God morgon!

Good morning from Sweden.

Today’s digest starts with a super interesting preprint on COVID-19 where the researchers have shown that anti-COVID-19 drugs induce lytic reactivation of an oncogenic virus. As if COVID-19 wasn’t dangerous enough, its treatment is now even more dangerous!

New research has revealed numerous genera of bacteria associated with Amoebozoa, which haven’t been looked into; polyamines as new substrates for a previously known efflux pump in Acinetobacter; genomic differences between the influenza viruses causing infections of different severity; and novel interactions between mycorrhizal fungi and plants.

Hope you’ll enjoy today’s digest!

COVID-19

Preprint: SARS-CoV-2 proteins and anti-COVID-19 drugs induce lytic reactivation of an oncogenic virus – Jungang Chen, et al.

Bacteria Hysteria

Preprint: Characterization of the antimicrobial activity of the cell-penetrating peptide TAT-RasGAP_317-326 – Maria Georgieva, et al.

Preprint: Bacteriophage Resistance Affects Flavobacterium columnare Virulence Partly via Mutations in Genes Related to Gliding Motility and Type IX Secretion System – Heidi MT Kunttu, et al.

Preprint: ROS-dependent innate immune mechanisms control Staphylococcus aureus MRSA virulence in the Drosophila larval model – Elodie Ramond, et al.

Preprint: Transposon-insertion sequencing in a clinical isolate of Legionella pneumophila identifies essential genes and determinants of natural transformation – Léo Hardy, et al.

Preprint: Spermidine and spermine are the natural substrates of the Acinetobacter baumannii AmvA multidrug efflux pump – Francesca L. Short, et al.

Gut Microbiome

Preprint: Comparing Fecal, Saliva, and Chicha Microbiomes Between Mothers and Children in an Indigenous Ecuadorian Cohort – Eric Daniel Adams, et al.

Preprint: Spatial analysis of gut microbiome reveals a distinct ecological niche associated with the mucus layer – Kellyanne Duncan, et al.

Preprint: Comprehensive Comparative Genomics Reveals Over 50 Phyla of Free-living and Pathogenic Bacteria are Associated with Diverse Members of the Amoebozoa – Yonas I. Tekle, et al.

β-glucan attenuates cognitive impairment via the gut-brain axis in diet-induced obese mice – Hongli Shi, et al., Microbiome

Faecal microbiota transplant from aged donor mice affects spatial learning and memory via modulating hippocampal synaptic plasticity- and neurotransmission-related proteins in young recipients – Alfonsina D’Amato, et al., Microbiome

Plants

Preprint: Comparative analysis of temporal transcriptome reveals the relationship between pectin degradation and pathogenicity of defoliating Verticillium dahliae to Upland cotton (Gossypium hirsutum) – Fan Zhang, et al.

Preprint: Silencing of ATP synthase β reduces phytoplasma multiplication in the leafhopper vector Euscelidius variegatus – Luciana Galetto, et al.

Trophic interactions as determinants of the arbuscular mycorrhizal fungal community with cascading plant-promoting consequences – Yuji Jiang, et al., Microbiome

Preprint: Characterization of Met25 as a Color Associated Genetic Marker in Yarrowia lipolytica – Harley Edwards, et al.

General Microbiome

Preprint: Fine scale sampling unveils diazotroph patchiness in the South Pacific Ocean – Mar Benavides, et al.

Preprint: Sedimentation rate and organic matter dynamics shape microbiomes across a continental margin – Sabyasachi Bhattacharya, et al.

Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula – Shawn P. Brown, et al., Microbiome

Viruses

Preprint: A potent neutralizing mouse monoclonal antibody specific to dengue virus type 1 Mochizuki strain recognized a novel epitope around the N-67 glycan on the E protein: a possible explanation of dengue virus evolution regarding the acquisition of N-67 glycan – Tomohiro Kotaki, et al.

Preprint: Differential Disease Severity and Whole Genome Sequence Analysis for Human Influenza A/H1N1pdm Virus in 2015-2016 Influenza Season – Hsuan Liu, et al.

Viral ecogenomics across the Porifera – Cecília Pascelli, et al., Microbiome

Infections

Preprint: A Universal Stress Protein upregulated by hypoxia may contribute to chronic lung colonisation and intramacrophage survival in cystic fibrosis – Andrew O’Connor, et al.

Preprint: Modulation of early host innate immune response by a Fowlpox virus (FWPV) lateral body protein – Efstathios S Giotis, et al.

Techniques

Preprint: Accurate Microbiome Sequencing with Synthetic Long Read Sequencing – Nico Chung, et al.

