Category Archives: Techniques

May 28, 2015

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Catching up after a couple of days in Paris…

General microbiome

Metagenomics meets time series analysis: unraveling microbial community dynamics – Karoline Faust – Current Opinion in Microbiology

What’s Bugging you and your Diet? – Bryn L Yeomans and Nicholas T Bello – Journal of Food and Nutritional Disorders

Pregnancy and birth microbiome

Comparison of Bacterial Composition in Blood and Placentas Using Conventional and Molecular Methods – Tingtao Chen – Clinical Microbiology: Open Access

Gut microbiome composition is associated with temperament during early childhood – Lisa M. Christian – Brain, Behavior, and Immunity

Human genital microbiome

Cervical Microbiota in Women with Preterm Prelabor Rupture of Membranes – Marian Kacerovsky – PLOS ONE

Re: The vaginal microbiome, vaginal anti-microbial defence mechanisms and the clinical challenge of reducing infection-related preterm birth – C Griffin – BJOG: An International Journal of Obstetrics & Gynaecology
Author’s reply re: The vaginal microbiome, vaginal anti-microbial defence mechanisms and the clinical challenge of reducing infection-related preterm birth – SS Witkin – BJOG: An International Journal of Obstetrics & Gynaecology

Human gut microbiome

Human seroreactivity to gut microbiota antigens – Benjamin S. Christmann – Journal of Allergy and Clinical Immunology

Models of microbiome research

A Role for Gut Microbiota and the Metabolite-Sensing Receptor GPR43 in a Murine Model of Gout – Angélica T. Vieira – Arthritis & Rheumatology

Tumor Grafting Induces Changes of Gut Microbiota in Athymic Nude Mice in the Presence and Absence of Medicinal Gynostemma Saponins – Lei Chen – PLOS ONE

Dynamic vaginal microbiota in pigtail macaques is associated with menstrual cycle and inflammation (MUC9P.753) – Nichole Klatt – The Journal of Immunology

Animal microbiome

Pyrosequencing Characterization of the Microbiota from Atlantic Intertidal Marine Sponges Reveals High Microbial Diversity and the Lack of Co-Occurrence Patterns – Anoop Alex – PLOS ONE

Characterization of the Bacterial Microflora on the Skin of Boreal toads, Anaxyrus (Bufo) boreas boreas, and Columbia Spotted Frogs, Rana luteiventris, in Grand Teton National Park, Wyoming USA – A.M. Hillis – International Journal of Microbiology Research

Soil microbiome

Niche and metabolic principles explain patterns of diversity and distribution: theory and a case study with soil bacterial communities – Jordan G. Okie – The Royal Society – Proceedings B

Book: The Soils of Antarctica – James G. Bockheim

Thesis: Role of Viruses Infecting Bacteria in Subsurface Sediments and Groundwater – Donald Pan – University of Nebraska-Lincoln

Water microbiome

Interaction and signalling between a cosmopolitan phytoplankton and associated bacteria – S. A. Amin – Nature

Towards a better quantitative assessment of the relevance of deep-sea viruses, Bacteria and Archaea in the functioning of the ocean seafloor – R. Danovaro – Aquatic Microbial Ecology

Bioreactor microbiome

Ecological Media Reveal Community Structure Shifts in a Municipal Wastewater Treatment Train – Bergmann RC – Bioremediation & Biodegradation

Extremophile microbiome

Deep-sea hydrothermal vent bacteria related to human pathogenic Vibrio species – Nur A. Hassan – PNAS

Book: The Soils of Antarctica – James G. Bockheim

Techniques

New Perspectives on Microbial Community Distortion after Whole-Genome Amplification – Alexander J. Probst – PLOS ONE

Human Bacterial and Fungal Amplicon Collection and Processing for Sequencing – Julia Oh – Bio-Protocol

Deconstructing the Polymerase Chain Reaction: Understanding and Correcting Bias Associated with Primer Degeneracies and Primer-Template Mismatches – Stefan J. Green – PLOS ONE

Microbial Ecology

Community quorum sensing signalling and quenching: microbial granular biofilm assembly – Chuan Hao Tan – NPJ Biofilms and Microbiomes

Theoretical analysis of the cost of antagonistic activity for aquatic bacteria in oligotrophic environments – Eneas Aguirre-von-Wobeser – Frontiers in Microbiology

More microbiology

Instrumentation: The mystery of the microscope in mud – Brian J. Ford – Nature

Antibiotic alternatives rev up bacterial arms race: From predatory microbes to toxic metals, nature is inspiring new ways to treat infections – Sara Reardon – Nature

Bioinformatics and Metagenomics

obitools: a unix-inspired software package for DNA metabarcoding – Frédéric Boyer – Molecular Ecology Resources

GenoLIB: a database of biological parts derived from a library of common plasmid features – Neil R. Adames – Nucleic Acids Research

PhD Thesis: Scalable Parallel Methods for Analyzing Metagenomics Data at Extreme Scale – Jeffrey A. Daily – Washington State University

Book Chapter: Lessons Learned from Simulated Metagenomic Datasets – Germán Bonilla-Rosso – Encyclopedia of Metagenomics

Review: Discovery of new protein families and functions: new challenges in functional metagenomics for biotechnologies and microbial ecology – Lisa Ufarté – Frontiers in Microbiology

Microbes in the news

The microbial world at our feet – Richard Burn – Society for General Microbiology

‘Bacteria Whisperer’ Bonnie Bassler reveals the secret lives of bacteria in Vancouver – CBC News

Google Ventures: These eight life sciences techs are the most promising – and worthy of investment – Meghana Keshavan – MedCityNews

Fast food versus the African diet, the bacteria battle waged in your gut – Carina Storrs – CNN

Toddler temperament could be influenced by different types of gut bacteria – Science Daily

Is Your Nervous System Being Hacked by Bacteria in Your Gut? – Gaia Vince – Gizmodo

Bacteria appears to help bats fight deadly white-nose syndrome – Mary Beth Griggs – Popular Science

Invisible helpers of the sea: Marine bacteria boost growth of tiny ocean algae – Phys.org

Some like it hot: Extremophile bacteria could be key to solving nuclear problems – Seaes Manchester

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May 20, 2015

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Human wound microbiome

Biochemical Association of Metabolic Profile and Microbiome in Chronic Pressure Ulcer Wounds – Mary Cloud B. Ammons – PLOS ONE

Human gut microbiome

Development and Validation of a Biomarker for Diarrhea-Predominant Irritable Bowel Syndrome in Human Subjects – Mark Pimentel – PLOS ONE

Editorial: Microbiota key to diet-associated risk of colon cancer – Nature Reviews Microbiology

