Category Archives: Metabolomics

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 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 14, 2014

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Microbiome of pregnancy and birth

Prevention of preterm birth: Harnessing science to address the global epidemic – Craig E. Rubens – Science Translational Medicine

Human skin microbiome

* The Skin Microbiome: A Focus on Pathogens and Their Association with Skin Disease – Keisha Findley, Elizabeth A. Grice – PLOS Pathogens

Human respiratory microbiome

* Profiling bacterial community in upper respiratory tracts – Hana Yi – BMC Infectious Disease

Human gut microbiome

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

Diversity and Composition of the Adult Fecal Microbiome Associated with History of Cesarean Birth or Appendectomy: Analysis of the American Gut Project – James J. Goedert – EBioMedicine

In vivo efficacy of microbiota-sensitive coatings for colon targeting: A promising tool for IBD therapy – Y. Karrout – Journal of Controlled Release

Animal microbiome

Inhibition of fish pathogens by the microbiota from rainbow trout (Oncorhynchus mykiss, Walbaum) and rearing environment – Carlos Araújo – Anaerobe

Description of Lacinutrix venerupis sp. nov., a novel bacterium associated with reared clams – Aide Lasa – Systematic and Applied Microbiology

Water microbiome

Changes in bacterial and eukaryotic communities during sewage decomposition in Mississippi river water – Asja Korajkic – Water Research

Metabolomics

Bacterial Metabolite Indole Modulates Incretin Secretion from Intestinal Enteroendocrine L Cells – Catalin Chimerel – Cell Reports

Microbial Bile Acid Metabolic Clusters: The Bouncers at the Bar – Joseph A. Sorg – Cell Host & Microbe

 

Bile provides key to CDI resistance – Cláudio Nunes Alves – Nature Reviews Microbiology

Immunology

ATP-Gated Ionotropic P2X7 Receptor Controls Follicular T Helper Cell Numbers in Peyer’s Patches to Promote Host-Microbiota Mutualism – Michele Proietti – Immunity

The Interplay between the Intestinal Microbiota and the Immune System – Yuk Man Kevin Lei – Clinics and Research in Hepatology and Gastroenterology

Microbes in the news

Gut–brain link grabs neuroscientists – Idea that intestinal bacteria affect mental health gains ground – Sara Reardon – Nature

* More Evidence That There’s a Connection Between a Person’s Gut Bacteria And Brain – Colin Schultz – Smithsonian Magazine

“Microbiome” of Sierra Nevada yellow-legged frogs shifts during infectious disease outbreaks – National Science Foundation

Bacteria become ‘genomic tape recorders’, recording chemical exposures in their DNA – ScienceDaily

Science, publishing, career

How to write a first draft – Annelie – WriteScience.org

Bik’s Picks

Premature infants are exposed to unsafe levels of chemical in medical products used to save their lives – Science Daily

The Dutch Village Where Everyone Has Dementia – The Atlantic

Keeping Mates Close and Competition Out in an Ocean Sponge – Casey Dunn – New York Times

20 Vintage Gadgets from Scientific American Readers [Slide Show] – Larry Greenemeier – Scientific American

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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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Microbiome digest, November 3, 2014

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Human oral and vaginal microbiomes, rumen microbiome of impalas, sample handling and sponges, and two remarkable pieces in the New York Times.

Human oral microbiome

The association between the upper digestive tract microbiota by HOMIM and oral health in a population-based study in Linxian, China – Guoqin Yu – BMC Public Health

“Human Oral Microbe Identification Microarrays were used to test for the presence of 272 human oral bacterial species (97 genera) in upper digestive tract (UDT) samples collected from 659 participants. “

Pregnancy and birth microbiome

Poster: Comparison of the Vaginal Microbiomes of Pregnant Women of Four Ethnicities
and Identification of Taxa Associated with Urogenital Disease – Mendz GL – ECCMID Poster

“Principal component analysis suggested differences in the bacterial populations of healthy women and those with genital infections, with clustering of the latter along the Protobacteria axis “

