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John Chaston

Assistant Professor
Plant & Wildlife Sciences

5132 LSB
Provo, UT 84602

Teaching Interests

The PWS470 course I teach is supported by DataCamp ( ) the most intuitive learning platform for data science. We use it for R and Shell instruction through a combination of short expert videos and hands-on-the-keyboard exercises. Additional resources are available for other purposes, including Python and SQL training. Take over 100+ courses by expert instructors on topics such as importing data, data visualization or machine learning and learn faster through immediate and personalised feedback on every exercise.


  • PhD, Microbiology Doctoral Training Program, University of Wisconsin-Madison, 2011
  • BS, Microbiology, Brigham Young University, 2005


Academic - Post-Secondary

  • Postdoctoral Associate, Cornell University, 2011-2014


  • Genetics Society of America, 2015-Present
  • American Society for Microbiology, 2012-Present

Honors and Awards

  • National Science Foundation : National Science Foundation Graduate Research Fellow
  • National Institutes of Health, University of Wisconsin-Madison : National Institutes of Health Microbes in Health and Disease Trainee

Courses Taught

Winter 2019

  • PWS 168: Personal Genomics Section 002, 003
  • PWS 470: Genomic Analysis Section 001
  • PWS 494R: Mentored Learning Experience Section 020
  • PWS 588: Metagenomics Section 001

Fall 2018

  • PWS 288: Molecular Genetics Laboratory Section 001
  • PWS 470: Genomic Analysis Section 001
  • PWS 494R: Mentored Learning Experience Section 021
  • PWS 699R: Master's Thesis Section 021

Summer 2018

  • PWS 494R: Mentored Learning Experience Section 022

Spring 2018

  • PWS 494R: Mentored Learning Experience Section 022
  • PWS 699R: Master's Thesis Section 019


Journal Articles

Carroll C, Olsen KD, Ricks NJ, Dill-McFarland KA, Suen G, Robinson TF, Chaston JM. 2019. Bacterial communities in the alpaca gastrointestinal tract vary with diet and body site. Frontiers in Microbiology.

Long E, Evans C, Chaston JM, Udall JA. 2018. Genomic Structural Variations Within Five Continental Populations of Drosophila melanogaster. G3. 8(10):3247-3253.

Judd AM, Matthews MK, Hughes RC, Veloz M, Sexton CE, Chaston JM. 2018. Bacterial methionine metabolism genes influence Drosophila melanogaster starvation resistance. Applied and Environmental Microbiology. 84:e00662-18.

Sexton CE, Smith HZ, Newell PD, Douglas AE, Chaston JM. 2018. MAGNAMWAR: An R package for genome-wide association studies of bacterial orthologs. Bioinformatics. 34:1951-1952.

White KM, Matthews MK, Hughes RC, Sommer AJ, Griffitts JS, Newell PD, Chaston JM. 2018. A Metagenome-wide association study and arrayed mutant library confirm Acetobacter lipopolysaccharide genes are necessary for association with Drosophila melanogaster. G3. 8(4):1119-1127.

Winans NJ, Walter A, Chouaia B, Chaston JM, Douglas AE, Newell PD. 2017. A genomic investigation of ecological differentiation between free-living and Drosophila-associated bacteria. Molecular ecology. 26(17):4536-4550.

Hammer AJ, Walters A, Carroll C, Newell PD, Chaston JM. 2017. Draft Genome Sequence of Lactobacillus paracasei DmW181, a Bacterium Isolated from Wild Drosophila. Genome announcements. 5(27).

Wright SM, Carroll C, Walters A, Newell PD, Chaston JM. 2017. Genome Sequence of Leuconostoc citreum DmW_111, Isolated from Wild Drosophila. Genome announcements. 5(24).

Ricks NJ, Carroll C, Walters A, Newell PD, Chaston JM. 2017. Genome Sequence of Weissella cibaria DmW_103, Isolated from Wild Drosophila. Genome announcements. 5(24).

Dobson AJ, Chaston JM, Douglas AE. 2016. The Drosophila transcriptional network is structured by microbiota. BMC genomics. 17(1):975.

Koyle ML, Veloz M, Judd AM, Wong AC, Newell PD, Douglas AE, Chaston JM. 2016. Rearing the fruit fly Drosophila melanogaster under axenic and gnotobiotic conditions. Journal of Visualized Experiments. 113:e54219.

Chaston JM, Dobson AJ, Newell PD, Douglas AE. 2015. Host genetic control of the microbiota mediates the Drosophila nutritional phenotype. Applied and Environmental Microbiology.

Dobson AJ, Chaston JM, Newell P, Donahue L, Hermann S, Sannino D, Westmiller S, Clark A, Lazzaro B, Douglas AE. 2015. Host genetic determinants of microbiota-dependent nutrition revealed by genome-wide analysis of Drosophila melanogaster. Nature Communications. 18(6):6312.

