January 7, 2015

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Human skin microbiome

Commensal–dendritic-cell interaction specifies a unique protective skin immune signature – Shruti Naik – Nature

Human gut microbiome

Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism – Fiona Cuskin – Nature

Animal models of microbiome research

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile – Charlie G. Buffie – Nature

Animal microbiome

Antibiotics in ingested human blood affect the mosquito microbiota and capacity to transmit malaria – Mathilde Gendrin – Nature Communications

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

Plant-Plant-Microbe Mechanisms Involved in Soil-Borne Disease Suppression on a Maize and Pepper Intercropping System – Min Yang – PLOS ONE

Water microbiome

Adapt or Die on the Highway To Hell: Metagenomic Insights into Altered Genomes of Firmicutes from the Deep Biosphere – Brandon Briggs, Frederick Colwell – AGU Fall Meeting San Francisco

Biodiversity hot spot on a hot spot: novel extremophile diversity in Hawaiian fumaroles – Kate Wall – Microbiology Open

Bioinformatics

Binpairs: Utilization of Illumina Paired-End Information for Improving Efficiency of Taxonomic Binning of Metagenomic Sequences – Anirban Dutta – PLOS ONE

Probiotics

Isolation and Characterization of Faecalibacterium prausnitzii from Calves and Piglets – Carla Foditsch – PLOS ONE

Antibiotics

A new antibiotic kills pathogens without detectable resistance – Losee L. Ling – Nature

Phages and viruses

Impact of Spontaneous Prophage Induction on the Fitness of Bacterial Populations and Host-Microbe Interactions – Arun M. Nanda – Journal of Bacteriology

More microbes

The Rebirth of Culture in Microbiology through the Example of Culturomics To Study Human Gut Microbiota – Jean-Christophe Lagier – Clinical Microbiology Reviews

Current and Past Strategies for Bacterial Culture in Clinical Microbiology – Jean-Christophe Lagier – Clinical Microbiology Reviews

Microbes in the news

How bacteria control their size – Diana Lutz – Washington University in St. Louis

Nestlé Health Science Invests $65M in Microbiome Therapy Startup – Drug Discovery and Development
Deep bacteria may evolve even without passing genes on – Colin Barras – New Scientist

Enough with the cleaning – it’s time we stopped giving bacteria such a hard time – Emer Sexton – Irish Examiner

Skin microbes trigger specific immune responses – Science Daily

Beer, bread yeast-eating bacteria aid human health – Science Daily

Science, publishing, career

Outreach: Speak up for science – Virginia Gewin – Nature

Science at risk as young researchers increasingly denied research grants – Phys.org

Science, in the Words of Alan Alda – Jessica Lahey – The Atlantic

University or University of Life? Neither provides workers with necessary people skills – Science Daily

English Is the Language of Science. That’s lousy luck for scientists in most of the world – Boer Deng – Slate.com

Bik’s Picks

Forget the selfish gene: Evolution of life is driven by the selfish ribosome, research suggests – Science Daily

Search for the First True Alien Earth Heats Up – Mike Wall – Space.com

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January 6, 2015

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Human gut microbiome

The involvement of gut microbiota in inflammatory bowel disease pathogenesis: potential for therapy – Giovanni Cammarota – Pharmacology & Therapeutics

Studies on Modulation of Gut Microbiota by Wine Polyphenols: From Isolated Cultures to Omic Approaches – Montserrat Dueñas – Antioxidants

Human respiratory microbiome

Cost-effective pooling of DNA from nasopharyngeal swab samples for large-scale detection of bacteria by real-time PCR – Sophie Edouard – Journal of Clinical Microbiology

Animal models of microbiome research

Effects of dietary mono- and multiprobiotic strains on growth performance, gut bacteria and body composition of Javanese carp (Puntius gonionotus, Bleeker 1850) – S.K. Allameh – Aquaculture Nutrition

Animal microbiome

Harlequin ladybird: Detection and decay rates of prey and prey symbionts in the gut of a predator through metagenomics – Débora P. Paula – Molecular Ecology Resources

Protist microbiome

Cytologic and Genetic Characteristics of Endobiotic Bacteria and Kleptoplasts of Virgulinella fragilis (Foraminifera) – Masashi Tsuchiya – The Journal of Eukaryotic Microbiology

Plant microbiome

Synergists and antagonists in the rhizosphere modulate microbial communities and growth of Quercus robur L. – Fuensanta Caravaca – Soil Biology and Biochemistry

Soil microbiome

Examination of biotic and abiotic controls of soil bacterial diversity under perennial shrubs in xeric soils – Naama Berg – CATENA

Two Metagenomes from Late Pleistocene Northeast Siberian Permafrost – Kirill Krivushin – Genome Announcements

Extractable N and microbial community structure respond to grassland restoration regardless of historical context and soil composition – Sara Jo M. Dickens – AoB Plants

Methane dynamics in an alpine fen: A field based study on methanogenic and methanotrophic microbial communities – Alessandro G. Franchini – FEMS Microbiology Ecology

Microbial community composition and functions are resilient to metal pollution along two forest soil gradients – Hamed Azarbad – FEMS Microbial Ecology

Effect of biostimulation, temperature and salinity on respiration activities and bacterial community composition in an oil polluted desert soil – Raeid M.M. Abed – International Biodeterioration & Biodegradation

High-throughput sequencing shows inconsistent results with a microscope-based analysis of the soil prokaryotic community – Masayuki Ushio – Soil Biology and Biochemistry

Water microbiome

Oil-derived marine aggregates – hot spots of polysaccharide degradation by specialized bacterial communities – Carol Arnosti – Deep Sea Research Part II: Topical Studies in Oceanography

Bioreactor and wastewater microbiomes

Overall functional gene diversity of microbial communities in three full-scale activated sludge bioreactors – Yu Xia – Applied Microbiology and Biotechnology

Metatranscriptomic analysis of lignocellulolytic microbial communities involved in high-solids decomposition of rice straw – Christopher W Simmons – Biotechnology for Biofuels

Techniques

Protocols for Metagenomic Library Generation and Analysis in Petroleum Hydrocarbon Microbe Systems – Stephanie M. Moormann – Springer Protocols Handbooks 2014

Science, publishing and career

Assessing Research Productivity: A new way of evaluating academics’ research output using easily obtained data – Ushma S. Neill – The Scientist

How many scientific papers are not original? – Michael Lesk – PNAS USA

Know Your PIO: Scientists and public information officers share several common goals. Here’s how to collaborate effectively – Tracy Vence – The Scientist

Microbes in the news

Signs of mother’s diet, birth delivery mode in human milk microbiome – EA Quinn – Genetic Literacy Project

Celebrate your fat – it’s fighting off infection – Clare Wilson – New Scientist

Common cold really is triggered by chilly weather, Yale scientists find – Sarah Knapton – The Telegraph

Picturing Infection: whole-animal, light-based imaging of infected small mammals – Kelly Rae Chi – The Scientist

Bik’s Picks

New evidence on the origin of carnivorous plants – Thomas J. Givnish – PNAS USA

Inching toward the 3D genome – Elizabeth Pennisi – Science

Chopsticks or spoon: The impact of eating methods on eating rate and glycemic response in healthy adults – Lijuan Sun – Physiology & Behavior

Anti-Vaxxers Are Idolizing the Amish, Inexplicably – Olga Khazan – The Atlantic

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January 5, 2015

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Happy New Year!

