September 8, 2020

Greetings, friends!

Today’s digest is a very heavy grab bag of articles! Included are many reviews on everything from the microbiome in forensic science to the gut-lung axis. Also included are original research articles focused on a variety of subjects including microplastics, extremophiles, and the bicycle microbiome! Finally, for those of you looking for practical advice, I’ve highlighted an article focused on best practices for writing genome announcements.

Happy reading!

General microbiome

Manipulating denitrifying sulfide removal of Pseudomonas sp. C27 with nitrite as sole nitrogen source: Shotgun proteomics analysis – Guo et al. – Bioresource Technology

Pseudomonas aeruginosa – Candida interplay: Effect on in vitro antibiotic susceptibility of Pseudomonas aeruginosa when grown in the presence Candida culture – Mcllroy et al. – British Journal of Biomedical Science

Impact of DNA extraction on whole genome sequencing analysis for characterization and relatedness of Shiga toxin-producing Escherichia coli isolates – Nouws et al. – Scientific Reports

Evolution of diversity explains the impact of pre-adaptation of a focal species on the structure of a natural microbial community – Padfield et al. – The ISME Journal

Biomass-degrading glycoside hydrolases of archaeal origin – Suleiman et al. – Biotechnology for Biofuels

Mining for novel antibiotics in the age of antimicrobial resistance – Udaondo and Matilla – Microbial Biotechology

Multi-site human microbiome

Association between the microbiomes of tonsil and saliva samples isolated from pediatric patients subjected to tonsillectomy for the treatment of tonsillar hyperplasia – Choi et al. – Experimental & Molecular Medicine

Review: The impact of the human microbiome in forensic sciences: A systematic review – García et al. – Applied and Enviornmental Microbiology

Human respiratory microbiome

Review: The evolving role of the lung microbiome in pulmonary fibrosis – Lipinski et al. – Lung Cellular and Molecular Physiology

Review: Recent advances in understanding the ecology of the lung microbiota and deciphering the gut-lung axis – Willis et al. – Lung Cellcular and Molecular Physiology

Human gut microbiome

Altered gut microbiota correlated with systemic inflammation in children with Kawasaki disease – Chen et al. – Scientific Reports

Review: Gut microbiota in human metabolic health and disease – Fan and Pedersen – Nature Reviews Microbiology

Lactose-reduced infant formula with added corn syrup solids is associated with a distinct gut microbiota in Hispanic infants – Jones et al. – Gut Microbes

Animal experiments

Gut bacterial communities and their contribution to performance of specialist Altica flea beetles – Wei et al. – Microbial Ecology

Dynamic changes of gut microbiota of discus fish (Symphysodon haraldi) at different feeding stages – Zhang et al. – Aquaculture

Plant, root, and soil microbiome

Diversity of cultivable microbes from soil of the Fildes Peninsula, Antarctica, and their potential application – Cong et al. – Frontiers in Microbiology

Structural and functional microbial diversity of sandy soil under cropland and grassland – Frąc et al. – PeerJ

Microbiome–environment interactions in antimony-contaminated rice paddies and the correlation of core microbiome with arsenic and antimony contamination – Li et al. – Chemosphere

Review: Implications of endophytic microbiota in Camellia Sinensis: A review on current understanding and future insights – Xie et al. – Bioengineered

Characterizing the nectar microbiome of the non-native tropical milkweed, Asclepias curassavica, in an urban environment – Warren et al. – PLOS ONE

Water and extremophile microbiome

Prokaryotic diversity in stream sediments affected by acid mine drainage – Carlier et al. – Extremophiles

Combination of genetic tools to discern Bacillus species isolated from hot springs in South Africa – Jardine and Ubomba-Jaswa – African Journal of Mirobiology Research

Bioleaching of pyritic coal wastes: bioprospecting and efficiency of selected consortia – Joulian et al. – Research in Microbiology

Genotypic and phylogenetic diversity of new isolates of terrestrial Xanthophyceae (Stramenopiles) from maritime sandy habitats – Rybalka et al. – Phycologia

Paucihalobacter ruber gen. nov., sp. nov., isolated from a haloalkaline lake sediment sample – Wu et al. – Microbiology Society

Comparative analysis of bacterial diversity and community structure in the rhizosphere and root endosphere of two halophytes, Salicornia europaea and Glaux maritima, collected from two brackish lakes in Japan – Yamamoto et al. – Microbes and Environments

Fungal diversity in deep-sea sediments from Magellan seamounts environment of the western Pacific revealed by high-throughput Illumina sequencing – Yang et al. – Journal of Microbiology

Effect of Ferrous Iron Addition on Ammonium Nitrogen Removal and Microbial Communities in Horizontal Subsurface Flow Constructed Wetlands – Zhang et al. – Wetlands

Built environment

Microplastics negatively affect soil fauna but stimulate microbial activity: insights from a field-based microplastic addition experiment – Lin et al. – Proceedings of the Royal Society B

Shared bicycle microbial community: a potential antibiotic-resistant bacteria warehouse – Wu et al. – Folia Microbiologica

Microbial carrying capacity and carbon biomass of plastic marine debris – Zhao et al. – The ISME Journal

Food microbiology

Proteolysis, lipolysis, texture and sensory properties of cheese ripened by Monascus fumeus – Xia et al. – Food Research International

Bioinformatics

Announcement: Best practices for successfully writing and publishing a genome announcement in microbiology resource announcements – Hotopp et al. – Microbiology Resource Announcements

Techniques

Flow-through stable isotope probing (Flow-SIP) minimizes cross-feeding in complex microbial communities – Mooshammer et al. – The ISME Journal

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