Category Archives: Metagenomics & Bioinformatics

May 8, 2015

Posted on by

Human oral microbiome

Published in Gut but also oral: Human buccal epithelium acquires microbial hyporesponsiveness at birth, a role for secretory leukocyte protease inhibitor – Celia L Menckeberg – Gut

 

Human gut microbiome

Cholesterol gallstones and bile host diverse bacterial communities with potential to promote the formation of gallstones – Yuhong Peng – Microbial Pathogenesis

Development of an enhanced human gastrointestinal epithelial culture system to facilitate patient-based assays – Kelli L VanDussen – Gut

Gut microbiome and innate immune response patterns in IgE-associated eczema – Christina E West – Clinical & Experimental Allergy

Review: The gut microbiome in autoimmunity: Sex matters – Andres Gomez – Clinical Immunology

Review: Chemical communication in the gut: Effects of microbiota-generated metabolites on gastrointestinal bacterial pathogens – Stefanie L. Vogt – Anaerobe

Special issue of Clinical Liver Disease about “Liver and the Microbiome”. Reviews include:

Human genital microbiome

The vaginal and gastrointestinal microbiomes in gynecologic cancers: A review of applications in etiology, symptoms and treatment – Dana Chase – Gynecologic Oncology

Animal models of microbiome

Effects of dietary inulin on bacterial growth, short-chain fatty acid production and hepatic lipid metabolism in gnotobiotic mice – Karolin Weitkunat – The Journal of Nutritional Biochemistry

Plant root and soil microbiome

Covariation of soil bacteria functional diversity and vegetation diversity along an altitudinal climatic gradient in the Western Carpathians – Beata Klimek – Pedobiologia

Changes in fungal communities along a boreal forest soil fertility gradient – Erica Sterkenburg – New Phytologist

Water microbiome

Editorial without citation to the original Nature paper: Deep-ocean microbe is closest living relative of complex cells – Mitch Leslie – Science

Parasites

Not all parasites are protective – Derek M. McKay – Parasite Immunology

Helminths and the microbiota: parts of the hygiene hypothesis – P. Loke – Parasite Immunology

Bioinformatics

Testing in Microbiome-Profiling Studies with MiRKAT, the Microbiome Regression-Based Kernel Association Test – Ni Zhao – AJHG

Sparse and Compositionally Robust Inference of Microbial Ecological Networks – Zachary D. Kurtz – PLOS Computational Biology

Demystifying computer science for molecular ecologists – Mahdi Belcaid and Robert J. Toonen

Techniques

TM7 detection in human microbiome: Are PCR primers and FISH probes specific enough? – Maria V. Sizova – Journal of Microbiological Methods

Microbes in the news

Man’s Best Germs: Does Your Dog Influence Your Health? – Heather Buschman – UC San Diego

Video: Can Poop Cure an Infection? – Anna Rothschild – Gross science

Science, publishing, and career

The Hitchhiker’s Guide to a Neuroscience Career – Marian Joels – Neuron

Recommendation letters: Give women an even chance – Marcia McNutt – Science

Bik’s Picks
Spiders Sprayed with Graphene Spin Super-Strong Silk – Renee Morad – Discovery

Mmm, I always have mixed feelings about papers using these types of animal models. “We made this mouse blind. And then we cured it!” Light in sight: A step towards a potential therapy for acquired blindness – Science Daily

Grocery lists may help shoppers stick to healthier diet, lower weight – Reuters

[hr]

 

 

May 7, 2015

Posted on by

Events

Human Gut Microbiome and Diseases Congress – 25-26 June 2015, Milano, Italy

Pregnancy and birth microbiome

The Canadian Healthy Infant Longitudinal Development (CHILD) birth cohort study: assessment of environmental exposures – Tim K Takaro – Journal of Exposure Science and Environmental Epidemiology

The Impact of Infancy Antibiotic Intake on Childhood Obesity; Review of Studies – Mohammad Reza Vafa – Advances in Obesity, Weight Management & Control

Human respiratory microbiome

The Host Response to the Lung Microbiome in Chronic Obstructive Pulmonary Disease
Marc A Sze – American Journal of Respiratory and Critical Care Medicine

Human gut microbiome

Approaches to studying and manipulating the enteric microbiome to improve autism symptoms – Richard E. Frye – Microbial Ecology in Health and Disease

Plant root and soil microbiome

Heading to the Origins – Rice Microbiome as Functional Extension of the Host – Pablo R. Hardoim – Journal of Rice Research

Inoculation of Phaseolus vulgaris with the nodule-endophyte Agrobacterium sp. 10C2 affects richness and structure of rhizosphere bacterial communities and enhances nodulation and growth – Saif-Allah Chihaoui – submitted paper

Biochar in Co-Contaminated Soil Manipulates Arsenic Solubility and Microbiological Community Structure, and Promotes Organochlorine Degradation – Samuel J. Gregory – PLOS ONE

Microbial quality of soil from the Pampa biome in response to different grazing pressures – Rafael S. Vargas – Genetics and Molecular Biology

Built environment microbiome

Dysbiotic drift: mental health, environmental grey space, and microbiota – Alan C Logan – Journal of Physiological Anthropology

Extremophiles

Sub-Ice Microalgal and Bacterial Communities in Freshwater Lake Baikal, Russia – Maria V. Bashenkhaeva – Microbial Ecology

Phages and viruses

Protist predation can select for bacteria with lowered susceptibility to infection by lytic phages – Anni-Maria Örmälä-Odegrip – BMC Evolutionary Biology

Microbial Ecology

Evolutionary ecology of microorganisms: from the tamed to the wild – Jay T Lennon – PeerJ

Metagenomics and bioinformatics

MyPro: A seamless pipeline for automated prokaryotic genome assembly and annotation – Yu-Chieh Liao – Journal of Microbiological Methods

PrePrint: Infer Metagenomic Abundance and Reveal Homologous Genomes Based on the Structure of Taxonomy Tree – Yu-Qing Qiu – IEEE/ACM Transactions on Computational Biology and Bioinformatics

Metabolomics

Effects of Uremic Toxins from the Gut Microbiota on Bone: A Brief Look at Chronic Kidney Disease – Ana Paula Black – Therapeutic Apheresis and Dialysis

Microbes in the news

Ulcer-causing bacteria induces stomach stem cell growth in mice, researchers find – Stanford Medicine

Newly named bacteria help honey bee larvae thrive – Kim Kaplan – Phys.org

The smell of death: Scientist reveals how 400 compounds mix to create heady mixture of scents as bacteria rips apart rotting flesh – Moheb Costandi – Daily Mail

Eat your vegetables, feed your microbiome – David Charbonneau – EyeViewKamloops

Microbiome Portrait Experiment for High School Students – Tufts

Bacteria redefine reinforced concrete – RSC Advances Blog

Possible role of gut bacteria in autism – Science Daily

Environmental exposures study tracks more than 3,200 Canadian babies – Simon Fraser University

Final Report Summary – TORNADO (Molecular Targets Open for Regulation by the gut flora – New Avenues for improved Diet to Optimize European health) – CORDIS Europa

Measles Vaccination Saves You From More Than Measles – Maggie Fox – NBC News

Microbes and money

‘Gut microbiome’ startup moving to science accelerator, seeks study volunteers: Prince William Science Accelerator – ISOThrive – Inside Nova

UBiome Seeks Academic Partnerships with the Launch of the uBiome Academic Consortium – WDRB

Science, publishing, and career

Science forum: RIPOSTE: a framework for improving the design and analysis of laboratory-based research – Nicholas G D Masca – eLife

Bik’s Picks

Listen To These Eerie ‘X-Files’ Sounds Recorded At The Edge Of Space – Macrina Cooper-White – Huffington Post

Finding That Babies Born at 22 Weeks Can Survive Could Change Abortion Debate – Lucy Westcott – Newsweek

Samantha Cristoforetti: 5 Memorable Moments From the Italian Astronaut’s Time in Space – Alyssa Newcomb – ABC News
[hr]

May 6, 2015

Posted on by

Human oral microbiome

The Impact of Various Time Intervals on the Supragingival Plaque Dynamic Core Microbiome – Wen-xin Jiang – PLOS ONE

Dental and Microbiological Risk Factors for Hospital-Acquired Pneumonia in Non-Ventilated Older Patients – Victoria C. Ewan – PLOS ONE

Human gut microbiome

Unraveling the Influence of Gut Microbes on the Mind – M.J. Friedrich – JAMA

Gut Microbiota and Colorectal Cancer – Yu Y.-N. – Gastrointestinal Tumors

Gut Microbiota and Hepatocellular Carcinoma – Tao X – Gastrointestinal Tumors

Editorial: Gut microbiota and inflammation in chronic kidney disease patients – Denise Mafra – Clinical Kidney Journal

Animal models

Chronic Trichuris muris Infection in C57BL/6 Mice Causes Significant Changes in Host Microbiota and Metabolome: Effects Reversed by Pathogen Clearance – Ashley Houlden – PLOS ONE

Animal microbiome

Bacterial Diversity Associated with Cinachyra cavernosa and Haliclona pigmentifera, Cohabiting Sponges in the Coral Reef Ecosystem of Gulf of Mannar, Southeast Coast of India – C. Jasmin – PLOS ONE

Plant microbiome

Shifts in Symbiotic Endophyte Communities of a Foundational Salt Marsh Grass following Oil Exposure from the Deepwater Horizon Oil Spill – Demetra Kandalepas – PLOS ONE

Endophytic and Epiphytic Microbes as “Sources” of Bioactive Agents – David J. Newman and Gordon M. Cragg – Frontiers in Chemistry

Review: Pivotal roles of phyllosphere microorganisms at the interface between plant functioning and atmospheric trace gas dynamics – Françoise Bringel – Frontiers in Microbiology

Soil and sediment microbiome

Metabolic Activity and Functional Diversity Changes in Sediment Prokaryotic Communities Organically Enriched with Mussel Biodeposits – Thomas Pollet – PLOS ONE

Impacts of dimethyl phthalate on the bacterial community and functions in black soils – Zhi-Gang Wang – Frontiers in Microbiology

Aquatic / Extremophile microbiome

Benthic microbial communities of coastal terrestrial and ice shelf Antarctic meltwater ponds – Stephen D. Archer – Frontiers in Microbiology

Microbial food web components, bulk metabolism, and single-cell physiology of piconeuston in surface microlayers of high-altitude lakes – Hugo Sarmento – Frontiers in Microbiology

Microbial communities of the Lemon Creek Glacier show subtle structural variation yet stable phylogenetic composition over space and time – Cody S. Sheik – Frontiers in Microbiology

Bioreactor microbiome

Bacterial Pathogens and Community Composition in Advanced Sewage Treatment Systems Revealed by Metagenomics Analysis Based on High-Throughput Sequencing – Xin Lu – PLOS ONE

Metagenomics, metabolomics, and bioinformatics

Expression of heterologous sigma factors enables functional screening of metagenomic and heterologous genomic libraries – Stefan M. Gaida – Nature Communications

TreeSeq, a Fast and Intuitive Tool for Analysis of Whole Genome and Metagenomic Sequence Data – Bastiaan Wintermans – PLOS ONE

Covariation is a poor measure of molecular coevolution – David Talavera – Molecular Biology and Evolution

Review: Data-driven integration of genome-scale regulatory and metabolic network models – Saheed Imam – Frontiers in Microbiology

Archaea

Complex archaea that bridge the gap between prokaryotes and eukaryotes – Anja Spang – Nature

More microbiology papers

The passenger-associated transport repeat promotes virulence factor secretion efficiency and delineates a distinct autotransporter subtype – Matthew Thomas Doyle – Molecular Microbiology

Microbes and art

Intestine-inspired 3D printed fashion will hold glowing bacteria – Chris Baraniuk – New Scientist

Microbes in the news

Who are the bioaerosols in your neighborhood? Find out by entering a chamber … – Jonathan Eisen – MicroBEnet

Exploring bacterial genes: New technique helps uncover useful functions in microbial genomes – University of Delaware

Newly discovered ‘missing link’ shows how humans could evolve from single-celled organisms: A new microbe found a mile and a half below the Atlantic Ocean  – Rachel Feltman – The Washington Post

Treating a bacterial infection with bacteria lowers chances of recurrence – Meryl Lin McKean – Fox4kc

Toxic Gut Bacteria: New Treatment Could Prevent Repeat Infections – Rachael Rettner – Live Science

Researchers produce jet fuel compounds from fungus – Science Daily

Molecular Homing Beacon Redirects Human Antibodies to Fight Pathogenic Bacteria – Heather Buschman – UC San Diego

Bacteria research opens way for new antibiotics: common building block, called the Passenger-associated Transport Repeat (PATR) present in many pathogens – University of Adelaide

Science, publishing, and career

‘Living figures’ make their debut: Published chart integrates data from outside scientists – Dalmeet Singh Chawla – Nature

The trouble with reference rot: Computer scientists are trying to shore up broken links in the scholarly literature – Jeffrey M. Perkel – Nature

The retirement debate: Stay at the bench, or make way for the next generation: When and how to exit research has become a charged issue in science – Megan Scudellari – Nature

Pint-sized DNA sequencer impresses first users: Portable device offers on-the-spot data to fight disease, catalogue species and more – Erika Check Hayden – Nature

Bik’s Picks

Recovering Sea Lions at Marine Center Deliberately Injured By Chlorine, Police Say – Avianne Tan – ABC News

People with Depression and Bipolar Disorder Feel Sadness Differently – Tanya Lewis – Live Science

Feasting on fruits may leave you craving for more – Silvia Fernandez – Pierce Pioneer News

Trouble Falling Asleep? Doctor Says This Trick Will Put You to Sleep in One Minute – Zachary Stieber – The Epoch Times
[hr]

May 5, 2015, part 2

Posted on by

There was so much literature today (more than 600 papers!) that I am doing a second digest today.

Human reproductive tract microbiome

Investigation and Characterization of the Microbiome of the Upper Female Reproductive Tract [10] – Shana M. Miles – Obstetrics & Gynecology

Animal and other models

Akkermansia muciniphila Adheres to Enterocytes and Strengthens the Integrity of the Epithelial Cell Layer – Justus Reunanen – Applied and Environmental Microbiology

Animal microbiome

Effect of Diet on the Rumen Microbial Community Composition of Growing Cattle and the Role It Plays in Methane Emissions – Allison L. Knoell – Digital Commons University of Nebraska – Lincoln

Amphibian Symbiotic Bacteria Do Not Show a Universal Ability To Inhibit Growth of the Global Panzootic Lineage of Batrachochytrium dendrobatidis – Rachael E. Antwis – Applied and Environmental Microbiology

Reptiles as Reservoirs of Bacterial Infections: Real Threat or Methodological Bias? – Giulia Zancolli – Microbial Ecology

Plant root, soil and sediment microbiome

Effects of cultivation ages and modes on microbial diversity in the rhizosphere soil of Panax ginseng – Chunping Xiao – Journal of Ginseng Research

Soil-foraging animals alter the composition and co-occurrence of microbial communities in a desert shrubland – David J Eldridge – The ISME Journal

The bacterial community inhabiting temperate deciduous forests is vertically stratified and undergoes seasonal dynamics – Rubén López-Mondéjar – Soil Biology and Biochemistry

Diversity of active microbial communities subjected to long-term exposure to chemical contaminants along a 40-year-old sediment core – Assia Kaci – Environmental Science and Pollution Research

Soil moisture and land use are major determinants of soil microbial community composition and biomass at a regional scale in northeastern China – L. Ma – Biogeosciences

Bacterial Community Diversity in Soil Under two Tillage Practices as Determined by Pyrosequencing – Aditi Sengupta – Microbial Ecology

Soil Microorganisms Contribute to Plant Nutrition and Root Health – Mark S. Coyne and Robert Mikkelsen – Better Crops

Changes in northern Gulf of Mexico sediment bacterial and archaeal communities exposed to hypoxia – R. Devereux – Geobiology

Effect of Nitrogen Management on Soil Microbial Community and Enzymatic Activities in Jatropha curcas L. Plantation – Doongar Ram Chaudhary – CLEAN – Soil, Air, Water

Response of maize and soil microorganisms to decomposing poplar root residues after shallow or homogenous mixing into soil – Hikal Gad – Journal of Plant Nutrition and Soil Science

Water microbiome

Metagenome Sequencing of a Coastal Marine Microbial Community from Monterey Bay, California – Ryan S. Mueller – Genome Announcements

Enrichment experiment changes microbial interactions in an ultra-oligotrophic environment – Gabriel Y. Ponce-Soto – Frontiers in Microbiology

Review: Marine-derived fungi: diversity of enzymes and biotechnological applications
Rafaella C. Bonugli-Santos – Frontiers in Microbiology

Review, but contains mostly plagiarized text: The Importance of Marine Genomics to Life – Popoola Raimot Titilade – Journal of Ocean Research

Extremophiles

Spatial microbial community structure and biodiversity analysis in “extreme” hypersaline soils of a semiarid Mediterranean area – Loredana Canfora – Applied Soil Ecology

Ecoenzymatic stoichiometry at the extremes: How microbes cope in an ultra-oligotrophic desert soil – Yunuen Tapia-Torres – Soil Biology and Biochemistry

Microbial and Enzyme Activities of Saline and Sodic Soils – Kripal Singh – Land Degradation & Development

Identification of Anthraquinone-Degrading Bacteria in Soil Contaminated with Polycyclic Aromatic Hydrocarbons – Elyse A. Rodgers-Vieira – Applied and Environmental Microbiology

Carbon Source Preference in Chemosynthetic Hot Spring Communities – Matthew R. Urschel – Applied and Environmental Microbiology

Isolating the effects of storm events on arctic aquatic bacteria: temperature, nutrients, and community composition as controls on bacterial productivity – Heather E. Adams – Frontiers in Microbiology

Bioreactor microbiology

Analysis of microbial communities in the oil reservoir subjected to CO2-flooding by using functional genes as molecular biomarkers for microbial CO2 sequestration – Jin-Feng Liu – Frontiers in Microbiology

Viruses

Combining genomic sequencing methods to explore viral diversity and reveal potential virus-host interactions – Cheryl-Emiliane T. Chow – Frontiers in Microbiology

More microbiology

Global trends in antimicrobial use in food animals – Thomas P. Van Boeckel – PNAS USA

Review: Sugar coating: bacterial protein glycosylation and host–microbe interactions – Felicia Y.Y. Tan – Trends in Biochemical Sciences

Assay for estimating total bacterial load: relative qPCR normalization of bacterial load with associated clinical implications – Ivan Brukner – Diagnostic Microbiology and Infectious Disease

Review: A review on computational systems biology of pathogen–host interactions – Saliha Durmuş – Frontiers in Microbiology

Metagenomics and bioinformatics

Contact genomics: Scaffolding and phasing (meta)genomes using chromosome 3D physical signatures – Jean-Francois Flot – FEBS Letters

Eco-Evolutionary Dynamics of Episomes among Ecologically Cohesive Bacterial Populations – Hong Xue – mBio

Whole genome sequencing of extended-spectrum β-lactamase producing Klebsiella pneumoniae isolated from a patient in Lebanon – Sima Tokajian – Frontiers in Cellular and Infection Microbiology

A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data – Stefan Spring – Frontiers in Microbiology

Review: Strategies and approaches in plasmidome studies – uncovering plasmid diversity disregarding of linear elements? – Julian R. Dib – Frontiers in Microbiology

Microbes in the news

Your Beard Is Covered in Bacteria: So is everything else. Don’t fall for the latest viral freak-out – David Coil – Slate

Longread: Gut Feelings – The Mysteries of the Microbiome – Jo Chandler – The Monthly

Bik’s Picks

Dolphins Living in Closer Quarters Are Friendlier – Lori Cuthbert – Discovery

Space might make astronauts dumber, study shows – Craig Hlavaty – Chron.com

We could use some in California – pipeline, please! Where does all the water go? Watch Oregon’s mysterious Lost Lake disappear down a lava tube – Aileen Donnelly – National Post
[hr]

May 1, 2015

Posted on by

A late post today – I was in meetings all day, and had no time to look at the 474 papers in my inbox until late. But let’s catch up!

General microbiome

Editorial: Bacteria make us human – Mohsin Ali – The Lancet

Microbiome of pregnancy and birth

Spotlight: Gut bacteria and necrotizing enterocolitis: cause or effect? – Christopher James Stewart – Trends in Microbiology

Editorial Harnessing the Early-Life Microbiota to Protect Children with Cystic Fibrosis – Leopoldo N. Segal and Martin J. Blaser – The Journal of Pediatrics

Human oral microbiome

Review: Dental Chatter: Bacterial Cross-Talk in the Biofilm of the Oral Cavity – Doron Steinberg – Israel Journal of Chemistry

The interaction between Streptococcus spp. and Veillonella tobetsuensis in the early stages of oral biofilm formation – Izumi Mashima – Journal of Bacteriology

Human gut microbiome

Antibiotic treatment of diarrhoea is associated with decreased time to the next diarrhoea episode among young children in Vellore, India – Elizabeth T Rogawski – International Journal of Epidemiology

High throughput sequencing reveals distinct microbial populations within the mucosal and luminal niches in healthy individuals – Yehuda Ringel – Gut Microbes

Gut Microbiota-Mediated Drug-Antibiotic Interactions – Dong-Hyun Kim – Drug Metabolism & Disposition

Humoral Immunity in the Gut Selectively Targets Phenotypically Virulent Attaching-and-Effacing Bacteria for Intraluminal Elimination – Nobuhiko Kamada – Cell Host & Microbe

MicroRNA-193a-3p Reduces Intestinal Inflammation in Response to Microbiota via Down-regulation of Colonic PepT1 – Xin Dai – The Journal of Biological Chemistry

Editorial: Some Reflections on the Microbiome and Obesity – Richard I. Shader – Clinical Therapeutics

Review: Regulation of body fat mass by the gut microbiota: Possible mediation by the brain – Erik Schéle – Peptides

Review: Role of Intestinal Microbiome in Lipid and Glucose Metabolism in Diabetes Mellitus – Casper van Olden – Clinical Therapeutics

Review: Gut microbiome, gut function, and probiotics: Implications for health – Neerja Hajela – Indian Journal of Gastroenterology

Review: Gut microbiota and the development of pediatric diseases – Chun-Yi Lu – Journal of Gastroenterology

Review: Regulation of body fat mass by the gut microbiota: Possible mediation by the brain – Erik Schéle – Peptides

Animal models

Transcriptional Modulation of Intestinal Innate Defense/Inflammation Genes by Preterm Infant Microbiota in a Humanized Gnotobiotic Mouse Model – Lei Lu – PLOS ONE

Pharmaceuticals and personal care products alter the holobiome and development of a medically important mosquito – Marcus J. Pennington – Environmental Pollution

Differences in the faecal microbiome of non-diarrhoeic clinically healthy dogs and cats associated with Giardia duodenalis infection: impact of hookworms and coccidia – Jan Šlapeta – International Journal for Parasitology

Ezetimibe and simvastatin modulate gut microbiota and expression of genes related to cholesterol metabolism – Emilie Catry – Life Sciences

Animal microbiome

Review: Tick microbiome: the force within – Sukanya Narasimhan – Trends in Parasitology

16S rRNA Amplicon Sequencing Demonstrates that Indoor-Reared Bumblebees (Bombus terrestris) Harbor a Core Subset of Bacteria Normally Associated with the Wild Host – Ivan Meeus – PLOS ONE

Plant microbiome

Plant and soil effects on bacterial communities associated with Miscanthus × giganteus rhizosphere and rhizomes – Dongfang Li – GCB Bioenergy

Soil microbiome

Distinct microbial populations are tightly linked to the profile of dissolved iron in the methanic sediments of the Helgoland mud area, North Sea – Oluwatobi Oni – Frontiers in Microbiology

Ecological effects of combined pollution associated with e-waste recycling on the composition and diversity of soil microbial communities – Jun Liu – Environmental Science & Technology

Water microbiome

Differences in organic matter and bacterioplankton between sections of the largest Arctic river: Mosaic or continuum? – Michail I. Gladyshev – Limnology and Oceanography

Extremophile microbiome

Insights from the Metagenome of an Acid Salt Lake: The Role of Biology in an Extreme Depositional Environment – Sarah Stewart Johnson – PLOS ONE

The microbial diversity, distribution, and ecology of permafrost in China: a review – Weigang Hu – Extremophiles

Bioreactor microbiology

Illumina MiSeq Sequencing Reveals Diverse Microbial Communities of Activated Sludge Systems Stimulated by Different Aromatics for Indigo Biosynthesis from Indole – Xuwang Zhang – PLOS ONE

Effects of garlic oil, nitrate, saponin and their combinations supplemented to different substrates on in vitro fermentation, ruminal methanogenesis, and abundance and diversity of microbial populations – A.K. Patra – Journal of Applied Microbiology

Food microbiology

Technological implications of reducing nitrate and nitrite levels in dry-fermented sausages: typical microbiota, residual nitrate and nitrite and volatile profile – Xavier F. Hospital – Food Control

Review: New Approaches for Bacteriotherapy: Prebiotics, New-Generation Probiotics, and Synbiotics – Rachna Patel – Clinical Infectious Diseases

Metagenomics and bioinformatics

DIDA: Distributed Indexing Dispatched Alignment – Hamid Mohamadi – PLOS ONE

Hybrid De Novo Genome Assembly Using MiSeq and SOLiD Short Read Data – Tsutomu Ikegami – PLOS ONE

Using populations of human and microbial genomes for organism detection in metagenomes – Sasha K Ames – Genome Research

Metabolomics

Systems biology of host–microbe metabolomics – Almut Heinken and Ines Thiele – Wiley Interdisciplinary Reviews: Systems Biology and Medicine

Microbes in the news

Don’t douche, and other lessons about the vaginal microbiome: Exploring the microscopic world between our legs – Susan Keown – Fred Hutch

Gut bacteria easy scapegoat to explain diseases, but connections hard to prove – Meredith Knight – Genetic Literacy Project

Find Out Just How Bacteria-Infested Houston Street Is During This Weekend of Walking Tours – Jaime Cone – Bedford and Bowery
and
The Artist & The Scientist: Microbial Maps – Festival Walk in New York City with Chris Mason – Jane’s Walk

Video: The Microbiome Project: Hospitals – Bacteria may actually be beneficial to hospitals – Argonne National Laboratory

Freshmen participate in huge research study on tiny viruses – University of Colorado Boulder

uBiome is launching an academic consortium to bring together researchers and industry teams with the hope of accelerating scientific understanding of the microbiome – uBiome

Each vineyard has a unique microbiome – Louise Lerner – Futurity

Science, publishing, and career

Ten Simple (Empirical) Rules for Writing Science – Cody J. Weinberger – PLOS Computational Biology

Honors Thesis: Students’ Knowledge and Opinions Concerning Genetically Modified Organisms: A Survey at University of Colorado Boulder – Connor Folkerth – University of Colorado at Boulder

Sexism in science: Peer editor tells female researchers their study needs a male author – Rachel Feltman – Washington Post

Bik’s Picks

How This Beetle Creates 500 Explosions Per Second In Its Bum – Ed Yong – National Geographic

Evidence that premature girls thrive more than premature boys – Science Daily

House GOP Wants to Eviscerate NASA Earth Sciences in New Budget – Phil Plait – Bad Astronomy – Slate
[hr]

April 29, 2015

Posted on by

Events

Friday May 1: Del Mar College, Corpus Christi, TX Hosts a Day of Science with “How to Train Your Superorganism: Via the Microbiome” – Record Star

Pregnancy and birth microbiome

Colostrum of Healthy Slovenian Mothers: Microbiota Composition and Bacteriocin Gene Prevalence – Tanja Obermajer – PLOS ONE

Human respiratory microbiome

The Importance of Bacterial and Viral Infections Associated with Adult Asthma Exacerbations in Clinical Practice – Motoyasu Iikura – PLOS ONE

Human gut microbiome

Fat, fibre and cancer risk in African Americans and rural Africans – Stephen J. D. O’Keefe – Nature Communications

Characterization of Bacterial and Fungal Microbiome in Children with Hirschsprung Disease with and without a History of Enterocolitis: A Multicenter Study – Philip K. Frykman – PLOS ONE

Animal models of microbiome research

Editorial: Host–microbe interactions and the enteric nervous system: a new connection? – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

Animal gut microbiome

Integrated Community Profiling Indicates Long-Term Temporal Stability of the Predominant Faecal Microbiota in Captive Cheetahs – Anne A. M. J. Becker – PLOS ONE

Plant microbiome

The Intracellular Scots Pine Shoot Symbiont Methylobacterium extorquens DSM13060 Aggregates around the Host Nucleus and Encodes Eukaryote-Like Proteins – Janne J. Koskimäki – mBio

Extremophile microbiome

Deep groundwater and potential subsurface habitats beneath an Antarctic dry valley –
J. A. Mikucki – Nature Communications

Microbial Diversity in a Permanently Cold and Alkaline Environment in Greenland – Mikkel A. Glaring – PLOS ONE

Bioinformatics

A Robust ANOVA Approach to Estimating a Phylogeny from Multiple Genes – Ximing Xu – Molecular Biology and Evolution

Maximum likelihood tree estimation using codon substitution models with multiple partitions – Stefan Zoller – Molecular Biology and Evolution

Techniques

Estimating Bacterial Diversity for Ecological Studies: Methods, Metrics, and Assumptions – Julia Birtel – PLOS ONE

From Benchtop to Desktop: Important Considerations when Designing Amplicon Sequencing Workflows – Dáithí C. Murray – PLOS ONE

Microbes in the news

Diet swap has dramatic effects on colon cancer risk for Americans and Africans – Science Daily

Mapping Genomes of Pine Bacteria Yields Unexpected Results – UC Merced

Salty aquifer, previously unknown microbial habitat discovered under Antarctica – Science Daily

Chemistry of seabed’s hot vents could explain emergence of life – Eureka Alert
and
Hydrothermal Vents Able to Create Simple Organic Molecules, Study Says – Sci-News

Understanding genetic diversity of bacteriophages – Phys.org

Deadly Gut Bacteria Peak in Spring (about C. difficile) – Rachael Rettner – LiveScience

30 min podcast about Antonie van Leeuwenhoek: The ‘first’ microbiologist and climate modelling – SocGenMicro – SoundCloud

Drug resistant bacteria common for nursing home residents with dementia – Science Daily

Rubella Has Been Eliminated From the Americas, Health Officials Say – Donald G. McNeil Jr. – New York Times

Science, publishing, and career

Symposium overview: Raising standards – International Symposium on Research Assessment and Evaluation in Shanghai, China – Michelle Grayson – Nature

Collateral damage: How one misconduct case brought a biology institute to its knees – The fall out from the STAP case is still being felt across Japan – David Cyranoski – Nature

Bik’s Picks

‘Obesity Signature’ Written in Pee – Rachael Rettner – LiveScience

Childhood bullying: Worse long-term mental health than maltreatment by adult – Science Daily

FDA Approves Double-Chin Eliminator Injection, Kybella – Sydney Lupkin – ABC News

[hr]

April 28, 2015

Posted on by

Wow, this was a busy day with about 700 new articles for y’all to screen. Here we go:

Events

May 7th Webinar: George Weinstock Ph.D., will present “The Human Microbiome: Impact on Health and Disease.”

May 13th Webcast at 11am EDT – “Innovations in the microbiome” with Annick Mercenier and Enea Rezzonico – Nature Publishing Group

Human oral microbiome

Periodontal disease in a remote Asian population: association between clinical and microbiological parameters – Christine Kvarnvik – Journal of Investigative and Clinical Dentistry

Human gut microbiome

Comparison of the gut microbiota of people in France and Saudi Arabia – M. Yasir – Nutrition and Diabetes

Fecal microbiota characteristics of patients with colorectal adenoma detected by screening: A population-based study – James J. Goedert – EBioMedicine

Review: Archaea associated with human surfaces: not to be underestimated – Corinna Bang , Ruth A. Schmitz – FEMS Microbiology Reviews

Review: Keeping bugs in check: The mucus layer as a critical component in maintaining intestinal homeostasis – Martin Faderl – IUBMB Life

Review: A day in the life of the meta-organism: diurnal rhythms of the intestinal microbiome and its host – Christoph A Thaiss – Gut Microbes

Review: Effect of Helicobacter pylori Infection on the Composition of Gastric Microbiota in the Development of Gastric Cancer – Cao L. · Yu J. – GastroIntestinal Tumors

Review: Immunogenetic control of the Intestinal Microbiota – Eric Marietta – Immunology

Review: Type 2 diabetes and gut microbiome: at the intersection of known and unknown – Smitha Upadhyaya – Gut Microbes

Review: Host-Microbiota Interactions in the Intestine – Elson C.O. – Digestive Diseases

Review: Control of commensal microbiota by the adaptive immune system – Husen Zhang – Gut Microbes

Animal models of microbiome research

Effects of low dietary protein on the metabolites and microbial communities in the caecal digesta of piglets – Zhen Luo – Archives of Animal Nutrition

Perturbation of the intestinal microbiota of mice infected with Cryptosporidium parvum – Refaat Ras – International Journal of Parasitology

Host litter-associated gut dynamics affect Escherichia coli abundance and adhesion genotype in rats – Michaela D. J. Blyton – Environmental Microbiology Reports

Regulation by gut commensal bacteria of carcinoembryonic antigen-related cell adhesion molecule expression in the intestinal epithelium – Yasuaki Kitamura – Genes to Cells

Bacteria-Mediated Effects of Antibiotics on Daphnia Nutrition – Elena Gorokhova – Environmental Science & Technology

Role of intestinal microbiota in the generation of polyphenol-derived phenolic acid mediated attenuation of Alzheimer’s disease β-amyloid oligomerization – Dongjie Wang – Molecular Nutrition & Food Research

Animal microbiome

Bacterial symbiont sharing in Megalomyrmex social parasites and their fungus-growing ant hosts – Joanito Liberti – Molecular Ecology

Microbial and sponge loops modify fish production in phase-shifting coral reefs – Cynthia B. Silveira – Environmental Microbiology

Coral symbiotic algae calcify ex hospite in partnership with bacteria – Jörg C. Frommlet – PNAS USA

Plant, plant root and soil microbiome

Yeast nitrogen utilization in the phyllosphere during plant lifespan under regulation of autophagy – Kosuke Shiraishi – Scientific Reports

Role of root microbiota in plant productivity – Andrzej Tkacz and Philip Poole – Journal of Experimental Botany

Seasonal variation of bacterial endophytes in urban trees – Shu Yi Shen – Frontiers in Microbiology

Plant polysaccharides initiate underground crosstalk with bacilli by inducing synthesis of the immunogenic lipopeptide surfactin – Delphine Debois – Environmental Microbiology Reports

Banana leaf and glucose mineralization and soil organic matter in microhabitats of banana plantations under long-term pesticide use – Elena Blume – Environmental Toxicology and Chemistry

Whole-genome comparative analysis of virulence genes unveils similarities and differences between endophytes and other symbiotic bacteria – Sebastian Lòpez-Fernàndez – Frontiers in Microbiology

Decreases in soil moisture and organic matter quality suppress microbial decomposition following a boreal forest fire – Sandra R. Holden – Soil Biology and Biochemistry

Soil bacterial community response to sulfadiazine in the soil–root zone – Rüdiger Reichel – Journal of Plant Nutrition and Soil Science

Three-dimensional structure and cyanobacterial activity within a desert biological soil crust – Hagai Raanan – Environmental Microbiology

Contrasting spatial patterns and ecological attributes of soil bacterial and archaeal taxa across a landscape – Florentin Constancias – Microbiology Open

Microbial 16S gene-based composition of a sorghum cropped rhizosphere soil under different fertilization managements – Anna Lavecchia – Biology and Fertility of Soils

Non-symbiotic Bradyrhizobium ecotypes dominate North American forest soils – David VanInsberghe – The ISME Journal

Deforestation fosters bacterial diversity and the cyanobacterial community responsible for carbon fixation processes under semiarid climate: a metaproteomics study – Felipe Bastida – Applied Soil Ecology

Soil pH effects on the interactions between dissolved zinc, non-nano- and nano-ZnO with soil bacterial communities – Daniel S. Read – Environmental Science and Pollution Research

Functional diversity of soil microbial communities under Scots pine, Norway spruce, silver birch and mixed boreal forests – Chodak Marcin – Pedobiologia

Water microbiome

Metabolic cascades in marine microbial communities – Andreas F. Haas and Forest Rohwer – PNAS USA

A Rickettsiales Symbiont of Amoebae with Ancient Features – Frederik Schulz – Environmental Microbiology

Bacterial communities of Beijing surface waters as revealed by 454 pyrosequencing of the 16S rRNA gene – Yu-Mei Wei – Environmental Science and Pollution Research

Cyanobacterial dynamics in shallow Lake Apopka (Florida, U.S.A.) before and after the shift from a macrophyte-dominated to a phytoplankton-dominated state – Matthew N. Waters – Freshwater Biology

Extremophile microbiome

Open Access: Metabolic and trophic interactions modulate methane production by Arctic peat microbiota in response to warming – Alexander Tøsdal Tveit – PNAS USA

Organic nitrogen cycling microbial communities are abundant in a dry Australian agricultural soil – Lori A. Phillips – Soil Biology and Biochemistry

Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystem – Karen Andrade – The ISME Journal

Microbiome of the built environment

From Lab to Field: The Influence of Urban Landscapes on the Invasive Potential of Wolbachia in Brazilian Aedes aegypti Mosquitoes – Heverton Leandro Carneiro Dutra – PLOS Neglected Tropical Diseases

Bioreactor microbiology

Deciphering Cyanide-Degrading Potential of Bacterial Community Associated with the Coking Wastewater Treatment Plant with a Novel Draft Genome – Zhiping Wang – Microbial Ecology

Seasonal Patterns in Microbial Community Composition in Denitrifying Bioreactors Treating Subsurface Agricultural Drainage – Matthew D. Porter – Microbial Ecology

Food microbiology

Analysis of Bacterial Diversity During Acetic Acid Fermentation of Tianjin Duliu Aged Vinegar by 454 Pyrosequencing – Qian Peng – Current Microbiology

Microbial Ecology

Field experimental evidence that stochastic processes predominate in the initial assembly of bacterial communities – Yi-Qi Hao – Environmental Microbiology

Effect of audible sound in form of music on microbial growth and production of certain important metabolites – Niral Sarvaiya, Vijay Kothari – Microbiology

Techniques

Optimized DNA extraction and metagenomic sequencing of airborne microbial communities – Wenjun Jiang – Nature Protocols
http://www.nature.com/nprot/journal/v10/n5/full/nprot.2015.046.html

Bioinformatics

phylogeo: an R package for geographic analysis and visualization of microbiome data –
Zachary Charlop-Powers and Sean F. Brady – Bioinformatics

PhD thesis: Statistical models for large-scale comparative metagenome analysis – Kathrin Petra Aßhauer – Georg-August-Universität Göttingen

Metagenomics

Prokaryotic genes in eukaryotic genome sequences: when to infer horizontal gene transfer and when to suspect an actual microbe – Irena I. Artamonova – Environmental Microbiology

Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes – Bing Li – The ISME Journal

Metabolomics and proteomics

Review: Microbial metaproteomics for characterizing the range of metabolic functions and activities of human gut microbiota – Weili Xiong – Proteomics

Fate of microbial metabolites of dietary polyphenols in rats: is the brain their target destination? – Mattia Gasperotti – ACS Chemical Neuroscience

Novel Systems Modeling Methodology in Comparative Microbial Metabolomics: Identifying Key Enzymes and Metabolites Implicated in Autism Spectrum Disorders – Colin Heberling – International Journal of Molecular Sciences

Navigating through metaproteomics data: A logbook of database searching –
Thilo Muth – Proteomics

Phages and viruses

Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity – Welkin H Pope – eLIFE

Linking environmental prokaryotic viruses and their host through CRISPRs
– Laura Sanguino – FEMS Microbiology Ecology

Microbes in the news

The Healthy Birth: Dyad or Triad? Exploring Birth and the Microbiome – Anne Estes – Science & Sensibility

Designing a Hospital to Better Fight Infection (about the Hospital Microbiome Project) – Robert Lee Hotz – Wall Street Journal
and
WSJ article on the Hospital Microbiome Project – Elisabeth Bik – MicroBEnet

Facts About Our Microbial Menagerie – Infection Control Today

Don’t Trust The Goats; Their Ticks Could Make You Sick – Poncie Rutsch – NPR

Tiny Creatures: The World of Microbes – Anne M. Estes – Mostly Microbes

Time-lapse movie of growth and death in bacterial communities – David Esteban – Experiment.com

Altered saliva shows increased risk for hospitalization in patients with cirrhosis, hepatic encephalopathy – Healio

An arms race of microbial proportions: A war between bacteria and bacteriophages is being fought at the genetic level – Jason Tetro – Popular Science

Microbes and money

uBiome Launches Clinical Laboratory: launch of their CLIA-regulated clinical laboratory to provide clinical tests based on its unique microbial assays – Globe News Wire

New report sheds light on the Global human microbiome market – size, share, segments analysis and outlook to 2020 – Whatech.com

Science, publishing and career

Five Non-Academic Careers for which Ph.D. Holders are Uniquely Qualified… – Colin White – Nature Careers

Study: Peer Review Predicts Success – Ruth Williams – The Scientist

Discussion paper: Appearance and Gender Bias in Academia – Tali Regev – Tel Aviv University

Bik’s Picks
Source of Antarctica’s Eerie ‘Bleeding Glacier’ Found – Becky Oskin – Live Science

Video: Watch an Algae Cell Turn Itself Inside Out – Douglas Main – NewsWeek

How do you find a Burmese python in the Everglades? – Michael Casey – CBS News

[hr]

April 27, 2015

Posted on by

Events:

Life Science Sunset Mixer and Protocols Hackathon – ZappyLab – Berkeley, CA – Thursday April 30 5:30 pm PDT

Microbiome webinar: can diet can modify GI bacteria? – May 6, 2015 at 1:00pm ET – American Society for Nutrition’s Nutritional Science Council

Microbiome of pregnancy and birth

The neonatal gut harbours distinct bifidobacterial strains – Eoin Barrett – Arch Dis Child Fetal Neonatal Ed

Doctoral thesis: Early Life Intestinal Microbiota in Health and in Atopic Eczema – Lotta Nylund – Turku, Finland

In mice: Cross-fostering immediately after birth induces a permanent microbiota shift that is shaped by the nursing mother – Joseph G Daft – Microbiome

Human gut microbiome

Gut microbiota trajectory in pediatric patients undergoing hematopoietic SCT – E Biagi – Bone Marrow Transplantation

Review: Characterization of the intestinal microbiota and its interaction with probiotics and health impacts – Carine Nunes de Almada – Applied Microbiology and Biotechnology

Commentary: The Gut Microbiome: A New Frontier for Alcohol Investigation – Gail A. Cresci – Alcoholism: Clinical and Experimental Research

Review: The Microbiome for Gastroenterologists – Amit Dutta – Gastroenterology & Endoscopy News

Animal microbiome

Dynamic Distribution of the Gut Microbiota and the Relationship with Apparent Crude Fiber Digestibility and Growth Stages in Pigs – Qing Niu – Scientific Reports

Rumen: A new family of hybrid virophages from an animal gut metagenome – Natalya Yutin – Biology Direct

Rumen: Exploring the sheep rumen microbiome for carbohydrate-active enzymes – Lucas Dantas Lopes – Antonie van Leeuwenhoek

Fish: Dietary input of microbes and host genetic variation shape among-population differences in stickleback gut microbiota – Chris CR Smith – The ISME Journal

Insects: Characterization of the microbiota in the guts of Triatoma brasiliensis and Triatoma pseudomaculata infected by Trypanosoma cruzi in natural conditions using culture independent methods – Marcia Gumiel – Parasites and Vectors

Plant root and soil microbiome

Link to PDF on Fierer lab website (PNAS link still not working): Continental-scale distributions of dust-associated bacteria and fungi – Albert Barberán – PNAS

Stability and succession of the rhizosphere microbiota depends upon plant type and soil composition – Andrzej Tkacz – The ISME Journal

Forest harvesting reduces the soil metagenomic potential for biomass decomposition – Erick Cardenas – The ISME Journal

Peatland vascular plant functional types affect methane dynamics by altering microbial community structure – Bjorn JM Robroek – Journal of Ecology

Structure and function of rhizosphere and non-rhizosphere soil microbial community respond differently to elevated ozone in field-planted wheat – Zhan Chen – Journal of Environmental Sciences

Review: Plant-microbe Cross-talk in the Rhizosphere: Insight and Biotechnological Potential – Shyamalina Haldar – The Open Microbiology Journal

Water microbiome

Pyrosequencing analysis of microbial communities reveals dominant cosmopolitan phylotypes in deep-sea sediments of the eastern Mediterranean Sea – Paraskevi N. Polymenakou – Research in Microbiology

Characterization of the Relative Importance of Human- and Infrastructure-Associated Bacteria in Graywater: A Case Study – Scott P. Keely – Journal of Applied Microbiology

Extremophiles

Calcite-accumulating large sulfur bacteria of the genus Achromatium in Sippewissett Salt Marsh – Verena Salman – The ISME Journal

Book: Microbial Evolution under Extreme Conditions – Corien Bakermans – Google Books/Nature

Microbiome of the built environment

Evolutionary dynamics of methicillin-resistant Staphylococcus aureus within a healthcare system – Li-Yang Hsu – Genome Biology

Food microbiology

Evolution of microbial counts and chemical and physico-chemical parameters in high-moisture Mozzarella cheese during refrigerated storage – Annamaria Ricciardi – LWT – Food Science and Technology

Phages, viruses, and CRISPRs

CRISPR Immunity Drives Rapid Phage Genome Evolution in Streptococcus thermophilus – David Paez-Espino – mBio

Perspective: Can Plant Viruses Cross the Kingdom Border and Be Pathogenic to Humans?
Fanny Balique – Viruses

Diversity of putative archaeal RNA viruses in metagenomic datasets of a yellowstone acidic hot spring – Hongming Wang – Springer Plus

