Category Archives: Animal experiments

Microbiome Digest, December 3, 2014

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Pregnancy and birth

Treatment of genital mycoplasma in colonized pregnant women in late pregnancy is associated with a lower rate of premature labour and neonatal complications – M. Vouga – Clinical Microbiology and Infection

Animal models of microbiome research

Early Canine Plaque Biofilms: Characterization of Key Bacterial Interactions Involved in Initial Colonization of Enamel – Lucy J. Holcombe – PLOS ONE

(Rat study) Dietary iron depletion at weaning imprints low microbiome diversity and this is not recovered with oral nano Fe(III) – Dore I. A. Pereira – MicrobiologyOpen

Soil microbiome

* Biology of a widespread uncultivated archaeon that contributes to carbon fixation in the subsurface – Alexander J. Probst – Nature Communications

Metabolomics

Microbiota-dependent metabolite trimethylamine-N-oxide is associated with disease severity and survival of patients with chronic heart failure – M. Trøseid – Journal of Internal Medicine

An ontology for microbial phenotypes – Marcus C Chibucos – BMC Microbiology

A chemo-centric view of human health and disease – Miquel Duran-Frigola – Nature Communications

Microbial Ecology

* Evolutionary limits to cooperation in microbial communities – Nuno M. Oliveira – PNAS USA

Microbes in the news

* Microbial Community Data Visualizations survey – Jonathan Eisen – MicroBEnet

* Microbiome: The bacterial tightrope – Katherine Bourzac – Nature

* Seth Bordenstein, Joël Doré, Paul Enck: a three-voice debate about gut microbiota research – Gut Microbiota Watch

Genes & cells: Gut microbes less diverse in humans: Great apes harbor more varied bacterial populations – Tina Hesman Saey – Science News

The nutritionists within: Firebugs depend on gut bacteria for vitamin supply – Phys.org

‘Friendly viruses’ as beneficial to gut health as ‘friendly bacteria’ – Medical News Today

Filth factor of public restrooms doesn’t live up to legends: study – Yahoo News

Fight off the flu with fermented foods – Katie Cavuto – Philly.com

* #BacteriaHysteria: These socks protect feet from bacteria – PhilStar

The Virus Detectives: Sifting Through Genes in Search of Answers on Ebola – Gina Kolata – NY Times

Science, publishing, and career

Harsh reality: Two reports highlight the plight of postdocs on both sides of the pond aiming for academia – Nature

* The automated lab: Start-up firms say robotics and software that autonomously record every detail of an experiment can transform the efficiency and reliability of research – Erika Check Hayden – Nature

* Essay Mills, not really plagiarism, but still disturbing:
Inside the Term Paper Plagiarism for Profit Industry – Joanna Evoniuk – GoLocalPDX

Bik’s Picks

Identification of the remains of King Richard III – Turi E. King – Nature Communications

People search for meaning when they approach a new decade in chronological age – Adam L. Alter – PNAS USA

Koalas Really Do Know Their Eucalyptus Leaves – Chris Pash – BusinessInsider

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Microbiome digest, December 2, 2014

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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

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Microbiome Digest, December 1, 2014

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Microbiome of pregnancy and birth

Increased periodontal inflammation in women with preterm premature rupture of membranes – Pascale F. M. Stadelmann- Clinical Oral Investigations

Human respiratory microbiome

Host–microorganism interactions in lung diseases – Benjamin J. Marsland & Eva S. Gollwitzer – Nature Reviews Immunology

Animal and reactor models of microbiome research

Effects of nitrate addition to a diet on fermentation and microbial populations in the rumen of goats, with special reference to Selenomonas ruminantium having the ability to reduce nitrate and nitrite – Narito Asanuma – Animal Science Journal

Modulation of the faecal microbiome of healthy adult dogs by inclusion of potato fibre in the diet – Matthew R. Panasevich – British Journal of Nutrition

To pool or not to pool? Impact of the use of individual and pooled fecal samples for in vitro fermentation studies – Aguirre M – Journal of Microbiology Methods (Pubmed link, link to article broken as of today)

Soil and sediment microbiome

Shifts of tundra bacterial and archaeal communities along a permafrost thaw gradient in Alaska – Jie Deng – Molecular Ecology

Production of gaseous hydrocarbons by microbial communities of Lake Baikal bottom sediments – O. N. Pavlova – Microbiology

Viruses and phages

Editorial on “Virus Ecology and Disturbances: Impact of Environmental Disruption on the Viruses of Microorganisms” – Heather K. Allen and Stephen T. Abedon – Frontiers in Microbiology

Transcriptomics, Proteomics

Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage – Emilie E. L. Muller – Nature Communications

Bioinformatics

A review of software for analyzing molecular sequences – Haema Nilakanta – BMC Research Notes

Other papers

Animal Phylogeny and Its Evolutionary Implications – Casey W Dunn – Annual Review of Ecology, Evolution, and Systematics

Microbes in the news

Without genes pilfered from bacteria, ticks would drop dead of the Lyme disease they carry – Darryl Fears – Washington Post

