Author Archives: eliesbik

June 3, 2016

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Microbes around a methane seep that look like ancient ruins, microbial metabolites protecting intestinal stem cells, and human-derived microbes in a Mars-like simulator.

Jobs and events

For everyone anxious to see the videos of the Stanford Bioinformatics for the Microbiome Symposium (including me!), please be patient. The AV team is working hard to generate videos for each individual talk, but that will take some time. Check in at this blog under the “Jobs and Events” header where I will post them once they are ready.

Assistant Professor in the Department of Biology – Macalester College, St. Paul, MN

Human vaginal microbiome

Predictive value of the composition of the vaginal microbiota in bacterial vaginosis, a dynamic study to identify recurrence-related flora – Bingbing Xiao – Scientific Reports

Human gut microbiome

Review: Reframing the Teenage Wasteland: Adolescent Microbiota-Gut-Brain Axis – Karen-Anne McVey Neufeld – The Canadian Journal of Psychiatry
Editorial to their own paper (?): Stress and the Microbiota-Gut-Brain Axis. An Evolving Concept in Psychiatry – John F. Cryan – The Canadian Journal of Psychiatry

Review: Emerging evidence of the role of gut microbiota in the development of allergic diseases – Kotryna Simonyte Sjödin – Current Opinion Allergy Clinical Immunology

Review: Microbiota and pathogen ‘pas de deux’: setting up and breaking down barriers to intestinal infection – Elizabeth S. McKenney – Pathogens and Disease

Review: Linking Gut Microbiota and Inflammation to Obesity and Insulin Resistance – M. J. A. Saad – Physiology

Research Highlight: Sensing gene–microbiota signals in IBD – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

Editorial: Probiotics and microbiota composition – Mary Ellen Sanders – BMC Medicine

Animal / tissue culture experiments

The Colonic Crypt Protects Stem Cells from Microbiota-Derived Metabolites – Gerard E. Kaiko – Cell

Press: Gut microbes’ metabolite dampens proliferation of intestinal stem cells – Science Daily

Animal microbiome

Unfortunately no reference to our recent paper,  which included dolphin blowhole samples: Isolation of culturable aerobic bacteria and evidence of Kerstersia gyiorum from the blowhole of captive Yangtze finless porpoises – Xiaoling Wan – Antonie van Leeuwenhoek

Plants, roots, and soil microbiome

Seeing is believing: cell biology at the plant–microbe interface: report from the 36th New Phytologist Symposium – Mike Deeks – New Phytologist

Bacteria with Phosphate Solubilizing Capacity Alter Mycorrhizal Fungal Growth Both Inside and Outside the Root and in the Presence of Native Microbial Communities – Yuli Marcela Ordoñez – PLOS ONE

Water and extremophile microbiome

Exhumed hydrocarbon-seep authigenic carbonates from Zakynthos island (Greece): Concretions not archaeological remains – Julian E Andrews – Marine and Petroleum Geology

Press:
Ancient Civilization of Microbes, Not Greeks, Built ‘Lost City’ – Henry Fountain – The New York Times
The lost (microbe) colony: bacteria make underwater ‘ruins’ off Greek island – Alan Yuhas – The Guardian
This “Lost Underwater City” Was Actually Made by Microbes. Though these formations may not be evidence of a lost city, they show off some intriguing chemistry – Danny Lewis – Smithsonian
Microfungal oasis in an oligotrophic desert: diversity patterns and community structure in three freshwater systems of Cuatro Ciénegas, Mexico – Patricia Velez – PeerJ

Built environment microbiome

Microbial succession in an inflated lunar/Mars analog habitat during a 30-day human occupation – Teresa Mayer – Microbiome

In Situ Microbial Community Succession on Mild Steel in Estuarine and Marine Environments: Exploring the Role of Iron-Oxidizing Bacteria – Joyce M. McBeth – Frontiers in Microbiology

Ecology and bioinformatics

Applications of species accumulation curves in large-scale biological data analysis – Chao Deng – Quantitative Biology

Microbes in the news

See beautiful gif below: Educate Your Immune System. Our bodies are confused by this 21st-century world – Moises Velasquez-Manoff – NY Times

Will Microbes Save Agriculture? Experts Aim To Find Out – Geoffrey Mohan – Sci Tech Today

Alzheimer’s May Defend Against Microbes – Paul Rodgers – Forbes

Methane-producing microbes in California rocks – Science Daily

Science, publishing, and career

Science launches the 2016 ‘Dance Your Ph.D.’ contest – John Bohannon – Science Magazine

Let’s talk about preprint servers – Emilie Marcus – Crosstalk Cell

Bik’s Picks

A New Origin Story for Dogs. The first domesticated animals may have been tamed twice – Ed Yong – The Atlantic

The meteoritic origin of Tutankhamun’s iron dagger blade – Daniela Comelli – Meteoritics & Planetary Science

