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

April 6, 2020

God morgon!

Good morning from Sweden. This is my first post and following the current trend, it starts with some articles on the COVID19 pandemic. Today’s digest is headlined by some interesting preprints reporting inhibitors of SARS-CoV2 virus, followed by another interesting read suggesting the link between the gut microbiome and ADHD, some articles on our struggle against pathogenic bacteria, virus and fungi, and capped off with a small but informative news article on things one should not do during the COVID19 lockdown.

You might notice that today’s post is dominated by preprints. These preprints, while being an excellent way to disperse information as rapidly as it emerges, aren’t peer-reviewed. Hence, always read them with a pinch of salt!


Preprint: In vitro screening of a FDA approved chemical library reveals potential inhibitors of SARS-CoV-2 replication – Franck Touret, et al.

Preprint: LY6E Restricts the Entry of Human Coronaviruses, including the currently pandemic SARS-CoV-2 – Xuesen Zhao, et al.

Preprint: Indomethacin has a potent antiviral activity against SARS CoV-2 in vitro and canine coronavirus in vivo – Tianhong Xu, et al.

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

Microbial interactions

Preprint: Enhanced nutrient uptake is sufficient to drive emergent cross-feeding between bacteria – Ryan K Fritts, et al.

Structure and function of the Arctic and Antarctic marine microbiota as revealed by metagenomics – Weipeng Zhang, et al. – Microbiome

Preprint: Accumulation of dead cells from contact killing facilitates coexistence in bacterial biofilms – Gabi Steinbach, et al.

Human microbiome

Preprint: Gut microbiota from persons with attention-deficit/hyperactivity disorder affects the brain in mice – Anouk C. Tengeler, et al.

Lung function and microbiota diversity in cystic fibrosis – Leah Cuthbertson, et al. – Microbiome

Animal microbiome

Preprint: Functional maturation of the gut microbiota at weaning is influenced by maternal environment in piglets – Martin Beaumont, et al.

Bacteria Hysteria

Preprint: The adaptive transcriptional response of pathogenic Leptospira to peroxide reveals new defenses against infection-related oxidative stress – Crispin Zavala-Alvarado, et al.

Preprint: Cytotoxicity of the effector protein BteA was attenuated in Bordetella pertussis by insertion of an alanine residue – Jan Bayram, et al.

Preprint: Antimicrobial peptide induced-stress renders Staphylococcus aureus susceptible to toxic nucleoside analogues – Alexandro Rodriguez-Rojas, et al.

Preprint: (p)ppGpp and malonyl-CoA set the pace for Staphylococcus aureus adaptation to FASII antibiotics and provide a basis for bi-therapy inhibition – Amit Pathania, et al.

Phages and viruses

Preprint: Viral RNA is a target for Wolbachia-mediated pathogen blocking – Tamanash Bhattacharya, et al.

Preprint: Synchronized infection identifies early rate-limiting steps in the hepatitis B virus life cycle – Anindita Chakraborty, et al.


Preprint: Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota – Takeo Shibata, et al.

Preprint: Biotinylated surfome profiling identifies potential biomarkers for diagnosis and therapy of Aspergillus fumigatus infection – Lei-Jie Jia, et al.


Preprint: Interpretable machine learning framework reveals novel gut microbiome features in predicting type 2 diabetes – Wanglong Gou, et al.

Preprint: Comprehensive single cell analysis of pandemic influenza A virus infection in the human airways uncovers cell-type specific host transcriptional signatures relevant for disease progression and pathogenesis – Jenna N Kelly, et al.

MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics – Eli Levy Karin, et al. – Microbiome

Preprint: Whole genome sequences of multi-drug resistant Escherichia coli isolated in a Pastoralist Community of Western Uganda: Phylogenomic changes, virulence and resistant genes – Jacob Stanley Iramiot, et al.

Microbes in news

News article: Experts study banana disease in Tanzania – The Guardian

News article: What not to do while on COVID-19 lockdown – Jamaica Observer

I know a lot of my fellow researchers are unable to continue their experiments and are yearning to get back to their respective labs. It is a testing time and I believe that patience and perseverance are the biggest strengths of a researcher. So, let’s bank on our strength and hope to see each other on the other side of this global pandemic soon!

With new information emerging every day about COVID19, there is a plethora of misinformation and myths surrounding the virus and the disease. As science enthusiasts, it is pertinent for us to dispel these myths. Here is a small list that I complied a few days back. Check it out!

April 4, 2020

Good morning and salutations from Singapore! This is the first digest that I’m contributing for the blog, so I hope my selections are interesting to you all! Today’s digest begins with some recent COVID-19 pre-prints, before getting into papers on a diverse range of microbiome-related topics. Highlights today include a study on cats potentially harbouring SARS-CoV-2 (nooo…), the effect of C-section birth on the vaginal microbiota of adult women, and the impact of the virome on biogeochemical cycling in Lake Baikal.


