Category Archives: Science – Career – Publishing

February 16, 2016

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Today we’ll go to the extremes: Life in hydrogen sulfide rich environments, subsurface Archaea, subseafloor Fungi, and pit latrines.

Events

NIOO Summer course: identifying terrestrial and freshwater nematodes – June 13-24, Wageningen, The Netherlands

Human respiratory microbiome

Concealed Carry: Hidden Staphylococcus aureus Carriage: Overrated or Underappreciated? – Alex van Belkum – mBio

Human gut microbiome

Review: Imbalance of Gastrointestinal Microbiota in the Pathogenesis of Helicobacter pylori-Associated Diseases – Cong He – Helicobacter

Editorial: We are not alone: Understanding the Contributions of Intestinal Microbial Communities and the Congested Gut in Heart Failure – WH Wilson Tang – JACC Heart Failure

Research Highlight: Microbiota predicts side-effects of immunotherapy – Yvonne Bordon – Nature Reviews Microbiology

Models of microbiome research

Rats: Effects of neutrophils peptide-1 transgenic Chlorella ellipsoidea on the gut microbiota of male Sprague–Dawley rats, as revealed by high-throughput 16S rRNA sequencing – Mingzhang Guo – World Journal of Microbiology and Biotechnology

Fish: Correlation between microbiota and growth in Mangrove Killifish (Kryptolebias marmoratus) and Atlantic cod (Gadus morhua) – Torunn Forberg – Scientific Reports

Rats: Diet-induced changes in maternal gut microbiota and metabolomic profiles influence programming of offspring obesity risk in rats – Heather A. Paul – Scientific Reports

Plant, root, and soil microbiome

Beneficial Microbes Affect Endogenous Mechanisms Controlling Root Development –
Eline H. Verbon – Trends in Plant Science

Water and extremophile microbiome

Mechanisms underlying adaptation to life in hydrogen sulfide rich environments – Joanna L. Kelley – Molecular Biology and Evolution

Deep Sequencing of Subseafloor Eukaryotic rRNA Reveals Active Fungi across Marine Subsurface Provinces – William Orsi – PLOS ONE

Succession of lignocellulolytic bacterial consortia bred anaerobically from lake sediment – Elisa Korenblum – Microbial Biotechnology

Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea – Brett J. Baker – Nature Microbiology

Built environment microbiome

Assessment of the influence of intrinsic environmental and geographical factors on the bacterial ecology of pit latrines – Belen Torondel – Microbial Biotechnology

Efficacy of dental unit waterlines disinfectants on a polymicrobial biofilm – Damien Costa – Water Research

Food microbiology

Warning: contains graphic images: Screening for Viral Pathogens in African Simian Bushmeat Seized at A French Airport – Sarah Temmam – Transboundary and Emerging Diseases

Next-generation sequencing analysis of lager brewing yeast strains reveals the evolutionary history of interspecies hybridization – Miki Okuno – DNA Research

Development of spoilage bacterial community and volatile compounds in chilled beef under vacuum or high oxygen atmospheres – Elina Jääskeläinen – International Journal of Food Microbiology

More microbiology

My favorite structure: Ribosomal small subunit domains radiate from a central core – Burak Gulen – Scientific Reports

Selection favors incompatible signaling in bacteria – Alfonso Pérez-Escudero – PNAS

Microbes in the news

Bacteria Can Convey Electrical Messages the Same Way Neurons Do – Diana Kwon – Scientific American

40 Trillion Bacteria on and in Us? Fewer Than We Thought – Nicholas Bakalar – New York Times

Scientists discover new microbes that thrive deep in the earth – Phys.org

Europe’s Richest Microbiome Biotech Acquires Irish Start-up To Accelerate – Labiotech

There are always bacteria lurking in dental equipment, suggests research – MedicalXpress

Genes, bugs and radiation: WHO backs new weapons in Zika fight – Ben Hirschler – Reuters

Gene Linked to Patients’ Response to Infectious Diseases – GenEngNews

Science, publishing, and career

Poisoning your lab mates? Simulating Scientific Sabotage, For Fun: With a card game, researchers make light of the “wacky aspects of scientific research.” – Tracy Vence – The Scientist

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February 13, 2016

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Fungal communities of bark beetles, microbiome in rhinosinusitis, deep-sea chemolithoautotrophic communities, talking walls (microbes in houses), and, for Valentine’s Day: cocoa bean fermentation. 

