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

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Publications Google Scholar: JF Rawls Pubmed: JF Rawls

2017 - 2016 - 2015 - 2014 - 2013 - 2012 - 20112010 - 2009 - 2008 - Pre-2008 - DATA
Lab members are underlined; *Co-first author

Kelly, MS, Surette, MG, Smieja, M, Pernica, JM, Rossi, L, Luinstra, K, Steenhoff, AP, Feemster, KA, Goldfarb, DM, Arscott-Mills, T, Boiditswe, S, Rulaganyang, I, Muthoga, C, Mazhani, T, Gaofiwe, L, Cunningham, CK, Rawls, JF, Shah, SS, and Seed, PC  (2017) The nasopharyngeal microbiota of children with respiratory infections in Botswana. Ped. Infect. Dis. J. (In press).
PMID: 28399056

Davison, J, Lickwar, CR, Song, L, Breton, G, Crawford, GE, and Rawls, JF (2017) Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha. Genome Research (In press).
PMID: 28385711

Minchin, JEN, and Rawls, JF (2017) A classification system for zebrafish adipose tissues. Disease Models & Mechanisms (In press).
PMID: 28348140

Leulier, F, McNeil, L, Lee, WJ, Rawls, JF, Cani, P, Schwarzer, M, Zhao, L and Simpson, S (2017) Integrative physiology:  at the crossroads of nutrition, microbiota and animal physiology. Cell Metabolism 25(3): 522–534.
PMID: 28273475

Minchin, JEN
, and Rawls, JF (2017) In vivo imaging and quantification of regional adiposity in zebrafish. Methods in Cell Biology 138: 3-27.
PMID: 28129849

Melancon, E, Gomez De La Torre Canny, S, Sichel, S, Kelly, M, Wiles, TJ, Rawls, JF, Eisen, J, and Guillemin, K (2017) Best practices for germ-free derivation and gnotobiotic zebrafish husbandry. Methods in Cell Biology 138: 61-100.
PMID: 28129860

Bae, S., Mueller, O., Wong, S., Rawls, J.F., and Valdivia, R.H. (2016) Genomic sequencing-based mutational enrichment analysis identifies motility genes in a genetically intractable gut microbe. Proc Natl Acad Sci USA 113(49): 14127-14132.
PMID: 27911803

Boursier, J, Mueller, O, Barret, M, Machado, M, Fizanne, L, Araujo-Perez, F, Guy, CD, Seed, PC, Rawls, JF, David, LA, Hunault, G, Oberti, F, Calès, P, and Diehl, AM (2016) The severity of NAFLD is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota. Hepatology 63(3): 764-75.
PMID: 26600078

Williamson, LL, McKenney, EA, Holzknecht, ZE, Belliveau, C, Rawls, JF, Poulton, S, Parker, W, and Bilbo, SD (2016) Got worms? Perinatal exposure to helminths prevents persistent immune sensitization and cognitive dysfunction induced by early-life infection. Brain, Behavior, & Immunity 51: 14-28.
PMID: 26162711

Stephens WZ, Burns AR, Stagaman K, Wong S, Rawls JF, Guillemin K, and Bohannan BJM. (2015) The composition of the zebrafish intestinal microbial community varies across development. ISME Journal 10(3): 644-54.
PMID: 26339860

Burns AR, Stephens WZ, Stagaman K, Wong S, Rawls JF, Guillemin K, and Bohannan, BJM (2016) Contribution of neutral processes to the assembly of gut microbial communities changes over host development. ISME Journal 10(3): 655-64.
PMID: 26296066

Gomez de la Torre Canny, S, and Rawls, JF (2015) Preview: Baby it’s cold outside: Host-microbiota relationships drive temperature adaptations. Cell Host & Microbe 18(6): 635-636.
PMID: 26651935

Wang L, Oehlers SH, Espenschied ST, Rawls JF, Tobin DM, and Ko DC (2015) CPAG: software for leveraging pleiotropy in GWAS to reveal similarity between human traits links plasma fatty acids and intestinal inflammation. Genome Biology. 16:190.
PMID: 26374098

