Author Archives: JP Cardenas

April 27, 2018

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Have a good Friday! Today’s Digest include a set of interesting reviews about the Hologenome concept, Clostridium difficile, the relation between microbiota and tuberculosis and microbiota transplantation. This digest also contains interesting articles about the use of dietary studies to control diet in microbiota studies, microbiome in cancer, microbiome and depression in rats and microbiome in soil from the Atacama’s desert.

 

Human and General Microbiome

Bile Acids and the Gut Microbiome as Potential Targets for NAFLD Treatment – Lixin Zhu – Journal of Pediatric Gastroenterology and Nutrition

Review: The role of fecal microbiota transplantation in inflammatory bowel disease – Irene D’Odorico – Journal of Digestive Diseases

Review: Put “gender glasses” on the effects of phenolic compounds on cardiovascular function and diseases – Ilaria Campesi – European Journal of Nutrition

Use of dietary indices to control for diet in human gut microbiota studies – Ruth C. E. Bowyer – Microbiome

Review: The hologenome concept of evolution after 10 years – Eugene Rosenberg – Microbiome

Pharmabiotic Manipulation of the Microbiota in Gastrointestinal Disorders: A Clinical Perspective – Fanny Giron – Journal of Neurogastroenterology and Motility

Microbiota potential for the treatment of sexual dysfunction – Hassan Tirandaz – Medical Hypotheses

Gut microbiome analysis identifies potential aetiological factors in acute gastroenteritis – Natalia Castaño-Rodríguez – Immunity and Infection

Skin microbiota and allergic symptoms associate with exposure to environmental microbes – Jenni Lehtimäki – PNAS

Gut microbiome of Moroccan colorectal cancer patients – Imane Allali – Medical Microbiology and Immunology

Systematic Review: Safety and efficacy of encapsulated fecal microbiota transplantation for recurrent Clostridium difficile infection: a systematic review – Umair Iqbal – European Journal of Gastroenterology & Hepatology

Alterations in Enteric Virome Associate With Colorectal Cancer and Survival Outcomes – Geicho Nakatsu – Gastroenterology

High relative abundance of firmicutes and increased TNF-α levels correlate with obesity in children – Yaneth C Orbe-Orihuela – Salud Pública de México (Article in English)

Perspective: Why does the microbiome affect behaviour? – Katerina V.-A. Johnson – Nature Reviews Microbiology

Research Highlight: Exercise affects gut microbiota and bone – Claire Greenhill – Nature Reviews Endocrinology

Review: Clostridium difficile – From Colonization to Infection – Holger Schäffler – Frontiers in Microbiology

MiniReview: New Players in Immunity to Tuberculosis: The Host Microbiome, Lung Epithelium, and Innate Immune Cells – Nancy Gupta – Frontiers in Immunology

 

Animal Microbiome

A meta-barcoding approach to assess and compare the storage temperature-dependent bacterial diversity of gilt-head sea bream (Sparus aurata) originating from fish farms from two geographically distinct areas of Greece – Foteini F.Parlapani – International Journal of Food Microbiology

High-fat diet induces depression-like behaviour in mice associated with changes in microbiome, neuropeptide Y, and brain metabolome – Ahmed M. Hassan – Nutritional Neuroscience

Cascading effects on bacterial communities: cattle grazing causes a shift in the microbiome of a herbivorous caterpillar – Tali S. Berman – The ISME Journal

Microbiomes associated with bovine periodontitis and oral health – Ana C.Borsanelli – Veterinary Microbiology

Microbiota-accessible carbohydrates suppress Clostridium difficile infection in a murine model – Andrew J. Hryckowian – Nature Microbiology

High-Fat Diet Induces Dysbiosis of Gastric Microbiota Prior to Gut Microbiota in Association With Metabolic Disorders in Mice – Cong He – Frontiers in Microbiology

Differential Microbial Communities of Omnivorous and Herbivorous Cattle in Southern China – Susanna K.P.Lau – Computational and Structural Biotechnology Journal

 

Plant/Soil Microbes

A microorganisms’ journey between plant generations – Nathan Vannier – Microbiome

MYB72-dependent coumarin exudation shapes root microbiome assembly to promote plant health – Ioannis A. Stringlis – PNAS

Bacterial potentials for uptake, solubilization and mineralization of extracellular phosphorus in agricultural soils are highly stable under different fertilization regimes – Martin Grafe – Environmental Microbiology Reports

 

Extremophiles

Microbiome analysis and bacterial isolation from Lejía Lake soil in Atacama Desert – Dinka Mandakovic – Extremophiles

 

Beneficial Microbes and Compounds

Current and future uses of probiotics – Georgia Tanner – JAAPA

Barley β-glucan improves metabolic condition via short-chain fatty acids produced by gut microbial fermentation in high fat diet fed mice – Junki Miyamoto – PLoS One

Systematic Review: Are probiotic treatments useful on fibromyalgia syndrome or chronic fatigue syndrome patients? A systematic review – P. Roman – Beneficial Microbes

Review: The application of in vitro human intestinal models on the screening and development of pre- and probiotics – V.T. Pham – Beneficial Microbes

 

Antimicrobial Resistance

Acquisition of multidrug-resistant organisms in the absence of antimicrobial exposure – E M C D’Agata – Clinical Infectious Diseases

 

Food Microbiome

Variation in the Microbiome, Trichothecenes, and Aflatoxins in Stored Wheat Grains in Wuhan, China – Qing-Song Yuan – Toxins

 

Methodologies

Review: Single-cell metagenomics: challenges and applications – Yuan Xu – Protein & Cell

 

April 24, 2018

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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

 

April 3, 2018

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Human Microbiome

Non-Ischemic Heart Failure With Reduced Ejection Fraction Is Associated With Altered Intestinal Microbiota – Themistoklis Katsimichas – Circulation Journal

The impact of antibiotics on the Intestinal microbiota needs to be re-defined in order to optimize the antibiotic usage – Bryan Coburn – Clinical Microbiology and Infection

