September 22, 2017

Human Microbiome

Microbiome profile of the amniotic fluid as a predictive biomarker of perinatal outcome – Daichi Urushiyama – Scientific Reports

Role of gut microbiota on cardio-metabolic parameters and immunity in coronary artery disease patients with and without type-2 diabetes mellitus – Lidia Sanchez-Alcoholado – Frontiers in Microbiology

Perspective: Linking the gut microbial ecosystem with the environment: does gut health depend on where we live? – Nishat Tasnim – Frontiers in Microbiology

Effect of caloric restriction on gut permeability, inflammation markers, and fecal microbiota in obese women – Beate Ott – Scientific Reports

Perspective: The immunology of the allergy epidemic and the hygiene hypothesis – Bart N Lambrecht – Nature Immunology

Pearls: The microbiome and the hallmarks of cancer – Laura E. Fulbright – PLoS Pathogens

Exploring the salivary microbiome of children stratified by the oral hygiene index – Izumi Mashima – PLoS ONE

 

Built Site Microbiome

Metagenomic characterization of ambulances across the USA – Niamh B. O’Hara – Microbiome (BMC)

 

Food Microbiome

Review: A Review on the Applications of Next Generation Sequencing Technologies as Applied to Food-Related Microbiome Studies – Yu Cao – Frontiers in Microbiology

Bottled aqua incognita: microbiota assembly and dissolved organic matter diversity in natural mineral waters – Celine C. Lesaulnier – Microbiome (BMC)

 

Pathogen Research

An engineered bispecific DNA-encoded IgG antibody protects against Pseudomonas aeruginosa in a pneumonia challenge model – Ami Patel – Nature Communications

Illusions regarding Helicobacter pylori clinical trials and treatment guidelines – David Y Graham – Gut (BMJ)

 

Beneficial Microbes

Akkermansia muciniphila May Determine the Ameliorating or Aggravating Effects of Chondroitin Sulfate on Osteoarthritis – Qing-Ping Zeng – Frontiers in Microbiology

Minireview: Next-Generation Beneficial Microbes: The Case of Akkermansia muciniphila – Patrice D. Cani – Frontiers in Microbiology

The PGPR Stenotrophomonas maltophilia SBP-9 augments resistance against biotic and abiotic stress in wheat plants – Prabhat N. Jha – Frontiers in Microbiology

 

Beneficial Molecules

pH-dependant antifungal activity of valproic acid against the human fungal pathogen Candida albicans – Julien Chaillot – Frontiers in Microbiology

Dietary teasaponin ameliorates alteration of gut microbiota and cognitive decline in diet-induced obese mice – Sen Wang – Scientific Reports

Mulberry leaf alleviates streptozotocin-induced diabetic rats by attenuating NEFA signaling and modulating intestinal microflora – Yao Sheng – Scientific Reports

 

Microbial Evolution

New Insights into the Diversity of the Genus Faecalibacterium – Leandro Benevides – Frontiers in Microbiology

 

Environmental Microbiology

Insights into microalga and bacteria interactions of selected phycosphere biofilms using metagenomic, transcriptomic and proteomic approaches – Ines Krohn-Molt – Frontiers in Microbiology

 

Bioinformatics, Genomics and Methodologies

Genomic GC-content affects the accuracy of 16S rRNA gene sequencing based microbial profiling due to PCR bias – Martin I. Bahl – Frontiers in Microbiology

Preprint: Optimizing scoring function of dynamic programming of pairwise profile alignment using derivative free neural network – Kazunori D. Yamada – BioRxiv

Improving contig binning of metagenomic data using dS2 oligonucleotide frequency dissimilarity – Ying Wang – BMC Bioinformatics

A Laboratory Methodology for Dual RNA-Sequencing of Bacteria and their Host Cells In Vitro – James W. Marsh – Frontiers in Microbiology

 

Other

Review: A review of the relationship between the gut microbiota and amino acid metabolism – Rui Lin – Amino Acids (Springer)

 

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September 21, 2017

Additional data and new analyses from the NIH Human Microbiome Project, understanding lambda phage integration in its effects on the host, a yeast fermentation method for use in wine making.

