Category Archives: Plant Root Soil microbiome

Microbiome digest, November 26

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

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

Human gut microbiome

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

Animal gut microbiome

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

Plant microbiome

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

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

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

Soil microbiome

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

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

Water microbiome

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

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

Metagenomics, microbial genomes

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

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

Microbes in the news

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

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

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

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

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

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

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

Science, publishing, and career

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

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

* Academia gets social – Brian Owens – The Lancet

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

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

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

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

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

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

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

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

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

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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 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 17, 2014

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Microbiome in pregnancy and birth

16S rRNA Gene Sequencing, Multilocus Sequence Analysis, and Mass Spectrometry Identification of the Proposed New Species “Clostridium neonatale” – Philippe Bouvet – Journal of Clinical Microbiology

Human oral microbiome

Shaping the oral microbiota through intimate kissing – Remco Kort – Microbiome

Distinct composition of the oral indigenous microbiota in South Korean and Japanese adults – Toru Takeshita – Scientific Reports

Periodontal and peri-implant microbiota in patients with healthy and inflamed periodontal and peri-implant tissues – Long-Fei Zhuang – Clinical Oral Implants Research

An in vivo comparison of internal bacterial colonization in two dental implant systems: Identification of a pathogenic reservoir – Joanne Mawhinney – Acta Odontologica Scandinavica

Oral pathogens in children with respiratory disease – Yumiko Endo – Pediatric Dental Journal

Severity-Related Changes of Bronchial Microbiome in Chronic Obstructive Pulmonary Disease – Marian Garcia-Nuñez – Journal of Clinical Microbiology

Human vaginal microbiome

Diversity of vaginal microbial communities and role of PAP smear in its detection – Neha Batra – International Journal of Current Microbiology and Applied Sciences

Human microbiome – other and general

The conjunctival microbiome in health and trachomatous disease: a case control study – Yanjiao Zhou – Genome Medicine

What is a host? Incorporating the Microbiota into the ‘Damage-Response Framework’ – Arturo Casadevall and Liise-anne Pirofski – Infection and Immunity

Plant microbiome

Plant–insect interactions under bacterial influence: ecological implications and underlying mechanisms – Akiko Sugio – Journal of Experimental Botany

Soils and sediments microbiome

Bacterial community composition and biogeochemical heterogeneity in PAH-contaminated riverbank sediments – Gloria P. Johnston, Laura G. Leff – Journal of Soils and Sediments

Diversity of acidophilic prokaryotes at two acid mine drainage sites in Turkey – Pınar Aytar – Environmental Science and Pollution Research

Ammonia-oxidizing archaea versus bacteria in two soil aquifer treatment systems – Kun Ding – Applied Microbiology and Biotechnology

Water microbiome

Community dynamics of prokaryotic and eukaryotic microbes in an estuary reservoir – Zhen Sun – Scientific Reports

454 Pyrosequencing reveals diversity of Bdellovibrio and like organisms in fresh and salt water – Nan Li – Antonie van Leeuwenhoek

Metabolomics

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

Immunology

Prevention and cure of rotavirus infection via TLR5/NLRC4–mediated production of IL-22 and IL-18 – Benyue Zhang – Science

Microbes in the news

Worm Defies Tradition, Stores Gut Bacteria in Gills Instead – Elizabeth Preston – Discover Magazine

Here’s How Many Bacteria Spread Through One Kiss – Mandy Oaklander – Time

How Bacteria In The Gut Help Fight Off Viruses – Michaeleen Doucleff – Goats and Soda – NPR

This could be the most important scientific breakthrough in our lifetimes – Bengt Saelensminde – MoneyWeek

Probing the Microbial Mysteries of Wine – Iratxe Zarraonaindia and Jack A. Gilbert – Microbe

Self-destructing drone is made of fungus, bacteria, and wasp spit – Lee Mathews – Geek.com

Bik’s Picks

Scientists Descend into Massive Crater in Yamal Peninsula in Siberia: Bermuda Triangle Mystery Solved? – Rhodi Lee – Tech Times

Lightning expected to increase by 50 percent with global warming – Science Daily

Sometimes a Shirt is More Than Just a Shirt.. – Isis the Scientist

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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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Microbiome digest, November 12, 2014

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Another short installment of the Digest. Two studies on microbial DNA contamination in reagents and laboratories, and gut microbiome in Down Syndrome.
Human gut microbiome

* Gut Microbiome in Down Syndrome – Elena Biagi – PLOS ONE

* Superresolution Imaging Captures Carbohydrate Utilization Dynamics in Human Gut Symbionts – Krishanthi S. Karunatilaka – mBio

Microbiota Talks Cholera out of the Gut – Amanda J. Hay, Jun Zhu – Cell Host & Microbe

 

Animal microbiome

Comparative Metagenomic Analysis of Coral Microbial Communities Using a Reference-Independent Approach – Camila Carlos – PLOS ONE

The Effect of Antibiotics on Associated Bacterial Community of Stored Product Mites – Jan Kopecky – PLOS ONE

 

Metagenomic Insights into the RDX-Degrading Potential of the Ovine Rumen Microbiome – Robert W. Li – PLOS ONE

Plant microbiome

Functional Potential of Soil Microbial Communities in the Maize Rhizosphere – Xiangzhen Li – PLOS ONE