Investigating host-microbiome interactions by droplet based microfluidics – Alexandra S. Tauzin, et al., Microbiome

Hello again everyone! Another change of seasons is upon us and I hope you all remain safe with the upcoming flu season as well as with the continuing covid-19 pandemic. Remember to continue hand washing, social distancing and masking to protect those most vulnerable. Todays post includes more interesting work relating to the gut microbiome with respect to obesity and also as a marker for the disease activity and therapeutic outcome in Inflammatory Bowel Disease. Enjoy!

ORAL MICROBIOME

Preprint: Longitudinal multi-omics along gingivitis development reveal a suboptimal-health gum state with periodontitis-like microbiome – Shi Huang, et al – bioRxiv

PREGNANCY AND EARLY LIFE

News Article: Maternal Microbes Support Fetal Brain Wiring – Nature

HUMAN GUT MICROBIOME

[HTML] Both Gut Microbiota and Differentially Expressed Proteins Are Relevant to the Development of Obesity – Y Li, et al – BioMed Research International

[PDF] How the intestinal microbiota may reflect disease activity and influence therapeutic outcome in inflammatory bowel disease – C Caenepeel, et al – Alimentary Pharmacology & …

ANIMAL MICROBIOME

News Article: Climate warming is altering animals’ gut microbes, which are critical to their health and survival – Fairfield Citizen

PLANT, ROOT AND SOIL MICROBIOME

Soil origin and plant genotype structure distinct microbiome compartments in the model legume …Microbiome – BioMed Central

WATER AND EXTREMOPHILE MICROBIOME

Effect of heavy metal-induced stress on two extremophilic microbial communities from Caviahue-Copahue, Argentina – LM Francisco, E Donati – Environmental Pollution

Fungi and viruses as important players in microbial mats – C Carreira, et al – FEMS Microbiology Ecology

FOOD MICROBIOLOGY

News Article: [PDF] Addition of Coriander during Fermentation of Korean Soy Sauce (Gangjang) Causes Significant Shift in Microbial Composition and Reduction in Biogenic Amine …M Mannaa, et al – Foods

SCIENCE, PUBLISHING AND CAREER

Post-doc in gut microbiome-behaviour research (0.8/1.0 fte) — AcademicTransfer

Space Exploration Plant and Microbiome Learning Sessions start this week – Space Ref

Human gut microbiome

Gut microbiota and old age: Modulating factors and interventions for healthy longevity – Coman and Vodnar – Experimental Gerontology

Role of Gut Microbiome and Microbial Metabolites in Alleviating Insulin Resistance After Bariatric Surgery – Wang et al. – Obesity Surgery

Analysis of the infant gut microbiome reveals metabolic functional roles associated with healthy infants and infants with atopic dermatitis using metaproteomics – Kingkaw et al. – PeerJ

Effects of β-Lactam Antibiotics on Gut Microbiota Colonization and Metabolites in Late Preterm Infants – Lu et al. – Current Microbiology

Review article: how the intestinal microbiota may reflect disease activity and influence therapeutic outcome in inflammatory bowel disease – Caenepeel et al. – Alimentary Pharmacology and Therapeutics

Human oral microbiome

Comparative evaluation of microbial profiles of oral samples obtained at different collection time points and using different methods – Omori et al. – Clinical Oral Investigations

Human vaginal microbiome

Identification of Bacteriophages in the Vagina of Pregnant Women: A Descriptive Study – da Costa et al. – International Journal of Obstetrics and Gynaecology

Pregnancy and early life

Microbiome Understanding in Maternity Study (MUMS), an Australian prospective longitudinal cohort study of maternal and infant microbiota: study protocol – Susic et al. – BMJ Open

Plant, root and soil microbiome

Bio-organic fertilizers stimulate indigenous soil Pseudomonas populations to enhance plant disease suppression – Tae et al. – Microbiome *

Breeding selection imposed a differential selective pressure on the wheat root-associated microbiome – Kinnunen et al. – FEMS MICROBIOLOGY ECOLOGY

Temporal dynamics of bacterial communities during seed development and maturation – Chesneau et al. – FEMS MICROBIOLOGY ECOLOGY

Comparative analysis of rhizosphere soil physiochemical characteristics and microbial communities between rusty and healthy ginseng root – Bian et al. – Scientific Reports

Environmental microbiology

Community, Distribution, and Ecological Roles of Estuarine Archaea – Zou et al. – Frontier in Microbiology

Aerobic microbial communities in the sediments of a marine oxygen minimum zone – Bhattacharya et al. – FEMS MICROBIOLOGY LETTERS

Microbial prospection of communities that produce biosurfactants from the water column and sediments of the Gulf of Mexico – Morales-Guzman et al. – Biotechnology an dApplied Biochemistry

Animal experiments

Anatomy, immunology, digestive physiology and microbiota of the salmonid intestine: Knowns and unknowns under the impact of an expanding industrialized production – Bjørgen et al. – Fish & Shellfish Immunology

