Greetings from Pittsburgh, PA! I’ve been following Microbiome Digest for several years, but this is my first contribution. Although my research is in a different subject area now, my PhD work focused on host-associated microbiota. That topic still has a special place in my heart, so below you’ll find research articles focused on the microbiota of calves, honey bees, dogs, giant clams, mosquitos, and bats! If host-associated microbiota isn’t your topic of interest, I’ve also included other articles so you can learn “WhatsGNU” in microbiology!
General microbiome
Review: A benchmark of algorithms for the analysis of pooled CRISPR screens – Bodapati et al. – Genome Biology
Animal experiments
Comparison of the ruminal and fecal microbiotas in beef calves supplemented or not with concentrate – Lourenco et al. – PLOS One
The trisaccharide melezitose impacts honey bees and their intestinal microbiota – Seeburger – PLOS One
Fecal shedding of Salmonella spp., Clostridium perfringens, and Clostridioides difficile in dogs fed raw meat-based diets in Brazil and their owners’ motivation – Viegas et al. – PLOS One
Mechanistic molecular responses of the giant clam Tridacna crocea to Vibrio coralliilyticus challenge – Xu et al. – PLOS One
Animal microbiome
Metagenomic analysis of Aedes aegypti and Culex quinquefasciatus mosquitoes from Grenada, West Indies – Ramos-Nino et al. – PLOS One
Detection of novel coronaviruses in bats in Myanmar – Valitutto et al. – PLOS One
Plant, root, and soil microbiome
Plant microbiome analysis after Metarhizium amendment reveals increases in abundance of plant growth-promoting organisms and maintenance of disease-suppressive soil – Barelli et al. – PLOS One
The genome evolution and domestication of tropical fruit mango – Wang et al. – Genome Biology
Water and extremophile microbiome
Environmental control on the distribution of metabolic strategies of benthic microbial mats in Lake Fryxell, Antarctica – Dillion et al. – PLOS One
Preprint: Experimentally-validated correlation analysis reveals new anaerobic methane oxidation partnerships with consortium-level heterogeneity in diazotrophy – Metcalfe et al. – bioRxiv
Built environment
A comparative analysis of drinking water employing metagenomics -Brumfield et al. – PLOS One
Prevalence and pollution characteristics of antibiotic resistant genes in one high anthropogenically-impacted river – Li and Zhang – PLOS One
Longitudinal survey of microbiome associated with particulate matter in a megacity – Qin et al. – Genome Biology
Phages and viruses
Ozone efficacy for the control of airborne viruses: Bacteriophage and norovirus models – Dubuis et al. – PLOS One
Bioinformatics
Decode-seq: a practical approach to improve differential gene expression analysis – Li et al. – Genome Biology
WhatsGNU: a tool for identifying proteomic novelty – Moustafa and Planet – Genome Biology
A Zipf-plot based normalization method for high-throughput RNA-seq data – Wang – PLOS One
Microbiome Digest - Bik's Picks 