title: Prokaryotic nucleotide composition is shaped by both phylogeny and the environment.
abstract: The causes of the great variation in nucleotide composition of prokaryotic genomes have long been disputed. Here, we use extensive metagenomic and whole-genome data to demonstrate that both phylogeny and the environment shape prokaryotic nucleotide content. We show that across environments, various phyla are characterized by different mean guanine and cytosine (GC) values as well as by the extent of variation on that mean value. At the same time, we show that GC-content varies greatly as a function of environment, in a manner that cannot be entirely explained by disparities in phylogenetic composition. We find environmentally driven differences in nucleotide content not only between highly diverged environments (e.g., soil, vs. aquatic vs. human gut) but also within a single type of environment. More specifically, we demonstrate that some human guts are associated with a microbiome that is consistently more GC-rich across phyla, whereas others are associated with a more AT-rich microbiome. These differences appear to be driven both by variations in phylogenetic composition and by environmental differences-which are independent of these phylogenetic composition differences. Combined, our results demonstrate that both phylogeny and the environment significantly affect nucleotide composition and that the environmental differences affecting nucleotide composition are far subtler than previously appreciated.
authors: Department of Biomedical Engineering, Science & Health Systems, Drexel University.
authors: Erin R
authors: ER
authors: Reichenberger
authors: Department of Computer and Electrical Engineering, Drexel University.
authors: Gail
authors: G
authors: Rosen
authors: Department of Biomedical Engineering, Science & Health Systems, Drexel University Department of Microbiology and Immunology, Drexel University College of Medicine uri.hershberg@drexel.edu ruthersh@tx.technion.ac.il.
authors: Uri
authors: U
authors: Hershberg
authors: Rachel and Menachem Mendelovitch Evolutionary Processes of Mutation and Natural Selection Research Laboratory, Department of Genetics and Developmental Biology, The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel uri.hershberg@drexel.edu ruthersh@tx.technion.ac.il.
authors: Ruth
authors: R
authors: Hershberg
mesh_terms: D001105:Archaea / Q000145:classification / Q000235:genetics; D001419:Bacteria / Q000145:classification / Q000235:genetics; D001482:Base Composition; D019641:DNA, Archaeal / Q000737:chemistry*; D004269:DNA, Bacterial / Q000737:chemistry*; D004777:Environment; D041981:Gastrointestinal Tract / Q000382:microbiology; D059647:Gene-Environment Interaction; D014644:Genetic Variation; D006801:Humans; D064307:Microbiota; D009711:Nucleotides / Q000032:analysis; D010802:Phylogeny
chemical_list: D019641:DNA, Archaeal; D004269:DNA, Bacterial; D009711:Nucleotides
keywords: GC-content; evolutionary forces; genomic variation; metagenomics; mutation; natural selection