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For: Laczny CC, Sternal T, Plugaru V, Gawron P, Atashpendar A, Margossian HH, Coronado S, der Maaten LV, Vlassis N, Wilmes P. VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data. Microbiome 2015;3:1. [PMID: 25621171 PMCID: PMC4305225 DOI: 10.1186/s40168-014-0066-1] [Citation(s) in RCA: 198] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 12/18/2014] [Indexed: 05/20/2023]
Number Cited by Other Article(s)
151
Spatafora JW, Aime MC, Grigoriev IV, Martin F, Stajich JE, Blackwell M. The Fungal Tree of Life: from Molecular Systematics to Genome-Scale Phylogenies. Microbiol Spectr 2017;5:10.1128/microbiolspec.funk-0053-2016. [PMID: 28917057 PMCID: PMC11687545 DOI: 10.1128/microbiolspec.funk-0053-2016] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Indexed: 12/23/2022]  Open
152
Emerson JB, Adams RI, Román CMB, Brooks B, Coil DA, Dahlhausen K, Ganz HH, Hartmann EM, Hsu T, Justice NB, Paulino-Lima IG, Luongo JC, Lymperopoulou DS, Gomez-Silvan C, Rothschild-Mancinelli B, Balk M, Huttenhower C, Nocker A, Vaishampayan P, Rothschild LJ. Schrödinger's microbes: Tools for distinguishing the living from the dead in microbial ecosystems. MICROBIOME 2017;5:86. [PMID: 28810907 PMCID: PMC5558654 DOI: 10.1186/s40168-017-0285-3] [Citation(s) in RCA: 265] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 06/05/2017] [Indexed: 05/16/2023]
153
Yang Y, Higgins SA, Yan J, Şimşir B, Chourey K, Iyer R, Hettich RL, Baldwin B, Ogles DM, Löffler FE. Grape pomace compost harbors organohalide-respiring Dehalogenimonas species with novel reductive dehalogenase genes. ISME JOURNAL 2017;11:2767-2780. [PMID: 28809851 DOI: 10.1038/ismej.2017.127] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 06/12/2017] [Accepted: 06/16/2017] [Indexed: 12/15/2022]
154
Feathermoss and epiphytic Nostoc cooperate differently: expanding the spectrum of plant-cyanobacteria symbiosis. ISME JOURNAL 2017;11:2821-2833. [PMID: 28800136 PMCID: PMC5702739 DOI: 10.1038/ismej.2017.134] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 06/20/2017] [Accepted: 07/07/2017] [Indexed: 11/09/2022]
155
Integrated meta-omic analyses of the gastrointestinal tract microbiome in patients undergoing allogeneic hematopoietic stem cell transplantation. Transl Res 2017;186:79-94.e1. [PMID: 28686852 DOI: 10.1016/j.trsl.2017.06.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 05/17/2017] [Accepted: 06/12/2017] [Indexed: 02/06/2023]
156
Laczny CC, Kiefer C, Galata V, Fehlmann T, Backes C, Keller A. BusyBee Web: metagenomic data analysis by bootstrapped supervised binning and annotation. Nucleic Acids Res 2017;45:W171-W179. [PMID: 28472498 PMCID: PMC5570254 DOI: 10.1093/nar/gkx348] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/11/2017] [Accepted: 04/21/2017] [Indexed: 12/20/2022]  Open
157
Interpreting Microbial Biosynthesis in the Genomic Age: Biological and Practical Considerations. Mar Drugs 2017;15:md15060165. [PMID: 28587290 PMCID: PMC5484115 DOI: 10.3390/md15060165] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 05/22/2017] [Accepted: 05/31/2017] [Indexed: 02/06/2023]  Open
158
Alvarenga DO, Fiore MF, Varani AM. A Metagenomic Approach to Cyanobacterial Genomics. Front Microbiol 2017;8:809. [PMID: 28536564 PMCID: PMC5422444 DOI: 10.3389/fmicb.2017.00809] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 04/20/2017] [Indexed: 01/08/2023]  Open
159
