Philip Hugenholtz

Summary

Affiliation: Lawrence Berkeley National Laboratory
Country: USA

Publications

  1. pmc Building on basic metagenomics with complementary technologies
    Falk Warnecke
    Microbial Ecology Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
    Genome Biol 8:231. 2007
  2. pmc SNP-VISTA: an interactive SNP visualization tool
    Nameeta Shah
    Institute for Data Analysis and Visualization, IDAV, Department of Computer Science, University of California, Davis, One ShieldsAve, Davis, CA 95616, USA
    BMC Bioinformatics 6:292. 2005
  3. pmc CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats
    Charles Bland
    Department of Computer Science, Jackson State University, Jackson, MS 39217, USA
    BMC Bioinformatics 8:209. 2007
  4. ncbi request reprint Reclassification of Sphaerobacter thermophilus from the subclass Sphaerobacteridae in the phylum Actinobacteria to the class Thermomicrobia (emended description) in the phylum Chloroflexi (emended description)
    Philip Hugenholtz
    Department of Environmental Science, Policy and Management, 151 Hilgard Hall, University of California Berkeley, Berkeley, CA 94720 3110, USA
    Int J Syst Evol Microbiol 54:2049-51. 2004
  5. pmc The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata
    Konstantinos Liolios
    Genome Biology Program, DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, USA
    Nucleic Acids Res 38:D346-54. 2010
  6. pmc A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
    Dongying Wu
    DOE Joint Genome Institute, Walnut Creek, California 94598, USA
    Nature 462:1056-60. 2009
  7. pmc Genome-directed isolation of the key nitrogen fixer Leptospirillum ferrodiazotrophum sp. nov. from an acidophilic microbial community
    Gene W Tyson
    Department of Environmental Science, Policy, and Management, 151 Hilgard Hall, University of California, Berkeley, CA 94720 3111, USA
    Appl Environ Microbiol 71:6319-24. 2005
  8. ncbi request reprint Lineages of acidophilic archaea revealed by community genomic analysis
    Brett J Baker
    Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720, USA
    Science 314:1933-5. 2006
  9. doi request reprint Validation of two ribosomal RNA removal methods for microbial metatranscriptomics
    Shaomei He
    Department of Energy Joint Genome Institute, Walnut Creek, California, USA
    Nat Methods 7:807-12. 2010
  10. pmc A bacterial metapopulation adapts locally to phage predation despite global dispersal
    Victor Kunin
    Microbial Ecology Program, Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
    Genome Res 18:293-7. 2008

Detail Information

Publications59

  1. pmc Building on basic metagenomics with complementary technologies
    Falk Warnecke
    Microbial Ecology Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
    Genome Biol 8:231. 2007
    ..Together, these approaches hold great promise for the study of microbial ecology and evolution...
  2. pmc SNP-VISTA: an interactive SNP visualization tool
    Nameeta Shah
    Institute for Data Analysis and Visualization, IDAV, Department of Computer Science, University of California, Davis, One ShieldsAve, Davis, CA 95616, USA
    BMC Bioinformatics 6:292. 2005
    ..The program is available at http://genome.lbl.gov/vista/snpvista1...
  3. pmc CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats
    Charles Bland
    Department of Computer Science, Jackson State University, Jackson, MS 39217, USA
    BMC Bioinformatics 8:209. 2007
    ..In this study, a new tool, CRT, is introduced that rapidly and accurately identifies CRISPRs in large DNA strings, such as genomes and metagenomes...
  4. ncbi request reprint Reclassification of Sphaerobacter thermophilus from the subclass Sphaerobacteridae in the phylum Actinobacteria to the class Thermomicrobia (emended description) in the phylum Chloroflexi (emended description)
    Philip Hugenholtz
    Department of Environmental Science, Policy and Management, 151 Hilgard Hall, University of California Berkeley, Berkeley, CA 94720 3110, USA
    Int J Syst Evol Microbiol 54:2049-51. 2004
    ..Descriptions for the phylum Chloroflexi and the class Thermomicrobia are emended to reflect the proposed changes in classification...
