August 17, 2019

Highlights: Role of microbiome in drug response, station and train surface microbiome, fish microbiome, bioreactor based microbial communities, many more articles and some news.


General microbiome

Microbial Taxon-Specific Isotope Incorporation with DNA Quantitative Stable Isotope Probing – Brianna K. Finley – Stable Isotope Probing

The Role of the Microbiome in Drug Response – Rosina Pryor – Annual Review of Pharmacology and Toxicology

Station and train surface microbiomes of Mexico City’s metro (subway/underground) – Apolinar Misael Hernández – bioRxiv

Animal experiments 

Alterations of the brain proteome and gut microbiota in D-galactose-induced brain aging mice with krill oil supplementation – Qinqin Jiang – ACS

Animal microbiome 

Low-load pathogen spillover predicts shifts in skin microbiome and survival of a terrestrial-breeding amphibian – C. Guilherme Becker – Proceedings B

Comparative analysis of the gut microbial communities between two dominant amphipods from the Challenger Deep, Mariana Trench – Xiang-yu Cheng – Deep Sea Research Part I: Oceanographic Research Papers

A microbial sea of possibilities: current knowledge and prospects for an improved understanding of the fish microbiome – Thibault P.R.A. Legrand – Reviews in Aquaculture

The microbiota in spider mite faeces potentially reflects intestinal bacterial communities in the host – Yu‐Xi Zhu – Insect Science

Plant, root, and soil microbiome

Agroforestry alters the rhizosphere soil bacterial and fungal communities of moso bamboo plantations in subtropical ChinaXiaoping Zhang – Applied Soil Ecology

Enhanced tomato plant growth in soil under reduced P supply through microbial inoculants and microbiome shifts – Namis Eltlbany – FEMS Microbiology Ecology

Microbiome in Plant Health and Disease: Challenges and Opportunities – Ranjini Ramesh – Microbiome in Plant Health and Disease

Exploring the Phyllosphere Bacterial Community for Improving Tree Crop Protection – Diogo Mina – Microbiome in Plant Health and Disease

Influence of the Rhizospheric Microbiome in Plant Health Management – Vankayalapati Vijaya Kumar – Microbiome in Plant Health and Disease

Circadian Rhythms in Plant-Microbe Interaction: For Better Performance of Bioinoculants in the Agricultural Fields – Raghavendra Maddur Puttaswamy –Biofertilizers for Sustainable Agriculture and Environment

Dynamics of the rice rhizosphere microbial community under continuous and intermittent flooding treatment – HaiLong Li – Journal of Environmental Management

Differential dynamics of microbial community networks help identify microorganisms interacting with residue-borne pathogens: the case of Zymoseptoria tritici in wheat – Lydie Kerdraon – bioRxiv

Water and extremophile microbiome 

Characterization of novel metagenomic–derived lipase from Indian hot spring – Rajesh Kumar Sahoo – International Microbiology

Built environment 

Multi-omics analysis reveals niche and fitness differences in typical denitrification microbial aggregations – Yale Deng – Environment International

Electricity generation and microbial community of single-chamber microbial fuel cells in response to Cu2O nanoparticles/reduced graphene oxide as cathode catalyst – ShuaishuaiXin – Chemical Engineering Journal

Effects of current intensities on the performances and microbial communities in a combined bio-electrochemical and sulfur autotrophic denitrification (CBSAD) system – Hongyu Wang – Science of The Total Environment

Sustained organic loading perturbation inhibits nitrite oxidation in bioreactors unveiling variable resistance and resilience of nitrification and nitrifiers – E. Santillan – bioRxiv

Food microbiology

Characterization of the Microbial Resistome in Conventional and “Raised Without Antibiotics” Beef and Dairy Production Systems – Pablo Rovira – Frontiers in Microbiology

Transcription Profiling Reveals Cooperative Metabolic Interactions in a Microbial Cheese-Ripening Community Composed of Debaryomyces hansenii, Brevibacterium aurantiacum, and Hafnia alvei – Nguyen-Phuong PHAM – Frontiers in Microbiology


Culture of salivary methanogens assisted by chemically produced hydrogen – CO Guindo – bioRxiv

Escherichia coli clonobiome: assessing the strains diversity in feces and urine by deep amplicon sequencing – Sofiya G. Shevchenko – bioRxiv

A new technique for use in the study of the microbiome: An evaluation of a three-dimensional cell culture technique in maintaining the gastrointestinal microbiome of four Balb/c female mice and implications for future studies – Everest Uriel Castaneda – bioRxiv

Microbes in the news

Genetic census of the human microbiome – ScienceDaily

When It Comes To Gut Health, Trust Science, Not Gimmicks – Futurism

UNSW unveils Microbiome Research Centre – What’s New in Food Technology & Manufacturing


UCSF, Stanford Receive $35 Million From Marc and Lynne Benioff – PND, Candid

Antiseptic resistance in bacteria ‘could lead to next generation of plastics’ – Dumbarton Reporter

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