AUTHOR=Leonard Michael T. , Davis-Richardson Austin G. , Ardissone Alexandria N. , Kemppainen Kaisa M. , Drew Jennifer C. , Ilonen Jorma , Knip Mikael , Simell Olli , Toppari Jorma , Veijola Riitta , Hyöty Heikki , Triplett Eric W. 

TITLE=The methylome of the gut microbiome: disparate Dam methylation patterns in intestinal Bacteroides dorei

JOURNAL=Frontiers in Microbiology

VOLUME=5

YEAR=2014

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2014.00361

DOI=10.3389/fmicb.2014.00361

ISSN=1664-302X

ABSTRACT=<p>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, <italic>Bacteroides dorei</italic>. Based on 16S rRNA analysis, this species represented over 45% of the bacteria present in these two samples. The <italic>B. dorei</italic> genome sequence from these samples was determined and the GATC methylation sites mapped. The <italic>Bacteroides dorei</italic> genome from one subject lacked any GATC methylation and lacked the DNA adenine methyltransferase genes. In contrast, <italic>B. dorei</italic> from another subject contained 20,551 methylated GATC sites. Of the 4970 open reading frames identified in the GATC methylated <italic>B. dorei</italic> 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.</p>