Today, after a hiatus, we have a new and big digest. Have a good Tuesday!
Gut Or General Microbiome
Editorial: Metagenomics, culturomics, and the human gut microbiota – Sophie Amrane – Expert Review of Anti-infective Therapy
Review: Disruptions in gut microbial-host co-metabolism and the development of metabolic disorders – Cynthia Rajani – Clinical Science
Metabolic retroconversion of trimethylamine N-oxide and the gut microbiota – Lesley Hoyles – Microbiome
Review: Factors influencing horizontal gene transfer in the intestine – Ximin Zeng – Animal Health Research Reviews
Commentary: Help, hope and hype: ethical considerations of human microbiome research and applications – Yonghui Ma – Protein & Cell
A System Biology Perspective on Environment-Host-Microbe Interactions – Lianmin Chen – Human Molecular Genetics
Comment on: effects of sleeve gastrectomy on the composition and diurnal oscillation of gut microbiota related to the metabolic improvements – Tammy L.Kindel – Surgery for Obesity and Related Diseases
Dietary Interventions to Modulate the Gut Microbiome—How Far Away Are We From Precision Medicine – Francesca De Filippis – Inflammatory Bowel Diseases
Targeting the gut microbiome to treat the osteoarthritis of obesity – Eric M. Schott – JCI Insight
Increased prevalence of pathogenic bacteria in the gut microbiota of infants at risk of developing celiac disease: the PROFICEL study – Marta Olivares – Gut Microbes
Genome sequence and description of Gracilibacillus timonensis sp. nov. strain Marseille-P2481T , a moderate halophilic bacterium isolated from the human gut microflora – Awa Diop – Microbiology Open
Inflammasomes make the case for littermate-controlled experimental design in studying host-microbiota interactions – Michail Mamantopoulos – Gut Microbes
No Significant Association Between the Fecal Microbiome and the Presence of Irritable Bowel Syndrome-type Symptoms in Patients with Quiescent Inflammatory Bowel Disease – Oliver Shutkever – Inflammatory Bowel Diseases
Research Highlight: Microbiome promotes pancreatic cancer – Iain Dickson – Nature Reviews Gastroenterology & Hepatology
Deciphering human gut microbiota-nutrient interactions: a role for biochemistry – Carina Chittim – Biochemistry
Letter: Defining the Impact of Host Genotypes on Microbiota Composition Requires Meticulous Control of Experimental Variables – Andy Wullaert – Cell Immunity
Review: Engineered Human Gastrointestinal Cultures to Study the Microbiome and Infectious Diseases – Sarah E.Blutt – Cellular and Molecular Gastroenterology and Hepatology
The Role of Macrophage Migration Inhibitory Factor in the Function of Intestinal Barrier – Milica Vujicic- Scientific Reports
Perspective: Urbanization and the gut microbiota in health and inflammatory bowel disease – Tao Zuo – Nature Reviews Gastroenterology & Hepatology
A systems biology approach to predict and characterize human gut microbial metabolites in colorectal cancer – QuanQiu Wang – Scientific Reports
Review: The human gut microbiota: metabolism and perspective in obesity – Aline Corado Gomes – Gut Microbes
Association between the Dietary Inflammatory Index (DII) and urinary enterolignans and C-reactive protein from the National Health and Nutrition Examination Survey-2003-2008 – Nitin Shivappa – European Journal of Nutrition
Case Report: The Effect of Fecal Microbiota Transplantation on a Child with Tourette Syndrome – Huijun Zhao – Case Reports in Medicine
Current evidence linking diet to gut microbiota and brain development and function – Florencia Ceppa – International Journal of Food Sciences and Nutrition
Using standard microbiome reference groups to simplify beta-diversity analyses and facilitate independent validation – Marlena Maziarz – Bioinformatics
Review: Gut microbiota, metabolism and psychopathology: A critical review and novel perspectives – Robin N. Groen – Critical Reviews in Clinical Laboratory Sciences