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Gif by Santtu Mustonen, New York Times

 

Microbes and art: Danino and Goodsell

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Two beautiful examples of the intersection of microbes and art:A Synthetic Biologist’s Beautiful Palette of Bacteria Art – Noémie Jennifer – The Creators Project

Tal Danino grows various strains of bacteria into detailed, microscopic patterns that pull you in close. During a recent residency at Eyebeam in New York City, he researched how bacteria could be used as inks in various printing processes, like silkscreening or stamping. The resulting series of works, Microuniverses, is a marriage of nature and engineering—in the artist’s words, “you can control these patterns, but then they evolve on their own.” The concept of “controlling universes” is part of Danino’s day job. As the director of the Synthetic Biological Systems Laboratory at Columbia University, Danino is figuring out how to program bacteria so it can detect and treat diseases in our bodies.

 

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It’s The Zika Virus In Action, Drawn By A Scientist-Artist – Maggie Zackowitz – NPR

A watercolor by scientist-artist David S. Goodsell just might make the Zika virus easier to visualize. The painting, which depicts an area about 110 nanometers wide (a nanometer is a billionth of a meter), shows the virus in the process of infecting a cell. (…) Of course the comic book-bright structures shown in the painting aren’t so simple and colorful in real, microscopic life. “These things are actually smaller than the wavelength of light, so they don’t really have a color,” Goodsell says. He chose his own color palette to highlight the function of each component — and to make them look beautiful.

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June 2, 2016

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Neck radiation and oral pathogen increase, menopause and the vaginal microbiome, nectar microbes, raw camel milk, and a review on short-chain fatty acids.

Human skin microbiome

Review: Microbial Ecology of the Human Skin – Anthony M. Cundell – Microbial Ecology

Human oral microbiome

Head and neck intensity modulated radiation therapy leads to an increase of opportunistic oral pathogens – Jennifer M. Schuurhuis – Oral Oncology

Human respiratory microbiome

Airway Microbiota Determines Innate Cell Inflammatory or Tissue Remodeling Profiles in Lung Transplantation – Eric Bernasconi – American Journal of Respiratory and Critical Care Medicine

Human vaginal microbiome

Review: Menopause and the Vaginal Microbiome – Alicia L. Muhleisen – Maturitas

Human gut microbiome

Not sure why this got published in Neurocomputing, also very poor English:
Gut microbiota community adaption during young children fecal microbiota transplantation by 16s rDNA sequencing – Jian-Lei Gu – Neurocomputing

Commentary: Transkingdom interactions: Liver flukes and the microbiota in cancer – Lisa Osborne – EBioMedicine

Review: Complex Relationships Between Food, Diet, and the Microbiome – Laura A. Pace – Gastroenterology Clinics of North America

Animal microbiome

Caribbean corals house shared and host-specific microbial symbionts over time and space – Nathaniel D. Chu – Environmental Microbiology Reports

Genome evolution and nitrogen-fixation in bacterial ectosymbionts of a protist inhabiting wood-feeding cockroaches – Vera Tai – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Nectar microbes can reduce secondary metabolites in nectar and alter effects on nectar consumption by pollinators – Rachel L. Vannette – Ecology

The Root-Associated Microbial Community of the World’s Highest Growing Vascular Plants – Roey Angel – Microbial Ecology

Plant community and soil chemistry responses to long-term nitrogen inputs drive changes in alpine bacterial communities – Xia Yuan – Ecology

Forest composition modifies litter dynamics and decomposition in regenerating tropical dry forest – Erik M. Schilling – Oecologia

Metal contamination status of the soil-plant system and effects on the soil microbial community near a rare metal recycling smelter – Zhu Li – Environmental Science and Pollution Research

Tree species, spatial heterogeneity, and seasonality drive soil fungal abundance, richness, and composition in Neotropical rainforests – Stephanie N. Kivlin – Environmental Microbiology

Review: Emerging Insights on Brazilian Pepper Tree (Schinus terebinthifolius) Invasion: The Potential Role of Soil Microorganisms – Karim Dawkins – Frontiers in Plant Science

Food microbiology

Bacteriological quality of raw camel milk along the market value chain in Fafen zone, Ethiopian Somali regional state – Tsegalem Abera – BMC Research Notes

Bioreactor microbiology

Comparison of microbial communities of activated sludge and membrane biofilm in 10 full-scale membrane bioreactors – Sung Jun Jo – Water Research

Phages and viruses

Phagonaute: A web-based interface for phage synteny browsing and protein function prediction – Hadrien Delattre – Virology

Assessing Illumina technology for the high-throughput sequencing of bacteriophage genomes – Branko Rihtman – PeerJ

Metagenomics and bioinformatics

Identification and analysis of integrons and cassette arrays in bacterial genomes – Jean Cury – Nucleic Acids Research

Uncovering oral Neisseria tropism and persistence using metagenomic sequencing – Claudio Donati – Nature Microbiology

