Publications

Publications

Google Scholar | PubMed

| 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | Pre-2008

Lab members are underlined; *Co-first author

2020

Cholan, P.M., Han, A., Woodie, B.R., Kurz, A.R.M., Britton, W.J., Ye, L., Holmes, Z.C., McCann, J.R., David, L.A., Rawls, J.F., and Oehlers, S.H. (2020) Conserved anti-inflammatory effects and sensing of butyrate in zebrafish. Gut Microbes 12(1):1-11.
PMID:33064972

Heppert, J., Davison, J.M., Kelly, C., Padilla Mercado, G., Lickwar, C.R., and Rawls, J.F.(2020) Transcriptional programmes underlying cellular identity and microbial responsiveness in the intestinal epithelium. Nature Reviews Gastroenterology and Hepatology. https://doi.org/10.1038/s41575-020-00357-6
PMID:33024279

Lickwar, C.R., and Rawls, J.F. (2020) Uncovering the history of intestinal host-microbiome interactions through vertebrate comparative genomics, Chapter 15 in Cellular Dialogues in the Holobiont, CRC Press, Edited by Thomas C. G. Bosch and Michael G. Hadfield, p. 244-264. https://doi.org/10.1201/9780429277375

Armstrong, S.C., Windom, M., Bihlmeyer, N., Li, J.S., Shah, S.H., Story, M., Zucker, N., Kraus, W.E., Pagidipati, N., Peterson, E., Wong, C., Wiefemeier, M., Sibley, L., Berchuck, S.I., Merrill, P., Zizzi, A., Sarria, C., Dressman, H.K., Rawls, J.F., and Skinner, A.C. (2020) Rationale and Design of “Hearts & Parks”: Study protocol for a pragmatic randomized clinical trial of an integrated clinic-community intervention to treat pediatric obesity. BMC Pediatrics 20(1):308.
PMID:32590958

*Loh, N.Y., *Pinnick, K.E., *Minchin, J.E.N., Neville, M.J., Kemp, J.P., Payne, A., Marinou, K., Gregson, C.L., Evans, D.M., Lindgren, C.M., Rawls, J.F., Karpe, F., and Christodoulides, C. (2020) RSPO3 functions via LGR4 to modulate human body fat distribution by eliciting diverse biological responses in abdominal and gluteal adipose progenitors. Nature Communications 11(1):2797.
PMID:32493999

2019

Ye, L., Mueller, O., Bagwell, J., Bagnat, M., Liddle, R.A., and Rawls, J.F. (2019) High fat diet induces microbiota-dependent silencing of enteroendocrine cells. eLife 8:e48479.
PMID:31793875

Martiny, J.B.H., Whiteson, K., Bohannan, B., David, L.A., Hynson, N., McFall-Ngai, M., Rawls, J.F., Schmidt, T., Abdo, Z., Blaser, M., Bordenstein, S., Bréchot, C., Bull, C., Dorrestein, P., Eisen, J., Garcia-Pichel, F., Gilbert, J., Hofmockel, K., Holtz, M., Knight, R., Welch, D.M., McDonald, D., Methe, B., Mouncey, N., Mueller, N., Pfister, C., Proctor, L., and Sachs, J. (2019) The Emergence of Microbiome Centers. Nature Microbiology 5: 2–3.
PMID:31857734

Murdoch, C.C., and Rawls, J.F. (2019) Commensal microbiota regulate vertebrate innate immunity – insights from the zebrafish. Frontiers in Immunology 10:2100. PMID:31555292

Casadei, E., Tacchi, L., Lickwar, C.R., Espenschied, S.T., Davison, J.M.,  Muñoz, P., Rawls, J.F., and Salinas, I. (2019) A conserved role for the microbiota in the control of olfactory systems in vertebrates. Chemical Senses 44(8):615-630.
PMID:31403159

Park, J., Levic, D.S., Sumigray, K.D., Bagwell, J., Eroglu, O., Block, C.L., Eroglu, C., Barry, R., Lickwar, C.R., Rawls, J.F., Watts, S.A., Lechler, T., and Bagnat, M. (2019) Lysosome-rich enterocytes mediate protein absorption in the vertebrate gut. Developmental Cell 51(1):7-20.e6.
PMID:31474562

Espenschied, S.T., Cronan, M.R., Matty, M.A., Mueller, O., Redinbo, M.R., Tobin, D.M., and Rawls, J.F. (2019) Epithelial delamination is protective during pharmaceutical-induced enteropathy. Proc. Natl. Acad. Sci. U.S.A 116(34):16961-16970.
PMID:31391308

Younge, N.E., Newgard, C.B., Cotton, C.M., Goldberg, R.N., Muehlbauer, M.J., Bain, J.R., Stevens, R.D., O’Connell, T.M., Rawls, J.F., Seed, P.C., and Ashley, P.L. (2019) Disrupted maturation of the microbiota and metabolome among extremely preterm infants with postnatal growth failure. Scientific Reports 9(1):8167.
PMID:31160673

Yan, C., Brunson, D.C., Tang, Q., Do, D., Iftimia, N.A., Moore, J.C., Hayes, M.N., Welker, A.M., Garcia, E.G., Dubash, T., Hong, X., Drapkin, B.J., Myers, D.T., Phat, S., Volorio, A., Marvin, D.L., Ligorio, M., Dershowitz, L., McCarthy, K.M., Karabacak, M., Fletcher, J.A., Sgroi, D., Iafrate, A.J., Maheswaran, S., Dyson, N.J., Haber, D.A., Rawls, J.F., and Langenau, D.M. (2019) Visualizing Engrafted Human Cancer and Therapy Responses in Immunodeficient Zebrafish. Cell 177(7): 1903-1914.
PMID:31031007

