Author Archives: eliesbik

November 23, 2016

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Why You Should Probably Be Glad You’re Not a Brown Bear or an Edible Dormouse – Julie Taylor – uBiome blog

“Thankfully, when you have your own microbiome analyzed by uBiome, you’ll be relieved to know that we won’t be sending round a guy in a helicopter with a tranquilizer gun. All you need to do is lightly swab a piece of used toilet paper.”

Human gut microbiome

Efficacy of Sterile Fecal Filtrate Transfer for Treating Patients With Clostridium difficile Infection – Stephan J. Ott – Gastroenterology

Research highlight: Microbiota under pressure – Andrea Aguilar – Nature Reviews Nephrology

Review: Candida albicans cell-type switching and functional plasticity in the mammalian host – Suzanne M. Noble – Nature Reviews Microbiology

Review: Gut Bacteria and Hydrogen Sulfide: The New Old Players in Circulatory System Homeostasis – Lenka Tomasova – MDPI Molecules

Microbiology of nearly sterile sites

Genomes of Gardnerella Strains Reveal an Abundance of Prophages within the Bladder Microbiome – Kema Malki – PLOS ONE

Animal experiments

Eye of the Finch: Characterization of the Ocular Microbiome of House Finches in Relation to Mycoplasmal Conjunctivitis – Courtney A. Thomason – Environmental Microbiology

Composition and diversity of mucosa-associated microbiota along the entire length of the pig gastrointestinal tract; dietary influences – Jennifer Kelly – Environmental Microbiology

Heat Stress Affects Facultative Symbiont-Mediated Protection from a Parasitoid Wasp – Eleanor R. Heyworth – PLOS ONE

Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium – Sandrine Brugiroux – Nature Microbiology

Assessment of the Fecal Microbiota in Beef Calves – J.S. Weese – Journal of Veterinary Internal Medicine

The role of microbiota in compensatory growth of protein-restricted rats – Yizhi Zhu – Microbial Biotechnology

Animal microbiome

Molecular diversity of bacterial endosymbionts associated with dagger nematodes of the genus Xiphinema (Nematoda: Longidoridae) reveals a high degree of phylogenetic congruence with their host – Juan E. Palomares-Rius – Molecular Ecology

Plant, root, and soil microbiome

Shared and host-specific microbiome diversity and functioning of grapevine and accompanying weed plants – Abdul Samad – Environmental Microbiology

Root isoflavonoids and hairy root transformation influence key bacterial taxa in the soybean rhizosphere – Laura J. White – Environmental Microbiology

Water and extremophile microbiome

Abundant and rare picoeukaryotic sub-communities present contrasting patterns in the epipelagic waters of marginal seas in the northwestern Pacific Ocean – Wenxue Wu – Environmental Microbiology

Bringing microbial diversity into focus: high-resolution analysis of iron mats from the Lō‘ihi Seamount – Jarrod J. Scott – Environmental Microbiology

Probing the evolution, ecology and physiology of marine protists using transcriptomics – David A. Caron – Nature Reviews Microbiology

Food microbiology

High-Throughput Sequencing of Viable Microbial Communities in Raw Pork Subjected to a Fast Cooling Process – Chao Yang – Journal of Food Science

Microbes in the news

Set of 12 microbiology postcards – PREORDER – Microbes and Molecules sciart card set featuring bacteria and fungi, gift for scientist – The Vexed Muddler – Etsy.com

Traces of antibiotic-resistant bacteria have been found in polluted city air. Not good – David Nield – ScienceAlert

Why Sprouts Are Especially Good At Harboring Dangerous Bacteria – Sara G. Miller – LiveScience / Huffington Post

Infectious Diseases Keep Delivering Surprises To The U.S. – Katherine Hobson – NPR

UVA Microbiologist Expands His Research Across the Atlantic – University of Virginia

By Wagging its ‘Tail,’ Bacteria Common in CF Lung Infections May Initiate Immune Reaction – Joana Fernandes – Cystic Fibrosis News Today

‘In five years this will be routine’: Map My Gut start-up offers personalised microbiome advice – Annie-Rose Harrison-Dunn – NutraIngredients

Can bacteria in yogurt calm your anxiety? – Jeff Sossamon – Futurity

November 22, 2016

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Vaginal Mirobiome in PPROM, Prevotella copri and rheumatoid arthritis, mice transplanted with stool from lean or obese humans, archaea in a pond.

