April 24, 2018

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

 

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April 11, 2018

In today’s digest, check among many interesting articles: the evolution within human microbiome by T.D. Lieberman,  unique microbial biodiversity residing in hadal trenches by L.M. Peoples, changes in community composition in coastal water following exposure to oil and oil dispersant by S.H. Doyle. While in news — a story about “microbial hitchhikers” in restroom hand dryers.

General microbiome

Seven Billion Microcosms: Evolution within Human Microbiomes – Tami D. Lieberman – mSystems

Using Cultivated Microbial Communities To Dissect Microbiome Assembly: Challenges, Limitations, and the Path Ahead – Benjamin E. Wolfe – mSystems

Understanding Microbiome Stability in a Changing World – Ashley Shade – mSystems

Horizontal gene transfer of Chlamydia: Novel insights from tree reconciliation –  Hyaekang Kim – PLOS One

New insight into the early stages of biofilm formation – Catherine R. Armbruster  – PNAS

Multicopy plasmids allow bacteria to escape from fitness trade-offs during evolutionary innovation – Jeronimo Rodriguez-Beltran – Nature Ecology & Evolution

Considering the Lives of Microbes in Microbial Communities – Elizabeth A. Shank – mSystems

Oral microbiome

Inflammatory Bacteriome and Oral Squamous Cell Carcinoma – M. Perera – Journal of Dental Research

Human gut microbiome

The cardiovascular macrophage: a missing link between gut microbiota and cardiovascular diseases? – X. Chen – European Review for Medical and Pharmacological Sciences

Can Diet Influence Our Health by Altering Intestinal Microbiota – Derived Fecal Metabolites? – Qiang Lyu – mSystems

Toward Personalized Control of Human Gut Bacterial Communities – Lawrence A. David – mSystems

Role of the Gut Microbiome in Vertebrate Evolution – Thomas J. Sharpton – mSystems

Dietary nutrition and gut microflora: A promising target for treating diseases – Ying Nie – Trends in Food Science & Technology

Reduction in hepatic secondary bile acids caused by short-term antibiotic-induced dysbiosis decreases mouse serum glucose and triglyceride levels – Takuya Kuno – Scientific Reports

A snapshot of gut microbiota of an adult urban population from Western region of India – Disha Tandon – PLOS One

Animal experiments 

Mice harboring pathobiont-free microbiota do not develop intestinal inflammation that normally results from an innate immune deficiency – Benoit Chassaing – PLOS One

Animal microbiome 

The cultivable autochthonous microbiota of the critically endangered Northern bald ibis (Geronticus eremita) – Joachim Spergser – PLOS One

Plant, root, and soil microbiome

Maize Phyllosphere Microbial Community Niche Development Across Stages of Host Leaf Growth – Heather C. Manching –  F1000 Research

Exploring the Potentiality of Novel Rhizospheric Bacterial Strains against the Rice Blast Fungus Magnaporthe oryzae – Narayanappa Amruta –  The Plant Pathology Journal

The sensitivity of soil enzymes, microorganisms and spring wheat to soil contamination with carfentrazone-ethyl – Monika Tomkiel – Journal of Environmental Science and Health, Part B

Water and extremophile microbiome 

Trophic-functional patterns of biofilm-dwelling ciliates at different water depths in coastal waters of the Yellow Sea, northern China – Mamun Abdullah Al – European Journal of Protistology

Vertically distinct microbial communities in the Mariana and Kermadec trenches – Logan M. Peoples – PLOS One

The redox-sensing protein Rex modulates ethanol production in Thermoanaerobacterium saccharolyticum – Tianyong Zheng – PLOS One

Subgroup characteristics of marine methane-oxidizing ANME-2 archaea and their syntrophic partners revealed by integrated multimodal analytical microscopy – Shawn E. McGlynn – Applied and Environmental Microbiology

Addressing Confounding Factors in Algal Phosphorus Limitation Experiments – Whitney S. Beck -bioRxiv

Effect of Siderophore on Iron Availability in a Diatom and a Dinoflagellate Species: Contrasting Response in Associated Bacteria – Nicolas Sanchez – Frontiers in Marine Science

Robust Mercury Methylation across Diverse Methanogenic Archaea – Cynthia C. Gilmour – mBio

Two Distinct Aerobic Methionine Salvage Pathways Generate Volatile Methanethiol in Rhodopseudomonas palustris – Anthony R. Miller – mBio

