A Case Study for the Recovery of Authentic Microbial Ancient DNA from Soil Samples

Environmental paleomicrobiology: using DNA preserved in aquatic sediments to its full potential

(2022) Eric Capo et al.   ENVIRONMENTAL MICROBIOLOGY

Benchmarking metagenomics classifiers on ancient viral DNA: a simulation study

(2022) Yami Ommar Arizmendi Cárdenas et al.   PeerJ

Reconstruction of ancient microbial genomes from the human gut

(2021) Marsha C. Wibowo et al.   NATURE

Effectiveness of decontamination protocols when analyzing ancient DNA preserved in dental calculus

(2021) Andrew G. Farrer et al.   Scientific Reports

GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy

(2021) Donovan H Parks et al.   NUCLEIC ACIDS RESEARCH

PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly

(2021) Maxime Borry et al.   PeerJ

Late Holocene climate anomaly concurrent with fire activity and ecosystem shifts in the eastern Australian Highlands

(2021) Zoë A. Thomas et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Early Last Interglacial ocean warming drove substantial ice mass loss from Antarctica

(2020) Chris S. M. Turney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Aquatic Thermal Reservoirs of Microbial Life in a Remote and Extreme High Andean Hydrothermal System

(2020) Vilma Pérez et al.   Microorganisms

An optimized method for the extraction of ancient eukaryote DNA from marine sediments

(2020) Linda Armbrecht et al.   Molecular Ecology Resources

Palaeomicrobiology: Application of Ancient DNA Sequencing to Better Understand Bacterial Genome Evolution and Adaptation

(2020) Luis A. Arriola et al.   Frontiers in Ecology and Evolution

Optimization of subsampling, decontamination, and DNA extraction of difficult peat and silt permafrost samples

(2020) Alireza Saidi-Mehrabad et al.   Scientific Reports

Evidence for signatures of ancient microbial life in paleosols

(2020) Katharina Frindte et al.   Scientific Reports

Do I have something in my teeth? The trouble with genetic analyses of diet from archaeological dental calculus

(2020) Allison E. Mann et al.   QUATERNARY INTERNATIONAL

Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments

(2019) Erik L. Clarke et al.   Microbiome

Assessing alignment-based taxonomic classification of ancient microbial DNA

(2019) Raphael Eisenhofer et al.   PeerJ

Laboratory contamination over time during low‐biomass sample analysis

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

An improved nucleic acid extraction method from dried blood spots for amplification of Plasmodium falciparum kelch13 for detection of artemisinin resistance

(2019) Kayvan Zainabadi et al.   MALARIA JOURNAL

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Ancient DNA from marine sediments: Precautions and considerations for seafloor coring, sample handling and data generation

(2019) Linda H. Armbrecht et al.   EARTH-SCIENCE REVIEWS

Consistent and correctable bias in metagenomic sequencing experiments

(2019) Michael R McLaren et al.   eLife

Comparison of extraction methods for recovering ancient microbial DNA from paleofeces

(2019) Richard W. Hagan et al.   AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY

More Arrows in the Ancient DNA Quiver: Use of Paleoepigenomes and Paleomicrobiomes to Investigate Animal Adaptation to Environment

(2019) Yichen Liu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Metabolic potential of microbial communities from ferruginous sediments

(2018) Aurèle Vuillemin et al.   ENVIRONMENTAL MICROBIOLOGY

A combined method for DNA analysis and radiocarbon dating from a single sample

(2018) Petra Korlević et al.   Scientific Reports

Differential preservation of endogenous human and microbial DNA in dental calculus and dentin

(2018) Allison E. Mann et al.   Scientific Reports

Proper Authentication of Ancient DNA Is Still Essential

(2018) Raphael Eisenhofer et al.   Genes

Mineral Facilitated Horizontal Gene Transfer: A New Principle for Evolution of Life?

(2018) Karina Krarup Sand et al.   Frontiers in Microbiology

Selection of Appropriate Metagenome Taxonomic Classifiers for Ancient Microbiome Research

(2018) Irina M. Velsko et al.   mSystems

Extraction of highly degraded DNA from ancient bones, teeth and sediments for high-throughput sequencing

(2018) Nadin Rohland et al.   Nature Protocols

A Low-Complexity GA-WSF Algorithm for Narrow-Band DOA Estimation

(2018) Haihua Chen et al.   International Journal of Antennas and Propagation

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

Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus

(2017) Laura S. Weyrich et al.   NATURE

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

GenBank

(2017) Dennis A Benson et al.   NUCLEIC ACIDS RESEARCH

Neandertal and Denisovan DNA from Pleistocene sediments

(2017) Viviane Slon et al.   SCIENCE

The influence of Antarctic subglacial volcanism on the global iron cycle during the Last Glacial Maximum

