Category Archives: Microbes in the News

December 12, 2014

Posted on by

Human oral microbiome

Periodontal microbiology in Latin America – Adolfo Contreras – Periodontology 2000

Current perspective of the impact of smoking on the progression and treatment of periodontitis – Francisco H. Nociti Jr – Periodontology 2000

Effect of periodontal treatment on preterm birth rate: a systematic review of meta-analyses – Néstor J. López, Sergio Uribe and Benjamín Martinez – Periodontology 2000

Pregnancy and birth

* The Infant Microbiome Development: Mom Matters – Noel T. Mueller – Trends in Molecular Medicine

(see also above) Effect of periodontal treatment on preterm birth rate: a systematic review of meta-analyses – Néstor J. López, Sergio Uribe and Benjamín Martinez – Periodontology 2000

Pre- and probiotics, functional foods

Repeated cooking and freezing of whole wheat flour increases resistant starch with beneficial impacts on in vitro fecal fermentation properties – Jennifer A. Arcila, Devin J. Rose – Journal of Functional Foods

Potential of cereal grains and grain legumes in modulating pigs’ intestinal microbiota – A review – Tobias Aumiller – Livestock Science

Significance of Inulin Fructans in the Human Diet – Gertjan Schaafsma and Joanne L. Slavin – Comprehensive Reviews in Food Science and Food Safety

Effects of targeted delivery of propionate to the human colon on appetite regulation, body weight maintenance and adiposity in overweight adults – Edward S Chambers – Gut

Animal models

P47 – A dietary-driven redox modulation of gut microbiome-host interactions: the rescue of epithelial barrier and mucus production during dysbiosis by dietary nitrate – Bárbara Rocha – Free Radical Biology and Medicine

Dietary Pectin–Derived Acidic Oligosaccharides Improve the Pulmonary Bacterial Clearance of Pseudomonas aeruginosa Lung Infection in Mice by Modulating Intestinal Microbiota and Immunity – Henry Bernard – The Journal of Infectious Diseases

Soil microbiome

Response of autochthonous microbiota of diesel polluted soils to land-farming treatments – Gloria Andrea Silva-Castro – Environmental Research

Are there links between responses of soil microbes and ecosystem functioning to elevated CO2, N deposition and warming? A global perspective – Pablo García-Palacios – Global Change Biology

Experimental evaluation of CO2 percolation effects on subsurface soil microbiota –
Patricia Österreicher-Cunha – International Journal of Greenhouse Gas Control

Water microbiome

In situ grazing experiments apply new technology to gain insights into deep-sea microbial food webs – Maria G. Pachiadaki – Deep Sea Research Part II: Topical Studies in Oceanography

Metabolomics

Microbial Urease in Health and Disease – Diego Mora, Stefania Arioli – PLOS Pathogens

Bioinformatics

“Bioinformatics: Introduction and Methods,” a Bilingual Massive Open Online Course (MOOC) as a New Example for Global Bioinformatics Education – Yang Ding – PLOS Computational Biology

Techniques
Effect of Two Different Commercial DNA Extraction Kits on the Bacterial 16S rRNA gene Denaturing Gradient Gel Electrophoresis Profile of Arabian Gelding Feces – Megan L. Shepherd – Journal of Equine Veterinary Science

More microbiology papers

mBio Addresses the Pause in Gain-of-Function (GOF) Experiments Involving Pathogens with Pandemic Potential (PPP) – Arturo Casadevall – mBio

The battle for iron – Andrew E. Armitage, Hal Drakesmith – Science

Bacteriophage exclusion, a new defense system – Rodolphe Barrangou and John van der Oost – The EMBO Journal

Microbes in the news

Poo And You: A Journey Into The Guts Of A Microbiome – Katherine Harmon Courage – NPR Health

The Gut and Arthritis: The Evidence Grows – Nancy Walsh and Diana Swift – MedPageToday

Gross! Apparently Your Bacteria Is What Makes or Breaks a Relationship? – Zahra Barnes – Glamour.com (who knew?)

A Powder Made From Bacteria Waste Could Curb Overeating – Sarah Zhang – Gizmodo

Science, publishing, career

Scientific Elevator Pitches: A number of competitions around the world are challenging young scientists to describe their research in mere minutes – Rina Shaikh-Lesko – The Scientist

More science doctorates, fewer postdoctorate science jobs – Beryl Lieff Benderly – Science Careers

Making science a desirable career – Jessica K. Polka, Kristin A. Krukenberg – Science Magazine

Tips for Talking to Politicians: Members of an American Society for Cell Biology panel urge their colleagues to consider science advocacy – Tracy Vence – The Scientist

What Should High School Students Learn About Science? – Ria Misra – Space io9

Faculty member leads development of webinars that improve science education – Samantha Schwartz – PennState News

In defamation case, PubPeer moves to quash subpoena to unmask anonymous commenters – Kelly Servick – Science Magazine

Scientific American’s Top 10 Science Stories of 2014 – Scientific American

Bik’s Picks

Why whale poo matters – George Monbiot – The Guardian

Introduction to special Science Issue on bird genomes: A flock of genomes – Guojie Zhang – Science

The Darwin Awards: sex differences in idiotic behaviour – Ben Alexander Daniel Lendrem – British Medical Journal

[hr]

December 11, 2014

Posted on by

The Bay Area is getting drenched with rain right now, and several leaks in our roof kept me busy with buckets and towels, but the power is still on, so here we go:

Human microbiome general

* Review: The demographic determinants of human microbiome health – Sylvie Estrela – Trends in Microbiology

Human oral microbiome

Salivary Mucins Protect Surfaces from Colonization by Cariogenic Bacteria – Erica Shapiro Frenkel – Applied and Environmental Microbiology

