OMB No. 0925-0001/0002 (Rev. 08/12 Approved Through 8/31/2015)
BIOGRAPHICAL SKETCH
Provide the following information for the Senior/key personnel and other significant contributors.
Follow this format for each person. DO NOT EXCEED FIVE PAGES.
NAME: Dr. Nathan C. VerBerkmoes
eRA COMMONS USER NAME (credential, e.g., agency login): VERBERKMOESN
POSITION TITLE: Research Associate Professor
EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, include postdoctoral training and residency
training if applicable. Add/delete rows as necessary.)
INSTITUTION AND LOCATION
DEGREE
(if applicable)
Completion Date
MM/YYYY
University of Tennessee, Knoxville TN
B.S.
05/01
University of Tennessee/Oak Ridge National Laboratory, Oak Ridge TN
Ph.D.
05/05
Oak Ridge National Laboratory, Oak Ridge, TN
Postdoctoral
02/06
A.
FIELD OF STUDY
Biochemistry and Cellular and
Molecular Biology
Life Science with focus on
Genomic Sciences and
Technology.
Biological Mass
Spectrometry/Proteomics
Research emphasis: Proteomic
analysis of microbes and
microbial communities.
Personal Statement
My research has focused on biological mass spectrometry and its applications in proteomics and
structural biology. Specifically, I employ multi-dimensional liquid chromatography coupled with electrospray ion
trap-Orbitrap mass spectrometry for the analysis of purified proteins, protein complexes, and single/multi-species
proteomes. The major focus of my research is the development and application of proteomics technologies to
the understanding of microbial physiology through the analysis of whole proteomes or enriched protein
complexes. The goal is to develop proteomic methodologies that allow for rapid data collection to gain greater
insight into the physiology of the large number of microbes that are being sequenced and thus available for
systems level studies. My research focus to date has been on those microbes that show promise for
bioremediation, bioenergy and carbon sequestration.
A recent goal is to develop proteome methodologies that will allow for the study of microbes and microbial
communities directly from environmental samples, a new subfield termed metaproteomics. My main focus with
microbial communities are the biofilms that grown and flourish is the hostile environment in Acid Mine Drainage
systems (Ram, Science, 2005 and Lo, Nature, 2007). We have extended this research to more complex
microbial communities such as sludge water samples, ground water samples, soil samples, oceans and the
human microbiome. Specifically, we focus on the human gastrointestinal flora from healthy and individuals with
Crohn’s disease. Recently we have begun to apply metaproteomics approaches to understanding the microbialhuman interactions in vaccine treatment. This has lead into research into human disease and mechanism such
as the application of MS-based proteomics to understand the disease mechanism in Autism.
B.
Positions and Honors
Positions and Employment:
2001-2005
Graduate Student, Advisor: Dr. Robert L. Hettich and Dr. Frank Larimer, Oak Ridge National
Laboratory, Oak Ridge, TN
2005-2006
Post-doctoral Associate, Dr. Robert L. Hettich, Oak Ridge National Laboratory, Oak Ridge, TN
2006-2012
Research Staff Member, Chemical Science Division, Oak Ridge National Laboratory, Oak Ridge,
TN
2012-2013
Staff Scientist and Group Leader, New England Biolabs Inc. Ipswich, MA.
2013-2014
Senior Staff Scientist and Director of Omics, BERG LLC, Framingham, MA
2015-Present Research Associate Professor, University of Texas El Paso, TX
2006-Present Adjunct faculty member, Department of Microbiology, University of Tennessee, Knoxville, TN
Service and synergistic activities:
2001-Present: Member of the American Society for Mass Spectrometry
2001-Present: Member of the East Tennessee Mass Spectrometry Discussion Group
2003-Present: Member of the American Society for Microbiology
Ad hoc reviewer: Journals including Journal of Proteome Research, Analytical Chemistry, ISME, and
Microbiology
Editor: Open access journal mSystems: http://msystems.asm.org
Teaching Experience:
Spring 2003: Teaching Assistant for Life Sciences 521 Analytical Technologies in UT/ORNL GST graduate
program.
