August 15th, 2022

God morgon!

Good morning from Sweden. Today’s digest is a bag full of articles, mostly preprints, from various fields. A newly published article reports that non-antibiotics, carbamazepine, ibuprofen, naproxen and propranolol, affect the horiontal gene transfer (HGT) and promote sharing of plasmids that encode antibiotic resistance genes. This is an important conclusion as so far we were bothered only about antibiotics but now there is evidence that even non-antibiotics can promote antimicrobial resistance.

Staying with antibiotics, a new preprint reports Ruthenium complexes as potent antibacterial compounds against clinical strains of Pseudomonas aeruginosa. The group was able to demonstrate the mode of action of these compounds and also find mutations that might promote supressor phenotype. These compounds also show synergism with Rifampicin, a known antibiotic. Another preprint about P. aeruginosa reports that the bacterium carries multitude of phage resistance mechanisms to fend of bacteriophages. These mechanisms determine the host specificity of phages as individual resistance mechanism only provide resistance against specific phages. This can be a vital information for planning phage therapies.

Elsewhere in the digest are reports on correlation between the presence of certain microbial species with the presence of Legionella in selected EU cities, importance of gut microbiota on glucose metabolism in offspring, and how the climate change induced influx of Atlantic waters in Arctic affects the microbial diversity.

In the end, there is a special report on how certain dietary compounds can alter the micrbes in our food and result in changes to our food. The scientists have proposed a new field of research – nutrifermentics. They report how Benzoic acid, a common food additive, can induce epigenetic changes in Saccharomyces cerevisiae that alter the characteristic of wine. This has important implications in strain developement where deliberate genetic modifications may be avoided by inducing epigenetic changes using such additives.

I hope you will enjoy reading today’s digest. Have a great week!

Water microbiome

Preprint: Genome-resolved community structure and function of freshwater bacteria at a continental scale – Rebecca E. Garner, et al.

Preprint: Bacterial communities of premise plumbing systems in four European cities, and their association with culturable Legionella – Maria Scaturro, et al.

Preprint: Variations in Atlantic water influx and sea-ice cover drive taxonomic and functional shifts in Arctic marine bacterial communities – Taylor Priest, et al.

Bacteria Hysteria

Non-antibiotic pharmaceuticals promote conjugative plasmid transfer at a community-wide level – Yue Wang, et al. Microbiome

Preprint: Screening Avian Pathogens in Eggs from Commercial Hatcheries in Nepal – an Effective Poultry Disease Surveillance Tool – Shreeya Sharma

Preprint: Negative interactions and virulence differences drive the dynamics in multispecies bacterial infections – Désirée A. Schmitz, Richard C. Allen, and Rolf Kümmerli

Preprint: Growth arrest of Staphylococcus aureus induces daptomycin tolerance via cell wall remodelling – Elizabeth V. K. Ledger and Andrew M. Edwards

Preprint: Polynuclear ruthenium complexes are effective antibiotics against Pseudomonas aeruginosa – Brent S. Weber, et al.

Preprint: Cryo-EM structure of the Type IV pilus extension ATPase from enteropathogenic Escherichia coli – Ashok R. Nayak, et al.

Preprint: Accumulation of defense systems drives panphage resistance in Pseudomonas aeruginosa – Ana Rita Costa, et al.

Preprint: Neisseria gonorrhoeae diagnostic escape from a gyrA-based test for ciprofloxacin susceptibility can lead to increased zoliflodacin resistance – Daniel H. F. Rubin, Tatum D. Mortimer, and Yonatan H. Grad

Preprint: A contractile injection system mediates developmentally regulated intra-strain cell death in Streptomyces coelicolor – Maria Vladimirov, et al.

Gut microbiome

Vertical transmission of the gut microbiota influences glucose metabolism in offspring of mice with hyperglycaemia in pregnancy – Cunxi Xue, et al. Microbiome

Phages and viruses

Preprint: Genetic differences between 129S substrains affect antiretroviral immune responses – Robert Z. Zhang, et al.

Preprint: The dissemination of Rift Valley fever virus to the eye and sensory neurons of zebrafish larvae is stat1 dependent – S. ter Horst, et al.

Preprint: HIV-1 latent infection triggers broader epigenomic and transcriptional changes in protein-coding and long non-coding RNAs than active infection of SupT1 cells – Gabrielle Lê-Bury, et al.

Preprint: Pelagibacter phage Skadi – An abundant polar specialist that exemplifies ecotypic niche specificity among the most abundant viruses on Earth – Holger H Buchholz, et al.

Preprint: A comprehensive single cell data analysis of in lymphoblastoid cells reveals the role of Super-enhancers in maintaining EBV latency – Bingyu Yan, et al.

Preprint: Identification of β2 microglobulin, the product of B2M gene, as a Host Factor for Vaccinia Virus Infection by Genome-Wide CRISPR genetic screens – Alejandro Matía, et al.

Preprint: Generation of Recombinant Rotaviruses Expressing Human Norovirus Capsid Proteins – Asha A. Philip and John T. Patton

Preprit: Distantly related hepaciviruses share common entry factor, Claudin-1 – Kamilla Toon, et al.

Preprint: Organisation of the orthobunyavirus tripodal spike and the structural changes induced by low pH and K+ during entry – Samantha Hover, et al.

General microbiome

Preprint: Effects of Cr stress on bacterial community structure and diversity in rhizosphere soils of Iris pseudacorus – Zhao Wei, et al.

Preprint: Lack of specificity in Geobacter periplasmic electron transfer – Sol Choi, Chi Ho Chan, and Daniel R. Bond

Preprint: Lipidomic analysis reveals differences in Bacteroides species driven largely by plasmalogens, glycerophosphoinositols and certain sphingolipids – Eileen Ryan, et al.

Preprint: Turnover of the extracellular polymeric matrix in an EBPR microbial community – Sergio Tomás-Martínez, et al.

Preprint: An Optimal Regulation of Fluxes Dictates Microbial Growth In and Out of Steady-State – Griffin Chure and Jonas Cremer

Preprint: Cryo-ET of infected cells reveals that a succession of two lattices drives vaccinia virus assembly – Miguel Hernandez-Gonzalez, et al.

Preprint: Soil protists can actively redistribute beneficial bacteria along Medicago truncatula roots – Christopher J. Hawxhurst, et al.

Developing whole cell standards for the microbiome field – Chrysi Sergaki, et al. Microbiome

Fungi

Preprint: The capacity to configure the hymenophore is not confined to the pore field in Oak mazegill (Daedalea quercina, Polyporales) – Bjarke Jensen

Preprint: Epigenetic Changes in Saccharomyces cerevisiae Alters the Aromatic Profile in Alcoholic Fermentation – Yanzhuo Kong, et al.

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