Pregnancy and early life

Pre-print: Genetic diversity and mother-child overlap of the gut associated microbiota determined by reduced genome sequencing – Anuradha Ravi – bioRxiv

Multi-site human microbiome

Strains, functions and dynamics in the expanded Human Microbiome Project – Jason Lloyd-Price – Nature

Phages and viruses

Combining Comprehensive Analysis of Off-Site Lambda Phage Integration with a CRISPR-Based Means of Characterizing Downstream Physiology – Yu Tanouchi – mBio

Techniques

The 16S rRNA gene-based PCR method used for the detection of segmented filamentous bacteria in the intestinal microbiota generates false-positive results – Forough L Nowrouzian – Acta Pathologica, Microbiologica, et Immunologica Scandinavica

Pre-print: Wine yeast phenomics: a standardized fermentation method for assessing quantitative traits of Saccharomyces cerevisiae strains in enological conditions – Emilien Peltier – bioRxiv

More microbes

Pre-print: Comprehensive analysis of central carbon metabolism reveals multiple connections between nutrients, biosynthetic capacity, and cell morphology in Escherichia coli – Corey S Westfall – bioRxiv

Microbes in the news

What’s the latest on gut microbiota? Concordia microbiology undergrads publish their findings – Phys.Org

Microbes on the market

Ixcela Launches Over-the-Counter Gut Health Test and Sophisticated Internal Wellness Program – Business Wire

Avadim Technologies Inc. Announces Partnership With Cardinal Health, Inc. – Market Wired

September 20, 2017

 

General microbiome

The human bitter taste receptor T2R38 is broadly tuned for bacterial compounds –  C Verbeurgt – PLoS One

Differential signal sensitivities can contribute to the stability of multispecies bacterial communities. – J Juhász – Biology Direct

Applying allometric theory to fungi – CA Aguilar-Trigueros – The ISME Journal

The Editorial on the Research Topic The Impact of Microorganisms on Consumption of Atmospheric Trace Gases – S Kolb – Frontiers in Microbiology

 

Human oral microbiome

Variations in oral microbiota associated with oral cancer. – H Zhao – Scientific Reports

Metabolic crosstalk regulates Porphyromonas gingivalis colonization and virulence during oral polymicrobial infection. – M Kuboniwa – Nature Microbiology

 

 

Human gut microbiome

Normalization of the microbiota in patients after treatment for colonic lesions – MA Sze – bioRxiv

Review: Modulation of the gut microbiome: a systematic review of the effect of bariatric surgery. – Y Guo – European Journal of Endocrinology

Urinary intermediates of tryptophan as indicators of the gut microbial metabolism. – T Pavlova – Analytica Chimica Acta

Recent urbanization in China is correlated with a Westernized microbiome encoding increased virulence and antibiotic resistance genes. – K Winglee – Microbiome

Continued Alcohol Misuse in Human Cirrhosis is Associated with An Impaired Gut-Liver Axis. – JS Bajaj – Alcoholism, Clinical and Experimental Research

Fructooligosaccharide (FOS) and Galactooligosaccharide (GOS) Increase Bifidobacterium but Reduce Butyrate Producing Bacteria with Adverse Glycemic Metabolism in healthy young population. – F Liu – Scientific Reports

 

Animal experiments 

Experimental colitis delays and reduces the severity of collagen-induced arthritis in mice – J Hablot – PLoS One

Identification of a mouse Lactobacillus johnsonii strain with deconjugase activity against the FXR antagonist T-β-MCA – M DiMarzio – PLoS One

The effect of age on the intestinal mucus thickness, microbiota composition and immunity in relation to sex in mice – M Elderman – PLoS One

Review:Role of the gastrointestinal microbiota in small animal health and disease. – A Redfern – The Veterinary Record

Gut Microbiota and IL-17A: Physiological and Pathological Responses. – B Douzandeh-Mobarrez – Probiotics and Antimicrobial Proteins

 

Animal microbiome 

The microbiota of water buffalo milk during mastitis – C Catozzi – PLoS One

What determines sclerobiont colonization on marine mollusk shells? – VO Agostini – PLoS One

Season, but not symbiont state, drives microbiome structure in the temperate coral Astrangia poculata. – KH Sharp – Microbiome

Metagenomic analysis of bacterial community structure and diversity of lignocellulolytic bacteria in Vietnamese native goat rumen. – HT Do – Asian-Australasian Journal of Animal Sciences

Comparative analysis of midgut bacterial communities in three aedine mosquito species from dengue-endemic and non-endemic areas of Rajasthan, India. – SS Charan – Medical and Veterinary Entomology

Microbiome of Pacific Whiteleg shrimp reveals differential bacterial community composition between Wild, Aquacultured and AHPND/EMS outbreak conditions. – F Cornejo-Granados – Scientific Reports