Fall 2003: Teaching Assistant for Life Sciences 695 Introduction to Biological Mass Spectrometry in UT/ORNL
GST graduate program.
Fall 2005: Life Sciences 695 Introduction to Biological Mass Spectrometry in UT/ORNL GST graduate program
C.
Contribution to Science
Over the last ten years my research has focused on the development of a subfield of proteomics termed
metaproteomics. While proteomics can be defined as the large scale study of protein structure and function
the advent of mass spectrometry based proteomics created a whole new field that attempted to rapidly identify
and quantify all of the proteins expressed in a given cell, tissue, body fluid, etc. This is one of the most difficult
analytical problems facing scientist today due to the fact that proteins exist in a given cell, tissue or body fluid
over a large dynamic range, with a wide array of post-translational modifications, protein size, and solubility.
Metaproteomics takes this analytical challenge one huge step further by attempting to identify and quantify all
of the proteins in a complex microbial community. Metaproteomics (also Community Proteomics,
Environmental Proteomics, or Community Proteogenomics) can be defined as “the study of all protein samples
recovered directly from environmental sources. Metaproteomics is used to classify experiments that deal with
all the genes and proteins identified from complex communities, where individuals cannot be binned into
species or organisms types. The metaproteomics approach is comparable to gene-centric environmental
genomics, or metagenomics”. To extend this complexity even further we have now attempted to apply
metaproteomics to the Human Microbiome Project (HMP) where the interface between microbe and host is so
critical to normal human health and disruption can lead to a wide variety of disease states. Below is a list of a
few important manuscripts that we have contributed to this field.
Selected Peer-reviewed Publications (Selected from 50 peer-reviewed publications)
H Index=34
1) Ram, R.J.; VerBerkmoes, N.C.; Thelen, M.P.; Tyson, G.W.; Shah, M.; Baker B.J.; Blake II, R.C.;
Hettich, R.L.; and J.F. Banfield. Community proteomics of a natural microbial biofilm. Science, 2005,
308, 1915-1920.
2) Lo I.; Denef V.J.; VerBerkmoes N.C.; Shah M.; Goltsman D.; DiBartolo G.; Tyson G.W.; Allen E.E;
Ram R.J.; Detter C.; Richardson P.; Thelen M.P.; Hettich R.L.; and Jillian F. Banfield. Strain-resolved
community proteomics reveals recombining genomes of acidophilic bacteria. Nature, 2007,
446(7135):537-541.
3) VerBerkmoes NC, Russell AL, Shah M, Godzik A, Rosenquist M, Halfvarson J, Lefsrud MG,
Apajalahti J, Tysk C, Hettich RL, Jansson JK. Shotgun metaproteomics of the human distal gut
microbiota. ISME J. 2009 Feb;3(2):179-89.
4) VerBerkmoes NC, Denef VJ, Hettich RL, Banfield JF. Systems biology: Functional analysis of
natural microbial consortia using community proteomics. Nat Rev Microbiol. 2009 Mar;7(3):196-205.
5) Denef VJ, Kalnejais LH, Mueller RS, Wilmes P, Baker BJ, Thomas BC, Verberkmoes NC, Hettich
RL, Banfield JF. Proteogenomic basis for ecological divergence of closely related bacteria in natural
acidophilic microbial communities. Proc Natl Acad Sci U S A. 2010 Feb 9;107(6):2383-90.
6) Baker BJ, Comolli LR, Dick GJ, Hauser LJ, Hyatt D, Dill BD, Land ML, Verberkmoes NC, Hettich
RL, Banfield JF. Enigmatic, ultrasmall, uncultivated Archaea. Proc Natl Acad Sci U S A. 2010 May
11;107(19):8806-11.
7) Gobler CJ, Berry DL, Dyhrman ST, Wilhelm SW, Salamov A, Lobanov AV, Zhang Y, Collier JL,
Wurch LL, Kustka AB, Dill BD, Shah M, VerBerkmoes NC, Kuo A, Terry A, Pangilinan J, Lindquist
EA, Lucas S, Paulsen IT, Hattenrath-Lehmann TK, Talmage SC, Walker EA, Koch F, Burson AM,
Marcoval MA, Tang YZ, Lecleir GR, Coyne KJ, Berg GM, Bertrand EM, Saito MA, Gladyshev VN,
Grigoriev IV. Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics.
