Category Archives: Human gut

May 6, 2015

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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
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May 5, 2015

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General human microbiome

Review: The Human Microbiota: The Rise of an “Empire” – Gidon Berger – Rambam Maimonides Medical Journal

Human gut microbiome

Human colon-derived soluble factors modulate gut microbiota composition – Arancha Hevia – Frontiers in Oncology

Dysbiosis of Intestinal Microbiota Associated With Inflammation Involved in the Progression of Acute Pancreatitis – Tan, Chaochao – Pancreas

Review: Does the Gut Microbiota Contribute to Obesity? Going beyond the Gut Feeling – Marisol Aguirre and Koen Venema – Microorganisms

Review: Alcohol Effects on the Composition of Intestinal Microbiota – Phillip A. Engen – The Gastrointestinal Microbiome – NIH

Human respiratory microbiome

Prevalence of oropharyngeal antibiotic-resistant flora among residents of aged care facilities: a pilot study – Christopher D. Etherton-Beer – Respirology

Animal models of microbiomes

Modulatory effects of a cranberry extract co-supplementation with Bacillus subtilis CU1 probiotic on phenolic compounds bioavailability and gut microbiota composition in high-fat diet-fed mice – Stéphanie Dudonné – PharmaNutrition

Animal microbiome

Characterization of the cellulolytic bacteria communities along the gastrointestinal tract of Chinese Mongolian sheep by using PCR-DGGE and real-time PCR analysis – Yan Zeng – World Journal of Microbiology and Biotechnology

Soil microbiome

Soil microbial community structure is unaltered by plant invasion, vegetation clipping, and nitrogen fertilization in experimental semi-arid grasslands – Chelsea J. Carey – Frontiers in Microbiology

Water microbiome

A metagenome for lacustrine Cladophora (Cladophorales) reveals remarkable diversity of eukaryotic epibionts and genes relevant to materials cycling – Linda E. Graham – Journal of Phycology

Bacterial and archaeal biogeography of the deep chlorophyll maximum in the South Pacific Gyre – Emily A. Walsh – Aquatic Microbial Ecology

Extremophiles

The influence of surface soil physicochemistry on the edaphic bacterial communities in contrasting terrain types of the Central Namib Desert – S. Gombeer – Geobiology

Microbial diversity and metabolic networks in acid mine drainage habitats – Celia Mendez-Garcia – Frontiers in Microbiology

Metabolomics

Structuring Microbial Metabolic Responses to Multiplexed Stimuli via Self-Organizing Metabolomics Maps – Cody R. Goodwin – Chemistry & Biology

Techniques

Deriving accurate microbiota profiles from human samples with low bacterial content through post-sequencing processing of Illumina MiSeq data – Jake Jervis-Bardy – Microbiome

More microbes

Antibacterial activity of silver-killed bacteria: the “zombies” effect – Racheli Ben-Knaz Wakshlak

Review: The dormant blood microbiome in chronic, inflammatory diseases – Marnie Potgieter – FEMS Microbiology Reviews

Microbes and art

Faecal transplants and bio-art – Eden Project’s latest exhibition Invisible You explores the science of microbes – Nicola Davis – The Guardian

Microbiology printable labels or buffet cards blue and black – LoveBacteriaArt – Etsy

Microbes in the news

1h Video: Seth Bordenstein: The microbiome and Darwin’s Mystery of Mysteries – University of Michigan Early Career Scientists Symposium

Cervicovaginal microbiome holds promise in preventing preterm birth – interview with Dr. Michal Elovitz at the annual meeting of the American Congress of Obstetricians and Gynecologists – Mary Ellen Schneider #ACOG15

Episode 6 of The Microbiome Podcast: The microbiome, autism, and serotonin production with Dr. Elaine Hsiao – MicrobiomeInstitute

Some beards as dirty as toilets: Microbiologist tests beards for germs – Royale Da – KOAT

(See more beard microbiome articles from these past days in The Beard Microbiome)