Pregnancy and early life

High Diversity and Variability in the Vaginal Microbiome in Women following Preterm Premature Rupture of Membranes (PPROM): A Prospective Cohort Study – Teenus Paramel Jayaprakash – PLOS ONE

Human oral microbiome

Review: The oral microbiome – an update for oral healthcare professionals – M. Kilian – British Dental Journal

Human gut microbiome

Chronic opioid use is associated with altered gut microbiota and predicts readmissions in patients with cirrhosis – C. Acharya – Alimentary Pharmacology and Therapeutics

In vitro fermentation of B-GOS: Impact on faecal bacterial populations and metabolic activity in autistic and non-autistic children – Roberta Grimaldi – FEMS Microbial Ecology

Evidence for Immune Relevance of Prevotella copri, a Gut Microbe, in Patients with Rheumatoid Arthritis – Annalisa Pianta – Arthitis & Rheumatology

Review: Human gut microbiota: the links with dementia development – Rashad Alkasir – Protein & Cell

Review: Gut hormones and gut microbiota: implications for kidney function and hypertensionGut hormones and gut microbiota: implications for kidney function and hypertension – Baris Afsar – Journal of the American Society of Hypertension

Review: Dysbiosis in the intensive care unit: Microbiome science coming to the bedside – Georgios D Kitsios – Journal of Critical Care

Review: Interactions between gut microbes and host cells control gut barrier and metabolism – P D Cani – International Journal of Obesity Supplements

Review: Life history and eco-evolutionary dynamics in light of the gut microbiota – Emilie Macke – Oikos

Animal experiments

Environmental spread of microbes impacts the development of metabolic phenotypes in mice transplanted with microbial communities from humans – Li Zhang – ISME Journal

Gut bacteria affect our metabolism – Science Daily

Animal microbiome

Gut microbiota of dung beetles correspond to dietary specializations of adults and larvae
– Shantanu P. Shukla – Molecular Ecology

Thesis: Characterization of the juvenile green turtle (Chelonia mydas) microbiome associated with the ontogenic shift from pelagic habitats to inshore resident areas – James T. Price – Purdue University

Tick microbiome and pathogen acquisition altered by host blood meal – Andrea Swei – The ISME Journal

Plant, root, and soil microbiome

Investigation of Endophytic Bacterial Community in Supposedly Axenic Cultures of Pineapple and Orchids with Evidence on Abundant Intracellular Bacteria – Natalia Pimentel Esposito-Polesi – Current Microbiology

Tree species, tree genotypes and tree genotypic diversity levels affect microbe-mediated soil ecosystem functions in a subtropical forest – Witoon Purahong – Scientific Reports

High-methionine soybean has no adverse effect on functional diversity of rhizosphere microorganisms -J.G. Liang – Plant Soil Environment

Illumina sequencing-based community analysis of bacteria associated with different bryophytes collected from Tibet, China – Jing Yan Tang – BMC Microbiology
https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-016-0892-3
Networks Depicting the Fine-Scale Co-Occurrences of Fungi in Soil Horizons – Hirokazu Toju – PLOS ONE

Isolation and Identification of Keratinolytic Bacteria that Exhibit Feather-degrading Potentials – F. O. Iruolaje – Journal of Advances in Biology & Biotechnology

Water and extremophile microbiome

Cryo-protective effect of an ice-binding protein derived from Antarctic bacteria – Marco Mangiagalli – The FEBS Journal

Unusually High Archaeal Diversity in a Crystallizer Pond, Pomorie Salterns, Bulgaria, Revealed by Phylogenetic Analysis – Margarita Kambourova – Archaea

Polymetallic nodules, sediments, and deep waters in the equatorial North Pacific exhibit highly diverse and distinct bacterial, archaeal, and microeukaryotic communities – Christine N. Shulse – Microbiology Open

Conference abstract: Defining the boarders of extreme life: The study of microbial communities and their settings gives insights into Mars analogue life within the MASE project – A Perras – 16th International Symposium on Microbial Ecology

