July 11, 2021

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.

General microbiome

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

Gut microbiome

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

Skin microbiome

Monitoring Infection and Antibiotic Treatment in the Skin Microbiota of Farmed European Seabass (Dicentrarchus Labrax) Fingerlings – Daniela Rosado – Microbial Ecology

Respiratory microbiome

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 communityXiunaRen – 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

Water microbiome

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

Methods/Tools/Pipelines

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 dataSebastian 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

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