“You’re covered in poo bacteria.” No, your beard isn’t full of poop (probably) – Rachel Feltman – The Washington Post

HuMiX – Emulating human microbiome on a chip – Bactavatchalou Sivakumar

Nanoparticles in consumer products can significantly alter normal gut microbiome – Phys.org

Never a dull day for microbiologist – Kathryn Bernard up for Women of Distinction prize – Winnipeg Free Press

Agricultural microbiology draws Chinese researchers to Argentina – Xinhua – Want China Times

Expert’s Corner: Physician-scientist on why he recommends probiotics – University of Massachusetts

Gut Wars: One Man’s Adventure With Antibiotics and Ulcerative Colitis – Alexandra Carmichael – uBiome blog

Show Me Your Moves: Updated classics and new techniques help microbiologists get up close and quantitative – Marissa Fessenden – The Scientist

‘Zombie’ Bacteria May Help Heal Wounds – Discovery

Ocean currents disturb methane-eating bacteria – Phys.org

Bacteria could prove key in the fight against cholesterol – Paul Healy – Independent

Free book (for a limited time): The Squid, the Vibrio & the Moon – Small Friends Books

Science, publishing, and career

DNA editing takes a serious step forward — for better or worse – Eryn Brown – LA Times

Bik’s Picks

Llamas as Lab Rats: From diagnostics to vaccines, llama antibodies point to new directions in HIV research – Jenny Rood – The Scientist

Big whales have stretchy nerves to help them gulp – Jonathan Webb – BBC

Is sleepwalking genetic? Study suggests it runs in the family – ZME Science

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May 4, 2015

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Grant opportunities

Newborn and Infant Gut Health – Application deadline : May 13, 2015 – Bill & Melinda Gates Foundation

Events

Free Webinar: The Human Microbiome: Beyond the Gut – May 5, 2:30 pm ET – The Scientist

General microbiome

Review: Sequencing and beyond: integrating molecular ‘omics’ for microbial community profiling – Eric A. Franzosa – Nature Reviews Microbiology

Reproductive Parasitism: Maternally Inherited Symbionts in a Biparental World
Gregory D.D. Hurst and Crystal L. Frost – Cold Spring Harbor Perspectives in Biology

Human oral microbiome

Editorial: Defining functional signatures of dysbiosis in periodontitis progression
Gary P Wang – Genome Medicine
belongs to:
Functional signatures of oral dysbiosis during periodontitis progression revealed by microbial metatranscriptome analysis – Susan Yost – Genome Medicine

Human gut microbiome

Intestinal dysbiosis in children with short bowel syndrome is associated with impaired outcome – Helene Engstrand Lilja – Microbiome

Intestinal Microbiota Signatures Associated With Histological Liver Steatosis in Pediatric-Onset Intestinal Failure – Katri Korpela – Journal of Parenteral & Enteral Nutrition

Differences of the Fecal Microflora With Clostridium difficile Therapies – Thomas J. Louie – Clinical Infectious Diseases

Review: The human gut resistome – Willem van Schaik – Philosophical Transactions B

Animal models

The intestinal microbiota influences Campylobacter jejuni colonization and extra-intestinal dissemination in mice – Jason L. O’Loughlin – Applied and Environmental Microbiology

Animal microbiome

Fish: Selection in the host structures the microbiota associated with developing cod larvae (Gadus morhua) – Ingrid Bakke – Environental Microbiology

Plant and soil microbiome

Crustose coralline algal species host distinct bacterial assemblages on their surfaces – Jennifer M Sneed – The ISME Journal

Influence of plant communities and soil properties during natural vegetation restoration on arbuscular mycorrhizal fungal communities in a karst region – Yueming Liang – Ecological Engineering

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

Predictable communities of soil bacteria in relation to nutrient concentration and successional stage, in a laboratory culture experiment – Woojin Song – Environmental Microbiology

Water microbiome

Accumulation of Clinically Relevant Antibiotic Resistant Genes, Bacterial load and Metals from a Freshwater Lake Sediments in Central Europe – Naresh Devarajan – Environmental Science & Technology