Microbiome models

Antibiotics in Early Life Alter the Gut Microbiome and Increase Disease Incidence in a Spontaneous Mouse Model of Autoimmune Insulin-Dependent Diabetes – Sophie Candon – PLOS ONE

Changes in Gut Microbiota in Rats Fed a High Fat Diet Correlate with Obesity-Associated Metabolic Parameters – Virginie Lecomte – PLOS ONE

Gut Microbiota Dynamics during Dietary Shift in Eastern African Cichlid Fishes – Laura Baldo – PLOS ONE

Metaproteomics reveals major microbial players and their biodegradation functions in a large-scale aerobic composting plant – Dongming Liu – Microbial Biotechnology

Animal microbiome

The Fecal Microbiome in Cats with Diarrhea – Jan S. Suchodolski – PLOS ONE

Plant and soil microbiome

Effect of crop management and sample year on abundance of soil bacterial communities in organic and conventional cropping systems – C.H. Orr – Journal of Applied Microbiology

Water microbiome

Characterization of the relative importance of human- and infrastructure-associated bacteria in grey water: a case study – S.P. Keely – Journal of Applied Microbiology

Techniques

PCR-Based Multiple Species Cell Counting for In Vitro Mixed Culture – Ruijie Huang – PLOS ONE

Bioinformatics

FuncTree: Functional Analysis and Visualization for Large-Scale Omics Data – Takeru Uchiyama – PLOS ONE

Microbes in the news

Manipulating the Microbiome Produces Hope, but Uneven Results – Monica J. Smith – Gastroenterology & Endoscopy News

In America, is our food, in fact, too clean? – Kate Murphy – Herald Tribune

Study reveals intestinal bacteria succession during recovery from cholera in Bangladesh – Eureka Alert

Targeting Antibiotic-Resistant Bacteria with CRISPR and Phages – Anna Azvolinsky – The Scientist

Marine Bacteria Can Control Chemistry of Sea Spray Ejected into Atmosphere – SciNews

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May 16, 2015

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Posting might be irregular in the coming days because of international travel, but I will try to keep you all updated as best as I can.

Human oral microbiome

Increased infection with key periodontal pathogens during gestational diabetes mellitus – Himabindu Gogeneni – Journal of Clinical Periodontology

Human respiratory microbiome

Airway microbiota and acute respiratory infection in children – Kohei Hasegawa – Expert Review of Clinical Immunology

Human gut microbiome

Microbiota—implications for immunity and transplantation – Jonathan S. Bromberg – Nature Reviews Nephrology

Poster: Association of classical microbiology and 16S rDNA metagenetic Aanalysis to evaluate the presence of Clostridium difficile ina a belgian nursing home (sic) – Rodriguez Diaz, Cristina – 5th International Human Microbiome Congres

Review: Probiotics, antibiotics and the immune responses to vaccines – Ira Praharaj – Philosophical Transactions B

Microbiome models

Exposure to soil, house dust, and decaying plants increases gut microbial diversity and decreases serum IgE levels in BALB/c mice – Dongrui Zhou – Environmental Microbiology

Water microbiome

Metagenomics reveals the high PAH-degradation potential of abundant uncultured bacteria from chronically-polluted subantarctic and temperate coastal marine environments – Claudia L. Loviso – Journal of Applied Microbiology

Plant root and soil microbiome

Early rhizosphere microbiome composition is related to the growth and Zn uptake of willows introduced to a former landfill – Terrence H. Bell – Environmental Microbiology

Not all are free-living: high-throughput DNA metabarcoding reveals a diverse community of protists parasitizing soil metazoa – S. Geisen – Molecular Ecology

Soil microbial communities vary as much over time as with chronic warming and nitrogen additions – Alexandra R. Contosta – Soil Biology and Biochemistry

Soil ecotoxicity assessment of glyphosate use under field conditions: microbial activity and community structure of Eubacteria and ammonia oxidizing bacteria – María C. Zabaloy – Pest Management Science

Changes in soil aggregation and microbial community structure control carbon sequestration after afforestation of semiarid shrublands – N. Garcia-Francoa – Soil Biology and Biochemistry

Air microbiome

Challenges and Opportunities of Airborne Metagenomics – Hayedeh Behzad – Genome Biology and Evolution

Food microbiology

Bacteriophages isolated from chicken meat and the horizontal transfer of antimicrobial resistance genes– Amira Shousha – Applied and Environmental Microbiology

Techniques

A simple method of normalization of DNA extraction for improving the quantitative detection of soil-borne plant pathogenic oomycetes by real-time PCR – M. Li – Letters in Applied Microbiology

Microbes in the news

The kittybiome Project – background and some plans – Jonathan Eisen – MicroBEnet

Science, publishing, and career

Why Medicine is Plagued with Fake Research – Chloe Della Costa – Business Cheat Sheet

Physics Paper on the Higgs Boson Has Record 5,154 Authors – Softpedia (link to actual pdf)

Bik’s Picks

Giant Squid Lore and Legends Date Back Centuries – Benjamin Radford – Discovery

Cocaine Use Could be Determined by a Fingerprint, New Study – Silvia Fernandez – Pierce Pioneer

New map shows most distinct causes of death by state – Marilyn Malara – UPI

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May 8, 2015

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Human oral microbiome

Published in Gut but also oral: Human buccal epithelium acquires microbial hyporesponsiveness at birth, a role for secretory leukocyte protease inhibitor – Celia L Menckeberg – Gut

 

Human gut microbiome

Cholesterol gallstones and bile host diverse bacterial communities with potential to promote the formation of gallstones – Yuhong Peng – Microbial Pathogenesis

Development of an enhanced human gastrointestinal epithelial culture system to facilitate patient-based assays – Kelli L VanDussen – Gut

Gut microbiome and innate immune response patterns in IgE-associated eczema – Christina E West – Clinical & Experimental Allergy

Review: The gut microbiome in autoimmunity: Sex matters – Andres Gomez – Clinical Immunology

Review: Chemical communication in the gut: Effects of microbiota-generated metabolites on gastrointestinal bacterial pathogens – Stefanie L. Vogt – Anaerobe

Special issue of Clinical Liver Disease about “Liver and the Microbiome”. Reviews include:

Human genital microbiome

The vaginal and gastrointestinal microbiomes in gynecologic cancers: A review of applications in etiology, symptoms and treatment – Dana Chase – Gynecologic Oncology

Animal models of microbiome

Effects of dietary inulin on bacterial growth, short-chain fatty acid production and hepatic lipid metabolism in gnotobiotic mice – Karolin Weitkunat – The Journal of Nutritional Biochemistry

