Category Archives: Built Environment Microbiology

January 22, 2017

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Events and Jobs

PhD scholarship in Molecular Microbiology– University of Copenhagen-Last Date: February 8, 2017

Quality Control Associate-Microbiology–US-CA-Del Mar

General Microbiome

Impacts of chemical gradients on microbial community structure-Jianwei Chen-The ISME Journal

Human Skin

Proteomic and peptidomic analysis of human sweat with emphasis on proteolysis-Yijing Yu-Journal of Proteomics

Human Respiratory Microbiome

Nasopharyngeal Microbiome Diversity Changes over Time in Children with Asthma–Marcos Pérez-Losada-PLOS One

Adherence of Pseudomonas aeruginosa to cystic fibrosis buccal epithelial cells–Meike Lingner-ERJ

Human Vaginal Microbiome

The interaction between vaginal microbiota, cervical length, and vaginal progesterone treatment for preterm birth risk-Lindsay M. Kindinger-Microbiome

Human Gut Microbiome

Role of Gastrointestinal Microbiota on Kidney Injury and the Obese Condition-Keerati Wanchai-The American Journal of the Medical Sciences

Review-Altered Molecular Signature of Intestinal Microbiota in Irritable Bowel Syndrome Patients Compared with Healthy Controls: a Systematic Review and Meta-analysis-Hai Ning Liu-Digestive and Liver Disease

Animal Microbiome

Bacterial community composition and fermentation in the rumen of Xinjiang brown cattle (Bos taurus), Tarim red deer (Cervus elaphus yarkandensis), and Karakul sheep (Ovis aries)-Wenxi Qian-Canadian Journal of Microbiology

The Gut Microbiome of the Vector Lutzomyia longipalpis Is Essential for Survival of Leishmania infantum–Stephen M. Beverley-mBio

The normal vaginal and uterine bacterial microbiome in giant pandas (Ailuropoda melanoleuca)-Xin Yang-Microbiological Research

Pathogen-mediated manipulation of arthropod microbiota to promote infection–Nabil M. Abraham-PNAS

The gastrointestinal tract of farmed mink (Neovison vison) maintains a diverse mucosa-associated microbiota following a 3-day fasting period-Martin I. Bahl-Microbiology Open

Ovarian cycling and reproductive state shape the vaginal microbiota in wild baboons–Elizabeth A. Miller-BMC Microbiome

Plant, root, and soil microbiome

A decade of irrigation transforms the soil microbiome of a semi-arid pine forest-Martin Hartmann-Molecular Ecology

Methane Emissions and Microbial Communities as Influenced by Dual Cropping of Azolla along with Early Rice-Jingna Liu-Scientific Reports

Differential responses of soil bacterial communities to long-term N and P inputs in a semi-arid steppe-Ning Ling-Geoderma

Mineralization of “non-metabolizable” glucose analogues in soil: potential chemosensory mimics of glucose-Kyle Mason-Jones-Journal of Plant Nutrition and Soil Science

Deciphering composition and function of the root microbiome of a legume plant-Kyle Hartman-BMC Microbiome

Isolation and characterization of Rhizobium sp. strain YS-1r that degrades lignin in plant biomass-Colin A. Jackson-Journal of Applied Microbiology

Metagenomic insights into effects of spent engine oil perturbation on the microbial community composition and function in a tropical agricultural soil–Lateef B. Salam-Environmental Science and Pollution Research

Biocontrol effects of Brevibacillus laterosporus AMCC100017 on potato common scab and its impact on rhizosphere bacterial communities-Shengfu Chen-Biological Control

Co-inoculation with Enterobacter and Rhizobacteria on Yield and Nutrient Uptake by Wheat (Triticum aestivum L.) in the Alluvial Soil Under Indo-Gangetic Plain of India-Ashok Kumar-Journal of Plant Growth Regulation

 Ornamental flowers in new light: Artificial lighting shapes the microbial phyllosphere community structure of greenhouse grown sunflowers (Helianthus annuus L.)–Beatrix W. Alsanius–Scientia Horticulturae

Extremophiles

Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats-Meinhard Simon-ISME

Review: Marine Bacterioplankton Seasonal Succession Dynamics-Carina Bunse-Trends in Microbiology

Review: Stress response physiology of thermophiles–Preeti Ranawat-Archives of Microbiology

The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights-Emanuele Bosi-BMC Genomics

Sulfur compound oxidation and carbon co-assimilation in the haloalkaliphilic sulfur oxidizers Thioalkalivibrio versutus and Thioalkalimicrobium aerophilum-Wee Kiong Ang-Research in Microbiology

Geological and Geochemical Controls on Subsurface Microbial Life in the Samail Ophiolite, Oman–Kaitlin R. Rempfert-Extreme Microbiology

Microbial character related sulfur cycle under dynamic environmental factors based on the microbial population analysis in sewerage system-Qian Dong-Aquatic Microbiology

Similar community assembly mechanisms underlie similar biogeography of rare and abundant bacteria in lakes on Yungui Plateau, China-Jingqiu Liao-Limnology and Oceanography

Unraveling the microbial processes of black band disease in corals through integrated genomics-Yui Sato-Scientific Reports

Preliminary Phylogenetic Analysis of Thermophilic Bacteria Producing Protease isolated from Kuantan Malaysia -Essam A. Makky-JBSR

Identification of a novel fatty acid in the cell membrane of Chryseobacterium frigidisoli PB4T isolated from an East Antarctic glacier forefield-Kai Mangelsdorf-Organic Geochemistry

Phosphorus removal by marine bacterium enhanced with iron in the presence of silicon–Yanru Wang-Journal of Chemical Technology and Biotechnology

 Built Environment Microbiology

Developing Evidence-based Tools for Designing and Evaluating Hospital Inpatient Rooms–Xiaobo Quan-Journal of Interior Design

Building-related symptoms are linked to the in vitro toxicity of indoor dust and airborne microbial propagules in schools: A cross-sectional study-J T Salin-Environmental Research

Techniques

Review:  Application of meta-omics techniques to understand greenhouse gas emissions originating from ruminal metabolism-Robert J. Wallace-Genetics Selection Evolution

Balance Trees Reveal Microbial Niche Differentiation–James T. Morton-Ecological and Evolutionary Science

Virus

Review: Virus–host interactions and their roles in coral reef health and disease–Rebecca Vega Thurber-Nature Reviews Microbiology

Virome of US bovine calf serum-Mohammadreza Sadeghi-Biologicals

More Microbes

Bacillus zeae sp. nov. isolated from the rhizosphere of Zea mays– Peter Kämpfer-International Journal of Systematic and Evolutionary Microbiology

Microbes in News

Capnophilic Enterobacteriaceae-JM. Sahuquillo Arce-Diagnostic Microbiology and Infectious Disease

January 18, 2017

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Biogeographical patterns and assembly processes of bacterial on glaciers. And, a critical review of interactions between central nervous system and microbiota during health and neurological disease.

