November 6, 2021

Have a nice weekend! Today we have a good variety of papers, in several different topics. Enjoy!

Human and General Microbiome

Metataxonomic investigation of the microbial community in the trachea and oropharynx of healthy controls and diabetic patients using endotracheal tubes – Sun Young Cho – PloS ONE

Characterization of the endometrial, cervicovaginal and anorectal microbiota in post-menopausal women with endometrioid and serous endometrial cancers – Gregory M Gressel – PloS ONE

Fecal Microbiota Transplantation Relieves Gastrointestinal and Autism Symptoms by Improving the Gut Microbiota in an Open-Label Study – Ning Li – Frontiers in Cellular and Infection Microbiology

Evaluation of vaginal microbiota in women admitted to the hospital for premature labour – Bruno Arena – Acta Bio-medica

The vaginal microbiota and innate immunity after local excisional treatment for cervical intraepithelial neoplasia – Anita Mitra – Genome Medicine

Comparative analysis of human facial skin microbiome between topical sites compared to entire face – Haeun Lee – Genes & Genomics

Lung Tissue Microbiome Is Associated With Clinical Outcomes of Idiopathic Pulmonary Fibrosis – Hee-Young Yoon – Frontiers in Medicine

Mechanisms underlying interactions between two abundant oral commensal bacteria – Dasith Perera – The ISME Journal

Epigenetic adaptations of the masticatory mucosa to periodontal inflammation – Gesa M Richter – Clinical Epigenetics

Increase of SARS-CoV-2 RNA load in faecal samples prompts for rethinking of SARS-CoV-2 biology and COVID-19 epidemiology – Mauro Petrillo – F1000Research

Microbiota-derived acetate enables the metabolic fitness of the brain innate immune system during health and disease – Daniel Erny – Cell Metabolism

Phage-delivered CRISPR-Cas9 for strain-specific depletion and genomic deletions in the gut microbiome – Kathy N Lam – Cell Reports

Cell-surface xyloglucan recognition and hydrolysis by the human gut commensal Bacteroides uniformis – Julie M Grondin – Applied and Environmental Microbiology

Dysbiosis of Gut Microbiome Is Associated With Rupture of Cerebral Aneurysms – Shuhei Kawabata – Stroke

Effect of Long-Term and Short-Term Imbalanced Zn Manipulation on Gut Microbiota and Screening for Microbial Markers Sensitive to Zinc Status – Lingjun Chen – Microbiology Spectrum

Dietary Modulation Alters Susceptibility to Listeria monocytogenes and Salmonella Typhimurium with or without a Gut Microbiota – Mathis Wolter – mSystems

Alterations in Gut Microbiome Composition and Function in Irritable Bowel Syndrome and Increased Probiotic Abundance with Daily Supplementation – Joann Phan – mSystems

The Future Is Big-and Small: Remote Sensing Enables Cross-Scale Comparisons of Microbiome Dynamics and Ecological Consequences – Deanna S Beatty – mSystems

Comprehensive functional core microbiome comparison in genetically obese and lean hosts under the same environment – Marina Martínez-Álvaro – Communications Biology

Vescimonas gen. nov., Vescimonas coprocola sp. nov., Vescimonas fastidiosa sp. nov., Pusillimonas gen. nov. and Pusillimonas faecalis sp. nov. isolated from human faeces – Maki Kitahara – International Journal of Systematic and Evolutionary Microbiology

Human and General Microbiome – Reviews

Engineering temporal dynamics in microbial communities – Carlotta Ronda – Current Opinion in Microbiology

From a parts list to assembly instructions and an operating manual: how small host models can re-write microbiome theory – Nic M Vega – Current Opinion in Microbiology

Microbiota-derived extracellular vesicles in interkingdom communication in the gut – Natalia Díaz-Garrido – Journal of Extracellular Vesicles

Multiple roles of short-chain fatty acids in Alzheimer disease – Hui Chen – Nutrition 

Role of gut microbiota in functional constipation – Shengsheng Zhang – Gastroenterology Report

Gut Feelings: The Microbiota-Gut-Brain Axis on Steroids – Sik Yu So – American Journal of Physiology. Gastrointestinal and Liver Physiology

Urobiome: An outlook on the metagenome of urological diseases – Rachel Shoemaker – Investigative and Clinical Urology