Improved metagenome screening efficiency by random insertion of T7 promoters – Yu Jung Kim – Journal of Biotechnology

Experiences in integrated data and research object publishing using GigaDB – Scott C Edmunds – International Journal on Digital Libraries

Techniques

An Improved Method for High Quality Metagenomics DNA Extraction from Human and Environmental Samples – Satyabrata Bag – Scientific Reports

Proteomics, metabolomics

In vitro metabolic labeling of intestinal microbiota for quantitative metaproteomics – Xu Zhang – Analytical Chemistry

Syntrophic metabolism of vitamins and amino acids in gut microbial community as revealed by in silico genomic analyses – Matvei Sergeevich Khoroshkin – The FASEB Journal

Review: From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites – Ara Koh – Cell

More microbiology

Survey of laboratory-acquired infections around the world in biosafety level 3 and 4 laboratories – N. Wurtz – European Journal of Clinical Microbiology & Infectious Diseases

Effects of temperature variability on community structure in a natural microbial food web – Axel Zander – Global Change Biology

Perspective: Cooperative Microbial Tolerance Behaviors in Host-Microbiota Mutualism – Janelle S. Ayres – Cell

Review: Multifaceted Interfaces of Bacterial Competition – Reed M. Stubbendieck – Journal of Bacteriology

Microbes in the news

Featuring our former lab member Kate Rubins: Napa native heading to International Space Station on 1st space mission – ABC7news

American Gut Project Expands to Asia – Crowdsourced microbiome sequencing effort seeks participant diversity – Heather Buschman – UC San Diego Health

Making sense of microbiomes – UCI biochemist studies the effect of unique virus, bacteria and fungi on kids’ health – Tom Vasich – UCI News

11 deaths at Huntington Hospital among patients infected by dirty scopes, city report says – LA Times
Deadly dirty medical scopes still threaten trusting patients – My News LA

Walnuts may improve your colon health: Eating walnuts changes the gut microbiome and reduces cancer growth – EurekAlert

Gluten-Free Diet Induces Changes In Gut Microbiome – Interview with Ettje Tigchelaar – Medical Research

Fecal Transplants Effective for Healing Ulcerative Colitis – HCP Live

Gut Microbiome Tied to Metabolic Hormones in Early Pregnancy – Doctors Lounge

Human Gut Microbiome May Help Identify New Ways of Preventing and Treating Diabetes – Endocrinology Advisor

Researchers poo poo antibiotics – Vet Practice Magazine

Video: Susannah Tringe talks about metagenomics analysis tools and the challenges of gaining a systems-level understanding of a microbial community – Vizbi

Cold shock: E.coli bacteria found in 92 per cent ice samples in Mumbai – MidDay

Science, publishing, and career

The scientist’s guide to summer reading – Science

What does scientific reproducibility mean, anyway? – Ivan Oransky and Adam Marcus – STAT News

June 1, 2016

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Cystic fibrosis, microbial detoxification in the Sage Grouse, salinity gradient in the Baltic Sea, and testing different 16S rRNA gene primer pairs.

Human respiratory microbiome

Microbiological profiles of sputum and gastric juice aspirates in Cystic Fibrosis patients – H. Al-momani – Scientific Reports

The Dynamics of Disease Progression in Cystic Fibrosis – Frederick R. Adler – PLOS ONE

Human gut microbiome

Alterations and correlations of the gut microbiome, metabolism, and immunity in patients with primary biliary cirrhosis – Long-Xian Lv – Environmental Microbiology

Review: Analysis and Interpretation of the Human Microbiome – Ashton, James J. – Inflammatory Bowel Diseases

Review: Gut microbiota and colorectal cancer – Mayuko Yamamoto – Genes and Environment

Animal experiments

The Impact of Lactobacillus casei on the Composition of the Cecal Microbiota and Innate Immune System Is Strain Specific – Busra Aktas – PLOS ONE

Metagenomic Analysis of the Rumen Microbiome of Steers with Wheat-Induced Frothy Bloat – D. W. Pitta – Frontiers in Microbiology

Intestinal Microbiota of Broiler Chickens As Affected by Litter Management Regimens – Lingling Wang – Frontiers in Microbiology

Animal microbiome

Snapshot of a Bacterial Microbiome Shift during the Early Symptoms of a Massive Sponge Die-Off in the Western Mediterranean – Andrea Blanquer – Frontiers in Microbiology

Microbial detoxification in the gut of a specialist avian herbivore, the Greater Sage-Grouse – Kevin D. Kohl – FEMS Microbiology Letters

Plant, root, and soil microbiome

Understory herb layer exerts strong controls on soil microbial communities in subtropical plantations – Kai Yin – Scientific Reports

Design defines the effects of nanoceria at a low dose on soil microbiota and the potentiation of impacts by canola plant – Mohamed Hamidat – Environmental Science & Technology

