Yearly Archives: 2017

March 11, 2017

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General microbiome

Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: a systematic review and meta-analysis – M Pammi – Microbiome

Is the 25 year hepatitis C marathon coming to an end to declare victory? – Khulood T Ahmed – bioRxiv

Natural antimicrobial peptide complexes in the fighting of antibiotic resistant biofilms: Calliphora vicina medicinal maggots – N Gordya – PLoS One

Complement inhibition by Sarcoptes scabiei protects Streptococcus pyogenes – An in vitro study to unravel the molecular mechanisms behind the poorly understood predilection of S. pyogenes to infect mite-induced skin lesions – PM Swe – PLoS Neglected Tropical Disease

CD40-signalling abrogates induction of RORγt+ Treg cells by intestinal CD103+ DCs and causes fatal colitis – C Barthels – Nature Communications

Antioxidant Supplements and Gastrointestinal Diseases: A Critical Appraisal – I Khan – Medical Principles and Practice

 

Human skin microbiome

Prenatal antibiotics and atopic dermatitis among 18-month old children in the Danish National Birth Cohort – S Timm – Clinical and Experimental Allergy

 

Human vaginal microbiome

*Review: Vaginal Microbiome and Its Relationship to Behavior, Sexual Health, and Sexually Transmitted Diseases – FM Lewis – Obstetrics and Gynecology

 

Human gut microbiome

*Review: Small Intestinal Bacterial Overgrowth and Irritable Bowel Syndrome: A Bridge between Functional Organic Dichotomy – UC Ghoshal – Gut and Liver

Beyond Digestion: The Pancreas Shapes Intestinal Microbiota and Immunity – H Tilg – Cell Metabolism

Melatonin prevents obesity through modulation of gut microbiota in mice – P Xu – Journal of Pineal Research

 

Animal microbiome

Dynamic changes of the respiratory microbiota and its relationship to fecal and blood microbiota in healthy young cats – Vientós-Plotts AI – PLoS One

A gut reaction: The combined influence of exercise and diet on gastrointestinal microbiota in rats – R Batacan – Journal of Applied Microbiology

Parasitism perturbs the mucosal microbiome of Atlantic Salmon – MS Llewellyn – Scientific Reports

Probiotic efficiency of Bacillus sp. in Labeo rohita challenged by Aeromonas hydrophila: assessment of stress profile, haemato-biochemical parameters and immune responses – A Nandi – Aquaculture Research

 

Plant, root and soil microbiome

Simplified and representative bacterial community of maize roots – B Niu – PNAS

Impact of three different fungicides on fungal epi- and endophytic communities of common bean (Phaseolus vulgaris) and broad bean (Vicia faba) – R Prior – Journal of Environmental Science and Health, Part B

Thermophilic microorganisms in arable land around medieval archaeological sites in Northern Caucasus, Russia: Novel evidence of past manuring practices – E Chernysheva – Geoarchaeology

 

Water and Extremophiles

In situ electrochemical enrichment and isolation of a magnetite-reducing bacterium from a high pH serpentinizing spring – AR Rowe – Environmental Microbiology

Niche specialization of bacteria in permanently ice-covered lakes of the McMurdo Dry Valleys, Antarctica – M Kwon – Environmental Microbiology

 

Transcriptomics and Proteomics

A Comprehensive Assessment of the Genetic Determinants in Salmonella Typhimurium for Resistance to Hydrogen Peroxide – Sardar Karash – bioRxiv

 

Techniques

Isolation and concentration of bacteria from blood using microfluidic membraneless dialysis and dielectrophoresis – L D’Amico – Lab on a Chip

A fast small-sample kernel independence test for microbiome community-level association analysis – X Zhan – Biometrics

 

More microbes

Integrative Physiology: At the Crossroads of Nutrition, Microbiota, Animal Physiology, and Human Health – Leulier F – Cell Metabolism

Phage therapy is highly effective against chronic lung infections with Pseudomonas aeruginosa – EM Waters – Thorax

*Review: Recent advances in genetic modification systems for Actinobacteria – Yu Deng – Applied Microbiology and Biotechnology

Meibomian gland disease and the microbiotome: is it time for ocular probiotics? – S Watson – Clinical & Experimental Ophthalmology

*Review: Infection in Organ Transplantation – JA Fishman – American Journal of Transplantation

Azole resistance in Candida albicans from animals: Highlights on efflux pump activity and gene overexpression – MFG Rocha – Mycoses

The Synonymy of the Toxic Dinoflagellates Prorocentrum mexicanum and P. rhathymum and the Description of P. steidingerae sp. nov. (Prorocentrales, Dinophyceae) – F Gomez – Journal of Eukaryotic Microbiology

Gut microbiota analysis in rats with methamphetamine-induced conditioned place preference – T Ning – bioRxiv

 

Microbes in news

What is Metagenomics? – Y Smith – News Medical

UCC researchers discover weapon to fight antibiotic resistance – D Ahlstrom – The Irish Times

Community gets an eye-opening lesson in human microbiome and our western lifestyle – C MacDonald – UToday

Microbiome Research Symposia Review: Microbiome and Diseases – J Phelan – Taconic Biosciences

Q&A with Zeus Capital’s Dr Gary Waanders: Live Biotherapeutics & 4D Pharma PLC (LON:DDDD) – A Stone – Directors Talk Interviews

Do You Have the Guts to Perform? Microbial Balance, the Brain and Athletic Performance – SJ Hewlings – Natural Products Insider

New probiotics meant to balance microbial, fungal communities in gut – H Schultz – NUTRAingredients

Google Leads $51M Investment in Startup Tackling Drug-Resistant Bacteria – R Bushey – R & D

Your bacteria-ridden makeup could be the reason you keep getting sick – A Mulvaney – Independent

March 10, 2017

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Ancient microbial DNA in Neanderthal dental calculus; the role of fungus in inflammatory bowel disease; symbiotic bacteria in the Hawaiian bobtail squid reproductive system; and a colorimetric/electrochemical device for detection of food and waterborne bacteria.

