Covid-19

Legal agreements: barriers and enablers to global equitable COVID-19 vaccine access – Phelan et al. -The Lancet

Science news

‘Scientific American’ Breaks 175 Years Of Tradition, Endorses A Presidential Nominee – NPR

Human microbiome

Early origin and global colonisation of foot-and-mouth disease virus – Aiewsakun et al. – Scientific Reports

Human gut microbiome

Alteration of Gut Microbiota in Patients With Epilepsy and the Potential Index as a Biomarker – Gong et al. – Frontiers in Microbiology

Plant, root, and soil microbiome

Amazonian soil metagenomes indicate different physiological strategies of microbial communities in response to land use change – Khan et al. – bioRxiv

Deciphering the Role of Trehalose in Tripartite Symbiosis Among Rhizobia, Arbuscular Mycorrhizal Fungi, and Legumes for Enhancing Abiotic Stress Tolerance in Crop Plants – Sharma et al. – Frontier in Microbiology

Animal experiments

Diet posttranslationally modifies the mouse gut microbial proteome to modulate renal function – Lobel et al. – Science

Investigation into the effect of divergent feed efficiency phenotype on the bovine rumen microbiota across diet and breed – McGovern et al. – Scientific Reports

We have got a human gut microbiome heavy edition today, with two reviews of the early life microbiome and its affects on physiological development.

I also want to highlight the work of Chen et al. 2020, who nicely demonstrate that the zebra finch early-life microbiome converges upon the microbiome of the parent that reared them (rather than their genetic parent) in cross-fostering experiments. This is important as cross-fostering experiments have been a staple in studies of avian micro-evolution and eco-physiology in captive and free-living system. Therefore, variation in offspring phenotypes attributable to the ‘early life environment’, ‘nest effects’, or ‘foster parent effects’ might in some cases be partly proximately driven by microbiome variation. This is an important point of clarification since, as Chen et al. 2020 and other researchers have demonstrated, the microbiome can be vertically transmitted—unlike most early-life environment sources of phenotypic variation. Thanks for indulging me in my musings 😉

Enjoy today’s list!

Human respiratory microbiome
Adhesion of Staphylococcus aureus to epithelial cells: an in vitro approach to study interactions within the nasal microbiota – Ménard et al. 2020 – Journal of Medical Microbiology

Human skin microbiome
Early development of the skin microbiome: therapeutic opportunities – Casterline and Paller 2020 – Pediatric Research

Human gut microbiome
Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria – Seelbinder et al. 2020 – Microbiome

Multi-omics analysis reveals the influence of genetic and environmental risk factors on developing gut microbiota in infants at risk of celiac disease – Leonard et al. 2020 – Microbiome

The effects of different dietary fiber pectin structures on the gastrointestinal immune barrier: impact via gut microbiota and direct effects on immune cells – Beukema et al. 2020 – Experimental & Molecular Medicine

Roles of the Polyphenol–Gut Microbiota Interaction in Alleviating Colitis and Preventing Colitis-Associated Colorectal Cancer – Zhao and Jiang – Advances in Nutrition

Stomach microbiota, Helicobacter pylori, and group 2 innate lymphoid cells – Ohno and Satoh-Takayama 2020 – Experimental & Molecular Medicine

Maternal supplementation with Bifidobacterium breve M-16V prevents their offspring from allergic airway inflammation accelerated by the prenatal exposure to an air pollutant aerosol – Terada-Ikeda et al. 2020 – PLOS ONE

[Review] Early Life Stress and the Development of the Infant Gut Microbiota: Implications for Mental Health and Neurocognitive Development – Vogel et al. 2020 – Current Psychiatry Reports

[Review] Early life interaction between the microbiota and the Enteric Nervous System – Foong et al. 2020 – Gastrointestinal and Liver Physiology

Animal experiments
Maternal gut microbes shape the early-life assembly of gut microbiota in passerine chicks via nests – Chen et al. 2020 – Microbiome

Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter – McKenna et al. 2020 –

Animal microbiome
Elucidation of Gut Microbiota in Mud Crab Scylla paramamosain Challenged to WSSV and Aeromonas hydrophila – Lin et al. 2020 – Marine Biotechnology

Plant, root, and soil microbiome
Soil microbial communities respond to an environmental gradient of grazing intensity in south Patagonia Argentina – Santiago et al. 2020 – Journal of Arid Environments

Different maturities drive proteomic and metabolomic changes in Chinese black truffle – Zhang et al. 2020 – Food Chemistry: X

Fungal Volatile Organic Compounds: More Than Just a Funky Smell? – Inamdar et al. 2020 – Annual Review of Microbiology

