Metagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data

AR Odom, T Faits, E Castro-Nallar, KA Crandall… - Scientific reports, 2023 - nature.com
Most experiments studying bacterial microbiomes rely on the PCR amplification of all or part
of the gene for the 16S rRNA subunit, which serves as a biomarker for identifying and …

Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank

M Steinegger, SL Salzberg - Genome biology, 2020 - Springer
Genomic analyses are sensitive to contamination in public databases caused by incorrectly
labeled reference sequences. Here, we describe Conterminator, an efficient method to …

A perspective on the role of lanthanides in biology: Discovery, open questions and possible applications

LJ Daumann, A Pol, HJMO den Camp… - Advances in microbial …, 2022 - Elsevier
Because of their use in high technologies like computers, smartphones and renewable
energy applications, lanthanides (belonging to the group of rare earth elements) are …

[PDF][PDF] The Dark mAtteR iNvestigator (DARN) tool: getting to know the known unknowns in COI amplicon data

H Zafeiropoulos, L Gargan… - MBMG …, 2021 - pdfs.semanticscholar.org
The mitochondrial cytochrome C oxidase subunit I gene (COI) is commonly used in
environmental DNA (eDNA) metabarcoding studies, especially for assessing metazoan …

Wochenende—modular and flexible alignment-based shotgun metagenome analysis

I Rosenboom, T Scheithauer, FC Friedrich, S Pörtner… - BMC genomics, 2022 - Springer
Background Shotgun metagenome analysis provides a robust and verifiable method for
comprehensive microbiome analysis of fungal, viral, archaeal and bacterial taxonomy …

Inline index helped in cleaning up data contamination generated during library preparation and the subsequent steps

Y Wang, H Yuan, J Huang, C Li - Molecular Biology Reports, 2022 - Springer
Background High-throughput sequencing involves library preparation and amplification
steps, which may induce contamination across samples or between samples and the …

Geographically diverse canid sampling provides novel insights into pre-industrial microbiomes

K Yarlagadda, AJ Zachwieja… - … of the Royal …, 2022 - royalsocietypublishing.org
Canine microbiome studies are often limited in the geographic and temporal scope of
samples studied. This results in a paucity of data on the canine microbiome around the …

Large-scale analysis of sheep rumen metagenome profiles captured by reduced representation sequencing reveals individual profiles are influenced by the …

MK Hess, HE Hodgkinson, AS Hess, L Zetouni… - BMC genomics, 2023 - Springer
Background Producing animal protein while reducing the animal's impact on the
environment, eg, through improved feed efficiency and lowered methane emissions, has …

Metagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data

T Faits, AR Odom-Mabey, E Castro-Nallar, KA Crandall… - bioRxiv, 2022 - biorxiv.org
Most experiments studying bacterial microbiomes rely on the PCR amplification of all or part
of the gene for the 16S rRNA subunit, which serves as a biomarker for identifying and …

Metascan: METabolic analysis, SCreening and annotation of metagenomes

G Cremers, MSM Jetten, HJM Op den Camp… - Frontiers in …, 2022 - frontiersin.org
Large scale next generation metagenomic sequencing of complex environmental samples
paves the way for detailed analysis of nutrient cycles in ecosystems. For such an analysis …