Human oral microbiome

Salivaomics – David T.W. Wong – The Journal of the American Dental Association

Human respiratory microbiome

The Bergen COPD microbiome study (MicroCOPD): rationale, design, and initial experiences – Rune Grønseth – European Clinical Respiratory Journal

Human skin microbiome

Interactions between host factors and the skin microbiome – Adam SanMiguel, Elizabeth A. Grice – Cellular and Molecular Life Sciences

Molecular Characterization of the Skin Fungal Microbiota in Patients with Seborrheic Dermatitis – Akiomi Tanaka – Clinical & Experimental Dermatology Research

Human gut microbiome

Microbiota-Mediated Inflammation and Antimicrobial Defense in the Intestine – Silvia Caballero and Eric G. Pamer – Annual Review of Immunology

* Role of the intestinal microbiota and fecal transplantation in inflammatory bowel diseases – Jie Liang – Journal of Digestive Diseases

Special Issue: Faecal transplantation and infectious diseases practitioners – D. Raoult – Clinical Microbiology and Infection

Human Clostridium difficile infection: Inhibition of NHE3 and microbiota profile – Melinda A Engevik – American Journal of Physiology – Gastrointestinal and Liver Physiology

Gut Fungal Microbiota: The Yin and Yang of Inflammatory Bowel Disease –
Richard, Mathias L. – Inflammatory Bowel Diseases

Gut-Microbiota and Mental Health: Current and Future Perspectives –
Ajit Kumar Thakur – Journal of Pharmacology & Clinical Toxicology

Microbiota, Biofilms and Helicobacter Pylori in the Diseases of Gastroduodenal Zone – G.Sh. Isaeva , V.B. Ziatdinov – Kazan Medical Journal

Prebiotic intake reduces the waking cortisol response and alters emotional bias in healthy volunteers – Kristin Schmidt – Psychopharmacology

The Human Microbiome, Ecological Ontology, and the Challenges of Community – Gregory W. Schneider and Russell Winslow – Perspectives in Biology and Medicine

Microbiome of pregnancy and birth

* Temporal dynamics of the very premature infant gut dominant microbiota – Fabien Aujoulat – BMC Biology

The Preterm Placental Microbiome Varies in Association with Excess Maternal Gestational Weight Gain – Kathleen M. Antony – American Journal of Obstetrics and Gynecology

* Study in 2 million children: Cesarean Section and Chronic Immune Disorders – Astrid Sevelsted – Pediatrics

Animal models

Directed shift of vaginal microbiota induced by vaginal application of sucrose gel in rhesus macaques – Kai-tao Hu – International Journal of Infectious Diseases

Investigating the long-term effect of subchronic phencyclidine-treatment on novel object recognition and the association between the gut microbiota and behavior in this animal model of schizophrenia – B. Pyndt Jørgensen – Physiology & Behavior

Red Ginseng and Semen Coicis can improve the structure of gut microbiota and relieve the symptoms of ulcerative colitis – Mingzhang Guo – Journal of Ethnopharmacology

Animal microbiome

Stability of the Gorilla Microbiome Despite SIV Infection – Andrew H. Moeller – Molecular Ecology

Antiviral immunity of Anopheles gambiae is highly compartmentalized, with distinct roles for RNA interference and gut microbiota – Guillaume Carissimo – PNAS USA

* Microbiota shifts in the surface mucopolysaccharide layer of corals transferred from natural to aquaria settings – Zoe A. Pratte – Journal of Invertebrate Pathology

Sponging up metals: Bacteria associated with the marine sponge Spongia officinalis – Cléa Bauvais – Marine Environment Research

Plant microbiome

Host identity is a dominant driver of mycorrhizal fungal community composition during ecosystem development – Laura B. Martínez-García – New Phytologist

* A Model to Explain Plant Growth Promotion Traits: A Multivariate Analysis of 2,211 Bacterial Isolates – Pedro Beschoren da Costa – PLOS ONE

The application of Arabidopsis thaliana in studying tripartite interactions among plants, beneficial fungal endophytes and biotrophic plant-parasitic nematodes – Alfonso Martinuz – Planta

Differences in thallus chemistry are related to species-specific effects of biocrust-forming lichens on soil nutrients and microbial communities – Manuel Delgado-Baquerizo – Functional Ecology

Halotolerant PGPRs Prevent Major Shifts in Indigenous Microbial Community Structure Under Salinity Stress – Nidhi Bharti – Microbial Ecology

Promoting effect of Fusarium oxysporum [f.sp. strigae] on abundance of nitrifying prokaryotes in a maize rhizosphere across soil types – Mary K. Musyoki – Biological Control

Preferential allocation, physio-evolutionary feedbacks, and the stability and environmental patterns of mutualism between plants and their root symbionts – James D. Bever – New Phytologist

Fungi in the future: interannual variation and effects of atmospheric change on arbuscular mycorrhizal fungal communities – T. E. Anne Cotton – New Phytologist

Soil and sediment microbiome

Prevalence of Antibiotic Resistance Genes and Bacterial Pathogens in Long-Term Manured Greenhouse Soils As Revealed by Metagenomic Survey – Hua Fang – Environmental Science & Technology

Water Content Differences Have Stronger Effects than Plant Functional Groups on Soil Bacteria in a Steppe Ecosystem – Ximei Zhang – PLOS ONE
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0115798

A Novel Sister Clade to the Enterobacteria Microviruses (family Microviridae) Identified in Methane Seep Sediments – Sam Bryson – Environmental Microbiology

Dynamics of Plant Nutrients, Utilization and Uptake, and Soil Microbial Community in Crops Under Ambient and Elevated Carbon Dioxide – Shardendu K. Singh – Nutrient Use Efficiency: from Basics to Advances

Water microbiome

Physical controls of variability in North Atlantic phytoplankton communities – Andrew D. Barton – Limnology and Oceanography

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

Unraveling the interactive effects of climate change and oil contamination on laboratory-simulated estuarine benthic communities – Francisco J. R. C. Coelho – Global Change Biology