McKenney EA, Williamson LL, Yoder AD, Rawls JF, Bilbo SD, and Parker, W (2015) Alteration of the rat cecal microbiota during colonization with the helminth Hymenolepis dimunita. Gut Microbes. 6(3):182-93.
PMID: 25942385

Wong, S., Burns, A.R., Stephens, W.Z., Stagaman, K., David, L.A., Guillemin, K., and Bohannan, B.J.M., and Rawls, J.F. (2015) Ontogenetic differences in dietary fat differentially influence microbiota assembly in the zebrafish gut and environment. mBio. 6(5):e00687-15.
PMID: 26419876

Williamson, L.L., McKenney, E.A., Holzknecht, Z.E., Belliveau, C., Rawls, J.F., Poulton, S., Parker, W., and Bilbo, S.D. (2015) Got worms? Perinatal exposure to helminths prevents persistent immune sensitization and cognitive dysfunction induced by early-life infection. Brain, Behavior, & Immunity (in press).pii: S0889-1591(15)00240-8
PMID: 26162711

Minchin JE, Dahlman I, Harvey CJ, Mejhert N, Singh MK, Epstein JA, Arner P, Torres-Vázquez J, and Rawls JF. (2015) Plexin D1 determines body fat distribution by regulating the type V collagen microenvironment in visceral adipose tissue. Proc Natl Acad Sci USA. 112(14):4363-4368.
PMID: 25831505  Cover

Marjoram L, Alvers A, Deerhake ME, Bagwell J, Mankiewicz J, Cocchiaro JL, Beerman RW, Willer J, Sumigray KD, Katsanis N, Tobin DM, Rawls JF, Goll MG, Bagnat M. (2015) Epigenetic control of intestinal barrier function and inflammation in zebrafish. Proc Natl Acad Sci USA.112(9):2770-5.
PMID: 25730872  Cover

Camp JG*, Frank CL*, Lickwar CR,  Guturu H, Rube T, Wenger AM, Chen J, Bejerano G, Crawford GE, Rawls JF. (2014) Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape. Genome Research. 24(9):1504-16.
PMID: 24963153  Data  Cover

Kanther M*, Tomkovich S*, Xiaolun S, Grosser MR, Koo J, Flynn EJ 3rd, Jobin C, Rawls JF. (2014) Commensal microbiota stimulate systemic neutrophil migration through induction of Serum amyloid A. Cell. Microbiol. 16(7):1053-67.
PMID: 24373309

Wong S*, Waldrop T*, Summerfelt S, Davidson J, Barrows F, Kenney PB, Welch T, Wiens GD, Snekvik K, Rawls JF, Good C. (2013) Aquacultured rainbow trout (Oncorhynchus mykiss) possess a large core intestinal microbiota that is resistant to variation in diet and rearing density. Appl Environ Microbiol. 79(16):4974-84.
PMID: 23770898     MG-RAST      Raw Data (ZIP: .sff, .fna.qual, mapping files)

Minchin JE, Williams VC, Hinits Y, Low SH, Tandon P, Fan CM, Rawls JF, and Hughes SM. (2013) Oesophageal and sternohyal muscle fibres are novel Pax3-dependent somite derivatives essential for ingestion. Development.  140(14):2972-2984.
PMID: 23760954

Getting the inside tract: new frontiers in zebrafish digestive system biology (2013) Sadler KC, Rawls JF , Farber SA. Zebrafish. 10(2):129-31.
PMID: 23738756

Mucosal candidiasis elicits activation of NF-κB, proinflammatory gene expression and localized neutrophilia in a transparent vertebrate host (2013) Gratacap RL, Rawls JF, Wheeler RT. Dis Model Mech. 6(5):1260-70.
PMID: 23720235

Obese Human Beings With Nonalcoholic Fatty Liver Disease Display Alterations in Fecal Microbiota and Volatile Organic Compounds (2013) Boursier J, Rawls JF, Diehl AM. Clin Gastroenterol Hepatol. 11(7):876-8.
PMID: 23628504

