March 5, 2019

A rich Digest for your Tuesday. Microbiome distinguishes atopic dermatitis from allergy, viruses hitchhike insect sperm for paternal transmission, and researchers test biofilms as water quality biosensor. Enjoy!


2017 NIH-wide workshop report on “The Human Microbiome: Emerging Themes at the Horizon of the 21st Century” – The 2017 NIH-wide microbiome workshop writing team – Microbiome

General microbiology

Adaptive laboratory evolution of a genome-reduced Escherichia coli – Donghui Choe et al. – Nature Communications

Frequency of disturbance alters diversity, function, and underlying assembly mechanisms of complex bacterial communities – Ezequiel Santillan et al. – npj Biofilms and Microbiomes

Interactions in self-assembled microbial communities saturate with diversity – Xiaoqian Yu et al. – The ISME Journal

Redox traits characterize the organization of global microbial communities – Salvador Ramírez-Flandes – PNAS

The genetic basis for adaptation of model-designed syntrophic co-cultures – Colton J. Lloyd et al. – PLoS Computational Biology

Antimicrobial resistance

Antibiotic resistance in urban runoff – Ayad Almakki et al. – Science of The Total Environment

Urban metagenomics uncover antibiotic resistance reservoirs in coastal beach and sewage waters – Pablo Fresia et al. – Microbiome

Pregnancy and early life

Longitudinal Microbiome Composition and Stability Correlate with Increased Weight and Length of Very-Low-Birth-Weight Infants – Alyson L. Yee et al. – mSystems

Human skin microbiome

** The nonlesional skin surface distinguishes atopic dermatitis with food allergy as a unique endotype – Donald Y. M. Leung et al. – Science Translational Medicine

Inverse association between the skin and oral microbiota in atopic dermatitis – Wei Li et al. – Journal of Investigative Dermatology

Dysbiosis of skin microbiota in psoriatic patients: co-occurrence of fungal and bacterial communities – Zuzana Stehlikova et al. – Frontiers in Microbiology

Human oral microbiome

Specific Gut and Salivary Microbiota Patterns Are Linked With Different Cognitive Testing Strategies in Minimal Hepatic Encephalopathy – Jasmohan Baja et al. – The American Journal of Gastroenterology

Human respiratory microbiome

A Haemophilus sp. dominates the microbiota of sputum from UK adults with non-severe community acquired pneumonia and chronic lung disease – Daniel G. Wootton et al. – Scientific Reports

Review: The Challenging Road of Moving from Association to Causation for Microbiome Research in IPF – Leopoldo N. Segal & Philip L Molyneaux – American Journal of Respiratory and Critical Care Medicine

Human gut microbiome

Molecular characterization of multidrug-resistant Pseudomonas aeruginosa isolates in hospitals in Myanmar – Tatsuya Tada et al. – Antimicrobial Agents and Chemotherapy

The Dimension of Time in Host-Microbiome Interactions – Giulia T. Uhr et al. – mSystems

The influence of probiotic bacteria and human gut microorganisms causing opportunistic infections on Blastocystis ST3 – M. Lepczyńska & E. Dzika – Gut Pathogens

Human gut-microbiome-brain axis

Review: Systematic Review of Gut Microbiota and Major Depression – Stephanie G. Cheung et al. – Frontiers in Psychiatry

Human multi-site microbiome

Influences on allergic mechanisms through gut, lung, and skin microbiome exposures – Andrea M. Kemter & Cathryn R. Nagler – The Journal of Clinical Investigation

Animal experiments

Metabolic and gut microbial characterization of obesity-prone mice under high-fat diet – Yu Gu et al. – Journal of Proteome Research

Mouse: Impact of 5 Fluorouracil Chemotherapy on Gut Inflammation, Functional Parameters, and Gut Microbiota – A.T.Sougiannis et al. – Brain, Behavior, and Immunity

Mouse: Antigen-presenting ILC3 regulate T cell–dependent IgA responses to colonic mucosal bacteria – Felipe Melo-Gonzalez et al. – Journal of Experimental Medicine