Trichodesmium physiological ecology and phosphate reduction in the western Tropical South Pacific – Kyle R. Frischkorn – Biogeosciences

Energy Gradients Structure Microbial Communities Across Sediment Horizons in Deep Marine Sediments of the South China Sea – Michael F. Graw- Frontiers in Microbiology

Rapid Formation of Microbe-Oil Aggregates and Changes in Community Composition in Coastal Surface Water Following Exposure to Oil and the Dispersant Corexit – Shawn M. Doyle – Frontiers in Microbiology

Understanding Diatom Cell Wall Silicification—Moving Forward – Mark Hildebrand – Frontiers in Marine Science

The hunt for the most-wanted chemolithoautotrophic spookmicrobes – Michiel H in ‘t Zandt – FEMS Microbiology Ecology

Biotechnology

Electron transport chains in organohalide-respiring bacteria and bioremediation implications – Shanquan Wang – Biotechnology Advances

Food microbiology

Listeria monocytogenes strains show large variations in competitive growth in mixed culture biofilms and suspensions with bacteria from food processing environments – Even Heir – International Journal of Food Microbiology

Review: Titanium dioxide (TiO2) photocatalysis technology for nonthermal inactivation of microorganisms in foods – Zhiwei Zhu – Trends in Food Science & Technology

The complexity of wine: clarifying the role of microorganisms – Sophie Tempère – Applied Microbiology and Biotechnology

Probiotics / prebiotics

The effect of Lactobacillus acidophilus and Lactobacillus casei on the in vitro bioaccessibility of flaxseed lignans (Linum usitatissimum L.) – O. Muñoz – Food & Function

The “Golden Age” of Probiotics: A Systematic Review and Meta-Analysis of Randomized and Observational Studies in Preterm Infants – Dermyshi E. – Neonatology

Phages and viruses

Screening of FDA-approved Drugs and Identification of Novel Lassa Virus Entry Inhibitors – Peilin Wang – bioRxiv

Reducing inherent biases introduced during DNA viral metagenome analyses of municipal wastewater – Nichole E. Brinkman – PLOS One

Sequence, genome organization, annotation and proteomics of the thermophilic, 47.7-kb Geobacillus stearothermophilus bacteriophage TP-84 and its classification in the new Tp84virus genus – Piotr M. Skowron – PLOS One

Bioinformatics

GMPR: A robust normalization method for zero-inflated count data with application to microbiome sequencing data – Li Chen – PeerJ

Techniques

Use of genomics to design a diagnostic assay to discriminate between Streptococcus pneumoniae and Streptococcus pseudopneumoniae – Matthew A. Croxen –  Microbial Genomics

Paraffin Embedding and Thin Sectioning of Microbial Colony Biofilms for Microscopic Analysis – William C. Cornell – Journal of Visualized Experiments (Jove)

Microbes in the news 

Bugs, microbes and death can inform the living

Gut bacteria keeps bears healthily obese

Restroom Hand Dryers Are Blowing Bacteria Everywhere

Survival strategy: How one enzyme helps bacteria recover from exposure to antibiotics

Oil-eating bacteria could clean up the next spill

 

April 3, 2018

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

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 29, 2018

Of special note today: gut microbiota species expressing orthologs of human Ro60 might be involved in triggering and sustaining chronic autoimmunity in lupus; The portal vein blood microbiome in patients with liver cirrhosis; A randomized clinical study suggests dietary promotion of short chain fatty acid producing gut microbes as an effective treatment for type 2 diabetes; and the sexual dimorphism of root, flower and leaf microbiomes in the wild strawberry plant

Events and jobs

Clinical Laboratory Technologist IV (SL-1), Microbiology Laboratory – Stony Brook University – NY

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General microbiome

Review: Discovering antibiotics from the global microbiome – Yick Chong Lam – Nature Microbiology

Pregnancy and early life

Review: Milk Glycans and Their Interaction with the Infant-Gut Microbiota – Nina Kirmiz – Annual Review of Food Science and Technology

Multi-site human microbiome

*Commensal orthologs of the human autoantigen Ro60 as triggers of autoimmunity in lupus – Teri M. Greiling – Science Translational Medicine

Human nearly-sterile sites

*Circulating microbiome in blood of different circulatory compartments – Robert Schierwagen – BMJ Blood

Human gut microbiome

*Gut bacteria selectively promoted by dietary fibers alleviate type 2 diabetes – Liping Zhao – Science

