Happy Monday! Today’s Microbiome Digest is chock-full. You’ll find: a review of approaches towards predictive microbial ecology, insights into function gleaned from rumen metatranscriptomics, diet studies in hunter-gatherers and mice, characterization of the mosquito and termite microbiota, the wild side of plant microbiomes, fermentation for traditional liquors, and much more!
General microbiome
Systems biology approaches towards predictive microbial ecology – Anne E. Otwell – Environmental Microbiology
One Health Relationships Between Human, Animal, and Environmental Microbiomes: A Mini-Review – Pauline Trinh – Frontiers in Public Health
Tuning of human MAIT cell activation by commensal bacteria species and MR1-dependent T-cell presentation – Cihan Tastan – Mucosal Immunology
Holistic Assessment of Rumen Microbiome Dynamics through Quantitative Metatranscriptomics Reveals Multifunctional Redundancy during Key Steps of Anaerobic Feed Degradation – Andrea Söllinger – mSystems
Multi-site human microbiome
A prospective study to examine the association of the urinary and fecal microbiota with prostate cancer diagnosis after transrectal biopsy of the prostate using 16sRNA gene analysis – Shaheen Alanee – Prostate
Streptococcus and Prevotella are associated with the prognosis of oesophageal squamous cell carcinoma – Yanfang Liu – Journal of Medical Microbiology
Urinary symptoms are associated with certain urinary microbes in urogynecologic surgical patients – Cynthia S. Fok – International Urogynecology Journal
Human gut microbiome
Links between environment, diet, and the hunter-gatherer microbiome – Gabriela K. Fragiadakis – Gut Microbes
Klebsiella oxytoca expands in cancer cachexia and acts as a gut pathobiont contributing to intestinal dysfunction – Sarah A. Pötgens – Scientific Reports
Co-Administration of Probiotics with Prescribed Antibiotics for Preventing Clostridium difficile Diarrhea – Ahmed S. I. Hamed – Academic Emergency Medicine
Animal experiments
Effect of industrial trans-fatty acids-enriched diet on gut microbiota of C57BL/6 mice – Yueting Ge – European Journal of Nutrition
AIEC infection triggers modification of gut microbiota composition in genetically predisposed mice, contributing to intestinal inflammation – Alexis Bretin – Scientific Reports
Effect of probiotic Bifidobacterium bifidum G9-1 on the relationship between gut microbiota profile and stress sensitivity in maternally separated rats – Hirokazu Fukui – Scientific Reports
Animal microbiome
Comparison of microbiomes of cold-water corals Primnoa pacifica and Primnoa resedaeformis, with possible link between microbiome composition and host genotype – Dawn B. Goldsmith – Scientific Reports
Neonatal gut and immune maturation is determined more by postnatal age than by post-conceptional age in moderately preterm pigs – Shuqiang Ren – American Journal of Physiology-Gastrointestinal and Liver Physiology
Functional metagenomics reveals abundant polysaccharide-degrading gene clusters and cellobiose utilization pathways within gut microbiota of a wood-feeding higher termite – Ning Liu – ISME Journal
Mosquito microbiota cluster by host sampling location – Ephantus J. Muturi – Parasites and Vectors
Plant, root, and soil microbiome|
The wild side of plant microbiomes – Juan E. Pérez-Jaramillo – Microbiome
Unraveling the Composition of the Root-Associated Bacterial Microbiota of Phragmites australis and Typha latifolia – Laura Pietrangelo – Frontiers in Microbiology
Vermicompost addition influences symbiotic fungi communities associated with leek cultivated in metal-rich soils – Antoine Pierart – Environmental Science and Pollution Research
Plant drought resistance is mediated by soil microbial community structure and soil-plant feedbacks in a savanna tree species – Nianxun Xi – Environmental and Experimental Botany
Metabolic specialization of denitrifiers in permeable sediments controls N2 O emissions – Hannah K. Marchant – Environmental Microbiology
Bacterial Biomarkers of Marcellus Shale Activity in Pennsylvania – Jeremy R. Chen See – Frontiers in Microbiology
Eighteen-Year Farming Management Moderately Shapes the Soil Microbial Community Structure but Promotes Habitat-Specific Taxa – Huaihai Chen – Frontiers in Microbiology
Water and extremophile microbiome
Bacterial and archaeal profiling of hypersaline microbial mats and endoevaporites, under natural conditions and methanogenic microcosm experiments – José Q. García-Maldonado – Extremophiles
Subsurface landfill leachate contamination affects microbial metabolic potential and their expression in the Banisveld aquifer – Neslihan Taş – FEMS Microbiology Ecology
Food microbiology
Robust Domination of Lactobacillus sakei in Microbiota During Traditional Japanese Sake Starter Yamahai-Moto Fermentation and the Accompanying Changes in Metabolites – Atsushi Tsuji – Current Microbiology
DaQu fermentation selects for heat resistant Enterobacteriaceae and bacilli – Zhiying Wang – Applied and Environmental Microbiology
Exploitation of autochthonous Tuscan sourdough yeasts as potential starters – Michela Palla – International Journal of Food Microbiology
Techniques
Conventional culture methods with commercially available media unveil the presence of novel culturable bacteria – Tamaki Ito – Gut Microbes