Human gut microbiome

* Effects of the gut microbiota on bone mass – Claes Ohlsson, Klara Sjögren – Trends in Endocrinology & Metabolism

Discovery of a Conjugative Megaplasmid in Bifidobacterium breve – Francesca Bottacini – Applied and Environmental Microbiology

Microbiome of pregnancy and birth

Microbiome of the placenta in pre-eclampsia supports the role of bacteria in the multifactorial cause of pre-eclampsia – Ranmalee Amarasekara – Journal of Obstetrics and Gynaecology Research
Animal and bioreactor models

Optimization of a rapid and efficient analytical pipeline for in-depth metaproteome characterization: evaluation on mock microbial mixtures and application to the mouse gut microbiome – Alessandro Tanca – Microbiome

* Microbial shifts in the aging mouse gut – Morgan GI Langille – Microbiome

Development of human colonic microbiota in the computer-controlled dynamic SIMulator of the GastroIntestinal tract SIMGI – Elvira Barroso – LWT – Food Science and Technology

Protocols for Microcosms for Growing Biofilms on Hydrophobic Substrates: A Polyphasic Approach to Study Biodiversity, Metabolic Activity, and Biofilm Architecture – Wolf-Rainer Abraham – Springer Protocols Handbooks 2014

Animal microbiome

Acidobacteria appear to dominate the microbiome of two sympatric Caribbean Sponges and one Zoanthid – Aileen O¿Connor-Sánchez – Biological Research

Plant microbiome

The impact of systemic and copper pesticide applications on the phyllosphere microflora of tomatoes – Andrea R Ottesen – Journal of the Science of Food and Agriculture

Soil and sediment microbiome

Linkages between the soil organic matter fractions and the microbial metabolic functional diversity within a broad-leaved Korean pine forest – Jing Tian – European Journal of Soil Biology

Carbon sequestration is related to mycorrhizal fungal community shifts during long-term succession in boreal forests – Karina E. Clemmensen – New Phytologist

Comparison of bacterial succession in green waste composts amended with inorganic fertiliser and wastewater treatment plant sludge – Sean Storey – Bioresource Technology

Water microbiome

Initial community and environment determine the response of bacterial communities to dispersant and oil contamination – Alice C. Ortmann – Marine Pollution Bulletin

Initial community and environment determine the response of bacterial communities to dispersant and oil contamination – Alice C. Ortmann, YueHan Lu – Marine Pollution Bulletin

Protistan diversity in a permanently stratified meromictic lake (Lake Alatsee, SW Germany) – Andreas Oikonomou – Environmental Microbiology

Exploration of Microbial Diversity of Taptapani (India) Hot Spring Through Molecular Phylogenetic Analysis – Sudip Kumar Sen – Arabian Journal for Science and Engineering

Food microbiology

Selection of Autochthonous Strains as Starter Cultures for Fermented Fish Products – Barbara Speranza – Journal of Food Science

Microbes in the news

Pregnancy Germs: Friend Or Foe? – How The Maternal Microbiome Influences Pregnancy Health – PR NewsWire / March of Dimes

Study Hints Gut Microbiome Plays A Role in Multiple Sclerosis –
Kate O’Rourke – Gastroenterology and Endoscopy News

“The Great Plate Count Anomaly” that is no more – Gemma Reguera – Small Things Considered ASM

Google Science Fair – Bacteria boosting cereal crop yields – Brett Worthington – ABC Net Australia

Guts of obese dogs look similar to those of obese people – Agata Blaszczak-Boxe – Science Magazine

Baby infected in birthing pool died of Legionnaire’s disease – Bahar Gholipour – CBS News

Science, publishing, and career

Scientists Often Skip A Simple Test That Could Verify Their Work – NPR Morning Edition

Study of massive preprint archive hints at the geography of plagiarism – John Bohannon – Science Insider

Bik’s Picks

Deep Neural Networks are Easily Fooled: High Confidence Predictions for Unrecognizable Images – Anh Nguyen – Arxiv

Three-in-one drug cuts body weight by a third – Nsikan Akpan – Science Magazine

Water vapor on Rosetta’s target comet significantly different from that found on Earth – Science Daily

[hr]

December 10, 2014

Posted on by

Food microbiome

The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types – Jenna M. Lang – PeerJ

Human oral microbiome

Subgingival microbial profiles of Sudanese patients with aggressive periodontitis – H. R. Z. Elabdeen – Journal of Periodontal Research

Human bladder microbiome

Interplay between Bladder Microbiota and Urinary Antimicrobial Peptides: Mechanisms for Human Urinary Tract Infection Risk and Symptom Severity – Vanessa Nienhouse – PLOS ONE

Human gut microbiome

Immunomodulatory Properties of Streptococcus and Veillonella Isolates from the Human Small Intestine Microbiota – Bartholomeus van den Bogert – PLOS ONE

Animal models of microbiome research

The Gut Commensal Bacteroides thetaiotaomicron Exacerbates Enteric Infection through Modification of the Metabolic Landscape – Meredith M. Curtis – Cell Host & Microbe

Gut Microbiota-Produced Succinate Promotes C. difficile Infection after Antibiotic Treatment or Motility Disturbance – Jessica A. Ferreyra – Cell Host & Microbe

Regionally Distinct Alterations in the Composition of the Gut Microbiota in Rats with Streptozotocin-Induced Diabetes – Roland Wirth – PLOS ONE

Animal microbiome

Environmentally Determined Differences in the Murine Lung Microbiota and Their Relation to Alveolar Architecture – Yeojun Yun – PLOS ONE

Bacteria and Methanogens Differ along the Gastrointestinal Tract of Chinese Roe Deer (Capreolus pygargus) – Zhipeng Li – PLOS ONE