● Hospital microbiome

Microbiota-targeted therapies on the intensive care unit. Haak, BW . Current opinions in Critical Care

● Human microbiome and nervous system

Review: Interactions between the microbiota, immune and nervous systems in health and disease. Thomas C Fung.Nature Neuroscience

● Human gut microbiome

A fibrolytic potential in the human ileum mucosal microbiota revealed by functional metagenomic. Patrascu O. Scientific Report

Fecal microbiota transplantation to fight Clostridium difficile infections and other intestinal diseases. Moelling, K. Bacteriophage

● Animal experiments 

Pepsin egg white hydrolysate modulates gut microbiota in Zucker obese rats. Requena T. Food & Function

Effect of early antibiotic administration on cecal bacterial communities and their metabolic profiles in pigs fed diets with different protein levels. Zhang C. Anaerobe

● Animal microbiome 

Fiber degradation potential of natural co-cultures of Neocallimastix frontalis and Methanobrevibacter ruminantium isolated from yaks (Bos grunniens) grazing on the Qinghai Tibetan Plateau. Wei YQ. Anaerobe

Gut microbiota isolated from the European pond turtle (Emys orbicularis) and its antimicrobial resistance. Ruzauskas M. Polish Journal of Veterinary Sciences

● Plant, root, and soil microbiome

Restoration using Azolla imbricata increases nitrogen functional bacterial groups and genes in soil. Xiao-Ming Lu. Applied Microbiology and Biotechnology

Ectomycorrhizal fungal diversity associated with endemic Tristaniopsis spp. (Myrtaceae) in ultramafic and volcano-sedimentary soils in New Caledonia. Waseem M. Mycorrhiza

Diversity and Assembling Processes of Bacterial Communities in Cryoconite Holes of a Karakoram Glacier.Ambrosini, R.Microbial Ecology

● Water and extremophile microbiome 

Bacterial community structure and prevalence of Pusillimonas-like bacteria in aged landfill leachate. Remmas, N. Environmental Science and Pollution Research

January 14, 2017

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So it is technically already January 15 most countries, but I have been busy today preparing to transfer Microbiome Digest to an eager group of 20 new contributors. It takes a lot of time to hopefully be able to safe some time – if that makes sense.

My inbox is still full of new alerts, but here is what I have been able to “digest” so far. It’s already a lot!

General human microbiome

Navigating social and ethical challenges of biobanking for human microbiome research –
Kim H. Chuong – BMC Medical Ethics

Editorial: Influence of the microbiota on host physiology – moving beyond the gut
– Kim E. Barrett – The Journal of Physiology

Pregnancy and early life

* Pregnant women carrying microcephaly foetuses and Zika virus contain potentially pathogenic microbes and parasites in their amniotic fluid – Diogo Antonio Tschoeke – BMC Medical Genomics

Growth and Morbidity of Gambian Infants are Influenced by Maternal Milk Oligosaccharides and Infant Gut Microbiota – Jasmine C. C. Davis – Scientific Reports

Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates – Matthew R Olm – Genome Research

The Microbiome and Complement Activation A Mechanistic Model for Preterm Birth – Alexis B. Dunn – Biological Research for Nursing

Review: Asthma and the microbiome: defining the critical window in early life – Leah T. Stiemsma – Allergy, Asthma & Clinical Immunology

Human gut microbiome

Alcohol, microbiome, life style influence alcohol and non-alcoholic organ damage – Manuela G. Neuman – Experimental and Molecular Pathology

Serum Trimethylamine N-oxide, Carnitine, Choline and Betaine in Relation to Colorectal Cancer Risk in the Alpha Tocopherol and Beta Carotene Study – Kristin A. Guertin – Cancer Epidemiology, Biomarkers & Prevention

Laboratory Testing of Donors and Stool for Fecal Microbiota Transplantation for Recurrent C. difficile Infection – Michael H. Woodwort – Journal of Clinical Microbiology

Editorial: Gut microbiota: implications for sports and exercise medicine – Owen Cronin – British Journal of Sports Medicine

Review/Addendum: Pathogen control at the intestinal mucosa – H2O2 to the rescue
Ulla G. Knaus – Gut Microbes

Editorial: Tune into the rhythm of your bugs – Purna Kashyap – Science Translational Medicine

Preview: Are Gut Microbes Responsible for Post-dieting Weight Rebound? – Julien Chilloux – Cell Metabolism

Review: Involvement of Reduced Microbial Diversity in Inflammatory Bowel Disease – Dawei Gong – Gastroenterology Research and Practice

Year in Review: Gut microbiota in 2016: A banner year for gut microbiota research – Wendy S. Garrett – Nature Reviews Gastroenterology & Hepatology

Review: Gut microbiota disturbance during helminth infection: can it affect cognition and behaviour of children? – Vanina Guernier – BMC Infectious Diseases

Review: An expanding stage for commensal microbes in host immune regulation – Yan Shi – Cellular & Molecular Immunology

Perspective: Decoding host–microbiota communication in the gut – now we’re flying!
– Stephen J. Keely – The Journal of Physiology

Just based on the abstract, this appears a wild hypothesis potentially ignoring economic status, fiber consumption etc:  Latitude as a co-driver of human gut microbial diversity? – Emma Dikongué – Ideas that Push the Boundaries

Book: Gut Microbiome and Behavior, Volume 131 – John F. Cryan, Gerard Clarke – Elsevier