Review: Impact of dietary compounds on cancer-related gut microbiota and microRNA – Muhammad Shahid Riaz Rajoka – Applied Microbiology and Biotechnology

Review: Influence of Altered Gut Microbiota Composition on Aging and Aging-Related Diseases – Jeonghyun Choi – Journal of Lifestyle Medicine

Review: Gut microbiome modulates efficacy of immune checkpoint inhibitors
Ming Yi – Journal of Hematology & Oncology

Protocol: Wisconsin microbiome study, a cross-sectional investigation of dietary fibre, microbiome composition and antibiotic-resistant organisms: rationale and methods  – Shoshannah Eggers – BMJ Journal

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Animal experiments

MicroRNA-146a Deficiency Protects against Listeria monocytogenes Infection by Modulating the Gut Microbiota – Chong-Tao Du – International Journal of Molecular Sciences

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

Towards an Integrative Understanding of tRNA Aminoacylation–Diet–Host–Gut Microbiome Interactions in Neurodegeneration – Elena L. Paley – Nutrients

Resilience of small intestinal beneficial bacteria to the toxicity of soybean oil fatty acids – Sara C Di Rienzi – eLife

Animal microbiome

Assessment of microbiome changes after rumen transfaunation: implications on improving feed efficiency in beef cattle – Mi Zhou – BMC Microbiology

Seasonal and algal diet-driven patterns of the digestive microbiota of the European abalone Haliotis tuberculata, a generalist marine herbivore – Angélique Gobet – BMC Microbiology

Diverse laboratory colonies of Aedes aegypti harbor the same adult midgut bacterial microbiome – Laura B. Dickson – BMC Parasites & Vectors

Plant, root, and soil microbiome

*The effects of host species and sexual dimorphism differ among root, leaf and flower microbiomes of wild strawberries in situ – Na Wei – Scientific Reports

The potential of plant microbiota in reducing postharvest food loss – Franziska Buchholz – Microbial Biotechnology

Root microbiota shift in rice correlates with resident time in the field and developmental – Jingying Zhang – Science China Life Sciences

Microbial Ecology

Allometry and Ecology of the Bilaterian Gut Microbiome – Scott Sherrill-Mix – mBio

Preprint: Changes in the genetic requirements for microbial interactions with increasing community complexity – Manon Morin – bioRxiv

Built environment

Drinking water microbiome assembly induced by water stagnation – Fangqiong Ling – The ISME Journal

Food microbiology

Constraint-based modeling in microbial food biotechnology – Martin H. Rau – Biochemical Society Transactions

Characterization of microbial community structure and metabolic potential using Illumina MiSeq platform during the black garlic processing – Zhichang Qiu – Food Research International

Guidance on the characterisation of microorganisms used as feed additives or as production organisms – EFSA Panel on Additives and Products or Substances used in Animal Feed (FEEDAP) – EFSA Journal

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Probiotics / prebiotics

Probiotic treatment reduces the autistic-like excitation/inhibition imbalance in juvenile hamsters induced by orally administered propionic acid and clindamycin – Afaf El-Ansary – Metabolic Brain Disease

Review: A review of probiotic supplementation in healthy adults: helpful or hype? – Saman Khalesi – European Journal of Clinical Nutrition

Fecal Transplants

Effect of Vegan Fecal Microbiota Transplantation on Carnitine‐ and Choline‐Derived Trimethylamine‐N‐Oxide Production and Vascular Inflammation in Patients With Metabolic Syndrome – Loek P. Smits – Journal of the American Heart Association

Bioinformatics

Review: Exploring Linkages between Taxonomic and Functional Profiles of the Human Microbiome – Morgan G. I. Langille – mSystems

Techniques

Hybridization capture reveals microbial diversity missed using current profiling methods – Cyrielle Gasc – BMC Microbiology

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Microbes in the news

Just passing through: fungi not part of the gut – Fungus species don’t play a role in healthy human microbiomes – Andrew Masterson – Cosmos

Plants, fungi and bacteria work together to clean polluted land – Genetic analysis shows microbial interactions help fast-growing trees break down petrochemical pollutants in soil – Science Daily

Bacteria and Art

Art and biology students participate in creative collaboration – Sierra Guardiola – The Ithacan

 

March 28, 2018

The impact of the microbiota on bone marrow transplantation in mice, differences in phage infection efficiency in nearly identical hosts, bacterial diversity of Brazilian artisanal cheese.

