Category Archives: General Microbiome

February 26, 2015

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After today’s #LlamaDrama, I was searching for some llama microbiome papers. Here is the best I could find:  Llama dung treats acid drainage – EnviroPaul – FlushItBlog

Microbiome of pregnancy and birth

Infant gut microbiota and food sensitization: associations in the first year of life – M. B. Azad – Clinical & Experimental Allergy

Human oral microbiome

Subgingival bacterial recolonization after scaling and root planing in smokers with chronic periodontitis – M Feres – Australian Dental Journal

Human skin microbiome

Review: The skin microbiome: Associations between altered microbial communities and disease – Laura S Weyrich – Australasian Journal of Dermatology

Human gut microbiome

Brief Report: Intestinal Dysbiosis in Ankylosing Spondylitis – Mary-Ellen Costello – Arthritis & Rheumatology

Animal microbiome

Olive Ridley Sea Turtle Hatching Success as a Function of the Microbial Abundance in Nest Sand at Ostional, Costa Rica – Vanessa S. Bézy – PLOS ONE

Can light intensity cause shifts in natural product and bacterial profiles of the sponge Aplysina aerophoba? – Oriol Sacristán-Soriano – Marine Ecology

Soil microbiome

Influence of edaphic and management factors on the diversity and abundance of ammonia-oxidizing thaumarchaeota and bacteria in soils of bioenergy crop cultivars
Anthony D. Bertagnolli – Environmental Microbiology Reports

Food microbiology

Dynamic variation of the microbial community structure during the long-time mono-fermentation of maize and sugar beet silage – Johanna Klang – Microbial Biotechnology

Metagenomics

Perspective: ‘Metagenomics 2.0’ – Katherine McMahon – Environmental Microbiology Reports

Bioinformatics

PathVisio 3: An Extendable Pathway Analysis Toolbox – Martina Kutmon – PLOS

Ecology and other microbiology papers

Perspective: From environmental microbiology to ecogenomics: spotting the emerging field of fungal–bacterial interactions – Paola Bonfante – Environmental Microbiology Reports

Perspective: The universe under a microscope – Arjun V. Raman and Nitin S. Baliga – Environmental Microbiology Reports

Perspective: Microbes don’t play solitaire: how cooperation trumps isolation in the microbial world – Steven J. Hallam – Environmental Microbiology Reports

Microbes in the news

 

Sewage provides insight into human microbiome – Biology News Net

Magazine Preview: Delving into the Depths of the Microbiome – Richard A. Stein – GenEngNews

Build a Better Microbiome: 7 Ways To Embrace More Microbes – Frank Lipman – Yahoo

Food emulsifiers linked to gut bacteria changes and obesity – Nathan Gray – Food Navigator
Emulsifiers Promote Obesity And Colitis In Mice – Science 2.0
Widely used food additive promotes colitis, obesity and metabolic syndrome, research shows – Medical Xpress

High bacteria counts on cellphone doesn’t determine rate of infection – Debbie Dujanovic – KSL.com

 

Suburban Birds Are Reservoirs for Lyme-Disease Bacteria – John Metcalfe – CityLab

Earth’s Deepest Spot Is Alive With ‘Unexpected’ Bacteria – Elizabeth Armstrong Moore – Newser

Report: Deadly Bacteria Lurking in Doctor, Dentist Offices and Why Hand Sanitizer Won’t Kill It – Elizabeth Cohen and Sandee LaMotte – CNN Wire

Science, publishing, and career

Scientific journal publishes papers of 200 words or less – We describe it briefly here – Francie Diep – Popular Science

 

What’s in a name? – Animals of all kinds have been named and remembered by scientists – Michael Erard – Science

Experts air concerns about federal gain-of-function review – Lisa Schnirring -CIDRAP University of Minnesota

Science and art

3D Laser Scanner Makes Haunting Works of Art – Calla Cofield – Live Science

Art’s place in the science world – Madlen Gubernick – iNSolution, Northeastern

Student Builds Replica Large Hadron Collider Out of Legos – NBC News

Bik’s Picks

Marine Shells’ Optical Structures Inspire Ideas For Transparent Displays – James Maynard – Tech Times

Florida snail species threatened by invasive parasites – David M. Demar – SMN Weekly

Feds spot third baby orca born recently to imperiled pods – Phuong Le – SF Gate

Doctor Seeking To Perform Head Transplant Is Out Of His Mind – Arthur Caplan – Forbes

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February 25, 2015

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Nature and Scientific American have a joint Microbiome special: “Innovations in the Microbiome” with several overview papers from Rob Knight, Ruth Ley,  Justin Sonnenburg et al. Articles include:

The Microbes Within – David Grogan
Why Microbiome Treatments Could Pay Off Soon – Rob Knight
Your Microbes at Work: Fiber Fermenters Keep Us Healthy
Mental Health: Thinking from the Gut – Charles Schmidt
Gut Microbiome: The Peacekeepers – Moises Velasquez-Manoff
The Gene–Microbe Link – Ruth E. Ley
Microbiome Engineering – Justin L. Sonnenburg
The Diverse Microbiome of the Hunter-Gatherer – Stephanie L. Schnorr

Human oral microbiome

Environment and Colonisation Sequence Are Key Parameters Driving Cooperation and Competition between Pseudomonas aeruginosa Cystic Fibrosis Strains and Oral Commensal Streptococci – Robert A. Whiley – PLOS ONE

Human skin microbiome

Malassezia Intra-Specific Diversity and Potentially New Species in the Skin Microbiota from Brazilian Healthy Subjects and Seborrheic Dermatitis Patients – Renan Cardoso Soares – PLOS ONE

Human gut microbiome

From the Gordon lab: Functional characterization of IgA-targeted bacterial taxa from undernourished Malawian children that produce diet-dependent enteropathy – Andrew L. Kau – Science Translational Medicine

Complementary Amplicon-Based Genomic Approaches for the Study of Fungal Communities in Humans – Timothy Heisel – PLOS ONE

Animal models of microbiome research

Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome – Benoit Chassaing – Nature

Animal microbiome

Heritable symbiosis: The advantages and perils of an evolutionary rabbit hole – Gordon M. Bennett and Nancy A. Moran

Endosymbiont Dominated Bacterial Communities in a Dwarf Spider – Bram Vanthournout, Frederik Hendrickx – PLOS ONE

Phylogenetic diversity of Archaea in the intestinal tract of termites from different lineages – Yu Shi – Journal of Basic Microbiology

Plant microbiome

Intercropped Silviculture Systems, a Key to Achieving Soil Fungal Community Management in Eucalyptus Plantations – Caio T. C. C. Rachid – PLOS ONE

Soil microbiome

Microbial dynamics in glacier forefield soils show succession is not just skin deep – Arwyn Edwards and Sophie Cook – Molecular Ecology

Microbial deposits in the aftermath of the end-Permian mass extinction: A diverging case from the Mineral Mountains (Utah, USA) – Emmanuelle Vennin – Sedimentology

Water microbiome

Characterizing variability in marine protist communities via ARISA fingerprints—a method evaluation – E.S. Kilias – Limnology and Oceanography: Methods

Characterisation of the Physical Composition and Microbial Community Structure of Biofilms within a Model Full-Scale Drinking Water Distribution System – Katherine E. Fish – PLOS ONE