The Food Web of Boiling Springs Lake Appears Dominated by the Heterolobosean Tetramitus thermacidophilus Strain BSL – William H.H. Reeder IV – Journal of Eukaryotic Microbiology

Microbiome of digesters and wastewater

Pyrosequencing of mcrA and Archaeal 16S rRNA Genes Reveals Diversity and Substrate Preferences of Methanogen Communities in Anaerobic Digesters – David Wilkins – Applied and Environmental Microbiology

Association of Biodiversity with the Rates of Micropollutant Biotransformations among Full-Scale Wastewater Treatment Plant Communities – David R. Johnson – Applied and Environmental Microbiology

Microbial Community Structure and Diversity in an Integrated System of Anaerobic-Aerobic Reactors and a Constructed Wetland for the Treatment of Tannery Wastewater in Modjo, Ethiopia – Adey Feleke Desta – PLOS ONE

Enhancement of sludge granulation in anaerobic acetogenesis by addition of nitrate and microbial community analysis – Yang Li – Biochemical Engineering Journal

Microbiome of the built environment

* Indoor Fungi: Companions and Contaminants – A. Nevalainen – Indoor Air

Food microbiology

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

Pyrosequencing vs. culture-dependent approaches to analyze lactic acid bacteria associated to chicha, a traditional maize-based fermented beverage from Northwestern Argentina – Patricia Elizaquível – International Journal of Food Microbiology

Metagenomics

Bacterial Phylogenetic Reconstruction from Whole Genomes Is Robust to Recombination but Demographic Inference Is Not – Jessica Hedge, Daniel J. Wilson – mBio

Reply to “Expanding the Conversation on High-Throughput Virome Sequencing Standards To Include Consideration of Microbial Contamination Sources” – Jason T. Ladner – mBio

Metabolomics

Response of Peripheral Rhythms to the Timing of Food Intake – Megumi Hatori, Satchidananda Panda – Methods in Enzymology

Techniques

The near-quantitative sampling of genomic DNA from various food-borne Eubacteria – Peter Irwin – BMC Microbiology

Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system – Patrick D. Schloss preprint

Preparation and Analysis of Metatranscriptomic Libraries in Petroleum Hydrocarbon Microbe Systems – Jarrad T. Hampton-Marcell – Springer Protocols Handbooks

Protocols for Handling, Storing, and Cultivating Oil Sands Tailings Ponds Materials for Microbial and Molecular Biological Study – J. M. Foght – Springer Protocols Handbooks

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples (video) – Yan Wei Lim – JOVE

Microbes in the news

Book: Principals of Microbial Diversity – James W. Brown – ASM Press

Bacteria hold clues to our health – Heather Kelly – CNN

11+ things everyone needs to know about microbes – Jonathan Eisen – MicrobeNet

How to Build a Healthy Microbiome, Before, During, and After Birth – Kelly Brogan – Mercola.com

Mining the microbiome: How the microbes that share our bodies could help prevent cancer – Leigh MacMillan – Vanderbilt-Ingram

The Surprising Link Between Gut Bacteria And Anxiety – Carolyn Gregoire – Huffington Post

Stress, Depression, & The Bacteria In Your Gut – Video with Professor John F. Cryan – Richard Zwolinski – PsychCentral

Really shameful overselling the microbiome from the American Society for Microbiology regarding lupus – Jonathan Eisen – The Tree of Life

Gut Microbiome Rebounds After Colonoscopy Bowel Preparation – Lara C. Pullen – Medscape

Elevator buttons at hospitals have more bacteria than the toilets – Nicole Oran – MedCityNews

Can Mars be terraformed with bacteria? The Cyano Knights think so! Scott Sutherland – The Weather Network

Cholera’s Method of Killing Identified – Jim Algar – Tech Times

Science, publishing and career

A Stronger Post-Publication Culture Is Needed for Better Science – Hilda Bastian – PLOS Medicine

Advocating for women in hiring decisions – Dr. Mellivora – Tenure She Wrote

Science and art

Stylish Silk Scarves, Dyed With Bacteria – Liz Stinson – Wired.com

Bik’s Picks

The global distribution of diet breadth in insect herbivores – Matthew L. Forister – PNAS USA

‘Bad luck’ of random mutations plays predominant role in cancer, study shows – Science Daily

Experimental Diet Pill Tricks Body into Thinking It Ate – Bahar Gholipour – Live Science

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December 30, 2014

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Human oral microbiome

Mucosal Microbiome in Patients with Recurrent Aphthous Stomatitis – K. Hijazi – Journal of Dental Research

Human respiratory microbiome

Impact of saline irrigation and topical corticosteroids on the postsurgical sinonasal microbiota – Cindy M. Liu – International Forum of Allergy & Rhinology

Human gut microbiome

The Gastrointestinal Microbiota and Colorectal Cancer – Temitope O. Keku – American Journal of Physiology – Gastrointestinal and Liver Physiology

The Impact of Diet and Lifestyle on Gut Microbiota and Human Health – Michael A. Conlon and Anthony R. Bird – Nutrients

Understanding How Commensal Obligate Anaerobic Bacteria Regulate Immune Functions in the Large Intestine – Eva Maier – Nutrients

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

Antibiotic activity and microbial community of the temperate sponge, Haliclona sp. – A. Hoppers – Journal of Applied Microbiology

Plant microbiome

Secondary successional trajectories of structural and catabolic bacterial communities in oil polluted soil planted with hybrid poplar – Shinjini Mukherjee – Molecular Ecology

Fungal Endophytes of Alpinia officinarum Rhizomes: Insights on Diversity and Variation across Growth Years, Growth Sites, and the Inner Active Chemical Concentration – Li Shubin – PLOS ONE

Endophytic microbial community in two transgenic maize genotypes and in their
near-isogenic non-transgenic maize genotype – Débora Alves Ferreira da Silva – BMC Microbiology

Soil, sediment, sludge, litter microbiome

Site properties have a stronger influence than fire severity on ectomycorrhizal fungi and associated N-cycling bacteria in regenerating post-beetle-killed lodgepole pine forests – Nabla M. Kennedy – Folia Microbiologica

Influence of Azo Dye Concentration on Activated Sludge Bacterial Community in the Presence of Functionalized Polyurethane Foam – Hong Lu – Applied Biochemistry and Biotechnology

The Potential of Antibiotic Alternatives for Enriching Beneficial Microbiota in Litter – Adriana A. Pedroso – SOJ Microbiology & Infectious Diseases

Water microbiome

Bacterial Community Composition in Three Freshwater Reservoirs of Different Alkalinity and Trophic Status – Marc Llirós – PLOS ONE

Bioinformatics
* Programming tools: Adventures with R – A guide to the popular, free statistics and visualization software that gives scientists control of their own data analysis – Sylvia Tippmann – Nature

