God morgon!

Good morning from ice-cold Sweden.

Today’s digest carries interesting preprints on microbiology. I really liked reading the report on a bacteriophage cocktail that kills Listeria without affecting the commensal microbiota and a novel rifampin derivative that is active against doxycycline resistant Francisella. Some preprints highlight the basic biology of bacteria. There is a study on genomic evolution in one of the most important bacterial species – Streptomyces, report on endopeptidases in E. coli, and more reports on methods for studying and annotating antibiotic resistance genes.

Elsewhere in the digest are prediction models for drug interaction iin Tuberculosis, interkingdom biofilms by Candida and Lactobacillus, and microbiome studies on human milk, metazoan-microbe interactions, and some marine microbes.

Finally, there is an interview with Pae-Ji soo, the CEO of Genome and Company who talks about the importance of microbiome in modulating the immunotherapy.

Happy reading!

Bacteria hysteria

Preprint: A bacteriophage cocktail significantly reduces Listeria monocytogenes without deleterious impact on the commensal gut microbiota under simulated gastro-intestinal conditions – Rasmus Riemer Jakobsen, et al.

Preprint: TPR1, a novel rifampin derivative demonstrates efficacy alone and in combination with doxycycline against the NIAID Category A Priority Pathogen F. tularensis – Jason E. Cummings, et al.

Preprint: A nadA mutation confers nicotinic acid auxotrophy in pro-carcinogenic intestinal Escherichia coli NC101 – Lacey R Lopez, et al.

Preprint: A non-adaptive demographic mechanism for genome expansion in Streptomyces – Mallory J Choudoir, et al.

Preprint: Role of endopeptidases in peptidoglycan synthesis mediated by alternative cross-linking enzymes in Escherichia coli – Henri Voedts, et al.

Viruses

Preprint: In vivo generation of BK and JC polyomavirus defective viral genomes in human urine samples associated with higher viral loads – Amin Addetia, et al.

Preprint: Methane-derived carbon flow through host-virus trophic networks in soil – Sungeun Lee, et al.

Preprint: Genome sequencing of the bacteriophage CL31 and interaction with the host strain Corynebacterium glutamicum ATCC 13032 – Max Hünnefeld, et al.

General microbiome

Preprint: Chlorine inactivation of Escherichia coli O157:H7 in fresh produce wash process: effectiveness and modeling – Mohammadreza Dehghan Abnavi, et al.

Subcellular view of host–microbiome nutrient exchange in sponges: insights into the ecological success of an early metazoan–microbe symbiosis – Meggie Hudspith, et al., Microbiome

Functional metagenomics reveals differential chitin degradation and utilization features across free-living and host-associated marine microbiomes – I. Raimundo, et al., Microbiome

Repeatability and reproducibility assessment in a large-scale population-based microbiota study: case study on human milk microbiota – Shirin Moossavi, et al., Microbiome

Preprint: Do size and shape matter? Exploring the interactions and the metabolome of the soil isolate Hylemonella gracilis – Olaf Tyc, et al.

Eukaryotes

Preprint: Modelling the impact of the macroalgae Asparagopsis taxiformis on rumen microbial fermentation and methane production – Rafael Muñoz-Tamayo, et al.

Preprint: Transcriptome signature of cell viability predicts drug response and drug interaction for Tuberculosis – Vivek Srinivas, et al.

Preprint: Chemical ecology of a tripartite symbiosis – Nicholas C Mucci, et al.

Preprint: Mapping global shifts in Saccharomyces cerevisiae gene expression across asynchronous time trajectories with diffusion maps – Taylor Reiter, et al.

Preprint: Recurrent Vulvovaginal Candidiasis; a dynamic interkingdom biofilm disease of Candida and Lactobacillus –
Emily McKloud, et al.

Methods

Preprint: Genie: An interactive real-time simulation for teaching genetic drift – Andreina I Castillo, et al.

Preprint: Direct-from-specimen microbial growth inhibition spectrums under antibiotic exposure and comparison to conventional antimicrobial susceptibility testing – Jade Chen, et al.

HMD-ARG: hierarchical multi-task deep learning for annotating antibiotic resistance genes – Yu Li,et al., Microbiome

Others

‘Microbiome to be game changer in immunotherapy‘ : The Korean Times