The Search Paradigm

Search" researchers use molecular methods such as cloning and sequencing to detect microorganisms in various environments. The circle to the left illustrates our basic "molecular method" for detecting organisms in a sample. These are the techniques used by both medical and environmental "search".

A significant part of what we do in environmental search is expansion of the three domain tree of life. Since many microbes are difficult to culture, many have only recently been discovered through sequencing of conserved genes such as that for the small subunit of the ribosomal RNA.

 

Environmental Search Projects

Drinking Water Microbiology -- This project aims to develop an understanding of the microbiology of drinking water and drinking water sources. As a new focus area of the project, samples will be collected from municipal drinking water taps and source water along major rivers. Graduate student Kim Ross, postdocs Kevin McCabe and Eric Holinger are the primary personnel. Our water supply work funded by the Sloan Foundation. Current project include sampling municipal water systems on the Colorado Front Range, the Los Angeles area, and along the Missouri/Mississippi river basin.

Indoor Environments -- This project, funded by the Sloan Foundation, examines the microbial communities in human environments incuding hospitals, homes, public buildings, and water systems. As a result of finding Mycobacterium spp. in many indoor and drinking water ecosystems, we are interested in finding a gene that successfully differentiates between different species/strains of Mycobacteria. Postdoc Kevin McCabe, graduate student Kim Ross and technician Kristen Peterson work on this project.

Microbially-induced Concrete Corrosion -- Concrete corrosion is a major financial drain for wastewater utilities. In this project, we aim to characterize what types of communities are present in different environments and to devise a metals-based inhibition material. Graduate student Ali Ling works on this project in collaboration with members of Dr. Mark Hernadez's laboratory in Environmental Engineering.

CAFOs -- Concentrated animal feeding operations bring together large numbers of people and animals in an enclosed environment. This project, funded by NIOSH, examines the microbial constituents of air in CAFOs to determine a) what microbes are present and b) whether we can detect specific microorganisms of concern. Work was previously completed by graduate student Mari Rodriguez and postdoc Piret Koll.

Guerrero Negro -- The Guerrero Negro hypersaline microbial mat of Baja California, Mexico has been a research site for the Pace Lab for years. The Bacterial, Archaeal, and Eukaryotic microbial diversity are the subjects of several studies previously conducted by Dr. John Spear, Dr. Ruth Ley, and undergraduates Alicia Berger and Leah Feazel, as well as ongoing investigation by Drs. Charles Robertson and Kirk Harris.

Yellowstone Microbial Mats -- This study is interested in dicovering what organisms form the multicolored microbial mats surrounding Yellowstone's hot springs. This study has been conducted by Kim Ross and Leah Feazel with the help of undergraduates Nikki Held, Mallory Chan, and graduate rotation students.

Environmental Search Publications

Rodriguez, M., J.J. Walker, N.R. Pace and M. Hernandez. (2010) Molecular source tracking of bioaerosols in the quarantined Katrina flood zone.  Aerosol Science Technol.  44:236-245.

Pace, N.R. (2009) Mapping the tree of life: progress and prospects. Microbiol. Mol. Biol. Rev. 73:564-576.

Baumgartner LK, Dupraz C, Buckley DH, Spear JR, Pace NR, and Visscher PT. (2009) Microbial species richness and metabolic activities in hypersaline microbial mats: Insight into biosignature formation through lithification. Astrobiology 9:861-874.

Feazel LM, Baumgartner LK, Peterson KL, Frank DN, Harris JK, and Pace NR. (2009) Opportunistic pathogens enriched in showerhead biofilms. PNAS 106: 16393-16399.

Baumgartner, LK, Spear, JR, Buckley, DH, Pace, NR, Reid, RP, Dupraz, C, and Visscher, PT (2009) Microbial diversity in modern marine stromatolites, Highborne Cay, Bahamas. Environ Microbiol. Published online July 6.

Robertson, CE, Spear, JR, Harris, JK, and Pace, NR (2009) Diversity and stratification of Archaea in a hypersaline microbial mat.
Appl Environ Microbiol 75:(7) 1801-1810.

Kunin, V, Raes, J, Harris, JK, Spear, JR, Walker, JJ, Ivanova, N, von Mering, C, Bebout, BM, Pace, NR, Bork, P, and Hugenholtz, P (2008) Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat. Mol Syst Biol 4:198.

Sahl, JW, Pace, NR, and Spear, JR. (2008) Comparative molecular analysis of endoevaporitic microbial communities. Appl Environ Microbiol 74(20):6444-6.

Feazel LM, Spear JR, Berger AB, Harris JK, Frank DN, Ley RE, Pace NR. (2008) Eucaryotic diversity in a hypersaline microbial mat. Appl Environ Microbiol. 74(1):329-32.

Ley RE, Harris JK, Wilcox J, Spear JR, Miller SR, Bebout BM, Maresca JA, Bryant DA, Sogin ML, Pace NR. (2006) Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat. Appl Environ Microbiol. 72(5):3685-95.

