Happy June! A rich Digest today featuring evolution of antibiotic resistant Enterobacter, a review on links between gut microbiota and gastrointestinal cancers, and functional variation in the gut microbiome of wild Drosophila populations. Enjoy!
General microbiology
Metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities – Manuel Kleiner et al. – PNAS
Commentary: The need for independent research on the health effects of glyphosate-based herbicides – Philip J. Landrigan and Fiorella Belpoggi – Environmental Health
Antibiotic resistance
** Genomic and Geographic Context for the Evolution of High-Risk Carbapenem-Resistant Enterobacter cloacae Complex Clones ST171 and ST78 – Angela Gomez-Simmonds, Medini K. Annavajhala and Zheng Wang et al. – mBio
Doctoral thesis: Implementation of an Antibiotic Stewardship Program for Urinary Tract Infections – Michel, Kaysha Pollyanna – Wilmington University
Preprint: Disrupting folate metabolism alters the capacity of bacteria in exponential growth to develop persisters to antibiotics – Jasmine Morgan et al. – bioRxiv
Pregnancy and early life
Probiotic supplementation and associated infant gut microbiome and health: a cautionary retrospective clinical comparison – C. Quin et al. – Scientific Reports
Human skin microbiome
The microbiota of traumatic, open fracture wounds is associated with mechanism of injury – Casey Bartow‐McKenney et al. – Wound Repair and Regeneration
Human gut microbiome
Review: Gut nutrient sensing and microbiota function in the control of energy homeostasis – Gilles Mithieux – Current Opinion in Clinical Nutrition and Metabolic Care
Gut Microbiota: FFAR Reaching Effects on Islets – Medha Priyadarshini et al. – Endocrinology
Pathophysiology of diverticular disease – Kathleen M. Schieffer et al. – Expert Review of Gastroenterology & Hepatology
** Review: Gut microbiota-mediated inflammation in obesity: a link with gastrointestinal cancer – Patrice D. Cani & Benedicte F. Jordan – Nature Reviews Gastroenterology & Hepatology
Combining amplicon sequencing and metabolomics in cirrhotic patients highlights distinctive microbiota features involved in bacterial translocation, systemic inflammation and hepatic encephalopathy – Valerio Iebba et al. – Scientific Reports
Human gut-microbiome-brain axis
Review: Recognizing Depression from the Microbiota–Gut–Brain Axis – Shan Liang et al. – International Journal of Molecular Sciences
Review: Microbiota‐gut‐brain axis: Interaction of gut microbes and their metabolites with host epithelial barriers – Y. Bhattarai – Neurogastroenterology & Motility
Animal experiments
Enterobacter cloacae administration induces hepatic damage and subcutaneous fat accumulation in high-fat diet fed mice – Anniina Keskitalo et al. – PLoS One
Mouse: Intestinal microbiota enhances pancreatic carcinogenesis in preclinical models – Ryan M Thomas et al. – Carcinogenesis
Consumption of transglycosylated starch down-regulates expression of mucosal innate immune response genes in the large intestine using a pig model – Barbara U. Metzler-Zebeli et al. – British Journal of Nutrition
N-Acetyl-Cysteine Alleviates Gut Dysbiosis and Glucose Metabolic Disorder in High-Fat Diet-Induced Mice – Junping Zheng et al. – Journal of Diabetes
The Ramazzini Institute 13-week pilot study on glyphosate and Roundup administered at human-equivalent dose to Sprague Dawley rats: effects on the microbiome – Qixing Mao and Fabiana Manservisi et al. – Environmental Health
Animal microbiome
Insights into the gut microbiota of freshwater shrimp and its associations with the surrounding microbiota and environmental factors – Yanting Zhao et al. – Journal of Microbiology and Biotechnology
Bacterial Microbiota Assemblage in Aedes albopictus Mosquitoes and Its Impacts on Larval Development – Xiaoming Wang et al. – Molecular Ecology
Cockroach: The role of gut microbiota in the regulation of standard metabolic rate in female Periplaneta americana – Paul A. Ayayee et al. – PeerJ
Preliminary Analysis of the Proteome of Exhaled Breath Condensate in Bottlenose Dolphins (Tursiops truncatus) – Bergfelt, Don R et al. – Aquatic Mammals
** Functional variation in the gut microbiome of wild Drosophila populations – Alyssa Bost et al. – Molecular Ecology
Plant, root and soil microbiome
Book chapter: Genomic Identification and Analysis of Specialized Metabolite Biosynthetic Gene Clusters in Plants Using PlantiSMASH – Satria A. Kautsar et al. – Plant Chemical Genomics
Compositional and abundance changes of nitrogen-cycling genes in plant-root microbiomes along a salt marsh chronosequence – Miao Wang et al. – Antonie van Leeuwenhoek
Effects of transgenic Bt rice on the active rhizospheric methanogenic archaeal community as revealed by DNA-based stable isotope probing – Cheng Han et al. – Journal of Applied Microbiology
Unlocking the bacterial and fungal communities assemblages of sugarcane microbiome – Rafael Soares Correa de Souza et al. – Scientific Reports
Diversity of culturable methylotrophic bacteria in different genotypes of groundnut and their potential for plant growth promotion – R. Krishnamoorthy et al. – 3 Biotech
Water and extremophile microbiome
Bacterial Communities Changes during Food Waste Spoilage – Shanghua Wu et al. – Scientific Reports
Impact of anti-acidification microbial consortium on carbohydrate metabolism of key microbes during food waste composting – Caihong Song et al. – Bioresource Technology
Exploratory Study of Archaebacteria and their Habitat in Underground, Opencast Coal Mines and Coal Mine Fire Areas of Dhanbad – D. Mukherjee et al. – Journal of the Geological Society of India
Book chapter: A Practical Guide to Studying the Microbiology of Karst Aquifers – Olivia S. Hershey et al. – Karst Water Environment
Phages and viruses
Responses of intestinal virome to silver nanoparticles: safety assessment by classical virology, whole-genome sequencing and bioinformatics approaches – Kuppan Gokulan and Aschalew Z Bekele et al. – International Journal of Nanomedicine
Technology
In silico design of novel proton-pump inhibitors with reduced adverse effects – Xiaoyi Li et al. – Frontiers of Medicine
Preprint: Diagnosing Bacterial Vaginosis with a Novel, Clinically-Actionable Molecular Diagnostic Tool – Joseph P Jarvis et al. – bioRxiv
Bioinformatics
PhyMet2: a database and toolkit for phylogenetic and metabolic analyses of methanogens – Burdukiewicz Michał et al. – Environmental Microbiology Reports
Microbes in the news
Robert Chapkin on Relationships Between the Gut Microbiome, Diet, and Colorectal Cancer – Cancer Network
What are bacteria doing in the bladder? – Gregor Reid – Nature Reviews Urology