Effects of Heavy Metal and Nutrients on Benthic Microbial Communities in Freshwater Sediment of Poyang Lake (China) – Cho Yu – Journal of Residuals Science & Technology

Review: Stream microbial diversity responds to environmental changes: Review and synthesis of existing research – Lydia Zeglin – Frontiers in Microbiology

Built environment microbiome

Indoor air bacterial communities in Hong Kong households assemble independently of occupant skin microbiomes – David Wilkins – Environmental Microbiology

Bioreactor microbiology

Bacterial community structure in treated sewage sludge with mesophilic and thermophilic anaerobic digestion – Hana Stiborova – Folia Microbiologica

Performance and microbial community dynamics in bioaugmented aerated filter reactor treating with coking wastewater – Shengnan Shi – Bioresource Technology

Phages and viruses

My life with Mu – Ariane Toussaint – Bacteriophage

Fungi

Fungal artificial chromosomes for mining of the fungal secondary metabolome – Jin Woo Bok – BMC Genomics

Review: The Human Mycobiome – Patrick C. Seed – Cold Spring Harbor Perspectives in Medicine

Antibiotic resistance

Antibiotic resistance genes in the environment: prioritizing risks – Johan Bengtsson-Palme & D. G. Joakim Larsson – Nature Reviews Microbiology

Review: The human gut resistome – Willem van Schaik – Philosophical Transactions B

Metagenomics

Under-detection of endospore-forming Firmicutes in metagenomic data – Sevasti Filippidou – Computational and Structural Biotechnology Journal

Microbes in the news

Each Vineyard Has a Unique Microbiome – University of Chicago – The Epoch Times

Viruses: You’ve heard the bad; here’s the good – American Society for Microbiology – Science Daily

Silver turns bacteria into deadly zombies – Emily Conover – Science Magazine

Rare plague outbreak in Colorado linked to pit bull, CDC says – CNN Wire

Science, publishing, and career

A time limit on postdoctoral contracts: The French experience – Elisabeth Pain – Science Careers

Follow the Funding – Bob Grant – The Scientist

Women Scientists Share Their Awful Stories Of Sexism In Publishing – Cat Ferguson – BuzzFeed Science

Science and art

The Microbiome Votes: I mixed my microbiome with the candidates and asked them to vote – Exploring the Invisible

Bik’s Picks

Horribly bleak study sees ‘empty landscape’ as large herbivores vanish at startling rate – Fred Barbash and Justin Wm. Moyer – Washington Post

Here’s How Coffee Cups in Space Could Help Save Lives on Earth – Helen Regan – Time

Why Hawaiians are protesting construction of the world’s second-largest telescope – Joseph Stromberg – Vox.com

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May 1, 2015

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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
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April 30, 2015

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General human microbiome

Microbiome Analysis: Trends in Cancer Epidemiology, Challenges and Opportunities – Elizabeth F. Hebert – International Journal of Cancer Research and Molecular Mechanisms

Human respiratory microbiome

Still under embargo/technical difficulties: Swine Farming Is a Risk Factor for Infection With and High Prevalence of Carriage of Multidrug-Resistant Staphylococcus aureus – Shylo E. Wardyn – Clinical Infectious Diseases

The Culturome of the Human Nose Habitats Reveals Individual Bacterial Fingerprint Patterns – Ursula Kaspar – Environmental Microbiome

Human gut microbiome

Determining the Long-term Effect of Antibiotic Administration on the Human Normal Intestinal Microbiota Using Culture and Pyrosequencing Methods – Mamun-Ur Rashid – Clinical Infectious Diseases

Animal models of microbiome research

Modulation of growth performances, survival, digestive enzyme activities and intestinal microbiota in common carp (Cyprinus carpio) larvae using short chain fructooligosaccharide – Seyed Hossein Hoseinifar – Aquaculture Research

Plant microbiome

Simulation of the evolution of the legume-rhizobia symbiosis under the conditions of ecological instability – N. I. Vorobyov – Russian Journal of Genetics: Applied Research

