Merry Christmas to those of you who celebrate, and Happy Holidays to those of you taking a break! Today’s Digest is dense, so get prepared. This Digest includes many articles in Animal Experiments and Plant, Root and Soil Microbiome. It also features finding antimicrobial resistance in indoor dust, how commensals help maintain epithelial homeostasis, and a carnivorous plant farming microbes for digesting preys. Enjoy!
Antimicrobial resistance
Bioaccumulation of antibiotics in crops under long-term manure application: Occurrence, biomass response and human exposure – Fangkai Zhao et al. – Chemosphere
Preprint: From genotype to antibiotic susceptibility phenotype in Enterobacteriaceae: a clinical perspective – Etienne Ruppé et al. – bioRxiv
Review: Action of Antimicrobial Peptides against Bacterial Biofilms – Muhammad Yasir et al. – Materials
** Antimicrobial Chemicals Associate with Microbial Function and Antibiotic Resistance Indoors – Ashkaan K. Fahimipour et al. – mSystems
Pregnancy and early life
Maternal antibiotic prophylaxis affects Bifidobacterium spp. counts in the human milk, during the first week after delivery – M. Padilha et al. – Beneficial Microbes
Human oral microbiome
Preprint: Microbiome composition comparison in oral and atherosclerotic plaque from patients with and without periodontitis – Daichi Isoshima et al. – bioRxiv
Meta-review: Barrett’s esophagus and esophageal cancer: Links to microbes and the microbiome – Teminioluwa A. Ajayi et al. – PLoS Pathogens
Human respiratory microbiome
Lower airway microbiota associates with inflammatory phenotype in severe preschool wheeze – Polly F.M. Robinson et al. – Journal of Allergy and Clinical Immunology
Human gut microbiome
Population-Based Gut Microbiome Associations With Hypertension – Hamdi Jama et al. – Circulation Research
Response to: Population-Based Gut Microbiome Associations With Hypertension – Claire J. Steves & Matthew A. Jackson – Circulation Research
Gut Microbiota and Endothelial Dysfunction Markers in Obese Mexican Children and Adolescents – Khemlal Nirmalkar et al. – Nutrients
Gut mucosal-associated microbiota better discloses Inflammatory Bowel Disease differential patterns than faecal microbiota – Annamaria Altomare et al. – Digestive and Liver Disease
Eczema-protective probiotic alters infant gut microbiome functional capacity but not composition: sub-sample analysis from a RCT – R. Murphy et al. – Beneficial Microbes
Review: Synthetic consortia of nanobody-coupled and formatted bacteria for prophylaxis and therapy interventions targeting microbiome dysbiosis-associated diseases and co-morbidities – Kenneth Timmis et al. – Microbial Biotechnology
Human gut-microbiome-brain axis
Review: A systematic review of enteric dysbiosis in chronic fatigue syndrome/myalgic encephalomyelitis – S. Du Preez et al. – Systematic Reviews
Built environment microbiome
Carbapenem-resistant Enterobacteriaceae dispersal from sinks is linked to drain position and drainage rates in a laboratory model system – P.Aranega Bou et al. – Journal of Hospital Infection
Enriching Beneficial Microbial Diversity of Indoor Plants and Their Surrounding Built Environment With Biostimulants – Alexander Mahnert et al. – Frontiers in Microbiology
Food microbiome
Bacterial diversity and community in Qula from the Qinghai–Tibetan Plateau in China – Yan Zhu & Yingying Cao et al. – PeerJ
Animal experiments
Gut microbiota profiling in Norwegian weaner pigs reveals potentially beneficial effects of a high-fiber rapeseed diet – Özgün Candan Onarman Umu et al. – PLoS One
** Mouse: Commensals Suppress Intestinal Epithelial Cell Retinoic Acid Synthesis to Regulate Interleukin-22 Activity and Prevent Microbial Dysbiosis – Mayara Grizotte-Lake et al. – Immunity
Non-isoflavones Diet Incurred Metabolic Modifications Induced by Constipation in Rats via Targeting Gut Microbiota – Jialin Liu & Ruirui Chang et al. – Frontiers in Microbiology
Genetic Effects on the Gut Microbiota Assemblages of Hybrid Fish From Parents With Different Feeding Habits – Wuhui Li, Junmei Liu & Hui Tan et al. – Frontiers in Microbiology
Mouse: Aspirin eugenol ester regulates cecal contents metabolomic profile and microbiota in an animal model of hyperlipidemia – Ning Ma et al. – BMC Veterinary Research
Effects of Early Intervention with Maternal Fecal Microbiota and Antibiotics on the Gut Microbiota and Metabolite Profiles of Piglets – Chunhui Lin et al. – Metabolites
Mouse: Impact of Cyanocobalamin and Methylcobalamin on Inflammatory Bowel Disease and the Intestinal Microbiota Composition – Xuan Zhu et al. – Journal of Agricultural and Food Chemistry
Impact of probiotics on development and behaviour in Drosophila melanogaster – a potential in vivo model to assess probiotics – E. Gómez et al. – Beneficial Microbes
