Topic 125

sequencing samples taxonomic sample method microbial amplicon reads throughput 16s metabarcoding dna communities library abundance community rrna mock taxa metagenomic primers microbiome libraries methods profiling environmental sequences cost high amplification composition identification species pcr pipeline illumina ribosomal protocol approach shotgun detection sequence efficient metagenomics used reference accurate based preparation workflow read sequenced primer organisms biodiversity available kits applied resolution present generation edna commercially genomics assessment bias biases microbiology bacterial low characterization microbiomes provides challenges tool rna effective datasets alternative abundances amplicons diversity microbes 18s widely next approaches reliable steps extraction monitoring using construction enables relative from technique bacteria commonly miseq

114 items. Top items listed below.

Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore sequencing confers species-level resolution 125 101 29 25 12 4

Quantitative microbiome profiling in lumenal and tissue samples with broad coverage and dynamic range via a single-step 16S rRNA gene DNA copy quantification and amplicon barcoding 125 29 4

Taxonomic classification method for metagenomics based on core protein families with Core-Kaiju 125 29 4

Speeding up the detection of invasive aquatic species using environmental DNA and nanopore sequencing 125 25 17 4

Comparing DNA Extraction and 16s Amplification Methods for Plant-Associated Bacterial Communities 125 29 12 5 4

Efficient and stable metabarcoding sequencing from DNBSEQ-G400 sequencer examined by large fungal community analysis 125 29 12 4

Sediment-associated microbial community profiling: sample pre-processing through sequential membrane filtration for 16s rDNA amplicon sequencing 125 29 25 15 5 4

A workflow for accurate metabarcoding using nanopore MinION sequencing 125 25 4

Evaluation of Compatibility of 16S rRNA V3V4 and V4 Amplicon Libraries for Clinical Microbiome Profiling 125 25 4

Optimal protocols for sequence-based characterization of the human vaginal microbiome 125 29 4

Illumina iSeq 100 and MiSeq exhibit similar performance in freshwater fish environmental DNA metabarcoding 125 17 5 4

Read counts from environmental DNA (eDNA) metabarcoding reflect fish abundance and biomass in drained ponds 125 17 5 4

Phylotype-Level Characterization of Complex Lactobacilli Communities Using a High-Throughput, High-Resolution Phenylalanyl-tRNA Synthetase (pheS) Gene Amplicon Sequencing Approach 125 29 4

Microbiome-based environmental monitoring of a dairy processing facility highlights the challenges associated with low microbial-load samples 125 29 4

Snipe: Highly sensitive pathogen detection from metagenomic sequencing data 125 25 12 4

PriSeT: Efficient De Novo Primer Discovery 125 25 4

Broad-Range Virus Detection and Discovery Using Microfluidic PCR Coupled with High-throughput Sequencing 125 35 25 4

PhenoGMM: Gaussian mixture modelling of microbial cytometry data enables efficient predictions of biodiversity 125 4

Obtaining deeper insights into microbiome diversity using a simple method to block host and non-targets in amplicon sequencing 125 29 4

Novel rRNA-depletion methods for total RNA sequencing and ribosome profiling developed for avian species 125 49 4

Generation of comprehensive ecosystems-specific reference databases with species-level resolution by high-throughput full-length 16S rRNA gene sequencing and automated taxonomy assignment (AutoTax) 125 29 25 4

Variant calling for cpn60 barcode sequence-based microbiome profiling 125 25 4

Accurate Microbiome Sequencing with Synthetic Long Read Sequencing 125 29 25 4

High-Resolution Phylogenetic and Population Genetic Analysis of Microbial Communities with RoC-ITS 125 25 5 4

eDNA metabarcoding outperforms traditional fisheries sampling and reveals fine-scale heterogeneity in a temperate freshwater lake 125 17 5 4

Rapid quantitative assessment of fish larvae community composition using metabarcoding 125 17 5 4

A simple, cost-effective, and robust method for rRNA depletion in RNA-sequencing studies 125 4

CaptureSeq: Hybridization-based enrichment of cpn60 gene fragments reveals the community structures of synthetic and natural microbial ecosystems 29 12 4

Status and prospects of marine NIS detection and monitoring through (e)DNA metabarcoding 125 84 17 5 4

Efficient and cost-effective bacterial mRNA sequencing from low input samples through ribosomal RNA depletion 125 43 4

Reverse transcriptase enzyme and priming strategy affect quantification and diversity of environmental transcripts 125 29 5

Bac-PULCE: Bacterial Strain and AMR Profiling Using Long Reads via CRISPR Enrichment 125 25 4

Optimised biomolecular extraction for metagenomic analysis of microbial biofilms from high-mountain streams 125 29 17 4

DNA extraction and host depletion methods significantly impact and potentially bias bacterial detection in a biological fluid 125 4

Using high abundance proteins as guides for fast and effective peptide/protein identification from metaproteomic data 125 29 4

An improved hgcAB primer set and direct high throughput sequencing expand Hg-methylator diversity in nature 125 29 5 4

Genome-based targeted sequencing as a reproducible microbial community profiling assay. 125 29 4

High-Throughput Stool Metaproteomics: Method and Application to Human Specimens 125 101 45 4

Accurate identification and quantification of commensal microbiota bound by host immunoglobulins 125 4

Inferring microbial co-occurrence networks from amplicon data: a systematic evaluation 125 13 4

Two-target quantitative PCR to predict library composition for shallow shotgun sequencing 125 29 4

A flexible pipeline combining clustering and correction tools for prokaryotic and eukaryotic metabarcoding 125 4

Freshwater diatom biomonitoring through benthic kick-net metabarcoding 125 17 4

The utility of a metagenomics approach for marine biomonitoring 125 17 5 4

Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets 125 25 4

MetaLab 2.0 enables accurate post-translational modifications profiling in metaproteomics 125 45 4

