A rich Digest today featuring the “Prime Editing” invented by the David R. Liu lab, which promises to correct 89% of point mutations, an ultra-deep metagenomic study of phages in aquatic systems and strain level interaction between bacteria and plants. Enjoy!

General microbiology

** Search-and-replace genome editing without double-strand breaks or donor DNA – Andrew V. Anzalone et al. – Nature

Resolving a piece of the archaeal lipid puzzle – Ann Pearson – PNAS

Antimicrobial resistance

Commentary: Surveillance and monitoring of antimicrobial resistance: limitations and lessons from the GRAM project – Jesse Schnall et al. – BMC Medicine

Preprint: In vitro Efficacy of Novel Glucan Synthase Inhibitor, Ibrexafungerp (SCY-078), Against Multidrug- and Pan-resistant Candida auris Isolates from the Outbreak in New York – Yan Chun Zhu et al. – bioRxiv
https://www.biorxiv.org/content/10.1101/811182v1.abstract

Review: Proteomics approach to understand bacterial antibiotic resistance strategies – Bo Peng et al. – Expert Review of Proteomics

Human oral microbiome

Subgingival Microbiota and Longitudinal Glucose Change: The Oral Infections, Glucose Intolerance and Insulin Resistance Study (ORIGINS) – R.T. Demmer et al. – Journal of Dental Research

Human gut microbiome

Review: Systems biology perspective for studying the gut microbiota in human physiology and liver diseases – Ozlem Altay et al. – EBioMedicine

Review: Intestinal microbiota and colorectal carcinoma: Implications for pathogenesis, diagnosis, and therapy – Ana Montalban-Arques & Michael Scharl – EBioMedicine

Perspective: Carbohydrate-based Prebiotics in Targeted Modulation of Gut Microbiome – Ka-Lung Lam & Peter Chi Keung Cheung – Journal of Agricultural and Food Chemistry

Metabolomics

Early Detection of Cystic Fibrosis Acute Pulmonary Exacerbations by Exhaled Breath Condensate Metabolomics – Xiaoling Zang et al. – Journal of Proteome Research

Food microbiome

Peer pressure: Evolutionary responses to biotic pressures in wine yeasts – C. G. Conacher et al. – FEMS Yeast Research

Animal experiments

Disruption of gut integrity and permeability contributes to enteritis in a fish-parasite model: a story told from serum metabolomics – Ariadna Sitjà-Bobadilla et al. – Parasites & Vectors

Animal microbiome

Estimating the burden of dengue and the impact of release of wMel Wolbachia-infected mosquitoes in Indonesia: a modelling study – Kathleen M. O’Reilly et al. – BMC Medicine

Plant, root and soil microbiome

Preprint: Insights into the desert living skin microbiome: geography, soil depth, and crust type affect biocrust microbial communities and networks in Mojave Desert, USA – Nuttapon Pombubpa et al. – bioRxiv

** Metabolites in the root exudates of groundnut change during interaction with plant growth promoting rhizobacteria in a strain-specific manner – Sravani Ankati & Appa Rao Podile – Journal of Plant Physiology

Environmental and biotic drivers of soil microbial β-diversity across spatial and phylogenetic scales – Loïc Chalmandrier et al. – Ecography

Soil hydrology drives ecological niche differentiation in a native prairie microbiome – James S Griffin et al. – FEMS Microbiology Ecology

Consistent host and organ occupancy of phyllosphere bacteria in a community of wild herbaceous plant species – Julien Massoni et al. – The ISME Journal

Effect of aridity and dune type on rhizosphere soil bacterial communities of Caragana microphylla in desert regions of northern China – Jiangli Gao et al. – PLoS One

Rhizosphere bacterial community in watermelon-wheat intercropping was more stable than in watermelon monoculture system under Fusarium oxysporum f. sp. niveum invasion – Hongjie Yu et al. – Plant and Soil

Phosphorus-acquisition strategies of canola, wheat and barley in soil amended with sewage sludges – C. Nobile et al. – Scientific Reports

Water and extremophile microbiome

Distinctive microbial communities in subzero hypersaline brines from Arctic coastal sea ice and rarely sampled cryopegs – Zachary S. Cooper et al. – FEMS Microbiology Ecology

Performance and microbial communities of different biofilm membrane bioreactors with pre-anoxic tanks treating mariculture wastewater – Huining Zhang et al. – Bioresource Technology

Do organic substrates drive microbial community interactions in Arctic snow? – Benoît Bergk Pinto et al. – Frontiers in Microbiology

Genomic signatures for sedimentary microbial utilization of phytoplankton detritus in a fast-flowing estuary – Mariya W. Smit et al. – Frontiers in Microbiology

pH control and microbial community analysis with HCl or CO2 addition in H2-based autotrophic denitrification – Wei Xing et al. – Water Research

Extremophilic nitrite-oxidizing Chloroflexi from Yellowstone hot springs – Eva Spieck et al. – The ISME Journal

Phages and viruses

** Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics – Vinicius S. Kavagutti et al. – Microbiome

Review: Phage Therapy with a Focus on the Human Microbiota – Sharita Divya Ganeshan & Zeinab Hosseinidoust – Antibiotics

Technology

Preprint: Gene copy normalization of the 16S rRNA gene cannot outweigh the methodological biases of sequencing – Robert Starke & Daniel Morais – bioRxiv

Review: Third generation sequencing in the clinical laboratory: Exploring the advantages and challenges of nanopore sequencing – Lauren M. Petersen et al. – Journal Clinical Microbiology

Microbes in the news

Which foods are beneficial for a healthy gut microbiome? – Ana Sandoiu – Medical News Today

Microbiome: Untapped source of novel antimicrobials – Delthia Ricks – Medical Xpress

The Problem With Labeling Gut Troubles ‘Dysbiosis’ – Elizabeth Preston – Undark

Bacteria for beauty: why you need to start thinking about your skin microbiome – Hannah Ebelthite – Telegraph

Research Finds These Mediterranean Diet Foods Protect The Gut Microbiome – Jamie Schneider – Mind Body Green

Are undiscovered antibiotics ‘silently waiting’ in our own bodies? Researchers scour microbiome for helpful genes – Shelly Fan – Genetic Literacy Project

Reprogramming the microbiome: Antara Lifesciences targets the human health space with dual targeted formulation – Tingmin Koe – Food Navigator Asia

Transient and long-term disruption of gut microbes after antibiotics – Jeff Hansen – UAB News

Microbes on the market

Microba, Psomagen Partner to Launch Microbiome Test in US – GenomeWeb