  5. pmc The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata
    Konstantinos Liolios
    Genome Biology Program, DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, USA
    Nucleic Acids Res 38:D346-54. 2010
    ..GOLD is available at: http://www.genomesonline.org and has a mirror site at the Institute of Molecular Biology and Biotechnology, Crete, Greece, at: http://gold.imbb.forth.gr/..
  6. pmc A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
    Dongying Wu
    DOE Joint Genome Institute, Walnut Creek, California 94598, USA
    Nature 462:1056-60. 2009
    ....
  7. pmc Genome-directed isolation of the key nitrogen fixer Leptospirillum ferrodiazotrophum sp. nov. from an acidophilic microbial community
    Gene W Tyson
    Department of Environmental Science, Policy, and Management, 151 Hilgard Hall, University of California, Berkeley, CA 94720 3111, USA
    Appl Environ Microbiol 71:6319-24. 2005
    ..We propose the name Leptospirillum ferrodiazotrophum sp. nov. for this iron-oxidizing, free-living diazotroph. This study highlights how environmental sequence data can provide insights for culturing previously uncultured microorganisms...
  8. ncbi request reprint Lineages of acidophilic archaea revealed by community genomic analysis
    Brett J Baker
    Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720, USA
    Science 314:1933-5. 2006
    ..45 micrometers in diameter is dominated by these organisms. Transmission electron microscope images revealed that the cells are pleomorphic with unusual folded membrane protrusions and have apparent volumes of <0.006 cubic micrometer...
  9. doi request reprint Validation of two ribosomal RNA removal methods for microbial metatranscriptomics
    Shaomei He
    Department of Energy Joint Genome Institute, Walnut Creek, California, USA
    Nat Methods 7:807-12. 2010
    ..Illumina sequencing itself also can compromise quantitative data analysis by introducing a G+C bias between runs...
  10. pmc A bacterial metapopulation adapts locally to phage predation despite global dispersal
    Victor Kunin
    Microbial Ecology Program, Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
    Genome Res 18:293-7. 2008
    ..Genomic signatures linking CAP to past phage exposures were observed mostly between local phage and host. We conclude that CAP strains disperse globally but must adapt to phage predation pressure locally...
  11. doi request reprint Annotation of metagenome short reads using proxygenes
    Daniel Dalevi
    Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Bioinformatics 24:i7-13. 2008
    ..We introduce a clustering method which significantly reduces the size of a metagenome dataset while maintaining a faithful representation of its functional and taxonomic content...
  12. ncbi request reprint Use of simulated data sets to evaluate the fidelity of metagenomic processing methods
    Konstantinos Mavromatis
    Department of Energy Joint Genome Institute DOE JGI, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
    Nat Methods 4:495-500. 2007
    ..The simulated data sets are available online to facilitate standardized benchmarking of tools for metagenomic analysis...
  13. ncbi request reprint Comparative metagenomics of microbial communities
    Susannah Green Tringe
    Department of Energy DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
    Science 308:554-7. 2005
    ..The identification of environment-specific genes through a gene-centric comparative analysis presents new opportunities for interpreting and diagnosing environments...
  14. pmc IMG/M: a data management and analysis system for metagenomes
    Victor M Markowitz
    Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, USA
    Nucleic Acids Res 36:D534-8. 2008
    ..IMG/M provides IMG's comparative data analysis tools extended to handle metagenome data, together with metagenome-specific analysis tools. IMG/M is available at http://img.jgi.doe.gov/m...
  15. ncbi request reprint CRISPR--a widespread system that provides acquired resistance against phages in bacteria and archaea
    Rotem Sorek
    Rotem Sorek, Victor Kunin and Philip Hugenholtz are at the Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
    Nat Rev Microbiol 6:181-6. 2008
    ..CRISPR arrays, together with a group of associated proteins, confer resistance to phages, possibly by an RNA-interference-like mechanism. This Progress discusses the structure and function of this newly recognized antiviral mechanism...