The direct and indirect association of cervical microbiota with the risk of cervical intraepithelial neoplasia – Chaoting Zhang – Cancer Medicine

Review: The use of probiotics in different phases of diverticular disease – Veronica Ojetti – Reviews on Recent Clinical Trials

Fecal microbiota transplantation and its potential therapeutic uses in gastrointestinal disorders – Ryan D. Heath – Northern clinics of Istanbul

Dysbiosis of the salivary microbiota in pediatric-onset primary sclerosing cholangitis and its potential as a biomarker – Kentaro Iwasawa – Scientific Reports

Microbiota Composition May Predict Anti-Tnf Alpha Response in Spondyloarthritis Patients: an Exploratory Study – Thomas Bazin – Scientific Reports

Research Highlight: Obesity: ANGPTL4 — the link binding obesity and glucose intolerance – Alan Morris – Nature Reviews Endocrinology

Influence of intrauterine administration of Lactobacillus buchneri on reproductive performance and pro-inflammatory endometrial mRNA expression of cows with subclinical endometritis – S. Peter – Scientific Reports

Review: Overview of Current Concepts in Gastric Intestinal Metaplasia and Gastric Cancer – David S. Jencks – Gastroenterology & Hepatology

 

Animal Microbiome

Psychoneuroimmunology and immunopsychiatry of zebrafish – Murilo S.de Abreu – Psychoneuroendocrinology

Regulation of growth, intestinal microbiota, non-specific immune response and disease resistance of sea cucumber Apostichopus japonicus (Selenka) in biofloc systems – Jinghua Chen – Fish & Shellfish Immunology

Loss of microRNA-21 Influences the Gut Microbiota Causing Reduced Susceptibility in a Murine Model of Colitis – Daniel G W Johnston – Journal of Crohn’s and Colitis

Influence of Long-Term Feeding Antibiotics on the Gut Health of Zebrafish – Zhou Li – Zebrafish

Effects of Intestinal Microbiota on Brain Development in Humanized Gnotobiotic Mice – Jing Lu – Scientific Reports

Long-term Western diet fed apolipoprotein E-deficient rats exhibit only modest early atherosclerotic characteristics – Ida Rune – Scientific Reports

 

Methods

Guided Protocol for Fecal Microbial Characterization by 16S rRNA-Amplicon Sequencing – Ayelet Di Segni – Journal Of Visualized Experiments (It includes a video)

 

Food Microbes

Tetracycline resistance in lactobacilli isolated from Serbian traditional raw milk cheeses – Tijana Ledina – Journal of Food Science and Technology

 

Pathogens

Case Report: Successful Fecal Microbiota Transplantation in a Patient with Severe Complicated Clostridium difficile Infection after Liver Transplantation – Schneider K.M. – Case Reports in Gastroenterology

Review: Significance of Streptococcus gallolyticus subsp. gallolyticus Association With Colorectal Cancer – Ewa Pasquereau-Kotula – Frontiers in Microbiology

Review: Helicobacter pylori the Latent Human Pathogen or an Ancestral Commensal Organism – Jackie Li –  Frontiers in Microbiology

Fungi-Induced Upper and Lower Respiratory Tract Allergic Diseases: One Entity – Aleksandra Barac – Frontiers in Microbiology

Genetic and Virulent Difference Between Pigmented and Non-pigmented Staphylococcus aureus – Jing Zhang – Frontiers in Microbiology

 

Environmental Microbes

Exploring Biogeochemistry and Microbial Diversity of Extant Microbialites in Mexico and Cuba – Patricia M. Valdespino-Castillo – Frontiers in Microbiology

Direct and Indirect Effects of Penguin Feces on Microbiomes in Antarctic Ornithogenic Soils – Yudong Guo – Frontiers in Microbiology

 

Other

Combination of peracetic acid and ultrasound reduces Salmonella Typhimurium on fresh lettuce (Lactuca sativa L. var. crispa) – Luiza Oliveira Silveira – Journal of Food Science and Technology

Recent advances in the physiopathology of IgA nephropathy – Renato C. Monteiro – Néphrologie & Thérapeutique

 

April 2, 2018

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Have a good monday! Today, in Microbiome Digest: interesting papers about Clostridium difficile, the use of Fecal Microbiota Transplant, studies in mice model, effect of Lactobacillus on Candida, antibiotic-resistant bacteria in sewerage biofilms, and more!

 

Human/General Microbiome

Diet, gut microbiota composition and feeding behavior – Jiyoung S. Kim – Physiology & Behavior

Fecal Microbiota Transplantation in Inflammatory Bowel Disease- a Primer for the Internists – Gaurav Syal – The American Journal of Medicine

Oral microbiota maturation during the first 7 years of life in relation to allergy development – Majda Dzidic – Allergy

The tangled web of interactions between host, pathogen and microbiota in C. difficile infection – Anna Maria Seekatz – Gastroenterology

Analysis of Treatment Outcomes for Recurrent Clostridium difficile Infections and Fecal Microbiota Transplantation in a Pediatric Hospital – Aileen Aldrich – The Pediatric Infectious Disease Journal

Role of microbiota in the autism spectrum disorders – Daniela Campion – Minerva Gastroenterologica e Dietologica

From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota – Eugen Bauer – mSystems

Developing a Bacteroides System for Function-Based Screening of DNA from the Human Gut Microbiome – Kathy N. Lam – mSystems

Is a Single Fecal Microbiota Transplant a Promising Treatment for Recurrent Clostridium difficile Infection? – Susy S Hota – Open Forum Infectious Diseases

Bronchoalveolar lavage fluid microbiota dysbiosis in infants with protracted bacterial bronchitis – Yanmin Bao – Journal of Thoracic Disease

Mother’s Milk: A Purposeful Contribution to the Development of the Infant Microbiota and Immunity – Kirsty Le Doare –  Frontiers in Immunology

Contributory Role of Gut Microbiota and Their Metabolites Toward Cardiovascular Complications in Chronic Kidney Disease – Daniel Y. Li – Seminars in Nephrology

