June 22, 2020

General microbiome
Impact of feeding and stirring regimes on the internal stratification of microbial communities in the fermenter of anaerobic digestion plants – Robert Heyera – Bioresource Technology

Human microbiome
REVIEW: Role of the Microbiome in Allergic Disease Development – Andrea C. Aguilera, – Pediatric Allergy and Immunology

Optimization and standardization of the culturomics technique for human microbiome exploration – Ami Diakite – Scientific Reports

Human skin microbiome
The microbiome of diabetic foot ulcers: a comparison of swab and tissue biopsy wound sampling techniques using 16S rRNA gene sequencing – J. Travis – BMC Microbiology

Human gut microbiome
Interpersonal Gut Microbiome Variation Drives Susceptibility and Resistance to Cholera Infection – Salma Alavi – Cell

EDITORIAL: Gut microbes effects on host metabolic alterations in health and disease – Suzana D. Savkovic – Gut Microbes

Revealing links between gut microbiome and its fungal community in Type 2 Diabetes Mellitus among Emirati subjects: A pilot study – Mohammad Tahseen Al Bataineh – Scientific Reports

Alterations in the Gut Microbiome in the Progression of Cirrhosis to Hepatocellular Carcinoma – Yelena Lapidot – mSystems

Human respiratory microbiome
Taxonomic diversity of sputum microbiome in lung cancer patients and its relationship with chromosomal aberrations in blood lymphocytes – V. G. Druzhinin – Scientific Reports

Pregnancy and early life
Human milk microbiota development during lactation and its relation to maternal geographic location and gestational hypertensive status – Yi Wan – Gut Microbes

Maternal Microbiota, Cortisol Concentration, and Post-PartumWeight Recovery Are Dependent on Mode of Delivery – Marta Selma-Royo – Nutrients

Human ancient microbiome
Analysis of oral microbiome from fossil human remains revealed the significant differences in virulence factors of modern and ancient Tannerella forsythia – Anna Philips – BMC Genomics

Animal experiments
Zebrafish microbiome studies make waves – Keaton Stagaman – Lab Animal

Animal microbiome
An Insight into Diversity and Functionalities of Gut Microbiota in Insects – Shengchen Wang – Current Microbiology

Plant, root, and soil microbiome
Microbial assimilation dynamics differs but total mineralization from added root and shoot residues is similar in agricultural Alfisols – Yingde Xu – Soil Biology and Biochemistry

Effects of increasing concentrations of unamended and gypsum modified bauxite residues on soil microbial community functions and structure – A mesocosm study – Camille Fourrier – Ecotoxicology and Environmental Safety

Microbiome approaches provide the key to biologically control postharvest pathogens and storability of fruits and vegetables – Peter Kusstatscher – FEMS Microbiology Ecology

Variations of rhizospheric soil microbial communities in response to continuous Andrographis paniculata cropping practices – Junren Li – Botanical Studies

Seed Metabolism and Pathogen Resistance Enhancement in Pisum sativum During Colonization of Arbuscular Mycorrhizal Fungi: An Integrative Metabolomics-Proteomics Approach – Nima Ranjbar Sistani – Frontiers in Plant Science

Water microbiome
Differential Responses of a Coastal Prokaryotic Community to Phytoplanktonic Organic Matter Derived from Cellular Components and Exudates – Hiroaki Takebe – Microbes and Environments

Built environment
MINI-REVIEW: Microorganisms populating the water-related indoor biome – Monika Novak Babič – Applied Microbiology and Biotechnology

Pre-print
Shotgun metagenomics reveals signicant gut microbiome features in different grades of acute pancreatitis – Shanshan Yu – Research Square

Characteristics of Esophagus Flora in Patients with Esophageal Squamous Cell Carcinoma in Central China – Shuixiang He – Research Square

Can root-associated fungi mediate the impact of abiotic conditions on the growth of a High Arctic herb? – Magdalena Wutkowska – bioRxiv

Microbes on the market
Finch Therapeutics Announces Positive Topline Results from Randomized Controlled Trial of CP101, an Oral Microbiome Drug, for the Prevention of Recurrent C. difficile Infection – Finch Therapeutics

Microbes in the news
Gut reaction: How the gut microbiome may influence the severity of COVID-19 – Shirin Moossavi – The Conversation

April 24, 2020

Events

Virtual Podium 2020 – Session 5 (Microbiome) – April 24, 2020

Scientific career and work-life balance – April 24, 2020

World Malaria Day – April 25, 2020 – Draws attention to the impact of the disease and (re)urges us to find a way to overcome it once and for all.
Join the #talkingmalaria tweetchat on April 24, 2020 at 12 noon BST.