Bik’s Picks

Ancient dental plaque: A ‘whey’ into our milk drinking past? – Science Daily

Does Intermittent Fasting Have Benefits? Science Suggests Yes – Charles Q. Choi – LiveScience

10 times science ruled in 2014 – Jacqui Devaney – Mashable

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Microbiome digest, November 25, 2014

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Human respiratory microbiome

Improved characterization of medically relevant fungi in the human respiratory tract using next-generation sequencing – Bittinger K – Genome Biology

Human gut microbiome

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

Intestinal dysbiosis in ankylosing spondylitis – Mary-Ellen Costello – Arthritis & Rheumatology

Systematic genomic analysis reveals the complementary aerobic and anaerobic respiration capacities of the human gut microbiota – Dmitry A. Ravcheev and Ines Thiele – Frontiers in Microbiology

* Bacteroides dorei dominates gut microbiome prior to autoimmunity in Finnish children at high risk for type 1 diabetes – Austin G. Davis-Richardson – Frontiers in Microbiology

* Children Living near a Sanitary Landfill Have Increased Breath Methane and Methanobrevibacter smithii in Their Intestinal Microbiota – Humberto Bezerra de Araujo Filho – Archaea

Gut microbiota and metabolic syndrome – Davide Festi – World Journal of Gastroenterology

Animal and other models of microbiome research

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

Infant formula supplemented with low protein and high carbohydrate alters the intestinal microbiota in neonatal SD rats – Wenguang Fan – BMC Microbiology

Comparing the effects of acute alcohol consumption in germ-free and conventional mice: the role of the gut microbiota – Canesso MCC – BMC Microbiology

The presence of nitrate dramatically changed the predominant microbial community in perchlorate degrading cultures under saline conditions – Victor G Stepanov – BMC microbiology

Intestinal Epithelial Cell Toll-like Receptor 5 Regulates the Intestinal Microbiota to Prevent Low-Grade Inflammation and Metabolic Syndrome in Mice – Benoit Chassaing – Gastroenterology

Model systems to analyze the role of miRNAs and commensal microflora in bovine mucosal immune system development – Guanxiang Liang – Molecular Immunology

Animal microbiome

* Gorilla gorilla gorilla gut: a potential reservoir of pathogenic bacteria as revealed using culturomics and molecular tools – Fadi Bittar – Scientific Reports

* Influence of dietary feathers on the fecal microbiota in captive Arctic fox: Do dietary hair or feathers play a role in the evolution of carnivorous mammals? – Liang Zhang – Integrative Zoology

An Antimethanogenic Nutritional Intervention in Early Life of Ruminants Modifies Ruminal Colonization by Archaea – Leticia Abecia – Archaea

The microbiome of New World vultures – Michael Roggenbuck – Nature Communications

* Uncovering the Cultivable Microbial Diversity of Costa Rican Beetles and Its Ability to Break Down Plant Cell Wall Components – Gabriel Vargas-Asensio – PLOS ONE

The effect of anthropogenic arsenic contamination on the earthworm microbiome – Pass D. A – Environmental Microbiology

Plant microbiome

Brassica seed meal soil amendments transform the rhizosphere microbiome and improve apple production though resistance to pathogen re-infestation – Mark Mazzola – Phytopathology

Water microbiome

* Deciphering Diversity and Ecological Function From Marine Metagenomes – Holly M. Bik – The Biological Bulletin

Ciliate Diversity, Community Structure, and Novel Taxa in Lakes of the McMurdo Dry Valleys, Antarctica – Yuan Xu – The Biological Bulletin

Impact of ocean phytoplankton diversity on phosphate uptake – Michael W. Lomas – PNAS USA

Metagenomes of Microbial Communities in Arsenic-and Pathogen-Contaminated Well and Surface Water from Bangladesh – AC Layton – Genome Announcements

 

Comparisons of the composition and biogeographic distribution of the bacterial communities occupying South African thermal springs with those inhabiting deep subsurface fracture water – Cara Magnabosco – Frontiers in Microbiology

Soil microbiome

Fluazifop-P-butyl (herbicide) affects richness and structure of soil bacterial communities
Trabelsi Darine – Soil Biology and Biochemistry

Prolonged irrigation with municipal wastewater promotes a persistent and active soil microbial community in a semiarid agroecosystem – F. García-Orenes – Agricultural Water Management

Long-term balanced fertilization increases the soil microbial functional diversity in a phosphorus-limited paddy soil – Jian-Qiang Su – Molecular Ecology

Different bulk and active bacterial communities in cryoconite from the margin and interior of the Greenland ice sheet – Marek Stibal – Environmental Microbiology Reports

Soil bacterial community structure remains stable over a five-year chronosequence of insect-induced tree mortality – Scott Ferrenberg – Frontiers in Microbiology

Metagenomics and genome organization

Rapid Core-Genome Alignment and Visualization for Thousands of Intraspecific Microbial Genomes – Treangen TJ – Genome Biology