Differential bacterial capture and transport preferences facilitate co-growth on dietary xylan in the human gut – Maria Louise Leth – Nature Microbiology

 

Animal Microbiome / Animal Experiments

Two new gene clusters involved in the degradation of plant cell wall from the fecal microbiota of Tunisian dromedary – Rihab Ameri – PLoS One

Honey Bee Antiviral Immune Barriers as Affected by Multiple Stress Factors: A Novel Paradigm to Interpret Colony Health Decline and Collapse – Francesco Nazzi – Viruses

Influence of Intestinal Microbiota Transplantation and NleH Expression on Citrobacter rodentium Colonization of Mice – Gaochan Wang – Pathogens

Shifts in the Gut Metabolome and Clostridium difficile Transcriptome throughout Colonization and Infection in a Mouse Model – Joshua R. Fletcher – mSystems

Akkermansia muciniphila is permissive to arthritis in the K/BxN mouse model of arthritis – Matthew L Stoll – Genes & Immunity

The Gut Microbiota Regulates Endocrine Vitamin D Metabolism through Fibroblast Growth Factor 23 – Stephanie A. Bora – Frontiers in Immunology

High diversity and variability in the bacterial microbiota of the coffee berry borer (Coleoptera: Curculionidae), with emphasis on Wolbachia – Yobana A Mariño – Journal of Applied Microbiology

Exercise prevents high fat diet-induced bone loss, marrow adiposity and dysbiosis in male mice – Laura R. McCabe – Bone

Protein- and RNA-Enhanced Fermentation by Gut Microbiota of the Earthworm Lumbricus terrestris – Lydia Zeibich – Applied and Environmental Microbiology

Canonical Wnt Signaling in CD11c+ APCs Regulates Microbiota-Induced Inflammation and Immune Cell Homeostasis in the Colon – Daniel Swafford – The Journal of Immunology

 

Beneficial Microbes

Culture Supernatants of Lactobacillus gasseri and L. crispatus Inhibit Candida albicans Biofilm Formation and Adhesion to HeLa Cells – Yuko Matsuda – Mycopathologia

 

Environmental and Water Microbiome

Prevalence of antibiotic resistant coliform bacteria, Enterococcus spp. and Staphylococcus spp. in wastewater sewerage biofilm – Kristína Lépesová – Journal of Global Antimicrobial Resistance

Occurrence of virulence-associated genes among Staphylococcus saprophyticus isolated from different sources – Weslley de Paiva-Santos – Microbial Pathogenesis

 

Other

Digest: Life history evolution in Darwin’s dream ponds – Foteini Spagopoulou – Evolution

Research Highlight: To grow, or not to grow – Ursula Hofer – Nature Reviews Microbiology

 

March 9, 2018

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Have a nice Friday! Today we have interesting papers about nasal/oral microbiota, some papers about studies in pathogens (including the use of bacteriophages for selective inhibition of E. coli), DNA extraction studies in meconium, and more!

 

Human/General Microbiome

Review: Microbiota metabolites: Pivotal players of cardiovascular damage in chronic kidney disease – Carmela Cosola – Pharmacological Research

Predictive biomarkers for type 2 of diabetes mellitus: bridging the gap between systems research and personalized medicine – Christina Kraniotou – Journal of Proteomics

The Nasal Microbiome in Asthma – Mina Fazlollahi – Journal of Allergy and Clinical Immunology

Metatranscriptome of the Oral Microbiome in Health and Disease – J. Solbiati – Journal of Dental Research

Nasal Microbiota and Respiratory Tract Infections: The Role of Viral Detection – Insa Korten – American Journal of Respiratory and Critical Care Medicine

Short term dynamics of the sputum microbiome among COPD patients – Rohita Sinha – Plos One

The effect of medical treatments on the bacterial microbiome in patients with chronic rhinosinusitis: a pilot study – Ravi Jain – International Forum of Allergy & Rhinology

The Influence of Cervicovaginal Microbiota on Mucosal Immunity and Prophylaxis in the Battle against HIV – Mara Farcasanu – Current HIV/AIDS Reports

Emerging Mechanisms of Innate Immunity and Their Translational Potential in Inflammatory Bowel Disease – Daniele Corridoni – Frontiers in Medicine

Oropharyngeal Microbiota in Frail Older Patients Unaffected by Time in Hospital – Victoria C. Ewan – Frontiers In Cellular And Infection Microbiology

Influence of Intestinal Indigenous Microbiota on Intrafamilial Infection by Helicobacter pylori in Japan – Takako Osaki – Frontiers in Immunology

Comparison of Meconium DNA Extraction Methods for Use in Microbiome Studies – Lisa F. Stinson – Frontiers in Microbiology

Minireview: Gut Microbiota: An Integral Moderator in Health and Disease – Qingqing Feng –   Frontiers in Microbiology

Activation of Notch-1 in oral epithelial cells by P. gingivalis triggers the expression of the antimicrobial protein PLA2-IIA – Ahmad Al-Attar – Mucosal Immunology

Gut microbial RNA and DNA analysis predicts hospitalizations in cirrhosis – Jasmohan S. Bajaj –  JCI Insight

Physiological Regulation of Drug Metabolism and Transport: Pregnancy, Microbiome, Inflammation, Infection, and Fasting – Edward T. Morgan – Drug Metabolism and Disposition

 

Pathogen Research

A bacteriophage cocktail targeting Escherichia coli reduces E. coli in simulated gut conditions, while preserving a non-targeted representative commensal normal microbiota – Tomasz Cieplak – Gut Microbes

Triclosan Enhances the Clearing of Pathogenic Intracellular Salmonella or Candida albicans but Disturbs the Intestinal Microbiota through mTOR-Independent Autophagy – Chao Wang – Frontiers In Cellular And Infection Microbiology

The Metabolic Sensor GPR43 Receptor Plays a Role in the Control of Klebsiella pneumoniae Infection in the Lung – Izabela Galvão – Frontiers in Immunology