Plant root and soil microbiome

Covariation of soil bacteria functional diversity and vegetation diversity along an altitudinal climatic gradient in the Western Carpathians – Beata Klimek – Pedobiologia

Changes in fungal communities along a boreal forest soil fertility gradient – Erica Sterkenburg – New Phytologist

Water microbiome

Editorial without citation to the original Nature paper: Deep-ocean microbe is closest living relative of complex cells – Mitch Leslie – Science

Parasites

Not all parasites are protective – Derek M. McKay – Parasite Immunology

Helminths and the microbiota: parts of the hygiene hypothesis – P. Loke – Parasite Immunology

Bioinformatics

Testing in Microbiome-Profiling Studies with MiRKAT, the Microbiome Regression-Based Kernel Association Test – Ni Zhao – AJHG

Sparse and Compositionally Robust Inference of Microbial Ecological Networks – Zachary D. Kurtz – PLOS Computational Biology

Demystifying computer science for molecular ecologists – Mahdi Belcaid and Robert J. Toonen

Techniques

TM7 detection in human microbiome: Are PCR primers and FISH probes specific enough? – Maria V. Sizova – Journal of Microbiological Methods

Microbes in the news

Man’s Best Germs: Does Your Dog Influence Your Health? – Heather Buschman – UC San Diego

Video: Can Poop Cure an Infection? – Anna Rothschild – Gross science

Science, publishing, and career

The Hitchhiker’s Guide to a Neuroscience Career – Marian Joels – Neuron

Recommendation letters: Give women an even chance – Marcia McNutt – Science

Bik’s Picks
Spiders Sprayed with Graphene Spin Super-Strong Silk – Renee Morad – Discovery

Mmm, I always have mixed feelings about papers using these types of animal models. “We made this mouse blind. And then we cured it!” Light in sight: A step towards a potential therapy for acquired blindness – Science Daily

Grocery lists may help shoppers stick to healthier diet, lower weight – Reuters

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May 6, 2015

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Human oral microbiome

The Impact of Various Time Intervals on the Supragingival Plaque Dynamic Core Microbiome – Wen-xin Jiang – PLOS ONE

Dental and Microbiological Risk Factors for Hospital-Acquired Pneumonia in Non-Ventilated Older Patients – Victoria C. Ewan – PLOS ONE

Human gut microbiome

Unraveling the Influence of Gut Microbes on the Mind – M.J. Friedrich – JAMA

Gut Microbiota and Colorectal Cancer – Yu Y.-N. – Gastrointestinal Tumors

Gut Microbiota and Hepatocellular Carcinoma – Tao X – Gastrointestinal Tumors

Editorial: Gut microbiota and inflammation in chronic kidney disease patients – Denise Mafra – Clinical Kidney Journal

Animal models

Chronic Trichuris muris Infection in C57BL/6 Mice Causes Significant Changes in Host Microbiota and Metabolome: Effects Reversed by Pathogen Clearance – Ashley Houlden – PLOS ONE

Animal microbiome

Bacterial Diversity Associated with Cinachyra cavernosa and Haliclona pigmentifera, Cohabiting Sponges in the Coral Reef Ecosystem of Gulf of Mannar, Southeast Coast of India – C. Jasmin – PLOS ONE

Plant microbiome

Shifts in Symbiotic Endophyte Communities of a Foundational Salt Marsh Grass following Oil Exposure from the Deepwater Horizon Oil Spill – Demetra Kandalepas – PLOS ONE

Endophytic and Epiphytic Microbes as “Sources” of Bioactive Agents – David J. Newman and Gordon M. Cragg – Frontiers in Chemistry

Review: Pivotal roles of phyllosphere microorganisms at the interface between plant functioning and atmospheric trace gas dynamics – Françoise Bringel – Frontiers in Microbiology

Soil and sediment microbiome

Metabolic Activity and Functional Diversity Changes in Sediment Prokaryotic Communities Organically Enriched with Mussel Biodeposits – Thomas Pollet – PLOS ONE

Impacts of dimethyl phthalate on the bacterial community and functions in black soils – Zhi-Gang Wang – Frontiers in Microbiology

Aquatic / Extremophile microbiome

Benthic microbial communities of coastal terrestrial and ice shelf Antarctic meltwater ponds – Stephen D. Archer – Frontiers in Microbiology

Microbial food web components, bulk metabolism, and single-cell physiology of piconeuston in surface microlayers of high-altitude lakes – Hugo Sarmento – Frontiers in Microbiology

Microbial communities of the Lemon Creek Glacier show subtle structural variation yet stable phylogenetic composition over space and time – Cody S. Sheik – Frontiers in Microbiology

Bioreactor microbiome

Bacterial Pathogens and Community Composition in Advanced Sewage Treatment Systems Revealed by Metagenomics Analysis Based on High-Throughput Sequencing – Xin Lu – PLOS ONE

Metagenomics, metabolomics, and bioinformatics

Expression of heterologous sigma factors enables functional screening of metagenomic and heterologous genomic libraries – Stefan M. Gaida – Nature Communications

TreeSeq, a Fast and Intuitive Tool for Analysis of Whole Genome and Metagenomic Sequence Data – Bastiaan Wintermans – PLOS ONE

Covariation is a poor measure of molecular coevolution – David Talavera – Molecular Biology and Evolution

Review: Data-driven integration of genome-scale regulatory and metabolic network models – Saheed Imam – Frontiers in Microbiology

Archaea

Complex archaea that bridge the gap between prokaryotes and eukaryotes – Anja Spang – Nature

More microbiology papers

The passenger-associated transport repeat promotes virulence factor secretion efficiency and delineates a distinct autotransporter subtype – Matthew Thomas Doyle – Molecular Microbiology

Microbes and art

Intestine-inspired 3D printed fashion will hold glowing bacteria – Chris Baraniuk – New Scientist

Microbes in the news

Who are the bioaerosols in your neighborhood? Find out by entering a chamber … – Jonathan Eisen – MicroBEnet

Exploring bacterial genes: New technique helps uncover useful functions in microbial genomes – University of Delaware

Newly discovered ‘missing link’ shows how humans could evolve from single-celled organisms: A new microbe found a mile and a half below the Atlantic Ocean  – Rachel Feltman – The Washington Post

Treating a bacterial infection with bacteria lowers chances of recurrence – Meryl Lin McKean – Fox4kc

Toxic Gut Bacteria: New Treatment Could Prevent Repeat Infections – Rachael Rettner – Live Science

Researchers produce jet fuel compounds from fungus – Science Daily

Molecular Homing Beacon Redirects Human Antibodies to Fight Pathogenic Bacteria – Heather Buschman – UC San Diego

Bacteria research opens way for new antibiotics: common building block, called the Passenger-associated Transport Repeat (PATR) present in many pathogens – University of Adelaide