Flexibility and Symmetry of Prokaryotic Genome Rearrangement Reveal Lineage-Associated Core-Gene-Defined Genome Organizational Frameworks – Yu Kang – mBio

Antibacterial gene transfer across the tree of life – Jason A Metcalf – eLife

Transcriptomics

Comparison of assembly algorithms for improving rate of metatranscriptomic functional annotation – Celaj A – Microbiome

Metabolomics

* Metabolomics reveals differential metabolic adjustments of normal and overweight subjects during overfeeding – Beatrice Morio – Metabolomics

Microbes in the news

* Healthy gut microbiota can prevent metabolic syndrome, researchers say – Science Daily

Microbiome Study Reveals Typically Pathogenic Bugs in Vulture Guts – GenomeWeb

The Excrement Experiment – Treating disease with fecal transplants – Emily Eakin – The New Yorker

Science and art

Maria Merian’s Butterflies: The Illustrated Story of How a 17th-Century Woman Forever Changed the Course of Science Through Art – Maria Popova – Brain Pickings

Bik’s Picks

Genome of the house fly, Musca domestica L., a global vector of diseases with adaptations to a septic environment – Jeffrey G Scott – Genome Biology

Museum specimens reveal loss of pollen host plants as key factor driving wild bee decline in The Netherlands – Jeroen Scheper – PNAS USA

* We don’t read about dinosaurs – Pat Schloss – Mothur blog

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Microbiome digest, November 24, 2014

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General microbiome

Microbial sequencing to improve individual and population health – Sharon J Peacock and George M Weinstock – Genome Medicine

Human oral microbiome

Shifts in Campylobacter species abundance may reflect general microbial community shifts in periodontitis progression – Karsten Henne – Journal of Oral Microbiology

Human respiratory microbiome

Analysis of the bacterial community in chronic obstructive pulmonary disease sputum samples by denaturing gradient Gel electrophoresis and real-time PCR – Dachang Wu – BMC Pulmonary Medicine

Human gut microbiome

Microbiome and cancer – Naoko Ohtani – Seminars in Immunopathology

The Gut Microbiome and the Brain – Leo Galland – Journal of Medicinal Food

The ELDERMET biobank: Isolation and characterization of the intestinal microbiota from elderly Irish subjects – Lakshminarayanan, Bhuvaneswari

Animal models of microbiome

Hydrogen sulphide protects against NSAID-enteropathy through modulation of bile and the microbiota – Rory W Blackler – British Journal of Pharmacology

Plant microbiome

Towards a holistic understanding of the beneficial interactions across the Populus microbiome – Stéphane Hacquard – New Phytologist

Soil microbiome

Soil Fungal Communities Respond to Grassland Plant Community Richness and Soil Edaphics – Nicholas LeBlanc – Microbial Ecology

Impact of plant species evenness, dominant species identity and spatial arrangement on the structure and functioning of soil microbial communities in a model grassland – L. Massaccesi – Oecologia

Contrasting assembly processes in a bacterial metacommunity along a desiccation gradient – Angel Valverde – Frontiers in Microbiology

 

Water microbiome

Metatranscriptome of marine bacterioplankton during winter time in the North Sea assessed by total RNA sequencing – Anna Kopf – Marine Genomics

Integrated metagenomic and metaproteomic analyses of marine biofilm communities – Dagmar H. Leary – Biofouling: The Journal of Bioadhesion and Biofilm Research

 

Spatial Diversity of Bacterioplankton Communities in Surface Water of Northern South China Sea – Jialin Li – PLOS ONE

* High Genetic Diversity and Novelty in Eukaryotic Plankton Assemblages Inhabiting Saline Lakes in the Qaidam Basin – Jiali Wang – PLOS ONE

Effects of ocean acidification on the biogenic composition of the sea-surface microlayer: Results from a mesocosm study – Luisa Galgani – Journal of Geophysical Research: Oceans

Other (Food, biotechnology)

Microbial Dynamics and Control in Shale Gas Production – Jason Gaspar – Environmental Science & Technology Letters

Dynamics and diversity of microbial community succession in traditional fermentation of Shanxi aged vinegar – Zhiqiang Nie – Food Microbiology

Resilience of Aggregated Microbial Communities Subjected to Drought—Small-Scale Studies – Amélie Barthès – Microbial Ecology

Microbial diversity in sugarcane ethanol production in a Brazilian distillery using a culture-independent method – Ohana Yonara Assis Costa – Journal of Industrial Microbiology & Biotechnology

 

Metagenomics and viromes

Evaluation of viral genome assembly and diversity estimation in deep metagenomes – Daniel Aguirre de Cárcer – BMC Genomics

Niche-dependent genetic diversity in Antarctic metaviromes – Olivier Zablocki – Bacteriophage

Metabolomics

The cross-talk between opportunistic fungi and the mammalian host via microbiota’s metabolism – Luigina Romani – Seminars in Immunopathology

The metabolomics of airway diseases, including COPD, asthma and cystic fibrosis – B. Fatemeh Nobakht M. Gh. – Biomarkers