Events and jobs
Microbiology/Immunology Faculty – West Virginia School of Osteopathic Medicine – Lewisburg, West Virginia

Pregnancy and early life
Association of Maternal Gestational Weight Gain With the Infant Fecal Microbiota – Alyssa Robinson – Journal of Pediatric Gastroenterology and Nutrition

Review: Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: a systematic review and meta-analysis – Mohan Pammi – Microbiome

Human oral microbiome
New approach for studying mobile genes using metagenomic analysis – K. Ishihara – Oral Diseases

Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus – Laura S. Weyrich – Nature

In the News: Prehistoric ‘Aspirin’ Found in Sick Neanderthal’s Teeth – National Geographic

Human skin microbiome
Using Shotgun Metagenomics to Examine the Use of Hand Microbiome as a Forensic Tool – Ning Chin – ProQuest Dissertations Publishing

Human vaginal microbiome
Review: The role of the vaginal microbiome in gynecological cancer: a review – Champer M. – BJOG

Human gut microbiome
A translational investigation into the role of dietary fatty acids in modulating endotoxemia and associated inflammation – Joshua Mark Lyte – ProQuest Dissertations Publishing

Orai1-Mediated Antimicrobial Secretion from Pancreatic Acini Shapes the Gut Microbiome and Regulates Gut Innate Immunity – Malini Ahuja – Cell Metabolism

Beyond Digestion: The Pancreas Shapes Intestinal Microbiota and Immunity – Herbert Tilg – Cell Metabolism

Low-dose penicillin exposure in early life decreases Th17 and the susceptibility to DSS colitis in mice through gut microbiota modification – Shuang Jin – Scientific Reports

Gut microbiota modulation of chemotherapy efficacy and toxicity – James. L. Alexander – Nature Reviews Gastroenterology & Hepatology

CD40-signalling abrogates induction of RORγt+ Treg cells by intestinal CD103+ DCs and causes fatal colitis – Christian Barthels – Nature Communications

Faecal microbiota transplantation in clinical practice – E M Terveer – Gut

Distinct Microbiome-Neuroimmune Signatures Correlate With Functional Abdominal Pain in Children With Autism Spectrum Disorder – Ruth Ann Luna – Cellular and Molecular Gastroenterology and Hepatology
Animal experiments
A gut reaction: The combined influence of exercise and diet on gastrointestinal microbiota in rats – Romeo Batacan – Journal of Applied Microbiology

A member of the gut mycobiota modulates host purine metabolism exacerbating colitis in mice – Chiaro TR – Science Translational Medicine

Animal microbiome
Diurnal dynamics of gaseous and dissolved metabolites and microbiota composition in the bovine rumen – Henk J. Van Lingen – Frontiers in Microbiology

Symbiotic bacteria associated with a bobtail squid reproductive system are detectable in the environment, and stable in the host and developing eggs – Allison H. Kerwin – Environmental Microbiology

Plant, root, and soil microbiome
Arsenic Transport in Rice and Biological Solutions to Reduce Arsenic Risk from Rice – Yanshan Chen – Frontiers in Plant Science

Pseudomonas fluorescens Transportome is Linked to Strain-Specific Plant Growth Promotion in Aspen Seedlings Under Nutrient Stress – Shalaka Shinde – Frontiers in Plant Science

Short-term exposure of paddy soil microbial communities to salt stress triggers different transcriptional responses of key taxonomic groups – Jingjing Peng – Frontiers in Microbiology

Fertilization of Phaseolus vulgaris with the Tunisian rock phosphate affects richness and structure of rhizosphere bacterial communities – Darin Trabelsi – Applied Soil Ecology

Bioprospecting plant-associated microbiomes – Christina A. Muller – Journal of Biotechnology

Water and extremophile microbiome
Isolation and identification of indigenous prokaryotic bacteria from arsenic-contaminated water resources and their impact on arsenic transformation – MA Jebelli – Ecotoxicology and Environmental Safety

Performance and kinetics of membrane and hybrid moving bed biofilm-membrane bioreactors treating salinity wastewater – Alejandro Rodriguez-Sanchez – AlChE Journal

Metabolomics
Technological development of high-performance MALDI mass spectrometry imaging for the study of metabolic biology – Adam D. Feenstra – ProQuest Dissertations Publishing

Food microbiology
The Biodiversity of the Microbiota Producing Heat-Resistant Enzymes Responsible for Spoilage in Processed Bovine Milk and Dairy Products – Solimar G. Machado – Frontiers in Microbiology

Culturable microorganisms during fermentation of Veltlínske zelené (Grüner Veltliner) ice wine – K. Ženišová – Journal of Food and Nutrition Research

Metabolomics for empirical delineation of the traditional Korean fermented foods and beverages – Digar Singh – Trends in Food Science & Technology

Probiotics/prebiotics
Case Study: Integrate genome-based assessment of safety for probiotic strains: Bacillus coagulans GBI-30, 6086 as a case study – Elisa Salvetti – Applied Microbiology and Biotechnology

Techniques
Colorimetric and Electrochemical Bacteria Detection Using Printed Paper- and Transparency-Based Analytic Devices – Jaclyn A. Adkins – Analytical Chemistry

Microbes in the news
Exciting Microbe Research? Temper That Giddy Feeling in Your Gut – The New York Times

Garrett’s non-microbiology picks
‘Plan bee’ drone artificially pollinates flowers on behalf of bees – Design Boom

March 9, 2017

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A variety of reviews about the oral microbiome and periodontal disease, a perspective piece on secondary metabolites mediating symbiotic interactions in the new Nature Reviews Chemistry journal, Akkermansia muciniphila’s involvement in host immune homeostasis, new insight into how raindrops disperse bacteria from soil into the air.

