Category Archives: Human oral

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 22, 2018

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Events and jobs

Microbiology Adjunct Instructor – Diablo Valley College

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Pregnancy and early life

Review: Maternal Microbiota, Prepregnancy Weight, and Mode of Delivery
Intergenerational Transmission of Risk for Childhood Overweight and Obesity – Giulia Paolella – JAMA Pediatrics

 

Human ear, nose and throat microbiome

*A microbiome case-control study of recurrent acute otitis media identified potentially protective bacterial genera – Rachael Lappan – BMC Microbiology

The Tracheal Microbiota in Patients with a Tracheostomy Before, During, and After an Acute Respiratory Infection – Pérez-Losada, Marcos – The Pediatric Infectious Disease Journal

Human oral microbiome

Shift of microbial composition of peri-implantitis-associated oral biofilm as revealed by 16S rRNA gene cloning – Ali Al-Ahmad – Journal of Medical Microbiology

Human vaginal microbiome

Short- and long-term influence of the levonorgestrel-releasing intrauterine system (Mirena®) on vaginal microbiota and Candida – Gilbert Gerard Ghislain Donders – Journal of Medical Microbiology

Human gut microbiome

Transitional and temporal changes in the mucosal and submucosal intestinal microbiota in advanced Crohn’s disease of the terminal ileum – Rodrick J. Chiodini – Journal of Medical Microbiology

Gut microbiota trajectory in early life may predict development of celiac disease – Marta Olivares – BMC Microbiome

A comparison of the microbial community structure between inflamed and non-inflamed sites in patients with ulcerative colitis – Atsushi Hirano – Journal of Gastroenterology and Hepatology

The Impact of NOD2 Variants on Fecal Microbiota in Crohn’s Disease and Controls Without Gastrointestinal Disease – Nicholas A Kennedy – Inflammatory Bowel Diseases

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Animal experiments

Regulation of vitamin D metabolism following disruption of the microbiota using broad spectrum antibiotics – Stephanie A. Bora – The Journal of Nutritional Biochemistry

Soluble dietary fiber improves energy homeostasis in obese mice by remodeling the gut microbiota – Haiyuan Wang – Biochemical and Biophysical Research Communications

Lactobacillus and Bifidobacterium Ameliorate Memory and Learning Deficits and oxidative stress in Aβ (1-42) Injected Rats – Somayeh Athari Nik Azm – Applied Physiology, Nutrition, and Metabolism

*Chronic helminth infection perturbs the gut-brain axis, promotes neuropathology and alters behaviour – Paul R Giacomin – The Journal of Infectious Diseases

*Endometriosis induces gut microbiota alterations in mice – Ming Yuan – Human Reproduction

*Strain differences in the susceptibility to the gut–brain axis and neurobehavioural alterations induced by maternal immune activation in mice – Morais, Livia H – Behavioural Pharmacology

Specific synbiotics in early life protect against diet-induced obesity in adult mice
Mona Mischke – Diabetes, Obesity, and Metabolism

Transcriptomic and Proteomic Profiling Revealed High Proportions of Odorant Binding and Antimicrobial Defense Proteins in Olfactory Tissues of the House Mouse – Barbora Kuntová – Frontiers in Genetics

Lactobacillus accelerates ISCs regeneration to protect the integrity of intestinal mucosa through activation of STAT3 signaling pathway induced by LPLs secretion of IL-22 – Qihang Hou – Cell Death and Differentiation

Animal microbiome

Review: Gut barrier function: Effects of (antibiotic) growth promoters on key barrier components and associations with growth performance – Leon J Broom – Poultry Science

Fecal microbiota transplantation in puppies with canine parvovirus infection – Giorgio Q. Pereira – Journal of Veterinary Internal Medicine

Water and extremophile microbiome

Phylogeny and bioactivity of epiphytic Gram-positive bacteria isolated from three co-occurring antarctic macroalgae – Pamela Alvarado – Antonie van Leeuwenhoek

 

Resistome

The antibiotic resistome and microbiota landscape of refugees from Syria, Iraq and Afghanistan in Germany – Robert Häsler – BMC Microbiome

Transferable vancomycin resistance in clade B commensal-type Enterococcus faecium – François Lebreton – Journal of Antimicrobial Chemotherapy

 

Bioinformatics

Deciphering the trophic interaction between Akkermansia muciniphila and the butyrogenic gut commensal Anaerostipes caccae using a metatranscriptomic approach – Loo Wee Chia – Antonie van Leeuwenhoek

Biotechnology

*A 3D intestinal tissue model supports Clostridioides difficile germination, colonization, toxin production and epithelial damage – Lamyaa Shaban – Anaerobe

Design of synthetic bacterial communities for predictable plant phenotypes – Sur Herrera Paredes – PLOS Biology

Harnessing a Methane-Fueled, Sediment-Free Mixed Microbial Community for Utilization of Distributed Sources of Natural Gas – Jeffrey J. Marlow – Biotechnology and Bioengineering

Dissertation: Microbial Communities Involved in Carbon Monoxide and Syngas Conversion to Biofuels and Chemicals – Sofia Victoria Esquivel Elizondo – Arizona State University

 

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Microbes in the news

This Vibrant Bacteria Could Be Used to “Grow” Paint – Meilan Solly – Smithsonian

Bacteria-eaters to prevent food poisoning? Phages eliminate Yersinia from food – Science Daily

A ‘Grueling and Grotesque’ Biohacking Experiment – Kate McLean – The Atlantic

 

February 20, 2018

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In today’s digest you can read: about advantages of Atomic Force Microscopy in studying of oral microbiota in the paper by S. S. Salavadhi; about gut microbiome association with Type 1 diabetes in the paper by J.A. Mullaney; about influence of steroids on the gut microbiota in the review by M.J Tetel and about the ability of Synechococcus cyanobacteria to dynamically change their pigment content to match the ambient light color, in the paper by T. Grébert. These are of course just a few of many interesting articles today. Enjoy!

Events and jobs

MS graduate position: Amoeba microbiome, Conway, Arkansas, US

Research Fellow in Cell Biology – Microscopy, Warwick, UK

PhD Student, ROYAL NIOZ-TEXEL, Texel, the Netherlands

General microbiome

Review: A new piece in the microbiome puzzle – Lindsay J. Pike – Nature Reviews Microbiology

The importance of resolving biogeographic patterns of microbial microdiversity – Alexander B Chase – Microbiology Australia

Consistent changes in the taxonomic structure and functional attributes of bacterial communities during primary succession – Rüdiger Ortiz-Álvarez – the ISME Journal

Pregnancy and early life

Infant formulae supplemented with prebiotics: Are they better than unsupplemented formulae? An updated systematic review – Agata Skórka – British Journal of Nutrition

Early Dietary Patterns and Microbiota Development: Still a Way to Go from Descriptive Interactions to Health-Relevant Solutions – Patricia Iozzo – Frontiers in Nutrition

Roles of Birth Mode and Infant Gut Microbiota in Intergenerational Transmission of Overweight and Obesity From Mother to Offspring – Hein M. Tun – JAMA Pediatrics

Multi-site human microbiome

A blinded observational cohort study of the microbiological ecology associated with pyuria and overactive bladder symptoms – Kiren Gill – International Urogynecology Journal

Oral microbiome

Atomic force microscopy: A three-dimensional reconstructive tool of oral microbiota in gingivitis and periodontitis – Shyam Sunder Salavadhi – Journal of Indian Society of Periodontology