Animal experiments

Intestinal microbiota as a tetrahydrobiopterin exogenous source in hph-1 mice – Jaques Belik – Scientific Reports

Oral treatment with Lactobacillus rhamnosus attenuates behavioural deficits and immune changes in chronic social stress – Aadil Bharwani – BMC Medicine

Year in review: Microbiome in 2016: T follicular helper cells and the gut microbiome in arthritis – Veena Taneja – Nature Reviews Rheumatology

Animal microbiome

* Bacterial Communities Associated with Houseflies (Musca domestica L.) Sampled within and between Farms – Simon Bahrndorff – PLOS ONE

Microbiome variation in corals with distinct depth distribution ranges across a shallow–mesophotic gradient (15–85 m) – Bettina Glasl – Coral Reefs

Symbiont-induced odorant binding proteins mediate insect host hematopoiesis – Joshua B Benoit – eLIFE

Drivers of variation in species impacts for a multi-host fungal disease of bats  –
Kate E. Langwig – Philosophical Transactions of the Royal Society B

Sponges: Evaluating the core microbiota in complex communities: A systematic investigation – Carmen Astudillo-Garcia – Environmental Microbiology

Plant, root, and soil microbiome

Bacterial community composition in costal dunes of the Mediterranean along a gradient from the sea shore to the inland – Haggai Wasserstrom – Scientific Reports

Phylogenetic relatedness, phenotypic similarity and plant–soil feedbacks – Connor R. Fitzpatrick

Review: Microbiome and the future for food and nutrient security – Brajesh K. Singh – Microbial Biotechnology

Water microbiome

Similar community assembly mechanisms underlie similar biogeography of rare and abundant bacteria in lakes on Yungui Plateau, China – Jingqiu Liao – Limnology and Oceanography

Built environment microbiome

Microbial diversity in different compartments of an aquaponics system – Zala Schmautz – Archives of Microbiology

Food microbiology

The influence of thiamine and riboflavin on various spoilage microorganisms commonly found in beer – Barry Hucker – The Journal of The Institue of Brewing

Waste and pollution microbiology

Microbial flora analysis for the degradation of beta-cypermethrin – Zhang Qi – Environmental Science and Pollution Research

Fungi (also see Animal Microbiome)

Medical mycology and fungal immunology: new research perspectives addressing a major world health challenge – Neil A. R. Gow – Philosophical Transactions of the Royal Society B

Proteomics and metabolomics

MAHMI database: a comprehensive MetaHit-based resource for the study of the mechanism of action of the human microbiota – Aitor Blanco-Míguez – Database

Perspective: Progress in the biology and analysis of short chain fatty acids – Roel J. Vonk – The Journal of Physiology

Bioinformatics and biostatistics

Using Machine Learning to Identify Major Shifts in Human Gut Microbiome Protein Family Abundance in Disease – Mehrdad Yazdani – IEEE

Microscale Insight into Microbial Seed Banks – Kenneth J. Locey – Frontiers in Microbiology

* EMPeror: Bringing the Dynamic Microbiome to Life with Animations – Yoshiki Vázquez-Baeza – Cell Host & Microbe

Parallel-META 3: Comprehensive taxonomical and functional analysis platform for efficient comparison of microbial communities – Gongchao Jing – Scientific Reports

Identifying Host Genetic Variants Associated with Microbiome Composition by Testing Multiple Beta Diversity Matrices – Hua X. – Human Heredity

MetaDP: a comprehensive web server for disease prediction of 16S rRNA metagenomic datasets – Xilin Xu – Biophysics Reports

Techniques

Methodological flaws introduce strong bias into molecular analysis of microbial populations – N. Krakat – Journal of Applied Microbiology

Editorial: Microbial Nanoscopy: Breakthroughs, Challenges, and Opportunities – Yves F. Dufrêne – ACS Nano

More microbes

* Asgard archaea illuminate the origin of eukaryotic cellular complexity – Katarzyna Zaremba-Niedzwiedzka – Nature

* Species-Independent Attraction to Biofilms through Electrical Signaling – Jacqueline Humphries – Cell

A bacterial global regulator forms a prion – Andy H. Yuan – Science

A periplasmic polymer curves Vibrio cholerae and promotes pathogenesis – Thomas M. Bartlett – Cell

Assembly of a nucleus-like structure during viral replication in bacteria – Vorrapon Chaikeeratisak – Science

Microbes in the news

Man’s best friend, bacteria’s worst enemy: dog sniffs out superbug in Canadian hospital – Ashifa Kassam – The Guardian

This article is not as bad as the title suggests but with photoshopped images:
Revealed: The millions of stomach-churning bacteria lurking in YOUR hair, skin, lungs, gut and mouth – and why – Mary Kekatos – Daily Mail

Video: Career profiles: Program Director at National Science Foundation Matthew Kane – American Society for Microbiology

A clear picture of bacteria: A new study has frozen bacteria extremely fast to gain a true-to-nature image of the internal and external structure – Science Daily

December 31, 2016

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Human lung microbiome

Study of the Lung Microbiome. Have We Reached the End of the Beginning?  – Alison Morris – American Journal of Respiratory and Critical Care Medicine

Microbes at nearly sterile sites

The Clinical Impact of Rapid, Direct MALDI-ToF Identification of Bacteria from Positive Blood Cultures – Kathryn French – PLOS ONE

Animal experiments

Impacts of resistant starch and wheat bran consumption on enteric inflammation in relation to colonic bacterial community structures and short-chain fatty acid concentrations in mice – Janelle A. Jiminez – Gut Pathogens

Animal microbiome

A Review of Bacterial Interactions With Blow Flies (Diptera: Calliphoridae) of Medical, Veterinary, and Forensic Importance – Jeffery K. Tomberlin – Annals of the Entomological Society of America

Comparative community structure of archaea in rumen of buffaloes and cattle – Shyam S Paul – Journal of the Science of Food and Agriculture

Plant, root, and soil microbiome

A decade of irrigation transforms the soil microbiome of a semi-arid pine forest – Martin Hartmann – Molecular Ecology

Water and extremophile microbiome

Exploration of cultivable fungal communities in deep coal-bearing sediments from ∼1.3 to 2.5 km below the ocean floor – Chang-Hong Liu – Environmental Microbiology

