Bacterial and Eukaryotic Small-Subunit Amplicon Data Do Not Provide a Quantitative Picture of Microbial Communities, but They Are Reliable in the Context of Ecological Interpretations

Seasonality of Planktonic Freshwater Ciliates: Are Analyses Based on V9 Regions of the 18S rRNA Gene Correlated With Morphospecies Counts?

(2019) Gianna Pitsch et al.   Frontiers in Microbiology

Weekly dynamics of abundance and size structure of specific nanophytoplankton lineages in coastal waters (Baltic Sea)

(2019) Kasia Piwosz   LIMNOLOGY AND OCEANOGRAPHY

Use and abuse of correlation analyses in microbial ecology

(2019) Alex Carr et al.   ISME Journal

Distinct relationships between fluorescence in situ hybridization and 16S rRNA gene- and amplicon-based sequencing data of bacterioplankton lineages

(2019) Insa Bakenhus et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

A comparative assessment of conventional and molecular methods, including MinION nanopore sequencing, for surveying water quality

(2019) Kishor Acharya et al.   Scientific Reports

Photochemical degradation of dissolved organic matter reduces the availability of phosphorus for aquatic primary producers

(2018) Petr Porcal et al.   CHEMOSPHERE

Determining lineage-specific bacterial growth curves with a novel approach based on amplicon reads normalization using internal standard (ARNIS)

(2018) Kasia Piwosz et al.   ISME Journal

Bioassessment of a Drinking Water Reservoir Using Plankton: High Throughput Sequencing vs. Traditional Morphological Method

(2018) Wanli Gao et al.   Water

Evaluating Established Methods for Rumen 16S rRNA Amplicon Sequencing With Mock Microbial Populations

(2018) Emily McGovern et al.   Frontiers in Microbiology

Dietary changes during weaning shape the gut microbiota of red pandas (Ailurus fulgens)

(2018) Candace L Williams et al.   Conservation Physiology

Taxon Disappearance from Microbiome Analysis Reinforces the Value of Mock Communities as a Standard in Every Sequencing Run

(2018) Yi-Chun Yeh et al.   mSystems

Molecular analyses of protists in long-term observation programmes—current status and future perspectives

(2018) Rowena Stern et al.   JOURNAL OF PLANKTON RESEARCH

NanoAmpli-Seq: A workflow for amplicon sequencing for mixed microbial communities on the nanopore sequencing platform.

(2018) Szymon T Calus et al.   GigaScience

Hunters or farmers? Microbiome characteristics help elucidate the diet composition in an aquatic carnivorous plant

(2018) Dagmara Sirová et al.   Microbiome

Distribution and ecological preferences of the freshwater lineage LimA (genus L imnohabitans) revealed by a new double hybridization approach

(2017) Tanja Shabarova et al.   ENVIRONMENTAL MICROBIOLOGY

Ubiquity and quantitative significance of bacterioplankton lineages inhabiting the oxygenated hypolimnion of deep freshwater lakes

(2017) Yusuke Okazaki et al.   ISME Journal

Assessment of the metabarcoding approach for community analysis of benthic-epiphytic dinoflagellates using mock communities

(2017) Kirsty F. Smith et al.   NEW ZEALAND JOURNAL OF MARINE AND FRESHWATER RESEARCH

Dynamics of the human gut microbiome in inflammatory bowel disease

(2017) Jonas Halfvarson et al.   Nature Microbiology

Detecting macroecological patterns in bacterial communities across independent studies of global soils

(2017) Kelly S. Ramirez et al.   Nature Microbiology

Structure and function of the microbial consortia of activated sludge in typical municipal wastewater treatment plants in winter

(2017) Bo Zhang et al.   Scientific Reports

Environmental Sequencing Provides Reasonable Estimates of the Relative Abundance of Specific Picoeukaryotes

(2016) Caterina R. Giner et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision

