454 Life Sciences

Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome.  Nossa CW, Oberdorf WE, Yang L, Aas JA, Paster BJ, Desantis TZ, Brodie EL, Malamud D, Poles MA, Pei Z. (9/7/2010) World J Gastroenterol 16(33): 4135-44.
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Gut microbial gene expression in mother-fed and formula-fed piglets.  Poroyko V, White JR, Wang M, Donovan S, Alverdy J, Liu DC, Morowitz MJ. (8/27/2010) PLoS One 5(8): e12459.
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A comparative molecular analysis of water-filled limestone sinkholes in north-eastern Mexico.  Sahl JW, Gary MO, Harris JK, Spear JR. (8/25/2010) Environ Microbiol ePub:
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Reshaping the gut microbiome with bacterial transplantation and antibiotic intake.  Manichanh C, Reeder J, Gibert P, Varela E, Llopis M, Antolin M, Guigo R, Knight R, Guarner F. (8/24/2010) Genome Research ePub:
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Characterization of Archaeal Community in Contaminated and Uncontaminated Surface Stream Sediments.  Porat I, Vishnivetskaya TA, Mosher JJ, Brandt CC, Yang ZK, Brooks SC, Liang L, Drake MM, Podar M, Brown SD, Palumbo AV. (8/20/2010) Microbial Ecology ePub:
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Evaluation of the bacterial diversity in the rumen and feces of cattle fed diets containing levels of dried distiller's grains plus solubles using bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP).  Callaway TR, Dowd SE, Edrington TS, Anderson RC, Krueger N, Bauer N, Kononoff PJ, Nisbet DJ. (8/20/2010) J Anim Sci ePub:
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A combined massively parallel sequencing - indicator species approach revealed significant association between sulfate-reducing bacteria and uranium-reducing microbial communities.  Cardenas E, Wu WM, Leigh MB, Carley J, Carroll S, Gentry T, Luo J, Watson D, Gu B, Ginder-Vogel M, Kitanidis PK, Jardine PM, Zhou J, Criddle CS, Marsh TL, Tiedje JM. (8/20/2010) Appl Environ Microbiol ePub:
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Horizon-specific bacterial community composition of German grassland soils as revealed by pyrosequencing-based analysis of 16S rRNA genes.  Will C, Thürmer A, Wollherr A, Nacke H, Herold N, Schrumpf M, Gutknecht J, Wubet T, Buscot F, Daniel R. (8/20/2010) Appl Environ Microbiol ePub:
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Bar-coded pyrosequencing of 16S rRNA gene amplicons reveals changes in ileal porcine bacterial communities due to high dietary zinc intake.  Vahjen W, Pieper R, Zentek J. (8/13/2010) Appl Environ Microbiol ePub:
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Analysis of human and animal fecal microbiota for microbial source tracking.  Lee JE, Lee S, Sung J, Ko G. (8/5/2010) ISME Journal ePub:
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Oral Bacterial Genome Sequencing Using the High-Throughput Roche Genome Sequencer FLX System.  Heng NC, Stanton JA. (8/1/2010) Methods in Molecular Biology 666: 197-218.
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Structure and dynamics of the microbial communities underlying the carboxylate platform for biofuel production.  Hollister EB, Forrest AK, Wilkinson HH, Ebbole DJ, Malfatti SA, Tringe SG, Holtzapple MT, Gentry TJ. (7/31/2010) Appl Microbiol Biotechnol ePub:
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Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags.  Wu GD, Lewis JD, Hoffmann C, Chen YY, Knight R, Bittinger K, Hwang J, Chen J, Berkowsky R, Nessel L, Li H, Bushman FD. (7/30/2010) BMC Microbiology 10(1): 206.
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Comparative metagenomics of bathypelagic plankton and bottom sediment from the Sea of Marmara.  Quaiser A, Zivanovic Y, Moreira D, López-García P. (7/29/2010) ISME Journal ePub:
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Vertical stratification of microbial communities in the Red Sea revealed by 16S rDNA pyrosequencing.  Qian PY, Wang Y, Lee OO, Lau SC, Yang J, Lafi FF, Al-Suwailem A, Wong TY. (7/29/2010) ISME Journal ePub:
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Phylogenetic and metabolic diversity of bacteria associated with cystic fibrosis.  Guss AM, Roeselers G, Newton IL, Young CR, Klepac-Ceraj V, Lory S, Cavanaugh CM. (7/15/2010) ISME Journal ePub:
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Viruses in the faecal microbiota of monozygotic twins and their mothers.  Reyes A, Haynes M, Hanson N, Angly FE, Heath AC, Rohwer F, Gordon JI. (7/15/2010) Nature 466(7304): 334-8.
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Analysis of Oral Microbiota in Children with Dental Caries by PCR-DGGE and Barcoded Pyrosequencing.  Analysis of Oral Microbiota in Children with Dental Caries by PCR-DGGE and Barcoded Pyrosequencing. (7/8/2010) Microbial Ecology ePub:
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Structural shifts of gut microbiota as surrogate endpoints for monitoring host health changes induced by carcinogen exposure.  Wei H, Dong L, Wang T, Zhang M, Hua W, Zhang C, Pang X, Chen M, Su M, Qiu Y, Zhou M, Yang S, Chen Z, Rantalainen M, Nicholson JK, Jia W, Wu D, Zhao L. (7/7/2010) FEMS Microbiol Ecol ePub:
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Pyrosequencing Study of Fecal Microflora of Autistic and Control Children.  Finegold SM, Dowd SE, Gontcharova V, Liu C, Henley KE, Wolcott RD, Youn E, Summanen PH, Granpeesheh D, Dixon D, Liu M, Molitoris DR, Green JA 3rd. (7/2/2010) Anaerobe ePub:
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Contrasting seasonal niche separation between rare and abundant taxa conceals the extent of protist diversity.  Nolte V, Pandey RV, Jost S, Medinger R, Ottenwälder B, Boenigk J, Schlötterer C. (7/1/2010) Molecular Ecology 19(14): 2908-15.
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Resistance and resilience of benthic biofilm communities from a temperate saltmarsh to desiccation and rewetting.  McKew BA, Taylor JD, McGenity TJ, Underwood GJ. (7/1/2010) ISME Journal ePub:
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454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases.  Tedersoo L, Nilsson RH, Abarenkov K, Jairus T, Sadam A, Saar I, Bahram M, Bechem E, Chuyong G, Kõljalg U. (7/1/2010) New Phytologist ePub:
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Microbes and Health Sackler Colloquium: Effect of broad- and narrow-spectrum antimicrobials on Clostridium difficile and microbial diversity in a model of the distal colon.  Rea MC, Dobson A, O'Sullivan O, Crispie F, Fouhy F, Cotter PD, Shanahan F, Kiely B, Hill C, Ross RP. (6/29/2010) PNAS ePub:
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Analysis of bacterial biofilm communities in water meters of a drinking water distribution system via pyrosequencing.  Hong PY, Hwang C, Ling F, Andersen GL, Lechevallier MW, Liu WT. (6/25/2010) Appl Environ Microbiol. ePub:
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TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets.  Schmieder R, Lim YW, Rohwer F, Edwards R. (6/23/2010) BMC Bioinformatics 11: 341.
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Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns.  Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N, Knight R. (6/21/2010) PNAS 107(26): 11971-5.
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VITCOMIC: visualization tool for taxonomic compositions of microbial communities based on 16S rRNA gene sequences.  Mori H, Maruyama F, Kurokawa K. (6/17/2010) BMC Bioinformatics 11(1): 332.