The Role of Gut Microbiota in Obesity and Type 2 and Type 1 Diabetes Mellitus: New Insights into “Old” Diseases – Igor Alexander Harsch – Medical Sciences
Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome – Geoffrey D. Hannigan – PLoS Computational Biology
Respiratory Microbiome
Prenatal antibiotic exposure and childhood asthma: a population-based study – Keely Loewen – European Respiratory Journal
Impact of gut colonization with butyrate producing microbiota on respiratory viral infection following allo-HCT – Bastiaan W. Haak – Blood
Oropharyngeal and nasopharyngeal decontamination with chlorhexidine gluconate in lung cancer surgery: a randomized clinical trial – Xavier Benoit D’Journo – Intensive Care Medicine
Impact of Long-Term Erythromycin Therapy on the Oropharyngeal Microbiome and Resistance Gene Reservoir in Non-Cystic Fibrosis Bronchiectasis – Jocelyn M. Choo – mSphere
Neonates colonized with pathogenic bacteria in the airways have a low-grade systemic inflammation – Nadia Rahman Fink – Allergy
Next-Generation Immune Repertoire Sequencing as a Clue to Elucidate the Landscape of Immune Modulation by Host–Gut Microbiome Interactions – Tatsuo Ichinohe – Frontiers in Immunology
Oral Microbiome
Metagenomic analysis of oral microbiome in young children aged 6‐8 y living in a rural isolated Chinese province – Yuan Xu – Oral Diseases
Microbiota and Metatranscriptome Changes Accompanying the Onset of Gingivitis – Emily M. Nowicki – mBio
Do we treat our patients or rather periodontal microbes with adjunctive antibiotics in periodontal therapy? A 16S rDNA microbial community analysis – Daniel Hagenfeld – PLoS One
The interplay between oral microbiome, lifestyle factors and genetic polymorphisms in the risk of oral squamous cell carcinoma – Jenn-Ren Hsiao – Carcinogenesis
Dynamic Alterations in Salivary Microbiota Related to Dental Caries and Age in Preschool Children With Deciduous Dentition: A 2-Year Follow-Up Study – Lei Xu – Frontiers in Physiology
Reproductive / Urinary tract Microbiome
How uterine microbiota might be responsible for a receptive, fertile endometrium – Marilen Benner – Human Reproduction Update
Culturing of female bladder bacteria reveals an interconnected urogenital microbiota – Krystal Thomas-White – Nature Communications
Fecal Microbiota Transplant
Editorial: Is fecal microbiota transplantation a temporary patch for treatment of Clostridium difficile infection or a new frontier of therapeutics? – Alexander Khoruts – Expert Review of Gastroenterology & Hepatology
Case Report: ANCA Vasculitis and Hemophagocytic Lymphohistiocytosis following a Fecal Microbiota Transplant – Adam Amlani – Case Reports in Rheumatology
Regional variability in fecal microbiota transplantation practices: a survey of the Southern Ontario Fecal Microbiota Transplantation Movement – Susy S. Hota – CMAJ Open
Commentary: Bacteriophage transfer during faecal microbiota transplantation in Clostridium difficile infection is associated with treatment outcome – Blessing O. Anonye – Frontiers in Cellular and Infection Microbiology
Fecal microbiota transplantation reverses antibiotic and chemotherapy-induced gut dysbiosis in mice – Quentin Le Bastard – Scientific Reports
Animal Microbiome and Animal Experiments
Evaluation of a therapy for Idiopathic Chronic Enterocolitis in rhesus macaques (Macaca mulatta) and linked microbial community correlates – Joshua M. Taylor – PeerJ
Comparative analyses of the gut microbiota among three different wild geese species in the genus Anser – Wen Wang – Journal of Basic Microbiology
Exposure to concentrated ambient PM2.5 alters the composition of gut microbiota in a murine model – Wanjun Wang – Particle and Fibre Toxicology
Imidacloprid decreases honey bee survival but does not affect the gut microbiome – Kasie Raymann – Applied and Environmental Microbiology
Letter: Bile Acids and the Microbiome in the Cow: Lack of Deoxycholic Acid Hydroxylation – Alan F. Hofmann – Lipids