Science, publishing, and career

‘Living figures’ make their debut: Published chart integrates data from outside scientists – Dalmeet Singh Chawla – Nature

The trouble with reference rot: Computer scientists are trying to shore up broken links in the scholarly literature – Jeffrey M. Perkel – Nature

The retirement debate: Stay at the bench, or make way for the next generation: When and how to exit research has become a charged issue in science – Megan Scudellari – Nature

Pint-sized DNA sequencer impresses first users: Portable device offers on-the-spot data to fight disease, catalogue species and more – Erika Check Hayden – Nature

Bik’s Picks

Recovering Sea Lions at Marine Center Deliberately Injured By Chlorine, Police Say – Avianne Tan – ABC News

People with Depression and Bipolar Disorder Feel Sadness Differently – Tanya Lewis – Live Science

Feasting on fruits may leave you craving for more – Silvia Fernandez – Pierce Pioneer News

Trouble Falling Asleep? Doctor Says This Trick Will Put You to Sleep in One Minute – Zachary Stieber – The Epoch Times
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May 5, 2015

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General human microbiome

Review: The Human Microbiota: The Rise of an “Empire” – Gidon Berger – Rambam Maimonides Medical Journal

Human gut microbiome

Human colon-derived soluble factors modulate gut microbiota composition – Arancha Hevia – Frontiers in Oncology

Dysbiosis of Intestinal Microbiota Associated With Inflammation Involved in the Progression of Acute Pancreatitis – Tan, Chaochao – Pancreas

Review: Does the Gut Microbiota Contribute to Obesity? Going beyond the Gut Feeling – Marisol Aguirre and Koen Venema – Microorganisms

Review: Alcohol Effects on the Composition of Intestinal Microbiota – Phillip A. Engen – The Gastrointestinal Microbiome – NIH

Human respiratory microbiome

Prevalence of oropharyngeal antibiotic-resistant flora among residents of aged care facilities: a pilot study – Christopher D. Etherton-Beer – Respirology

Animal models of microbiomes

Modulatory effects of a cranberry extract co-supplementation with Bacillus subtilis CU1 probiotic on phenolic compounds bioavailability and gut microbiota composition in high-fat diet-fed mice – Stéphanie Dudonné – PharmaNutrition

Animal microbiome

Characterization of the cellulolytic bacteria communities along the gastrointestinal tract of Chinese Mongolian sheep by using PCR-DGGE and real-time PCR analysis – Yan Zeng – World Journal of Microbiology and Biotechnology

Soil microbiome

Soil microbial community structure is unaltered by plant invasion, vegetation clipping, and nitrogen fertilization in experimental semi-arid grasslands – Chelsea J. Carey – Frontiers in Microbiology

Water microbiome

A metagenome for lacustrine Cladophora (Cladophorales) reveals remarkable diversity of eukaryotic epibionts and genes relevant to materials cycling – Linda E. Graham – Journal of Phycology

Bacterial and archaeal biogeography of the deep chlorophyll maximum in the South Pacific Gyre – Emily A. Walsh – Aquatic Microbial Ecology

Extremophiles

The influence of surface soil physicochemistry on the edaphic bacterial communities in contrasting terrain types of the Central Namib Desert – S. Gombeer – Geobiology

Microbial diversity and metabolic networks in acid mine drainage habitats – Celia Mendez-Garcia – Frontiers in Microbiology

Metabolomics

Structuring Microbial Metabolic Responses to Multiplexed Stimuli via Self-Organizing Metabolomics Maps – Cody R. Goodwin – Chemistry & Biology

Techniques

Deriving accurate microbiota profiles from human samples with low bacterial content through post-sequencing processing of Illumina MiSeq data – Jake Jervis-Bardy – Microbiome

More microbes

Antibacterial activity of silver-killed bacteria: the “zombies” effect – Racheli Ben-Knaz Wakshlak

Review: The dormant blood microbiome in chronic, inflammatory diseases – Marnie Potgieter – FEMS Microbiology Reviews

Microbes and art

Faecal transplants and bio-art – Eden Project’s latest exhibition Invisible You explores the science of microbes – Nicola Davis – The Guardian

Microbiology printable labels or buffet cards blue and black – LoveBacteriaArt – Etsy

Microbes in the news

1h Video: Seth Bordenstein: The microbiome and Darwin’s Mystery of Mysteries – University of Michigan Early Career Scientists Symposium

Cervicovaginal microbiome holds promise in preventing preterm birth – interview with Dr. Michal Elovitz at the annual meeting of the American Congress of Obstetricians and Gynecologists – Mary Ellen Schneider #ACOG15

Episode 6 of The Microbiome Podcast: The microbiome, autism, and serotonin production with Dr. Elaine Hsiao – MicrobiomeInstitute

Some beards as dirty as toilets: Microbiologist tests beards for germs – Royale Da – KOAT

(See more beard microbiome articles from these past days in The Beard Microbiome)

“You’re covered in poo bacteria.” No, your beard isn’t full of poop (probably) – Rachel Feltman – The Washington Post

HuMiX – Emulating human microbiome on a chip – Bactavatchalou Sivakumar

Nanoparticles in consumer products can significantly alter normal gut microbiome – Phys.org

Never a dull day for microbiologist – Kathryn Bernard up for Women of Distinction prize – Winnipeg Free Press

Agricultural microbiology draws Chinese researchers to Argentina – Xinhua – Want China Times

Expert’s Corner: Physician-scientist on why he recommends probiotics – University of Massachusetts

Gut Wars: One Man’s Adventure With Antibiotics and Ulcerative Colitis – Alexandra Carmichael – uBiome blog

Show Me Your Moves: Updated classics and new techniques help microbiologists get up close and quantitative – Marissa Fessenden – The Scientist

‘Zombie’ Bacteria May Help Heal Wounds – Discovery

Ocean currents disturb methane-eating bacteria – Phys.org

Bacteria could prove key in the fight against cholesterol – Paul Healy – Independent

Free book (for a limited time): The Squid, the Vibrio & the Moon – Small Friends Books

Science, publishing, and career

DNA editing takes a serious step forward — for better or worse – Eryn Brown – LA Times

Bik’s Picks

Llamas as Lab Rats: From diagnostics to vaccines, llama antibodies point to new directions in HIV research – Jenny Rood – The Scientist

Big whales have stretchy nerves to help them gulp – Jonathan Webb – BBC

Is sleepwalking genetic? Study suggests it runs in the family – ZME Science

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April 21, 2015

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I don’t always eat steak, but when I do, I will put some garlic on it.