  16. pmc A bioinformatician's guide to metagenomics
    Victor Kunin
    Microbial Ecology Program, DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, USA
    Microbiol Mol Biol Rev 72:557-78, Table of Contents. 2008
    ..Finally, data management issues are presented and discussed. We hope that this review will assist bioinformaticians and biologists in making better-informed decisions on their journey during a metagenomic project...
  17. doi request reprint Experimental factors affecting PCR-based estimates of microbial species richness and evenness
    Anna Engelbrektson
    Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
    ISME J 4:642-7. 2010
    ..However, estimates of species evenness are consistent among different primer pairs targeting the same region. These results highlight the importance of experimental methodology when comparing diversity estimates across communities...
  18. ncbi request reprint Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite
    Falk Warnecke
    DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
    Nature 450:560-5. 2007
    ..Our results underscore how complex even a 1-microl environment can be...
  19. pmc Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix orenii
    Konstantinos Mavromatis
    DOE Joint Genome Institute, Walnut Creek, California, United States of America
    PLoS ONE 4:e4192. 2009
    ....
  20. pmc Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium
    Athanasios Lykidis
    Joint Genome Institute, Lawrence National Berkeley Laboratory, Walnut Creek, CA, USA
    ISME J 5:122-30. 2011
    ..These observations suggest that the TA-degrading consortium consists of additional syntrophic interactions beyond the standard H(2)-producing syntroph-methanogen partnership that may serve to improve community stability...
  21. doi request reprint Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates
    Victor Kunin
    Microbial Ecology Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
    Environ Microbiol 12:118-23. 2010
    ..We suggest that stringent quality-based trimming of 16S pyrotags and clustering thresholds no greater than 97% identity should be used to avoid overestimates of the rare biosphere...
  22. doi request reprint Fixation-free fluorescence in situ hybridization for targeted enrichment of microbial populations
    Suzan Yilmaz
    Microbial Ecology Program, DOE Joint Genome Institute, Walnut Creek, CA, USA
    ISME J 4:1352-6. 2010
    ..This approach should facilitate subsequent genomic sequencing and analysis of targeted populations as DNA is not compromised by crosslinking during fixation...
  23. ncbi request reprint Community structure and metabolism through reconstruction of microbial genomes from the environment
    Gene W Tyson
    Department of Environmental Science, Policy and Management, University of California, Berkeley, California 94720, USA
    Nature 428:37-43. 2004
    ..Analysis of the gene complement for each organism revealed the pathways for carbon and nitrogen fixation and energy generation, and provided insights into survival strategies in an extreme environment...
  24. pmc Evolutionary conservation of sequence and secondary structures in CRISPR repeats
    Victor Kunin
    DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
    Genome Biol 8:R61. 2007
    ..It has been recently shown that CRISPR provides acquired resistance against viruses in prokaryotes...
  25. doi request reprint Insights into the phylogeny and coding potential of microbial dark matter
    Christian Rinke
    DOE Joint Genome Institute, Walnut Creek, California 94598, USA
    Nature 499:431-7. 2013
    ..This study greatly expands the genomic representation of the tree of life and provides a systematic step towards a better understanding of biological evolution on our planet...
  26. pmc Comparative metagenomic and metatranscriptomic analysis of hindgut paunch microbiota in wood- and dung-feeding higher termites
    Shaomei He
    Energy Biosciences Institute, University of California, Berkeley, California, USA
    PLoS ONE 8:e61126. 2013
    ..corniger microbiota. These observations are consistent with dietary differences in carbohydrate composition and nutrient contents, but may also reflect the phylogenetic difference between the hosts...
  27. pmc Automated group assignment in large phylogenetic trees using GRUNT: GRouping, Ungrouping, Naming Tool
    Daniel Dalevi
    Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
    BMC Bioinformatics 8:402. 2007
    ..Hierarchical group names are typically manually assigned in trees, an approach that becomes unfeasible for very large topologies...