Events and jobs

Research Associate in the Department of Twin Research and Genetic Epidemiology, School of Life Cours – King’s College London

Research Associate in Department of Twin Research_School of Life Course Sciences – King’s College London

General microbiome

Variations in the relative abundance of Wolbachia in the gut of Nasutitermes arborum across life stages and castes – Michel Diouf – FEMS Microbiology Letters

Pregnancy and early life

HIV-exposure, early life feeding practices and delivery mode impacts on faecal bacterial profiles in a South African birth cohort – Shantelle Claassen-Weitz – Scientific Reports

Human respiratory microbiome

Exacerbation induces a microbiota shift in sputa of COPD patients – Eric Jubinville – PLOS ONE

Human oral microbiome

Review: Insights into the human oral microbiome – Digvijay Verma – Archives of Microbiology

Pre-print: Characterization of the salivary microbiome in people with obesity – Yujia Wu – PeerJ

Review: The oral microbiota – a mechanistic role for systemic diseases – G Jia – British Dental Journal

Human gut microbiome

Differences in epidemiological features between ulcerative colitis and Crohn’s disease: the early life-programmed versus late dysbiosis hypothesis – Laurent Beaugerie – Medical Hypotheses

Analysis of changes in intestinal flora and intravascular inflammation and coronary heart disease in obese patients – Xv Li – Experimental and Therapeutic Medicine

Animal experiments

Nutritional Support from the Intestinal Microbiota Improves Hematopoietic Reconstitution after Bone Marrow Transplantation in Mice – Anna Staffas – Cell Host & Microbe

High salt intake increases plasma trimethylamine N-oxide (TMAO) concentration and produces gut dysbiosis in rats – Klaudia Bielinska – Nutrition

High salt diet exacerbates colitis in mice by decreasing Lactobacillus levels and butyrate production – Pedro M Miranda – Microbiome

The Pancreatic Cancer Microbiome Promotes Oncogenesis by Induction of Innate and Adaptive Immune Suppression – Smruti Pushalkar – Cancer Discovery

Predominant gut Lactobacillus murinus strain mediates anti-inflammaging effects in calorie-restricted mice – Fengwei Pan – Microbiome

Deletion of choline acetyltransferase in enteric neurons results in postnatal intestinal dysmotility and dysbiosis – Carl D Johnson – The FASEB Journal

At-hatch administration of probiotic to chickens can introduce beneficial changes in gut microbiota – Stephen Baldwin – PLOS ONE

Impact of parenteral antimicrobial administration on the structure and diversity of the fecal microbiota of growing pigs – Mohamed Zeineldin – Microbial Pathogenesis

Pre-print: Metabolic retroconversion of trimethylamine N-oxide and the gut microbiota – Lesley Hoyles – bioRxiv

Pre-print: Isolation of a natural DNA virus of Drosophila melanogaster, and characterisation of host resistance and immune responses – William H Palmer – bioRxiv

Proanthocyanidin‐Rich Grape Seed Extract Modulates Intestinal Microbiota in Ovariectomized Mice – Guangwen Jin – Journal of Food Science

Evaluation of the nutrition and function of cow and goat milk based on intestinal microbiota by metagenomic analysis – Zhaoxia Wang – Food & Function

Animal microbiome

Pre-print: Characterisation of gut microbiota of farmed Chinook salmon using metabarcoding – Milica Ciric – bioRxiv

Variation in the microbiome of the urogenital tract of Chlamydia-free female koalas (Phascolarctos cinereus) with and without ‘wet bottom’ – Alistair R Legione – PLOS ONE

Pre-print: Characterization of shifts of koala (Phascolarctos cinereus) intestinal microbial communities associated with antibiotic treatment – Katherine E Dahlhausen – PeerJ

Comparison of gizzard and intestinal microbiota of wild neotropical birds – M Alexandra García-Amado – PLOS ONE

Fecal microbiota in the female prairie vole (Microtus ochrogaster) – J Thomas Curtis – PLOS ONE

Disentangling factors that shape the gut microbiota in German Shepherd dogs – Åsa Vilson – PLOS ONE

Yeast culture dietary supplementation modulates gut microbiota, growth and biochemical parameters of grass carp – Han Liu – Microbial Biotechnology

Fecal Microbiota Transplantation in Gestating Sows and Neonatal Offspring Alters Lifetime Intestinal Microbiota and Growth in Offspring – Ursula M McCormack – mSystems

