Category Archives: Built Environment Microbiology

September 22, 2016

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Jobs at Second Genome, endohyphal bacteria in fungi on tropical seeds and leaves, designing buildings to house our germs.

Jobs and events

Second Genome (San Francisco, CA) is hiring.

Southern California Microbiome Symposium – Connections to the Environment and Health – Sept 23, UC Irvine

Human gut microbiome

Review: Current Hypothesis for the Relationship between Dietary Rice Bran Intake, the Intestinal Microbiota and Colorectal Cancer Prevention – Winnie K. W. So – MDPI Nutrients

Animal models

Temporal Development of Gut Microbiota in Triclocarban Exposed Pregnant and Neonatal Rats – Rebekah C. Kennedy – Scientific Reports

Animal microbiome

Parasitic Infection by Pseudocapillaria tomentosa is Associated with a Longitudinal Restructuring of the Zebrafish Gut Microbiome – Christopher A Gaulke – bioRxiv

Biology, Pest Status, Microbiome and Control of Kudzu Bug (Hemiptera: Heteroptera: Plataspidae): A New Invasive Pest in the U.S. – Anirudh Dhammi – International Journal of Molecular Sciences

Plant, root, and soil microbiome

A Hardy Plant Facilitates Nitrogen Removal via Microbial Communities in Subsurface Flow Constructed Wetlands in Winter – Penghe Wang – Scientific Reports

Diversity, Specificity, and Phylogenetic Relationships of Endohyphal Bacteria in Fungi That Inhabit Tropical Seeds and Leaves – Justin P. Shaffer – Frontiers in Ecology and Evolution

More microbiology

Nuclear pore-like structures in a compartmentalized bacterium – Evgeny Sagulenko – bioRxiv

Review: Molecular microbiology methods for environmental diagnosis – T. Bouchez – Environmental Chemistry Letters

Self-healing cementitious materials based on bacteria and nutrients immobilized respectively – Huaicheng Chen – Construction and Building Materials

Techniques

An Enteric Micromotor Can Selectively Position and Spontaneously Propel in the Gastrointestinal Tract – Jinxing Li – ACS Nano

Microbes in the news

Black Slime Is Coating World Monuments—And That May Be Good – Michelle Z. Donahue – National Geographic

Designing Buildings to House Our Favorite Germs – Melissa Pandika – Ozy

Very cool talks: Lake Arrowhead Microbial Genomes #LAMG16: Day 3 – David Coil – MicroBEnet

Prairies Yield Clues for Antibiotic Resistance – AgResearch Magazine

Genetically Engineered Bacteria Can Grow Food, Forks on Mars – Jacqueline Ronson – Inverse.com

CosmoCrops! – The 2016 winners of the Nordic Mini-Jamboree! – Copenhagen University iGEM
UW Medical Center takes action after finding bacteria in medical devices – Coral Garnick – BizJournals

Gut bacteria explain insects’ tolerance to a toxic diet – Science Daily

A field guide to dangerous bacteria – Tabletopwhale

Science, publishing, and career

The natural selection of bad science – Paul E. Smaldino – Royal Society Open Science

Press: The Inevitable Evolution of Bad Science – Ed Yong – The Atlantic

Salaries: Reality check: A feeling that good performance is not adequately rewarded is pervading the research world – Chris Woolston – Nature Careers

September 20, 2016

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A review of antibiotics’ effect on the human microbiome, the pig gut microbiome, microbiome of Green Design, expanding Unifrac, and GutCheck, the Microbiome Game.

General human microbiome

Review: Antibiotic use and microbiome function – Manuel Ferrer – Biochemical Pharmacology

Human respiratory microbiome

Taxa of the Nasal Microbiome Are Associated with Influenza-Specific IgA Response to Live Attenuated Influenza Vaccine – Hannah M. Salk – PLOS ONE

Changes in the bacterial microbiome of patients with chronic rhinosinusitis after endoscopic sinus surgery – Ravi Jain – International Forum of Allergy & Rhinology

Human gut microbiome

Gastric microbiota in the functional dyspepsia patients treated with probiotic yogurt – Hirohiko Nakae – BMJ Open Gastroenterology

Animal microbiome

A reference gene catalogue of the pig gut microbiome – Liang Xiao – Nature Microbiology

Press: Gut Microbial Genes Profiled in Pigs From Diverse Breeds, Locations – Genome Web

The Prevalence of Canine Oral Protozoa and Their Association with Periodontal Disease – Niran Patel – The Journal of Eukaryotic Microbiology

Functional diversity of ant-associated bacterial communities – A. A. Dymova – Biology Bulletin

Plant, root, and soil microbiome

Can inoculation with living soil standardize microbial communities in soilless potting substrates? – Petra Bukovská – Applied Soil Ecology