 

Plant, root, and soil microbiome

Evolution with a seed bank: the population genetic consequences of microbial dormancy – WR Shoemaker – bioRxiv

Longispora urticae sp. nov., isolated from rhizosphere soil of Urtica urens L., and emended descriptions of the species Longispora albida and Longisporafulva. – C Piao – International Journal of Systematic and Evolutionary Microbiology

Actinomycetes benefaction role in soil and plant health. – AA Bhatti – Microbial Pathogenesis

Environmental parameters altered by climate change affect the activity of soil microorganisms involved in bioremediation – I Alkorta – FEMS Microbiology Letters

Micropredator niche differentiation between bulk soil and rhizosphere of an agricultural soil depends on bacterial prey. – L Zhang – FEMS Microbiology Ecology

Soil microbial communities drive the resistance of ecosystem multifunctionality to global change in drylands across the globe. – M Delgado-Baquerizo  – Ecology Letters

Paenibacillus arcticus sp. nov., isolated from Arctic soil. – IT Cha – International Journal of Systematic and Evolutionary Microbiology

Mineral phosphorus fertilization modulates interactions between maize, rhizosphere yeasts and arbuscular mycorrhizal fungi – M Sarabia – Rhizosphere

Zinc Solubilizing Bacillus cereus and related species Modulates Growth, Yield and Zinc Biofortification of Soybean and Wheat Seeds Cultivated in Central India – R Khande – Rhizosphere

Utilisation of mucilage C by microbial communities under drought – MA Ahmed – Biology and Fertility of Soils

 

Built environment

Walker occupancy has an impact on changing airborne bacterial communities in an underground pedestrian space, as small-dust particles increased with raising both temperature and humidity – T Okubo – PLoS One

 

Food microbiology

Diversity and dynamics stability of bacterial community in traditional solid-state fermentation of Qishan vinegar – X Gan – Annals of Microbiology

 

Phages and viruses

Isolation and identification of enteroviruses from sewage and sewage-contaminated water samples from Ibadan, Nigeria, 2012-2013. – JA Adeniji – bioRxiv

The virome of Drosophila suzukii, an invasive pest of soft fruit – NC Medd – bioRxiv

Immune Loss as a Driver of Coexistence During Host-Phage Coevolution – JL Weissman – bioRxiv

 

Bioinformatics

Bioinformatics in the Netherlands: the value of a nationwide community  – CWG  van Gelder – Briefings in Bioinformatics

 

Techniques

Longitudinal multiparameter single-cell analysis of macaques immunized with pneumococcal protein-conjugated or unconjugated polysaccharide vaccines reveals distinct antigen specific memory B cell repertoires – B Lia – PLoS One

Methods matter: Influential purification and analysis parameters for intracellular parasite metabolomics – MA Carey – bioRxiv

COREMIC: a web-tool to search for a root-zone associated CORE MICrobiome – RR Rodrigues – bioRxiv

Quorum sensing improves current output with Acidithiobacillus ferrooxidans. – N Chabert – Microbial Biotechnology

Transcriptome analysis of Pseudostellaria heterophylla in response to the infection of pathogenic Fusarium oxysporum. – X Qin – BMC Plant Biology

Regulatory networks underlying mycorrhizal development delineated by genome-wide expression profiling and functional analysis of the transcription factor repertoire of the plant symbiotic fungus Laccaria bicolor. – Y Daquerre – BMC Genomics

 

Microbes in the news

Rocks, not bacteria, triggered Earth’s oxidation – Cosmos

The Table At Your Favorite Restaurant May Be Way Grosser Than You ThoughtThe Table At Your Favorite Restaurant May Be Way Grosser Than You Thought – Men’s Health

Researchers unlock potential pathway to treat flesh-eating bacteria – Phys.org

Revealed: The nasty infections you can pick up at the gym – and how to avoid deadly bacteria lingering on your workout gear  – Daily Mail Online

Flagship seeks $500M for sixth fund; unveils another microbiome firm – Fierce Biotech

CAN SPRAYING BACTERIA IN YOUR FACE ACTUALLY HAVE HEALTH BENEFITS? – CDA Press

Space-Grown Bacteria Could Pose Major Problems for Astronauts – Health Line

See jerkface bacteria hiding in tumors and gobbling chemotherapy drugs – Ars Technica

How BIOHM’s At Home Candida Test Is Giving Consumers Peace of Mind – Forbes

September 17, 2017

Sunday dose- lots of techniques and news on microbes!