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Production of ectomycorrhizal mycelium peaks during canopy closure in Norway spruce forests.  Wallander H, Johansson U, Sterkenburg E, Brandström Durling M, Lindahl BD. (6/15/2010) New Phytology ePub:
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Multivariate Cutoff Level Analysis (MultiCoLA) of large community data sets.  Gobet A, Quince C, Ramette A. (6/14/2010) Nucleic Acids Research ePub:
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Pyrosequencing of the 16S rRNA gene to reveal bacterial pathogen diversity in biosolids.  Bibby K, Viau E, Peccia J. (6/9/2010) Water Research 44(14): 4252-60.
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Discovery of commonly existing anode biofilm microbes in two different wastewater treatment MFCs using FLX Titanium pyrosequencing.  Lee TK, Van Doan T, Yoo K, Choi S, Kim C, Park J. (6/8/2010) Appl Microbiol Biotechnol 87(6): 2335-43.
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Effect of Dechlorination and Sulfate Reduction on the Microbial Community Structure in Denitrifying Membrane-Biofilm Reactors.  Zhang H, Ziv-El M, Rittmann BE, Krajmalnik-Brown R. (6/4/2010) Environ Sci Technology 44(13): 5159-64.
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Microbes and Health Sackler Colloquium: Vaginal microbiome of reproductive-age women.  Ravel J, Gajer P, Abdo Z, Schneider GM, Koenig SS, McCulle SL, Karlebach S, Gorle R, Russell J, Tacket CO, Brotman RM, Davis CC, Ault K, Peralta L, Forney LJ. (6/3/2010) PNAS ePub:
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Postprandial remodeling of the gut microbiota in Burmese pythons.  Costello EK, Gordon JI, Secor SM, Knight R. (6/3/2010) ISME Journal ePub:
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Analyzing Endodontic Infections by Deep Coverage Pyrosequencing.  Li L, Hsiao WW, Nandakumar R, Barbuto SM, Mongodin EF, Paster BJ, Fraser-Liggett CM, Fouad AF. (6/2/2010) Journal of Dental Research ePub:
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Viral and microbial community dynamics in four aquatic environments.  Rodriguez-Brito B et al. (6/1/2010) ISME Journal 4(6): 739-51.
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The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves.  Redford AJ, Bowers RM, Knight R, Linhart Y, Fierer N. (6/1/2010) Environmental Microbiology ePub:
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Assessment of soil fungal communities using pyrosequencing.  Lim YW, Kim BK, Kim C, Jung HS, Kim BS, Lee JH, Chun J. (6/1/2010) Journal of Microbiology 48(3): 284-9.
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Comparison of normalization methods for construction of large, multiplex amplicon pools for next-generation sequencing.  Harris JK, Sahl JW, Castoe TA, Wagner BD, Pollock DD, Spear JR. (6/1/2010) Applied Environmental Microbiology 76(12): 3863-8.
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A catalog of reference genomes from the human microbiome.  Human Microbiome Jumpstart Reference Strains Consortium (5/21/2010) Science 328(5981): 994-9.
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Isolated communities of Epsilonproteobacteria in hydrothermal vent fluids of the Mariana Arc seamounts.  Huber JA, Cantin HV, Huse SM, Mark Welch DB, Sogin ML, Butterfield DA. (5/14/2010) FEMS Microbiol Ecol ePub:
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Transcriptomic analysis of a marine bacterial community enriched with dimethylsulfoniopropionate.  Vila-Costa M, Rinta-Kanto JM, Sun S, Sharma S, Poretsky R, Moran MA. (5/13/2010) ISME Journal ePub:
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Soil bacterial and fungal communities across a pH gradient in an arable soil.  Rousk J, Bååth E, Brookes PC, Lauber CL, Lozupone C, Caporaso JG, Knight R, Fierer N. (5/6/2010) ISME Journal ePub:
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Quantitative assessment of the human gut microbiome using multitag pyrosequencing.  Gillevet P, Sikaroodi M, Keshavarzian A, Mutlu EA. (5/1/2010) Chem Biodivers 7(5): 1065-75.
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Analysis of multitag pyrosequence data from human cervical lavage samples.  Naqvi A, Rangwala H, Spear G, Gillevet P. (5/1/2010) Chemistry & Biodiversity 7(5): 1076-85.
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QIIME allows analysis of high-throughput community sequencing data.  Caporaso JG et al. (5/1/2010) Nature Methods 7(5): 335-6.
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Pyrosequencing Reveals a Highly Diverse and Cultivar-Specific Bacterial Endophyte Community in Potato Roots.  Manter DK, Delgado JA, Holm DG, Stong RA. (4/23/2010) Microbial Ecology ePub:
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Metagenome of the Mediterranean deep chlorophyll maximum studied by direct and fosmid library 454 pyrosequencing.  Ghai R, Martin-Cuadrado AB, Molto AG, Heredia IG, Cabrera R, Martin J, Verdú M, Deschamps P, Moreira D, López-García P, Mira A, Rodriguez-Valera F. (4/15/2010) ISME Journal ePub:
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Freshwater Perkinsea and marine-freshwater colonizations revealed by pyrosequencing and phylogeny of environmental rDNA.  Bråte J, Logares R, Berney C, Ree DK, Klaveness D, Jakobsen KS, Shalchian-Tabrizi K. (4/15/2010) ISME Journal ePub:
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The functional potential of high Arctic permafrost revealed by metagenomic sequencing, qPCR and microarray analyses.  Yergeau E, Hogues H, Whyte LG, Greer CW. (4/15/2010) ISME Journal ePub:
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The Analysis of Oral Microbial Communities of Wild-type and Toll-Like Receptor 2-deficient Mice Using a 454 GS FLX Titanium Pyrosequencer.  Chun J, Kim KY, Lee JH, Choi Y. (4/6/2010) BMC Microbiology 10(1): 101.
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Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins.  Turnbaugh PJ, Quince C, Faith JJ, McHardy AC, Yatsunenko T, Niazi F, Affourtit J, Egholm M, Henrissat B, Knight R, Gordon JI. (4/2/2010) PNAS 107(16): 7503-8.
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Comparative analysis of fecal microbiota in infants with and without eczema.  Hong PY, Lee BW, Aw M, Shek LP, Yap GC, Chua KY, Liu WT. (4/1/2010) PLoS One 5(4): e9964.
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Molecular characterization of the polymicrobial flora in chronic rhinosinusitis.  Stephenson MF, Mfuna L, Dowd SE, Wolcott RD, Barbeau J, Poisson M, James G, Desrosiers M. (4/1/2010) J Otolaryngol Head Neck Surg 39(2): 182-7.
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Bacterial diversity in rhizosphere soil from Antarctic vascular plants of Admiralty Bay, maritime Antarctica.  Teixeira LC, Peixoto RS, Cury JC, Sul WJ, Pellizari VH, Tiedje J, Rosado AS. (4/1/2010) ISME Journal 4(8): 989-1001.
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Composition and genetic diversity of picoeukaryotes in subtropical coastal waters as revealed by 454 pyrosequencing.  Cheung MK, Au CH, Chu KH, Kwan HS, Wong CK. (3/25/2010) ISME Journal 4(8): 1053-9.
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Nitrite-driven anaerobic methane oxidation by oxygenic bacteria.  Ettwig et al. (3/25/2010) Nature 464(7288): 543-8.
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Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples.  Lauber CL, Zhou N, Gordon JI, Knight R, Fierer N. (3/25/2010) FEMS Microbiology Letters 307(1): 80-6.