General microbiome

* Perspective: Hijacking exogenous signals to generate new secondary metabolites during symbiotic interactions – Rurun Wang – Nature Reviews Chemistry

Cooperation of Gastric Mononuclear Phagocytes with Helicobacter pylori during Colonization – Monica Viladomiu – Journal of Immunology

Human respiratory microbiome

Longitudinal sampling of the lung microbiota in individuals with cystic fibrosis – Fiona J. Whelan – PLoS ONE

Human oral microbiome

Review: Role of microbial communities in the pathogenesis of periodontal diseases and caries – Alex Mira – Journal of Clinical Periodontology

Review: Dental biofilm: ecological interactions in health and disease – P. D. Marsh – Journal of Clinical Periodontology

Review: The oral cavity microbiota: between health, oral disease and cancers of the aerodigestive tract – Pierre Le Bars – Canadian Journal of Microbiology

A new mathematical model of bacterial interactions in two-species oral biofilms – Bénédicte Martin – PLoS ONE

Human urinary microbiome

Alterations of Urinary Microbiota in Type 2 Diabetes Mellitus with Hypertension and/or Hyperlipidemia – Fengping Liu – Frontiers in Physiology

Human gut microbiome

Impact of Bariatric Surgery on Metabolic and Gut Microbiota Profile: a Systematic Review and Meta-analysis – Dimitrios E. Magouliotis – Obesity Surgery

Commensal gut bacteria modulate phosphorylation-dependent PPARγ transcriptional activity in human intestinal epithelial cells – Malgorzata Nepelska – Scientific Reports

* Pili-like proteins of Akkermansia muciniphila modulate host immune responses and gut barrier function – Noora Ottman – PLoS ONE

Altered intestinal microbiota in patients with chronic pancreatitis: implications in diabetes and metabolic abnormalities – Sai Manasa Jandhyala – Scientific Reports

Disease-Associated Changes in Bile Acid Profiles and Links to Altered Gut Microbiota – Susan A. Joyce – Digestive Diseases

One-year calorie restriction impacts gut microbial composition but not its metabolic performance in obese adolescents – Alicia Ruiz – Environmental Microbiology

Dysbiosis of Gut Microbiota Associated with Clinical Parameters in Polycystic Ovary Syndrome – Rui Liu – Frontiers in Microbiology

Animal experiments

Bifidobacterium breve with α-linolenic acid alters the composition, distribution and transcription factor activity associated with metabolism and absorption of fat – Elaine Patterson – Scientific Reports

Exploring gastric bacterial community in young pigs – Vincenzo Motta – PLoS ONE

Animal microbiome

Parasitism perturbs the mucosal microbiome of Atlantic Salmon – M. S. Llewellyn – Scientific Reports

The microbiome composition of Aedes aegypti is not critical for Wolbachia-mediated inhibition of dengue virus – Michelle D. Audsley – PLoS Neglected Tropical Diseases

Endosymbiotic calcifying bacteria across sponge species and oceans – Leire Garate – Scientific Reports

Bacterial communities associated with Shinkaia crosnieri from the Iheya North, Okinawa Trough: Microbial diversity and metabolic potentials – Jian Zhang – Journal of Marine Systems

Diet affects arctic ground squirrel gut microbial metatranscriptome independent of community structure – Jasmine J. Hatton – Environmental Microbiology

Plant, root, and soil microbiome

Microbial Communities as Environmental Indicators of Ecological Disturbance in Restored Carbonate Fen-Results of 10 Years of Studies – Tomasz Mieczan – Microbial Ecology

Rhizospheric microbial community of Caesalpinia spinosa (Mol.) Kuntze in conserved and deforested zones of the Atiquipa fog forest in Peru – Irene Cordero – Applied Soil Ecology

Abundance and diversity of ammonia-oxidizing archaea and bacteria in the rhizosphere soil of three plants in the Ebinur Lake wetland – Yuan He – Canadian Journal of Microbiology

Alphaproteobacteria fix nitrogen in a Sphagnum-dominated peat bog using molybdenum-dependent nitrogenase – Melissa J. Warren – bioRxiv

Water and extremophile microbiome

Quantifying the importance of the rare biosphere for microbial community response to organic pollutants in a freshwater ecosystem – Yuanqi Wang – Applied and Environmental Microbiology

Comparison of Prokaryotic Diversity in Cold, Oligotrophic Remote Lakes of Chilean Patagonia – Paulina Aguayo – Current Microbiology

Plasmid DNA analysis of pristine groundwater microbial communities reveal extensive presence of metal resistance genes – Ankita Kothari – bioRxiv

Food microbiology

Characterization of microbial population of breba and main crops (Ficus carica) during cold storage: Influence of passive modified atmospheres (MAP) and antimicrobial extract application – María del Carmen Villalobos – Food Microbiology

Genetic diversity, safety and technological characterization of lactic acid bacteria isolated from artisanal Pico cheese – M. F. P. Domingos-Lopes – Food Microbiology

Probiotics/prebiotics

A proliferative probiotic Bifidobacterium strain in the gut ameliorates progression of metabolic disorders via microbiota modulation and acetate elevation – Ryo Aoki – Scientific Reports

More microbes

* Bioaerosol generation by raindrops on soil – Young Soo Joung – Nature Communications

Cooperation in carbon source degradation shapes spatial self-organization of microbial consortia on hydrated surfaces – Robin Tecon – Scientific Reports

Microbes in the news

The ‘Dark Matter’ of the Microbial World – Sarah Zhang – The Atlantic

Scientists Make Art From Objects Invisible to the Naked Eye – Marissa Fessenden – Smithsonian

March 8th, 2017

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Today is the International Women’s Day! This is a day for awareness about the importance of support equality in rights and opportunities for women.