Murdoch, C.C., Espenschied, S.T., Matty, M.A., Mueller, O., Tobin, D.M., Rawls, J.F. (2019) Intestinal Serum amyloid A suppresses systemic neutrophil activation and bactericidal activity in response to microbiota colonization. PLoS Pathogens. 15(3).
PMID:30845179

 

2018

Cronan, M.R., Matty, M.A., Rosenberg, A.F., Blanc, L., Pyle, C.J., Espenschied, S.T., Rawls, J.F., Dartois, V., Tobin, D.M (2018) An explant technique for high-resolution imaging and manipulation of mycobacterial granulomas. Nat Methods.15(12):1098-1107.
PMID:30504889

Kelly, M.S., Surette, M.G., Smieja, M., Rossi, L., Luinstra, K., Steenhoff, A.P., Goldfarb, D.M., Pernica, J.M., Arscott-Mills, T., Boiditswe, S., Mazhani, T., Rawls, J.F., Cunningham, C.K., Shah, S.S., Feemster, K.A., and Seed P.C. (2018) Pneumococcal Colonization and the Nasopharyngeal Microbiota of Children in Botswana. Pediatr Infect Dis J. 37(11):1176-1183.
PMID:30153231

Williamson, I.A., Arnold, J.W., Samsa, L.A., Gaynor, L. DeSalvo, M., Cocchiaro, J.L., Carroll, I., Azcarate-Peril, A., Rawls, J.F., Allbritton, N.L., and Magness, S.T. (2018) A high-throughput organoid microinjection platform to study gastrointestinal luminal physiology and the microbiome. Cellular and Molecular Gastroenterology and Hepatology. 6(3):301-319. 45.
PMID:30123820 | Cover

Minchin, J.E.N., Scahill, C.M., Staudt, N., Busch-Nentwich, E.M., and Rawls, J.F. (2018) Deep phenotyping in zebrafish reveals genetic and diet-induced adiposity changes that may inform disease risk. J Lipid Res. 59(8):1536-1545.
PMID:29794036

King, J., Foster, J., Davison, J.M., Rawls, J.F., and Breton, G. (2018) Zebrafish transcription factor ORFeome for gene discovery and regulatory network elucidation. Zebrafish 15(2):202-205
PMID:29173090

2017

Lickwar, C.R., Camp, J.G., Weiser, M., Kingsley, D.M., Furey, T.S., Sheikh, S.Z., and Rawls, J.F. (2017) Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells. PLoS Biology. 15(8):e2002054
PMID: 28850571

McCann, J.R., Rawls, J.F., Seed, P.C., Armstrong S.C. (2017)The Intestinal Microbiome and Childhood Obesity. Current Pediatrics Reports. 5(3): 150-155
Link

Phelps, D., Brinkman, N.E., Keely, S.P., Anneken, E.M., Gearhart, A., Catron, T.R., Betancourt, D., Wood, C.E., Espenschied, S.T., Rawls, J.F., and Tal, T. (2017) Microbial colonization is required for normal neurobehavioral development in zebrafish. Scientific Reports. 7(1): 11244
PMID: 28894128 

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. 36(9): e211-e218
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. 27(7): 1195-1206
PMID: 28385711

Minchin JEN, and Rawls JF. (2017) A classification system for zebrafish adipose tissues. Disease Models & Mechanisms. 10: 797-809
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

2016

Bae S, Mueller O, Wong S, Rawls JF, and Valdivia RH. (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

2015

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 AR, Stephens WZ, Stagaman K, David LA, Guillemin K, and Bohannan BJM, and Rawls JF. (2015) Ontogenetic differences in dietary fat differentially influence microbiota assembly in the zebrafish gut and environment. mBio. 6(5):e00687-15.
PMID: 26419876

Williamson LL, McKenney EA, Holzknecht ZE, Belliveau C, Rawls JF, Poulton S, Parker W, and Bilbo SD. (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

2012

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 |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

2013

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

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

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

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

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

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

McMenamin SK*, Minchin JE*, Gordon TN, Rawls JF, Parichy DM. (2013) Dwarfism and Increased Adiposity in the gh1 Mutant Zebrafish vizzini. Endocrinology. 154(4):1476-87.
PMID: 23456361

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. (2013) Animals in a bacterial world, a new imperative for the life sciences. Proc Natl Acad Sci USA. 110(9):3229-36.
PMID: 23391737

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. (2013) Carbon monoxide and heme oxygenase-1 prevent intestinal inflammation in mice by promoting bacterial clearance. Gastroenterology. 144(4):789-98.
PMID: 23266559

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

2012

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

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

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

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. (2012) Increased rectal microbial richness is associated with the presence of colorectal adenomas in humans. ISME J. (10):1858-68.
PMID: 22622349

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

2011

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

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

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

Kanther M, Sun X, Mühlbauer M, Mackey LC, Flynn EJ 3rd, Bagnat M, Jobin C, Rawls JF. (2011) Microbial colonization induces dynamic temporal and spatial patterns of NF-κB activation in the zebrafish digestive tract. Gastroenterology.  141(1):197-207
PMID: 21439961 | GEO:GSE16857

2010

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

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

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

2009

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

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

2008

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

Pre-2008

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

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

Rawls JF, Mahowald MA, Ley RE, Gordon JI. (2006) Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection. Cell. 127(2):423-33.
PMID: 17055441 | GEO:GSE5198

Rawls JF, Samuel BS, Gordon JI. (2004) Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota. Proc Natl Acad Sci USA. 101(13):4596-601.
PMID: 15070763

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

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

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

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

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

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

Parichy DM, Rawls JF, Pratt SJ, Whitfield TT, Johnson SL. (1999) 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. Development. 126(15):3425-36.
PMID: 10393121

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