May 9, 2020

Among the highlights for today, there’s an unusual preprint on using honeybees for proxy sampling of the urban microbiome, as well as a paper on the effect of captivity on the microbiome of raptors.

In some non-microbiome related news, the summarized highlights from the 5th International One Health Congress were recently published. Some of their recommendations regarding science and public health are particularly apt considering the present pandemic, and I found it to be quite an interesting read. You can find it here:

Make science evolve into a One Health approach to improve health and security: a white paper – Osterhaus et al. – One Health Outlook

I hope you’re all doing well, wherever you are!


Preprint: The coding capacity of SARS-CoV-2 – Finkel et al. – bioRxiv

Pregnancy and early life

An individualized mosaic of maternal microbial strains is transmitted to the infant gut microbial community – Koo et al. – Royal Society of Open Science

Animal microbiome

Preprint: Host evolutionary history and ecology shape virome composition in fishes – Geoghegan et al. – bioRxiv

The fecal microbiota of wild and captive raptors – Oliveira et al. – Animal Microbiome

Plant, root, and soil microbiome

Phylogenetic farming: Can evolutionary history predict crop rotation via the soil microbiome? – Kaplan et al. – Evolutionary Applications

Built environment

Preprint: Holobiont urbanism: sampling urban beehives reveals cities’ metagenomes – Henaff et al. – bioRxiv


Preprint: Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore sequencing confers species-level resolution – Matsuo et al. – bioRxiv

Quantifying technical confounders in microbiome studies – Bartolomaeus et al. – Cardiovascular Research

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 😀