About International Women’s Day

Gender at Nature Ecology & Evolution

Helping women progress in traditionally male dominated fields

Rosalind Franklin: Navigating workplace politics to gain recognition in science

International Women’s Day 2017: pursuing a career in science

BMC Series Blog: International Women’s Day

Events and Webinars

3rd Annual Translational Microbiome Conference, April 12-13, 2017 in Boston, MA

Webinar: Nomadic nanopore sequencing of metagenomes with the MinION

Microbiome research

Salivary Gluten Degradation and Oral Microbial Profiles in Healthy Individuals and Celiac Disease Patients – Na Tian – Applied and Environmental Microbiology

Impact of Westernized Diet on Gut Microbiota in Children on Leyte Island – Jiro Nakayama – Frontiers in Microbiology

Comparison of culture-dependent and culture-independent molecular methods for characterization of vaginal microflora – Shirali Pandya – Journal of Medical Microbiology

Effect of predatory bacteria on the gut bacterial microbiota in rats – Kenneth Shatzkes – Scientific Reports

Methods article: Critical Issues in Mycobiota Analysis – Bettina Halwachs – Frontiers in Microbiology

Microbiota alteration is associated with the development of stress-induced despair behavior – Ioana A. Marin – Scientific Reports

Review: Beyond Hygiene: Commensal Microbiota and Allergic Diseases – Sung-Wook Hong – Immune Network

Fecal Bacterial Communities in treated HIV infected individuals on two antiretroviral regimens – Sandra Pinto-Cardoso – Scientific Reports

Editorial: How can the gut microbiota affect immune recovery in HIV-infected individuals? – Sergio Serrano-Villar – Future Microbiology

Unexplored Archaeal Diversity in the Great Ape Gut Microbiome – Kasie Raymann – mSphere

Probiotics

Lactobacillus rhamnosus GG supernatant enhance neonatal resistance to systemic Escherichia coli K1 infection by accelerating development of intestinal defense – Xiaolong He – Scientific Reports

Bifidobacterium breve with α-linolenic acid alters the composition, distribution and transcription factor activity associated with metabolism and absorption of fat  – Elaine Patterson – Scientific Reports

Timely use of Probiotics in Hospitalized Adults Prevents Clostridium difficile Infection: a Systematic Review with Meta-Regression Analysis – Nicole T. Shen – Gastroenterology

Metagenomics

Review: Beneficial Microorganisms for Corals (BMC): Proposed Mechanisms for Coral Health and Resilience – Raquel S. Peixoto – Frontiers in Microbiology

Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples – Feiqiao Yu – bioRxiv

Untangling Genomes of Novel Planctomycetal and Verrucomicrobial Species from Monterey Bay Kelp Forest Metagenomes by Refined Binning – John Vollmers – Frontiers in Microbiology

Environmental Viral Genomes Shed New Light on Virus-Host Interactions in the Ocean – Yosuke Nishimura – mSphere

Pathogens

Metabolic activity, urease production, antibiotic resistance and virulence in dual species biofilms of Staphylococcus epidermidis and Staphylococcus aureus – Ilse Vandecandelaere – PLoS ONE

Review: Mollicutes in vaginal microbiology: Mycoplasma hominis, Ureaplasma urealyticum, Ureaplasma parvum and Mycoplasma genitalium – David Taylor-Robinson – Research in Microbiology

Case report: Contribution of Ultra Deep Sequencing in the Clinical Diagnosis of a New Fungal Pathogen Species: Basidiobolus meristosporus – Emilie Sitterlé – Frontiers in Microbiology

The Chlamydia suis genome exhibits high levels of diversity, plasticity and mobile antibiotic resistance: comparative genomics of a recent livestock cohort shows influence of treatment regimes – Helena M.B. Seth-Smith – Genome Biology and Evolution

Extremophiles

Reducing salinity by flooding an extremely alkaline and saline soil changes the bacterial community but its effect on the archaeal community is limited – Arit S de León-Lorenzana – Frontiers in Microbiology

Early life

Paleoproterozoic sterol biosynthesis and the rise of oxygen – David A. Gold – Nature

March 7, 2017

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Events and jobs

Professor Of Microbiology – University of Western Australia – Last date: Friday, May 12, 2017

 

General microbiome

Biofilms: Microbial Cities Wherein Flow Shapes Competition – Su Chuen Chew – Trends in Microbiology

*Review: Critical Streptococcus suis Virulence Factors: Are They All Really Critical? – Mariela Segura – Trends in Microbiology

*Review: Collective Infectious Units in Viruses – Rafael Sanjuán – Trends in Microbiology

*Review: KSHV microRNAs: Tricks of the Devil – Jie Qin – Trends in Microbiology

Significant disparities in allergy prevalence and microbiota between the young people in Finnish and Russian Karelia – Lasse Ruokolainen – Clinical & Experimental Allergy

 

Human oral microbiome

Chemotherapeutic decontamination of dental implants colonized by mature multispecies oral biofilm – Sebastien Dostie – Journal of Clinical Periodontology

 

Human vaginal microbiome

The presence of vaginal Lactobacillus species does not contribute to a measureable difference in amniotic fluid lactate levels collected from the vaginal tract of laboring women – Beverley Hall – AOGS

 

