July 24, 2020

Good afternoon all!

Today’s digest is a bit on the lighter side, nevertheless, there are some great papers to sink your teeth into.

Those with an interest in tropical diseases will want to read an investigation into the three-way relationship between humans, their microbiotas and the protozoan cause of Chagas disease.

History buffs, and fans of the epic novel ‘Romance of the Three Kingdoms’ may be interested by an analysis of the soil microbiome of the Jinsha relic, which is found at the site of the former Chinese Shu state capital.

For those more philosophically inclined, there is an interesting discussion on the impact of human space activity on the search for extra-terrestrial life. So that’s ancient history and space-age wizardry all covered in today’s rather modest digest. What more could you want?!


Preprint: Rapid in vitro assays for screening neutralizing antibodies and antivirals against SARS-CoV-2 – Oark et al.

Preprint: The D614G mutation in the SARS-CoV2 Spike protein increases infectivity in an ACE2 receptor dependent manner – Ogawa et al.

Preprint: Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants – Weisblum et al.

General microbiome

Mapping of host-parasite-microbiome interactions reveals metabolic determinants of tropism and tolerance in Chagas disease – Hossain et al.Science Advances

Animal experiments

Host immunity and the colon microbiota of mice infected with Citrobacter rodentium are beneficially modulated by lipid-soluble extract from late-cutting alfalfa in the early stages of infection – Fries-Craft et al.PLOS One

Plant, root, and soil microbiome

Diversity and structure of soil microbiota of the Jinsha earthen relic – Yang et al.PLOS One

Quantitative detection of economically important Fusarium oxysporum f. sp. cubense strains in Africa in plants, soil and water – Matthews et al. – PLOS One

Fungi, bacteria and oomycota opportunistically isolated from the seagrass, Zostera marina – Ettinger and Eisen – PLOS One


Majority sensing in synthetic microbial consortia – Alnahhas et al. – Nature Communications

Microbes in the news

Should we disinfect outer space?: Jenna Sutela and Sophia Roosth in conversation – Sutela and Roosth – Art in America

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

May 19, 2020

Good afternoon from sunny South Wales!

Today’s digest has a lot of great papers, with something for just about everyone. We’ll start off with a bang, and highlight a great paper in which Rajasekaran and collegaues challenge the current dogma that human intervertebral discs are sterile using a 16S rRNA sequencing approach.

We then have an interesting, or perhaps concerning paper looking at the prevalence of underreported parasites in laboratory zebrafish populations. A must read for anybody using zebrafish models. We also have plenty of papers concerning plant and water microbiomes, including a rather huge report on ocean systems.

Finally, with the current health climate, what better paper peruse than the contribution of Qureshi et al. who have demonstrated that gender neutral bathrooms are more rapidly colonised than single gender bathrooms. If recent anecdotal news articles are to be believed (although they seldom are) it’s usually the men letting the side down. You’ve got to wash those hands!

I hope everyone is staying safe, and enjoys today’s post!


Preprint: Identification of five antiviral compounds from the Pandemic Response Box targeting SARS-CoV-2 – Holwerda et al.

General microbiome

Longitudinal Study of Oral Microbiome Variation in Twins – Freire et al.Sci Rep

Human nearly-sterile sites

Human intervertebral discs harbour a unique microbiome and dysbiosis determines health and disease – Rajasekaran et al.European Spine Journal

Human gut microbiome

Early signs of gut microbiome aging: biomarkers of inflammation, metabolism, and macromolecular damage in young adulthood – Gaydosh et al. The Journals of Gerontology

Animal experiments

Behavioural effects of the common brain-infecting parasite Pseudoloma neurophilia in laboratory zebrafish (Danio rerio) – Midttun et al.Sci Rep

Lactobacillus plantarum FRT10 alleviated high-fat diet–induced obesity in mice through regulating the PPARα signal pathway and gut microbiota – Cai et al.Applied Microbial and Cell Physiology

Animal microbiome

Factors affecting the microbiome of Ixodes scapularis and Amblyomma americanum – Brinkerhoff et al.PLoS ONE

Preprint: Distinct Microbial Assemblages Associated with Genetic Selection for High- and Low- Muscle Yield in Rainbow Trout – Walker et al.