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Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome.  Jakobsson HE, Jernberg C, Andersson AF, Sjölund-Karlsson M, Jansson JK, Engstrand L. (3/24/2010) PLoS One 5(3): e9836.
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Metagenomic analysis reveals a marked divergence in the structure of belowground microbial communities at elevated CO.  He Z, Xu M, Deng Y, Kang S, Kellogg L, Wu L, Van Nostrand JD, Hobbie SE, Reich PB, Zhou J. (3/23/2010) Ecology Letters 13(5): 564-75.
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Phylogenetic Characterization of Fecal Microbial Communities of Dogs Fed Diets with or without Supplemental Dietary Fiber Using 454 Pyrosequencing.  Middelbos IS, Vester Boler BM, Qu A, White BA, Swanson KS, Fahey GC. (3/22/2010) PLoS One 5(3): e9768.
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Novel Microbial Diversity Retrieved by Autonomous Robotic Exploration of the World's Deepest Vertical Phreatic Sinkhole.  Sahl JW, Fairfield N, Harris JK, Wettergreen D, Stone WC, Spear JR. (3/19/2010) Astrobiology 10(2): 201-13.
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The obligate endobacteria of arbuscular mycorrhizal fungi are ancient heritable components related to the Mollicutes.  Naumann M, Schüßler A, Bonfante P. (3/18/2010) ISME Journal 4(7): 862-71.
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A comparison of bacterial composition in diabetic ulcers and contralateral intact skin.  Gontcharova V, Youn E, Sun Y, Wolcott RD, Dowd SE. (3/17/2010) Open Microbiol J 4: 8-19.
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Forensic identification using skin bacterial communities.  Fierer N, Lauber CL, Zhou N, McDonald D, Costello EK, Knight R. (3/15/2010) PNAS 107(14): 6477-81.
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Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics.  Stewart FJ, Ottesen EA, Delong EF. (3/11/2010) ISME Journal 4(7): 896-907.
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The effect of nutrient deposition on bacterial communities in Arctic tundra soil.  Campbell BJ, Polson SW, Hanson TE, Mack MC, Schuur EA. (3/7/2010) Environmental Microbiology 12(7): 1842-54.
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Metabolic Syndrome and Altered Gut Microbiota in Mice Lacking Toll-Like Receptor 5.  Vijay-Kumar M, Aitken JD, Carvalho FA, Cullender TC, Mwangi S, Srinivasan S, Sitaraman SV, Knight R, Ley RE, Gewirtz AT. (3/4/2010) Science 328(5975): 228-31.
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Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises.  Creer S, Fonseca VG, Porazinska DL, Giblin-Davis RM, Sung W, Power DM, Packer M, Carvalho GR, Blaxter ML, Lambshead PJ, Thomas WK. (3/1/2010) Molecular Ecology 19 Suppl 1: 4-20.
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Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water.  Stoeck T, Bass D, Nebel M, Christen R, Jones MD, Breiner HW, Richards TA. (3/1/2010) Molecular Ecology 19 Suppl 1: 21-31.
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Massively parallel 454-sequencing of fungal communities in Quercus spp. ectomycorrhizas indicates seasonal dynamics in urban and rural sites.  Jumpponen A, Jones KL, David Mattox J, Yaege C. (3/1/2010) Molecular Ecology 19 Suppl 1: 41-53.
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Ecogenomics: using massively parallel pyrosequencing to understand virus ecology.  Roossinck MJ, Saha P, Wiley GB, Quan J, White JD, Lai H, Chavarría F, Shen G, Roe BA. (3/1/2010) Molecular Ecology 19 Suppl 1: 81-8.
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Metagenomic analyses reveal antibiotic-induced temporal and spatial changes in intestinal microbiota with associated alterations in immune cell homeostasis.  Hill DA, Hoffmann C, Abt MC, Du Y, Kobuley D, Kirn TJ, Bushman FD, Artis D. (3/1/2010) Mucosal Immunology 3(2): 148-58.
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Stressor exposure disrupts commensal microbial populations in the intestines and leads to increased colonization by Citrobacter rodentium.  Bailey MT, Dowd SE, Parry NM, Galley JD, Schauer DB, Lyte M. (2/9/2010) Infection and Immunity 78(4): 1509-19.
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Gut Microbiota in Human Adults with Type 2 Diabetes Differs from Non-Diabetic Adults.  Larsen N, Vogensen FK, van den Berg FW, Nielsen DS, Andreasen AS, Pedersen BK, Al-Soud WA, Sørensen SJ, Hansen LH, Jakobsen M. (2/5/2010) PLoS One 5(2): e9085.
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Shifts in microbial community structure along an ecological gradient of hypersaline soils and sediments.  Hollister EB, Engledow AS, Hammett AJ, Provin TL, Wilkinson HH, Gentry TJ. (2/4/2010) ISME Journal 4(6): 829-38.
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The structure of bacterial communities in the western Arctic Ocean as revealed by pyrosequencing of 16S rRNA genes.  Kirchman DL, Cottrell MT, Lovejoy C. (2/3/2010) Environmental Microbiology 12(5): 1132-43.
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Identification of Rhesus Macaque Genital Microbiota by 16S Pyrosequencing Shows Similarities to Human Bacterial Vaginosis: Implications for Use as an Animal Model for HIV Vaginal Infection.  Spear GT, Gilbert D, Sikaroodi M, Doyle L, Green L, Gillevet PM, Landay AL, Veazey RS. (2/1/2010) AIDS Res Hum Retroviruses 26(2): 193-200.
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Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment.  Iwai S, Chai B, Sul WJ, Cole JR, Hashsham SA, Tiedje JM. (2/1/2010) ISME Journal 4(2): 279-85.
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Pyrosequencing reveals contrasting seasonal dynamics of taxa within Baltic Sea bacterioplankton communities.  Andersson AF, Riemann L, Bertilsson S. (2/1/2010) ISME Journal 4(2): 171-81.
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Interactions between gut microbiota, host genetics and diet relevant to development of metabolic syndromes in mice.  Zhang C, Zhang M, Wang S, Han R, Cao Y, Hua W, Mao Y, Zhang X, Pang X, Wei C, Zhao G, Chen Y, Zhao L. (2/1/2010) ISME Journal 4(2): 232-41.
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Bacterial communities of disease vectors sampled across time, space, and species.  Jones RT, Knight R, Martin AP.  (2/1/2010) ISME Journal 4(2): 223-31.
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The carnivorous Pale Pitcher Plant harbors diverse, distinct and temporally dependent bacterial communities.  Koopman MM, Fuselier DM, Hird S, Carstens BC. (1/22/2010) Applied Evironmental Microbiology 76(6): 1851-60.
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Experimental factors affecting PCR-based estimates of microbial species richness and evenness.  Engelbrektson A, Kunin V, Wrighton KC, Zvenigorodsky N, Chen F, Ochman H, Hugenholtz P. (1/21/2010) ISME Journal 4(5): 642-7.
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Seasonally dynamic fungal communities in the Quercus macrocarpa phyllosphere differ between urban and nonurban environments.  Jumpponen A, Jones KL. (1/17/2010) New Phytologist 186(2): 496-513.
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PyNAST: a flexible tool for aligning sequences to a template alignment.  Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R. (1/15/2010) Bioinformatics 26(6): 266-7.
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CANGS: a user-friendly utility for processing and analyzing 454 GS-FLX data in biodiversity studies.  Pandey RV, Nolte V, Schlötterer C. (1/11/2010) BMC Research Notes 3(1): 3.