Animal microbiome

Effects of Pediococcus pentosaceus supplementation on growth performance, intestinal microflora and disease resistance of white shrimp, Litopenaeus vannamei – M. Adel – Aquaculture Nutrition

 

Plant, root and soil microbiome

Effects of the Inoculant Strain Pseudomonas sp. SPN31 nah + and of 2-Methylnaphthalene Contamination on the Rhizosphere and Endosphere Bacterial Communities of Halimione portulacoides – V Oliveira – Current Microbiology

Microbial-enhanced lindane removal by sugarcane (Saccharum officinarum) in doped soil-applications in phytoremediation and bioaugmentation. – J A Salam – Journal of Environmental Management

Immobilization remediation of Cd-polluted soil with different water condition – J Li – Journal of Environmental Management

Disentangling above- and below-ground facilitation drivers in arid environments: the role of soil microorganisms, soil properties and microhabitat – Yudi M Lozano – New Phytologist

A long-term study of burning effects on a plant pathogen in tallgrass prairie – S. P. Dendy – Plant Pathology

 

Water and extremophile microbiome

Temperature–nutrient interactions exacerbate sensitivity to warming in phytoplankton – Mridul K. Thomas – Global Change Biology

 

Metagenomics and Bioinformatics

Omics for Understanding the Gut-Liver-Microbiome Axis and Precision Medicine – Jag Khalsa – Clinical Pharmacology in Drug Development

 

Techniques

Drug–Drug Interactions and Diagnostics for Drug Users With HIV and HIV/HCV Coinfections: Introduction – Jag H. Khalsa – Clinical Pharmacology in Drug Development

 

More Microbes

Influence of key physicochemical and hydrodynamic specifications of three packing materials on both performance and bacterial community structure of gas-biofilters – Luc Malhautier – Journal of Chemical Technology and Biotechnology

Metabolic coupling in bacteria – Shraddha Shitut – bioRxiv

Fungal derived 15-keto-prostaglandin E2 and host peroxisome proliferator-activated receptor gamma (PPAR-γ) promote C. neoformans growth during infection – Robert J Evans – bioRxiv

 

Microbes in news

Parkinson’s Linked to Changes in Gut Bacteria – T Pedersen – Psych Central

3.77 billion year old bacteria fossil may be Earth’s oldest, scientists say – J Leone – Journal-News

Bacterial vaginosis: A common health concern women must not take lightly – S Kantengwa – The New Times

This Drugstore Face Cream Is A Game Changer For People With Dry Skin – L Lebsack – Refinery29

UT researchers take new approach in cholera prevention – C Deangelis – The Blade

Bacteriophages Offer Potential for Helping Reduce Dependence on In-Feed Antibiotics – The Pig Site

Exciting Microbe Research? Temper That Giddy Feeling in Your Gut – AE Carroll – The Upshot

Human Microbiome Market Worth 899.1 Million USD by 2025 – PRNewswire

Native Squid Used in Research of Environment and Human Health – Maui Now

March 6, 2017

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Interesting articles on the how the interactions between bacteria and fungi influence N cycling in soils. Also, fecal sample collection methods influence microbial community structure.

General microbiome

The National Biome Initiative: An Allergy Perspective. Furuta GT. Journal of Allergy and Clinical Immunology

The Microbiome in Allergic Disease: Current Understanding and Future Opportunities – 2017 PRACTALL Document of the American Academy of Allergy, Asthma & Immunology and the European Academy of Allergy and Clinical Immunology. Huang YJ. Journal of Allergy and Clinical Immunology

Oral and nasal microbiome

Community analysis of dental plaque and endotracheal tube biofilms from mechanically ventilated patients.      Marino PJ. Journal of Critical Care

Oral and nasal microbiota in Parkinson’s disease. Pereira PA. Parkinsonism and Related Disorders

Gut microbiome

The effect of omeprazole treatment on the gut microflora and neutrophil function. Kostrzewska M. Clinics and Research in Hepatology and Gastroenterology

Water and extremophile microbiome

Bacterial interactions and implications for oil biodegradation process in mangrove sediments. Grativol AD. Marine Pollution Bulletin

Quantifying the importance of the rare biosphere for microbial community response to organic pollutants in a freshwater ecosystem. Wang Y. Applied and Environmental Microbiology

Probiotics

Probiotic treatment reduces depressive-like behaviour in rats independently of diet. Abildgaard A. Psychoneuroendocrinology

Techniques

Comparison of fecal collection methods for microbiota studies in Bangladesh. Vogtmann E. Applied and Environmental Microbiology

Plant, root, and soil microbiome

How interacting fungal species and mineral nitrogen inputs affect transfer of nitrogen from litter via arbuscular mycorrhizal mycelium. He Y. Environmental Science and Pollution Research

Salmonella Senftenberg adaptation to linalool and its association with antibiotic resistance and environmental persistence. Hollander K. Applied and Environmental Microbiology

Fungal and bacterial contributions to nitrogen cycling in cheatgrass-invaded and uninvaded native sagebrush soils of the western USA.  DeCrappeo NM. Plant and Soil

Native soil organic matter as a decisive factor to determine the arbuscular mycorrhizal fungal community structure in contaminated soils. Montiel-Rozas. Biology and Fertility of Soils

March 5, 2017

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Here are few interesting articles for your Sunday morning edition. Canadian bacteria-like fossils may be the oldest evidence of life yet.  Black carbon, one of the main components of air pollution,  is reported to drastically change the development of bacterial biofilms and key aspects of bacterial colonization and survival.  A novel organ culture system described for the mouse intestine shows that the nervous system influences the microbiome/immune system crosstalk.  And the power of alternative assays for discovery: Deep sequencing of cell-free DNA from a large patient cohort revealed previously unknown and highly prevalent microbial and viral diversity in humans.