Microbiome of the built environment

Sewage Reflects the Microbiomes of Human Populations – Ryan J. Newton – mBio

Phages and viruses

The targeted recognition of Lactococcus lactis phages to their polysaccharide receptors – Orla McCabe – Molecular Microbiology

Bioinformatics

Tools for Bacterial Comparative Genomics – Kat Holt – Holt Lab

Techniques

Comparison of different methods for the recovery of DNA from spores of mycotoxin producing moulds in spiked food samples – Sabrina Grube – Letters in Applied Microbiology

Metabolomics

Nutritional stress induces exchange of cell material and energetic coupling between bacterial species – Saida Benomar – Nature Communications

Other papers of interest

Climate-driven introduction of the Black Death and successive plague reintroductions into Europe – Boris V. Schmid – PNAS USA

Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs – Eric Londin – PNAS USA

Microbes in the news

Fishing For the Microbes Behind Malnutrition – Ed Yong – National Geographic

4th World Summit ‘Gut Microbiota For Health’ to be held in Barcelona – Phys.org

Indian scientist awarded 1.5 million euros grant to investigate the role of gut microbiota in autoimmune diseases – Economic Times India

Johnson & Johnson Bets On Alzheimer’s Vaccine, Disease Prediction, Human ‘Microbiome’ – Amy Nordrum – International Business Times

Altered microbiome may lead to liver disease in patients with cystic fibrosis – Healio

Cystic Fibrosis Liver Cirrhosis Associated with Intestinal Microbiome – Maureen Newmn – LungDiseaseNews

Linoleic acid role balanced by changes to gut microbiota: Study – Annie-Rose Harrison-Dunn – NutraIngredients

My Microbiome Experience from Start to Results – Alexandra Carmichael – uBiome Blog

Session Report: Citizen Microbiology at Citizen Science 2015 – David Coil – MicroBEnet

Bacteria pipe food to each other using tiny tubes – Francie Diep – Popular Science

CSU study finds that Leprosy bacteria can survive in unusual environments – Emily Vavra – Collegian

Science, publishing and career

Scientists are cautious about public outreach – Chris Woolston – Nature

It’s Time for More Racial Diversity in STEM Toys – Maia Weinstock – Scientific American

Science and art

Science and Culture: Data visualization nurtures an artistic movement – J. D. Talasek – PNAS USA

Bik’s Picks

Wanted: 80,000 British babies for massive study – Helen Pearson – Nature

28.8 million tons of Sahara desert fertilize the Amazon – Deborah Netburn – LA Times

Your Eyelashes Should Be This Long, Science Says – Megan Gannon – Scientific American [hr]

February 24, 2015

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Human oral microbiome

Review: The Oral Microbiome and Cancer – A. Ross Kerr – Journal of Dental Hygiene

Human esophageal/stomach microbiome

Association between tobacco use and the upper gastrointestinal microbiome among Chinese men – Emily Vogtmann – Cancer Causes & Control

Human gut microbiome

Diversity in gut bacterial community of school-age children in Asia – Jiro Nakayama – Scientific Reports

Characterization of the human gut microbiome during travelers’ diarrhea – Bonnie P. Youmans – Gut Microbes

Review: Interactive roles of gut microbiota and gastrointestinal motility in the
development of inflammatory disorders – Hirofumi Okubo – Macrophage

Review: Microbial endocrinology: the interplay between the microbiota and the endocrine system – Hadar Neuman – Microbiology Reviews

Review: Gut/brain axis and the microbiota – Emeran A. Mayer – The Journal of Clinical Investigation

Animal models of microbiome research

Exercise training modifies gut microbiota in normal and diabetic mice – Jennifer Elizabeth Lambert – Applied Physiology, Nutrition, and Metabolism

Impact of dietary deviation on disease progression and gut microbiome composition in lupus-prone SNF1 mice – Benjamin M. Johnson – Clinical & Experimental Immunology

Host genetic determinants of microbiota-dependent nutrition revealed by genome-wide analysis of Drosophila melanogaster – Adam J. Dobson – Nature Communications

Microbial community structure in the gut of the New Zealand insect Auckland tree weta (Hemideina thoracica) – David W. Waite – Archives of Microbiology

Animal microbiome

Rumen Bacterial Diversity of 80 to 110-Day-Old Goats Using 16S rRNA Sequencing – Xufeng Han – PLOS ONE

Phosphorus sequestration in the form of polyphosphate by microbial symbionts in marine sponges – Fan Zhang – PNAS USA

Plant microbiome

Identification of novel Bromus- and Trifolium-associated circular DNA viruses – Simona Kraberger – Archives of Virology

Effects of chemical and biological pesticides on plant growth parameters and rhizospheric bacterial community structure in Vigna radiata – Sunil Singh – Journal of Hazardous Materials

Review: Microbial Symbionts: A Potential Bio-Boom – Mustafa Morsy – Journal of Investigative Genomics

Water microbiome

Hadal biosphere: Insight into the microbial ecosystem in the deepest ocean on Earth – Takuro Nunoura – PNAS USA

Resilience and recovery: the effect of triclosan exposure timing during development, on the structure and function of river biofilm communities – J.R. Lawrence – Aquatic Toxicology

Adaption of the microbial community to continuous exposures of multiple residual antibiotics in sediments from a salt-water aquacultural farm – Min Wang – Journal of Hazardous Materials

Metagenomics

Whole-genome assembly of Akkermansia muciniphila sequenced directly from human stool – Aurélia Caputo – Biology Direct

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage – Nicholas H. Putnam – ArXiv

Direct multiplexed whole genome sequencing of respiratory tract samples reveals full viral genomic information – Jan Zoll – Journal of Clinical Virology

Less is more: extreme genome complexity reduction with ddRAD using Ion Torrent semiconductor technology – Lilian Pukk – Molecular Ecology Resources

AMAS: optimizing the partition and filtration of adaptive seeds to speed up read mapping – Ngoc Hieu Tran, Xin Chen – arXiv

The Genome 10K Project: A Way Forward – Klaus-Peter Koepfli – Annual Reviews of Animal Biosciences

Other papers of interest

Allergy in Children in Hand Versus Machine Dishwashing – Bill Hesselmar – Pediatrics

Thiopeptide antibiotics stimulate biofilm formation in Bacillus subtilis – Rachel Bleich – PNAS USA

Microbes in the news

Were early seas transformed by sponge microbiome? – Catherine Brahic – New Scientist

Bacteria Thrive in the Ocean Depths of Challenger Deep – NBC News

Scientists discover bacteria in marine sponges harvest phosphorus for the reef community – Phys.org

Infant Gut Microbiome Linked to Allergic Predisposition (interview with Christine Cole Johnson) – Medical Research

Genetic variety in gut critters tied to disease – Max Green – Columbia Chronicle

Exposure to bacteria, good for a strong immune system? – Justin J Reyes – KGNS

After 8 centuries, rats exonerated in spread of Black Death. Gerbils implicated. – Sarah Kaplan – Washington Post

Your Soap Has Bacteria In It, But It Still Gets You Clean – Poncie Rutsch – NPR Shots

Antibiotics cause dangerous bacteria communities to appear, study says – Suzanne Plunkett – Reuters

Antibiotics give rise to new communities of harmful bacteria – Science Daily

Hand-wash your dishes to help protect kids from allergies – Jessica Firger – CBS News