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Characterization of the oral fungal microbiome (mycobiome) in healthy individuals.  Ghannoum MA, Jurevic RJ, Mukherjee PK, Cui F, Sikaroodi M, Naqvi A, Gillevet PM. (1/8/2010) PLoS Pathogens 6(1): e1000713.
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Like will to like: abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria.  Stecher B, Chaffron S, Käppeli R, Hapfelmeier S, Freedrich S, Weber TC, Kirundi J, Suar M, McCoy KD, von Mering C, Macpherson AJ, Hardt WD. (1/6/2010) PLoS Pathogens 6(1): e1000711.
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The effects of circumcision on the penis microbiome.  Price LB, Liu CM, Johnson KE, Aziz M, Lau MK, Bowers J, Ravel J, Keim PS, Serwadda D, Wawer MJ, Gray RH. (1/6/2010) PLoS One 5(1): e8422.
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Effect of the herbicide glyphosate on glyphosate-tolerant maize rhizobacterial communities: a comparison with pre-emergency applied herbicide consisting of a combination of acetochlor and terbuthylazine.  Barriuso J, Marín S, Mellado RP. (1/1/2010) Environmental Microbiology 12(4): 1021-30.
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Deep Sequencing of a DMSP-Degrading Gene (dmdA) Using PCR Primer Pairs Designed from Marine Metagenomic Data.  Varaljay VA, Howard EC, Sun S, Moran MA. (1/1/2010) Applied Environmental Microbiology 76(2): 609-17.
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Moussa virus: A new member of the Rhabdoviridae family isolated from Culex decens mosquitoes in Côte d'Ivoire.  Quan PL, Junglen S, Tashmukhamedova A, Conlan S, Hutchison SK, Kurth A, Ellerbrok H, Egholm M, Briese T, Leendertz FH, Lipkin WI. (1/1/2010) Virus Research 147(1): 17-24.
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Intestinal Microbial Ecology in Premature Infants Assessed with Non-Culture-Based Techniques.  Mshvildadze M, Neu J, Shuster J, Theriaque D, Li N, Mai V. (1/1/2010) Journal of Pediatrics 156(1): 20-5.
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Photoperiod Modulates Gut Bacteria Composition in Male Siberian Hamsters (Phodopus sungorus).  Bailey MT, Walton JC, Dowd SE, Weil ZM, Nelson RJ. (12/30/2009) Brain Behav Immun 24(4): 577-84.
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Rumen Bacterial Diversity Dynamics Associated with Changing from Bermudagrass Hay to Grazed Winter Wheat Diets.  Pitta DW, Pinchak WE, Dowd SE, Osterstock J, Gontcharova V, Youn E, Dorton K, Yoon I, Min BR, Fulford JD, Wickersham TA, Malinowski DP. (12/29/2009) Microbial Ecology 59(3): 511-22.
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Bacterial community variation in human body habitats across space and time.  Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R. (12/18/2009) Science 326(5960): 1694-7.
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Defining the healthy "core microbiome" of oral microbial communities.  Zaura E, Keijser BJ, Huse SM, Crielaard W. (12/10/2009) BMC Microbiology 9(1): 259.
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Hydrography shapes bacterial biogeography of the deep Arctic Ocean.  Galand PE, Potvin M, Casamayor EO, Lovejoy C. (12/10/2009) ISME Journal 4(4): 564-76.
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Metagenomic islands of hyperhalophiles: the case of Salinibacter ruber.  Pasic L, Rodriguez-Mueller B, Martin-Cuadrado AB, Mira A, Rohwer F, Rodriguez-Valera F. (12/2/2009) BMC Genomics 10(1): 570.
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Disclosing arbuscular mycorrhizal fungal biodiversity in soil through a land-use gradient using a pyrosequencing approach.  Lumini E, Orgiazzi A, Borriello R, Bonfante P, Bianciotto V. (11/17/2009) Environmental Microbiology ePub:
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The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice.  Peter J. Turnbaugh, Vanessa K. Ridaura, Jeremiah J. Faith, Federico E. Rey, Rob Knight and Jeffrey I. Gordon (11/12/2009) Science Translational Medicine 1(6):
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High diversity of the viral community from an Antarctic lake.  López-Bueno A, Tamames J, Velázquez D, Moya A, Quesada A, Alcamí A. (11/6/2009) Science 326(5954): 858-61.
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Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities.  Stoeck T, Behnke A, Christen R, Amaral-Zettler L, Rodriguez-Mora MJ, Chistoserdov A, Orsi W, Edgcomb VP. (11/3/2009) BMC Biology 7(1): 72.
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Systematic artifacts in metagenomes from complex microbial communities.  Gomez-Alvarez V, Teal TK, Schmidt TM. (11/1/2009) ISME Journal 3(11): 1314-7.
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High-fat diet determines the composition of the murine gut microbiome independently of obesity.  Hildebrandt MA, Hoffmann C, Sherrill-Mix SA, Keilbaugh SA, Hamady M, Chen YY, Knight R, Ahima RS, Bushman F, Wu GD. (11/1/2009) Gastroenterology 137(5): 1716-24.
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Evaluation of the bacterial diversity among and within individual venous leg ulcers using bacterial tag-encoded FLX and Titanium amplicon pyrosequencing and metagenomic approaches.  Wolcott RD, Gontcharova V, Sun Y, Dowd SE. (10/27/2009) BMC Microbiology 9: 226.
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Generalized antifungal activity and 454-screening of Pseudonocardia and Amycolatopsis bacteria in nests of fungus-growing ants.  Sen R, Ishak HD, Estrada D, Dowd SE, Hong E, Mueller UG. (10/20/2009) PNAS 106(42): 17805-10.
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Diversity and population structure of sewage-derived microorganisms in wastewater treatment plant influent.  McLellan SL, Huse SM, Mueller-Spitz SR, Andreishcheva EN, Sogin ML. (10/16/2009) Environmental Microbiology 12(2): 378-92.
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Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals.  Willner D, Furlan M, Haynes M, Schmieder R, Angly FE, Silva J, Tammadoni S, Nosrat B, Conrad D, Rohwer F. (10/9/2009) PLoS One 4(10): e7370.
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Windshield splatter analysis with the Galaxy metagenomic pipeline.  Kosakovsky Pond S, Wadhawan S, Chiaromonte F, Ananda G, Chung WY, Taylor J, Nekrutenko A; The Galaxy Team. (10/9/2009) Genome Research 19(11): 2144-53
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Introducing mothur: Open Source, Platform-independent, Community-supported Software for Describing and Comparing Microbial Communities.  Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF. (10/2/2009) Applied Environmental Microbiology 75(23): 7537-41.
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Phylogenetic diversity and metabolic potential encoded by a glacial ice metagenome.  Simon C, Wiezer A, Strittmatter AW, Daniel R. (10/2/2009) Applied Environmental Microbiology 75(23): 7519-26.
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Confirmation of the Sequence of 'Candidatus Liberibacter asiaticus' and Assessment of Microbial Diversity in Huanglongbing-Infected Citrus Phloem Using a Metagenomic Approach.  Tyler HL, Roesch LF, Gowda S, Dawson WO, Triplett EW. (10/1/2009) Molecular Plant Microbial Interactions 22(12): 1624-34.
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Deep sequencing reveals exceptional diversity and modes of transmission for bacterial sponge symbionts.  Webster NS, Taylor MW, Behnam F, Lücker S, Rattei T, Whalan S, Horn M, Wagner M. (9/29/2009) Environmental Microbiology ePub:
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Community proteogenomics reveals insights into the physiology of phyllosphere bacteria.  Delmotte N, Knief C, Chaffron S, Innerebner G, Roschitzki B, Schlapbach R, von Mering C, Vorholt JA. (9/22/2009) PNAS 106(38): 16428-33.
