Hyvää Päivää from Helsinki, Finland ! Today’s digest contains quite a lot of different topics. If you are interested in marine microbiology and virology, I recommend taking a look at the paper by Gazitúa and collaborators. In this study they investigated the role of phages in shaping the metabolism metabolic networks along redox gradients associated with marine oxygen minimum zones. To do so, they investigated the phage contents in auxiliary metabolic genes involved in bacterial photosynthesis, central carbon metabolism, and nutrient cycling.
Today’s non-microbiology pick is a web-platform, called Sysrev, built to aid in systematic evidence reviews. Sysrev contains thousands of Findable, Accessible, Iteroperable and Reusable (FAIR) datasets from a large variety of disciplines.
Have a great Sunday!
Human gut microbiome
Preprint: Fecal microbiome of children with norovirus gastroenteritis – Merces Hernandez et al. – bioRxiv
Plant, root, and soil microbiome
Preprint: Eukaryotic rather than prokaryotic microbiomes change over seasons in rewetted fen peatlands – Wang et al. – bioRxiv
Plant part and a steep environmental gradient predict plant microbial composition in a tropical watershed. – Bernard et al. – ISME J
Distribution patterns of Acidobacteriota in different fynbos soils – Conradie and Jacobs – PLOS
Water and extremophile microbiome
Preprint: Epidemiological dynamics of viral infection in a marine pico-eukaryote – Listmann et al. – bioRxiv
Preprint: A deep-sea sulfate reducing bacterium directs the formation of zero-valent sulfur via sulfide oxidation – Liu et al. – bioRxiv
Preprint: Integrated multi-omics investigations reveal the key role of synergistic microbial networks in removing plasticizer di-(2-ethylhexyl) phthalate from estuarine sediments – Ting-Shyang Wei et al. – bioRxiv
Time-series transcriptomics from cold, oxic subseafloor crustal fluids reveals a motile, mixotrophic microbial community – Seyler et al. – ISME J
Food microbiology
Preprint: Biofilm-forming capacity of Escherichia coli isolated from cattle and beef packing plants: relation to virulence attributes, stage of processing, antimicrobial interventions, and heat tolerance – Stanford et al. – bioRxiv
Phages and viruses
Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters – Gazitúa et al. – ISME J
Bioinformatics
Umibato: estimation of time-varying microbial interaction using continuous-time regression hidden Markov model
Shion et al. – bioRxiv
My non-microbiology picks
Preprint: Sysrev: A FAIR Platform For Data Curation And Systematic Evidence Review – Bozada et al. – bioRxiv
Microbiome Digest - Bik's Picks 