Good morning from sunny San Francisco, California! Today’s digest shares some fascinating in vivo studies including a paper from Ou et al. examining the role of host antimicrobial proteins α-definsins in bacterial colonization and epithelial cell adherence in the gut and a proof-of-concept paper from Hsu et al. in which the authors orally delivered an engineered phage to the gut of mice that was capable of specifically repressing gene expression in bacteria. Additionally, there are some great plant, root, and soil microbiome papers (Kusstatscher et al. show that treating maize seeds with a plant growth-promoting rhizobacteria improves plant health) and water microbiome papers (León-Zayas et al. published a super collaborative paper looking at microbiome sharing between sediments, seagrasses, and reef fish at multiple sites). Finally, I wanted to highlight a paper by Zelaya et al. outlining a course-based undergraduate research experience for teaching microbiology that focuses on the bean beetle microbiome. Happy reading!
Pregnancy and Early Life
Review: The early life education of the immune system: Moms, microbes and (missed) opportunities. – Nitya, J. et al., Gut Microbes
Delayed Establishment of Gut Microbiota in Infants Delivered by Cesarean Section. – Kim, G. et al., Frontiers in Microbiology
Human Respiratory Microbiome
Proteins produced by Streptococcus species in the lower respiratory tract can modify antiviral responses against influenza virus in respiratory epithelial cells. – Nishioka, K. et al., Microbes and Infection
Human Vaginal Microbiome
Vaginal host immune-microbiome interactions in a cohort of primarily African-American women who ultimately underwent spontaneous preterm birth or delivered at term. – Florova, V. et al., Cytokine
Human Oral Microbiome
Isolation and Characterization of Nitrate-Reducing Bacteria as Potential Probiotics for Oral and Systemic Health. – Rosier, B.T. et al., Frontiers in Microbiology
Human Gut Microbiome
Translocation of Viable Gut Microbiota to Mesenteric Adipose Drives Formation of Creeping Fat in Humans. – Ha, C.W.Y. et al., Cell
Gastrointestinal Surgery for Inflammatory Bowel Disease Persistently Lowers Microbiome and Metabolome Diversity. – Fang, X. et al., Inflammatory Bowel Diseases
Animal Experiments
α-Defensins Promote Bacteroides Colonization on Mucosal Reservoir to Prevent Antibiotic-Induced Dysbiosis. – Ou, J. et al., Frontiers in Immunology
In situ reprogramming of gut bacteria by oral delivery. – Hsu, B.B. et al., Nature Communications
The intestinal microbial metabolite desaminotyrosine is an anti‐inflammatory molecule that modulates local and systemic immune homeostasis. – Wei, Y. et al., The FASEB Journal
Modulation of experimental autoimmune encephalomyelitis through colonisation of the gut with Escherichia coli. – Libbey, J.E. et al., Beneficial Microbes
Molecular patterns from a human gut-derived Lactobacillus strain suppress pathogenic infiltration of leukocytes into the central nervous system. -Sanchez, J.M.S. et al., Journal of Neuroinflammation
Plant, Root, and Soil Microbiome
Soil-microorganism-mediated invasional meltdown in plants. – Zhang, Z. et al., Nature Ecology and Evolution
Microbiome Management by Biological and Chemical Treatments in Maize Is Linked to Plant Health. – Kusstatscher, P. et al., Microorganisms
Disruption of Firmicutes and Actinobacteria abundance in tomato rhizosphere causes the incidence of bacterial wilt disease. – Lee, S-M. et al., The ISME Journal
Keystone Microbiomes Revealed by 14 Years of Field Restoration of the Degraded Agricultural Soil Under Distinct Vegetation Scenarios. – Zhang, Z. et al., Frontiers in Microbiology
Dynamic Changes in the Microbiome of Rice During Shoot and Root Growth Derived From Seeds. – Wang, M. et al., Frontiers in Microbiology
Root-Secreted Coumarins and the Microbiota Interact to Improve Iron Nutrition in Arabidopsis. – Harbort, C.J. et al., Cell Host & Microbe
Review: Pinpointing secondary metabolites that shape the composition and function of the plant microbiome. – Jacoby, R.P. et al., Journal of Experimental Botany
Water and Extremophile Microbiome
Microbiomes of fish, sediment and seagrass suggest connectivity of coral reef microbial populations. – León-Zayas, R. et al., PeerJ
Size Shapes the Active Microbiome of Methanogenic Granules, Corroborating a Biofilm Life Cycle. – Trego, A.C. et al., mSystems
Self-regulating microbiome networks ensure functional resilience of biofilms in sand biofilters during manganese load fluctuations. – Zhao, X. et al., Water Research
Review: Groundwater Microbial Communities in Times of Climate Change. -Retter, A. et al., Current Issues in Molecular Biology
Probiotics/Prebiotics
Combining IL-2-based immunotherapy with commensal probiotics produces enhanced antitumor immune response and tumor clearance. – Shi, L. et al., Journal for the ImmunoTherapy of Cancer
Mom’s diet matters: Maternal prebiotic intake in mice reduces anxiety and alters brain gene expression and the fecal microbiome in offspring. – Hebert, J.C. et al., Brain, Behavior, and Immunity
Prophylactic effects of oral administration of Lactobacillus casei on house dust mite-induced asthma in mice. – Lingzhi, L. et al., Food & Function
Bioinformatics
INTEDE: interactome of drug-metabolizing enzymes. – Yin, J. et al., Nucleic Acid Research.
GIMICA: host genetic and immune factors shaping human microbiota. – Tang, J. et al., Nucleic Acid Research
metaFlye: scalable long-read metagenome assembly using repeat graphs. – Kolmogorov, M. et al., Nature Methods
Diagnosing and Predicting Mixed-Culture Fermentations with Unicellular and Guild-Based Metabolic Models. – Scarborough, M.J. et al., mSystems
Education
The Bean Beetle Microbiome Project: A Course-Based Undergraduate Research Experience in Microbiology. – Zelaya, A.J. et al., Frontiers in Microbiology
Microbiome Digest - Bik's Picks 