Using strain-resolved analysis to identify contamination in metagenomics data

inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains

(2021) Matthew R. Olm et al.   NATURE BIOTECHNOLOGY

Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants

(2021) Alexander Crits-Christoph et al.   mBio

Genome-resolved metagenomics of eukaryotic populations during early colonization of premature infants and in hospital rooms

(2019) Matthew R. Olm et al.   Microbiome

Laboratory contamination over time during low‐biomass sample analysis

(2019) Laura S. Weyrich et al.   Molecular Ecology Resources

Quantifying and Understanding Well-to-Well Contamination in Microbiome Research

(2019) Jeremiah J. Minich et al.   mSystems

Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life

(2018) Moran Yassour et al.   Cell Host & Microbe

Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome

(2018) Pamela Ferretti et al.   Cell Host & Microbe

Computational correction of index switching in multiplexed sequencing libraries

(2018) Anton J M Larsson et al.   NATURE METHODS

The human skin microbiome

(2018) Allyson L. Byrd et al.   NATURE REVIEWS MICROBIOLOGY

Recognizing the reagent microbiome

(2018) Marcus C. de Goffau et al.   Nature Microbiology

KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples

(2018) Jeremiah J. Minich et al.   mSystems

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

(2018) Nicole M. Davis et al.   Microbiome

Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations

(2018) Raphael Eisenhofer et al.   TRENDS IN MICROBIOLOGY

Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates

(2017) Matthew R. Olm et al.   GENOME RESEARCH

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

(2017) Matthew R Olm et al.   ISME Journal

The Source and Evolutionary History of a Microbial Contaminant Identified Through Soil Metagenomic Analysis

(2017) Matthew R. Olm et al.   mBio

Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome

(2017) Brandon Brooks et al.   Nature Communications

Evidence for persistent and shared bacterial strains against a background of largely unique gut colonization in hospitalized premature infants

(2016) Tali Raveh-Sadka et al.   ISME Journal

Propionibacterium acnes: Disease-Causing Agent or Common Contaminant? Detection in Diverse Patient Samples by Next-Generation Sequencing

(2016) Sarah Mollerup et al.   JOURNAL OF CLINICAL MICROBIOLOGY

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

Strategies for Achieving High Sequencing Accuracy for Low Diversity Samples and Avoiding Sample Bleeding Using Illumina Platform

(2015) Abhishek Mitra et al.   PLoS One

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

(2014) Susannah J Salter et al.   BMC BIOLOGY

Common Contaminants in Next-Generation Sequencing That Hinder Discovery of Low-Abundance Microbes

(2014) Martin Laurence et al.   PLoS One

Tracking a Hospital Outbreak of Carbapenem-Resistant Klebsiella pneumoniae with Whole-Genome Sequencing

(2012) E. S. Snitkin et al.   Science Translational Medicine