Address: 12700 E. 19th Avenue, Room 3113
Anschutz Medical Campus, Aurora, CO 80045
Phone: (303) 724-7942
University, Villanova PA (1993-1997); BS: Colorado State University, Fort
Collins, CO (1997-1999); MS: University of Colorado, Boulder (2003-2007); PhD:
Postdoctoral Training, University of Colorado, Boulder (2007-2013)
main focus of my lab is to understand factors that shape human microbiota
composition in health and disease (particularly in the gastrointestinal tract) and
to elucidate the functional consequences of compositional differences, both in
terms of the biological/metabolic properties of individual bacteria and host
interactions. Although my formal training is entirely in the biological
sciences, I have substantial experience in the development and application of
computational tools for the analysis of metagenomic (primarily 16S ribosomal
RNA) and bacterial genome sequences for culture-independent analysis of
microbial populations. During my pre-doctoral work with Dr. Rob Knight and as a
joint post-doctoral fellow with Dr. Knight and Dr. Jeffrey Gordon, I was
heavily involved in the development of very popular tools for microbial
community analysis; I am the primary developer of the UniFrac algorithm for
comparing microbial diversity among many samples using phylogenetic
information, and am a contributor to the QIIME software package. My goal is to
continue to innovate in the area of bioinformatics analysis of sequence data
while exploring links between microbiota composition/function with disease.
work includes extensive meta-analyses of 16S rRNA and genomic sequences in the
public domain, analysis of new datasets that I have had access to through an
extensive network of collaborators, and most recently 16S rRNA datasets of
human microbiota samples generated in my own lab. Ongoing projects in my lab
explore associations between the human microbiota and HIV-infection, asthma,
autism spectrum disorders, metabolic disease, and graft versus host disease in
cancer patients who have undergone stem cell transplant. Working across such a
breadth of datasets/diseases has given me a unique perspective towards
understanding parallels between compositional changes that occur in different
developmental, physiological and disease states.
the end of my post-doctoral training and as new faculty, I have been continuing
to couple 16S rRNA based analyses of microbial distribution with comparative
genomics analysis and functional experiments with cultured isolates to predict
and test which biological functions are shared by bacteria that change in
relative abundance in disease states. This work has involved use of anaerobic
culture techniques that will allow my laboratory to follow up on genomics based
functional predictions. This will help me to reach my goal of moving beyond
descriptive studies of how human microbiota composition differs with disease to
studies that also elucidate the functional consequences of those differences.
A. Livraghi-Butrico, A.A. Fletcher, M.M.
McElwee, S.E. Evans, et al. “Muc5b is required for airway defense.”
(2014). Nature. 505:412-416.
C., M. Li, T.B. Campbell, S.C. Flores, D. Linderman, M.J. Gebert, R. Knight,
A.P. Fontenot, and B.E. Palmer. “Alterations in the Gut Microbiota Associated
with HIV-1 Infection.” (2013). Cell Host and Microbe. 14(3):329-339.
C.*, J. Stombaugh*, A. Gonzalez*, G.
Ackermann, D. Wendel, Y. Vázquez-Baeza, J.K. Jansson, J.I. Gordon, and R.
Knight. “Meta-analyses of studies of the human microbiota.” (2013) Genome Res.
S., C. Lauber, E.K. Costello, C.A. Lozupone, G. Humphrey, D. Berg-Lyons,
J.G. Caporaso, D. Knights, J.C. Clemente, S. Nakielny, J.I. Gordon, N. Fierer,
R. Knight. “Cohabiting family members
share microbiota with one another and with their dogs.” (2013). eLife. 2:e00458.
(5) Lozupone, C., A. Cota-Gomez, B.E.
Palmer, D.J. Linderman, E.S. Charlson, E. Sodergren, M. Mitreva, S. Abubucker,
J. Martin, G. Yao, T.B. Campbell, S.C. Flores, G. Ackerman, J. Stombaugh, L.
Ursell, J.M. Beck, J.L. Curtis, V.B. Young, S.V. Lynch, L. Huang, G.M.
Weinstock, K.S. Knox, H. Twigg, A. Morris, E. Ghedin, F.D. Bushman, R.G.
Collman, R. Knight, and A.P. Fontenot; for the Lung HIV Microbiome Project. “Widespread Colonization of the Lung by Tropheryma whipplei in HIV Infection.”
(2013). Am J Respir Crit Care Med. 187(10)1110-7.