Strengths and Biases of High-Throughput Sequencing Data in the Characterization of Freshwater Ciliate Microbiomes – Vittorio Boscaro – Microbial Ecology

Microbial diversity and autotrophic activity in Kamchatka hot springs – Alexander Yu – Extremophiles

Cyanobacterial harmful algal blooms are a biological disturbance to western Lake Erie bacterial communities – Michelle A. Berry – Environmental Microbiology

Built environment microbiome

An emerging paradox: Toward a better understanding of the potential benefits and adversity of microbe exposures in the indoor environment – J. Mensah-Attipoe – Indoor Air

Sandpits as a reservoir of potentially pathogenic fungi for children – Anna Wójcik – Ann Agric Environ Med

Food microbiome

Microbiological characterization of vegetables and their rhizosphere soil in Eastern Poland – Teresa Kłapeć – Ann Agric Environ Med

Proteomics

Comparing genome versus proteome-based identification of clinical bacterial isolates
Valentina Galata – Briefings Bioinformatics

Microbes in the news

Now Sixty food poisoning cases ‘from farm’s trendy raw milk’ leads a judge to slap a ban on the business to block them from selling any more – Liz Hull – The Daily Mail

The Changing Face of American Forests. How pollution deposes dominant tree species and releases soil carbon – Nala Rogers – Inside Science

Can Bacteria Help Stop the Spread of Disease? – Infection Control Today

How Do Multidrug-Resistant Bacteria Survive Antibiotics Without Resistance Genes? – Contagion LIve

Easy, crunchy, healthy sauerkraut – Cindy Grace – AJC

Science, publishing, and career

Who Believes in the Storybook Image of the Scientist? – Coosje L. S. Veldkamp – Accountability in Research

What Scientists Think About Scientists – Neuroskeptic – Discover

November 19, 2016

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Metformin and diabetes, lizards, Brazilian tree phyllosphere, Amazonian dark earth, air pollution in China, microbiomes of ice cream and cannabis.

General microbiome

Phylosymbiosis: Relationships and Functional Effects of Microbial Communities across Host Evolutionary History – Andrew W. Brooks – PLOS Biology

Review: A place for host–microbe symbiosis in the comparative physiologist’s toolbox – Kevin D. Kohl – Journal of Experimental Biology

Human skin and wound microbiology

Review: Cooperative Evolutionary Strategy between the Bacteriome and Mycobiome – Mahmoud Ghannoum – mBio

Human gut microbiome

Metformin Is Associated With Higher Relative Abundance of Mucin-Degrading Akkermansia muciniphila and Several Short-Chain Fatty Acid–Producing Microbiota in the Gut – Jacobo de la Cuesta-Zuluaga – Diabetes Care

News: Metformin Alters Gut Microbiota Composition in Diabetes – Doctors Lounge

Review (Blastocystis) : Modulating the Gut Micro-Environment in the Treatment of Intestinal Parasites – Luis Vitetta – Journal of Clinical Medicine

Review: Recent advances in Entamoeba biology: RNA interference, drug discovery, and gut microbiome – Pedro Morgado – F1000 Research

Microbes in blood, urine, and tissue

Changes in blood microbiota profiles associated with liver fibrosis in obese patients: A pilot analysis – Benjamin Lelouvier – Hepatology

Review: The Urinary Tract Microbiome in Health and Disease – Isabel M. Aragón – European Urology Focus

Animal experiments

A High-Fat High-Sucrose Diet Rapidly Alters Muscle Integrity, Inflammation and Gut Microbiota in Male Rats – Kelsey H. Collins – Scientific Reports

Animal microbiome

Gut microbial ecology of lizards: insights into diversity in the wild, effects of captivity, variation across gut regions, and transmission – Kevin D. Kohl – Molecular Ecology

In liver, not in feces: Metagenomic Evaluation of Bacteria from Voles – Katja A. Koskela – Vector-Borne and Zoonotic Diseases

Plant, root, and soil microbiome

Phyllosphere Metaproteomes of Trees from the Brazilian Atlantic Forest Show High Levels of Functional Redundancy – M.R. Lambais – Microbial Ecology

Metagenome sequencing of the microbial community of two Brazilian anthropogenic Amazon dark earth sites, Brazil – Leandro Nascimento Lemos – Genomics Data

Metal-resistant rhizobacteria isolates improve Mucuna deeringiana phytoextraction capacity in multi-metal contaminated soils from a gold mining area – Cácio Luiz Boechat – Environmental Science and Pollution Research

Identification of the Core Set of Carbon-Associated Genes in a Bioenergy Grassland Soil
Adina Howe – PLOS ONE

The nutrient preference of plants influences their rhizosphere microbiome – Feng Cai – Applied Soil Ecology

Effect of microbial-based inoculants on nutrient concentrations and early root morphology of corn (Zea mays) – Pamela Calvo – Journal of Plant Nutrition and Soil Science

The impact of winter legume and cereal cover crops on rhizosphere microbial communities of subsequent vegetable crops for contrasting crop decline – L.M. Manici – Biological Control

Impacts of protected colonial birds on soil microbial communities: When protection leads to degradation – María T. Domínguez – Soil Biology and Biochemistry

Water and pollution microbiome

Nearshore Pelagic Microbial Community Abundance Affects Recruitment Success of Giant Kelp, Macrocystis pyrifera – Megan M. Morris – Frontiers in Microbiology

Biostimulation and microbial community profiling reveal insights on RDX transformation in groundwater – Dongping Wang – Microbiology Open

Screening and In Situ Monitoring of Potential Petroleum Hydrocarbon Degraders in Contaminated Surface Water – Bulent Icgen – Clean Soil Air Water

Source tracking using microbial community fingerprints: Method comparison with hydrodynamic modelling – D.T. McCarthy – Water Research

Air microbiology

Airborne particulate matter pollution in urban China: A chemical mixture perspective from sources to impacts – Ling Jin – National Science Review

Review: Monitoring of the airborne biological particles in outdoor atmosphere. Part 1: Importance, variability and ratios – Andrés Núñez – International Microbiology

Review: Monitoring of airborne biological particles in outdoor atmosphere. Part 2: Metagenomics applied to urban environments – Andrés Núñez – International Microbiology