Salmassi TM, Walker JJ, Newman DK, Leadbetter JR, Pace NR, Hering JG. (2006) Community and cultivation analysis of arsenite oxidizing biofilms at Hot Creek. Environ Microbiol;8(1):50-9.

Robertson CE, Harris JK, Spear JR, Pace NR. (2005) Phylogenetic diversity and ecology of environmental Archaea. Curr Opin Microbiol. 8(6):638-42. Review.

Papineau D, Walker JJ, Mojzsis SJ, Pace NR. (2005) Composition and structure of microbial communities from stromatolites of Hamelin Pool in Shark Bay, Western Australia. Appl Environ Microbiol. 71(8):4822-32.

Jakosky BM, Anbar AD, Des Marais D, Morrison D, Pace NR. (2005) Don't dismiss astrobiology. Science. 308(5721):495-7.

Walker JJ, Spear JR, Pace NR. (2005) Geobiology of a microbial endolithic community in the Yellowstone geothermal environment.Nature. 434(7036):1011-4.

Spear JR, Walker JJ, McCollom TM, Pace NR.(2005) Hydrogen and bioenergetics in the Yellowstone geothermal ecosystem. Proc Natl Acad Sci U S A. 102(7):2555-60.

Kelley ST, Theisen U, Angenent LT, St Amand A, Pace NR. (2004) Molecular analysis of shower curtain biofilm microbes. Appl Environ Microbiol. 70(7):4187-92.

Harris JK, Kelley ST, Pace NR. (2004) New perspective on uncultured bacterial phylogenetic division OP11. Appl Environ Microbiol. 70(2):845-9.

 

RNAse P Projects

This research area includes studies of RNase P RNA, its catalytic function and associated proteins, as well as other functional RNAs such as miRNAs.

Analysis of Bacterial RNase P Structure--The fine structure of bacterial Ribonuclease P is still being resolved by comparing structures from different bacteria. Kinetics, mutational analyses, covariation, and X-RAY crystallography,are techniques commonly utilized by the P researchers: Alexei, Lika, Donnie, Katrina and Sina.

Eukaryal RNase P--Steve Marquez studies the RNase P molecule of eucaryotic organisms. In eucaryotes there are many more affiliated proteins needed for the catalytic function of RNase P

RNAse P Publications

Kazantsev, AV, Krivenko, AA, and Pace, NR (2008) Mapping metal-binding sites in the catalytic domain of bacterial RNase P RNA.
RNA 15: 266-276.

Marquez SM, Chen JL, Evans D, Pace NR. (2006) Structure and function of eukaryotic Ribonuclease P RNA. Mol Cell. 24(3):445-56.

Dalby AB, Frank DN, St Amand AL, Bendele AM, Pace NR. (2006) Culture-independent analysis of indomethacin-induced alterations in the rat gastrointestinal microbiota. Appl Environ Microbiol. 72(10):6707-15.

Kazantsev AV, Pace NR.(2006) Bacterial RNase P: a new view of an ancient enzyme.
Nat Rev Microbiol. 4(10):729-40. Review.

Evans D, Marquez SM, Pace NR. (2006) RNase P: interface of the RNA and protein worlds. Trends Biochem Sci. 31(6):333-41.

Marquez SM, Chen J, Evans D, Pace NR. (2006) Structure and function of eukaryotic ribonuclease P RNA. Mol. Cell. 24:445-56.

Kazantsev AV, Pace NR. (2006) Bacterial RNase P: a new view of an ancient enzyme. Nature Rev. Microbiol. 4:729-40.

Buck AH, Kazantsev AV, Dalby AB, Pace NR. (2005) Structural perspective on the activation of RNAse P RNA by protein. Nat Struct Mol Biol. 12(11):958-64.

Buck AH, Dalby AB, Poole AW, Kazantsev AV, Pace NR. (2005) Protein activation of a ribozyme: the role of bacterial RNase P protein. EMBO J. 24(19):3360-8.

Kazantsev AV, Krivenko AA, Harrington DJ, Holbrook SR, Adams PD, Pace NR. (2005) Crystal structure of a bacterial ribonuclease P RNA. Proc Natl Acad Sci U S A. 102(38):13392-7.

Marquez SM, Harris JK, Kelley ST, Brown JW, Dawson SC, Roberts EC, Pace NR. (2005) Structural implications of novel diversity in eucaryal RNase P RNA. RNA. 11(5):739-51

Kazantsev AV, Krivenko AA, Harrington DJ, Carter RJ, Holbrook SR, Adams PD, Pace NR. (2003) High-resolution structure of RNase P protein from Thermotoga maritima. Proc Natl Acad Sci U S A. 100(13):7497-502

Krivenko AA, Kazantsev AV, Adamidi C, Harrington DJ, Pace NR. (2002) Expression, purification, crystallization and preliminary diffraction analysis of RNase P protein from Thermotoga maritima. Acta Crystallogr D Biol Crystallogr. 58(Pt 7):1234-6.

