Monthly Archives: April 2021

April 07, 2021

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General microbiome

Primate phageomes are structured by superhost phylogeny and environment – Gogarten et al. – PNAS

Fungal‐induced glycolysis in macrophages promotes colon cancer by enhancing innate lymphoid cell secretion of IL‐22 – Zhu et al. – The EMBO Journal

A method for detection of SARS-CoV-2 RNA in healthy human stool: a validation study – Coryell et al. – The Lancet Microbe

The Ocular Microbiome and Microbiota and their Effects on Ocular Surface Pathophysiology and Disorders – Aragona et al. – Survey of Ophthalmology

Human oral microbiome

Multi-dimensional study of the oral microbiome, metabolite, and immunologic environment in peanut allergy – Ho et al. – Journal of Allergy and Clinical Immunology

Human skin microbiome

Temporal Variation in Staphylococcus aureus Protein A Genotypes from Nose and Skin in Atopic Dermatitis Patients – van Mierlo et al. – Dermatology

Sex‐Based Differences in Fecal Short‐Chain Fatty Acid and Gut Microbiota in Irritable Bowel Syndrome Patients – Sun et al. – Journal of Digestive Diseases

Human gut microbiome

[REVIEW]Ecological and evolutionary responses to antibiotic treatment in the human gut microbiota – Pennycook & Scanlan – FEMS Microbiology Reviews

Animal microbiome (for animals in the wild)

The Fecal and Serum Metabolomics of Giant Pandas Based on Untargeted Metabolomics – Yang et al. – Zoological Scienc

Microbes in space

Astrobiology of life on Earth – Hallsworth et al. – Environmental Microbiology
Mars’ surface is not universally biocidal – Hallsworth – Environmental Microbiology

Bioinformatics

Draft Genome Sequences and Antimicrobial Profiles of Three Staphylococcus epidermidis Strains from Neonatal Blood Samples – Afeke et al. – Microbiology Resource Announcements

CoCoNet: An Efficient Deep Learning Tool for Viral Metagenome Binning – Arisdakessian et al. – Bioinformatics

Techniques

Rank normalization empowers a t-test for microbiome differential abundance analysis while controlling for false discoveries – Davis, Huang & Wang – Briefings in Bioinformatics

Discovering multiple types of DNA methylation from bacteria and microbiome using nanopore sequencing – Tourancheau et al. – Nature Methods

April 6, 2021

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Human gut microbiome

Thousands of previously unknown phages discovered in whole-community human gut metagenomes – Benler et al. – Microbiome

*Elevated rates of horizontal gene transfer in the industrialized human microbiome – Groussin et al. – Cell

Animal microbiome

Combined effects of composting and antibiotic administration on cattle manure–borne antibiotic resistance genes – Keenum et al. – Microbiome

Swine growth promotion with antibiotics or alternatives can increase antibiotic resistance gene mobility potential – Muurinen et al. – Scientific Reports

Methods

Using high-abundance proteins as guides for fast and effective peptide/protein identification from human gut metaproteomic data – Stamboulian et al. – Microbiome

High throughput sequencing provides exact genomic locations of inducible prophages and accurate phage-to-host ratios in gut microbial strains – Zünd et al. – Microbiome

A comprehensive metagenomics framework to characterize organisms relevant for planetary protection – Danko et al. – Microbiome

April 3, 2021

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Have a nice weekend! Today we want to highlight a new podcast about Microbiome and Health, available in Spotify. We also have today a set of studies, covering aspects of the urinary microbiome, drug-microbiome dynamics, and cancer microbiota.

Microbes in the Media

Biomes Podcast with Dr. Ruairi Robertson (Available in Spotify)

Human and General Microbiome

Microbiome and Metabolome Analyses Reveal Novel Interplay Between the Skin Microbiota and Plasma Metabolites in Psoriasis – Dongmei Chen – Frontiers in Microbiology

Microreview: Organ-on-chip to investigate host-pathogens interactions – Thomas Feaugas – Cellular Microbiology

Investigating colonization patterns of the infant gut microbiome during the introduction of solid food and weaning from breastmilk: A cohort study protocol – Sara Dizzell – PLoS One

Urinary Microbiota; Which Non-Invasive Urine Collection Method Should We Use? – Muhammed Selcuk Ozer – IJCP

A specific association between laxative misuse and suicidal behaviours in patients with anorexia nervosa and bulimia nervosa – Aiste Lengvenyte – Eating and Weight Disorders – Studies on Anorexia, Bulimia and Obesity