Metagenomics and Bioinformatics

He’s alive! Elviz – exploration of metagenome assemblies with an interactive visualization tool – Michael Cantor – BMC Bioinformatics

Genome assembly using Nanopore-guided long and error-free DNA reads – Mohammed-Amin Madoui – BMC Genomics

Protocol: Generating Enriched Metagenomes from Active Microorganisms with DNA Stable Isotope Probing – Carolina Grob – Springer Protocols Handbooks 2015

PhD thesis: MetaPathways : a modular pipeline for the analysis of environmental sequence information – Niels William Hanson – University of British Columbia

Metabolomics

Identification of Metabolic Signatures Linked to Anti-Inflammatory Effects of Faecalibacterium prausnitzii – Sylvie Miquel – mBio

MetaboAnalyst 3.0—making metabolomics more meaningful – Jianguo Xia – Nucleic Acids Research

Microbes in the news

Crowd funding: Stayin’ alive: how do microbes help corals recover from bleaching? The roles of bacteria in corals – Laura Núñez-Pons – Experiment.com

Building a better microbiome – Richard A. Marini – Express News

The Truth About C-Sections, Probiotics, and the Bacteria in Your Gut: Dr. Neil Stollman on fecal microbiota transplants

Your make-up could be a breeding ground for bacteria – Kimberley Hibbert – Jamaica Observer

Learning from Earth’s Smallest Ecosystems (Kavli Hangout) – Alan Brown – Live Science

Spoiled rotten: how breweries are trying to spot bad beer through DNA – Josh Lowensohn -The Verge

The Fecal Bacterium You’ll Learn to Love – Jason Tetro – Huffington Post

Pet Talk: Research reveals canine skin microbiome – Your Houston News

Physician-scientist cautions against indiscriminate use of antibiotics – Bob Kustra – Idaho Statesman

Waterproof bacteria inspire special coatings – Tim Sandle – Digital Journal

Metanome changes name to Diversigen – News Medical

Solving Real-World Problems With Unconventional Solutions: Using Bacteria To Heal Wounds – Texas A&M Today

Strike a healthy bacteria balance in your gut – Scott Scanlon – Buffalo News

How Safe is Your Shrimp? – Consumer Reports study finds 60% of frozen shrimp contaminated with bacteria – Food Safety News

Science, publishing, and career

Trove of VA reports reveals research misconduct, medical malpractice – Brendan Borrell – Retraction Watch

Lab Bloopers: Reddit users share the worst mishaps they’ve witnessed while working in the lab – Jenny Rood – The Scientist

Peer review, explained (cartoon) – Academia Obscura

Bik’s Picks

Why pregnant women in Mississippi keep dying – Danielle Paquette – Washington Post

Oil May Have Killed Gulf Dolphins – David Biello – Scientific American

Photos: 7-Year-Old Boy Discovers T. Rex Cousin – Live Science
[hr]

April 23, 2015

Posted on by

Earth Day initiative by Jonathan Eisen – I took the pledge! Become a Guardian of Microbial Diversity – Jonathan Eisen – Change.org

Due to the importance of microbes and microbial diversity to the planet, and due the risks that may come from a reduction in this diversity, we are calling here for people to take a pledge to become “A Guardian of Microbial Diversity” By taking this pledge you state that you will make efforts to consider the effects of your actions on microbes and their diversity. In addition, you pledge here to support efforts to limit and prevent unnecessary damage to the diversity of microbes on the planet.

Call for Grant Applications (deadline April 30): Gut Microbiome Grant Program – DNA Genotek

Animal models of microbiome research

Dysbiotic gut microbiota causes transmissible Crohn’s disease-like ileitis independent of failure in antimicrobial defence – Monika Schaubeck – Gut

Oral ampicillin inhibits liver regeneration by breaking hepatic innate immune tolerance normally maintained by gut commensal bacteria – Xunyao Wu – Hepatology

Animal microbiome

Alligator: The Good, the Bad, and the Unknown: Microbial Symbioses of the American Alligator – Sarah W. Keenan and Ruth M. Elsey – Integrative & Comparative Biology

Ticks: Concordance of bacterial communities of two tick species and blood of their shared rodent host – Evelyn C. Rynkiewicz – Molecular Ecology

Plant and soil microbiome

A new look at plant viruses and their potential beneficial roles in crops – Marilyn J. Roossinck – Molecular Plant Pathology

Molecular signals required for the establishment and maintenance of ectomycorrhizal symbioses – Kevin Garcia – New Phytologist

Fungus: Metagenome sequence of Elaphomyces granulatus from sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome expansion and a Proteobacteria-rich microbiome – C. Alisha Quandt – Environmental Microbiology

Understanding fungal functional biodiversity during the mitigation of environmentally dispersed pentachlorophenol in cork oak forest soils – Adélia Varela – Environmental Microbiology

Effects of diurnal temperature variation on microbial community and petroleum hydrocarbon biodegradation in contaminated soils from a sub-Arctic site – Ali Akbari – Environmental Microbiology

Impacts of Dimethyl Phthalate on the Bacterial Community and Functions in Black Soils – Zhigang Wang – Frontiers in Microbiology

Enzymatic and biological assessment of sulfonylurea herbicide impact on soil bacterial communities – Marioara Nicoleta Filimon – African Journal of Agricultural Research

Water microbiome

Water column methanotrophy controlled by a rapid oceanographic switch – Lea Steinle – Nature Geoscience

Microbial metabolism of transparent exopolymer particles during the summer months along a eutrophic estuary system – Edo Bar-Zeev – Frontiers in Microbiology

Extremophiles

Distinct summer and winter bacterial communities in the active layer of Svalbard permafrost revealed by DNA- and RNA-based analyses – Anders Prieme – Frontiers in Microbiology

Bioreactor microbiome

The Impact of Injections of Different Nutrients on the Bacterial Community and Its Dechlorination Activity in Chloroethene-Contaminated Groundwater  – Takamasa Miura – Microbes and Environments

Metagenomics and bioinformatics

PDF, in press: Detecting bacterial genomes in a metagenomic sample using NGS reads – Camilo Valdes – Statistics and Its Interface

Metabolomics

Editorial about colibactin paper: Natural products: Hunting microbial metabolites – Eric W. Schmidt – Nature Chemistry

Microbial Ecology

Deciphering microbial community robustness through synthetic ecology and molecular systems synecology – Ben Stenuit – Current Opinion in Biotechnology

Microbes in the news

What about Earth’s Microbiome? – Raina Maier – Scientific American

Effectiveness of methane-consuming bacteria in the ocean moderated by ocean currents – Anthony Watts – Watts Up With That

Researchers discover new method to detect most common bacteria contaminating oysters – Phys.org

DNA of bacteria crucial to the ecosystem defies explanation – Robert Perkins – University of Southern California

Bacteria Can Aid Aphids Against Predation and Parasitism – Meredith Swett Walker – Entomology Today

Editorial: Bacterial bonanza far from the West – Nature

Researchers develop computer model of bacterial colony interactions – Christopher Packham – Phys.org

DuPont buying microbiome firm, seeks edge in emerging crop products – Carey Gillam – Reuters

Science and Art

Artists Make Human Cheese From Toe, Armpit, And Belly Button Bacteria: Collaborative art project called Selfmade by Christina Agapakis and Sissel Tolaas – James Mailer -Smash.com
and
Scientists create cheese from human toe bacteria – IndiaToday

Science, publishing and career

Beyond Bar and Line Graphs: Time for a New Data Presentation Paradigm – Tracey L. Weissgerber – PLOS Biology

Bik’s Picks

Colour As a Signal for Entraining the Mammalian Circadian Clock – Lauren Walmsley – PLOS Biology

Peering Inside Yellowstone’s Supervolcano – Larry O’Hanlon – Discovery

World Happiness Report 2015 ranks happiest countries – Science Daily

Kermit the Frog Reacts to His Newly Discovered Lookalike: “Shorten your name if you want to make it in show business.” – Kermit – Disney Channel

[hr]

April 21, 2015

Posted on by

I don’t always eat steak, but when I do, I will put some garlic on it.