Microgavage of zebrafish larvae (2013) Cocchiaro JL, Rawls JF. J Vis Exp. (72):e4434.
Video    PMID: 23463135  

Dwarfism and Increased Adiposity in the gh1 Mutant Zebrafish vizzini (2013) McMenamin SK*, Minchin JE*, Gordon TN, Rawls JF, Parichy DM. Endocrinology.154(4):1476-87.
PMID: 23456361
Animals in a bacterial world, a new imperative for the life sciences (2013) McFall-Ngai M, Hadfield MG, Bosch TC, Carey HV, Domazet-Loso T, Douglas AE, Dubilier N, Eberl G, Fukami T, Gilbert SF, Hentschel U, King N, Kjelleberg S, Knoll AH, Kremer N, Mazmanian SK, Metcalf JL, Nealson K, Pierce NE, Rawls JF, Reid A, Ruby EG, Rumpho M, Sanders JG, Tautz D, Wernegreen JJ. Proc Natl Acad Sci USA. 110(9):3229-36.
PMID: 23391737  

Carbon monoxide and heme oxygenase-1 prevent intestinal inflammation in mice by promoting bacterial clearance (2013) Onyiah JC, Sheikh SZ, Maharshak N, Steinbach EC, Russo SM, Kobayashi T, Mackey LC, Hansen JJ, Moeser AJ, Rawls JF, Borst LB, Otterbein LE, Plevy SE. Gastroenterology. 144(4):789-98.
PMID: 23266559

Glafenine-induced intestinal injury in zebrafish is ameliorated by μ-opioid signaling via enhancement of Atf6-dependent cellular stress responses. (2013) Goldsmith JR, Cocchiaro JL, Rawls JF, Jobin C. Dis Model Mech. (1):146-59.
PMID: 22917923

Microbiota regulate intestinal absorption and metabolism of fatty acids in the zebrafish. (2012) Semova I, Carten JD, Stombaugh J, Mackey LC, Knight R, Farber SA, Rawls JF. Cell Host Microbe. 12(3):277-88.
PMID: 22980325

Intestinal microbiota composition in fishes is influenced by host ecology and environment. (2012) Wong S, Rawls JF. Mol Ecol. 21(13):3100-2.
PMID: 22916346

Special issue: gut microbial communities in health and disease. (2012) Rawls JF. Gut Microbes. (4):277-8.
PMID: 22688724

Increased rectal microbial richness is associated with the presence of colorectal adenomas in humans. (2012) Sanapareddy N, Legge RM, Jovov B, McCoy A, Burcal L, Araujo-Perez F, Randall TA, Galanko J, Benson A, Sandler RS, Rawls JF, Abdo Z, Fodor AA, Keku TO. ISME J. (10):1858-68.
PMID: 22622349

Intronic cis-regulatory modules mediate tissue-specific and microbial control of angptl4/fiaf transcription. (2012) Camp JG, Jazwa AL, Trent CM, Rawls JF. PLoS Genet. 8(3):e1002585.
PMID: 22479192

Study of host-microbe interactions in zebrafish. (2011) Milligan-Myhre K, Charette JR, Phennicie RT, Stephens WZ, Rawls JF, Guillemin K, Kim CH. Methods Cell Biol. 105:87-116.
PMID: 21951527

In vivo analysis of white adipose tissue in zebrafish. (2011) Minchin JE, Rawls JF.
Methods Cell Biol. 105:63-86.
PMID: 21951526

Evidence for a core gut microbiota in the zebrafish. (2011) Roeselers G, Mittge EK, Stephens WZ, Parichy DM, Cavanaugh CM, Guillemin K, Rawls JF. ISME J. 5(10):1595-608.
PMID: 21472014 

Microbial colonization induces dynamic temporal and spatial patterns of NF-κB activation in the zebrafish digestive tract.(2011) 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