Effects of saline water irrigation and fertilization regimes on soil microbial metabolic activity – Li -Juan Chen – Journal of Soils and Sediments

More on the Centralia coal mine fire (see yesterday’s post): Diversity and mechanisms of arsenic resistance among soil bacteria impacted by the ongoing Centralia coal mine fire – Taylor K Dunivin – PeerJ Preprint

Water and extremophile microbiome

Metagenomics as a preliminary screen for antimicrobial bioprospecting – Soha Al-Amoudi – Gene

Built environment microbiome

The Microbiome of Green Design: Sustainable building practices may have unforeseen consequences for microbial communities and human health – Carolyn Beans – BioScience

More microbiology

Cat-Scratch Disease in the United States, 2005–2013 – Christina A. Nelson – Emerging Infectious Diseases

Press: Don’t Kiss That Kitty: Cat-Scratch Fever Is Making People Sicker – Erin Ross – NPR

Bioinformatics and proteomics

Strategies to improve usability and preserve accuracy in biological sequence databases – Johan Bengtsson-Palme – Proteomics

Expanding the UniFrac Toolbox – Ruth G. Wong – PLOS ONE

MetaStorm: A Public Resource for Customizable Metagenomics Annotation – Gustavo Arango-Argoty – PLOS ONE

Microbes in the news

Gut Check: The Microbiome Game – MoBio
Gut Check: The Microbiome Game now available for purchase – David Coil – MicroBEnet

Antibiotic Resistant Bacteria and the World’s Peril: The U.N. General Assembly is taking on a danger that threatens the health of our entire species – Laurie Garrett – Scientific American

Scientists uncover a clever ranking strategy bacteria use to fight off viruses – NewsWire Rockefeller

Oetzi Iceman Update: Bacteria Found In Mummy’s Stomach May Lead To Cancer Research – Janice Williams – International Business News

Stone Age mummy still revealing secrets, 25 years on – Simon Sturdee – Phys.org

Lake Arrowhead Microbial Genomics #LAMG16 Report: Day 1 – David Coil – MicroBEnet

September 17, 2016

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Metabolic interactions between a 4-species community, captive and wild red-crowned cranes, microbial life around a coal mine fire that’s been burning for over 50 years.

Pregnancy and early life

Associations between EBV and CMV Seropositivity, Early Exposures, and Gut Microbiota in a Prospective Birth Cohort: A 10-Year Follow-up – Claudia Carvalho-Queiroz – Frontiers in Pediatrics

Human oral microbiome

The Oral Microbiome of Children: Development, Disease, and Implications Beyond Oral Health – Andres Gomez – Microbial Ecology

Human gut microbiome

Gut microbiota, metabolome and immune signatures in patients with uncomplicated diverticular disease – Giovanni Barbara – Gut

Faecal Concentrations of Short-chain Fatty Acids and Selected Bacteria in Healthy and Celiac Children – Maša Primec – International Journal of Celiac Disease

Animal and in vitro experiments

Impact of Gluten-Friendly Bread on the Metabolism and Function of In Vitro Gut Microbiota in Healthy Human and Coeliac Subjects – Antonio Bevilacqua – PLOS ONE

Protocol: Intestinal Organoids as a Novel Tool to Study Microbes–Epithelium Interactions – Giulia Nigro – Methods in Molecular Biology

The Contribution of High-Order Metabolic Interactions to the Global Activity of a Four-Species Microbial Community – Xiaokan Guo – PLOS Computational Biology

Animal microbiome

Effects of captivity and artificial breeding on microbiota in feces of the red-crowned crane (Grus japonensis) – Yuwei Xie – Scientific Reports

Compartmentalization of microbial communities that inhabit the hindguts of millipedes – James B. Nardi – Arthropod Structure & Development

Plant, root, and soil microbiome

Seasonal and altitudinal changes of culturable bacterial and yeast diversity in Alpine forest soils – Luís França – Extremophiles

Niche filtering of bacteria in soil and rock habitats of the Colorado Plateau Desert, Utah, USA – Kevin Lee – Frontiers in Microbiology

The Centralia, PA, coal mine fire has been burning since 1962. Stochastic extremes but convergent recovery of bacterial and archaeal soil communities to an ongoing subterranean coal mine fire – Sang-Hoon Lee – PeerJ Preprint

Water and extremophile microbiome

Functional ecology of soil microbial communities along a glacier forefield in Tierra de Fuego (Chile) – Miguel Angel Fernández-Martínez – Frontiers in Microbiology

Riverine Bacterial Communities Reveal Environmental Disturbance Signatures within the Betaproteobacteria and Verrucomicrobia – John Paul Balmonte – Frontiers in Microbiology