 

Metabolomics as a tool for diagnosis and monitoring in coeliac disease – Danielle Ryan – Metabolomics

 

Transcriptomics

Single-cell transcriptomics for microbial eukaryotes – Martin Kolisko – Current Biology

Bioinformatic tools

The R package otu2ot for implementing the entropy decomposition of nucleotide variation in sequence data – Alban Ramette and Pier Luigi Buttigieg – Frontiers in Microbiology

Techniques

Introduction to Genetic, Genomic, and System Analyses for Communities – Jack A. Gilbert, Nicole M. Scott – Springer Protocols Handbooks 2014

Microbes in the news

It’s all around us: Three scientists on how the microbiome shapes our world – Plus: Why you shouldn’t give probiotics to your dog – Brooke Borel

Professor’s new book aims to advance microbiome research – Brian McNeill – Phys.org

Book: Metagenomics for Microbiology, 1st Edition – Izard and Rivera – Elsevier

Symbiota Maps Plant Microbiome to Boost Crop Yields – Martin LaMonica – Xconomy

* History Lessons from Bacteria – Cindy Lu – Cell

 

Revolutionizing the interaction between plants and bacteria – Phys.org

Life’s extremists may be an untapped source of antibacterial drugs – David Salisbury – VanderBilt.edu

 

Science, publishing, career

Point of view: How postdocs benefit from building a union – Benjamin Cain

Bik’s Picks

The XKCD guid to the universe’s most bizarre physics – Randall Munroe – Wired.com

Physicists Solve Mystery of Scotch Whisky Rings – Rachel Nuwer – Scientific American

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Microbiome digest, November 21, 2014

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Microbiome general

Rare biosphere exploration using high-throughput sequencing: research progress and perspectives – Aibin Zhan, Hugh J. MacIsaac – Conservation Genetics

Human oral microbiome

Polymicrobial synergy and dysbiosis in inflammatory disease – Richard J. Lamonta, George Hajishengallis – Trends in Molecular Medicine

Human skin microbiome

* Dialogue between skin microbiota and immunity – Yasmine Belkaid, Julia A. Segre – Science

Human respiratory microbiome

Asthma 2014: from monoclonals to the microbiome – Peter G Gibson, Paul S Foster – The Lancet Respiratory Medicine

Human gut microbiome

Development of Fecal Microbiota Transplantation Suitable for Mainstream Medicine – Alexander Khoruts – Clinical Gastroenterology and Hepatology

The role of the gut and microbes in the pathogenesis of spondyloarthritis – Mark Asquith – Best Practice & Research Clinical Rheumatology

From lifetime to evolution: timescales of human gut microbiota adaptation – Sara Quercia – Frontiers in Microbiology

Animal and other models of microbiome research

Development of aminoglycoside and β-lactamase resistance among intestinal microbiota of swine treated with lincomycin, chlortetracycline, and amoxicillin – Jian Sun – Frontiers in Microbiology

Model systems to analyze the role of miRNAs and commensal microflora in bovine mucosal immune system development – Guanxiang Liang – Molecular Immunology

Gut Microbial Colonization Orchestrates TLR2 Expression, Signaling and Epithelial Proliferation in the Small Intestinal Mucosa – Nives Hörmann – PLOS ONE

The effects of elevated CO2 concentration on competitive interaction between aceticlastic and syntrophic methanogenesis in a model microbial consortium – Souichiro Kato – Frontiers in Microbiology

Animal microbiome

Aerobic cloacal and pharyngeal bacterial flora in six species of free-living birds – J. Stenkat – Journal of Applied Microbiology

Plant microbiome

Expanding genomics of mycorrhizal symbiosis – Alan Kuo – Frontiers in Microbiology

Soil and sediment microbiome

* Impact of interspecific interactions on antimicrobial activity among soil bacteria – Olaf Tyc – Frontiers in Microbiology

* Application of ancient DNA to the reconstruction of past microbial assemblages and for the detection of toxic cyanobacteria in subtropical freshwater ecosystems – Gabriela Martínez de la Escalera – Molecular Ecology

Characterisation of the soil microbial community of cultivated and uncultivated vertisol in Australia under several management regimes – Karuna Shrestha – Agriculture, Ecosystems & Environment

Wastewater reuse in irrigation: A microbiological perspective on implications in soil fertility and human and environmental health – Cristina Becerra-Castro – Environment International

Kotuikan Formation assemblage: a diverse organic-walled microbiota in the Mesoproterozoic Anabar succession, northern Siberia – Natalya G. Vorob’eva – Precambrian Research

Water microbiome

Diurnal expression of SAR11 proteorhodopsin and 16S rRNA genes in coastal North Atlantic waters – Raphaël Lami, David L. Kirchman – Aquatic Microbial Ecology

Leaf-litter-associated fungi and bacteria along temporal and environmental gradients in boreal streams – Jenny Bergfur, Carina Sundberg – Aquatic Microbial Ecology