Pregnancy and early life

Prediction of complicated disease course for children newly diagnosed with Crohn’s disease: a multicenter inception cohort study – Subra Kugathasan – The Lancet

Multi-site human microbiome

Humans are colonized by many uncharacterized and highly divergent microbes -Mark A. Kowarsky -bioRxiv

Human respiratory microbiome

Air pollution alters Staphylococcus aureus and Streptococcus pneumonia biofilms, antibiotic tolerance and colonization – Shane J. K. Hussey – Journal of Environmental Microbiology

Human vaginal microbiome

The global health impact of vaginal dysbiosis – Janneke H.H.M. van de Wijgert – Research in Microbiology

Human gut microbiome

An Intestinal Organ Culture System Uncovers a Role for the Nervous System in Microbe-Immune Crosstalk – Nissan Yissachar – Cell

Animal microbiome

Genetic and functional analysis of the bovine uterine microbiota. Part I: Metritis versus healthy cows, Part II: Purulent vaginal discharge versus healthy cows – M.L.S. Bicalho – The journal of Dairy Science

Plant, root, and soil microbiome

Review: Soil-Plant-Microbe Interactions in Stressed Agriculture Management– Shobhit Raj Vimal – Pedosphere

Water and extremophile microbiome

Evidence for early life in Earth’s oldest hydrothermal vent precipitates – Matthew S. Dodd – Nature

Microbes in the news

Study Shows Link Between Microbiome in the Gut and Parkinson’s – University of Alabama at Birmingham

A Japanese study performed by sequencing the gut microbiota of 367 healthy individuals ranging from newborn to 104 years old shows microbiome changes with age

UN issues list of 12 most worrying bacteria

Microbes on the market

Rebiotix Inc. has its lead product for C. diff. treatment granted Fast Track, Orphan Drug, and Breakthrough Therapy status by the FDA.  

March 4th, 2017

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Events and jobs

Head, Microbiome Discovery Research – Johnson & Johnson

Multi-site human microbiome

Characterization of oral and gut microbiome temporal variability in hospitalized cancer patients – Jessica R. Galloway-Peña – Genome Medicine

Human gut microbiome

Childhood BMI in relation to microbiota in infancy and lifetime antibiotic use – K. Korpela – Microbiome

Animal experiments

Metaproteogenomics reveals taxonomic and functional changes between cecal and fecal microbiota in mouse – Alessandro Tanca – Frontiers in Microbiology

Animal microbiome

Cultivable gut bacteria provide a pathway for adaptation of Chrysolina herbacea to Mentha aquatica volatiles – Graziano Pizzolante – BMC Plant Biology

Gut bacteria oversee the special relationship between the green mint leaf beetle and watermint – BMC Series Blog

Effects of tussah immunoreactive substances on growth, immunity, disease resistance against Vibrio splendidus and gut microbiota profile of Apostichopus japonicus – Shuhui Ma – Fish & Shellfish Immunology

Community-Level Differences in the Microbiome of Healthy Wild Mallards and Those Infected by Influenza A Viruses – Holly H. Ganz – mSystems

The microbiome of the ant-built home: the microbial communities of a tropical arboreal ant and its nest – Jane Lucas – Ecosphere

*Perspective: Gut microbiome transmission in lizards – Timothy J. Colston – Molecular Ecology

Plant, root, and soil microbiome

Microbial communities in soil chronosequences with distinct parent material: the effect of soil pH and litter quality – Fernando D. Alfaro – Journal of Ecology

Water and extremophile microbiome

Volcanic ash supports a diverse bacterial community in a marine mesocosm – V. Witt – Geobiology

Methylamine as a Nitrogen Source for Microorganisms from a Coastal Marine Environment – Martin Taubert – Environmental Microbiology

Built environment

Response of microbial community structure to pre-acclimation strategies in microbial fuel cells for domestic wastewater treatment – Younghyun Park – Bioresource Technology

Food microbiology

Viable microbial loads on citrus carpoplane during packhouse processing and survival of foodborne pathogens in reconstituted postharvest fungicides – A. Gomba – Journal of Food Safety

Bacterial and fungal core microbiomes associated with small grain silages during ensiling and aerobic spoilage – Lysiane Duniere – BMC Microbiology

Probiotics / prebiotics

Microbiome dynamic modulation through functional diets based on pre- and probiotics (mannan-oligosaccharides and Saccharomyces cerevisiae) in juvenile rainbow trout (Oncorhynchus mykiss) – Ana Teresa Gonçalves – Journal of Applied Microbiology

Exploration of the effect of probiotics supplementation on intestinal microbiota of food allergic mice – Bo Yang – American Journal of Translational Research

Phages and viruses

Human norovirus binding to select bacteria representative of the human gut microbiota – Erin A. Almand – PLoS ONE

Environmental Viral Genomes Shed New Light on Virus-Host Interactions in the Ocean – Yosuke Nishimura – mSphere

Bioinformatics

REPARATION: Ribosome Profiling Assisted (Re-)Annotation of Bacterial
genomes – Elvis Ndah – BioRxiv

Normalization and microbial differential abundance strategies depend upon data characteristics – Sophie Weiss – Microbiome

How conserved are the conserved 16S-rRNA regions? – Marcel Martinez-Porchas – PeerJ

Microbes in the news

Gut bacteria affect intestines and brain in IBS patients – Medical News Today

Intestinal Bacteria Alter Gut and Brain Function – Neuroscience News

Why Are People Sending Poop Through the Mail? For Their Health – GQ Magazine

Microbes on the market

Next-gen microbiome drugs are now on sale, should you buy them? – New Scientist

 

March 3, 2017

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Our post today has been remodeled after some small technical problems, but here’s your fresh Friday digest of microbiome papers!