Shifts in Microbial Community Structure and Activity in the Ultra-Oligotrophic Eastern Mediterranean Sea Driven by the Deposition of Saharan Dust and European Aerosols – Cui Guo- Frontiers in Marine Science

Phylogenetic Characterization of Marine Benthic Archaea in Organic-Poor Sediments of the Eastern Equatorial Pacific Ocean (ODP Site 1225) – Antje Lauer – Microorganisms

Built environment microbiome

Occurrence and diversity of both bacterial and fungal communities in dental unit waterlines subjected to disinfectants – Damien Costa – Pathogens and Disease

Techniques

Stable Isotope Techniques for the Assessment of Host and Microbiota Response During Gastrointestinal Dysfunction – Butler, Ross N. – Journal of Pediatric Gastroenterology and Nutrition

Microbes in the news

Get Your Children Good and Dirty – B. Brett Finlay and Marie-Claire Arrieta – Wall Street Journal

NASA Space Biology Fellowships to Study the Microbiome of the ISS as a Built Environment Research Announcement – SpaceRef

Intercontinental Plant Microbiome Research Earns UBiome Grant – Haverford.edu

Scientific research shows how corrugated stops bacteria – Packaging World

Bacterial Predators Surprise Scientists with Hidden Diversity – Jennifer Frazer – Scientific American

Bacteria Hysteria

Fear-mongering story sponsored by industry, performed by microbiology professor: Petri dishes you can wear: UA researchers study the bacteria on the bottoms of your shoes – Courtney Gallant – The Daily Wildcat

September 14, 2016

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Testing antibacterial and antismelly capacities of deodorant with a sniffer panel, uncovering trophic interactions by metagenomic sequencing of ladybugs’ gut contents.

Events

6th ASM Beneficial Microbes meeting, Days 3-4 – Tera Levin – Storify

Human armpit microbiome

Smelly armpits, bacteria, and a sniffer panel: Effective axillary malodour reduction by polyquaternium-16-containing deodorants – B. Traupe – International Journal of Cosmetic Science

Human gut microbiome

Review: Pathogenesis of acute graft-versus-host disease: from intestinal microbiota alterations to donor T cell activation – Robert Zeiser – British Journal of Haemotology

Review: Role of the gut microbiota in host appetite control: bacterial growth to animal feeding behaviour – Sergueï O. Fetissov – Nature Reviews Endocrinology

Animal microbiome

Ladybugs: Uncovering Trophic Interactions in Arthropod Predators through DNA Shotgun-Sequencing of Gut Contents – Débora P. Paula – PLOS ONE

Does adaptive radiation of a host lineage promote ecological diversity of its bacterial communities? A test using gut microbiota of Anolis lizards – Tiantian Ren – Molecular Ecology

Built Environment microbiome

Previously in preprint, now published: Microbial diversity of extreme habitats in human homes – Amy M. Savage – PeerJ

Techniques / Bioreactors

Quantitative high-throughput population dynamics in continuous-culture by automated microscopy – Jason Merritt – Scientific Reports

Microbes in the news

Genevieve Sullivan: Bacteria and Food Packaging – Darren Chow – Cornell Sun

Samantha VanWees: Bacteria, Light and Milk Processing – Isabelle Philippe – CornellSun

This should be Open Access, because it is just a list of links. But it is not unfortunately: Web Alert: Ecophysiology of anaerobes: An annotated selection of World Wide Web sites relevant to the topics in environmental microbiology – Lawrence P. Wackett

An arms race with a superbug: Study shows how pneumonia-causing bacteria invade the body – Phys.org

Coming together for microbiology: new network for scientists working in forensic medicine – Labnews UK

The possible link between bacteria and chronic disease? – Jason Tetro – PopSci

See paper in Advanced Materials featured yesterday: Delivering beneficial bacteria to the GI tract. Method that transports microbes through the stomach to the intestine may benefit human health – Anne Trafton – MIT News Office

Science, publishing, and career

Mansplaining: how not to talk to female Nasa astronauts – Laura Bates – The Guardian

 

 

September 12, 2016

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Individual response of gut microbiota to diet (in mice), appendicitis, adaptive evolution of goose with its microbiome, fungi in rubber plantations.

Events

Storify of days 1-2 of the 6th ASM Beneficial Microbes Meeting, Sept 9-12, Seattle, WA.