Molecular characterization of mucosal adherent bacteria and associations with colorectal adenomas. (2010) Shen XJ, Rawls JF, Randall T, Burcal L, Mpande CN, Jenkins N, Jovov B, Abdo Z, Sandler RS, Keku TO. Gut Microbes.1(3):138-47.
PMID: 20740058

Host-microbe interactions in the developing zebrafish. (2010) Kanther M, Rawls JF. Curr Opin Immunol. 22(1):10-9.
PMID: 20153622

Tuberculous granuloma induction via interaction of a bacterial secreted protein with host epithelium. (2010) Volkman HE, Pozos TC, Zheng J, Davis JM, Rawls JF, Ramakrishnan L. Science. 327(5964):466-9.
PMID: 20007864

Patterns and scales in gastrointestinal microbial ecology. (2009) Camp JG, Kanther M, Semova I, Rawls JF. Gastroenterology. 136(6):1989-2002.
PMID: 19457423

Ontogeny and nutritional control of adipogenesis in zebrafish (Danio rerio). (2009)
Flynn EJ 3rd*, Trent CM*, Rawls JF. J Lipid Res. 50(8):1641-52.
PMID: 19366995

Methods for generating and colonizing gnotobiotic zebrafish. (2008) Pham LN, Kanther M, Semova I, Rawls JF. Nat Protoc. 3(12):1862-75.
PMID: 19008873

Enteric infection and inflammation alter gut microbial ecology. (2007)
Rawls JF. Cell Host Microbe. 2(2):73-4.
PMID: 18005720

In vivo imaging and genetic analysis link bacterial motility and symbiosis in the zebrafish gut. (2007) Rawls JF, Mahowald MA, Goodman AL, Trent CM, Gordon JI. Proc Natl Acad Sci USA.104(18):7622-7.
PMID: 17456593

Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection. (2006) 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. (2004) Rawls JF, Samuel BS, Gordon JI. Proc Natl Acad Sci USA. 101(13):4596-601.
PMID: 15070763  Supplemental Data

Temporal and molecular separation of the kit receptor tyrosine kinase's roles in zebrafish melanocyte migration and survival. (2003) Rawls JF, Johnson SL.
Dev Biol. 262(1):152-61.
PMID: 14512025

Coupled mutagenesis screens and genetic mapping in zebrafish. (2003) Rawls JF, Frieda MR, McAdow AR, Gross JP, Clayton CM, Heyen CK, Johnson SL.
Genetics. 163(3):997-1009.
PMID: 12663538

How the zebrafish gets its stripes. (2001) Rawls JF, Mellgren EM, Johnson SL.
Dev Biol. 240(2):301-14. Review.
PMID: 11784065

Requirements for the kit receptor tyrosine kinase during regeneration of zebrafish fin melanocytes. (2001) Rawls JF, Johnson SL. Development. 128(11):1943-9.
PMID: 11493518

Mutational analysis of endothelin receptor b1 (rose) during neural crest and pigment pattern development in the zebrafish Danio rerio. (2000) Parichy DM, Mellgren EM, Rawls JF, Lopes SS, Kelsh RN, Johnson SL. Dev Biol. 227(2):294-306.
PMID: 11071756

Zebrafish kit mutation reveals primary and secondary regulation of melanocyte development during fin stripe regeneration. (2000) Rawls JF, Johnson SL.
Development. 127(17):3715-24.
PMID: 10934016

Zebrafish sparse corresponds to an orthologue of c-kit and is required for the morphogenesis of a subpopulation of melanocytes, but is not essential for hematopoiesis or primordial germ cell development. (1999) Parichy DM, Rawls JF, Pratt SJ, Whitfield TT, Johnson SL. Development. 126(15):3425-36.
PMID: 10393121

SCAR, a WASP-related protein, isolated as a suppressor of receptor defects in late Dictyostelium development. (1998) Bear JE, Rawls JF, Saxe CL 3rd. J Cell Biol. 142(5):1325-35.
PMID: 9732292