title: The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes.
abstract: Metagenomic studies characterize both the composition and diversity of uncultured viral and microbial communities. BLAST-based comparisons have typically been used for such analyses; however, sampling biases, high percentages of unknown sequences, and the use of arbitrary thresholds to find significant similarities can decrease the accuracy and validity of estimates. Here, we present Genome relative Abundance and Average Size (GAAS), a complete software package that provides improved estimates of community composition and average genome length for metagenomes in both textual and graphical formats. GAAS implements a novel methodology to control for sampling bias via length normalization, to adjust for multiple BLAST similarities by similarity weighting, and to select significant similarities using relative alignment lengths. In benchmark tests, the GAAS method was robust to both high percentages of unknown sequences and to variations in metagenomic sequence read lengths. Re-analysis of the Sargasso Sea virome using GAAS indicated that standard methodologies for metagenomic analysis may dramatically underestimate the abundance and importance of organisms with small genomes in environmental systems. Using GAAS, we conducted a meta-analysis of microbial and viral average genome lengths in over 150 metagenomes from four biomes to determine whether genome lengths vary consistently between and within biomes, and between microbial and viral communities from the same environment. Significant differences between biomes and within aquatic sub-biomes (oceans, hypersaline systems, freshwater, and microbialites) suggested that average genome length is a fundamental property of environments driven by factors at the sub-biome level. The behavior of paired viral and microbial metagenomes from the same environment indicated that microbial and viral average genome sizes are independent of each other, but indicative of community responses to stressors and environmental conditions.
authors.affiliation: Biology Department, San Diego State University, San Diego, California, United States of America. forent.angly@gmail.com
authors.forename: Florent E
authors.initials: FE
authors.lastname: Angly
authors.forename: Dana
authors.initials: D
authors.lastname: Willner
authors.forename: Alejandra
authors.initials: A
authors.lastname: Prieto-Davó
authors.forename: Robert A
authors.initials: RA
authors.lastname: Edwards
authors.forename: Robert
authors.initials: R
authors.lastname: Schmieder
authors.forename: Rebecca
authors.initials: R
authors.lastname: Vega-Thurber
authors.forename: Dionysios A
authors.initials: DA
authors.lastname: Antonopoulos
authors.forename: Katie
authors.initials: K
authors.lastname: Barott
authors.forename: Matthew T
authors.initials: MT
authors.lastname: Cottrell
authors.forename: Christelle
authors.initials: C
authors.lastname: Desnues
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Dinsdale
authors.forename: Mike
authors.initials: M
authors.lastname: Furlan
authors.forename: Matthew
authors.initials: M
authors.lastname: Haynes
authors.forename: Matthew R
authors.initials: MR
authors.lastname: Henn
authors.forename: Yongfei
authors.initials: Y
authors.lastname: Hu
authors.forename: David L
authors.initials: DL
authors.lastname: Kirchman
authors.forename: Tracey
authors.initials: T
authors.lastname: McDole
authors.forename: John D
authors.initials: JD
authors.lastname: McPherson
authors.forename: Folker
authors.initials: F
authors.lastname: Meyer
authors.forename: R Michael
authors.initials: RM
authors.lastname: Miller
authors.forename: Egbert
authors.initials: E
authors.lastname: Mundt
authors.forename: Robert K
authors.initials: RK
authors.lastname: Naviaux
authors.forename: Beltran
authors.initials: B
authors.lastname: Rodriguez-Mueller
authors.forename: Rick
authors.initials: R
authors.lastname: Stevens
authors.forename: Linda
authors.initials: L
authors.lastname: Wegley
authors.forename: Lixin
authors.initials: L
authors.lastname: Zhang
authors.forename: Baoli
authors.initials: B
authors.lastname: Zhu
authors.forename: Forest
authors.initials: F
authors.lastname: Rohwer
mesh_terms: D030561:Databases, Nucleic Acid; D016680:Genome, Bacterial; D016679:Genome, Viral; D056186:Metagenomics / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012985:Software Design