Hyvää Päivää from Helsinki, Finland ! Today’s digest contains a wide range of topics to explore! I particularly recommend taking the time to read at the fascinating review listed below exploring horizontal gene transfer in environmental microbial communities. They describe how advances in the computational analysis of metagenomic data has allowed us to dive deeper in understanding these processes in microbiomes.
Among the list of very interesting research papers in this digest, you’ll find a fascinating study exploring the symbiotic microbial communities associated with deeper corals. Although extensive litterature has been published on coral microbiomes from shallow waters, this papers is the first to examine microbial communities associated with the deep photosymbiotic corals, living at more than 150 m of depth!
Today’s non-microbiology pick is a really interesting paper from Faldelmola and collaborators reporting on the development by the Pan-African H3Africa Bioinformatics Network of two data portals for African genomic medicine and African microbiomes datasets. The paper explore how they lead a very successful 6-days hackathon allowing to efficiently develop these two important scientific ressources, but also how they build a collaborative community of African researchers and experts.
Have a great Weekend!
General microbiome
Review: Examining horizontal gene transfer in microbial communities – Brito – Nature reviews microbiology
Preprint: Evidence for a billion-years arms race between viruses, virophages and eukaryotes – Barreat and Katzourakis – BioRxiV
Unifying community detection across scales from genomes to landscapes – Hudon et al. – Oikos
Human gut microbiome
Preprint: Adaptive ecological processes and metabolic independence drive microbial colonization and resilience in the human gut – Watson et al. – BioRxiV
Animal experiments
Diversity and characteristics of raw milk microbiota from Korean dairy farms using metagenomic and culturomic analysis – Ryu et al. – Food control
Animal microbiome
Preprint: Reclassification of seven honey bee symbiont strains as Bombella apis – Smith et al. – BioRxiV
Symbiotic associations of the deepest recorded photosynthetic scleractinian coral (172 m depth) – Rouzé et al. – ISME Journal
Metagenomic shotgun sequencing reveals host species as an important driver of virome composition in mosquitoes – Thongsripong et al. – Scientific reports
Water and extremophile microbiome
Aerobic and anaerobic iron oxidizers together drive denitrification and carbon cycling at marine iron-rich hydrothermal vents – McAllister et al. – ISME Journal
Microbial niche differentiation explains nitrite oxidation in marine oxygen minimum zones – Sun et al. – ISME Journal
Morphological complexity affects the diversity of marine microbiomes – Lemay et al. – ISME Journal
Preprint: Abundance and Microbial Diversity from Surface to Deep Water Layers Over the Rio Grande Rise, South Atlantic – Ferreira et al. – BioRxiV
Bioinformatics
Supervised extraction of near-complete genomes from metagenomic samples: A new service in PATRIC – Parrello et al. – Plos One
A roadmap for metagenomic enzyme discovery – Robinson et al. – Natural Product Reports
Techniques
Preprint: Synergistic effect of short- and long-read sequencing on functional meta-omics – Galata et al. – BioRxiV
My non-microbiology picks
H3ABioNet genomic medicine and microbiome data portals hackathon proceedings – Fadlelmola et al. – Database
Microbiome Digest - Bik's Picks 