Phages and viruses
Potential applications of human viral metagenomics and reference materials: 2 considerations for current and future viruses – Santiago-Rodriguez and Hollister 2020 – Applied and Environmental Microbiology

Bioinformatics
Estimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC – Saary et al. 2020 – Genome Biology

Techniques
Hill-based dissimilarity indices and null models for analysis of microbial community assembly – Modin et al. 2020 –

A gene prioritization method based on a swine multi-omics knowledgebase and a deep learning model – Fu et al. 2020 – Communications Biology

Human vaginal microbiome
Lactobacillus species signature in association with term and preterm births from low-income group of Pakistan – Aslam et al. – The Journal of Maternal-Fetal & Neonatal Medicine

Human gut microbiome
Long-term use of antibiotics and risk of type 2 diabetes in women: a prospective cohort study – Yuan et al. – International Journal of Epidemiology

The Impact of Diabetes on the Gut and Salivary IgA Microbiomes – Brown et al. – Infection and Immunity

Animal experiments
Effects of dietary replacement of soybean meal with dried distillers grains with solubles on the microbiota occupying different ecological niches in the rumen of growing Hu lambs – Shen et al. – Journal of Animal Science and Biotechnology

Pathogen identification and epidemiological assessment in recirculation aquaculture system based on Illumina sequencing technology – Sugachenko et al. – Limnology and Freshwater Biology

How oral probiotics affect the severity of an experimental model of progressive multiple sclerosis? Bringing commensal bacteria into the neurodegenerative process – Mestre et al. – Gut Microbes

Animal microbiome
General Microbiota of the Soft TickOrnithodoros turicataParasitizing the Bolson Tortoise(Gopherus flavomarginatus) in the Mapimi BiosphereReserve, Mexico – Barraza-Guerrero et al. – Biology

Water and extremophile microbiome
Bioturbation by the marine polychaete Capitella teleta alters sediment microbial community by ingestion and defecation of sediment particles – Jang et al. – Science of the Total Environment

Bacteria in the lakes of the Tibetan Plateau and polar regions – Liu et al. – Science of the Total Enivornment

Sulfate-reducing bacterial community shifts in response to acid mine drainage in the sediment of the Hengshi watershed, South China – Bao et al. – Environmental Science and Pollution Research

Bioinformatics
Review: Predictive interactome modeling for precision microbiome engineering – Kessell et al – Current Opinion in Chemical Engineering

God morgon!

Good morning from Sweden. Today’s digest is a loaded one with a lot of new preprints and news from the world of microbiology.

As someone who suffers from allergic rhinitis my mind was blown when I read the article that linked gut microbiota to allergic rhinitis! I am waiting for someone to come up with a gut microflora based treatment now! Further in the area of microbiome are preprints on assessment of antibiotic use in neonates and barcoding of about 1000 new marine yeast isolates.

A new preprint details the mechanism of action of a very effective new antibiotic armeniaspirol against Gram positive bacteria. Yet another preprint describes the potent antimycobaterial activity of synthetic Azetidines derivatives, which could be a great tool in our fight against tuberculosis. Further in bacteriology are preprints providing new information about host-pathogen interactions during Helicobacter infections, dynamics in persisting and resuscitating bacteria, RNA metabolism and metabolic homeostasis in bacteria.

A super interesting preprint describes a new form of on-chip microscopy and I must confess that the authors did a great job at giving their manuscript a catchy, short and yet informative title!

Bioinformatic studies using thousands of nCoV genomes have unearthed some mutations that might be responsible for its human adaptation (although computational studies without any experimental biological evidence are not my favourite, it might provide a starting point for scientists interested in COVID19.

There are a lot of more interesting articles and I wish I could write about all of them! I hope you will enjoy today’s selection.

COVID-19

Preprint: The discovery of gene mutations making SARS-CoV-2 well adapted for humans: host-genome similarity analysis of 2594 genomes from China, the USA and Europe – Weitao Sun

Preprint: Mutation in position of 32 (G>U) of S2M differentiate human SARS-CoV2 from Bat Coronavirus – Majid Vahed, et al.

Preprint: Development of SARS-CoV-2 Nucleocapsid Specific Monoclonal Antibodies – James S. Terry, et al.

Preprint: A Mental Health Paradox: Mental health was both a motivator and barrier to physical activity during the COVID-19 pandemic – Maryam Marashi, et al.

Bacteria Hysteria

Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments – Da-Shuai Mu, et al., Microbiome

Preprint: Armeniaspirols inhibit the AAA+ proteases ClpXP and ClpYQ leading to cell division arrest in Gram-positive bacteria – Puneet Labana, et al.