C., J.I. Stombaugh, J.I. Gordon, J.K. Jansson and R. Knight. “Diversity,
stability and resilience of the human gut microbiota.” (2012). Nature. 489(7415):220-30.
C., K. Faust, J. Raes, J.J. Faith, D.N. Frank, J. Zaneveld, J.I. Gordon, and R.
Knight. “Identifying genomic and metabolic features that can underlie early
successional and opportunistic lifestyles of human gut symbionts.” (2012)
Genome Res. 22(10):1974-84.
(8) Yatsunenko, T. F.E. Rey, M.J. Manary, I.
Trehan, M.G. Dominguez-Bello, M. Contreras, M. Magris, G. Hidalgo, R.N.
Baldassano, A.P. Anokhin, A.C. Heath, B. Warner, J. Reeder, J. Kuczynski, J. G.
Caporaso, C.A. Lozupone, C. Lauber, J.C. Clemente, D. Knights, R. Knight and
J.I. Gordon. “Human gut microbiome viewed across age and geography” (2012). Nature. 486(7402):222-7.
(9) The Human Microbiome Consortium. “Structure,
function, and diversity of the healthy human microbiome.” (2012) Nature.
(10) The Human Microbiome Consortium. “A framework
for human microbiome research” (2012). Nature. 486(7402):215-21.
J., J. Stombaugh, D. McDonald, J. Chocholousova, P. Gardner, M.K. Iyer, Z. Liu,
C.A. Lozupone, J. Quinn, S. Smit, S. Wikman, J.R. Zaneveld, and R. Knight.
“RNASTAR: An RNA STructural Alignment Repository that provides insight into the
evolution of natural and artificial RNAs.” (2012) RNA. 18(7):1319-27.
K.E., S.D. Essinger, C.A. Lozupone, M.P. O'Connor, G.L. Rosen, R. Knight, S.S.
Kilham, and J.A. Russell. “Environmental and ecological factors that shape the
gut bacterial communities of fish: a meta-analysis.” (2012) Mol Ecol. 21(13):3363-78.
S., R. Knight, A.A. Allshouse, S. Roemer, C. Lozupone, D. McDonald, J. Widmann,
N.F. Voelkel, R.J. Shelton, E.B. Suarez, K.W. Hammer, C. Goujard, N.
Petrosillo, G. Simonneau, P.Y. Hsue, M. Humbert, and S.C. Flores. “Human
Immunodeficiency Virus nef Signature Sequences Are Associated with Pulmonary
Hypertension.“ (2012) AIDS Res Hum Retroviruses. 28(6):607-18.
N.P., T. Yatsunenko, A. Hsiao, J.J. Faith, B.D. Muegge, A.L. Goodman, B.
Henrissat, R. Oozeer, S. Cools-Portier, G. Gobert, C. Chervaux, D. Knights,
C.A. Lozupone, R. Knight, A.E. Duncan, J.R. Bain, M.J. Muehlbauer, C.B.
Newgard, A.C. Heath, and J.I. Gordon. “The impact of a consortium of fermented
milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins.”
(2011) Sci Transl Med. 3(106):106ra106.
D., L.W. Parfrey, J. Zaneveld, C. Lozupone, and R. Knight. “Human-associated
microbial signatures: examining their predictive value.” (2011) Cell Host
J.R., L.W. Parfrey, W. Van Treuren, C. Lozupone, J.C. Clemente, D. Knights, J.
Stombaugh, J. Kuczynski, and R. Knight. “Combined phylogenetic and genomic
approaches for the high-throughput study of microbial habitat adaptation.”
(2011) Trends Microbiol. 19(10):472-82.
E.E., C.A. Lozupone, F.E. Rey, J. Guruge, A. Narra, J. Goodfellow, M. Wu, A.C.
Heath, R. Knight, and J.I. Gordon. “Pan-genome of the dominant human
gut-associated archaeon, Methanobrevibacter
smithii, studied in twins.” (2011) Proc Natl Acad Sci. 108:4599-606.
A., J. Stombaugh, C. Lozupone, P.J. Turnbaugh, J.I. Gordon, and R. Knight. “The
mind-body-microbial continuum” (2011) Dialogues Clin Neurosci. 13(1):55-62.
P., Kottmann R., et al. “Minimum information about a marker gene
sequence (MIMARKS) and minimum information about any (x) sequence (MIxS)
specifications.” (2011) Nature Biotech. 29(5):415-420.
A.J., K.R. Freeman, K.F. McCormick, R.C. Lynch, C. Lozupone, R. Knight, and S.