COVID-19

GRAND CHALLENGE: A billion molecules against COVID-19 – Joint European Disruptive Initiative

General microbiome

Reversibility of propionic acid inhibition to anaerobic digestion: Inhibition kinetics and microbial mechanism – Youl Han – Chemosphere

Responses of microbial structures, functions, metabolic pathways and community interactions to different C/N ratios in aerobic nitrification – Hongwei Sun – Bioresource Technology

PERSPECTIVE: Cultivating fungal research – Heidi H. Kong – Science

Human microbiome

REVIEW: Microbiota–immune interactions in asthma pathogenesis and phenotype – Nicholas W.Lukacs – Current Opinion in Immunology

CANCER IN TRANSLATION: Microbiome genomics for cancer prediction – Lorenz Adlung – Nature Cancer

Human skin microbiome

BOOK CHAPTER: The wound microbiome – Aayushi Uberoi – In: Wound Healing, Tissue Repair, and Regeneration in Diabetes.

Human gut microbiome

BOOK CHAPTER: Dietary Fiber and Gut Microbiota – Carolina Senés-Guerrero – In: Science and Technology of Fibers in Food Systems

Animal experiments

Effect of in feed administration of different butyrate formulations on Salmonella Enteritidis colonization and cecal microbiota in broilers – Lonneke Onrust – Veterinary Research

Stochasticity constrained by deterministic effects of diet and age drive rumen microbiome assembly dynamics – Ori Furman – Nature Communications

Sequence variant analysis reveals poor correlations in microbial taxonomic abundance between humans and mice after gnotobiotic transfer – Farnaz Fouladi – ISME Journal

Temporal changes in microbial communities attached to forages with different lignocellulosic compositions in the cattle rumen – Javad Gharechahi – FEMS Microbiology Ecology

Animal microbiome

Host-microbiota interaction helps to explain the bottom-up effects of climate change on a small rodent species – Guoliang Li – ISME Journal

Plant, root, and soil microbiome

Tapping into the maize root microbiome to identify bacteria that promote growth under chilling conditions – Stien Beirinckx – Microbiome

Regulatory relationship between quality variation and environment of Cistanche deserticola in three ecotypes based on soil microbiome analysis – Xiao Sun – Scientific Reports

Effects of biodegradable plastic film mulching on soil microbial communities in two agroecosystems – Sreejata Bandopadhyay – PeerJ

Water microbiome

Total Microbial Activity and Sulfur Cycling Microbe Changes in Response to the Development of Hypoxia in a Shallow Estuary – Yunjung Park – Ocean Science Journal

Built environment

Associations Between Respiratory Infections and Bacterial Microbiome in Student Dormitories in Northern China – Xi Fu – Indoor Air

Bacterial community analysis of floor dust and HEPA filters in air purifiers used in office rooms in ILAS, Beijing – Jianguo Guo – Scientific Reports

Microbes in space

The influence of spaceflight on the astronaut salivary microbiome and the search for a microbiome biomarker for viral reactivation – Camilla Urbaniak – Microbiome

Food microbiology

Insights into the Microbiological Safety of Wooden Cutting Boards Used for Meat Processing in Hong Kong’s Wet Markets: A Focus on Food-Contact Surfaces, Cross-Contamination and the Efficacy of Traditional Hygiene Practices – Patrick T. Sekoai – Microorganisms

Pre-print

MicrobioLink: An integrated computational pipeline to infer functional effects of microbiome-host interactions – Tahila Andrighetti – bioRxiv

Repeatability and reproducibility assessment in a large-scale population-based microbiota study: case study on human milk microbiota – Shirin Moossavi – bioRxiv

Mendelian randomization analysis revealed causal effects from gut microbiota to abdominal obesity – Qian Xu – bioRxiv

A quantitative measure of functional redundancy in microbial ecosystems – Taylor M Royalty – bioRxiv

Host association induces genome changes in Candida albicans which alters its virulence – Amanda C Smith – bioRxiv

Shirin’s non-microbiology picks

CAREER FEATURE: Safely conducting essential research in the face of COVID-19 – Virginia Gewin – Nature

Reaching a Large Urban Undergraduate Population through Microbial Ecology Course-Based Research Experiences – Samantha Parks – Journal of Microbiology & Biology Education

POLICY FORUM: Against pandemic research exceptionalism – Alex John London – Science

WORLD VIEW: On the 50th Earth Day, take collective action for the planet – Emma Marris – Nature

BEHIND THE PAPER: Annotating the unknown: Functional Gene Annotation using Untargeted Metabolomics – Robert Jansen – Nature Microbiology Community

March 27, 2020

We begin with a few updates about the recent research news about COVID 19 and how as a scientist you might be able to help. As a result of the global lock down, many conferences and seminars have moved online. You will find some of the microbiome-related online events in today’s post. Please also have a look at a special issue of the Philosophical Transactions of the Royal Society for conceptual challenges in microbial community ecology.