Preprint: Characterization and treatment of SARS-CoV-2 in nasal and bronchial human airway epithelia – Pizzorno et al.

* Preprint: SARS-CoV-2 neutralizing serum antibodies in cats: a serological investigation – Zhang et al.

Preprint: Direct RNA sequencing and early evolution of SARS-CoV-2 – Taiaroa et al.

General microbiome

Review: Microbiota and metabolites in rheumatic diseases – Tong et al. – Autoimmunity Reviews

Human respiratory microbiome

Preprint: Distinctive airway microbial ecology of smokers and asthmatics – Turek et al.

Microbial burden and viral exacerbations in a longitudinal multicenter COPD cohort – Bouquet et al.Respiratory Research

Human gut microbiome

An in vitro evaluation of the effects of different statins on the structure and function of human gut bacterial community – Zhao et al.PLoS ONE

Human vaginal microbiome

* A cross-sectional pilot study of birth mode and vaginal microbiota in reproductive-age women – Stennett et al.PLoS ONE

Animal experiments

Polysaccharide extracted from WuGuChong reduces high-fat diet-induced obesity in mice by regulating the composition of intestinal microbiota – Wang et al.Nutrition & Metabolism

Animal microbiome

Intestinal microbes: an axis of functional diversity among large marine consumers – Scott et al.Proceedings of the Royal Society B

Plant, root, and soil microbiome

The response of soil and phyllosphere microbial communities to repeated application of the fungicide iprodione: Accelerated biodegradation or toxicity? – Katsoula et al.FEMS Microbiology Ecology

Divergent patterns of microbial community composition shift under two fertilization regimes revealed by responding species – Yao et al.Applied Soil Ecology

Water and extremophile microbiome

* Preprint: New Viral Biogeochemical Roles Revealed Through Metagenomic Analysis of Lake Baikal – Coutinho et al.


Ten simple rules for providing effective bioinformatics research support – Kumuthini et al.PLoS Computational Biology

Finally, remember that physical isolation doesn’t have to mean social isolation. Call someone you haven’t talked to in a while, I’m sure they’ll appreciate it! You’re doing great 😀

April 2, 2020

Today’s digest starts with a recent study from The Lancet linking antibiotic usage and the gut microbiome with asthma incidence, before moving onto a range of other papers covering multiple human body sites and environmental microbiome studies.

General microbiome
*** Decreasing antibiotic use, the gut microbiota, and asthma incidence in children: evidence from population-based and prospective cohort studies – Patrick et al. – The Lancet

Human respiratory microbiome

Lung function and microbiota diversity in cystic fibrosis – Cuthbertson et al. – BMC Microbiome

Human gut microbiome

Colonic microbiota is associated with inflammation and host epigenomic alterations in inflammatory bowel disease – Ryan et al. – Nature Communications

Fecal microbiota transplantation for the improvement of metabolism in obesity: The FMT-TRIM double-blind placebo-controlled pilot trial – Yu et al. – PLOS Medicine

Effects of underfeeding and oral vancomycin on gut microbiome and nutrient absorption in humans – Basolo et al. – Nature Medicine

The Gut Microbial Diversity of Newly Diagnosed Diabetics but Not of Prediabetics Is Significantly Different from That of Healthy Nondiabetics – Gaike et al. – MSystems

Shotgun Metagenomics of Gut Microbiota in Humans with up to Extreme Longevity and the Increasing Role of Xenobiotic Degradation – Rampelli et al. MSystems

Animal experiments

Gut microbiota from persons with attention-deficit/hyperactivity disorder affects the brain in mice – Tengeler et al. – BMC Microbiome

Unraveling Assemblage, Functions and Stability of the Gut Microbiota of Blattella germanica by Antibiotic Treatment – Domínguez-Santos et al. – Frontiers in Microbiology

Plant, root, and soil microbiome

Novel phosphate-solubilizing bacteria enhance soil phosphorus cycling following ecological restoration of land degraded by mining – Liang et al.  – ISME

Water and extremophile microbiome

Genomic and transcriptomic evidence of light-sensing, porphyrin biosynthesis, Calvin-Benson-Bassham cycle, and urea production in Bathyarchaeota – Pan et al. BMC Microbiome

Microbial community profiling of ammonia and nitrite oxidizing bacterial enrichments from brackishwater ecosystems for mitigating nitrogen species – Baskaran et al. – Nature Scientific Reports


Lactobacillus reuteri 5454 and Bifidobacterium animalis ssp. lactis 5764 improve colitis while differentially impacting dendritic cells maturation and antimicrobial responses – Hrdý et al. Nature Scientific Reports

April 1, 2020

Hello Everyone, I am excited for my first post here. Continuing the trend the first few papers are on COVID-19 : first one talks about its classification and nomenclature. I hope everyone is staying safe and healthy. Last but not the least, keep up the hand washing.


