Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data

Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies

(2023) Katherine M. Kennedy et al.   NATURE

Trait biases in microbial reference genomes

(2023) Sage Albright et al.   Scientific Data

Metagenome assembly of high-fidelity long reads with hifiasm-meta

(2022) Xiaowen Feng et al.   NATURE METHODS

Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing

(2022) Mantas Sereika et al.   NATURE METHODS

Batch effects account for the main findings of an in utero human intestinal bacterial colonization study

(2021) Marcus C. de Goffau et al.   Microbiome

Comparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota

(2021) Francesco Durazzi et al.   Scientific Reports

A Fast and Efficient Single-stranded Genomic Library Preparation Method Optimized for Ancient DNA

(2021) Joshua D Kapp et al.   JOURNAL OF HEREDITY

Validation and standardization of DNA extraction and library construction methods for metagenomics-based human fecal microbiome measurements

(2021) Dieter M. Tourlousse et al.   Microbiome

Disentangling host–microbiota complexity through hologenomics

(2021) Antton Alberdi et al.   NATURE REVIEWS GENETICS

Optimizing liquefaction and decontamination of sputum for DNA extraction from Mycobacterium tuberculosis

(2021) Anzaan Dippenaar et al.   TUBERCULOSIS

Sequencing artifacts derived from a library preparation method using enzymatic fragmentation

(2020) Norio Tanaka et al.   PLoS One

The effect of storage conditions on microbial communities in stool

(2020) Kristien Nel Van Zyl et al.   PLoS One

DNA extraction approaches substantially influence the assessment of the human breast milk microbiome

(2020) Chloe A. Douglas et al.   Scientific Reports

Emerging Priorities for Microbiome Research

(2020) Chad M. Cullen et al.   Frontiers in Microbiology

GC bias affects genomic and metagenomic reconstructions, underrepresenting GC-poor organisms

(2020) Patrick Denis Browne et al.   GigaScience

Comparison of Methods To Collect Fecal Samples for Microbiome Studies Using Whole-Genome Shotgun Metagenomic Sequencing

(2020) Doratha A. Byrd et al.   mSphere

Quantifying sample completeness and comparing diversities among assemblages

(2020) Anne Chao et al.   ECOLOGICAL RESEARCH

Impact of DNA Extraction Method on Variation in Human and Built Environment Microbial Community and Functional Profiles Assessed by Shotgun Metagenomics Sequencing

(2020) Hui-yu Sui et al.   Frontiers in Microbiology

Direct Comparison of Fecal and Gut Microbiota in the Blue Mussel (Mytilus edulis) Discourages Fecal Sampling as a Proxy for Resident Gut Community

(2020) Tyler W. Griffin et al.   MICROBIAL ECOLOGY

Multicenter assessment of microbial community profiling using 16S rRNA gene sequencing and shotgun metagenomic sequencing

(2020) Dongsheng Han et al.   Journal of Advanced Research

Holo-Omics: Integrated Host-Microbiota Multi-omics for Basic and Applied Biological Research

(2020) Lasse Nyholm et al.   iScience

Metagenomics-Based Proficiency Test of Smoked Salmon Spiked with a Mock Community

(2020) Claudia Sala et al.   Microorganisms

Microbial abundance, activity and population genomic profiling with mOTUs2

(2019) Alessio Milanese et al.   Nature Communications

Challenges of next-generation sequencing targeting anaerobes

(2019) Georg Conrads et al.   ANAEROBE

Investigation of the skin microbiome: swabs vs. biopsies

(2019) S. Prast‐Nielsen et al.   BRITISH JOURNAL OF DERMATOLOGY

Quantitative and qualitative evaluation of the impact of the G2 enhancer, bead sizes and lysing tubes on the bacterial community composition during DNA extraction from recalcitrant soil core samples based on community sequencing and qPCR

(2019) Alex Gobbi et al.   PLoS One

Recentrifuge: Robust comparative analysis and contamination removal for metagenomics

(2019) Jose Manuel Martí   PLoS Computational Biology

The Impact of DNA Extraction Methods on Stool Bacterial and Fungal Microbiota Community Recovery

(2019) Kristýna Fiedorová et al.   Frontiers in Microbiology

MGS-Fast: Metagenomic shotgun data fast annotation using microbial gene catalogs

(2019) Stuart M Brown et al.   GigaScience

Quantifying spatiotemporal variability and noise in absolute microbiota abundances using replicate sampling

(2019) Brian W. Ji et al.   NATURE METHODS

Microbiota data from low biomass milk samples is markedly affected by laboratory and reagent contamination

(2019) Josef Dahlberg et al.   PLoS One

Incomplete cell disruption of resistant microbes

(2019) Robert Starke et al.   Scientific Reports

Controlling for Contaminants in Low-Biomass 16S rRNA Gene Sequencing Experiments

(2019) Lisa Karstens et al.   mSystems

Variations in the microbiome due to storage preservatives are not large enough to obscure variations due to factors such as host population, host species, body site, and captivity

