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Catherine Lozupone, PhD


​​Address: 12700 E. 19th Avenue, Room 3113
Anschutz Medical Campus, Aurora, CO 80045
Phone: (303) 724-7942
 
Education:
Villanova 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)
 
Research areas:
  • Microbiology of the human gut and impacts on health.
  • The development of bioinformatics techniques for analysis of marker gene and genomic sequence data.
 
The 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.
 
My 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.
 
Towards 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.
 
Publications:
(1)   Roy, M.G., 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.
(2)   Lozupone, 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.
(3)   Lozupone, 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. 23(10):1704-14.
(4)   Song, 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.
(6)   Lozupone, 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.
(7)   Lozupone, 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. 486(7402):207-14.
(10)  The Human Microbiome Consortium. “A framework for human microbiome research” (2012). Nature. 486(7402):215-21.
(11)  Widmann 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.
(12)  Sullam, 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.
(13)  Almodovar, 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.
(14)  McNulty, 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.
(15)  Knights, D., L.W. Parfrey, J. Zaneveld, C. Lozupone, and R. Knight. “Human-associated microbial signatures: examining their predictive value.” (2011) Cell Host Microbe. 10(4):292-6.
(16)  Zaneveld 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.
(17)  Hansen, 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.
(18)  Gonzalez, 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.
(19)  Yilmaz, 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.
(20)  King, 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.
(21)  Lozupone, C., M.E. Lladser, D. Knights, J. Stombaugh, and R. Knight. “UniFrac: an effective distance metric for microbial community comparison.” (2010) ISME J. 5(2):169-72.
(22)  Kuczynski 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.
(23)  Nemergut, 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.
(24)  Caporaso 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.
(25)  Widmann, 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.
(26)  Rousk, 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.
(27)  Caporaso, 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. 7(5):335-6.
(28)  Zaneveld, 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 Res. 38(12):3869-79.
(29)  Hamady, 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.
(30)  Faith, 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.
(31)  Goodman, 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.
(35)  Lozupone, C.A. and R. Knight. “Species divergence and the measurement of microbial diversity.” (2008) FEMS Microbiol Reviews. 32(4):557-78.
(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.
(38)  Liu, Z., C. Lozupone, M. Hamady, F.D. Bushman, and R. Knight. “Short pyrosequencing reads suffice for accurate microbial community analysis.” (2007) Nucleic Acids Res. 35:e120.
(39)  Lozupone, C.A. and R. Knight. "Global patterns of bacterial diversity." (2007) Proc Natl Acad Sci. 104(27):11436-40.
(40)  Knight, 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.
(41)  Fierer, 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.
(42)  D'Souza, 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.
(43)  Xu, 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. 5(7)e156.
(44)  Lozupone 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.
(45)  Lozupone, 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.
(46)  Lozupone, C.A.  and R.D. Knight. "UniFrac: A new phylogenetic method for comparing microbial communities." (2005). Appl Environ Microbiol. 71:8228-35.
(47)  Legiewicz, M., C. Lozupone, R. Knight, and M. Yarus. "Size and constant sequences alter selection." (2005) RNA. 11:1701-9.
(48)  Ley, 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. 102:11070-11075.
(49)  De 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.
(50)  Lozupone C.*, S. Changayil*, I. Majerfeld I, and M. Yarus. “Selection of the simplest RNA that binds isoleucine.” (2003) RNA. 11:1315-1322.
(51)  Ardell, 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.
(52)  Lozupone, C.A., R. Knight, and L. Landweber. “The molecular basis of nuclear genetic code change in ciliates.” (2001) Current Biol. 11(2):65-74.
(53)  Lozupone, C.A., and D.A. Klein. “Molecular and cultural assessment of chytrid and Spizellomyces populations in grassland soils.” (2002) Mycologia. 94:411-420.
(54)   Lozupone, C.A., and D.A. Klein. “Chytridiomycota of little importance in soils?” (1999) ASM News. 65:662-663.