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Zachery Lewis















Postdoctoral Researcher

2014 Alfred P. Sloan Foundation Microbiology of the Built Environment Postdoctoral Fellow

Department of Food Science & Technology

UC Davis

ztlewis {at}


Personal Blog


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BABE Microbiome Project


Research Interests:

Microbial ecology using DNA-sequencing based approaches

The interface of the human microbiome with diet and immunity

Probiotics, prebiotics, and intestinal health

Breast-feeding and infant health

Influence of human genetics on the human microbiome

Hygiene hypothesis and microbial "old friends"


Skills and Training

Microbial ecology

  • Expertise analyzing DNA sequencing-based datasets of fungal and bacterial communities
    • Amplicon-based (16S rRNA) and shotgun metagenomics from humans and several animal species
  • Experience with TRFLP-based methods
  • Attended the Strategies and Techniques for Analyzing Microbial Population Structure (STAMPS) 2-week intensive course at the Marine Biological Laboratory in Woods Hole, Massachusetts



  • Experienced with microbial ecology- and metagenomics-focused analysis programs (QIIME, QIITA, PICRUSt, STAMP, MaAsLin, LEfSe, MG-RAST) and their statistical approaches to data analysis
  • Familiar with JMP (an SAS-based statistical analysis program)
  • Proficient with command-line interfaces, analysis on remote servers, SSH protocol, version control
  • Completed Software Carpentry workshop to learn basic skills for programming in Python (see for example of code I helped write)
  • Basic-level experience with R statistical programming
  • Graduate of Joint Genome Institute’s Microbial Genomics and Metagenomics workshop. Familiar with the Integrated Microbial Genomics (IMG) system
  • Basic bioinformatics tools (primer design, plasmid restriction mapping, BLAST, etc.)
  • Experience with Linux, PC, and Mac operating systems
  • Experienced with all MS Office suite programs


Microbiology & Molecular biology

  • DNA prep kits, PCR, qPCR, cloning, DNA restriction & ligation, etc.
  • Isolation, growth, and study of microorganisms using selective and differential media
  • Experience culturing strict anaerobe species
  • Study of bacterial metabolic pathways using various enzyme activity assays, genetic knock-outs, growth & substrate utilization assays, etc.
  • Experience in studying the relationship of human genetics with microbial abundances and functions.
  • Development and validation of new methods/assays



  • Successful cross-disciplinary collaborations with chemists, nutritionists, clinicians, statisticians, bioinformaticists, food scientists, animal scientists, ecologists, anthropologists, electrical engineers, etc.
    • Supervisory experience in research lab setting
      • More than 20 individuals supervised during course of graduate school
      • Currently leading a team of 10 undergraduates as part of my postdoctoral fellowship
  • Graduate of UC Davis School of Management Food and Health Entrepreneurship Academy
    • Learned about how start-up companies function, venture capital, business management, market analysis



  • Two quarters of TA experience teaching a food safety/quality control lab class
  • One quarter TAing an introductory biology course
  • Consistently praised in student evaluations for engaging teaching style


Field Work

  • Experience with in-field sample collection for study on the ecology of native fishes in Costa Rica



  • English (native)
    • Excellent technical writing skills
  • Spanish – fluent (speak, read, and write)
    • Achieved “Advanced” level on the American Council on the Teaching of Foreign Languages Spanish oral proficiency interview and writing proficiency test



PhD in Microbiology

University of California- Davis                                                                   March 2015

  • Dissertation Topic: How breast milk affects infant gut microbiota
    • Probiotics and prebiotics
    • Microbial ecology
    • Human genetics
    • Research Advisor- Prof. David A. Mills, Department of Food Science and Technology


B.S. in Microbiology with minor in Spanish

Brigham Young University, Provo, UT                                                           Aug. 2008


