Today’s Digest features several soil and environmental microbiome papers, including the effect of fire on soil ecosystems, insights into the freshwater microbiome associated with the world’s largest mining disaster, applications of soils in forensics, and chemical leaching from LCD screens due to synergistic bacteria. Plus, check out some animal work in marine invertebrates (Sea stars and Ascidians) as well as minks, flying squirrels, and bees!
Pregnancy and early life
The profile of human milk metabolome, cytokines and antibodies in inflammatory bowel diseases versus healthy mothers and potential impact on the newborn – Xuanyi Meng -Journal of Crohn’s and Colitis
Human multi-site microbiome
Shared gut, but distinct oral microbiota composition in primary Sjögren’s syndrome and systemic lupus erythematosus – Taco A. van der Meulen – Journal of Autoimmunity
Urine Bacteria-Derived Extracellular Vesicles and Allergic Airway Diseases in Children – Mona Samra – International Archives of Allergy and Immunology
Review: Repertoire of bacterial species cultured from the human oral cavity and respiratory tract – Maxime DM Fonkou – Future Microbiology
Gut-brain axis
Schizophrenia and gut-flora related epigenetic factors – Chuanjun Zhuo – Progress in Neuro-Psychopharmacology and Biological Psychiatry
The structure of resilience in irritable bowel syndrome and its improvement through hypnotherapy: Cross-sectional and prospective longitudinal data – Johannes Peter – PLOS One
Fermented foods, the gut and mental health: a mechanistic overview with implications for depression and anxiety – Hajara Aslam – Nutritional Neuroscience
Chronic alcohol exposure induced gut microbiota dysbiosis and its correlations with neuropsychic behaviors and brain BDNF/Gabra1 changes in mice – Zheng Xu – Biofactors
Microbial treatment: the potential application for Parkinson’s disease – Xin Fang – Neurological Sciences
Multiple Sclerosis-Associated Changes in the Composition and Immune Functions of Spore-Forming Bacteria. – Egle Cekanaviciute – mSystems
Human gut microbiome
The effect of drinking water pH on the human gut microbiota and glucose regulation: results of a randomized controlled cross-over intervention – Tue H. Hansen – Scientific Reports
Composition of gut microbiota and its association with body mass index and lifestyle factors in a cohort of 7–18 years old children from the American Gut Project – Jinbing Bai – Pediatric Obesity
Long-term impact of oral vancomycin, ciprofloxacin and metronidazole on the gut microbiota in healthy humans. – Bastiaan W Haak – Journal of Antimicrobial Chemotherapy
Helicobacter pylori Infection: New Facts in Clinical Management. – Peter Malfertheiner – Current Treatment Options in Gastroenterology
Animal experiments
The protective effects of fecal microbiota transplantation in an experimental model of necrotizing enterocolitis – Christian Prado – Journal of Pediatric Surgery
Intestinal Snakeskin Limits Microbial Dysbiosis during Aging and Promotes Longevity – Anna M. Salazar – iScience
Animal microbiome
Microbiome shifts with onset and progression of Sea Star Wasting Disease revealed through time course sampling – Melanie M. Lloyd – Scientific Reports
Core and Dynamic Microbial Communities of Two Invasive Ascidians: Can Host–Symbiont Dynamics Plasticity Affect Invasion Capacity?– Hila Dror – Microbial Ecology
Fecal bacterial microbiota of Canadian commercial mink (Neovison vison): Yearly, life stage, and seasonal comparisons – Nicole R. Compo – PLOS One
Variations in Gut Microbiota of Siberian Flying Squirrels Correspond to Seasonal Phenological Changes in Their Hokkaido Subarctic Forest Ecosystem – Po-Yu Liu – Microbial Ecology
Influence of Feeding Type and Nosema ceranae Infection on the Gut Microbiota of Apis cerana Workers – Shao K. Huang – mSystems
Host selectively contributes to shaping intestinal microbiota of carnivorous and omnivorous fish – Kristian Daly – The Journal of General and Applied Microbiology
Plant, root, and soil microbiome
Fire modulates ecosystem functioning through the phylogenetic structure of soil bacterial communities – Eduardo Pérez-Valera – Soil Biology and Biochemistry
Assessment of soil microbial communities involved in cellulose utilization at two contrasting Alpine forest sites – José A. Siles – Soil Biology and Biochemistry
Experimental Testing of Dispersal Limitation in Soil Bacterial Communities with a Propagule Addition Approach – Fen-Guo Zhang – Microbial Ecology
Influence of different biological control agents and compost on total and nitrification driven microbial communities at rhizosphere and soil level in a lettuce – Fusarium oxysporum f. sp. lactucae pathosystem – Maria Alexandra Cucu – Journal of Applied Microbiology
Assessment of 16S rRNA gene primers for studying bacterial community structure and function of aging flue-cured tobaccos. – Fan Wang – AMB Express
Changes in bacterial diversity and catabolic gene abundance during the removal of dimethylphenol isomers in laboratory-scale constructed wetlands. – Mónica A. Vásquez Piñeros – Applied Microbiology and Biotechnology
Abiotic factors determine functional outcomes of microbial inoculation of soils from a metal contaminated brownfield – Jay Prakash Singh – Ecotoxicology and Environmental Safety
Applying microbial biogeography in soil forensics – Habteab Habtom – Forensic Science International: Genetics
eDNA metabarcoding supporting community assessment of environmental stressor in a field-based sediment microcosm study – Jianghua Yang – Environmental Science and Technology
Water and extremophile microbiome
Analysis of the diversity of aerobic, thermophilic endospore-forming bacteria in two Algerian hot springs using cultural and non-cultural methods – Mohamed Amine Gomri – Annals of Microbiology
Anaerobic biological treatment of industrial saline wastewater: Fixed bed Reactor performance and analysis of the microbial community structure and abundance – Mariem Jeddi – Environmental Technology
Microbiome triggered transformations of trace organic chemicals in the presence of effluent organic matter in managed aquifer recharge (MAR) systems – Karin Hellauer – Environmental Science and Technology
Insights on the freshwater microbiomes metabolic changes associated with the world’s largest mining disaster – Marcelle C. Cordeiro – Science of the Total Environment
Microbial Functional Responses to Cholesterol Catabolism in Denitrifying Sludge – Sean Ting-Shyang Wei – mSystems
Built environment
Leaching of indium from end-of-life LCD panels via catalysis by synergistic microbial communities – Yaling Xie – Science of the Total Environment
Probiotics/Prebiotics
Probiotic and synbiotic therapy in the critically ill: State of the art – James M. Davison – Nutrition
Butyrate Producers as Potential Next-Generation Probiotics: Safety Assessment of the Administration of Butyricicoccus pullicaecorum to Healthy Volunteers. – Leen Boesmans – mSystems
Divergent short-chain fatty acid production and succession of colonic microbiota arise in fermentation of variously-sized wheat bran fractions – Yunus E. Tuncil – Scientific Reports
Bioinformatics
Machine Learning Reveals Missing Edges and Putative Interaction Mechanisms in Microbial Ecosystem Networks – Demetrius DiMucci – mSystems
Techniques
A tridecaptin-based fluorescent probe for differential staining of Gram-negative bacteria. – Wei Wang – Analytical and Bioanalytical Chemistry
High-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome Integrity – Jeremiah J. Minich – mSystems
Book Chapter: Activity-Based Protein Profiling—Enabling Multimodal Functional Studies of Microbial Communities – Christopher Whidbey – Current Topics in Microbiology and Immunology
Microbiome Digest - Bik's Picks 