Schmidt. “Biogeography and habitat
modeling of high-alpine bacteria." (2010) Nature Commun. 1(5):1-6.
C., M.E. Lladser, D. Knights, J. Stombaugh, and R. Knight. “UniFrac: an
effective distance metric for microbial community comparison.” (2010) ISME J.
J., Z. Liu Z, C. Lozupone, D. McDonald, N. Fierer, and R. Knight. “Microbial
community resemblance methods differ in their ability to detect biologically
relevant patterns. (2010) Nat Methods. 7(10):813-9.
D.R, E.K. Costello, M. Hamady, C. Lozupone, et al. “Global patterns in the
biogeography of bacterial taxa” (2010) Environ. Microbiol. 13(1):135-44.
J.G., C.L. Lauber, W.A. Walters, D. Berg-Lyons, C.A. Lozupone, P.J. Turnbaugh,
N. Fierer, and R. Knight. “Microbes and Health Sackler Colloquium: Global
patterns of 16S rRNA diversity at a depth of millions of sequences per sample.”
(2011) Proc Natl Acad Sci. 108:4516-22.
J., J.K. Harris, C. Lozupone, A.Wolfson and R. Knight. “Stable tRNA-based
phylogenies using only 76 nucleotides.” (2010). RNA. 16(8):1469-77.
J., E. Baath, P.C. Brookes, C.L. Lauber, C. Lozupone, C. Lozupone, J.G.
Caporaso, R. Knight, and N. Fierer. “Soil bacterial and fungal communities
across a pH gradient in arable soil.” (2010) ISME J. 4:1340-51.
J.G*., J. Kuczynski*, J. Stombaugh*, K. Bittinger, F.D. Bushman, E.K. Costello,
N. Fierer, A.G. Peña, J.K. Goodrich, J.I. Gordon, G. Huttley, S.T. Kelley, D.
Knights, J.E. Koenig, R.E. Ley, C.A. Lozupone, et al. “QIIME Allows Integration
and Analysis of High-Throughput Community Sequencing Data.” (2010) Nat Methods.
J.R., C. Lozupone, J.I. Gordon and R. Knight. “Ribosomal RNA diversity predicts
genome diversity in gut bacteria and their relatives.” (2010). Nucleic Acids
M.*, C. Lozupone*, R. Knight. “Fast UniFrac: Facilitating high-throughput
phylogenetic analyses of microbial communities including analysis of
pyrosequencing and phylochip data.” (2010) ISME J. 4(1):17-27.
D.P., C.A. Lozupone, D. Nipperess, and R. Knight. “The cladistic basis for the
PD (Phylogenetic Diversity) measure links evolutionary features to
environmental gradients and supports broad applications of microbial ecology’s
‘phylogenetic beta diversity’ framework.” (2009) Int. J. Mol. Sci. 10(11):4723-4741.
A.L., N.P McNulty, Y. Zhao, D. Leip, R. Mitra, C.A. Lozupone, R. Knight, and
J.I. Gordon. “Identifying genetic determinants needed to establish a human gut
symbiont in its habitat.” (2009) Cell Host Microbe. 6(3):279-89.
(32) Ley R.E.*, C.A. Lozupone*, M. Hamady, R.
Knight, and J.I. Gordon. “Worlds within worlds: evolution of the vertebrate gut
microbiota.” (2008) Nat Rev Microbiol. 6(10):776-88.
(33) Lozupone C.A.,
M. Hamady, B.L. Cantarel, P.M. Coutinho, B. Henrissat, J.I. Gordon, and R.
Knight. “The convergence of carbohydrate active gene repertoires in human gut
microbes.” (2008) Proc Natl Acad Sci. 105(39):15076-81.
(34) Ley R.E., M. Hamady, C. Lozupone, P.J.
Turnbaugh, R.R. Ramey, J.S. Bircher, M.L. Schlegel, T.A. Tucker, M.D.
Schrenzel, R. Knight, and J.I. Gordon. “Evolution of mammals and their gut
microbes.” (2008) Science. 320(5883):1647-51.
C.A. and R. Knight. “Species
divergence and the measurement of microbial diversity.” (2008) FEMS Microbiol
(36) Zaneveld J, P.J. Turnbaugh, C. Lozupone, R.E.
Ley, M. Hamady, J.I. Gordon, and R. Knight. “Host-bacterial coevolution and the
search for new drug targets.” (2008) Curr Opin Chem Biol. 12(1):109-14.
