June 28, 2020

Greetings from Wiltshire, England!

Today’s digest brings a little bit of everything. We’ve been cataloguing the latest COVID-19 publications during this pandemic, and today I’m please to bring you a paper combining both COVID-19 and microbiome research!

Elsewhere, there are plenty of environmental microbiome publications, including a great paper on the challenges of studying microbiology in space, an analysis of how aerosols spread COVID-19 and other infectious agents in dental practices, and plenty of articles on various aspects of soil microbiomes.

I hope everyone’s coping well during these times. On a personal level, I’m delighted to be returning to the lab this week to resume my PhD research into gut microbiomes and cancer. I’m glad to be back, but worried about how my pipetting skills have suffered during my time off!

Stay safe, and happy reading!


Intestinal Flora as a Potential Strategy to Fight SARS-CoV-2 Infection – He et al.Frontiers in Microbiology

Preprint: Naturally mutated spike proteins of SARS-CoV-2 variants show differential levels of cell entry – Ozono et al.

Human vaginal microbiome

Novel Potential Probiotic Lactobacilli for Prevention and Treatment of Vulvovaginal Infections – Kumherová et al. – Probiotics and Antimicrobial Proteins

Preprint: The structure and diversity of strain level variation in vaginal bacteria –Tortelli et al.

Human gut microbiome

Early exposure to food contaminants reshapes maturation of the human brain-gut-microbiota axis – Sarron et al.World Journal of Gastroenterology

Luminal microbiota related to Crohn’s disease recurrence after surgery – Hamilton et al.Gut Microbes

Animal experiments

Preprint: The gut mycobiome of healthy mice is shaped by the environment and shapes metabolic outcomes in response to diet – Mims et al.

Animal microbiome

Germ-free housing conditions do not affect aortic root and aortic arch lesion size of late atherosclerotic low-density lipoprotein receptor-deficient mice – Kiouptsi et al.Gut Microbes

The effects of environment and ontogeny on the skin microbiome of two Stegastes damselfishes (Pomacentridae) from the eastern Caribbean Sea – Xavier et al.Marine Biology

Variations and Potential Factors of Gut Prokaryotic Microbiome During Spawning Migration in Coilia nasus – Ying et al.Current Microbiology

Plant, root, and soil microbiome

Genetic diversity of Agrobacterium species isolated from nodules of common bean and soybean in Brazil, Mexico, Ecuador and Mozambique, and description of the new species Agrobacterium fabacearum sp. nov. – Delamuta et al.International Journal of Systematic and Evolutionary Microbiology

Efects of cadmium perturbation on the microbial community structure and heavy metal resistome of a tropical agricultural soil – Salam et al.Bioresources and Bioprocessing

Differences in soil microbial communities and enzyme activity due to the application of bioslurry under cultivation – Mofokeng et al.South African Journal of Plant and Soil

Microbial Communities in the Fynbos Region of South Africa: What Happens during Woody Alien Plant Invasions – Jacobs et al.Diversity

Water and extremophile microbiome

Sierra Nevada mountain lake microbial communities are structured by temperature, resources and geographic location – Schulhof et al.Molecular Ecology

Preprint: Fungal communities in sediments along a depth gradient in the Eastern Tropical Pacific – Rojas-Jimenez et al

Built environment

Preprint: Evaluating aerosol and splatter following dental procedures – Allison et al.

Microbes in space

Current Progression: Application of High-Throughput Sequencing Technique in Space Microbiology – Chen et al.BioMed Research International

Food microbiology

Swine Methicillin-resistant Staphylococcus aureus carrying toxic-shock syndrome toxin gene in Hong Kong, China – Sapugahawatte et al. – Emerging Microbes and Infections

Probiotics / prebiotics

Moving from probiotics to precision probiotics – Veiga, et al. – Nature Microbiology

Phages and viruses

Fetal inheritance of chromosomally integrated human herpesvirus 6 predisposes the mother to pre-eclampsia – Gaccioli et al. – Nature Microbiology


Developing standards for the microbiome field – Amos et al.Microbiome

Microbes in the news

Team Examines Microbiome of Marine Invertebrate That Produces Anticancer CompoundTechnology Networks

Bacteria live on our eyeballs — and understanding their role could help treat common eye diseasesYahoo! News

June 12, 2020

Buenos dias and greetings from Spain!

