March 28th, 2021

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

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