Insights into the phylogeny and coding potential of microbial dark matter

Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng J-F, Darling A, Malfatti S, Swan BK, Gies EA, Dodsworth JA, et al. (2013)
Nature 499(7459): 431-437.

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Abstract / Bemerkung
Genome sequencing enhances our understanding of the biological world by providing blueprints for the evolutionary and functional diversity that shapes the biosphere. However, microbial genomes that are currently available are of limited phylogenetic breadth, owing to our historical inability to cultivate most microorganisms in the laboratory. We apply single-cell genomics to target and sequence 201 uncultivated archaeal and bacterial cells from nine diverse habitats belonging to 29 major mostly uncharted branches of the tree of life, so-called 'microbial dark matter'. With this additional genomic information, we are able to resolve many intra- and inter-phylum-level relationships and to propose two new superphyla. We uncover unexpected metabolic features that extend our understanding of biology and challenge established boundaries between the three domains of life. These include a novel amino acid use for the opal stop codon, an archaeal-type purine synthesis in Bacteria and complete sigma factors in Archaea similar to those in Bacteria. The single-cell genomes also served to phylogenetically anchor up to 20% of metagenomic reads in some habitats, facilitating organism-level interpretation of ecosystem function. 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.
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Nature
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499
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7459
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431-437
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Rinke C, Schwientek P, Sczyrba A, et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature. 2013;499(7459):431-437.
Rinke, C., Schwientek, P., Sczyrba, A., Ivanova, N. N., Anderson, I. J., Cheng, J. - F., Darling, A., et al. (2013). Insights into the phylogeny and coding potential of microbial dark matter. Nature, 499(7459), 431-437. doi:10.1038/nature12352
Rinke, C., Schwientek, P., Sczyrba, A., Ivanova, N. N., Anderson, I. J., Cheng, J. - F., Darling, A., Malfatti, S., Swan, B. K., Gies, E. A., et al. (2013). Insights into the phylogeny and coding potential of microbial dark matter. Nature 499, 431-437.
Rinke, C., et al., 2013. Insights into the phylogeny and coding potential of microbial dark matter. Nature, 499(7459), p 431-437.
C. Rinke, et al., “Insights into the phylogeny and coding potential of microbial dark matter”, Nature, vol. 499, 2013, pp. 431-437.
Rinke, C., Schwientek, P., Sczyrba, A., Ivanova, N.N., Anderson, I.J., Cheng, J.-F., Darling, A., Malfatti, S., Swan, B.K., Gies, E.A., Dodsworth, J.A., Hedlund, B.P., Tsiamis, G., Sievert, S.M., Liu, W.-T., Eisen, J.A., Hallam, S.J., Kyrpides, N.C., Stepanauskas, R., Rubin, E.M., Hugenholtz, P., Woyke, T.: Insights into the phylogeny and coding potential of microbial dark matter. Nature. 499, 431-437 (2013).
Rinke, Christian, Schwientek, Patrick, Sczyrba, Alexander, Ivanova, Natalia N, Anderson, Iain J, Cheng, Jan-Fang, Darling, Aaron, Malfatti, Stephanie, Swan, Brandon K, Gies, Esther A, Dodsworth, Jeremy A, Hedlund, Brian P, Tsiamis, George, Sievert, Stefan M, Liu, Wen-Tso, Eisen, Jonathan A, Hallam, Steven J, Kyrpides, Nikos C, Stepanauskas, Ramunas, Rubin, Edward M, Hugenholtz, Philip, and Woyke, Tanja. “Insights into the phylogeny and coding potential of microbial dark matter”. Nature 499.7459 (2013): 431-437.

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Leveraging single-cell genomics to expand the fungal tree of life.
Ahrendt SR, Quandt CA, Ciobanu D, Clum A, Salamov A, Andreopoulos B, Cheng JF, Woyke T, Pelin A, Henrissat B, Reynolds NK, Benny GL, Smith ME, James TY, Grigoriev IV., Nat Microbiol 3(12), 2018
PMID: 30297742
Functional shifts in microbial mats recapitulate early Earth metabolic transitions.
Gutiérrez-Preciado A, Saghaï A, Moreira D, Zivanovic Y, Deschamps P, López-García P., Nat Ecol Evol 2(11), 2018
PMID: 30297749
Programmed DNA destruction by miniature CRISPR-Cas14 enzymes.
Harrington LB, Burstein D, Chen JS, Paez-Espino D, Ma E, Witte IP, Cofsky JC, Kyrpides NC, Banfield JF, Doudna JA., Science 362(6416), 2018
PMID: 30337455
Repertoire of the gut microbiota from stomach to colon using culturomics and next-generation sequencing.
Mailhe M, Ricaboni D, Vitton V, Gonzalez JM, Bachar D, Dubourg G, Cadoret F, Robert C, Delerce J, Levasseur A, Fournier PE, Angelakis E, Lagier JC, Raoult D., BMC Microbiol 18(1), 2018
PMID: 30355340
Metagenomics meets read clouds.
Goordial J, Ronholm J., Nat Biotechnol 36(11), 2018
PMID: 30412190
Members of the Genus Methylobacter Are Inferred To Account for the Majority of Aerobic Methane Oxidation in Oxic Soils from a Freshwater Wetland.
Smith GJ, Angle JC, Solden LM, Borton MA, Morin TH, Daly RA, Johnston MD, Stefanik KC, Wolfe R, Gil B, Wrighton KC., MBio 9(6), 2018
PMID: 30401770
Metatranscriptomes Reveal That All Three Domains of Life Are Active but Are Dominated by Bacteria in the Fennoscandian Crystalline Granitic Continental Deep Biosphere.
Lopez-Fernandez M, Simone D, Wu X, Soler L, Nilsson E, Holmfeldt K, Lantz H, Bertilsson S, Dopson M., MBio 9(6), 2018
PMID: 30459191
Supragingival Plaque Microbiome Ecology and Functional Potential in the Context of Health and Disease.
Espinoza JL, Harkins DM, Torralba M, Gomez A, Highlander SK, Jones MB, Leong P, Saffery R, Bockmann M, Kuelbs C, Inman JM, Hughes T, Craig JM, Nelson KE, Dupont CL., MBio 9(6), 2018
PMID: 30482830
Next-generation sequencing (NGS) in the microbiological world: How to make the most of your money.
Vincent AT, Derome N, Boyle B, Culley AI, Charette SJ., J Microbiol Methods 138(), 2017
PMID: 26995332
Regulation of infection efficiency in a globally abundant marine Bacteriodetes virus.
Howard-Varona C, Roux S, Dore H, Solonenko NE, Holmfeldt K, Markillie LM, Orr G, Sullivan MB., ISME J 11(1), 2017
PMID: 27187794
Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2 concentrations.
Probst AJ, Castelle CJ, Singh A, Brown CT, Anantharaman K, Sharon I, Hug LA, Burstein D, Emerson JB, Thomas BC, Banfield JF., Environ Microbiol 19(2), 2017
PMID: 27112493
Gifted microbes for genome mining and natural product discovery.
Baltz RH., J Ind Microbiol Biotechnol 44(4-5), 2017
PMID: 27520548
Impact of 6:2 fluorotelomer alcohol aerobic biotransformation on a sediment microbial community.
Zhang S, Merino N, Wang N, Ruan T, Lu X., Sci Total Environ 575(), 2017
PMID: 27756549
Single-cell genomics based on Raman sorting reveals novel carotenoid-containing bacteria in the Red Sea.
Song Y, Kaster AK, Vollmers J, Song Y, Davison PA, Frentrup M, Preston GM, Thompson IP, Murrell JC, Yin H, Hunter CN, Huang WE., Microb Biotechnol 10(1), 2017
PMID: 27748032
Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements.
Mukherjee S, Stamatis D, Bertsch J, Ovchinnikova G, Verezemska O, Isbandi M, Thomas AD, Ali R, Sharma K, Kyrpides NC, Reddy TB., Nucleic Acids Res 45(d1), 2017
PMID: 27794040
Quest for Ancestors of Eukaryal Cells Based on Phylogenetic Analyses of Aminoacyl-tRNA Synthetases.
Furukawa R, Nakagawa M, Kuroyanagi T, Yokobori SI, Yamagishi A., J Mol Evol 84(1), 2017
PMID: 27889804
Variability in Metagenomic Count Data and Its Influence on the Identification of Differentially Abundant Genes.
Jonsson V, Österlund T, Nerman O, Kristiansson E., J Comput Biol 24(4), 2017
PMID: 27892712
Gaia and her microbiome.
Stolz JF., FEMS Microbiol Ecol 93(2), 2017
PMID: 27940647
Strategies to improve reference databases for soil microbiomes.
Choi J, Yang F, Stepanauskas R, Cardenas E, Garoutte A, Williams R, Flater J, Tiedje JM, Hofmockel KS, Gelder B, Howe A., ISME J 11(4), 2017
PMID: 27935589
A report on extensive lateral genetic reciprocation between arsenic resistant Bacillus subtilis and Bacillus pumilus strains analyzed using RAPD-PCR.
Khowal S, Siddiqui MZ, Ali S, Khan MT, Khan MA, Naqvi SH, Wajid S., Mol Phylogenet Evol 107(), 2017
PMID: 27956257
New CRISPR-Cas systems from uncultivated microbes.
Burstein D, Harrington LB, Strutt SC, Probst AJ, Anantharaman K, Thomas BC, Doudna JA, Banfield JF., Nature 542(7640), 2017
PMID: 28005056
Cheating fosters species co-existence in well-mixed bacterial communities.
Leinweber A, Fredrik Inglis R, Kümmerli R., ISME J 11(5), 2017
PMID: 28060362
Unusual respiratory capacity and nitrogen metabolism in a Parcubacterium (OD1) of the Candidate Phyla Radiation.
Castelle CJ, Brown CT, Thomas BC, Williams KH, Banfield JF., Sci Rep 7(), 2017
PMID: 28067254
Ecology of the Oral Microbiome: Beyond Bacteria.
Baker JL, Bor B, Agnello M, Shi W, He X., Trends Microbiol 25(5), 2017
PMID: 28089325
All together now: experimental multispecies biofilm model systems.
Tan CH, Lee KW, Burmølle M, Kjelleberg S, Rice SA., Environ Microbiol 19(1), 2017
PMID: 27878947
MetaSort untangles metagenome assembly by reducing microbial community complexity.
Ji P, Zhang Y, Wang J, Zhao F., Nat Commun 8(), 2017
PMID: 28112173
Development of a facile droplet-based single-cell isolation platform for cultivation and genomic analysis in microorganisms.
Zhang Q, Wang T, Zhou Q, Zhang P, Gong Y, Gou H, Xu J, Ma B., Sci Rep 7(), 2017
PMID: 28112223
Accessing the genomic information of unculturable oceanic picoeukaryotes by combining multiple single cells.
Mangot JF, Logares R, Sánchez P, Latorre F, Seeleuthner Y, Mondy S, Sieracki ME, Jaillon O, Wincker P, Vargas C, Massana R., Sci Rep 7(), 2017
PMID: 28128359
Mineralizing Filamentous Bacteria from the Prony Bay Hydrothermal Field Give New Insights into the Functioning of Serpentinization-Based Subseafloor Ecosystems.