Broeksema B, Calusinska M, McGee F, Winter K, Bongiovanni F, Goux X, Wilmes P, Delfosse P, Ghoniem M. ICoVeR - an interactive visualization tool for verification and refinement of metagenomic bins. BMC Bioinformatics 2017;18:233. [PMID: 28464793 PMCID: PMC5414344 DOI: 10.1186/s12859-017-1653-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 04/26/2017] [Indexed: 12/20/2022]  Open
160
Volokhov DV, Hwang J, Chizhikov VE, Danaceau H, Gottdenker NL. Prevalence, Genotype Richness, and Coinfection Patterns of Hemotropic Mycoplasmas in Raccoons (Procyon lotor) on Environmentally Protected and Urbanized Barrier Islands. Appl Environ Microbiol 2017;83:e00211-17. [PMID: 28258139 PMCID: PMC5394313 DOI: 10.1128/aem.00211-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 02/22/2017] [Indexed: 11/20/2022]  Open
161
Danovaro R, Canals M, Tangherlini M, Dell'Anno A, Gambi C, Lastras G, Amblas D, Sanchez-Vidal A, Frigola J, Calafat AM, Pedrosa-Pàmies R, Rivera J, Rayo X, Corinaldesi C. A submarine volcanic eruption leads to a novel microbial habitat. Nat Ecol Evol 2017;1:144. [PMID: 28812643 DOI: 10.1038/s41559-017-0144] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 03/20/2017] [Indexed: 11/09/2022]
162
Ludington WB, Seher TD, Applegate O, Li X, Kliegman JI, Langelier C, Atwill ER, Harter T, DeRisi JL. Assessing biosynthetic potential of agricultural groundwater through metagenomic sequencing: A diverse anammox community dominates nitrate-rich groundwater. PLoS One 2017;12:e0174930. [PMID: 28384184 PMCID: PMC5383146 DOI: 10.1371/journal.pone.0174930] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 03/18/2017] [Indexed: 12/12/2022]  Open
163
Taubert M, Grob C, Howat AM, Burns OJ, Pratscher J, Jehmlich N, von Bergen M, Richnow HH, Chen Y, Murrell JC. Methylamine as a nitrogen source for microorganisms from a coastal marine environment. Environ Microbiol 2017;19:2246-2257. [PMID: 28244196 DOI: 10.1111/1462-2920.13709] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/13/2017] [Accepted: 02/19/2017] [Indexed: 11/27/2022]
164
Draft Genome Sequence of Pseudomonas sp. BDAL1 Reconstructed from a Bakken Shale Hydraulic Fracturing-Produced Water Storage Tank Metagenome. GENOME ANNOUNCEMENTS 2017;5:5/11/e00033-17. [PMID: 28302780 PMCID: PMC5356057 DOI: 10.1128/genomea.00033-17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
165
Draft Genome Sequence of "Candidatus Synechococcus spongiarum" m9, Binned from a Metagenome of South China Sea Sponge Theonella swinhoei. GENOME ANNOUNCEMENTS 2017;5:5/6/e01307-16. [PMID: 28183779 PMCID: PMC5331489 DOI: 10.1128/genomea.01307-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
166
Washburne AD, Silverman JD, Leff JW, Bennett DJ, Darcy JL, Mukherjee S, Fierer N, David LA. Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets. PeerJ 2017;5:e2969. [PMID: 28289558 PMCID: PMC5345826 DOI: 10.7717/peerj.2969] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/09/2017] [Indexed: 01/06/2023]  Open
167
Huang AD, Luo C, Pena-Gonzalez A, Weigand MR, Tarr CL, Konstantinidis KT. Metagenomics of Two Severe Foodborne Outbreaks Provides Diagnostic Signatures and Signs of Coinfection Not Attainable by Traditional Methods. Appl Environ Microbiol 2017;83:e02577-16. [PMID: 27881416 PMCID: PMC5244306 DOI: 10.1128/aem.02577-16] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 11/15/2016] [Indexed: 12/17/2022]  Open
168
Lagkouvardos I, Fischer S, Kumar N, Clavel T. Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons. PeerJ 2017;5:e2836. [PMID: 28097056 PMCID: PMC5234437 DOI: 10.7717/peerj.2836] [Citation(s) in RCA: 260] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 11/28/2016] [Indexed: 01/01/2023]  Open