The Problem With Dirty Money – Paul Rodgers – Forbes

Bik’s Picks

Peanut consumption in infancy prevents peanut allergy, study finds – Science Daily

Climate change is really bad news if you like oysters, scallops and clams – Puneet Kollipara – Washington Post

Space is cool, but NASA’s cheeseburgers look gross – Brian Koerber – Mashable

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February 23, 2015

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General human microbiome

Review: Human Microbiome: When a Friend Becomes an Enemy – Magdalena Muszer – Archivum Immunologiae et Therapiae Experimentalis

Microbiome of pregnancy and birth

Probiotics and gut health in infants: A preliminary case–control observational study about early treatment with Lactobacillus reuteri DSM 17938 – Francesco Savino – Clinica Chimica Acta

Review: Clinical impact of human breast milk metabolomics – Flaminia Cesare Marincola – Clinica Chimica Acta

Human oral microbiome

Review: A review on microbiological cause of periodontal disease: disease and treatment. – Durgesh, Bangalore H – Reviews in Medical Microbiology $$$

Human gut microbiome

No difference in small bowel microbiota between patients with irritable bowel syndrome and healthy controls – Aldona Dlugosz – Scientific Reports

Microbiota disbiosis is associated with colorectal cancer – Zhiguang Gao – Frontiers in Microbiology

Pilot Dietary Intervention with Heat-Stabilized Rice Bran Modulates Stool Microbiota and Metabolites in Healthy Adults – Amy M. Sheflin – Nutrients

Contrasting effects of fresh and fermented kimchi consumption on gut microbiota composition and gene expression related to metabolic syndrome in obese Korean women
Kyungsun Han – Molecular Nutrition & Food Research

Review: Gut microbiota: Microbiota organisation—a key to understanding CRC development – Georgina L. Hold & Wendy S. Garrett – Nature Reviews Gastroenterology & Hepatology

Review: Changing views on diverticular disease: impact of aging, obesity, diet, and microbiota – R. C. Spiller – Neurogastroenterology & Motility

Animal models of microbiome research

Oral microbiome composition changes in mouse models of colitis – Jaana Rautava – Journal of Gastroenterology and Hepatology

Animal microbiome

Diverse small circular DNA viruses circulating amongst estuarine molluscs – Anisha Dayaram – Infection, Genetics and Evolution

Plant microbiome

Moth Outbreaks Alter Root-Associated Fungal Communities in Subarctic Mountain Birch Forests – Karita Saravesi – Microbial Ecology

The Microbiome of Pinus muricata Ectomycorrhizae: Community Assemblages, Fungal Species Effects, and Burkholderia as Important Bacteria in Multipartnered Symbioses – Nhu H. Nguyen, Thomas D. Bruns – Microbial Ecology

Soil microbiome

Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill – Luis M Rodriguez-R – The ISME Journal

The microbe-mediated mechanisms affecting topsoil carbon stock in Tibetan grasslands – Haowei Yue – The ISME Journal

Resource Type and Availability Regulate Fungal Communities Along Arable Soil Profiles – Julia Moll – Microbial Ecology

Characteristic microbial communities in the continuous permafrost beside the bitumen in Qinghai-Tibetan Plateau – Nan Jiang – Environmental Earth Sciences

Effect of early dry season induced by the Three Gorges Dam on the soil microbial biomass and bacterial community structure in the Dongting Lake wetland – Haipeng Wu – Ecological Indicators

Disentangling plant and soil microbial controls on carbon and nitrogen loss in grassland mesocosms – Franciska T. De Vries – Journal of Ecology

Water microbiome

Evidence for an active rare biosphere within freshwater protists community – Didier Debroas – Molecular Ecology

Response of the microbial community to seasonal groundwater level fluctuations in petroleum hydrocarbon-contaminated groundwater – Ai-xia Zhou – Environmental Science

Microbiome of the built environment

Isolation of Vermamoeba vermiformis and associated bacteria in hospital water – Isabelle Pagnier – Microbial Pathogenesis

Dynamics of bacterial communities before and after distribution in a full-scale drinking water network – Joline El-Chakhtoura – Water Research

Marine bioerosion of lapideous archaeological artifacts found in the Grotta Azzurra (Capri, Naples, Italy): Role of microbiota and boring Porifera – Carlotta Sacco Perasso – International Biodeterioration & Biodegradation

Bioreactor microbiome

Chemotactic preferences govern competition and pattern formation in simulated two-strain microbial communities – Florian Centler and Martin Thullner – Frontiers in Microbiology

Review: Microbial management of anaerobic digestion: exploiting the microbiome-functionality nexus – Marta Carballa – Current Opinion in Biotechnology

Metagenomics, Sequencing and Bioinformatics

Improved detection of artifactual viral minority variants in high-throughput sequencing data – Matthijs R. A. Welkers – Frontiers in Microbiology

Bioinformatics approaches for viral metagenomics in plants using short RNAs: model case of study and application to a Cicer arietinum population – Walter Pirovano – Frontiers in Microbiology

Accurate multiplexing and filtering for high-throughput amplicon-sequencing – Esling Philippe – Nucleic Acids Research

Uploaded manuscript: Metagenomic Assembly Validation of an in vitro Mock Community [PDF] – Ino de Bruijn – Authorea

DIME: A Novel Framework for De Novo Metagenomic Sequence Assembly – Guo Xuan – Journal of Computational Biology

Clustering of reads with alignment-free measures and quality values – Matteo Comin – Algorthms for Molecular Biology

Improved data analysis for the MinION nanopore sequencer – Miten Jain – Nature Methods

Genome-wide gene order distances support clustering the gram-positive bacteria – Christopher H. House – Frontiers in Microbiology

Perspective: Current strategies for mobilome research – Tue S. Jørgensen – Frontiers in Microbiology

Metabolomics

Species-specific dynamic responses of gut bacteria to a mammalian glycan – Varsha Raghavan and Eduardo A. Groisman – Journal of Bacteriology

Role of intestinal microbiota in the generation of polyphenol derived phenolic acid mediated attenuation of Alzheimer’s disease β-amyloid oligomerization – Dongjie Wang – Molecular Nutrition & Food Research

Pilot Dietary Intervention with Heat-Stabilized Rice Bran Modulates Stool Microbiota and Metabolites in Healthy Adults – Amy M. Sheflin – Nutrients

Review: Does Our Gut Microbiome Predict Cardiovascular Risk? – A Review of the Evidence From Metabolomics – Julian L. Griffin – Circulation: Cardiovascular Genetics

http://intl-circgenetics.ahajournals.org/content/8/1/187.full

Other microbiology papers of interest

Review: Interactions of Salmonella with animals and plants – Agnès Wiedemann – Frontiers in Microbiology

Microbes in the news

Rob Knight awarded Vilcek Prize 2015 – Vilcek Foundation

AAAAI Annual Meeting Research Links Infants’ Microbiome to Development of Immune System, Allergic Diseases and Asthma – Our Midland

Examining the Hygiene Hypothesis and the Role of the Microbiome in Allergic Disease – Rodrigo Barros – HCP Live

The Role of the Skin Microbiome in Health and Disease – Rodrigo Barros – HCP Live

Facebook banned “Human Microbiome” artist picture for being ‘overly sexual’ – Hannah Parry – Mail Online

