March 20, 2020

Good morning! I hope this post finds you well. There are lots of new microbiome papers to share, including work on the disruption of E. coli biofilms, inconsistent diets used in Drosophila microbiome studies, and the effects of pollution on soil microbial communities.

General microbiome

Biosynthesis of silver nanoparticles by Fusarium scirpi and its potential as antimicrobial agent against uropathogenic Escherichia coli biofilms, Candelario Rodríguez-Serrano et al., PLOS ONE


Human gut microbiome

Targeted inhibition of gut bacterial β-glucuronidase activity enhances anticancer drug efficacy, Aadra P. Bhatt et al., PNAS

Gut Microbiome Pattern Reflects Healthy Aging and Predicts Extended Survival in Humans (preprint), Tomasz Wilmanski et al., bioRxiv

Propionic Acid Shapes the Multiple Sclerosis Disease Course by an Immunomodulatory Mechanism, Alexander Duscha et al., Cell

Adjusting for age improves identification of gut microbiome alterations in multiple diseases, Tarini S Ghosh et al., eLife

Environmental remodeling of human gut microbiota and antibiotic resistome in livestock farms, Jian Sun et al., Nature Communications

Review – Altering Routine Intensive Care Unit Practices to Support Commensalism, Hamilton and Behal, Nutrition in Clinical Practice

Household Pet Ownership and the Microbial Diversity of the Human Gut Microbiota, Ashley E. Kates et al., Frontiers in Cellular and Infection Microbiology

Meta-analysis – Assessing the efficacy and safety of fecal microbiota transplantation and probiotic VSL#3 for active ulcerative colitis: A systematic review and meta-analysis, Xiaofei Dang et al., PLOS ONE


Other human microbiome

Subgingival Host-Microbial Interactions in Hyperglycemic Individuals, P.S. Kumar et al., Journal of Dental Research

Investigating Bifidobacteria and Human Milk Oligosaccharide Composition of Lactating Mothers, Gabriele Andrea Lugli et al., FEMS Microbiology Ecology


Animal experiments

Effects of intestinal flora on the pharmacokinetics and pharmacodynamics of aspirin in high-altitude hypoxia, Sun and Zhang et al., PLOS ONE

Meta-analysis of diets used in Drosophila microbiome research and introduction of the Drosophila Dietary Composition Calculator (DDCC) (preprint), Broderick and Lesperance, bioRxiv

The Carnivorous Digestive System and Bamboo Diet of Giant Pandas May Shape Their Low Gut Bacterial Diversity, Wei Gui et al., Conservation Physiology


Animal microbiome

Non-invasive evaluation of the equine gastrointestinal mucosal transcriptome, Coleman and Whitfield-Cargile et al., PLOS ONE

Dietary substitution of soybean oil with coconut oil in the absence of dietary antibiotics supports growth performance and immune function in nursery and grower pigs, Andrea G. Braundmeier-Fleming et al., Journal of Animal Science and Biotechnology

Isoflavone supplementation, via red clover hay, alters the rumen microbial community and promotes weight gain of steers grazing mixed grass pastures, Brittany E. Harlow et al., PLOS ONE

Domesticated equine species and their derived hybrids differ in their fecal microbiota, J.E. Edwards et al., Animal Microbiome

Integrative analysis of gut microbiome and metabolites revealed novel mechanisms of intestinal Salmonella carriage in chicken, Khin K.Z. Mon et al., Scientific Reports


Plant, root, and soil microbiome

Acute effects of PAH contamination on microbial community of different forest soils, Enrica Picariello et al., Environmental Pollution

Context-dependent Dynamics Lead to the Assembly of Functionally Distinct Microbial Communities, Leonora S Bittleston et al., Nature Communications

Lifting the veil on arid-to-hyperarid Antarctic soil microbiomes: a tale of two oases, Eden Zhang et al., Microbiome

Perspective – Toward Comprehensive Plant Microbiome Research, Kari Saikkonen et al., Frontiers in Ecology and Evolution


Water and extremophile microbiome

Deep-sea corals provide new insight into the ecology, evolution, and the role of plastids in widespread apicomplexan symbionts of anthozoans, Samuel A. Vohsen et al., Microbiome


Food microbiology

Lactic Acid Bacteria Isolated From Korean Kimchi Activate the Vitamin D Receptor–autophagy Signaling Pathways, Rong Lu et al., Inflammatory Bowel Diseases

Consumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and Metabolome, Bryn C. Taylor et al., mSystems

Differential Microbial Composition of Monovarietal and Blended Extra Virgin Olive Oils Determines Oil Quality During Storage, Zullo and Ciafardini, Microorganisms


Phages and viruses

Honey bees harbor a diverse gut virome engaging in nested strain-level interactions with the microbiota, Germán Bonilla-Rosso et al., PNAS


Bioinformatics

FORENSIC: an Online Platform for Fecal Source Identification, Adélaïde Roguet et al., mSystems

Review – Accurate and complete genomes from metagenomes, Lin-Xing Chen et al., Genome Research

Powmic: An R Package for Power Assessment in Microbiome Case-Control Studies, Li Chen, Bioinformatics


Techniques

RapidAIM: a culture- and metaproteomics-based Rapid Assay of Individual Microbiome responses to drugs, Leyuan Li et al., Microbiome


Non-microbiology picks

Marketplace shrimp mislabeling in North Carolina, Morgan L. Korzik et al., PLOS ONE

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