Diversity Enhances NPP, N Retention, and Soil Microbial Diversity in Experimental Urban Grassland Assemblages – Grant L. Thompson – PLOS ONE

Water and extremophile microbiome

Diversity of Pico- to Mesoplankton along the 2000 km Salinity Gradient of the Baltic Sea – Tue O. O. Hu – Frontiers in Microbiology

Superimposed Pristine Limestone Aquifers with Marked Hydrochemical Differences Exhibit Distinct Fungal Communities – Ali Nawaz – Frontiers in Microbiology

Culture-independent characterization of novel psychrophilic magnetotactic cocci from Antarctic marine sediments – Fernanda Abreu – Environmental Microbiology

Food microbiology

Metagenomic sequencing reveals the relationship between microbiota composition and quality of Chinese Rice Wine – Xutao Hong – Scientific Reports

Exploring flavour-producing core microbiota in multispecies solid-state fermentation of traditional Chinese vinegar – Zong-Min Wang – Scientific Reports

Bioreactor microbiology

Mycoalgae biofilm: development of a novel platform technology using algae and fungal cultures – Aravindan Rajendran – Biotechnology for Biofuels

Techniques

Performance of 16s rDNA Primer Pairs in the Study of Rhizosphere and Endosphere Bacterial Microbiomes in Metabarcoding Studies – Bram Beckers – Frontiers in Microbiology

Misguided phylogenetic comparisons using DGGE excised bands may contaminate public sequence databases – Victor Satler Pylro – Journal of Microbiological Methods

Microbes in the news

Unlocking the secrets of bacterial biofilms – to use against them – Karin Sauer – The Conversation

CDC to set up network of labs to fight tough bacteria – Dale Shoemaker – The Morning Call

Stick insects produce bacterial enzymes themselves. In the course of evolution, genes of gut microbes ‘jumped’ to their insect host – EurekAlert

Tobacco Smoke Makes Germs More Resilient – University of Louisville – NewsWise

Malaria, Zika and Dengue Could Meet Their Match in Mosquito-Borne Bacteria. A common bacteria that infects mosquitoes seems to prevent them from carrying more deadly diseases – Brian Handwerk – Smithsonian

Wild Culture: The Wild Side of Beer Brewing – Anna Brones – Paste Magazine

Unlocking the Mysteries of the Microbiome – J Craig Venter Institute

Science, publishing, and career

Nondisclosure of Financial Interest in Clinical Practice Guideline Development: An Intractable Problem? – Hilda Bastian – PLOS Medicine

Financial Relationships between Organizations That Produce Clinical Practice Guidelines and the Biomedical Industry: A Cross-Sectional Study – Paul Campsall – PLOS Medicine

Pseudoscience

Why Is Big Naturopathy Afraid Of This Lone Whistleblower? – Kavin Senapathy – Forbes

Bik’s Brain: Monet

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Welcome in my brain, which is full of completely useless associations. Here is another edition of #ICouldNotResist.

Today, with help from a Tweet by @MarylandMunros, I associated a graph made by the J. Craig Venter Institute (JCVI) with a painting by Claude Monet.

Top: a visualization of ocean microbial data collected on JCVI’s Global Ocean Sampling Expedition (GOS). See the original post here.

Bottom: “Houses of Parliament, Sunset, 1903” painting by Claude Monet (image taken from Wikipedia).

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May 31, 2016

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Feces for forensic investigations, respiratory tract microbiome in premature infants, soil microbes in cereal rotation, sourdough microbiota, kombucha bacteria making cellulose, GutCyc metabolic models, and 157 new microbial genomes from biogas reactors.

Pregnancy and birth

The Microbiome of the Lower Respiratory Tract in Premature Infants with and without Severe Bronchopulmonary Dysplasia – Takashi Imamura – American Journal of Perinatology

High fecal IgA is associated with reduced Clostridium difficile colonization in infants – Sarah L. Bridgman – Microbes and Infection

Human gut microbiome

Microbial population analysis improves the evidential value of faecal traces in forensic investigations – Frederike C. A. Quaak – International Journal of Legal Medicine

Composition and function of the pediatric colonic mucosal microbiome in untreated patients with ulcerative colitis – Rajesh Shah – Gut Microbes

Active and Secretory IgA-Coated Bacterial Fractions Elucidate Dysbiosis in Clostridium difficile Infection – Mária Džunková – mSphere

Review: Tolerance to the Intestinal Microbiota Mediated by ROR(γt)+ Cells – Caspar Ohnmacht – Trends in Immunology

Review: Vegetarian diets and gut microbiota: important shifts in markers of metabolism and cardiovascular disease – Vinicius A. do Rosario – Nutrition Reviews

Review: Microbiome and its Impact on Gastrointestinal Atopy – Amanda B. Muir – Allergy