Campus bacteria: The whats and wheres of Columbia’s most infamous bacteria (e.g. the Sweatococcus @ Dodge Gym Equipment) – Sophia Hotung – Columbia Spectator

Bacteria connect to each other and exchange nutrients – Phys.org

Researchers explore influence of host organisms on bacterial metabolism – News Medical

Blood tests indicate scientist may not have been sickened at Tulane primate center – Kim Chatelain – Nola

We’re all hosts on a viral planet: E. coli O157 edition – Doug Powell – BarfBlog

Bik’s Picks

Surprise! 1,000-Year-Old Mummy Found in Buddha Statue – NBC News

Crews free humpback whale tangled in fishing line off Hawaii – Fox News

Satire: Collective Cleanliness: A Meta-Discursive Study of Academic Tearoom Culture – Lotta Washinup and Duya Dishez – Journal of Applied Elbow Grease

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February 20, 2015

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Human microbiome, general

Article collection (n=1?): Microbiota: Coevolution and the Modern Environment – Martin Katzman, Alan C. Logan – Journal of Physiological Anthropology

Review: Natural environments, ancestral diets, and microbial ecology: is there a modern “paleo-deficit disorder”? Part I – Alan C Logan – Journal of Physiological Anthropology

Human respiratory microbiome

Chronic Obstructive Pulmonary Disease Lung Microbiota Diversity May Be Mediated by Age or Inhaled Corticosteroid Use – Alexa A. Pragman – Journal of Clinical Microbiology

Reply to “Chronic Obstructive Pulmonary Disease Lung Microbiota Diversity May Be Mediated by Age or Inhaled Corticosteroid Use” – Marian Garcia-Nuñez – Journal of Clinical Microbiology

Fecal microbiota transplantation

ECCO congress abstract: FMT not effective in active UC patients – Haelio

MALDI-Tof MS

Microbial Typing by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry: Do We Need Guidance for Data Interpretation? – Sébastien Spinali – Journal of Clinical Microbiology

Immunology

Perspective: A common origin for immunity and digestion – Nichole A. Broderick – Frontiers in Immunology

Microbes in the news

Engineering the Human Microbiome Shows Promise for Treating Disease – Justin L. Sonnenburg – Scientific American

Book Review: “Philosophy of Microbiology”, by Maureen A. O’Malley – Adrian Woolfson – Science

UCLA Outbreak Highlights Challenge Of Curbing Infections – Jordan Rau – NPR

Title seems incorrect: Your Genes May Be Part Mom, Part Dad and Part Bacteria – Krystnell Storr – Science.Mic

Host influences bacterial metabolism – Phys.org

Bacteria-killing virus may help prevent root canal infections – DrBicuspid

Virus-cutting enzyme helps bacteria remember a threat – Phys.org

Science, publishing, and career

Putting the ‘Media’ in ‘Academia’ – Stewart Barker – MicrobeStew

College Faculties Have a Serious Diversity Problem – Marcus Woo – Wired.com

Satire: Grad Student Diagnosed With Early-Onset Thesis Fear – The Allium

Bik’s Picks

Nest Etiquette—Where Ants Go When Nature Calls – Tomer J. Czaczkes, Jürgen Heinze, Joachim Ruther – PLOS ONE

Why I’m Volunteering to Die on Mars – Sonia Van Meter – Time.com

How the sun can damage your skin even in the dark – Deborah Netburn – LA Times

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February 19, 2015

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A new edition of Frontiers in Microbiology, and pretty much the whole Table of Contents was of interest! Here we go:

Human gut microbiome

Perspective: Aging and the human gut microbiota—from correlation to causality – Sitaraman Saraswati and Ramakrishnan Sitaraman – Frontiers in Microbiology

Review: Intestinal mucosal tolerance and impact of gut microbiota to mucosal tolerance – Dimitry A. Chistiakov – Frontiers in Microbiology

Animal models of microbiome research

Effects of Vendor and Genetic Background on the Composition of the Fecal Microbiota of Inbred Mice – Aaron C. Ericsson – PLOS ONE

Germ-free mice, but still of interest: Microbiota-Independent Ameliorative Effects of Antibiotics on Spontaneous Th2-Associated Pathology of the Small Intestine – Daehee Han – PLOS ONE

Maternal Antibiotic-Induced Early Changes in Microbial Colonization Selectively Modulate Colonic Permeability and Inducible Heat Shock Proteins, and Digesta Concentrations of Alkaline Phosphatase and TLR-Stimulants in Swine Offspring – Marie-Edith Arnal – PLOS ONE

Workshop: Mouse Microbiota: genotype-phenotype control and technological challenges (March 2015, in Portugal) – Infrafrontier

Animal microbiome

The Dynamic Distribution of Porcine Microbiota across Different Ages and Gastrointestinal Tract Segments – Wenjing Zhao – PLOS ONE

Characterization of shed medicinal leech mucus reveals a diverse microbiota -Brittany M. Ott – Frontiers in Microbiology

Effect of polybrominated diphenyl ether (PBDE) treatment on the composition and function of the bacterial community in the sponge Haliclona cymaeformis
Ren-Mao Tian – Frontiers in Microbiology

Review: Microbes in the coral holobiont: partners through evolution, development, and ecological interactions – Janelle R. Thompson – Frontiers in Cellular and Infection Microbiology

Plant microbiome

Hypothesis: Mutualism–parasitism paradigm synthesized from results of root-endophyte models – Keerthi G. Mandyam and Ari Jumpponen – Frontiers in Microbiology

Soil microbiome

Metagenomic insights into S(0) precipitation in a terrestrial subsurface lithoautotrophic ecosystem – Trinity L. Hamilton – Frontiers in Microbiology

Microbial Community Dynamics during the Bioremediation Process of Chlorimuron-Ethyl-Contaminated Soil by Hansschlegelia sp. Strain CHL1 – Liqiang Yang – PLOS ONE

Water microbiome

High pH microbial ecosystems in a newly discovered, ephemeral, serpentinizing fluid seep at Yanartaş (Chimera), Turkey – D’Arcy R. Meyer-Dombard – Frontiers in Microbiology

Competition and facilitation between the marine nitrogen-fixing cyanobacterium Cyanothece and its associated bacterial community – Verena S. Brauer – Frontiers in Microbiology

Editorial: Metal economy in host-microbe interactions – Frédéric J. Veyrier and Mathieu F. Cellier – Frontiers in Cellular and Infection Microbiology

Editorial: Antibiotic resistance genes in food and gut (non-pathogenic) bacteria. Bad genes in good bugs – Henk Aarts and Abelardo Margolles – Frontiers in Microbiology

Metagenomics

Phylogenetic Profiling: How Much Input Data Is Enough? – Nives Škunca, Christophe Dessimoz – PLOS ONE

Deconstruction of Archaeal Genome Depict Strategic Consensus in Core Pathways Coding Sequence Assembly – Ayon Pal – PLOS ONE

Perspective: Reconstructing each cell’s genome within complex microbial communities—dream or reality? – Scott Clingenpeel – Frontiers in Microbiology

Perspective: Finding and identifying the viral needle in the metagenomic haystack: trends and challenges – Hayssam Soueidan – Frontiers in Microbiology

Perspective: Metagenomics of plant and fungal viruses reveals an abundance of persistent lifestyles – Marilyn J. Roossinck – Frontiers in Microbiology