Animal microbiome

Host plant and population source drive diversity of microbial gut communities in two polyphagous insects – Asher G. Jones et al. – Scientific Reports

Bacterial Community of the Digestive Tract of the European Medicinal Leech (Hirudo verbana) from the Danube River – Saraswoti Neupane et al. – Microbial Ecology

Gut microbiota of the European Brown Hare (Lepus europaeus) – G. L. Stalder et al. – Scientific Reports

Plant, root and soil microbiome

Soil microbial functions are affected by organic matter removal in temperate deciduous forest – François Maillard et al. – Soil Biology and Biochemistry

Warming counteracts grazing effects on the functional structure of the soil microbial community in a Tibetan grassland – Li Tang et al. – Soil Biology and Biochemistry

Soil Bacterial Communities From the Chilean Andean Highlands: Taxonomic Composition and Culturability – Felipe Maza et al. – Frontiers in Bioengineering and Biotechnology

Foliar Application of Vegetal-Derived Bioactive Compounds Stimulates the Growth of Beneficial Bacteria and Enhances Microbiome Biodiversity in Lettuce – Francesca Luziatelli et al. – Frontiers in Plant Science

Creek to Table: Tracking fecal indicator bacteria, bacterial pathogens, and total bacterial communities from irrigation water to kale and radish crops – Sarah M.Allard et al. – Science of The Total Environment

Water and extremophile microbiome

Contrasting Pathways for Anaerobic Methane Oxidation in Gulf of Mexico Cold Seep Sediments – Adrien Vigneron et al. – mSystems

Diversity, spatial distribution and activity of fungi in freshwater ecosystems – Cécile Lepère​ et al. – PeerJ

Spatial variability of Antarctic surface snow bacterial communities – Lucie A. Malard et al. – Frontiers in Microbiology

Impacts of microbial assemblage and environmental conditions on the distribution of anatoxin-a producing cyanobacteria within a river network – Keith Bouma-Gregson et al. – The ISME Journal

Vertical stratification of bacteria and archaea in sediments of a small boreal humic lake – Antti J Rissanen et al. – FEMS Microbiology Letters

Airborne Microbial Communities at High-Altitude and Suburban Sites in Toyama, Japan Suggest a New Perspective for Bioprospecting – Daisuke Tanaka et al. – Frontiers in Bioengineering and Biotechnology

Coral microbiome diversity reflects mass coral bleaching susceptibility during the 2016 El Niño heat wave – Stephanie G. Gardner et al. – Ecology and Evolution

Phages and viruses

** Viral pathogens hitchhike with insect sperm for paternal transmission – Qianzhuo Mao et al. – Nature Communications

Early respiratory viral infections in infants with cystic fibrosis – Ashley R. Deschamp et al. – Journal of Cystic Fibrosis


** Oxygen-reducing microbial cathodes monitoring toxic shocks in tap water – Antonin Prévoteau et al. – Biosensors and Bioelectronics

Inhibition of methanogens decreased sulfadiazine removal and increased antibiotic resistance gene development in microbial fuel cells – Shuai Zhang et al. – Bioresource Technology

Effect of the extraction and purification of soil DNA and pooling of PCR amplification products on the description of bacterial and archaeal communities – Johan S. Sáenz et al. – Journal of Applied Microbiology

Impact of Preservation Method and 16S rRNA Hypervariable Region on Gut Microbiota Profiling – Zigui Chen et al. – mSystems

Ultrahigh-Throughput Multiplexing and Sequencing of >500-Base-Pair Amplicon Regions on the Illumina HiSeq 2500 Platform – Johanna B. Holm et al. – mSystems

Fungal Cells Recovery From Air Samples: A Tale of Loss And Gain – Hamza Mbareche et al. – Applied and Environmental Microbiology


Genome and pan-genome analysis to classify emerging bacteria – Aurélia Caputo et al. – Biology Direct

16S rRNA sequence embeddings: Meaningful numeric feature representations of nucleotide sequences that are convenient for downstream analyses – Stephen Woloszynek et al. – PLoS Computational Biology


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