Animal microbiome

Examination of the Rumen Bacteria and Methanogenic Archaea of Wild Impalas (Aepyceros melampus melampus) from Pongola, South Africa – Laura M. Cersosimo – Microbial Ecology

“In the present study, next-generation sequencing and real-time polymerase chain reaction were used to investigate the diversity and density of the bacteria and methanogenic archaea residing in the rumen of five adult male impalas”

Effects of sample handling and cultivation bias on the specificity of bacterial communities in keratose marine sponges – Cristiane C. Hardoim – Frontiers in Microbiology

Bacterial community profiling of the sympatric keratose species Sarcotragus spinosulus and Ircinia variabilis (Dictyoceratida, Irciniidae) was performed by polymerase chain reaction-denaturing gradient gel electrophoresis and 454-pyrosequecing of 16S rRNA gene fragments. “

Plant microbiome

Soil type-dependent effects of a potential biocontrol inoculant on indigenous bacterial communities in the rhizosphere of field-grown lettuce – Susanne Schreiter – FEMS Microbiology Ecology

“16S rRNA gene fragments amplified from total community DNA were analyzed by denaturing gradient gel electrophoresis (DGGE) and pyrosequencing. “

Are heterotrophic and silica-rich eukaryotic microbes an important part of the lichen symbiosis? – David M Wilkinson – Mycology: An International Journal on Fungal Biology

“In this necessarily speculative paper we highlight areas for future research and how newer technologies may be useful for understanding the full suite of organisms involved in the lichen symbiosis.”

Soil microbiome

Selection on soil microbiomes reveals reproducible impacts on plant function – Kevin Panke-Buisse – ISME Journal

“Analysis of the soil microbial community using 16 S rRNA gene sequencing showed distinct microbiota profiles assembling by flowering time treatment.”

Chemolithotrophy in the continental deep subsurface: Sanford Underground Research Facility (SURF), USA – Magdalena R. Osburn – Frontiers in Microbiology

“Geochemical data, energetic modeling, and DNA sequencing were combined with principle component analysis to describe this deep (down to 8100 ft below surface), terrestrial environment.”

Bioinformatic tools

* Seeing the forest for the genes: Using metagenomics to infer the aggregated traits of microbial communities – Noah Fierer – Frontiers in Microbiology

“Microbial ecologists could benefit by borrowing the concept of community-aggregated traits (CATs) from plant ecologists to glean more insight from the ever-increasing amount of metagenomic data being generated.”

Metabolomics

Fructan supplementation of senior cats affects stool metabolite concentrations and fecal microbiota concentrations, but not nitrogen partitioning in excreta – K.A. Barry – Journal of Animal Science

“Fructan supplementation may benefit senior cats as it modulates stool odor-forming compounds and decreases some protein catabolites and pathogenic gut microbiota concentrations without affecting N retention.”

Proteomics

From the Banfield lab: Development of an enhanced metaproteomic approach for deepening the microbiome characterization in the human infant gut – Weili Xiong – Journal of Proteome Research

“….we have designed a novel metaproteomic strategy based on double filtering (DF) the raw samples, a method that fractionates microbial from human cells to enhance microbial protein identification and characterization in complex fecal samples from healthy premature infants. “

More microbiology

Complementarity between targeted real-time specific PCR and conventional broad-range 16S rDNA PCR in the syndrome-driven diagnosis of infectious diseases – A.-S. Morel – European Journal of Clinical Microbiology & Infectious Diseases

“Herein, we report our experience in the diagnosis of infectious diseases over two years, during which 32,948 clinical samples from 18,056 patients were received from France and abroad.”

Microbes in the news

* There Is No ‘Healthy’ Microbiome – Ed Yong – New York Times

“The microbiome is complex, varied, ever changing and context-dependent — qualities that are the enemies of easy categorization.”

Study: Ice Man has traces of bacteria that undermined his health – BetaWired

“…they found evidence of the presence of Treponema denticola, an opportunistic pathogen implicated in the development of periodontal diseases. “

Science, publishing, and career

How Do Small Things Make a Big Difference? Activities to Teach about Human–Microbe Interactions – Chandana Jasti – The American Biology Teacher

“In these guided inquiry activities, students investigate human–microbe interactions as they work together to interpret and analyze authentic data from published articles and develop scientific models.”