Li X, Frank DN, Zengel JM. (2002) Phylogenetic analysis of the strucutre of RNase MRP RNA in yeasts. RNA. 8:741-52

Johne's Disease Acid fast and FISH Images

Medical Microbiology Projects

Cystic Fibrosis -- Kirk Harris uses sequencing to analyze bacterial community composition in lung sputum and bronchial lavages of CF patients. This is useful because frequently the exacerbation-causing organisms are not brought into culture in the hospital lab. Potentially, this work could be used to drive treatment of CF patients based on the bacterial pathogens identified through sequencing.

Johnes's Disease -- An ongoing study of the microbial community composition in the intestines of Crohn's Disease cattle. This is a gastro-intestinal disease that may be caused by bacteria and is becoming more prevalent. Previous studies in the lab have studied inflammatory bowel disease (IBD) and chrone's disease in humans.

MRSA -- Methicillin-resistant Staphylococcus aureus (MRSA) represents an increasing risk especially in hospital nosocomial infections.

Atopic Dermatitis -- increasingly common skin condition in children, causes inflammation, lesions, and itchiness. Often associated with microbial infection.

Prostatitis -- inflamation of the prostate affects 50% of all men at some point in their life. Prostatitis maybe bacterial or non-bacterial by hospital culture results.

 

University of Colorado Health Sciences Center

Cystic Fibrosis Foundation

Crohn's and Colitis Foundation

 

 

 

Tuberculosis Images

Medical Microbiology Publications

Frank, D.N., L.M. Feazel, M.T. Bessesen, C.S. Price,  E.N. Janoff and N.R. Pace.  (2010) The human nasal microbiota and Staphylococcus aureus carriage.  PLoS ONE 5:e10598 (15 pp.).

Frank, D.N., S.S. Wilson, A.L. St. Amand, and N.R. Pace. (2009) Culture-independent microbiological analysis of Foley urinary catheter biofilms.  PLoS ONE 4:e7811 (7 pp.).

Frank, DN, Wysocki, A, Specht-Glick, DD, Rooney, A, Feldman, RA, St Amand, AL, Pace, NR, and Trent, JD (2009) Microbial diversity in chronic open wounds.
Wound Repair Regen 17(2):163-72.

Frank, DN (2008) XplorSeq: A software environment for integrated management and phylogenetic analysis of metagenomic sequence data. BMC Bioinformatics 9: 420.

Frank, DN and Pace, NR (2008) Gastrointestinal microbiology enters the metagenomics era. Curr Opin Gastroenterol, 24(1):4-10.

Peterson, DA, Frank, DN, Pace, NR, and Gordon, JI (2008) Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases.
Cell Host Microbe 3(6):417-27.

Harris JK, De Groote MA, Sagel SD, Zemanick ET, Kapsner R, Penvari C, Kaess H, Deterding RR, Accurso FJ, Pace NR.(2007) Molecular identification of bacteria in bronchoalveolar lavage fluid from children with cystic fibrosis.Proc Natl Acad Sci 104(51):20529-33.

Frank DN, St Amand AL, Feldman RA, Boedeker EC, Harpaz N, Pace NR. (2007) Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci. 104(34):13780-5

St Amand AL, Frank DN, De Groote MA, Basaraba RJ, Orme IM, Pace NR. (2005) Use of specific rRNA oligonucleotide probes for microscopic detection of Mycobacterium tuberculosis in culture and tissue specimens. J Clin Microbiol. 2005 Oct;43(10):5369-71.

Gardner EM, Burman WJ, DeGroote MA, Hildred G, Pace NR. (2005) Conventional and molecular epidemiology of macrolide resistance among new Mycobacterium avium complex isolates recovered from HIV-infected patients. Clin Infect Dis. 41(7):1041-4.

St Amand AL, Frank DN, De Groote MA, Pace NR.(2005) Use of specific rRNA oligonucleotide probes for microscopic detection of Mycobacterium avium complex organisms in tissue. J Clin Microbiol. 43(4):1505-14

Angenent LT, Kelley ST, St Amand A, Pace NR, Hernandez MT. (2005) Molecular identification of potential pathogens in water and air of a hospital therapy pool. Proc Natl Acad Sci U S A. 102(13):4860-5.

De Groote MA, Frank DN, Dowell E, Glode MP, Pace NR. (2005) Lactobacillus rhamnosus GG bacteremia associated with probiotic use in a child with short gut syndrome. Pediatr Infect Dis J. 24(3):278-80.

Frank DN, Spiegelman GB, Davis W, Wagner E, Lyons E, Pace NR. (2003) Culture-independent molecular analysis of microbial constituents of the healthy human outer ear. J Clin Microbiol. 41(1):295-303.