Good morning from smokey, apocalyptic San Francisco! The world outside my window may be in sepia tones, but the articles I’m highlighting here are helping to brighten my day. Today’s digest has some fascinating insect and environmental microbiome research including a paper about the gut microbiota of a beetle that lives in the mixed forest of northeastern Asia and its capacity to efficiently degrade polystyrene. Additionally, there’s a paper characterizing the community structure and metabolic capacity of a biofilm-like microbial community lining the wall of the Yumugi river cave in a remote part of Western New Guinea. I’ve also included a paper examining availability of microbial community sequencing data which found that much of this data is not available and offers suggestions for improving data archiving practices. Finally, there is a very interesting technique paper about an orally ingestible microdevice that can be used to sample the gut microbiota in the upper gastrointestinal tract. Happy reading!
General Microbiome
Influence of Intratumor Microbiome on Clinical Outcome and Immune Processes in Prostate Cancer. – Ma, J. et al., Cancers
Experimental (co)evolution in a multi-species microbial community results in local maladaptation. – Castledine, M. et al., Ecology Letters
Pregnancy and Early Life
Mothers of Preterm Infants Have Individualized Breast Milk Microbiota that Changes Temporally Based on Maternal Characteristics. – Asbury, M.R et al., Cell Host Microbe
The meconium microbiota shares more features with the amniotic fluid microbiota than the maternal fecal and vaginal microbiota. – He, Q. et al., Gut Microbes
Skin microbiome
Stratum Corneum Lipidomics Analysis Reveals Altered Ceramide Profile in Atopic Dermatitis Patients Across Body Sites With Correlated Changes in Skin Microbiome. – Emmert, H. et al., Experimental Dermatology
Vaginal microbiome
Diverse vaginal microbiome was associated with pro-inflammatory vaginal milieu among pregnant women in Uganda. – Bayigga, L. et al. Human Microbiome Journal
Gut microbiome
Diet Diurnally Regulates Small Intestinal Microbiome-Epithelial-Immune Homeostasis and Enteritis. – Tuganbeav, T. et al., Cell
Microbiota-modulated CART + enteric neurons autonomously regulate blood glucose. – Muller, P.A. et al., Science
Succinate Produced by Intestinal Microbes Promotes Specification of Tuft Cells to Suppress Ileal Inflammation. -Banerjee, A. et al., Gastroenterology
Animal Experiments
Gut microbiome improves postoperative cognitive function by decreasing permeability of the blood-brain barrier in aged mice. – Wen, J. et al., Brain Research Bulletin
Indolepropionic Acid, a Metabolite of the Microbiome, Has Cytostatic Properties in Breast Cancer by Activating AHR and PXR Receptors and Inducing Oxidative Stress. – Sári, Z. et al., Cancers
Angiogenin maintains gut microbe homeostasis by balancing α-Proteobacteria and Lachnospiraceae. – Sun, D. et al., Gut
Gut Microbiota-Associated Activation of TLR5 Induces Apolipoprotein A1 Production in the Liver. – Yiu, J.H.C. et al., Circulation Research
Animal and insect microbiome
Cross-generational effects of climate change on the microbiome of a photosynthetic sponge. – Luter, H.M. et al., Environmental Microbiology
Symbionts shape host innate immunity in honeybees. – Horak, R.D. et al., Proceedings Biological Sciences
Parental Microbiota Modulates Offspring Development, Body Mass and Fecundity in a Polyphagous Fruit Fly. – Nguyen, B. et al. Microorganisms
Fast and Facile Biodegradation of Polystyrene by the Gut Microbial Flora of Plesiophthalmus davidis Larvae. – Woo, S. et al., Applied and Environmental Microbiology
Gut microbiota protects honey bees (Apis mellifera L.) against polystyrene microplastics exposure risks. – Wang, K. et al., Journal of Hazardous Materials
Plant, root, and soil microbiome
Characteristics of microbial community of soil subjected to industrial production of antibiotics. – Borčinová, M. et al., Folia Microbiologica
Host selection shapes crop microbiome assembly and network complexity. -Xiong, C. et al., The New Phytologist
Microbiome of root vegetables-a source of gluten-degrading bacteria. – Kõiv, V. et al., Applied Microbiology and Biotechnology
Water and extremophile microbiome
Environmental stability impacts the differential sensitivity of marine microbiomes to increases in temperature and acidity. – Wang, Z. et al., ISME Journal
Insights into the Vertical Stratification of Microbial Ecological Roles across the Deepest Seawater Column on Earth. – Xue, C-X et al., Microorganisms
The microbial community of a biofilm lining the wall of a pristine cave in Western New Guinea. – Turrini, P. et al., Microbiological Research
Built environment
Airborne bacteria in outdoor air and air of mechanically ventilated buildings at city-scale in Hong Kong across seasons. – Zhou, Y. et al., Environmental Science and Technology
Phages and viruses
Review: Phages and their potential to modulate the microbiome and immunity. Federici, S. et al., Cellular and Molecular Immunology
Bioinformatics
Generalized estimating equation modeling on correlated microbiome sequencing data with longitudinal measures. – Chen, B. and Xu, W., PLoS Computational Biology
The Nubeam reference-free approach to analyze metagenomic sequencing reads. – Dai, H. and Guan, Y., Genome Research
The archives are half-empty: an assessment of the availability of microbial community sequencing data. – Jurburg, S.D. et al., Communications Biology
Techniques
An effective culturomics approach to study the gut microbiota of mammals. – Pereira, A.C. and Cunha, M.V., Research in Microbiology
Activity-based cell sorting reveals responses of uncultured archaea and bacteria to substrate amendment. – Reichart, N.J. et al., ISME Journal
An Ingestible Self-Polymerizing System for Targeted Sampling of Gut Microbiota and Biomarkers. – Chen, L. et al., ACS Nano
Microbiome Digest - Bik's Picks 