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Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development

Overview of attention for article published in Genome Medicine, April 2018
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  • In the top 5% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (92nd percentile)
  • Good Attention Score compared to outputs of the same age and source (73rd percentile)

Mentioned by

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1 news outlet
blogs
2 blogs
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22 X users
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1 Google+ user

Citations

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117 Dimensions

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150 Mendeley
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Title
Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development
Published in
Genome Medicine, April 2018
DOI 10.1186/s13073-018-0534-5
Pubmed ID
Authors

Wei-Hung Pan, Felix Sommer, Maren Falk-Paulsen, Thomas Ulas, Philipp Best, Antonella Fazio, Priyadarshini Kachroo, Anne Luzius, Marlene Jentzsch, Ateequr Rehman, Fabian Müller, Thomas Lengauer, Jörn Walter, Sven Künzel, John F. Baines, Stefan Schreiber, Andre Franke, Joachim L. Schultze, Fredrik Bäckhed, Philip Rosenstiel

Abstract

The interplay of epigenetic processes and the intestinal microbiota may play an important role in intestinal development and homeostasis. Previous studies have established that the microbiota regulates a large proportion of the intestinal epithelial transcriptome in the adult host, but microbial effects on DNA methylation and gene expression during early postnatal development are still poorly understood. Here, we sought to investigate the microbial effects on DNA methylation and the transcriptome of intestinal epithelial cells (IECs) during postnatal development. We collected IECs from the small intestine of each of five 1-, 4- and 12 to 16-week-old mice representing the infant, juvenile, and adult states, raised either in the presence or absence of a microbiota. The DNA methylation profile was determined using reduced representation bisulfite sequencing (RRBS) and the epithelial transcriptome by RNA sequencing using paired samples from each individual mouse to analyze the link between microbiota, gene expression, and DNA methylation. We found that microbiota-dependent and -independent processes act together to shape the postnatal development of the transcriptome and DNA methylation signatures of IECs. The bacterial effect on the transcriptome increased over time, whereas most microbiota-dependent DNA methylation differences were detected already early after birth. Microbiota-responsive transcripts could be attributed to stage-specific cellular programs during postnatal development and regulated gene sets involved primarily immune pathways and metabolic processes. Integrated analysis of the methylome and transcriptome data identified 126 genomic loci at which coupled differential DNA methylation and RNA transcription were associated with the presence of intestinal microbiota. We validated a subset of differentially expressed and methylated genes in an independent mouse cohort, indicating the existence of microbiota-dependent "functional" methylation sites which may impact on long-term gene expression signatures in IECs. Our study represents the first genome-wide analysis of microbiota-mediated effects on maturation of DNA methylation signatures and the transcriptional program of IECs after birth. It indicates that the gut microbiota dynamically modulates large portions of the epithelial transcriptome during postnatal development, but targets only a subset of microbially responsive genes through their DNA methylation status.

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X Demographics

The data shown below were collected from the profiles of 22 X users who shared this research output. Click here to find out more about how the information was compiled.
Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 150 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 150 100%

Demographic breakdown

Readers by professional status Count As %
Researcher 37 25%
Student > Ph. D. Student 25 17%
Student > Master 16 11%
Student > Bachelor 12 8%
Professor 5 3%
Other 18 12%
Unknown 37 25%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 32 21%
Agricultural and Biological Sciences 27 18%
Immunology and Microbiology 20 13%
Medicine and Dentistry 6 4%
Nursing and Health Professions 5 3%
Other 16 11%
Unknown 44 29%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 34. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 20 January 2019.
All research outputs
#1,143,257
of 24,933,778 outputs
Outputs from Genome Medicine
#230
of 1,537 outputs
Outputs of similar age
#25,294
of 333,629 outputs
Outputs of similar age from Genome Medicine
#7
of 23 outputs
Altmetric has tracked 24,933,778 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 95th percentile: it's in the top 5% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 1,537 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 27.1. This one has done well, scoring higher than 85% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 333,629 tracked outputs that were published within six weeks on either side of this one in any source. This one has done particularly well, scoring higher than 92% of its contemporaries.
We're also able to compare this research output to 23 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 73% of its contemporaries.