Inter-comparison of marine microbiome sampling protocols.

[1]  Tom O. Delmont,et al.  Priorities for ocean microbiome research , 2022, Nature Microbiology.

[2]  Austin D. Swafford,et al.  A comparison of six DNA extraction protocols for 16S, ITS, and shotgun metagenomic sequencing of microbial communities , 2022, bioRxiv.

[3]  G. Garrity,et al.  Valid publication of the names of forty-two phyla of prokaryotes. , 2021, International journal of systematic and evolutionary microbiology.

[4]  P. Duarte,et al.  Exploration of the Types of Rarity in the Arctic Ocean from the Perspective of Multiple Methodologies , 2021, Microbial Ecology.

[5]  J. Baum,et al.  Inconsistent Patterns of Microbial Diversity and Composition Between Highly Similar Sequencing Protocols: A Case Study With Reef-Building Corals , 2021, bioRxiv.

[6]  J. Fuhrman,et al.  Comprehensive single-PCR 16S and 18S rRNA community analysis validated with mock communities, and estimation of sequencing bias against 18S. , 2021, Environmental microbiology.

[7]  M. Oren,et al.  Identification of plastic-associated species in the Mediterranean Sea using DNA metabarcoding with Nanopore MinION , 2020, Scientific Reports.

[8]  G. Cochrane,et al.  Tara Oceans: towards global ocean ecosystems biology , 2020, Nature Reviews Microbiology.

[9]  F. Aylward,et al.  Strong Purifying Selection Is Associated with Genome Streamlining in Epipelagic Marinimicrobia , 2019, Genome biology and evolution.

[10]  Randle Aaron M. Villanueva,et al.  ggplot2: Elegant Graphics for Data Analysis (2nd ed.) , 2019, Measurement: Interdisciplinary Research and Perspectives.

[11]  Jennifer M. Fettweis,et al.  The Integrative Human Microbiome Project , 2019, Nature.

[12]  Luis Pedro Coelho,et al.  Microbial abundance, activity and population genomic profiling with mOTUs2 , 2019, Nature Communications.

[13]  P. Duarte,et al.  Diversity and Composition of Pelagic Prokaryotic and Protist Communities in a Thin Arctic Sea-Ice Regime , 2019, Microbial Ecology.

[14]  J. Claverie,et al.  Diatom diversity through HTS-metabarcoding in coastal European seas , 2018, Scientific Reports.

[15]  Erin K. Grey,et al.  Optimising the detection of marine taxonomic richness using environmental DNA metabarcoding: the effects of filter material, pore size and extraction method , 2018, Metabarcoding and Metagenomics.

[16]  M. Huggett,et al.  Coral microbiome database: Integration of sequences reveals high diversity and relatedness of coral‐associated microbes , 2018, Environmental microbiology reports.

[17]  D. Read,et al.  The effect of filtration method on the efficiency of environmental DNA capture and quantification via metabarcoding , 2018, Molecular ecology resources.

[18]  Jean M. Macklaim,et al.  Microbiome Datasets Are Compositional: And This Is Not Optional , 2017, Front. Microbiol..

[19]  Robert D. Finn,et al.  Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families , 2017, Nucleic Acids Res..

[20]  Dawn B. Goldsmith,et al.  Evaluation of Filtration and DNA Extraction Methods for Environmental DNA Biodiversity Assessments across Multiple Trophic Levels , 2017, Front. Mar. Sci..

[21]  Fang Liu,et al.  The sponge microbiome project , 2017, GigaScience.

[22]  Christian von Mering,et al.  MAPseq: highly efficient k-mer search with confidence estimates, for rRNA sequence analysis , 2017, Bioinform..

[23]  Michael W Taylor,et al.  Diversity, structure and convergent evolution of the global sponge microbiome , 2016, Nature Communications.

[24]  J. Fuhrman,et al.  Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. , 2016, Environmental microbiology.

[25]  Simon Bahrndorff,et al.  The Microbiome of Animals: Implications for Conservation Biology , 2016, International journal of genomics.

[26]  J. L. Green,et al.  A unified initiative to harness Earth's microbiomes , 2015, Science.

[27]  J. Claverie,et al.  Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing. , 2015, Environmental microbiology.

[28]  Rachelle M. Jensen,et al.  The ocean sampling day consortium , 2015, GigaScience.

[29]  Brian C. Thomas,et al.  Unusual biology across a group comprising more than 15% of domain Bacteria , 2015, Nature.