Preprint: Effect of polyethylene glycol on growth of Escherichia coli DH5α and Bacillus subtilis NRS-762 – Wenfa Ng

Preprint: Essentiality of c-di-AMP in Bacillus subtilis: Bypassing mutations converge in potassium and glutamate homeostasis – Larissa Krüger, et al.

Preprint: Comparative genomics of Clostridium species associated with vacuum-packed meat spoilage – Nikola Palevich, et al.

Preprint: Antibiotics and the developing intestinal microbiome, metabolome and inflammatory environment: a randomized trial of preterm infants – Jordan T. Russell, et al.

Preprint: Azetidines kill Mycobacterium tuberculosis without detectable resistance by blocking mycolate assembly – Alice Lanne, et al.

Preprint: Proteome dynamics in persisting and resuscitating bacterial cells – Maja Semanjski, et al.

Preprint: Limitation of phosphate assimilation maintains cytoplasmic magnesium homeostasis – Roberto E. Bruna, et al.

Preprint: RecA levels modulate biofilm development in Acinetobacter baumannii – Carly Ching, et al.

Preprint: Distinct survival, growth lag, and ribosomal RNA degradation kinetics during long-term starvation for carbon or phosphate – Yusuke Himeoka, et al.

General microbiome

Gut microbial characteristics of adult patients with allergy rhinitis – Libing Zhu, et al., Microbial Cell Factories

Impact of investigational microbiota therapeutic RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trial – Suryang Kwak, et al., Microbiome

Preprint: Soil characteristics constrain the response of bacterial and fungal communities and hydrocarbon degradation genes to phenanthrene soil contamination and phytoremediation with poplars – Sara Correa-García, et al.

Preprint: Microbial bioprospecting for lignocellulose degradation at a unique Greek environment – Daphne N. Georgiadou, et al.

Preprint: DNA barcoding analysis of more than 1000 marine yeast isolates reveals previously unrecorded species – Chinnamani PrasannaKumar, et al.

Viruses

Preprint: Mammalian ANP32A and ANP32B proteins drive alternative avian influenza virus polymerase adaptations – Thomas. P. Peacock, et al.

Preprint: Development of Resistance to 4′-Ethynyl-2-Fluoro-2′-Deoxyadenosine (EFdA) by Wild-Type and Nucleoside Reverse Transcriptase Inhibitor Resistant Human Immunodeficiency Virus Type 1 – Maria E Cilento, et al.

Host-pathogen interactions

Preprint: NHR-49/PPAR-α and HLH-30/TFEB promote C. elegans host defense via a flavin-containing monooxygenase – Khursheed A. Wani, at al.

Preprint: Role of ERK activation in H. pylori-induced disruption of cell-cell tight junctions – Amita Sekar and Bow Ho

Preprint: Cellular co-infection can modulate the efficiency of influenza A virus production and shape the interferon response – Brigitte E Martin, et al.

Preprint: Non-permissive human conventional CD1c⁺ dendritic cells enable trans-infection of human primary renal tubular epithelial cells and protect BK polyomavirus from neutralization – Mathieu Sikorski, et al.

Techniques

Preprint: Nanoscopy on the Chea(i)p – Benedict Diederich, et al.

Preprint: Visualizing Borrelia burgdorferi infection using a small molecule imaging probe – Madeline G Sell, et al.

Microbiology in News

Malibu Microbiome Meeting Virtual Prelude Shares New Data – PR Newswire

Human Microbiome-Based Drugs And Diagnostics Market An Insight On the Important Factors and Trends Influencing the Market – Daily Research Chronicle

Autism and the Microbiome – The New Indian Express

Human gut microbiome

Keystone taxa indispensable for microbiome recovery – Sean M. Gibbons – Nature Microbiology

Metagenomics analysis of gut microbiota in response to diet intervention and gestational diabetes in overweight and obese women: a randomised, double-blind, placebo-controlled clinical trial – Mokkala et al. – Gut

Environmental microbiome

Preprint: Bacterial Community Assemblages in Classroom Floor Dust of 50 Public Schools in a Large City: Characterization Using 16s rRNA Sequences and Associations with Environmental Factors – Park et al.

A nitrogenase-like enzyme system catalyzes methionine, ethylene, and methane biogenesis – North et al. – Science

Animal microbiome

Effect of glycerol feed-supplementation on seabass metabolism and gut microbiota – Louvado et al. – Applied Microbiology and Biotechnology

Food microbiome

Secrets of the cheese microbiome – Danilo Ercolini – Nature Food

Biotechnology

A heterogeneous microbial consortium producing short-chain fatty acids from lignocellulose – Shahab et al. – Science

Non-microbiology pics

One Health(y) Cities: Cities are pandemic ecosystems and that’s where the action ought to happen – Evelyne de Leeuw – Cities and Health