Transcriptomic Immune Response of the Cotton Stainer Dysdercus fasciatus to Experimental Elimination of Vitamin-Supplementing Intestinal Symbionts – Eugen Bauer – PLOS ONE

Metabolomics

Stool Phospholipid Signature is Altered by Diet and Tumors – Julie M. Davies – PLOS ONE

Pathogens’ Exploitation of the Intestinal Food Web
Tu Anh Pham N., Trevor D. Lawley – Cell Host & Microbe

Could resistant starch be the redeemer of dietary carbohydrate? – M Denise Robertson – Practical Diabetes

A New Insight into the Physiological Role of Bile Salt Hydrolase among Intestinal Bacteria from the Genus Bifidobacterium – Piotr Jarocki – PLOS ONE

Metagenomics

Maths on microbes: adding microbial ecophysiology to metagenomics – Wilfred F. M. Röling – Microbial Biotechnology

Functional optimization of gene clusters by combinatorial design and assembly – Michael J Smanski – Nature Biotechnology

More microbiology

Microbiology: Ditch the term pathogen – Arturo Casadevall & Liise-anne Pirofski – Nature

New sequencing technique: MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island – Philip M Ashton – Nature Biotechnology

Microbes in the news

NASA ISS On-Orbit Status 5 December 2014: Microbiome Experiment – SpaceRef

Bacteria’s Game of ‘Telephone’ Foils Microbiologists’ Eavesdropping – Kim Krieger – UConnToday

Science, publishing, career

The Point When Science Becomes Publicity – James Hamblin – The Atlantic

No Lovin’ Feeling… for Science Fair – Claire Wapole – Huffington Post

How to cope when things go wrong in academia – Julie Gould – Nature Jobs

Scientific Peer Review Is Broken. We’re Fighting to Fix It With Anonymity – The Founders of PubPeer – Wired.com

Not sure how old this is, but I liked the graph: The illustrated guide to a Ph.D. – Matt Might

Ocean biology: Marine dreams – Chris Woolston – Nature

New postdoc report covers familiar ground – Beryl Lieff Benderly, Jim Austin – Science Careers

Bik’s Picks

Injectable 3-D vaccines could fight cancer, infectious diseases – ScienceDaily

Glittering Nobel Gown Represents Scientist’s Work – Joanne Manaster – Scientific American

This Commuter Bus Runs On Poop- A U.K.-based biogas plant has developed a 40-seater than runs on converted sewage and food waste – Corinne Iozzio – Smithsonian

[hr]

December 9, 2014

Posted on by

Human oral microbiome

* Characterization and comparison of bacterial communities in benign vocal fold lesions – Alissa S Hanshew – Microbiome

Bacterial invasion and persistence: critical events in the pathogenesis of periodontitis? – S. Ji – Journal of Periodontal Research

Human skin microbiome

This took two years to publish, but here it is: Meeting report for the 1st skin microbiota workshop, Boulder, CO October 15-16 2012 – Jack A Gilbert – Standards in Genomic Sciences

Human respiratory microbiome

Assessment of Airway Microbiota and Inflammation in Cystic Fibrosis Using Multiple Sampling Methods – Edith T. Zemanick – Annals of the American Thoracic Society

Human gut microbiome

* Stability of Gut Enterotypes in Korean Monozygotic Twins and Their Association with Biomarkers and Diet – Mi Young Lim – Scientific Reports

* Microbiota organization is a distinct feature of proximal colorectal cancers – Christine M. Dejea – PNAS USA

Review: Crosstalk between intestinal microbiota, adipose tissue and skeletal muscle as an early event in systemic low-grade inflammation and the development of obesity and diabetes – Christian Bleau – Diabetes/Metabolism Research and Reviews

Pathophysiological responses from human gut microbiome – Anindya Roy Chowdhury, Utpal Bakshi – World Journal of Translational Medicine

Animal models of microbiome research

Microbiome-metabolome analysis reveals unhealthy alterations in the composition and metabolism of ruminal microbiota with increasing dietary grain in a goat model – Sheng-yong Mao – Environmental Microbiology

Animal microbiome

Carpoglyphus lactis (Acari: Astigmata) from various dried fruits differed in associated microorganisms – Jan Hubert – Journal of Applied Microbiology

Bacterial dynamics within the mucus, tissue and skeleton of the coral Porites lutea during different seasons – Jie Li – Scientific Reports

 

Investigation of biotechnological potential of sponge-associated bacteria collected in Brazilian coast – O.C.S. Santos – Letters in Applied Microbiology

Plant microbiome

* Removal of floral microbiota reduces floral terpene emissions – Josep Peñuelas – Scientific Reports

Contrasting diversity of epibiotic bacteria and surrounding bacterioplankton of a common submerged macrophyte, Potamogeton crispus, in freshwater lakes – Dan He – FEMS Microbiology Ecology

Review: Sphagnum physiology in the context of changing climate: emergent influences of genomics, modelling and host–microbiome interactions on understanding ecosystem function – David J. Weston – Plant, Cell & Environment

Book: Principles of Plant-Microbe Interactions – Springer

Soil and sediment microbiome

Anthropogenic land use shapes the composition and phylogenetic structure of soil arbuscular mycorrhizal fungal communities – Mari Moora – FEMS Microbiology Ecology

Halophyte plant colonization as a driver of the composition of bacterial communities in salt marshes chronically exposed to oil hydrocarbons – Vanessa Oliveira – FEMS Microbiology Ecology

Changes in microbial communities in coastal sediments along natural CO2 gradients at a volcanic vent in Papua New Guinea – Felix F. Raulf – Environmental Microbiology

Nitrogen Cycling Processes and Microbial Community Composition in Bed Sediments in the Yukon River at Pilot Station – Deborah A. Repert – Journal of Geophysical Research: Biogeosciences