Akkermansia muciniphila can reduce the damage of gluco/lipotoxicity, oxidative stress, and inflammation and normalize intestine microbiota in streptozotocin-induced diabetic rats – Ling Zhang – Pathogens and Disease
The impact of genome variation and diet on the metabolic phenotype and microbiome composition of Drosophila melanogaster – Lisa Jehrke – Scientific Reports
Fecal microbial composition associated with variation in feed efficiency in pigs depends on diet and sex – Lisanne M G Verschuren – Journal of Animal Science
Discovery of a mcr-1-bearing plasmid in commensal colistin-resistant Escherichia coli from healthy broilers in Faisalabad, Pakistan – Jiali Lv – Virulence
Pre-colonization with the commensal fungus Candida albicans reduces murine susceptibility to Clostridium difficile infection – Laura Markey – Gut Microbes
PCBs-high-fat diet interactions as mediators of gut microbiota dysbiosis and abdominal fat accumulation in female mice – Yulang Chi – Environmental Pollution
Metagenome and Culture-Based Methods Reveal Candidate Bacterial Mutualists in the Southern House Mosquito (Diptera: Culicidae) – Aparna Telang – Journal of Medical Entomology
Polysaccharide of Hericium erinaceus attenuates colitis in C57BL/6 mice via regulation of oxidative stress, inflammation-related signaling pathways and modulating the composition of the gut microbiota – Yilin Ren – The Journal of Nutritional Biochemistry
Potent SGLT1/2 Dual Inhibition Improves Glycemic Control Without Marked Gastrointestinal Adaptation or Colonic Microbiota Changes in Rodents – Fuyong Du – Journal of Pharmacology and Experimental Therapeutics
Similarity of the dog and human gut microbiomes in gene content and response to diet – Luis Pedro Coelho – Microbiome
Direct and Indirect Effects of Penguin Feces on Microbiomes in Antarctic Ornithogenic Soils – Yudong Guo – Frontiers in Microbiology
Stem Cell Transcription Factor FoxO Controls Microbiome Resilience in Hydra – Benedikt M. Mortzfeld – Frontiers in Microbiology
The effects of baicalein on cortical pro-inflammatory cytokines and the intestinal microbiome in senescence accelerated mouse prone 8 – Li Gao – ACS Chemical Neuroscience
Biases from different DNA extraction methods in intestine microbiome research based on 16S rDNA sequencing: a case in the koi carp, Cyprinus carpio var. Koi – Zhuoran Han – Microbiology Open
Built Environments
A comparison of methods used to unveil the genetic and metabolic pool in the built environment – Cinta Gomez-Silvan – Microbiome
Metabolism and Biodegradation of Spacecraft Cleaning Reagents by Strains of Spacecraft-Associated Acinetobacter – Mogul Rakesh – Astrobiology
Pathogen Research
The Critical Role of Zinc in a New Murine Model of Enterotoxigenic E. coli 1 (ETEC) Diarrhea – DT Bolick – Infection and Immunity
Review: Effects of antibiotic resistance (AR) and microbiota shifts on Campylobacter jejuni-mediated diseases – Phillip T. Brooks – Animal Health Research Reviews
A quality improvement initiative to reduce necrotizing enterocolitis across hospital systems – Amy T. Nathan – Journal of Perinatology
Quantitative Simulations Predict Treatment Strategies Against Fungal Infections in Virtual Neutropenic Patients – Sandra Timme – Frontiers in Immunology
Review: Helicobacter pylori the Latent Human Pathogen or an Ancestral Commensal Organism – Jackie Li – Frontiers in Microbiology
Heterogeneous ceramide distributions alter spatially resolved growth of Staphylococcus aureus on human stratum corneum – Joseph M. Cleary – Journal of the Royal Society Interface
Viruses
Viral Diversity of House Mice in New York City – Simon H. Williams – mBio
Subclinical cytomegalovirus infection associates with altered host immunity, gut microbiota and vaccine responses – Clarissa Santos Rocha – Journal of Virology
Antimicrobial Research
Antimicrobial resistance: from basic science to translational innovation – Jun Lin – Animal Health Research Reviews