Research/ Work Experience

Graduate Student Researcher 2009-2015

Laboratory of David Mills, UC Davis Department of Food Science and Technology

  • Use of DNA-based methods to investigate microbial ecology of infant guts
  • Cloning, restriction digests, electrophoresis gels, enzyme assays, reagent prep
  • Training and mentoring of new lab members
  • Extensive safety training


Food Quality Control Lab Technician, R&D Department 2008-2009

Tahitian Noni International, American Fork UT

  • Ran microbiology lab testing for presence of pathogens in food and cosmetic products
  • Kept strict records and generated of Certificates of Analysis
  • Developed and validated new testing methods
  • Performed research on antimicrobial properties of Morinda citrifolia juice
  • Gained intimate knowledge of nutraceutical businesses


Undergraduate Research Assistant 2007-2008

Dr. William McCleary’s Lab, Brigham Young University, Provo UT

  • Studied phosphate uptake regulation in E. coli by making mutants
  • Performed lab upkeep and maintenance, preparation of reagents
  • Analyzed data on the effects of mutations in phosphate regulon


Public Health Laboratories Virology Unit Intern Summer 2007

State of New Hampshire Public Health Laboratories, Concord NH

  • Assisted in testing specimens for presence of various arboviruses
  • Designed data entry system to save lab dozens of person-hours per year
  • Performed lab stocking and upkeep


Science Reference Desk Assistant 2006-2008

Harold B. Lee Library Science Reference Desk, Provo UT

  • Helped patrons with research in scientific journals, books, and databases
  • Shelved and repaired books
  • Carried out other projects as assigned by subject librarian


  • Alfred P. Sloan Foundation Microbiology of the Built

Environment Postdoctoral Fellowship                                                                  2014

  • Henry A. Jastro Graduate Research Scholarship                                              2010, 2011, 2013
  • Honorable Mention NSF Graduate Research Fellowship Program                      2011
  • BYU Academic Scholarship (Spring/Summer)                                                 2008
  • William Hebard Academic Scholarship                                                             2007
  • BYU Bicentennial Scholarship                                                                          2002


Public Service

Volunteer for BioTech SYSTEM program, which promotes K-12 biotech education.             2009-2014

  • Gave multiple lab tours yearly and talked to high-school-age youth about opportunities in science. Coordinated by UC Davis Designated Emphasis in Biotechnology program.



  • Lewis, Z. T., J. Davis, J. T. Smilowitz, J B. German, C. B Lebrilla, D. A Mills. 2016.  The impact of freeze-drying infant fecal samples on measures of their bacterial community profiles and milk-derived oligosaccharide content. PeerJ  (In Press).
  • Lewis, Z. T., G. Shani, C. Masarweh, M. Popovic, S. A. Frese, D. A. Sela, M. A. Underwood and D. A. Mills. 2016. Validating bifidobacterial species and subspecies identity in commercial probiotic products.  Pediatrics Research (In Press).
  • Hinde, K. & Lewis, Z. T. Mother’s littlest helpers. Science 348, 1427–1428 (2015).
  • Lewis, Z. T. et al., Mills, D. A. Maternal Fucosyltransferase 2 Status Affects the Gut Bifidobacterial Communities of Breastfed Infants. Microbiome 3, 1–21 (2015)
  • Huda, M. N., Lewis Z. T. et al., Stephensen, C. B. Stool Microbiota and Vaccine Responses of Infants. Pediatrics 134, e362–72 (2014).
  • Lewis, Z. T. et al., Mills, D. A. Use of bifidobacterial specific terminal restriction fragment length polymorphisms to complement next generation sequence profiling of infant gut communities. Anaerobe 19, 62–9 (2013).
  • Lewis, Z. T. & Mills, D. A. Oligosaccharides as Functional Foods. Encycl. Biotechnol. Agric. Food 1–4 (2013)
  • Underwood, M. A. Kalanetra K. M., Bokulich, N. A., Lewis Z. T. et al., Mills, D. A. A Comparison of Two Probiotic Strains of Bifidobacteria in Premature Infants. J. Pediatr. 163, 1585–1591 (2013).
  • Zivkovic, A. M., Lewis, Z. T., German, J. B. & Mills, D. A. Establishment of a Milk-Oriented Microbiota ( MOM ) in early life : How Babies Meet Their MOMs. Funct. Food Rev. 5, 3–12 (2013).
  • Rice, C., Pollard, J., Lewis, Z. T. & McCleary, W. Employment of a Promoter-Swapping Technique Shows that PhoU Modulates the Activity of the PstSCAB(2) ABC Transporter in Escherichia coli. Appl. Environ. Microbiol. 75, 573–582 (2009).



