Hyvää Päivää from Helsinki, Finland ! Today’s digest contains a selection of really interesting preprints and published studies. If you are interested in soil microbiology, take a look at the preprint by Nelson and collaborators, who characterized the soil microbiome across a wildfire burn severity gradients in coniferous forests and made their dataset available in the Fire Responding Ecogenomic database (FiRE-db).
Looking at a large variety of ecosystems, Rodriguez-Gijon and collaborators used a vast collection of Metagenomes Assembled Genomes (MAGs), to investigate the genomes size of prokaryotes in these ecosystems. They show that, while the environment of origin can be linked to genome size, it seems like evolutionary phylogenetic history is in many cases a stronger predictor.
Finally, today’s non-microbiology pick is a great “10 simples rules” paper reviewing best practices on organizing bioinformatics workshops in low and middle-income countries.
Have a great Weekend!
General microbiome
Preprint: A genomic perspective across Earth’s microbiomes reveals that genome size in Archaea and Bacteria is linked to ecosystem type and trophic strategy – Rodriguez-Gijon et al. – BioRXiV
Multi-site human microbiome
Review : Host-Microbe Metagenomics: a Lens To Refocus Our Perspective
on Infectious and Inflammatory Diseases – Kalantar and Langelier – mSystems
Human gut microbiome
Rectal bacteriome and virome signatures and clinical outcomes in community-acquired pneumonia: An exploratory study – Kullberg et al. – EClinicalMedicine
Review: The important role of fungi in inflammatory bowel diseases – Wang et al. – Scandinavian Journal of Gastroenterology
Animal experiments (mouse/rat experiments, chickens/pigs on different diets)
Preprint: A bacterial genome and culture collection of gut microbial in weanling piglet – Dong et al. – BioRXiV
Characterization of the fecal microbiota of sows and their offspring from German commercial pig farms – Lührmann et al. – Plos One
Plant, root, and soil microbiome
Preprint: Does plant diversity determine the diversity of the rhizosphere microbial community? – Zverev et al. – BioRXiV
Preprint: Playing with FiRE: A genome resolved view of the soil microbiome responses to high severity forest wildfire – Nelson et al. – BioRXiV
Peatland microbial community responses to plant functional group and drought are depth-dependent – Lamit et al. – Molecular ecology
Soil pH determines bacterial distribution and assembly processes in natural mountain forests of eastern China – Ni et al. – Global ecology and Biogeography
Water and extremophile microbiome
Preprint: The OceanDNA MAG catalog contains over 50,000 prokaryotic genomes originated from various marine environments – Nishimura et al. – BioRXiV
Food microbiology
Preprint: Mixed culture metagenomics of the microbes making sour beer – Piraine et al. – BioRXiV
Preprint: Insights into the nutritional properties and microbiome diversity in sweet and sour yogurt manufactured in Bangladesh – Tanzina et al. – BioRXiV
Preprint: Microbial communities in retail draft beers and the biofilms they produce – Bose et al. – BioRXiV
Bioinformatics
Book chapter: Bioinformatics Tools and Software – Gupta et al. – Advances in Bioinformatics, Springer, Singapore
MiDSystem: A comprehensive online system for de novo assembly and analysis of microbial genomes – Lee et al. – New biotechnology
My non-microbiology picks
Ten simple rules for organizing a bioinformatics training course in low– and middle-income countries – Moore et al. – PLOS computational biology
Microbiome Digest - Bik's Picks 