Today we can announce a Virtual Skin Microbiome Symposium held by New York Society of Cosmetic Chemists (NYSCC), that will start on June 15 to June 22, 2020, will include five on-demand sessions, a live panel Q&A and the Suppliers’ Day Digital Pop-Up & Solutions Center.


Epidemiological models are important tools for guiding COVID-19 interventions – Robin N. Thompson – BMC Medicine

Diagnosis of COVID-19 in children: the story evolves – R. Harwood and I. Sinha – BMC Medicine

Africa’s response to COVID-19 – Chikwe Ihekweazu and Emmanuel Agogo – BMC Medicine

Evaluation of the potential incidence of COVID-19 and effectiveness of containment measures in Spain: a data-driven approach – Alberto Aleta and Yamir Moreno – BMC Medicine

Pre-print – Identification of unique mutations in SARS-CoV-2 strains isolated from India suggests its attenuated pathotype – Shubham Gaurav – bioRxiv

General microbiome

Feasibility of collection and analysis of microbiome data in a longitudinal randomized trial of community gardening – Mireia Gascon – Future microbiology

Targeted microbiome depletion – A Du ToitNature Reviews Microbiology

Combining proteogenomics and metaproteomics for deep taxonomic and functional characterization of microbiomes from a non-sequenced host D Gouveia et al. – Biofilms and Microbiomes

Microbiome factors in HPV-driven carcinogenesis and cancers D Lin et al. – Plos Pathogens

Human respiratory microbiome

Clinical diagnostic application of metagenomic next-generation sequencing in children with severe nonresponding pneumonia – Heping Wang – PLOS ONE

Human vaginal microbiome

Exploring potential of vaginal Lactobacillus isolates from South African women for enhancing treatment for bacterial vaginosis – Anna-Ursula Happel – PLOS ONE

Human nearly-sterile sites

Parapseudoflavitalea muciniphila gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from a human peritoneal tumour and reclassification of Pseudobacter ginsenosidimutans as Pseudoflavitalea ginsenosidimutans comb. nov. – Paul A. Lawson et al. – Microbiology society

Animal experiments

Evaluation of the bacterial ocular surface microbiome in ophthalmologically normal dogs prior to and following treatment with topical neomycin-polymyxin-bacitracin – Callie M Rogers et al. – PLOS ONE

Short-chain fructo-oligosaccharides supplementation to suckling piglets: Assessment of pre- and post-weaning performance and gut health – Miriam Ayuso – PLOS ONE

Polysaccharides isolated from Cordyceps Sinensis contribute to the progression of NASH by modifying the gut microbiota in mice fed a high-fat diet – Lei Chen et al. – PLOS ONE

Effect of dietary gossypol supplement on fermentation characteristics and bacterial diversity in the rumen of sheep – CaiDie Wang – PLOS ONE

Polysaccharides isolated from Cordyceps Sinensis contribute to the progression of NASH by modifying the gut microbiota in mice fed a high-fat diet – Lei Chen – PLOS ONE

β-glucan administration improves growth performance and gut health in New Zealand White and APRI rabbits with different breed responses – Mahmoud M Abo Ghanima – PLOS ONE

Comparative study of gut microbiota in Tibetan wild asses (Equus kiang) and domestic donkeys (Equus asinus) on the Qinghai-Tibet plateau – H Liu, X Zhao – PeerJ

Pre-print – Differential genes and microbiota revealed by serum metabolomics of obese rats after intervention by Rhizoma Coptidis – K Luo et al. – Research Square

Pre-print – Quantifying fluorescent glycan uptake to elucidate strain-level variability in foraging behaviors of rumen bacteria – Leeann Klassen et al. – bioRxiv

Animal microbiome

Characterizing the microbiome of ectoparasitic louse flies feeding on migratory raptors – Rebecca A McCabe et al. – PLOS ONE

Characterization of the microbiota of commercially-traded finfish fillets – HR Shehata et al. – Food Research International

A bug’s life-delving into the challenges of helminth microbiome studies – F Formenti et al. – PLoS Neglected Tropical Diseases