Pollution microbiology

Influence of plantation on microbial community in porous concrete treating polluted surface water – Yan Long – International Biodeterioration & Biodegradation

Food microbiology

Study of the bacterial diversity of foods: PCR-DGGE versus LH-PCR – Cristiana Garofalo – International Journal of Food Microbiology

Viruses and phages

Viral coinfection is shaped by host ecology and virus-virus interactions across diverse microbial taxa and environments – Samuel L Diaz-Munoz – bioRxiv

More microbiology

Uncovering new drugs and targets – Andrea Du Toit – Nature Reviews Microbiology

Microbiota under pressure – Andrea Aguilar – Nature Reviews Nephrology

Microbes in the news

‘Bacteria beaters’ win Longitude Prize Discovery Award – Shan Ross – The Scotsman

Bacteria for bio-toilets by February 15 – The Times of India

Your Office Has a Microbiome, and It Might Make You Sick – Zoe Schlanger – Wired

Tomato plants are more resistant against nematodes when colonized by a fungus – Farming Futures

Scientists use bacteria to map out NZ. A team of scientists growing bacteria in the shape of New Zealand have caught the attention of their colleagues across the globe – News Australia

The cover image is a map of New Zealand drawn with pyoverdine-producing P. aeruginosa cells in an ocean of indigoidine-synthesizing E. coli. – Cell Chemical Biology

Science, publishing, and career

Citizen science: The people behind the data – Mary Goodchild – NERC Planet Earth

November 21, 2016

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Why is the human vaginal microbiome unique, multiple sclerosis, fiber-deprived gut microbes eating mucus, vertical structure of the phyllospere, cave microbiome, resistome.

Pregnancy and early life

Associations between changes in the maternal gut microbiome and differentially methylated regions of diabetes-associated genes in fetuses: A pilot study from a birth cohort study – Kaori Tachibana – Journal of Diabetes Investigation

Human vaginal microbiome

Lactobacilli Dominance and Vaginal pH: Why is the Human Vaginal Microbiome Unique? – Elizabeth A. Miller – Frontiers in Microbiology

Human gut microbiome

Prevalence of Small Intestinal Bacterial Overgrowth in Multiple Sclerosis: a Case-Control Study from China – Yongbo Zhang – Journal of Neuroimmunology

MyNewGut: Insulin resistance as key factor for linking modulation of gut microbiome to health claims and dietary recommendations to tackle obesity – Stoffer Loman -Trends in Food Science & Technology

Review: The Multibiome: The Intestinal Ecosystem’s Influence on Immune Homeostasis, Health, and Disease – Heather A Filyk – EBioMedicine

Review: Microbiome and nutrition in autism spectrum disorder: current knowledge and research needs – Kirsten Berding – Nutrition Reviews

Review: Th Role of Short-Chain Fatty Acids in Kidney Injury Induced by Gut-derived Inflammatory Response – Wei Huang – Metabolism

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

Animal and in vitro experiments

A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility – Mahesh S. Desai – Cell
Editorial: Veggies and Intact Grains a Day Keep the Pathogens Away – Francesca S. Gazzaniga – Cell
Press: High-fiber diet keeps gut microbes from eating the colon’s lining, protects against infection, animal study shows – Science Daily

Coevolutionary dynamics between a defensive microbe and a pathogen driven by fluctuating selection – Suzanne A. Ford – Molecular Ecology

Gut microbiota in Drosophila melanogaster interacts with Wolbachia but does not contribute to Wolbachia-mediated antiviral protection – Yixin H. Ye – Journal of Invertebrate Pathology

Modulation of the cytokine profile in Caco-2 cells by faecal lactobacilli and bifidobacteria from individuals with distinct dietary habits – Diomira Luongo – Cytokine

An Alteration in the Cecal Microbiota Composition by Feeding of 1-Kestose Results in a Marked Increase in the Cecal Butyrate Content in Rats – Takumi Tochio – PLOS ONE

Animal microbiome

Proteome data on the microbial microbiome of grasshopper feces – Nico Jehmlich – Data in Brief

Plant, root, and soil microbiome

Vertical Structure of Phyllosphere Fungal Communities in a Tropical Forest in Thailand Uncovered by High-Throughput Sequencing – Ayako Izuno – PLOS ONE

