When to suspect contamination rather than colonization – lessons from a putative fetal sheep microbiome

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

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

Microbiome or no microbiome: are we looking at the prenatal environment through the right lens?

(2021) W. Florian Fricke et al.   Microbiome

Lessons learned from the prenatal microbiome controversy

(2021) Martin J. Blaser et al.   Microbiome

Group therapy on in utero colonization: seeking common truths and a way forward

(2021) Rachel B. Silverstein et al.   Microbiome

A philosophical perspective on the prenatal in utero microbiome debate

(2021) Jens Walter et al.   Microbiome

Multiomics analysis reveals the presence of a microbiome in the gut of fetal lambs

(2021) Yanliang Bi et al.   GUT

Strain inheritance and neonatal gut microbiota development: A meta-analysis

(2021) Daniel Podlesny et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Microbial exposure during early human development primes fetal immune cells

(2021) Archita Mishra et al.   CELL

Interaction of bacterial communities and indicators of water quality in shoreline sand, sediment, and water of Lake Michigan

(2020) Meredith B. Nevers et al.   WATER RESEARCH

A high-resolution map of bacteriophage øX174 transcription

(2020) Dominic Y. Logel et al.   VIROLOGY

Diversity within species: interpreting strains in microbiomes

(2020) Thea Van Rossum et al.   NATURE REVIEWS MICROBIOLOGY

No evidence for a placental microbiome in human pregnancies at term

(2020) Irene Sterpu et al.   AMERICAN JOURNAL OF OBSTETRICS AND GYNECOLOGY

What is new and relevant for sequencing-based microbiome research? A minireview

(2019) Alena M. Fricker et al.   Journal of Advanced Research

Human placenta has no microbiome but can contain potential pathogens

(2019) Marcus C. de Goffau et al.   NATURE

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

(2019) Jeremiah J. Minich et al.   mSystems

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient

(2018) Xin Fang et al.   Frontiers in Microbiology

Qualitative and Quantitative DNA- and RNA-Based Analysis of the Bacterial Stomach Microbiota in Humans, Mice, and Gerbils

(2018) Philipp Wurm et al.   mSystems

Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations

(2018) Raphael Eisenhofer et al.   TRENDS IN MICROBIOLOGY

A critical assessment of the “sterile womb” and “in utero colonization” hypotheses: implications for research on the pioneer infant microbiome

(2017) Maria Elisa Perez-Muñoz 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

Large-scale contamination of microbial isolate genomes by Illumina PhiX control

(2015) Supratim Mukherjee et al.   Standards in Genomic Sciences

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

(2014) Susannah J Salter et al.   BMC BIOLOGY

Comparison of Gull Feces-Specific Assays Targeting the 16S rRNA Genes of Catellicoccus marimammalium and Streptococcus spp.

(2012) Hodon Ryu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genomic Diversity of Escherichia Isolates from Diverse Habitats

(2012) Seungdae Oh et al.   PLoS One

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS