Category Archives: Phages and viruses

Microbiome digest, November 28, 2014

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Human gut microbiome

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

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

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

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

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

Metagenomic analysis of the gastric microbiota cultivable from a patient 

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

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

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

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

Animal microbiome

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

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

Chironomid Microbiome – Malka Halpern, Yigal Senderovich – Microbial Ecology

Plant microbiome

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

Soil and sludge microbiome

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

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

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

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

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

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

Water microbiome

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

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

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

Food microbiology

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

Bioinformatics

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

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

Phages and viruses

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

Metabolomics

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

Transcriptomics

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

More microbiology

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

Microbes in the news

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

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

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

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

Science and art

It’s a microbial world – protozoa pancakes

Bik’s Picks

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

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

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

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

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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 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 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 4, 2014

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Tomorrow, Wednesday November 5, at 1:00pm USA-EST : Upcoming AMA (Ask Me Anything) in reddit/r/science: “Microbiota of the human gut” with my co-worker Les Dethlefsen. Ask him anything! You can submit questions, vote for the best questions, and the top questions will be answered by Les.

Human gut microbiome

* Rapid changes in the gut microbiome during human evolution – Andrew H. Moeller – PNAS USA

“To establish how the gut microbiome has changed since the diversification of human and ape species, we characterized the microbial assemblages residing within hundreds of wild chimpanzees, bonobos, and gorillas.”

and: Human Gut Bacteria Much Different Than Apes – Science 2.0

* Blastocystis Is Associated with Decrease of Fecal Microbiota Protective Bacteria: Comparative Analysis between Patients with Irritable Bowel Syndrome and Control Subjects – Céline Nourrisson – PLOS ONE

“Here, we first compared the prevalence of Blastocystis among 56 IBS patients (40 IBS with constipation (IBS-C), 9 IBS with diarrhea (IBS-D), 4 mixed IBS (IBS-M) and 3 unsubtyped IBS (IBS-U) according to the Rome III criteria) and 56 control (i.e. without any diagnosed chronic or acute gastrointestinal disorder) subjects. “

Animal models of microbiome research

* Bone Marrow Dendritic Cells from Mice with an Altered Microbiota Provide Interleukin 17A-Dependent Protection against Entamoeba histolytica Colitis – Stacey L. Burgess – mBio

“In studies utilizing a murine model, we demonstrated that colonization of the gut with the commensal Clostridia-related bacteria known as segmented filamentous bacteria (SFB) is protective during E. histolytica infection.”

Animal microbiome

Effect of Copper Treatment on the Composition and Function of the Bacterial Community in the Sponge Haliclona cymaeformis – Ren-Mao Tian – mBio

“16S rRNA gene sequencing results showed that the sponge Haliclona cymaeformis harbored symbiotic sulfur-oxidizing Ectothiorhodospiraceae and photosynthetic Cyanobacteria as dominant species. “

Bioinformatics tools

Massive fungal biodiversity data re-annotation with multi-level clustering – Duong Vu – Scientific Reports

“An implementation of the algorithm allowed clustering of all 344,239 ITS (Internal Transcribed Spacer) fungal sequences from GenBank”

Viruses and phages

Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry applied to virus identification – Adriana Calderaro – Scientific Reports

“The results revealed MALDI-TOF MS to be an effective and inexpensive tool for the identification of the three poliovirus serotypes. “

More microbiology

Occurrence and expression of bacterial human virulence gene homologues in natural soil bacteria – Ditte A. Søborg – FEMS Microbial Ecology

“About 25% of the bacterial isolates contained virulence gene homologues representing toxin (hblA, cytK2), adhesin (fimH), regulator (phoQ) and resistance (yfbI) determinants in pathogenic bacteria.”

Science, publishing, and career

* Don’t Worry Your Pretty Little Heads – Rebecca Schuman – Slate

“I don’t understand how they wrote the paper or the op-ed they did while looking at the same results I see in their paper. … Where I come from,” she concludes, “we call that institutional bias.”

Bik’s Picks

Birds found using human musical scales for the first time – Virginia Morell – Science Blog

“The flutelike songs of the male hermit thrush (Catharus guttatus) are some of the most beautiful in the animal kingdom.”

Vaccine-resistant polio strain discovered – Science Daily

“The DNA sequence shows two mutations, unknown until now, of the proteins that form the “shell” (capsid) of the virus.”

The appliance of science: home experiments with your kids – Louise Holden – Irish Times

“Next week is Science Week, and one of the messages that McCarthy is hoping to put out there is that science is for everybody, not just those hoping to work in the sector. Helping your child to become science-literate is a great gift.”

The top 20 catchiest songs of all time, according to science – Michelle Starr – CNET

“A year-long survey by the Museum of Science and Industry in Manchester has revealed the top 10 most persistent earworms — with the Spice Girls topping the list.”

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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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