Food and cannabis microbiology

Metagenomic analysis of medicinal Cannabis samples; pathogenic bacteria, toxigenic fungi, and beneficial microbes grow in culture-based yeast and mold tests – Kevin McKernan – F1000 Research

Enrichment dynamics of Listeria monocytogenes and the associated microbiome from naturally contaminated ice cream linked to a listeriosis outbreak – Andrea Ottesen – BMC Microbiology

Bioinformatics

[PDF] A small-sample multivariate kernel machine test for microbiome association studies – Xiang Zhan – Fred Hutch Research

More microbiology

Quorum Sensing Controls Adaptive Immunity through the Regulation of Multiple CRISPR-Cas Systems – Adrian G. Patterson – Molecular Cell

Bacteria communicate to ramp up collective immune response to viral threats – Science Daily

A Molecular Genetic Basis Explaining Altered Bacterial Behavior in Space – Luis Zea – PLOS ONE

Alabama researcher helps solve mystery of runaway bacteria on spaceships – AL.com

Microbes in the news

Podcast: This Week in Microbiology: microbial DNA found on ATM machines in New York City, and how hydraulic fracturing, or fracking, alters microbial ecosystems deep in the Earth – TWIM

One swab from the surface of your smartphone can tell scientists all about your lifestyle
– Karen Turner – Washington Post

This bacteria is getting harder for kids to fight – Mashable

Armpit Bacteria Transplants Could Save Us From Our Stink – Kaleigh Rogers – Motherboard

Worrying traces of resistant bacteria in air – EurekAlert

 

Science, publishing, and career

An Open Letter from and to Female Scientists – Kelly Ramirez – Scientific American
500 Women Scientists: An open letter from women of science

Who Will Advise Trump on Science? – Ed Yong – The Atlantic

 

 

 

November 18, 2016

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Pathogens in rheumatoid arthritis, Staph in hog workers, pathogens in bat guano, host colonization determinants, microbes on New York ATM keypads.

Human oral microbiome

Clinical effects of probiotics containing Bacillus species on gingivitis: a pilot randomized controlled trial – B. Alkaya – Journal of Periodontal Research

Human respiratory microbiome

Livestock-Associated, Antibiotic-Resistant Staphylococcus aureus Nasal Carriage and Recent Skin and Soft Tissue Infection among Industrial Hog Operation Workers – Maya Nadimpalli – PLOS ONE

Hog workers carrying livestock-related, drug-resistant bacteria may be developing skin infections – News Medical

Human gut microbiome

A method for automated pathogenic content estimation with application to rheumatoid arthritis – Xiaoyuan Zhou and Christine Nardini – BMC Systems Biology

Imbalance of bacteriome profiles within the Finnish Diabetes Prediction and Prevention study: Parallel use of 16S profiling and virome sequencing in stool samples from children with islet autoimmunity and matched controls – Ondrej Cinek – Pediatric Diabetes

Review: Diet, microorganisms and their metabolites, and colon cancer – Stephen J. D. O’Keefe – Nature Reviews Gastroenterology & Hepatology

Review: Gut microbiota and functional diseases of the gastrointestinal tract – Nicola Imperatore – Minerva Gastroenterologica e Dietologlica

Animal experiments

Gram-positive bacteria are held at a distance in the colon mucus by the lectin-like protein ZG16 – Joakim H. Bergström – PNAS

In bees: Genome-wide screen identifies host colonization determinants in a bacterial gut symbiont – J. Elijah Powell – PNAS

A new pathway for the gut microbiota to modulate the brain: activation of pattern-recognition receptors by microbial products – P Zheng – Mol Psychiatry

The bacterial peptidoglycan-sensing molecule Pglyrp2 modulates brain development and behavior – T Arentsen – Mol Psychiatry

Animal microbiome

Bats: Microbiome analysis reveals the abundance of bacterial pathogens in Rousettus leschenaultii guano – Sunil Banskar – Scientific Reports

Plant, root, and soil microbiome

Plant nodulation inducers enhance horizontal gene transfer of Azorhizobium caulinodans symbiosis island – Jun Ling – PNAS

Built environment microbiome

Microbial Community Patterns Associated with Automated Teller Machine Keypads in New York City – Holly M. Bik – mSphere

Food microbiome

Inferring the role of microorganisms in water kefir fermentations – Abigail Martínez-Torre – International Journal of Food Science & Technology

Microbes in the news

Australian Academy of Sciences announces 2017 honorific awardees, including infectious diseases professor Kathryn Elizabeth Holt

Common Skin Bacteria Could Save You From Other Skin Diseases – Monica U Santos – iTechPost
Skin bacterium releases enzyme that may protect against damage and disease – Catherine Paddock – Medical News Today

The Microbiome’s Role in Precision Medicine, with Jun Sun and Jack Gilbert – Kristen Thometz – WTTW

Microbes on the market

uBiome in the news: Startup will ‘DNA test’ your poop to analyze your gut health – Natural News

Bristol-Myers Squibb and Enterome Announce Immuno-Oncology Collaboration Focused on Microbiome-Derived Biomarkers, Drug Targets and Bioactive Molecules – BusinessWire

November 15, 2016

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Microbial profiling in the classroom, viral abundance in seawater membrane vesicles, two Akkermansia in vitro studies, the phyllospere of Phoenix’ urban forest, the (im)possibility to reconstruct plasmids, high confidence protein annotations.

