Composition, abundance, diversity, and new investigative tools

Ruminants are able to degrade and use fibrous feed as a source of energy and nutrients because of the presence of complex anaerobic microbiota in the rumen, composed mainly of bacteria, fungi, and ciliate protozoa. Ruminal microorganisms play different roles in feed digestion and act synergistically to ferment plant structural and nonstructural carbohydrates and proteins. This review reports the latest assessment of microbiota diversity in the rumen ecosystem and summarizes the molecular techniques and the newly available “omic” technologies, based on DNA and RNA sequence analysis, which allow for new insights into the structure and functions of these complex microbial communities.

• Publication year

  2014

• Venue

  The Professional Animal Scientist

• Publication date

  2014-02-01

• Fields of study

  Biology, Environmental Science

• Identifiers
  DOI 10.15232/S1080-7446(15)30076-0
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

• Exploring the bovine rumen bacterial community from birth to adulthood

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• The Genome of the Anaerobic Fungus Orpinomyces sp. Strain C1A Reveals the Unique Evolutionary History of a Remarkable Plant Biomass Degrader

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• Rumen microbial (meta)genomics and its application to ruminant production.

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• Board-invited review: Rumen microbiology: leading the way in microbial ecology.

  2013cited by this paper
• Storage conditions of intestinal microbiota matter in metagenomic analysis

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  2012cited by this paper
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• Similarity of the ruminal bacteria across individual lactating cows.

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• Relative diversity and community structure analysis of rumen protozoa according to T-RFLP and microscopic methods.

  2012cited by this paper
• Commission on Genetic Resources for Food and Agriculture. Micro-organisms and ruminant digestion: State of knowledge, trends and future prospects

  2012cited by this paper
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  2012cited by this paper
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• [Construction and analysis of rumen bacterial artificial chromosome library from a dairy cow rumen microflora].

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• Molecular ecological analysis of the gastrointestinal microbiota: a review.

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