Human gut microbiome

Review: Steroids, stress and the gut microbiome-brain axis – M. J. Tetel – Journal of Neuroendocrinology

Alterations of the Gut Microbiota in Hashimoto’s Thyroiditis Patients – Zhao Fuya – Thyroid

Endospores and other lysis-resistant bacteria comprise a widely shared core community within the human microbiota – Sean Michael Kearney – bioRxiv

Alterations in Intestinal Microbiota Lead to Production of Interleukin 17 by Intrahepatic γδ T-cell Receptor-positive Cells and Pathogenesis of Cholestatic Liver Disease – Dana Tedesco – Gastroenterology

Type 1 diabetes susceptibility alleles are associated with distinct alterations in the gut microbiota – Jane A. Mullaney – BMC Microbiome

Animal experiments

Effect of Dietary Chestnut or Quebracho Tannin Supplementation on Microbial Community and Fatty Acid Profile in the Rumen of Dairy Ewes – Arianna Buccioni – BioMed Research International

Long-Term Treatment with Green Tea Polyphenols Modifies the Gut Microbiome of Female Sprague-Dawley Rats – Jincheng Wang – The Journal of Nutritional Biochemistry

Microbiota-Derived Indole Metabolites Promote Human and Murine Intestinal Homeostasis through Regulation of Interleukin-10 Receptor – Erica E. Alexeev – The Americn Journal of Pathology

Interrelations between the rumen microbiota and production, behavioral, rumen-fermentation, metabolic, and immunological attributes of dairy cows – M. Schären – Journal of Diary Science

Animal microbiome

Disentangling metabolic functions of bacteria in the honey bee gut – Lucie Kešnerová – PLOS One

Plant, root, and soil microbiome

Soil mixture composition alters Arabidopsis susceptibility to Pseudomonas syringae infection – Jana A. Hassan – Plant Direct

Taxonomic structure and function of seed-inhabiting bacterial microbiota from common reed (Phragmites australis) and narrowleaf cattail (Typha angustifolia L.) – Ting Gao – Archives of Microbiology

The soil microbiome — from metagenomics to metaphenomics – Janet K Jansson – Current Opinion in Microbiology

Exometabolomic profiling of bacterial strains cultivated using Arabidopsis root extract as the sole carbon source – Richard Paul Jacoby – Molecular Plant-Microbiome Interactions

A strain of Streptomyces sp. isolated from rhizospheric soil of Crataegus oxycantha producing Nalidixic acid, a synthetic antibiotic – Nidhi Arora – Journal of Applied Microbiology

High microbial diversity promotes soil ecosystem functioning – Pierre-Alain Maron – Applied and Environmental Microbiology

Water and extremophile microbiome 

Apportioning bacterial carbon source utilization in soil using 14C isotope analysis of FISH-targeted bacterial populations sorted by Fluorescence Activated Cell Sorting (FACS): 14C-FISH-FACS – Christos Gougoulias – Environmental Microbiology Reports

Insights into the fundamental physiology of the uncultured Fe-oxidizing bacterium Leptothrix ochracea – E. J. Fleming – Applied and Environmental Microbiology

Light color acclimation is a key process in the global ocean distribution of Synechococcus cyanobacteria – Théophile Grébert – PNAS

Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning – Zhili He – mBio

Iron and phosphorus deprivation induce sociality in the marine bloom-forming cyanobacterium Trichodesmium – Yael Tzubari – the ISME Journal

Cryptophyta as major bacterivores in freshwater summer plankton – Vesna Grujcic – the ISME Journal

Phages and viruses

The impact of bacteriophages on phyllosphere bacterial abundance and composition – Norma M. Morella – Molecular Ecology

Microbes in the news 

Guts and gory: vampire bats need bacteria to digest blood

Using mutant bacteria to study how changes in membrane proteins affect cell functions

February 19, 2018

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Events and jobs

Research Technician I – University at Buffalo

General microbiome

Non-antibiotic antimicrobial triclosan induces multiple antibiotic resistance through genetic mutation – Ji Lu, bioRxiv

Oncologists tap the microbiome in bid to improve immunotherapy outcomes – Asher Mullard, Nature Reviews Drug Discovery

Nasal microbiome

Establishment of the Nasal Microbiota in the first 18 Months of Life – Correlation with Early Onset Rhinitis and Wheezing – Le Duc Huy Ta, Journal of Allergy and Clinical Immunology

The nasal microbiome in chronic rhinosinusitis: analyzing the effects of atopy and bacterial functional pathways in 111 patients – Mahboobeh Mahdavinia, Journal of Allergy and Clinical Immunology

Pregnancy and early life

Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome – Daniela S. A. Goltsman, bioRxiv

Human vaginal microbiome

Microbiota changes impact on sexually transmitted infections and the development of pelvic inflammatory disease – Nathalie Loeper, Microbes and Infection

Human gut microbiome

Efficacy of Bifidobacterium breve Fermented Milk in Maintaining Remission of Ulcerative Colitis – Katsuyoshi Matsuoka, Digestive Diseases and Sciences

Comparison of Different Strategies for Providing Fecal Microbiota Transplantation to Treat Patients with Recurrent Clostridium difficile Infection in Two English Hospitals: A Review – Simon D. Goldenberg, Infectious Diseases and Therapy

Fecal Microbiota Transplant for Refractory Clostridium difficile Infection Interrupts 25-Year History of Recurrent Urinary Tract Infections – Tiffany Wang, Open Forum Infectious Diseases

Fecal microbiota transplantation for severe complicated C. difficile colitis in a patient with acquired immunodeficiency syndrome – P. Martínez-Ayala, Revista de Gastroenterología de México

Microbial Engraftment and Efficacy of Fecal Microbiota Transplant for Clostridium difficile Patients With and Without IBD – Robert P Hirten, bioRxiv

The impact of a helminth-modified microbiome on host immunity – Tara P. Brosschot &
Lisa A. Reynolds, Mucosal Immunology

Depression and obesity: evidence of shared biological mechanisms – Yuri Milaneschi, Molecular Psychiatry

Delayed gut microbiota development in high-risk for asthma infants is temporarily modifiable by Lactobacillus supplementation – Juliana Durack, Nature Communications

Roux-en-Y Gastric-Bypass and sleeve gastrectomy induces specific shifts of the gut microbiota without altering the metabolism of bile acids in the intestinal lumen – Henri Duboc, International Journal of Obesity

Effects of ewe’s milk yogurt (whole and semi-skimmed) and cow’s milk yogurt on inflammation markers and gut microbiota of subjects with borderline-high plasma cholesterol levels: a crossover study – Noemí Redondo, European Journal of Nutrition

Impact of food additives on the gut-brain axis – Mary K. Holder, Physiology & Behavior

Gut microbiota injury in allogeneic haematopoietic stem cell transplantation – Yusuke Shono, Nature Reviews Cancer

Microbiota: Pathobiont peacekeepers – Kirsty Minton, Nature Reviews Immunology

Gut Microbiomics—A Solution to Unloose the Gordian Knot of Biological Effects of Ionizing Radiation – Amy Zhang, Journal of Heredity

Oral microbiome

Host defense against oral microbiota by bone-damaging T cells – Masayuki Tsukasaki, Nature Communications

Beyond Streptococcus mutans: clinical implications of the evolving dental caries aetiological paradigms and its associated microbiome – N. Philip, BDJ

Animal experiments

The Divergence in Bacterial Components Associated with Bactrocera dorsalis across Developmental Stages – Xiaofeng Zhao, Frontiers in Microbiology

