Good morning! There’s a diverse set of microbiome papers to share today, ranging from the human microbiome in Lynch Syndrome to the microbes that flavor wine and degrade paintings in art galleries. You may also want to check out the recent news that popular video game Borderlands 3 is introducing a new mini-game that prompts players to help “map” the human gut microbiome—technical details are hard to come by, but it appears to be alignment related. There is also a study that found more than 20 percent of recently published metagenomes are not accessible.
In addition, Microbiome Data Congress 2020 will be held online on May 6 and is offering free registration through tomorrow (Friday, April 10). Speakers include human microbiome researcher Dr. Nikos Kyrpides of the (U.S.) DOE Joint Genome Institute and soil microbiologist Dr. Kari Dunfield of the University of Guelph.
Human gut microbiome
Structure of the Mucosal and Stool Microbiome in Lynch Syndrome, Yan Yan et al., Cell Host & Microbe
Effects of sex and chronic cigarette smoke exposure on the mouse cecal microbiome, Tam and Filho et al., PLOS ONE
The gut microbiome but not the resistome is associated with urogenital schistosomiasis in preschool-aged children, Derick N. M. Osakunor et al., Communications Biology
Perspective: Developing a new class of engineered live bacterial therapeutics to treat human diseases, Mark R. Charbonneau et al., Nature Communications
Review: The gut mycobiome: The overlooked constituent of clinical outcomes and treatment complications in patients with cancer and other immunosuppressive conditions, Galloway-Peña and Kontoyiannis, PLOS Pathogens
Intestinal enteroids recapitulate the effects of short-chain fatty acids on the intestinal epithelium, Sarah C. Pearce et al., PLOS ONE
A combination of monosodium glutamate and high-fat and high-fructose diets increases the risk of kidney injury, gut dysbiosis and host-microbial co-metabolism, Thatsanapong Pongking et al., PLOS ONE
Plant, root, and soil microbiome
Preprint: Vineyard ecosystems are structured and distinguished by fungal communities impacting the flavour and quality of wine, Di Liu et al., bioRxiv
Bacterial community composition of vermicompost-treated tomato rhizospheres, Juana Munoz-Ucros et al., PLOS ONE
Field Performance of Mixtures of Pseudomonas and Bacillus spp. in Managing Papaya Ringspot Virus Disease and their Effect on Plant Defense Enzyme Activity, Ranasinghe and De Costa, Tropical Agricultural Research
Detection of potential biodeterioration risks for tempera painting in 16th century exhibits from State Tretyakov Gallery, Alexander Zhgun et al., PLOS ONE
Microbiome and antibiotic resistome in household dust from Beijing, China, Long-Jun Ding et al., Environment International
Preprint: Microbial dark matter driven degradation of carbon fiber polymer composites, Adam M. Breister et al., bioRxiv
Phages and viruses
Preprint: Primate phageomes are structured by superhost phylogeny and environment, Jan-Frederik Gogarten et al., bioRxiv
PIA: More Accurate Taxonomic Assignment of Metagenomic Data Demonstrated on sedaDNA From the North Sea, Becky Cribdon et al., Frontiers in Ecology and Evolution
A restriction enzyme reduced representation sequencing approach for low-cost, high-throughput metagenome profiling, Melanie K. Hess et al., PLOS ONE
Science, publishing, and career
Every fifth published metagenome is not available to science, Eckert, Di Cesare and Fontaneto et al., PLOS Biology
Thanks for heads up on the Microbiome Data Congress 2020!