Pregnancy and birth

Urinary Microbiota Associated with Preterm Birth: Results from the Conditions Affecting Neurocognitive Development and Learning in Early Childhood (CANDLE) Study – Nicholas J. Ollberding – PLOS ONE

Review: The role of the bacterial microbiota on reproductive and pregnancy health – Deborah B. Nelson – Anaerobe

Human skin microbiome

Skin microbiome prior to development of atopic dermatitis: early colonization with commensal staphylococci at 2 months is associated with a lower risk of atopic dermatitis at 1 year – Elizabeth A. Kennedy – Journal of Allergy and Clinical Immunology

Human respiratory microbiome (and Methods)

Note that 2 different amplification strategies were performed, so IMHO this is more reflection of primer differences than sequencing differences: Different next generation sequencing platforms produce different microbial profiles and diversity in cystic fibrosis sputum – Andrea Hahn – Journal of Microbiological Methods

Human gut microbiome

Evaluation of the microbiome in children’s appendicitis – Martin Salö – International Journal of Colorectal Disease

Review: Food: a new form of personalised (gut microbiome) medicine for chronic diseases? – Tess Pallister – Journal of the Royal Society of Medicine

Review: Linking the Microbiota, Chronic Disease, and the Immune System – Timothy W. Hand – Trends in Endocrinology & Metabolism

Animal and bioreactor experiments

From the Sonnenburg lab @Stanford: Individualized Responses of Gut Microbiota to Dietary Intervention Modeled in Humanized Mice – Samuel A. Smits – mSystems

An In Vitro Approach to Study Effects of Prebiotics and Probiotics on the Faecal Microbiota and Selected Immune Parameters Relevant to the Elderly – Yue Liu – PLOS ONE

Animal microbiome

Genome and metagenome analyses reveal adaptive evolution of the host and interaction with the gut microbiota in the goose – Guangliang Gao – Scientific Reports

Hold off on the orange oil: Characterization of Antibacterial Activities of Eastern Subterranean Termite, Reticulitermes flavipes, against Human Pathogens – Yuan Zeng – PLOS ONE

Use of MALDI-TOF MS and culturomics to identify mosquitoes and their midgut microbiota – Fatalmoudou Tandina – Parasites & Vectors

Plant, root, and soil microbiome

Drought history affects grassland plant and microbial carbon turnover during and after a subsequent drought event – Lucia Fuchslueger – Journal of Ecology

Effect of organic matter enrichment on the fungal community in limestone cave sediments – ELS Marques – Genetics and Molecular Research

Contrasting elevational diversity patterns for soil bacteria between
two ecosystems divided by the treeline – Guixiang Li – Science China Life Sciences

Review: Diversity and ecology of soil fungal communities in rubber plantations – Jutamart Monkai – Fungal Biology Reviews

Illumina sequencing reveals a rhizosphere bacterial community associated with foxtail millet smut disease suppression – Yansha Han – Plant and Soil

Water and extremophile microbiome

Viruses-to-mobile genetic elements skew in the deep Atlantis II brine pool sediments – Mustafa Adel – Scientific Reports

Built environment microbiome

Review: The Microbiome of the Built Environment and Human Behavior: Implications for Emotional Health and Well-Being in Postmodern Western Societies – C.E. Stamper – International Review of Neurobiology

Microbes in the news

The Bacteria on Your Skin Are Safer Than These Two Chemicals the FDA Just Banned From Your Soap – Jill Richardson – Truth Digg

DNA in London Grave May Help Solve Mysteries of the Great Plague – Roff Smith – National Geographic

Bik’s Non-Microbiology Picks

This paper was discussed on Twitter this weekend because of a conflict of interest of one of the authors (Deepak Chopra) and the design and interpretation of the study:

Identification of Altered Metabolomic Profiles Following a Panchakarma-based Ayurvedic Intervention in Healthy Subjects: The Self-Directed Biological Transformation Initiative (SBTI) – Christine Tara Peterson – Scientific Reports

September 10, 2016

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Bifidobacteria and ulcerative colitis, the pollen microbiome, busting the 5-second rule, resistance genes in 23,000 microbial genomes, and a cool video of evolution of bacterial resistance.

Events

Gut health, microbiota & probiotics throughout the lifespan – Metabolic & Brain function 2016 – Sept 15-16, Harvard Medical School, Boston, MA

Human oral microbiome

Deep sequencing reveals microbiota dysbiosis of tongue coat in patients with liver carcinoma – Haifeng Lu – Scientific Reports

Human respiratory microbiome

Review: The microbiome in asthma – Magali Noval Rivas – Current Opinion Pediatrics

Human gut microbiome

Elucidating the gut microbiome of ulcerative colitis: bifidobacteria as novel microbial biomarkers – Sabrina Duranti – FEMS Microbiology Ecology

Review: Gut Microbiota, Inflammation, and Colorectal Cancer – Caitlin A. Brennan – Annual Review of Microbiology

Review: Microbiota—myeloid cell crosstalk beyond the gut – Sayeh Gorjifard – Journal of Leukocyte Biology

Four reviews in Current Pharmaceutical Design in the category “Could the gut microbiota perhaps be involved in disease X?” – with 4 different X’s. 