Microbiota in fermented feed and swine gut – Cheng Wang, Applied Microbiology and Biotechnology

Biogeographical Differences in the Influence of Maternal Microbial Sources on the Early Successional Development of the Bovine Neonatal Gastrointestinal tract – Carl J. Yeoman, Scientific Reports

Animal microbiome

Amphibian chytridiomycosis outbreak dynamics are linked with host skin bacterial community structure – Kieran A. Bates, Nature Communications

The effect of cadmium exposure on diversity of intestinal microbial community of Rana chensinensis tadpoles – Danyang Mu, Ecotoxicology and Environmental Safety

A new cell extraction method reveals hemolymph microbiome of three aquatic invertebrates – Xinxu Zhang, Applied Microbiology and Biotechnology

The gastrointestinal tract microbiota of northern white-cheeked gibbons (Nomascus leucogenys) varies with age and captive condition – Ting Jia, Scientific Reports

Plant, root, and soil microbiome

Manipulation of the rhizosphere microbial community through application of a new bio-organic fertilizer improves watermelon quality and health – Jia Zhao, PLOS One

Water and extremophile microbiome

Seasonal dynamics of tetracycline resistance gene transport in the Sumas River agricultural watershed of British Columbia, Canada – Patricia L. Keen, Science of The Total Environment

Microbial diversity and toxin risk in tropical freshwater reservoirs of Cape Verde – Ana Paula Semedo-Aguiar, bioRxiv

Common hydraulic fracturing fluid additives alter the structure and function of anaerobic microbial communities – Adam C. Mumford, Applied and Environmental Microbiology

Bacterial Community Shift and Coexisting/Coexcluding Patterns Revealed by Network Analysis in A Bioreduced Uranium Contaminated Site after Reoxidation – Bing Li, Applied and Environmental Microbiology

Properties of bacterial communities attached to artificial substrates in a hypereutrophic urban river – Xianlei Cai, AMB Express

Food microbiology

Nitrogen removal enhancement using lactic acid fermentation products from food waste as external carbon sources: performance and microbial communities – Jialing Tang, Bioresource Technology

Probiotics/Prebiotics

Advances in Probiotic Regulation of Bone and Mineral Metabolism – Laura R. McCabe, Calcified Tissue International

Prebiotics as functional food ingredients preventing diet-related diseases – A. Florowska, Food and Function

A prebiotic mixture improved Lactobacillus acidophilus and Bifidobacterium animalisgastrointestinal in vitro resistance in petit-suisse – Marina Padilha, Food and Function

Bioinformatics

SEED 2: a user-friendly platform for amplicon high-throughput sequencing data analyses – Tomáš Větrovský, Bioinformatics

Techniques

Use of Rectal Swab Samples for Analysis of the Intestinal Microbiome in Children – Nan Zhang, Chinese Medical Journal

February 18, 2018

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Quite a few articles with alerts from today and the day before. Many interesting articles on microbe/microbe and microbe-host interactions, enjoy!

Events and jobs
Senior Bioinformatician – Host Microbiota Interactions – Wellcome Trust Sanger Institute

Postdoctoral Fellow – ‘Microbiome of intestinal tract cancers’ – Centre for Molecular and Biomolecular Informatics (CMBI)

Department Chair – Department of Microbiology and Immunology – College of Veterinary Medicine Cornell University, Ithaca, New York

Associate Scientist- Microbiology – Aerotek, Los Angeles, CA

Multi-site human microbiome
Differential contributions of specimen types, culturing, and 16S – Lone Heimann Larsen – Journal Of Clinical Microbiology

Analysis of microbial sequences in plasma cell-free DNA for early-onset breast cancer patients and healthy females – Yu-Feng Huang – BMC Medical Genomics

Human oral microbiome
Bacterial microleakage at the abutment-implant interface, in vitro study. – Carlos Larrucea – Clinical Implant Dentistry And Related Research

Comparison of Oropharyngeal Microbiota from Children with Asthma and Cystic Fibrosis. – Sébastien Boutin – Mediators Of Inflammation

Human vaginal microbiome
Review: Cervicovaginal Microbiota and Reproductive Health: The Virtue of Simplicity. – Melis N Anahtar – Cell Host & Microbe

Human gut microbiome
The effect of Clostridium butyricum on symptoms and fecal microbiota in diarrhea-dominant irritable bowel syndrome: a randomized, double-blind, placebo-controlled trial. – Yi-Yuan Sun – Scientific Reports

Association of gut microbial communities with plasma lipopolysaccharide-binding protein (LBP) in premenopausal women – Jessica S Citronberg – ISME

Microbiota Accessible Carbohydrates Suppress Clostridium difficile in a Murine Model – Andrew J Hryckowian – bioRxiv

Review: Gut Microbiota-Based Therapies for Irritable Bowel Syndrome. – Emily K Stern – Clinical And Translational Gastroenterology

Review: A neuroscience perspective of the gut theory of Parkinson’s disease. – Lisa M Smith – The European Journal Of Neuroscience

Microbial-microbial/host interactions
Interactions between predation and disturbances shape prey communities. – Canan Karakoç – Scientific Reports

Elevated success of multispecies bacterial invasions impacts community composition during ecological succession. – Damian W Rivett – Ecology Letters

Competition in biofilms between cystic fibrosis isolates of Pseudomonas aeruginosa is driven by R-pyocins – Olubukola Oluyombo – bioRxiv

Linking associations of rare low-abundance species to their environments by association networks – Tatiana V. Karpinets – Frontiers in Microbiology

Genetic Ablation of Butyrate Utilization Attenuates Gastrointestinal Salmonella Disease. – Denise N Bronner – Cell Host & Microbe

Goblet cell associated antigen passages are inhibited during Salmonella typhimur/cium infection to prevent pathogen dissemination and limit responses to dietary antigens. – Devesha H Kulkarni – Mucosal Immunology

Animal experiments
Cytosolic and secreted peptidoglycan-degrading enzymes in Drosophila respectively control local and systemic immune responses to microbiota – Bernard Charroux – Cell Host & Microbe

Differences in the intestinal microbiota between uninfected piglets and piglets infected with porcine epidemic diarrhea virus. – Mei-Zhou Huang – Plos One

Rumen-protected methionine during the peripartal period in dairy cows and its effects on abundance of major species of ruminal bacteria. – Mohamed K Abdelmegeid – Journal Of Animal Science And Biotechnology

Impact of Chestnut and Quebracho Tannins on Rumen Microbiota of Bovines. – Juan María Díaz Carrasco – Biomed Research International

Starvation influences the microbiota assembly and expression of immunity-related genes in the intestine of grass carp (Ctenopharyngodon idellus) – Ngoc Tuan Tran – Aquaculture

Animal microbiome
The Dynamic Distribution of Small-Tail Han Sheep Microbiota across Different Intestinal Segments. – Hao Zhang – Frontiers In Microbiology

Microbiome assembly of avian eggshells and their potential as transgenerational carriers of maternal microbiota. – H Pieter J van Veelen – The Isme Journal

Plant, root, and soil microbiome
Photoautotrophic organisms control microbial abundance, diversity, and physiology in different types of biological soil crusts. – Stefanie Maier – The Isme Journal

Long-term use of cover crops and no-till shift soil microbial community life strategies in agricultural soil. – Radomir Schmidt – Plos One

Genome mining of Streptomyces scabrisporus NF3 reveals symbiotic features including genes related to plant interactions. – Corina Diana Ceapă – Plos One

Select and resequence reveals relative fitness of bacteria in symbiotic and free-living environments – Liana T. Burghardt – PNAS