Events and jobs

Senior Laboratory Technician (Microbiology) – Symbio Laboratories, Perth, Australia

Two Assistant Professor Positions: Microbiology (0709823) or Ecology (0709824) – School of Biological Sciences, Illinois State University in Normal, IL

 

General microbiome

Review: Seeing is understanding: Salmonella’s way to penetrate the intestinal epithelium – K Zhang – International Journal of Medical Microbiology

 

 

Human nearly-sterile sites 

Metabolomic findings in sepsis as a damage of host-microbial metabolism integration – NV Beloborodova – Journal of Critical Care

 

Human gut microbiome

Molecular estimation of alteration in intestinal microbial composition in Hashimoto’s thyroiditis patients – HM Ishaq – Biomedicine & Pharmacotherapy

Immune regulation by histamine and histamine-secreting bacteria – W Barcik – Current Opinion in Immunology

Comparison of gut microbiota in adult patients with type 2 diabetes and healthy individuals – M Sedhigi – Microbial Pathogenesis

Review: Do Bacteria Shape our Development? Crosstalk between Intestinal Microbiota and HPA Axis – C de Weerth – Neuroscience & Biobehavioral Reviews

Corrigendum: Corrigendum to “Bifidobacterium animalis subsp. lactis LKM512 reduces levels of intestinal trimethylamine produced by intestinal microbiota in healthy volunteers: A double-blind, placebo-controlled study” [J. Funct. Food 36 (2017) 94–101] – M Matsumoto – Journal of Functional Foods

 

Animal experiments

Sulfate-reducing bacteria stimulate gut immune responses and contribute to inflammation in experimental colitis – VR Figliuolo – Life Sciences

Dietary pomegranate extract and inulin affect gut microbiome differentially in mice fed an obesogenic diet – S Zhang – Anaerobe

Gut Microbe–Mediated Suppression of Inflammation-Associated Colon Carcinogenesis by Luminal Histamine Production – C Gao – The American Journal of Pathology

Food restriction followed by refeeding with a casein- or whey-based diet differentially affects the gut microbiota of pre-pubertal male rats – M Masarwi – The Journal of Nutritional Biochemistry

 

Animal microbiome 

Metarhizium brunneum – an enzootic wireworm disease and evidence for its suppression by bacterial symbionts – T Kabaluk – Journal of Invertebrate Pathology

 

Plant, root and soil microbiome

Biodiversity of soil bacteria exposed to sub-lethal concentrations of phosphonium-based ionic liquids: Effects of toxicity and biodegradation – M Sydow – Ecotoxicology and Environmental Safety

A metagenomic-based, cross-seasonal picture of fungal consortia associated with Italian soils subjected to different agricultural managements – S Panelli – Fungal Ecology

The importance of plants to development and maintenance of soil structure, microbial communities and ecosystem functions – FM Vezzani – Soil and Tillage Research

Distribution of apple and blackcurrant microbiota in Lithuania and the Czech Republic – I Vepštaitė-Monstavičė – Microbiological Research

 

Built environment 

Ecotoxicological and microbiological assessment of sewage sludge associated with sugarcane bagasse – LRD Sommaggio – Ecotoxicology and Environmental Safety

 

Food microbiology

Review: Seafood Pathogens and Information on Antimicrobial Resistance: A Review – S Elbashir – Food Microbiology

Microbial diversity on commercial eggs as affected by the production system. A first approach using PGM – C Neira – International Journal of Food Microbiology

 

 

Techniques

To engraft or not to engraft: an ecological framework for gut microbiome modulation with live microbes – J Walter – Current Opinion in Biotechnology

Review: Worms, Bugs and Drugs: C. elegans as a Model for Host-Microbe-Drug Interactions – AP García-González – Current Opinion in Systems Biology

Metagenomic Shotgun Sequencing and Unbiased Metabolomic Profiling Identify Specific Human Gut Microbiota and Metabolites Associated with Immune Checkpoint Therapy Efficacy in Melanoma Patients – AE Frankel – Neoplasia

A comparative study to evaluate natural attenuation, mycoaugmentation, phytoremediation, and microbial-assisted phytoremediation strategies for the bioremediation of an aged PAH-polluted soil – M García-Sánchez – Ecotoxicology and Environmental Safety

Aronia (Aronia melanocarpa) phenolics bioavailability in a combined in vitro digestion/Caco-2 cell model is structure and colon region dependent – J Wu – Journal of Functional Foods

