June 19, 2021

Have a nice weekend (¡Tengan un muy buen fin de semana!) In this Digest, a set of papers released during this latter month were selected, covering some of the most remarkable articles for this week. Please, if you want to highlight another article, please suggest it in the comments.  


NGLess tutorial for processing metagenomes – Big Data Biology LabJune 25
Registration available (closing June 22) at: https://docs.google.com/forms/d/e/1FAIpQLSebHvVFknM4Sy3ztMQbwQVxJ441VgRjJDPgCAPD4opse4znhQ/viewform

Human and General Microbiome

The Bacterial Microbiota Of Hunner Lesion Interstitial Cystitis/Bladder Pain Syndrome – J Curtis Nickel – BJU International

Microbiome-encoded Bile Acid Metabolism Modulates Colonic Transit Times – Naisi Li – IScience

Psychobiotics For Patients With Chronic Gastrointestinal Disorders Having Anxiety Or Depression Symptoms – Viet Hang Dao – Journal Of Multidisciplinary Healthcare

Homeostasis Of Mucosal Glial Cells In Human Gut Is Independent Of Microbiota – Timna Inlender – Scientific Reports

Yearly Changes In The Composition Of Gut Microbiota In The Elderly, And The Effect of lactobacilli intake on these changes – Ryuta Amamoto – Scientific Reports

Don’t Worry, Heavy Moms; Just Eat Your Broccoli(or Kimchi)! Co-diet Of High-fiber and high-fat helps give birth to healthy offspring through gut microbiota-to-brain signaling –  Sun-Kyung Lee – Molecules And Cells

Dietary Fiber Intake, The Gut Microbiome, And Chronic Systemic Inflammation In A cohort of adult men – Wenjie Ma – Genome Medicine

Commentary: The Role Of The Microbiome In Inflammation During Tuberculosis – Anou M Somboro – EBioMedicine

Vaginal Bacterial Load In The Second Trimester Is Associated With Early Preterm birth recurrence: a nested case-control study – Laura Goodfellow – BJOG

Bacteria-Mediated Synergistic Cancer Therapy: Small Microbiome Has A Big Hope – Xinyu Lou – Nano-micro Letters

Spatial Heterogeneity Analysis Of The Human Virome With Taylor’s Power Law – Zhanshan Sam Ma – Computational And Structural Biotechnology Journal

The Influence Of Nutritional Factors On Immunological Outcomes – Evanthia Tourkochristou – Frontiers In Immunology

Gut Microbial SNPs Induced By High-Fiber Diet Dominate Nutrition Metabolism And Environmental Adaption of Faecalibacterium prausnitzii in Obese Children – Hui Li – Frontiers In Microbiology

Gut Microbiota Regulate Gut-Lung Axis Inflammatory Responses By Mediating ILC2 Compartmental Migration – Qinqin Pu – Journal Of Immunology

Effects Of Cat Ownership On The Gut Microbiota Of Owners – Guankui Du – PloS One

Effect Of COVID-19 Precautions On The Gut Microbiota And Nosocomial Infections – Armin Rashidi –  Gut Microbes

Association Between Oral Microflora And Gastrointestinal Tumors (Review)– Xiaoxiao Li – Oncology Reports

Bacteroides-dominant Gut Microbiome Of Late Infancy Is Associated With Enhanced neurodevelopment – Sukhpreet K Tamana – Gut Microbes

Proteome-wide Prediction Of Bacterial Carbohydrate-binding Proteins As A Tool For understanding commensal and pathogen colonisation of the vaginal microbiome – François Bonnardel  – NPJ Biofilms And Microbiomes

Investigating The Origin Of The Fetal Gut And Placenta Microbiome In Twins – Nayo Williams – The Journal Of Maternal-fetal & Neonatal Medicine

Levels Of Trimethylamine N-Oxide Remain Elevated Long Term After Left Ventricular Assist Device and Heart Transplantation and Are Independent From Measures of  Inflammation and Gut Dysbiosis – Melana Yuzefpolskaya – Circulation: Heart Failure

The Impact Of Device-assisted Therapies On The Gut Microbiome In Parkinson’s disease – Michal Lubomski – Journal Of Neurology

Alterations In Microbiome Composition And Metabolic Byproducts Drive Behavioral And transcriptional responses to morphine – Rebecca S Hofford – Neuropsychopharmacology

Structural Specificities Of Cell Surface Beta-glucan Polysaccharides Determine commensal yeast mediated immuno-modulatory activities – Changhon Lee – Nature Communications

Integrated Omics Endotyping Of Infants With Respiratory Syncytial Virus bronchiolitis and risk of childhood asthma – Yoshihiko Raita – Nature Communications

Fecal Short-chain Fatty Acids And Obesity In A Community-based Japanese Population: The DOSANCO Health Study – Ryodai Yamamura – Obesity Research & Clinical Practice

Anaerobic Microbiota Derived From The Upper Airways Impact Staphylococcus Aureus physiology –  Sarah K Lucas – Infection And Immunity

Review: A New Biological Triangle In Cancer: Intestinal Microbiota, Immune Checkpoint inhibitors and antibiotics – Jie Zhang – Clinical & Translational Oncology