2014 Life Sciences Salary Survey – Jyoti Madhusoodanan – The Scientist

“This year’s data reveal notable variation in compensation for life scientists working in different fields, sectors, and regions of the world.”

Academic Science Isn’t Sexist – Wendy M. Williams and Stephen J. Ceci – New York Times

“Our analyses show that women can and do prosper in math-based fields of science, if they choose to enter these fields in the first place.”

and two rebuttals:
Academic science is sexist: We do have a problem here – Emily Willingham
* The flawed and offensive logic of “Academic Science Isn’t Sexist” in the @nytimes – Jonathan Eisen – The Tree of Life

Bik’s Picks

Standing time and all-cause mortality in a large cohort of Australian adults – Hidde P. van der Ploeg – Preventive Medicine

“Increasing standing may hold promise for alleviating the health risks of prolonged sitting.”

A Face to Remember – Kerry Grens – The Scientist

“Once dominated by correlational studies, face-perception research is moving into the realm of experimentation—and gaining tremendous insight.”

* With a very cute picture: Rovers Disguised as Baby Penguins Can Quietly Infiltrate Penguin Colonies – Rachel Nuwer – Smithsonian

“Pursuing this hunch, they outfitted the rover with a big ball of fluff and a little penguin head and arms. ”

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Microbiome Digest, October 29, 2014

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The genome of Mycoplasma Mnola, helminths in wild rats, fungi in strawberry roots, and the top 100 most cited papers of all time. Can you guess which one is #1?

Human genital microbiome

An Emerging Mycoplasma Associated with Trichomoniasis, Vaginal Infection and Disease – Jennifer M. Fettweis – PLOS ONE

“In this study, the mycoplasma was found almost exclusively in women infected with the sexually transmitted pathogen Trichomonas vaginalis, but rarely observed in women with no diagnosed disease.”

Human gut microbiome

Bacteriology and Changes in Antibiotic Susceptibility in Adults with Community-Acquired Perforated Appendicitis – Hong Gil Jeon – PLOS ONE

“We retrospectively reviewed records of adult patients diagnosed with perforated appendicitis at an 800-bed teaching hospital between January 2000 and December 2011. “

Animal microbiome

Changes in the intestinal bacterial community during the growth of white shrimp, Litopenaeus vannamei – Zhaobin Huang – Aquaculture Research

“In this study, we documented the changes in the intestinal bacterial community at four stages in Litopenaeus vannamei…, using 454 pyrosequencing techniques. “

* Assessment of Helminth Biodiversity in Wild Rats Using 18S rDNA Based Metagenomics – Ryusei Tanaka – PLOS ONE

“In this study, we assessed parasite diversity in wild rats using 18S rDNA-based metagenomics. 18S rDNA PCR products were sequenced using an Illumina MiSeq sequencer and the analysis of the sequences using the QIIME software successfully classified them into several parasite groups.”

Soil microbiome

Linking soil microbial communities to vascular plant abundance along a climate gradient – Luca Bragazza – New Phytologist

“Microbial community structure and function were measured seasonally in four peatlands located along an altitude gradient representing a natural gradient of climate and associated vascular plant abundance.”

* Influence of Soil Type, Cultivar and Verticillium dahliae on the Structure of the Root and Rhizosphere Soil Fungal Microbiome of Strawberry – Srivathsa Nallanchakravarthula – PLOS ONE

“In this study we examined the effects of different soils and cultivars, and the presence of a soil-borne fungal pathogen, Verticillium dahliae, on the fungal microbiome of the rhizosphere soil and roots of strawberry plants, using high-throughput pyrosequencing.”

