July 11, 2020

Good morning everyone. Today’s digest includes various interesting articles such as: 1) mNGS-based approach for broad-range detection of pathogens associated with CNS infections, 2) dynamics of diarrheal pathogenesis and antimicrobial resistance transmission using gut microbiome and resistome profiling, 3) comparison urinary and bladder mucosa-associated microbiome composition in bladder cancer patients, 4) regulation of vaginal microbiome composition and stability by ovarian hormones, diet and exercise, 5) Chokeberry polyphenols can reduce the body weight of HFD-fed rats by accelerating energy homeostasis and thermogenesis in interscapular brown adipose tissue, 6) Comparison of taxonomic composition and diversity of bacterial and fungal communities in synanthropic and non-synanthropic mound-building mouse, and 7) an information retrieval system for large metagenomic datasets to recover missing content from genome bins. Enjoy reading. Happy weekend.

General microbiome

Commentary: mSphere of Influence: Translating Gut Microbiome Studies To Benefit Human Health – Anna M. Seekatz – mSphere

A metagenomics-based diagnostic approach for central nervous system infections in hospital acute care setting – Mohammad Rubayet Hasan – Scientific Reports

Human microbiome

Metagenomic analysis of gut microbiome and resistome of diarrheal fecal samples from Kolkata, India, reveals the core and variable microbiota including signatures of microbial dark matter – Rituparna De – Gut Pathogens

Bladder cancer-related microbiota: examining differences in urine and tissue samples– Bassel Mansour – Scientific Reports

Daily Vaginal Microbiota Fluctuations Associated with Natural Hormonal Cycle, Contraceptives, Diet, and Exercise – Stephanie D. Song – mSphere

Dynamics of the lung microbiome in intensive care patients with chronic obstructive pulmonary disease and community-acquired pneumonia – Wei-Chang Huang – Scientific Reports

Animal microbiome / Animal experiments

The polyphenol-rich extract from chokeberry (Aronia melanocarpa L.) modulates gut microbiota and improves lipid metabolism in diet-induced obese rats – Yue Zhu – Nutrition and Metabolism

Changes in the gut microbiota mediate the differential regulatory effects of two glucose oxidases produced by Aspergillus niger and Penicillium amagasakiense on the meat quality and growth performance of broilers – Shengru Wu – Journal of Animal Science and Biotechnology

The effects of atrazine on the microbiome of the eastern oyster: Crassostrea virginicaAdrian Britt – Scientific Reports

How being synanthropic affects the gut bacteriome and mycobiome: comparison of two mouse species with contrasting ecologies – Barbora Bendová – BMC Microbiology

Fruit and vegetable microbiome

Exploring bacteria diversity in commercialized table olive biofilms by metataxonomic and compositional data analysis – Antonio Benítez-Cabello – Scientific Reports

Plant, root and soil microbiome

Deconstructing the Soil Microbiome into Reduced-Complexity Functional Modules – Dan Naylor – mBio

Water microbiome

Metagenomic water quality monitoring with a portable laboratory – Kishor Acharya – Water Research

Methods

Exploring neighborhoods in large metagenome assembly graphs using spacegraphcats reveals hidden sequence diversity – C. Titus Brown – Genome Biology

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