Fish skin and gut microbiomes show contrasting signatures of host species and habitat – FÉ Sylvain et al. – Applied and Environmental

Plant, root, and soil microbiome

Isolation, Screening and Identification of Free-Living Diazotrophic Bacteria from Salinated Arid Soils – SA Begmatova et al. – Microbiology

Eukaryotic Microbial Communities in Japanese Arable AndisolsInvestigated by Amplicon Sequencing of 18S rRNA – GenesKazumori Mise et al. – American Society for microbiology

Combined effects of green manure returning and addition of sewage sludge compost on plant growth and microorganism communities in gold tailings. – YJ Ai et al. – Environmental Science and Pollution

Taxonomic shifts in arbuscular mycorrhizal fungal communities with shade and soil nitrogen across conventionally managed and organic coffee agroecosystems. – L Aldrich-Wolfe et al. – Mycorrhiza

Metagenomics Framework for the study of Soil Microbial Communities Based 16s rRNA Gene profiling approach – A Basu et al. – International Journal of Biotechnology

Soil microbial communities in the rhizosphere of Robinia pseudoacacia L. after being exposed to elevated atmospheric CO2 and cadmium for 4 years – X Jia et al. – Applied Soil Ecology

Soil aggregates by design: Manufactured aggregates with defined microbial composition for interrogating microbial activities in soil microhabitats – HJ Harvey et al – Soil Biology and Biochemistry

Would fertilization history render the soil microbial communities and their activities more resistant to rainfall fluctuations? J Kátai et al. – biorxiv

Pre-print – Meta-transcriptomic detection of diverse and divergent RNA viruses in green and chlorarachniophyte algae – Justine Charon et al. – bioRxiv

Water and extremophile microbiome

Comparative metagenomics reveals the microbial diversity and metabolic potentials in the sediments and surrounding seawaters of Qinhuangdao mariculture area – Shuping Wang et al. – PLOS ONE

Spatial dynamics of eukaryotic microbial communities in the German Bight – PAA Sprong et al. – Journal of Sea Research

Temporal distribution of microbial community in an industrial wastewater treatment system following crash and during recovery periods – H Barak et al. – Chemosphere

Pre-print – Characterizing the growing microorganisms at species level in 46 anaerobic digesters at Danish wastewater treatment plants: A six-year survey on microbiome structure and key drivers – Chenjing Jiang et al. – bioRxiv

Pre-print – Ozone nanobubble treatment effectively reduced pathogenic Gram positive and negative bacteria in freshwater and safe for tilapia – Chayuda Jhunkeaw et al. – bioRxiv

Pre-print – Impact of trimethoprim on the river microbiome and antimicrobial resistance. James Delaney et al. – bioRxiv


gutMEGA: a database of the human gut MEtaGenome Atlas – Q Zhang et al. – Briefings in Bioinformatics

May 12, 2020

Buenos dias!! Greetings from Spain.

Today we can highlight a very interesting article of gut–brain modulation of a monkey model of human depression, MELODY a new trial to improve the future microbiome of the offspring of mothers with Crohn’s disease, or how It’s the fertilization the main agent in rhizosphere composition.

I hope you enjoy reading this as much as I did making it!
Stay safe, Jose


Pre-print: Prediction analysis of SARS-COV-2 entry in Livestock and Wild animals – Manas Ranjan Praharaj et al. – bioRxiv

Pre-print: Clinical performance of SARS-CoV-2 IgG antibody tests and potential protective immunity – Niko Kohmer et al. – bioRxiv

Pre-print: The role of high cholesterol in age related COVID19 lethality. – Hao Wang et al. – bioRxiv

Human vaginal microbiome

Effect of commercial vaginal products on the growth of uropathogenic and commensal vaginal bacteria – Kristin J. Hung et al. – Scientific Reports

Human respiratory microbiome

Differences in airway microbiome and metabolome of single lung transplant recipients – Nirmal S. Sharma et al. – Respiratory Research

Pre-print: Assessing the variation within the oral microbiome of healthy adults – Jacob T. Nearing et al. – bioRxiv

Microbiome profile associated with malignant pleural effusion – Samira Shojaee et al. – PLOS ONE

Composition and function of oral microbiota between gingival squamous cell carcinoma and periodontitis – Yuchao Li et al. – Oral Oncology