Disruption of ruminal homeostasis by malnutrition involved in systemic ruminal microbiota-host interactions in a pregnant sheep model – Xue et al. – Microbiome

Techniques

Method development and validation for the quantification of organic acids in microbial samples using anionic exchange solid-phase extraction and gas chromatography-mass spectrometry – Heyen et al. – Analytical and Bioanalytical Chemistry

A novel universal primer pair for prokaryotes with improved performances for anammox containing communities – Mazzoli et al. – Scientific Reports

Good morning, a few interesting papers today. In particular one paper finding a link between the meconium microbiome and head circumference is a great read, and the paper on the package MicrobiomeExplorer for R.

Pregnancy and Early Life

Meconium microbiome and its relation to neonatal growth and head circumference catch-up in preterm infants. Terrazza Nutricioist et al. PLOS ONE.

Human mouth microbiome

Photobiomodulation modulates inflammation and oral microbiome: a pilot study. Zanotta et al. Biomarkers.

Human vaginal microbiome

Changes in Vaginal Microbiome in Pregnant and Nonpregnant Women with Bacterial Vaginosis: Toward Microbiome Diagnostics? Mohamed et al. OMICS: A Journal Of Integrative Biology.

Human gut microbiome

Role of Gut Microbiome and Microbial Metabolites in Alleviating Insulin Resistance After Bariatric Surgery. Wang et al. Obesity Surgery

[Pre-print] Multi-omic Characterization of the Taxa-function Relationship in Infant Gut Microbiomes. Nguyen et al. Research Square.

Bioinformatics

MicrobiomeExplorer: An R package for the analysis and visualization of microbial communities. Reeder et al. Bioinformatics

Animal experiments

[Pre-print] Preventive Antibiotic Treatment Increases Neonatal Chicks Susceptibility to Salmonella Infection Via Disrupting Gut Microbiota and Linoleic Acid Metabolism. Mei et al. Research Square.

Plant, root and soil microbiome

Rhizospheric microbiomes help Dongxiang common wild rice (Oryza rufipogon Griff.) rather than Leersia hexandra Swartz survive under cold stress. Xu et al. Archives of Agronomy and Soil Science

Covid-19

Respiratory disease in cats associated with human-to-cat transmission of SARS-CoV-2 in the UK – Hosie et al. – bioRxiv

Human gut microbiome

The intestinal microbiome is a co-determinant of the postprandial plasma glucose response – Søndertoft et al. – PLOS ONE

Supplementation of a lacto-fermented rapeseed-seaweed blend promotes gut microbial- and gut immune-modulation in weaner piglets – Hui et al. – bioRxiv

Human vaginal microbiome

Changes of vaginal microbiota during cervical carcinogenesis in women with human papillomavirus infection – So et al. 2020 – PLOS ONE

Human fecal microbiome

Fecal microbiota transplantation in inflammatory bowel disease patients: A systematic review and meta-analysis – Caldeira et al. – PLOS ONE

Pregnancy and early life

Meconium microbiome and its relation to neonatal growth and head circumference catch-up in preterm infants – Terrazzan et al. – PLOS ONE

Plant, root and soil microbiome

Augmented Biodegradation of Textile Azo Dye Effluents by Plant Endophytes: A Sustainable, Eco-Friendly Alternative – Goud et al. 2020 – Current Microbiology

Regional Differences in the Structure of Juglans nigra Phytobiome Reflect Geographical Differences in Thousand Cankers Disease Severity – Onufrak et al. – Phytobiomes

Using the Microbiome Amplification Preference Tool (MAPT) to Reveal Medicago sativa-Associated Eukaryotic Microbes – Moccia et al. – Phytobiomes

Temporal variation in soil bacterial communities can be confounded with spatial variation – Hermans et al. – FEMS Microbial Ecology

A multi-omics approach to solving problems in plant disease ecology – Crandall et al. 2020 – PLOS ONE

Impact of Water Stress on Microbial Community and Activity in Sandy and Loamy Soils – Siebielec et al. – Agronomy

Animal experiments

The microbiota of the surface, dermis and subcutaneous tissue of dog skin – Garcia-Fonticoba et al. – Animal Microbiome

Host and altitude factors affect rumen bacteria in cattle – Wu et al. – Brazilian Journal of Microbiology

Environmental microbiology

Macroecological laws describe variation and diversity in microbial communities – Jacopo Grilli – Nature communications

Alpha-, beta-, and gamma-diversity of bacteria varies across habitats – Walters and Martiny – PLOS ONE

Linking microbial Sphagnum degradation and acetate mineralization in acidic peat bogs: from global insights to a genome-centric case study – James et al. – The ISME