Parasite-Vector Interaction of Chagas Disease: A Mini-Review – Ana Beatriz Bortolozo de Oliveira – The American Journal of Tropical Medicine and Hygiene – Current Issue

Bacillus subtilis spore with surface display of paramyosin from Clonorchis sinensis potentializes a promising oral vaccine candidate – Hengchang Sun – Parasites & Vectors

 

Animal Microbiome

Instar- and host-associated differentiation of bacterial communities in the Mediterranean fruit fly Ceratitis capitata – Antonino Malacrinò – Plos One

Concurrent gut transcriptome and microbiota profiling following chronic ethanol consumption in nonhuman primates – Tasha Barr – Gut Microbes

Integrating molecular and ecological approaches to identify potential polymicrobial pathogens over a shrimp disease progression – Wenfang Dai – Applied Microbiology And Biotechnology

Intestinal bacterial signatures of white feces syndrome in shrimp – Dongwei Hou – Applied Microbiology And Biotechnology

Bile acid metabolism regulated by the gut microbiota promotes non-alcoholic steatohepatitis-associated hepatocellular carcinoma in mice – Shoji Yamada – Oncotarget

Early-life exposure to low-dose oxidants can increase longevity via microbiome remodelling in Drosophila – Fumiaki Obata – Nature Communications

Physiological mechanisms of sustained fumagillin-induced weight loss – Jie An – JCI Insight

Gpr109a Limits Microbiota-Induced IL-23 Production To Constrain ILC3-Mediated Colonic Inflammation – Brinda Bhatt – The Journal in Immunology

Fuzhuan brick tea polysaccharides attenuate metabolic syndrome in high-fat diet induced mice in association with modulation in the gut microbiota – Guijie Chen – Journal Of Agricultural And Food Chemistry

 

Extremophiles

Metagenomic Insights into the Phylogenetic and Metabolic Diversity of the Prokaryotic Community Dwelling in Hypersaline Soils from the Odiel Saltmarshes (SW Spain) – Blanca Vera-Gargallo – Genes

 

Plant Microbiome

Disease-induced assemblage of a plant-beneficial bacterial consortium – Roeland L. Berendsen – The ISME Journal

March 7, 2018

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Human Microbiome

The Effect of Lean-Seafood and Non-Seafood Diets on Fecal Metabolites and Gut Microbiome: Results From a Randomized Crossover Intervention Study – Mette Schmedes – Molecular Nutrition & Food Research

Addendum – Invited: Gut Microbiota in Toxicological Risk Assessment of Drugs and Chemicals: The Need of Hour – Ganesan Velmurugan – Gut Microbes

Effects of different thickening agents on infant gut microbiota – C. A. González-Bermúdez – Food & Function

The Impact of Laparoscopic Sleeve Gastrectomy with Duodenojejunal Bypass on Intestinal Microbiota Differs from that of Laparoscopic Sleeve Gastrectomy in Japanese Patients with Obesity – Rieko Kikuchi – Clinical Drug Investigation

Perspective: Precision antimicrobial therapeutics: the path of least resistance? – Caitlin N. Spaulding – npj Biofilms and Microbiomes

Convergent shifts in host-associated microbial communities across environmentally elicited phenotypes – Tyler J. Carrier – Nature Communications

Case report: Successful faecal microbiota transplant for recurrent Clostridium difficile infection delivered by colonoscopy through a diverted ileostomy in a patient with severe perianal Crohn’s disease – Jonathan Digby-Bell – BMJ Case Reports

Outlook: How baby’s first microbes could be crucial to future health – Sarah DeWeerdt – Nature

Correspondence: Bile acid–microbiota crosstalk in gastrointestinal inflammation and carcinogenesis: a role for bifidobacteria and lactobacilli? – Borja Sánchez – Nature Reviews Gastroenterology & Hepatology

Inter-niche and inter-individual variation in gut microbial community assessment using stool, rectal swab, and mucosal samples – Roshonda B. Jones – Scientific Reports

Review: Gastrointestinal toxicity of immune checkpoint inhibitors: from mechanisms to management – Mark A. Samaan – Nature Reviews Gastroenterology & Hepatology

Reply: Probiotics, bile acids and gastrointestinal carcinogenesis – Wei Jia – Nature Reviews Gastroenterology & Hepatology

Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid – Philipp Kirstahler – Scientific Reports

 

Animal microbiome

Performance, egg quality, nutrient digestibility, and excreta microbiota shedding in laying hens fed corn-soybean-meal-wheat-based diets supplemented with xylanase – X. J. Lei – Poultry Science

Next generation sequencing for gut microbiome characterization in rainbow trout (Oncorhynchus mykiss) fed animal by-product meals as an alternative to fishmeal protein sources – Simona Rimoldi – Plos One

Sugary Kefir Strain Lactobacillus mali APS1 Ameliorated Hepatic Steatosis by Regulation of SIRT-1/Nrf-2 and Gut Microbiota in Rats – Yung-Tsung Chen – Molecular Nutrition & Food Research

Pyrroloquinoline quinone prevents developmental programming of microbial dysbiosis and macrophage polarization to attenuate liver fibrosis in offspring of obese mice – Jacob E. Friedman – Hepatology Communications

Inulin-type fructan improves diabetic phenotype and gut microbiota profiles in rats – Qian Zhang​ – PeerJ

Early-life exposure to low-dose oxidants can increase longevity via microbiome remodelling in Drosophila – Fumiaki Obata – Nature Communications

The influence of caging, bedding, and diet on the composition of the microbiota in different regions of the mouse gut – Aaron C. Ericsson – Scientific Reports

News & Views: The intestinal microbiome influences checkpoint blockade – Cynthia L Sears – Nature Medicine

News Feature: Gut checkpoint: A rising cancer treatment may get a boost from intestinal bacteria – Anna Azvolinsky – Nature Medicine

Herbivorous turtle ants obtain essential nutrients from a conserved nitrogen-recycling gut microbiome – Yi Hu – Nature Communications

