Research Topics
| Philip HugenholtzSummaryAffiliation: Lawrence Berkeley National Laboratory Country: USA Publications
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Detail Information
Publications
Building on basic metagenomics with complementary technologiesFalk 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...
SNP-VISTA: an interactive SNP visualization toolNameeta 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...- CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeatsCharles 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... 
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...- The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadataKonstantinos 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/.. - A phylogeny-driven genomic encyclopaedia of Bacteria and ArchaeaDongying Wu
DOE Joint Genome Institute, Walnut Creek, California 94598, USA
Nature 462:1056-60. 2009.... - Genome-directed isolation of the key nitrogen fixer Leptospirillum ferrodiazotrophum sp. nov. from an acidophilic microbial communityGene 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... - Lineages of acidophilic archaea revealed by community genomic analysisBrett 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... 
Validation of two ribosomal RNA removal methods for microbial metatranscriptomicsShaomei 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...- A bacterial metapopulation adapts locally to phage predation despite global dispersalVictor 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... - Annotation of metagenome short reads using proxygenesDaniel 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... - Use of simulated data sets to evaluate the fidelity of metagenomic processing methodsKonstantinos 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... - IMG/M: a data management and analysis system for metagenomesVictor 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... - Comparative metagenomics of microbial communitiesSusannah 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... - A bioinformatician's guide to metagenomicsVictor 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... - CRISPR--a widespread system that provides acquired resistance against phages in bacteria and archaeaRotem 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... - Experimental factors affecting PCR-based estimates of microbial species richness and evennessAnna 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... - Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termiteFalk 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... - Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix oreniiKonstantinos Mavromatis
DOE Joint Genome Institute, Walnut Creek, California, United States of America
PLoS ONE 4:e4192. 2009.... - Fixation-free fluorescence in situ hybridization for targeted enrichment of microbial populationsSuzan 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... - Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortiumAthanasios 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... - Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimatesVictor 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... - Evolutionary conservation of sequence and secondary structures in CRISPR repeatsVictor 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... - Community structure and metabolism through reconstruction of microbial genomes from the environmentGene 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... - Automated group assignment in large phylogenetic trees using GRUNT: GRouping, Ungrouping, Naming ToolDaniel 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... - A renaissance for the pioneering 16S rRNA geneSusannah 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... - Riding giantsPhilip Hugenholtz
DOE Joint Genome Institute, Walnut Creek, CA, USA
Environ Microbiol 9:5. 2007 - Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial matVictor Kunin
Microbial Ecology Program, DOE Joint Genome Institute, Walnut Creek, CA, USA
Mol Syst Biol 4:198. 2008.... - The integrated microbial genomes (IMG) systemVictor 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... - Glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrassJohn M Gladden
Joint BioEnergy Institute, Emeryville, CA 94608, USA
Appl Environ Microbiol 77:5804-12. 2011.... - Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communitiesHector 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... - Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cowsFilipa 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... - Extremely acidophilic protists from acid mine drainage host Rickettsiales-lineage endosymbionts that have intervening sequences in their 16S rRNA genesBrett J Baker
Department of Earth and Planetary Sciences, University of California at Berkeley, Berkeley, California 94720, USA
Appl Environ Microbiol 69:5512-8. 2003..quot; To our knowledge, this is the first report of an endosymbiotic relationship in an extremely acidic habitat... - Microbiology: metagenomicsPhilip Hugenholtz
Nature 455:481-3. 2008 - 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. novHui 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)... - Kinetic and phylogenetic characterization of an anaerobic dechlorinating microbial communitySimona 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... - Bellerophon: a program to detect chimeric sequences in multiple sequence alignmentsThomas Huber
ComBinE group, Advanced Computational Modelling Centre, The University of Queensland, Brisbane 4072, Australia
Bioinformatics 20:2317-9. 2004..AVAILABILITY: Bellerophon is available as an interactive web server at http://foo.maths.uq.edu.au/~huber/bellerophon.pl.. - Filamentous Chloroflexi (green non-sulfur bacteria) are abundant in wastewater treatment processes with biological nutrient removalLovisa 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... - In situ studies of the phylogeny and physiology of filamentous bacteria with attached growthTrine 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... - Exploring prokaryotic diversity in the genomic eraPhilip 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... - Laboratory cultivation of widespread and previously uncultured soil bacteriaShayne J Joseph
Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia
Appl Environ Microbiol 69:7210-5. 2003.... - Accurate phylogenetic classification of variable-length DNA fragmentsAlice 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... - Environmental distribution and population biology of Candidatus Accumulibacter, a primary agent of biological phosphorus removalS 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... - The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwideKonstantinos 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/.. - Characterization of filamentous bacteria, belonging to candidate phylum KSB3, that are associated with bulking in methanogenic granular sludgesTakeshi 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... - Chthoniobacter flavus gen. nov., sp. nov., the first pure-culture representative of subdivision two, Spartobacteria classis nov., of the phylum VerrucomicrobiaParveen 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... - Liquid serial dilution is inferior to solid media for isolation of cultures representative of the phylum-level diversity of soil bacteriaLiesbeth 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... - Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveysMichelle Sait
Department of Microbiology and Immunology, The University of Melbourne, Victoria 3010, Australia
Environ Microbiol 4:654-66. 2002.... - Fermentation of glycolate by a pure culture of a strictly anaerobic gram-positive bacterium belonging to the family LachnospiraceaePeter 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... - Non-sulfate-reducing, syntrophic bacteria affiliated with desulfotomaculum cluster I are widely distributed in methanogenic environmentsHiroyuki 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.... - Evolution of the hyaluronic acid synthesis (has) operon in Streptococcus zooepidemicus and other pathogenic streptococciLars 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... - Molecular analysis of dimethyl sulphide dehydrogenase from Rhodovulum sulfidophilum: its place in the dimethyl sulphoxide reductase family of microbial molybdopterin-containing enzymesChristopher 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.... - Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouthYann 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... - 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... - Use of stable-isotope probing, full-cycle rRNA analysis, and fluorescence in situ hybridization-microautoradiography to study a methanol-fed denitrifying microbial communityManeesha 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...