Plant, root, and soil microbiome

Tetracycline resistance genes are more prevalent in wet soils than in dry soils – Yijun Kang – Ecotoxicology and Environmental Safety

Functional diversity of ectomycorrhizal fungal communities is reduced by trace element contamination – Álvaro López-García – Soil Biology and Biochemistry

Long- and short-term effects of mercury pollution on the soil microbiome – Aline Frossard – Soil Biology and Biochemistry

Structure of surface polysaccharides from Aeromonas sp. AMG272, a plant-growth promoting rhizobacterium isolated from rice rhizosphere – Rocío Contreras Sánchez-Matamoros – Carbohydrate Research

Review: Sniffing bacterial volatile compounds for healthier plants – Rouhallah Sharifi – Current Opinion in Plant Biology

Arbuscular mycorrhizal fungi influence decomposition and the associated soil microbial community under different soil phosphorus availability – Jing Xu – Soil Biology and Biochemistry

Water and extremophile microbiome

Habitat filtering of bacterioplankton communities above polymetallic nodule fields and sediments in the Clarion-Clipperton zone of the Pacific Ocean – Markus V Lindh – Environmental Microbiology Reports

Microbial communities in seawater from an Arctic and a temperate Norwegian fjord and their potentials for biodegradation of chemically dispersed oil at low seawater temperatures – Deni Ribicic – Marine Pollution Bulletin

Built environment

Pre-print: Half-lives of PAHs and temporal microbiota changes in commonly used urban landscaping materials – Marja I Roslund – PeerJ

Food microbiology

Interspecies variation in biofilm-forming capacity of psychrotrophic bacterial isolates from Chinese raw milk – Lei Yuan – Food Control

Bacterial diversity of artisanal cheese from the Amazonian region of Brazil during the dry and rainy seasons – Mayra Carla de Freitas Martins – Food Research International

Probiotics/prebiotics

Salecan stabilizes the microstructure and improves the rheological performance of yogurt – Renjie Fu – Food Hydrocolloids

Probiotic Lactobacillus casei Zhang (LCZ) alleviates respiratory, gastrointestinal & RBC abnormality via immuno-modulatory, anti-inflammatory & anti-oxidative actions – Yan-Yan Hor – Journal of Functional Foods

Routine Supplementation of Lactobacillus rhamnosus GG and Risk of Necrotizing Enterocolitis in Very Low Birth Weight Infants – Andrea F Kane – The Journal of Pediatrics

Phages and viruses

Continued Need for Comprehensive Genetic and Phenotypic Characterization of Viruses: Benefits of Complementing Sequence Analyses with Functional Determinations – Aaron C Brault – The American Journal of Tropical Medicine and Hygiene

Detection of Hantaviruses and Arenaviruzses in three-toed jerboas from the Inner Mongolia Autonomous Region, China – Zhiqiang Wu – Emerging Microbes & Infections

Enteric Virome Sensing—Its Role in Intestinal Homeostasis and Immunity – Rebecca N Metzger – Viruses

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

Multiple mechanisms drive phage infection efficiency in nearly identical hosts – Cristina Howard-Verona – The ISME Journal

Early MinION™ nanopore single-molecule sequencing technology enables the characterization of hepatitis B virus genetic complexity in clinical samples – Virginie Sauvage – PLOS ONE

A metagenomic viral discovery approach identifies potential zoonotic and novel mammalian viruses in Neoromicia bats within South Africa – Marike Geldenhuys – PLOS ONE

Pre-print: Ecological and evolutionary consequences of viral plasticity – Melinda Choua – bioRxiv

Bioinformatics

Pre-print: Taxonomy annotation errors in 16S rRNA and fungal ITS sequence databases – Robert C Edgar – bioRxiv

Metabolomics

Analysis of paper foxing by newly available omics techniques – Justyna Szulc – International Biodeterioration & Biodegradation

Review: Targeting human urinary metabolome by LC–MS/MS: a review – Jose Rodríguez-Morató – Bioanalysis

GC-MS Based Metabolomics and NMR Spectroscopy Investigation of Food Intake Biomarkers for Milk and Cheese in Serum of Healthy Humans – Alessia Trimigno – Metabolites

Techniques

KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples – Jeremiah J Minich – mSystems

eDNA from roots: a robust tool for determining Phytophthora communities in natural ecosystems – Ihsanul Khaliq – FEMS Microbiology Ecology