Conferences

WAO Symposium on Food Allergy and the Microbiome – December 2015 – Miami, FL, USA

Call for papers: Interactions of the Human Microbiome and Immune System in Health Resilience and Disease Pathogenesis – Journal of Immunology Research

Microbiome of pregnancy and birth

Impact of human milk bacteria and oligosaccharides on neonatal gut microbiota establishment and gut health – Ted Jost – Nutrition Reviews

Human oral microbiome

Editorial on “The oral microbiome in an ecological perspective: More than just a sum of microbes” – Egija Zaura and Alex Mira – Frontiers in Cellular and Infection Microbiology

Human respiratory microbiome

Rapid detection of emerging pathogens and the loss of microbial diversity associated with severe lung disease in cystic fibrosis – William G. Flight – Journal of Clinical Microbiology

Review behind a thick paywall: The pediatric microbiome and the lung – Michael Tracy – Current Opinion in Pediatrics

Review: Lung Microbiomes: New Frontiers? – Kathryn DeRiemer – American Journal of Respiratory and Critical Care Medicine

Review: A systematic review and meta-analysis of probiotics for the treatment of allergic rhinitis – Alexander E. Zajac – International Forum of Allergy & Rhinology

Human gut microbiome

Ménage-à-trois of bariatric surgery, bile acids and the gut microbiome – Rajendra Raghow – World Journal of Diabetes

Gut Microbiome Compositional and Functional Differences between Tumor and Non-tumor Adjacent Tissues from Cohorts from the US and Spain – Gut Microbes

Review: No Vacancy: How Beneficial Microbes Cooperate with Immunity To Provide Colonization Resistance to Pathogens – Martina Sassone-Corsi and Manuela Raffatellu – The Journal of Immunology

Review on chronic kidney disease: Altered intestinal microbial flora and impaired epithelial barrier structure and function in CKD: the nature, mechanisms, consequences and potential treatment – Nosratola D. Vaziri – Nephrology Dialysis Transplantation

Review: The Role of Microbial Amino Acid Metabolism in Host Metabolism – Evelien P. J. G. Neis – Nutrients

Review: Linking Smoking, Coffee, Urate, and Parkinson’s Disease – A Role for Gut Microbiota? – Filip Scheperjans – Journal of Parkinson’s Disease

Animal and other models of microbiome research

Have some garlic with your steak: Dietary allicin reduces transformation of L-carnitine to TMAO through impact on gut microbiota – Wei-Kai Wu – Journal of Functional Foods

Innate Lymphoid Cells Control Early Colonization Resistance against Intestinal Pathogens through ID2-Dependent Regulation of the Microbiota – Xiaohuan Guo – Immunity

Effect of donor animal species and their feeding on the composition of the microbial community establishing in a rumen simulation – M. Witzig – Journal of Applied Microbiology

Impact of a novel protein meal on the gastrointestinal microbiota and host transcriptome of larval zebrafish Danio rerio – Eugene Rurangwa – Frontiers in Physiology

Animal microbiome

Shit happens: Shifts in the gut microbiome observed in wildlife (Giraffa camelopardalis, Antidorcas marsupialis) fecal samples exposed to natural weather conditions: lessons from time series analyses using next generation sequencing for application in field studies – Sebastian Menke – Methods in Ecology and Evolution

Caste-Specific Differences in Hindgut Microbial Communities of Honey Bees (Apis mellifera) – Karen M. Kapheim – PLOS ONE

Molecular Survey of Bacterial Communities Associated with Bacterial Chondronecrosis with Osteomyelitis (BCO) in Broilers – Tieshan Jiang – PLOS ONE

Plant root and soil microbiome

Bacterial diversity amplifies nutrient-based plant–soil feedbacks – Simone Weidner – Functional Ecology

Non-random species loss in bacterial communities reduces antifungal volatile production –
W. H. Gera Hol – Ecology

Application of a new purification method of West-Kazakhstan chestnut soil microbiota DNA for metagenomic analysis – N. Kh. Sergaliev – Eurasian Soil Science

Physiological profiles of microbial communities in mine soils afforested with different tree species – Marcin Chodak – Ecological Engineering

Microbial lipid and amino sugar responses to long-term simulated global environmental changes in a California annual grassland – Chao Liang – Frontiers in Microbiology

Water microbiome

Seasonal diversity and dynamics of haptophytes in the Skagerrak, Norway, explored by high-throughput sequencing – Elianne Sirnæs Egge – Molecular Ecology

Extremophiles

Relationship between phylogenetic and nutritional diversity in Arctic (Kandalaksha Bay) seawater planktonic bacteria – Chiara Pesciaroli – Annals of Microbiology

Geochemical Characteristics and Microbial Community Composition in Toxic Metal-Rich Sediments Contaminated with Au-Ag Mine Tailings – Man Jae Kwon – Journal of Hazardous Materials

Uranium isotopes fingerprint biotic reduction – Malgorzata Stylo – PNAS

Bioreactor microbiome

Metaproteomics of complex microbial communities in biogas plants – Robert Heyer – Microbial Biotechnology

Similar PAH Fate in Anaerobic Digesters Inoculated with Three Microbial Communities Accumulating Either Volatile Fatty Acids or Methane – Florence Braun – PLOS ONE

Reactor performance and methanogenic archaea species in thermophilic anaerobic co-digestion of waste activated sludge mixed with food wastewater – Hyun Min Jang – Chemical Engineering Journal

Functional food microbiology

A proposed framework for an appropriate evaluation scheme for microorganisms as novel foods with a health claim in Europe – Sylvie Miquel – Microbial Cell Factories

Metagenomics and bioinformatics

CoMeta: Classification of Metagenomes Using k-mers – Jolanta Kawulok, Sebastian Deorowicz – PLOS ONE

Large-scale contamination of microbial isolate genomes by Illumina PhiX control – Supratim Mukherjee – Standards in Genomic Sciences

NGS-eval: NGS Error analysis and novel sequence VAriant detection tooL – Ali May – Nucleic Acids Research

Mini review: The Turbulent Network Dynamics of Microbial Evolution and the Statistical Tree of Life – Eugene V. Koonin – Journal of Molecular Evolution

Not really metagenomics but of interest: Ecological overlap and horizontal gene transfer in Staphylococcus aureus and Staphylococcus epidermidis – Guillaume Méric – Genome Biology and Evolution

Haven’t we microbiologists already been doing this for years?
Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform – Shadi Shokralla – Scientific Reports

Techniques

Method Optimization for Fecal Sample Collection and Fecal DNA Extraction – Conny Mathay – Biopreservation and Biobanking

Microbes in the news

Housing characteristics and microbial communities in homes of asthmatic children – Elisabeth Bik – MicroBEnet

OCHS science experiment finds space a hospitable place for bacteria – Cindy Nevitt – Press of Atlantic City

Uranium isotopes carry the fingerprint of ancient bacterial activity – Phys.org

Immune cells support good gut bacteria in fight against harmful bacteria – University of Chicago

Q&A: What Is Listeria? Bacteria Found in Blue Bell Ice Cream – Mary Clare Jalonick – ABC News

Grant will help University of Minnesota study antibiotic-resistant bacteria – Star Tribune

Science, publishing, and career

Mya Breitbart awarded the 2015 STEM Woman of the Year – University of South Florida

Bik’s Picks

Fast imaging of live organisms with sculpted light sheets – Aleksander K. Chmielewski – Scientific Reports

Cheesy, metallic, sweet: 170-year-old champagne is clue to winemaking’s past – Allie Wilkinson – Nature

New Evidence of Prehistoric Trade With Asia Found at Bering Land Bridge Site – Huffington Post
[hr]