Research Highlight: Comparative genomics: Blood, guts and vampire bats – Linda Koch – Nature Reviews Genetics

 

Pathogen research

Serial Clustering of Late Onset Group B Streptococcal Infections in the Neonatal Unit – a Genomic Re-Evaluation of Causality – Elita Jauneikaite – Clinical Infectious Diseases

A multi-omic analysis reveals the role of fumarate in regulating the virulence of enterohemorrhagic Escherichia coli – Cheng-Ju Kuo – Cell Death & Disease

Occurrence of blaNDM Variants Among Enterobacteriaceae From a Neonatal Intensive Care Unit in a Northern India Hospital – Nayeem Ahmad – Frontiers in Microbiology

 

Food Microbes

Lactobacillus rossiae strain isolated from sourdough produces putrescine from arginine – Beatriz del Rio – Scientific Reports

 

Environmental Microbiology

Microbial diversity associated to the anaerobic sediments of a soda lake (Mono Lake, CA) – Patricia Rojas – Canadian Journal of Microbiology

February 28, 2018

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Have a good Wednesday! After few days of inactivity, we bring this digest with several reviews from different aspects of microbiome research. We included also some papers about microbiota and antibiotic resistance, microbiota and metabolism, and more.

 

Human and General microbiome

Review: Microbiota and Metabolism — What’s New in 2018 – Alexis Bretin – American Journal of Physiology-Endocrinology and Metabolism

Review: Eicosanoids in the GI Tract – John L Wallace – British Journal of Pharmacology

Review: Gut : liver : brain axis: the microbial challenge in the hepatic encephalopathy – Andrea Mancini – Food and Function

Meeting update: faecal microbiota transplantation–bench, bedside, courtroom? – Nik Sheng Ding – . Frontline Gastroenterology

Mini-Review: Involvement of Corticotropin-Releasing Factor and Receptors in Immune Cells in Irritable Bowel Syndrome – Mahanand Chatoo – Frontiers in Endocrinology

Gut microbiome composition in lean patients with NASH is associated with liver damage independent of caloric intake: A prospective pilot study – S.M.B.Duarte – Nutrition, Metabolism and Cardiovascular Diseases

Study protocol: Antifibrotic and molecular aspects of rifaximin in alcoholic liver disease: study protocol for a randomized controlled trial – Bjørn Stæhr Madsen – Trials

Gut microbiota characterisation in obese patients before and after bariatric surgery – G. Campisciano – Beneficial Microbes

Effect of sodium fluoride on oral biofilm microbiota and enamel demineralization – Thomas Thurnheer – Archives of Oral Biology

Review: Human Gut Microbiota in Health and Alzheimer’s Disease – Leszek Szablewski –  Journal of Alzheimer’s Disease

Fecal microbiota profile in atopic asthmatic adult patients – A.M. Okba – European annals of allergy and clinical immunology

Cervicovaginal microbiota composition correlates with the acquisition of high-risk human papillomavirus types – Xiaojie Huang – International journal of cancer

Review: Dysbiosis of gut microbiota in promoting the development of colorectal cancer – Shaomin Zou – Gastroenterology Report

In Brief: Microbiome: Principles of microbiota engraftment – Andrea Du Toit – Nature Reviews Microbiology

Clearance of Carbapenem-resistant Enterobacteriaceae versus Vancomycin-resistant enterococci carriage after fecal microbiota transplant: a prospective comparative study – Aurélien Dinh – The Journal of Hospital Infection

Alterations of the human gut Methanobrevibacter smithii as a biomarker for inflammatory bowel diseases – Shaghayegh Baradaran Ghavami – Microbial Pathogenesis

Forum: Inadequate Production of H2 by Gut Microbiota and Parkinson Disease – Sergej M.Ostojic – Trends in endocrinology and metabolism

Review: Brain Feeding Circuits after Roux-en-Y Gastric Bypass – Mohammed K.Hankir – Trends in endocrinology and metabolism

Temporal variability of oral microbiota over 10 months and the implications for future epidemiologic studies – Emily Vogtmann – Cancer Epidemiology, Biomarkers & Prevention

Review: Psoriatic arthritis: tissue-directed inflammation? – Giacomo Cafaro – Clinical Rheumatology

 

Animal Microbiome

Intestine farnesoid X receptor agonist and the gut microbiota activate G-protein bile acid receptor-1 signaling to improve metabolism – Preeti Pathak – Hepatology

Primary murine mucosal response during cephalosporin-induced intestinal colonization by Enterococcus faecium – Antoni P. A. Hendrickx – MicrobiologyOpen

Respiratory Disease following Viral Lung Infection Alters the Murine Gut Microbiota – Helen T. Groves – Frontiers in Immunology

Tartary buckwheat protein prevented dyslipidemia in high-fat diet-fed mice associated with gut microbiota changes – Xiao-Li Zhou – Food and chemical toxicology

When Darwin’s Special Difficulty Promotes Diversification in Insects – Frederic Legendre – Systematic Biology

Commensal Microbes Induce Serum IgA Responses that Protect against Polymicrobial Sepsis – Joel R.Wilmore – Cell host and microbe

Brain-derived neurotrophic factor preserves intestinal mucosal barrier function and alters gut microbiota in mice – Chen Li – The Kaohsiung Journal of Medical Sciences

Microbiota-mediated modulation of organophosphate insecticide toxicity by species-dependent lactobacilli interactions in a Drosophila melanogaster insect model – Brendan A. Daisley – Applied And Environmental Microbiology

Assessing bacterial community dynamics across the gastrointestinal tract of dairy calves during pre-weaning development – Juliana Dias – Applied And Environmental Microbiology

Microbial community dynamics during rearing of black soldier fly larvae (Hermetia illucens) and its impact on exploitation potential – Jeroen De Smet – Applied And Environmental Microbiology

Microbiota promote secretory cell determination in the intestinal epithelium by modulating host Notch signaling – Joshua V. Troll – Development

Hypoglycemic and hypolipidemic effect of S-allyl-cysteine sulfoxide (alliin) in DIO mice – Baiqiang Zhai – Scientific Reports

