After a week, our Microbiome Digest is back online with a rich collection of articles in all fields microbiome. Highlights include a review on colonization resistance to bacterial pathogens in the gut, a report on daily sampling of the individual microbiome response to similar diets, and, have you heard of the FAIR principles for scientific data? Happy reading!
General microbiology
Bacillus cereus infection in neonates and the absence of evidence for the role of banked human milk: Case reports and literature review – Antoine Lewin et al. – Infection Control & Hospital Epidemiology
Comment: Multiple levels of the unknown in microbiome research – Andrew Maltez Thomas & Nicola Segata – BMC Biology
Comparative genome analysis reveals niche-specific genome expansion in Acinetobacter baumannii strains – Harshita Yakkala & Devyani Samantarrai et al. – PLoS One
Antimicrobial resistance
Definitions and guidelines for research on antibiotic persistence – Nathalie Q. Balaban et al. – Nature Reviews Microbiology
Review: Genomic and metagenomic approaches for predictive surveillance of emerging pathogens and antibiotic resistance – Kimberley V. Sukhum et al. – Clinical Pharmacology & Therapeutics
Review: Antimicrobial Tolerance and Metabolic Adaptations in Microbial Biofilms – Aurélie Crabbé et al. – Trends in Microbiology
Human oral microbiome
Dysbiotic salivary microbiota in dry mouth and primary Sjögren’s syndrome patients – S. Rusthen et al. – PLoS One
Human gut microbiome
** Review: Gut Microbiota and Colonization Resistance against Bacterial Enteric Infection – Q. R. Ducarmon et al. – Microbiology and Molecular Biology Reviews
Review: Gastrointestinal Microbiota in Patients with Chronic Kidney Disease: A Systematic Review – SeonYoon Chung et al. – Advances in Nutrition
Gut Microbial Associations to Plasma Metabolites Linked to Cardiovascular Phenotypes and Risk – Alexander Kurilshikov et al. – Circulation Research
Commentary: The Microbiome, Plasma Metabolites, Dietary Habits, and Cardiovascular Risk Unravelling Their Interplay – Dariush Mozaffarian – Circulation Research
Review: Macronutrient metabolism by the human gut microbiome: major fermentation by-products and their impact on host health – Kaitlyn Oliphant & Emma Allen-Vercoe – Microbiome
Review: Lactose digestion in humans: intestinal lactase appears to be constitutive whereas the colonic microbiome is adaptable – Richard A Forsgård – The American Journal of Clinical Nutrition
** Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans – Abigail J. Johnson et al – Cell Host & Microbe
Review: HIV, Cancer, and the Microbiota: Common Pathways Influencing Different Diseases – Sergio Serrano-Villar et al. – Frontiers in Immunology
IDDF2019-ABS-0157 Fecal microbiota transplantations reconstitute gut fungal and viral microbiota in graft-versus-host disease – Fen Zhang et al. – Gut
Exploring the impact of Helicobacter pylori on gut microbiome composition – Nihar Ranjan Dash et al. – PLoS One
Metabolomics
Review: Translational Metabolomics: Current Challenges and Future Opportunities – Farhana R. Pinu et al. – Metabolites
Animal experiments
Consumption of post-fermented Jing-Wei Fuzhuan brick tea alleviates liver dysfunction and intestinal microbiota dysbiosis in high fructose diet-fed mice – Xiangnan Zhang et al. – RSC Advance
Mouse: B vitamin sharing promotes stability of gut microbial communities – Vandana Sharma et al. – Frontiers in Microbiology
Variability of the ability of complex microbial communities to exclude microbes carrying antibiotic resistance genes in rabbits – caroline s. achard et al. – Frontiers in Microbiology
Effects of BARLEYmax and high-β-glucan barley line on short-chain fatty acids production and microbiota from the cecum to the distal colon in rats – Seiichiro Aoe et al. – PLoS One
Animal microbiome
The “wildness” of the giant panda gut microbiome and its relevance to effective translocation – Ran Yao & Liangliang Xu et al. – Global Ecology and Conservation
Host genetics influence the rumen microbiota and heritable rumen microbial features associate with feed efficiency in cattle – Fuyong Li et al – Microbiome
Mosquito: Host species and site of collection shape the microbiota of Rift Valley fever vectors in Kenya – David P. Tchouassi et al – PLoS NTD
Longitudinal microbiome profiling reveals impermanence of probiotic bacteria in domestic pigeons – Kirsten Grond, Julie M. Perreau & Wesley T. Loo et al. – PLoS One
Food microbiome
Ground beef microbiome changes with antimicrobial decontamination interventions and product storage – Margaret D. Weinroth et al. – PLoS One