(2019) Abigail E. Asangba et al.   AMERICAN JOURNAL OF PRIMATOLOGY

Benchmarking Metagenomics Tools for Taxonomic Classification

(2019) Simon H. Ye et al.   CELL

Efficacy of Fecal Sampling as a Gut Proxy in the Study of Chicken Gut Microbiota

(2019) Wei Yan et al.   Frontiers in Microbiology

Sample Preservation and Storage Significantly Impact Taxonomic and Functional Profiles in Metaproteomics Studies of the Human Gut Microbiome

(2019) Oskar Hickl et al.   Microorganisms

Membrane-sensitive bacterial DNA extractions and absolute quantitation of recovery efficiencies

(2019) Xiao Jie Shi et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Effects of sampling strategy and DNA extraction on human skin microbiome investigations

(2019) Rie Dybboe Bjerre et al.   Scientific Reports

Optimization of fecal sample processing for microbiome study — The journey from bathroom to bench

(2018) Wei-Kai Wu et al.   JOURNAL OF THE FORMOSAN MEDICAL ASSOCIATION

Comparison of DNA extraction methods for human gut microbial community profiling

(2018) Mi Young Lim et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Proper experimental design requires randomization/balancing of molecular ecology experiments

(2018) Miklós Bálint et al.   Ecology and Evolution

Guano exposed: Impact of aerobic conditions on bat fecal microbiota

(2018) Viacheslav Y. Fofanov et al.   Ecology and Evolution

Correcting for batch effects in case-control microbiome studies

(2018) Sean M. Gibbons et al.   PLoS Computational Biology

Improving saliva shotgun metagenomics by chemical host DNA depletion

(2018) Clarisse A. Marotz et al.   Microbiome

Absolute quantitation of microbiota abundance in environmental samples

(2018) Andrzej Tkacz et al.   Microbiome

Batch effects correction for microbiome data with Dirichlet-multinomial regression

(2018) Zhenwei Dai et al.   BIOINFORMATICS

Community profiling of the urinary microbiota: considerations for low-biomass samples

(2018) Lisa Karstens et al.   Nature Reviews Urology

A Comparison of Techniques for Collecting Skin Microbiome Samples: Swabbing Versus Tape-Stripping

(2018) Kazuhiro Ogai et al.   Frontiers in Microbiology

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data

(2018) Nicole M. Davis et al.   Microbiome

Evaluating the Information Content of Shallow Shotgun Metagenomics

(2018) Benjamin Hillmann et al.   mSystems

Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations

(2018) Raphael Eisenhofer et al.   TRENDS IN MICROBIOLOGY

Microbial life on a sand grain: from bulk sediment to single grains

(2017) David Probandt et al.   ISME Journal

Impact of sample processing on human airways microbial metagenomes

(2017) Lutz Wiehlmann et al.   JOURNAL OF BIOTECHNOLOGY

Library Construction from Subnanogram DNA for Pelagic Sea Water and Deep-Sea Sediments

(2017) Miho Hirai et al.   MICROBES AND ENVIRONMENTS

Environmental DNA metabarcoding: Transforming how we survey animal and plant communities

(2017) Kristy Deiner et al.   MOLECULAR ECOLOGY

Shotgun metagenomics, from sampling to analysis

(2017) Christopher Quince et al.   NATURE BIOTECHNOLOGY

Towards standards for human fecal sample processing in metagenomic studies

(2017) Paul I Costea et al.   NATURE BIOTECHNOLOGY

Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

(2017) Alexander Sczyrba et al.   NATURE METHODS

Home-Made Cost Effective Preservation Buffer Is a Better Alternative to Commercial Preservation Methods for Microbiome Research

(2017) Sebastian Menke et al.   Frontiers in Microbiology

Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing

(2017) Sarah Siu Tze Mak et al.   GigaScience

Optimizing methods and dodging pitfalls in microbiome research

(2017) Dorothy Kim et al.   Microbiome

Comparison of vaginal microbiota sampling techniques: cytobrush versus swab

(2017) Anita Mitra et al.   Scientific Reports

Toward Accurate and Quantitative Comparative Metagenomics

(2016) Stephen Nayfach et al.   CELL

A comparison of DNA extraction methods for high-throughput DNA analyses

(2016) Lauren M. Schiebelhut et al.   Molecular Ecology Resources

Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation

(2016) Hilary P. Browne et al.   NATURE

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples

(2016) Angela Glassing et al.   Gut Pathogens

Comparison of capture and storage methods for aqueous macrobial eDNA using an optimized extraction protocol: advantage of enclosed filter

(2016) Johan Spens et al.   Methods in Ecology and Evolution

Rapid Microbiome Changes in Freshly Deposited Cow Feces under Field Conditions

(2016) Kelvin Wong et al.   Frontiers in Microbiology

Two sampling methods yield distinct microbial signatures in the nasopharynges of asthmatic children