[30]  R. Parsons,et al.  Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton , 2015 .

[31]  C. Padilla,et al.  Standard filtration practices may significantly distort planktonic microbial diversity estimates , 2015, Front. Microbiol..

[32]  Luis Pedro Coelho,et al.  Structure and function of the global ocean microbiome , 2015, Science.

[33]  C. Duarte,et al.  Seafaring in the 21St Century: The Malaspina 2010 Circumnavigation Expedition , 2015 .

[34]  R. Costa,et al.  Effects of sample handling and cultivation bias on the specificity of bacterial communities in keratose marine sponges , 2014, Front. Microbiol..

[35]  R. Knight,et al.  The Earth Microbiome project: successes and aspirations , 2014, BMC Biology.

[36]  Naomi S. Altman,et al.  Points of Significance: Visualizing samples with box plots , 2014, Nature Methods.

[37]  Susan P. Holmes,et al.  Waste Not , Want Not : Why Rarefying Microbiome Data is Inadmissible . October 1 , 2013 , 2013 .

[38]  Sean R. Eddy,et al.  Infernal 1.1: 100-fold faster RNA homology searches , 2013, Bioinform..

[39]  A. Keeley,et al.  Filtration recovery of extracellular DNA from environmental water samples. , 2013, Environmental science & technology.

[40]  Pelin Yilmaz,et al.  The SILVA ribosomal RNA gene database project: improved data processing and web-based tools , 2012, Nucleic Acids Res..

[41]  Katherine H. Huang,et al.  The Human Microbiome Project: A Community Resource for the Healthy Human Microbiome , 2012, PLoS biology.

[42]  William A. Walters,et al.  Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms , 2012, The ISME Journal.

[43]  P. Bork,et al.  A Holistic Approach to Marine Eco-Systems Biology , 2011, PLoS biology.

[44]  Rick L. Stevens,et al.  The Earth Microbiome Project: Meeting report of the “1st EMP meeting on sample selection and acquisition” at Argonne National Laboratory October 6th 2010. , 2010, Standards in genomic sciences.

[45]  William A. Walters,et al.  Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample , 2010, Proceedings of the National Academy of Sciences.

[46]  M. Cottrell,et al.  The structure of bacterial communities in the western Arctic Ocean as revealed by pyrosequencing of 16S rRNA genes. , 2010, Environmental microbiology.

[47]  P. Bork,et al.  A human gut microbial gene catalogue established by metagenomic sequencing , 2010, Nature.

[48]  H. Ducklow,et al.  Correction: A Method for Studying Protistan Diversity Using Massively Parallel Sequencing of V9 Hypervariable Regions of Small-Subunit Ribosomal RNA Genes , 2009, PLoS ONE.

[49]  S. Hallam,et al.  Large volume (20L+) filtration of coastal seawater samples. , 2009, Journal of visualized experiments : JoVE.

[50]  E. Rosenberg,et al.  Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution. , 2008, FEMS microbiology reviews.

[51]  A. Halpern,et al.  The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific , 2007, PLoS biology.

[52]  L. Riemann,et al.  Optimization of DNA extraction for quantitative marine bacterioplankton community analysis , 2004 .

[53]  Z. Kawabata,et al.  Use of the SYBR Green I fluorescent dye and a centrifugal filter device for rapid determination of dissolved DNA concentration in fresh water , 2004 .

[54]  O. White,et al.  Environmental Genome Shotgun Sequencing of the Sargasso Sea , 2004, Science.

[55]  Victor Smetacek,et al.  Pelagic ecosystem structure: Heterotrophic compartments of the plankton and their relationship to plankton size fractions 1 , 1978 .

[56]  D. Bauer.  Constructing Confidence Sets Using Rank Statistics , 1972 .

[57]  O. J. Dunn.  Multiple Comparisons Using Rank Sums , 1964 .

[58]  Francisco M. Cornejo-Castillo,et al.  Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition , 2017, Scientific Data.

[59]  F. Maruyama,et al.  Application of real-time long and short polymerase chain reaction for sensitive monitoring of the fate of extracellular plasmid DNA introduced into river waters. , 2008, Microbes and environments.

[60]  H. Toutenburg.  Hollander, M., D. A. Wolfe: Nonparametric statistical methods. John Wiley & Sons, New York-Sydney-Tokyo-Mexico City 1973. 503 S., $9.50 , 1975 .