November 1, 2020

Hello from the Sonoran Desert! In today’s digest, you’ll find several interesting works, in particular on recent advances in understanding the gut microbiome! Iandaza and collaborators review the rise of machine learning and deep learning methods in exploring the gut microbiota and the potential of these methods in the diagnosis and treatment of diseases. Additionally, this digest links to a freely-accessible webinar series from the university of Illinois on gut-brain connections.

If you are interested in microbial ecology, I also recommend taking a look at a very interesting preprint from Ettinger and collaborators. The authors investigate the distribution of fungi associated with a widely distributed seagrass, Zostera marina. This work is particularly relevant since the role and diversity of fungi in marine ecosystems are often overlooked in microbiome studies, while terrestrial fungi have been shown to have critical roles as decomposers, pathogens and endophytes.

Finally, you’ll find in this digest a non-microbiology pick: an amazing preprint where authors assessed 2.75 million open access articles on their transparency (data sharing, code sharing, conflicts of interest disclosures, funding disclosures and protocol registration)!

Have a great Sunday!


Events and webinars

Webinar: Scientific Webinars on the Gut-Brain Connection Spotlight Spike in Research


Pregnancy and early life

Review: The dark matter of microbiome: the mother-infant pair virome – Comitini et al. – Minerva Pediatrica

Human vaginal microbiome

Intrauterine Growth Restriction Is Associated with Unique Features of the Reproductive Microbiome – Hu et al. – Reproductive sciences

Human gut microbiome

Review: Gut microbiota and artificial intelligence approaches: A scoping review – Iadanza et al. – Health and Technology

Review: Circadian rhythms and the gut microbiota: from the metabolic syndrome to cancer – Bishehsari et al. – Nature Reviews Endocrinology

Ecological Structuring of Temperate Bacteriophages in the Inflammatory Bowel Disease-Affected Gut – Nishiyama et al. – Microorganisms


Animal microbiome

Preprint: Genomic and microscopic evidence of stable high density and maternally inherited Wolbachia infections in Anopheles mosquitoes – Walker et al. – BioRxiV

Plant, root, and soil microbiome

Testosterone amendment alters metabolite profiles of the soil microbial community – Ding et al. – Environmental Pollution

Host population size is linked to orchid mycorrhizal fungal communities in roots and soil, which are shaped by microenvironment – Kaur et al. – Mycorrhiza

Root exudates drive soil‐microbe‐nutrient feedbacks in response to plant growth – Zhao et al. – Plant, Cell & Environment

Microbial activity and metamitron degrading microbial communities differ between soil and water-sediment systems – Wang et al. – Journal of hazardous materials

Water and extremophile microbiome

Review: Insights into ‘Symbiodiniaceae phycosphere’ in a coral holobiont – Guedes Garrido et al. – Symbiosis

Diversity and Dynamics of Seaweed Associated Microbial Communities Inhabiting the Lagoon of Venice – Juhmani et al. – Microorganisms

Preprint: Global diversity and biogeography of the Zostera marina mycobiome – Ettinger et al. – BioRxiV

Built environment

Analysis of Microbial Community Structure and Diversity in Surrounding Rock Soil of Different Waste Dump Sites in Fushun Western Opencast Mine – Jiang et al. – Chemosphere


My non-microbiology picks

Preprint: Assessment of transparency indicators across the biomedical literature: how open is open? – Serghiou et al. – BioRxiV

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