Soil bacterial and fungal communities respond differently to various isothiocyanates added for biofumigation – Ping Hu – Frontiers in Microbiology

Primary succession of soil enzyme activity and heterotrophic microbial communities along the chronosequence of Tianshan Mountains No. 1 Glacier, China – Jun Zeng – Antonie van Leeuwenhoek

Water microbiome

Off-site impacts of agricultural composting: role of terrestrially derived organic matter in structuring aquatic microbial communities and their metabolic potential – Thomas Pommier – FEMS Microbiology Ecology

Microbiome of the built environment

* Diversity of Bacterial Communities of Fitness Center Surfaces in a U.S. Metropolitan Area – Nabanita Mukherjee – International Journal of Environmental Research and Public Health

Food microbiology

Potentially probiotic acetic acid bacteria isolation and identification from traditional dairies microbiota – Babak Haghshenas – International Journal of Food Science & Technology

Metagenomics

Microbial community pattern detection in human body habitats via ensemble clustering framework – Peng Yang – BMC Systems Biology

Proteomics and metabolomics

Insights on the human microbiome and its xenobiotic metabolism: what is known about its effects on human physiology? – Tewes Tralau – Expert Opinion on Drug Metabolism & Toxicology

Proteomic tools to decipher microbial community structure and functioning – Florence Arsène-Ploetze – Environmental Science and Pollution Research

Systems-based approaches to unravel multi-species microbial community functioning – Florence Abram – Computational and Structural Biotechnology Journal

Amplification and other techniques

* Multi-template polymerase chain reaction – Elena Kalle – Biomolecular Detection and Quantification

Microfluidic static droplet array for analyzing microbial communication on a population gradient – Heon-Ho Jeong – Lab Chip

More microbiology papers

* Gain-of-function experiments: time for a real debate – W. Paul Duprex (with David Relman) – Nature Reviews Microbiology

Ciprofloxacin mechanism: Emergence of antibiotic resistance from multinucleated bacterial filaments – Julia Bos – PNAS USA

Microbes in the news

The fragrance of flowers depends on the fungi and bacteria that coated – Beta Wired

The Human Microbiome: Getting Personal – Katy Califf – ASM Microbe

Science, publishing, career

Scientists Are Not That Smart – Chad Orzel – New York Magazine

io9 Science Survey: Tell Us About Working With Rodents in the Lab – Annalee Newitz – io9

Best Way for Professors to Get Good Student Evaluations? Be Male – Amanda Marcotte – Slate

Bik’s Picks

Unfortunately sold out, but really cute: DNA Molecule Plush – ThinkGeek

The birth of a dinosaur footprint: Subsurface 3D motion reconstruction and discrete element simulation reveal track ontogeny (with movies) – Peter L. Falkingham – PNAS USA

Billionaire’s New Science Institute Plans “Google Maps” View of Cells – Joshn Fischman – Scientific American

Expanded DNA alphabet wins Science award – Bradley J. Fikes – UT San Diego

[hr]

Microbiome digest, December 8, 2014

Posted on by

Human microbiome general

The human microbiome: opportunities and challenges for clinical care – Geraint B. Rogers – Internal Medicine Journal

Evaluative Profiling of Arsenic Sensing and Regulatory Systems in the Human Microbiome Project Genomes – Raphael D Isokpehi – Microbiology Insights

Human oral microbiome

* High resolution taxonomic profiling of the subgingival microbiome for biomarker discovery and periodontitis diagnosis – Szymon P. Szafranski – Applied and Environmental Microbiology

Human gut microbiome

Crosstalk at the mucosal border: importance of the gut microenvironment in IBS – Lena Öhman – Nature Reviews Gastroenterology & Hepatology

Antimicrobial resistance characteristics and fitness of Gram negative faecal bacteria from volunteers treated with minocycline or amoxicillin – Miranda Kirchner – Frontiers in Microbiology

Decrease in lactobacilli in the intestinal microbiota of celiac children with a gluten-free diet, and selection of potentially probiotic strains – María J. Lorenzo Pisarello – Canadian Journal of Microbiology

Safety assessment of genetically modified rice expressing human serum albumin from urine metabonomics and fecal bacterial profile – Xiaozhe Qi – Food and Chemical Toxicology

Pregnancy and birth microbiome

Placental Microbiome and Its Role in Preterm Birth – Bin Cao – NeoReviews

High A. vaginae and G. vaginalis vaginal loads are associated with preterm birth – Florence Bretelle – Clinical Infectious Diseases

Cesarean Section and Chronic Immune Disorders – Astrid Sevelsted – Pediatrics

Animal and other models of microbiome research

Intestinal epithelial ​MyD88 is a sensor switching host metabolism towards obesity according to nutritional status – Amandine Everard – Nature Communications

Bugs and Food: A Recipe for Cancer? – Christina L. Ohland, Christian Jobin – Cell Metabolism

The current provided by oxygen-reducing microbial cathodes is related to the composition of their bacterial community – Mickaël Rimboud – Bioelectrochemistry

Animal microbiome

The putative functional ecology and distribution of archaeal communities in sponges, sediment and seawater in a coral reef environment – Ana R.M. Polónia – Molecular Ecology

Plant microbiome

* The role of bacteria and mycorrhiza in plant sulfur supply – Jacinta M. Gahan and Achim Schmalenberger – Frontiers in Plant Science

Arctic fungal communities associated with roots of Bistorta vivipara do not respond to the same fine-scale edaphic gradients as the aboveground vegetation – Sunil Mundra – New Phytologist

Soil and sediment microbiome

Impacts of altered precipitation regimes on soil communities and biogeochemistry in arid and semi-arid ecosystems – Uffe N. Nielsen – Global Change Biology