Pisapia C, Gérard E, Gérard M, Lecourt L, Lang SQ, Pelletier B, Payri CE, Monnin C, Guentas L, Postec A, Quéméneur M, Erauso G, Ménez B., Front Microbiol 8(), 2017
PMID: 28197130
The Timetree of Prokaryotes: New Insights into Their Evolution and Speciation.
Marin J, Battistuzzi FU, Brown AC, Hedges SB., Mol Biol Evol 34(2), 2017
PMID: 27965376
Validation of Metagenomic Next-Generation Sequencing Tests for Universal Pathogen Detection.
Schlaberg R, Chiu CY, Miller S, Procop GW, Weinstock G, Professional Practice Committee and Committee on Laboratory Practices of the American Society for Microbiology, Microbiology Resource Committee of the College of American Pathologists., Arch Pathol Lab Med 141(6), 2017
PMID: 28169558
Geological and Geochemical Controls on Subsurface Microbial Life in the Samail Ophiolite, Oman.
Rempfert KR, Miller HM, Bompard N, Nothaft D, Matter JM, Kelemen P, Fierer N, Templeton AS., Front Microbiol 8(), 2017
PMID: 28223966
Molecular Taxonomic Profiling of Bacterial Communities in a Gilthead Seabream (Sparus aurata) Hatchery.
Califano G, Castanho S, Soares F, Ribeiro L, Cox CJ, Mata L, Costa R., Front Microbiol 8(), 2017
PMID: 28261166
Improvement of phytoplankton culture isolation using single cell sorting by flow cytometry.
Marie D, Le Gall F, Edern R, Gourvil P, Vaulot D., J Phycol 53(2), 2017
PMID: 27878810
Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota.
Kublanov IV, Sigalova OM, Gavrilov SN, Lebedinsky AV, Rinke C, Kovaleva O, Chernyh NA, Ivanova N, Daum C, Reddy TB, Klenk HP, Spring S, Göker M, Reva ON, Miroshnichenko ML, Kyrpides NC, Woyke T, Gelfand MS, Bonch-Osmolovskaya EA., Front Microbiol 8(), 2017
PMID: 28265262
Symbiosis in eukaryotic evolution.
López-García P, Eme L, Moreira D., J Theor Biol 434(), 2017
PMID: 28254477
New Allometric Scaling Laws Revealed for Microorganisms.
Kieft TL., Trends Ecol Evol 32(6), 2017
PMID: 28285792
Using natural products for drug discovery: the impact of the genomics era.
Zhang MM, Qiao Y, Ang EL, Zhao H., Expert Opin Drug Discov 12(5), 2017
PMID: 28277838
The gut microbiome in human neurological disease: A review.
Tremlett H, Bauer KC, Appel-Cresswell S, Finlay BB, Waubant E., Ann Neurol 81(3), 2017
PMID: 28220542
The preservation of microbial DNA in archived soils of various genetic types.
Ivanova EA, Korvigo IO, Aparin BF, Chirak EL, Pershina EV, Romaschenko NS, Provorov NA, Andronov EE., PLoS One 12(3), 2017
PMID: 28339464
High-resolution sequencing reveals unexplored archaeal diversity in freshwater wetland soils.
Narrowe AB, Angle JC, Daly RA, Stefanik KC, Wrighton KC, Miller CS., Environ Microbiol 19(6), 2017
PMID: 28217877
Organismal and spatial partitioning of energy and macronutrient transformations within a hypersaline mat.
Mobberley JM, Lindemann SR, Bernstein HC, Moran JJ, Renslow RS, Babauta J, Hu D, Beyenal H, Nelson WC., FEMS Microbiol Ecol 93(4), 2017
PMID: 28334407
Retroelement-guided protein diversification abounds in vast lineages of Bacteria and Archaea.
Paul BG, Burstein D, Castelle CJ, Handa S, Arambula D, Czornyj E, Thomas BC, Ghosh P, Miller JF, Banfield JF, Valentine DL., Nat Microbiol 2(), 2017
PMID: 28368387
Ferrous iron- and ammonium-rich diffuse vents support habitat-specific communities in a shallow hydrothermal field off the Basiluzzo Islet (Aeolian Volcanic Archipelago).
Bortoluzzi G, Romeo T, La Cono V, La Spada G, Smedile F, Esposito V, Sabatino G, Di Bella M, Canese S, Scotti G, Bo M, Giuliano L, Jones D, Golyshin PN, Yakimov MM, Andaloro F., Geobiology 15(5), 2017
PMID: 28383164
Dynamics of archaea at fine spatial scales in Shark Bay mat microbiomes.
Wong HL, Visscher PT, White RA, Smith DL, Patterson MM, Burns BP., Sci Rep 7(), 2017
PMID: 28397816
Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.).
Waite DW, Vanwonterghem I, Rinke C, Parks DH, Zhang Y, Takai K, Sievert SM, Simon J, Campbell BJ, Hanson TE, Woyke T, Klotz MG, Hugenholtz P., Front Microbiol 8(), 2017
PMID: 28484436
Diversity of Metabolically Active Bacteria in Water-Flooded High-Temperature Heavy Oil Reservoir.
Nazina TN, Shestakova NM, Semenova EM, Korshunova AV, Kostrukova NK, Tourova TP, Min L, Feng Q, Poltaraus AB., Front Microbiol 8(), 2017
PMID: 28487680
PALADIN: protein alignment for functional profiling whole metagenome shotgun data.
Westbrook A, Ramsdell J, Schuelke T, Normington L, Bergeron RD, Thomas WK, MacManes MD., Bioinformatics 33(10), 2017
PMID: 28158639
Global Distribution Patterns and Pangenomic Diversity of the Candidate Phylum "Latescibacteria" (WS3).
Farag IF, Youssef NH, Elshahed MS., Appl Environ Microbiol 83(10), 2017
PMID: 28314726
ICoVeR - an interactive visualization tool for verification and refinement of metagenomic bins.
Broeksema B, Calusinska M, McGee F, Winter K, Bongiovanni F, Goux X, Wilmes P, Delfosse P, Ghoniem M., BMC Bioinformatics 18(1), 2017
PMID: 28464793
Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics.
Lee STM, Kahn SA, Delmont TO, Shaiber A, Esen ÖC, Hubert NA, Morrison HG, Antonopoulos DA, Rubin DT, Eren AM., Microbiome 5(1), 2017
PMID: 28473000
Empirical genome evolution models root the tree of life.
Harish A, Kurland CG., Biochimie 138(), 2017
PMID: 28478110
Novel Large Sulfur Bacteria in the Metagenomes of Groundwater-Fed Chemosynthetic Microbial Mats in the Lake Huron Basin.
Sharrar AM, Flood BE, Bailey JV, Jones DS, Biddanda BA, Ruberg SA, Marcus DN, Dick GJ., Front Microbiol 8(), 2017
PMID: 28533768
RNA-Dependent Cysteine Biosynthesis in Bacteria and Archaea.
Mukai T, Crnković A, Umehara T, Ivanova NN, Kyrpides NC, Söll D., MBio 8(3), 2017
PMID: 28487430
Unveiling microbial interactions in stratified mat communities from a warm saline shallow pond.
Saghaï A, Gutiérrez-Preciado A, Deschamps P, Moreira D, Bertolino P, Ragon M, López-García P., Environ Microbiol 19(6), 2017
PMID: 28489281
Technological Microbiology: Development and Applications.
Vitorino LC, Bessa LA., Front Microbiol 8(), 2017
PMID: 28539920
Spatiotemporal analysis of microbial community dynamics during seasonal stratification events in a freshwater lake (Grand Lake, OK, USA).
Morrison JM, Baker KD, Zamor RM, Nikolai S, Elshahed MS, Youssef NH., PLoS One 12(5), 2017
PMID: 28493994
Mechanisms of gene flow in archaea.
Wagner A, Whitaker RJ, Krause DJ, Heilers JH, van Wolferen M, van der Does C, Albers SV., Nat Rev Microbiol 15(8), 2017
PMID: 28502981
Integrative modeling of gene and genome evolution roots the archaeal tree of life.
Williams TA, Szöllősi GJ, Spang A, Foster PG, Heaps SE, Boussau B, Ettema TJG, Embley TM., Proc Natl Acad Sci U S A 114(23), 2017
PMID: 28533395
Kisameet Glacial Clay: an Unexpected Source of Bacterial Diversity.
Svensson SL, Behroozian S, Xu W, Surette MG, Li L, Davies J., MBio 8(3), 2017
PMID: 28536287
Bioturbation as a key driver behind the dominance of Bacteria over Archaea in near-surface sediment.
Chen X, Andersen TJ, Morono Y, Inagaki F, Jørgensen BB, Lever MA., Sci Rep 7(1), 2017
PMID: 28546547
A Small Number of Low-abundance Bacteria Dominate Plant Species-specific Responses during Rhizosphere Colonization.
Dawson W, Hör J, Egert M, van Kleunen M, Pester M., Front Microbiol 8(), 2017
PMID: 28611765
Calorithrix insularis gen. nov., sp. nov., a novel representative of the phylum Calditrichaeota.
Kompantseva EI, Kublanov IV, Perevalova AA, Chernyh NA, Toshchakov SV, Litti YV, Antipov AN, Bonch-Osmolovskaya EA, Miroshnichenko ML., Int J Syst Evol Microbiol 67(5), 2017
PMID: 27983475
Emulating Host-Microbiome Ecosystem of Human Gastrointestinal Tract in Vitro.
Park GS, Park MH, Shin W, Zhao C, Sheikh S, Oh SJ, Kim HJ., Stem Cell Rev 13(3), 2017
PMID: 28488235
1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life.
Mukherjee S, Seshadri R, Varghese NJ, Eloe-Fadrosh EA, Meier-Kolthoff JP, Göker M, Coates RC, Hadjithomas M, Pavlopoulos GA, Paez-Espino D, Yoshikuni Y, Visel A, Whitman WB, Garrity GM, Eisen JA, Hugenholtz P, Pati A, Ivanova NN, Woyke T, Klenk HP, Kyrpides NC., Nat Biotechnol 35(7), 2017
PMID: 28604660
Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes.
Da Cunha V, Gaia M, Gadelle D, Nasir A, Forterre P., PLoS Genet 13(6), 2017
PMID: 28604769
Archaeal Diversity and CO2 Fixers in Carbonate-/Siliciclastic-Rock Groundwater Ecosystems.
Lazar CS, Stoll W, Lehmann R, Herrmann M, Schwab VF, Akob DM, Nawaz A, Wubet T, Buscot F, Totsche KU, Küsel K., Archaea 2017(), 2017
PMID: 28694737
Bioprospecting challenges in unusual environments.
Tanner K, Vilanova C, Porcar M., Microb Biotechnol 10(4), 2017
PMID: 28612429
The metabolic potential of the single cell genomes obtained from the Challenger Deep, Mariana Trench within the candidate superphylum Parcubacteria (OD1).
León-Zayas R, Peoples L, Biddle JF, Podell S, Novotny M, Cameron J, Lasken RS, Bartlett DH., Environ Microbiol 19(7), 2017
PMID: 28474498
Unexplored diversity and strain-level structure of the skin microbiome associated with psoriasis.
Tett A, Pasolli E, Farina S, Truong DT, Asnicar F, Zolfo M, Beghini F, Armanini F, Jousson O, De Sanctis V, Bertorelli R, Girolomoni G, Cristofolini M, Segata N., NPJ Biofilms Microbiomes 3(), 2017
PMID: 28649415
Single-virus genomics reveals hidden cosmopolitan and abundant viruses.