Metabolomics, Proteomics

Symbiosis, dysbiosis, and rebiosis — The value of metaproteomics in human microbiome monitoring – Lei Mao and Jacqueline Franke – Proteomics

Viruses and Phages

Virus evolution towards limited dependence on the non-essential functions of the host: the bacteriophage SPP1 case – Virginija Cvirkaite-Krupovic – Journal of Virology

Microbial Ecology

Review: Metacommunity organisation, spatial extent and dispersal in aquatic systems: patterns, processes and prospects – Jani Heino – Freshwater Biology

Microbes in the news

Is the Bacteria in Our Gut the Key to Our Health? (Podcast with Ed Yong, Jack Gilbert, Jonathan Eisen, Margaret McFall-Ngai starts at 9 min) – To The Point – Barbara Bogaev – KCRW

9 Amazing and Gross Things Scientists Discovered About Microbes This Year – Greg Miller – Wired.com

The Right Chemistry: Exposure to bacteria can help keep us healthy – Joe Schwarcz – Montreal Gazette

Scientists Discover How Mouth Microbes Cause Gum Disease – Randall Mayes – Design & Trend

Microbiologists cultivate “microbial dark matter” – Eric Hopton – RedOrbit

Science, Publishing, and Career

Open Access 2014: A Year that Data Cracked Through Secrecy and Myth – Hilda Bastian- PLOS Blogs

Bik’s Picks

Watch raindrops make asteroid-like collisions (slo-mo video) – Popular Science

An ‘Otter-This-World’ Christmas! – Total cuteness courtesy of the Monterey Bay Aquarium – Susan C. Schena – Patch.com

Go Outside Tonight and Take a Look at Comet Lovejoy in the Sky – Dan Van Winkle – The Mary Sue

46 Important Things Science Taught Us In 2014 – It was a big year for robot penguins, snake penises, and space exploration. Sadly not all at the same time – Kelly Oakes – BuzzFeed

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December 28, 2014

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Human oral microbiome

Periodontitis: from microbial immune subversion to systemic inflammation – George Hajishengallis – Nature Reviews Immunology

Microbiology of Oral Biofilm-Dependent Diseases: Have We Made Significant Progress to Understand and Treat These Diseases? – Ana Paula Vieira Colombo – Current Oral Health Reports

Human skin microbiome

Dynamics of the surgical microbiota along the cardiothoracic surgery pathway – Sara Romano-Bertrand – Frontiers in Microbiology

Human gut microbiome

Decreased Bacterial Diversity Characterizes the Altered Gut Microbiota in Patients With Psoriatic Arthritis, Resembling Dysbiosis in Inflammatory Bowel Disease – Jose U. Scher – Arthritis & Rheumatology

Insights Into the Role of the Microbiome in Obesity and Type 2 Diabetes – Annick V. Hartstra – Diabetes Care

* The gut microbiota and its role in the development of allergic disease: a wider perspective – C. E. West – Clinical & Experimental Allergy

The power in numbers: Gut microbiota in Parkinson’s disease – Joaquin A. Vizcarra – Movement Disorders

Childhood Obesity: A Role for Gut Microbiota? – Marina Sanchez – Int. J. Environ. Res. Public Health

Animal models of microbiome

Impact of the gut microbiota on rodent models of human disease – Axel Kornerup Hansen – World Journal of Gastroenterology

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

Alteration of the fecal microbiota and serum metabolite profiles in dogs with idiopathic inflammatory bowel disease – Yasushi Minamoto – Gut Microbes

Intermittent hypoxia alters gut microbiota diversity in a mouse model of sleep apnoea
Isabel Moreno-Indias – European Respiratory Journal

Bioreactor models

Lead toxicity to the performance, viability, and community composition of activated sludge microorganisms – Husen Zhang – Environmental Science & Technology

Animal microbiome

Diet strongly influences the gut microbiota of surgeonfishes – Sou Miyake – Molecular Ecology

Plant microbiome

21st century agriculture: integration of plant microbiomes for improved crop production and food security – Angela Sessitsch and Birgit Mitter – Microbial Biotechnology

Soil microbiome

Vertical distribution of the soil microbiota along a successional gradient in a glacier forefield – Thomas Rime – Molecular Ecology

Changes in the composition and diversity of bacterial communities 13 years after soil reclamation of abandoned mine land in eastern China – Yuanyuan Li – Ecological Research

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

Clay minerals and metal oxides strongly influence the structure of alkane-degrading microbial communities during soil maturation – Annelie Steinbach – ISME Journal

Different vegetable crop rotations affect soil microbial communities and soilborne diseases of potato and onion: literature review and a long-term field evaluation – PJ Wright – New Zealand Journal of Crop and Horticultural Science

Water microbiome

* Biogeography and ecology of the rare and abundant microbial lineages in deep-sea – Rika E. Anderson – FEMS Microbiology Ecology

Comparative metagenomic and metatranscriptomic analyses of microbial communities in acid mine drainage – Lin-xing Chen – ISME Journal

Microbes of the built environment

Indoor bioaerosol dynamics – William W Nazaroff – Indoor Air

Bioinformatics

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

Metabolomics

Reevaluating the hype: Four bacterial metabolites under scrutiny – Esther Eleonore Fröhlich – European Journal of Microbiology and Immunology

Microbes in the news

Discovering microbiology – Nicholas P Money – Oxford University Press

The Microbes in Your Kitchen (Or in your Starbucks mocha) – Kevin Bonham – Scientific American

Science, Publishing, Career

Science is the most ‘future proof’ degree: Engineering and chemistry seen as courses likely to lead to an adaptable career – Laura Clark – Daily Mail

Bik’s Picks

Dr. Oz gets roasted in science journal’s Christmas edition — science roundup extra (video, links) – Susannah L. Bodman – Oregon Live

Science Explains Why The Best BBQ Is Slow Cooked – Patrick Allan – LifeHacker

The Shapes of Snowflakes – CompoundChem

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December 26, 2014

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Pregnancy and birth

* Early Childhood Gut Microbiomes Show Strong Geographic Differences Among Subjects at High Risk for Type 1 Diabetes – Kaisa M. Kemppainen – Diabetes Care

Human skin microbiome

* Spatial variations in the microbial community structure and diversity of the human foot is associated with the production of odorous volatiles – Deborah Stevens – FEMS Microbiology Ecology

Human respiratory microbiome

Microbiota profiling of bronchial fluids of elderly patients with pulmonary carcinoma – Naoko Ishida – Journal of Oral Biosciences

Human gut microbiome

* Microbial culturomics: paradigm shift in the human gut microbiome study – J.-C. Lagier
Clinical Microbiology and Infection