Events and jobs

Full-time visiting faculty position in biochemistry and microbiology (2017-18)
College of the Holy Cross – Worcester, Massachussets

Microbiology Laboratory Technician
Symbio Laboratories – Brisbane, Australia

Team Manager – Microbiology
AstraZeneca – Cambridge, UK

27th European Congress of Clinical Microbiology & Infectious Diseases
Vienna – Austria

General microbiome

Cryptic biogeochemical cycles: unravelling hidden redox reactions
Andreas Kappler – Environmental Microbiology

Multi-site human microbiome

Microbe-microbe and host-microbe interactions drive microbiome dysbiosis and inflammatory processes
AD Proal – Discovery Medicine

The human microbiome: an emerging tool in forensics
Jarrad T. Hampton-Marcell – Microbial Biotechnology

The salivary microbiome is altered in the presence of a high salivary glucose concentration
J. Max Goodson – Plos One

Human vaginal microbiome

Review: The role of Escherichia coli in reproductive health: state of the art.
P. Cools – Research in Microbiology

Survival of vaginal microorganisms in three commercially available transport systems.
Allison L DeMarco – Anaerobe

Human gut microbiome

Small Intestinal Bacterial Overgrowth Is Associated with Non-Alcoholic Fatty Liver Disease.
A. Fialho – Journal of Gastrointestinal and Liver Disease

Review: Roles of the intestinal microbiota in pathogen protection.
C. Ubeda – Clinical Translational Immunology

Atopic dermatitis and gut microbiota
M. Lindberg – British Journal of Dermatology

Editorial: The gut microbiota and psychiatric illness
Glenda MacQueen – Journal of Psychiatry and Neuroscience

Commentary: For Health Disparities, Don’t Ignore the Microbiome
Jennifer Abbasi – JAMA

Faecal microbiota transplantation protects against radiation-induced toxicity.
M Cui – EMBO Molecular Medicine

Multi-Omics Reveals that Lead Exposure Disturbs Gut Microbiome Development, Key Metabolites and Metabolic Pathways
Bei Gao – Chemical Research in Toxicology

Animal experiments

Transplantation of fecal microbiota from patients with irritable bowel syndrome alters gut function and behavior in recipient mice.
Giada de Palma – Science Translational Medicine

Targeting the Microbiota-Gut-Brain Axis: Prebiotics Have Anxiolytic and Antidepressant-like Effects and Reverse the Impact of Chronic Stress in Mice
Aurelijus Burokas – Biological Psychiatry

Animal microbiome

Unraveling the processes shaping mammalian gut microbiomes over evolutionary time
Mathieu Groussin – Nature Communications

Transition of the intestinal microbiota of dogs with age.
H. Masuoka – Biosciences Microbiota Food Health

Comparative analysis of gut microbiota of mosquito communities in central Illinois.
EJ Muturi – PLoS Neglected Tropical Diseases

Transformation, Proliferation, and Influence on Host Performance by Three Gut Bacteria in the Rice Water Weevil (Coleoptera: Curculionidae)
Yunshan Huang – Annals of the Entomological Society of America

Succession and dynamics of Pristionchus nematodes and their microbiome during decomposition of Oryctes borbonicus on La Réunion Island
Jan M. Meyer – Environmental Microbiology

MALDI-TOF MS identification of microbiota associated with pest insect Diabrotica speciosa
Bruno Perlatti – Agricultural and Forest Entomology

Culture-independent genomics of a novel chlamydial pathogen of fish provides new insight into host-specific adaptations utilized by these intracellular bacteria
Alyce Taylor-Brown – Environmental Microbiology

Plant, root, and soil microbiome

Syntrophobacteraceae-affiliated species are major propionate-degrading sulfate reducers in paddy soil
Pengfei Liu – Environmental Microbiology

Next-Generation Sequencing Analyses of Bacterial Community Structures in Soybean Pastes Produced in Northeast China
Mi-Hwa Lee – Journal of Food Science

Community Structure, Species Variation, and Potential Functions of Rhizosphere-Associated Bacteria of Different Winter Wheat (Triticum aestivum) Cultivars
AK Mahoney – Frontiers in Plant Science

Water and extremophile microbiome

Metagenomic analysis reveals unusually high incidence of proteorhodopsin genes in the ultraoligotrophic Eastern Mediterranean Sea
Vadim Dubinsky – Environmental Microbiology

Bacterial activity in hydrogenetic ferromanganese crust from the Indian Ocean: a combined geochemical, experimental and pyrosequencing study
PP Sujith – Environmental Earth Sciences

Stoichiometry of Prochlorococcus, Synechococcus, and small eukaryotic populations in the western North Atlantic Ocean
Steven E. Baer – Environmental Microbiology

Built environment

Microbial population dynamics in continuous anaerobic digester systems during start up, stable conditions and recovery after starvation.
N. de Jonge – Bioresource Technology

Spread from the Sink to the Patient: in situ Study Using Green Fluorescent Protein (GFP) Expressing- Escherichia coli to Model Bacterial Dispersion from Hand Washing Sink Trap Reservoirs
Shireen Kotay – Applied and Environmental Microbiology

Phages and viruses

Pre-print: How to name and classify your phage: an informal guide
Evelien M. Adriaenssens – bioRxiv

Review: Tumor-associated macrophages: implications in cancer immunotherapy
Amy J Petty – Immunotherapy

Predation by Bdellovibrio bacteriovorus significantly reduces viability and alters the microbial community composition of activated sludge flocs and granules
Shugeng Feng – FEMS Microbiology Ecology

Techniques

The choice of the DNA extraction method may influence the outcome of the soil microbial community structure analysis
Sylwia Zielinska – MicrobiologyOpen

Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis
Jason L. Weirather – F1000 Open Research

A High-Throughput Screening Platform of Microbial Natural Products for the Discovery of Molecules with Antibiofilm Properties against Salmonella
Sonia Paytubi – Frontiers in Microbiology

From reads to operational taxonomic units: an ensemble processing pipeline for MiSeq amplicon sequencing data
Mohamed Mysara – GigaDB

Misc

Highlights: Evolving as a holobiont
Lauren A. Richardson – Plos Biology

Microbes in the news

Gut microbes and poor artery health – researchers probe possible link
Jim Scott – CU Boulder Today

March 2, 2017

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Events and jobs
Postdoctoral Teaching and Learning Fellow in Microbiome Data Analysis – Department of Microbiology and Immunology (MICB) – University of British Columbia

Commercial Support Manager, Probiotics for Human Health & Microbiome – Hørsholm, Denmark – Chr. Hansen

Position in experimental biochemistry including microbiology – University of Warsaw

Microbiology Laboratory Technician – Milwaukee, WI – Aerotek

Human vaginal microbiome
Specific vaginal lactobacilli suppress the inflammation induced by lipopolysaccharide stimulation through downregulation of toll-like receptor 4 expression in human embryonic intestinal epithelial cells – Keisuke Tobita – Bioscience of Microbiota, Food and Health

Human gut microbiome
Editorial: The gut microbiota and psychiatric illness – Glenda MacQueen – Journal of Psychiatry and Neurosciece

Animal experiments
Understanding the mechanisms of zinc bacitracin and avilamycin on animal production: linking gut microbiota and growth performance in chickens – Eduardo Crisol-Martínez – Applied Microbiology and Biotechnology

Transition of the intestinal microbiota of dogs with age – Hiroaki Masuoka – Bioscience of Microbiota, Food and Health

Faecal microbiota transplantation protects against radiation-induced toxicity – Ming Cui – EMBO Molecular Medicine

Animal microbiome
Comparative analysis of gut microbiota of mosquito communities in central Illinois – Ephantus J. Muturi – PLoS Neglected Tropical Diseases

Plant, root, and soil microbiome
Community Structure, Species Variation, and Potential Functions of Rhizosphere-Associated Bacteria of Different Winter Wheat (Triticum aestivum) Cultivars – Aaron K Mahoney – Frontiers in Plant Science

Water and extremophile microbiome
Microbial community assembly and evolution in subseafloor sediment – Piotr Starnawski – PNAS

Phylogenetic Diversity and Anti-MRSA Activity of Halotolerant Actinobacteria from sediments in Great Salt Plains, Oklahoma – Ahmed H Gad – bioRxiv

Investigating the Microbial Degradation Potential in Oil Sands Fluid Fine Tailings Using Gamma Irradiation: A Metagenomic Perspective – Danielle VanMensel – Microbial Ecology

Food microbiology
Boswellia serrata resin extract alleviates azoxymethane (AOM)/dextran sodium sulfate (DSS)-induced colon tumorigenesis – YC Chou – Molecular Nutrition Food Research

A series of review articles on the FODMAP diet has been published in the most recent issue of the Journal of Gastroenterology and Hepatology
Review: Use of the low-FODMAP diet in inflammatory bowel disease – Peter R Gibson – Journal of Gastroenterology and Hepatology
Review: How to institute the low-FODMAP diet – Jacqueline S Barrett – Journal of Gastroenterology and Hepatology
Review: When the low FODMAP diet does not work – Emma P Halmos – Journal of Gastroenterology and Hepatology
Review: Nutritional, microbiological and psychosocial implications of the low FODMAP diet – Heidi Maria Staudacher – Journal of Gastroenterology and Hepatology

The spxB gene as a target to identify Lactobacillus casei group species in cheese – Maria Luisa Savo Sardaro – Food Microbiology

Bioinformatics
GMPR: A novel normalization method for microbiome sequencing data – Jun Chen – bioRxiv

Cohesion: A method for quantifying the connectivity of microbial communities – Cristina Herren – bioRxiv

Techniques
Microbial population dynamics in continuous anaerobic digester systems during start up, stable conditions and recovery after starvation – Nadieh de Jonge – Bioresource Technology

Microbes in the news
How Bacteria Interfere with Insect Reproduction – Ruth Williams – The Scientist
This references two important papers on Wolbachia:
A Wolbachia deubiquitylating enzyme induces cytoplasmic incompatibility – John F Beckmann – Nature Microbiology
Prophage WO genes recapitulate and enhance Wolbachia-induced cytoplasmic incompatibility – Daniel P LePage – Nature

Synopsis: Racing Bacteria – Katherine Wright – APS Physics

Meet green bacteria, airport’s eco-friendly toilet cleaners – Times of India

Assessing Host-Microbiota Relationships – Richard A Stein – Genetic Engineering and Biotechnology News

Bacteria from the ancient city of Troy – Caitlin Pepperell – Microbe Post

Gut bacteria determines the beneficial impacts of soy food on heart health – David Templeton – Pittsburgh Post-Gazette

Microbes on the market
Vaginal Microbiota May Affect Tenofovir Applied Intravaginally – John Schieszer – Infectious Disease Advisor

The Human Microbiome: Advancing New Frontiers in a Rapidly Emerging Market – PR Newswire – Yahoo Finance

New research data published in Frontiers in Microbiology confirm the microbiome’s potential to impact plant health – PR Newswire – Yahoo Finance

Microbiome Therapeutics Market Growth, Forecast and Value Chain 2017-2027 – Future Market Insights – OpenPR

Random Science
Editorial: Microbiome yarns: microbiomology of curly and straight hair – Kenneth Timmis – Microbial Biotechnology