General microbiome

Microorganisms as Scaffolds of Host Individuality: An Eco-Immunity Account of the Holobiont – Lynn Chiu – PhilSci Archive

Microbial Community-Level Physiological Profiling as an Inquiry Laboratory Exercise – Pamela A. Marshall – The American Biology Teacher

Human oral microbiome

Bacterial communities associated with apical periodontitis and dental implant failure – Simon Dingsdag – Microbial Ecology in Health and Disease

Human respiratory microbiome

Review: Development of the respiratory tract microbiota in cystic fibrosis – Emma M. de Koff –  Current Opinion in Pulmonary Medicine

Human gut microbiome

Oral application of Escherichia coli bacteriophage: safety tests in healthy and diarrheal children from Bangladesh – Shafiqul Alam Sarker – Environmental Microbiology

The SURMetaGIT study: Design and rationale for a prospective pan-omics examination of the gastrointestinal response to Roux-en-Y gastric bypass surgery – Priscila Sala – Journal of International Medical Research

Review: The Human Microbiome and I-Cubed: A Modern Medical Paradigm – David S. Younger – World Journal of Neuroscience

Animal and in vitro models

In vitro colonisation of the distal colon by Akkermansia muciniphila is largely mucin and pH dependent – F. Van Herreweghen – Beneficial Microbes

Akkermansia muciniphila mediates negative effects of IFNγ on glucose metabolism – Renee L. Greer – Nature Communications

Animal microbiome

Black rhinoceros (Diceros bicornis) and domestic horse (Equus caballus) hindgut microflora demonstrate similar fermentation responses to grape seed extract supplementation in vitro – N. F. Huntley – Journal of Animal Physiology and Animal Nutrition

Plant, root, and soil microbiome

Sensitive responders among bacterial and fungal microbiome to pyrogenic organic matter (biochar) addition differed greatly between rhizosphere and bulk soils – Zhongmin Dai – Scientific Reports

Thesis: The Phyllosphere of Phoenix’s Urban Forest: Insights from a Publicly-Funded Microbial Environment – Benjamin C. MacNeille – Arizona State University

Diversity of phylloplane microflora in certain tea cultivars of Assam, North-East India – Amarjyoti Tanti – European Journal of Biological Research

Review: Do genetically modified plants affect adversely on soil microbial communities?
– Zheng-jun Guan – Agriculture, Ecosystems & Environment

Water and extremophile microbiome

The Microbiota of Recreational Freshwaters and the Implications for Environmental and Public Health – Chang Soo Lee – Frontiers in Microbiology

Functional diversity of microbial communities in pristine aquifers inferred by PLFA – and sequencing – based approaches – Valerie F. Schwab – Biogeosciences

Trade-off between taxon diversity and functional diversity in European lake ecosystems – Lars Grossmann – Molecular Ecology

Glycerol enhances fungal germination at the water-activity limit for life – Andrew Stevenson – Environmental Microbiology

Bacterial and archeal community composition in hot springs from Indo-Burma region, North-east India – Amrita Kumari Panda – AMB Express

Phages and viruses

Next-generation sequencing and norovirus – Matthew Cotten & Marion Koopmans – Future Virology

Membrane vesicles in sea water: heterogeneous DNA content and implications for viral abundance estimates – Steven J Biller – ISME Journal

Metagenomics and bioinformatics

On the (im)possibility to reconstruct plasmids from whole genome short-read sequencing data – Sergio Arredondo-Alonso – bioRxiv

EMDUnifrac: Exact linear time computation of the Unifrac metric and identification of differentially abundant organisms – Jason McClelland – bioRxiv

Optimal prediction of the number of unseen species – Alon Orlitsky – PNAS

Constraint-based stoichiometric modelling from single organisms to microbial communities
– Willi Gottstein – Journal of the Royal Society Interface

Metabolomics, culturomics, proteomics

Critical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns – Emma Timmins-Schiffman – The ISME Journal

Prioritizing Natural Product Diversity in a Collection of 146 Bacterial Strains Based on Growth and Extraction Protocols – Max Crüsemann – Journal of Natural Products

Probiotics

Review: Probiotics and Subclinical Psychological Symptoms in Healthy Participants: A Systematic Review and Meta-Analysis – Jennifer McKean – The Journal of Alternative and Complementary Medicine

Microbes in the news

Good News at Fred Hutch: Evolutionary biologists Drs. Harmit Malik and Jesse Bloom win American Society for Microbiology awards – Fred Hutch

NTU don once downed a dish of live bacteria, for science’s sake – Straits Times

MCR-1 resistance gene could make its way into bacteria and superbugs in Australia – NT News
Biofilm battle is key to antibiotic war – University of Queensland

‘Probiotics’ on salad greens could make them safer, healthier – The University of Queensland

Monique Keiran: Laziness and hubris making us sick – Times Colonist

From the American Heart Association annual meeting: Could C-Section Birth Raise Child’s Risk of Obesity? – Dennis Thompson – Pantagraph

November 14, 2016

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Infant gut microbiota, oral microbiota of farmworkers with pesticide exposure, critically ill patients, probiotics and Alzheimer’s, Sutterella is a commensal.

Events

Cheese Cultures & Microbiology Class, December 2, 2016, Petaluma – California Artisan Cheese Guild – Eventbrite

Pregnancy and early life

A comparison of intestinal microbiota in a population of low-risk infants exposed and not exposed to intrapartum antibiotics: The Baby & Microbiota of the Intestine cohort study protocol – Julia Simioni – BMC Pediatrics

Establishment and development of the intestinal microbiota of preterm infants in a Lebanese tertiary hospital – Tarek Itania – Anaerobe

Human oral microbiome

Human Oral Buccal Microbiomes Are Associated with Farmworker Status And Azinphos-methyl Agricultural Pesticide Exposure – Ian B. Stanaway – Applied and Environmental Microbiology

News: Study finds link between pesticide exposure and microbiome changes – Brooks Hays – UPI
Pesticide exposures can cause changes in oral microbiome – ASM

Molecular detection of bacteria associated to caries activity in dentinal lesions – Beatriz Gonçalves Neves – Clinical Oral Investigations

Review: Microbial Profiles and Detection Techniques in Peri-Implant Diseases: a Systematic Review – Miguel Padial-Molina – J Oral Maxillofac Res

Human skin microbiome

A Precision Microbiome Approach Using Sucrose for Selective Augmentation of Staphylococcus epidermidis Fermentation against Propionibacterium acnes – Yanhan Wang – Int J Mol Sci

A novel enzyme with antioxidant capacity produced by the ubiquitous skin colonizer Propionibacterium acnes – Maria Allhorn – Scientific Reports

Skin bacteria could protect against disease – Science Daily

Human vaginal microbiome

Escherichia coli and Enterococcus faecalis are able to incorporate and enhance a pre-formed Gardnerella vaginalis biofilm – Joana Castro – Pathogens and Disease