Plant, root and soil microbiome
Biocontrol of Root Diseases and Growth Promotion of the Tuberous Plant Aconitum carmichaelii Induced by Actinomycetes Are Related to Shifts in the Rhizosphere Microbiota – Yulong Li et al. – Microbial Ecology
Microbial communities from different soil types respond differently to organic waste input – Sophie Sadet-Bourgeteau et al. – Applied Soil Ecology
Plant-based oil-sorbents harbor native microbial communities effective in spilled oil-bioremediation under nitrogen starvation and heavy metal-stresses – N. Dashti et al. – Ecotoxicology and Environmental Safety
Effects of agricultural management on rhizosphere microbial structure and function in processing tomato – Jennifer E. Schmidt et al. – Applied and Environmental Microbiology
Microbial diversity in bulk and rhizosphere soil of Ranunculus glacialis along a high-alpine altitudinal gradient – Nadine Praeg et al. – Frontiers in Microbiology
Tripartite Interactions Between Endophytic Fungi, Arbuscular Mycorrhizal Fungi, and Leymus chinensis – Hui Liu et al. – Microbial Ecology
Review: Plant host-associated mechanisms for microbial selection – Piet Jones et al. – Frontiers in Plant Science
Soil Microbial Biomass and Fungi Reduced with Canola Introduced into Long-Term Monoculture Wheat Rotations – Jeremy C. Hansen et al. – Frontiers in Microbiology
Pearls: Microbiota-mediated disease resistance in plants – Nathan Vannier et al. – PLoS Pathogens
Effects of maize rotation on the physicochemical properties and microbial communities of American ginseng cultivated soil – Xiao-Lin Jiao et al. – Scientific Reports
Linking the response of soil microbial community structure in soils to long-term wastewater irrigation and soil depth – Qiuling Dang et al. – Science of the Total Environment
One-time nitrogen fertilization shifts switchgrass soil microbiomes within a context of larger spatial and temporal variation – Huaihai Chen et al. – PLoS One
Water and extremophile microbiome
Comparison of bacterial community structure and potential functions in hypoxic and non-hypoxic zones of the Changjiang Estuary – Dong-Mei Wu & Qiu-Ping Dai et al. – PLoS One
Review: Progress and promise of omics for predicting the impacts of climate change on harmful algal blooms – Gwenn M.M.Hennon & Sonya T.Dyhrman – Harmful Algae
Position-specific metabolic probing and metagenomics of microbial communities reveal conserved central carbon metabolic network activities at high temperatures – Scott C. Thomas et al. – Frontiers in Microbiology
Chemical composition of extracellular polymeric substances and evolution of microbial community in activated sludge exposed to ibuprofen – Guangqing Zhou et al. – Journal of Environmental Management
Enhancement of facultative anaerobic denitrifying communities by oxygen release from roots of the macrophyte in constructed wetlands – Haishu Sun et al. – Journal of Environmental Management
How does environmental inter-annual variability shape aquatic microbial communities? A 40-year annual record of sedimentary DNA from a boreal lake (Nylandssjön, Sweden) – Eric Capo et al. – Frontiers in Ecology and Evolution
Phages and viruses
Review: Virome and bacteriome: two sides of the same coin – Jonathan Stern et al. – Current Opinion in Virology
Technology
Gut microbiome analysis by post: Evaluation of the optimal method to collect stool samples from infants within a national cohort study – Georgina M. Williams et al. – PLoS One
Microbiota data from low biomass milk samples is markedly affected by laboratory and reagent contamination – Josef Dahlberg et al. – PLoS One
Bioinformatics
GRASP2: fast and memory-efficient gene-centric assembly and homolog search for metagenomic sequencing data – Cuncong Zhong et al. – BMC Bioinformatics
Proficiency testing of virus diagnostics based on bioinformatics analysis of simulated in silico high-throughput sequencing datasets – Annika Brinkmann et al. – Journal of Clinical Microbiology
Microbes in the news
FDA recalls certain tattoo inks for bacterial contamination – Fox 13 News
Viruses found to use intricate ‘treadmill’ to move cargo across bacterial cells – ScienceDaily
USDA issues reminder about how to safely meal prep – Erica Chayes Wida – Today
Highlights and key takeaways from the 2019 Boston Bacterial Meeting (BBM) – Dr. Tomislav Meštrović, MD, Ph.D. – News Medical
Non-microbiology picks
** The State of Open Data Report 2018
Network analysis to evaluate the impact of research funding on research community consolidation – Daniel J. Hicks et al. – PLoS One
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