Conferences

WAO Symposium on Food Allergy and the Microbiome – December 2015 – Miami, FL, USA

Call for papers: Interactions of the Human Microbiome and Immune System in Health Resilience and Disease Pathogenesis – Journal of Immunology Research

Microbiome of pregnancy and birth

Impact of human milk bacteria and oligosaccharides on neonatal gut microbiota establishment and gut health – Ted Jost – Nutrition Reviews

Human oral microbiome

Editorial on “The oral microbiome in an ecological perspective: More than just a sum of microbes” – Egija Zaura and Alex Mira – Frontiers in Cellular and Infection Microbiology

Human respiratory microbiome

Rapid detection of emerging pathogens and the loss of microbial diversity associated with severe lung disease in cystic fibrosis – William G. Flight – Journal of Clinical Microbiology

Review behind a thick paywall: The pediatric microbiome and the lung – Michael Tracy – Current Opinion in Pediatrics

Review: Lung Microbiomes: New Frontiers? – Kathryn DeRiemer – American Journal of Respiratory and Critical Care Medicine

Review: A systematic review and meta-analysis of probiotics for the treatment of allergic rhinitis – Alexander E. Zajac – International Forum of Allergy & Rhinology

Human gut microbiome

Ménage-à-trois of bariatric surgery, bile acids and the gut microbiome – Rajendra Raghow – World Journal of Diabetes

Gut Microbiome Compositional and Functional Differences between Tumor and Non-tumor Adjacent Tissues from Cohorts from the US and Spain – Gut Microbes

Review: No Vacancy: How Beneficial Microbes Cooperate with Immunity To Provide Colonization Resistance to Pathogens – Martina Sassone-Corsi and Manuela Raffatellu – The Journal of Immunology

Review on chronic kidney disease: Altered intestinal microbial flora and impaired epithelial barrier structure and function in CKD: the nature, mechanisms, consequences and potential treatment – Nosratola D. Vaziri – Nephrology Dialysis Transplantation

Review: The Role of Microbial Amino Acid Metabolism in Host Metabolism – Evelien P. J. G. Neis – Nutrients

Review: Linking Smoking, Coffee, Urate, and Parkinson’s Disease – A Role for Gut Microbiota? – Filip Scheperjans – Journal of Parkinson’s Disease

Animal and other models of microbiome research

Have some garlic with your steak: Dietary allicin reduces transformation of L-carnitine to TMAO through impact on gut microbiota – Wei-Kai Wu – Journal of Functional Foods

Innate Lymphoid Cells Control Early Colonization Resistance against Intestinal Pathogens through ID2-Dependent Regulation of the Microbiota – Xiaohuan Guo – Immunity

Effect of donor animal species and their feeding on the composition of the microbial community establishing in a rumen simulation – M. Witzig – Journal of Applied Microbiology

Impact of a novel protein meal on the gastrointestinal microbiota and host transcriptome of larval zebrafish Danio rerio – Eugene Rurangwa – Frontiers in Physiology

Animal microbiome

Shit happens: Shifts in the gut microbiome observed in wildlife (Giraffa camelopardalis, Antidorcas marsupialis) fecal samples exposed to natural weather conditions: lessons from time series analyses using next generation sequencing for application in field studies – Sebastian Menke – Methods in Ecology and Evolution

Caste-Specific Differences in Hindgut Microbial Communities of Honey Bees (Apis mellifera) – Karen M. Kapheim – PLOS ONE

Molecular Survey of Bacterial Communities Associated with Bacterial Chondronecrosis with Osteomyelitis (BCO) in Broilers – Tieshan Jiang – PLOS ONE

Plant root and soil microbiome

Bacterial diversity amplifies nutrient-based plant–soil feedbacks – Simone Weidner – Functional Ecology

Non-random species loss in bacterial communities reduces antifungal volatile production –
W. H. Gera Hol – Ecology

Application of a new purification method of West-Kazakhstan chestnut soil microbiota DNA for metagenomic analysis – N. Kh. Sergaliev – Eurasian Soil Science

Physiological profiles of microbial communities in mine soils afforested with different tree species – Marcin Chodak – Ecological Engineering

Microbial lipid and amino sugar responses to long-term simulated global environmental changes in a California annual grassland – Chao Liang – Frontiers in Microbiology

Water microbiome

Seasonal diversity and dynamics of haptophytes in the Skagerrak, Norway, explored by high-throughput sequencing – Elianne Sirnæs Egge – Molecular Ecology

Extremophiles

Relationship between phylogenetic and nutritional diversity in Arctic (Kandalaksha Bay) seawater planktonic bacteria – Chiara Pesciaroli – Annals of Microbiology

Geochemical Characteristics and Microbial Community Composition in Toxic Metal-Rich Sediments Contaminated with Au-Ag Mine Tailings – Man Jae Kwon – Journal of Hazardous Materials

Uranium isotopes fingerprint biotic reduction – Malgorzata Stylo – PNAS

Bioreactor microbiome

Metaproteomics of complex microbial communities in biogas plants – Robert Heyer – Microbial Biotechnology

Similar PAH Fate in Anaerobic Digesters Inoculated with Three Microbial Communities Accumulating Either Volatile Fatty Acids or Methane – Florence Braun – PLOS ONE

Reactor performance and methanogenic archaea species in thermophilic anaerobic co-digestion of waste activated sludge mixed with food wastewater – Hyun Min Jang – Chemical Engineering Journal

Functional food microbiology

A proposed framework for an appropriate evaluation scheme for microorganisms as novel foods with a health claim in Europe – Sylvie Miquel – Microbial Cell Factories

Metagenomics and bioinformatics

CoMeta: Classification of Metagenomes Using k-mers – Jolanta Kawulok, Sebastian Deorowicz – PLOS ONE

Large-scale contamination of microbial isolate genomes by Illumina PhiX control – Supratim Mukherjee – Standards in Genomic Sciences

NGS-eval: NGS Error analysis and novel sequence VAriant detection tooL – Ali May – Nucleic Acids Research

Mini review: The Turbulent Network Dynamics of Microbial Evolution and the Statistical Tree of Life – Eugene V. Koonin – Journal of Molecular Evolution

Not really metagenomics but of interest: Ecological overlap and horizontal gene transfer in Staphylococcus aureus and Staphylococcus epidermidis – Guillaume Méric – Genome Biology and Evolution

Haven’t we microbiologists already been doing this for years?
Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform – Shadi Shokralla – Scientific Reports

Techniques

Method Optimization for Fecal Sample Collection and Fecal DNA Extraction – Conny Mathay – Biopreservation and Biobanking

Microbes in the news

Housing characteristics and microbial communities in homes of asthmatic children – Elisabeth Bik – MicroBEnet