Martinez-Hernandez F, Fornas O, Lluesma Gomez M, Bolduc B, de la Cruz Peña MJ, Martínez JM, Anton J, Gasol JM, Rosselli R, Rodriguez-Valera F, Sullivan MB, Acinas SG, Martinez-Garcia M., Nat Commun 8(), 2017
PMID: 28643787
Unexpected genomic features in widespread intracellular bacteria: evidence for motility of marine chlamydiae.
Collingro A, Köstlbacher S, Mussmann M, Stepanauskas R, Hallam SJ, Horn M., ISME J 11(10), 2017
PMID: 28644443
Energy and carbon metabolisms in a deep terrestrial subsurface fluid microbial community.
Momper L, Jungbluth SP, Lee MD, Amend JP., ISME J 11(10), 2017
PMID: 28644444
Evolutionary Origins of Two-Barrel RNA Polymerases and Site-Specific Transcription Initiation.
Fouqueau T, Blombach F, Werner F., Annu Rev Microbiol 71(), 2017
PMID: 28657884
Novel approaches in function-driven single-cell genomics.
Doud DFR, Woyke T., FEMS Microbiol Rev 41(4), 2017
PMID: 28591840
Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information.
Barberán A, Caceres Velazquez H, Jones S, Fierer N., mSphere 2(4), 2017
PMID: 28776041
Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples.
Yu FB, Blainey PC, Schulz F, Woyke T, Horowitz MA, Quake SR., Elife 6(), 2017
PMID: 28678007
'ARMAN' archaea depend on association with euryarchaeal host in culture and in situ.
Golyshina OV, Toshchakov SV, Makarova KS, Gavrilov SN, Korzhenkov AA, La Cono V, Arcadi E, Nechitaylo TY, Ferrer M, Kublanov IV, Wolf YI, Yakimov MM, Golyshin PN., Nat Commun 8(1), 2017
PMID: 28680072
Massively parallel whole genome amplification for single-cell sequencing using droplet microfluidics.
Hosokawa M, Nishikawa Y, Kogawa M, Takeyama H., Sci Rep 7(1), 2017
PMID: 28701744
Improved genome recovery and integrated cell-size analyses of individual uncultured microbial cells and viral particles.
Stepanauskas R, Fergusson EA, Brown J, Poulton NJ, Tupper B, Labonté JM, Becraft ED, Brown JM, Pachiadaki MG, Povilaitis T, Thompson BP, Mascena CJ, Bellows WK, Lubys A., Nat Commun 8(1), 2017
PMID: 28729688
Comparative genomics of the DNA damage-inducible network in the Patescibacteria.
Sánchez-Osuna M, Barbé J, Erill I., Environ Microbiol 19(9), 2017
PMID: 28618189
Unusual metabolic diversity of hyperalkaliphilic microbial communities associated with subterranean serpentinization at The Cedars.
Suzuki S, Ishii S, Hoshino T, Rietze A, Tenney A, Morrill PL, Inagaki F, Kuenen JG, Nealson KH., ISME J 11(11), 2017
PMID: 28731475
Present and Future of Culturing Bacteria.
Overmann J, Abt B, Sikorski J., Annu Rev Microbiol 71(), 2017
PMID: 28731846
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.
Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C, Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T., Nat Biotechnol 35(8), 2017
PMID: 28787424
Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life.
Spang A, Caceres EF, Ettema TJG., Science 357(6351), 2017
PMID: 28798101
Many More Microbes in Humans: Enlarging the Microbiome Repertoire.
Lagier JC, Drancourt M, Charrel R, Bittar F, La Scola B, Ranque S, Raoult D., Clin Infect Dis 65(suppl_1), 2017
PMID: 28859350
Genotyping of Bartonella bacteria and their animal hosts: current status and perspectives.
Kosoy M, McKee C, Albayrak L, Fofanov Y., Parasitology (), 2017
PMID: 28764816
Influence of Igneous Basement on Deep Sediment Microbial Diversity on the Eastern Juan de Fuca Ridge Flank.
Labonté JM, Lever MA, Edwards KJ, Orcutt BN., Front Microbiol 8(), 2017
PMID: 28824568
The growing tree of Archaea: new perspectives on their diversity, evolution and ecology.
Adam PS, Borrel G, Brochier-Armanet C, Gribaldo S., ISME J 11(11), 2017
PMID: 28777382
Grape pomace compost harbors organohalide-respiring Dehalogenimonas species with novel reductive dehalogenase genes.
Yang Y, Higgins SA, Yan J, Şimşir B, Chourey K, Iyer R, Hettich RL, Baldwin B, Ogles DM, Löffler FE., ISME J 11(12), 2017
PMID: 28809851
Actinobacterial Rare Biospheres and Dark Matter Revealed in Habitats of the Chilean Atacama Desert.
Idris H, Goodfellow M, Sanderson R, Asenjo JA, Bull AT., Sci Rep 7(1), 2017
PMID: 28827739
Response to nitrogen addition reveals metabolic and ecological strategies of soil bacteria.
Samad MS, Johns C, Richards KG, Lanigan GJ, de Klein CAM, Clough TJ, Morales SE., Mol Ecol 26(20), 2017
PMID: 28752622
Prokaryotic diversity and community composition in the Salar de Uyuni, a large scale, chaotropic salt flat.
dC Rubin SS, Marín I, Gómez MJ, Morales EA, Zekker I, San Martín-Uriz P, Rodríguez N, Amils R., Environ Microbiol 19(9), 2017
PMID: 28752915
Stress and stability: applying the Anna Karenina principle to animal microbiomes.
Zaneveld JR, McMinds R, Vega Thurber R., Nat Microbiol 2(), 2017
PMID: 28836573
Meta-analysis of Liver and Heart Transcriptomic Data for Functional Annotation Transfer in Mammalian Orthologs.
Reyes PFL, Michoel T, Joshi A, Devailly G., Comput Struct Biotechnol J 15(), 2017
PMID: 29187960
Illuminating microbial diversity.
Forster SC., Nat Rev Microbiol 15(10), 2017
PMID: 28852214
Shotgun metagenomics, from sampling to analysis.
Quince C, Walker AW, Simpson JT, Loman NJ, Segata N., Nat Biotechnol 35(9), 2017
PMID: 28898207
Salinirussus salinus gen. nov., sp. nov., isolated from a marine solar saltern.
Cui HL, Lü ZZ, Li Y, Zhou Y., Int J Syst Evol Microbiol 67(9), 2017
PMID: 28875907
Evaluation of single-cell genomics to address evolutionary questions using three SAGs of the choanoflagellate Monosiga brevicollis.
López-Escardó D, Grau-Bové X, Guillaumet-Adkins A, Gut M, Sieracki ME, Ruiz-Trillo I., Sci Rep 7(1), 2017
PMID: 28887541
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life.
Parks DH, Rinke C, Chuvochina M, Chaumeil PA, Woodcroft BJ, Evans PN, Hugenholtz P, Tyson GW., Nat Microbiol 2(11), 2017
PMID: 28894102
Novel arsenic-transforming bacteria and the diversity of their arsenic-related genes and enzymes arising from arsenic-polluted freshwater sediment.
Suhadolnik MLS, Salgado APC, Scholte LLS, Bleicher L, Costa PS, Reis MP, Dias MF, Ávila MP, Barbosa FAR, Chartone-Souza E, Nascimento AMA., Sci Rep 7(1), 2017
PMID: 28894204
BeerDeCoded: the open beer metagenome project.
Sobel J, Henry L, Rotman N, Rando G., F1000Res 6(), 2017
PMID: 29123645
Metabolic Roles of Uncultivated Bacterioplankton Lineages in the Northern Gulf of Mexico "Dead Zone".
Thrash JC, Seitz KW, Baker BJ, Temperton B, Gillies LE, Rabalais NN, Henrissat B, Mason OU., MBio 8(5), 2017
PMID: 28900024
Bacterial, Archaeal, and Eukaryotic Diversity across Distinct Microhabitats in an Acid Mine Drainage.
Mesa V, Gallego JLR, González-Gil R, Lauga B, Sánchez J, Méndez-García C, Peláez AI., Front Microbiol 8(), 2017
PMID: 28955322
Geochemical and Microbial Community Attributes in Relation to Hyporheic Zone Geological Facies.
Hou Z, Nelson WC, Stegen JC, Murray CJ, Arntzen E, Crump AR, Kennedy DW, Perkins MC, Scheibe TD, Fredrickson JK, Zachara JM., Sci Rep 7(1), 2017
PMID: 28931901
Tools for Genomic and Transcriptomic Analysis of Microbes at Single-Cell Level.
Chen Z, Chen L, Zhang W., Front Microbiol 8(), 2017
PMID: 28979258
Individual Patterns of Complexity in Cystic Fibrosis Lung Microbiota, Including Predator Bacteria, over a 1-Year Period.
de Dios Caballero J, Vida R, Cobo M, Máiz L, Suárez L, Galeano J, Baquero F, Cantón R, Del Campo R., MBio 8(5), 2017
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The trajectory of microbial single-cell sequencing.
Woyke T, Doud DFR, Schulz F., Nat Methods 14(11), 2017
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Towards a balanced view of the bacterial tree of life.
Schulz F, Eloe-Fadrosh EA, Bowers RM, Jarett J, Nielsen T, Ivanova NN, Kyrpides NC, Woyke T., Microbiome 5(1), 2017
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Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents.
Anderson RE, Reveillaud J, Reddington E, Delmont TO, Eren AM, McDermott JM, Seewald JS, Huber JA., Nat Commun 8(1), 2017
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Genomic Comparison of Two Family-Level Groups of the Uncultivated NAG1 Archaeal Lineage from Chemically and Geographically Disparate Hot Springs.
Becraft ED, Dodsworth JA, Murugapiran SK, Thomas SC, Ohlsson JI, Stepanauskas R, Hedlund BP, Swingley WD., Front Microbiol 8(), 2017
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Finding life's missing pieces.
Solden LM, Wrighton KC., Nat Microbiol 2(11), 2017
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Archaea and the origin of eukaryotes.
Eme L, Spang A, Lombard J, Stairs CW, Ettema TJG., Nat Rev Microbiol 15(12), 2017
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Metabolic potential and in situ activity of marine Marinimicrobia bacteria in an anoxic water column.
Bertagnolli AD, Padilla CC, Glass JB, Thamdrup B, Stewart FJ., Environ Microbiol 19(11), 2017
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The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota.
Milani C, Duranti S, Bottacini F, Casey E, Turroni F, Mahony J, Belzer C, Delgado Palacio S, Arboleya Montes S, Mancabelli L, Lugli GA, Rodriguez JM, Bode L, de Vos W, Gueimonde M, Margolles A, van Sinderen D, Ventura M., Microbiol Mol Biol Rev 81(4), 2017
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First Insights into the Diverse Human Archaeome: Specific Detection of Archaea in the Gastrointestinal Tract, Lung, and Nose and on Skin.
Koskinen K, Pausan MR, Perras AK, Beck M, Bang C, Mora M, Schilhabel A, Schmitz R, Moissl-Eichinger C., MBio 8(6), 2017
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Diverse Marinimicrobia bacteria may mediate coupled biogeochemical cycles along eco-thermodynamic gradients.