Animal Models

Utilizing a reductionist model to study host-microbe interactions in intestinal inflammation – Amy M Tsou – Microbiome

Disruption of autophagy by increased 5-HT alters gut microbiota and enhances susceptibility to experimental colitis and Crohn’s disease – Sabah Haq – Science Advances

Differences in the gut microbiota composition of rats fed with soybean protein and their derived peptides – Wenhui Li – Journal of Food Science

Animal Microbiome (non-model)

Unraveling differences in fecal microbiota stability in mammals: from high variable carnivores and consistently stable herbivores – Franziska Zoelzer – Animal Microbiome

The Role Transition of Dietary Species Richness in Modulating the Gut Microbial Assembly and Postweaning Performance of a Generalist Herbivore – Guoliang Li – mSystems

Age Associated Microbiome and Microbial Metabolites Modulation and Its Association With Systemic Inflammation in a Rhesus Macaque Model – Suresh Pallikkuth – Frontiers in Immunology

Strain-level analysis reveals the vertical microbial transmission during the life cycle of bumblebee – Qinzhi Su – Microbiome

Social convergence of gut microbiomes in vampire bats – Karthik Yarlagadda – Biology Letters

Shrimp AHPND Causing Vibrio anguillarum Infection: Quantitative Diagnosis and Identifying Antagonistic Bacteria – Huiyu Shen – Marine Biotechnology

Naturally occurring fire coral clones demonstrate a genetic and environmental basis of microbiome composition – C E Dubé – Nature Communications

Dry and Rainy Seasons Significantly Alter the Gut Microbiome Composition and Reveal a Key Enterococcus sp. (Lactobacillales: Enterococcaceae) Core Component in Spodoptera frugiperda (Lepidoptera: Noctuidae) Corn Strain From Northwestern Colombia – Marlon Felipe Higuita Palacio – Journal of Insect Science

Invasive Amphibian Gut Microbiota and Functions Shift Differentially in an Expanding Population but Remain Conserved Across Established Populations – Carla Wagener – Microbial Ecology

Review: Microbiome Studies in Non-human Primates – Jason M Brenchley – Current HIV/AIDS Reports

Beneficial Microbes and Compounds

Regulation divergences of Lactobacillus fermentum PCC and Lactobacillus paracasei 431 on penicillin-induced upper respiratory tract microbial dysbiosis in BALB/c mice – Feng Gao – Food & Function

Dietary calcium phosphate strongly impacts gut microbiome changes elicited by inulin and galacto-oligosaccharides consumption – Jori Fuhren – Microbiome

Plant Microbiome

Effects of growth promoting microorganisms on tomato seedlings growing in different media conditions – Robert Pokluda – PloS ONE

Inter-Kingdom Networks of Canola Microbiome Reveal Bradyrhizobium as Keystone Species and Underline the Importance of Bulk Soil in Microbial Studies to Enhance Canola Production – Jean-Baptiste Floc’h – Microbial Ecology

Built Environment Microbiome

City-Scale Meta-Analysis of Indoor Airborne Microbiota Reveals that Taxonomic and Functional Compositions Vary with Building Types – You Zhou – Environmental Science & Technology

Environmental Microbiome

Heavy metals and microbiome are negligible drivers than mobile genetic elements in determining particle-attached and free-living resistomes in the Yellow River – Qiaoling Yu – Journal of Hazardous Materials

Forensic Microbiome

Assessment of the link between evidence and crime scene through soil bacterial and fungal microbiome: A mock case in forensic study – Sukriye Karadayı – Forensic Science International

Microbiome Analysis Methods; Bioinformatics 

Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification – Oliver Schwengers – Microbial Genomics

Compositional Data Analysis of Microbiome and Any-Omics Datasets: A Validation of the Additive Logratio Transformation – Michael Greenacre – Frontiers in Microbiology

Machine Learning Based Metagenomic Prediction of Inflammatory Bowel Disease – Andrea Mihajlović – Studies in Health Technology and Informatics

Evaluating de Novo Assembly and Binning Strategies for Time Series Drinking Water Metagenomes – Solize Vosloo – Microbiology Spectrum

Evaluation of the effect of antibiotics on gut microbiota in early life based on culturomics, SMRT sequencing and metagenomics sequencing methods – Lihan Wang – Analytical Methods

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