Root nodule symbiosis in Lotus japonicus drives the establishment of distinctive rhizosphere, root, and nodule bacterial communities – Rafal Zgadzaj – PNAS

Press: Nitrogen-fixing symbiosis is crucial for legume plant microbiome assembly – EurekAlert

Influence of salt tolerant Trichoderma spp. on growth of maize (Zea mays) under different salinity conditions – Krishna Kumar – Journal of Basic Microbiology

Review: Recent changes to the classification of symbiotic, nitrogen-fixing, legume-associating bacteria: a review – Abdelaal Shamseldin – Symbiosis

Review: Forest microbiome: diversity, complexity and dynamics – Petr Baldrian – FEMS Microbiology Reviews

Review: The cave microbiome as a source for drug discovery: reality or pipe dream? – Soumya Ghosh – Biochemical Pharmacology

Extremophile microbiome

Opinion: Colonization of Black Smokers by Hyperthermophilic Microorganisms – Reinhard Wirth – Trends in Microbiology

Food microbiology

Biofilms formed by microbiota recovered from fresh produce: Bacterial biodiversity, and inactivation by benzalkonium chloride and enterocin AS-48 – Mª José Grande Burgos – LWT – Food Science and Technology

Metabolomics

Comparative in silico analysis of butyrate production pathways in gut commensals and pathogens – Swadha Anand – Frontiers in Microbiology

Resistome

Prevalence of antibiotic resistance genes among human gut-derived bifidobacteria – Sabrina Duranti – Applied and Environmental Microbiology

Review: Genomic and metagenomic technologies to explore the antibiotic resistance mobilome
– José L. Martínez – Annals of the New York Academy of Sciences

Microbes in the news

I got my gut sequenced – and found out I need to go to the dentist – Liam Mannix – Sydney Morning Herald

Bighorn sheep transfer OK’d despite concerns about disease – Brett French – Missoulian
http://missoulian.com/news/state-and-regional/bighorn-sheep-transfer-ok-d-despite-

High-Fat Diets Alter Gut Microbiota, Leading to Increased Choroidal Neovascularization – Dava Stewart – HCP Live

Student scientists engineer bacteria to break down plastic, hope to help clean Baltimore harbor – Scott Dance – The Baltimore Sun

Soil bacteria helps protect rice plants from arsenic and fungus. ‘Cocktail’ of soil bacteria can protect rice plants from deadly forces – Science Daily
Bacteria Might Be Able To Help Rice Affected By Fungus – Rodney Rafols – iTechPost

Microbes and art: van Dongen, Parreno, Park and more.

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Electricity-Free Lamp Is Powered by Octopus Bacteria – Dutch designer Teresa Van Dongen has merged design and biology in her new project – Kiran Umapathy – PSFK

“Electricity? So passé. Dutch designer Teresa van Dongen dared to combine biology with the technology by creating an electricity-free lamp—the Ambio—that runs on octopus bacteria.  “

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The Ambio lamp is filled with living bioluminescent bacteria. Source: PSFK.com

An artwork controlled by a colony of bacteria – Aaron Souppouris – Engadget

“Anywhen is an immersive artwork by French avant-garde artist Philippe Parreno. (…) It features an ever-changing mix of sound, light and shadow, augmented by fish-shaped balloons, a transforming array of suspended speakers and a cinema that seemingly appears at random. Except, it’s not random. The individual elements of Anywhen are at the whim of bacteria.”

An art of loopholes. How the French artist Philippe Parreno studiously avoids having ideas – Emily Nathan  – The New Yorker

“I want to turn the museum into a similar kind of instrument, a weird hybrid made out of light and recorded sound and bacteria and acoustic panels, with sequences and motifs that recur and retreat,” he said. “Unless you want to spend eight hours there, you will definitely miss something. But that’s part of it, no? You always miss something in life.”

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Philippe Pareno’s “Anywhen”, an exhibition controlled by bacteria. Source: Engadget.com.

This Scientist crystallises Bacteria for Stained Glass and Lace! – Evelyn Warner – Labiotech

“Simon Park is a scientist who wants to teach us about the microbiome through his art. Among his works are a self-portrait, lace and stained glass, all of which have been produced from bacteria! (…) Through his art, he aims to draw our attention to them and make them more familiar. (The apotheosis of the latter is his self-portrait from his own microbial flora!) “

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Bacterial Stained Glass by Simon Park. Source: Labiotech.eu.