* The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2- Coronaviridae Study – Group of the International Committee on Taxonomy of Viruses – Nature Microbiology

Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses – Letko et al. – Nature Microbiology

General microbiome
Variation in prostaglandin metabolism during growth of the diatom Thalassiosira rotula – Dato et al. – Scientific Reports

Pregnancy and early life
Factors affecting early-life intestinal microbiota development – Vandenplas et al. – Nutrition

Multi-site human microbiome
Gut, oral and skin microbiome of Indian patrilineal families reveal perceptible association with age – Chaudhari et al. – Scientific Reports

Human gut microbiome
Implication of the gut microbiome composition of type 2 diabetic patients from northern China – Li et al. – Scientific Reports

The microbiota programs DNA methylation to control intestinal homeostasis and inflammation– Ansari et al. – Nature Microbiology

Animal microbiome
The Contest of Microbial Pigeon Neighbors: Interspecies Competition Between Serratia marcescens and the Human Pathogen Cryptococcus neoformans – Haleva et al. – Fungal Biology

Plant, root, and soil microbiome
Pseudomonas PS01 Isolated from Maize Rhizosphere Alters Root System Architecture and Promotes Plant Growth – Chu et al. – Microorganisms

Phages and viruses
Viruses with different genome types adopt a similar strategy to pack nucleic acids based on positively charged protein domains – Requião et al. – Scientific Reports

*Review: 5 challenges in understanding the role of the virome in health and disease – Wang David – PLOS Pathogens

Whole-genome sequencing of Burkholderia pseudomallei from an urban melioidosis hot spot reveals a fine-scale population structure and localised spatial clustering in the environment – Rachlin et al. – Scientific Reports

Comprehensive evaluation of complex polymicrobial specimens using next generation sequencing and standard microbiological culture – Cummings et al. – Scientific Reports

Review: Potential of proteomics to probe microbes – Matilda et al. – Journal of Basic Microbiology

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.

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

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

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

March 25, 2020

Today’s digest features an article about colorectal cancer signatures and E. coli and a study about the microbiome and resistome of great apes and human.


News: How blood from coronavirus survivors might save lives – Nature

General microbiome

What is the Origin of Human Bacterial Flora? – Alen J Salerian – Journal of Applied & Environmental Microbiology

The Microbiome of the Nose—Friend or Foe? – Sofia Dimitri-Pinheiro – Allergy Rhinol.

Pregnancy and early life

Non-targeted urinary metabolomics in pregnancy and associations with fetal growth restriction – Chelsea M. Clinton – Scientific Reports

Multi-site human microbiome

Effects of Chlorhexidine mouthwash on the oral microbiome – Raul Bescos – Scientific Reports

Human gut microbiome

Mutational signature in colorectal cancer caused by genotoxic pks+ E. coli – Cayetano Pleguezuelos-Manzano – Nature

Animal experiments

Natural agents inhibit colon cancer cell proliferation and alter microbial diversity in mice – Lulu Farhana – PLOS One

Animal microbiome (for animals in the wild)

Co-abundance analysis reveals hidden players associated with high methane yield phenotype in sheep rumen microbiome – Leila Ghanbari Maman – Scientific Reports

Effects of heat stress on the gut health of poultry – Marcos H Rostagno – Journal of Animal Science

The microbiome and resistome of chimpanzees, gorillas, and humans across host lifestyle and geography – Tayte P. Campbell – THE ISME Journal

Plant, root, and soil microbiome

Impact of molasses and microbial inoculants on fermentation quality, aerobic stability, and bacterial and fungal microbiomes of barley silage – Beiyi Liu – Scientific Reports

Bacterial analysis in the early developmental stages of the black tiger shrimp (Penaeus monodon) – Pacharaporn Angthong – Scientific Reports

Water and extremophile microbiome

Microbial community profiling of ammonia and nitrite oxidizing bacterial enrichments from brackishwater ecosystems for mitigating nitrogen species – Viswanathan Baskaran – Scientific Reports

Vertical Beta-Diversity of Bacterial Communities Depending on Water Stratification – Wan-Hsuan Cheng – Frontiers in Microbiology


Artificial microbiome heterogeneity spurs six practical action themes and examples to increase study power-driven reproducibility – Abigail R. Basson – Scientific Reports


Benchmarking the MinION: Evaluating long reads for microbial profiling – Robert M. Leidenfrost – Scientific Reports