Jobs and events

Postdoc opportunity, University of Notre Dame: 20,000 longitudinal gut microbiome samples from wild baboons

Pregnancy and birth

Review: Prevention of Necrotizing Enterocolitis Through Manipulation of the Intestinal Microbiota of the Premature Infant – Kannikar Vongbhavit – Clinical Therapeutics

Human oral microbiome

Analysis of bacterial community profiles of endodontically infected primary teeth using pyrosequencing – Kwan Hee Yun – International Journal of Paediatric Dentistry

Human respiratory microbiome

Composition and dynamics of the respiratory tract microbiome in intubated patients – Brendan J. Kelly – Microbiome Journal

Metagenomic Sequencing of the Chronic Obstructive Pulmonary Disease Upper Bronchial Tract Microbiome Reveals Functional Changes Associated with Disease Severity – Simon J. S. Cameron- PLOS ONE

The bacterial microbiome in chronic rhinosinusitis: Richness, diversity, postoperative changes, and patient outcomes – Edward John Cleland – American Journal of Rhinology & Allergy

Review: Microbiome of the paranasal sinuses: Update and literature review – Jivianne T. Lee – American Journal of Rhinology & Allergy

Editorial: The microbiome of the sinuses and its relevance in health and disease – Simon A. Carney

Human reproductive tract microbiome

Molecular detection of intrauterine microbial colonization in women with endometriosis – Khaleque N. Khan – European Journal of Obstetrics & Gynecology and Reproductive Biology

Review: The Basics of Bacteriuria: Strategies of Microbes for Persistence in Urine – Deepak S. Ipe – Frontiers in Cellular and Infection Microbiology

Review: The Human Microbiome during Bacterial Vaginosis – Andrew B. Onderdonk – Clinical Microbiology Reviews

Human gut microbiome

Allergy associations with the adult fecal microbiota: Analysis of the American Gut Project – Xing Hua – EBioMedicine

An Integrated Metabolomic and Microbiome Analysis Identified Specific Gut Microbiota Associated with Fecal Cholesterol and Coprostanol in Clostridium difficile Infection – Vijay C. Antharam – PLOS ONE

Review: The Role of Probiotics on the Microbiota: Effect on Obesity – Esther Nova – Nutrition in Clinical Practice

Editorial: Policing of gut microbiota by the adaptive immune system – Laurent Dollé – BMC Medicine

Review: Fostering of advanced mutualism with gut microbiota by Immunoglobulin A – Duncan B. Sutherland – Immunological Reviews

Perspective: The Second Brain: Is the Gut Microbiota a Link Between Obesity and Central Nervous System Disorders? – Javier Ochoa-Repáraz – Current Obesity Reports

Review: Butyrate, Neuroepigenetics and the Gut Microbiome: Can a High Fiber Diet Improve Brain Health? – Megan W. Bourassa – Neuroscience Letters

Gut passage

Colonic response to laxative ingestion as assessed by MRI differs in constipated irritable bowel syndrome compared to functional constipation – C. Lam – Neurogastroenterology & Motility

How do primates affect seed germination? A meta-analysis of gut passage effects on neotropical plants – Lisieux F. Fuzessy – Oikos

Models of microbiome research

Drosophila: Effects of co-occurring Wolbachia and Spiroplasma endosymbionts on the Drosophila immune response against insect pathogenic and non-pathogenic bacteria – Upasana Shokal – BMC Microbiology

Rats: Diet-induced changes in maternal gut microbiota and metabolomic profiles influence programming of offspring obesity risk in rats – Heather A. Paul – Scientific Reports

Thesis, mice: The effects of nicotine on the gut microbiome and the serum metabolite profile of mice – Ridwan Amin Mahbub – University of Georgia

Contains several cases of image duplication (might be error): Dietary Fiber Intake Regulates Intestinal Microflora and Inhibits Ovalbumin-Induced Allergic Airway Inflammation in a Mouse Model – Zhiyu Zhang – PLOS ONE

Animal microbiome

Metabarcoding of fungal communities associated with bark beetles – Kirsten E. Miller – Ecology and Evolution

Deep 16S rRNA gene sequencing of anterior foregut microbiota from the blue-green sharpshooter (Graphocephala atropunctata) – E. E. Rogers – Journal of Applied Entomology