Fecal microbiota transplantation through mid-gut for refractory Crohn’s disease: Safety, feasibility, and efficacy trial results – Bota Cui – Journal of Gastroenterology and Hepatology

Culturomics: a new approach to study the human microbiome – G. Greub – Clinical Microbiology and Infection

The influence of the human microbiome and probiotics on cardiovascular health – Race Ettinger – Gut Microbes

Prolonged use of a proton pump inhibitor reduces microbial diversity: implications for Clostridium difficile susceptibility – Charlie T Seto – Microbiome

Animal microbiome

Use of metagenomic high-throughput sequencing technology and robust bioinformatics to assess the microbiome of cattle, their environments, and beef products to determine the degree of antimicrobial resistance – X. Yang – Meat Science

News in livestock research – use of Omics-technologies to study the microbiota in the gastrointestinal tract of farm animals – Simon Deusch – Computational and Structural Biotechnology Journal

Birds: Bacteria and the evolution of honest signals. The case of ornamental throat feathers in spotless starlings – Magdalena Ruiz-Rodríguez – Functional Ecology

Silverleaf whitefly: Diversity of symbiotic bacteria associated with Bemisia tabaci (Homoptera: Aleyrodidae) in cassava mosaic disease pandemic areas of Tanzania – L.S. Tajebe – Annals of Applied Biology

Physicochemical conditions, metabolites, and community structure of the bacterial microbiota in the gut of wood-feeding cockroaches (Blaberidae: Panesthiinae) – Eugen Bauer – FEMS Microbiology Ecology

Sea urchin larvae decipher the epiphytic bacterial community composition when selecting sites for attachment and metamorphosis – Shaun J. Nielsen – FEMS Microbiology Ecology

Plant microbiome

Land-use intensity and host plant identity interactively shape communities of arbuscular mycorrhizal fungi in roots of grassland plants – Kriszta Vályi – New Phytologist

Temporal patterns of orchid mycorrhizal fungi in meadows and forests as revealed by 454 pyrosequencing – Jane Oja – New Phytologist

Review: Exploring interactions of plant microbiomes – Fernando Dini Andreote – Scienta Agricola

Drying effects on archaeal community composition and methanogenesis in bromeliad tanks – Franziska B. Brandt – FEMS Microbiology Ecology

The effect of psychrotrophic bacteria isolated from the root zone of winter wheat on selected biotic and abiotic factors – Sebastian Wojciech Przemieniecki – Journal of Plant Protection Research

Soil microbiome

Influence of exogenous organic matter on prokaryotic and eukaryotic microbiota in an agricultural soil. A multidisciplinary approach – Daniela Pezzolla – Soil Biology and Biochemistry

Soil bacteria hold the key to root cluster formation – Byron B. Lamont – New Phytologist

Distinct composition signatures of archaeal and bacterial phylotypes in the Wanda Glacier forefield, Antarctic Peninsula – Igor S. Pessi – FEMS Microbiology Ecology

The effect of storage on microbial activity and bacterial community structure of drained and flooded paddy soil – Juan Wang – Journal of Soils and Sediments

Detection and diversity of copper containing nitrite reductase genes (nirK) in prokaryotic and fungal communities of agricultural soils – Andrew Long – FEMS Microbiology Ecology

Archaeal community diversity and abundance changes along a natural salinity gradient in estuarine sediments – Gordon Webster – FEMS Microbiology Ecology

Water microbiome

Molecular analysis of the benthos microbial community in Zavarzin thermal spring (Uzon Caldera, Kamchatka, Russia) – Alexey S Rozanov – BMC Genomics

Food microbiology

Cheese rind microbial communities: diversity, composition and origin – Françoise Irlinger – FEMS Microbiology Letters

Microbiome and immunology

The role of IL-10 in microbiome-associated immune modulation and disease tolerance – Benoît Levast – Cytokine

TL1A regulates TCRγδ+ intraepithelial lymphocytes and gut microbial composition – Peter Tougaard – European Journal of Immunology

Microbiome components with probiotic or other interesting properties

Miniaturized Cultivation of Microbiota for Antimalarial Drug Discovery – Carrie Waterman – Medicinal Research Reviews

Antagonism against fish pathogens by cellular components and verification of probiotic properties in autochthonous bacteria isolated from the gut of an Indian major carp, Catla catla (Hamilton) – Anjan Mukherjee and Koushik Ghosh – Aquaculture Research

Probiotic strains introduced through live feed and rearing water have low colonizing success in developing Atlantic cod larvae – Jorunn Skjermo – Aquaculture

Metabolomics

Introducing the USA Plant, Algae and Microbial Metabolomics Research Coordination Network (PAMM-NET) – Lloyd W. Sumner – Metabolomics

Towards the Fecal Metabolome Derived from Moderate Red Wine Intake – Ana Jiménez-Girón – Metabolites

Bioinformatics

Inconsistent Denoising and Clustering Algorithms for Amplicon Sequence Data – Koskinen Kaisa – Journal of Computational Biology

Microbes in the news

Is 2015 the Year We All Sequence Our Microbiomes?– The Atlantic

Do new natural products lurk in genes of bacteria? – Kevin Stacey-Brown – Futurity

Discovery holds promise for decoding elusive bacteria – Business Standard

Experimental Drugs Target Bacteria’s Social Network – Carl Zimmer – Scientific American

Did Microbes Shape the Human Life Span? – Tia Ghose – LiveScience

Does the Gut Microbiome Play a Role in Autoimmune Disease? – Amy Nett – ChrisKresser.com

Bik’s Picks

To Raise Science Scores, Colleges Look Beyond the Lecture – Richard Perez-Pena – New York Times

Tsunami Science: Advances Since the 2004 Indian Ocean Tragedy – Becky Oskin – Live Science

Rudimentary egg and sperm cells made from stem cells – David Cyranoski – Nature

Who Patented ‘My Favorite Things’? – Robinson Meyer – The Atlantic

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December 23, 2014

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Microbiome publications are definitely not taking a winter break, so here is your holiday update. Merry Christmas to those who celebrate!