Belowground visions of life: Soil makes Art – Global Soil Biodiversity

“How can soil biodiversity scientists share their knowledge with the public? Art is the answer given by “Belowground visions of life: Soil makes Art”, a project funded by the Leverhulme Trust in the UK. This project supports an artist in residence, Ed Reynolds, working with Dr Tancredi Caruso, soil ecologist at the School of Biological Sciences, Queen’s University Belfast.”

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Original artwork by Ed Reynolds. Source: Global Soil Biodiversity.com

Microbial Awards Season in Biology 350! – Mark O. Martin – Microbes Rule

“Who knows if I can change lives? I do know that I can change the way my students view the world, using “microbial-colored glasses.” I also believe that art can intersect with science, often in ways that enhance learning. This semester, I had my Biology 350 micronauts try it two different ways, with (hopefully) some success. First, the Vexed Muddler and I cooked up a #MicrobialArt competition.”

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Josh’s art won First Prize: unfair and inaccurate assumptions about the microbial world.

“That was a heck of a #MicrobialMorning, but there was more to come. That’s right: it was then time for the #LuxAcademyAwards! Earlier this semester, I had students create “microbial art” by “painting” with luminous bacteria (Photobacterium leignothi) on Petri dishes. I then wanted folks across the Internet to vote on their favorites, and distribute yet more #MicrobialSwag to lucky #MicrobialArtists!”

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Molly created #LuxArt2016 4th place winner.

Bacteria-Inspired Art Infects a Chelsea Gallery – Andrew Nunes — The Creators Project

“Bacteria are more than just the building blocks of microorganisms in art collective Slavs and Tatars’ latest exhibition at Tanya Bonakdar Gallery. Titled Afteur Pasteur, an homage to the microbiologist who discovered microbial fermentation and pasteurization, the exhibition uses references to bacteria and microbes as unlikely lenses to examine larger cultural and historical ideas. (…) A fully functional ‘bacteria bar’ serves the yogurt drink ayran (sorry, there’s no kombucha here) allowing visitors to ingest a constituent life form while perusing the remaining works.”

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Ayran bar, Slavs and Tatars, 2016. Source: The Creators Project.

 

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

Upcoming North American Microbiome Congress in San Diego

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A while ago I wrote about the (North American) Microbiome Congress, to be held in San Diego in January 2017, because of the lack of women among the speakers. Jonathan Eisen also wrote a post about that.

I was pleasantly surprised to see that the conference organizer, Kisaco Research, has taken our criticism to heart, and has worked hard to improve the diversity of the invited speakers. They now have a great line-up with Jessica Metcalf, Emma Taylor, David Pride, Julia Oh, Sarkis Mazmanian, Embriette Hyde, Susan Holmes, Rob Knight, Jeff Leach, George Weinstock, Curtis Huttenhower, and Catherine Lozupone.

They also feature the following statement on the conference’s website:

“The process of choosing a speaker faculty has many complicated variables, but it is clear that our choices should have been more diverse. I sincerely apologize to those who are offended by the decisions we have made. We recognize that it is our responsibility to help ensure that the speaker faculty reflect the diversity and culture of the field and science as a whole. In this instance we failed to live up to our own standards of sensitivity and diversity, for which we sincerely apologize. Kisaco Research is deeply committed to producing events that represent the diversity of the scientific fields we work with. We are embarrassed that this has been previously overlooked and are currently working to make this, and all other programmes, ones that the leading scientists are proud to be a part of.

Stephanie Jaczniakowska-McGirr
Conference Director
Kisaco Research
sjm@kisacoresearch.com”

Kudos to Kisaco Research for listening, apologizing, and taking action. That takes courage and I so, so, appreciate this.

Their new line-up looks like a wonderful set of speakers, and you might want to give this conference a second look. The North American Microbiome Congress from January 24-25 in San Diego.

Full disclosure: Kisaco Research has invited me to come to the congress, which I accepted. I might see you there!