To rarefy or not to rarefy: Enhancing microbial community analysis through next-generation sequencing 125 4

Equivolumetric protocol generates library sizes proportional to total microbial load in next-generation sequencing 125 29 4

A low-cost pipeline for soil microbiome profiling 125 25 4

Tagsteady: a metabarcoding library preparation protocol to avoid false assignment of sequences to samples 125 4

Measuring both microbial load and diversity with a single amplicon sequencing library 7 4

Ultrafast and accurate 16S microbial community analysis using Kraken 2 125 29 4

Assessment of current taxonomic assignment strategies for metabarcoding eukaryotes 125 4

Accurate and sensitive detection of microbial eukaryotes from metagenomic shotgun sequencing 125 29 12 4

Monitoring the microbiome for food safety and quality using deep shotgun sequencing 125 29 12 5 4

Metagenomic evidence for a polymicrobial signature of sepsis 125 112 4

Evaluating Methods for Differential Gene Expression And Alternative Splicing Using Internal Synthetic Controls. 125 43 4

Validation of a PNA clamping method for reducing host DNA amplification and increasing eukaryotic diversity in rhizosphere microbiome studies 125 29 12 5

Biodiversity Soup II: A bulk-sample metabarcoding pipeline emphasizing error reduction 125 4

Discovering and exploiting multiple types of DNA methylation from individual bacteria and microbiome using nanopore sequencing 125 4

The use of CRISPR-Cas Selective Amplicon Sequencing (CCSAS) to reveal the eukaryotic microbiome of metazoans 125 29 12 4

A step-by-step sequence-based analysis of virome enrichment protocol for freshwater and sediment samples 29 17 5 4

High quality single amplicon sequencing method for illumina platforms using N (0-10) spacer primer pool without PhiX spik-in 125 25 4

Fast and inexpensive whole genome sequencing library preparation from intact yeast cells 125 33 4

Optimization of cerebrospinal fluid microbial metagenomic sequencing diagnostics 125 12 4

A Rapid, Cost-Effective Tailed Amplicon Method for Sequencing SARS-CoV-2 25 1

Harnessing the power of eDNA metabarcoding for the detection of deep-sea fishes 84 17 5 4

Spider webs as eDNA tool for biodiversity assessment of life's domains 125 17 5 4

Competitive mapping allows to identify and exclude human DNA contamination in ancient faunal genomic datasets 125 25 4

MinION-in-ARMS: Nanopore Sequencing To Expedite Barcoding Of Specimen-Rich Macrofaunal Samples From Autonomous Reef Monitoring Structures 125 4

A novel metabarcoding strategy for studying nematode communities 125 25 4

SCRAPP: A tool to assess the diversity of microbial samples from phylogenetic placements 162 13 4

Metalign: Efficient alignment-based metagenomic profiling via containment min hash 13 4

Considerations for metabarcoding-based port biological baseline surveys aimed at marine non-indigenous species monitoring and risk-assessments 125 84 17 5 4

Implications of error-prone long-read whole-genome shotgun sequencing on characterizing reference microbiomes 25 4

Improved freshwater macroinvertebrate detection from eDNA through minimized non-target amplification 125 17 5 4

Efficient assessment of nocturnal flying insect communities by combining automatic light traps and DNA metabarcoding 125 84 17 5 4

Demonstrating the utility of flexible sequence queries against indexed short reads with FlexTyper 25 13 4

Balrog: A universal protein model for prokaryotic gene prediction 162 13 4

Estimating the quality of eukaryotic genomes recovered from metagenomic analysis 125 4

A Tree of Human Gut Bacterial Species and its Applications to Metagenomics and Metaproteomics Data Analysis 13 4

A Quantitative Sequencing Framework for Absolute Abundance Measurements of Mucosal and Lumenal Microbial Communities 29 12 5 4

TRAPID 2.0: a web application for taxonomic and functional analysis of de novo transcriptomes 125 43 25 4

Nuclease-mediated depletion biases in ribosome footprint profiling libraries 125 4

Probabilistic Ranking Of Microbiomes Plus Taxa Selection to discover and validate microbiome function models for multiple litter decomposition studies 29 26 4

Ribo-Pop: Simple, cost-effective, and widely applicable ribosomal RNA depletion 125 4

NGPINT: A Next-generation protein-protein interaction software 125 4

Ligation bias is a major contributor to nonstoichiometric abundances of secondary siRNAs and impacts analyses of microRNAs 125 4

AmpliCI: A High-resolution Model-Based Approach for Denoising Illumina Amplicon Data 13 4

Highly Multiplexed Single-Cell Full-Length cDNA Sequencing of human immune cells with 10X Genomics and R2C2 25 4

MAUI-seq: Metabarcoding using amplicons with unique molecular identifiers to improve error correction 125 29 4

Probabilistic gene expression signatures identify cell-types from single cell RNA-seq data 43 4

Terminitor: Cleavage Site Prediction Using Deep Learning Models 105 26 4

Rapid cost-effective viral genome sequencing by V-seq 35 4

An enhanced characterization of the human skin microbiome: a new biodiversity of microbial interactions 29 12 5

Methods for Extraction and Detection of Bacteriophage DNA from the Sputum of Patients with Cystic Fibrosis 125 29 12 4

Error correction enables use of Oxford Nanopore technology for reference-free transcriptome analysis 25 4

Quantitative profiling of microbial communities by de novo metaproteomics 125 4

Bacterial single-cell genomics enables phylogenetic analysis and reveals population structures from in vitro evolutionary studies 107 52 12 9 5 4

Shotgun Metagenomic Analysis Reveals New Insights on Bacterial Community Profiles in Tempeh 29 12