(2017) Silvia Frisia et al.   Nature Communications

Preservation and Significance of Extracellular DNA in Ferruginous Sediments from Lake Towuti, Indonesia

(2017) Aurèle Vuillemin et al.   Frontiers in Microbiology

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography

(2016) Stephen Nayfach et al.   GENOME RESEARCH

Centrifuge: rapid and sensitive classification of metagenomic sequences

(2016) Daehwan Kim et al.   GENOME RESEARCH

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data

(2016) Daniel H. Huson et al.   PLoS Computational Biology

Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons

(2016) C. Ryan Penton et al.   Frontiers in Microbiology

Large Differences in Bacterial Community Composition among Three Nearby Extreme Waterbodies of the High Andean Plateau

(2016) Pablo Aguilar et al.   Frontiers in Microbiology

Microbial Activity Response to Solar Radiation across Contrasting Environmental Conditions in Salar de Huasco, Northern Chilean Altiplano

(2016) Klaudia L. Hernández et al.   Frontiers in Microbiology

Isolation and Characterization of the First Xylanolytic Hyperthermophilic Euryarchaeon Thermococcus sp. Strain 2319x1 and Its Unusual Multidomain Glycosidase

(2016) Sergey N. Gavrilov et al.   Frontiers in Microbiology

Removal of Exogenous Materials from the Outer Portion of Frozen Cores to Investigate the Ancient Biological Communities Harbored Inside

(2016) Robyn A. Barbato et al.   Jove-Journal of Visualized Experiments

Residual soil DNA extraction increases the discriminatory power between samples

(2015) Jennifer M. Young et al.   Forensic Science Medicine and Pathology

Subsistence strategies in traditional societies distinguish gut microbiomes

(2015) Alexandra J. Obregon-Tito et al.   Nature Communications

Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification

(2015) Kirsten A. Ziesemer et al.   Scientific Reports

Microbial diversity and trophic components of two high altitude wetlands of the Chilean Altiplano

(2015) SERGIO SCOTT et al.   GAYANA

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Susannah J Salter et al.   BMC BIOLOGY

Prevention, diagnosis and treatment of high-throughput sequencing data pathologies

(2014) Xiaofan Zhou et al.   MOLECULAR ECOLOGY

Pathogens and host immunity in the ancient human oral cavity

(2014) Christina Warinner et al.   NATURE GENETICS

Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX

(2014) Mikkel Schubert et al.   Nature Protocols

Ancient and modern environmental DNA

(2014) Mikkel Winther Pedersen et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Strategic use of the underground in an energy mix plan: Synergies among CO2, CH4 geological storage and geothermal energy. Latium Region case study (Central Italy)

(2013) M. Procesi et al.   APPLIED ENERGY

Influence of Methanogenic Populations in Holocene Lacustrine Sediments Revealed by Clone Libraries and Fatty Acid Biogeochemistry

(2013) A. Vuillemin et al.   GEOMICROBIOLOGY JOURNAL

Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions

(2013) Christina J Adler et al.   NATURE GENETICS

Monitoring DNA Contamination in Handled vs. Directly Excavated Ancient Human Skeletal Remains

(2013) Elena Pilli et al.   PLoS One

Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments

(2013) J. Dabney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters

(2012) Kjersti Aagaard et al.   FASEB JOURNAL

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Temporal Patterns of Nucleotide Misincorporations and DNA Fragmentation in Ancient DNA

(2012) Susanna Sawyer et al.   PLoS One

Setting the stage – Building and working in an ancient DNA laboratory

(2011) Michael Knapp et al.   ANNALS OF ANATOMY-ANATOMISCHER ANZEIGER

Addressing challenges in the production and analysis of illumina sequencing data

(2011) Martin Kircher et al.   BMC GENOMICS

Impact of Small Repeat Sequences on Bacterial Genome Evolution

(2011) Nicholas Delihas   Genome Biology and Evolution

Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death

(2011) V. J. Schuenemann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The functional potential of high Arctic permafrost revealed by metagenomic sequencing, qPCR and microarray analyses

(2010) Etienne Yergeau et al.   ISME Journal

Fluid geochemistry of hydrothermal systems in the Arica-Parinacota, Tarapacá and Antofagasta regions (northern Chile)

(2010) F. Tassi et al.   JOURNAL OF VOLCANOLOGY AND GEOTHERMAL RESEARCH

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

An Efficient Multistrategy DNA Decontamination Procedure of PCR Reagents for Hypersensitive PCR Applications

(2010) Sophie Champlot et al.   PLoS One

The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information

(2010) T. Chen et al.   Database-The Journal of Biological Databases and Curation

Soil sampling based on field spatial variability of soil microbial indicators

(2009) Joséphine Peigné et al.   EUROPEAN JOURNAL OF SOIL BIOLOGY