OCHS science experiment finds space a hospitable place for bacteria – Cindy Nevitt – Press of Atlantic City

Uranium isotopes carry the fingerprint of ancient bacterial activity – Phys.org

Immune cells support good gut bacteria in fight against harmful bacteria – University of Chicago

Q&A: What Is Listeria? Bacteria Found in Blue Bell Ice Cream – Mary Clare Jalonick – ABC News

Grant will help University of Minnesota study antibiotic-resistant bacteria – Star Tribune

Science, publishing, and career

Mya Breitbart awarded the 2015 STEM Woman of the Year – University of South Florida

Bik’s Picks

Fast imaging of live organisms with sculpted light sheets – Aleksander K. Chmielewski – Scientific Reports

Cheesy, metallic, sweet: 170-year-old champagne is clue to winemaking’s past – Allie Wilkinson – Nature

New Evidence of Prehistoric Trade With Asia Found at Bering Land Bridge Site – Huffington Post
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April 20, 2015

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Happy 4/20! Here is a paper from last June that deserves renewed attention today: 

Understanding Cultivar-Specificity and Soil Determinants of the Cannabis Microbiome – Max E. Winston – PLOS ONE

Human oral microbiome

Review: Ecological Approaches to Oral Biofilms: Control without Killing – Marsh P.D. – Caries Research

Human vaginal microbiome

A multi-platform metabolomics approach identifies novel biomarkers associated with bacterial diversity in the human vagina – Amy McMillan – ArXiv

Comparison of detection methods for vaginal lactobacilli – I. Smidt – Beneficial Microbes

Human gut microbiome

Differences in Gut Microbiota Between Atopic and Healthy Children – Tiina Drell – Current Microbiology

DGGE: Is there interaction between gut microbial profile and cardiovascular risk in chronic kidney disease patients? – Amanda F Barros – Future Medicine

Thesis: Characterization and Investigation of Fungi Inhabiting the Gastrointestinal Tract of Healthy and Diseased Humans – Mallory J Suhr – University of Nebraska-Lincoln

Poster: The MS Microbiome Consortium (MSMC): an academic multi-disciplinary collaborative effort to elucidate the role of the gut microbiota in MS (P2.205)
Ilana Katz Sand – Neurology

Review: Gut microbiota and Ma-Pi 2 macrobiotic diet in the treatment of type 2 diabetes – Francesco Fallucca – World Journal of Diabetes

Animal microbiome

The coral core microbiome identifies rare bacterial taxa as ubiquitous endosymbionts
Tracy D Ainsworth – The ISME Journal

Plant root and soil microbiome

Tree: Genetic Diversity and Functional Traits of Pterocarpus officinalis Jacq. Associated with Symbiotic Microbial Communities in Caribbean Swamp Forests in Relation to Insular Distribution, Salinity and Flooding – Amadou M. Bâ, Elsie Rivera-Ocasio – Wetlands

Plant: Effects of cowpea (Vigna unguiculata) root mucilage on microbial community response and capacity for phenanthrene remediation – Ran Sun – Journal of Environmental Sciences

Effect of conventional and organic orchard floor management practices on enzyme activities and microbial counts in a ‘Cripp’s Pink’/M7 apple orchard – André H Meyer – South African Journal of Plant and Soil

Successional and seasonal variations in soil and litter microbial community structure and function during tropical post-agricultural forest regeneration: A multi-year study
A. Peyton Smith – Global Change Biology

Editorial: Increasing diversity – Andrea Du Toit – Nature Reviews Microbiology

Soils naturally suppressive to banana Fusarium wilt disease harbor unique bacterial communities – Zongzhuan Shen – Plant and Soil

Cropping systems modulate the rate and magnitude of soil microbial autotrophic CO2 fixation in soil – Xiao H. Wu – Frontiers in Microbiology

Cave microbiome
Nutrient input influences fungal community composition and size and can stimulate Mn(II) oxidation in caves – SK Carmichael – Environmental Microbiology Reports

Water microbiome

Temporal and spatial constraints on community assembly during microbial colonization of wood in seawater – Dimitri Kalenitchenko – The ISME Journal

Extremophiles

In situ expression of eukaryotic ice-binding proteins in microbial communities of Arctic and Antarctic sea ice – Christiane Uhlig – The ISME Journal

Metatranscriptomes reveal functional variation in diatom communities from the Antarctic Peninsula – Gareth A Pearson – The ISME Journal

Venn Diagrams galore: Multi-scale variability analysis reveals the importance of spatial distance in shaping Arctic soil microbial functional communities – Yu Shi – Soil Biology and Biochemistry

Microbes of the built environment

Influence of housing characteristics on bacterial and fungal communities in homes of asthmatic children – K. C. Dannemiller – Indoor Air

Microbial diversity in bioaerosol samples causing ODTS compared to reference bioaerosol samples as measured using Illumina sequencing and MALDI-TOF – Anne Mette Madsen – Environmental Research

Molecular characterization of microbial communities and quantification of Mycobacterium immunogenum in metal removal fluids and their associated biofilms
Jianfeng Wu – Environmental Science and Pollution Research

Bioreactor and wastewater microbiology

Microbial Mats as a Biological Treatment Approach for Saline Wastewaters: The Case of Produced Water from Hydraulic Fracturing – Benay Akyon – Environmental Science & Technology

Dynamics and distribution of bacterial and archaeal communities in oil-contaminated temperate coastal mudflat mesocosms – Gbemisola O. Sanni – Environmental Science and Pollution Research

Techniques

Flow cytometry as an auxiliary tool for the selection of probiotic bacteria – D. Mudroňová – Beneficial Microbes

Other microbiology papers

Shattering old beliefs: Gram’s stain does not cross the bacterial cytoplasmic membrane – Michael J. Wilhelm – ACS Chemical Biology

Dynamic Clustering in Suspension of Motile Bacteria – Xiao Chen – ArXiv

Microbes in the news

Jessica Richman, CEO of uBiome joins for short Toolmaker Talk about microbiome – Quantified Self Radio

Top 100 Most Influential People, with Martin Blaser – Almudena Bernabea – Time

Video: David Sela, PhD: Probiotics, nutrition & the microbiome – UMass Amherst – YouTube

Can Specks of Dust Help Solve Crimes? – Mandy Oaklander – Time

Bacterial flora of remote tribespeople carries antibiotic resistance genes – Science Daily

In fight against Crohn’s, professor battles bacteria – Scott Goss – USA Today

Are gut bacteria manipulating your mood? – Viviane Richter – Cosmos Magazine

To fight nasty digestive bugs, U-M scientists set out to build a better gut – using stem cells – HealthCanal