Review: Gut microbiota and inflammatory joint diseases – Maxime Breban – Joint Bone Spine

Review: Faecal microbiota transplantation: applications and limitations in treating gastrointestinal disorders – Hani Sbahi – BMJ Open Gastroenterology

Book chapter with not a lot of data: Gut Microbiota: A Possible Role in the Pathogenesis of Multiple Sclerosis – Takashi Yamamura – Neuro-Immuno-Gastroenterology

Review: Recent Advances and Understanding of Using Probiotic-Based Interventions to Restore Homeostasis of the Microbiome for the Prevention/Therapy of Bacterial Diseases – Jan S. Suchodolski – Microbiology Spectrum

Review: The human gut microbiome impacts health and disease – Stanislav Dusko Ehrlich – Comptes Rendus Biologies

Animal microbiology

Analysis of cultivable microbiota and diet intake pattern of the long-lived naked mole-rat – Tewodros Debebe – Gut Pathogens

Editorial: Microbial ecology: Algae feed a shift on coral reefs – Melissa Garren – Nature Microbiology

Grandeur Alliances: Symbiont Metabolic Integration and Obligate Arthropod Hematophagy – Rita V.M. Rio – Trends in Parasitology

Plant, root, and soil microbiome

Pastures to woodlands: changes in soil microbial communities and carbon following reforestation – T.R. Cavagnaro – Applied Soil Ecology

The legacy effect of cover crops on soil fungal populations in a cereal rotation – Andrew P. Detheridge – Agriculture, Ecosystems & Environment

Microbial utilization of double-labeled aspen litter in boreal aspen and spruce soils – Charlotte E. Norris – Soil Biology and Biochemistry

Isolating a functionally relevant guild of fungi from the root microbiome of Populus – Gregory Bonito – Fungal Ecology

Review – Lichen-Associated Bacteria as a Hot Spot of Chemodiversity: Focus on Uncialamycin, a Promising Compound for Future Medicinal Applications – Delphine Parrot – Planta Med

Book Chapter: Plant-Rhizobacteria Interaction and Drought Stress Tolerance in Plants – Cohen Ana Carmen – Drought Stress Tolerance in Plants, Vol 1

Water microbiology

Response of bacterial communities from California coastal waters to alginate particles and an alginolytic Alteromonas macleodii strain – Maximilian Mitulla – Environmental Microbiology

Food microbiology

New insight into microbial diversity and functions in traditional Vietnamese alcoholic fermentation – Vu Nguyen Thanh – International Journal of Food Microbiology

Evolution of sourdough microbiota in spontaneous sourdoughs started with different plant materials – Valery Ripari – International Journal of Food Technology

Review: Drivers for the establishment and composition of the sourdough lactic acid bacteria biota – Marco Gobbetti – International Journal of Food Microbiology

Pollution and waste microbiology

Deeper insight into the structure of the anaerobic digestion microbial community; the biogas microbiome database is expanded with 157 new genomes – Laura Treu – Bioresource Technology

Differential impacts of willow and mineral fertilizer on bacterial communities and biodegradation in diesel fuel oil-contaminated soil – Mary-Cathrine C. Leewis – Frontiers in Microbiology

Spatial variation of microbial community structure in the Zijinshan commercial copper heap bioleaching plant – Xingyu Liu – Minerals Engineering

Techniques

Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples – Angela Glassing – Gut Pathogens

Viruses

A metagenomic comparison of endemic viruses from broiler chickens with runting stunting syndrome and from normal birds – Ryan Devaney – Avian Pathology

Bioinformatics

GutCyc: a Multi-Study Collection of Human Gut Microbiome Metabolic Models – Aria S. Hahn – bioRxiv

metaBIT, an integrative and automated metagenomic pipeline for analyzing microbial profiles from high-throughput sequencing shotgun data – Guillaume Louvel – Molecular Ecology Resources

A resource-frugal probabilistic dictionary and applications in (meta)genomics – Camille Marchet – arXiv

Book Chapter: An Efficient Algorithm for Finding All Pairs k-Mismatch Maximal Common Substrings – Sharma V. Thankachan – Bioinformatics Research and Applications

More microbiology

Engineering control of bacterial cellulose production using a genetic toolkit and a new cellulose-producing strain – Michael Florea – PNAS

Bacteria In Kombucha Tea Could Be Key To Materials Useful For Mars Mission – Ted Ranosa – Tech Times
Engineering ‘tea bacteria’ could lead to advanced materials – Colin Smith – Imperial College London

Microbes in the news

This genetically engineered bacteria can inhale CO2 and produce energy – Futurism
Harvard Scientist Engineers Bacterium That Inhales CO2, Produces Energy – Jeff McMahon – Forbes

Daily Beast Fails in Its Reporting on Probiotics – David Wild – Gastroenterology & Endoscopy News

Why Ice Cream And Peanut Butter May Promote Gut Inflammation – Both contain emulsifiers, which are added to improve texture and extend shelf life – Rachael Rettner – Huffington Post

Scientists find novel enzymes encoded by giant virus – TASS Russian News Agency

Science, publishing and career

We need to do more for women in science – H. Ahmed – Science

May 30, 2016

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Blogging from AMS Airport, with just a couple of new papers that came out yesterday.