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November 17, 2016

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Sepsis diagnosis through fecal gases, colonic lesion detection, microbiological map of the horse GI tract, beachgrass invasion, thromobolites.

Pregnancy and early life

Detection of Sepsis in Preterm Infants by Fecal Volatile Organic Compounds Analysis: A Proof of Principle StudyDetection of Sepsis in Preterm Infants by Fecal Volatile Organic Compounds Analysis: A Proof of Principle Study – Berkhout, Daniel J.C. – Journal of Pediatric Gastroenterology and Nutrition

Human gut microbiome

DNA from fecal immunochemical test can replace stool for detection of colonic lesions using a microbiota-based model – Nielson T. Baxter – Microbiome

Disturbances of the Perioperative Microbiome Across Multiple Body Sites in Patients Undergoing Pancreaticoduodenectomy – Rogers, Matthew B. – Pancreas

Animal experiments

Lactobacillus salivarius Isolated from Patients with Rheumatoid Arthritis Suppresses Collagen-Induced Arthritis and Increases Treg Frequency in Mice – Liu Xiaofei – Journal of Interferon & Cytokine Research

Animal microbiome

Horse: A Microbiological Map of the Healthy Equine Gastrointestinal Tract – Aaron C. Ericsson – PLOS ONE

Scallop: Characterization of the microbiota associated to Pecten maximus gonads using 454-pyrosequencing – Aide Lasa – International Microbiology

Catfish: Ontogenetic Characterization of the Intestinal Microbiota of Channel Catfish through 16S rRNA Gene Sequencing Reveals Insights on Temporal Shifts and the Influence of Environmental Microbes – Jacob W. Bledsoe – PLOS ONE

Bacteria discovery offers possible new means of controlling crop pest – Phys.org

Plant, root, and soil microbiome

Combined effects of reduced irrigation and water quality on the soil microbial community of a citrus orchard under semi-arid conditions – F. Bastida – Soil Biology and Biochemistry

Seasonality and partitioning of root allocation to rhizosphere soils in a midlatitude forest – Rose Z. Abramoff – Ecosphere

Beachgrass invasion in coastal dunes is mediated by soil microbes and lack of disturbance dependence – Aaron S. David – Ecosphere

Thirty-one years of rice-rice-green manure rotations shape the rhizosphere microbial community and enrich beneficial bacteria – Xiaoxia Zhang – Soil Biology and Biochemistry

Points of View: Dinner in the dark: Illuminating drivers of soil organic matter decomposition – Annemieke van der Wal – Soil Biology and Biochemistry

Water and extremophile microbiome

Spatial homogeneity of bacterial and archaeal communities in the deep eastern Mediterranean Sea surface sediments – Sabine Keuter – International Microbiology

Thrombolite fabrics and origins: Influences of diverse microbial and metazoan processes on Cambrian thrombolite variability in the Great Basin, California and Nevada – Cara Harwood Theisen – Sedimentology

Three-Dimensional Structure of the Ultra-oligotrophic Marine Bacterium Pelagibacter – Xiaowei Zhao – Applied and Environmental Microbiology

Metagenomics and bioinformatics

Deconvoluting simulated metagenomes: the performance of hard- and soft- clustering algorithms applied to metagenomic chromosome conformation capture (3C) – Matthew Z. DeMaere

Proteomics and metabolomics

Discovery of MRSA active antibiotics using primary sequence from the human microbiome – John Chu – Nature Chemical Biology – DOI: 10.1038/nchembio.2207

Researchers discover new antibiotics by sifting through the human microbiome – Phys.org

Sequencing techniques

Evaluation of PacBio sequencing for full-length bacterial 16S rRNA gene classification -Josef Wagner – BMC Microbiology

Bacteria in the news

Solving how harmless bacteria become an unwelcome guest – University at Buffalo

MRSA and other superbugs: could you be at risk when flying? – Lisa Salmon – BT

‘Sweet’ solution to kill bacteria in drinking water developed – Economic Times

Prenatal stress alters gut bacteria to cause lifelong problems in offspring – Medical News Today

How Drug-Resistant Bacteria Travel from the Farm to Your Table – Melinda Wenner Moyer – Scientific American

Simple changes to antibiotic treatment of MRSA may help beat the bacteria – Medical Xpress

Gut microbiota may play important role in influencing onset of blinding wet AMD – News Medical

Gut Microbiome May Determine Immunotherapy Response – Liam Davenport – Medscape

Feeling Hangry? The Science Behind Gut Health and Mood – Dana Angelo White – FoodNetwork

Gut bacteria diversity linked to immunotherapy response in melanoma patients – LabNews

Microbes on the market

Modified Bacteria Could Cure a Fatal Genetic Disorder Found in Infants – Futurism

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

November 16, 2016

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Infants with and without colic, supplementing adults with breastmilk sugars, honey bee viruses, and forensic metabolomics of cell phones.