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454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity.  Buée M, Reich M, Murat C, Morin E, Nilsson RH, Uroz S, Martin F. (8/22/2009) New Phytologist 184(2): 449-56.
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Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine.  Claesson MJ, O'Sullivan O, Wang Q, Nikkilä J, Marchesi JR, Smidt H, de Vos WM, Ross RP, O'Toole PW. (8/20/2009) PLoS One 4(8): e6669.
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Analysing diet of small herbivores: the efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures.  Soininen EM, Valentini A, Coissac E, Miquel C, Gielly L, Brochmann C, Brysting AK, Sonstebo JH, Ims RA, Yoccoz NG, Taberlet P. (8/20/2009) Frontiers in Zooology 6(1): 16.
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Microbial community structure in a biofilm anode fed with a fermentable substrate: The significance of hydrogen scavengers.  Parameswaran P, Zhang H, Torres CI, Rittmann BE, Krajmalnik-Brown R. (8/17/2009) Biotechnology and Bioengineering 105(1): 69-78.
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Identification of a novel astrovirus (Astrovirus VA1) associated with an outbreak of acute gastroenteritis.  Finkbeiner SR, Li Y, Ruone S, Conrardy C, Gregoricus N, Toney D, Virgin HW, Anderson LJ, Vinjé J, Wang D, Tong S. (8/12/2009) Journal of Virology 83(20): 10836-9.
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Focused-Pulsed sludge pre-treatment increases the bacterial diversity and relative abundance of acetoclastic methanogens in a full-scale anaerobic digester.  Zhang H, Banaszak JE, Parameswaran P, Alder J, Krajmalnik-Brown R, Rittmann BE. (8/5/2009) Water Research 43(18): 4517-26.
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Bacterial diversity in surgical site infections: not just aerobic cocci any more.  Wolcott RD, Gontcharova V, Sun Y, Zischakau A, Dowd SE. (8/1/2009) Journal of Wound Care 18(8): 317-23.
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Community analysis of chronic wound bacteria using 16S rRNA gene-based pyrosequencing: impact of diabetes and antibiotics on chronic wound microbiota.  Price LB, Liu CM, Melendez JH, Frankel YM, Engelthaler D, Aziz M, Bowers J, Rattray R, Ravel J, Kingsley C, Keim PS, Lazarus GS, Zenilman JM. (7/31/2009) PLoS One 4(7): e6462.
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The seasonal structure of microbial communities in the Western English Channel.  Gilbert JA, Field D, Swift P, Newbold L, Oliver A, Smyth T, Somerfield PJ, Huse S, Joint I. (7/31/2009) Environmental Microbiology. 11(12): 3132-9.
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Community-wide response of gut microbiota to enteropathogenic Citrobacter infection revealed by deep sequencing.  Hoffmann C, Hill DA, Minkah N, Kirn T, Troy A, Artis D, Bushman F. (7/27/2009) Infection and Immunity 77(10): 4668-78.
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Microbial community structure in the North Pacific ocean.  Brown MV, Philip GK, Bunge JA, Smith MC, Bissett A, Lauro FM, Fuhrman JA, Donachie SP. (7/23/2009) ISME Journal 3(12): 1374-86.
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Universal DNA-based methods for assessing the diet of grazing livestock and wildlife from feces.  Pegard A, Miquel C, Valentini A, Coissac E, Bouvier F, François D, Taberlet P, Engel E, Pompanon F. (7/8/2009) J Agric Food Chem 57(13): 5700-6.
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Regulation of myocardial ketone body metabolism by the gut microbiota during nutrient deprivation.  Crawford PA, Crowley JR, Sambandam N, Muegge BD, Costello EK, Hamady M, Knight R, Gordon JI. (7/7/2009) PNAS 106(27): 11276-81.
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Next-generation sequencing and metagenomic analysis: a universal diagnostic tool in plant virology.  Adams IP, Glover RH, Monger WA, Mumford R, Jackeviciene E, Navalinskiene M, Samuitiene M, Boonham N. (7/1/2009) Molecular Plant Pathology 10(4): 537-45.
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Assessment of bias associated with incomplete extraction of microbial DNA from soil.  Feinstein LM, Sul WJ, Blackwood CB. (6/26/2009) Appl Environ Microbiol 75(16): 5428-33.
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A Comparative study of species richness estimates obtained using nearly complete fragments and simulated pyrosequencing-generated fragments in 16S rRNA gene-based environmental surveys.  Youssef N, Sheik CS, Krumholz LR, Najar FZ, Roe BA, Elshahed MS. (6/25/2009) Appl Environ Microbiol 75(16): 5227-36.
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Large-scale parallel 454 sequencing reveals host ecological group specificity of arbuscular mycorrhizal fungi in a boreonemoral forest.  Opik M, Metsis M, Daniell TJ, Zobel M, Moora M. (6/24/2009) New Phytology 184(2): 424-37.
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Genetic detection and characterization of Lujo virus, a new hemorrhagic fever-associated arenavirus from southern Africa.  Briese T, Paweska JT, McMullan LK, Hutchison SK, Street C, Palacios G, Khristova ML, Weyer J, Swanepoel R, Egholm M, Nichol ST, Lipkin WI. (6/2/2009) PLoS Pathogens 5(5): e1000455.
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Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing.  Kröber M, Bekel T, Diaz NN, Goesmann A, Jaenicke S, Krause L, Miller D, Runte KJ, Viehöver P, Pühler A, Schlüter A. (6/1/2009) Journal of Biotechnology 142(1): 38-49.
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Microbial diversity in the sputum of a cystic fibrosis patient studied with 16S rDNA pyrosequencing.  Armougom F, Bittar F, Stremler N, Rolain JM, Robert C, Dubus JC, Sarles J, Raoult D, La Scola B. (5/16/2009) Eur J Clin Microbiol Infect Dis. 28(9): 1151-4.
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Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column.  Yanmei Shi, Gene W. Tyson, Edward F. DeLong (5/14/2009) Nature 459: 266-269.
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SOrt-ITEMS : Sequence Orthology based approach for Improved Taxonomic Estimation of Metagenomic Sequences.  Monzoorul HM, Tarini S, Dinakar K, Sharmila S M. (5/13/2009) Bioinformatics 25(14): 1722-30.
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Deep sequencing analysis of RNAs from a grapevine showing Syrah decline symptoms reveals a multiple virus infection that includes a novel virus.  Al Rwahnih M, Daubert S, Golino D, Rowhani A. (5/10/2009) Virology 387(2): 395-401.
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Barcoded Pyrosequencing Reveals Shared Bacterial Community Properties along Two Alkaline Hot Spring Temperature Gradients in Yellowstone National Park.  Miller SR, Strong AL, Jones KL, Ungerer MC. (5/7/2009) Applied Environmental Microbiology 75(13): 4565-72.
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Evaluating high-throughput sequencing as a method for metagenomic analysis of nematode diversity.  Porazinska et al. (5/5/2009) Molecular Ecology Resources 9(6): 1439-1450.
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Comparative analysis of human saliva microbiome diversity by barcoded pyrosequencing and cloning approaches.  Nasidze I, Quinque D, Li J, Li M, Tang K, Stoneking M. (5/3/2009) Analytical Biochemistry 391(1): 64-8.
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The ITS region as a target for characterization of fungal communities using emerging sequencing technologies.  Nilsson RH, Ryberg M, Abarenkov K, Sjökvist E, Kristiansson E. (5/1/2009) FEMS Microbiol Letter 296(1): 97-101.