The Microbiome And Gynecologic Cancer: Current Evidence And Future Opportunities – Laura M Chambers Current – Oncology Reports

Increased Bacterial Proteolytic Activity Detected Before Diagnosis Of Ulcerative Colitis – Heather J Galipeau – Inflammatory Bowel Diseases

Characterization Of An Alpha-glucosidase Enzyme Conserved In Gardnerella spp. Isolated from the human vaginal microbiome – Pashupati Bhandari – Journal Of Bacteriology

Catechin Metabolites Along With Curcumin Inhibit Proliferation And Induce Apoptosis in Cervical Cancer Cells by Regulating VEGF Expression In-Vitro – Elnaz Khojaste – Nutrition And Cancer

Review: The Lung Microbiome In Lung Transplantation – John E McGinniss – The Journal Of Heart And Lung Transplantation

Vaginal Microbiome: Normalcy Vs Dysbiosis – Viqar Sayeed Saraf – Archives Of Microbiology

Beneficial Microbes, Compounds and Interventions

Lactobacillus acidophilus LA14 Alleviates Liver Injury – Longxian Lv – mSystems

Desulfovibrio vulgaris, A Potent Acetic Acid-producing Bacterium, Attenuates nonalcoholic fatty liver disease in mice – Ying Hong – Gut Microbes

Review: The Interaction Of Akkermansia muciniphila With Host-derived Substances, Bacteria and diets – Tatsuro Hagi – Applied Microbiology And Biotechnology

Ganoderma lucidum Polysaccharide Modulates Gut Microbiota And Immune Cell Function to inhibit inflammation and tumorigenesis in colon – Cuiling Guo – Carbohydrate Polymers

The Outer Membrane Protein Amuc_1100 Of Akkermansia muciniphila Alleviates The depression-like behavior of depressed mice induced by chronic stress – Rongrong Cheng – Biochemical And Biophysical Research Communications

JianpiQinghua Granule Reduced PPI Dosage In Patients With Nonerosive Reflux Disease: A multicenter, randomized, double-blind, double-dummy, noninferiority study – Jiaqi Zhang –  Phytomedicine

Circadian Disruption-induced Metabolic Syndrome In Mice Is Ameliorated By Oat Beta-glucan mediated by gut microbiota – Wai-Yin Cheng – Carbohydrate Polymers

Effects Of Mediterranean Diet On Plasma Metabolites And Their Relationship With insulin resistance and gut microbiota composition in a crossover randomized clinical trial – Serena Galié – Clinical Nutrition

Calorie Restriction Conferred Improvement Effect On Long-term Rehabilitation Of ischemic stroke via gut microbiota Jia-Ting Huang – Pharmacological Research

Animal Models / Animal Microbiome

Holdemanella biformis Improves Glucose Tolerance And Regulates GLP-1 Signaling In obese mice –  Marina Romaní-Pérez – The FASEB Journal

Gut Microbiota Composition Affects Procyanidin A2-Attenuated Atherosclerosis In ApoE(-/-) Mice by Modulating the Bioavailability of Its Microbial Metabolites – Shiying Yang – Journal Of Agricultural And Food Chemistry

The Gut Microbiome Of The Sunda Pangolin (Manis javanica) Reveals Its Adaptation To specialized myrmecophagy – Fuhua Zhang – PeerJ

A Rise In Proteobacteria Is An Indicator Of Gut-liver Axis-mediated Nonalcoholic fatty liver disease in high-fructose-fed adult mice. Isabela Macedo Lopes Vasques-Monteiro – Nutrition Research

Plant Microbiome

Extension Of Plant Phenotypes By The Foliar Microbiome – Christine V Hawkes – Annual Review Of Plant Biology

Plant Genetics As A Tool For Manipulating Crop Microbiomes: Opportunities And Challenges – Kayla M Clouse – Frontiers In Bioengineering And Biotechnology

Development Of An Inexpensive Matrix-assisted Laser Desorption-time Of Flight Mass spectrometry method for the identification of endophytes and rhizobacteria cultured from the microbiome associated with maize – Michael G LaMontagne – PeerJ

Opinion: Assessing The Potential To Harness The Microbiome Through Plant Genetics – Joy Bergelson – Current Opinion In Biotechnology

Experimental and Computational Tools and Techniques

An Integrated Gene Catalog And Over 10,000 Metagenome-assembled Genomes From The gastrointestinal microbiome of ruminants – Fei Xie – Microbiome (BMC)

Antibiotic Resistance: Time Of Synthesis In A Post-genomic Age – Teresa Gil-Gil – Computational And Structural Biotechnology Journal

Efam: An Expanded, Metaproteome-supported HMM Profile Database Of Viral Protein families – Ahmed A Zayed – Bioinformatics

The Future Of Microbial Ecological Niche Theory And Modeling – Stephanie N Kivlin – The New Phytologist

DNA Extraction And Host Depletion Methods Significantly Impact And Potentially Bias Bacterial Detection in a Biological Fluid – Erika Ganda – mSystems


Electrical Conductivity As A Driver Of Biological And Geological Spatial heterogeneity in the Puquios, Salar de Llamara, Atacama Desert, Chile –  R P Reid – Scientific Reports

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