Good morning from New Jersey! Tons of papers to share with you today, including three about the role of the microbiome in COVID-19 and multiple new analysis tools and techniques.
Human respiratory microbiome
Functional profiling of COVID-19 respiratory tract microbiomes, Niina Haiminen et al., Scientific Reports
[Preprint] Mild CF Lung Disease is Associated with Bacterial Community Stability, Thomas H. Hampton et al., bioRxiv
Human skin microbiome
[Preprint] On-person adaptive evolution of Staphylococcus aureus during atopic dermatitis increases disease severity, Felix M. Key et al., bioRxiv
Human gut microbiome
[Mini-Review] The Unique Impact of COVID-19 on Human Gut Microbiome Research, Ella Burchill et al., Frontiers in Medicine
Variability in digestive and respiratory tract Ace2 expression is associated with the microbiome, Koester and Li et al., PLOS ONE
[Review] Towards a mechanistic understanding of reciprocal drug–microbiome interactions, Michael Zimmermann et al., Molecular Systems Biology
[Review] The Microbiome Meets Nanotechnology: Opportunities and Challenges in Developing New Diagnostic Devices, Celia Fuentes‐Chust et al., Advanced Materials
[Preprint] The capacity to produce hydrogen sulfide (H2S) via cysteine degradation is ubiquitous in the human gut microbiome, Domenick J Braccia et al., bioRxiv
Model experiments
[Preprint] Species richness determines C. difficile invasion outcome in synthetic human gut communities, Susan Hromada et al., bioRxiv
Gut microbiota determines the social behavior of mice and induces metabolic and inflammatory changes in their adipose tissue, Oryan Agranyoni et al., npj Biofilms and Microbiomes
Improvement of loperamide-induced slow transit constipation by Bifidobacterium bifidum G9-1 is mediated by the correction of butyrate production and neurotransmitter profile due to improvement in dysbiosis, Yutaka Makizaki et al., PLOS ONE
Animal microbiome
A Preliminary Comparison on Faecal Microbiomes of Free-Ranging Large Baleen (Balaenoptera musculus, B. physalus, B. borealis) and Toothed (Physeter macrocephalus) Whales, Stefanie P. Glaeser et al., Microbial Ecology
Host–microbial systems as glass cannons: Explaining microbiome stability in corals exposed to extrinsic perturbations, Courtney M. Dunphy et al., Journal of Animal Ecology
Fish predation on corals promotes the dispersal of coral symbionts, Carsten G. B. Grupstra et al., Animal Microbiome
Plant, root, and soil microbiome
Global analysis of the apple fruit microbiome: Are all apples the same?, Ahmed Abdelfattah et al., Environmental Microbiology
Water and extremophile microbiome
[Preprint] Uncharted biosynthetic potential of the ocean microbiome, Lucas Paoli et al., bioRxiv
The microbiome of the Black Sea water column analyzed by shotgun and genome centric metagenomics, Pedro J. Cabello-Yeves et al., Environmental Microbiome
Revealing taxon-specific heavy metal-resistance mechanisms in denitrifying phosphorus removal sludge using genome-centric metaproteomics, Yuan Lin et al., Microbiome
Bioinformatics
Forensic Microbiome Database: A Tool for Forensic Geolocation Meta-Analysis Using Publicly Available 16S rRNA Microbiome Sequencing, Singh and Clarke et al., Frontiers in Microbiology
ProgPerm: Progressive permutation for a dynamic representation of the robustness of microbiome discoveries, Liangliang Zhang et al., BMC Bioinformatics
Model-Based Microbiome Data Ordination: A Variational Approximation Approach, Yanyan Zeng et al., Journal of Computational and Graphical Statistics
Techniques
Blue poo: impact of gut transit time on the gut microbiome using a novel marker, Francesco Asnicar et al., Gut
Benchmarking DNA isolation kits used in analyses of the urinary microbiome, Lisa Karstens et al., Scientific Reports
Choice of library preparation affects sequence quality, genome assembly, and precise in silico prediction of virulence genes in shiga toxin-producing Escherichia coli, Julie Haendiges et al., PLOS ONE
Microbiome Digest - Bik's Picks 