Esophageal microbiome signature in patients with Barrett’s esophagus and esophageal adenocarcinoma – Loris Riccardo Lopetuso et al. – PLOS ONE

Human gut microbiome

Subtle Variations in Dietary-Fiber Fine Structure Differentially Influence the Composition and Metabolic Function of GutMicrobiota – Tuncil, Y. E et al. – mSphere

Intestinal parasites in rural communities in Nan Province, Thailand: Changes in bacterial gut microbiota associated with minute intestinal fluke infection – Ajala Prommi et al. – Cambridge University Press

Perturbations of the Gut Microbiome and Metabolome in Children with Calcium Oxalate Kidney Stone Disease – Michelle R et al. – Journal of the American Society of Nephrology

The gut microbiome modulates gut–brain axis glycerophospholipid metabolism in a region-specific manner in a non-human primate model of depression – Peng Zheng et al. – Molecular Psychiatry

A dietary intervention to improve the microbiome composition of pregnant women with Crohn’s disease and their offspring: The MELODY (Modulating Early Life Microbiome through Dietary Intervention in Pregnancy) trial design – Peter Inga et al. – Contemporary Clinical Trials Communications

Gut Microbiota Dysbiosis Associated with Bile Acid Metabolism in Neonatal Cholestasis Disease – Meng Li et al. – Scientific Reports

Individual and cohort-specific gut microbiota patterns associated with tissue-specific insulin sensitivity in overweight and obese males – Gerben D. A. Hermes et al. – Scientific Reports

Fecal microbiota composition is linked to the postoperative disease course in patients with Crohn’s disease – Anna Strömbeck et al. – BMC Gastroenterology

Human skin microbiome

Diversity of navel microbiome in young adults Free – Shreya Shah et al. – Journal of Medical Microbiology

Animal experiments

Wild primate microbiomes prevent weight gain in germ-free mice – Dimitrios N. Sidiropoulos et al. – Animal Microbiome

Changes in the microbiome of mariculture feed organisms after treatment with a potentially probiotic strain of Phaeobacter inhibens – Karen K. Dittmann et al. – Applied and Environmental Microbiology

Alterations of fecal microbiome characteristics by dietary soy isoflavone ingestion in growing pigs infected with porcine reproductive and respiratory syndrome virus – B N Smith et al. – Journal of Animal Science

Influenza infection elicits an expansion of gut population of endogenous Bifidobacterium animalis which protects mice against infection – Qiang Zhang et al. – Genome Biology

Pre-print: Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter – Aaron McKenna et al. – bioRxiv

Administration of Bifidobacterium bifidum CGMCC 15068 modulates gut microbiota and metabolome in azoxymethane (AOM)/dextran sulphate sodium (DSS)-induced colitis-associated colon cancer (CAC) in mice – Qing Wang et al. – Applied Microbiology and Biotechnology

Animal microbiome

Structure and membership of gut microbial communities in multiple fish cryptic species under potential migratory effects – My Hanh Le et al. – Scientific Reports

Seasonal habitat drives intestinal microbiome composition in anadromous Arctic char (Salvelinus alpinus) – Geraint Element et al. – Envariomental microbiology

Honeybee microbiome is stabilized in the presence of propolisPerot Saelao et al. – Biology letters

Body-size Scaling is Related to Gut Microbial Diversity, Metabolism and Dietary Niche of Arboreal Folivorous Flying Squirrels – Po-Yu Liu et al. – Scientific Reports

Preprint: Differential Response of Digesta- and Mucosa-Associated Intestinal Microbiota to Dietary Black Soldier Fly (Hermetia illucens) Larvae Meal in Seawater Phase Atlantic Salmon (Salmo salar) – Yanxian Li et al. – bioRxiv

Plant, root, and soil microbiome

Liming reduces N2O emissions from Mediterranean soil after-rewetting and affects the size, structure and transcription of microbial communities – Eduardo Vázquez et al – Soil Biology and Biochemistry

Significant effects on soil microbial communities were not detected after strategic tillage following 44 years of conventional or no-tillage management – Vivian A. Rincon-Florez – Pedobiologia

Seasonal variations in soil microbial communities under different land restoration types in a subtropical mountains region, Southwest China – Denggao Fu et al. – Applied Soil Ecology