169
Wilkins D, Leung MHY, Lee PKH. Microbiota fingerprints lose individually identifying features over time. MICROBIOME 2017;5:1. [PMID: 28086968 PMCID: PMC5234115 DOI: 10.1186/s40168-016-0209-7] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 11/22/2016] [Indexed: 05/19/2023]
170
Morrow KM, Bromhall K, Motti CA, Munn CB, Bourne DG. Allelochemicals Produced by Brown Macroalgae of the Lobophora Genus Are Active against Coral Larvae and Associated Bacteria, Supporting Pathogenic Shifts to Vibrio Dominance. Appl Environ Microbiol 2017;83:e02391-16. [PMID: 27795310 PMCID: PMC5165121 DOI: 10.1128/aem.02391-16] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 10/07/2016] [Indexed: 11/20/2022]  Open
171
Umu ÖCO, Rudi K, Diep DB. Modulation of the gut microbiota by prebiotic fibres and bacteriocins. MICROBIAL ECOLOGY IN HEALTH AND DISEASE 2017;28:1348886. [PMID: 28959178 PMCID: PMC5614387 DOI: 10.1080/16512235.2017.1348886] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 06/24/2017] [Indexed: 12/21/2022]
172
Metagenome-Assembled Genome Sequence of Pseudomonas stutzeri Strain CO183 Isolated from a Coalbed Methane Well. GENOME ANNOUNCEMENTS 2016;4:4/6/e01237-16. [PMID: 27811112 PMCID: PMC5095482 DOI: 10.1128/genomea.01237-16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
173
Narayanasamy S, Jarosz Y, Muller EEL, Heintz-Buschart A, Herold M, Kaysen A, Laczny CC, Pinel N, May P, Wilmes P. IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses. Genome Biol 2016;17:260. [PMID: 27986083 PMCID: PMC5159968 DOI: 10.1186/s13059-016-1116-8] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 11/22/2016] [Indexed: 01/28/2023]  Open
174
Draft Genome Sequence of Antarctic Methanogen Enriched from Dry Valley Permafrost. GENOME ANNOUNCEMENTS 2016;4:4/6/e01362-16. [PMID: 27932654 PMCID: PMC5146446 DOI: 10.1128/genomea.01362-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
175
Sedlar K, Kupkova K, Provaznik I. Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics. Comput Struct Biotechnol J 2016;15:48-55. [PMID: 27980708 PMCID: PMC5148923 DOI: 10.1016/j.csbj.2016.11.005] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 11/24/2016] [Accepted: 11/26/2016] [Indexed: 12/11/2022]  Open
176
Nitrogen fixation in a chemoautotrophic lucinid symbiosis. Nat Microbiol 2016;2:16193. [PMID: 27775698 DOI: 10.1038/nmicrobiol.2016.193] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 09/07/2016] [Indexed: 02/03/2023]
177
Mikaelyan A, Meuser K, Brune A. Microenvironmental heterogeneity of gut compartments drives bacterial community structure in wood- and humus-feeding higher termites. FEMS Microbiol Ecol 2016;93:fiw210. [PMID: 27798065 DOI: 10.1093/femsec/fiw210] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2016] [Indexed: 11/13/2022]  Open
178
Reconstruction of a Nearly Complete Pseudomonas Draft Genome Sequence from a Coalbed Methane-Produced Water Metagenome. GENOME ANNOUNCEMENTS 2016;4:4/5/e01024-16. [PMID: 27795237 PMCID: PMC5054310 DOI: 10.1128/genomea.01024-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
179
Vanwonterghem I, Evans PN, Parks DH, Jensen PD, Woodcroft BJ, Hugenholtz P, Tyson GW. Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota. Nat Microbiol 2016;1:16170. [PMID: 27694807 DOI: 10.1038/nmicrobiol.2016.170] [Citation(s) in RCA: 289] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 08/12/2016] [Indexed: 11/09/2022]
