Hyvää Päivää from Helsinki, Finland ! Today’s digest contains quite a lot of different topics. If you are interested in early-life microbiome, I recommend taking a look at the paper from Mortensen and collaborators. To understand the role of the maternal vaginal microbiome’s in seeding their child and the importance of the delivery mode in early-life microbiome acquisition, they studied 665 mother–child dyads and modeled the transfer of the vaginal microbiota from mother to infants.
In today’s digest, you’ll also find a really interesting preprint from Abiriga and collaborators, looking at the microbiome of a groundwater aquifer contaminated by a municipal landfill while undergoing intrinsic bioremediation. This preprint is particularly notable because studies looking at the microbiome of contaminated aquifers are particularly rare, despite groundwater contaminations from landfills being a very common issue.
Today’s non-microbiology pick takes a look at the difficulty of detecting scientificly fraudulent images produced by Generative Adversarial Networks (GANs). They demonstrate that this deep-learning method can generate realistic western blot images that are indistinguishable from real western blots. In conclusion, the authors argues that additional information should be required to ensure that the western blots published in scientific publication are not generated images.
Have a great Sunday!
Human respiratory microbiome
Functional lower airways genomic profiling of the microbiome to capture active microbial metabolism – Sulaiman et al. – European respiratory journal
Human skin microbiome
Preprint: Comparative investigation of the Diabetic foot ulcer microbiome – Saeb et al. – BioRxiv
Human vaginal microbiome
Preprint: Vaginal bacterial load in the second trimester is associated with early preterm birth recurrence: a nested case-control – Goodfellow et al. – MedRxiv
Modeling transfer of vaginal microbiota from mother to infant in early life – Mortensen et al. – eLife
Human gut microbiome
Review: Linking Gut Microbiome and Lipid Metabolism: Moving beyond Associations – Lamichhane et al. – Metabolites
Animal microbiome
Individual fate and gut microbiome composition in the European wild rabbit (Oryctolagus cuniculus) – Funosas et al. – Scientific reports
Plant, root, and soil microbiome
Microbiome structure and functional potential in permafrost soils of the Western Canadian Arctic – Varsadiya et al. – FEMS Microbial ecology
Book chapter: Microbial Diversity of Phyllosphere – Dhankhar et al. – Phytomicrobiome Interactions and Sustainable Agriculture
Review: Novel and Emerging Capabilities that Can Provide a Holistic Understanding of the Plant Root Microbiome – Singer et al. – Phytomes journal
Water and extremophile microbiome
Book chapter: Potential of Extremophiles for Bioremediation – Kaushik et al. – Microbial Rejuvenation of Polluted Environment. Microorganisms for Sustainability, vol 25. Springer, Singapore.
Built environment
Microbial Diversity Analysis of Sediment from Yeosu New Harbor of South Korea Using 16S rRNA Gene Amplicon Sequencing – Lee et al. – Microbiology ressource announcements
Preprint: Characterisation of the bacterial microbiota of a landfill-contaminated confined aquifer undergoing intrinsic remediation – Abiriga et al. – BioRxiv
Phages and viruses
Reduced metagenomic sequencing (RMS) approach to determine the gut-associated phageome in mother-child – Manohar et al. – Human Microbiome Journal
Review: Enteric Viruses and Inflammatory Bowel Disease – Tarris et al. – Viruses
Bioinformatics
book chapter: Advances in Omics and Bioinformatics Tools for Phyllosphere Studies – Bansal – Phytomicrobiome Interactions and Sustainable Agriculture
MegaR: an interactive R package for rapid sample classification and phenotype prediction using metagenome profiles and machine learning – Dhungel et al. – BMC Bioinformatics
My non-microbiology picks
Preprint: Emerging Concern of Scientific Fraud: Deep Learning and Image Manipulation – Qi et al. – BioRxiv
Microbiome Digest - Bik's Picks 