Microbial Flora Associated with the Halophyte- – Fehmida Bibi – Frontiers In Microbiology

Root growth improvement of mesquite seedlings and bacterial rhizosphere and soil community changes are induced by inoculation with plant growth-promoting bacteria and promote restoration of eroded desert soil – Cristina Galaviz – Land Degradation and Development

Diversity of root-associated microbial populations of Tamarix parviflora cultivated under various conditions – Marketa Polivkova – Applied Soil Ecology

Succession of the functional microbial communities and the metabolic functions in maize straw composting process – Huawei Wei – Bioresource Technology

Rhizospheric microbial communities are driven by Panax ginseng at different growth stages and biocontrol bacteria alleviates replanting mortality – Linlin Dong – Acta Pharmaceutica Sinica B

Review: Soil protists: a fertile frontier in soil biology research. – Stefan Geisen – Fems Microbiology Reviews

Water and extremophile microbiome
Composition and Activity of Microbial Communities along the Redox Gradient of an Alkaline, Hypersaline, Lake. – Christian F Edwardson – Frontiers In Microbiology

Phosphorus Solubilizing and Releasing Bacteria Screening from the Rhizosphere in a Natural Wetland – Ying Cao – Water

Effects of water flow on submerged macrophyte-biofilm systems in constructed wetlands – Bing Han – Scientific Reports

Dispersal limitation and thermodynamic constraints govern spatial structure of permafrost microbial communities – Eric M Bottos – bioRxiv

Metagenomic exploration of soils microbial communities associated to Antarctic vascular plants – Marco A. Molina-Montenegro – PeerJ Preprints

Built environment
Liquid co-substrates repower sewage microbiomes – Justus Hardegen – bioRxiv

Investigating antibiotics, antibiotic resistance genes, and microbial contaminants in groundwater in relation to the proximity of urban areas – Edina Szekeres – Environmental Pollution

Influence of secondary water supply systems on microbial community structure and opportunistic pathogen gene markers – Huan Li – Water Research

Review: A review on the applications of microbial electrolysis cells in anaerobic digestion. – Zhengsheng Yu – Bioresource Technology

Probiotics / prebiotics / antibiotics
Tacrolimus concentration to dose ratio in solid organ transplant patients treated with fecal microbiota transplantation for recurrent Clostridium difficile infection. – Michael H Woodworth – Transplant Infectious Disease : An Official Journal Of The Transplantation Society

Techniques
Functional imaging of the interaction between gut microbiota and the human host: A proof-of-concept clinical study evaluating novel use for 18F-FDG PET-CT. – Ben Boursi – Plos One

A 3D intestinal tissue model supports Clostridioides difficile germination, colonization, toxin production and epithelial damage – Lamyaa Shaban – Anaerobe

How to isolate, identify and determine antimicrobial susceptibility of anaerobic bacteria in routine laboratories? – Elisabeth Nagy – Clinical Microbiology and Infection

Microbes in the news
A trip to ‘the poopy lab’ in the interest of drug development – Eric Boodman – STAT News

Probe provides rapid lung investigation – Pallab Ghosh – BBC News

February 14, 2018

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The role of saliva in structuring human oral bacterial communities, effects of permafrost thaw on methanogenic communities, and articles on the microbiomes of termites, burying beetles, honey bees, and mosquitoes.

Human oral microbiome

A spatial gradient of bacterial diversity in the human oral cavity shaped by salivary flow – Diana M Proctor – Nature Communications

Human vaginal microbiome

To ‘douche’ or not to ‘douche’: hygiene habits may have detrimental effects on vaginal microbiota – Erdogan Aslan – Journal of Obstetrics and Gynaecology

Human gut microbiome

Elevated circulating levels of succinate in human obesity are linked to specific gut microbiota – Carolina Serena – The ISME Journal

Infection and Microbiome: Impact of Tuberculosis on Human Gut Microbiome of Indian Cohort – Utkarsh Sood – Indian Journal of Microbiology

Comparative metaproteomics analysis shows altered fecal microbiota signatures in patients with major depressive disorder – Zhi Chen – NeuroReport

Animal experiments

Protective effect of Group B Streptococcus type-III polysaccharide conjugates against maternal colonization, ascending infection and neonatal transmission in rodent models – Emiliano Chiarot – Scientific Reports

Animal microbiome

Pre-print: Axenic Aedes aegypti develop without live bacteria, but exhibit delayed development and reduced oviposition – Maria A Correa – bioRxiv

Two novel strains of Torulaspora delbrueckii isolated from the honey bee gut microbiome and their use in honey fermentation – Joseph P Barry – bioRxiv

Gut microbiota in the burying beetle, Nicrophorus vespilloides, provide colonization resistance against larval bacterial pathogens – Yin Wang – Ecology and Evolution

Rampant Host Switching Shaped the Termite Gut Microbiome – Thomas Bourguignon – Current Biology

Plant, root, and soil microbiome

Melanization of mycorrhizal fungal necromass structures microbial decomposer communities – Christopher W Fernandez – Journal of Ecology

Fungal community shifts underpin declining mycelial production and turnover across a Pinus sylvestris chronosequence – Andreas Hagenbo – Journal of Ecology

Mycorrhizal symbioses influence the trophic structure of the Serengeti – Bo Maxwell Stevens – Journal of Ecology

The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome – M A Cregger – Microbiome

Water and extremophile microbiome

Pre-print: Transgenerational inheritance of shuffled symbiont communities in the coral Montipora digitata – Kate Quigley – bioRxiv

Shifts of methanogenic communities in response to permafrost thaw results in rising methane emissions and soil property changes – Shiping Wei – Extremophiles

Food microbiology

Dynamic correlations between microbiota succession and flavor development involved in the ripening of Kazak artisanal cheese – Xiaoji Zheng – Food Research International

Application of high-throughput pyrosequencing in the analysis of microbiota of food commodities procured from small and large retail outlets in a U.S. metropolitan area – A pilot study – Daleniece Higgins – Food Research International

Phages and viruses

The analysis of the oral DNA virome reveals which viruses are widespread and rare among healthy young adults in Valencia (Spain) – Vicente Pérez-Brocal – PLOS ONE

More microbes

Lactobacillus plantarum lipoteichoic acid inhibits biofilm formation of Streptococcus mutans – Ki Bum Ahn – PLOS ONE

Microbes in the news

In soil-dwelling bacteria, scientists find a new weapon to fight drug-resistant superbugs – Melissa Healy – Los Angeles Times

Interdisciplinary approach yields new insights into human evolution – Liz Entman – Vanderbilt University News

Viruses and Bacteria Travel Along a High-Altitude Superhighway – Dave Roos – Seeker

Science, career, and publishing

Pre-print: The impact on authors and editors of introducing Data Availability Statements at Nature journals – Rebecca Grant – bioRxiv

February 8, 2018

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Many interesting articles today: the geographical location of habitat has a stronger impact on the fecal microbiome of lemurs than sex, age, or species;  the mechanism for pathobiont-dependent inflammatory bowel disease involves microbiota reactive T cells; highly active antiretroviral therapy can restore gut microbiome diversity in AIDS patients; host immunity can interact with skin microbiota composition as shown in two species of giant salamander; the development of the small intestine microbiome in silka deer; and the gut microbiome of preterm infants that are breastfed develops normally.