(2016) Sophie Weiss et al.   ISME Journal

Repeated flood disturbance enhances rotifer dominance and diversity in a zooplankton community of a small dammed mountain pond

(2016) Carmen Gabaldón et al.   JOURNAL OF LIMNOLOGY

Phenology of cryptomonads and the CRY1 lineage in a coastal brackish lagoon (Vistula Lagoon, Baltic Sea)

(2016) Kasia Piwosz et al.   JOURNAL OF PHYCOLOGY

Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies

(2016) Daryl M Gohl et al.   NATURE BIOTECHNOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics

(2016) Juan Jovel et al.   Frontiers in Microbiology

Eukaryotic plankton diversity in the sunlit ocean

(2015) C. de Vargas et al.   SCIENCE

A brief history of bacterial growth physiology

(2015) Moselio Schaechter   Frontiers in Microbiology

Bacterial community structure and dissolved organic matter in repeatedly flooded subsurface karst water pools

(2014) Tanja Shabarova et al.   FEMS MICROBIOLOGY ECOLOGY

The Bias Associated with Amplicon Sequencing Does Not Affect the Quantitative Assessment of Bacterial Community Dynamics

(2014) Federico M. Ibarbalz et al.   PLoS One

Diversity and abundance of “Pelagibacterales” (SAR11) in the Baltic Sea salinity gradient

(2014) Daniel P.R. Herlemann et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Distribution of the verrucomicrobial cladeSpartobacteriaalong a salinity gradient in the Baltic Sea

(2014) Benjamin Bergen et al.   Environmental Microbiology Reports

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

454 Pyrosequencing to Describe Microbial Eukaryotic Community Composition, Diversity and Relative Abundance: A Test for Marine Haptophytes

(2013) Elianne Egge et al.   PLoS One

Extremely High Copy Numbers and Polymorphisms of the rDNA Operon Estimated from Single Cell Analysis of Oligotrich and Peritrich Ciliates

(2013) Jun Gong et al.   PROTIST

The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy

(2012) Laure Guillou et al.   NUCLEIC ACIDS RESEARCH

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

(2012) Anna Klindworth et al.   NUCLEIC ACIDS RESEARCH

Direct Comparisons of Illumina vs. Roche 454 Sequencing Technologies on the Same Microbial Community DNA Sample

(2012) Chengwei Luo et al.   PLoS One

Microplanktonic Community Structure in a Coastal System Relative to a Phaeocystis Bloom Inferred from Morphological and Tag Pyrosequencing Methods

(2012) Sébastien Monchy et al.   PLoS One

Which sequencing depth is sufficient to describe patterns in bacterial α- and β-diversity?

(2012) Daniel Lundin et al.   Environmental Microbiology Reports

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

The ecophysiology and bloom dynamics of Prymnesium spp.

(2011) Edna Granéli et al.   HARMFUL ALGAE

Seasonal bloom dynamics and ecophysiology of the freshwater sister clade of SAR11 bacteria ‘that rule the waves’ (LD12)

(2011) Michaela M Salcher et al.   ISME Journal

Vertical and longitudinal distribution patterns of different bacterioplankton populations in a canyon-shaped, deep prealpine lake

(2011) Michaela M. Salcher et al.   LIMNOLOGY AND OCEANOGRAPHY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water

(2010) THORSTEN STOECK et al.   MOLECULAR ECOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Seasonal population dynamics and trophic role of planktonic nanoflagellates in coastal surface waters of the Southern Baltic Sea

(2009) Kasia Piwosz et al.   ENVIRONMENTAL MICROBIOLOGY

Protistan assemblages across the Indian Ocean, with a specific emphasis on the picoeukaryotes

(2008) Fabrice Not et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques

(2008) Rudolf Amann et al.   NATURE REVIEWS MICROBIOLOGY

rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea

(2008) Z. M.-P. Lee et al.   NUCLEIC ACIDS RESEARCH