* Genome-wide association study of Arabidopsis thaliana leaf microbial community – Matthew W. Horton – Nature Communications

Environmental microbiome

A method for sampling microbial aerosols using high altitude balloons – N.C. Bryan – Journal of Microbiological Methods

Techniques

(preprint already featured here in July, but now officially out)
* Reagent and laboratory contamination can critically impact sequence-based microbiome analyses – Susannah J Salter – BMC Biology

* Diverse and Widespread Contamination Evident in the Unmapped Depths of High Throughput Sequencing Data – Richard W. Lusk – PLOS ONE

 

Reconceptualising the beta diversity-environmental heterogeneity relationship in running water systems – Jani Heino – Freshwater Biology

Microbes in the news

* Contaminomics: Why Some Microbiome Studies May Be Wrong – Ed Yong – National Geographic

* The Kitome: Dealing with the reagent microbiome – Pat Schloss – Mothur.org

DNA Extraction Kits Contaminated – Kerry Grens – The Scientist

Bik’s Picks

Serotonin lies at the intersection of pain and itch – Bethany Brookshire – ScienceNews

Rainbow palette found in Brooklyn’s contaminated water – Aviva Rutkin – New Scientist

This did not work on my cats, but feel free to try:
‘Cat Circles’, The Amazing Phenomenon In Which a Cat Will Always Sit Inside a Circle on the Floor – Lori Dorn – Laughing Squid

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Microbiome digest, November 10, 2014

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Pregnancy and birth microbiome

* Intestinal Microbiota is Different in Women with Preterm Birth: Results from Terminal Restriction Fragment Length Polymorphism Analysis – Arihiro Shiozaki – PLOS ONE

Ureaplasma species and Mycoplasma hominis in cervical fluid of pregnancies complicated by preterm prelabor rupture of membranes – Ivana Musilova – Journal of Maternal-Fetal and Neonatal Medicine

Human respiratory microbiome

Characterization and quantification of the fungal microbiome in serial samples from individuals with cystic fibrosis – Sven D Willger – Microbiome

Human gut microbiome

* The human intestinal microbiome at extreme ages of life. Dietary intervention as a way to counteract alterations – Nuria Salazar – Frontiers in Genetics

Nanosilver-Mediated Change in Human Intestinal Microbiota – Pranab Das – Journal of Nanomedicine & Nanotechnology

Animal microbiome

Bacterial Diversity Dynamics Associated with Different Diets and Different Primer Pairs in the Rumen of Kankrej Cattle – Dipti W. Pitta – PLOS ONE

Think laterally: horizontal gene transfer from symbiotic microbes may extend the phenotype of marine sessile hosts– Sandie M. Degnan – Frontiers in Microbiology

* Temporal changes in the bacterial community of animal feces and their correlation with stable fly oviposition, larval development, and adult fitness – Thais A. Albuquerque and Ludek Zurek – Frontiers in Microbiology

Plant microbiome

Bacterial networks and co-occurrence relationships in the lettuce root microbiota – Massimiliano Cardinale – Environmental Microbiome

Fungicide Effects on Fungal Community Composition in the Wheat Phyllosphere – Ida Karlsson – PLOS ONE

* Spatial structuring of bacterial communities within individual Ginkgo biloba trees – Jonathan W. Leff – Environmental Microbiology

Soil microbiome

Printing Soil: A single-step, high throughput method to isolate microorganisms and near-neighbor microbial consortia from a complex environmental sample – Bradley R. Ringeisen – Methods in Ecology and Evolution

Microbial communities of frozen soils of the Tuimaada Valley in Central Sakha – T. I. Ivanova – Biology Bulletin

Metabolomics

Automatic Prediction of Polysaccharide Utilization Loci in Bacteroidetes Species –
Nicolas Terrapon – Bioinformatics

Microbial Ecology

* The importance of sample archiving in microbial ecology – S. Craig Cary & Noah Fierer – Nature Reviews Microbiology

“it is an unwritten rule that all freezers will rapidly become filled to capacity, no matter how many freezers are purchased”

Coincidental Loss of Bacterial Virulence in Multi-Enemy Microbial Communities – Ji Zhang – PLOS ONE

Top-down effects of a lytic bacteriophage and protozoa on bacteria in aqueous and biofilm phases – Ji Zhang – Ecology and Evolution

Bioinformatics

Toward a better understanding of Apis mellifera and Varroa destructor microbiomes: introducing “PhyloH” as a novel phylogenetic diversity analysis tool – A Sandionigi – Molecular Ecology Resources

SRI International’s BioCyc Database Collection Expanded for Easy Access to Information about Microbes and Metabolic Pathways

Microbes in the news

* Will You Donate Your Poop To Science? – Christopher Robbins – Gothamist

Pediatric Research | Microbiome research exploding with new revelations – John Barnard – Dispatch

Line Dancing Bacteria on a Chip – UTwente.nl

* Researcher studies microbiome of the dead – Melissa Benmark – WKAR Michigan State University

Bik’s Picks

The Unbelievable Skepticism of the Amazing Randi – Adam Higginbotham – New York Times

Winners Announced For The World’s Richest Science Award: The $3 Million Breakthrough Prize – F.D. Flam – Forbes

* The Challenge of Teaching Science in Rural America – Alexandra Ossola – The Atlantic

Don’t swallow it: Six health myths you should ignore – New Scientist

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