God morgon!

Good morning from Sweden. I know everyone is looking forward to a long weekend, but today is just Monday.

Today’s digest begins with a new visualisation tool for microbiome analysis in R – animalcules. In another study, probiotic yeast metabolites were reported to inhibit bacterial virulence. It is yet another evidence in support of the fermented milk-based probiotic drinks. Talking about the diet, a team of researchers has found the commonly used dietary emulsifiers have a detrimental impact on the gut microbiome. A new study on studying the microbiome using PCR amplification and sequencing illustrates how off-target amplification can introduce a lot of problems. The study in question compared the brain microbiome of healthy individuals and individuals with Parkinson’s disease. Another study has shown how reduced genome provides certain bacteria an advantage in thriving during coastal dinoflagellate blooms.

Elsewhere in the digest are preprints describing a new broad spectrum antifungal, Kenyan traditional medicine as an approach to tackle antibiotic resistance, and prediction of antibiotic resistance using machine learning approach.

Hope you like today’s collection!

Computational Biology

animalcules: interactive microbiome analytics and visualization in R – Yue Zhao, et al., Microbiome

Phylogenetic Core Groups: a promising concept in search of a consistent methodological framework – Alberto Pascual-García, Microbiome

Preprint: Machine-learning prediction of resistance to sub-inhibitory antimicrobial concentrations from Escherichia coli genomes– Sam Benkwitz-Bedford, et al.

Environmental Microbiome

Opportunistic bacteria with reduced genomes are effective competitors for organic nitrogen compounds in coastal dinoflagellate blooms – Yu Han, et al., Microbiome

Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals– T. Keller-Costa, et al., Microbiome

Age and sex-associated variation in the multi-site microbiome of an entire social group of free-ranging rhesus macaques – Mareike C. Janiak, et al., Microbiome

Holo-omics for deciphering plant-microbiome interactions – Ling Xu, et al., Microbiome

General Microbiome

Much ado about nothing? Off-target amplification can lead to false-positive bacterial brain microbiome detection in healthy and Parkinson’s disease individuals – Janis R. Bedarf, et al., Microbiome

Diet and gut microbiome interactions of relevance for symptoms in irritable bowel syndrome – Julien Tap, et al., Microbiome

Cross-kingdom inhibition of bacterial virulence and communication by probiotic yeast metabolites – Orit Malka, et al., Microbiome

Revealing taxon-specific heavy metal-resistance mechanisms in denitrifying phosphorus removal sludge using genome-centric metaproteomics – Yuan Lin, et al., Microbiome

Direct impact of commonly used dietary emulsifiers on human gut microbiota – Sabrine Naimi, et al., Microbiome

Preprint: Paenibacillus sp. strain UY79, isolated from a root nodule of Arachis villosa, displays a broad spectrum of antifungal activity – Andrés Costa, et al.

Bacteria Hysteria

Preprint: Accessory genomic epidemiology of co-circulating Acinetobacter baumannii clones – Valeria Mateo-Estrada, et al.

Preprint: Kenyan Traditional Medicine: Exploring Old Solutions to the Modern Antibacterial Crises Through Natural Products Chemistry – Fidensio K. Ndegwa, et al.

Preprint: The Detection of Bergeyella zoohelcum in Young Children after Cat Bite – Min Hu, et al.

Preprint: Chromatic bacteria version 2 – A Himar1 transposon based delivery vector to extend the host range of a toolbox to fluorescently tag bacteria – Christian F Stocks, et al.

Viruses

Preprint: Human herpesvirus 8 molecular mimicry of ephrin ligands facilitates cell entry and triggers EphA2 signaling – Taylor L. Light, et al.

Preprint: Th17 cell master transcription factor RORC2 regulates HIV-1 gene expression and viral outgrowth – Tomas Raul Wiche Salinas, et al.

Preprint: Rapid evolutionary turnover of mobile genetic elements drives microbial resistance to viruses – Fatima Aysha Hussain, et al.