Seasonal variation in marine-snow-associated and ambient-water prokaryotic communities in the northern Adriatic Sea – Jana Vojvoda – Aquatic Microbial Ecology

Microbial eukaryote diversity in the marine oxygen minimum zone off northern Chile – Darren J. Parris – Frontiers in Microbiology

* Resolving the abundance and air-sea fluxes of airborne microorganisms in the North Atlantic Ocean – Eva Mayol – Frontiers in Microbiology

Microbial contributions to coupled arsenic and sulfur cycling in the acid-sulfide hot spring Champagne Pool, New Zealand – Katrin Hug – Frontiers in Microbiology

Food microbiology

* Unpasteurised commercial boza as a source of microbial diversity – Andrea Osimani – International Journal of Food Microbiology

Metabolomics

* Prediction and quantification of bioactive microbiota metabolites in the mouse gut –
Gautham V. Sridharan – Nature Communications

An isotope-labeled chemical derivatization method for the quantitation of short-chain fatty acids in human feces by liquid chromatography–tandem mass spectrometry – Jun Han – Analytica Chimica Acta

Metagenomics / Bioinformatics

Key roles for freshwater Actinobacteria revealed by deep metagenomic sequencing – Rohit Ghai – Molecular Ecology

* BiomeNet: A Bayesian Model for Inference of Metabolic Divergence among Microbial Communities – Mahdi Shafiei – PLOS Computational Biology

Phylogeny and phylogeography of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships – Maggie C. Y. Lau – Frontiers in Microbiology

Techniques

Microbial Contamination in Next Generation Sequencing: Implications for Sequence-Based Analysis of Clinical Samples – Michael J. Strong – PLOS Pathogens

Comparing High-throughput Platforms for Sequencing the V4 Region of SSU-rDNA in Environmental Microbial Eukaryotic Diversity Surveys – Frédéric Mahé – Journal of Eukaryotic Microbiology

More microbiology papers

The Red Queen Model of Recombination Hotspots Evolution in the Light of Archaic and Modern Human Genomes – Yann Lesecque – PLOS Genetics

Association between Footwear Use and Neglected Tropical Diseases: A Systematic Review and Meta-Analysis – Sara Tomczyk – PLOS Neglected Tropical Diseases

Impact of wash cycle time, temperature and detergent formulation on the hygiene effectiveness of domestic laundering – M. Honisch – Journal of Applied Microbiology

Microbes in the news

Contaminated samples point the finger at the wrong suspects – Dalmeet Chawla – Imperial College London

Analyzing COPD Patients’ Sputum And Microbiota Composition Might Improve Treatment – Isaura Santos – Lung Disease News

Willy Burgdorfer, Who Found Bacteria That Cause Lyme Disease, Is Dead at 89 – William Yardley – The New York Times

Plants talk to each other using an internet of fungus – Nic Fleming – BBC

Bacteria on Russian ‘sex satellite’ survive reentry – Alec Luhn – The Guardian

Body’s bacteria may keep our brains healthy – Elizabeth Pennisi – Science Magazine

Hand dryers ‘splatter’ users with bacteria, scientists warn – Sarah Knapton – Telegraph UK

Unique sense of ‘touch’ gives a prolific bacterium its ability to infect anything – Morgan Kelly – Princeton

Science, publishing and career

Gates Foundation announces world’s strongest policy on open access research – Richard Van Noorden – Nature News Blog

Bogus Journal Accepts Profanity-Laced Anti-Spam Paper – Jeffrey Beal – Scholarly Open Access

* Sh*t My Reviewers Say – Collecting the finest real specimens of reviewer comments since 1456

Ten Simple Rules to Achieve Conference Speaker Gender Balance – Jennifer L. Martin – PLOS ONE

Bik’s Picks

Shedding light on skin color – Ann Gibbons – Science

Flashback Friday: Does garlic protect against vampires? An experimental study – Seriously Science – Discover Magazine

The Secret Life of Passwords – Ian Urbina – New York Times

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Microbiome digest, November 20, 2014

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Human gut microbiome

* Altered Duodenal Microbiota Composition in Celiac Disease Patients Suffering From Persistent Symptoms on a Long-Term Gluten-Free Diet – Pirjo Wacklin – American

Friend and foe: factors influencing the movement of the bacterium Helicobacter pylori along the parasitism–mutualism continuum – Derek Lin and Britt Koskella – Evolutionary Applications

 

Investigation of pH and Temperature Profiles in the GI Tract of Fasted Human Subjects Using the Intellicap® System – Mirko Koziolek – Journal of Pharmaceutical Sciences

Human vaginal microbiome

Vaginal Microbiota and Sexually Transmitted Infections That May Influence Transmission of Cell-Associated HIV – Richard A. Cone – Journal of Infectious Diseases

Animal models of microbiome research

The gut microbiota influences blood-brain barrier permeability in mice – Viorica Braniste – Science Translational Medicine

Association of Obesity with Serum Leptin, Adiponectin, and Serotonin and Gut Microflora in Beagle Dogs – H.-J. Park – Journal of Veterinary Internal Medicine