A silica sands-based method for faithful analysis of microbial communities and DNA isolation from a wide range of species – Xia Liu – Preparative Biochemistry and Biotechnology

More microbes

Review: New therapeutics from Nature: The odd case of the bacterial cytotoxic necrotizing factor 1 – Zaira Maroccia – Biomedicine & Pharmacotherapy

Pre-print: An attenuated CRISPR-Cas system in Enterococcus faecalis permits DNA acquisition – Karthik Hullahalli – bioRxiv

Microbes in the news

Here’s Why Antibiotics May Give Viruses a Leg Up – Christopher Wanjek – Live Science

‘Nanobot’ viruses tag and round up bacteria in food and water – Carolyn Wilke – ScienceNews

Your rubber ducky is probably crawling with bacteria, scientists say – STAT

Newly discovered bacteria can break down biomass – Phys.Org

Microbes on the market

Biocodex funds microbiome research on link between diet, colon cancer, IBD – Healio

Rebiotix’s Lee Jones to Receive TRUST 2018 Courageous Women in Health Care Award – PR Newswire

March 26, 2018

Suggestions to read in today’s digest are: a review about microbiological methods applied in studies following the deepwater horizon oil spill by S.Zhang, a paper by W. Pootakham on dynamics of coral‐associated microbiomes during a thermal bleaching event and a paper by X. Jiang on a novel auxotrophic interaction among soil microbes. Enjoy!

Oral microbiome

Reduced salivary secretion contributes more to changes in the oral microbiome of patients with primary Sjögren’s syndrome than underlying disease – Taco A van der Meulen – Annals of the Rheumatic Diseases

Insights into the human oral microbiome – Digvijay Verma – Archives of Microbiology

Human gut microbiome

Plant sterols and human gut microbiota relationship: An in vitro colonic fermentation study – María Cuevas-Tena – Journal of Functional Foods

Fecal microbiome composition and stability in 4- to 8-year old children is associated with dietary patterns and nutrient intake  – Kirsten Berding – The Journal of Nutritional Biochemistry

Gut Microbiota Profiles in Treatment-naïve Children with Attention Deficit Hyperactivity Disorder – Hai-yin Jiang – Behavioural Brain Research

Vitamin D administration leads to a shift of the intestinal bacterial composition in Crohn’s Disease patients, but not in healthy controls – Holger Schäffler – Journal of Digestive Diseases

Review: The Impact of Klebsiella pneumoniae in Lower Gastrointestinal Tract Diseases – Christina Parvinder Kaur – Journal of Digestive Diseases

Differential immune responses and microbiota profiles in children with autism spectrum disorders and co-morbid gastrointestinal symptoms – Destanie R. Rose – Brain, Behavior, and Immunity

Methodology challenges in studying human gut microbiota – effects of collection, storage, DNA extraction and next generation sequencing technologies – Marina Panek – Scientific Reports

Microbial communities inhabiting the fairy ring of Floccularia luteovirens and isolation of potential mycorrhiza helper bacteria – Rui Xing – Journal of Basic Microbiology

Animal experiments 

Chitosan oligosaccharides improve the disturbance in glucose metabolism and reverse the dysbiosis of gut microbiota in diabetic mice – Junping Zheng – Carbohydrate Polymers

Comparative study of effects of assemblages AII and BIV of Giardia duodenalis on mucosa and microbiota of the small intestine in mice – Mariana Felgueira Pavanelli – Biomedicine & Pharmacotherapy

Lifelong calorie restriction affects indicators of colonic health in aging C57Bl/6J mice – Dieuwertje E.G. Kok – The Journal of Nutritional Biochemistry

Effects of oxidative stress induced by high dosage of dietary iron ingested on intestinal damage and caecal microbiota in Chinese Yellow broilers – Z. Y. Gou – Journal of Animal Physiology and Animal Nutrition

Animal microbiome 

Effects of short term lead exposure on gut microbiota and hepatic metabolism in adult zebrafish – Jizhou Xia – Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology

Effects of commercial dietary prebiotic and probiotic supplements on growth, innate immune responses, and intestinal microbiota and histology of Totoaba macdonaldi – Mayra L. González-Félix – Aquaculture

Plant, root, and soil microbiome

Phage particles harboring antibiotic resistance genes in fresh-cut vegetables and agricultural soil – Olatz Larrañaga – Environment International

