Happy Monday morning from San Francisco, California! Hope everyone had a restful weekend. For those who aren’t quite ready for the working week, how about easing in to things with a warm beverage and some great microbiome reads?
Today’s digest includes two papers that blew my mind. The first is a paper by van Tatenhove-Pel et al. which looks at how cell-to-cell distance in 3D space impacts the metabolic interactions between bacteria. The second, by Nowosad et al., examines the role of the gut microbiota on B cell selection and antibody affinity maturation in gut-associated germinal centers. Other fascinating papers include: a pilot study profiling the gut microbiomes of South Africans in an urban cohort and a transitioning rural cohort which was designed collaboratively with community leaders (Oduaran et al.); a review paper about using brachyuran crabs as a model for studying how animal-microbiome symbioses evolve when aquatic organisms transition to land (Cannicci et al.); and a paper that used shotgun metagenomics to identify current and historical microbiomes in lake sediment which could help our understanding of how humans impact lake ecosystems over time (Garner et al.). Happy reading, y’all!
General Microbiome
Microbial competition reduces metabolic interaction distances to the low µm-range. – van Tatenhove-Pel, R.J. et al., The ISME Journal
Human Respiratory Microbiome
Developmental patterns in the nasopharyngeal microbiome during infancy are associated with asthma risk. – Tang, H.H.F, et al., Journal of Allergy and Clinical Immunology
Human Gut Microbiome
Distinct Fecal and Plasma Metabolites in Children with Autism Spectrum Disorders and Their Modulation after Microbiota Transfer Therapy. – Kang, D-W et al., mSphere
Gut Microbiome in Children from Indigenous and Urban Communities in México: Different Subsistence Models, Different Microbiomes. – Sánchez-Quinto, A. et al., Microorganisms
Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle transition. – Oduaran, O.H. et al., BMC Microbiology
Maturation of the gut microbiome during the first year of life contributes to the protective farm effect on childhood asthma. – Depber, M. et al., Nature Medicine
Fecal Microbiota Changes in Patients With Postpartum Depressive Disorder. – Zhou, Y. et al., Frontiers in Cellular and Infection Microbiology
Animal Experiments
Tunable dynamics of B cell selection in gut germinal centres. – Nowosad, C.R. et al., Nature
Acute liver failure is regulated by MYC- and microbiome-dependent programs. – Kolodziejczyk, A.A. et al., Nature Medicine
Epithelial TLR4 signaling activates DUOX2 to induce microbiota-driven tumorigenesis. – Burgueño, J.F. et al., Gastroenterology
Gut Microbiome Alters the Activity of Liver Cytochromes P450 in Mice With Sex-Dependent Differences. – Jourová, L. et al., Frontiers in Pharmacology
Distinct Polysaccharide Utilization Determines Interspecies Competition between Intestinal Prevotella spp. – Gálvez, E.J.C. et al., Cell Host & Microbe
FXR in the dorsal vagal complex is sufficient and necessary for upper small intestinal microbiome-mediated changes of TCDCA to alter insulin action in rats. – Zhang, S-Y et al., Gut
Animal Microbiome
Review: To the Land and Beyond: Crab Microbiomes as a Paradigm for the Evolution of Terrestrialization. – Cannicci, S. et al., Frontiers in Microbiology
Insect Microbiome
The direct and indirect effects of environmental toxicants on the health of bumblebees and their microbiomes. – Rothman, J.A. et al., Proceedings of the Royal Society B, Biological Sciences
A Very Hungry Caterpillar: Polyethylene Metabolism and Lipid Homeostasis in Larvae of the Greater Wax Moth ( Galleria mellonella). – LeMoine, C.M. et al., Environmental Science and Technology
Plant, Root, and Soil Microbiome
Deciphering the Microbial Taxonomy and Functionality of Two Diverse Mangrove Ecosystems and Their Potential Abilities To Produce Bioactive Compounds. – Liao, S. et al., mSystems
Introducing the Mangrove Microbiome Initiative: Identifying Microbial Research Priorities and Approaches To Better Understand, Protect, and Rehabilitate Mangrove Ecosystems. – Allard, S.M. et al., mSystems
Water and Extremophile Microbiome
The water chemistry and microbiome of household wells in Medawachchiya, Sri Lanka, an area with high prevalence of chronic kidney disease of unknown origin (CKDu). McDonough, L.K. et al., Scientific Reports
Sediment Metagenomes as Time Capsules of Lake Microbiomes. – Garner, R.E. et al., mSphere
Built Environment
Bioaerosols in the Athens Metro: Metagenetic insights into the PM 10 microbiome in a naturally ventilated subway station. – Grydaki, N. et al., Environment International
Probiotics
Biotic Interactions Are More Important than Propagule Pressure in Microbial Community Invasions. – Albright, M.B.N. et al., mBio
Microbiological, immunological, and histological changes in the gut of Salmonella Enteritidis-challenged rats fed goat cheese containing Lactobacillus rhamnosus EM1107. – Rolim, F.R.L. et al., Journal of Dairy Science
Comparative Genome Analysis of Bifidobacterium longum subsp. infantis Strains Reveals Variation in Human Milk Oligosaccharide Utilization Genes among Commercial Probiotics. – Duar, R.M. et al., Nutrients
Persistence of Suspected Probiotic Organisms in Preterm Infant Gut Microbiota Weeks After Probiotic Supplementation in the NICU. – Yousuf, E.I. et al., Frontiers in Microbiology
Bioinformatics
Model-based and phylogenetically adjusted quantification of metabolic interaction between microbial species. – Lam, T.J. et al., PLoS Computational Biology
Comprehensive screening of genomic and metagenomic data reveals a large diversity of tetracycline resistance genes. – Berglund, F. et al., Microbial Genomics
Review: Naught all zeros in sequence count data are the same. – Silverman, J.S. et al., Computational and Structural Biotechnology Journal
Techniques
Microbiomic Analysis on Low Abundant Respiratory Biomass Samples; Improved Recovery of Microbial DNA From Bronchoalveolar Lavage Fluid. – Saladié, M. et al., Frontiers in Microbiology
Jumping the green wall: The use of PNA-DNA clamps to enhance microbiome sampling depth in wildlife microbiome research. – Víquez-R, L. et al., Ecology and Evolution
Microbiome Digest - Bik's Picks 