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!

COVID-19

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

Techniques

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!

COVID-19

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!