* Effects of tree identity dominate over tree diversity on the soil microbial community structure – Andrea Scheibe – Soil Biology and Biochemistry

Smooth brome invasion increases rare soil bacterial species prevalence, bacterial species richness and evenness – Candace L. Piper – Journal of Ecology

The interactive effects of elevated ozone and wheat cultivars on soil microbial community composition and metabolic diversity – Xuelian Bao – Applied Soil Ecology

Seasonal variations of the composition of microbial biofilms in sandy tidal flats: Focus of fatty acids, pigments and exopolymers – Claire Passarelli – Estuarine, Coastal and Shelf Science

Pharmaceuticals in the environment: Biodegradation and effects on natural microbial communities. A Review – Anna Barra Caracciolo – Journal of Pharmaceutical and Biomedical Analysis

Water microbiome

Successional Change in Microbial Communities of Benthic Phormidium-Dominated Biofilms – Katie A. Brasell – Microbial Ecology

Microbiome of the built environment

Characterizing airborne fungal and bacterial concentrations and emission rates in six occupied children’s classrooms – D. Hospodsky – Indoor Air

Food microbiology

Analysis of the bacterial community in aged and aging pit mud of Chinese Luzhou-flavour liquor by combined PCR-DGGE and quantitative PCR assay – Huipeng Liang – Journal of the Science of Food and Agriculture

Phages and viruses

Emerging methods to study bacteriophage infection at the single-cell level – Vinh T. Dang and Matthew B. Sullivan – Frontiers in Microbiology

Metabolomics

* The Community Ecology of Microbial Molecules – Robert A. Quinn, Theodore Alexandrov – Journal of Chemical Ecology

Ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry for rapid analysis of the metabolites of morroniside produced by human intestinal bacteria – Min Zhao – Journal of Chromatography B

Small-intestinal or colonic microbiota as a potential amino acid source in animals – Werner G. Bergen – Amino Acids

Techniques

Comparative assessment of next-generation sequencing, denaturing gradient gel electrophoresis, clonal restriction fragment length polymorphism and cloning-sequencing as methods for characterizing commercial microbial consortia – A.D. Samarajeewa – Journal of Microbiological Methods

Microbes in the news

Now We Know Some Creepy Things About How Penicillin Destroys Bacteria – Esther Inglis-Arkell – IO9

Arctic bacteria converts mercury – Kristian Sjøgren – ScienceNordic

Should I Eat Greek Yogurt? – Mandy Oaklander – Time

CSU team examines dairy-cattle microorganisms to improve food safety – Kristen Browning-Blas – Bovine Vet Online

Glyphosate used with GMO crops under attack for disrupting microbiome: Science or a gut feeling? – David Warmflash – Genetic Literacy Project

#BacteriaHysteria: Why it’s time to detox your desk: Average worker comes into contact with more than 10 MILLION disease-causing bacteria lurking on their keyboard, phone and mouse – Lizzie Parry – Daily Mail

Bik’s Picks

The Yearbook: Our list of newsmakers this year – Manasi Vaidya & Shraddha Chakradhar – Nature Medicine

Notable advances 2014 – Amanda Keener – Nature Medicine

Let’s face it, for robots, falling down is easy. But how do you teach them to land safely? – Maki Naro – Popular Science

Force-feeding a human to a snake is not science (and is also super dumb) – Rachel Feltman – Washington Post

[hr]

Microbiome Digest, December 5, 2014

Posted on by

Human oral microbiome

* Noma Affected Children from Niger Have Distinct Oral Microbial Communities Based on High-Throughput Sequencing of 16S rRNA Gene Fragments – Katrine L. Whiteson – PLOS Neglected Tropical Diseases

* Ancient DNA analysis of dental calculus – Laura S. Weyrich – Journal of Human Evolution

Human gut microbiome

* Gut microbiota are related to Parkinson’s disease and clinical phenotype – Filip Scheperjans – Movement Disorders

The role of the microbiome in immune cell development – Nita H. Salzman – Annals of Allergy, Asthma & Immunology

Ezakiella peruensis gen. nov., sp. nov. isolated from human fecal sample from a coastal traditional community in Peru – Nisha B. Patel – Anaerobe

Microbiome and Immunology

Microbial Programming of Systemic Innate Immunity and Resistance to Infection – Thomas B. Clarke – PLOS Pathogens

Animal models of microbiome research

* (see also Metabolomics) Diet and Feeding Pattern Affect the Diurnal Dynamics of the Gut Microbiome – Amir Zarrinpar – Cell Metabolism

Effects of cyclophosphamide on immune system and gut microbiota in mice – Xiaofei Xu, Xuewu Zhang – Microbiological Research

Gut microbiota and environment in patients with major burns – A preliminary report – Kentaro Shimizu – Burns

Animal microbiome

* The Feline Oral Microbiome: A Provisional 16S rRNA gene based Taxonomy with Full-length Reference Sequences – Floyd E. Dewhirst – Veterinary Microbiology

Diversity and health status specific fluctuations of intrauterine microbial communities in postpartum dairy cows – K. Wagener – Veerinary Microbiology

* Evidence of Polyethylene Biodegradation by Bacterial Strains from the Guts of Plastic-Eating Waxworms – Jun Yang – Environmental Science & Technology

Metabolomics

* Diet and Feeding Pattern Affect the Diurnal Dynamics of the Gut Microbiome – Amir Zarrinpar – Cell Metabolism

A Systematic Computational Analysis of Biosynthetic Gene Cluster Evolution: Lessons for Engineering Biosynthesis – Marnix H. Medema – PLOS Computational Biology

The Evolution of Fungal Metabolic Pathways – Jennifer H. Wisecaver – PLOS Genetics

