A comprehensive method for amplicon-based and metagenomic characterization of viruses, bacteria, and eukaryotes in freshwater samples

作者：Uyaguari Diaz Miguel I; Chan Michael; Chaban Bonnie L; Croxen Matthew A; Finke Jan F; Hill Janet E; Peabody Michael A; Van Rossum Thea; Suttle Curtis A; Brinkman Fiona S L; Isaac Renton Judith; Prystajecky Natalie A; Tang Patrick^*

来源：Microbiome, 2016, 4(1): 20.

DOI：10.1186/s40168-016-0166-1

• Microbiome
• Watersheds
• Amplicon sequencing
• Metagenomes
• Metagenomics
• Microbial fractions

Background: Studies of environmental microbiota typically target only specific groups of microorganisms, with most focusing on bacteria through taxonomic classification of 16S rRNA gene sequences. For a more holistic understanding of a microbiome, a strategy to characterize the viral, bacterial, and eukaryotic components is necessary.
Results: We developed a method for metagenomic and amplicon-based analysis of freshwater samples involving the concentration and size-based separation of eukaryotic, bacterial, and viral fractions. Next-generation sequencing and culture-independent approaches were used to describe and quantify microbial communities in watersheds with different land use in British Columbia. Deep amplicon sequencing was used to investigate the distribution of certain viruses (g23 and RdRp), bacteria (16S rRNA and cpn60), and eukaryotes (18S rRNA and ITS). Metagenomic sequencing was used to further characterize the gene content of the bacterial and viral fractions at both taxonomic and functional levels.
Conclusion: This study provides a systematic approach to separate and characterize eukaryotic-, bacterial-, and viral-sized particles. Methodologies described in this research have been applied in temporal and spatial studies to study the impact of land use on watershed microbiomes in British Columbia.

• 出版日期2016-7-19
• 单位Saskatchewan; Saskatoon