<abstract xmlns="http://www.w3.org/1999/xhtml"><p>Unlike classical microbiology which focuses on bacteria capable of growing <italic>in vitro</italic>, metagenomics is a study of genetic information originating from microflora which aims to characterise the microbiome, namely the common genome of bacteria, archaea, fungi, protozoa and viruses living in the host. Metagenomics relies on next-generation sequencing (NGS), a large-scale sequencing technique which allows millions of sequential reactions to be carried out in parallel to decode entire communities of microorganisms. Metagenomic analyses support taxonomic analyses (involving gene fragments encoding ribosomal RNAs 5S and 16S in bacteria) or functional analyses for identifying genes encoding proteins that participate in the regulation of metabolic pathways in the body. New metagenomics technologies expand our knowledge of the phylogenetic structure of microflora in the gastrointestinal tract of poultry, and they support the identification of previously unknown groups of microbiota, mainly those occurring in small numbers. Next-generation sequencing also provides indirect information about the quantitative structure of the genes of gut microorganisms, but microbial activity and changes in the proportions of microbial metabolites that affect the host’s intestinal integrity and metabolism remain insufficiently investigated. Therefore, research studies are undertaken to investigate the proportions of the key microbial metabolites in the intestinal contents of poultry relative to changes in the population size of the most important bacterial groups, including those determined by cheaper techniques.</p></abstract>

Unlike classical microbiology which focuses on bacteria capable of growing in vitro, metagenomics is a study of genetic information originating from microflora which aims to characterise the microbiome, namely the common genome of bacteria, archaea, fungi, protozoa and viruses living in the host. Metagenomics relies on next-generation sequencing (NGS), a large-scale sequencing technique which allows millions of sequential reactions to be carried out in parallel to decode entire communities of microorganisms. Metagenomic analyses support taxonomic analyses (involving gene fragments encoding ribosomal RNAs 5S and 16S in bacteria) or functional analyses for identifying genes encoding proteins that participate in the regulation of metabolic pathways in the body. New metagenomics technologies expand our knowledge of the phylogenetic structure of microflora in the gastrointestinal tract of poultry, and they support the identification of previously unknown groups of microbiota, mainly those occurring in small numbers. Next-generation sequencing also provides indirect information about the quantitative structure of the genes of gut microorganisms, but microbial activity and changes in the proportions of microbial metabolites that affect the host’s intestinal integrity and metabolism remain insufficiently investigated. Therefore, research studies are undertaken to investigate the proportions of the key microbial metabolites in the intestinal contents of poultry relative to changes in the population size of the most important bacterial groups, including those determined by cheaper techniques.

Functioning of the Intestinal Ecosystem: From New Technologies in Microbial Research to Practical Poultry Feeding – A Review

Institute of Animal Reproduction and Food Research, Polish Academy of Sciences

Annals of Animal Science

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Unlike classical microbiology which focuses on bacteria capable of growing in vitro, metagenomics is a study of genetic information originating from microflora...

Functioning of the Intestinal Ecosystem: From New Technologies in Microbial Research to Practical Poultry Feeding – A Review

Published Online: May 02, 2019

Page range: 239 - 256

Received: Aug 08, 2018

Accepted: Jan 29, 2019

DOI: https://doi.org/10.2478/aoas-2019-0007

Keywords
intestinal microbiota, metagenomics, next-generation sequencing, intestinal ecosystem, poultry nutrition

© 2019 Zenon Zduńczyk, published by Sciendo

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Functioning of the Intestinal Ecosystem: From New Technologies in Microbial Research to Practical Poultry Feeding – A Review

Published Online: May 02, 2019

Page range: 239 - 256

Received: Aug 08, 2018

Accepted: Jan 29, 2019

DOI: https://doi.org/10.2478/aoas-2019-0007

Keywordsintestinal microbiota, metagenomics, next-generation sequencing, intestinal ecosystem, poultry nutrition

© 2019 Zenon Zduńczyk, published by Sciendo

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Keywords
intestinal microbiota, metagenomics, next-generation sequencing, intestinal ecosystem, poultry nutrition