 

Pathogen research

Immunization with intestinal microbiota-derived Staphylococcus aureus and Escherichia coli reduces bacteria-specific recolonization of the intestinal tract – Julio Adrián Garfias-López – Immunology Letters

Salmonella-mediated inflammation eliminates competitors for fructose-asparagine in the gut – Jikang Wu – Infection and immunity

Treatment of Clostridium difficile infection with a small molecule inhibitor of toxin UDP-glucose hydrolysis activity – Ilana L. Stroke – Antimicrobial agents and chemotherapy

Review: Treatment of recurrent Clostridium difficile colitis: a narrative review – Roy J Hopkins – Gastroenterology Report

Review: Pseudomonas syringae: what it takes to be a pathogen – Xiu-Fang Xin – Nature Reviews Microbiology

 

Food Microbiome

Review: Seafood spoilage microbiota and associated volatile organic compounds at different storage temperatures and packaging conditions – Olumide A.Odeyemi – International journal of food microbiology

 

Water Microbiome

A closer look at the antibiotic-resistant bacterial community found in urban wastewater treatment systems – Amir H. Tehrani – MicrobiologyOpen

 

Extremophiles

Transitory microbial habitat in the hyperarid Atacama Desert – Dirk Schulze-Makuch – PNAS

 

Other papers

Microbial diversity in biodeteriorated Greek historical documents dating back to the 19th and 20th century: A case study – Kiriaki Karakasidou – MicrobiologyOpen

A novel affordable reagent for room temperature storage and transport of fecal samples for metagenomic analyses – Mo Han – Microbiome

Identification of a highly active tannase enzyme from the oral pathogen Fusobacterium nucleatum subsp. polymorphum – Julen Tomás-Cortázar – Microbial Cell Factories

Effect of Bacillus subtilis C-3102 on loose stools in healthy volunteers – M. Hatanaka – Beneficial Microbes

In situ biomolecule production by bacteria; a synthetic biology approach to medicine – Yensi Flores Bueso – Journal of Controlled Release

February 23, 2018

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This Friday: A nice set of papers focused in pathogens such as Salmonella and C. difficile, several papers about soil/root microbiome and more…

Human Microbiome

Review: Skin microbiota and human 3D skin models – Franziska Rademacher – Experimental Dermatology

News and Views: Gut microbiota: Beyond metagenomics, metatranscriptomics illuminates microbiome functionality in IBD – Aonghus Lavelle – Nature Reviews Gastroenterology & Hepatology

Letter: Concomitant resolution through fecal microbiota transplantation of Clostridium difficile and OXA-48-producing Klebsiella pneumoniae –  Giovanni Bruno – Infectious Diseases

Oral cholera vaccination promotes homing of IgA+ memory B cells to the large intestine and the respiratory tract – M van Splunter – Mucosal Immunology

Review: Signalling from the periphery to the brain that regulates energy homeostasis – Ki-Suk Kim – Nature Reviews Neuroscience

Research Highlight: Colorectal cancer: Bacterial biofilms and toxins prompt a perfect storm for colon cancer – Iain Dickson – Nature Reviews Gastroenterology & Hepatology

Research Highlight: Metabolism: The small intestine — a new player in fructose metabolism – Ivone Leong – Nature Reviews Endocrinology

Akkermansia muciniphila-derived extracellular vesicles influence gut permeability through the regulation of tight junctions – Chaithanya Chelakkot – Experimental & Molecular Medicine

 

Animal Microbiome / Animal Experiments

Effects of a galacto-oligosaccharide-rich diet on fecal microbiota and metabolite profiles in mice – W. Cheng – Food and Function

Impact of oral fidaxomicin administration on the intestinal microbiota and susceptibility to Clostridium difficile colonization in mice – N. J. Ajami – Antimicrobial Agents and Chemotherapy

Interplay between gut microbiota and p66Shc affects obesity-associated insulin resistance – Stefano Ciciliot – The FASEB Journal

CD Obesity-Prone Rats, but not Obesity-Resistant Rats, Robustly Ferment Resistant Starch Without Increased Weight or Fat Accretion – Diana Obanda – Obesity

Dietary live yeast and increased water temperature influence the gut microbiota of rainbow trout – David Huyben – Journal of Applied Microbiology

Remodeling of the Candida glabrata cell wall in the gastrointestinal tract affects the gut microbiota and the immune response – Rogatien Charlet – Scientific Reports

Absence of receptor guanylyl cyclase C enhances ileal damage and reduces cytokine and antimicrobial peptide production during oral Salmonella Typhimurium infection – Shamik Majumdar – Infection and Immunity

Thermal regime and host clade, rather than geography, drive Symbiodinium and bacterial assemblages in the scleractinian coral Pocillopora damicornis sensu lato – Kelly Brener-Raffalli – Microbiome

Chitin Oligosaccharide Modulates Gut Microbiota and Attenuates High-Fat-Diet-Induced Metabolic Syndrome in Mice – Junping Zheng – Marine Drugs

Targeting the PXR–TLR4 signaling pathway to reduce intestinal inflammation in an experimental model of necrotizing enterocolitis – Kezhen Huang – Pediatric Research

Hypoglycemic and hypolipidemic effect of S-allyl-cysteine sulfoxide (alliin) in DIO mice – Baiqiang Zhai –  Scientific Reports

 

Human Pathogens

Clostridioides (Clostridium) difficile infection: current and alternative therapeutic strategies – Fernando Gil – Future Medicine

Emergence of an Extensively Drug-Resistant Salmonella enterica Serovar Typhi Clone Harboring a Promiscuous Plasmid Encoding Resistance to Fluoroquinolones and Third-Generation Cephalosporins – Elizabeth J. Klemm – mBio

Metronidazole-Loaded Polyethyleneimine and Chitosan-Based Liquid Crystalline System for Treatment of Staphylococcal Skin Infections – Francesca Damiani Victorelli –  Journal of Biomedical Nanotechnology