Metabolomics

Statistical methods for handling unwanted variation in metabolomics data – Alysha M. De Livera – Analytical Chemistry

Review: Fungal secondary metabolite dynamics in fungus–grazer interactions: novel insights and unanswered questions – Marko Rohlfs – Frontiers in Microbiology

Other articles of interest

Improving the Robustness of Complex Networks with Preserving Community Structure – Yang Yang – PLOS ONE

Techniques

A Simple Method for Encapsulating Single Cells in Alginate Microspheres Allows for Direct PCR and Whole Genome Amplification – Saharnaz Bigdeli – PLOS ONE

Microbes in the news

Innovations in the microbiome – Nature/Scientific American collaboration on the human microbiome. Some articles:
Microbiome Research May Soon Pay Off Big – Rob Knight – Scientific American
Genes and Microbes Influence One Another, Scientists Find – Ruth Ley – Scientific American

Pull Up A Stool And Let’s Talk About Your Microbiome – Bill Sullivan – The Scope

L.A. hospital warns 179 patients possibly exposed to “superbug” from endoscopies – Steve Gorman – Reuters

Stalking a wily foe: U-M scientists figure out how C. difficile bacteria wreak havoc in the gut – Kara Gavin – University of Michigan

Studying microbes in health and disease – Katherine Unger Baillie – Penn Current

And they still do! Microbes may have covered Earth 3.2 billion years ago – Charles Q Choi – Mother Nature Network

Toothpaste-mouth rinse combo washes out harmful bacteria – Janice Neumann – Reuters

Aetokthonos hydrillicola – the “eagle killer”: Bald eagles are starting to flourish again — but hold the confetti – The Washington Post

Virus found in sewage shows promise in treating dental procedure infections – Catherine Paddock – Medical News Today

Science, publishing, and career

What pushes scientists to lie? The disturbing but familiar story of Haruko Obokata – John Rasko and Carl Power – The Guardian

Science and art

Wind-Created Sand Sculptures on Lake Michigan Beach – Josh Nowicki – WILX.com

Bik’s picks

New York City Could See 6-Foot Sea Rise, Tripling of Heat Waves by 2100 – Colin Sullivan – Scientific American

Starving Sea Lion Pups in California: Warmer Ocean Could Be to Blame – NBC News

Changing insights: Love to eat eggs? U.S. panel now says they’re not a health risk – Yasmeen Abutaleb – Reuters

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February 17, 2015

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Too little time to cover everything from this 3-day weekend, but hopefully I can catch up tomorrow.

Microbiome of pregnancy and birth

Milk- and solid-feeding practices and daycare attendance are associated with differences in bacterial diversity, predominant communities, and metabolic and immune function of the infant gut microbiome – Amanda L. Thompson – Frontiers in Cellular and Infection Microbiology

Human oral microbiome

Dynamic Changes in the Subgingival Microbiome and Their Potential for Diagnosis and Prognosis of Periodontitis – Baochen Shi – mBio

The hidden ‘mycobacteriome’ of the human healthy oral cavity and upper respiratory tract
Lilia Macovei – Journal of Oral Microbiology

Human vaginal microbiome

The Vaginal Microbiota over an 8- to 10-Year Period in a Cohort of HIV-Infected and HIV-Uninfected Women – Supriya D. Mehta – PLOS ONE

Human gut microbiome

Effects of polysaccharopeptide from Trametes versicolor and amoxicillin on the gut microbiome of healthy volunteers – Kumar Pallav – Gut Microbes

Animal models of microbiome research

Vertically transmitted faecal IgA levels determine extra-chromosomal phenotypic variation – Clara Moon – Nature

Voluntary and forced exercise differentially alter the gut microbiome in C57BL/6J mice – Jacob M. Allen – Journal of Applied Physiology

Commentary: Secret behind commensal resilience revealed – Christina Tobin Kåhrström – Nature Reviews Microbiology

Animal microbiome

Community structure of gut fungi during different developmental stages of the Chinese white pine beetle (Dendroctonus armandi) – Xia Hu – Scientific Reports

Persistent Shifts in Caribbean Coral Microbiota are Linked to the 2010 Warm Thermal Anomaly – Allison Tracy – Environmental Microbiology Reports

Review: Pathogenesis of canine atopic dermatitis: skin barrier and host–micro-organism interaction – Domenico Santoro – Veterinary Dermatology

Plant microbiome

Whose truffle is this? Distribution patterns of ectomycorrhizal fungal diversity in Tuber melanosporum brûlés developed in multi-host Mediterranean plant communities – Elisa Taschen – Environmental Microbiology

The composition of arbuscular mycorrhizal fungal communities differs among the roots, spores and extraradical mycelia associated with five Mediterranean plant species – Sara Varela-Cervero – Environmental Microbiology

Plant and soil effects on bacterial communities associated with Miscanthus ×giganteus rhizosphere and rhizomes – Dongfang Li – GCB bioenergy

Soil microbiome

Plant diversity, soil biota and resistance to exotic invasion – Huixuan Liao – Diversity and Distributions

Global biogeographic sampling of bacterial secondary metabolism – Zachary Charlop-Powers – eLife

Water microbiome

Illumina sequencing-based analysis of free-living bacterial community dynamics during an Akashiwo sanguine bloom in Xiamen sea, China – Caiyun Yang – Scientific Reports

Transient Changes in Bacterioplankton Communities Induced by the Submarine Volcanic Eruption of El Hierro (Canary Islands) – Isabel Ferrera – PLOS ONE

Bioreactor microbiology

Analysis of microbial community composition in a lab-scale membrane distillation bioreactor – Q. Zhang – Journal of Applied Microbiology

Temperature and solids retention time control microbial population dynamics and volatile fatty acid production in replicated anaerobic digesters – Inka Vanwonterghem – Scientific Reports

Phages and viruses

Sequences spanning the leader-repeat junction mediate CRISPR adaptation to phage in Streptococcus thermophilus – Yunzhou Wei – Nucleic Acids Research

Microbial Ecology

Patterns, causes and consequences of defensive microbiome dynamics across multiple scales – Andrew H. Smith – Molecular Ecology

Niche construction by growth forms is as strong a predictor of species diversity as environmental gradients – Kari Anne Bråthen and Virve Tuulia Ravolainen – Journal of Ecology

Comment: The importance of soil archives for microbial ecology – Jan Dolfing & Youzhi Feng – Nature Reviews Microbiology

Editorial: Metabolites in differentiation – Andrea Du Toit – Nature Reviews Microbiology

Bioinformatics, metagenomics

RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes – Thomas Brettin – Scientific Reports

An improved method to set significance thresholds for β diversity testing in microbial community comparisons – Arda Gülay and Barth F. Smets – Environmental Microbiology

Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses – Marie Lisandra Zepeda Mendoza – Briefings in Bioinformatics

Correcting Illumina sequencing errors for human data – Heng Li – ArXiv

Not really microbial, but of possible interest: ModuleBlast: identifying activated sub-networks within and across species – Guy E. Zinman – Nucleic Acids Research

Metabolomics

A high-resolution 2D J-resolved NMR detection technique for metabolite analyses of biological samples – Yuqing Huang – Scientific Reports

Pseudomonas aeruginosa manipulates redox and iron homeostasis of its microbiota partner Aspergillus fumigatus via phenazines – Benoit Briard – Scientific Reports