Events and jobs

FEMS Project: Volunteer for the Opportunities Board Taskforce

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General microbiome

Can social partnerships influence the microbiome? Insights from ant farmers and their trophobiont mutualists – A. B. F. Ivens – Molecular Ecology

Pregnancy and early life

Maternal antibiotic exposure during pregnancy and hospitalization with infection in offspring: a population-based cohort study – Jessica Eden Miller – International Journal of Epidemiology

*Intestinal microbiota development and gestational age in preterm neonates – Katri Korpela – Scientific Reports

Human oral microbiome

Diversity analysis of subgingival microbial bacteria in peri-implantitis in Uygur population – Gao, Xiaowei MM – Medicine

Human vaginal microbiome

Commentary: The implausible “in vivo” role of hydrogen peroxide as an antimicrobial factor produced by vaginal microbiota – Gilda Tachedjian – Microbiome

Human gut microbiome

Microbiome–host systems interactions: Protective effects of propionate upon the blood–brain barrier – Lesley Hoyles – bioRxiv

*Alterations in the gut microbiota of patients with acquired immune deficiency syndrome – Youlian Zhou – Journal of Cellular and Molecular Medicine

Open-label pilot for treatment targeting gut dysbiosis in myalgic encephalomyelitis/chronic fatigue syndrome: neuropsychological symptoms and sex comparisons – Amy Wallis – Microbiome

Review: Diet and microbiota linked in health and disease  – T. Requena – Food And Function

Review: The role of gut microbiota and IL-23/IL-17 pathway in ankylosing spondylitis immunopathogenesis: New insights and updates – Farhad Babaie – Immunology Letters

Dissertation: Interaction of Cocoa Powder with Intestinal Microbiota – Zuyin Li – Louisiana State University


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Animal experiments

*c-MAF-dependent regulatory T cells mediate immunological tolerance to a gut pathobiont – Mo Xu – Nature

Dysregulated bile acid synthesis and dysbiosis are implicated in Western diet–induced systemic inflammation, microglial activation, and reduced neuroplasticity – Prasant Kumar Jena – The FASEB Journal

High-fat diet stimulates the gut pathogenic microbiota and maintains hepatic injury in antibiotic-treated rats – Sooad Al-Daihan – Cellular and Molecular Biology

Review: Searching for the gut microbial contributing factors to social behavior in rodent models – Brittany D. Needham – Developmental Neurobiology

Metatranscriptome Sequencing Reveals Insights into the Gene Expression and Functional Potential of Rumen Wall Bacteria – Evelyne Mann – Frontiers in Microbiology


Animal microbiome

*Occupancy strongly influences faecal microbial composition of wild lemurs – Alexander Umanets – FEMS Microbiology Ecology

*Influence of immunogenetics, sex, and body condition on the cutaneous microbial communities of two giant salamanders – Obed Hernández-Gómez – Molecular Ecology

Transient influence of blood meal and natural environment on blacklegged tick bacterial communities – Christine P. Zolnik – Tick and Tick-borne Diseases

The Development of Microbiota and Metabolome in Small Intestine of Sika Deer (Cervus nippon) from Birth to Weaning – Zhipeng Li – Frontiers in Microbiology

Exploring coral microbiome assemblages in the South China Sea – Lin Cai – Scientific Reports

Biogeographic Differences in the Microbiome and Pathobiome of the Coral Cladocora caespitosa in the Western Mediterranean Sea – Esther Rubio-Portillo – Frontiers in Microbiology

Survival and growth of Stenotrophomonas maltophilia in free-living amoebae (FLA) and bacterial virulence properties – Elodie Denet – PLOSone

Gut Microbiota Mediate Insecticide Resistance in the Diamondback Moth, Plutella xylostella (L.) – Xiaofeng Xia – Frontiers in Microbiology

Effects of predation stress and food ration on perch gut microbiota – Yinghua Zha – Microbiome

Longitudinal Effects of Supplemental Forage on the Honey Bee (Apis mellifera) Microbiota and Inter- and Intra-Colony Variability – Jason A. Rothman – Microbial Ecology


Plant, root, and soil microbiome

Spatial scale affects the relative role of stochasticity versus determinism in soil bacterial communities in wheat fields across the North China Plain – Yu Shi – Microbiome

Soil incubation studies with Cry1Ac protein indicate no adverse effect of Bt crops on soil microbial communities – Li Zhaolei – Ecotoxicology and Environmental Safety

The influence of cattle grazing on methane fluxes and engaged microbial communities in alpine forest soils – Mira Mutschlechner – FEMS Microbiology Ecology

Diversity and metabolic potential of the microbiota associated with a soil arthropod – Simon Bahrndorff – Scientific Reports

Soil pH rather than nutrients drive changes in microbial community following long-term fertilization in acidic Ultisols of southern China – Jia Liu – Journal of Soils and Sediments

Halotolerant microbial consortia able to degrade highly recalcitrant plant biomass substrate – Larisa Cortes-Tolalpa – Applied Microbiology and Biotechnology

Commentary: Putting concerns for caution into perspective: microbial plant protection products are safe to use in agriculture – Ben Lugtenberg – Journal of Plant Diseases and Protection

Review: Does genotypic and species diversity of mycorrhizal plants and fungi affect ecosystem function? – Christina Hazard – New Phytologist

Review: Putting concerns for caution into perspective: microbial plant protection products are safe to use in agriculture – Ben Lugtenberg – Journal of Plant Diseases and Protection


Water and extremophile microbiome

Ultra-rare marine microbes contribute to key sulfur related ecosystem functions – Dimitri Kalenitchenko – Molecular Ecology

Review: The microbial contribution to reactive oxygen species dynamics in marine ecosystems – Erik R. Zinser – Environmental Microbiology Reports

Application of metagenome analysis to characterize the molecular diversity and saxitoxin-producing potentials of a cyanobacterial community: a case study in the North Han River, Korea – Keon Hee Kim – Applied Biological Chemistry

Built environment

Airborne microbial communities in the atmospheric environment of urban hospitals in China – Xin-Lei Gao – Journal of Hazardous Materials


Food microbiology

Effects of chitosan oligosaccharides on microbiota composition of silver carp (Hypophthalmichthys molitrix) determined by culture-dependent and independent methods during chilled storage – Shiliang Jia – International Journal of Food Microbiology

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Probiotics / prebiotics

Lactobacillus plantarum AN1 cells increase caecal L. reuteri in an ICR mouse model of dextran sodium sulphate-induced inflammatory bowel disease – Yasushi Yokota – International Immunopharmacology

Lactobacillus salivarius LA307 and Lactobacillus rhamnosus LA305 attenuate skin inflammation in mice – S. Holowacz – Beneficial Microbes

Bifidobacteria and its rice fermented products on diet induced obese mice: analysis of physical status, serum profile and gene expressions – M. Ray – Beneficial Microbes

Lactobacillus rhamnosus GG Affects Microbiota and Suppresses Autophagy in the Intestines of Pigs Challenged with Salmonella Infantis – Wei Zhang – Frontiers in Microbiology

Probiotic Use in Equine Gastrointestinal Disease – Angelika Schoster – Veterinary Clinics: Equine Practice

Review: The Role of Prebiotics and Probiotics in Gastrointestinal Disease – Martin H. Floch – Gastroenterology Clinics

Effects of Bentonite Bgp35b-p on the Gut Microbiota of Mice Fed a High-Fat Diet – Eun-Sook Lee – Journal of the Science of Food and Agriculture

Feeding the developing brain: Juvenile rats fed diet rich in prebiotics and bioactive milk fractions exhibit reduced anxiety-related behavior and modified gene expression in emotion circuits – Agnieszka Mika – Neuroscience Letters