Student Travel Award Speaker: International Milk Genomics Conference, Davis CA. Oct 2013 Talk title: "Maternal FUT2 Polymorphisms Influence the Gut Microbial Communities of Breastfed Infants" Poster presentation of the same name at conference.

Speaker, 8th Annual UC Davis Research Retreat on Host Microbe Interactions, Tahoe City, CA, Oct 2013 Talk title: "Maternal FUT2 Polymorphisms Influence the Gut Microbial Communities of Breastfed Infants"

Speaker, UC Davis Microbiology Department Seminar (MIC 291) Davis, CA. Oct 23 2013, Talk title: "Maternal FUT2 Polymorphisms Influence the Gut Microbial Communities of Breastfed Infants"

Poster presentation at: Human Microbiome Science: Vision for the Future, Washington DC. July 2013 "Maternal FUT2 Polymorphisms Influence the Gut Microbial Communities of Breastfed Infants."


Hobbies and interests

  • Anthropology
  • Economics and Politics
  • Playing Basketball
  • Fan of various NFL and NBA teams
  • Document Actions

    Dr. Mills interviewed by Reno News & Review Oct 15, 2016
    UC Davis Milk Group Profiled in New Yorker Magazine Aug 18, 2016
    mBio paper profiled Jul 13, 2016
    Sercan Karav's AEM paper profiled Apr 17, 2016
    Cell paper profiled Apr 17, 2016
    Nina Kirmiz wins poster award Jan 10, 2016
    Zach Lewis's Paper on Bifidobacterial Species QC profiled Nov 26, 2015
    Frese & Mills interviewed by Proto Magazine on infant microbiome Nov 24, 2015
    Wine microbiome work profiled by Nature Plants Nov 24, 2015
    Liver Cancer-Gut Microbiome work profiled by Synthesis May 04, 2015
    Bokulich interviewed on eLife brewery paper Apr 25, 2015
    Zachery Lewis's paper in Microbiome Profiled by NPR and UC Davis Apr 11, 2015
    Dr. Mills Elected Fellow in American Academy of Microbiology Feb 25, 2015
    Milk Bioactives Group profiled by UC Davis Office of Research Dec 11, 2014
    NIH Grant Success on Milk Bioactives!! Nov 26, 2014
    UC Davis Milk Bioactives Group Profiled in Science Sep 26, 2014
    Steve Frese honored by European Probiotics Association Sep 07, 2014
    Nick Bokulich garners 2013-14 Kinsella Thesis award Sep 07, 2014
    Bangladesh infant cohort paper profiled Jul 26, 2014
    Milk Bioactives Program Profiled in Davis Enterprise Jul 26, 2014
    Bokulich Sake Paper Profiled Jul 26, 2014
    Gates project profiled Apr 03, 2014
    Milk bioactives work profiled in Science News Dec 30, 2013
    PNAS paper on wine microbial terroir profiled Dec 03, 2013
    Bokulich garners Brewing award Oct 26, 2013
    Premie probiotic paper profiled Oct 22, 2013
    Bokulich beer microbiome work profiled Aug 29, 2013
    Dr. Mills NIH talk online Aug 22, 2013
    Dave Sela begins faculty position at University of Massachusetts-Amherst Aug 17, 2013
    Chemical Engineering News article profiles milk glycan work Jul 08, 2013