Mouth bacteria can tell the status of liver disease – Zee News

How the gut garden affects fat-burning – Sylvia Harral, Michele Stewart – Recorder Online

Maple Syrup Extract May Fight Infection-Causing Bacteria: Study – Joanna Adams – Huffington Post

How Things Work: Phages occupy bacteria to cure infection – Sharon Wu – The Tartan

The Bacteria Will See You Now: How Little Bugs Create Big Problems in Hospitals – Brian Krans – HealthLine

Cytokinins Cannot Be Associated with Plants Only: Being Present in Bacteria, They Also Affect Resistance to TB – Martina Šaradínová

Microbes and art

Video: Anna Dumitriu – “Don’t try this at home” – creating microbial artwork from faecal transplants – YouTube

Now with a Colon and Rectum – but Super Stomach and Tremendous Testicle are cute too. Bladder is on sale! I Heart Guts Plush Organs

Science, publishing, and career

University of Victoria student diving for his master’s – Jeff Bell – Times Colonist (HT: Ed Yong)

Bik’s Picks

Roundup and Risk Assessment – Michael Specter – New Yorker

Vampire Squid Outlast Their Shallower Peers – SindyaN. Bhanoo – New York Times

New species of frog found in Costa Rica looks just like Kermit – Andrea Romano – Mashable

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April 16, 2015

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Human gut microbiome

Alcoholic Liver Disease: The Gut Microbiome and Liver Cross Talk – Phillipp Hartmann – Alcoholism: Clinical and Experimental Research

Animal models of microbiome research

Xylo-oligosaccharides and virginiamycin differentially modulate gut microbial composition in chickens – Mohsen Pourabedin – Microbiome

Taking advantage of quorum sensing – Cláudio Nunes-Alves – Nature Reviews Microbiology

Changes in the colon microbiota and intestinal cytokine gene expression following minimal intestinal surgery – Susan Lapthorne – World Journal of Gastroenterology

Animal microbiome

Insect life history and the evolution of bacterial mutualism – Lee M. Henry – Ecology Letters

Bugs full of viruses – Astrid Gall – Nature Reviews Microbiology

Similar sponge-associated bacteria can be acquired via both vertical and horizontal transmission – Detmer Sipkema – Environmental Microbiology

Transcriptional activity of the giant barrel sponge, Xestospongia muta Holobiont: Molecular Evidence for Metabolic Interchange – Cara L. Fiore – Frontiers in Microbiology

Water microbiome

Shift of anammox bacterial community structure along the Pearl Estuary and the impact of environmental factors – Bingbing Fu – Journal of Geophysical Research

Metatranscriptome analyses indicate resource partitioning between diatoms in the field – Harriet Alexander – PNAS USA

Microbiome of the built environment

Total Concentrations of Virus and Bacteria in Indoor and Outdoor Air – Aaron J. Prussin – Environmental Science and Technology Letters
See also my blog post on MicroBE.net about this paper, with a lively discussion on filters and pore sizes

Food microbiology

Effect of Gamma Irradiation on the Bacteriological and Sensory Analysis of Raw Whole Milk under Refrigeration – Adriana Cristina de Oliveira Silva

Bioreactor microbiology

Disturbance opens recruitment sites for bacterial colonization in activated sludge – David C. Vuono – Environmental Microbiology

Metaproteomics of complex microbial communities in biogas plants – Robert Heyer – Microbial Biotechnology

16S rRNA gene analysis, not metagenomics: Metagenomic analysis for the microbial consortium of anaerobic CO oxidizers – Ying Guo – Microbial Biotechnology

Bioinformatics

Protocol: Bioinformatics and Microarray Data Analysis on the Cloud – Barbara Calabrese, Mario Cannataro – Methods in Molecular Biology

An Ontology-Based GIS for Genomic Data Management of Rumen Microbes – Saber Jelokhani-Niaraki – Genomics & Informatics

Behind a very thick paywall: Application of Meta-Mesh on the analysis of microbial communities from human associated-habitats – Xiaoquan Su – Quantitative Biology

Metagenomics

The metagenomic approach and causality in virology – Silvana Beres Castrignano and Teresa Keico Nagasse-Sugahara – Rev Saúde Pública

Techniques

Use of pressure cycling technology for cell lysis and recovery of bacterial and fungal communities from soil – Emily A. Bruner – BioTechniques

Microbial Ecology

Estimating and Mapping Ecological Processes Influencing Microbial Community Assembly – James C. Stegen – Frontiers in Microbiology

More microbiology

The Infallible Microbial Identification Test: Does It Exist? – Alex van Belkum – Journal of Clinical Microbiology

Microbes in the news

Synthetic Cheese and the Microbiome – Alex A. — MicroBE.net

Total Concentrations of Virus and Bacteria in Indoor and Outdoor Air – Elisabeth Bik – MicroBE.net

A Review of the Oral Microbiome: Orli Reports – Orli Kadoch – uBiome Blog

To fight nasty digestive bugs, scientists set out to build a better gut—using stem cells – Medical Xpress

#BacteriaArePlural The bacteria that steals DNA from its surroundings – Mette Risbråthe – Norwegian University of Life Sciences

#BacteriaHysteria: Germ warfare: Kitchens can harbor hidden bacteria – Katherine Roth – The Pueble Chieftain

Science, publishing, and career

A resource for cell line authentication, annotation and quality control – Mamie Yu – Nature

Science AMA Series: We are Charon Pierson, journal editor and elected member of the Governing Council for the Committee on Publication Ethics (COPE) and Ivan Oransky, co-founder of Retraction Watch. AUA about publication ethics and retractions.

Rule rewrite aims to clean up scientific software – Nature Biotechnology asks peer reviewers to check accessibility of code used in computational studies – Erika Check Hayden – Nature

Bik’s Picks

Response of seafloor ecosystems to abrupt global climate change – Sarah E. Moffitt – PNAS USA

Longread: The Pollen Detective – He’d used science to crack cases from art forgery to bank robbery. But then a murder took place in his own backyard – David Wolman – Medium

This professor measured his fingernail growth for 35 years. The results will amaze you! – Seriously, Science? – Discover

April 14, 2015

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Human oral microbiome

Bacteriophage and their potential roles in the human oral cavity – Anna Edlund – Journal of Oral Microbiology

A Potential Biofilm Metabolite Signature for Caries Activity – A Pilot Clinical Study
Zandona F – Metabolomics

Human gut microbiome

Functional Dynamics of the Gut Microbiome in Elderly People during Probiotic Consumption – Emiley A. Eloe-Fadrosh – mBio

Siblings of patients with Crohn’s disease exhibit a biologically relevant dysbiosis in mucosal microbial metacommunities – Charlotte Hedin – Gut