  28. ncbi request reprint Riding giants
    Philip Hugenholtz
    DOE Joint Genome Institute, Walnut Creek, CA, USA
    Environ Microbiol 9:5. 2007
  29. doi request reprint A renaissance for the pioneering 16S rRNA gene
    Susannah G Tringe
    DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
    Curr Opin Microbiol 11:442-6. 2008
    ..The standard conclusion that microbial ecosystems are remarkably complex and diverse is now being replaced by detailed insights into microbial ecology and evolution based only on this one historically important marker gene...
  30. pmc Genome sequence of the flexirubin-pigmented soil bacterium Niabella soli type strain (JS13-8(T))
    Iain Anderson
    DOE Joint Genome Institute, Walnut Creek, California, USA
    Stand Genomic Sci 7:210-20. 2012
    ..The 4,697,343 bp long chromosome with its 3,931 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia ofBacteria andArchaea project...
  31. pmc Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat
    Victor Kunin
    Microbial Ecology Program, DOE Joint Genome Institute, Walnut Creek, CA, USA
    Mol Syst Biol 4:198. 2008
    ....
  32. pmc The integrated microbial genomes (IMG) system
    Victor M Markowitz
    Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, USA
    Nucleic Acids Res 34:D344-8. 2006
    ..IMG allows users to focus their analysis on subsets of genes and genomes of interest and to save the results of their analysis. IMG is available at http://img.jgi.doe.gov...
  33. pmc Glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass
    John M Gladden
    Joint BioEnergy Institute, Emeryville, CA 94608, USA
    Appl Environ Microbiol 77:5804-12. 2011
    ....
  34. ncbi request reprint Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities
    Hector Garcia Martin
    DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
    Nat Biotechnol 24:1263-9. 2006
    ..The present study provides a much needed blueprint for a systems-level understanding of EBPR and illustrates that metagenomics enables detailed, often novel, insights into even well-studied biological systems...
  35. pmc Complete genome sequence of the moderately thermophilic mineral-sulfide-oxidizing firmicute Sulfobacillus acidophilus type strain (NAL(T))
    Iain Anderson
    DOE Joint Genome Institute, Walnut Creek, California, USA
    Stand Genomic Sci 6:1-13. 2012
    ..acidophilus. The genome, which consists of one chromosome and one plasmid with a total size of 3,557,831 bp harbors 3,626 protein-coding and 69 RNA genes, and is a part of the GenomicEncyclopedia ofBacteria andArchaea project...
  36. pmc Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows
    Filipa Godoy-Vitorino
    Department of Biology, University of Puerto Rico, Rio Piedras, San Juan, Puerto Rico
    ISME J 6:531-41. 2012
    ..Regardless of the independent origin of foregut fermentation in birds and mammals, organ function has led to convergence of the microbial community structure in phylogenetically distant hosts...
  37. pmc Extremely acidophilic protists from acid mine drainage host Rickettsiales-lineage endosymbionts that have intervening sequences in their 16S rRNA genes
    Brett J Baker
    Department of Earth and Planetary Sciences, University of California at Berkeley, Berkeley, California 94720, USA
    Appl Environ Microbiol 69:5512-8. 2003
    ..To our knowledge, this is the first report of an endosymbiotic relationship in an extremely acidic habitat...
  38. ncbi request reprint Gemmatimonas aurantiaca gen. nov., sp. nov., a gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov
    Hui Zhang
    Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology AIST, Tsukuba, Ibaraki 305 8566, Japan
    Int J Syst Evol Microbiol 53:1155-63. 2003
    ..nov. Environmental sequence data indicate that this phylum is widespread in nature and has a phylogenetic breadth (19% 16S rDNA sequence divergence) that is greater than well-known phyla such as the Actinobacteria (18% divergence)...
  39. pmc Exploring prokaryotic diversity in the genomic era
    Philip Hugenholtz
    ComBinE group, Advanced Computational Modelling Centre, The University of Queensland, Brisbane 4072, Australia
    Genome Biol 3:REVIEWS0003. 2002
    ..This bias is beginning to be rectified by the use of phylogenetically directed isolation strategies and by directly accessing microbial genomes from environmental samples...