Hawley AK, Nobu MK, Wright JJ, Durno WE, Morgan-Lang C, Sage B, Schwientek P, Swan BK, Rinke C, Torres-Beltrán M, Mewis K, Liu WT, Stepanauskas R, Woyke T, Hallam SJ., Nat Commun 8(1), 2017
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Increased Biosynthetic Gene Dosage in a Genome-Reduced Defensive Bacterial Symbiont.
Lopera J, Miller IJ, McPhail KL, Kwan JC., mSystems 2(6), 2017
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Bacterial Succession on Sinking Particles in the Ocean's Interior.
Pelve EA, Fontanez KM, DeLong EF., Front Microbiol 8(), 2017
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Phylogenomics of Cas4 family nucleases.
Hudaiberdiev S, Shmakov S, Wolf YI, Terns MP, Makarova KS, Koonin EV., BMC Evol Biol 17(1), 2017
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Bacteriophage Distributions and Temporal Variability in the Ocean's Interior.
Luo E, Aylward FO, Mende DR, DeLong EF., MBio 8(6), 2017
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Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla.
Becraft ED, Woyke T, Jarett J, Ivanova N, Godoy-Vitorino F, Poulton N, Brown JM, Brown J, Lau MCY, Onstott T, Eisen JA, Moser D, Stepanauskas R., Front Microbiol 8(), 2017
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Decontaminating eukaryotic genome assemblies with machine learning.
Fierst JL, Murdock DA., BMC Bioinformatics 18(1), 2017
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Ammonia-oxidising archaea living at low pH: Insights from comparative genomics.
Herbold CW, Lehtovirta-Morley LE, Jung MY, Jehmlich N, Hausmann B, Han P, Loy A, Pester M, Sayavedra-Soto LA, Rhee SK, Prosser JI, Nicol GW, Wagner M, Gubry-Rangin C., Environ Microbiol 19(12), 2017
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Atmospheric trace gases support primary production in Antarctic desert surface soil.
Ji M, Greening C, Vanwonterghem I, Carere CR, Bay SK, Steen JA, Montgomery K, Lines T, Beardall J, van Dorst J, Snape I, Stott MB, Hugenholtz P, Ferrari BC., Nature 552(7685), 2017
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The Emergency Medical Service Microbiome.
Hudson AJ, Glaister GD, Wieden HJ., Appl Environ Microbiol (), 2017
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Archaeal S-Layers: Overview and Current State of the Art.
Rodrigues-Oliveira T, Belmok A, Vasconcellos D, Schuster B, Kyaw CM., Front Microbiol 8(), 2017
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Tritagonist as a new term for uncharacterised microorganisms in environmental systems.
Freimoser FM, Pelludat C, Remus-Emsermann MN., ISME J 10(1), 2016
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ProDeGe: a computational protocol for fully automated decontamination of genomes.
Tennessen K, Andersen E, Clingenpeel S, Rinke C, Lundberg DS, Han J, Dangl JL, Ivanova N, Woyke T, Kyrpides N, Pati A., ISME J 10(1), 2016
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Phylogeny and physiology of candidate phylum 'Atribacteria' (OP9/JS1) inferred from cultivation-independent genomics.
Nobu MK, Dodsworth JA, Murugapiran SK, Rinke C, Gies EA, Webster G, Schwientek P, Kille P, Parkes RJ, Sass H, Jørgensen BB, Weightman AJ, Liu WT, Hallam SJ, Tsiamis G, Woyke T, Hedlund BP., ISME J 10(2), 2016
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Ecophysiology of an uncultivated lineage of Aigarchaeota from an oxic, hot spring filamentous 'streamer' community.
Beam JP, Jay ZJ, Schmid MC, Rusch DB, Romine MF, Jennings Rde M, Kozubal MA, Tringe SG, Wagner M, Inskeep WP., ISME J 10(1), 2016
PMID: 26140529
Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages.
Hug LA, Thomas BC, Sharon I, Brown CT, Sharma R, Hettich RL, Wilkins MJ, Williams KH, Singh A, Banfield JF., Environ Microbiol 18(1), 2016
PMID: 26033198
Single-cell genomics of uncultivated deep-branching magnetotactic bacteria reveals a conserved set of magnetosome genes.
Kolinko S, Richter M, Glöckner FO, Brachmann A, Schüler D., Environ Microbiol 18(1), 2016
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Competitive strategies differentiate closely related species of marine actinobacteria.
Patin NV, Duncan KR, Dorrestein PC, Jensen PR., ISME J 10(2), 2016
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Insights in the ecology and evolutionary history of the Miscellaneous Crenarchaeotic Group lineage.
Fillol M, Auguet JC, Casamayor EO, Borrego CM., ISME J 10(3), 2016
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Experimental insights into the importance of aquatic bacterial community composition to the degradation of dissolved organic matter.
Logue JB, Stedmon CA, Kellerman AM, Nielsen NJ, Andersson AF, Laudon H, Lindström ES, Kritzberg ES., ISME J 10(3), 2016
PMID: 26296065
Predicting microbial traits with phylogenies.
Goberna M, Verdú M., ISME J 10(4), 2016
PMID: 26371406
Genomic and metagenomic surveys of hydrogenase distribution indicate H2 is a widely utilised energy source for microbial growth and survival.
Greening C, Biswas A, Carere CR, Jackson CJ, Taylor MC, Stott MB, Cook GM, Morales SE., ISME J 10(3), 2016
PMID: 26405831
Identification and Resolution of Microdiversity through Metagenomic Sequencing of Parallel Consortia.
Nelson WC, Maezato Y, Wu YW, Romine MF, Lindemann SR., Appl Environ Microbiol 82(1), 2016
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Proteogenomics of rare taxonomic phyla: A prospective treasure trove of protein coding genes.
Kumar D, Mondal AK, Kutum R, Dash D., Proteomics 16(2), 2016
PMID: 26773550
Comparative Genomics of Candidate Phylum TM6 Suggests That Parasitism Is Widespread and Ancestral in This Lineage.
Yeoh YK, Sekiguchi Y, Parks DH, Hugenholtz P., Mol Biol Evol 33(4), 2016
PMID: 26615204
Single-Cell-Genomics-Facilitated Read Binning of Candidate Phylum EM19 Genomes from Geothermal Spring Metagenomes.
Becraft ED, Dodsworth JA, Murugapiran SK, Ohlsson JI, Briggs BR, Kanbar J, De Vlaminck I, Quake SR, Dong H, Hedlund BP, Swingley WD., Appl Environ Microbiol 82(4), 2016
PMID: 26637598
Computational approaches to predict bacteriophage-host relationships.
Edwards RA, McNair K, Faust K, Raes J, Dutilh BE., FEMS Microbiol Rev 40(2), 2016
PMID: 26657537
Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome.
Kuleshov V, Jiang C, Zhou W, Jahanbani F, Batzoglou S, Snyder M., Nat Biotechnol 34(1), 2016
PMID: 26655498
Metagenomic investigation of the geologically unique Hellenic Volcanic Arc reveals a distinctive ecosystem with unexpected physiology.
Oulas A, Polymenakou PN, Seshadri R, Tripp HJ, Mandalakis M, Paez-Espino AD, Pati A, Chain P, Nomikou P, Carey S, Kilias S, Christakis C, Kotoulas G, Magoulas A, Ivanova NN, Kyrpides NC., Environ Microbiol 18(4), 2016
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Cultivating microbial dark matter in benzene-degrading methanogenic consortia.
Luo F, Devine CE, Edwards EA., Environ Microbiol 18(9), 2016
PMID: 26549712
Genome Reconstruction from Metagenomic Data Sets Reveals Novel Microbes in the Brackish Waters of the Caspian Sea.
Mehrshad M, Amoozegar MA, Ghai R, Shahzadeh Fazeli SA, Rodriguez-Valera F., Appl Environ Microbiol 82(5), 2016
PMID: 26729711
Molecular Ecology of Hypersaline Microbial Mats: Current Insights and New Directions.
Wong HL, Ahmed-Cox A, Burns BP., Microorganisms 4(1), 2016
PMID: 27681900
Assessing Bacterial Diversity in the Rhizosphere of Thymus zygis Growing in the Sierra Nevada National Park (Spain) through Culture-Dependent and Independent Approaches.
Pascual J, Blanco S, García-López M, García-Salamanca A, Bursakov SA, Genilloud O, Bills GF, Ramos JL, van Dillewijn P., PLoS One 11(1), 2016
PMID: 26741495
Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations.
Bendall ML, Stevens SL, Chan LK, Malfatti S, Schwientek P, Tremblay J, Schackwitz W, Martin J, Pati A, Bushnell B, Froula J, Kang D, Tringe SG, Bertilsson S, Moran MA, Shade A, Newton RJ, McMahon KD, Malmstrom RR., ISME J 10(7), 2016
PMID: 26744812
Prokaryotic Community Structure Driven by Salinity and Ionic Concentrations in Plateau Lakes of the Tibetan Plateau.
Zhong ZP, Liu Y, Miao LL, Wang F, Chu LM, Wang JL, Liu ZP., Appl Environ Microbiol 82(6), 2016
PMID: 26746713
Metabolic traits of an uncultured archaeal lineage--MSBL1--from brine pools of the Red Sea.
Mwirichia R, Alam I, Rashid M, Vinu M, Ba-Alawi W, Anthony Kamau A, Kamanda Ngugi D, Göker M, Klenk HP, Bajic V, Stingl U., Sci Rep 6(), 2016
PMID: 26758088
A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling.
D'Amore R, Ijaz UZ, Schirmer M, Kenny JG, Gregory R, Darby AC, Shakya M, Podar M, Quince C, Hall N., BMC Genomics 17(), 2016
PMID: 26763898
Archaeal Distribution in Moonmilk Deposits from Alpine Caves and Their Ecophysiological Potential.
Reitschuler C, Spötl C, Hofmann K, Wagner AO, Illmer P., Microb Ecol 71(3), 2016
PMID: 26790864
Single-cell genome sequencing: current state of the science.
Gawad C, Koh W, Quake SR., Nat Rev Genet 17(3), 2016
PMID: 26806412
Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs.
Eloe-Fadrosh EA, Paez-Espino D, Jarett J, Dunfield PF, Hedlund BP, Dekas AE, Grasby SE, Brady AL, Dong H, Briggs BR, Li WJ, Goudeau D, Malmstrom R, Pati A, Pett-Ridge J, Rubin EM, Woyke T, Kyrpides NC, Ivanova NN., Nat Commun 7(), 2016
PMID: 26814032
Microbial diversity in European alpine permafrost and active layers.
Frey B, Rime T, Phillips M, Stierli B, Hajdas I, Widmer F, Hartmann M., FEMS Microbiol Ecol 92(3), 2016
PMID: 26832204
Metagenomics uncovers gaps in amplicon-based detection of microbial diversity.
Eloe-Fadrosh EA, Ivanova NN, Woyke T, Kyrpides NC., Nat Microbiol 1(), 2016
PMID: 27572438
Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy.
Campanaro S, Treu L, Kougias PG, De Francisci D, Valle G, Angelidaki I., Biotechnol Biofuels 9(), 2016
PMID: 26839589
Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems.
Burstein D, Sun CL, Brown CT, Sharon I, Anantharaman K, Probst AJ, Thomas BC, Banfield JF., Nat Commun 7(), 2016
PMID: 26837824
High-resolution phylogenetic microbial community profiling.