Human gut microbiome

Critically ill patients demonstrate large interpersonal variation in intestinal microbiota dysregulation: a pilot study – Jacqueline M. Lankelma – Intensive Care Medicine

Mucosal Prevalence and Interactions with the Epithelium Indicate Commensalism of Sutterella spp. – Kaisa Hiippala – Frontiers in Microbiology

Review: Impact of Microbes on the Pathogenesis of Primary Biliary Cirrhosis (PBC) and Primary Sclerosing Cholangitis (PSC) – Jochen Mattner – Int J Mol Sci

Animal microbiome

Review: Microbiota-host interplay at the gut epithelial level, health and nutrition – Jean-Paul Lallès – Journal of Animal Science and Biotechnology

Plant, root, and soil microbiome

Root bacterial endophytes alter plant phenotype, but not physiology – Jeremiah A. Henning – Peer J

Cultivation Versus Molecular Analysis of Banana (Musa sp.) Shoot-Tip Tissue Reveals Enormous Diversity of Normally Uncultivable Endophytic Bacteria – Pious Thomas – Microbial Ecology

Water microbiome

Unraveling the microbial community of a cold groundwater catchment system – Burga Braun – Water Research

Built environment microbiome

Size-related bacterial diversity and tetracycline resistance gene abundance in the air of concentrated poultry feeding operations – Min Gao – Environmental Pollution

Metabolomics

Review: Emerging roles of xenobiotic detoxification enzymes in metabolic diseases – Michael C. Petriello – Reviews on Environmental Health

Probiotics

Effect of probiotic supplementation on cognitive function and metabolic status in Alzheimer’s disease: a randomized, double-blind, and controlled trial – Elmira Akbari -Frontiers in Aging Neuroscience

News: Probiotics improve cognition in Alzheimer’s patients – Medical Xpress

More microbiology

tRNA-mediated codon-biased translation in mycobacterial hypoxic persistence – Yok Hian Chionh – Nature Communications

Cracking the code for dormant bacteria. Newly discovered genetic code controls bacterial survival during infections – Anne Trafton – MIT News Office

Microbes in the news

Monitoring in Real Time the Formation and Removal of Biofilms From Clinically Relevant Pathogens – PR Web

From the American College of Rheumatology Annual Scientific Meeting: Gut bacteria may be a trigger for antiphospholipid syndrome – EurekAlert

Three University of Maryland students are sending bacteria samples into space – Rachel Kuipers – the Diamondback

University of Texas at Dallas named “Milestones in Microbiology” – Joanna Urban – ASM

Bethany professor Matthew Swearingen receives research grant – Weirton Daily Times

Scientists try bacteria to halt invasive cheatgrass overwhelming the West – Keith Ridler – LA Times

November 11, 2016

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The human microbiome before birth, the HIV lung microbiome, leprosy in squirrels, and ticklish rats. That latter story has nothing to do with microbiology, but we can all use some uplifting stories.

Events

Advancing Microbiome Research Symposium: Microbiome & Disease – November 17, 2016 – Chicago, IL, USA

HIV Microbiome Workshop 2016 – November 17-18, 2016 – Bethesda, MD, USA.

2nd Annual European Microbiome Congress – November 30-Dec 1, 2016 – London, UK

Microbiome Drug Development Summit Europe – Jan 24-26 January 2017. Paris, France

North American Microbiome Congress / Human Microbiome Conference January 24-25 2017, San Diego, CA

Pregnancy and early life

The Human Microbiome before Birth – Martin J. Blaser and Maria G. Dominguez-Bello

Human respiratory microbiome

The bronchial epithelial cell bacterial microbiome and host response – Marc A. Sze – BMC Pulmonary Medicine

Biofilms in ventilator-associated pneumonia – Laia Fernández-Barat – Future Microbiology

Human gut microbiome

An evaluation of the therapeutic potential of fecal microbiota transplantation to treat infectious and metabolic diseases – Albert K Groen – EMBO Molecular Medicine

Association of colorectal carcinogenesis pathway with life style and intestinal microbiome based on the genome and epigenome abnormalities – Nihon Shokakibyo Gakkai Zasshi

Perspective: The Liver at the Nexus of Host-Microbial Interactions – Andrew J. MacPharson – Cell Host & Microbe

Animal experiments

Expression of recombinant human lysozyme in transgenic chicken promotes the growth of Bifidobacterium in the intestine and improves postnatal growth of chicken – Hai Wang – AMB Express

Chronic Early-life Stress in Rat Pups Alters Basal Corticosterone, Intestinal Permeability, and Fecal Microbiota at Weaning: Influence of Sex – Nabila Moussaoui – J Neurogastroenterol Motil.

Animal microbiome (and infection)

Red squirrels in the British Isles are infected with leprosy bacilli – Charlotte Avanzi – Science
Red squirrels in the British Isles are infected with leprosy bacteria – Phys.org
Leprosy Surprise: Medieval Scourge Is Lurking In British Squirrels – Michaeleen Doucleff – NPR

Bacterial Associations Across House Fly Life History: Evidence for Transstadial Carriage From Managed Manure – Klara Zurek – Journal of Insect Science

Built environment microbiology

Review: Constructed Wetlands Revisited: Microbial Diversity in the -omics Era. – Olga Sánchez – Microbial Ecology

Metagenomics and bioinformatics

Commentary: Insights into microbial ecosystems using a new computational approach – Thuy Do – Oral Diseases

Microbes in the news

Are we ready for consumer microbiome testing? – Juliet Preston – MedCityNews

Raining Cats and Dogs… and Bacteria? – Julie Taylor – uBiome

Scientists Try Bacteria to Halt Invading Cheatgrass in West – Keith Ridler – ABC News / Associated Press

Targeting pathogenic bacteria – using phage-derived proteins, proteins developed from the bacteria-invading viruses, for detection of pathogenic bacteria – Science Daily

Your flu risk may be linked to the year you were born – Jacqueline Howard – CNN

How ‘Psychobiotics’ Use Gut Bacteria To Treat Mental Illness. Targeting the gut could create a new class of psychiatric treatments – Carolyn Gregoire – The Huffington Post

Animal Science Professor Identifies Gut Microbiota Signatures of Healthy Aging – ScienceBlog

Quest to map Africa’s soil microbiome begins. Sub-Saharan project could one day help ecosystems to resist climate change and improve agriculture – Sarah Wild – Nature

Microbiome, Hidden Chemical Secrets, Being Accessed At Scripps Pier In San Diego – PR Newswrire

New Method Allows Scientists to Detect the Presence in Ham of the Parasite that Causes Toxoplasmosis – SciCasts

Bik’s non-microbiology Picks

Why are we ticklish? Scientists who tickled rats offer an intriguing answer – Karen Kaplan – LA Times
Neural correlates of ticklishness in the rat somatosensory cortex – S. Ishiyama – Science

November 10, 2016

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Fanconi anemia, Clostridium subcluster decreased in UC, ectomycorrhizas in oak forests, cryoconite hole anaerobes.