Animal models

Antibiotic Treatment Induces Long-lasting Changes in the Fecal Microbiota that Protect Against Colitis – Naomi L. Ward – Inflammatory Bowel Diseases

Differences In CD8αα And Cecal Microbiome Community During Proliferation And Late Cytolytic Phases Of Marek’s Disease Virus (MDV) Infection Are Associated With Genetic Resistance To Marek’s Disease – Sudeep Perumbakkam – FEMS Microbiology Ecology

Plant, root, and soil microbiome

Bacterial microbiota associated with flower pollen is influenced by pollination type, and shows a high degree of diversity and species-specificity – Binoy Ambika Manirajan – Environmental Microbiology

Land use intensification in the humid tropics increased both alpha and beta diversity of soil bacteria – Teotonio Soares de Carvalho – Ecology

Small-scale spatial heterogeneity of ecosystem properties, microbial community composition and microbial activities in a temperate mountain forest soil – Martina Štursová – FEMS Microbiology Ecology

Extremophile microbiome

Seasonal dynamics of extremely halophilic microbial communities in three Argentinian salterns – Leonardo Di Meglio – FEMS Microbiology Ecology

Built environment microbiome

screen-shot-2016-09-10-at-10-44-32-am

Christin Lola / Fotolia (via Science Direct)

Longer Contact Times Increase Cross-Contamination of Enterobacter aerogenes from Surfaces to Food – Robyn C. Miranda – Applied and Environmental Microbiology

Researchers debunk ‘five-second rule’: Eating food off the floor isn’t safe. Sometimes bacteria transfer in less than a second – Science Daily

Forget the ‘five-second rule’: Food dropped on the floor picks up bacteria in just ONE second – David Gardner – Daily Mail

Antimicrobial Chemicals Are Associated with Elevated Antibiotic Resistance Genes in the Indoor Dust Microbiome – Erica M. Hartmann – Environmental Science & Technology

Antibiotic Resistance Genes in Indoor Dust – Technology Networks

Metagenomics and bioinformatics

The transfer network of bacterial mobile resistome connecting animal and human microbiome – Yongfei Hu – Applied and Environmental Microbiology

Catalog of Mobile Antibiotic Resistance Genes Helps Explain Transfer to Human Pathogens – Genome Web

Chinese investigators characterize the world of resistance gene exchange among bacteria – Phys.org

Phages and viruses

Bacteriophages in clinical samples can interfere with microbiological diagnostic tools – Maryury Brown-Jaque – Scientific Reports

Techniques

Absolute quantification of microbial taxon abundances – Ruben Props – The ISME Journal

Microbes in the news

Jo Handelsman of White House Office of Science and Technology to Speak Monday – University of Tennessee

WATCH: Bacteria Invade Antibiotics And Transform Into Superbugs – Angus Chen – NPR
This might be the coolest visualization of evolution ever. Watch these bacteria evolve antibiotic resistance in just 12 days – Brian Resnick – Vox

These researchers would like you to mail them your gut bacteria – Katherine Lindemann – Research Gate Blog

Hepatitis A Outbreak Linked to Strawberries at Smoothie Chain – Daniel Victor – New York Times

Bacteria Hysteria

M&S becomes first supermarket to offer anti-bacterial shopping bags to banish bugs such as E. coli –  Katie Morley – The Telegraph

Bik’s non-microbiology Picks

Microbiome analysis, please! Giraffes aren’t just giraffes. Turns out there are four species – Rachel Feltman – Washington Post

Flatworm parasite named after Barack Obama: Is that a compliment? – Rowena Lindsay Christian Science Monitor

 

September 9, 2016

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Microbiome and tuberculosis, mangoes, lessons from amphibians, and the microbiome of buildings.

Human gut microbiome

Oral, frozen fecal microbiota transplant (FMT) capsules for recurrent Clostridium difficile infection – Ilan Youngster – BMC Medicine

Review: Microbiome Changes during Tuberculosis and Antituberculous Therapy – Bo-Young Hong – Clinical Microbiology Reviews

No consensus on how the microbiome affects tuberculosis, review finds – Science Daily

Animal models

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Mango, “hedgehog” style – Wikipedia

Mango Supplementation Modulates Gut Microbial Dysbiosis and Short-Chain Fatty Acid Production Independent of Body Weight Reduction in C57BL/6 Mice Fed a High-Fat Diet – Babajide Ojo – Journal of Nutrition

Mango and the Microbiota: New Research Reveals Potential Role of this Superfruit in Maintaining Gut Health – National Mango Board – PR Newswire

Antibiotics Suppress Activation of Intestinal Mucosal Mast Cells and Reduce Dietary Lipid Absorption in Sprague-Dawley Rats – Hirokazu Sato – Gastroenterology