Intermittent Fasting Promotes White Adipose Browning and Decreases Obesity by Shaping the Gut Microbiota – G Li – Cell Metabolism

High-throughput sequencing analysis reveals different Lactobacillus populations that dominate during “Chorizo de León” cured meat making – NM Quijada – Food Microbiology

Whole-genome Comparison of Urinary Pathogenic Escherichia coli and Faecal Isolates of UTI Patients and Healthy Controls – KL Nielsen – International Journal of Medical Microbiology

 

Microbes in the news

Swapping Spit: You Likely Share Your Roommate’s Microbiome, Even Without Kissing – Seeker

Microbiome in Ear May Play Role in Ear Infections – Contagion Live

Human Microbiome Market Size, Status and Forecast To 2025 – Med Gadget

Science spotlight: in-cosmetics Formulation Summit approaching – Cosmetics Design-Europe

JooMo launches new body-wash with skin bacteria tech – Cosmetics Design-Europe

Data from: Microbiome symbionts and diet diversity incur costs on the immune system of insect larvae – DRYAD

Legionella bacteria found in water at Ludlow Community Hospital – BBC News

Researchers take first steps towards development of biosensor for detection of bacteria – News Medical

 

September 15, 2017

Events and jobs

 
Assistant or Associate Professor – Microbiology/Infectious Disease, Farmington, US

 
General microbiome

 
Review: Human microbiota in aging and infection: A review – Elisavet Stavropoulou  – Critical Reviews in Food Science and Nutrition

 

Phylogeographic, genomic, and meropenem susceptibility analysis of Burkholderia ubonensis – Erin P. Price – PLOS

 
Pregnancy and early life

 
The relation between cesarean birth and child cognitive development – Cain Polidano – Scientific Reports

 

Simultaneously Monitoring Immune Response and Microbial Infections During Pregnancy through Plasma cfRNA Sequencing – Wenying Pan – Clinical Chemistry

 
Human respiratory microbiome

 
Oral microbiomeTooth Be Told, Genetics Influences Oral Microbiome – Emily R. Davenport – Cell Host & Microbe

 
Host Genetic Control of the Oral Microbiome in Health and Disease – Andres Gomez – Cell Host & Microbe

 

Human nearly-sterile sites 

 

Evaluation of the Bacterial Diversity in the Human Tongue Coating Based on Genus-Specific Primers for 16S rRNA Sequencing – Beili Sun – BioMed Research International

 

Review: Microbiota-Derived Uremic Retention Solutes: Perpetrators of Altered Nonrenal Drug Clearance in Kidney Disease – Alexander J. Prokopienko – Expert Review of Clinical Pharmacology

 

Human gut microbiome

 
Microbial metabolites as mimickers of human molecules – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

 
The intestinal microbiota regulates body composition through NFIL3 and the circadian clock – Yuhao Wang – Science

 
The Landscape of Type VI Secretion across Human Gut Microbiomes Reveals Its Role in Community Composition – Adrian J. Verster – Cell Host & Microbe

 
Butyrate-producing bacteria supplemented in vitro to Crohn’s disease patient microbiota increased butyrate production and enhanced intestinal epithelial barrier integrity – Annelies Geirnaert – Scientific Reports

 
Linking Spatial Structure and Community-Level Biotic Interactions through Cooccurrence and Time Series Modeling of the Human Intestinal Microbiota – Eric J. de Muinck –  mSystems
Review: Microbiota and neurodegenerative diseases – Moira Marizzonip – Current Opinion in Neurology

 
Effect of cytomegalovirus and Epstein–Barr virus replication on intestinal mucosal gene expression and microbiome composition of HIV-infected and uninfected individuals – Gianella Sara – AIDS

 
Systematic Review and Meta-analysis: Fecal Microbiota Transplantation for Treatment of Active Ulcerative Colitis – Narula Neeraj – Inflammatory Bowel Diseases

 
Signatures in the gut microbiota of Japanese infants who developed food allergies in early childhood – Masaru Tanaka – FEMS Microbiology Ecology

 
Quantity and source of dietary protein influence metabolite production by gut microbiota and rectal mucosa gene expression: a randomized, parallel, double-blind trial in overweight humans – Martin Beaumont – The American Journal of Clinical Nutrition
Analysis of Mucosa-Associated Microbiota in Colorectal Cancer – Kehan Xu – Medical Science Monitor

