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