Animal microbiome

Evaluation of five antibiotics on larval gut bacterial diversity of Plutella xylostella (Lepidoptera: Plutellidae) – Xiao-Li Lin – Insect Science

Soil microbiome

Regional-scale patterns of soil microbes and nematodes across grasslands on the Mongolian plateau: relationships with climate, soil, and plants – Dima Chen – Ecography

Water microbiome

Using a “time machine” to test for local adaptation of aquatic microbes to temporal and spatial environmental variation – Jeremy W. Fox andLawrence D. Harder – Evolution

Role of microorganisms in oceanic anoxic events (OAEs) – Muriel Pacton and Georges E. Gorin – Geology Today

Microbiome of the built environment

* Environmental contamination and hospital-acquired infection: factors that are easily overlooked – C. Beggs – Indoor Air

Bioinformatics

* rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development – Steven F. Stoddard – Nucleic Acids Research

Microbes in the news

Shift in gut bacteria observed in fiber supplement study may offer good news for weight loss – Science Daily – November 18 2014

Altered microbiota linked to GI symptoms in celiac patients on strict diet – Healio.com

Interview with David Sela: Food scientist proposes way to improve health via breast milk – Cecilia Prado – Daily Collegian

* Mother’s Microbes Protect Baby’s Brain – Ruth Williams – The Scientist

Germophobes, spoiler alert: WSU presentation to suggest not all bacteria is bad – Marcia Ratcliff – Winona Daily News

How Gut Bacteria Can Lead to Weight Gain (video) – Melinda Beck – Wall Street Journal

Genes Revealed that May Impact the Colonization of Beneficial Bacteria – Sarah Plumridge – Northwestern.edu

Microbiome Move Over: the Gut Virome Makes Its Debut – Lara C. Pullen – Medscape

Virus Protects Mouse Gut – Tracy Vence – The Scientist

Upcoming events

2014-15: Bioinformatics: Discovering Patterns in Human Microbiome Data (HMD): March 16-18, 2015

Science and Art

If you are looking for Herpes virus pillows: Virus Cushions – Ohh Reindeer

3D printed giant germs help visually impaired see the world of microorganisms – Nanowerk

Doing science experiments on music: Cymatics: Science Vs. Music – Nigel Stanford – Vimeo.com

Bik’s Picks

Magic shoes: How to hear yourself instantly happy – Corrinne Burns – New Scientist

Out of India: Finding the origins of horses, rhinos – Science Daily

Here’s Why Cats Keep Rubbing Against Our Legs (And Why Catnip Makes Them Go Crazy) – Jacueline Howard – The Huffington Post

Here’s Why Dogs Kick Their Legs When You Rub Their ‘Sweet Spot” – Jacueline Howard – The Huffington Post

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Microbiome digest, November 19, 2014

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Skin microbiome of infants, viruses can replace bacteria for proper development of gut anatomy, and Amazon reviews of note.

Human skin microbiome

Evolving Concepts of Neonatal Skin – Carrie C. Coughlin and Alain Taïeb – Pediatric Dermatology

Clinical Approaches to Skin Cleansing of the Diaper Area: Practice and Challenges – Carrie C. Coughlin – Pediatric Dermatology

Psoriasis is not an autoimmune disease? – Lionel Fry – Experimental Dermatology

Animal models of microbiome research

* An enteric virus can replace the beneficial function of commensal bacteria – Elisabeth Kernbauer, Yi Ding & Ken Cadwell – Nature

Microbiology: A backup for bacteria – Yao Wang & Julie K. Pfeiffer – Nature

Animal microbiome

An Experimental Test of whether the Defensive Phenotype of an Aphid Facultative Symbiont Can Respond to Selection within a Host Lineage – Ailsa H.C. McLean – PLOS ONE

Effect of yeast with bacteriocin from rumen bacteria on laying performance, blood biochemistry, faecal microbiota and egg quality of laying hens – H. T. Wang – Journal of Animal Physiology and Animal Nutrition

* Symbiotic bacteria enable olive flies (Bactrocera oleae) to exploit intractable sources of nitrogen – M. Ben-Yosef – Journal of Evolutionary Biology

Plant microbiome

* Bacterial Endophytic Communities in the Grapevine Depend on Pest Management – Andrea Campisano – PLOS ONE

Metagenomics, transcriptomics

Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics – Zheng-Shuang Hua – ISME Journal

Community transcriptomics reveals unexpected high microbial diversity in acidophilic biofilm communities – Daniela S Aliaga Goltsman – ISME Journal

Ecology

Evolution of species interactions determines microbial community productivity in new environments – Francesca Fiegna – ISME Journal

Microbes in the news

Viruses as a Cure – Carl Zimmer – New York Times

A Lack of Bacteria Can Make You Overweight – Melinda Beck – The Wall Street Journal

Science, publishing and career

* Stereotyping: PhD costume slammed – Nature

* She still needs help from Ken: Amazon reviews trash Barbie computer engineering book – Kevin Allen – Ragan’s PR Daily