 
Animal experiments 

 
Short-term dietary methionine supplementation affects one-carbon metabolism and DNA methylation in the mouse gut and leads to altered microbiome profiles, barrier function, gene expression and histomorphology – Isabelle R. Miousse – Genes & Nutrition

 
Development of Inflammatory Bowel Disease Is Linked to a Longitudinal Restructuring of the Gut Metagenome in Mice – Thomas Sharpton – mSystems

 
Development of a Stable Lung Microbiome in Healthy Neonatal Mice – Matea Kostric – Microbial Ecology

 

Animal microbiome

 

Seasonal variation in nutrient utilization shapes gut microbiome structure and function in wild giant pandas – Qi Wu  – Proceedings of the Royal Society of London B

 
Plant, root, and soil microbiome

 
Soil microbial community responses to acid exposure and neutralization treatment – Doyun Shin – Journal of Environmental Management

 
Spatial patterns of hypolithic cyanobacterial diversity in Northern Australia –  Keith Christian – Ecology & Evolution

 

Food microbiology

 

Short-Term Intake of a Fructose-, Fat- and Cholesterol-Rich Diet Causes Hepatic Steatosis in Mice: Effect of Antibiotic Treatment – Annette Brandt – Nutrients

 
Overview of craft brewing specificities and potentially associated microbiota – Lindsey Rodhouse – Critical Reviews in Food Science and Nutrition

 

Probiotics / prebiotics
Isolation of probiotic piliated Lactobacillus rhamnosus strains from human faecal microbiota using SpaAantiserum-based colony immunoblotting – Zhen-quan Yang – Journal of Microbiology and Biotechnology

 

Phages and viruses
CRISPR-based Herd Immunity Limits Phage Epidemics in Bacterial Populations – Pavel Payne – bioRxiv

 
Bioinformatics
A comparison of sequencing platforms and bioinformatics pipelines for compositional analysis of the gut microbiome – Imane Allali – BMC Microbiology

 
Minimizing mixing intensity to improve the performance of rice straw anaerobic digestion via enhanced development of microbe-substrate aggregates – Moonkyung Kim – Bioresource Technology

 
Long term effects of cerium dioxide nanoparticles on the nitrogen removal, micro-environment and community dynamics of a sequencing batch biofilm reactor – Yi Xu – Bioresource Technology

 

Microbes in the news 
NIPGR scientists identify bacteria that can devour fungi

 
Are Genes to Blame for Cavity-causing Bacteria?

 
Microbes on the market (news about biotech companies)

 
Newly Launched CoreBiome Touts Microbiome ‘Profiling’ Services

 
Inventor converts waste plastics to fertilizer, fuel

 
Science, publishing, and career

 
The hundred most-cited publications in microbiota of diabetes research: A bibliometric analysis – Jiaxing Tian – Medicine

September 11, 2017

General microbiome

The evolutionary logic of sepsis – Lajos Rózsa, Infection, Genetics and Evolution

Pan-genome analysis of Bacillus for microbiome profiling – Yihwan Kim, Scientific Reports

Using CRISPR-Cas systems as antimicrobials – David Bikard, Current Opinion in Microbiology

Pregnancy and early life

The composition of the vaginal microbiome in first trimester pregnant women influences the level of autophagy and stress in vaginal epithelial cells – Dimitrios Nasioudis, Journal of Reproductive Immunology

Multi-site human microbiome

Veterinary antibiotics in food, drinking water, and the urine of preschool children in Hong Kong – Na Li, Environment International

Acne vulgaris patients have a distinct gut microbiota in comparison with healthy controls – Y. Deng, Journal of Investigative Dermatology

Immune mechanisms of food allergy and its prevention by early intervention – Victor Turcanu, Current Opinion in Immunology

Intestinal microbiome-gut-brain axis and irritable bowel syndrome – Moser G., Wiener Medizinische Wochenschrift

Human skin microbiome

Integrated metabolome-microbiome analyses to evaluate the alleviating effects of short-term green tea supplementation for UVB-induced erythema – E. Jung, Journal of Investigative Dermatology

Isomerization of urocanic acid by ultraviolet radiation and its role in modulation of skin microbiome, antimicrobial peptides, and immune function – V. Patra, Journal of Investigative Dermatology

Universal transcriptomic analysis of host-microbiome interactions in psoriasis – T. Furnholm, Journal of Investigative Dermatology