Review: Plant-associated fungal communities in the light of meta’omics – Derek Peršoh – Fungal Diversity

Water microbiome

Editorial : Roles and mechanisms of parasitism in aquatic microbial communities – Télesphore Sime-Ngando – Frontiers in Microbiology

Picoplankton and nanoplankton variability in an Antarctic shallow coastal zone (Admiralty Bay) during the austral summer of 2010/2011 – Mariana Vanzan – Polar Biology

Relationships between Microbial Compositions and Hydrochemical Factors in Nitrate Contaminated Groundwater of Hun River Alluvial Proluvial Fan, China – A.X. Zhou – Journal of Agricultural Science and Technology

Extremophile microbiome

Picoplankton and nanoplankton variability in an Antarctic shallow coastal zone (Admiralty Bay) during the austral summer of 2010/2011 – Mariana Vanzan – Polar Biology

Microbiome of the built environment

Screening of bacteria and concrete compatible protection materials – Yusuf Çağatay Erşan – Construction and Building Materials

Bioreactor microbiology

Metal Oxide Nanoparticles Induce Minimal Phenotypic Changes in a Model Colon Gut Microbiota – Alicia A Taylor – Environmental Engineering Science

Metagenomics

Genome mining: Prediction of lipopeptides and polyketides from Bacillus and related Firmicutes – Gajender Aleti – Computational and Structural Biotechnology Journal

Book: VIRONOMICS: The Study of Viral Genomics in Human Cancer and Disease – Dirk P. Dittmer – Next Generation Sequencing in Cancer Research, Volume 2

Microbes in the news

An Atlas of the Bacteria and Fungi We Breathe Every Day – Neel V. Patel – Wired

Deadly Gut Bacteria Infections Peak in Spring – Rachael Rettner – Live Science

Study finds swine farming is a risk factor for drug-resistant staph infections – University of Iowa

Turning to Bacteria to Fight the Effects of Climate Change – Esther Ngumbi – Scientific American

Are We Less “Gutsy” Than we Used to Be? New Clues about the Evolution of the Human Microbiome from Research in Apes – Sharon Greenblum – Food Insight

How Fluid Flow Affects Bacteria – Science 2.0

Four Exceptional Contributions to the Advancement of Clinical Microbiology and Infectious Diseases Recognised at ECCMID – Select Science

Microbiome Hypome (articles that overstate microbiome importance)

The Cure for Brain Diseases Is in Your Gut – David Perlmutter – The Daily Beast

Microbes and money

Irish Microbiome Research Institute Partners With San-Francisco Based Second Genome On Bowel Disease Research – IBD News Today

Bik’s Picks

Low Sunlight Increases Pancreatic Cancer Risk; Why It’s Important To Get Enough Vitamin D – Justin Caba – Medical Daily

Bat Wings Harbor Special Sensory Cells – Stephanie Pappas – Live Science

Sea Lion Pup Waddling Around San Francisco’s Marina District Safely Captured – KPIX / KCBS

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April 29, 2015

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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

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April 28, 2015

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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

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April 27, 2015

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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
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April 24, 2015

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Events

MetaSUB: First International Summit of Metagenomics & Metadesign of Subways and Urban Biomes – June 2015 – Christopher Mason – MicroBE.net

Human oral microbiome

Comparison of Bacterial Community Composition of Primary and Persistent Endodontic Infections Using Pyrosequencing – Giorgos N. Tzanetakis – Journal of Endodontics

Total and Specific Bacterial Levels in the Apical Root Canal System of Teeth with Post-treatment Apical Periodontitis – Henrique S. Antunes – Journal of Endodontics

Ability of Human Oral Microbiota to Produce Wine Odorant Aglycones from Odourless Grape Glycosidic Aroma Precursors – Carolina Muñoz-González – Food Chemistry

Human gut microbiome

Ecological effect of ceftazidime/avibactam on the normal human intestinal microbiota – Mamun-Ur Rashid – International Journal of Antimicrobial Agents