Science and Art

This looks more like a genome than a plasmid, but it is pretty: ”Plasmid 29″ – Sandra Culliton – Etsy

Bik’s Picks

A hip-hop state of mind – Akeem Sule, Becky Inkster – The Lancet

 

House Passes Bill That Makes It Harder For Scientists To Advise The EPA – Emily Atkin – Think Progress

Mother’s soothing presence makes pain go away, changes gene activity in infant brain – Science Daily

Science (and Quacks) vs. the Aging Process – Tracey Samuelson – New York Times

Sorting Fact From Fiction and What the Best Science Writing Can Teach Us – Barbara J. King – Time

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Microbiome digest, November 18, 2014

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Pregnancy and birth microbiome

Fetal exposures and perinatal influences on the stool microbiota of premature infants – Diana A. Chernikova – Journal of Maternal-Fetal and Neonatal Medicine

* The Origin of Human Milk Bacteria: Is There a Bacterial Entero-Mammary Pathway during Late Pregnancy and Lactation? – Juan M. Rodríguez – Advances in Nutrition

Human oral microbiome

Dysbiosis and alterations in predicted functions of subgingival microbiome in chronic periodontitis – Mariana E. Kirst – Applied and Environmental Microbiology

Human respiratory microbiome

Analysis of Changes in Diversity and Abundance of the Microbial Community in a Cystic Fibrosis Patient Over a Multi-Year Period – Joshua R. Stokell – Journal of Clinical Microbiology

Human gut microbiome

* Gut Microbes and the Brain: Paradigm Shift in Neuroscience – Emeran A. Mayer – Journal of Neuroscience

Fiber supplementation influences phylogenetic structure and functional capacity of the human intestinal microbiome: follow-up of a randomized controlled trial – Hannah D Holscher – American Journal of Clinical Nutrition

Enteric microbiota leads to new therapeutic strategies for ulcerative colitis – Wei-Xu Chen – World Journal of Gastroenterology

Intestinal microbiota: The explosive mixture at the origin of inflammatory bowel disease? – Roberto Bringiotti – – World Journal of Gastroenterology

Direct Detection and Quantification of Bacterial Genes Associated with Inflammation in DNA Isolated from Stool – Ramon Gomez-Moreno – Advances in Microbiology

Review: The gut microbiome in health and in disease – Shreiner, Andrew B – Current Opinion in Gastroenterology

Animal models of microbiome research

* Composition of Intestinal Microbiota in Immune-Deficient Mice Kept in Three Different Housing Conditions – Christa Thoene-Reineke – PLOS ONE

The Gut Microbiota Modulates Glycaemic Control and Serum Metabolite Profiles in Non-Obese Diabetic Mice – Thomas U. Greiner – PLOS ONE

Animal microbiome

* Convergent Bacterial Microbiotas in the Fungal Agricultural Systems of Insects – Frank O. Aylward – mBio

* Optimization of preservation and processing of sea anemones for microbial community analysis using molecular tools – Joana Rocha – Scientific Reports

Global discovery of colonization determinants in the squid symbiont Vibrio fischeri – John F. Brooks, II – PNAS US

Plant microbiome

It takes an individual plant to raise a community: TRFLP analysis of the rhizosphere microbial community of two pairs of high- and low-metal-accumulating plants – Melanie P. Columbus – Soil Biology and Biochemistry

Soil and sediment microbiome

* Uncoupling of microbial community structure and function in decomposing litter across beech forest ecosystems in Central Europe – Witoon Purahong – Scientific Reports

Different Continuous Cropping Spans Significantly Affect Microbial Community Membership and Structure in a Vanilla-Grown Soil as Revealed by Deep Pyrosequencing – Wu Xiong – Microbial Ecology

Deforestation and cultivation with Maize (Zea mays L.) has a profound effect on the bacterial community structure in soil – Elizabeth Selene Gómez-Acata – Land Degradation & Development

Soil pH Determines Microbial Diversity and Composition in the Park Grass Experiment – Kateryna Zhalnina – Microbial Ecology

Shifts in carbon substrate utilization in sediment microbial communities along the Llobregat River – Anna Freixa – Fundamental and Applied Limnology / Archiv für Hydrobiologie

Salt effects on the soil microbial decomposer community and their role in organic carbon cycling: A review – Kristin M. Rath – Soil Biology and Biochemistry

Water microbiome

* Metagenome Sequencing of the Microbial Community of a Solar Saltern Crystallizer Pond at Cáhuil Lagoon, Chile – Alvaro M. Plominsky – Genome Announcements

Experimental evidence for strong stabilizing forces at high functional diversity of aquatic microbial communities – Francesco Carrara – ESA Ecology

Microbiome of the built environment

* Ecological succession and viability of human-associated microbiota on restroom surfaces – Sean M. Gibbons – Applied and Environmental Microbiology

* Seasonal Variability in Airborne Biotic Contaminants in Swine Confinement Buildings – Priyanka Kumari – PLOS ONE