Plant/Environment Microbiome
Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria – Ling Xu – PNAS
Assessment of toxic impact of metals on proline, antioxidant enzymes, and biological characteristics of Pseudomonas aeruginosa inoculated Cicer arietinum grown in chromium and nickel-stressed sandy clay loam soils – Saima Saif – Environmental Monitoring and Assessment
The first Taxus rhizosphere microbiome revealed by shotgun metagenomic sequencing – Da‐Cheng Hao – Journal of Basic Microbiology
Exposure to nanoplastics disturbs the gut microbiome in the soil oligochaete Enchytraeus crypticus – Bo-Kai Zhu – Environmental Pollution
Comparative Microbiome Analysis of a Fusarium Wilt Suppressive Soil and a Fusarium Wilt Conducive Soil From the Châteaurenard Region – Katarzyna Siegel-Hertz – Frontiers in Microbiology
Food Microbes
Towards better microbial safety of fresh produce: Chlorophyllin-based photosensitization for microbial control of foodborne pathogens on cherry tomatoes – Egle Paskeviciute – Journal of Photochemistry and Photobiology B: Biology
Metaproteomics of Microbiota in Naturally Fermented Soybean Paste, Da‐jiang – Ping Zhang – Journal of Food Science
Drugs, Beneficial Microbes and Compounds
Age-Related Changes in the Natural Killer Cell Response to Seasonal Influenza Vaccination Are Not Influenced by a Synbiotic: a Randomised Controlled Trial – Agnieszka Przemska-Kosicka – Frontiers in Immunology
4G-β-D-galactosylsucrose as a prebiotics may improve underweight in inpatients with schizophrenia – Takahiko Nagamine – Nihon Shokuhin Men’eki Gakkai
An approach on the potential use of probiotics in the treatment of skin conditions: acne and atopic dermatitis – Vitória H. M. Mottin – International Journal of Dermatology
Effects of Prebiotic Fiber Xylooligosaccharide in Adenine induced Nephropathy in Mice – Jieping Yang – Molecular Nutrition and Food Research
Anti-inflammatory effect of multistrain probiotic formulation (L. rhamnosus, B. lactis, and B. longum) – Marzia Sichetti – Nutrition
A combination of Lactobacillus mali APS1 and dieting improved the efficacy of obesity treatment via manipulating gut microbiome in mice – Yung-Tsung Chen – Scientific Reports
The Potential Effect of Chinese Herbal Formula Hongqijiangzhi Fang in Improving NAFLD: Focusing on NLRP3 Inflammasome and Gut Microbiota – Shu Liang – Evidence-Based Complementary and Alternative Medicine
Cationic amphiphilic bolaamphiphile-based delivery of antisense oligonucleotides provides a potentially microbiome sparing treatment for C. difficile – Arun K. Sharma – The Journal of Antibiotics
A probiotic modulates the microbiome and immunity in multiple sclerosis – Stephanie K. Tankou – Annals of Neurology
Comprehensive comparison of polysaccharides from Ganoderma lucidum and G. sinense: chemical, antitumor, immunomodulating and gut-microbiota modulatory properties – Li-Feng Li – Scientific Reports
Anti-diabetic mechanism of dietary polysaccharides based on their gastrointestinal functions – Jie-Lun Hu – Journal of Agricultural and Food Chemistry
The Effects of Synbiotic Supplementation on Body Mass Index, Metabolic and Inflammatory Biomarkers, and Appetite in Patients with Metabolic Syndrome: A Triple-Blind Randomized Controlled Trial – Samira Rabiei – Journal of Dietary Supplements
Bioinformatics and Methods
MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs – Daniel H. Huson – Biology Direct
KDiamend: a package for detecting key drivers in a molecular ecological network of disease – Mengxuan Lyu – BMC Systems Biology
ViDiT-CACTUS: an inexpensive and versatile library preparation and sequence analysis method for virus discovery and other microbiology applications – Joost Theo Petra Verhoeven – Canadian Journal of Microbiology
Phylogenomic Analysis of β-Lactamase in Archaea and Bacteria Enables the Identification of Putative New Members – Vivek Keshri – Genome Biology and Evolution
Microbiome Digest - Bik's Picks 