Press (with ugly title): The influence of fat when gut bacteria is reduced by antibioticsm – Science Daily

Animal microbiome

Harnessing the Microbiome to Prevent Fungal Infections: Lessons from Amphibians – Jenifer B. Walke – PLOS Pathogens

Built environment microbiome

Ten questions concerning the microbiomes of buildings – Rachel I. Adams – Building and Environment

The hot new 10 questions concerning the microbiomes of buildings will surprise you – Jonathan Eisen – MicroBEnet

Microbes in the news

“I’ll never let go, Jack I promise”
Titanic expected to disappear by 2030 thanks to hungry bacteria – Matthew Humphries – Geek.com
Video: Will Bacteria Completely Destroy The Titanic’s Remains? – MSN Video

Scientists find deadly scrub typhus bacteria in South America – Reuters

Mount Sinai Beth Israel Says Legionella Bacteria Found in Several Areas of Hospital – NY1.com

Mood, mind and memory: can gut bacteria meddle with the brain? – Dyani Lewis – Cosmos Magazine
Bugs as drugs – medicine’s next frontier – Dyani Lewis – Cosmos Magazine

Driving Microbiome Science: PKU and Probiotics – Raredr

Experts urge a defensive stance in efforts against antimicrobial resistance – EurekAlert

Microbes and money

Microban Opens Microbiology Testing Services to Non-Partners – Genevieve Scarano – Sourcing Journal

Science, publishing, and career

Your toughest experiment: taking the lead in the lab. Eight scientists share the secrets of being a successful PI – Times Higher Education

September 6, 2016

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Tongue diagnostics and bacterial communities, microbiome and ALS, flowers and bees sharing microbes, and CRISPR assembly.

Events

4th World Congress on Targeting Microbiota is organized at Institut Pasteur, Paris, France – October 17-19, 2016

How the Indoor Microbiome Influence Health, with Jack A. Gilbert – October 27, 2016 at British International School of Chicago – Lincoln Park in Chicago

Human oral microbiome

Bacillus as a potential diagnostic marker for yellow tongue coating – Juan Ye – Scientific Reports

Human skin microbiome

Redefining the Chronic-Wound Microbiome: Fungal Communities Are Prevalent, Dynamic, and Associated with Delayed Healing – Lindsay Kalan – mBio

Human respiratory tract microbiome

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

Human urinary tract microbiome

Commentary: “Urinary tract infection” and the microbiome – Thomas E. Finucane – The American Journal of Medicine

Human gut microbiome

Pitfalls in Inferring Human Microbial Dynamics from Temporal Metagenomics Data – Hong-Tai Cao – bioRxiv

Evaluation of the microbial diversity in amyotrophic lateral sclerosis using high-throughput sequencing – Xin Fang – Frontiers in Microbiology

Review: Beyond 16S rRNA community profiling: intra-species diversity in the gut microbiota – Kirsten M. Ellegaard – Frontiers in Microbiology

Review: Epigenetic mechanisms in microbial members of the human microbiota: current knowledge and perspectives – Natacha Cureau – Future Medicine

Microbiology and immunology

Perspective: Autoimmunity and the microbiome: T-cell receptor mimicry of “self” and microbial antigens mediates self tolerance in holobionts – Robert Root-Bernstein – BioEssays

Animal models of microbiome research

Ketogenic diet modifies the gut microbiota in a murine model of autism spectrum disorder – Christopher Newell – Molecular Autism

Animal microbiome

Disentangling a holobiont – recent advances and perspectives in Nasonia wasps – Jessica Dittmer – Frontiers in Microbiology

Review: The terrestrial isopod microbiome: An all-in-one toolbox for animal-microbe interactions of ecological relevance – Didier Bouchon – Frontiers in Microbiology

Plant, root, and soil microbiome

Microbial communities in passive remediation systems at three abandoned coal mine sites in the United Kingdom – Carmen Falagán – Proceedings IMWA 2016, Freiberg

Primary Succession of Nitrogen Cycling Microbial Communities Along the Deglaciated Forelands of Tianshan Mountain, China – Jun Zeng – Frontiers in Microbiology

Flowers and Wild Megachilid Bees Share Microbes – Quinn S. McFrederick – Microbial Ecology

Triclosan Resistome from Metagenome Reveals Diverse Enoyl Acyl Carrier Protein Reductases and Selective Enrichment of Triclosan Resistance Genes – Raees Khan – Scientific Reports

Water and extremophile microbiome

Oligotrophic Lagoons of the South Pacific Ocean Are Home to a Surprising Number of Novel Eukaryotic Microorganisms – Eunsoo Kim – Environmental Microbiology

Upstream freshwater and terrestrial sources are differentially reflected in the bacterial community structure along a small Arctic river and its estuary – Aviaja L. Hauptmann – Frontiers in Microbiology