COVID-19
Coronavirus vaccines: five key questions as trials begin – Nature News


How blood from coronavirus survivors might save lives – Nature News

COVID-19 Pandemic: Scientist volunteer form

An initiative to redirect scientific resources towards the fight against COVID-19

Virtual Events
Virtual Conference: 6th Annual Translational Microbiome Conference

Guts & Bugs: A virtual GI seminar series by Edelblum Lab

Let’s go viral: online microbiology seminars in partnership with International Society of Microbial Ecology
Schedule can be found via Twitter #MicroSeminar @MicroSeminar

General microbiome
SPECIAL ISSUE: Phillosophical Transactions of the Royal Society B : Conceptual challenges in microbial community ecology

Human respiratory microbiome
Review: Respiratory microbiome and epithelial interactions shape immunity in the lungs – Invernizzi et al. – Immunology

Human oral microbiome
Polymicrobial periodontal disease triggers a wide radius of effect and unique virome – Gao et al. – npj Biofilms and Microbiomes

Metagenomic analysis of bacterial species in tongue microbiome of current and never smokers – Sato et al. – npj Biofilms and Microbiomes

Spatial Ecology of the Human Tongue Dorsum Microbiome – Wilbert et al. – Cell Reports

Oral biofilms exposure to chlorhexidine results in altered microbial composition and metabolic profile – Chatzigiannidou et al. – npj Biofilms and Microbiomes

Dysbiotic oral microbiota and infected salivary glands in Sjögren’s syndrome – Alam et al. – PLOS ONE

Animal experiments
Drosophila-associated bacteria differentially shape the nutritional requirements of their host during juvenile growth – Consuegra et al. – PLOS Biology

Bacterially produced metabolites protect C. elegans neurons from degeneration – Urrutia et al. – PLOS Biology

Dynamic interactions within the host-associated microbiota cause tumor formation in the basal metazoan Hydra – Rathje et al. – PLOS Pathogens

Association of colitis with gut-microbiota dysbiosis in clathrin adapter AP-1B knockout mice – Jangid et al. – PLOS ONE

Variations in microbiota composition of laboratory mice influence Citrobacter rodentium infection via variable short-chain fatty acid production – Osbelt et al. – PLOS Pathogens

Changes in the faecal microbiota of horses and ponies during a two-year body weight gain programme – Langner et al. – PLOS ONE

Animal microbiome
Microbiomes in the insectivorous bat species Mops condylurus rapidly converge in captivity – Edenborough et al. – PLOS ONE

Plant, root, and soil microbiome
Towards Nutrition-Sensitive Agriculture: An evaluation of biocontrol effects, nutritional value, and ecological impact of bacterial inoculants – Passera et al. – Science of The Total Environment

Book Chapter: Rhizobacteria Versus Chelating Agents: Tool for Phytoremediation – Kaur et al. – Microbial Technology for Health and Environment

Book Chapter: Applications of Microorganisms in Agriculture – Doley et al. – Microbial Technology for Health and Environment

Plant Invasion Has Limited Impact on Soil Microbial alpha Diversity: A Meta-Analysis – Custer & van Diepen – Diversity

Water microbiome
Carbonate facies‐specific stable isotope data record climate, hydrology, and microbial communities in Great Salt Lake, UT – Ingalls et al. – Geobiology

The microbiome of modern microbialites in Bacalar Lagoon, Mexico – Yanez-Montalvo et al. – PLOS ONE

Food microbiology
Variations in Fungal Community and Diversity in Doushen With Different Flavors – Luo et at. – Frontiers in Microbiology

Bioinformatics
MetaBridge: An Integrative Multi‐Omics Tool for Metabolite‐Enzyme Mapping – Blimkie et al. – Current Protocols in Bioinformatics

Validating metabarcoding-based biodiversity assessments with multi-species occupancy models: A case study using coastal marine eDNA – McClenaghan et al. – PLOS ONE

PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph – Gautreau et al. – PLOS Computational Biology

The Community Simulator: A Python package for microbial ecology – Marsland et al. – PLOS ONE

Techniques
Genome-based species-specific primers for rapid identification of six species of Lactobacillus acidophilusgroup using multiplex PCR – You & Kim – PLOS ONE

Pathogens and microbiome
Commensal Neisseria cinerea impairs Neisseria meningitidis microcolony development and reduces pathogen colonisation of epithelial cells – Custodio et al. – PLOS Pathogens

Swimming motility of a gut bacterial symbiont promotes resistance to intestinal expulsion and enhances inflammation – Wiles et al. – PLOS Biology