Pregnancy and birth

Randomized Control Trial of Human Recombinant Lactoferrin: A Substudy Reveals Effects on the Fecal Microbiome of Very Low Birth Weight Infants – Michael P. Sherman – The Journal of Pediatrics

Editorial: Clinical Benefits of Lactoferrin for Infants and Children – Paolo Manzoni – The Journal of Pediatrics

Human oral microbiome

Initial oral biofilm formation on titanium implants with different surface treatments: An in vivo study – Cyntia Ferreira Ribeiro – Archives of Oral Biology

Human gut microbiome

Research Highlight: Helminths and Intestinal Flora Team Up to Improve Gut Health – Paul Giacomin – Trends in Parasitology

Plant, root, and soil microbiome

How to live with phosphorus scarcity in soil and sediment: Lessons from bacteria.– Yunuen Tapia-Torres – Applied and Environmental Microbiology

Waste and pollution microbiology

Evolution of microbial community along with increasing solid concentration during high-solids anaerobic digestion of sewage sludge – Can Liu – Bioresource Technology

Is there a distance-decay relationship in biological wastewater treatment plants? – Xiaohui Wang – Applied and Environmental Microbiology

Microbes in the news

UCSB Professor Wins Bacteria-Killing Grant – Microbial Geneticist David Low Receives Award to Pinpoint BamA Protein – Santa Barbara Independent

Minnesota chief epidemiologist: No cause for concern after anthrax detection
An initial positive test was followed by negative ones, said Dr. Ruth Lynfield. The bacteria can occur naturally. – Beatrice Dupuy – Star Tribune

Master Gardener Explains Soil Nitrogen – Frank Rauchschwalbe – My Mother Lode

US reports first case of bacteria resistant to antibiotic of last resort – The Guardian

May 28, 2016

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Gut microbiota in stunted children in India, Chinese children with diabetes, Tibetan and Han populations at different altitudes, and searching for Darwin’s Warm Little Pond.

Human skin microbiome

Review: The influence of skin microorganisms on cutaneous immunity – Yasmine Belkaid – Nature Reviews Immunology

Human oral microbiome

Study recruitment: Reducing oral bacteria in those with mild dementia – Shelley Allen – ISRCTN Registry

Human gut microbiome

Weight gain in anorexia nervosa does not ameliorate the faecal microbiota, branched chain fatty acid profiles, and gastrointestinal complaints – Isabelle Mack – Scientific Reports

Longitudinal Analysis of the Intestinal Microbiota in Persistently Stunted Young Children in South India – Duy M. Dinh – PLOS ONE

Effects of Rifaximin on Transit, Permeability, Fecal Microbiome, and Organic Acid Excretion in Irritable Bowel Syndrome – Andrés Acosta – Clinical and Translational Gastroenterology

Imbalance of Fecal Microbiota at Newly Diagnosed Type 1 Diabetes in Chinese Children – Cui-Juan Qi – Chinese Medical Journal

Comparative Analysis of Gut Microbiota of Native Tibetan and Han Populations Living at Different Altitudes – Kang Li – PLOS ONE

Intestinal Microbiota Is Influenced by Gender and Body Mass Index – Carmen Haro – PLOS ONE

Associations between common intestinal parasites and bacteria in humans as revealed by qPCR – L. O’Brien Andersen – European Journal of Clinical Microbiology & Infectious Diseases
Review: Gut microbiota, metabolites and host immunity – Michelle G. Rooks – Nature Reviews Immunology

Review: The behaviour of dietary fibre in the gastrointestinal tract determines its physiological effect – Edoardo Capuano – Critical Reviews in Food Science and Nutrition

Animal experiments

Effects of dietary fibre source on microbiota composition in the large intestine of suckling piglets – Lingli Zhang – FEMS Microbiology Letters

Investigations on the possible impact of a glyphosate-containing herbicide on ruminal metabolism and bacteria in vitro by means of the “Rumen Simulation Technique” – Susanne Riede – Journal of Applied Microbiology

Piglet nasal microbiota at weaning may influence the development of Glässer’s disease during the rearing period – Florencia Correa-Fiz – BMC Genomics

Effects of a Broad-Spectrum Antibiotic on the Siberian Hamster (Phodopus sungorus) Gut Microbiome – Emma A. St. John – The FASEB Journal

Animal microbiome

Comparison of archaeal and bacterial communities in two sponge species and seawater from an Indonesian coral reef environment – Ana Rita Moura Polónia – Marine Genomics

