ArticleFrontiers in microbiology2014
The methylome of the gut microbiome: disparate Dam methylation patterns in intestinal Bacteroides dorei.
Article in Frontiers in microbiology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
20 citing papers in PubMed, 39 citations in OpenAlex.
- Emerging methylation-based approaches in microbiome engineering.Biotechnology for biofuels and bioproducts · 2024Review
- Extension of bacterial rDNA sequencing for simultaneous methylation detection and its application in microflora analysis.Scientific reports · 2023Article
- Examining horizontal gene transfer in microbial communities.Nature reviews. Microbiology · 2021Review
- Epigenetic interaction of microbes with their mammalian hosts.Journal of biosciences · 2021Article
- The Human Gut Phageome: Origins and Roles in the Human Gut Microbiome.Frontiers in cellular and infection microbiology · 2021Review
- Gut Microbiota Alterations from Three-Strain Yogurt Formulation Treatments in Slow-Transit Constipation.The Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale · 2020Article
- Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system.BMC microbiology · 2019Article
- Deciphering bacterial epigenomes using modern sequencing technologies.Nature reviews. Genetics · 2019Review
- High-quality genome sequences of uncultured microbes by assembly of read clouds.Nature biotechnology · 2018Article
- Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation.Nature biotechnology · 2018Article
- Is there foul play in the leaf pocket? The metagenome of floating fern Azolla reveals endophytes that do not fix NThe New phytologist · 2018Article
- Association Between Early-Life Antibiotic Use and the Risk of Islet or Celiac Disease Autoimmunity.JAMA pediatrics · 2017Article
- Modulation of Type 1 Diabetes Risk by the Intestinal Microbiome.Current diabetes reports · 2017Review
- Toward a genetic tool development pipeline for host-associated bacteria.Current opinion in microbiology · 2017Review
- Human epigenetics and microbiome: the potential for a revolution in both research areas by integrative studies.Future science OA · 2017Article
- The role of the intestinal microbiota in type 1 diabetes mellitus.Nature reviews. Endocrinology · 2016Review
- Integrating DNA Methylation and Gene Expression Data in the Development of the Soybean-Bradyrhizobium N2-Fixing Symbiosis.Frontiers in microbiology · 2016Article
- A model for the role of gut bacteria in the development of autoimmunity for type 1 diabetes.Diabetologia · 2015Review
- Bacteroides dorei dominates gut microbiome prior to autoimmunity in Finnish children at high risk for type 1 diabetes.Frontiers in microbiology · 2014Article
- Review
Corrections and comments
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Authors and funding
12 authors at 6 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.