Hyvää Päivää from Helsinki, Finland ! Today’s digest contains a variety of interesting papers, in particular in bioinformatics! I recommend anyone interesting in metagenomic read classification to take a look at the benchmark study by Arizmendi Cardenas and collaborators. They compared read-based taxonomic classification tools on their capacity to handle ancient DNA sequences, characterized by a higher mutation rate and shorter sequences.
This digest also contains a very good review on the current state of the art network analysis methods for exploring interaction in complex microbial communities.
Finally, today’s non-microbiology pick is a piece exploring the current challenges and limitations for the annotation of microbiome dataset with high-quality metadata.
Have a great Weekend!
Human gut microbiome
Systematic Review: The Gut Microbiome and Its Potential Clinical Application in Inflammatory Bowel Disease – Aldars-Garcia et al. – Microorganisms
Millet-based supplement restored gut microbial diversity of acute malnourished pigs – Li et al. – PLOS One
A mixture of quebracho and chestnut tannins drives butyrate-producing bacteria populations shift in the gut microbiota of weaned piglets – Miragoli et al. – PLOS One
Dynamic changes occur in the DNA gut virome of female cynomolgus macaques during aging – Tan et al. – Microbiology Open
Virome Diversity among Mosquito Populations in a Sub-Urban Region of Marseille, France – Nebbak et al. – Viruses
Plant, root, and soil microbiome
Preprint: Mapping the microbial diversity and natural resistome of north Antarctica soils – Marcoleta et al. – BioRXiv
Community dynamics in rhizosphere microorganisms at different development stages of wheat growing in confined isolation environments – Ma et al. – Applied Microbiology and Biotechnology
Water and extremophile microbiome
Book chapter: Bioprospecting Extreme Ecosystems Before They Vanish: The (Poorly Studied) Microbiology of Tropical Glaciers – Yarzabal – Extreme environment (CRC press)
Investigating variability in microbial community composition in replicate environmental DNA samples down lake sediment cores – Pearman et al. – PLOS One
Preprint: Benchmarking metagenomics classifiers on ancient viral DNA: a simulation study – Arizmendi Cardenas et al. – BioRXiv
Review: Network analysis methods for studying microbial communities: A mini review – Matchado et al. – Computational and sctructural Biotechnology Journal
Improving metagenomic binning results with overlapped bins using assembly graphs – Mallawaarachchi et al. – Algorithms for molecular biology
My non-microbiology picks
Preprint: Current challenges in microbiome metadata collection – Rosenfeld et al. – BioRXiv