November 20, 2021

Highlights!

Review: Reporting guidelines for human microbiome research: the STORMS checklist – Chloe Mirzayi – Nature Medicine → The following article “provides guidance for concise and complete reporting of microbiome studies that will facilitate manuscript preparation, peer review, and reader comprehension of publications and comparative analysis of published results”

Honey bee genetics shape the strain-level structure of gut microbiota in social transmission – Jiaqiang Wu – Microbiome → “Our results indicated that host genetics influence the bee gut composition and suggest a gut-brain connection implicated in the gut bacterial strain preference”

Metatranscriptomics to characterize respiratory virome, microbiome, and host response directly from clinical samples – Seesandra V Rajagopala – Cell Reports Methods → This study reports a method to study virome and microbiome of clinically relevant respiratory samples, using a children cohort. 

Human and General Microbiome

Response of Lung Microbiota to Changes of Pulmonary Innate Immunity Under Healthy Conditions – Taro Yasuma – American Journal of Respiratory and Critical Care Medicine

Small intestinal bacterial overgrowth in Alzheimer’s disease – Karol Kowalski – Journal of Neural Transmission 

Periodontitis Salivary Microbiota Worsens Colitis – J Qian – Journal of Dental Research

The Effects of Moderate Alcohol Consumption on Circulating Metabolites and Gut Microbiota in Patients With Coronary Artery Disease – Xinyue Zhao – Frontiers in Cardiovascular Medicine

Integrative Analysis of LGR5/6 Gene Variants, Gut Microbiota Composition and Osteoporosis Risk in Elderly Population – Dong-Sheng Di – Frontiers in Microbiology

Comparison of the Gut Microbiota in Patients with Benign and Malignant Breast Tumors: A Pilot Study – Peidong Yang – Evolutionary Bioinformatics Online

Temporal variability in quantitative human gut microbiome profiles and implications for clinical research – Doris Vandeputte – Nature Communications

Association between Parkinson’s disease and the faecal eukaryotic microbiota – Severin Weis – NPJ Parkinson’s Disease

Micronutrient supplements can promote disruptive protozoan and fungal communities in the developing infant gut – Ana Popovic – Nature Communications

An integrative understanding of the large metabolic shifts induced by antibiotics in critical illness – Andrea Marfil-Sánchez – Gut Microbes

Efficacy and Outcomes of Fecal Microbiota Transplantation for Recurrent Clostridioides difficile Infection in Children with Inflammatory Bowel Disease – Maribeth R Nicholson – Journal of Crohn’s & Colitis

The anti-inflammatory effect of bacterial short chain fatty acids is partially mediated by endocannabinoids – Amrita Vijay – Gut Microbes

Human and General Microbiome – Reviews

Bile acids as regulatory molecules and potential targets in metabolic diseases – Ai-Jin Xie – Life Sciences

Renaissance for Phage-Based Bacterial Control – Cory Schwarz – Environmental Science & Technology

Sulphur metabolism in colon cancer tissues: a case report and literature review – Hironori Fukuoka – The Journal of International Medical Research

Dietary fatty acids in gut health: Absorption, metabolism and function – E Xu – Animal Nutrition

The search for aliens within us: a review of evidence and theory regarding the foetal microbiome – Richard Cariño III – Critical Reviews in Microbiology

Human immune diversity: from evolution to modernity – Adrian Liston – Nature Immunology 

Beneficial Microbes and Compounds

Review: Human Milk Oligosaccharides as a Missing Piece in Combating Nutritional Issues during Exclusive Breastfeeding – Verawati Sudarma – Pediatric Gastroenterology, Hepatology & Nutrition

Review: Advancements in the Pharmaceutical Applications of Probiotics: Dosage Forms and Formulation Technology – Kshitis Chandra Baral – International Journal of Nanomedicine

Lactobacillus rhamnosus strain LRH05 intervention ameliorated body weight gain and adipose inflammation via modulating the gut microbiota in high-fat diet-induced obese mice – Yung-Tsung Chen – Molecular Nutrition & Food Research

Bifidobacterium infantis Maintains Genome Stability in Ulcerative Colitis via Regulating Anaphase-Promoting Complex Subunit 7 – Taotao Han – Frontiers in Microbiology

Galacto-oligosaccharide Supplementation Modulates Pathogen-Commensal Competition between Streptococcus agalactiae and Streptococcus salivarius – Rebecca E Moore – Chembiochem

Animal Microbiome (Non-models)

Metagenome-assembled genomes and gene catalog from the chicken gut microbiome aid in deciphering antibiotic resistomes – Yuqing Feng – Communications Biology

Contrasting microbiome dynamics of putative denitrifying bacteria in two octocoral species exposed to dissolved organic carbon (DOC) and warming – Nan Xiang – Applied and Environmental Microbiology

Plant Microbiome

Emergent bacterial community properties induce enhanced drought tolerance in Arabidopsis – Nan Yang – NPJ Biofilms and Microbiomes

Drops join to make a stream: high-throughput nanoscale cultivation to grasp the lettuce root microbiome – Antoine Persyn – Environmental Microbiology Reports

Pan-genome analysis identifies intersecting roles for Pseudomonas specialized metabolites in potato pathogen inhibition – Alba Pacheco-Moreno – eLife

Small-scale agricultural grassland management can affect soil fungal community structure as much as continental scale geographic patterns – A Fox – FEMS Microbiology Ecology

Geographic and position-based variations in phyllospheric bacterial communities present on flue-cured tobacco – Jianbin Ye – Applied Microbiology and Biotechnology

Other Microbes

Improved quantitative microbiome profiling for environmental antibiotic resistance surveillance – Amelie Ott – Environmental Microbiome

Sediment Microbiota in Response to Circuitry of Sediment Microbial Fuel Cells, Revealed by 16S rRNA Gene Amplicon Sequencing – Yasuyuki Takemura – Microbiology Resource Announcements

Bacterial response to spatial gradients of algal-derived nutrients in a porous microplate – Hyungseok Kim – The ISME Journal

Review: Microbial ecology of tourist Paleolithic caves – Zelia Bontemps – The Science of the Total Environment

Microbiome Analysis and Bioinformatics

Multivariate statistical monitoring system for microbial population dynamics – Koji Ishiya – Physical Biology

GMrepo v2: a curated human gut microbiome database with special focus on disease markers and cross-dataset comparison – Die Dai – Nucleic Acids Research

metaSNV v2: detection of SNVs and subspecies in prokaryotic metagenomes – Thea Van Rossum – Bioinformatics

Assessing saliva microbiome collection and processing methods – Abigail J S Armstrong – NPJ Biofilms and Microbiomes

Analysing microbiome intervention design studies: Comparison of alternative multivariate statistical methods – Maryia Khomich – PloS ONE

Technical note: overcoming host contamination in bovine vaginal metagenomic samples with Nanopore adaptive sequencing – Chian Teng Ong – Journal of Animal Science

Mian: Interactive Web-Based Microbiome Data Table Visualization and Machine Learning Platform – Boyang Tom Jin – Bioinformatics

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