Human oral microbiome

Serum IgG Antibody Levels to Periodontal Microbiota Are Associated with Incident Alzheimer Disease – James M. Noble – PLOS ONE

Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle – Xuesong He – PNAS USA

Pyrosequencing of supra- and subgingival biofilms from inflamed peri-implant
and periodontal sites – Simone Schaumann – BMC Oral Health

Human respiratory microbiome

The Microbial Community of the Cystic Fibrosis Airway Is Disrupted in Early Life – Julie Renwick – PLOS ONE

Human gut or general microbiome
Effects of bowel cleansing on the intestinal microbiota – Jonna Jalanka – Gut

The Microbiome of Aging and Age-Related Disease – 2014 Meeting Abstracts

Microbial community pattern detection in human body habitats via ensemble clustering framework – Peng Yang – ArXiv.org

Cancer and the microbiome: potential applications as new tumor biomarker – Khan Shahanavaj – Expert Review of Anticancer Therapy

Influence of Intestinal Microbiota on Body Weight Gain: a Narrative Review of the Literature – Camila S. Cardinelli – Obesity Surgery

Animal models of microbiome research

Host genetics and diet, but not immunoglobulin A expression, converge to shape
compositional features of the gut microbiome in an advanced intercross population
of mice – Larry J Leamy – Genome Biology

Animal microbiome

Microbiomes, plausible players or not in alteration of host behaviour – David G. Biron – Frontiers in Microbiology

The Howler Monkey as a Model for Exploring Host-Gut Microbiota Interactions in Primates – Katherine R. Amato, Nicoletta Righini – Howler Monkeys

The Gut Microbiota Appears to Compensate for Seasonal Diet Variation in the Wild Black Howler Monkey (Alouatta pigra) – Katherine R. Amato – Microbial Ecology

Application of the Human Intestinal Tract Chip to the non-human primate gut microbiota – T.D.J. Bello González – Beneficial Microbes

Effects of dietary supplementation of a commercial prebiotic Previda® on survival, growth, immune responses and gut microbiota of Pacific white shrimp, Litopenaeus vannamei – J.D. Anuta – Aquaculture Nutrition

Metagenomic-Based Study of the Phylogenetic and Functional Gene Diversity in Galápagos Land and Marine Iguanas – Pei-Ying Hong – Microbial Ecology

Plant microbiome

The plant microbiome at work – Klaus Schlaeppi and Davide Bulgarelli – Molecular Plant-Microbe Interactions

Tree communities rapidly alter soil microbial resistance and resilience to drought – David Rivest – Functional Ecology

The Sesquiterpene Biosynthesis and Vessel-Occlusion Formation in Stems of Aquilaria sinensis (Lour.) Gilg Trees Induced by Wounding Treatments without Variation of Microbial Communities – Zheng Zhang – International Journal of Molecular Sciences

Analysis of microbial taxonomical groups present in maize stalks suppressive to colonization by toxigenic Fusarium spp.: A strategy for the identification of potential antagonists – Jürgen Köhl – Biological Control

Soil and sediment microbiome

Diversity, Distribution and Hydrocarbon Biodegradation Capabilities of Microbial Communities in Oil-Contaminated Cyanobacterial Mats from a Constructed Wetland – Raeid M. M. Abed – PLOS ONE

Do climate factors govern soil microbial community composition and biomass at a regional scale? – L. Ma – Biogeosciences Discuss

Water microbiome

Early succession of micro-periphyton communities in kelp bed and barren ground ecological systems – Roberto A. Uribe – Marine Ecology

Greater temporal changes of sediment microbial community than its waterborne counterpart in Tengchong hot springs, Yunnan Province, China – Shang Wang – Scientific Reports

Effects of warming on microbial communities in the coastal waters of temperate and subtropical zones in the Northern Hemisphere, with a focus on Gammaproteobacteria
Dao Thi Anh Tuyet – Journal of Oceanography

Colonization in the photic zone and subsequent changes during sinking determines bacterial community composition in marine snow – Stefan Thiele – Applied and Environmental Microbiology

Diversity, Distribution and Hydrocarbon Biodegradation Capabilities of Microbial Communities in Oil-Contaminated Cyanobacterial Mats from a Constructed Wetland
Raeid M. M. Abed – PLOS ONE

Bioreactor microbiology

Comparative analysis of microbial community of novel lactic acid fermentation inoculated with different undefined mixed cultures – Shaobo Liang – Bioresource Technology

A framework for establishing predictive relationships between specific bacterial 16S rRNA sequence abundances and biotransformation rates – Damian E. Helbling – Water Research

Metagenomics

Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India – Johan Bengtsson-Palme – Frontiers in Microbiology

Challenges of metagenomics and single-cell genomics approaches for exploring cyanobacterial diversity – Michelle Davison – Photosynthesis Research

Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms – Martial Marbouty – eLIFE

Development and validation of an rDNA operon based primer walking strategy applicable to de novo bacterial genome finishing – Alexander W. Eastman and Ze-Chun Yuan – Frontiers in Microbiology

Metabolomics and transcriptomics

Terpene synthases are widely distributed in bacteria – Yuuki Yamada – PNAS USA

Scaling microbial biomass, metabolism and resource supply – Robert L. Sinsabaugh – Biogeochemistry

Metatranscriptomics of N2-fixing cyanobacteria in the Amazon River plume – Jason A Hilton – ISME Journal

Mining Soil Metagenomes to Better Understand the Evolution of Natural Product Structural Diversity: Pentangular Polyphenols as a Case Study – Hahk-Soo Kang and Sean F. Brady – Journal of the American Chemical Society

Molecular details of a starch utilization pathway in the human gut symbiont Eubacterium rectale – Darrell W. Cockburn – Molecular Microbiology

Techniques

Deciphering the Prokaryotic Community and Metabolisms in South African Deep-Mine Biofilms through Antibody Microarrays and Graph Theory – Yolanda Blanco – PLOS ONE

Rapid species-level identification of vaginal and oral lactobacilli using MALDI-TOF MS analysis and 16S rDNA sequencing – Annette Carola Anderson – BMC Microbiology

Probiotics

Probiotic and technological properties of Lactobacillus spp. strains from the human stomach in the search for potential candidates against gastric microbial dysbiosis – Susana Delgado – Frontiers in Microbiology

Phages and viruses

Effectiveness of bacteriophages in the sputum of cystic fibrosis patients – E. Saussereau – Clinical Microbiology and Infection

More Microbiology

Bridging the gap between viable but non-culturable and antibiotic persistent bacteria – Mesrop Ayrapetyan – Trends in Microbiology

Bacterial microcompartments and the modular construction of microbial metabolism – Cheryl A. Kerfeldemail, Onur Erbilgin – Trends in Microbiology

The impact of triclosan on the spread of antibiotic resistance in the environment – Daniel E. Carey – Frontiers in Microbiology

Microbes in the news

At Last, I Meet My Microbes – Katherine Harmon Courage – NPR Shots

This Is Your Microbiome: Katherine Harmon Courage at NPR is taking a tour through her microbiome and that of her husband, mother, and dog, as she recounts in a four-part series – Genome Web

Big Idea 2015: Medicine, Wellbeing, and the Microbiome – Deepak Chopra – LinkedIn

When Threatened By Worms, Bacteria Summon Killer Fungi – Ed Yong – National Geographic

Parkinson’s disease linked to gut bacteria – Tim Sandle – Digital Journal

Bacteria in 550-million-year-old fossils provide new clues about fossil formation – Science Codex