Built environment microbiology

Review: Emerging Investigators Series: Sewer surveillance for monitoring antibiotic use and prevalence of antibiotic resistance: urban sewer epidemiology – Nicole Fahrenfeld – Environmental Science: Water Research & Technology

Food microbiology

High-throughput identification of the microbial biodiversity of cocoa bean fermentation by MALDI-TOF MS – S. Miescher Schwenninger – Letters in Applied Microbiology

Bioinformatics and metagenomics

Assemble CRISPRs from metagenomic sequencing data – Jikai Lei – Bioinformatics

Contig annotation tool CAT robustly classifies assembled metagenomic contigs and long sequences – Diego D. Cambuy – bioRxiv

Techniques

High throughput sequencing of multiple amplicons for barcoding and integrative taxonomy – Perrine Cruaud – bioRxiv

Microbes in the news

Podcast (12 min) with Stephen Pointing: Protecting the Earth’s Microbiome – Jesse Mulligan – Radio NZ

Biochemists’ discovery could lead to vaccine against ‘flesh-eating’ bacteria – Science Daily

Enzyme from oral bacteria could be potential therapy for celiac disease – News Medical

Bik’s Non-Microbiology Picks

Bizarre ant colony discovered in an abandoned Polish nuclear weapons bunker – Annalee Newitz – ArsTechnica

September 1, 2016

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Bedouins, urban Saoudis and monkeys, a subglacial lake, and the oldest microbial fossils.

Events

Alfred P. Sloan Foundation Workshop on Viruses to be Held in Singapore, January 2017 – David Coil – MicroBEnet

Human respiratory microbiome

News: Does barnyard dust protect Amish children from asthma? – Bryant Furlow – The Lancet

Human gut microbiome

Gut microbiome and dietary patterns in different Saudi populations and monkeys – Emmanouil Angelakis – Scientific Reports

Fecal Microbiota Transplantation is Safe and Efficacious for Recurrent or Refractory Clostridium difficile Infection in Patients with Inflammatory Bowel Disease – Monika Fischer

Animal experiments

High fat diet drives obesity regardless the composition of gut microbiota in mice – Sylvie Rabot – Scientific Reports

Gut Microbiota Promote Angiotensin II–Induced Arterial Hypertension and Vascular Dysfunction – Susanne H. Karbach – Hypertension

Plant, root, and soil microbiome

Forest area and connectivity influence root-associated fungal communities in a fragmented landscape – Rachel L. Vannette – Ecology

Review: Comparative phylogenomics of symbiotic associations – Pierre-Marc Delaux – New Phytologist

Water and extremophile

Microbial Community Structure of Subglacial Lake Whillans, West Antarctica – Amanda M. Achberger – Frontiers in Microbiology

Dust microbiome

Poultry houses: DNA from dust: comparative genomics of large DNA viruses in field surveillance samples – Utsav Pandey – bioRxiv

Techniques

Direct 16S rRNA-seq from bacterial communities: a PCR-independent approach to simultaneously assess microbial diversity and functional activity potential of each taxon – Riccardo Rosselli – Scientific Reports

More microbiology

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Geological map and location of microbial structures

Rapid emergence of life shown by discovery of 3,700-million-year-old microbial structures – Allen P. Nutman – Nature

Press: Life thrived on young Earth: scientists discover 3.7-billion-year-old fossils – Science Daily
The World’s Oldest Fossils Are 3.7 Billion Years Old. The newly discovered rocks suggest that life arose very quickly after the Earth was formed – Ed Yong – The Atlantic

Microbes in the news

Microbial genomics and the future of food microbiology – Julie Wolf – American Society for Microbiology

Space Microbiome? Yes Please! and I’ll take a minION sequencer as well if you don’t mind – Ben Libberton – NPJ Biofilms Community

Multitalented microbiology student is highly lauded for her scholarship – Western Michigan University

Manuka honey makes bacteria less resistant to antibiotics – Rowena Jenkins – The Conversation

Changes in Gut microflora – early warning of Equine Metabolic Syndrome (EMS)? – Jackie Bellamy-Zions – Harness Link

uBiome Hires New Vice President of Research and Development: Dr. Audrey Goddard Joins from Genomic Health and Genentech – PR Web

Samorost 3’s fairy tale of microbiology is now on iPhone – Chris Priestman – Kill Screen

Science, publishing, and career

How to Motivate Your Employees: Give Them Compliments and Pizza – Melissa Dahl – New York Magazine

Opinion: Fixing Science’s Human Bias. It’s time to accelerate the conversation about why the research community is still not diverse – Edward Courchaine and Sarah Smaga – The Scientist

Thanks to the glass ceiling breakers – Yarrow Axford – Science

Peer review

HT: Tomer Altman: Stupid Patent of the Month: Elsevier Patents Online Peer Review – Electronic Frontier Foundation

Research Integrity

OMICS vs. The FTC: Plagiarism at a Predatory Publisher – Neuroskeptic – Discover

 

August 26, 2016

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MRI scans of colonic contents in setting of diet or defaecation, fecal transplants, the microbiome of ambulances, and a core taxa tool.