Skin microbiota alteration link to skin symptoms after a harsh cleanser – A.G. Gueniche, Journal of Investigative Dermatology

Forensic human identification using skin microbiomes – Sarah E. Schmedes, Applied Environmental Microbiology

Human gut microbiome

“Clostridium mediterraneense” a new bacterial species isolated from the human gut – Sokhna Ndongo, New Microbes and New Infections

Definition, Pathogenesis and Management of that cursed Dyspepsia – Pramoda Koduru, Clinical Gastroenterology and Hepatology

Gastrointestinal Conditions in the Female Athlete – Barry Kent Diduch, Clinics in Sports Medicine

Human oral microbiome

Location-Specific Oral Microbiome Possesses Features Associated with Chronic Kidney Disease – Jianzhong Hu, Kidney International Reports

The salivary microbiome is consistent between subjects and resistant to impacts of short-term hospitalization – Damien J. Cabral, Scientific Reports

Animal experiments

Effects of dietary fructooligosaccharide on the growth, antioxidants, immunity and disease resistance of Chinese mitten crab – Erteng Jia, Aquaculture

The microbiota influences cell death and microglial colonization in the perinatal mouse brain – Alexandra Castillo-Ruiz, Brain, Behavior, and Immunity

Differences in amino acid catabolism by gut microbes with/without prebiotics inclusion in GDDY-based diet affect feed utilization in rainbow trout – Omolola C. Betiku, Aquaculture

Effects of organic acids and essential oils blend on growth, gut microbiota, immune response and disease resistance of Pacific white shrimp (Litopenaeus vannamei) against Vibrio parahaemolyticus – Wangquan He, Fish & Shellfish Immunology

Imazalil exposure induces gut microbiota dysbiosis and hepatic metabolism disorder in zebrafish – Cuiyuan Jin, Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology

Local immune response of two mucosal surfaces of the European seabass, Dicentrarchus labrax, fed tryptophan- or methionine-supplemented diets – R. Azeredo, Fish & Shellfish Immunology

Segment specific responses of intestinal epithelium transcriptome to in-feed antibiotics in pigs – Kaifan Yu, Physiological Genomics

Animal microbiome

Inside the guts of the city: Urban-induced alterations of the gut microbiota in a wild passerine – Aimeric Teyssier, Science of The Total Environment

Bacterial microbiota associated with Rhipicephalus sanguineus(s.l.) ticks from France, Senegal and Arizona – Magalie René-Martellet, Parasites & Vectors

Introduced ascidians harbor highly diverse and host-specific symbiotic microbial assemblages – James S. Evans, Scientific Reports

The interactions between gut microbiota and entomopathogenic fungi: a potential approach for biological control of Blattella germanica (L.) – Fan Zhang, Pest Management Science

Plant, root, and soil microbiome

Volatiles of roots of wild-growing and cultivated Armoracia macrocarpa and their antimicrobial activity, in comparison to horseradish, A. rusticana – Silvana Petrović, Industrial Crops and Products

Rhizospheric metagenome of the terrestrial mangrove fern Acrostichum from Indian Sunderbans – Sayak Ganguli, Genomics Data

Paddy soil microbial communities driven by environment- and microbe-microbe interactions: A case study of elevation-resolved microbial communities in a rice terrace – Weimin Sun, Science of The Total Environment

Identifying the active microbiome associated with roots and rhizosphere soil of oilseed rape – Konstantia Gkarmiri, Applied Environmental Microbiology

Effect of Extracellular Electron Shuttles on Arsenic-Mobilizing Activities in Soil Microbial Communities – Shigeki Yamamura, Journal of Hazardous Materials

Water and extremophile microbiome

Microbiological studies of hot springs in India: a review – Poddar A., Archives of Microbiology

Impact of pyrene and cadmium co-contamination on prokaryotic community in coastal sediment microcosms – Qifang Ding, Chemosphere

Food microbiology

Analysis of bacterial and fungal communities in Marcha and Thiat, traditionally prepared amylolytic starters of India – Shankar Prasad Sha, Scientific Reports

Probiotics / prebiotics

Passion fruit by-product and fructooligosaccharides stimulate the growth and folate production by starter and probiotic cultures in fermented soymilk – Marcela Albuquerque Cavalcanti Albuquerque, International Journal of Food Microbiology

Gut microbiota alterations from different Lactobacillus probiotic-fermented yoghurt treatments in slow-transit constipation – Chen-Jian Liu, Journal of Functional Foods