Metabolomics

Bacterial microcompartments and the modular construction of microbial metabolism – Cheryl A. Kerfeld – Trends in Microbiology

* Suppression of Microbial Metabolic Pathways Inhibits the Generation of the Human Body Odor Component Diacetyl by Staphylococcus spp – Takeshi Hara – PLOS ONE

Bioinformatics

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

* Poster: Assessment of eukaryotic communities in environmental samples: A workflow comparison for next-generation sequencing data – Kristin Hardge – ePIC

Archaea

Phylogenetically Driven Sequencing of Extremely Halophilic Archaea Reveals Strategies for Static and Dynamic Osmo-response – Erin A. Becker – PLOS Genetics

More microbiology papers

* The commonly used antimicrobial additive triclosan is a liver tumor promoter – Mei-Fei Yueh – PNAS USA

Microbes in the News

Virus linked to mass die-off of sea stars – Craig Welch – The Seattle Times

Bik’s Picks

Wild chimpanzees plan their breakfast time, type, and location – Karline R. L. Janmaat – PNAS USA

Here Are 4 More Vulnerable Fish to Avoid Next Time You’re at the Sushi Bar – Dan Kedmey – Time

Comet landing: Organic molecules detected by Philae – Paul Rincon – BBC News

Correlation instead of causation?: Coffee Creamer, Crackers Linked To Worse Memory – Science2.0

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Microbiome digest, November 13, 2014

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Microbiome of pregnancy and birth

Hyaluronan in cervical epithelia protects against infection-mediated preterm birth – Yucel Akgul – Journal of Clinical Investigation

The Impact of the Milk Glycobiome on the Neonate Gut Microbiota – Alline R. Pacheco – Annual Review of Animal Biosciences

Human oral microbiome

The oral microbiome and the immunobiology of periodontal disease and caries – Massimo Costalonga – Immunology Letters

Human gut microbiome

Intestinal microbiota as modulators of the immune system and neuro-immune system: impact on the host health and homeostasis – Carlos Magno da Costa Maranduba – Journal of Immunology Research

The role of the microbiota in inflammation, carcinogenesis, and cancer therapy – Amiran Dzutsev – European Journal of Immunology

Animal microbiome

The Insect Microbiome Modulates Vector Competence for Arboviruses – Natapong Jupatanakul – Viruses

Bacterial community structure in Apis florea larvae analyzed by denaturing gradient gel electrophoresis and 16S rRNA gene sequencing – Prakaimuk Saraithong – Insect Science

Pezizomycotina dominates the fungal communities of South China Sea Sponges Theonella swinhoei and Xestospongia testudinaria – Liling Jin – FEMS Microbiology Ecology

Plant microbiome

Plant lignin content altered by soil microbial community – Alison E. Bennett – New Phytologist

Bioreactor microbiome

Ciprofloxacin Residues in Municipal Biosolid Compost Do Not Selectively Enrich Populations of Resistant Bacteria – Caitlin P. Youngquist – Applied and Environmental Microbiology

Food microbiology

Spatial Distribution of Bacterial Communities and Related Biochemical Properties in Luzhou-Flavor Liquor-Fermented Grains – Jia Zheng- Journal of Food Science

Bacterial Community Dynamics of Salted and Fermented Shrimp based on Denaturing Gradient Gel Electrophoresis – Kook-Il Han – Journal of Food Science

Metabolomics

Microbiota-dependent metabolite trimethylamine-N-oxide is associated with disease severity and survival of patients with chronic heart failure – Marius Trøseid – Journal of Internal Medicine

Techniques

* Performance Comparison of Illumina and Ion Torrent Next-Generation Sequencing Platforms for 16S rRNA-Based Bacterial Community Profiling – Stephen J. Salipante – Applied and Environmental Microbiome

Impact of T-RFLP data analysis choices on assessments of microbial community structure and dynamics – Nils Johan Fredriksson – BMC Bioinformatics

A Hidden Pitfall in the Preparation of Agar Media Undermines Microorganism Cultivability – Tomohiro Tanaka – Applied and Environmental Microbiome

Microbes in the news

Contamination plagues some microbiome studies – Elizabeth Pennisi – Science Magazine

37 Trillion Invaders: We Are Not Alone – Science 2.0

Spilling Our Guts: Decreased Diversity in the Human Microbiome (podcast) – ScienceFriday

Nature, as Well as Nurture, Shapes Human Gut Microbiome – Lara C. Pullen – Medscape

Enterome Enters into a Microbiome-Based Development Collaboration with AbbVie in Crohn’s Disease – PRNewsWire

Pillow germs: Testing revealed bacteria growing on bed pillows; how often you should replace them – KJRH

“The Lung Ranger” Cystic Fibrosis Device From Dundee University Wins 3 Awards – Anna Tan – CysticFibrosisNewsToday

Science and Career

The point of it all – Joseph Swift – Science Magazine

No sexism in science? Not so fast, critics say – Rachel Bernstein – Science Magazine

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