Whole-genome sequences of an abortive Bacillus safensis strain isolated from a mare’s uterus – Little, Hillhouse and Lawhorn – Genome Sequences

Plant, root, and soil microbiome

Preprint: A fungal member of the microbial phyllosphere antagonizes infection of Arabidopsis thaliana by the oomycete pathogen Albugo laibachii via a putative secreted hydrolase – Eitzen et al.

Preprint: Diazotrophic bacteria from maize exhibit multifaceted plant growth promotion traits in multiple hosts – Higdon et al.

Fungal communities and their association with nitrogen-fixing bacteria affect early decomposition of Norway spruce deadwood – Gómez-Brandón et al. – Sci Rep

Fruitbody chemistry underlies the structure of endofungal bacterial communities across fungal guilds and phylogenetic groups – Pent, Bahram and Põldmaa – ISME J

Endophytic fungal community in grape is correlated to foliar age and domestication – Fan et al.Annals of Microbiology

Water and extremophile microbiome

Microbial genomics of the global ocean system – Joye and Kostka – Coloqium Report

How do microbiota associated with an invasive seaweed vary across scales? – Bonthond et al.Molecular Ecology

Preprint: Differences in the microbiota of native and non-indigenous gelatinous zooplankton organisms in a low saline environment – Jaspers et al.

Built environment

Gender‐neutral bathroom surfaces recolonized by microbes more quickly than single gender bathrooms – Qureshi, Kedo and Berthrong – Letters in Applied Microbiology

Food microbiology

Dynamic distribution of gut microbiota in meat rabbits at different growth stages and relationship with average daily gain (ADG) – Fang et al.BMC Microbiology


Preprint: Evaluation of Methods to Optimise Shotgun Metagenomic Sequencing-Based Analysis of the Microbiome of Milk – Feehily et al.

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

Longing for the lab

I’m a final year PhD student, studying the relationship between gut bacteria and colon cancer using a benign cell line model. Last Tuesday, the UK government announced a lockdown, and those institutions that were still open, closed their doors.

So, like a batch of fresh samples, my experiments have been put on ice. It’s a scary time for a lot of fledgling researchers, with no contingency plan for bursary or lab time extensions currently in place. Many PhD students, like myself, will find themselves attempting to write thesis chapters a lot earlier than they had planned.

I’ve witnessed first hand, as my peers have battled through the ordeal, that tackling the big beast of thesis writing can lead to all kinds of delirium. In my recent writing-induced malaise, I’ve found myself longing to be back in lab. Surprisingly, I’m even finding myself reminiscing about some of the more tedious tasks, such as:

  1. Passaging cell lines. Looking after cells, particular benign or primary cell lines, is like having a child. They always need something, and if you dare to upset them, pray for your lab results/sanity. Shared tissue culture facilities also pose their own problems, and I’m sure most cell biologists would admit to a small level of constant paranoia: Are my cells ok? But, what I wouldn’t give for the simplicity of easing myself into a busy week of lab work by splitting a flask of cells on a Monday morning.
  2. Visiting the liquid nitrogen freezer. Liquid nitrogen freezers are scary. Lab managers just love to regale fresh inductees with horror stories as a way of teaching the importance of appropriate eye protection. They’re also usually kept somewhere out of the way and with good ventilation. In my experience, this is almost exclusively a damp, cold, cellar-like room somewhere far, far away from where you actually conduct your lab work. There is, however, a sort of tranquility about lifting the lid off of the freezer, and watching the gas silently flow out like the world’s quietest volcano.
  3. Transporting samples between labs. As part of my work, I’m lucky enough to work with some foul-smelling anaerobic bacteria. Fortunately, the university moved on from anaerobic jars long before I started, and we have a rather high-end anaerobic workstation. The problem, however, is that this workstation is not in the main microbiology lab, but a smaller lab approximately 3 feet down the corridor. We have no open lab zone, so this means painstakingly sealing, bagging and boxing all cultures, in order to, for example, read them on a spectrophotometer that’s a mere 20 paces away. Come to think of it, maybe I don’t miss this so much.

Perhaps the biggest challenge many of us are facing right now is that of isolation. The hustle and bustle of a busy lab is gone, supervisors are more distant, and there are no fellow researchers to complain to about a failed experiment (or a cantankerous lab manager). Hopefully by facilitating discussion and keeping connected, we can make getting through this difficult time a little easier.

What are you missing about science? Comment below!