Jeffrey S McLean

Summary

Affiliation: J. Craig Venter Institute
Country: USA

Publications

  1. doi request reprint Quantification of electron transfer rates to a solid phase electron acceptor through the stages of biofilm formation from single cells to multicellular communities
    Jeffrey S McLean
    The J Craig Venter Institute, San Diego, CA, USA
    Environ Sci Technol 44:2721-7. 2010
  2. pmc An in vitro biofilm model system maintaining a highly reproducible species and metabolic diversity approaching that of the human oral microbiome
    Anna Edlund
    Microbial and Environmental Genomics, J, Craig Venter Institute, 10355 Science Center Drive, CA 921 21 San Diego, USA
    Microbiome 1:25. 2013
  3. pmc Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum
    Jeffrey S McLean
    Microbial and Environmental Genomics, J Craig Venter Institute, San Diego, CA 92121, USA
    Proc Natl Acad Sci U S A 110:E2390-9. 2013
  4. pmc Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform
    Jeffrey S McLean
    Microbial and Environmental Genomics, J Craig Venter Institute, San Diego, California 92121, USA
    Genome Res 23:867-77. 2013
  5. pmc Identifying low pH active and lactate-utilizing taxa within oral microbiome communities from healthy children using stable isotope probing techniques
    Jeffrey S McLean
    Microbial and Environmental Genomics, The J Craig Venter Institute, San Diego, California, United States of America
    PLoS ONE 7:e32219. 2012
  6. pmc Correlated biofilm imaging, transport and metabolism measurements via combined nuclear magnetic resonance and confocal microscopy
    Jeffrey S McLean
    Environmental Microbial Genomics, J Craig Venter Institute, 111 49 N Torrey Pines Rd, Suite 220, La Jolla, CA 92037, USA
    ISME J 2:121-31. 2008
  7. pmc Meta-omics uncover temporal regulation of pathways across oral microbiome genera during in vitro sugar metabolism
    Anna Edlund
    Microbial and Environmental Genomics, J Craig Venter Institute, La Jolla, CA, USA
    ISME J 9:2605-19. 2015
  8. pmc The social structure of microbial community involved in colonization resistance
    Xuesong He
    UCLA School of Dentistry, Los Angeles, CA, USA
    ISME J 8:564-74. 2014
  9. pmc High-Quality Draft Genome Sequence of Low-pH-Active Veillonella parvula Strain SHI-1, Isolated from Human Saliva within an In Vitro Oral Biofilm Model
    Anna Edlund
    Microbial and Environmental Genomics, J Craig Venter Institute, La Jolla, California, USA School of Dentistry, University of California, Los Angeles, Los Angeles, California, USA
    Genome Announc 4:. 2016
  10. pmc Metagenome and Metatranscriptome Analyses Using Protein Family Profiles
    Cuncong Zhong
    J Craig Venter Institute, La Jolla, California, United States of America
    PLoS Comput Biol 12:e1004991. 2016

Collaborators

  • Karen E Nelson
  • J Craig Venter
  • Robert Friedman
  • Andrew E Allen
  • Christopher L Dupont
  • Haluk Beyenal
  • Shun ichi Ishii
  • Mark E Shirtliff
  • Orianna Bretschger
  • Yuri A Gorby
  • R A Wind
  • Byung Hong Kim
  • Liang Shi
  • Anna Edlund
  • Xuesong He
  • Wenyuan Shi
  • Renate Lux
  • Youngik Yang
  • Shibu Yooseph
  • Paul D Majors
  • Batbileg Bor
  • Cuncong Zhong
  • James K Fredrickson
  • Adam P Hall
  • Lihong Guo
  • Dwayne A Elias
  • David W Kennedy
  • Eric A Hill
  • Grigoriy E Pinchuk
  • Matthew J Marshall
  • Scott D Harvey
  • Morris S Good
  • David S Wunschel
  • Joseph K Bedree
  • Justin S Bois
  • Thao T To
  • Quanhui Liu
  • Lujia Cen
  • Michael Watling
  • Z Hong Zhou
  • Nicole Poweleit
  • Robert P Gunsalus
  • Roger E Bumgarner
  • Pieter C Dorrestein
  • Don D Nguyen
  • Kenneth H Nealson
  • Heather M Mottaz
  • Carol S Giometti
  • Mary S Lipton
  • Sandra L Tollaksen
  • Johannes C M Scholten
  • Salahuddin Ahmed
  • Maxim I Boyanov
  • Paul D Panetta
  • Shannon M Goodwin
  • Susan L Crawford
  • Nancy B Valentine
  • Samantha B Reed
  • John M Zachara
  • Daad A Saffarini
  • Gary M Mong
  • Alice C Dohnalkova
  • Cody J Simonson
  • Richard M Ozanich
  • Zheming Wang
  • David E Culley
  • Kenneth M Kemner
  • Jim K Fredrickson
  • Barry Lai
  • Vanessa L Bailey
  • Margaret F Romine
  • Christopher F Wend
  • Alexander S Beliaev
  • Don S Daly
  • Leonard J Bond
  • Nancy Valentine
  • Kristin Jarman
  • Kevin R Minard
  • Karen Wahl