Metagenomics / Bioinformatics

* Evaluation of a Hybrid Approach Using UBLAST and BLASTX for Metagenomic Sequences Annotation of Specific Functional Genes – Ying Yang – PLOS ONE

“A hybrid annotation pipeline proposed previously for taxonomic assignments was evaluated in this study for metagenomic sequences annotation of specific functional genes, such as antibiotic resistance genes, arsenic resistance genes and key genes in nitrogen metabolism. “

Metabolomics

Long-term phenotypic evolution of bacteria – Germán Plata – Nature

“Here we perform a comparative analysis of bacterial growth and gene deletion phenotypes using hundreds of genome-scale metabolic models. “

Phages and viruses

Conditional tolerance of temperate phages via transcription-dependent CRISPR-Cas targeting – Gregory W. Goldberg – Nature

“Here we show that the Staphylococcus epidermidis CRISPR-Cas system can prevent lytic infection but tolerate lysogenization by temperate phages. “

Science, publishing and career

The top 100 papers – Richard Van Noorden – Nature

“To mark the anniversary, Nature asked Thomson Reuters, which now owns the SCI, to list the 100 most highly cited papers of all time.”

Bibliometrics: Is your most cited work your best? – John P. A. Ioannidis – Nature

“John P. A. Ioannidis and colleagues asked the most highly cited biomedical scientists to score their top-ten papers in six ways.”

Recommendations for the Role of Publishers in Access to Data – Jennifer Lin, Carly Strasser – PLOS Biology

“As appeals for public access of research data continue to proliferate, many scholarly publishers—alongside funders, institutions, and libraries—are expanding their role to address this need. “

How to Make More Published Research True – John P. A. Ioannidis – PLOS ONE

“Currently, many published research findings are false or exaggerated, and an estimated 85% of research resources are wasted.”

* Prominent Geomicrobiologist Dies – Tracy Vence – The Scientist

“Katrina Edwards, whose research focus was on discovering life beneath the ocean floor, has passed away at age 46.”

Bik’s Picks

* The Art of Science: Popsicles Go Viral – The Finch and Pea

“Lick a virus? Probably not a good idea, unless it’s a Dangerous Popsicle, a sweet treat created by artist and designer Wei Li. “

Dozens of genes associated with autism in new research – Science Direct

“Two major genetic studies of autism, involving more than 50 laboratories worldwide, have newly implicated dozens of genes in the disorder. “

Antares Rocket Explosion Destroyed These Kids’ Science Projects – Rheana Murray – ABC News

“Students across the nation watched their science projects go up in flames as the rocket bound for the International Space Station exploded moments after takeoff.”

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General microbiology and science digest, October 28, 2014

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Viruses in humans and caribous, metabolomics of losing weight, and microbes on rough surfaces.
Metabolomics

Impact of a 6-week very low-calorie diet and weight reduction on the serum and fecal metabolome of overweight subjects – Mette S. Schmedes – European Food Research and Technology

“NMR-based metabolomics was carried out on serum and fecal samples obtained from healthy female subjects pre- and post-weight reduction. “

Book with lots of plagiarized text (in at least 3 chapters), so not worth the $25 for the physical book, or even the free download:
Metabonomics and Gut Microbiota in Nutrition and Disease – Springer Link

Metagenomics

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes – Donovan H. Parks – PeerJ Preprints

“Here we introduce CheckM, an automated method for assessing the quality of a genome using a broader set of marker genes specific to the position of a genome within a reference genome tree along with information about the collocation of these genes. “

Viruses and phages

Expanding the Conversation on High-Throughput Virome Sequencing Standards To Include Consideration of Microbial Contamination Sources – Michael J. Strong, Zhen Lin, Erik K. Flemington – mBio

“We thank Ladner and colleagues for their conversation about standardizing viral genome sequences derived from high-throughput (HT) sequencing technology.”

Chlorovirus ATCV-1 is part of the human oropharyngeal virome and is associated with changes in cognitive functions in humans and mice – Robert H. Yolken – PNAS USA

“Unexpectedly, we identified DNA sequences homologous to virus ATCV-1, an algal virus not previously known to infect humans, in oropharyngeal samples obtained from healthy adults. “

* Preservation of viral genomes in 700-y-old caribou feces from a subarctic ice patch – Terry Fei Fan Ng – PNAS USA

“Using a viral particle-associated nucleic acid enrichment approach, we genetically characterized one complete DNA and one partial RNA viral genome from a 700-y-old fecal sample preserved in ice. “

Microbial Ecology

Trophic interactions induce spatial self-organization of microbial consortia on rough surfaces – Gang Wang, Dani Or – Scientific Reports

“A mechanistic model of cell-level interactions among multispecies microbial populations grown on hydrated rough surfaces facilitated systematic evaluation of how trophic dependencies shape spatial self-organization of microbial consortia in complex diffusion fields.”