Microbes in the news

Scientists to Study Health of Plant-Bacteria Symbiosis in California –  Iqbal Pittalwala, UCR Today

Sugars in breast milk may fight harmful bacteria directly – Laura Sanders, Science News

Atopic dermatitis associated with different bacteria depending on disease severity – Andrew Bowser, Dermatology Times

Park Service using lasers to remove Jefferson Memorial’s grimy coating – Jack Moore, WTOP

Startups focus on the microbiome as an organic solution to increase crop yields – Jonathan Shieber, Tech Crunch

September 5, 2017

Jobs

Postdoctoral fellow in genomics of uncultured microbial parasites (SciLifeLab, Sweden) via Science Careers

Call for Assistant Professors and Professors (IST Austria, including for Life Sciences) via Science Careers

 

Human Microbiome

Characterization of cervico-vaginal microbiota in women developing persistent high-risk Human Papillomavirus infection – Monica Di Paola – Scientific Reports

Collection of non-meconium stool on fecal occult blood cards is an effective method for fecal microbiota studies in infants – Wendy S.W. Wong – Microbiome (BMC)

Influence of Pregnancy History on the Vaginal Microbiome of Pregnant Women in their First Trimester – Dimitrios Nasioudis – Scientific Reports

Gut microbiome in ADHD and its relation to neural reward anticipation – Esther Aarts – PLoS ONE

A cross-sectional comparative study of gut bacterial community of Indian and Finnish children – Shreyas V. Kumbhare – Scientific Reports

Dysbiosis contributes to chronic constipation development via regulation of serotonin transporter in the intestine – Hailong Cao – Scientific Reports

Review article: the human intestinal virome in health and disease – S. R. Carding – Alimentary Pharmacology and Therapeutics

Review: Organ-specific protection mediated by cooperation between vascular and epithelial barriers – Ilaria Spadoni – Nature Reviews Immunology

Review: Microbiota of chronic diabetic wounds: ecology, impact and potential for innovative healing strategies – Sonia Gonçalves Pereira – Frontiers in Microbiology

Animal Microbiome

Comparative Analysis of the Gut Microbiota Composition between Captive and Wild Forest Musk Deer – Yimeng Li – Frontiers in Microbiology

High-fat diet increases pain behaviors in rats with or without obesity – Zongbin Song – Scientific Reports

Research Highlights: The microbiota maintains oxygen balance in the gut – Irene Vacca – Nature Reviews Microbiology

Studying the Differences of Bacterial Metabolome and Microbiome in the Colon between Landrace and Meihua Piglets – Zhuang Chen – Frontiers in Microbiology

Dietary heme induces gut dysbiosis, worsens colitis and potentiates the development of adenomas in mice – Marco Constante – Frontiers in Microbiology

Antibiotic-induced perturbations in microbial diversity during post-natal development alters amyloid pathology in an aged APPSWE/PS1ΔE9 murine model of Alzheimer’s disease – Myles R. Minter – Scientific Reports

Enrichment of beneficial bacteria in the skin microbiota of bats persisting with white-nose syndrome – Virginie Lemieux-Labonté – Microbiome (BMC)

 

Environmental and Soil Microbiome

Composted Cattle Manure Increases Microbial Activity and Soil Fertility More Than Composted Swine Manure in a Submerged Rice Paddy – Suvendu Das – Frontiers in Microbiology

Fermentative Bacteria Influence the Competition between Denitrifiers and DNRA Bacteria – Eveline M. van den Berg – Frontiers in Microbiology

Beneficial microbes

Lactobacillus casei BL23 produces microvesicles carrying proteins associated with its probiotic effect – Ana P. Domínguez Rubio – Frontiers in Microbiology

Probiotic mixture Golden Bifido prevents neonatal Escherichia coli K1 translocation via enhancing intestinal defense – Qing Zeng – Frontiers in Microbiology

Protective Effect of Akkermansia muciniphila against Immune-mediated Liver Injury in a Mouse Model – Wenrui Wu – Frontiers in Microbiology

 

Methods

Review: Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing – Luisa W. Hugerth – Frontiers in Microbiology

Total rRNA-Seq analysis gives insight into bacterial, fungal, protozoal and archaeal communities in the rumen using an optimized RNA isolation method – Chijioke O. Elekwachi – Frontiers in Microbiology

Non-Microbiology picks

The contribution of Nintendo Wii Fit series in the field of health: a systematic review and meta-analysis – Julien Tripette – PeerJ