Detail Information

Publications20

  1. doi request reprint Quantification of electron transfer rates to a solid phase electron acceptor through the stages of biofilm formation from single cells to multicellular communities
    Jeffrey S McLean
    The J Craig Venter Institute, San Diego, CA, USA
    Environ Sci Technol 44:2721-7. 2010
    ..These data suggest a link between the ability of a surface to accept electrons and biofilm structure development...
  2. pmc An in vitro biofilm model system maintaining a highly reproducible species and metabolic diversity approaching that of the human oral microbiome
    Anna Edlund
    Microbial and Environmental Genomics, J, Craig Venter Institute, 10355 Science Center Drive, CA 921 21 San Diego, USA
    Microbiome 1:25. 2013
    ....
  3. pmc Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum
    Jeffrey S McLean
    Microbial and Environmental Genomics, J Craig Venter Institute, San Diego, CA 92121, USA
    Proc Natl Acad Sci U S A 110:E2390-9. 2013
    ..Phylogenomic analysis of conserved single-copy genes confirms that TM6SC1 is a deeply branching phylum. ..
  4. pmc Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform
    Jeffrey S McLean
    Microbial and Environmental Genomics, J Craig Venter Institute, San Diego, California 92121, USA
    Genome Res 23:867-77. 2013
    ..Here we show for the first time that it also enables comparative genomic analysis of strain variation in a pathogen captured from complex biofilm samples in a healthcare facility...
  5. pmc Identifying low pH active and lactate-utilizing taxa within oral microbiome communities from healthy children using stable isotope probing techniques
    Jeffrey S McLean
    Microbial and Environmental Genomics, The J Craig Venter Institute, San Diego, California, United States of America
    PLoS ONE 7:e32219. 2012
    ....
  6. pmc Correlated biofilm imaging, transport and metabolism measurements via combined nuclear magnetic resonance and confocal microscopy
    Jeffrey S McLean
    Environmental Microbial Genomics, J Craig Venter Institute, 111 49 N Torrey Pines Rd, Suite 220, La Jolla, CA 92037, USA
    ISME J 2:121-31. 2008
    ....
  7. pmc Meta-omics uncover temporal regulation of pathways across oral microbiome genera during in vitro sugar metabolism
    Anna Edlund
    Microbial and Environmental Genomics, J Craig Venter Institute, La Jolla, CA, USA
    ISME J 9:2605-19. 2015
    ....
  8. pmc The social structure of microbial community involved in colonization resistance
    Xuesong He
    UCLA School of Dentistry, Los Angeles, CA, USA
    ISME J 8:564-74. 2014
    ..Furthermore, our results emphasize the importance of 'Facilitation' or positive interactions in the development of community-level functions, such as colonization resistance. ..
  9. pmc High-Quality Draft Genome Sequence of Low-pH-Active Veillonella parvula Strain SHI-1, Isolated from Human Saliva within an In Vitro Oral Biofilm Model
    Anna Edlund
    Microbial and Environmental Genomics, J Craig Venter Institute, La Jolla, California, USA School of Dentistry, University of California, Los Angeles, Los Angeles, California, USA
    Genome Announc 4:. 2016
    ..The genome is composed of 7 contigs, for a total of 2,200,064 bp. ..
  10. pmc Metagenome and Metatranscriptome Analyses Using Protein Family Profiles
    Cuncong Zhong
    J Craig Venter Institute, La Jolla, California, United States of America
    PLoS Comput Biol 12:e1004991. 2016
    ..HMM-GRASPx is freely available online from http://sourceforge.net/projects/hmm-graspx. ..
  11. pmc Phenotypic and Physiological Characterization of the Epibiotic Interaction Between TM7x and Its Basibiont Actinomyces
    Batbileg Bor
    Section of Oral Biology, School of Dentistry, University of California, Los Angeles, CA, 90095, USA