Manually curated database: Mycobiome: Approaches to analysis of intestinal fungi – Jie Tang – Journal of Immunological Methods

No abstract, behind paywall – Isoflavones and the gut microbiome – Herman Depypere – Maturitas

Animal models of microbiome research

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

Dysbiosis and Staphyloccus aureus Colonization Drives Inflammation in Atopic Dermatitis – Tetsuro Kobayashi – Immunity

Animal microbiome

Evaluation of Composition and Individual Variability of Rumen Microbiota in Yaks by 16S rRNA High-throughput Sequencing Technology – Wei Guo – Anaerobe

Diversity and phylogenetic analysis of endosymbiotic bacteria of the date palm root borer Oryctes agamemnon (Coleoptera: Scarabaeidae) – Wael S El-Sayed and Reda A Ibrahim – BMC Microbiology

Review: Genomics of the honey bee microbiome – Nancy A. Moran – Current Opinion in Insect Science

Review: Hologenome theory and the honey bee pathosphere – Ryan S. Schwarz – Current Opinion in Insect Science

Water microbiome

Metagenome-assembled genomes uncover a global brackish microbiome – Luisa W Hugerth – BioRxiv

Built environment microbiome

Review: Hospital-associated microbiota and implications for nosocomial infections – Simon Lax and Jack A Gilbert – Trends in Molecular Medicine

Microbes and immunology

Of mice, macaques and men: scaling of virus dynamics and immune responses – Christian L. Althaus – Frontiers in Microbiology

Extremophiles

Deciphering the microbiota of Tuwa hot spring, India using shotgun metagenomic sequencing approach – Amitsinh Mangrola – Genomics Data

Review: Thermophiles in the genomic era: Biodiversity, science, and applications – M. Sofía Urbieta – Biotechnology Advances

Microbes in the news

Justin and Erica Sonnenburg: Cute Family. And You Should See Their Bacteria –  John Swansburg @thescienceofus @NYMag

Episode 5 of The Microbiome Podcast: Diet and its impact on our microbiota and health with Drs. Erica and Justin Sonnenburg – American Microbiome Institute

The Man Who Drank Cholera and Launched the Yogurt Craze – Ilya Metchnikoff laid the foundation for modern probiotics – Lina Zeldovich- Nautilus

Dirk Gevers, heading the Janssen Human Microbiome Institute – Nature Reviews Drug Discovery

Science, publishing, and career

Big names or big ideas: Do peer-review panels select the best science proposals? – Danielle Li, Leila Agha – Science

Bik’s Picks

When Hubble Stared at Nothing for 100 Hours – Nadia Drake – National Geographic

Neuroscientists Create Illusion of Having Invisible Body – Sci-News

Entire genomes of woolly mammoths mapped: Clues to extinction, possibility of bringing mammoths back – Science Daily

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April 22, 2015

Posted on by

Happy Earth Day! Today, I screened 371 papers for you from ISME Journal, Nature, Applied and Environmental Microbiology, PLOS ONE, and others. Here is what I found:

Human oral microbiome

Quorum-Sensing Dysbiotic Shifts in the HIV-Infected Oral Metabiome – Robert E. Brown – PLOS ONE

Full mouth periodontal debridement with or without adjunctive metronidazole gel in smoking patients with chronic periodontitis: A pilot study – C. C. Bergamaschi – Journal of Periodontal Research

Human respiratory microbiome

Changes in Cystic Fibrosis Airway Microbial Community Associated with a Severe Decline in Lung Function – Patrizia Paganin – PLOS ONE

Bacteriological Assessment of Healthcare-Associated Pneumonia Using a Clone Library Analysis – Shingo Noguchi – PLOS ONE

Human gut microbiome

Sex, Body Mass Index, and Dietary Fiber Intake Influence the Human Gut Microbiome – Christine Dominianni – PLOS ONE

Editorial: Gut Bacteria Combined With Poor Diet May Promote Childhood Malnutrition – M. J. Friedrich – JAMA