Biotechnology

Effects of voltage on sulfadiazine degradation and the response of sul genes and microbial communities in biofilm-electrode reactors – Xiao-Li Yang – Ecotoxicology and Environmental Safety

Waste and Pollution

Biodegradation of n-alkanes on oil–seawater interfaces at different temperatures and microbial communities associated with the degradation – Synnøve Lofthus – Biodegradation

Techniques

The application of rumen simulation technique (RUSITEC) for studying dynamics of the bacterial community and metabolome in rumen fluid and the effects of a challenge with Clostridium perfringens – Stefanie U. Wetzels – PLOSone

More bang for the buck? Can arbuscular mycorrhizal fungal communities be characterized adequately alongside other fungi using general fungal primers? – Ylva Lekberg – New Phytologist


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Microbes in the news

These Bacteria Digest Toxic Metals And Poop Out Tiny Gold Nuggets – Signe Dean – Science Alert

The discovery of a third form of flagella-mediated motility in symbiotic bacteria – Phys.org

Phage or foe? – In light of new evidence, we have to reassess the role of bacteriophages in microbial communities: are they always the enemy? – Lucía Fernández – npj Biofilms and Microbiomes

The effect of gut bacteria on bone health cannot be generalized – Randi Lundberg – Taconic

Here’s What You Need To Know About The Bacteria In Your Vagina
A microbiome doesn’t just exist in your gut – Sarah DiGiulio – Huffington Post

Understanding Microbial Communities Living On Amphibian Skin – Sofia Prado-Irwin – Science Trends

In the battle against cancer, microbes could be the answer – Nicola Davison – Wired


February 7, 2018

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Today we have many “gut microbiota” and “water microbiome” articles, as well as quite a few reviews in “Food microbiology” sector. One article (among many interesting today) I would like to highlight is the one from Guillaume Bernard and how unraveling the microbial dark matter should be identified as a central priority for biologists.

Jobs

Microbiology Technician -R&D, Lille, France

Consultant Medical Microbiologist, Birmingham, UK

Events

1st International Conference on Microbial Food and Feed Ingredients (MiFFI2018): 2-4 May 2018, Denmark

12th Vaccine Congress, Budapest, Hungary

General microbiome

Synergistic gold–copper detoxification at the core of gold biomineralisation in Cupriavidus metallidurans  – L. Bütof – Metallomics

The role of the type VI secretion system vgrG gene in the virulence and antimicrobial resistance of Acinetobacter baumannii ATCC 19606 – Jianfeng Wang – PLOS One

Genome-Based Characterization of Biological Processes That Differentiate Closely Related Bacteria – Marike Palmer – Frontiers in Microbiology

Microbial dark matter investigations: how microbial studies transform biological knowledge and empirically sketch a logic of scientific discovery – Guillaume Bernard – Genome Biology and Evolution

Draft genome sequence of Paenibacillus strain LK1, a phytohormone producing bacterium – Kun Liu – 3 Biotech

Pregnancy and early life

Review: Urinary tract infection during pregnancy: current concepts on a common multifaceted problem – Kallirhoe Kalinderi – Journal of Obstetrics and Gynaecology

Human respiratory microbiome

In children, the microbiota of the nasopharynx and brochoalveolar lavage fluid are both similar and different – Kirsten M. Kloepfer – Pediatric Pulmonology

At the Root: Defining and Halting Progression of Early Chronic Obstructive Pulmonary Disease – Fernando J. Martinez – American Journal of Respiratory and Critical Care Medicine

Oral microbiome

Transcriptome of healthy gingival tissue from edentulous sites in patients with a history of generalized aggressive periodontitis – Tiago Taiete – Journal of Periodontology

Evaluation of oxidative status in patients with chronic periodontitis and polycystic ovary syndrome: A cross-sectional study – Ebru Saglam – Journal of Periodontology

Selection of appropriate metagenome taxonomic classifiers for ancient microbiome research – Irina Marie Velsko – bioRxiv

Presence of the esp gene in Enterococcus faecium derived from oropharyngeal microbiota of haematology patients – Milica Jovanović – Archives of Oral Biology

Short-term microbiological effects of photodynamic therapy in non-surgical periodontal treatment of residual pockets: A split-mouth RCT – Mônica Grazieli Corrêa – Lasers in Surgery and Medicine

Human skin microbiome

Platelet activation and aggregation by the opportunistic pathogen Cutibacterium (Propionibacterium) acnes – Frida Petersson – PLOS One

Human vaginal microbiome

Dysbiosis of the Vaginal Microbiota and Higher Vaginal Kynurenine/Tryptophan Ratio Reveals an Association with Chlamydia trachomatis Genital Infections – Noa Ziklo – Frontiers in Celular & Infection Microbiology

Human gut microbiome

Report: Patients with familial adenomatous polyposis harbor colonic biofilms containing tumorigenic bacteria – Christine M. Deje – Science

Bacteroides fragilis Toxin Coordinates a Pro-carcinogenic Inflammatory Cascade via Targeting of Colonic Epithelial Cells – Liam Chung – Cell Host & Microbe

Longitudinal microbiome analysis of single donor fecal microbiota transplantation in patients with recurrent Clostridium difficile infection and/or ulcerative colitis – Michael Mintz – PLOS One

Infectious bursal disease virus infection leads to changes in the gut associated-lymphoid tissue and the microbiota composition – Li Li – PLOS One

Enterohemorrhagic Escherichia coli O157 subclade 8b strains in Chiba Prefecture, Japan, produced larger amounts of Shiga toxin 2 than strains in subclade 8a and other clades – Shinichiro Hirai – PLOS One

Gut microbiome and depression: what we know and what we need to know – Gal Winter – Reviews in the Neurosciences

Connection between BMI related plasma metabolite profile and gut microbiota – Filip Ottosson – The Journal of Clinical Endocrinology & Metabolism

Overview and systematic review of studies of microbiome in schizophrenia and bipolar disorder – Tanya T. Nguyen – Journal of Psychiatric Research

Maturation of the gut microbiome and risk of asthma in childhood – Jakob Stokholm – Nature Communications

Anaerobic 4-hydroxyproline utilization: discovery of a new glycyl radical enzyme in the human gut microbiome uncovers a widespread microbial metabolic activity – Yolanda Y. Huang – Gut Microbes

Micro Integral Membrane Protein (MIMP), a Newly Discovered Anti-Inflammatory Protein of Lactobacillus Plantarum, Enhances the Gut Barrier and Modulates Microbiota and Inflammatory Cytokines – Yin M. – Cellular Physiology and Biochemistry

Detection of stable community structures within gut microbiota co-occurrence networks from different human populations – Matthew A. Jackson – PeerJ

Animal experiments 

Comparative genomics reveals differences in mobile virulence genes of Escherichia coli O103 pathotypes of bovine fecal origin – Lance W. Noll – PLOS One

Shift of uterine microbiota associated with antibiotic treatment and cure of metritis in dairy cows – Soo Jin Jeon – Veterinary Microbiology

Microbiota-derived Metabolic Factors Reduce Campylobacteriosis in Mice  – Xiaolun Sun – Gastroenterology

Comprehensive Profiling of Fecal Metabolome of Mice by Integrated Chemical Isotope Labeling-Mass Spectrometry Analysis – Bi-Feng Yuan – Analitical Chemistry

Influence of a diet enriched with virgin olive oil or butter on mouse gut microbiota and its correlation to physiological and biochemical parameters related to metabolic syndrome – Isabel Prieto – PLOS One