The microbial degradation of onion flavonol glucosides and their roasting products by the human gut bacteria Eubacterium ramulus and Flavonifractor plautii – Katrin Ulbrich – Food Research International

Desulfovibrio desulfuricans isolates from the gut of a single individual: Structural and biological lipid a characterization – Wei Zhang-Sun – FEBS Letters

Metagenomics

Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies – James F. Denton – PLOS Computational Biology

Microbes in the news

A Worm’s Gut Could Help Dispose of Plastic Trash: Microbes found in the guts of waxworms like to feast on polyethylene – Rachel Nuwer – Smithsonian Magazine

Friendly bacteria are protective against malaria – MedicalXpress

Self-healing Concrete Vanishes Potholes Using Bacteria. Here’s How it Works – Jan Dizon – TechTimes

Wireless Implant Eliminates Bacteria, Then Dissolves – WND

Science, publishing and career

* Ten Simple Rules for Finishing Your PhD – Jacopo Marino – PLOS Computational Biology

Bik’s Picks

Amid Bugs, Hail, Floods and Bacteria, Italian Olives Take a Beating – Elisabetta Povoledo – New York Times

See it, touch it, feel it: Researchers use ultrasound to make invisible 3-D haptic shape that can be seen and felt – Science Daily

Satire: Breaking: James Watson Faked Winning A Nobel Prize – The Allium

[hr]

Microbiome digest, December 4, 2014

Posted on by

Human (gut and other) microbiome

* Temporal variability is a personalized feature of the human microbiome – Gilberto E Flores – Genome Biology

The rest of the story: the microbiome and gastrointestinal infections – Jhansi L Leslie, Vincent B Young – Current Opinion in Microbiology

* Gut Microbiota Elicits a Protective Immune Response against Malaria Transmission – Bahtiyar Yilmaz – Cell

Pregnancy and birth

The infant airway microbiome in health and disease impacts later asthma development –
Shu Mei Teo – BioRxiv

Animal models of microbiome research

Dietary Yeasts Reduce Inflammation in Central Nerve System via Microflora – Kazushiro Takata – Annals of Clinical and Translational Neurology

Effects of dietary supplementation of modified zinc oxide on growth performance, nutrient digestibility, blood profiles, fecal microbial shedding and fecal score in weanling pigs –

Jin Ho Cho – Animal Science Journal

Bioinformatics

ITScan: a web-based analysis tool for Internal Transcribed Spacer (ITS) sequences – Milene Ferro – BMC Research Notes

Next generation sequencing reads comparison with an alignment-free distance – Emanuel Weitschek – BMC Research Notes

Microbes in the news

Go Ahead, Use the Restroom – Nicholas Bakalar – New York Times

Trusting your gut, and the importance of your microbiome: Words on Wellness – Daniel Neides – Cleveland.com

Microbiome component fights malaria – Bradley J. Fikes – UT San Diego

Gut Microbes May Play a Role in AS – Diana Swift – MedPageToday

Science, publishing, and career

Getting Credit for Data – Eric Martens and Jennifer Lin – PLOS Blogs

What do young scientists want? – Beryl Lieff Benderly – Science Careers

Why Don’t More Minority Students Seek Careers In STEM Fields? – David Orenstein – RedOrbit

Bik’s Picks

Revealed: 100 safety breaches at UK labs handling potentially deadly diseases – Ian Sample – The Guardian

Why DNA pioneer James Watson just sold his Nobel Prize for $4.1 million – Susannah Locke – Vox.com

The Corrupting Power of Cancer – Lauren Richardson – PLOS Blogs

Is The Food Babe A Fearmonger? Scientists Are Speaking Out – Maria Godoy – NPR The Salt

[hr]

Microbiome digest, December 2, 2014

Posted on by

General microbiome

Microbiome, holobiont and the net of life – Emiliano Salvucci – Critical Reviews in Microbiology

Pregnancy and birth

Infectious Causes of Necrotizing Enterocolitis – Sarah A. Coggins – Clinics in Perinatology

Human oral microbiome

Solving the etiology of dental caries – Aurea Simón-Soro, Alex Mira – Trends in Microbiology

Oral Microbiota in Crevices Around Dental Implants: Profiling of Oral Biofilm – Takuichi Sato – Interface Oral Health Science

Human respiratory microbiome

* Temporal profiling of the bacterial and fungal communities in ΔF508 adult cystic fibrosis sputum – Andrew Nelson – PeerJ Preprint

Human gut microbiome

* Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production – Gary D Wu – Gut

Microbiome of death

* Initial insights into bacterial succession during human decomposition – Embriette R. Hyde – International Journal of Legal Medicine

Animal and other models of microbiome research

Natural killer T cells play a necessary role in modulating of immune-mediated liver injury by gut microbiota – Jianing Chen – Scientific Reports

Effect of stoned olive pomace on rumen microbial communities and polyunsaturated fatty acids biohydrogenation: an in vitro study – Grazia Pallara – BMC Veterinary Research

Successional changes in the chicken cecal microbiome during 42 days of growth are independent of organic acid feed additives – Brian B Oakley – BMC Veterinary Research

Animal microbiome

The role of host phylogeny varies in shaping microbial diversity in the hindguts of lower termites – Vera Tai – Applied and Environmental Microbiology

Plant microbiome

Relocation, high-latitude warming and host genetic identity shape the foliar fungal microbiome of poplars – Miklós Bálint – Molecular Ecology

Soil and sediment microbiome

Distribution of sediment bacterial and archaeal communities in plateau freshwater lakes – Jingxu Zhang – Applied Microbiology and Biotechnology

Effects of Phragmites invasion on soil microbial activity and structure in a brackish marsh – Keunyea Song – Plant and Soil

Water microbiome

* High temporal and spatial diversity in marine RNA viruses implies that they have an important role in mortality and structuring plankton communities – Julia A. Gustavsen – Frontiers in Microbiology