Singer E, Bushnell B, Coleman-Derr D, Bowman B, Bowers RM, Levy A, Gies EA, Cheng JF, Copeland A, Klenk HP, Hallam SJ, Hugenholtz P, Tringe SG, Woyke T., ISME J 10(8), 2016
PMID: 26859772
Back to the Future of Soil Metagenomics.
Nesme J, Achouak W, Agathos SN, Bailey M, Baldrian P, Brunel D, Frostegård Å, Heulin T, Jansson JK, Jurkevitch E, Kruus KL, Kowalchuk GA, Lagares A, Lappin-Scott HM, Lemanceau P, Le Paslier D, Mandic-Mulec I, Murrell JC, Myrold DD, Nalin R, Nannipieri P, Neufeld JD, O'Gara F, Parnell JJ, Pühler A, Pylro V, Ramos JL, Roesch LF, Schloter M, Schleper C, Sczyrba A, Sessitsch A, Sjöling S, Sørensen J, Sørensen SJ, Tebbe CC, Topp E, Tsiamis G, van Elsas JD, van Keulen G, Widmer F, Wagner M, Zhang T, Zhang X, Zhao L, Zhu YG, Vogel TM, Simonet P., Front Microbiol 7(), 2016
PMID: 26903960
Improved Environmental Genomes via Integration of Metagenomic and Single-Cell Assemblies.
Mende DR, Aylward FO, Eppley JM, Nielsen TN, DeLong EF., Front Microbiol 7(), 2016
PMID: 26904016
Novel microbial assemblages inhabiting crustal fluids within mid-ocean ridge flank subsurface basalt.
Jungbluth SP, Bowers RM, Lin HT, Cowen JP, Rappé MS., ISME J 10(8), 2016
PMID: 26872042
Archaeal Community Changes Associated with Cultivation of Amazon Forest Soil with Oil Palm.
Tupinambá DD, Cantão ME, Costa OY, Bergmann JC, Kruger RH, Kyaw CM, Barreto CC, Quirino BF., Archaea 2016(), 2016
PMID: 27006640
Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines.
Vavourakis CD, Ghai R, Rodriguez-Valera F, Sorokin DY, Tringe SG, Hugenholtz P, Muyzer G., Front Microbiol 7(), 2016
PMID: 26941731
Culture-independent method for identification of microbial enzyme-encoding genes by activity-based single-cell sequencing using a water-in-oil microdroplet platform.
Nakamura K, Iizuka R, Nishi S, Yoshida T, Hatada Y, Takaki Y, Iguchi A, Yoon DH, Sekiguchi T, Shoji S, Funatsu T., Sci Rep 6(), 2016
PMID: 26915788
Bacterial Communities of Three Saline Meromictic Lakes in Central Asia.
Baatar B, Chiang PW, Rogozin DY, Wu YT, Tseng CH, Yang CY, Chiu HH, Oyuntsetseg B, Degermendzhy AG, Tang SL., PLoS One 11(3), 2016
PMID: 26934492
Advanced tools in marine natural drug discovery.
Zhang G, Li J, Zhu T, Gu Q, Li D., Curr Opin Biotechnol 42(), 2016
PMID: 26954946
Delta-proteobacterial SAR324 group in hydrothermal plumes on the South Mid-Atlantic Ridge.
Cao H, Dong C, Bougouffa S, Li J, Zhang W, Shao Z, Bajic VB, Qian PY., Sci Rep 6(), 2016
PMID: 26953077
Novel, Deep-Branching Heterotrophic Bacterial Populations Recovered from Thermal Spring Metagenomes.
Colman DR, Jay ZJ, Inskeep WP, Jennings Rd, Maas KR, Rusch DB, Takacs-Vesbach CD., Front Microbiol 7(), 2016
PMID: 27014227
MeCorS: Metagenome-enabled error correction of single cell sequencing reads.
Bremges A, Singer E, Woyke T, Sczyrba A., Bioinformatics 32(14), 2016
PMID: 27153586
Consortia of low-abundance bacteria drive sulfate reduction-dependent degradation of fermentation products in peat soil microcosms.
Hausmann B, Knorr KH, Schreck K, Tringe SG, Glavina Del Rio T, Loy A, Pester M., ISME J 10(10), 2016
PMID: 27015005
Genome-based microbial ecology of anammox granules in a full-scale wastewater treatment system.
Speth DR, In 't Zandt MH, Guerrero-Cruz S, Dutilh BE, Jetten MS., Nat Commun 7(), 2016
PMID: 27029554
The bulk and the tail of minimal absent words in genome sequences.
Aurell E, Innocenti N, Zhou HJ., Phys Biol 13(2), 2016
PMID: 27043075
Metagenomic analysis of nitrogen and methane cycling in the Arabian Sea oxygen minimum zone.
Lüke C, Speth DR, Kox MAR, Villanueva L, Jetten MSM., PeerJ 4(), 2016
PMID: 27077014
Genomic insights into members of the candidate phylum Hyd24-12 common in mesophilic anaerobic digesters.
Kirkegaard RH, Dueholm MS, McIlroy SJ, Nierychlo M, Karst SM, Albertsen M, Nielsen PH., ISME J 10(10), 2016
PMID: 27058503
A new view of the tree of life.
Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, Butterfield CN, Hernsdorf AW, Amano Y, Ise K, Suzuki Y, Dudek N, Relman DA, Finstad KM, Amundson R, Thomas BC, Banfield JF., Nat Microbiol 1(), 2016
PMID: 27572647
Phylogenetic diversity and ecophysiology of Candidate phylum Saccharibacteria in activated sludge.
Kindaichi T, Yamaoka S, Uehara R, Ozaki N, Ohashi A, Albertsen M, Nielsen PH, Nielsen JL., FEMS Microbiol Ecol 92(6), 2016
PMID: 27090759
Raman activated cell sorting.
Song Y, Yin H, Huang WE., Curr Opin Chem Biol 33(), 2016
PMID: 27100046
Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics.
Jovel J, Patterson J, Wang W, Hotte N, O'Keefe S, Mitchel T, Perry T, Kao D, Mason AL, Madsen KL, Wong GK., Front Microbiol 7(), 2016
PMID: 27148170
A multi-omic future for microbiome studies.
Jansson JK, Baker ES., Nat Microbiol 1(), 2016
PMID: 27572648
Microbial diversity: The tree of life comes of age.
Spang A, Ettema TJ., Nat Microbiol 1(), 2016
PMID: 27572651
Physiology, Biochemistry, and Applications of F420- and Fo-Dependent Redox Reactions.
Greening C, Ahmed FH, Mohamed AE, Lee BM, Pandey G, Warden AC, Scott C, Oakeshott JG, Taylor MC, Jackson CJ., Microbiol Mol Biol Rev 80(2), 2016
PMID: 27122598
Carbon and Sulfur Cycling below the Chemocline in a Meromictic Lake and the Identification of a Novel Taxonomic Lineage in the FCB Superphylum, Candidatus Aegiribacteria.
Hamilton TL, Bovee RJ, Sattin SR, Mohr W, Gilhooly WP, Lyons TW, Pearson A, Macalady JL., Front Microbiol 7(), 2016
PMID: 27199928
Metagenomic analysis of rapid gravity sand filter microbial communities suggests novel physiology of Nitrospira spp.
Palomo A, Jane Fowler S, Gülay A, Rasmussen S, Sicheritz-Ponten T, Smets BF., ISME J 10(11), 2016
PMID: 27128989
Culture-Independent Diagnostics for Health Security.
Doggett NA, Mukundan H, Lefkowitz EJ, Slezak TR, Chain PS, Morse S, Anderson K, Hodge DR, Pillai S., Health Secur 14(3), 2016
PMID: 27314653
Single cell stable isotope probing in microbiology using Raman microspectroscopy.
Wang Y, Huang WE, Cui L, Wagner M., Curr Opin Biotechnol 41(), 2016
PMID: 27149160
Falsirhodobacter sp. alg1 Harbors Single Homologs of Endo and Exo-Type Alginate Lyases Efficient for Alginate Depolymerization.
Mori T, Takahashi M, Tanaka R, Miyake H, Shibata T, Chow S, Kuroda K, Ueda M, Takeyama H., PLoS One 11(5), 2016
PMID: 27176711
Toward a Predictive Understanding of Earth's Microbiomes to Address 21st Century Challenges.
Blaser MJ, Cardon ZG, Cho MK, Dangl JL, Donohue TJ, Green JL, Knight R, Maxon ME, Northen TR, Pollard KS, Brodie EL., MBio 7(3), 2016
PMID: 27178263
Status of the Archaeal and Bacterial Census: an Update.
Schloss PD, Girard RA, Martin T, Edwards J, Thrash JC., MBio 7(3), 2016
PMID: 27190214
Comparison of archaeal and bacterial communities in two sponge species and seawater from an Indonesian coral reef environment.
Polónia AR, Cleary DF, Freitas R, Coelho FJ, de Voogd NJ, Gomes NC., Mar Genomics 29(), 2016
PMID: 27225825
Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling.
Flygare S, Simmon K, Miller C, Qiao Y, Kennedy B, Di Sera T, Graf EH, Tardif KD, Kapusta A, Rynearson S, Stockmann C, Queen K, Tong S, Voelkerding KV, Blaschke A, Byington CL, Jain S, Pavia A, Ampofo K, Eilbeck K, Marth G, Yandell M, Schlaberg R., Genome Biol 17(1), 2016
PMID: 27224977
Genome-Based Microbial Taxonomy Coming of Age.
Hugenholtz P, Skarshewski A, Parks DH., Cold Spring Harb Perspect Biol 8(6), 2016
PMID: 26988968
Archaeal communities of Arctic methane-containing permafrost.
Shcherbakova V, Yoshimura Y, Ryzhmanova Y, Taguchi Y, Segawa T, Oshurkova V, Rivkina E., FEMS Microbiol Ecol 92(10), 2016
PMID: 27312964
Indirect Evidence Link PCB Dehalogenation with Geobacteraceae in Anaerobic Sediment-Free Microcosms.
Praveckova M, Brennerova MV, Holliger C, De Alencastro F, Rossi P., Front Microbiol 7(), 2016
PMID: 27379063
Sporulation, bacterial cell envelopes and the origin of life.
Tocheva EI, Ortega DR, Jensen GJ., Nat Rev Microbiol 14(8), 2016
PMID: 28232669
Visualizing in situ translational activity for identifying and sorting slow-growing archaeal-bacterial consortia.
Hatzenpichler R, Connon SA, Goudeau D, Malmstrom RR, Woyke T, Orphan VJ., Proc Natl Acad Sci U S A 113(28), 2016
PMID: 27357680
A catalogue of 136 microbial draft genomes from Red Sea metagenomes.
Haroon MF, Thompson LR, Parks DH, Hugenholtz P, Stingl U., Sci Data 3(), 2016
PMID: 27377622
Genomics-informed isolation and characterization of a symbiotic Nanoarchaeota system from a terrestrial geothermal environment.
Wurch L, Giannone RJ, Belisle BS, Swift C, Utturkar S, Hettich RL, Reysenbach AL, Podar M., Nat Commun 7(), 2016
PMID: 27378076
Metagenome-wide association studies: fine-mining the microbiome.
Wang J, Jia H., Nat Rev Microbiol 14(8), 2016
PMID: 27396567
Genome Evolution and Nitrogen Fixation in Bacterial Ectosymbionts of a Protist Inhabiting Wood-Feeding Cockroaches.