Injectable antimicrobials in commercial feedlot cattle and their effect on the nasopharyngeal microbiota and antimicrobial resistance – Devin B.Holman – Veterinary Microbiology

IL-6-mediated signaling pathways limit Chlamydia muridarum infection and exacerbate its pathogenicity in the mouse genital tract  – Xin Sun – Microbes and Infection

Gut microbial composition can differentially regulate bile acid synthesis in humanized mice – Dae Joong Kang – Hepatology Communications

Gut Microbiota Offers Universal Biomarkers across Ethnicity in Inflammatory Bowel Disease Diagnosis and Infliximab Response Prediction – Youlian Zhou – mSystems

Intratumoral bacteria may elicit chemoresistance by metabolizing anticancer agents – Leore T. Geller – Molecular & Cellular Oncology

Interaction of genotype and diet on small intestine microbiota of Japanese quail fed a cholesterol enriched diet – Shasha Liu – Scientific Reports

Dietary supplementation with a nucleotide-rich yeast extract modulates gut immune response and microflora in weaned pigs in response to a sanitary challenge – S. M. Waititu – Animal

Animal microbiome 

Cellulose-dependent expression and antibacterial characteristics of surfactin from Bacillus subtilis HH2 isolated from the giant panda – Ziyao Zhou – PLOS One

Assessment of the gorilla gut virome in association with natural simian immunodeficiency virus infection – Mirela D’arc – BMC Retrovirology

Temperature variation, bacterial diversity and fungal infection dynamics in the amphibian skin – Ana V. Longo – Molecular Ecology

Plant, root, and soil microbiome

Effects of an EPSPS-transgenic soybean line ZUTS31 on root-associated bacterial communities during field growth – Gui-Hua Lu – PLOS One

Linking Nitrogen Load to the Structure and Function of Wetland Soil and Rhizosphere Microbial Communities – Eric R. Hester – mSystems

Abiotic Stresses Shift Belowground Populus-Associated Bacteria Toward a Core Stress Microbiome – Collin M. Timm – mSystems

Metagenomic and Metatranscriptomic Analyses of Diverse Watermelon Cultivars Reveal the Role of Fruit Associated Microbiome in Carbohydrate Metabolism and Ripening of Mature Fruits – Thangasamy Saminathan – Frontiers in Plant Science

Links between nanoscale and macroscale surface properties of natural root mucilage studied by atomic force microscopy and contact angle – Robin Kaltenbach – Journal of Colloid and Interface Science

Induced Salt Tolerance of Perennial Ryegrass by a Novel Bacterium Strain from the Rhizosphere of a Desert Shrub Haloxylon ammodendron – Ao-Lei He – International Journal of Molecular Science

Water and extremophile microbiome 

High growth potential and nitrogen removal performance of marine anammox bacteria in shrimp-aquaculture sediment – LuongVan Duc – Chemosphere

Establishment and convergence of photosynthetic microbial biomats in shallow unit process open-water wetlands – Zackary L.Jones – Water Research

Review: Bioactive compounds from marine macroalgae and their hypoglycemic benefits – ChaoZhao – Trends in Food Science & Technology

A Short Comparison of Two Marine Planktonic Diazotrophic Symbioses Highlights an Un-quantified Disparity – Andrea Caputo – Frontiers in Marine Science

Evidence for Coupling of the Carbon and Phosphorus Biogeochemical Cycles in Freshwater Microbial Communities – O. Roger Anderson – Frontiers in Marine Science

Spatiotemporal dynamics of river viruses, bacteria and microeukaryotes – Thea Van Rossum  – bioRxiv

Trace Metal Requirements and Interactions in Symbiodinium kawagutii – Irene B. Rodriguez – Frontiers in Microbiology

Depth-Resolved Variations of Cultivable Bacteria and Their Extracellular Enzymes in the Water Column of the New Britain Trench – Qianfeng Liu – Frontiers in Microbiology

Cyanophage-encoded lipid desaturases: oceanic distribution, diversity and function – Sheila Roitman – The ISME Journal

Picoplankton distribution influenced by thermohaline circulation in the southern Adriatic – Tina Šilović – Continental Shelf Research

Evaluation of the relationship of picoplankton and viruses to environmental variables in a lagoon system (Çakalburnu Lagoon, Turkey) – Yucel-Gier – Chemistry and Ecology

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

Distribution of bacterial communities along the spatial and environmental gradients from Bohai Sea to northern Yellow Sea – Shu-Xian Yu – PeerJ

Environmental Factors Support the Formation of Specific Bacterial Assemblages on Microplastics – Sonja Oberbeckmann – Frontiers in Microbiology

Abrupt changes in the composition and function of fungal communities along an environmental gradient in the high Arctic – Oriol Grau – Molecular Ecology

Built environment 

Effects of copper on the composition and diversity of microbial communities in laboratory-scale swine manure composting – Yanan Yin – Canadian Journal of Microbiology

Characteristics of microbial community functional structure of a biological coking wastewater treatment system – Dev Raj Josh – Journal of Environmental Sciences

Stripping Away the Soil: Plant Growth Promoting Microbiology Opportunities in Aquaponics – Ryan P. Bartelme – Frontiers in Microbiology

Food microbiology

Review: Recent advances in understanding the anti-obesity activity of anthocyanins and their biosynthesis in microorganisms – Lianghua Xie – Trends in Food Science & Technology

Review: Combining reformulation, active packaging and non-thermal post-packaging decontamination technologies to increase the microbiological quality and safety of cooked ready-to-eat meat products – Claudia N.Horita – Trends in Food Science & Technology

Review: Impact of curcumin nanoformulation on its antimicrobial activity – Anderson Clayton da Silva – Trends in Food Science & Technology

Review: Antimicrobial potential of legume extracts against foodborne pathogens: A review – M.C.Pina-Pérez – Trends in Food Science & Technology

Long-term kinetics of Salmonella Typhimurium ATCC 14028 survival on peanuts and peanut confectionery products – Maristela S. Nascimento – PLOS One

Impact of Lactobacillus curvatus 54M16 on microbiota composition and growth of Listeria monocytogenes in fermented sausages – Marina Giello – Food Microbiology

Effects of microbial diversity on nitrite concentration in pao cai, a naturally fermented cabbage product from China – Zhaoxia Wang – Food Microbiology

Bacterial and fungal microbiota of spontaneously fermented Chinese products, Rubing milk cake and Yan-cai vegetable pickles – Xin Liu – Food Microbiology

Omics-Based Insights into Flavor Development and Microbial Succession within Surface-Ripened Cheese – A. S. Bertuzzi – mSytems

Variation in Raw Milk Microbiota Throughout 12 Months and the Impact of Weather Conditions – Nan Li – Scientific Reports

Phages and viruses

The Human Virome – Selene Zárate – Archives of Medical Research

Microreview: Contractile injection systems of bacteriophages and related systems – Nicholas M.I. Taylor – Molecular Microbiology

In vitro models for deciphering the mechanisms underlying the sexual transmission of viruses at the mucosal level – Julie Frouard – Virology

Bioinformatics

xenoGI: reconstructing the history of genomic island insertions in clades of closely related bacteria – Eliot C. Bush – BMC Bioinformatics

Microbes in the news

Scientists say Earth’s atmosphere is raining viruses and bacteria down on the entire planet

Medicines from engineered bacteria offer promise — and pitfalls

Microbes on the market 

uBiome, the Leader in Microbial Genomics, Launches New Research Study Allowing SmartGut™ Patients to Assess the Impact of Diet and Lifestyle on Gut Conditions