Bile Microbiota in Liver Transplantation: Proof of Concept Using Gene Amplification in a Heterogeneous Clinical Scenario – Francesco D’Amico – Frontiers in Surgery

The Unique Impact of COVID-19 on Human Gut Microbiome Research – Ella Burchill – Frontiers in Medicine

Modeling of Urinary Microbiota Associated With Cystitis – Marina Ceprnja – Frontiers in Cellular and Infection Microbiology

Identification of Microbiome Etiology Associated With Drug Resistance in Pleural Empyema – Zhaoyan Chen – Frontiers in Cellular and Infection Microbiology

Analysis of Gut Microbiome Using Explainable Machine Learning Predicts Risk of Diarrhea Associated With Tyrosine Kinase Inhibitor Neratinib: A Pilot Study – Chi Wah Wong – Frontiers in Oncology 

Antitumor efficacy of a neoantigen cancer vaccine delivered by electroporation is influenced by microbiota composition – Lucia Lione – OncoImmunology 

Associations between dysbiosis-inducing drugs, overall survival and tumor response in patients treated with immune checkpoint inhibitors – Louis Gaucher – Therapeutic Advances in Medical Oncology

The Hygiene Hypothesis – Learning From but Not Living in the Past – Petra I. Pfefferle – Frontiers in Immunology

Strength Exercise Confers Protection in Central Nervous System Autoimmunity by Altering the Gut Microbiota – Hao Chen – Frontiers in Immunology

Beneficial Microbes and Compounds

Enrichment of Food With Tannin Extracts Promotes Healthy Changes in the Human Gut Microbiota – Silvia Molino – Frontiers in Microbiology

Bifidobacterium Lactis Probio-M8 regulates gut microbiota to alleviate Alzheimer’s disease in the APP/PS1 mouse model – Jianing Cao – European Journal of Nutrition 

Animal Microbiome

Re-Analysis of 16S rRNA Gene Sequence Data Sets Uncovers Disparate Laboratory-Specific Microbiomes Associated with the Yellow Fever Mosquito (Aedes aegypti) – Jonas Frankel-Bricker – Microbial Ecology 

FOXO regulates the expression of antimicrobial peptides and promotes phagocytosis of hemocytes in shrimp antibacterial immunity – Cang Li – PLoS Pathogens

Environmental Microbiome

Microbial characteristics response to the soil quality of newly created farmland on the Loess Plateau – Chen Xu – Environmental Science and Pollution Research

Bioinformatics

Human microbiome privacy risks associated with summary statistics – Jae-Chang Cho – PLoS One

ResistoXplorer: a web-based tool for visual, statistical and exploratory data analysis of resistome data – Achal Dhariwal – NAR Genomics and Bioinformatics

April 2, 2021

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Good morning and happy Friday!

In my last blog post I requested reader contributions and many of you reached out! Below are some of the highlights which include a commentary on phylogenetic core groups, a preprint on viral RNA methylation in Wolbachia, a database for the murine oral bacterial community, and a research article on fungal modification in the leaf-cutter ant fungal garden ecosystem.

Events and jobs

Biological Sciences Laboratory Instructor Position at Smith College in Northampton, MA

General microbiome

***Commentary: Phylogenetic Core Groups: a promising concept in search of a consistent methodological framework – Pascual-García – Microbiome

Animal microbiome

***Preprint: Differential viral RNA methylation contributes to pathogen blocking in Wolbachia-colonized arthropod – Bhattacharya et al. – bioRxiv

Preprint: Isolation and characterization of a novel Wolbachia bacteriophage from Allonemobius socius crickets in Missouri – Fischer et al. – bioRxiv

***From plants to ants: Fungal modification of leaf lipids for nutrition and communication in the leaf-cutter ant fungal garden ecosystem – Khadempour et al. – mSystems

Plant, root, and soil microbiome

Preprint: Experimental evolution-driven identification of Arabidopsis rhizosphere competence genes in Pseudomonas protegens – Zhang et al. – bioRxiv

Built environment

Metagenomic profile of microbial communities in a drinking water storage tank sediment after sequential exposure to monochloramine, free chlorine, and monochloramine – Gomez-Alvarez et al. – ACS EST Water

Bioinformatics

***A 16S rRNA gene and draft genome database for the murine oral bacterial community – Joesph et al. – mSystems