Tai V, Carpenter KJ, Weber PK, Nalepa CA, Perlman SJ, Keeling PJ., Appl Environ Microbiol 82(15), 2016
PMID: 27235430
Metagenomic signatures of a tropical mining-impacted stream reveal complex microbial and metabolic networks.
Reis MP, Dias MF, Costa PS, Ávila MP, Leite LR, de Araújo FMG, Salim ACM, Bucciarelli-Rodriguez M, Oliveira G, Chartone-Souza E, Nascimento AMA., Chemosphere 161(), 2016
PMID: 27441985
Let microorganisms do the talking, let us talk more about microorganisms.
Nai C, Magrini B, Offe J., Fungal Biol Biotechnol 3(), 2016
PMID: 28955464
Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants.
Stolze Y, Bremges A, Rumming M, Henke C, Maus I, Pühler A, Sczyrba A, Schlüter A., Biotechnol Biofuels 9(), 2016
PMID: 27462367
Are multi-omics enough?
Vilanova C, Porcar M., Nat Microbiol 1(8), 2016
PMID: 27573112
Virtual microfluidics for digital quantification and single-cell sequencing.
Xu L, Brito IL, Alm EJ, Blainey PC., Nat Methods 13(9), 2016
PMID: 27479330
Toward Accurate and Quantitative Comparative Metagenomics.
Nayfach S, Pollard KS., Cell 166(5), 2016
PMID: 27565341
SAR11 bacteria linked to ocean anoxia and nitrogen loss.
Tsementzi D, Wu J, Deutsch S, Nath S, Rodriguez-R LM, Burns AS, Ranjan P, Sarode N, Malmstrom RR, Padilla CC, Stone BK, Bristow LA, Larsen M, Glass JB, Thamdrup B, Woyke T, Konstantinidis KT, Stewart FJ., Nature 536(7615), 2016
PMID: 27487207
Draft genome sequence of Pseudomonas moraviensis strain Devor implicates metabolic versatility and bioremediation potential.
Miller NT, Fuller D, Couger MB, Bagazinski M, Boyne P, Devor RC, Hanafy RA, Budd C, French DP, Hoff WD, Youssef N., Genom Data 9(), 2016
PMID: 27583206
Culture Independent Genomic Comparisons Reveal Environmental Adaptations for Altiarchaeales.
Bird JT, Baker BJ, Probst AJ, Podar M, Lloyd KG., Front Microbiol 7(), 2016
PMID: 27547202
Draft genome sequence of Micrococcus luteus strain O'Kane implicates metabolic versatility and the potential to degrade polyhydroxybutyrates.
Hanafy RA, Couger MB, Baker K, Murphy C, O'Kane SD, Budd C, French DP, Hoff WD, Youssef N., Genom Data 9(), 2016
PMID: 27583205
LCA*: an entropy-based measure for taxonomic assignment within assembled metagenomes.
Hanson NW, Konwar KM, Hallam SJ., Bioinformatics 32(23), 2016
PMID: 27515739
Metagenomic applications in environmental monitoring and bioremediation.
Techtmann SM, Hazen TC., J Ind Microbiol Biotechnol 43(10), 2016
PMID: 27558781
Bipartite graph analyses reveal interdomain LGT involving ultrasmall prokaryotes and their divergent, membrane-related proteins.
Jaffe AL, Corel E, Pathmanathan JS, Lopez P, Bapteste E., Environ Microbiol 18(12), 2016
PMID: 27485833
North-Seeking Magnetotactic Gammaproteobacteria in the Southern Hemisphere.
Leão P, Teixeira LC, Cypriano J, Farina M, Abreu F, Bazylinski DA, Lins U., Appl Environ Microbiol 82(18), 2016
PMID: 27401974
Enrichment of Root Endophytic Bacteria from Populus deltoides and Single-Cell-Genomics Analysis.
Utturkar SM, Cude WN, Robeson MS, Yang ZK, Klingeman DM, Land ML, Allman SL, Lu TY, Brown SD, Schadt CW, Podar M, Doktycz MJ, Pelletier DA., Appl Environ Microbiol 82(18), 2016
PMID: 27422831
Dissecting host-associated communities with DNA barcodes.
Baker CC, Bittleston LS, Sanders JG, Pierce NE., Philos Trans R Soc Lond B Biol Sci 371(1702), 2016
PMID: 27481780
The Atacama Desert: Technical Resources and the Growing Importance of Novel Microbial Diversity.
Bull AT, Asenjo JA, Goodfellow M, Gómez-Silva B., Annu Rev Microbiol 70(), 2016
PMID: 27607552
A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data.
Spatafora JW, Chang Y, Benny GL, Lazarus K, Smith ME, Berbee ML, Bonito G, Corradi N, Grigoriev I, Gryganskyi A, James TY, O'Donnell K, Roberson RW, Taylor TN, Uehling J, Vilgalys R, White MM, Stajich JE., Mycologia 108(5), 2016
PMID: 27738200
Label-free isolation and deposition of single bacterial cells from heterogeneous samples for clonal culturing.
Riba J, Gleichmann T, Zimmermann S, Zengerle R, Koltay P., Sci Rep 6(), 2016
PMID: 27596612
Draft Genome Sequence of the Bactrocera oleae Symbiont "Candidatus Erwinia dacicola".
Blow F, Gioti A, Starns D, Ben-Yosef M, Pasternak Z, Jurkevitch E, Vontas J, Darby AC., Genome Announc 4(5), 2016
PMID: 27634990
Draft genome sequence of Microbacterium oleivorans strain Wellendorf implicates heterotrophic versatility and bioremediation potential.
Avramov AP, Couger MB, Hartley EL, Land C, Wellendorf R, Hanafy RA, Budd C, French DP, Hoff WD, Youssef N., Genom Data 10(), 2016
PMID: 27699150
Draft genome sequence and detailed analysis of Pantoea eucrina strain Russ and implication for opportunistic pathogenesis.
Moghadam F, Couger MB, Russ B, Ramsey R, Hanafy RA, Budd C, French DP, Hoff WD, Youssef N., Genom Data 10(), 2016
PMID: 27699151
The changing view of eukaryogenesis - fossils, cells, lineages and how they all come together.
Dacks JB, Field MC, Buick R, Eme L, Gribaldo S, Roger AJ, Brochier-Armanet C, Devos DP., J Cell Sci 129(20), 2016
PMID: 27672020
Structure, Evolution, and Functions of Bacterial Type III Toxin-Antitoxin Systems.
Goeders N, Chai R, Chen B, Day A, Salmond GP., Toxins (Basel) 8(10), 2016
PMID: 27690100
Single sample resolution of rare microbial dark matter in a marine invertebrate metagenome.
Miller IJ, Weyna TR, Fong SS, Lim-Fong GE, Kwan JC., Sci Rep 6(), 2016
PMID: 27681823
Freshwater bacteria release methane as a byproduct of phosphorus acquisition.
Yao M, Henny C, Maresca JA., Appl Environ Microbiol (), 2016
PMID: 27694233
Bacterial Community Structures in Freshwater Polar Environments of Svalbard.
Ntougias S, Polkowska Ż, Nikolaki S, Dionyssopoulou E, Stathopoulou P, Doudoumis V, Ruman M, Kozak K, Namieśnik J, Tsiamis G., Microbes Environ 31(4), 2016
PMID: 27725345
Picodroplet partitioned whole genome amplification of low biomass samples preserves genomic diversity for metagenomic analysis.
Hammond M, Homa F, Andersson-Svahn H, Ettema TJ, Joensson HN., Microbiome 4(1), 2016
PMID: 27716450
Draft genome sequence of Staphylococcus hominis strain Hudgins isolated from human skin implicates metabolic versatility and several virulence determinants.
Calkins S, Couger MB, Jackson C, Zandler J, Hudgins GC, Hanafy RA, Budd C, French DP, Hoff WD, Youssef N., Genom Data 10(), 2016
PMID: 27766204
Archaea in Natural and Impacted Brazilian Environments.
Rodrigues T, Belmok A, Catão E, Kyaw CM., Archaea 2016(), 2016
PMID: 27829818
The landscape of microbial phenotypic traits and associated genes.
Brbić M, Piškorec M, Vidulin V, Kriško A, Šmuc T, Supek F., Nucleic Acids Res 44(21), 2016
PMID: 27915291
Combined genomic and structural analyses of a cultured magnetotactic bacterium reveals its niche adaptation to a dynamic environment.
Araujo AC, Morillo V, Cypriano J, Teixeira LC, Leão P, Lyra S, Almeida LG, Bazylinski DA, Ribeiro de Vasconcelos AT, Abreu F, Lins U., BMC Genomics 17(suppl 8), 2016
PMID: 27801294
Lack of Overt Genome Reduction in the Bryostatin-Producing Bryozoan Symbiont "Candidatus Endobugula sertula".
Miller IJ, Vanee N, Fong SS, Lim-Fong GE, Kwan JC., Appl Environ Microbiol 82(22), 2016
PMID: 27590822
Shedding light on cell compartmentation in the candidate phylum Poribacteria by high resolution visualisation and transcriptional profiling.
Jahn MT, Markert SM, Ryu T, Ravasi T, Stigloher C, Hentschel U, Moitinho-Silva L., Sci Rep 6(), 2016
PMID: 27796326
[Culturomics: a method to study human gut microbiota].
Lagier JC, Raoult D., Med Sci (Paris) 32(11), 2016
PMID: 28008829
SSUnique: Detecting Sequence Novelty in Microbiome Surveys.
Lynch MD, Neufeld JD., mSystems 1(6), 2016
PMID: 28028549
From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer.
Weimann A, Mooren K, Frank J, Pope PB, Bremges A, McHardy AC., mSystems 1(6), 2016
PMID: 28066816
Culture of previously uncultured members of the human gut microbiota by culturomics.
Lagier JC, Khelaifia S, Alou MT, Ndongo S, Dione N, Hugon P, Caputo A, Cadoret F, Traore SI, Seck EH, Dubourg G, Durand G, Mourembou G, Guilhot E, Togo A, Bellali S, Bachar D, Cassir N, Bittar F, Delerce J, Mailhe M, Ricaboni D, Bilen M, Dangui Nieko NP, Dia Badiane NM, Valles C, Mouelhi D, Diop K, Million M, Musso D, Abrahão J, Azhar EI, Bibi F, Yasir M, Diallo A, Sokhna C, Djossou F, Vitton V, Robert C, Rolain JM, La Scola B, Fournier PE, Levasseur A, Raoult D., Nat Microbiol 1(), 2016
PMID: 27819657
Measurement of bacterial replication rates in microbial communities.
Brown CT, Olm MR, Thomas BC, Banfield JF., Nat Biotechnol 34(12), 2016
PMID: 27819664
Polycyclic Aromatic Hydrocarbon-Induced Changes in Bacterial Community Structure under Anoxic Nitrate Reducing Conditions.
Martirani-Von Abercron SM, Pacheco D, Benito-Santano P, Marín P, Marqués S., Front Microbiol 7(), 2016
PMID: 27877167
Genomic and Transcriptomic Evidence for Carbohydrate Consumption among Microorganisms in a Cold Seep Brine Pool.