  40. ncbi request reprint Filamentous Chloroflexi (green non-sulfur bacteria) are abundant in wastewater treatment processes with biological nutrient removal
    Lovisa Björnsson
    Advanced Wastewater Management Centre, Department of Microbiology and Parasitology, The University of Queensland, Brisbane 4072, Australia
    Microbiology 148:2309-18. 2002
    ..It is suggested that filamentous bacteria belonging to the Chloroflexi phylum account for a large fraction of phylogenetically uncharacterized filaments in BNR systems and are likely to be abundant in such systems on a global scale...
  41. ncbi request reprint Kinetic and phylogenetic characterization of an anaerobic dechlorinating microbial community
    Simona Rossetti
    Water Research Institute, Via Reno 1, 00198, Rome, Italy
    Microbiology 149:459-69. 2003
    ..The predominance of Spirochaetes in the microbial consortium, the main group revealed by clone library analysis, was confirmed by FISH using a purposely developed probe...
  42. doi request reprint Microbiology: metagenomics
    Philip Hugenholtz
    Nature 455:481-3. 2008
  43. ncbi request reprint In situ studies of the phylogeny and physiology of filamentous bacteria with attached growth
    Trine Rolighed Thomsen
    Department of Environmental Engineering, Aalborg University, Sohngardsholmsvej 57, DK 9000 Aalborg, Denmark
    Environ Microbiol 4:383-91. 2002
    ..These are the first data on the physiology of the almost entirely uncharacterized TM7 phylum and show that TM7 filamentous bacteria can uptake carbon substrates under aerobic and anaerobic conditions...
  44. pmc Laboratory cultivation of widespread and previously uncultured soil bacteria
    Shayne J Joseph
    Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia
    Appl Environ Microbiol 69:7210-5. 2003
    ....
  45. ncbi request reprint Accurate phylogenetic classification of variable-length DNA fragments
    Alice Carolyn McHardy
    Bioinformatics and Pattern Discovery Group, IBM Thomas J Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, New York 10598, USA
    Nat Methods 4:63-72. 2007
    ..The method requires no more than 100 kb of training sequence for the creation of accurate models of sample-specific populations and can assign fragments >or=1 kb with high specificity...
  46. pmc The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide
    Konstantinos Liolios
    Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
    Nucleic Acids Res 34:D332-4. 2006
    ..GOLD is available at http://www.genomesonline.org. It is also mirrored at the Institute of Molecular Biology and Biotechnology, Crete, Greece at http://gold.imbb.forth.gr/..
  47. pmc Chthoniobacter flavus gen. nov., sp. nov., the first pure-culture representative of subdivision two, Spartobacteria classis nov., of the phylum Verrucomicrobia
    Parveen Sangwan
    Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia
    Appl Environ Microbiol 70:5875-81. 2004
    ..Environmental sequences indicate that the class Spartobacteria is largely represented by globally distributed, abundant, and active soil bacteria...
  48. ncbi request reprint Bellerophon: a program to detect chimeric sequences in multiple sequence alignments
    Thomas Huber
    ComBinE group, Advanced Computational Modelling Centre, The University of Queensland, Brisbane 4072, Australia
    Bioinformatics 20:2317-9. 2004
    ..Bellerophon was specifically developed to detect 16S rRNA gene chimeras in PCR-clone libraries of environmental samples but can be applied to other nucleotide sequence alignments...
  49. ncbi request reprint Characterization of filamentous bacteria, belonging to candidate phylum KSB3, that are associated with bulking in methanogenic granular sludges
    Takeshi Yamada
    Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology AIST, Tsukuba, Ibaraki, Japan
    ISME J 1:246-55. 2007
    ..Bacteria closely related to the characterized KSB3 filaments were present in two types of mesophilically grown UASB sludge granules treating actual wastewater discharged from sugar-processing industries...