Animal models of microbiome research

Effects of dietary supplementation of selenium-enriched probiotics on production performance and intestinal microbiota of weanling piglets raised under high ambient temperature – C. H. Lv – Journal of Animal Physiology and Animal Nutrition

Phylogenetic and Functional Alterations in Bacterial Community Compositions in Broiler Ceca as a Result of Mannan Oligosaccharide Supplementation – A. Corrigan – Applied and Environmental Microbiology

Animal microbiome

Taxonomic Identification of Ruminal Epithelial Bacterial Diversity during Rumen Development in Goats – Jinzhen Jiao – Applied and Environmental Microbiology

Shifts in Bacterial Communities of Eggshells and Antimicrobial Activities in Eggs during Incubation in a Ground-Nesting Passerine – Stéphanie Grizard – PLOS ONE

Plant microbiome

Fungi on leaves: Host genotype is an important determinant of the cereal phyllosphere mycobiome – Rumakanta Sapkota – New Phytologist

Soil and plant soil microbiome

Continental-scale distributions of dust-associated bacteria and fungi – Albert Barberán – PNAS USA

Missing forests: Soil microbiome responses to the short-term effects of Amazonian deforestation – Acacio A. Navarrete – Molecular Ecology

Distinct soil microbial diversity under long-term organic and conventional farming – Martin Hartmann – The ISME Journal

Genomic signature of selective sweeps illuminates adaptation of Medicago truncatula to root-associated microorganisms – Maxime Bonhomme – Molecular Biology and Evolution

Differential Assemblage of Functional Units in Paddy Soil Microbiomes – Yongkyu Kim – PLOS ONE

The Effect of Biochar and Its Interaction with the Earthworm Pontoscolex corethrurus on Soil Microbial Community Structure in Tropical Soils – Jorge Paz-Ferreiro – PLOS ONE

Water microbiome

Species Richness and Adaptation of Marine Fungi from Deep-Subseafloor Sediments – Vanessa Rédou – Applied and Environmental Microbiology

Environmental metabarcoding reveals heterogeneous drivers of microbial eukaryote diversity in contrasting estuarine ecosystems – Delphine Lallias – The ISME Journal

Food microbiology

Spoiler alert: Origin and ecological selection of core and food-specific bacterial communities associated with meat and seafood spoilage – Stéphane Chaillou – ISME Journal

Proteomics

“You produce while I clean up,” a strategy revealed by exoproteomics during Synechococcus–Roseobacter interactions – Joseph A. Christie-Oleza – Proteomics

Microbes in the news

How Modern Life Depletes Our Gut Microbes – Michaeleen Doucleff – NPR Goats and Soda

Great longread: Forensic science: The soil sleuth – Forensic geologist Lorna Dawson helps convict criminals using the dirt from their shoes – Chelsea Wald – Nature

A Microbiome Three-Conference Summary – Kristina Campbell – The Intestinal Gardener

University brews up artificial kopi luwak coffee with even more flavor using civet microbiome – Katherine Wei – China Post

Science, publishing, and career

The postdoc series: What comes next? A postdoc sets you up for a variety of careers, including academia, editing, working in industry, core laboratories and more – Julie Gould – Nature Jobs

Is it fair to evaluate Ph.D. students based on their personalities? Fallout from a gutless adviser – Alice Huang – Science

Minority Ph.D. students: Where do they go? – Beryl Lieff Benderly – Science

Bibliometrics: The Leiden Manifesto for research metrics – Diana Hicks – Nature

Rita Colwell: Women in science still battle bias – Mike McInally – Mid-Valley Health

Bik’s Picks

The genome of cultivated sweet potato contains Agrobacterium T-DNAs with expressed genes: An example of a naturally transgenic food crop – Tina Kyndt – PNAS

How exactly do mosquitoes track us down – and what makes humans their meal of choice? – Biodetectives

Construction workers in China accidentally unearth dinosaur eggs – Sean O’Kane – The Verge
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