Scaling laws governing stochastic growth and division of single bacterial cells – Srividya Iyer-Biswas – PNAS USA

“Now, by using a unique combination of measurement and analysis technologies, together with mathematical modeling, we discover quantitative features that are conserved across physiological conditions. “

Microbes in the news

Gut feelings – Microbiome and mental health – Fabio Piccini – Wall Street International

“Might people suffering from certain forms of mental health problems benefit from a fecal transplant from someone with more happy-go-lucky bacteria? “

Small Things Considered: Bacteria Allow Woodrats to Eat Poison – Anne A. Madden – ASM blog

“Despite such dire consequences, woodrats ingest enough of these plant toxins to kill a lab rat. Every day. But the desert is not littered with woodrat corpses, so clearly they are able to detoxify this poisonous salad somehow. “

Saving The Bees Using Microscopic Bugs – RedOrbit

“Phages are the most abundant life form on the planet and each phage has a unique bacteria that it will attack,” said Sandra Burnett, BYU professor of microbiology and molecular biology. “This makes phage an ideal treatment for bacterial disease because it can target specific bacteria while leaving all other cells alone.”

Science, publishing, and career

Reputation and impact in academic careers – Alexander Michael Petersen – PNAS USA

“Here, we develop a framework for quantifying the influence author reputation has on a publication’s future impact.”

NPRs All Things Considered (Podcast, 5 min): Is ‘Leaning In’ The Only Formula For Women’s Success In Science? – Kelly McEvers – NPR

“Don’t wait to be invited or encouraged to make a career in science, engineering or technology, Frances Arnold advises the young women she teaches at the California Institute of Technology. “

Bik’s Picks

Doctors Making Housecalls: Better, Cheaper Care at Home? – Jennifer Ferris – MedPageToday

“In a little over a decade the practice has exploded in popularity — with Taavoni and more than 40 other providers in North Carolina innovating new ways to bring healthcare home.”

Oil platforms off California are among the most productive marine fish habitats globally –
Jeremy T. Claisse – PNAS USA

“Here, we find that fish communities living on the complex hardscape habitat created throughout the water column by the structure of oil and gas platforms off California have the highest secondary production per unit area of seafloor of any marine ecosystem for which similar estimates exist.”

Can Science Perfect Food? – Daniela Galarza – Eater.com

“A research team in Japan is blowing past molecular gastronomy to discover new ways of perfecting already flawless dishes.”

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General microbiology and science digest, October 27, 2014

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A new Shiny R tool for microbial communities, virus-like pictures in human distal gut, interaction between oral bacteria, dancing your PhD, and X-ray movies of human joints in action.

Bioinformatics

* Seed: a user-friendly tool for exploring and visualizing microbial community data –
Daniel Beck – Bioinformatics

“Seed is written in R using the Shiny library. This provides access to powerful R based functions and libraries through a simple user interface. “

Viruses and phages

With cool pictures: Characterization of virus-like particles associated with the human faecal and caecal microbiota – Lesley Hoyles – Research in Microbiology

“Various methodologies for the recovery of VLPs from faeces were tested and optimized, including successful down-stream processing of such samples for the purpose of an in-depth electron microscopic analysis, pulsed-field gel electrophoresis and efficient DNA recovery.”

Transcriptomics / Proteomics / Metabolomics

Thermophilic microbial cellulose decomposition and methanogenesis pathways recharacterized by metatranscriptomic and metagenomic analysis – Yu Xia – Scientific Reports

“The metatranscriptomic recharacterization in the present study captured microbial enzymes at the unprecedented scale of 40,000 active genes belonged to 2,269 KEGG functions were identified.”

