Joyeuses fêtes from Paris, France ! In today’s digest, you will find great papers looking at various animal and plant microbiomes. In particular, I recommend taking some time to look at a preprint from Brealey and collaborators exploring the impact of human antibiotic use on oral microbiome in wild animals. The authors used shotgun metagenomics to determine the abundance and diversity of antimicrobial resistance genes in the oral microbiome of brown bears from Swedish museum specimens. Importantly, they show a significant increase in antimicrobial resistance genes in correlation with modern human antibiotics use, showing an impact even on wildlife of our antibiotic consumption.
Today’s non-microbiology pick takes a look back at the history of bioinformatics through the data analysis and visualization of papers published between 1998 and 2019. In addition of reading this very interesting paper, you can take a look at the data collected through interactive visualizations available at http://bioinfo.dcc.ufmg.br/history !
Have a great Sunday!
Pregnancy and early life
Preprint: Metabolomic signature of the maternal microbiota in the fetus – Pessa-Morikawa et al. – BioRXiv
Human nearly-sterile sites
Preprint: The urinary microbiome in postmenopausal women with recurrent urinary tract infections – Hiersoux Vaughan et al. – BioRXiv
Preprint: Biofilm development on urinary catheters promotes the appearance of viable but non-culturable (VBNC) bacteria – Wilks et al. – BioRXiv
Animal microbiome
Preprint: Wild animal oral microbiomes reflect the history of human antibiotics use – Brealey et al. – BioRXiV
Plant, root, and soil microbiome
Dissimilarity analysis of microbial communities in the rhizosphere and tissues of diseased and healthy cherry trees (Cerasus pseudocerasus) – Ding et al. – Canadian Journal of Plant Pathology
First Recorded Account of Arbuscular Mycorrhizal Fungi in Sand Dunes in South Eastern Australia: Biogeography and Species Richness – Hanlon et al. – Journal of Coastal Research
Diversity and structural differences of bacterial microbial communities in rhizocompartments of desert leguminous plants – Zhou et al. – PLOS ONE
Preprint: Orchard management and landscape context mediate the floral microbiome of pear – Schaeffer et al. – BioRXiv
Water and extremophile microbiome
Interplay of microbial communities with mineral environments incoralline algae – Valdespino-Castillo et al. – Science of the total environment
Acid Mine Drainage as Energizing Microbial Niches for the Formation of Iron Stromatolites: The Tintillo River in Southwest Spain – Chacon-Baca et al. – Astrobiology
Bioinformatics
PStrain: An Iterative Microbial Strains Profiling Algorithm for Shotgun Metagenomic Sequencing Data – Wang et al. – Bioinformatics
MegaPath: sensitive and rapid pathogen detection using metagenomic NGS data – Leung et al. – BMC Genomics
My non-microbiology picks
A Brief History of Bioinformatics Told by Data Visualization – Mariano et al. – Brazilian Symposium on Bioinformatics
Microbiome Digest - Bik's Picks 