Hello from the Sonoran Desert! In today’s digest, you’ll find two very interesting reviews! Stagaman and collaborators come back on years of Zebra-fish gut microbiome research and explore the insights gleaned from this awesome model animal. On the other hand, François and Pybus review our understanding of avian viromes in both wild and domesticated bird populations, highlighting the current limitations and pitfalls in this research area.
But today’s digest also contains very interesting research papers! Gulino and collaborators are exploring viromes in New York city wastewater systems. This paper is particularly interesting as bacteriophages are typically left out from urban environments microbiomes studies, despite their abundance and importance in ecosystems.
Finally, today’s non-microbiology pick is a review that comes back on how information theory, developped by Claude Shannon in the late 40s, have been used in computational biology. This paper is particularly interesting for readers wanting to learn more about the basics of information theory and how it is applied today in bioinformatics.
Have a great Sunday!
Pregnancy and early life
Review: The microbiome in pediatric oncology – Rotz et al. – Cancer
Human respiratory microbiome
Metagenomic analysis of the lung microbiome in pulmonary tuberculosis – a pilot study – Hu et al. – Emerging Microbes & infections
Human vaginal microbiome
Taxonomic and Functional Differences in Cervical Microbiome Associated with Cervical Cancer Development –Nkufi Tange et al. – Scientific reports
Human gut microbiome
Preprint: The gut microbiome regulates memory function – Noble et al. – BioRxiV
Animal experiments (mouse/rat experiments, chickens/pigs on different diets)
review: Zebrafish microbiome studies make waves – Stagaman et al. – Lab Animal
Built environment (subways, indoor surfaces)
Revealing antimicrobial resistance in stormwater with MinION – Bialasek et al. – Chemosphere
Phages and viruses
Review: Towards an understanding of the avian virome –François et al. – Journal of general Virology
Initial Mapping of the New York City Wastewater Virome –Gulino et al. – mSystems
Higher order Markov models for metagenomic sequence classification – Burks et al. –Bioinformatics
Preprint: Combinatorial Algorithms for Strain Level Metagenomic Microbial Detection and Quantification –Zhu et al. –BioRxiV
Preprint: Ultra-rapid metagenotyping of the human gut microbiome – Shi et al. – BioRxiV
My non-microbiology pick
Review: Information Theory in Computational Biology: Where We Stand Today – Chanda et al. – Entropy