Pregnancy and birth

Longitudinal study on clinical and microbial analysis of periodontal status in pregnancy – Fernanda Campos Machado – Brazilian Oral Research

Review: Role of microbiota function during early life and children neurodevelopment – Tomás Cerdó – Trends in Food Science & Technology

Human oral microbiome (also see above)

Evaluation of oral microbiota in undernourished and eutrophic children using checkerboard DNA-DNA hybridization – M. Testa – Anaerobe

Review: Human neutrophils and oral microbiota: a constant tug-of-war between a harmonious and a discordant coexistence – Silvia M. Uriarte – Immunological Reviews

Human skin microbiome

Temporal stability in chronic wound microbiota is associated with poor healing – Michael Loesche – Journal of Investigative Dermatology

Human gut microbiome

Colonic content: effect of diet, meals, and defecation – R. A. Bendezú – Neurogastroenterology & Motility

Gut microbiota associated with HIV infection is significantly enriched in bacteria tolerant to oxygen – Grégory Dubourg – BMJ Open Gastroenterology

Prevalence and genetic diversity of Blastocystis in family units living in the United States – Pauline D. Scanlan – Infection, Genetics and Evolution

Nitrogen fixation and nifH diversity in human gut microbiota – Katsura Igai – Scientific Reports

Letter: Intestinal Microbiota and Health of Adults Who Were Born by Cesarean Delivery – James J. Goedert – JAMA Pediatrics

Opinion: The microbiome, microbial generated pro-inflammatory neurotoxins, and Alzheimer’s disease – Walter J. Lukiw – Journal of Sport and Health Science

Review: Estrogen and Microbiota Crosstalk: Should We Pay Attention? – Karen L. Chen – Trends in Endocrinology & Metabolism

Review: Gender, aging and longevity in humans: an update of an intriguing/neglected scenario paving the way to a gender-specific medicine – Rita Ostan – Clinical Science

Fecal transplants

Estimating the risks of faecal transplants – K. Patel – The Journal of Hospital Infection

Effect of Fecal Microbiota Transplantation on Recurrence in Multiply Recurrent Clostridium difficile Infection: A Randomized Trial – Colleen R. Kelly – Annals of Internal Medicine

Plant, root, and soil microbiome

Arbuscular mycorrhizal fungi communities from tropical Africa reveal strong ecological structure – Susana Rodríguez-Echeverría – New Phytologist

Gall-ID: tools for genotyping gall-causing phytopathogenic bacteria – Edward W. Davis II – PeerJ

Water microbiome

Structure and function of methanogenic microbial communities in sediments of Amazonian lakes with different water types – Yang Ji – Environmental Microbiology

Built environment microbiome

Detection and characterization of surface microbial contamination in emergency ambulances – Aketza Varona-Barquin – American Journal of Infection Control

Fitness and recovery of bacterial communities and antibiotic resistance genes in urban wastewaters exposed to classical disinfection treatments – Andrea Di Cesare – Environmental Science & Technology

Bioinformatics and metagenomics

PhyloCore: A phylogenetic approach to identifying core taxa in microbial communities – Tiantian Ren – Gene

Microbes in the news

Gut reaction: the surprising power of microbes – Ed Yong – The Guardian

Want to feel better? Be kind to your bugs. Ed Yong’s new book will give you a positive outlook on your body’s trillions of bacteria – Kate Womersley – The Spectator

The world’s largest bacterial study of baby poo – MedicalXpress

What’s in Your Poo? The nonmicrobial components of feces may have important consequences as we try to grapple with microbiome research – Kevin Bonham – Scientific American

Solving a 48-year-old mystery: scientists succeed at growing noroviruses in human intestinal cell cultures in the lab – Graciela Gutierrez – Baylor College of Medicine

MSU researchers spread the buzz about bee viruses – Marshall Swearingen – Montana State University

Science, publishing, and career

Family ties ‘help scientists to get ahead’ in some countries. Levels of nepotism in scientific publishing have been revealed by report – Jack Grove  – Times Higher Education

Supervisors can do a lot more to support PhD students. Many doctoral candidates feel poorly looked after. More awareness and empathy from academics can help fight that – Geoffrey Cantor – Times Higher Education

New leader of NIH’s research watchdog faces staff revolt – Jocelyn Kaiser – Science