(2016) Marcos Pérez-Losada et al.   Microbiome

Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota

(2016) Abigail P. Lauder et al.   Microbiome

Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition

(2016) Berith E. Knudsen et al.   mSystems

Effect of short-term room temperature storage on the microbial community in infant fecal samples

(2016) Yong Guo et al.   Scientific Reports

Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community

(2015) Robert M. Bowers et al.   BMC GENOMICS

Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses

(2015) Marie Lisandra Zepeda Mendoza et al.   BRIEFINGS IN BIOINFORMATICS

Microbiota and Host Nutrition across Plant and Animal Kingdoms

(2015) Stéphane Hacquard et al.   Cell Host & Microbe

A comparison of four methods for PCR inhibitor removal

(2015) Qingqing Hu et al.   Forensic Science International-Genetics

Fecal microbiota analysis: an overview of sample collection methods and sequencing strategies

(2015) Vincent Thomas et al.   Future Microbiology

Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates

(2015) Doris Vandeputte et al.   GUT

Implications of multiple freeze-thawing on respiratory samples for culture-independent analyses

(2015) Leah Cuthbertson et al.   Journal of Cystic Fibrosis

Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform

(2015) Melanie Schirmer et al.   NUCLEIC ACIDS RESEARCH

Library preparation methodology can influence genomic and functional predictions in human microbiome research

(2015) Marcus B. Jones et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rhythmicity of the intestinal microbiota is regulated by gender and the host circadian clock

(2015) Xue Liang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Shifts in the gut microbiome observed in wildlife faecal samples exposed to natural weather conditions: lessons from time-series analyses using next-generation sequencing for application in field studies

(2015) Sebastian Menke et al.   Methods in Ecology and Evolution

How Much DNA Is Lost? Measuring DNA Loss of Short-Tandem-Repeat Length Fragments Targeted by the PowerPlex 16® System Using the Qiagen MinElute Purification Kit

(2015) Brian M. Kemp et al.   HUMAN BIOLOGY

The Effects of Freezing on Faecal Microbiota as Determined Using MiSeq Sequencing and Culture-Based Investigations

(2015) Fiona Fouhy et al.   PLoS One

The Effect of Sampling and Storage on the Fecal Microbiota Composition in Healthy and Diseased Subjects

(2015) Danyta I. Tedjo et al.   PLoS One

Evaluating Bias of Illumina-Based Bacterial 16S rRNA Gene Profiles

(2014) Katherine Kennedy et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

Gut microbiome of the Hadza hunter-gatherers

(2014) Stephanie L. Schnorr et al.   Nature Communications

Non-random DNA fragmentation in next-generation sequencing

(2014) Maria S. Poptsova et al.   Scientific Reports

Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis

(2014) Agata Wesolowska-Andersen et al.   Microbiome

Sequencing platform and library preparation choices impact viral metagenomes

(2013) Sergei A Solonenko et al.   BMC GENOMICS

Chemical fragmentation for massively parallel sequencing library preparation

(2013) P. Gyarmati et al.   JOURNAL OF BIOTECHNOLOGY

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

Absolute quantification by droplet digital PCR versus analog real-time PCR

(2013) Christopher M Hindson et al.   NATURE METHODS

The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses

(2013) Tomáš Větrovský et al.   PLoS One

Comparison of Sequencing Platforms for Single Nucleotide Variant Calls in a Human Sample

(2013) Aakrosh Ratan et al.   PLoS One

Biases during DNA extraction of activated sludge samples revealed by high throughput sequencing

(2012) Feng Guo et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Coverage-based rarefaction and extrapolation: standardizing samples by completeness rather than size

(2012) Anne Chao et al.   ECOLOGY

PCR inhibitors - occurrence, properties and removal

(2012) C. Schrader et al.   JOURNAL OF APPLIED MICROBIOLOGY

Library Preparation and Multiplex Capture for Massive Parallel Sequencing Applications Made Efficient and Easy

(2012) Mårten Neiman et al.   PLoS One

Characterization of the Fecal Microbiota Using High-Throughput Sequencing Reveals a Stable Microbial Community during Storage

(2012) Ian M. Carroll et al.   PLoS One

Bayesian community-wide culture-independent microbial source tracking

(2011) Dan Knights et al.   NATURE METHODS

Survival and recovery of DNA from ancient teeth and bones

(2010) C.J. Adler et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

Metagenomics: Facts and Artifacts, and Computational Challenges

(2010) John C. Wooley et al.   JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY

Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: Effective recovery of bacterial and archaeal DNA using mechanical cell lysis

(2010) Anne Salonen et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition

(2010) Andrew Adey et al.   GENOME BIOLOGY

Next Generation Sequencing of Ancient DNA: Requirements, Strategies and Perspectives

(2010) Michael Knapp et al.   Genes

Genomic DNA k-mer spectra: models and modalities

(2009) Benny Chor et al.   GENOME BIOLOGY

Selective isolation of bacterial DNA from human clinical specimens

(2007) Hans-Peter Horz et al.   JOURNAL OF MICROBIOLOGICAL METHODS