Proc Natl Acad Sci U S A. 2011 Mar 15;108(11):4352-7.
8) Kleiner M, Wentrup C, Lott C, Teeling H, Wetzel S, Young J, Chang YJ, Shah M, VerBerkmoes
NC, Zarzycki J, Fuchs G, Markert S, Hempel K, Voigt B, Becher D, Liebeke M, Lalk M, Albrecht D,
Hecker M, Schweder T, Dubilier N. Metaproteomics of a gutless marine worm and its symbiotic
microbial community reveal unusual pathways for carbon and energy use. Proc Natl Acad Sci U S A.
2012 May 8;109(19):E1173-82.
9) Wrighton KC, Thomas BC, Sharon I, Miller CS, Castelle CJ, VerBerkmoes NC, Wilkins MJ, Hettich
RL, Lipton MS, Williams KH, Long PE, Banfield JF. Fermentation, hydrogen, and sulfur metabolism
in multiple uncultivated bacterial phyla. Science. 2012 Sep 28;337(6102):1661-5.
10) Twelve previously unknown phage genera are ubiquitous in global oceans. Holmfeldt K,
Solonenko N, Shah M, Corrier K, Riemann L, VerBerkmoes NC, Sullivan MB. Proc Natl Acad Sci U S
A. 2013 Jul 30;110(31):12798-803.
11) Multi-omics of permafrost soil microbiome before and after natural thaw. Hultman et al. Nature.
2015 May 14;521(7551):208-12.
D.
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Research Support
“Meta-“omics” analysis of microbial carbon cycling responses to altered rainfall inputs in native prairie soils”.
3 years funding to ORNL, David Myrold, Oregon State University, PI; Nathan VerBerkmoes co-PI, DOEBER Carbon Cycle
“Development and integration of genome-enabled techniques to track and predict the cycling of carbon in
model microbial communities”. 3 years funding to ORNL, Jill Banfield University of California Berkeley,
PI; Nathan VerBerkmoes co-PI, DOE-BER Carbon Cycle
“Development of advanced proteomic methods to monitor baseline and post-immunization mucosal
immunological profiles of the gastrointestinal tract via stool samples.” 2 years funding to ORNL, Nathan
VerBerkmoes PI. NIH CCHI Pilot Project
“Immunological studies in subjects Immunized with Ty21a Typhoid Vaccine using advanced proteomics.” 1
year funding to ORNL. Nathan VerBerkmoes PI. NIH CCHI Pilot Project.
“Microbiological, Geochemical, and Hydrologic Processes Controlling Uranium Mobility: An Integrated FieldScale Subsurface Research Challenge at Rifle, Colorado.” 5 years funding to ORNL, Phil Long Pacific
Northwest National Laboratory, PI; Nathan VerBerkmoes co-PI; DOE-BER.
Proteogenomic Studies of a Natural Microbial Community from Acid Mine Drainage,” UC-Berkeley-LLNLORNL research effort, Banfield PI, NCV collaborator, DOE-BER Genomes:GTL, 10/01/05 – 9/30/10.
“Optimization and Directed, Natural Evolution of Biologically-Mediated Chromate Reduction in Subsurface
Soil Microcosms”. ORNL, Hettich PI, NCV Co-PI, DOE-BER ERSP, 02/01/07-09/30/09.
“Development of Proteogenomic Approaches to Analyze the Role of Virus-Microbe Interactions in Shaping
Natural Microbial Communities” ORNL, Jillian Banfield (UCB), PI, NCV Co-PI, DOE-BER Genomes:GTL
10/01/07-9/30/10.
“Whole Community Proteome Characterization of Synthetic Human Gut Microbiomes in Gnotobiotic Mice”,
Hettich PI, NCV Co-PI, ORNL Seed Grant 01/01/09-01/01/10.