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Diet-induced metabolic improvements in a hamster model of hypercholesterolemia are strongly linked to alterations of the gut microbiota.  Martínez I, Wallace G, Zhang C, Legge R, Benson AK, Carr TP, Moriyama EN, Walter J. (5/1/2009) Applied Environmental Microbiology 75(12): 4175-84.
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16SrRNA bacterial tag-encoded amplicons pyrosequencing for rapid deciphering of the microbiome of fermented foods: the case of fermented pearl-millet slurries.  Humblot C, Guyot JP. (5/1/2009) Applied Environmental Microbiology 75(13): 4354-61.
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Metagenomic Analyses of Viruses in Stool Samples from Children with Acute Flaccid Paralysis.  Victoria JG, Kapoor A, Li L, Blinkova O, Slikas B, Wang C, Naeem A, Zaidi S, Delwart E. (5/1/2009) Journal of Virology 83(9): 4642-51
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Culture-independent identification of gut bacteria correlated with the onset of diabetes in a rat model.  Roesch LF, Lorca GL, Casella G, Giongo A, Naranjo A, Pionzio AM, Li N, Mai V, Wasserfall CH, Schatz D, Atkinson MA, Neu J, Triplett EW. (5/1/2009) ISME Journal 3(5): 536-48
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Effects of experimental choices and analysis noise on surveys of the "rare biosphere".  Hamp TJ, Jones WJ, Fodor AA. (5/1/2009) Applied Environmental Microbiology 75(10): 3263-70.
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The Expansion of the Microbiological Spectrum of Brain Abscesses with Use of Multiple 16S Ribosomal DNA Sequencing.  Al Masalma M, Armougom F, Scheld WM, Dufour H, Roche PH, Drancourt M, Raoult D. (5/1/2009) Clinical Infectious Diseases 48(9): 1169-78.
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Metagenomic analysis of stressed coral holobionts.  Thurber RV, Willner-Hall D, Rodriguez-Mueller B, Desnues C, Edwards RA, Angly F, Dinsdale E, Kelly L, Rohwer F. (4/22/2009) Environmental Microbiology 11(8): 2148-63.
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Comparative metagenomics of Daphnia symbionts.  Qi W, Nong G, Preston JF, Ben-Ami F, Ebert D. (4/21/2009) BMC Genomics 10: 172.
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Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla.  Mahowald MA, Rey FE, Seedorf H, Turnbaugh PJ, Fulton RS, Wollam A, Shah N, Wang C, Magrini V, Wilson RK, Cantarel BL, Coutinho PM, Henrissat B, Crock LW, Russell A, Verberkmoes NC, Hettich RL, Gordon JI. (4/7/2009) PNAS 106(14): 5859-64.
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Bias in assessments of marine microbial biodiversity in fosmid libraries as evaluated by pyrosequencing.  Temperton B, Field D, Oliver A, Tiwari B, Mühling M, Joint I, Gilbert JA. (4/2/2009) ISME Journal 3(7): 792-6.
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An oligarchic microbial assemblage in the anoxic bottom waters of a volcanic subglacial lake.  Gaidos E, Marteinsson V, Thorsteinsson T, Jóhannesson T, Rúnarsson AR, Stefansson A, Glazer B, Lanoil B, Skidmore M, Han S, Miller M, Rusch A, Foo W. (4/1/2009) ISME Journal 3(4): 486-97.
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A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses.  Jones RT, Robeson MS, Lauber CL, Hamady M, Knight R, Fierer N. (4/1/2009) ISME Journal 3(4): 442-53
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Unique archaeal assemblages in the Arctic Ocean unveiled by massively parallel tag sequencing.  Galand PE, Casamayor EO, Kirchman DL, Potvin M, Lovejoy C. (3/26/2009) The ISME Journal 3(7): 860-9.
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Influence of fecal sample storage on bacterial community diversity.  Roesch LF, Casella G, Simell O, Krischer J, Wasserfall CH, Schatz D, Atkinson MA, Neu J, Triplett EW. (3/24/2009) Open Microbiology Journal 3: 40-6
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Reproducible Community Dynamics of the Gastrointestinal Microbiota Following Antibiotic Perturbation.  Antonopoulos DA, Huse SM, Morrison HG, Schmidt TM, Sogin ML, Young VB. (3/23/2009) Infection and Immunity 77(6): 2367-75.
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Metagenomic signatures of 86 microbial and viral metagenomes.  Willner D, Thurber RV, Rohwer F. (3/18/2009) Environmental Microbiology ePub:
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Molecular Diversity of a North Carolina Wastewater Treatment Plant As Revealed by Pyrosequencing.  Sanapareddy N, Hamp TJ, Gonzalez LC, Hilger HA, Fodor AA, Clinton SM. (3/1/2009) Applied Environmental Microbiology 75(6): 1688-96
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Identification of yeast in chronic wounds using new pathogen-detection technologies.  Leake JL, Dowd SE, Wolcott RD, Zischkau AM. (3/1/2009) Journal of Wound Care 18(3): 103-8
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Human gut microbiota in obesity and after gastric bypass.  Zhang H, Dibaise JK, Zuccolo A, Kudrna D, Braidotti M, Yu Y, Parameswaran P, Crowell MD, Wing R, Rittmann BE, Krajmalnik-Brown R. (2/17/2009) PNAS 106(7): 2365-70
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Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases.  Brulc JM, Antonopoulos DA, Miller ME, Wilson MK, Yannarell AC, Dinsdale EA, Edwards RE, Frank ED, Emerson JB, Wacklin P, Coutinho PM, Henrissat B, Nelson KE, White BA. (2/10/2009) PNAS 106(6): 1948-53
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Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre.  Poretsky RS, Hewson I, Sun S, Allen AE, Zehr JP, Moran MA. (2/3/2009) Environmental Microbiology 11(6): 1358-75.
