January 06, 2021

Good morning, today we selected papers about the cancer microbiome atlas, detection of blood parasites, antibiotics and gut microbiome, metabolome and a new binning approach for metagenomic data using auto-encoders.

General microbiome

The cancer microbiome atlas: a pan-cancer comparative analysis to distinguish tissue-resident microbiota from contaminants – Dohlaman et al. – Cell Host & Microbe

Human nearly-sterile sites (blood, organs, brain)

Sensitive universal detection of blood parasites by selective pathogen-DNA enrichment and deep amplicon sequencing – Flaherty et al. – Microbiome

Human gut microbiome

Long-Term Impact of Suppressive Antibiotic Therapy on Intestinal Microbiota – Escudero-Sanchez et al. – genes

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Metagenomics dataset used to characterize microbiome in water and sediments of the lake Solenoe (Novosibirsk region, Russia) – Bryanskaya et al. – Data in Brief

*Metabolome

Changes in the Serum Metabolome of Patients Treated With Broad-Spectrum Antibiotics – Kaskiw et al. – Pathogens and Immunity

Walnut Consumption, Plasma Metabolomics, and Risk of Type 2 Diabetes and Cardiovascular Disease – Guasch-Ferre et al. – The Journal of Nutrition

Bioinformatics

Improved metagenome binning and assembly using deep variational autoencoders – Nissen et al. – Nature Biotechnology

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