An overview of fecal preparation for global metabolic profiling – O. Deda – Journal of Pharmaceutical and Biomedical Analysis

Increased urinary indoxyl sulfate (indican): new insights into gut dysbiosis in Parkinson’s Disease – Cassani Erica – Parkinsonism & Related Disorders

Microbes in the news

Overselling the microbiome award: CBC Fresh Air & JA Tetro on kissing microbiomes – Jonathan Eisen – Phylogenomics / The Tree of Life Blog

A (not so!) Surprising Comparison of Male vs. Female Microbiomes – Alexandra Carmichael – uBiome

Microbes in the Gut Are Essential to Our Well-Being – David Grogan – Scientific American

Inflammatory Bowel Disease May Be from Mom’s Bacteria, not DNA – Christopher Wanjek – LiveScience

Mothers can pass traits to offspring through bacteria’s DNA, mouse study shows – Science Daily (about the Clara Moon paper in Nature; see above)

How Can Rivers And Streams Be Sources Of Antibiotic Resistant Bacteria? – James Maynard – TechTimes

Cooperative Control: With the help of a virus that infects its prey’s nervous system, a parasitoid wasp coerces a lady beetle to protect its young – Sandhya Sekar – The Scientist

Scientists turn the tables on drug-resistant bacteria by infecting them with bacteriophages – Phys.org

Science and career

Seven myths about scientists debunked – Jeffrey Craig, Marguerite Evans-Galea – the Conversation

Science and art

Microbial Masterpieces: Artist Anicka Yi explores the beauty of bacteria – Jenny Rood – The Scientist

2015 Year of the Phage – Life in our Phage World (Book, download)

Bik’s Picks

Demographic Clusters Identified within the Northern Gulf of Mexico Common Bottlenose Dolphin (Tursiops truncates) Unusual Mortality Event: January 2010 – June 2013 – Stephanie Venn-Watson – PLOS ONE

BP cherry-picks study to dodge blame for massive deaths of gulf dolphins – Michael Hiltzik – Los Angeles Times

Satire: Study Finds Jack Shit – The Onion

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February 13, 2015

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Happy Valentine’s Day tomorrow! The totally awesome Michele Banks @artologica made a super-special #ScienceValentines for all microbiome lovers.

Microbiome of pregnancy and birth

Review (but plagiarism alert!): Gut microbiota biomodulators: When the stork comes by the scalpel – Vito Leonardo Miniello – Clinica Chimica Acta

Human oral microbiome

Preliminary Report of the Effect of A New Saliva Substitute Based on Chamomile (Matricaria Chamomilla) and Flax Seed (Linum Usitatissimum) on the Oral Microbiota of Patients with Xerostomia – Blanca Urzúa Orellana – Oral Surgery, Oral Medicine, Oral Pathology and Oral Radiology

Human vaginal microbiome

Also check out “Animal microbiome” section below.

Review: The biology of Trichomonas vaginalis in the light of urogenital tract infection – Gary Kusdian, Sven B. Gould – Molecular and Biochemical Parasitology

Human gut microbiome

Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species – Sharon Greenblum – Cell

Review: Impact of diet on the human intestinal microbiota – Huizi Tan, Paul W. O’Toole – Current Opinion in Food Science

Fecal Microbiota Transplantation

Review: Fecal Microbiota Transplantation for the Management of Clostridium difficile Infection – Krishna Rao – Infectious Disease Clinics of North America

Survey: Faecal Microbiota Transplantation for Clostridium difficile infection in the UK – Robert James Porter, Carole Fogg – Clinical Microbiology and Infection

Animal models

Dynamics and Establishment of Clostridium difficile Infection in the Murine Gastrointestinal Tract – Mark J. Koenigsknecht – Infection and Immunity

Animal microbiome

Influence of age, reproductive cycling status, and menstruation on the vaginal microbiome in baboons (Papio anubis) – M. Uchihashi – American Journal of Primatology

Genetically Modifying the Insect Gut Microbiota to Control Chagas Disease Vectors through Systemic RNAi – Mabel L. Taracena – PLOS Neglected Tropical Diseases

Habitat-specific environmental conditions primarily control the microbiomes of the coral Seriatopora hystrix – Olga Pantos – ISME Journal

Soil microbiology

Review: Microbial hotspots and hot moments in soil: Concept & review – Yakov Kuzyakov, Evgenia Blagodatskaya – Soil Biology and Biochemistry

Water microbiology

Origins and environmental mobility of antibiotic resistance genes, virulence factors and bacteria in a tidal creek’s watershed – A.L. Barkovskii – Journal of Applied Microbiology

Food microbiology

Microbial biogeography of the transnational fermented milk Matsoni – Nicholas A. Bokulich – Food Microbiology

The microbial diversity of an industrially produced lambic beer shares members of a traditionally produced one and reveals a core microbiota for lambic beer fermentation – Freek Spitaels – Food Microbiology

Bacteria and yeast microbiota in milk kefir grains from different Italian regions – Cristiana Garofalo – Food Microbiology

Review: Phages in the global fruit and vegetable industry – M. Żaczek – Journal of Applied Microbiology

Metabolomics

Review: The human gut sterolbiome: bile acid-microbiome endocrine aspects and therapeutics – Jason M. Ridlon, Jasmohan S. Bajaj – Acta Pharmaceutica Sinica B

Bioinformatics

Reconstructing (super)trees from data sets with missing distances: Not all is lost – George Kettleborough – Molecular Biology and Evolution

Microbial evolution

Harnessing Evolution to Elucidate the Consequences of Symbiosis – Nicole M. Gerardo – PLOS Biology

GC-Content Evolution in Bacterial Genomes: The Biased Gene Conversion Hypothesis Expands – Florent Lassalle – PLOS Genetics

Microbes in the news

Nicely timed: Romance and Microbes: The Science Behind Shared Bacteria – Brittany Dingler – Skidmore News

Negative Effects of Long-Term Antibiotic Use Even Far-More Reaching Than Estimated – Heather Johnson – Business2Community

Antibiotic use has more unwanted effects than previously thought – Catharine Paddock – Medical News Today

Not gross if you love microbes: 5 Gross Things Inside Your Body Right Now! (video) – Scientiflix

The 3 strangest facts about all that bacteria on the New York City subway – Erin Brodwin – BusinessInsider

What do the bacteria living in your gut have to do with your immune system? – Elizabeth Bent – The Conversation

Pensioner Peter cured by groundbreaking transplant – West Briton

Since 1938: Autism, The Microbiome and Donald Triplett, Case 1 – Teresa Conrick – The Age of Autism

Captive pandas succumb to killer virus – Mara Hvistendahl – Science

Does the Cold Really Cause a Cold? – James Gilbert – NewsPlex

Study: Listeria pathogen is prevalent, persistent in retail delis – Purdue University

Toxic Ganges adds to spread of drug-resistant bacteria – Victor Mallet and Clive Cookson – FT

Science, publishing, and career

Slideshow: So you want to be an academic? – Josh Neufeld – SlideShare

The science of schmoozing – about scientist Hugues Lantuit – Eli Kintisch – Science

Inspiring Women Scientists in Microbiology and Ecology (part 1) – Suzanne Kennedy – MoBio

Inspiring Women Scientists in Microbiology and Ecology: Part Deux – Emelia DeForce – MoBio

Why Did WNYC Delete Its Podcast on the Male “Expert” on Women in Tech? – Kate Knibbs – Gizmodo

Bik’s Picks – Valentine’s day’s edition

The Chemical Compounds Behind the Smell of Flowers – Compound Chemistry

This Valentine’s Day, Say ‘I Love You’ With Science – Brandon Echter – Science Friday

7 DIY valentine ideas for science nerds – Jenn Savedge – Mother Nature Network

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February 12, 2015

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Happy Darwin Day! To celebrate, I’ll start of with an older paper:

What did Darwin say about microbes, and how did microbiology respond? – Maureen A. O’Malley – Trends in Microbiology

Two San Francisco Bay Area events of interest

Sat/Sun Feb 14/15: Family Science Days. Free event. Join the LSA, NASA, Science is Elementary (where I volunteer) and more at #FamSciDays!

Tue Feb 17, VLAB forum discussion: Gut-Feeling — Ventures into the Microbiome. Will bacteria enable personalized medicine?

General human microbiome

Review: Microbial Diversity: Relevance and Relationship Between Environmental Conservation And Human Health – Jeremias Pakulski Panizzon – Brazilian Archives of Biology and Technology

Human skin microbiome

Editorial: S. epidermidis Influence on Host Immunity: More Than Skin Deep – Richard L. Gallo – Cell Host & Microbe

Human gut microbiome

What role do bacteria play in persisting fistula formation in idiopathic and Crohn’s anal fistula? – P. J. Tozer – Colorectal Disease

Review: Spondyloarthritis and the Microbiome: New Insights From an Ancient Hypothesis – Julia Manasson, Jose U. Scher – Current Rheumatology Reports

Animal models of microbiome research

Editorial: TFH-IgA Responses Keep Microbiota in Check – Kanya Honda – Cell Host & Microbe

Effects of rearing temperature and dietary short-chain fructooligosaccharides supplementation on allochthonous gut microbiota, digestive enzymes activities and intestine health of turbot (Scophthalmus maximus L.) juveniles – I. Guerreiro – Aquaculture Nutrition

Animal microbiome

Symbiotic bacteria contribute to increasing the population size of a freshwater crustacean, Daphnia magna – Saranya Peerakietkhajorn – Environmental Microbiology Reports

Catacombs microbiome

When in Rome: Complex bacterial diversity in the white biofilms of the Catacombs of St. Callixtus in Rome evidenced by different investigation strategies – Lucia Krakova – Environmental Microbiology

Soil and sediment microbiome

Depth shapes α- and β-diversities of microbial eukaryotes in surficial sediments of coastal ecosystems – Jun Gong – Environmental Microbiology

The archaeal lipidome in estuarine sediment dominated by members of the Miscellaneous Crenarchaeotal Group – Travis B. Meador – Environmental Microbiology

Genetic signatures indicate widespread antibiotic resistance and phage infection in microbial communities of the McMurdo Dry Valleys, East Antarctica – Sean T. S. Wei – Polar Biology

Exposure to vancomycin causes a shift in the microbial community structure without affecting nitrate reduction rates in river sediments – Anniet M. Laverman – Environmental Science and Pollution Research

Temperature Sensitivity of Microbial Respiration of Fine Root Litter in a Temperate Broad-Leaved Forest – Naoki Makita, Ayumi Kawamura – PLOS ONE

Water microbiome

Review: Marine microbial community dynamics and their ecological interpretation – Jed A. Fuhrman – Nature Reviews Microbiology

Bioreactor microbiome

Comprehensive microbial analysis of combined mesophilic anaerobic-thermophilic aerobic process treating high-strength food wastewater – Hyun Min Jang – Water Research

Culture-dependent and culture-independent characterization of potentially functional biphenyl-degrading bacterial community in response to extracellular organic matter from Micrococcus luteus – Xiao-Mei Su – Microbial Biotechnology

The fate of oxytetracycline in two-phase and single-phase anaerobic cattle manure digesters and its effects on microbial communities – Çağrı Akyol – Journal of Chemical Technology and Biotechnology

Opinion/review: Integrated omics for the identification of key functionalities in biological wastewater treatment microbial communities – Shaman Narayanasamy – Microbial Biotechnology

Metabolomics and Proteomics

Metabolomic Analysis of Human Fecal Microbiota: A Comparison of Feces-Derived Communities and Defined Mixed Communities – Sandi Yen – Journal of Proteome Research

Surveillance for lower airway pathogens in mechanically ventilated patients by metabolomic analysis of exhaled breath: a case-control study – Stephen J Fowler – Thorax

The Unipept metaproteomics analysis pipeline – Bart Mesuere – Proteomics

Review: A Biotechnological Approach to Microbial Based Perfumes and Flavours – Charu Gupta – Journal of Microbiology & Experimentation

Microbial Ecology

Ecological Perspectives on Synthetic Biology: Insights from Microbial Population Biology – Ana E. Escalante – Frontiers in Microbiology

Bioinformatics

A machine learning pipeline to improve De Bruijn graph metatranscriptomic assemblies – Hussein Mohsen – Bioinformatics

Techniques

Identification of response classes from heavy metal-tolerant soil microbial communities by highly resolved concentration-dependent screenings in a microfluidic system – Dana Kürsten – Methods in Ecology and Evolution

Evaluation of revised polymerase chain reaction primers for more inclusive quantification of ammonia-oxidizing archaea and bacteria – Kelley A. Meinhardt – Environmental Microbiology Reports

Phylogenetic analysis of cultivation-resistant terrestrial cyanobacteria with massive sheaths (Stigonema spp. and Petalonema alatum, Nostocales, Cyanobacteria) using single-cell and filament sequencing of environmental samples – Jan Mareš – Journal of Phycology

Other microbiology papers

Binding of the Fap2 Protein of Fusobacterium nucleatum to Human Inhibitory Receptor TIGIT Protects Tumors from Immune Cell Attack – Chamutal Gur – Immunity

Microbes in the news

Podcast on the NY Subway Microbiome paper (19 min): Listen To Our Conversation With The Microbe Map Man – Jody Avirgan – Five Thirty Eight

Another short Podcast: Subway DNA Survey Finds Microbes, Mozzarella and Mystery – Christopher Intagliata – Scientific American

What The Bacteria In Your Gut Have To Do With Your Physical And Mental Health – Carolyn Gregoire – The Huffington Post
Cecilia Westbrook Makes Yogurt With Her Own Vaginal Bacteria (NSFW) – David Moye – The Huffington Post

Bacteria, economics and our aging population – Julie Flaherty – MedicalXpress

Session Recap: Therapeutic Workshop “Trust Your Gut” with Martin Blaser et al. – BiotechNow

Is there a link between gut microbiota and Parkinson’s disease? – GutMicrobiotaWatch

Early microbiome development impacts later weight gain – Nathan Gray – NutraIngredients

Not all microbial strains are equally efficient – Kemin – All About Feed

The Nanotech View of the Microbiome (Kavli Roundtable) – Alan Brown – LiveScience

Bacteria protect intestinal tumor model from being killed by immune cells – Cell Press – Eureka Alert

A discussion of Casadevall and Pirofski’s Nature commentary: What’s The Damage? – Amesh Adalja – BifurcatedNeedle

New Non-Stick Coating Will Stop Bacteria Sticking to Medical Materials – Jamie Condliffe – GizModo

Science, publishing, and career

NIH proposal to create grant for aging scientists hits a nerve – Jocelyn Kaiser – Science

Social media: A network boost – How scientists can use Twitter to expand their social contacts and find jobs – Monya Baker – Nature

Elsevier Valentines – It all started with an innocent tweet. – Sylvain Deville – Storify

Bik’s Picks

U.S. Droughts Will Be the Worst in 1,000 Years – Mark Fischetti – Scientific American

Emaciated sea lion pup rescued from side of San Francisco highway – Reuters.com

Happy Darwin Day! Here are our favorite stories about evolution – Rachel Feltman – Washington Post

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February 10, 2015

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Microbiome of pregnancy and birth

Network analysis suggests a potentially ‘evil’ alliance of opportunistic pathogens inhibited by a cooperative network in human milk bacterial communities – Zhanshan (Sam) Ma – Scientific Reports

Human respiratory microbiome

The nasal microbiota in health and disease: variation within and between subjects – Kristi Biswas – Frontiers in Microbiology

Analysis of the nasal vestibule mycobiome in patients with allergic rhinitis – Won Hee Jung – Mycoses

Human oral microbiome

Review: Salivary Diagnostics and the Oral Microbiome – Jennifer E. Kerr – Advances in Salivary Diagnostics

Review: Microbiome of peri-implant infections: lessons from conventional, molecular and metagenomic analyses – Georgios Charalampakis – Virulence

Review: On the dynamics of root canal infections – what we understand and what we don’t – Matthias Zehnder – Virulence

Human gut microbiome

See also Rojo paper under Metabolomics

Evaluating variation in human gut microbiota profiles due to DNA extraction method and inter-subject differences – Brett Wagner Mackenzie – Frontiers in Microbiology

Dysbiosis gut microbiota associated with inflammation and impaired mucosal immune function in intestine of humans with non-alcoholic fatty liver disease – Weiwei Jiang – Scientific Reports

Intestinal Lesions Are Associated with Altered Intestinal Microbiome and Are More Frequent in Children and Young Adults with Cystic Fibrosis and Cirrhosis – Thomas Flass – PLOS ONE

The impact of oral consumption of Lactobacillus plantarum P-8 on faecal bacteria revealed by pyrosequencing – LY Kwok – Beneficial Microbes

Review: Contribution of diet to the composition of the human gut microbiota – Daniela Graf – Microbial Ecology in Health and Disease

Animal microbiome

Characterization of the Fecal Microbial Communities of Duroc Pigs Using 16S rRNA Gene Pyrosequencing – Edward Alain B. Pajarillo – Asian-Australasian Journal of Animal Sciences

Metagenomic analysis of the gut microbiota of the Timber Rattlesnake, Crotalus horridus – Richard William McLaughlin – Molecular Biology Reports

Larval exposure to polychlorinated biphenyl 126 (PCB-126) causes persistent alteration of the amphibian gut microbiota – Kevin D. Kohl – Environmental Toxicology and Chemistry

Abstract: Bugs in bats 2: Analysis of microbial communities in faecal samples obtained from bats in the Netherlands – JCM Wolkers-Rooijackers – 11th Conference of the Dutch Society for Wildlife Health

Plant microbiome

Rapid quantification of rice root-associated bacteria by flow cytometry – G. Valdameri – Letters in Applied Microbiology

Elevated atmospheric CO2 levels affect community structure of rice root-associated bacteria – Kiwamu Minamisawa – Frontiers in Microbiology

Characterization of Leaf Blade- and Leaf Sheath-Associated Bacterial Communities and Assessment of Their Responses to Environmental Changes in CO2, Temperature, and Nitrogen Levels under Field Conditions – Seishi Ikeda – Microbes and Environments

Soil, sediment, and rock microbiome

Community Structure and Biogeochemical Impacts of Microbial Life on Floating Pumice – J. J. Elser – Applied and Environmental Microbiology

Variability in responses of bacterial communities and nitrogen oxide emission to urea fertilization among various flooded paddy soils – Ning Wang – FEMS Microbiology Ecology

Analysis of Sclerotia-Associated Fungal Communities in Cool-Temperate Forest Soils in North Japan – Anzilni F. Amasya – Microbes and Environments

Water microbiome

Bacterial Diversity in the South Adriatic Sea during a Strong, Deep Winter Convection Year – M. Korlević – Applied and Environmental Microbiology

Viruses and phages

Traces of ATCV-1 associated with laboratory component contamination – Kristín Rós Kjartansdóttir – PNAS USA

Reply to Kjartansdóttir et al.: Chlorovirus ATCV-1 findings not explained by contamination – Robert H. Yolken – PNAS USA

Microbial Ecology

Temporal patterns of rarity provide a more complete view of microbial diversity – Ashley Shade, Jack A. Gilbert – Trends in Microbiology

Metagenomics

Genomes of Planktonic Acidimicrobiales: Widening Horizons for Marine Actinobacteria by Metagenomics – Carolina Megumi Mizuno – mBio

Metabolomics

Ranking the impact of human health disorders on gut metabolism: Systemic lupus erythematosus and obesity as study cases – David Rojo – Scientific Reports

Review: Animals in a bacterial world: opportunities for chemical ecology – Alexandra M. Cantley and Jon Clardy – Natural Product Reports

Bioinformatics

CATCh, an Ensemble Classifier for Chimera Detection in 16S rRNA Sequencing Studies – Mohamed Mysara – Applied and Environmental Microbiology

Techniques

Best practices for sample processing and storage prior to microbiome DNA analysis freeze? buffer? process? – Jonathan Eisen – MicroBEnet

More microbes

Natural Green Coating Inhibits Adhesion of Clinically Important Bacteria – Danielle S. Trentin – Scientific Reports

 

Chemical signature of magnetotactic bacteria – Matthieu Amor – PNAS USA

Microbes in the news

Breastfeeding prepares a baby for solid food – Tim Sandle – Digital Journal

Gut microbiota reveal better ways of detecting (and preventing) colorectal cancer – Kristina Campbell – Microbiome Institute

Our Inner Viruses: Forty Million Years In the Making – Carl Zimmer – National Geographic

Our wine owes a debt to ancient viruses – Andrew Geering – Phys.org

Diet is the Chief Factor Behind Gut Microbiome Diversity, Study Shows – Patricia Inacio – IBD News Today

Citizen Oceanography Meets the Marine Microbiome – Rachelle Lauro – Mission Blue

Fecal Microbiota Transplants: An Insider’s Guide – Monica J. Smith

Science and Art

Researcher Determined to Play Piano Duet With Yellow Slime Mold – The Mary Sue

And the winners of the #spacemicrobes Microbial Playoffs are… – Arvind Suresh – Discover Magazine

A Beautiful Wallpaper Made With Smallpox Vaccine – Joseph Flaherty – Wired.com

Bik’s Picks
Stressed Young Bees Linked To Colony Collapse – Jim Algar – Tech Times

Meet Spot: New Breed of Robot Dog Climbs and Trots – Elizabeth Palermo – Live Science

Australia’s Shocking Rate Of Mammal Extinction Blamed On Cats And Red Foxes Brought Over By European Settlers – Rebekah Marcarelli – Headlines and Global News

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