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Coastal Synechococcus metagenome reveals major roles for horizontal gene transfer and plasmids in population diversity.  Palenik B, Ren Q, Tai V, Paulsen IT. (2/1/2009) Environmental Microbiology 11(2): 349-59
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Evaluation of the bacterial diversity in cecal contents of laying hens fed various molting diets by using bacterial tag-encoded FLX amplicon pyrosequencing.  Callaway TR, Dowd SE, Wolcott RD, Sun Y, McReynolds JL, Edrington TS, Byrd JA, Anderson RC, Krueger N, Nisbet DJ. (2/1/2009) Poultry Science 88(2): 298-302
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Disease-specific motifs can be identified in circulating nucleic acids from live elk and cattle infected with transmissible spongiform encephalopathies.  Gordon PM, Schütz E, Beck J, Urnovitz HB, Graham C, Clark R, Dudas S, Czub S, Sensen M, Brenig B, Groschup MH, Church RB, Sensen CW. (2/1/2009) Nucleic Acids Research 37(2): 550-6
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A core gut microbiome in obese and lean twins.  Turnbaugh P, Hamady M, Yatsunenko T, Cantarel B, Duncan A, Ley R, Sogin M, Jones W, Roe B, Affourtit J, Egholm M, Henrissat B, Heath A, Knight R, Gordon J. (1/22/2009) Nature 457: 480-484
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Direct metagenomic detection of viral pathogens in nasal and fecal specimens using an unbiased high-throughput sequencing approach.  Nakamura S, Yang CS, Sakon N, Ueda M, Tougan T, Yamashita A, Goto N, Takahashi K, Yasunaga T, Ikuta K, Mizutani T, Okamoto Y, Tagami M, Morita R, Maeda N, Kawai J, Hayashizaki Y, Nagai Y, Horii T, Iida T, Nakaya T. (1/19/2009) PLoS One 4(1): e4219
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Characterization of denitrification gene clusters of soil bacteria via a metagenomic approach.  Demanèche S, Philippot L, David MM, Navarro E, Vogel TM, Simonet P. (1/1/2009) Applied Environmental Microbiology 75(2): 534-7
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Potential for phosphonoacetate utilization by marine bacteria in temperate coastal waters.  Gilbert JA, Thomas S, Cooley NA, Kulakova A, Field D, Booth T, McGrath JW, Quinn JP, Joint I. (1/1/2009) Environmental Microbiology 11(1): 111-25
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Metagenomic and stable isotopic analyses of modern freshwater microbialites in Cuatro Ciénegas, Mexico.  Breitbart M, Hoare A, Nitti A, Siefert J, Haynes M, Dinsdale E, Edwards R, Souza V, Rohwer F, Hollander D. (1/1/2009) Environmental Microbiology 11(1): 16-34
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Laboratory procedures to generate viral metagenomes.  Thurber RV, Haynes M, Breitbart M, Wegley L, Rohwer F. (1/1/2009) Nature Protocols 4(4): 470-83
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Use of pyrosequencing and DNA barcodes to monitor variations in Firmicutes and Bacteroidetes communities in the gut microbiota of obese humans.  Armougom F, Raoult D. (12/1/2008) BMC Genomics 9: 576
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Metagenomic analysis indicates that stressors induce production of herpes-like viruses in the coral Porites compressa.  Vega Thurber RL, Barott KL, Hall D, Liu H, Rodriguez-Mueller B, Desnues C, Edwards RA, Haynes M, Angly FE, Wegley L, Rohwer FL. (11/25/2008) PNAS 105: 18413-8
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Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing.  Huse SM, Dethlefsen L, Huber JA, Welch DM, Relman DA, Sogin ML. (11/21/2008) PLoS Genetics 4: e1000255
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Novel Borna Virus in psittacine birds with Proventricular Dilatation Disease.  Honkavuori K, Shivaprasad H, Williams B, Quan P, Hornig M, Street C, Palacios G, Hutchison S, Franca M, Egholm M, Briese T, Lipkin I. (11/19/2008) Emerging Infectious Diseases 14(12): 1883-6.
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The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing.  Dethlefsen L, Huse S, Sogin ML, Relman DA. (11/18/2008) PLoS Biology 6(110): e280
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The influence of sex, handedness, and washing on the diversity of hand surface bacteria.  Fierer N, Hamady M, Lauber CL, Knight R. (11/18/2008) PNAS 105(46): 17994-9
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The Ribosomal Database Project: improved alignments and new tools for rRNA analysis.  Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM. (11/12/2008) Nucleic Acids Research 37: D141-5
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The complete genome sequence of Thermococcus onnurineus NA1 reveals a mixed heterotrophic and carboxydotrophic metabolism.  Lee HS, Kang SG, Bae SS, Lim JK, Cho Y, Kim YJ, Jeon JH, Cha SS, Kwon KK, Kim HT, Park CJ, Lee HW, Kim SI, Chun J, Colwell RR, Kim SJ, Lee JH. (11/1/2008) Journal of Bacteriology 190: 7491-9
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Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use.  V. Acosta-Martínez, S. Dowd, Y. Sun and V. Allen (11/1/2008) Soil Biology and Biochemistry 40: 2762-2770
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Pyrosequencing analysis of the Oral Microflora of healthy adults.  Keijser BJ, Zaura E, Huse SM, van der Vossen JM, Schuren FH, Montijn RC, Ten Cate JM, Crielaard W. (11/1/2008) Journal of Dental Research 87: 1016-20
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Metagenomic diagnosis of bacterial infections.  Nakamura S, Maeda N, Miron IM, Yoh M, Izutsu K, Kataoka C, Honda T, Yasunaga T, Nakaya T, Kawai J, Hayashizaki Y, Horii T, Iida T. (11/1/2008) Emerging Infectious Disease 14: 1784-6
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Comparison of the Diversity of the Vaginal Microbiota in HIV-Infected and HIV-Uninfected Women with or without Bacterial Vaginosis.  Spear GT, Sikaroodi M, Zariffard MR, Landay AL, French AL, Gillevet PM. (10/15/2008) Journal of Infectious Disease 198: 1131-40
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Environmental genomics reveals a single-species ecosystem deep within Earth.  Chivian D, Brodie EL, Alm EJ, Culley DE, Dehal PS, Desantis TZ, Gihring TM, Lapidus A, Lin LH, Lowry SR, Moser DP, Richardson PM, Southam G, Wanger G, Pratt LM, Andersen GL, Hazen TC, Brockman FJ, Arkin AP, Onstott TC. (10/10/2008) Science 322: 275-8
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Polymicrobial nature of chronic diabetic foot ulcer biofilm infections determined using bacterial tag encoded FLX amplicon pyrosequencing (bTEFAP).  Dowd SE, Wolcott RD, Sun Y, McKeehan T, Smith E, Rhoads D. (10/3/2008) PLoS ONE 3: e3326
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Metagenomic Analysis of Lysogeny in Tampa Bay: Implications for Prophage Gene Expression.  Lauren McDaniel, Mya Breitbart, Jennifer Mobberley, Amy Long, Matthew Haynes, Forest Rohwer, John H. Paul (9/23/2008) PLoS ONE 3: e3263
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Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities.  Gilbert JA, Field D, Huang Y, Edwards R, Li W, Gilna P, Joint I. (8/22/2008) PLoS ONE 3: e3042
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Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome.  Qu A, Brulc JM, Wilson MK, Law BF, Theoret JR, Joens LA, Konkel ME, Angly F, Dinsdale EA, Edwards RA, Nelson KE, White BA. (8/13/2008) PLoS ONE 3: e2945
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Comparative analysis of human gut microbiota by barcoded pyrosequencing.  Andersson AF, Lindberg M, Jakobsson H, Bäckhed F, Nyrén P, Engstrand L. (7/30/2008) PLoS One 3: e2836
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Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment.  Biddle JF, Fitz-Gibbon S, Schuster SC, Brenchley JE, House CH. (7/29/2008) PNAS 105: 10583–10588