Pregnancy and early life

Comparison of formula-fed infants with and without colic revealed significant differences in total bacteria, Enterobacteriaceae and faecal ammonia – Francesco Savino – Acta Pediatrica

Human gut microbiome

Bacterially-Associated Transcriptional Remodelling in a Distinct Genomic Subtype of Colorectal Cancer Provides a Plausible Molecular Basis for Disease Development – Katie S. Lennard – PLOS ONE

Oral supplementation of healthy adults with 2′-O-fucosyllactose and lacto-N-neotetraose is well tolerated and shifts the intestinal microbiota – Emma Elison – British Journal of Nutrition

News: Effects of Human Milk Oligosaccharides Supplementation on Adult Gut Microbiota – Hummer Aslam – Medical News Bulletin

Gut microbiota influences pathological angiogenesis in obesity-driven choroidal neovascularization – Elisabeth MMA Andriessen – EMBO Molecular Medicine

Gut flora connects obesity with pathological angiogenesis in the eye – Rebecca Scholz – EMBO Molecular Medicine

Animal microbiome

Ontogenetic Characterization of the Intestinal Microbiota of Channel Catfish through 16S rRNA Gene Sequencing Reveals Insights on Temporal Shifts and the Influence of Environmental Microbes – Jacob W. Bledsoe – PLOS ONE

Year-Long Monitoring of Physico-Chemical and Biological Variables Provide a Comparative Baseline of Coral Reef Functioning in the Central Red Sea – Anna Roik – PLOS ONE

Honey Bee Viruses in Wild Bees: Viral Prevalence, Loads, and Experimental Inoculation – Adam G. Dolezal – PLOS ONE

Plant, root, and soil microbiome

Microbiome engineers: Grazers, browsers, and the phytobiome stampede – Karen A Garrett – BioRxiv

Fine-scale spatial distribution of orchid mycorrhizal fungi in the soil of host-rich grasslands` – Samuele Voyron – New Phytologist

Water and extremophile microbiome

Shifting microbial communities sustain multi-year iron reduction and methanogenesis in ferruginous sediment incubations – Marcus S Bray – bioRxiv

Ordination obscures the influence of environment on plankton metacommunity structure – Tad A. Dallas – Limnology and Oceanography Letters

Metabolomics

Lifestyle chemistries from phones for individual profiling – Amina Bouslimani – PNAS

Cellphone Smudges Yield a Trove of Forensic Data. Researchers say molecules and microbes left on phone, keys, credit cards can linger for months – Wall Street Journal
Chemical traces on your phone reveal your lifestyle, scientists say – The Guardian
Cellphone crud could help I.D. crime victims – Gary Robbins – San Diego Union Tribune
The Grime on Your Smartphone Can Reveal Your Secrets – Christopher Wanjek – Live Science

Effects of Liver Resection on Hepatic Short-Chain Fatty Acid Metabolism in Humans – Evelien P. J. G. Neis – PLOS ONE

Microbes in the news

Biologists give bacteria thermostat controls – Whitney Clavin – Phys.org

Yes, your beer pong cup is teeming with bacteria – Alexandra Ossola – Popular Science

Scientists discover important link between immune system, gut bacteria and glucose metabolism – News Medical

Immune system uses gut bacteria to control glucose metabolism – Oregon State

Bacteria turn trees into pollution-eating machines – Anthony King – Horizon

From the 2016 European Society for Medical Oncology (ESMO) Congress: The Future of Cancer Drugs: RNA Therapies, Bacteria, and Viruses – Kate M. O’Rourke – Medscape

Bile duct bacteria pose cancer risk – Biotech in Asia