Baboons: Vaginal Dysbiosis from an Evolutionary Perspective – Natalia Schlabritz-Loutsevitch – Scientific Reports

Review: Longevity-modulating effects of symbiosis: insights from Drosophila–Wolbachia interaction – Oleksandr M. Maistrenko – Biogerontology

Water and extremophile microbiome

Essay: A Field Trip to the Archaean in Search of Darwin’s Warm Little Pond – Bruce Damer- MDPI Life

Identification and characterization of yeasts isolated from sedimentary rocks of Union Glacier at the Antarctica – Salvador Barahona – Extremophiles

Ionic Strength Is a Barrier to the Habitability of Mars – Mark G. Fox-Powell – Astrobiology

Built environment microbiology

Urban Dust Microbiome: Impact on Later Atopy and Wheezing – Christina Tischer – Environmental Health Perspectives

Review: Pediatric Asthma and the Indoor Microbial Environment – Lidia Casas – Current Environmental Health Reports

Waste and pollution microbiology

Enhanced methane production via repeated batch bioaugmentation pattern of enriched microbial consortia – Zhiman Yang – Bioresource Technology

Techniques

Effect of short-term room temperature storage on the microbial community in infant fecal samples – Yong Guo – Scientific Reports

Microbial Ecology

Review: Microbial interactions and community assembly at microscales – Otto X Cordero – Current Opinion in Microbiology

Microbes in the news

How to feed a happy, healthy gut – Carrie Dennett – The Washington Post

Development of Gut Microbes and Gut Immunity Linked – Julia Evangelou Strait – Washington University School of Medicine

Newly Discovered Phages Can Target Antibiotic Resistance – Interview with Paul E. Turner PhD – Medical Research

Specter of Oyster Bacteria Brings Suit Against FDA – Lorraine Bailey – Courthouse News

Xenex Germ-Zapping Robot Kills CRE; Robot Destroys Nightmare Bacteria Like CRE, Ebola & C.Diff before They Make People Sick – Business Wire

Science, publishing and career

Excellent podcast for all genders: Sexism in biotech, from scantily clad models to how gender affects this podcast – Meg Tirrell and Luke Timmerman – STAT News

May 27, 2016

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image1Just a short Microbiome Digest in between funeral ceremonies today. But today also brought good news: Microbiome Digest / Bik’s Picks received the “Microbiome Pioneer Award” today at Stanford’s Bioinformatics for the Microbiome Symposium. Professor Ami Bhatt handed out the prize, and Professor Christina Vandenbroucke-Grauls took the photo. I am very honored and thankful for this award, and I owe a big thank you for Tomer Altman for helping me start the blog and David Relman for helping me run it!

Human skin and hair microbiome

Physiological and microbiological verification of the benefit of hair washing in patients with skin conditions of the scalp – Miwa Kobayashi – Journal of Cosmetic Dermatology

Animal microbiome

Bacterial and Archaeal Diversity in the Gastrointestinal Tract of the North American Beaver (Castor canadensis) – Robert J. Gruninger – PLOS ONE

Beaver Gut Microbiome Provides Clues to Plant Material Breakdown – Genome Web

Plant, root, and soil microbiome

Rapid identification of bacteria associated with Acute Oak Decline by high resolution melt (HRM) analysis – Carrie Brady – Letters in Applied Microbiology

Sediment microbial communities rely on different dissolved organic matter sources along a Mediterranean river continuum – A. Freixa – Limnology and Oceanography

More Microbiology

A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria
Jason M. Peters – Cell

Survivability of bare, individual Bacillus subtilis spores to high-velocity surface impact: Implications for microbial transfer through space – Brandon L. Barney – Planetary and Space Science

Crash test bacteria study at BYU could shed light on outer space – Daniel Woodruff – KUTV

Microbes in the news

Bacterial diversity in soils was shaped by ice ages – Amanda Garris – Cornell

Superbugs for dummies: Explaining the battle between bacteria and antibiotics – Helen Branswell – STAT News

Goose Island identifies bacteria that caused tainted beer, but not source – Josh Noel – Chicago Tribune

Cork scientists win funding from Bill Gates’ foundation for Africa study – Gordon Hunt – Silicon Republic

High-dose vitamin D may boost diversity of the gut microbiome – Nutraingredients

 

UCSB receives Grand Challenges Explorations grant – EurekAlert

Science, publishing, and career

Should researchers publish their findings before peer review? – Ivan Oransky and Adam Marcus – STAT News

May 26, 2016

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Bioinformatics Symposium tomorrow at Stanford with free live stream, development of upper respiratory tract microbiome in infants, coral microbiome in Hawaii, calcified red algae microbiome, and metagenomics pathogen detection tool.