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Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP)  Scot E Dowd,Todd R Callaway, Randall D Wolcott, Yan Sun, Trevor McKeehan, Robert G Hagevoort, Thomas S Edrington (7/24/2008) BMC Microbiology 8: 125
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Genetic diversity and composition of a plasmid metagenome from a wastewater treatment plant  Andreas Schlüter, Lutz Krause, Rafael Szczepanowski, Alexander Goesmann, Alfred Pühler (4/8/2008) Journal of Biotechnology :
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Functional metagenomic profiling of nine biomes  Dinsdale EA, Edwards RA, Hall D, Angly F, Breitbart M, Brulc JM, Furlan M, Desnues C, Haynes M, Li L, McDaniel L, Moran MA, Nelson KE, Nilsson C, Olson R, Paul J, Brito BR, Ruan Y, Swan BK, Stevens R, Valentine DL, Thurber RV, Wegley L, White BA, Rohwer F (4/3/2008) Nature 452: 629-632
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Phylogenetic classification of short environmental DNA fragments  Lutz Krause, Naryttza N. Diaz, Alexander Goesmann, Scott Kelley, Tim W. Nattkemper, Forest Rohwer, Robert A. Edwards and Jens Stoye (4/1/2008) Nucleic Acids Research 36: 2230-2239
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Biodiversity and biogeography of phages in modern stromatolites and thrombolites  Desnues C, Rodriguez-Brito B, Rayhawk S, Kelley S, Tran T, Haynes M, Liu H, Furlan M, Wegley L, Chau B, Ruan Y, Hall D, Angly FE, Edwards RA, Li L, Thurber RV, Reid RP, Siefert J, Souza V, Valentine DL, Swan BK, Breitbart M, Rohwer F (3/20/2008) Nature 452: 7185
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Microbial community gene expression in ocean surface waters  Jorge Frias-Lopez, Yanmei Shi, Gene W. Tyson, Maureen L. Coleman, Stephan C. Schuster, Sallie W. Chisholm, and Edward F. DeLong (3/11/2008) PNAS 105: 3805–3810
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Survey of bacterial diversity in chronic wounds using Pyrosequencing, DGGE, and full ribosome shotgun sequencing  Dowd SE, Sun Y, Secor PR, Rhoads DD, Wolcott BM, James GA, Wolcott RD (3/6/2008) BMC Microbiology 8:
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Metagenomics: Read Length Matters  K. Eric Wommack, Jaysheel Bhavsar, and Jacques Ravel (3/1/2008) Applied Environmental Microbiology 74: 1453-1463
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Microbial ecology of four coral atolls in the northern line islands  Dinsdale EA, Pantos O, Smriga S, Edwards RA, Angly F, Wegley L, Hatay M, Hall D, Brown E, Haynes M, Krause L, Sala E, Sandin SA, Thurber RV, Willis BL, Azam F, Knowlton N, Rohwer F (2/27/2008) PLoS ONE 3:
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Analyzing gene expression from marine microbial communities using environmental transcriptomics.  Poretsky RS, Gifford S, Rinta-Kanto J, Vila-Costa M, Moran MA. (2/18/2008) Journal of Visualized Experiments 24:
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Bacterial carbon processing by generalist species in the coastal ocean  Mou X, Sun S, Edwards RA, Hodson RE, Moran MA (2/7/2008) Nature 451: 708-711
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A New Arenavirus in a Cluster of Fatal Transplant-Associated Diseases  Gustavo Palacios, Julian Druce, Lei Du, Thomas Tran, Chris Birch, Thomas Briese, Sean Conlan, Phenix-Lan Quan, Jeffrey Hu, John Marshall, Jan Fredrik Simons, Michael Egholm, Christopher D. Paddock, Wun-Ju Shieh, Cynthia S. Goldsmith, Sherif R. Zaki, Mike Catton, and W. Ian Lipkin (2/6/2008) New England Journal of Medicine 358: 991-998
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The Macaque Gut Microbiome in Health, Lentiviral Infection, and Chronic Enterocolitis  McKenna P, Hoffmann C, Minkah N, Aye PP, Lackner A, Liu Z, Lozupone CA, Hamady M, Knight R, Bushman FD (2/4/2008) PLoS Pathogens 4:
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Bacterial flora typing with deep, targeted, chip-based Pyrosequencing  Sundquist A, Bigdeli S, Jalili R, Druzin ML, Waller S, Pullen KM, El-Sayed YY, Taslimi MM, Batzoglou S, Ronaghi M (11/30/2007) BMC Microbiology 7:
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Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite  Falk Warnecke, Peter Luginbuhl, Natalia Ivanova, Majid Ghassemian, Toby H. Richardson, Justin T. Stege, Michelle Cayouette, Alice C. McHardy, Gordana Djordjevic, Nahla Aboushadi, Rotem Sorek, Susannah G. Tringe, Mircea Podar, Hector Garcia Martin, Victor Kunin, Daniel Dalevi, Julita Madejska, Edward Kirton, Darren Platt, Ernest Szeto, Asaf Salamov, Kerrie Barry, Natalia Mikhailova, Nikos C. Kyrpides, Eric G. Matson, Elizabeth A. Ottesen, Xinning Zhang, Myriam Hernandez, Catalina Murillo, Luis G. Acosta, Isidore Rigoutsos, Giselle Tamayo, Brian D. Green, Cathy Chang, Edward M. Rubin, Eric J. Mathur, Dan E. Robertson, Philip Hugenholtz & Jared R. Leadbetter (11/22/2007) Nature 450: 487-488
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Metagenomic analysis of the microbial community associated with the coral Porites astreoides  Wegley L, Edwards R, Rodriguez-Brito B, Liu H, Rohwer F (11/1/2007) Environmental Microbiology 9: 2707-2719
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Microbial population structures in the deep marine biosphere  Huber JA, Welch DB, Morrison HG, Huse SM, Neal PR, Butterfield DA, Sogin ML (10/5/2007) Science 318: 97-100
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A Metagenomic Survey of Microbes in Honey Bee Colony Collapse Disorder  Diana L. Cox-Foster, Sean Conlan, Edward C. Holmes, Gustavo Palacios, Jay D. Evans, Nancy A. Moran, Phenix-Lan Quan, Thomas Briese, Mady Hornig, David M. Geiser, Vince Martinson, Dennis vanEngelsdorp, Abby L. Kalkstein, Andrew Drysdale, Jeffrey Hui, Junhui Zhai,2Liwang Cui, StephenK. Hutchison, Jan Fredrik Simons, Michael Egholm, Jeffery S. Pettis, W. Ian Lipkin (9/6/2007) Science :
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MEGAN analysis of metagenomic data  Daniel H. Huson, Alexander F. Auch, Ji Qi and Stephan C. Schuster (1/25/2007) Genome Research :
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An obesity-associated gut microbiome with increased capacity for energy harvest  Peter J. Turnbaugh, Ruth E. Ley, Michael A. Mahowald, Vincent Magrini, Elaine R. Mardis & Jeffrey I. Gordon (12/21/2006) Nature 444: 1027-1031
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The Marine Viromes of Four Oceanic Regions  Florent E. Angly, Ben Felts, Mya Breitbart, Peter Salamon, Robert A. Edwards, Craig Carlson, Amy M. Chan, Matthew Haynes, Scott Kelley, Hong Liu, Joseph M. Mahaffy, Jennifer E. Mueller, Jim Nulton, Robert Olson, Rachel Parsons, Steve Rayhawk, Curtis A. Suttle, Forest Rohwer (11/1/2006) PLoS Biology 4: 2121-2131
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Archaea predominate among ammonia-oxidizing prokaryotes in soils  S. Leininger, T. Urich, M. Schloter, L. Schwark, J. Qi, G. W. Nicol, J. I. Prosser, S. C. Schuster, C. Schleper (8/17/2006) Nature 442: 806-809
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Microbial diversity in the deep sea and the underexplored ‘‘rare biosphere’’   Mitchell L. Sogin, Hilary G. Morrison, Julie A. Huber, David Mark Welch, Susan M. Huse, Phillip R. Neal, Jesus M. Arrieta, and Gerhard J. Herndl   (8/8/2006) PNAS 103: 12115–12120
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Finding novel genes in bacterial communities isolated from the environment   Lutz Krause, Naryttza N. Diaz, Daniela Bartels, Robert A. Edwards, Alfred Puhler, Forest Rohwer, Folker Meyer and Jens Stoye  (7/15/2006) Bioinformatics 22: 281-289
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Using pyrosequencing to shed light on deep mine microbial ecology   Robert A. Edwards, Beltran Rodriguez-Brito, Linda Wegley, Matthew Haynes, Mya Breitbart, Dean M. Peterson, Martin O. Saar, Scott Alexander, E. Calvin Alexander, Jr., Forest Rohwer (3/20/2006) BMC Genomics 7: 57
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