  50. pmc Environmental distribution and population biology of Candidatus Accumulibacter, a primary agent of biological phosphorus removal
    S Brook Peterson
    Microbiology Doctoral Training Program, University of Wisconsin Madison, 1550 Linden Drive, Madison, WI, USA
    Environ Microbiol 10:2692-703. 2008
    ..These results provide evidence of ecological differences among Candidatus Accumulibacter lineages...
  51. ncbi request reprint Numbers and locations of native bacteria on field-grown wheat roots quantified by fluorescence in situ hybridization (FISH)
    Michelle Watt
    CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia
    Environ Microbiol 8:871-84. 2006
    ..001) and 1.4%Pseudomonas (P = 0.014). Efforts to manage rhizosphere bacteria for sustainable agricultural systems should continue to focus on root cap and mucilage chemistry, and remnant roots as sources of beneficial bacteria...
  52. ncbi request reprint Fermentation of glycolate by a pure culture of a strictly anaerobic gram-positive bacterium belonging to the family Lachnospiraceae
    Peter H Janssen
    Department of Microbiology and Immunology, University of Melbourne, 3010, Victoria, Australia
    Arch Microbiol 179:321-8. 2003
    ..There was no evidence for homoacetogenic metabolism. This bacterium therefore differs in metabolism from previously reported glycolate-utilising anaerobes...
  53. doi request reprint Evolution of the hyaluronic acid synthesis (has) operon in Streptococcus zooepidemicus and other pathogenic streptococci
    Lars M Blank
    Department of Chemical Engineering, The University of Queensland, Brisbane, Australia
    J Mol Evol 67:13-22. 2008
    ..The intragene rearrangements appear to be ongoing events and the two has operons of the S. equi subspecies represent two alternatives of the same gene arrangement. A scenario for the evolution of streptococcal has operons is proposed...
  54. pmc Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth
    Yann Marcy
    Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 104:11889-94. 2007
    ..This approach enables single-cell genetic analysis of any uncultivated minority member of a microbial community...
  55. pmc Liquid serial dilution is inferior to solid media for isolation of cultures representative of the phylum-level diversity of soil bacteria
    Liesbeth Schoenborn
    Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia
    Appl Environ Microbiol 70:4363-6. 2004
    ..We conclude that, contrary to expectation, liquid serial dilution culture is inferior to culturing on solid media for isolating representatives of many bacterial phyla from soil...
  56. ncbi request reprint Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys
    Michelle Sait
    Department of Microbiology and Immunology, The University of Melbourne, Victoria 3010, Australia
    Environ Microbiol 4:654-66. 2002
    ....
  57. pmc Use of stable-isotope probing, full-cycle rRNA analysis, and fluorescence in situ hybridization-microautoradiography to study a methanol-fed denitrifying microbial community
    Maneesha P Ginige
    Advanced Wastewater Management Centre, The University of Queensland, St Lucia 4072, Queensland, Australia
    Appl Environ Microbiol 70:588-96. 2004
    ..We conclude that Methylophilales bacteria are the dominant denitrifiers in our SBR system and likely are important denitrifiers in full-scale methanol-fed denitrifying sludges...
  58. ncbi request reprint Molecular analysis of dimethyl sulphide dehydrogenase from Rhodovulum sulfidophilum: its place in the dimethyl sulphoxide reductase family of microbial molybdopterin-containing enzymes
    Christopher A McDevitt
    Centre for Metals in Biology, Department of Microbiology and Parasitology, School of Molecular and Microbial Sciences, The University of Queensland, St Lucia 4072, Australia
    Mol Microbiol 44:1575-87. 2002
    ....
  59. pmc Non-sulfate-reducing, syntrophic bacteria affiliated with desulfotomaculum cluster I are widely distributed in methanogenic environments
    Hiroyuki Imachi
    Department of Environmental Systems Engineering, Nagaoka University of Technology, 1603 1 Kamitomioka, Nagaoka, Niigata 940 2188, Japan
    Appl Environ Microbiol 72:2080-91. 2006
    ....