Hello all from another new Microbiome Digest volunteer! This post is coming to you straight from the heart of New York City – being surrounded everywhere by COVID-19 (and related research!), it’s been good to get back into the microbiome world 🙂 I love all things microbiology but am partial to bacteria, especially multidrug-resistant pathogens and communities involved in biological nutrient removal/recovery from waste.

Today’s roundup is heavy on the soil and environmental microbiomes and some interesting preprints, with some unique finds – indigenous yeasts in winemaking, gut microbiomes after dietary interventions in adult dogs, and much more!

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Human gut microbiome

Characterization of Gut Microbiota in Hospitalized Patients with Clostridioides difficile Infection – Bahareh Vakili – Current Microbiology

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Animal experiments
Genetic and metabolic links between the murine microbiome and memory – Jian-Hua Mao – Microbiome

A human-origin probiotic cocktail ameliorates aging-related leaky gut and inflammation via modulating microbiota-taurine-tight junction axis
Shokouh Ahmadi – JCI Insight

Animal microbiome

Preprint: CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content – Maxime Borry – bioRxiv

Phylogenetic analysis of intestinal microbiota reveals novel Mycoplasma phylotypes in salmonid species – Brenda Mora-Sánchez – Microbial Pathogenesis

Rapid Reconstitution of the Faecal Microbiome after Extended Diet-Induced Changes Indicate a Stable Gut Microbiome in Healthy Adult Dogs – David Allaway – Applied and Environmental Microbiome

Plant, root, and soil microbiome

Review: Harnessing rhizosphere microbiomes for drought-resilient crop production – Franciska T. de Vries – Science

Book Chapter: Endophytic Actinomycetes-Mediated Modulation of Defense and Systemic Resistance Confers Host Plant Fitness Under Biotic Stress Conditions – Waquar Akhter Ansari – Microbial Versatility in Varied Environments

Elevated CO2 mitigates the negative effect of CeO2 and Cr2O3 nanoparticles on soil bacterial communities by alteration of microbial carbon use – Jipeng Luo – Environmental Pollution

Periodic waterlogging consistently shapes agricultural soil microbiomes by promoting specific taxa – Florian Gschwend – Applied Soil Ecology

Food microbiology

Review:Indigenous yeasts: Emerging Trends and Challenges in winemaking – Iliada K. Lappa – Current Opinion in Food

Ecology of lactobacilli present in Italian cheeses produced from raw milk
Christian Milani – Applied and Environmental Microbiology

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Probiotics / prebiotics
Probiotic supplementation improves cognitive function and mood with changes in gut microbiota in community-dwelling elderly: A randomized, double-blind, placebo-controlled, multicenter trial – Chong-Su Kim – The Journals of Gerontology

Phages and viruses
Intestinal microbiome‐macrophage crosstalk contributes to cholestatic liver disease by promoting intestinal permeability – Anna Isaacs-Ten – Hepatology

Bioinformatics
Preprint: hogwash: Three Methods for Genome-Wide Association Studies in Bacteria – Katie Saund – bioRxiv

Mycobiome

Preprint: Mycobiome analysis in fungal Infected formalin-fixed and paraffin-embedded tissues for identification of pathogenic fungi: A pilot study – Taebum Lee – bioRxiv

Host-Pathogen Interactions
Preprint: Human GBP1 differentially targets Salmonella and Toxoplasma to license recognition of microbial ligands and caspase-mediated death – Daniel Fisch – bioRxiv

Preprint: Mechanical competition triggered by innate immune signaling drives the collective extrusion of bacterially-infected epithelial cells – Effie E. Bastounis – bioRxiv

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Microbes on the market

Genome & Company receives FDA IND clearance for GEN-001, its first anti-cancer microbiome therapeutic (Press Release, BioSpace)