September 16, 2018

Good morning! the publications from today’s microbiome digest covering the followings: Tick Microbiome, Chronic fatigue syndrome and alteration in the oral microbiome, CRC associated metabolites quantified from the faecal extracts, vaginal microbiome during cytolytic vaginosis, rumen and fecal bacterial community in high-production dairy cattle, and estimation of the expected variation in microbiome measurements (methodological research). Enjoy reading.

General microbiome

Thesis: Investigating the effects of the gut-associated microbial community on the growth of the eastern spruce budworm – Melbert Schwarz – Thesis

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing – Lisa Couper – Journal of Visualized Experiments: JoVE

Alcohol consumption increase susceptibility to pneumococcal pneumonia in a humanized murine HIV model mediated by intestinal dysbiosis – Derrick R.Samuelson – Alcohol 

Oral microbiome

Chronic fatigue syndrome patients have alterations in their oral microbiome composition and function – Taiwu Wang – PLOSONE

Human gut microbiome

Metabolite quantification of faecal extracts from colorectal cancer patients and healthy controls – Gwénaëlle Le Gall – Oncotarget

Vaginal microbiome

Characterization of the vaginal microbiome during cytolytic vaginosis using high-throughput sequencing – Haihong Xu – Wiley

Animal microbiome

High-production dairy cattle exhibit different rumen and fecal bacterial community and rumen metabolite profile than low-production cattle – Yingyu Mu – MicrobiologyOpen

Characterization of the Functional Changes in Mouse Gut Microbiome Associated with Increased Akkermansia muciniphila Population Modulated by Dietary Black Raspberries – Pengcheng Tu – ACS Omega

Plant, root, and soil microbiome

Dynamics of soil respiration and microbial communities: Interactive controls of temperature and substrate quality – Rana ShahbazAli – Soil Biology and Biochemistry

Microbial community structure and functions differ between native and novel (exotic-dominated) grassland ecosystems in an 8-year experiment – Aleksandra Checinska Sielaff – Plant and Soil

Impacts of heavy metals and soil properties at a Nigerian e-waste site on soil microbial community – Bo Jiang – Journal of Hazardous Material

Insight into Bacterial Community Diversity and Monthly Fluctuations of Medicago sativa Rhizosphere Soil in Response to Hydrogen Gas Using Illumina High-Throughput Sequencing – Zhiying Li – Current Microbiology

Extreme environmental microbiome

Bacterial diversity in snow from mid-latitude mountain areas: Alps, Eastern Anatolia, Karakoram and Himalaya – Roberto Sergio AZZONI – Annals of Glaciology

Water and extremophile microbiome

Characterization of bacterial and microbial eukaryotic communities associated with an ephemeral hypoxia event in Taihu Lake, a shallow eutrophic Chinese lake – Jian Cai – Environmental Science and Pollution Research

Inherent bacterial community response to multiple heavy metals in sediment from river-lake systems in the Poyang Lake, China – Hua Zhang – Ecotoxicology and Environmental Safety


Machine learning analysis of microbial flow cytometry data from nanoparticles, antibiotics and carbon sources perturbed anaerobic microbiomes – Abhishek S. Dhoble – Journal of Biological Engineering


Methodology: Quantification of variation and the impact of biomass in targeted 16S rRNA gene sequencing studies – Jeffrey M. Bender – Microbiome

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