Proteomic and transcriptional analysis of interaction between oral microbiota Porphyromonas gingivalis and Streptococcus oralis – Kazuhiko Maeda – Journal of Proteome Research

“Here, using shotgun proteomics we examined the molecular basis of mixed-biofilm formation by P. gingivalis with Streptococcus oralis.”

Review: Toward the comprehensive understanding of the gut ecosystem via metabolomics-based integrated omics approach – Wanping Aw, Shinji Fukuda – Seminars in Immunopathology

“In this review, we discuss in detail the relationship between gut microbiota and its metabolites … in the host health and etiopathogenesis of various pathological states such as multiple sclerosis, autism, obesity, diabetes, and chronic kidney disease. “

More Microbiology

Biofilms: Five-Star Accommodations for the Aerobically Challenged – Robert A. Cramer – Current Biology

“A recent study finds that fungal biofilms are capable of supporting growth of anaerobic bacteria, suggesting that these fungi can promote bacterial growth in otherwise toxic environments.”

Microbes in the news

* Sorry, Your Gut Bacteria Are Not the Answer to All Your Health Problems – Gabrielle Canon – Mother Jones

“We’re told that tweaks to the microbiome can cure everything from allergies to Ebola. Not exactly, say experts. …despite the optimism, some researchers caution that much of what we hear about microbiome science isn’t always, well, science. “

* Orthopedic surgeon studies bear bacteria to aid bear attack victims – Healio

“Working with the Montana Fish, Wildlife & Parks, Iwersen has been collecting cultures of bacteria from the mouths of grizzly bears and correlating them with the types of bacteria found in the bear bites on patients. “

Mexican scientist investigates intestinal bacteria – BetaWired

“Recent findings of the investigator Xicotencatl Gracida Canales…at Harvard University in Cambridge, USA, suggest that in the absence of an intestinal shield, variations in bacterial metabolism can affect reproductive cells and cause infertility in an animal model called C. Elegans.”

Algae-Based Material Takes On Body Odor – Dana Dovey – NewsWeek

“A team of Swedish researchers from the KTH Royal Institute of Technology has found a way to eliminate the growth of this smell-inducing bacteria using one of nature’s best antimicrobials, algae.”

MoBE Postdoctoral Fellowship: From Source to Tap: Linking the Drinking Water Microbiome to Human Health – Sarah Haig – MicroBEnet

“We hypothesize that the microbial communities in municipally treated drinking water are a source of opportunistic pathogens, posing a risk to people with cystic fibrosis”

Science, publishing, career

Is NIH policy the best way to sex equality in studies? – Bethany Brookshire – Science News

“The end goal will be to make sure that NIH-funded scientists “balance male and female cells and animals in preclinical studies in all future [grant] applications” to the NIH.”

Some suggestions for having diverse speakers at meetings – Jonathan Eisen – The Tree of Life

“Some people were asking what one can do to improve gender diversity at meetings so I thought I would post this which I was meaning to do anyway “

‘Dance Your Ph.D.’ finalists announced – John Bohannon – Science

“Rather than reading a paper about it, why not watch a dance? A ballet and a modern dance on those very topics have made it into the finals of this year’s “Dance Your Ph.D.” contest.”

Bik’s Picks

Interactive world map of vaccine-preventable outbreaks – Council for Foreign Relations

“This interactive map visually plots global outbreaks of measles, mumps, whooping cough, polio, rubella, and other diseases that are easily preventable by inexpensive and effective vaccines.”

Dietary cocoa flavanols reverse age-related memory decline in mice – Science Daily

“Dietary cocoa flavanols —- naturally occurring bioactives found in cocoa —- reversed age-related memory decline in healthy older adults, according to a new study. Flavanols are also found naturally in tea leaves and in certain fruits and vegetables”

Amazing X-ray GIFs Show Joints In Motion – Lisa Winter – IFL Science

“Cameron Drake of San Francisco has created a collection of magnificent images showing joints in motion. He was aided by orthopedic physician Dr. Noah Weiss and the finished product is completely amazing. “

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