The fruit microbiome: A new frontier for postharvest biocontrol and postharvest biology – Samir Droby – Postharvest Biology and Technology

Earthworms differentially modify the microbiome of arable soils varying in residue management – Xin Gong – Soil Biology and Biochemistry

Subterranean infestation by Holotrichia parallela larvae is associated with changes in the peanut (Arachis hypogaea L.) rhizosphere microbiome – Li-Li Geng – Microbiological Research

Microbial communities inhabiting the fairy ring of Floccularia luteovirens and isolation of potential mycorrhiza helper bacteria – Rui Xing – Journal of Basic Microbiology

Mycobiota of maize seeds revealed by rDNA‐ITS sequence analysis of samples with varying storage times – Hui – Qin Xing – Microbiology Open

Multiscale patterns and drivers of arbuscular mycorrhizal fungal communities in the roots and root‐associated soil of a wild perennial herb – Pil U. Rasmussen – New Phytologist

Impact of spatial organization on a novel auxotrophic interaction among soil microbes – Xue Jiang – The ISME Journal

Water and extremophile microbiome 

Nutrient enrichment during shrimp cultivation alters bacterioplankton assemblies and destroys community stability – Wen Yang – Ecotoxicology and Environmental Safety

Specific enrichment of hyperthermophilic electroactive Archaea from deep-sea hydrothermal vent on electrically conductive support – Guillaume Pillot – Bioresource Technology

Changes in microbial communities during volatile fatty acid production from cyanobacterial biomass harvested from a cyanobacterial bloom in a river – Hyun Uk Cho – Chemosphere

Emerging contaminants and nutrients synergistically affect the spread of class 1 integron-integrase (intI1) and sul1 genes within stable streambed bacterial communities – Jèssica Subirats – Water Research

Assessing the origin of bacteria in tap water and distribution system in an unchlorinated drinking water system by SourceTracker using microbial community fingerprints – Gang Liu – Water Research

Large buoyant particles dominated by cyanobacterial colonies harbor distinct bacterial communities from small suspended particles and free‐living bacteria in the water column – Limei Shi – Microbiology Open

Dynamics of coral‐associated microbiomes during a thermal bleaching event – Wirulda Pootakham – Microbiology Open

Effects of bottom-water hypoxia on sediment bacterial community composition in a seasonally hypoxic enclosed bay (Omura Bay, West Kyushu, Japan) – FEMS Microbiology Ecology

Review: A Retrospective Review of Microbiological Methods Applied in Studies Following the Deepwater Horizon Oil Spill – Shuangfei Zhang – Frontiers in Microbiology

Built environment

Sulfate-reducing mixed communities with the ability to generate bioelectricity and degrade textile diazo dye in microbial fuel cells – Waheed Miran – Journal of Hazardous Materials

Work scheme to isolate the different microorganisms found in hydrogen-producing reactors: A study of effectiveness by pyrosequencing analysis – Laura Fuentes  – Journal of Applied Microbiology

Effect of hydraulic retention time on microbial community structure in wastewater treatment electro-bioreactors – Nancy A. ElNaker – Microbiology Open

Food microbiology

Presence of Clostridium difficile in poultry and poultry meat in Egypt – Mostafa Y. Abdel-Glil – Anaerobe

Isolation and characterization of microorganisms and volatiles associated with Moroccan saffron during different processing treatments – Francesco Fancello – International Journal of Food Microbiology

Post-harvest processing decreases the richness of bacterial taxa in the phyllosphere of broccoli – Min-Soo Kim  – Journal of Applied Microbiology

Probiotics / prebiotics

Probiotic Lactobacillus casei Zhang (LCZ) alleviates respiratory, gastrointestinal & RBC abnormality via immuno-modulatory, anti-inflammatory & anti-oxidative actions – Yan-Yan Hor – Journal of Functional Foods

Complete genome sequence of Bifidobacterium choerinum FMB-1, a resistant starch-degrading bacterium – Dong-Hyun Jung – Journal of Biotechnology

Structural studies of the cell wall polysaccharide from Lactococcus lactis UC509.9 – Evgeny Vinogradov – Carbohydrate Research

Lactobacillus paracasei CNCM I-3689 reduces vancomycin-resistant Enterococcus persistence and promotes Bacteroidetes resilience in the gut following antibiotic challenge – Laureen Crouzet – Scientific Reports

Microbes in the news

 

 

This Hungry Bacteria Could Help Clean Up Heavy Metals And Greenhouse Gases