High throughput sequencing methods for microbiome profiling: application to food animal systems

• Published in: Animal health research reviews Vol. 13; no. 1; pp. 40 - 53
• Main Author: Highlander, Sarah K.
• Format: Journal Article
• Language: English
• Published: Cambridge, UK Cambridge University Press 01.06.2012
• Subjects: Animals; Animals, Domestic - microbiology; Archaea - genetics; Bacteria - classification; Bacteria - genetics; Biosphere; Cell culture; Data processing; DNA, Ribosomal - chemistry; DNA, Ribosomal - genetics; Food; food animals; Food production; genes; Genes, rRNA; genome assembly; Genomes; high-throughput nucleotide sequencing; High-Throughput Nucleotide Sequencing - methods; High-Throughput Nucleotide Sequencing - veterinary; host specificity; Humans; Meat; Metagenome; Metagenomics - methods; Microbial activity; microbial communities; microbiome; Nucleotide sequence; nucleotide sequences; Reminder; ribosomal DNA; ribosomal RNA; RNA, Ribosomal, 16S - genetics; rRNA 16S; Sequence Analysis, RNA - veterinary; surveys; viruses; Viruses - genetics; microbial community analysis; metagenomics; genome sequencing; 16S rRNA gene sequencing; whole genome shotgun sequencing; Roche 454; microbial diversity; Illumina
• DOI: 10.1017/S1466252312000126
• ISSN: 1466-2523; 1475-2654

Analysis of microbial communities using high throughput sequencing methods began in the mid 2000s permitting the production of 1000s to 10,000s of sequence reads per sample and megabases of data per sequence run. This then unprecedented depth of sequencing allowed, for the first time, the discovery of the ‘rare biosphere’ in environmental samples. The technology was quickly applied to studies in several human subjects. Perhaps these early studies served as a reminder that though the microbes that inhabit mammals are known to outnumber host cells by an order of magnitude or more, most of these are unknown members of our second genome, or microbiome (as coined by Joshua Lederberg), because of our inability to culture them. High throughput methods for microbial 16S ribosomal RNA gene and whole genome shotgun (WGS) sequencing have now begun to reveal the composition and identity of archaeal, bacterial and viral communities at many sites, in and on the human body. Surveys of the microbiota of food production animals have been published in the past few years and future studies should benefit from protocols and tools developed from large-scale human microbiome studies. Nevertheless, production animal-related resources, such as improved host genome assemblies and increased numbers and diversity of host-specific microbial reference genome sequences, will be needed to permit meaningful and robust analysis of 16S rDNA and WGS sequence data.