December 17, 2020

Bonjour from Paris, France ! In today’s digest, readers interested in viromes will find a nice selection of papers looking at the viral populations associated to deep lake waters, birds, star fish and human gut! I also recommend anyone interested in this topic to take a look at a preprint from Amgarten and collaborators presenting a new computational tool called “vHULK”, allowing an in-silico bacteriophage host prediction!

Readers may also be interested in taking a look at the announcement of a new web interface allowing the exploration of the Human Microbiome Project (HMP). The ressource, called HMPDACC, provides a unified data repository for the two phases of the HMP, allows to search samples on a multitude of metadata, and provides analysis pipelines and standardized protocols to facilitate community use of HMP dataset.

Finally, today’s non-microbiology digest is a paper taking a look at the avalanche of papers and preprints published this year around the COVID-19 pandemic. Impressively, 84,180 indexed publications were relevant to COVID-19 written by 322,279 unique authors from all scientific subfields (except for Automobile Design & Engineering scientists!)

Have a great Saturday!


General microbiome

Preprint: Trait Evolution in Microbial Communities – Zhao et al. – BioRXiv

Human gut microbiome

The Pre‐treatment Gut Microbiome is Associated with Lack of Response to Methotrexate in New Onset Rheumatoid Arthritis – Artacho et al. – Arthitis and Rheumatology

Chapter: Oral Microbes: A Hidden Yet Powerful Evidence for Futuristic Forensic Investigation – Patel and Ganguly Soni – In: Shrivastava P., et al. (eds) Forensic DNA Typing: Principles, Applications and Advancements. Springer.

Microbiome Analysis from Paired Mucosal and Fecal Samples of a Colorectal Cancer Biobank – Wirth et al. – Cancers


Animal microbiome

Not That Close to Mommy: Horizontal Transmission Seeds the Microbiome Associated with the Marine Sponge Plakina cyanorosea – Oliveira et al. – mircoorganisms


Phages and viruses

Comparative Metagenomics of Palearctic and Neotropical Avian Cloacal Viromes Reveal Geographic Bias in Virus Discovery – Truchado et al. – microorganisms

Virome Analysis of Near-Bottom Coastal Water of Lake Baikal – Butina et al. – Microbiology ressource announcements

Virome Variation during Sea Star Wasting Disease Progression in Pisaster ochraceus (Asteroidea, Echinodermata) – Hewson et al. – Viruses

Gut eukaryotic virome in colorectal carcinogenesis: Is that a trigger? – Massimino et al. – Computational and structural biotechnology journal

Bioinformatics

Preprint: vHULK, a new tool for bacteriophage host prediction based on annotated genomic features and deep neural networks – Amgarten et al. – BioRXiv

HMPDACC: a Human Microbiome Project Multi-omic data resource – Huot Creasy et al. Nucleic Acids Research

Review: Literature on Applied Machine Learning in Metagenomic Classification: A Scoping Review – Tonkovic et al. – biology


My non-microbiology picks

Preprint: The rapid, massive infection of the scientific literature and authors by COVID-19 – Ioannidis et al. – BioRXiv

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