Good morning everyone!
In today’s microbiome digest, we can learn more about the influence of host genetics on the gut microbiome from the research by Laura et. al., and a perspective by Liliana et. al. Also, this digest contains interesting methods/tools/pipelines such as a Robust covariance estimation method by Yong He et. Al., a new pipeline for structural characterization and classification of RNA-Seq microbiome data by Racedo et. Al, and a k-mer based tool ‘kASA’ for taxonomic analysis of metagenomic data.
Enjoy reading. Happy Sunday.
Review: Non-zero-sum microbiome immune system interactions – Timur Tuganbaev – European Journal of Immunology
Review: Intersection of FcγRIIB, the microbiome, and checkpoint inhibitors in antitumor immunity – Kirsten M. Baecher – Cancer Immunology, Immunotherapy
Evaluating extraction methods to study canine urine microbiota – Ryan Mrofchak – PLOS ONE
Review: The potential of outdoor environments to supply beneficial butyrate-producing bacteria to humans – Joel E. Brame – Science of The Total Environment
Gut microbiome heritability is nearly universal but environmentally contingent – Laura Grieneisen – Science
Perspective: Host genetics influence the gut microbiome– Liliana Cortes-Ortiz – Science
Isoflavone diet ameliorates experimental autoimmune encephalomyelitis through modulation of gut bacteria depleted in patients with multiple sclerosis – Samantha N. Jensen – Science Advances
Monitoring Infection and Antibiotic Treatment in the Skin Microbiota of Farmed European Seabass (Dicentrarchus Labrax) Fingerlings – Daniela Rosado – Microbial Ecology
Metagenomic Next-Generation Sequencing for the Diagnosis of Pneumocystis jirovecii Pneumonia in Non-HIV-Infected Patients: A Retrospective Study – Juan Jiang – Infectious Diseases and Therapy
Optimal primer selection for sinus microbiome profiling: A comparative analysis of the V1-V3 and V3-4 16S target regions – James Connell – International forum of Allergy and Rhinology
Detection of Chlamydia psittaci in both blood and bronchoalveolar lavage fluid using metagenomic next-generation sequencing – Yuan, Yingpu – Medicine
Animal microbiome / Animal experiments
Review: New insights into the microbiota of wild mice – Ho-Keun Kwon – Mammalian Genome
Bacterial communities of indoor surface of stingless bee nests – Leandro Pio de Sousa – PLOS ONE
Elucidating the optimum added dosage of Diatomite during co-composting of pig manure and sawdust: Carbon dynamics and microbial community – XiunaRen – Science of The Total Environment
Punicic acid ameliorates obesity and liver steatosis by regulating gut microbiota composition in mice – Gaofeng Yuan – Food and Function
Arc1 and the microbiota together modulate growth and metabolic traits in Drosophila – Scott A. Keith – Development
Plant, root and soil microbiome
Diversity and Interactomics of Bacterial Communities Associated with Dominant Trees During Tropical Forest Recovery – Angel A. Becerra-Lucio – Current Microbiology
Land-use types shape soil microbial compositions under rapid urbanization in the Xiong’an New Area, China – Can Wang – Science of The Total Environment
Insights into the Endophytic Bacterial Microbiome of Crocus sativus: Functional Characterization Leads to Potential Agents that Enhance the Plant Growth, Productivity, and Key Metabolite Content – Tanveer Ahmad – Microbial Ecology
Using a high-throughput sequencing technology to evaluate the various forage source epiphytic microbiota and their effect on fermentation quality and microbial diversity of Napier grass – Niaz Ali – Archives of Microbiology
Global homogenization of the structure and function in the soil microbiome of urban greenspaces – Manuel Delgado-Baquerizo – Science Advances
Anaerobic fermentation of hydrothermal liquefaction wastewater of dewatered sewage sludge for volatile fatty acids production with focuses on the degradation of organic components and microbial community compositions – Zheng Chen – Science of The Total Environment
Robust covariance estimation for high-dimensional compositional data with application to microbial communities analysis – Yong He – Statistics in Medicine
A new pipeline for structural characterization and classification of RNA-Seq microbiome data – Sebastian Racedo – BioData Mining.
Taxonomic analysis of metagenomic data with kASA – Silvio Weging – Nucleic Acids Res
Rapid and simultaneous determination of histidine metabolism intermediates in human and mouse microbiota and biomatrices – Inmaculada Acuña – Biofactors