Yellowstone Thermal Pools Colored by Pollution – Patrick J Kiger – Discovery

Floating Toilets That Clean Themselves Grow On A Lake – Nsikan Akpan – NPR Goats and Soda

Bettendorf wrestling coach’s invention tackles germs and bacteria on sporting mats and floors – Dennis Moran – QC Online

People on Craigslist Want to Give You Bacteria for Free – Natalie Kitroeff – BusinessWeek

Science, publishing, career

Patterns of text reuse in a scientific corpus – Daniel T. Citron and Paul Ginsparg – PNAS USA

The Anti-Plagiarism Machine: An analysis of hundreds of thousands of scientific papers finds text re-use is rampant, but it isn’t always malicious – Adrienne Lafrance – The Atlantic

“You Are Welcome Here”: Small Stickers Make a Big Difference for LGBTQ Scientists – Kyle Frischkorn – Scientific American

Science and Art

Incredible Bacteria-Laced Fabric Combines Art, Biology And Fashion – Priscilla Frank – Huffington Post
Bik’s Picks

Evolutionary perspectives on human height variation – Gert Stulp and Louise Barrett – Biological Reviews

What the ‘marshmallow test’ can teach you about your kids – Chuck Hadad – CNN

7 of the Ocean’s Strangest Creatures, Including a Fish With a Flashlight – Matt Simon – Wired

Modern genetics confirm ancient relationship between fins and hands – Science Daily

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December 19, 2014

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Pregnancy and Birth

Lots of abstracts (mostly from the group of Kjersti Aagaard) from the 35th Annual Meeting of the Society for Maternal-Fetal Medicine — The Pregnancy Meeting in the American Journal of Obstetrics and Gynecology

13: Association of preterm birth with alterations in the microbiome and linkage to host mtDNA variants – Kjersti Aagaard

57: Alterations in the intestinal microbiome of infants are associated with breastfeeding practice – Derrick Chu

78: Distinct alterations in the placental microbiome among spontaneous preterm births – Kjersti Aagaard

79: Metagenomics of a population-based prospective cohort reveals no discernable impact of mode of delivery (MOD) on the infant microbiome by 6 weeks of age – Derrick Chu

122: The microbiome of the placenta is altered among subjects with severe chorioamnionitis & spontaneous preterm birth – Amanda Prince

282: Chorioamnionitis induced by intramniotic injection of IL1, LPS or Ureaplasma parvum is associated with an altered microbiome in a primate model of inflammatory preterm birth (PTB) – Amanda Prince

283: Amniotic fluid microbiome community and inflammation in women with second trimester cervical changes – Amanda Roman

342: Poor maternal nutrition is associated with alterations in the maternal and neonatal microbiome communities – Kathleen Antony

650: Characterization of the vaginal microbiome following preterm premature rupture of membranes (PPROM) – Janet Hill

709: Race, latency, and fetal membrane microbiota diversity in preterm premature rupture of membranes – Sarahn Wheeler

Human oral microbiome

* Comparative analysis of the human saliva microbiome from different climate zones: Alaska, Germany, and Africa – Li J – BMC Microbiology

Human respiratory microbiome

* The adult nasopharyngeal microbiome as a determinant of pneumococcal acquisition – Cremers AJ – Microbiome Journal

Human gut microbiome

* The gut microbiota of Colombians differs from that of Americans, Europeans and Asians – Escobar JS – BMC Microbiology

Gut Microbiota: Its Role in Hepatic Encephalopathy – Rahul Rai – Journal of Clinical and Experimental Hepatology

The fungal microbiota of de-novo paediatric inflammatory bowel disease – I. Mukhopadhya – Microbes and Infection

Human vaginal microbiome

Colonization of the upper genital tract by vaginal bacterial species in non-pregnant women  – Caroline M. Mitchell – American Journal of Obstetrics and Gynecology

Transcriptional fingerprints of antigen-presenting cell subsets in the human vaginal mucosa and skin reflect tissue-specific immune microenvironments – Dorothée Duluc – Genome Medicine

Animal models

Microbially Driven TLR5-Dependent Signaling Governs Distal Malignant Progression through Tumor-Promoting Inflammation – Melanie R. Rutkowski – Cancer Cell

Intestinal microbiota diversity and expression of pattern recognition receptors in newly weaned piglets – Xin Tao – Anaerobe

Host genetics and diet, but not immunoglobulin A expression, converge to shape
compositional features of the gut microbiome in an advanced intercross population
of mice – Larry J Leamy – Genome Biology

The effects of Lactobacillus acidophilus as feed supplement on skin mucosal immune parameters, intestinal microbiota, stress resistance and growth performance of black swordtail (Xiphophorus helleri) – Seyed Hossein Hoseinifar – Fish & Shellfish Immunology

Animal microbiome

Investigation of a new acetogen isolated from an enrichment of the tammar wallaby forestomach – Gagen EJ – BMC Microbiology

Metagenomics, bioinformatics

Determining the quality and complexityof next-generation sequencing data without
a reference genome – Seyed Yahya Anvar – Genome Biology

Techniques

Tracking down the sources of experimental contamination in microbiome studies – Sophie Weiss – Genome Biology

More microbiology

Single cell genomics of bacterial pathogens: outlook for infectious disease research – Jeffrey S McLean and Roger S Lasken – Genome Medicine

A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens – Maha R Farhat – Genome Medicine

Environmental enteropathy and malnutrition: do we know enough to intervene? – William A Petri – BMC Medicine

Microbes in the news

Mix of Bacteria in Gut May Depend More on Diet than Genes – Microbiota, Microbiome Change Quickly, UCSF Researchers Find – Jeffrey Norris – UCSF

Protection of the mouse gut by mucus depends on microbes – Phys.org

Life would go on if all bacteria disappeared (but it would totally suck) – Rachel Feltman – Washington Post

New technology using bacteria from dung helps coffee farmers to purify water – Oliver Balch – The Guardian

Science, publishing, career

Dragging scientific publishing into the 21st century – Razib Khan – Genome Biology

Training for peer review: why we need it and how to get there – David Moher – Biome BioMedCentral

Along with the privilege of authorship come important responsibilities – David Moher – BMC Medicine

Crashing the Old Boys’ Science Club – Yamina Berchiche – Live Science

Bik’s Picks

‘People Can Be Afraid of Anything’ – There are plenty of people afraid of whales who will never even see one. How I learned about, and tried to conquer, my own cetaphobia – Kate Horowitz – The Atlantic

Playlist: Science! – NPR/TED staff – NPR

Birds sensed severe storms and fled before tornado outbreak – Science Daily

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December 18, 2014

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Human gut microbiome

* Metagenomic Analysis of Viruses in Feces from Unsolved Outbreaks of Gastroenteritis in Humans – Nicole E. Moore – Journal of Clinical Microbiology

