Good morning! There’s a particularly broad collection of microbiome papers to share with you today, from the bacteria that hang onto wounds after debridement to the biofilms that form in the ancient ruins of a town buried by the eruption of Mount Vesuvius. A few unusual highlights include the sexually transmitted microbiome of bedbugs and the gut microbes that colonize a sea cucumber after it grows up, remove its own digestive tract and grows a new one. Some interesting new software tools are hiding in the “Bioinformatics” section at the bottom as well.
General microbiome
Intracellular Staphylococcus aureus persisters upon antibiotic exposure, Frédéric Peyrusson et al., Nature Communications
Human respiratory microbiome
Investigation of the human nasal microbiome in persons with long- and short-term exposure to methicillin-resistant Staphylococcus aureus and other bacteria from the pig farm environment, Md Zohorul Islam et al., PLOS ONE
Human skin microbiome
Microbial predictors of healing and short-term effect of debridement on the microbiome of chronic wounds, Samuel Verbanic et al., npj Biofilms and Microbiomes
Human gut microbiome
Systemic short chain fatty acids limit antitumor effect of CTLA-4 blockade in hosts with cancer, Clélia Coutzac et al., Nature Communications
Functional and phylogenetic alterations in gut microbiome are linked to graft-versus-host disease severity, Mathilde Payen et al., Blood Advances
Animal experiments
Preprint: Metagenomic alterations in gut microbiota precede and predict onset of colitis in the IL10 gene-deficient murine model, Miyoshi and Lee et al., bioRxiv
Dietary Fiber Protects against Diabetic Nephropathy through Short-Chain Fatty Acid–Mediated Activation of G Protein–Coupled Receptors GPR43 and GPR109A, Yan Jun Li et al., Journal of the American Society of Nephrology
Probiotic strain Lactobacillus plantarum YYC-3 prevents colon cancer in mice by regulating the tumour microenvironment, Yuanchun Yue et al., Biomedicine & Pharmacotherapy
Effect of stevia on the gut microbiota and glucose tolerance in a murine model of diet-induced obesity, Sarah L. Becker et al., FEMS Microbiology Ecology
Animal microbiome
Sea cucumber intestinal regeneration reveals deterministic assembly of the gut microbiome, Brooke L. Weigel, Applied and Environmental Microbiology
Mating changes the genital microbiome in both sexes of the common bedbug Cimex lectularius across populations, Sara Bellinvia et al., Proceedings of the Royal Society B
Plant, root, and soil microbiome
Mutualist and pathogen traits interact to affect plant community structure in a spatially explicit model, John W. Schroeder et al., Nature Communications
Preprint: Seasonal dynamics of methane cycling microbial communities in Amazonian floodplain sediments, Julia B. Gontijo et al., bioRxiv
Preprint: Community succession of the grapevine fungal microbiome in the annual growth cycle, Liu and Howell, bioRxiv
Characterizing changes in soil microbiome abundance and diversity due to different cover crop techniques, Wang and Wu et al., PLOS ONE
Preprint: Specific and conserved patterns of microbiota-structuring by maize benzoxazinoids in the field, Selma Cadot et al., bioRxiv
Water and extremophile microbiome
The role of changing temperature in microbial metabolic processes during permafrost thaw, Komi S. Messan et al., PLOS ONE
Built environment
Microbial biofilm community structure and composition on the lithic substrates of Herculaneum Suburban Baths, De Natale and Mele et al., PLOS ONE
Probiotics/prebiotics
Comparative effectiveness of probiotic-based formulations on cecal microbiota modulation in broilers, Denise R. Rodrigues et al., PLOS ONE
Phages and viruses
Weirdo19ES is a novel singleton mycobacteriophage that selects for glycolipid deficient phage-resistant M. smegmatis mutants, Cristian Alejandro Suarez et al., PLOS ONE
Bioinformatics
Decoding the language of microbiomes using word-embedding techniques, and applications in inflammatory bowel disease, Tataru and David, PLOS Computational Biology
Sequence count data are poorly fit by the negative binomial distribution, Stijn Hawinkel et al., PLOS ONE
Preprint: sPepFinder expedites genome-wide identification of small proteins in bacteria, Li and Chao, bioRxiv
Logicome Profiler: Exhaustive detection of statistically significant logic relationships from comparative omics data, Fukunaga and Iwasaki, PLOS ONE
Microbiome Digest - Bik's Picks 