Newell PD, Chaston JM, Wang Y, Winans NJ, Sannino D, Wong AC, Dobson AJ, Kagle J, Douglas AE. 2014. In vivo function and comparative genomic analyses of the Drosophila gut microbiota identify candidate symbiosis factors. Frontiers in Microbiology - Microbial Symbioses.

Chaston JM, Newell PD, Douglas AE. 2014. Metagenome-Wide Association of Microbial Determinants of Host Phenotype in Drosophila melanogaster. mBio. 5(5):e01631-14.

Veesenmeyer JL, Andersen AW, Lu X, Hussa EA, Murfin KE, Chaston JM, Dillman A, Wassarman KM, Sternberg PW, Goodrich-Blair H. 2014. NilD CRISPR RNA contributes to Xenorhabdus nematophila colonization of symbiotic host nematodes. Molecular microbiology. 93(5):1026-42.

Jing X, Wong AC, Chaston JM, Colvin J, McKenzie CL, Douglas AE. 2014. The bacterial communities in plant phloem-sap-feeding insects. 23(6):1433-44.

Wong AC, Chaston JM, Douglas AE. 2013. The inconstant gut microbiota of Drosophila species revealed by 16S rRNA gene analysis. The ISME journal. 7(10):1922-32.

Chaston JM, Murfin KE, Heath-Heckman EA, Goodrich-Blair H. 2013. Previously unrecognized stages of species-specific colonization in the mutualism between Xenorhabdus bacteria and Steinernema nematodes. Cellular microbiology. 15(9):1545-59.

Murfin KE, Chaston JM, Goodrich-Blair H. 2012. Visualizing bacteria in nematodes using fluorescent microscopy. Journal of visualized experiments : JoVE.

Chaston JM, Douglas AE. 2012. Making the most of "omics" for symbiosis research. The Biological bulletin. 223(1):21-9.

Bhasin A, Chaston JM, Goodrich-Blair H. 2012. Mutational analyses reveal overall topology and functional regions of NilB, a bacterial outer membrane protein required for host association in a model of animal-microbe mutualism. Journal of bacteriology. 194(7):1763-76.

Sugar DR, Murfin KE, Chaston JM, Andersen AW, Richards GR, deLéon L, Baum JA, Clinton WP, Forst S, Goldman BS, et al. 2012. Phenotypic variation and host interactions of Xenorhabdus bovienii SS-2004, the entomopathogenic symbiont of Steinernema jollieti nematodes. Environmental microbiology. 14(4):924-39.

Dillman A, Chaston JM, Adams BJ, Ciche TA, Goodrich-Blair H, Stock SP, Sternberg PW. 2012. An entomopathogenic nematode by any other name. PLoS pathogens. 8(3):e1002527.

Chaston JM, Dillman A, Shapiro-Ilan DI, Bilgrami AL, Gaugler R, Hopper KR, Adams BJ. 2011. Outcrossing and crossbreeding recovers deteriorated traits in laboratory cultured Steinernema carpocapsae nematodes. International journal for parasitology. 41(7):801-9.

Chaston JM, Suen G, Tucker SL, Andersen AW, Bhasin A, Bode E, Bode HB, Brachmann AO, Cowles CE, Cowles KN, et al. 2011. The entomopathogenic bacterial endosymbionts Xenorhabdus and Photorhabdus: convergent lifestyles from divergent genomes. PloS one. 6(11):e27909.

Chaston JM, Goodrich-Blair H. 2010. Common trends in mutualism revealed by model associations between invertebrates and bacteria. FEMS microbiology reviews. 34(1):41-58.

Adhikari BN, Lin CY, Bai X, Ciche TA, Grewal PS, Dillman A, Chaston JM, Shapiro-Ilan DI, Bilgrami AL, Gaugler R, et al. 2009. Transcriptional profiling of trait deterioration in the insect pathogenic nematode Heterorhabditis bacteriophora. BMC genomics. 10:609.

Adams BJ, Wall DH, Gozel U, Dillman A, Chaston JM, Hogg ID. 2007. The southernmost worm, Scottnema lindsayae (Nematoda): diversity, dispersal and ecological stability. Polar Biology. 30:809-815.


Chaston JM. Genetic influence of the Drosophila melanogaster microbiome on host nutrition and behavior. University of Nevada-Las Vegas. Las Vegas, NV. 2015 .

Chaston JM, Dobson AJ, Douglas AE. Effects of Wolbachia on Drosophila nutrition and microbiome. Drosophila Conference 2015. Chicago, IL. 2015 .

Chaston JM. Finding determinants of microbial community structure and function using genome-wide association. 5th ASM Conference on Beneficial Microbes. Washington, DC. 2014 .

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