(37) McKenna P., C. Hoffmann, N. Minkah, P.P. Aye,
A. Lackner, Z. Liu, C.A. Lozupone, M. Hamady, R. Knight, and F.D. Bushman. “The
macaque gut microbiome in health, lentiviral infection, and chronic
enterocolitis.” (2008) PLoS Pathog. 4(2):e20.
Z., C. Lozupone, M. Hamady, F.D. Bushman, and R. Knight. “Short pyrosequencing
reads suffice for accurate microbial community analysis.” (2007) Nucleic Acids
C.A. and R. Knight. "Global
patterns of bacterial diversity." (2007) Proc Natl Acad Sci.
R., P. Maxwell, A. Birmingham, J. Carnes, J.G. Caporaso, B.C. Easton, M.
Hamady, Z. Liu, C. Lozupone, R. Sammut, S. Smit, M. Wakefield, J. Widmann, S.
Wikman, S. Wilson, and G.A. Huttley. “PyCogent: a toolkit for making sense from
sequence.” (2007) Genome Biol. 8(8):R171.
N., M. Breitbart, J. Nulton, P. Salamon, C. Lozupone, R. Jones, M. Robeson, R.
Edwards, B. Felts, S. Rayhawk, R. Knight, F. Rohwer, and R.B. Jackson. “Metagenomic and small-subunit rRNA analyses
of the genetic diversity of bacteria, archaea, fungi, and viruses in soil.”
(2007) Appl Environ Microbiol. 73:7059-66.
M., A.P. Fontenot, D.G. Mack, C. Lozupone, S. Dillon, A. Meditz, C.C. Wilson,
E. Connick, and B.E. Palmer. “Programmed
death 1 expression on HIV-specific CD4+ T Cells is driven by viral replication
and associated with T cell dysfunction.” (2007) J Immunology. 179:1979-87.
J., M.A. Mahowald, R.E. Ley, C. A. Lozupone, M. Hamady, E.C. Martens, B.
Henrissat, P.M. Coutinho, P. Minx, P. Latreille, H. Cordum, A. Van Brunt, K.
Kim, R. Fulton, S.W. Clifton, R.K. Wilson, R.D. Knight, and J.I. Gordon. “Evolution
of symbiotic bacteria in the distal human intestine.” (2007) PLoS Biol.
C.A., M. Hamady, S. Kelley, and R.
Knight. "Quantitative and qualitative diversity
measures lead to different insights into factors that structure microbial
communities." (2007) Appl Environ Microbiol. 73:1576-1585.
C.*, M. Hamady*, and R. Knight.
“UniFrac—an online tool for comparing microbial community diversity in a
phylogenetic context.” (2006) BMC Bioinformatics. 7:371-384.
C.A. and R.D. Knight. "UniFrac: A new
phylogenetic method for comparing microbial communities." (2005). Appl
Environ Microbiol. 71:8228-35.
M., C. Lozupone, R. Knight, and M. Yarus. "Size and constant sequences
alter selection." (2005) RNA. 11:1701-9.
R.E., F. Backhed, P. Turnbaugh, C.A. Lozupone, R.D. Knight, and J.I. Gordon.
"Obesity alters gut microbial ecology." (2005) Proc Natl Acad Sci.
Zwart, I, C. Lozupone et al. “Artificial Selection: Finding function amongst
randomized sequences” in Handbook of RNA Biochemistry. (2005) Edited by
R. K. Hartmann, A. Bindereif, A. Schon, E. Westhof. Chapter 47, p 783-806.
C.*, S. Changayil*, I. Majerfeld I, and M. Yarus. “Selection of the simplest
RNA that binds isoleucine.” (2003) RNA. 11:1315-1322.
D, C. Lozupone, and L. Landweber.
“Polymorphism, recombination and alternative unscrambling in the DNA polymerase
alpha gene of the ciliate Stylonychia
lemnae (Alveolata; class Spirotrichea).” (2003). Genetics. 165(4):1761-77.
C.A., R. Knight, and L. Landweber. “The molecular basis of nuclear genetic code
change in ciliates.” (2001) Current Biol. 11(2):65-74.
C.A., and D.A. Klein. “Molecular and cultural assessment of chytrid and Spizellomyces populations in grassland
soils.” (2002) Mycologia. 94:411-420.
C.A., and D.A. Klein.
“Chytridiomycota of little importance in soils?” (1999) ASM News. 65:662-663.