Hello from the Sonoran Desert! In today’s digest, you’ll find quite a few exciting reads about ancient microbes!
Duchêne and collaborators review recents efforts in paleopathology leading to the genome sequencing of ancient pathogens of historical interest such as the pre-modern bubonic plague (Yersinia pestis), smallpox (Variola virus) and cholera (Vibrio cholerae). In their review, the authors explore this amazing topic that aims to broaden our understanding of the past infectious disease.
On the other hand, Eisenhofer and collaborators examine ancient microbial DNA preserved within dental calculus samples from two major cultural periods in Japan: the Jomon period circa 3000 years ago and the Edo period circa 400–150 ago. In this piece, they explore how human oral microbiomes have changed through time in ancient Japanese populations.
Finally, you’ll find in this digest a non-microbiology pick: a “10 simple rules” paper outlining best practices for annotating and submitting sequencing data! Indeed, metadata accompanying sequence datasets is critical to ensure data longevity and reusability by both human and machine agents, and poor metadata can drastically reduce the value of sequencing experiments by limiting its reuse in integrative analyses!
Have a great Sunday!
General Microbiology
Review: The Recovery, Interpretation and Use of Ancient Pathogen Genomes – Duchêne et al. – Current Biology
Multi-site human microbiome
Functional diversity of microbial ecologies estimated from ancient human coprolites and dental calculus – Jacobson et al. – Philosphical transactions of the royal society of Biological sciences.
Human respiratory and oral microbiome
Investigating the demographic history of Japan using ancient oral microbiota – Eisenhofer et al. – Philosphical transactions of the royal society of Biological sciences.
Human gut microbiome
Preprint: Distinct human gut microbial taxonomic signatures uncovered with different sample processing and microbial cell disruption methods for metaproteomic analysis – Garcia-Duran et al. – BioRxiv.
Review: Deciphering diet-gut microbiota-host interplay: Investigations of pectin. – Tan and Nie – Trends in Food Science & Technology
Plant, root, and soil microbiome
Book Chapter: Microbes and Environment: Global Warming Reverting the Frozen Zombies. In: Fahad et al. (eds) Environment, Climate, Plant and Vegetation Growth. Springer, Cham.
Taxonomic Diversity of Bacteria and Their Filterable Forms in the Soils of Eastern Antarctica (Larsemann Hills and Bunger Hills) – Kudinova et al. – Microbiology.
Preprint: Long-term warming effects on the microbiome and nitrogen fixation associated with the moss Racomitrium lanuginosum in Icelandic tundra – Klarenberg et al. – bioRxiv
Water and extremophile microbiome
Diversity of Eukaryotic Microorganisms in the Drainage Waters of a Coal Open-Cast Mine – Gruzdev et al. – Microbiology
Dissimilarity of microbial diversity of pond water, shrimp intestine and sediment in Aquamimicry system – Zeng et al. – AMB express.
Comparative diversity analysis of halophiles at two polar saltern systems in Indramayu, West Java, Indonesia – Chasanah et al. – Letters in Applied Microbiology.
Mechanistic model of nutrient uptake explains dichotomy between marine oligotrophic and copiotrophic bacteria – Norris et al. – BioRxiv.
Food microbiology
Review: Microbial diversity of seafood. Parlapani. Current Opinion in Food Science.
Phages and viruses
The first head‐tailed virus, MFTV1, produced by a hyperthermophilic methanogenic deep‐sea archaea – Thiroux et al. – Environmental microbiology.
Review: Single-virus genomics and beyond – Martinez et al. – Nature reviews Microbiology
Bioinformatics
A Rapid Automated Process for Organizing Bacterial Cluster Segments Using Deep Neural Networks – Elroy Martis et al. – IEEE conference
Techniques
FACS-iChip: a high-efficiency iChip system for microbial ‘dark matter’ mining – Liu et al. – Marine Life Science and Technology
Comparison of Nucleic Acid Extraction Methods for a Viral Metagenomics Analysis of Respiratory Viruses – Sabatier et al. – Microorganisms
Science, publishing, and career
Preprint: Advancing science or advancing careers? Researchers’ opinions on success indicators – Aubert Bonn and Pinxten – BioRxiv.
My non-microbiology picks
Ten simple rules for annotating sequencing experiments – Stevens et al. – Plos Computational Biology
Microbiome Digest - Bik's Picks 