Impact of atmospheric deposition on the metabolism of coastal microbial communities

Sandra Martínez-García – Estuarine, Coastal and Shelf Science

Assessment of Bacterial and Archaeal Community Structure in Swine Wastewater Treatment Processes – Marcio Luis Busi Da Silva – Microbial Ecology

Food microbiology

Evaluation of microbial diversity in the pilot-scale beer brewing process by culture-dependent and culture-independent method – Masayuki Takahashi- Journal of Applied Microbiology

Pre- and probiotics

Recent developments in prebiotics to selectively impact beneficial microbes and promote intestinal health – Robert A. Rastall , Glenn R. Gibson – Current Opinion in Biotechnology

* The domestication of the probiotic bacterium Lactobacillus acidophilus – Matthew J. Bull – Scientific Reports

Microbes in the news

Mining industry could benefit from Wheatbelt discovery of salt and acid tolerant bacteria – Lucinda Jose – ABC Australia

Science, publishing, and career

The never-ending Ph.D. – By Adam Ruben – Science Careers

Clueless Reporter from the Mirror Bases Story on Withdrawn OMICS Publishing Group Article – Jeffrey Beall – ScholaryOA

The Next Enlightenment: Sharing Science With the World – Marietta DiChristina – Huffington Post

Bik’s Picks

Actor Alan Alda Challenges Scientists to Explain ‘What is Sleep?’ – Laura Geggel – LiveScience

Ability to consume alcohol may have shaped primate evolution – Sarah C. P. Williams – Science News

#Shirtgate inspires a Kickstarter for shirts covered in (science) ladies – Rachel Feltman – Washington Post

[hr]

Microbiome digest, November 28, 2014

Posted on by

Human gut microbiome

Effects of Surgical and Dietary Weight Loss Therapy for Obesity on Gut Microbiota Composition and Nutrient Absorption – Antje Damms-Machado – BioMed Research International

Collateral damage from oral ciprofloxacin versus nitrofurantoin in outpatients with urinary tract infections: a culture-free analysis of gut microbiota – Andrew J. Stewardson – Clinical Microbiology and Infection

Potential of fecal microbiota for early-stage detection of colorectal cancer – Georg Zeller – Molecular Systems Biology

Does the microbiota play a role in the pathogenesis of autoimmune diseases? – Mairi H McLean – Gut

The gut microbiota and inflammatory bowel disease – Katsuyoshi Matsuoka and Takanori Kanai – Seminars in Immunopathology

Metagenomic analysis of the gastric microbiota cultivable from a patient 

with gastritis concomitant with Barrett’s esophagus – Andrés Julián Gutiérrez-Escobar – Rev Gastroenterol Peru

Gut microbiota in patients with type 2 diabetes mellitus – Kristine H Allin – European Journal of Endocrinology

Gut brain axis: diet microbiota interactions and implications for modulation of anxiety and depression – Ruth Ann Luna, Jane A Foster

Behçet’s syndrome patients exhibit specific microbiome signature – Clarissa Consolandi – Autoimmunity Reviews

Animal microbiome

Complete genome sequence and comparative genome analysis of Klebsiella oxytoca HKOPL1 isolated from giant panda feces – Jingwei Jiang – BMC Research Notes

Few highly abundant operational taxonomic units dominate within rumen methanogenic archaeal species in New Zealand sheep and cattle – Henning Seedorf – Applied and Environmental Microbiology

Chironomid Microbiome – Malka Halpern, Yigal Senderovich – Microbial Ecology

Plant microbiome

Understanding and engineering beneficial plant–microbe interactions: plant growth promotion in energy crops – Kerrie Farrar – Plant Biotechnology Journal

Soil and sludge microbiome

Global diversity and geography of soil fungi – Leho Tedersoo – Science

Effects of the Biocontrol Agent Aspergillus flavipes on the Soil Microflora and Soil Enzymes in the Rooting Zone of Pepper Plants Infected with Phytophthora capsici – Hui Wang – Journal of Phytopathology

Plant diversity predicts beta but not alpha diversity of soil microbes across grasslands worldwide – Suzanne M. Prober – Ecology Letters

Soil chemical properties affect the reaction of forest soil bacteria to drought and rewetting stress – Marcin Chodak – Annals of Microbiology

Cyanobacteria and algae of buried soils and their modern analogues – A. D. Temraleeva – Paleontological Journal

Diversity and efficiency of anthracene-degrading bacteria isolated from a denitrifying activated sludge system treating municipal wastewater – Spyridon Ntougias – International Biodeterioration & Biodegradation

Water microbiome

Profile of bacterial communities in South African mine-water samples using Illumina next-generation sequencing platform – Jitendra Keshri – Applied Microbiology and Biotechnology

Temporal and Vertical Distribution of Bacterioplankton at the Gray’s Reef National Marine Sanctuary – Xinxin Lu – Applied and Environmental Microbiology

Identification of Microorganisms in Hydrocarbon-Contaminated Aquifer Samples by Fluorescence In Situ Hybridization (CARD-FISH) – Schattenhofer Martha – Springer Protocols Handbooks

Food microbiology

Influence of pig rennet on proteolysis, organic acids content and microbiota of Pecorino di Farindola, a traditional Italian ewe’s raw milk cheese – Tofalo Rosanna – Food Chemistry

Bioinformatics

Alternative for USEARCH: VSEARCH: Open and free 64-bit multithreaded tool for processing metagenomic sequences, including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling – Github

svaseq: removing batch effects and other unwanted noise from sequencing data – Jeffrey T. Leek – Nucleic Acids Research

Phages and viruses

Automated classification of tailed bacteriophages according to their neck organization – Anne Lopes – BMC Genomics