Cost-Effectiveness of Competing Treatment Strategies for Clostridium difficile Infection: A Systematic Review – Phuc Le – Infection Control & Hospital Epidemiology

 

Food Microbiome

Antibiotic Resistance Genetic Markers and Integrons in White Soft Cheese: Aspects of Clinical Resistome and Potentiality of Horizontal Gene Transfer –  Ana Caroline L. de Paula – Genes

Effect of the environment microbiota on the flavour of light-flavour Baijiu during spontaneous fermentation – Xiao-Na Pang – Scientific Reports

 

Plant and Environmental Microbiomes

Pseudomonas rhizophila S211, a New Plant Growth-Promoting Rhizobacterium with Potential in Pesticide-Bioremediation – Wafa Hassen – Frontiers in Microbiology

Indigenous Pseudomonas spp. Strains from the Olive (Olea europaea L.) Rhizosphere as Effective Biocontrol Agents against Verticillium dahliae: From the Host Roots to the Bacterial Genomes – Carmen Gómez-Lama Cabanás – Frontiers in Microbiology

Preprint: Network hubs in root-associated fungal metacommunities – Hirokazu Toju – BioRxiv

Preprint: Microbial Treatment of Soil Contaminated with Spent engine Oil / Biotreatment of Soil Contaminated with Spent Engine by Microorganisms – Abiodun A. Ayandele – BioRxiv

Bacterial Preferences for Specific Soil Particle Size Fractions Revealed by Community Analyses – Michael Hemkemeyer – Frontiers in Microbiology

Peatland Acidobacteria with a dissimilatory sulfur metabolism – Bela Hausmann – The ISME Journal

Systemic Homeostasis in Metabolome, Ionome, and Microbiome of Wild Yellowfin Goby in Estuarine Ecosystem – Feifei Wei – Scientific Reports

 

Microbes in General

Review: Ethanolamine Utilization in Bacteria – Karan Gautam Kavala – mBio

Review: The Genome-Scale Integrated Networks in Microorganisms – Tong Hao – Frontiers in Microbiology

 

January 31, 2018

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Today, research in prediabetes microbiome, bacteriophages in urinary microbiota, several reviews and a good number of papers focused in animal microbiome.

 

Human Microbiome

Review: Influence of functional food components on gut health – Murphy L.Y. Wan – Critical Reviews in Food Science and Nutrition

Review: Gut Microbiota and the Neuroendocrine System – Aitak Farzi – Neurotherapeutics

Laxative effect of repeated Daiokanzoto is attributable to decrease in aquaporin-3 expression in the colon – Risako Kon – Journal of Natural Medicines

Aberrant intestinal microbiota in individuals with prediabetes – Kristine H. Allin – Diabetologia

Perspective: The Potential for Topical Probiotic Treatment of Chronic Rhinosinusitis, a Personal Perspective – Anders U. Cervin – Frontiers in cellular and infection microbiology

The third tier in treatment: Attending to the growing connection between gut health and emotional well-being – Joseph Verdino – Health psychology open

Bifidobacteria and lactobacilli in the gut microbiome of children with non-alcoholic fatty liver disease: which strains act as health players? – Valerio Nobili – Archives of medical science

Kynurenic Acid: The Janus-Faced Role of an Immunomodulatory Tryptophan Metabolite and Its Link to Pathological Conditions – Elisa Wirthgen – Frontiers in immunology

Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis – Susana Matamouros – Proceedings of the National Academy of Sciences of the United States of America

Review: Gut as an emerging organ for the treatment of diabetes – Martin Haluzik – The Journal of endocrinology

Bacteriophages Of The Urinary Microbiome – Taylor Miller-Ensminger – Journal of bacteriology

Commensal microbiota modulate gene expression in the skin – Jacquelyn S. Meisel – Microbiome

Host genetic variation and its microbiome interactions within the Human Microbiome Project – Raivo Kolde – Genome medicine

 

Animal Microbiome

Comparison of Microbial Communities in Swine Manure at Various Temperatures and storage times – Joung-Soo Lim – Asian-Australasian journal of animal sciences

Effects of different dietary ratio of metabolizable glucose and metabolizable protein on growth performance, rumen fermentation, blood biochemical indices and ruminal microbiota of 8 to 10-month-old heifers – Jie Sun – Asian-Australasian journal of animal sciences

Effects of dietary fiber levels on cecal microbiota composition in geese – Yanpin Li – Asian-Australasian journal of animal sciences

Annotation of gut bacterial taxonomic and functional diversity in Spodoptera litura and Spilosoma obliqua – Kiran G. Bapatla – Journal of Basic Microbiology

Variations in diet cause alterations in microbiota and metabolites that follow changes in disease severity in a multiple sclerosis model – J.E. Libbey – Beneficial Microbes

Impact of beneficial bacteria supplementation on the gut microbiota, colony development and productivity of Apis mellifera L. – D. Alberoni – Beneficial Microbes

Gut microbiota modulates type I interferon and antibody-mediated immune responses in chickens infected with influenza virus subtype H9N2 – A. Yitbarek – Beneficial Microbes

Appropriate dose of Lactobacillus buchneri supplement improves intestinal microbiota and prevents diarrhoea in weaning Rex rabbits – Y. Zhou – Beneficial Microbes

The Inner Workings of the Outer Surface: Skin and Gill Microbiota as Indicators of Changing Gut Health in Yellowtail Kingfish – Thibault P. R. A. Legrand – Frontiers in microbiology

 

Plant/Soil Microbiome

Integrated multi-omic analysis of host-microbiota interactions in acute oak decline – Martin Broberg – Microbiome

Antibiotics Disturb the Microbiome and Increase the Incidence of Resistance Genes in the Gut of a Common Soil Collembolan – Dong Zhu – Environmental science & technology

 

Environmental Microbiome

Coordinated gene expression between Trichodesmium and its microbiome over day–night cycles in the North Pacific Subtropical Gyre – Kyle R Frischkorn – The ISME Journal

 

General Microbiome

Cross-regulatory circuit between AHR and microbiota – Jian Ji – Current Drug Metabolism

‘Massilimalia timonensis’ sp. nov., a new bacterium species isolated from human faeces after decontamination with alcohol – P. Afouda – New microbes and new infections

Taxonomy of anaerobic digestion microbiome reveals biases associated with the applied high throughput sequencing strategies – Stefano Campanaro – Scientific Reports

January 30, 2018

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Today, the exposome on acne, eukaryotes in gut microbiota and chronic fatigue, oral and intestinal microbiome comparison in colorectal cancer, several studies in pathogen research, a review about rhizobia and more!