Zhang W, Ding W, Yang B, Tian R, Gu S, Luo H, Qian PY., Front Microbiol 7(), 2016
PMID: 27895636
Bacterial Active Community Cycling in Response to Solar Radiation and Their Influence on Nutrient Changes in a High-Altitude Wetland.
Molina V, Hernández K, Dorador C, Eissler Y, Hengst M, Pérez V, Harrod C., Front Microbiol 7(), 2016
PMID: 27909430
Growth of magnetotactic sulfate-reducing bacteria in oxygen concentration gradient medium.
Lefèvre CT, Howse PA, Schmidt ML, Sabaty M, Menguy N, Luther GW, Bazylinski DA., Environ Microbiol Rep 8(6), 2016
PMID: 27701830
A novel open-type biosensor for the in-situ monitoring of biochemical oxygen demand in an aerobic environment.
Yamashita T, Ookawa N, Ishida M, Kanamori H, Sasaki H, Katayose Y, Yokoyama H., Sci Rep 6(), 2016
PMID: 27917947
Towards quantitative viromics for both double-stranded and single-stranded DNA viruses.
Roux S, Solonenko NE, Dang VT, Poulos BT, Schwenck SM, Goldsmith DB, Coleman ML, Breitbart M, Sullivan MB., PeerJ 4(), 2016
PMID: 28003936
A Single-Granule-Level Approach Reveals Ecological Heterogeneity in an Upflow Anaerobic Sludge Blanket Reactor.
Kuroda K, Nobu MK, Mei R, Narihiro T, Bocher BT, Yamaguchi T, Liu WT., PLoS One 11(12), 2016
PMID: 27936088
Genome sequence and overview of Oligoflexus tunisiensis Shr3T in the eighth class Oligoflexia of the phylum Proteobacteria.
Nakai R, Fujisawa T, Nakamura Y, Baba T, Nishijima M, Karray F, Sayadi S, Isoda H, Naganuma T, Niki H., Stand Genomic Sci 11(), 2016
PMID: 27999625
Insights into the metabolism, lifestyle and putative evolutionary history of the novel archaeal phylum 'Diapherotrites'.
Youssef NH, Rinke C, Stepanauskas R, Farag I, Woyke T, Elshahed MS., ISME J 9(2), 2015
PMID: 25083931
Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea.
Kamanda Ngugi D, Blom J, Alam I, Rashid M, Ba-Alawi W, Zhang G, Hikmawan T, Guan Y, Antunes A, Siam R, El Dorry H, Bajic V, Stingl U., ISME J 9(2), 2015
PMID: 25105904
Magnetic nanoparticle-mediated isolation of functional bacteria in a complex microbial community.
Zhang D, Berry JP, Zhu D, Wang Y, Chen Y, Jiang B, Huang S, Langford H, Li G, Davison PA, Xu J, Aries E, Huang WE., ISME J 9(3), 2015
PMID: 25191996
The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification.
Reddy TB, Thomas AD, Stamatis D, Bertsch J, Isbandi M, Jansson J, Mallajosyula J, Pagani I, Lobos EA, Kyrpides NC., Nucleic Acids Res 43(database issue), 2015
PMID: 25348402
Assessing the global phylum level diversity within the bacterial domain: A review.
Youssef NH, Couger MB, McCully AL, Criado AE, Elshahed MS., J Adv Res 6(3), 2015
PMID: 26257925
Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics.
Hua ZS, Han YJ, Chen LX, Liu J, Hu M, Li SJ, Kuang JL, Chain PS, Huang LN, Shu WS., ISME J 9(6), 2015
PMID: 25361395
Microbial community composition and diversity in Caspian Sea sediments.
Mahmoudi N, Robeson MS, Castro HF, Fortney JL, Techtmann SM, Joyner DC, Paradis CJ, Pfiffner SM, Hazen TC., FEMS Microbiol Ecol 91(1), 2015
PMID: 25764536
The eukaryotic ancestor had a complex ubiquitin signaling system of archaeal origin.
Grau-Bové X, Sebé-Pedrós A, Ruiz-Trillo I., Mol Biol Evol 32(3), 2015
PMID: 25525215
Rooting the domain archaea by phylogenomic analysis supports the foundation of the new kingdom Proteoarchaeota.
Petitjean C, Deschamps P, López-García P, Moreira D., Genome Biol Evol 7(1), 2015
PMID: 25527841
Microbial taxonomy in the post-genomic era: rebuilding from scratch?
Thompson CC, Amaral GR, Campeão M, Edwards RA, Polz MF, Dutilh BE, Ussery DW, Sawabe T, Swings J, Thompson FL., Arch Microbiol 197(3), 2015
PMID: 25533848
Current and past strategies for bacterial culture in clinical microbiology.
Lagier JC, Edouard S, Pagnier I, Mediannikov O, Drancourt M, Raoult D., Clin Microbiol Rev 28(1), 2015
PMID: 25567228
The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota.
Lagier JC, Hugon P, Khelaifia S, Fournier PE, La Scola B, Raoult D., Clin Microbiol Rev 28(1), 2015
PMID: 25567229
Single cell biotechnology to shed a light on biological 'dark matter' in nature.
Huang WE, Song Y, Xu J., Microb Biotechnol 8(1), 2015
PMID: 25627841
Expanding the World of Marine Bacterial and Archaeal Clades.
Yilmaz P, Yarza P, Rapp JZ, Glöckner FO., Front Microbiol 6(), 2015
PMID: 26779174
Antibiotics: An irresistible newcomer.
Wright G., Nature 517(7535), 2015
PMID: 25561172
Where next for microbiome research?
Waldor MK, Tyson G, Borenstein E, Ochman H, Moeller A, Finlay BB, Kong HH, Gordon JI, Nelson KE, Dabbagh K, Smith H., PLoS Biol 13(1), 2015
PMID: 25602283
Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor.
Nobu MK, Narihiro T, Rinke C, Kamagata Y, Tringe SG, Woyke T, Liu WT., ISME J 9(8), 2015
PMID: 25615435
High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats.
Zhou J, He Z, Yang Y, Deng Y, Tringe SG, Alvarez-Cohen L., MBio 6(1), 2015
PMID: 25626903
The effects of variable sample biomass on comparative metagenomics.
Chafee M, Maignien L, Simmons SL., Environ Microbiol 17(7), 2015
PMID: 25329041
Microbes don't play solitaire: how cooperation trumps isolation in the microbial world.
Hallam SJ, McCutcheon JP., Environ Microbiol Rep 7(1), 2015
PMID: 25721597
Re-defining microbial diversity from its single-celled building blocks.
Stepanauskas R., Environ Microbiol Rep 7(1), 2015
PMID: 25721601
Extending the conserved phylogenetic core of archaea disentangles the evolution of the third domain of life.
Petitjean C, Deschamps P, López-García P, Moreira D, Brochier-Armanet C., Mol Biol Evol 32(5), 2015
PMID: 25660375
Accurate, multi-kb reads resolve complex populations and detect rare microorganisms.
Sharon I, Kertesz M, Hug LA, Pushkarev D, Blauwkamp TA, Castelle CJ, Amirebrahimi M, Thomas BC, Burstein D, Tringe SG, Williams KH, Banfield JF., Genome Res 25(4), 2015
PMID: 25665577
Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling.
Castelle CJ, Wrighton KC, Thomas BC, Hug LA, Brown CT, Wilkins MJ, Frischkorn KR, Tringe SG, Singh A, Markillie LM, Taylor RC, Williams KH, Banfield JF., Curr Biol 25(6), 2015
PMID: 25702576
Microbial diversity: a bonanza of phyla.
Eme L, Doolittle WF., Curr Biol 25(6), 2015
PMID: 25784040
Ecology and exploration of the rare biosphere.
Lynch MD, Neufeld JD., Nat Rev Microbiol 13(4), 2015
PMID: 25730701
Metagenome of a microbial community inhabiting a metal-rich tropical stream sediment.
Costa PS, Reis MP, Ávila MP, Leite LR, de Araújo FM, Salim AC, Oliveira G, Barbosa F, Chartone-Souza E, Nascimento AM., PLoS One 10(3), 2015
PMID: 25742617
Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount.
Field EK, Sczyrba A, Lyman AE, Harris CC, Woyke T, Stepanauskas R, Emerson D., ISME J 9(4), 2015
PMID: 25303714
Inter-phylum HGT has shaped the metabolism of many mesophilic and anaerobic bacteria.
Caro-Quintero A, Konstantinidis KT., ISME J 9(4), 2015
PMID: 25314320
Targeted diversity generation by intraterrestrial archaea and archaeal viruses.
Paul BG, Bagby SC, Czornyj E, Arambula D, Handa S, Sczyrba A, Ghosh P, Miller JF, Valentine DL., Nat Commun 6(), 2015
PMID: 25798780
The unique chemistry of Eastern Mediterranean water masses selects for distinct microbial communities by depth.
Techtmann SM, Fortney JL, Ayers KA, Joyner DC, Linley TD, Pfiffner SM, Hazen TC., PLoS One 10(3), 2015
PMID: 25807542
Structure, mineralogy, and microbial diversity of geothermal spring microbialites associated with a deep oil drilling in Romania.
Coman C, Chiriac CM, Robeson MS, Ionescu C, Dragos N, Barbu-Tudoran L, Andrei AŞ, Banciu HL, Sicora C, Podar M., Front Microbiol 6(), 2015
PMID: 25870594
Large-scale contamination of microbial isolate genomes by Illumina PhiX control.
Mukherjee S, Huntemann M, Ivanova N, Kyrpides NC, Pati A., Stand Genomic Sci 10(), 2015
PMID: 26203331
The changing landscape of microbial biodiversity exploration and its implications for systematics.
Hedlund BP, Dodsworth JA, Staley JT., Syst Appl Microbiol 38(4), 2015
PMID: 25921438
Single-cell genomics of a rare environmental alphaproteobacterium provides unique insights into Rickettsiaceae evolution.
Martijn J, Schulz F, Zaremba-Niedzwiedzka K, Viklund J, Stepanauskas R, Andersson SG, Horn M, Guy L, Ettema TJ., ISME J 9(11), 2015
PMID: 25848874
Wiretapping into microbial interactions by single cell genomics.
Stepanauskas R., Front Microbiol 6(), 2015
PMID: 25904902
Combining genomic sequencing methods to explore viral diversity and reveal potential virus-host interactions.
Chow CE, Winget DM, White RA, Hallam SJ, Suttle CA., Front Microbiol 6(), 2015
PMID: 25914678
Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystem.
Andrade K, Logemann J, Heidelberg KB, Emerson JB, Comolli LR, Hug LA, Probst AJ, Keillar A, Thomas BC, Miller CS, Allen EE, Moreau JW, Brocks JJ, Banfield JF., ISME J 9(12), 2015
PMID: 25918833
Contrasting taxonomic stratification of microbial communities in two hypersaline meromictic lakes.
Andrei AŞ, Robeson MS, Baricz A, Coman C, Muntean V, Ionescu A, Etiope G, Alexe M, Sicora CI, Podar M, Banciu HL., ISME J 9(12), 2015
PMID: 25932617
Stable-Isotope Probing Identifies Uncultured Planctomycetes as Primary Degraders of a Complex Heteropolysaccharide in Soil.
Wang X, Sharp CE, Jones GM, Grasby SE, Brady AL, Dunfield PF., Appl Environ Microbiol 81(14), 2015
PMID: 25934620
Advances and applications of single-cell sequencing technologies.
