April 10, 2018

After a brief hiatus, your Digest is back! After screening several hundred papers, progress seems to concentrate on a selected fields, including human gut microbiome and plant/soil microbiome. The WHO advocates for a global atlas of zoonotic viruses, a PDF link to a book volume full of application of microbiome engineering in agriculture, environmental protection and industry, and 16s rDNA primers can cross-react with mitochondrial sequences in eukaryotic cells. Last but not least, what can we all do to help young scientists, including ourselves, cope with immense pressure and distress?

General microbiology

Role of Partially Saturated Canthaxanthin and Ergosterol in the Survival of Aspergillus carbonarius Mutant at Extreme Acidic Condition – A. Kumar et al. – Microbiology

Coupled iron-microbial catalysis for CO2 hydrogenation with multispecies microbial communities – Elise Blanchet et al. – Chemical Engineering Journal

An integrated membrane bioreactor system with iron-dosing and side-stream co-fermentation for enhanced nutrient removal and recovery: System performance and microbial community analysis – Ruo-hong Li et al. – Bioresource Technology

The Microbiome and Population Health: Considerations to Enhance Study Design and Data Analysis in Observational and Interventional Epidemiology – Ryan T Demmer – American Journal of Epidemiology

Robust, linear correlations between growth rates and β-lactam–mediated lysis rates – Anna J. Lee et al. – PNAS USA

Human oral microbiome

Apical periodontitis: preliminary assessment of microbiota by 16S rRNA high throughput amplicon target sequencing – Federico Mussano and Ilario Ferrocino et al. – BMC Oral Health

Human gut microbiome

A feasibility study: association between gut microbiota enterotype and antibody response to seasonal trivalent influenza vaccine in adults – Nick Shortt and Hazel Poyntz et al. – Clinical & Translational Immunology

Gut-dependent microbial translocation induces inflammation and cardiovascular events after ST-elevation myocardial infarction – Xin Zhou, Jing Li and Junli Guo et al. – Microbiome

Book chapter: Influence of the Gut Microbiome on Immune Development During Early Life – Shankar S. Iyer and Richard S. Blumberg – Physiology of the Gastrointestinal Tract (Sixth Edition)

Book chapter: Gut Barrier: Innate Immunity – Gerco den Hartog et al. – Physiology of the Gastrointestinal Tract (Sixth Edition)

Review: Molecular Pathophysiology of Epithelial Barrier Dysfunction in Inflammatory Bowel Diseases – Jessica Y. Lee et al. – Proteomes

Impact of tart cherries polyphenols on the human gut microbiota and phenolic metabolites in vitro and in vivo – Alba C. Mayta-Apaza et al. – The Journal of Nutritional Biochemistry

Characterization of the duodenal bacterial microbiota in patients with pancreatic head cancer vs. healthy controls – Qi-Xiang Mei et al. – Pancreatology

Human multi-site microbiome

Microbiota potential for the treatment of sexual dysfunction – Hassan Tirandaz et al. – Medical Hypotheses

Animal experiments

Nile tilapia: Effects of Lactogen 13, a New Probiotic Preparation, on Gut Microbiota and Endocrine Signals Controlling Growth and Appetite of Oreochromis niloticus Juveniles – Gioacchini Giorgia et al. – Microbial Ecology

Effects of shenling baizhu powder herbal formula on intestinal microbiota in high-fat diet-induced NAFLD rats – Yupei Zhang et al. – Biomedicine & Pharmacotherapy

Gut Microbiota Promotes Tumor Growth in Mice by Modulating Immune Response – Vrishketan Sethi et al. – Gastroenterology

The effects of feeding monensin on rumen microbial communities and methanogenesis in bred heifers fed in a drylot – E.A. Melchior et al. – Livestock Science

Identification, characterization and selection of autochthonous lactic acid bacteria as probiotic for feedlot cattle – Natalia C. Maldonado et al. – Livestock Science

Glyphosate based- herbicide exposure affects gut microbiota, anxiety and depression-like behaviors in mice – Yassine Aitbali et al. – Neurotoxicology and Teratology

Animal microbiome

Characterization of the bacterial community in different parts of the gut of sea cucumber (Apostichopus Japonicus) and its variation during gut regeneration – Luo Wang et al. – Aquaculture Research

Review: The adherence and colonization of microorganisms in fish gastrointestinal tract – Xuemei Li et al. – Reviews in Aquaculture

Effect of Saccharomyces boulardii and Bacillus subtilis B10 on gut microbiota modulation in broiler – Chubin Qin and Li Gong et al. – Animal Nutrition

Metabolomics Study of Immune Responses of New Zealand Greenshell™ Mussels (Perna canaliculus) Infected with Pathogenic Vibrio sp. – Thao V. Nguyen et al. – Marine Biotechnology

Review: Use of antibiotics in broiler production: Global impacts and alternatives – Youcef Mehdi et al. – Animal Nutrition

Food Microbiome

PDF: High-Throughput rRNA Gene Sequencing Reveals High and Complex Bacterial Diversity Associated with Brazilian Coffee Bean Fermentation – Dão Pedro de Carvalho Neto et al. – Food Technology and Biotechnology

The impact of vegan production on the kimchi microbiome – Michelle Zabat et al. – Food Microbiology

Plant, root and soil microbiome

Soil abiotic variables are more important than Salicaceae phylogeny or habitat specialization in determining soil microbial community structure – Sonya Erlandson et al. – Molecular Ecology

RNA-based analyses reveal fungal communities structured by a senescence gradient in the moss Dicranum scoparium and the presence of putative multi-trophic fungi – Ko‐Hsuan Chen et al. – New Phytologist