Human oral microbiome

The Salivary Microbiome and Oral Cancer Risk: A Pilot Study in Fanconi Anemia – C.P. Furquim – Journal of Dental Research

Human gut microbiome

A Single Species of Clostridium Subcluster XIVa Decreased in Ulcerative Colitis Patients – Kozue Takeshita – Inflammatory Bowel Diseases

Composition of gut microbiota in infants in China and global comparison – Ya-Shu Kuang – Scientific Reports

Changes in duodenal tissue-associated microbiota following hookworm infection and consecutive gluten challenges in humans with coeliac disease – Paul Giacomin – Scientific Reports

Making sense of the cause of Crohn’s – a new look at an old disease – Anthony W. Segal – F1000 Research

Metaanalysis: The Emerging Role of the Gut Microbiome in Adult Patients With Multiple Sclerosis – Pamela K. Newland – Journal of Neuroscience Nursing

Review: Escherichia coli Nissle 1917 in Ulcerative Colitis Treatment: Systematic Review and Meta-analysis – Giuseppe Losurdo – Journal of Gastrointestinal and Liver Diseases

Human blood and tissue microbiology

Comparing culture and molecular methods for the identification of microorganisms involved in necrotizing soft tissue infections – Vibeke Børsholt Rudkjøbing – BMC Infectious Diseases

Review: Mechanisms of Bacterial Colonization of Implants and Host Response – Christof Wagner – Advances in Experimental Medicine and Biology

Animal models

Fecal Microbiota and Metabolome in a Mouse Model of Spontaneous Chronic Colitis: Relevance to Human Inflammatory Bowel Disease – Ainsley M. Robinson – Inflammatory Bowel Diseases

Microbiota induces tonic CCL2 systemic levels that control pDC trafficking in steady state – M Swiecki – Mucosal Immunology

Siderophore-based immunization strategy to inhibit growth of enteric pathogens – Martina Sassone-Corsia – PNAS

Akkermansia muciniphila improves metabolic profiles by reducing inflammation in chow diet-fed mice – Shaoqian Zhao – Journal of Molecular Endocrinology

The highly variable microbiota associated to intestinal mucosa correlates with growth and hypoxia resistance of sea bass, Dicentrarchus labrax, submitted to different nutritional histories – François-Joël Gatesoupe – BMC Microbiology

Plant, root, and soil microbiome

Plant growth patterns in a tripartite strip relay intercrop are shaped by asymmetric aboveground competition – Chengdong Huang – Field Crops Research

First detection of Endogone ectomycorrhizas in natural oak forests – Kohei Yamamoto – Mycorrhiza

[PFD] Grape berry bacterial inhibition by different copper fungicides – Guilherme Martins – BIO Web of Conferences

Sensitive responders among bacterial and fungal microbiome to pyrogenic organic matter (biochar) addition differed greatly between rhizosphere and bulk soils – Z Dai – Scientific Reports

Water and extremophile microbiome

Enrichment of Cryoconite Hole Anaerobes: Implications for the Subglacial Microbiome – Marek K. Zdanowski – Microbial Ecology

Food microbiology

Sensory, microbiological and physico-chemical characterization of Klila, a traditional cheese made in the south-west of Algeria – Benamara R. N. – African Journal of MIcrobiology Research

Does organically produced lettuce harbor higher abundance of antibiotic resistance genes than conventionally produced? – Bokai Zhu – Environment International

Built environment microbiology

Microbiological evaluation of drinking water available in schools in Cruz das Almas, Brazil – Marcos Vinicius Silva de Andrade – African Journal of MIcrobiology Research

Bioinformatics and metagenomics

Book chapter: DecontaMiner: A Pipeline for the Detection and Analysis of Contaminating Sequences in Human NGS Sequencing Data – Ilaria Granata – Dynamics of Mathematical Models in Biology

More microbiology

Predatory Bacteria Attenuate Klebsiella pneumoniae Burden in Rat Lungs – Kenneth Shatzkes – mBio

Predatory bacteria offer potential solution to drug resistance problem – Phys.org
Predatory Bacteria Can Cannibalize Drug-Resistant Bugs – Seeker

Bik’s non-microbiology Picks

Beyond Our Borders? Public Resistance to Global Genomic Data Sharing – Mary A. Majumder – PLOS Biology

Origins of Biodiversity – Michael J. Benton – PLOS Biology

Microbes in the news

Researchers exploring new platform for detecting pathogenic bacteria using bacteriophages – News Medical

Novel vaccines block iron scavenging by bacteria. Agents starve bacteria by raising antibodies to capture the small molecules the microbes release to harvest iron – Stu Borman – Chemical & Engineering News

What’s lurking in the water in Shedd Aquarium – Lisa Bertagnoli – Chicago Business

New biophotonic light sensor can detect Legionella bacteria in minutes – News Medical

Scrubs And Superbug Transmission In ICUs: What We Still Don’t Know Can Kill You – Judy Stone – Forbes
Dangerous bacteria could hitch a ride on nurses’ scrubs – Rachel Sereix – Duke Chronicle

Microbes and the market

Clinical Microbiology Market Expected to Reach $6.72 billion by 2022 – Medgadget

Science, publishing, and career

Rosalind’s Ghost: Biology, Collaboration, and the Female – Caroline Wagner – PLOS Biology

Differences in Collaboration Patterns across Discipline, Career Stage, and Gender – Xiao Han T. Zeng – PLOS Biology