    Microb Ecol 71:243-55. 2016
    ....
  12. doi request reprint Investigations of structure and metabolism within Shewanella oneidensis MR-1 biofilms
    Jeffrey S McLean
    Pacific Northwest National Laboratory, MSIN P7 50, Richland, WA 99354, United States
    J Microbiol Methods 74:47-56. 2008
    ....
  13. ncbi request reprint NMR methods for in situ biofilm metabolism studies
    Paul D Majors
    Pacific Northwest National Laboratory, MSIN K8 98, Richland, WA 99352, USA
    J Microbiol Methods 62:337-44. 2005
    ..These results represent progress toward our ultimate goal of correlating time- and depth-resolved metabolism and mass transport with gene expression in live in situ biofilms using combined NMR/optical microscopy techniques...
  14. ncbi request reprint An estimate of biofilm properties using an acoustic microscope
    Morris S Good
    Laboratory Directed Research and Development Program, Northwest National Laboratory, Richland, WA, USA
    IEEE Trans Ultrason Ferroelectr Freq Control 53:1637-48. 2006
    ..The experimental acoustic and optical systems, methods used to estimate biofilm properties, and potential applications for the resulting data are discussed...
  15. pmc c-Type cytochrome-dependent formation of U(IV) nanoparticles by Shewanella oneidensis
    Matthew J Marshall
    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
    PLoS Biol 4:e268. 2006
    ..In the environment, such association of UO(2) nanoparticles with biopolymers may exert a strong influence on subsequent behavior including susceptibility to oxidation by O(2) or transport in soils and sediments...
  16. pmc The influence of cultivation methods on Shewanella oneidensis physiology and proteome expression
    Dwayne A Elias
    Department of Biochemistry, University of Missouri Columbia, Columbia, MO 65211, USA
    Arch Microbiol 189:313-24. 2008
    ..By decreasing cell to cell variability, higher quality samples will allow for the interpretive accuracy necessary for drawing conclusions relevant to microbial systems biology research...
  17. pmc Electrically conductive bacterial nanowires produced by Shewanella oneidensis strain MR-1 and other microorganisms
    Yuri A Gorby
    Pacific Northwest National Laboratory, Richland, WA 99352, USA
    Proc Natl Acad Sci U S A 103:11358-63. 2006
    ....
  18. doi request reprint NMR bioreactor development for live in-situ microbial functional analysis
    Paul D Majors
    Biological Sciences Division, Pacific Northwest National Laboratory, 3335 Q Avenue, MSIN K8 98, Richland, WA 99352, USA
    J Magn Reson 192:159-66. 2008
    ..The advantages of live in-situ microbial metabolomics analysis and its complementariness with functional genomics/systems biology methods are discussed...
  19. ncbi request reprint Effects of varied pH, growth rate and temperature using controlled fermentation and batch culture on matrix assisted laser desorption/ionization whole cell protein fingerprints
    David S Wunschel
    Analytical Chemistry, Pacific Northwest National Laboratory, MS P8 08, PO Box 999, Richland WA 99352, USA
    J Microbiol Methods 62:259-71. 2005
    ..The effect of varying growth temperature on Y. enterocolitica was also examined. While the anticipated effects on phenotype were observed, the MALDI-MS technique provided the proper identification...
  20. ncbi request reprint Preparation and evaluation of spore-specific affinity-augmented bio-imprinted beads
    Scott D Harvey
    Pacific Northwest National Laboratory, P O Box 999 MSIN P8 50, Richland, WA 99352, USA
    Anal Bioanal Chem 386:211-9. 2006
    ..The binding assay results also indicated that further refinement of the surface deactivation procedure would enhance the performance of the imprinted substrate...