February 1, 2020

Today’s Digest brings you an Outlook collection on human gut microbiome by Nature, a Hi-C investigation of the evolution of the gut microbiota, and be careful with the dust, there’s transferrable antimicrobial genes within!


Reshaping the Microbiome through Nutrition – Nature Conference – San Diego, CA

General microbiology

Commensal Bacteroidetes protect against Klebsiella pneumoniae colonization and transmission through IL-36 signalling – Richard P. Sequeira et al. – Nature Microbiology

** The gut microbiome – Nature Outlook

Antimicrobial resistance

The negative cofactor 2 complex is a key regulator of drug resistance in Aspergillus fumigatus – Takanori Furukawa et al. – Nature Communications

Plasmid-mediated metronidazole resistance in Clostridioides difficile – Ilse M. Boekhoud et al. – Nature Communications

A Common Practice of Widespread Antimicrobial Use in Horse Production Promotes Multi-Drug Resistance – S. Álvarez–Narváez et al. – Scientific Reports

Surveys of knowledge and awareness of antibiotic use and antimicrobial resistance in general population: A systematic review – PLoS One

Antimicrobial resistance patterns and molecular resistance markers of Campylobacter jejuni isolates from human diarrheal cases – Mohamed Elhadidy et al. – PLoS One

Review: Antibiotic resistance: turning evolutionary principles into clinical reality – Dan I Andersson et al. – FEMS Microbiology Reviews

Antibiotic resistome associated with microbial communities in an integrated wastewater reclamation system – Kaifeng Yu et al. – Water Research

Human gut microbiome

** Tracking microbial evolution in the human gut using Hi-C reveals extensive horizontal gene transfer, persistence and adaptation – Eitan Yaffe & David A. Relman – Nature Microbiology

Growth effects of N-acylethanolamines on gut bacteria reflect altered bacterial abundances in inflammatory bowel disease – Nadine Fornelos et al. – Nature Microbiology

Human cancer microbiome

The Influence of Lung Microbiota on Lung Carcinogenesis, Immunity, and Immunotherapy – Ariel G. Ramírez-Labrada et al. – Trends in Cancer

Built environment microbiome

** Mobilizable antibiotic resistance genes are present in dust microbial communities – Sarah Ben Maamar et al. – PLoS Pathogens

Indoor and outdoor airborne bacterial and fungal air quality in kindergartens: seasonal distribution, genera, levels, and factors influencing their concentration – Farhad Mirkhond Chegini et al. – Building and Environment


Targeted metabolomics of pellicle and saliva in children with different caries activity – Annika Schulz et al. – Scientific Reports

Animal experiments

Review: The role of the microbiota in sedentary life style disorders and ageing: Lessons from the animal kingdom – P.W. O’Toole & P.G. Shiels – Journal of Internal Medicine

Animal microbiome

Dietary effects on gut microbiota of the mesquite lizard Sceloporus grammicus (Wiegmann, 1828) across different altitudes – Nina Montoya-Ciriaco et al. – Microbiome

Late weaning is associated with increased microbial diversity and Faecalibacterium prausnitzii abundance in the fecal microbiota of piglets – Francesca Romana Massacci et al. – Animal Microbiome

Plant, root and soil microbiome

Effects of soil chemical properties and fractions of Pb, Cd, and Zn on bacterial and fungal communities – Xiaomei Pan et al. – Science of the Total Environment

Resilience of the microbial communities of semiarid agricultural soils during natural climatic variability events – Lumarie Pérez-Guzmán et al. – Applied Soil Ecology

Effects of microbial inoculants on the fermentation characteristics and microbial communities of sweet sorghum bagasse silage – Miaoyin Dong et al. – Scientific Reports

Water and extremophile microbiome

Diversity of Bacterial Community in the Oxygen Minimum Zones of Arabian Sea and Bay of Bengal as Deduced by Illumina Sequencing – Genevieve L. Fernandes et al. – Frontiers in Microbiology

Ionic Liquid Enriches the Antibiotic Resistome, Especially Efflux Pump Genes, Before Significantly Affecting Microbial Community Structure – Xiaolong Wang et al. – Environmental Science & Technology

Methane yield enhancement of mesophilic and thermophilic anaerobic co-digestion of algal biomass and food waste using algal biochar: Semi-continuous operation and microbial community analysis – Le Zhang et al. – Bioresource Technology

Characterization and co-occurrence of microbial community in epiphytic biofilms and surface sediments of wetlands with submersed macrophytes – Yuansi Liu et al. – Science of the Total Environment

Phages and viruses

** Giant virus diversity and host interactions through global metagenomics – Frederik Schulz et al. – Nature

Reassortment and adaptive mutations of an emerging avian influenza virus H7N4 subtype in China – Bingqian Qu et al. – PLoS One

Outbreak of Pneumonia of Unknown Etiology in Wuhan China: the Mystery and the Miracle – Hongzhou Lu et al. – Journal of Medical Virology


Comparing bioinformatic pipelines for microbial 16S rRNA amplicon sequencing – Andrei Prodan et al. – PLoS One

Microbes in the news

Walnuts May Benefit Gut Bacteria and Improve Heart Health – Karina Lichtenstein – Medicine Net

How to create living art with microbes – Eugenia Angulo – BBVA OpenMind

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