Short term effects of biochar with different particle sizes on phosphorous availability and microbial communities – Rubab Sarfraz et al. – Chemosphere

Microbial community responses to different volatile petroleum hydrocarbon class mixtures in an aerobic sandy soil – George Mangse et al.– Environmental Pollution

Plant litter amendments in restored wetland soils altered microbial communities more than clay additions – Christine E. Maietta et al. – Soil Biology and Biochemistry

Long-term fertilization rather than plant species shapes rhizosphere and bulk soil prokaryotic communities in agroecosystems – Mikhail V. Semenov et al. – Applied Soil Ecology

Effect of compost amendment and bioaugmentation on PAH degradation and microbial community shifting in petroleum-contaminated soil – Manli Wu et al. – Chemosphere

Review: The use of -omics tools for assessing biodeterioration of cultural heritage: A review – GutarowskaBeata – Journal of Cultural Heritage

Water and extremophile

Tagging the vanA gene in wastewater microbial communities for cell sorting and taxonomy of vanA carrying cells – Sara Gallego et al – Science of The Total Environment

High-Throughput Sequencing Reveals a Potentially Novel Sulfurovum Species Dominating the Microbial Communities of the Seawater–Sediment Interface of a Deep-Sea Cold Seep in South China Sea – Qing-Lei Sun et al. – Microorganisms

Glacial microbiota are hydrologically connected and temporally variable – Karen A Cameron et al. – Enviromental microbiology

Built environment

The microbiome driving anaerobic digestion and microbial analysis – Jun Wei Lim et al. – Advances in Bioenergy


MG-MLST: Characterizing the Microbiome at the Strain Level in Metagenomic Data – Nathanael J. Bangayan et al. – Microorganisms

Inference of single-cell phylogenies from lineage tracing data using Cassiopeia – Matthew G Jones et al. – Genome Biology

TaxIt: An iterative computational pipeline for untargeted strain-level identification using MS/MS spectra from pathogenic single-organism samples – Mathias Kuhring et al. Journal of Proteome Research

Review: The Computational Diet: A Review of Computational Methods Across Diet, Microbiome, and Health – Ameen Eetemadi et al. – Frontiers in Microbiology

General microbiology

Review: Diversity, ecology and evolution of Archaea – Brett J. Baker et al – Nature Microbiology

Microbes on the market

Microbiome Sequencing Services Market 2020-2024 – husain – NJ MMA News

April 7, 2020

Hi everyone! This is my first contribution to the daily digest, and I’ll follow others’ lead by starting with the latest preprints concerning Covid-19. Away from the ongoing pandemic, some of the highlights include a look at how commensal gut microbes interact with pathogens, and an insight into deep sea oceanic crust microbiomes.

It seems to be a relatively quiet day today, so I’ve included an article from the University of Bristol which looks at how nanoscopic pillars on the surface of some insect wings protect them against bacteria. Perhaps only loosely a microbiome paper, but it’s worth a read for its electron microscopy alone!


Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor – Lan et al. – Nature

Preprint: Atazanavir inhibits SARS-CoV-2 replication and pro-inflammatory cytokine production – Fintelman-Rodrigues et al.

Preprint: Amantadine disrupts lysosomal gene expression; potential therapy for COVID19 – Smieszek et al.

Preprint: Potent Antiviral Activities of Type I Interferons to SARS-CoV-2 Infection – Mantlo et al.

Human gut microbiome

Dissecting individual pathogen-commensal interactions within a complex gut microbiota community – Hassall and Unnikrishnan

Animal microbiome

Antibacterial effects of nanopillar surfaces are mediated by cell impedance, penetration and induction of oxidative stress – Jenkins et al. – Nature Communications

Water and extremophile microbiome

Deep microbial proliferation at the basalt interface in 33.5–104 million-year-old oceanic crust – Suzuki et al.Communications Biology

Food microbiology

How does the microbiome impact pig health? – Sarah Mikesell – The Pig Site

Microbes in the news

Lifestyle trumps geography in determining makeup of gut microbiomeEurekAlert!

Microbes on the market

Gilead taps Second Genome for microbiome biomarker help in a potential $1.5B deal – Connor Hale – FierceBiotech.com