Hello from the Sonoran Desert! In today’s digest, you’ll find find a lot of very interesting papers! For those interested in host-phages interactions, there is an amazing work from Ping and collaborators looking at phage infections dynamics in migrating bacterial populations. Interestingly, the authors suggests that phages may be able to “hitchhike” with moving bacteria.
To continue with our viral readings, you’ll also find an interesting perspective paper from Kuprovic and collaborators. In this piece, the authors attempt to reconstruct the virome associated to LUCA (Last Universal Cellular Ancestor). Amazingly, their reconstruction shows that a remarkably complex virome would have been associated to LUCA, suggesting an extensive viral evolution antedating LUCA!
Finally, today’s non-microbiology pick is a book, looking at the fascinating Cuatro Ciénegas Basin, located in México, a site that is often described as a real outdoor laboratory for astrobiology. Indeed, the Basin site contains gypsum-rich soil analogous to the Gale Crater in Mars, and the ponds contains extremely oligotrophic waters, which can be used to model ancient oceans chemistry. You’ll explore along the chapters the history, ecology, microbiology and evolution of this amazing site, to unravel the mysteries of this site absolutely unique on the planet.
Have a great Sunday!
Human respiratory microbiome
Review: Insights gained into respiratory infection pathogenesis using lung tissue metabolomics – Bernatchez and McCall – PLOS Pathogens
Human gut microbiome
Description and determinants of the faecal resistome and microbiome of farmers and slaughterhouse workers: A metagenome-wide cross-sectional study – Van Gompel et al. – Environment International
Review: The influence of the gut microbiome on obesity – Blanco – Journal of the American Association of Nurse Practitioners
Animal microbiome (for animals in the wild)
Comparative analysis of the gut microbiota of Apis cerana in Yunnan using high-throughput sequencing. – Luo et al. – Archives of Microbiology
Plant, root, and soil microbiome
Higher tree diversity increases soil microbial resistance to drought. – Gillespie et al. – Communications Biology
Effect of land uses on soil microbial community structures among different soil depths in northeastern China. – Ji et al. – European Journal of soil Biology
Structural variability and niche differentiation of the rhizosphere and endosphere fungal microbiome of Casuarina equisetifolia at different ages. – Huang et al. – Environmental Microbiology
Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)
Substrate regulation leads to differential responses of microbial ammonia-oxidizing communities to ocean warming. – Zheng et al. – Nature communications
Diversity and dynamics of relevant nanoplanktonic diatoms in the Western English Channel. – Arsenieff et al. – The ISME Journal
Lake characteristics influence how methanogens in littoral sediments respond to terrestrial litter inputs. – Yakimovich et al. – The ISME Journal
Built environment (subways, indoor surfaces)
Heavy metal concentrations in Brazilian port areas and their relationships with microorganisms: can pollution in these areas change the microbial community? – Del Busso Zampieri et al. – Environmental Monitoring and Assessment
Food microbiology
Material conversion, microbial community composition and metabolic functional succession during green soybean hull composting. – Zhang et al. – Bioresource Technology
Phages and viruses
Hitchhiking, collapse, and contingency in phage infections of migrating bacterial populations. – Ping et al. – The ISME Journal
Review: The LUCA and its complex virome. – Krupovic et al. – Nature Review Microbiology
Insights into the dynamics between viruses and their hosts in a hot spring microbial mat. – Jarett et al. – ISME Journal
Bioinformatics
IDMIL: an alignment-free Interpretable Deep Multiple Instance Learning (MIL) for predicting disease from whole-metagenomic data. – Rahman and Rangwala – Bioinformatics
My non-microbiology pick
Book: Astrobiology and Cuatro Ciénegas Basin as an Analog of Early Earth. – Medina-Chávez et al. – Cuatro Ciénegas Basin: An Endangered Hyperdiverse Oasis. Springer
Microbiome Digest - Bik's Picks 