December 2, 2019

Good Morning! Highlights of today’s digest include investigation of microbial communities from ground water sources to develop bioremediation strategies for removal of contaminating micropollutants for production of drinking water, another study with whole-virome analysis identifies changes in the human gut virome in inflammatory bowl diseases with a hope to develop biomarkers and therapeutics. Also, take a look at cool techniques such as Photo-PCR with gold nanorods and irradiation that shortens time for cell lysis and termocycling allowing rapid detection of bacteria as a point-of-care diagnostic tool. Enjoy!

Human skin microbiome
Review: Revealing the secret life of skin With the microbiome you never walk alone – Sfriso et al. – International Journal of Cosmetic Science

Human urinary tract microbiome
ANTIBIOTIC EXPOSURE IN LONG-TERM CARE FACILITIES IS ASSOCIATED WITH URINARY MICROBIOME PERTURBATIONS – Schell et al. – Innovation in Aging

Human gut microbiome
In silico Identification of Riboswitches in the Human Gut Microbiome for
Therapeutic Applications
– Kumari and Som – Journal of RNA and Genomics

Animal microbiome
Age, gut location and diet impact the gut microbiome of a tropical herbivorous surgeonfish – Parata et al. – FEMS Microbial Ecology

Microbial signatures of protected and impacted Northern Caribbean reefs: changes from Cuba to the Florida Keys – Weber et al. – Environmental Microbiology

Geographically isolated Colorado potato beetle mediating distinct defense responses in potato is associated with the alteration of gut microbiota – Wang et al. – Journal of Pest Science

Plant, root and soil microbiome
Dynamics of bacterial community in litter and soil along a chronosequence of Robinia pseudoacacia plantations – Xu et al. – Science of The Total Environment

Influence of invasion by Sosnowsky’s hogweed on nematode communities and microbial activity in forest and grassland ecosystems – Cerevkova et al. – Global Ecology and Conservation

Water and extremophile microbiome
*Exploring groundwater microbial communities for natural attenuation potential of micropollutants – Aldas-Vargas et al. – bioRxiv

Shifts in dimethylated sulfur concentrations and microbiome composition in the red-tide causing dinoflagellate Alexandrium minutum during a simulated marine heatwave – Deschaseaux et al. – Biogeosciences

Artificial light at night erases positive interactions across trophic levels – Maggi et al. – Functional Ecology

Review: Linking metagenomics to aquatic microbial ecology and biogeochemical cycles – Grossart et al. – Limnology and Oceanography

Anaerobic microbial communities can influence algal growth and nutrient removal from anaerobic digestate – Bankston and Higgins – Bioresource Technology

Analysis of microbial communities involved in organic matter and nitrogen removal in a full-scale moving bed biofilm reactor located near the Polar Arctic Circle – Rodriguez-Sanchez et al. – International Biodeterioration & Biodegradation

Enhanced volatile fatty acid production and microbial population analysis in anaerobic treatment of high strength wastewater – Lim et al. – Journal of Water Process Engineering

Rainfall Influences on Microbial Community Dynamics in an Urban Watershed – Banka et al. – Journal of Student-Scientists’ Research

Management of water bodies in show caves – A microbial approach – Moldovan et al. – Tourism Management

Built-environment
Continental-scale microbiome study reveals different environmental characteristics determining microbial richness and composition/quantity in hotel rooms – Fu et al. – bioRxiv

Food microbiology
Integrated Meta-omics Approaches To Understand the Microbiome of Spontaneous Fermentation of Traditional Chinese Pu-erh Tea – Zhao et al. – mSystems

Phages and viruses
*Whole-Virome Analysis Sheds Light on Viral Dark Matter in Inflammatory Bowel Disease – Clooney et al. – Cell Host & Microbe

Metagenomics of the faecal virome indicate a cumulative effect of enterovirus and gluten amount on the risk of coeliac disease autoimmunity in genetically at risk children: the TEDDY study – Lindfors et al. – BMJ Gut

Bioinformatics
Detecting contamination in viromes using ViromeQC – Zolfo et al. – Nature Biotechnology

Review: Metagenomics: Is it a powerful tool to obtain lipases for application in biocatalysis? – Almeida et al. – Biochimica et Biophysica Acta (BBA) – Proteins and Proteomics

Techniques
In-depth serum virome analysis in patients with acute liver failure with indeterminate etiology – Ren et al. – Archives of Virology

Visualization of viral infection dynamics in a unicellular eukaryote and quantification of viral production using VirusFISH – Castillo et al. – bioRxiv

High-efficiency multi-site genomic editing (HEMSE) of Pseudomonas putida through thermoinducible ssDNA recombineering – Aparicio et al. – bioRxiv

A user guide to environmental protistology: primers, metabarcoding, sequencing, and analyses – Geisen et al. – bioRxiv

MiniReview: Next-Generation Sequencing Coupled With in situ Hybridization: A Novel Diagnostic Platform to Investigate Swine Emerging Pathogens and New Variants of Endemic Viruses – Resende et al. – Frontiers in Veterinary Science

*Gold Nanorod-based Photo-PCR System for One-Step, Rapid Detection of Bacteria – Kim et al. – Nanotheranostics

Science career
Using a Systems Change Framework to Evaluate Academic Equity & Climate Efforts in a Graduate Program – Wallace and York – bioRxiv

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