Effect of iron supplementation with or without vitamin E (VE) on gut microbiome (MB) in iron deficient (ID) infants and toddlers – Minghua Tang – The FASEB Journal

Molecular assessment of differences in the duodenal microbiome in subjects with irritable bowel syndrome – Evangelos Giamarellos-Bourboulis – Scandinavian Journal of Gastroenterology

Review: Viruses, Other Pathogenic Microorganisms and Esophageal Cancer – Xu W. – Gastrointestinal Tumors

Human genital tract microbiome

True love: Complementary seminovaginal microbiome in couples – Reet Mändar – Research in Microbiology

Metabolic Signatures of Bacterial Vaginosis – Sujatha Srinivasan – mBio

Pregnancy and birth microbiome

Low birthweight, gestational age, need for surgical intervention and gram-negative bacteraemia predict intestinal failure following necrotising enterocolitis – Anders Elfvin – Acta Paediatrica

Animal models of microbiome research

Gut microbiota depletion from early adolescence in mice: Implications for brain and behaviour – Lieve Desbonnet – Brain, Behavior, and Immunity

Animal microbiome

Dog: Draft Genome Sequences of 26 Porphyromonas Strains Isolated from the Canine Oral Microbiome – David A. Coil – Genome Announcements

Ragworm: Polychaete burrows harbour distinct microbial communities in oil-contaminated coastal sediments – Joe D Taylor and Michael Cunliffe – Environmental Microbiology Reports

Just dropping by (Aphids): Do Bacterial Symbionts Govern Aphid’s Dropping Behavior? – Omer Lavy – Environmental Entomology

Review (corals): Nitrogen cycling in corals: the key to understanding holobiont functioning? – Nils Rädecker – Trends in Microbiology

Plant and soil microbiome

Below-ground abiotic and biotic heterogeneity shapes above-ground infection outcomes and spatial divergence in a host–parasite interaction – Ayco J. M. Tack – New Phytologist

A pyrosequencing insight into sprawling bacterial diversity and community dynamics in decaying deadwood logs of Fagus sylvatica and Picea abies – Björn Hoppe – Scientific Reports

Effect of crop management and sample year on abundance of soil bacterial communities in organic and conventional cropping systems – Caroline H. Orr – Journal of Applied Microbiology

Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics – Carmelo Andújar – Molecular Ecology

Soil treatment-induced differential gene expression in tomato: Relationships between defense gene expression and soil microbial community composition – Shawn T. Lucas – Applied Soil Ecology

Diversity and characterization of Cd-tolerant dark septate endophytes (DSEs) associated with the roots of Nepal alder (Alnus nepalensis) in a metal mine tailing of southwest China – Runbing Xu – Applied Soil Ecology

Plant traits related to nitrogen uptake influence plant-microbe competition – Delphine Moreau – Ecology

Soil microbial functionality in response to dairy sewage sludge and mineral fertilisers application under winter rape – K. Oszust – International Journal of Environmental Science and Technology

Water microbiome

Dynamic succession of groundwater functional microbial communities in response to emulsified vegetable oil amendment during sustained in situ U(VI) reduction – Ping Zhang – Applied and Environmental Microbiology

Distribution of PAHs and the PAH-degrading bacteria in the deep-sea sediments of the high-latitude Arctic Ocean – C. Dong – Biogeosciences

Sulfate-reducing bacterial communities in the water column of the Gdansk Deep (Baltic Sea) – V. A. Korneeva – Microbiology

Bioreactor microbiology

Rare taxa have potential to make metabolic contributions in enhanced biological phosphorus removal ecosystems – Christopher E. Lawson – Environmental Microbiology

Extremophile microbiome

Archaeal Viruses Multiply: Temporal Screening in a Solar Saltern – Nina S. Atanasova – Viruses

Review: 40 Years of archaeal virology: Expanding viral diversity – Jamie C. Snyder – Virology

Methane Yield Database: Online Infrastructure and Bioresource for Methane Yield Data and Related Metadata – Boštjan Murovec – Bioresource Technology

Call for papers: BIODESERT: Exploring and Exploiting the Microbial Resource of Hot and Cold Deserts – Hindawi BioMed Research International

Metagenomics and metabolomics

Reconstructing Rare Soil Microbial Genomes using in situ Enrichments and Metagenomics – Tom O. Delmont – Frontiers in Microbiology

Characterization and Detection of a Widely Distributed Gene Cluster That Predicts Anaerobic Choline Utilization by Human Gut Bacteria – Ana Martínez-del Campo – mBio

Metabolic Signatures of Bacterial Vaginosis – Sujatha Srinivasan – mBio

Review: Prokaryotic functional gene diversity in the sunlit ocean: Stumbling in the dark
Isabel Ferrera – Current Opinion in Microbiology

Techniques

Specific amplification of bacterial DNA by optimized so-called universal bacterial primers in samples rich of plant DNA – Samart Dorn-In – Journal of Microbiological Methods

More microbiology papers

Bacterial Raincoats: Interfacial self-assembly of a bacterial hydrophobin – Keith M. Bromley – PNAS USA

A New Synthesis for Dual Use Research of Concern – Michael J. Imperiale, Arturo Casadevall – PLOS Biology

Microbes in the news

Here’s Your New Science-Backed Reason to Eat More Cheese Your good bacteria love stinky fromage as much as you do – Mandy Oaklander – Time

Making a microbe subway map – Bethany Brookshire – Student Science

Video: Can gut bacteria help us live longer? – Simin Nikbin Meydani – Tufts University

Bacterial raincoat discovery paves way to better crop protection – Phys.org

CRISPR Shows How A Bacterial Cell Can Recognize Its Own DNA – Science 2.0

Spotlight on the Banfield lab: Longer DNA fragments reveal rare species diversity  – TANN – Archaeology News Network

Submission for the ASM Global Video Challenge 2015: Bacterial Friends Within You – YouTube

Spread of bacteria an issue in doctors’ white coat debate – Murray Feingold – Standard Speaker

Science, publishing, and career

How should journalists cover quacks like Dr. Oz or the Food Babe? – Julia Belluz – Vox

Great news: National hiring experiments reveal 2:1 faculty preference for women on STEM tenure track – Wendy M. Williams and Stephen J. Ceci – PNAS USA

Bik’s Picks

Four Corners Methane ‘Hot Spot’: NASA Joins Team Of Scientists Attempting To Pinpoint Source Of Gas – Avaneesh Pandey – International Business Times

Natural Selection May Help Account for Dutch Height Advantage – Carl Zimmer – New York Times

This Doughnut In Space Went Where No Breakfast Pastry Has Been Before – Cameron Keady – Huffington Post
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