title: The methylome of the gut microbiome: disparate Dam methylation patterns in intestinal Bacteroides dorei.
abstract: Despite the large interest in the human microbiome in recent years, there are no reports of bacterial DNA methylation in the microbiome. Here metagenomic sequencing using the Pacific Biosciences platform allowed for rapid identification of bacterial GATC methylation status of a bacterial species in human stool samples. For this work, two stool samples were chosen that were dominated by a single species, Bacteroides dorei. Based on 16S rRNA analysis, this species represented over 45% of the bacteria present in these two samples. The B. dorei genome sequence from these samples was determined and the GATC methylation sites mapped. The Bacteroides dorei genome from one subject lacked any GATC methylation and lacked the DNA adenine methyltransferase genes. In contrast, B. dorei from another subject contained 20,551 methylated GATC sites. Of the 4970 open reading frames identified in the GATC methylated B. dorei genome, 3184 genes were methylated as well as 1735 GATC methylations in intergenic regions. These results suggest that DNA methylation patterns are important to consider in multi-omic analyses of microbiome samples seeking to discover the diversity of bacterial functions and may differ between disease states.
authors.affiliation: Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida Gainesville, FL, USA.
authors.forename: Michael T
authors.initials: MT
authors.lastname: Leonard
authors.affiliation: Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida Gainesville, FL, USA.
authors.forename: Austin G
authors.initials: AG
authors.lastname: Davis-Richardson
authors.affiliation: Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida Gainesville, FL, USA.
authors.forename: Alexandria N
authors.initials: AN
authors.lastname: Ardissone
authors.affiliation: Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida Gainesville, FL, USA.
authors.forename: Kaisa M
authors.initials: KM
authors.lastname: Kemppainen
authors.affiliation: Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida Gainesville, FL, USA.
authors.forename: Jennifer C
authors.initials: JC
authors.lastname: Drew
authors.affiliation: Department of Clinical Microbiology, University of Eastern Finland Kuopio, Finland ; Immunogenetics Laboratory, University of Turku Turku, Finland.
authors.forename: Jorma
authors.initials: J
authors.lastname: Ilonen
authors.affiliation: Children's Hospital, University of Helsinki and Helsinki University Central Hospital Helsinki, Finland ; Diabetes and Obesity Research Program, University of Helsinki Helsinki, Finland ; Department of Pediatrics, Tampere University Hospital Tampere, Finland.
authors.forename: Mikael
authors.initials: M
authors.lastname: Knip
authors.affiliation: Department of Pediatrics, Turku University Hospital, University of Turku Turku, Finland.
authors.forename: Olli
authors.initials: O
authors.lastname: Simell
authors.affiliation: Department of Pediatrics, Turku University Hospital, University of Turku Turku, Finland.
authors.forename: Jorma
authors.initials: J
authors.lastname: Toppari
authors.affiliation: Department of Pediatrics, Oulu University Hospital, University of Oulu Oulu, Finland.
authors.forename: Riitta
authors.initials: R
authors.lastname: Veijola
authors.affiliation: School of Medicine, University of Tampere Tampere, Finland.
authors.forename: Heikki
authors.initials: H
authors.lastname: Hyöty
authors.affiliation: Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida Gainesville, FL, USA.
authors.forename: Eric W
authors.initials: EW
authors.lastname: Triplett
keywords: DNA adenine methyltransferase; GATC; epigenetics; genomics; metagenomics
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