Wang Y, Navin NE., Mol Cell 58(4), 2015
PMID: 26000845
Marine biology. Uncovering hidden worlds of ocean biodiversity.
Armbrust EV, Palumbi SR., Science 348(6237), 2015
PMID: 25999494
The dormant blood microbiome in chronic, inflammatory diseases.
Potgieter M, Bester J, Kell DB, Pretorius E., FEMS Microbiol Rev 39(4), 2015
PMID: 25940667
Classification and identification of pigmented cocci bacteria relevant to the soil environment via Raman spectroscopy.
Kumar V, Kampe B, Rösch P, Popp J., Environ Sci Pollut Res Int 22(24), 2015
PMID: 25940486
Complex archaea that bridge the gap between prokaryotes and eukaryotes.
Spang A, Saw JH, Jørgensen SL, Zaremba-Niedzwiedzka K, Martijn J, Lind AE, van Eijk R, Schleper C, Guy L, Ettema TJG., Nature 521(7551), 2015
PMID: 25945739
The two-domain tree of life is linked to a new root for the Archaea.
Raymann K, Brochier-Armanet C, Gribaldo S., Proc Natl Acad Sci U S A 112(21), 2015
PMID: 25964353
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW., Genome Res 25(7), 2015
PMID: 25977477
Acetogenesis from H2 plus CO2 and nitrogen fixation by an endosymbiotic spirochete of a termite-gut cellulolytic protist.
Ohkuma M, Noda S, Hattori S, Iida T, Yuki M, Starns D, Inoue J, Darby AC, Hongoh Y., Proc Natl Acad Sci U S A 112(33), 2015
PMID: 25979941
Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains.
Whitman WB, Woyke T, Klenk HP, Zhou Y, Lilburn TG, Beck BJ, De Vos P, Vandamme P, Eisen JA, Garrity G, Hugenholtz P, Kyrpides NC., Stand Genomic Sci 10(), 2015
PMID: 26203337
Synergistic function of four novel thermostable glycoside hydrolases from a long-term enriched thermophilic methanogenic digester.
Wang M, Lai GL, Nie Y, Geng S, Liu L, Zhu B, Shi Z, Wu XL., Front Microbiol 6(), 2015
PMID: 26052323
New perspectives on microbial community distortion after whole-genome amplification.
Probst AJ, Weinmaier T, DeSantis TZ, Santo Domingo JW, Ashbolt N., PLoS One 10(5), 2015
PMID: 26010362
VirSorter: mining viral signal from microbial genomic data.
Roux S, Enault F, Hurwitz BL, Sullivan MB., PeerJ 3(), 2015
PMID: 26038737
Origin and evolution of lysyl oxidases.
Grau-Bové X, Ruiz-Trillo I, Rodriguez-Pascual F., Sci Rep 5(), 2015
PMID: 26024311
In Silico Analysis of the Metabolic Potential and Niche Specialization of Candidate Phylum "Latescibacteria" (WS3).
Youssef NH, Farag IF, Rinke C, Hallam SJ, Woyke T, Elshahed MS., PLoS One 10(6), 2015
PMID: 26039074
New aminopeptidase from "microbial dark matter" archaeon.
Michalska K, Steen AD, Chhor G, Endres M, Webber AT, Bird J, Lloyd KG, Joachimiak A., FASEB J 29(9), 2015
PMID: 26062601
Complete Genome Sequence of the Bacterium Aalborg_AAW-1, Representing a Novel Family within the Candidate Phylum SR1.
Dueholm MS, Albertsen M, Stokholm-Bjerregaard M, McIlroy SJ, Karst SM, Nielsen PH., Genome Announc 3(3), 2015
PMID: 26067967
Bacterial gene import and mesophilic adaptation in archaea.
López-García P, Zivanovic Y, Deschamps P, Moreira D., Nat Rev Microbiol 13(7), 2015
PMID: 26075362
Unusual biology across a group comprising more than 15% of domain Bacteria.
Brown CT, Hug LA, Thomas BC, Sharon I, Castelle CJ, Singh A, Wilkins MJ, Wrighton KC, Williams KH, Banfield JF., Nature 523(7559), 2015
PMID: 26083755
A primase subunit essential for efficient primer synthesis by an archaeal eukaryotic-type primase.
Liu B, Ouyang S, Makarova KS, Xia Q, Zhu Y, Li Z, Guo L, Koonin EV, Liu ZJ, Huang L., Nat Commun 6(), 2015
PMID: 26095544
Uncultivated thermophiles: current status and spotlight on 'Aigarchaeota'.
Hedlund BP, Murugapiran SK, Alba TW, Levy A, Dodsworth JA, Goertz GB, Ivanova N, Woyke T., Curr Opin Microbiol 25(), 2015
PMID: 26113243
Faustovirus, an asfarvirus-related new lineage of giant viruses infecting amoebae.
Reteno DG, Benamar S, Khalil JB, Andreani J, Armstrong N, Klose T, Rossmann M, Colson P, Raoult D, La Scola B., J Virol 89(13), 2015
PMID: 25878099
Coupling of diversification and pH adaptation during the evolution of terrestrial Thaumarchaeota.
Gubry-Rangin C, Kratsch C, Williams TA, McHardy AC, Embley TM, Prosser JI, Macqueen DJ., Proc Natl Acad Sci U S A 112(30), 2015
PMID: 26170282
IMG-ABC: A Knowledge Base To Fuel Discovery of Biosynthetic Gene Clusters and Novel Secondary Metabolites.
Hadjithomas M, Chen IM, Chu K, Ratner A, Palaniappan K, Szeto E, Huang J, Reddy TB, Cimermančič P, Fischbach MA, Ivanova NN, Markowitz VM, Kyrpides NC, Pati A., MBio 6(4), 2015
PMID: 26173699
Functional Classification of Uncultured "Candidatus Caldiarchaeum subterraneum" Using the Maple System.
Takami H, Arai W, Takemoto K, Uchiyama I, Taniguchi T., PLoS One 10(7), 2015
PMID: 26196861
The universal tree of life: an update.
Forterre P., Front Microbiol 6(), 2015
PMID: 26257711
Complex coupled metabolic and prokaryotic community responses to increasing temperatures in anaerobic marine sediments: critical temperatures and substrate changes.
Roussel EG, Cragg BA, Webster G, Sass H, Tang X, Williams AS, Gorra R, Weightman AJ, Parkes RJ., FEMS Microbiol Ecol 91(8), 2015
PMID: 26207045
Biocatalysts for biomass deconstruction from environmental genomics.
Armstrong Z, Mewis K, Strachan C, Hallam SJ., Curr Opin Chem Biol 29(), 2015
PMID: 26231123
Toward the identification of methanogenic archaeal groups as targets of methane mitigation in livestock animalsr.
St-Pierre B, Cersosimo LM, Ishaq SL, Wright AD., Front Microbiol 6(), 2015
PMID: 26284054
Rational and combinatorial tailoring of bioactive cyclic dipeptides.
Giessen TW, Marahiel MA., Front Microbiol 6(), 2015
PMID: 26284060
Dominant ectosymbiotic bacteria of cellulolytic protists in the termite gut also have the potential to digest lignocellulose.
Yuki M, Kuwahara H, Shintani M, Izawa K, Sato T, Starns D, Hongoh Y, Ohkuma M., Environ Microbiol 17(12), 2015
PMID: 26079531
Abundant Atribacteria in deep marine sediment from the Adélie Basin, Antarctica.
Carr SA, Orcutt BN, Mandernack KW, Spear JR., Front Microbiol 6(), 2015
PMID: 26379647
Computational approaches to natural product discovery.
Medema MH, Fischbach MA., Nat Chem Biol 11(9), 2015
PMID: 26284671
Changing ideas about eukaryotic origins.
Williams TA, Embley TM., Philos Trans R Soc Lond B Biol Sci 370(1678), 2015
PMID: 26323752
Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes.
Saw JH, Spang A, Zaremba-Niedzwiedzka K, Juzokaite L, Dodsworth JA, Murugapiran SK, Colman DR, Takacs-Vesbach C, Hedlund BP, Guy L, Ettema TJ., Philos Trans R Soc Lond B Biol Sci 370(1678), 2015
PMID: 26323759
New substitution models for rooting phylogenetic trees.
Williams TA, Heaps SE, Cherlin S, Nye TM, Boys RJ, Embley TM., Philos Trans R Soc Lond B Biol Sci 370(1678), 2015
PMID: 26323766
Metaproteomics of aquatic microbial communities in a deep and stratified estuary.
Colatriano D, Ramachandran A, Yergeau E, Maranger R, Gélinas Y, Walsh DA., Proteomics 15(20), 2015
PMID: 26223443
Monodisperse Picoliter Droplets for Low-Bias and Contamination-Free Reactions in Single-Cell Whole Genome Amplification.
Nishikawa Y, Hosokawa M, Maruyama T, Yamagishi K, Mori T, Takeyama H., PLoS One 10(9), 2015
PMID: 26389587
Advancing understanding of microbial bioenergy conversion processes by activity-based protein profiling.
Liu Y, Fredrickson JK, Sadler NC, Nandhikonda P, Smith RD, Wright AT., Biotechnol Biofuels 8(), 2015
PMID: 26413155
MICROBIOLOGY. Beyond known methanogens.
Lloyd K., Science 350(6259), 2015
PMID: 26494746
Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics.
Evans PN, Parks DH, Chadwick GL, Robbins SJ, Orphan VJ, Golding SD, Tyson GW., Science 350(6259), 2015
PMID: 26494757
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The candidate phylum Poribacteria by single-cell genomics: new insights into phylogeny, cell-compartmentation, eukaryote-like repeat proteins, and other genomic features.
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Adding genomic 'foliage' to the tree of life.
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Dynamics in the microbial cytome-single cell analytics in natural systems.
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Capturing and cultivating single bacterial cells in gel microdroplets to obtain near-complete genomes.
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Archaeal "dark matter" and the origin of eukaryotes.
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Intestinal microbiome and digoxin inactivation: meal plan for digoxin users?
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Single cell genomic study of Dehalococcoidetes species from deep-sea sediments of the Peruvian Margin.
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Ecological understanding of root-infecting fungi using trait-based approaches.
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Phylogeny, culturing, and metagenomics of the human gut microbiota.
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Gut microbiome of the Hadza hunter-gatherers.
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The hybrid nature of the Eukaryota and a consilient view of life on Earth.
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Mutational analysis of the (p)ppGpp synthetase activity of the Rel enzyme of Mycobacterium tuberculosis.
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Nitrososphaera viennensis gen. nov., sp. nov., an aerobic and mesophilic, ammonia-oxidizing archaeon from soil and a member of the archaeal phylum Thaumarchaeota.
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The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing.
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Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters.
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Unveiling viral-host interactions within the 'microbial dark matter'.
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ExaBayes: massively parallel bayesian tree inference for the whole-genome era.
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Antibiotic genes spread far and wide.
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Evolutionary ecology of the marine Roseobacter clade.
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Planning considerations related to the organic contamination of Martian samples and implications for the Mars 2020 Rover.
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Metagenomic ventures into outer sequence space.
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Emerging methods to study bacteriophage infection at the single-cell level.
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Being Aquifex aeolicus: Untangling a hyperthermophile's checkered past.
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Sequencing the human microbiome in health and disease.
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