February 11, 2017

Changes in the gut microbiota during aging is associated with increased gut permeability and peripheral inflammation and may mediate cognitive decline. An overview of the gut microbiome in Crohn’s Disease and insight into how extremophiles might maintain protein folding. 

General microbiome

Whole genome sequence of lactic acid bacterium Pediococcus acidilactici strain S1 – Gun-Seok Park  Brazilian Journal of Microbiology

Pygmaiobacter massiliensis’ sp. nov., a new bacterium isolated from the human gut of a Pygmy woman – M. Bilen – NMNI

Human and rat gut microbiome composition is maintained following sleep restriction – Zhang SL – PNAS

Palaeogeographic variation in the Permian−Triassic boundary microbialites: A discussion of microbial and ocean processes after the end-Permian mass extinction – Stephen Kershaw – Journal of Palaeogeography

Assessment of bacterial profiles in aged, home-made Sichuan paocai brine with varying titratable acidity by PacBio SMRT sequencing technology – Jialu Cao – Food Control


Human gut microbiome

A microbial signature for Crohn’s disease – Victoria Pascal – Gut

Differences in Gut Metabolites and Microbial Composition and Functions between Egyptian and U.S. Children Are Consistent with Their Diets  – V. Shankar – mSystems

*PrePrint:  Postmortem succession of gut microbial communities in human cadavers – Jennifer M DeBruyn – PeerJ Preprints

Substituting whole grains for refined grains in a 6-wk randomized trial has a modest effect on gut microbiota and immune and inflammatory markers of healthy adults – Vanegas SM – American Journal of Clinical Nutrition

Altered molecular signature of intestinal microbiota in irritable bowel syndrome patients compared with healthy controls: A systematic review and meta-analysis – Hai-Ning Liu – Digestive and Liver Disease

Animal experiments 

Revisiting Metchnikoff: Age-related Alterations in Microbiota-Gut-Brain Axis in the Mouse – Karen A. Scott – Brain, Behavior, and Immunity

Animal microbiome 

Immune system stimulation by the native gut microbiota of honey bees – Waldan K. Kwong – Royal Society for Open Science

Deep Sequencing Reveals Highly Variable Gut Microbial Composition of Invasive Fish Mossambicus Tilapia (Oreochromis mossambicus) Collected from Two Different Habitats – Swapnil Sopan Gaikwad – Indian Journal of Microbiology

The gastrointestinal tract microbiota of the Japanese quail, Coturnix japonica –  Ngare Wilkinson – Environmental Biotechnology

Plant, root, and soil microbiome

Hydrogen Peroxide and Strigolactones Signaling Are Involved in Alleviation of Salt Stress Induced by Arbuscular Mycorrhizal Fungus in Sesbania cannabina Seedlings – Cun-Cui Kong – Journal of Plant Growth Regulation

Potential Role of Plant-Associated Bacteria in Plant Metal Uptake and Implications in Phytotechnologies – Petra S. Kidd – Advances in Botanical Research

Application of bacteria from non-cultivated plants to promote growth, alter root architecture and alleviate salt stress of cotton – Ivelisse Irizarry – Journal of Applied Microbiology

*Reference:  Phytomyxea – Simon Bulman – Springer Reference – Handbook of the Protists

Water and extremophile microbiome 

Molecular determinant of the effects of hydrostatic pressure on protein folding stability – Calvin R. Chen – Nature Communications

Microarray analysis of the benthic bacterium Shewanella piezotolerans WP3 at low temperature – Huahua Jian – Marine Genomics

Metagenomic exploration of microbial community in mine tailings of Malanjkhand copper project, India – Abhishek Gupta – Genomics Data

Illumina sequencing-based analysis of sediment bacteria community in different trophic status freshwater lakes – Yu Wan – Microbiology Open

Variations in airborne bacterial communities at high altitudes over the Noto Peninsula (Japan) in response to Asian dust events – Teruya Maki – Atmospheric Chemistry and Physics Discussions

Phages and viruses

Viruses comprise an extensive pool of mobile genetic elements in eukaryote cell cultures and human clinical samples – Thannesberger J – The FASEB Journal


Community-level physiological profiling analyses show potential to identify the copiotrophic bacteria present in soil environments – Salvador Llado – PLOS one

Cultivation-Free Raman Spectroscopic Investigations of Bacteria – Björn Lorenz – Trends in Microbiology

*Review:  Proteomics Tracing the Footsteps of Infectious Disease – Todd M Greco – Molecular and Cellular Proteomics

Metabolomics as a Challenging Approach for Medicinal Chemistry and Personalized Medicine – Michel Fredérich – Journal of Medical Chemistry

An integrative Bayesian Dirichlet-multinomial regression model for the analysis of taxonomic abundances in microbiome data – Wadsworth WD – BMC Bioinformatics

Microbes on the market 

Lipid accumulation in prokaryotic microorganisms from arid habitat – Philippa Hauschild – Applied Microbiology and Biotechnology



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