Microbial diversity changes with rhizosphere and hydrocarbons in contrasting soils – Muhammad Atikul Islam Khan et al. – Ecotoxicology and Environmental Safety

Effects of redox potential on soil Cadmium solubility: Insight into microbial community – Delong Meng et al. – Journal of Environmental Sciences

Long-term phosphorus application to a maize monoculture influences the soil microbial community and its feedback effects on maize seedling biomass – Ming Lang et al. – Applied Soil Ecology

Book chapter: Differential Responses of Plants to Biotic Stress and the Role of Metabolites – Maham Saddique et al. – Plant Metabolites and Regulation Under Environmental Stress

Role of Phenolic Acids from the Rhizosphere Soils of Panax notoginseng as a Double-Edge Sword in the Occurrence of Root-Rot Disease – Ya-Meng Zhao et al. – Molecules

Forum: From Petri Dishes to Model Ecosystems – Oskar Siemianowski et al. – Trends in Plant Science

An Insight into Catechins Metabolic Pathways of Camellia sinensis Based on Genome and Transcriptome Analysis – Wenzhao Wang et al. – Journal of Agricultural and Food Chemistry

Seasonal characterization of sugarcane vinasse: Assessing environmental impacts from fertirrigation and the bioenergy recovery potential through biodigestion – Lucas Tadeu Fuess et al. – Science of The Total Environment

Soil microbial biomass: A key soil driver in management of ecosystem functioning – Jay Shankar Singh and Vijay Kumar Gupta – Science of The Total Environment

Phosphorus fertilising potential of fly ash and effects on soil microbiota and crop – Deborah Schönegger et al. – Resources, Conservation and Recycling

Response of the soil microbial community to different fertilizer inputs in a wheat-maize rotation on a calcareous soil – Shuikuan Bei et al. – Agriculture, Ecosystems & Environment

Water and extremophile microbiome

Bacterial Diversity and Functional Activity of Microbial Communities in Hot Springs of the Baikal Rift Zone – E. V. Lavrentyeva et al. – Microbiology

Microbial Community Composition and Rates of the Methane Cycle Microbial Processes in the Upper Sediments of the Yamal Sector of the Southwestern Kara Sea – A. S. Savvichev et al. – Microbiology

Nematode-associated microbial taxa do not correlate with host phylogeny, geographic region or feeding morphology in marine sediment habitats – Taruna Schuelke et al. – Molecular Ecology

Discriminating activated sludge flocs from biofilm microbial communities in a novel pilot-scale reciprocation MBR using high-throughput 16S rRNA gene sequencing – Ryan De Sotto et al. – Journal of Environmental Management

PDF: Divergent assemblage patterns of abundant and rare microbial sub-communities in response to inorganic carbon stresses in a simultaneous anammox and denitrification (SAD) system – Duntao Shu et al. – Bioresource Technology

Antibiotic resistance in wastewater treatment plants: Tackling the black box – Célia M. Manaia et al. – Environment International

Phages and viruses

** Building a global atlas of zoonotic viruses – Dennis Carroll et al. – Bulletin of WHO

Phages infecting Faecalibacterium prausnitzii belong to novel viral genera that help to decipher intestinal viromes – Jeffrey K. Cornuault et al. – Microbiome

Dual Insect specific virus infection limits Arbovirus replication in Aedes mosquito cells – Michaela J. Schultz et al. – Virology


** Taxon Disappearance from Microbiome Analysis Reinforces the Value of Mock Communities as a Standard in Every Sequencing Run – Yi-Chun Yeh et al. – mSystems

Hemolymph Microbiomes of Three Aquatic Invertebrates as Revealed by a New Cell Extraction Method – Xinxu Zhang et al. – Applied and Environmental Microbiology

Clinical impact of rapid bacterial identification by MALDI-TOF MS combined with the bêta-LACTA™ test on early antibiotic adaptation by an antimicrobial stewardship team in bloodstream infections – A. Mizrahi et al. – Infectious Diseases

Genetic engineering of bee gut microbiome bacteria with a toolkit for modular assembly of broad-host-range plasmids – Sean P. Leonard et al. – ACS Synthetic Biology

** Cross-Reactivity of Prokaryotic 16S rDNA-Specific Primers to Eukaryotic DNA: Mistaken Microbial Community Profiling in Environmental Samples – Shailendra Yadav et al. – Current Microbiology

Detection of Pathogenic Microorganisms by Microfluidics Based Analytical Methods – Dongxue Zhang et al. – Analytical Chemistry

** Book chapter PDF: Microbial, Plant, Environmental and Industrial Technologies – Debmalya Barh and Vasco Azevedo – Microbial Omics: Applications in Biotechnology

Metabolome- and genome-scale model analyses for engineering of Aureobasidium pullulans to enhance polymalic acid and malic acid production from sugarcane molasses – Jun Feng and Jing Yang et al. – Biotechnology for Biofuels

eDNA-based bioassessment of coastal sediments impacted by an oil spill – Yuwei Xie et al. – Environmental Pollution

Using natural biomass microorganisms for drinking water denitrification – Darleila Damasceno Costa et al. – Journal of Environmental Management


Cluster and Multiple Correspondence Analyses in Rheumatology: Paths to Uncovering Relationships in a Sea of Data – Lu Han et al. – Rheumatic Disease Clinics of North America

Microbes in the news

Faecal transplantation: do not try this at home – Talha Khan Burki – The Lancet Gastroenterology & Hepatology

Non-microbiology picks

** Editorial: Time to talk about why so many postgrads have poor mental health – Nature

Editorial: Using Preprints for Journal Clubs – Arturo Casadevall and Neil Gow – mBio


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