180
Single sample resolution of rare microbial dark matter in a marine invertebrate metagenome. Sci Rep 2016;6:34362. [PMID: 27681823 PMCID: PMC5041132 DOI: 10.1038/srep34362] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 09/13/2016] [Indexed: 12/31/2022]  Open
181
Draft Genome Sequence of Methanohalophilus mahii Strain DAL1 Reconstructed from a Hydraulic Fracturing-Produced Water Metagenome. GENOME ANNOUNCEMENTS 2016;4:4/5/e00899-16. [PMID: 27587817 PMCID: PMC5009974 DOI: 10.1128/genomea.00899-16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
182
Genome Evolution and Nitrogen Fixation in Bacterial Ectosymbionts of a Protist Inhabiting Wood-Feeding Cockroaches. Appl Environ Microbiol 2016;82:4682-4695. [PMID: 27235430 DOI: 10.1128/aem.00611-16] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/18/2016] [Indexed: 12/30/2022]  Open
183
McKenney ES, Kendall MM. Microbiota and pathogen 'pas de deux': setting up and breaking down barriers to intestinal infection. Pathog Dis 2016;74:ftw051. [PMID: 27252177 PMCID: PMC5985477 DOI: 10.1093/femspd/ftw051] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 02/04/2016] [Accepted: 05/24/2016] [Indexed: 02/07/2023]  Open
184
Lymperopoulou DS, Adams RI, Lindow SE. Contribution of Vegetation to the Microbial Composition of Nearby Outdoor Air. Appl Environ Microbiol 2016;82:3822-33. [PMID: 27107117 PMCID: PMC4907200 DOI: 10.1128/aem.00610-16] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 04/12/2016] [Indexed: 11/20/2022]  Open
185
Moissl-Eichinger C, Cockell C, Rettberg P. Venturing into new realms? Microorganisms in space. FEMS Microbiol Rev 2016;40:722-37. [PMID: 27354346 DOI: 10.1093/femsre/fuw015] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2016] [Indexed: 12/15/2022]  Open
186
Laczny CC, Muller EEL, Heintz-Buschart A, Herold M, Lebrun LA, Hogan A, May P, de Beaufort C, Wilmes P. Identification, Recovery, and Refinement of Hitherto Undescribed Population-Level Genomes from the Human Gastrointestinal Tract. Front Microbiol 2016;7:884. [PMID: 27445992 PMCID: PMC4914512 DOI: 10.3389/fmicb.2016.00884] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 05/25/2016] [Indexed: 12/05/2022]  Open
187
Laffy PW, Wood-Charlson EM, Turaev D, Weynberg KD, Botté ES, van Oppen MJH, Webster NS, Rattei T. HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts. Front Microbiol 2016;7:822. [PMID: 27375564 PMCID: PMC4899465 DOI: 10.3389/fmicb.2016.00822] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 05/16/2016] [Indexed: 11/13/2022]  Open
188
Mayer T, Blachowicz A, Probst AJ, Vaishampayan P, Checinska A, Swarmer T, de Leon P, Venkateswaran K. Microbial succession in an inflated lunar/Mars analog habitat during a 30-day human occupation. MICROBIOME 2016;4:22. [PMID: 27250991 PMCID: PMC4890489 DOI: 10.1186/s40168-016-0167-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 04/18/2016] [Indexed: 05/04/2023]
189
Russell JA, León-Zayas R, Wrighton K, Biddle JF. Deep Subsurface Life from North Pond: Enrichment, Isolation, Characterization and Genomes of Heterotrophic Bacteria. Front Microbiol 2016;7:678. [PMID: 27242705 PMCID: PMC4861733 DOI: 10.3389/fmicb.2016.00678] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 04/26/2016] [Indexed: 12/04/2022]  Open
190