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

January 26, 2018

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Here’s your daily Digest after a burst of articles. High-intensity swimming can impact immunity and microbial diversity in mice. Intestinal microbiota can alter host epigenetic in mice. A sad story of an eight year old boy killed by flesh eating bacteria…

Jobs and events

The Human Microbiome – Heidelberg, Germany

2018 MICROBIOME CONFERENCES – Taconic

General microbiology

Peptidoglycan compositional analysis of Enterococcus faecalis biofilm by stable isotope labeling by amino acids in bacterial culture – James D. Chang et al. – Biochemistry

Pregnancy and early life

Vaginal dysbiosis increases risk of preterm fetal membrane rupture, neonatal sepsis and is exacerbated by erythromycin – Richard G. Brown et al. – BMC Medicine

Human skin microbiome

* Review: Skin microbiota–host interactions – Y. Erin Chen et al. – Nature

Human vaginal microbiome

Probiotics in the Prevention and Treatment of Postmenopausal Vaginal Infections: Review Article – Jun-Mo Kim and Yoo Jin Park – Journal of Menopausal Medicine

Human oral microbiome

Silver Fluoride as a Treatment for Dental Caries – J.A. Horst – Advances in Dental Research

Therapeutic Strategies Targeting Cariogenic Biofilm Microenvironment – Y. Liu & Z. Ren et al. – Advances in Dental Research

Video protocol: Oral Biofilm Sampling for Microbiome Analysis in Healthy Children – Elisabeth Santigli et al. – JoVE

Human gut microbiome

Review: Clostridium difficile control measures: current and future methods for prevention – Erik R. Dubberke & Carlos Mejia-Chew – Expert Review of Anti-infective Therapy

Review: Colorectal Cancers: An Update on Their Molecular Pathology – Kentaro Inamura – Cancers

Review: Role of microbiota-derived lipopolysaccharide in adipose tissue inflammation, adipocyte size and pyroptosis during obesity – Lars-Georg Hersoug et al. – Nutrition Research Reviews

* Review: Role of priority effects in the early-life assembly of the gut microbiota – Daniel Sprockett et al. – Nature Reviews Gastroenterology & Hepatology

Review: Upper Respiratory Symptoms, Gut Health and Mucosal Immunity in Athletes – Candice Colbey et al. – Sports Medicine

Review: Microbiota in obesity: interactions with enteroendocrine, immune and central nervous systems – R. J. Mulders et al. – Obesity Reviews

Factors Associated with the Use of Fecal Microbiota Transplant in Patients with Recurrent Clostridium difficile Infections – Sehrish Jamot et al. – Infection Control & Hospital Epidemiology

Animal experiments

Zebrafish: Dysregulation of Intestinal Health by Environmental Pollutants: Involvement of the Estrogen Receptor and Aryl Hydrocarbon Receptor – Lianguo Chen et al. – Environmental Science & Technology

Probiotic/prebiotic correction for adverse effects of iron fortification on intestinal resistance to Salmonella infection in weaning mice – Feifei Lin et al. – Food & Function

Beneficial effects of consumption of acerola, cashew or guava processing by-products on intestinal health and lipid metabolism in dyslipidaemic female Wistar rats – Kamila Sabino Batista et al. – British Journal of Nutrition

Rat: Berberine Modulates Gut Microbiota and Reduces Insulin Resistance via the TLR4 Signaling Pathway – Dan Liu & Yiyi Zhang et al. – Experimental and Clinical Endocrinology & Diabetes

Early microbial colonization affects DNA methylation of genes related to intestinal immunity and metabolism in preterm pigs – Xiaoyu Pan et al. – DNA Research

Mouse: Innate and adaptive lymphocytes sequentially shape the gut microbiota and lipid metabolism – Kairui Mao et al. – Nature

* Influence of excessive exercise on immunity, metabolism and gut microbial diversity in an overtraining mice model – Xin Yuan et al. – Scandinavian Journal of Medicine & Science in Sports

* Mouse: An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression – Yufeng Qin et al. – Genome Biology

* Gut Microbiota-Derived Short Chain Fatty Acids Induce Circadian Clock Entrainment in Mouse Peripheral Tissue – Yu Tahara et al. – Scientific Reports

Time-course responses of ileal and fecal microbiota and metabolite profiles to antibiotics in cannulated pigs – Kan Gao et al. – Applied Microbiology and Biotechnology

Preprint: Toxoplasma gondii infection triggers chronic cachexia and sustained commensal dysbiosis in mice – Jessica A Hatter et al. – bioRxiv

Animal microbiome

Rapid and Specific Methods to Differentiate Foodborne Pathogens, Campylobacter jejuni, Campylobacter coli, and the New Species Causing Spotty Liver Disease in Chickens, Campylobacter hepaticus – Thi Thu Hao Van et al. – Foodborne Pathogens and Disease

Microbial community and short-chain fatty acid profile in gastrointestinal tract of goose – H Yang et al. – Poultry Science

Exploration of the faecal microbiota and biomarker discovery in equine grass sickness – Joy Leng et al. – Journal of Proteome Research

Plant, root and soil microbiome

Amendment of Agricultural Soil with Metal Nanoparticles: Effects on Soil Enzyme Activity and Microbial Community Composition – Bahareh Asadishad et al. – Environmental Science & Technology

Induction of abiotic stress tolerance in plants by endophytic microbes – Rusi Lata et al. – Letters in Applied Microbiology

Opinion piece: Plant pathogen effector proteins as manipulators of host microbiomes? – Nick C. Snelders et al. – Molecular Plant Pathology

Water and extremophile microbiome

Metabarcoding analysis on European coastal samples reveals new molecular metazoan diversity – David Lopez-Escardo et al. – bioRxiv

Food microbiome

Fungal networks shape dynamics of bacterial dispersal and community assembly in cheese rind microbiomes – Yuanchen Zhang et al. – Nature Communications

Phages and viruses

Distinct Effects of Type I and III Interferons on Enteric Viruses – Harshad Ingle et al. – Viruses

Technology

GC-MS Analysis of Short-Chain Fatty Acids in Feces, Cecum Content, and Blood Samples – Lisa R. Hoving et al. – Clinical Metabolomics

NMR Analysis of Fecal Samples – Hye Kyong Kim et al. – Clinical Metabolomics

Bioinformatics

Spherical: an iterative workflow for assembling metagenomic datasets – Thomas C. A. Hitch and Christopher J. Creevey – BMC Bioinformatics

Microbes in the news

Middle Eastern diet increases gut microbiota diversity, shows benefit in cirrhosis – Healio

Bacterial DNA sequencing could help design ‘friendlier’ nanoparticles – Belle Dumé – Nanotechweb

Consumption of Dietary Fiber May Prevent Metabolic Syndrome – Anamika P – TGHN

Researchers Discover 10 New Immune Systems in Bacteria – Jim Daley – The Scientist

New Ocean-Dwelling, Bacteria-Killing Tailless Virus Hid in Plain Sight – Mindy Weisberger – Live Science

New method developed to detect bacteria in food and water – Ananya Mandal – News Medical

eNose Successfully Recognizes Bacteria in Common Soft Tissue Infections – Michaela Fleming – Contagion Live

Are There Zombie Viruses In The Thawing Permafrost? – Michaeleen Doucleff – NPR

* ‘He was so strong’: Boy, 8, dies from flesh-eating bacteria – by Associated Press – New York Post

Publishing and education

Preprint: Harmonizing semantic annotations for computational models in biology – Maxwell L Neal et al. – bioRxiv