Events

Tomorrow, starts at 8am Pacific Time: Bioinformatics for the Microbiome, Stanford University. Will also be live streamed (and recording will be kept here for a while too) at Stanford Webcast. Due to family circumstances I won’t be able to be there, unfortunately 😦

Targeting the Microbiome – September 19-22, Boston, MA

Report from meeting earlier this week: Frontiers in Human Microbiota Symbiotic Interactions” 3rd Annual Meeting of the Bridging Biomedical Worlds Series

Jobs

Postdoc position in Pat Schloss group – Department of Microbiology & Immunology at the University of Michigan

General microbiome

Bioengineering microbial communities: Their potential to help, hinder and disgust – Diane Sivasubramaniama – Bioengineered

Pregnancy and birth

Development of Upper Respiratory Tract Microbiota in Infancy is Affected by Mode of Delivery – Astrid A.T.M. Bosch – EBioMedicine

Human respiratory microbiome

Long-Term Evolution of Burkholderia multivorans during a Chronic Cystic Fibrosis Infection Reveals Shifting Forces of Selection – Inês N. Silva – mSystems

Study shows how bacteria evolve in lungs of cystic fibrosis patients – Science Daily

Upper airway microbial colonization in patients with neuromuscular disorders – Florian Stehling – Respirology

Human gut microbiome

Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study – Toshitaka Odamaki – BMC Microbiology

Metagenomic characterization of microbial communities in situ within the deeper layers of the ileum in Crohn’s Disease – Chandra Sekhar Pedamallu – CMGH Cellular and Molecular Gastroenterology and Hepatology

Association of Systemic Sclerosis With a Unique Colonic Microbial Consortium – Elizabeth R. Volkmann – Arthritis & Rheumatology

Development of the gut microbiota and mucosal IgA responses in twins and gnotobiotic mice – Joseph D. Planer – Nature

Animal experiments

Impact of a High-Fat or High-Fiber Diet on Intestinal Microbiota and Metabolic Markers in a Pig Model – Sonja N. Heinritz – MDPI Nutrients

Immunological Consequences of Intestinal Fungal Dysbiosis – Matthew L. Wheeler – Cell Host & MIcrobe

Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease – Hiutung Chu – Science

Editorial: Microbiome: Does the brain listen to the gut? – Thomas Kuntz – eLIFE

Animal microbiome

Biogeography of planktonic and coral-associated microorganisms across the Hawaiian Archipelago – Jennifer L. Salerno – FEMS Microbiology Ecology

Codivergence of the primary bacterial endosymbiont of psyllids versus host switches and replacement of their secondary bacterial endosymbionts – Aidan A. G. Hall – Environmental Microbiology

An exploration of the fungal assemblage in each life history stage of the butterfly, Lycaeides melissa (Lycaenidae), as well as its host plant Astragalus canadensis (Fabaceae) – Joshua G. Harrison – Fungal Ecology

Comparison of the fecal microbiota in horses with Equine Metabolic Syndrome (EMS) and metabolically normal controls fed a similar all forage diet – S. Elzinga – Journal of Equine Veterinary Science

Plant, root, and soil microbiome

Characterising the microbiome of Corallina officinalis, a dominant calcified intertidal red alga – Juliet Brodie – FEMS Microbiology Ecology

Relative importance of soil properties and microbial community for soil functionality: insights from a microbial swap experiment – Manuel Delgado-Baquerizo – Functional Ecology

Effect of agricultural practices and coastal constraints on soil microbial functional properties in Mediterranean olive orchards – N. Boukhdoud – European Journal of Soil Science

Functional breadth and home-field advantage generate functional differences among soil microbial decomposers – Nicholas Fanin – Ecology

Book Chapter: Bacteria and Non-lichenized Fungi Within Biological Soil Crusts – Stefanie Maier – Biological Soil Crusts: An Organizing Principle in Drylands

Metagenomics, bioinformatics, and techniques

HoloVir: A workflow for investigating the diversity and function of viruses in invertebrate holobionts – Patrick W. Laffy – Frontiers in Microbiology

Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling – Steven Flygare – Genome Biology

Metagenomics pathogen detection tool could change how infectious diseases are diagnosed – EurekAlert

Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing – Matthew Thoendel – Journal of Microbiological Methods

BMPOS: a Flexible and User-Friendly Tool Sets for Microbiome Studies – Victor S. Pylro – Microbial Ecology

Functional foods

Reviewing Classical and Molecular Techniques Regarding Profiling of Probiotic Character of Microorganisms – Christos Stefanis – Current Research in Nutrition and Food Science

Microbes in the news

Polio-free world? Not if scientists refuse to destroy their research specimens – Helen Branswell – STAT news

The secret history of ancient toilets. By scouring the remains of early loos and sewers, archaeologists are finding clues to what life was like in the Roman world and in other civilizations – Chelsea Wald – Nature

Using Gut Bacteria To Save The Planet – John Farrell – Forbes

The Emergent Microbiome: A Revolution for the Life Sciences – Part VI, Diagnostics – Jessica L. Miles and Anthony D. Sabatelli – Lexology