The Digest is back with a lot of plant and soil microbiome papers. Highlights include how nematodes may alter microbial communities to benefit the host, a review on host-microbe interactions affecting acne, and a common garden study on causal relationship between plant phenotype and its rhizosphere microbiome.
General microbiology
A Candida auris Outbreak and Its Control in an Intensive Care Setting – David W. Eyre et al. – New England Journal of Medicine
** Diplogastrellus nematodes are sexually transmitted mutualists that alter the bacterial and fungal communities of their beetle host – Cristina C. Ledón-Rettig et al. – PNAS
Cross-talk between MarR-like transcription factors coordinates the regulation of motility in uropathogenic Escherichia coli – Courtney L. Luterbach & Harry L.T. Mobley – Infection and Immunity
Antibiotic resistance
Environmental dimensions of antibiotic resistance: Assessment of basic science gaps – Kornelia Smalla et al. – FEMS Microbiology Ecology
Human skin microbiome
** Host-microbiome interactions and recent progress into understanding the biology of acne vulgaris – Alan M. O’Neill & Richard L. Gallo – Microbiome
Human oral microbiome
Molecular analysis of oral microflora in patients with primary Sjögren’s syndrome by using high-throughput sequencing – Zhifang Zhou et al. – PeerJ
Human repiratory microbiome
Genomics, Microbiomics, Proteomics, and Metabolomics in Bronchopulmonary Dysplasia – Charitharth Vivek Lal et al. – Seminars in Perinatology
Human gut microbiome
Association of metformin administration with gut microbiome dysbiosis in healthy volunteers – Ilze Elbere et al. – PLoS One
Oral probiotic combination of Lactobacillus and Bifidobacterium alters the gastrointestinal microbiota during antibiotic treatment for Clostridium difficile infection – T. J. De Wolfe et al. – PLoS One
Review: Impact of the gut microbiota on chemical risk assessment – Tine Rask Licht & Martin Iain Bahl – Current Opinion in Toxicology
Alterations in gut bacterial and fungal microbiomes are associated with bacterial Keratitis, an inflammatory disease of the human eye – Rajagopalaboopathi Jayasudha et al. – Journal of Biosciences
The Microbiome and Radiation Induced-Bowel Injury: Evidence for Potential Mechanistic Role in Disease Pathogenesis – Tomoko Kumagai et al. – Nutrients
Impact of Agaricus bisporus Mushroom Consumption on Gut Health Markers in Healthy Adults – Julie Hess et al. – Nutrients
Animal experiments
Effect of probiotic treatment on the clinical course, intestinal microbiome, and toxigenic Clostridium perfringens in dogs with acute hemorrhagic diarrhea – Anna-Lena Ziese et al. – PLoS One
Caloric restriction promotes functional changes involving short-chain fatty acid biosynthesis in the rat gut microbiota – Alessandro Tanca et al. – Scientific Reports
Animal microbiome
Evidence for Gut-Associated Serratia symbiotica in Wild Aphids and Ants Provides New Perspectives on the Evolution of Bacterial Mutualism in Insects – François Renoz et al. – Microbial Ecology
Plant, root and soil microbiome
Vertical stratification of bacteria and the chemical compounds in crude oil-contaminated soil layers of the semi-deserted Dzungharian Basin – Jiang-Ke Yang et al. – PLoS One
Dynamics of Changes in Microbiological Composition of Stored Sediments – Aleksandra Sałata et al. – Journal of Ecological Engineering
Review: Nano-scale undead drivers of microbial life, biogeochemical turnover and ecosystem functions – Yakov Kuzyakov & Kyle Mason-Jones – Soil Biology and Biochemistry
Response of microbial communities to different organochlorine pesticides (OCPs) contamination levels in contaminated soils – Yu Du et al. – Chemosphere
Changes in the soil microbial communities of alpine steppe at Qinghai-Tibetan Plateau under different degradation levels – Heng Zhou et al. – Science of The Total Environment
Responses of the endophytic bacterial communities of Juncus acutus to pollution with metals, emerging organic pollutants and to bioaugmentation with indigenous strains – Evdokia Syranidou et al. – Frontiers in Plant Science
Desert and steppe soils exhibit lower autotrophic microbial abundance but higher atmospheric CO2 fixation capacity than meadow soils – Kang Zhao et al. – Soil Biology and Biochemistry
Bacterial microbiota and metabolic character of traditional sour cream and butter in Buryatia, Russia – Jie Yu et al. – Frontiers in Microbiology
Interactions between soil properties, soil microbes and plants in remnant-grassland and old-field areas: a reciprocal transplant approach – Monique E. Smith et al. – Plant and Soil
Exploration of the Biosynthetic Potential of the Populus Microbiome – Patricia M. Blair et al. – mSystems
Soil microbial community structure in the rhizosphere of Robinia pseudoacacia L. seedlings exposed to elevated air temperature and cadmium-contaminated soils for 4 years – X. Jia et al. – Science of The Total Environment
** Plant Phenotypic Traits Eventually Shape Its Microbiota：A Common Garden Test – Yunshi Li et al. – Frontiers in Microbiology
Soil Type-Dependent Interactions of P-Solubilizing Microorganisms with Organic and Inorganic Fertilizers Mediate Plant Growth Promotion in Tomato – Isaac Kwadwo Mpanga et al. – Agronomy
Water and extremophile microbiome
Distinct community structure and microbial functions of biofilms colonizing microplastics – Lingzhan Miao et al. – Science of The Total Environment
Mature biofilm communities on synthetic polymers in seawater – Specific or general? – Inga V. Kirstein et al. – Marine Environmental Research
Phages and viruses
Virome definition in cerebrospinal fluid of patients with neurological complications after hematopoietic stem cell transplantation – C. Pou et al. – Journal of Clinical Virology
Metagenomic sequencing from mosquitoes in China reveals a variety of insect and human viruses – Pengpeng Xiao et al. – Frontiers in Cellular and Infection Microbiology
Technology
Review: Practical considerations for sampling and data analysis in contemporary metagenomics-based environmental studies – Christopher Staley & Michael J. Sadowsky –
Bioinformatics
Postnovo: Post-Processing Enables Accurate and FDR-Controlled De Novo Peptide Sequencing – Samuel E. Miller et al. – Journal of Proteome Research
Microbiome Digest - Bik's Picks 