Altered faecal and mucosal microbial composition in post-infectious irritable bowel syndrome patients correlates with mucosal lymphocyte phenotypes and psychological distress – J. Sundin – Alimentary Pharmacology & Therapeutics

Animal models of microbiome research

* The composition of the gut microbiota shapes the colon mucus barrier – Hedvig E Jakobsson – EMBO Reports

Diet Dominates Host Genotype in Shaping the Murine Gut Microbiota – Rachel N. Carmody – Cell Host & Microbe

Animal microbiome

Fish: The Gastrointestinal Phage Communities of the Cultivated Freshwater Fishes – Yang He – FEMS Microbiology Letters

Mussel: Algae Consumption and Nitrate Removal in a Raw Water Transport System by Limnoperna fortunei and its Associated Microorganisms – Ruijian Zhang – Water Environment Research

Plant microbiome

Meeting report: A snapshot of molecular plant–microbe interaction research – Sebastian Wittulsky – New Phytologist

Plant–microbe interactions change along a tallgrass prairie restoration chronosequence – Anna J. Herzberger – Restoration Ecology

Water microbiome

The influence of iron and siderophores on eukaryotic phytoplankton growth rates and community composition in the Ross Sea – Adam B. Kustka – Marine Chemistry

Food microbiology

Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products – Mathieu Almeida – BMC Genomics

Metabolomics

Identification and characterization of intestinal lactobacilli strains capable of degrading immunotoxic peptides present in gluten – R.M. Duar – Journal of Applied Microbiology

Microbes in the news

Behind The Scenes At The Lab That Fingerprints Microbiomes – Katherine Harmon Courage – NPR Shots Health News

Complex genome-microbiome link may influence risk for IBD – Healio

Patients don’t understand risks of unnecessary antibiotics, study shows – Science Daily

The Microbiota Crisis: How the Herbicide Glyphosate is Killing Microbiomes – Martin Michener – Health Impact News

Bik’s Picks

Asian Glow May Indicate Lower Pain Tolerance – Stephani Sutherland – Scientific American

What was the Worst #ScienceFail of 2014? (Op-Ed) – Aaron Huertas – LiveScience

Breakthrough of the year 2014 – Science

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December 17, 2014

Posted on by

A late digest today – I have been busy writing a paper and cooking for our lab’s annual holiday potluck party tomorrow. But here we go:

Human gut microbiome

Complex host genetics influence the microbiome in inflammatory bowel disease – Dan Knights – Genome Medicine

Microbiota and the human nature: know thyself – Harald Brüssow – Environmental Microbiology

Animal and bioreactor models of microbiome

Simulating distal gut mucosal and luminal communities using packed-column biofilm reactors and an in vitro chemostat model – Julie A.K. McDonald – Journal of Microbiological Methods

A novel method to characterize bacterial communities affected by carbon source and electricity generation in microbial fuel cells using stable isotope probing and Illumina sequencing – Yang Song – Journal of Microbiological Methods

Animal microbiome
Crab: Linking regional variation of epibiotic bacterial diversity and trophic ecology in a new species of Kiwaidae (Decapoda, Anomura) from East Scotia Ridge (Antarctica) hydrothermal vents – Katrin Zwirglmaier – MicrobiologyOpen

Soil microbiome

Minireview: The soil resistome: a critical review on antibiotic resistance origins, ecology and dissemination potential in telluric bacteria – Joseph Nesme and Pascal Simonet – Environmental Microbiology

The soil microbial community predicts the importance of plant traits in plant–soil feedback – Po-Ju Ke – New Phytologist

Metagenomics

Tle distribution and diversity in metagenomic datasets reveal niche specialization – Frank Egan – Environmental Microbiology Reports

Techniques

Application of a single-colony coculture technique to the isolation of unculturable gut bacteria – Yoshiki Tanaka – Microbiology and Immunology

A novel universal DNA labeling and amplification system for rapid microarray-based detection of 117 antibiotic resistance genes in Gram-positive bacteria – Christian Strauss – Journal of Microbiological Methods

Microbial Ecology

Microbial biogeography: the end of the ubiquitous dispersal hypothesis? – Christopher J. van der Gast – Environmental Microbiology

Bacteria can mobilize nematode-trapping fungi to kill nematodes – Xin Wang – Nature Communications

Microfluidic single-cell analysis links boundary environments and individual microbial phenotypes – Christian Dusny and Andreas Schmid – Environmental Microbiology

Microbes in the News

Microbiome may have shaped early human populations – Phys.org

Commensal bacteria were critical shapers of early human populations – Phys.org

Microbes played a significant role in human evolution, study says – Chuck Bednar – RedOrbit

The microbes we eat: Study investigates bacteria in different diets – Nathan Gray – NutraIngredients

Researchers source stool samples to study gut bacteria – Nicole Kwan – FOX News

Bacterial biofilms are associated with colon cancer, imaging technique reveals – Science Daily

Do Autoimmune Diseases Begin in the Gut? – Stephen Paget – Medscape

People may inherit ‘gut’ bacteria that cause Crohn’s disease and ulcerative colitis – MedicalXpress

* 2015 will be the year of the Microbiome (and 28 other predictions) – Fortune

#BacteriaHysteria: The hidden dangers lurking in your kitchen: Chopping boards harbour 200% more faecal bacteria than toilet seats and potatoes and leeks can give you food poisoning – Lizzie Parry – Daily Mail Online

Scientists Debate If It’s OK To Make Viruses More Dangerous In The Lab – Nell Greenfieldboyce – NPR Shots Health News

Science, publishing, and career

12 Unimpressed Comments From Peer Reviewers – Kristy Hamilton – IFL Science (for more entertaining quotes in Environmental Microbiology, see here)

Journalists to Catalog Retractions: Staff of the blog Retraction Watch will create a database of papers retracted from the scientific literature – Kerry Grens – The Scientist

Here’s What Happens When Female MIT PhDs Do a Reddit AMA About Computer Science – Lauren Landry – BostInno

How to be a science girl in a Barbie world – Eve Andrews – Grist.org

For Sale: “Your Name Here” in a Prestigious Science Journal – Charles Seife – Scientific American

These Beautiful Women in Science Art Prints Feature Rad As Heck Ladies – Sam Maggs – The Mary Sue

Bik’s Picks

Happy Holidays from the Corals! – Ocean Portal – Smithsonian

Science’s good, bad, ugly year – Tom Siegfried – Science News

Meet Bill Nye, The Anti-Science Guy – Robert Tracinski – The Federalist

10 Cutest Animals in Science in 2014 – Megan Gannon – Live Science

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