How do intestinal microbiota interact with host genome-encoded
processes to impact vertebrate health and disease

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Microbiota modulate transcription in the intestinal epithelium without
remodeling the accessible chromatin landscape.
J. Gray Camp, Christopher L. Frank, Colin R. Lickwar, Harendra Guturu, Tomas Rube, Aaron M. Wenger, Jenny Chen, Gill Bejerano, Gregory E. Crawford, and John F. Rawls.
Genome Research. 24(9):1504-16.

PMID 24963153     GEO GSE57919     UCSC Track Hub     Supplemental Data    More..


Aquacultured rainbow trout (Oncorhynchus mykiss) possess a large core intestinal microbiota that is resistant to variation in diet and rearing density.
Wong S, Waldrop T, Summerfelt S, Davidson J, Barrows F, Kenney PB, Welch T, Wiens GD, Snekvik K, Rawls JF, Good C.
Appl Environ Microbiol. 79(16):4974-84.
PMID: 23770898       MG-RAST      Raw Data (ZIP: .sff, .fna.qual, mapping files)


Microbial colonization induces dynamic temporal and spatial patterns of NF-κB activation in the zebrafish digestive tract.
Kanther M, Sun X, Mühlbauer M, Mackey LC, Flynn EJ 3rd, Bagnat M, Jobin C, Rawls JF. Gastroenterology.  141(1):197-207.
PMID: 21439961     GEO:GSE16857   


Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection.
Rawls JF, Mahowald MA, Ley RE, Gordon JI. Cell.127(2):423-33.
PMID: 17055441      GEO:GSE5198

Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota.
Rawls JF, Samuel BS, Gordon JI.
Proc Natl Acad Sci USA
. 101(13):4596-601.
PMID: 15070763    Supplemental Data