Selection of appropriate metagenome taxonomic classifiers for ancient microbiome research
Metagenomics enables the study of complex microbial communities from myriad sources,
including the remains of oral and gut microbiota preserved in archaeological dental calculus …
including the remains of oral and gut microbiota preserved in archaeological dental calculus …
[HTML][HTML] Benchmarking Metagenomic Classifiers on Simulated Ancient and Modern Metagenomic Data
V Pusadkar, RK Azad - Microorganisms, 2023 - mdpi.com
Taxonomic profiling of ancient metagenomic samples is challenging due to the
accumulation of specific damage patterns on DNA over time. Although a number of methods …
accumulation of specific damage patterns on DNA over time. Although a number of methods …
[HTML][HTML] Quantitative metaproteomics of medieval dental calculus reveals individual oral health status
The composition of ancient oral microbiomes has recently become accessible owing to
advanced biomolecular methods such as metagenomics and metaproteomics, but the utility …
advanced biomolecular methods such as metagenomics and metaproteomics, but the utility …
[HTML][HTML] Assessing alignment-based taxonomic classification of ancient microbial DNA
R Eisenhofer, LS Weyrich - PeerJ, 2019 - peerj.com
The field of palaeomicrobiology—the study of ancient microorganisms—is rapidly growing
due to recent methodological and technological advancements. It is now possible to obtain …
due to recent methodological and technological advancements. It is now possible to obtain …
[HTML][HTML] Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification
KA Ziesemer, AE Mann, K Sankaranarayanan… - Scientific reports, 2015 - nature.com
To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has
been primarily accomplished through a metataxonomic approach involving targeted …
been primarily accomplished through a metataxonomic approach involving targeted …
[HTML][HTML] aMeta: an accurate and memory-efficient ancient metagenomic profiling workflow
Abstract Analysis of microbial data from archaeological samples is a growing field with great
potential for understanding ancient environments, lifestyles, and diseases. However, high …
potential for understanding ancient environments, lifestyles, and diseases. However, high …
[HTML][HTML] The postmedieval Latvian oral microbiome in the context of modern dental calculus and modern dental plaque microbial profiles
A Kazarina, E Petersone-Gordina, J Kimsis, J Kuzmicka… - Genes, 2021 - mdpi.com
Recent advantages in paleomicrobiology have provided an opportunity to investigate the
composition of ancient microbial ecologies. Here, using metagenome analysis, we …
composition of ancient microbial ecologies. Here, using metagenome analysis, we …
Comprehensive analysis of microorganisms accompanying human archaeological remains
Metagenome analysis has become a common source of information about microbial
communities that occupy a wide range of niches, including archaeological specimens. It has …
communities that occupy a wide range of niches, including archaeological specimens. It has …
[HTML][HTML] decOM: similarity-based microbial source tracking of ancient oral samples using k-mer-based methods
Background The analysis of ancient oral metagenomes from archaeological human and
animal samples is largely confounded by contaminant DNA sequences from modern and …
animal samples is largely confounded by contaminant DNA sequences from modern and …
Correcting index databases improves metagenomic studies
Assessing the taxonomic composition of metagenomic samples is an important first step in
understanding the biology and ecology of microbial communities in complex environments …
understanding the biology and ecology of microbial communities in complex environments …