Effects of chronic caffeine exposure during adolescence and subsequent acute caffeine challenge during adulthood on rat brain serotonergic systems – M.R. Arnold et al. – Neuropharmacology
Mouse: A Microtube Array Membrane (MTAM) Encapsulated Live Fermenting Staphylococcus epidermidis as a Skin Probiotic Patch against Cutibacterium acnes – Albert-Jackson Yang et al. – International Journal of Molecular Sciences
Animal microbiome
Wild bees and their nests host Paenibacillus bacteria with functional potential of avail – Alexander Keller et al. – Microbiome
Field-level clothianidin exposure affects bumblebees but generally not their pathogens – Dimitry Wintermantel et al. – Nature Communications
Plant, root and soil microbiome
** Hunters or farmers? Microbiome characteristics help elucidate the diet composition in an aquatic carnivorous plant – Dagmara Sirová & Jiří Bárta et al. – Microbiome
The influence of Bt maize cultivation on communities of arbuscular mycorrhizal fungi revealed by MiSeq sequencing – Huilan Zeng et al. – Frontiers in Microbiology
Evaluation of the possible persistence of potential human pathogenic bacteria in olive orchards irrigated with treated urban wastewater – Adriano Sofo et al. – Science of The Total Environment
Relationships between the properties of Spitsbergen soil, number and biodiversity of rhizosphere microorganisms, and heavy metal concentration in selected plant species – Agnieszka Hanaka et al. – Plant and Soil
Deciphering differences in the chemical and microbial characteristics of healthy and Fusarium wilt-infected watermelon rhizosphere soils – Tianzhu Meng et al. – Applied Microbiology and Biotechnology
Shift of millet rhizosphere bacterial community during the maturation of parent soil revealed by 16S rDNA high-throughput sequencing – Lixia Xu et al. – Applied Soil Ecology
Molecular characterization of eukaryotic algal communities in the tropical phyllosphere based on real-time sequencing of the 18S rDNA gene – Huang Zhu et al. – BMC Plant Biology
The impact of carbon addition on the organisation of rhizosheath of chickpea – Sheikh M. F. Rabbi et al. – Scientific Reports
Feedbacks of plant identity and diversity on the diversity and community composition of rhizosphere microbiomes from a long-term biodiversity experiment – Marc W. Schmid et al. – Molecular Ecology
Review: The role of water in plant-microbe interactions – Kyaw Aung et al. – The Plant Journal
Toxicity of phthalate esters to lettuce (Lactuca sativa) and the soil microbial community under different soil conditions – Tingting Ma et al. – PLoS One
Water and extremophile microbiome
Review: Acidithiobacillus ferrooxidans – Raquel Quatrini & D. Barrie Johnson – Trends in Microbiology
Phages and viruses
Perspective: Minimum Information about an Uncultivated Virus Genome (MIUViG) – Simon Roux et al. – Nature Biotechnology
Data: Whole-genome of Mexican-crAssphage isolated from the human gut microbiome – Melany Cervantes-Echeverría et al. – BMC Research Notes
Virome analysis of tick-borne viruses in Heilongjiang Province, China – Fei Meng et al. – Ticks and Tick-borne Diseases
Preprint: Human cytomegalovirus genomes sequenced directly from clinical material: variation, multiple-strain infection, recombination and mutation – Nicolas M Suarez et al. – bioRxiv
Simultaneous Detection of Beta and Gamma Human Herpesviruses by Multiplex qPCR Reveals Simple Infection and Coinfection Episodes Increasing Risk for Graft Rejection in Solid Organ Transplantation – Yessica Sánchez-Ponce et al. – Viruses
Finer-Scale Phylosymbiosis: Insights from Insect Viromes – Brittany A. Leigh – mSystems
Technology
Design and application of a novel two-amplicon approach for defining eukaryotic microbiota – Ana Popovic et al. – Microbiome
Preprint: Optimization of DNA extraction from human urinary samples for mycobiome community profiling – A. Lenore Ackerman et al. – bioRxiv
Bioinformatics
Combining multiple functional annotation tools increases coverage of metabolic annotation – Marc Griesemer & Jeffrey A. Kimbrel et al. – BMC Genomics
Scientific Communication and Education
Preprint: The economy and environmental attitudes: Does a good economy make citizens care more about the environment? – Stephanie Marie Rizio & Yoshihisa Kashima – bioRxiv
Preprint: Professional medical writing support and the quality, ethics and timeliness of clinical trial reporting: a systematic review – Obaro Evuarherhe et al. – bioRxiv
Preprint: A data-driven approach to reduce gender disparity in invited speaker programs at scientific meetings – Ann-Maree Vallence – bioRxiv
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