Metabolomics

Metabolic fate of neutral human milk oligosaccharides in exclusively breast-fed infants –
Viktoria Dotz – Molecular Nutrition & Food Research
http://onlinelibrary.wiley.com/doi/10.1002/mnfr.201400160/abstract

Transcriptomics

Transcriptome analysis reveals novel regulatory mechanisms in a genome-reduced bacterium – Pavel V. Mazin – Nucleic Acids Research

More microbiology

In vivo treatment of Helicobacter pylori infection with liposomal linolenic acid reduces colonization and ameliorates inflammation – Soracha Thamphiwatana – PNAS USA

Microbes in the news

How bacteria in your gut could be making you fat, allergic, or anxious – Susannah Locke – Vox

Interview with Dan Knights: UMN professor solves problems from ‘gut bugs’ to Rubik’s Cube – Richard Chin – Twin Cities

Artificial Sweeteners May Have Despicable Impacts on Gut Microbes – Sheena Faherty – Scientific American

The Human Microbiome, An Issue of Clinics in Laboratory Medicine – Google eBook

Science and art

It’s a microbial world – protozoa pancakes

Bik’s Picks

Detection of fraudulent addition of bovine whey in Ricotta cheese by iso-electric focusing
– Fabio Fuselli – Journal of Science of Food and Agriculture

DNA survives critical entry into Earth’s atmosphere – Science Daily

Bill Nye: ‘Science is true, whether or not you believe it’ – Brad Wheeler – The Globe and Mail

The Best Gifts of 2014 for Science Geeks – Smithsonian.com

[hr]

Microbiome digest, November 26

Posted on by

Happy Thanksgiving, everyone! A big thanks to all my readers, and please share this blog with others. The more readers, the better.

December 8th (4pm GMT): eLife Google Hangout on the link between gut bacteria and arthritis, featuring Stephen Baker, Rajat Rohatgi, and Curtis Huttenhower.

Human gut microbiome

* Maternal Obesity Is Associated with Alterations in the Gut Microbiome in Toddlers
Jeffrey D. Galley – PLOS ONE

Animal gut microbiome

Prevalence and Characterization of Escherichia coli and Salmonella Strains Isolated from Stray Dog and Coyote Feces in a Major Leafy Greens Production Region at the United States-Mexico Border – Michele T. Jay-Russell – PLOS ONE

Plant microbiome

Effects of a Ciliate Protozoa Predator on Microbial Communities in Pitcher Plant (Sarracenia purpurea) Leaves – Taylor K. Paisie – PLOS ONE

A Novel Interaction between Plant-Beneficial Rhizobacteria and Roots: Colonization Induces Corn Resistance against the Root Herbivore Diabrotica speciosa – Franciele Santos – PLOS ONE

* Towards the unification of sequence-based classification and sequence-based identification of host-associated microorganisms – Joshua R. Herr – New Phytologist

Soil microbiome

Belowground biodiversity and ecosystem functioning – Richard D. Bardgett & Wim H. van der Putten – Nature

* Printing soil: a single-step, high-throughput method to isolate micro-organisms and near-neighbour microbial consortia from a complex environmental sample – Bradley R. Ringeisen – Methods in Ecology and Evolution

Water microbiome

Integrating Bacterial and Viral Water Quality Assessment to Predict Swimming-Associated Illness at a Freshwater Beach: A Cohort Study – Jason W. Marion – PLOS ONE

Massive Regime Shifts and High Activity of Heterotrophic Bacteria in an Ice-Covered Lake – Mina Bižić-Ionescu – PLOS ONE

Metagenomics, microbial genomes

Transferred interbacterial antagonism genes augment eukaryotic innate immune function – Seemay Chou – Nature

Evolutionary Ecology of the Marine Roseobacter Clade – Haiwei Luo and Mary Ann Moran – Microbial and Molecular Biology Reviews

Microbes in the news

* This Forgotten Turkey Bacteria Could Lead to the Super-Antibiotic of the Future – Motherboard

* BacteriaHysteria – Turkeys raised with antibiotics could carry bacteria – 9News

* Tech Dudes Take Credit For Female Scientist’s Work; Plan To “Hack” Vaginas So They Smell Like Peaches – Carolyn Cox

* Bacteria central: how to stop your boxing gloves from stinking – MMA Kanvas

The Oral Microbiome: From Bad Bugs to Bad Biofilm Behaviors – NIH NIDCR

Are Human Breast Milk Microbiomes ‘neutral’? – Chinese Academy of Sciences

Vultures survive toxic diet with bacterial help – ABC.AU Science

Science, publishing, and career

* Open access is tiring out peer reviewers – Martijn Arns – Nature

* Publishing: The peer-review scam – Cat Ferguson, Adam Marcus& Ivan Oransky – Nature

* Academia gets social – Brian Owens – The Lancet

* The outsourcing and commercialization of science – Is the lab CEO the future of academic research? – David R Smith – EMBO Reports

* No women alas this year: Five Stanford professors named fellows of American Association for the Advancement of Science – Stanford News

Bik’s Picks – some cool non-microbiome science articles for your Thanksgiving break

The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima – Ariel D. Chipman – PLOS ONE

Identification of a Buried Cadaver Based on Finger Ridge Characteristics of a Hand Protected by a Latex Glove – Krzysztof Klemczak M.A. – Journal of Forensic Science

Polish ‘vampire’ burials weren’t just for outsiders – New Scientist

Satire: Investigator To Immediately Offer Job To Sender Of Unsolicited Email – The Allium

Recalculating: The Mind and the Map – Elizabeth Preston – The Atlantic

Science-Based Hacks For Making Your Thanksgiving Meal Perfect – Kevin Loria – BusinessInsider

[hr]