Wasmund K, Cooper M, Schreiber L, Lloyd KG, Baker BJ, Petersen DG, Jørgensen BB, Stepanauskas R, Reinhardt R, Schramm A, Loy A, Adrian L. Single-Cell Genome and Group-Specific dsrAB Sequencing Implicate Marine Members of the Class Dehalococcoidia (Phylum Chloroflexi) in Sulfur Cycling. mBio 2016;7:e00266-16. [PMID: 27143384 PMCID: PMC4959651 DOI: 10.1128/mbio.00266-16] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 04/05/2016] [Indexed: 11/20/2022]  Open
191
Metagenomic analysis of rapid gravity sand filter microbial communities suggests novel physiology of Nitrospira spp. ISME JOURNAL 2016;10:2569-2581. [PMID: 27128989 DOI: 10.1038/ismej.2016.63] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 02/29/2016] [Accepted: 03/19/2016] [Indexed: 01/30/2023]
192
Lin HH, Liao YC. Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes. Sci Rep 2016;6:24175. [PMID: 27067514 PMCID: PMC4828714 DOI: 10.1038/srep24175] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 03/22/2016] [Indexed: 12/18/2022]  Open
193
Stedtfeld RD, Williams MR, Fakher U, Johnson TA, Stedtfeld TM, Wang F, Khalife WT, Hughes M, Etchebarne BE, Tiedje JM, Hashsham SA. Antimicrobial resistance dashboard application for mapping environmental occurrence and resistant pathogens. FEMS Microbiol Ecol 2016;92:fiw020. [PMID: 26850162 PMCID: PMC5968356 DOI: 10.1093/femsec/fiw020] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 01/30/2016] [Indexed: 02/04/2023]  Open
194
Tegtmeier D, Thompson CL, Schauer C, Brune A. Oxygen Affects Gut Bacterial Colonization and Metabolic Activities in a Gnotobiotic Cockroach Model. Appl Environ Microbiol 2016;82:1080-1089. [PMID: 26637604 PMCID: PMC4751835 DOI: 10.1128/aem.03130-15] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 11/24/2015] [Indexed: 12/21/2022]  Open
195
Itävaara M, Salavirta H, Marjamaa K, Ruskeeniemi T. Geomicrobiology and Metagenomics of Terrestrial Deep Subsurface Microbiomes. ADVANCES IN APPLIED MICROBIOLOGY 2016;94:1-77. [PMID: 26917241 DOI: 10.1016/bs.aambs.2015.12.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
196
Lewis ZT, Davis JCC, Smilowitz JT, German JB, Lebrilla CB, Mills DA. The impact of freeze-drying infant fecal samples on measures of their bacterial community profiles and milk-derived oligosaccharide content. PeerJ 2016;4:e1612. [PMID: 26819854 PMCID: PMC4727960 DOI: 10.7717/peerj.1612] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 12/29/2015] [Indexed: 12/13/2022]  Open
197
Güllert S, Fischer MA, Turaev D, Noebauer B, Ilmberger N, Wemheuer B, Alawi M, Rattei T, Daniel R, Schmitz RA, Grundhoff A, Streit WR. Deep metagenome and metatranscriptome analyses of microbial communities affiliated with an industrial biogas fermenter, a cow rumen, and elephant feces reveal major differences in carbohydrate hydrolysis strategies. BIOTECHNOLOGY FOR BIOFUELS 2016;9:121. [PMID: 27279900 PMCID: PMC4897800 DOI: 10.1186/s13068-016-0534-x] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/26/2016] [Indexed: 05/13/2023]
198
Prussin AJ, Marr LC. Sources of airborne microorganisms in the built environment. MICROBIOME 2015;3:78. [PMID: 26694197 PMCID: PMC4688924 DOI: 10.1186/s40168-015-0144-z] [Citation(s) in RCA: 196] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 12/14/2015] [Indexed: 05/20/2023]
199
Eren AM, Esen ÖC, Quince C, Vineis JH, Morrison HG, Sogin ML, Delmont TO. Anvi'o: an advanced analysis and visualization platform for 'omics data. PeerJ 2015;3:e1319. [PMID: 26500826 PMCID: PMC4614810 DOI: 10.7717/peerj.1319] [Citation(s) in RCA: 1123] [Impact Index Per Article: 112.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 09/22/2015] [Indexed: 12/13/2022]  Open
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