Today’s microbiome digest is a grab bag that includes ten simple rules for working with other people’s code, an article examining Wolbachia infections in native cockroach populations, and an article examining the role in lactic acid in shaping the human microbiome. Also highlighted is an article focused on human viruses residing within our cells and tissues, which demonstrated a unique virome in nine different human organs through targeted-enrichment viral metagenomics and virus specific qPCRs.
Happy reading!
General microbiome
The structure of prevacuolar compartments in Neurospora crassa as observed with super-resolution microscopy – Bowman – PLOS One
Phylogenetic trees of closely related bacterial species and subspecies based on frequencies of short nucleotide sequences – Nakano et al. – PLOS One
***Unmasking the tissue-resident eukaryotic DNA virome in humans – Pyöriä et al. – Nucleic Acids Research
Predicting partner fitness based on spatial structuring in a light-driven microbial community – Sakkos et al. – PLOS Computational Biology
Multi-site human microbiome
Evaluation of alcohol-free mouthwash for studies of the oral microbiome – Yano et al. – PLOS One
A systematically biosynthetic investigation of lactic acid bacteria reveals diverse antagonistic bacteriocins that potentially shape the human microbiome – Zhang et al. – Microbiome
Human gut microbiome
Positive mood-related gut microbiota in a long-term closed environment: a multiomics study based on the “Lunar Palace 365” experiment – Hao et al. – Microbiome
Animal microbiome
Wolbachia infection in native populations of Blattella germanica and Periplaneta americana – Choubdar et al. – PLOS One
Plant, root, and soil microbiome
Bacterial and fungal community composition and community-level physiological profiles in forest soils – Kunito et al. – PLOS One
Water and extremophile microbiome
Predicting microbial community compositions in wastewater treatment plants using artificial neural networks – Liu et al. – Microbiome
Open ocean and coastal strains of the N2-fixing cyanobacterium UCYN-A have distinct transcriptomes – Muñoz-Marín et al. – PLOS One
Meta-organism gene expression reveals that the impact of nitrate enrichment on coral larvae is mediated by their associated Symbiodiniaceae and prokaryotic assemblages – Tong et al. – Microbiome
Bioinformatics
Ten simple rules for working with other people’s code – Pilgrim et al. – PLOS Computational Biology
Predicting microbe organisms using data of living micro forms of life and hybrid microbes classifier – Raza et al. – PLOS One
iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria – Roux et al. – PLOS Biology
Microbiome Digest - Bik's Picks 