 

Human Microbiome

Short-Term Overfeeding with Dairy Cream Does Not Modify Gut Permeability, the Fecal Microbiota, or Glucose Metabolism in Young Healthy Men – Beate Ott – The Journal of Nutrition

The influence of exposome on acne – Brigitte Dréno – Journal of the European Academy of Dermatology and Venereology

Geographical Distribution and Diversity of Gut Microbial NADH:Ubiquinone Oxidoreductase Sequence Associated with Alzheimer’s Disease – Elena Paley – Journal of Alzheimer’s Disease

Book review: Microbiota in health and disease: from pregnancy to childhood in Beneficial Microbes

Eukaryotes in the gut microbiota in myalgic encephalomyelitis/chronic fatigue syndrome – Alexandra H. Mandarano – PeerJ

Preliminary Comparison of Oral and Intestinal Human Microbiota in Patients with Colorectal Cancer: A Pilot Study – Edda Russo – Frontiers in Microbiology

Review: The Role of Skin and Orogenital Microbiota in Protective Immunity and Chronic Immune-Mediated Inflammatory Disease – Young Joon Park – Frontiers in Immunology

Short-Chain Fatty Acids Differentially Affect Intracellular Lipolysis in a Human White Adipocyte Model – Johan W. E. Jocken – Frontiers in Endocrinology

Year in Review: Cancer immunotherapy in 2017: The breakthrough of the microbiota – Guido Kroemer – Nature Reviews Immunology

 

Animal Microbiome

Sinus Microanatomy and Microbiota in a Rabbit Model of Rhinosinusitis – Do-Yeon Cho – Frontiers in Cellular and Infection Microbiology

EPSP of L. casei BL23 Protected against the Infection Caused by Aeromonas veronii via Enhancement of Immune Response in Zebrafish – Chubin Qin – Frontiers in Microbiology

Mosquito vector-associated microbiota: Metabarcoding bacteria and eukaryotic symbionts across habitat types in Thailand endemic for dengue and other arthropod-borne diseases – Panpim Thongsripong – Ecology and Evolution

Exogenous Fecal Microbiota Transplantation from Local Adult Pigs to Crossbred Newborn Piglets – Luansha Hu – Frontiers in Microbiology

Composition and Functional Specialists of the Gut Microbiota of Frogs Reflect Habitat Differences and Agricultural Activity – Bing-Hong Huang – Frontiers in Microbiology

Hydrogen-water ameliorates radiation-induced gastrointestinal toxicity via MyD88’s effects on the gut microbiota – Hui-wen Xiao – Experimental & Molecular Medicine

Bacillus licheniformis normalize the ileum microbiota of chickens infected with necrotic enteritis – Shuai Xu – Scientific Reports

 

Beneficial Bacteria and Compounds

Review: Potential interactions among phenolic compounds and probiotics for mutual boosting of their health-promoting properties and food functionalities – A review – Evandro Leite de Souza – Critical Reviews in Food Science and Nutrition

Review: Impact of Dietary Fiber Consumption on Insulin Resistance and the Prevention of Type 2 Diabetes – Martin O Weickert – The Journal of Nutrition

Traditional Herbal Medicine-Derived Sulforaphene LFS-01 Reverses Colitis in Mice by Selectively Altering the Gut Microbiota and Promoting Intestinal Gamma-Delta T Cells – Ming Li – Frontiers in Pharmacology

Antimicrobial activity of apple cider vinegar against Escherichia coli, Staphylococcus aureus and Candida albicans; downregulating cytokine and microbial protein expression – Darshna Yagnik – Scientific Reports

 

Food Microbiome

Assertiveness of meat-borne Lactococcus piscium strains and their potential for competitive exclusion of spoilage bacteria in situ and in vitro – Maik Hilgarth – Journal of Applied Microbiology

 

Pathogen Research

Editorial: Do tetracyclines have the potential to reduce the risk of Clostridium difficile infection? – Sahil Khanna – Expert Review of Anti-infective Therapy

Minireview: Immunological roulette: Luck or something more? Considering the connections between host and environment in TB – John E Pearl – Cellular and Molecular Immunology

Review: Applications for Bacteriophage Therapy during Pregnancy and the Perinatal Period – Lucy L. Furfaro – Frontiers in Microbiology

Antibiotic-Induced Pathobiont Dissemination Accelerates Mortality in Severe Experimental Pancreatitis – Fernanda S. Soares – Frontiers in Immunology

Molecular epidemiology and comparative genomics of Campylobacter concisus strains from saliva, faeces and gut mucosal biopsies in inflammatory bowel disease – Karina Frahm Kirk – Scientific Reports

Exploration of the role of the virulence factor ElrA during Enterococcus faecalis cell infection – Natalia Nunez – Scientific Reports

 

Environmental Microbiome

Review: Rhizobia: from saprophytes to endosymbionts – Philip Poole – Nature Reviews Microbiology

Suppression of the activity of arbuscular mycorrhizal fungi by the soil microbiota – Nanna B Svenningsen – The ISME Journal

 

Microbiology – Other

News and Analysis: Genome watch: Keeping tally in the microbiome – Alexandre Almeida – Nature Reviews Microbiology

 

Non-microbiology picks

A meta-analysis of the diagnostic sensitivity and clinical utility of genome sequencing, exome sequencing and chromosomal microarray in children with suspected genetic diseases – Michelle M Clark – BioRxiv