A bacterial filter protects and structures the gut microbiome of an insect – Michele Caroline Lanan – The ISME Journal

Plant, root, and soil microbiome

Isolation and Identification of Plant Growth Promoting Rhizobacteria from Cucumber Rhizosphere and Their Effect on Plant Growth Promotion and Disease Suppression – Shaikhul Islam – Frontiers in Microbiology

Microbial biomass and soil organic carbon accumulation on a former lakebed near Novosibirsk, Russia – Mikhail. V. Yakutin – Journal of Plant Nutrition and Soil Science

A cost-effective and efficient strategy for Illumina sequencing of fungal communities: A case study of beech endophytes identified elevation as main explanatory factor for diversity and community composition – A.B. Siddique – Fungal Ecology

Primer: Networking in the Plant Microbiome – Marcel G. A. van der Heijden – PLOS Biology

Thesis: Next generation sequencing on soil samples from Etosha National Park: Diversity studies of an anthrax reservoir – Valseth, Karoline

Water and extremophile microbiome

Coupled RNA-SIP and metatranscriptomics of active chemolithoautotrophic communities at a deep-sea hydrothermal vent – Caroline S Fortunato – The ISME Journal

Novel microbial assemblages inhabiting crustal fluids within mid-ocean ridge flank subsurface basalt – Sean P Jungbluth – The ISME Journal

Context dependency in biodiversity patterns of central German stream metacommunities – Jonathan D. Tonkin – Freshwater Biology

Microbial community composition in the marine sediments of Jeju Island: next-generation sequencing surveys – Heebok Choi – Journal of Microbiology and Biotechnology

Effects of temperature stress and aquarium conditions on the red macroalga Delisea pulchra and its associated microbial community – Enrique Zozaya-Valdés – Frontiers in Microbiology

Using in situ bacterial communities to monitor contaminants in river sediments – Yuwei Xie – Environmental Pollution

DGGE: Effects of fullerene (C60), multi-wall carbon nanotubes (MWCNT), single wall carbon nanotubes (SWCNT) and hydroxyl and carboxyl modified single wall carbon nanotubes on riverine microbial communities – J. R. Lawrence – Environmental Science and Pollution Research

Built environment microbiome

Walls talk: Microbial biogeography of homes spanning urbanization – Jean F. Ruiz-Calderon – Science Advances

Microbial communities affecting albumen photography heritage: a methodological survey – Andrea Puškárová – Scientific Reports

Food microbiology

Characterization of microbiota in Plaisentif cheese by high-throughput sequencing –
Alessandra Dalmasso – LWT-Food Science and Technology

Metagenomic analysis of viruses associated with field-grown and retail lettuce identifies human and animal viruses – Tiong Gim Aw – International Journal of Food Microbiology

Bacterial diversity of floor drain biofilms and drain waters in a Listeria monocytogenes contaminated food processing environment – Monika Dzieciol

Review: The cocoa bean fermentation process: from ecosystem analysis to starter culture development – L. De Vuyst – Journal of Applied Microbiology

Techniques

Oufti: an integrated software package for high-accuracy, high-throughput quantitative microscopy analysis – Ahmad Paintdakhi – Molecular Microbiology

Viruses and phages

Perspective: A Virological Perspective on Cancer – Blossom Damania – PLOS Pathogens

Bioinformatics and metagenomics

Fast search of thousands of short-read sequencing experiments – Brad Solomon – Nature Biotechnology

Open-Source Sequence Clustering Methods Improve the State Of the Art – Evguenia Kopylova

Editorial: Bacterial Speciation: Genetic Sweeps in Bacterial Species -Frederick M. Cohan – Current Biology

Microbes in the news

Walls talk – or at least hold many secrets a wall whisperer can reveal – Jonathan Eisen – MicroBEnet

Country microbes, city microbes—where you live can change how you get sick – Annalee Newitz – Ars Technica

Urbanization Leads to Change in Type of Bacteria in the Home – Lauran Neergaard – ABC News

Fun list: Ranking the Top 10 Best Bacteria on Earth – Ben Guarino – Inverse

Science, publishing and career

The Research Pirates of the Dark Web – Kaveh Waddell  – The Atlantic

Researcher illegally shares millions of science papers free online to spread knowledge – Science Alert

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February 10, 2016

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Socioeconomic status and microbiota diversity, metagenome of a carnivorous plant, microbiota of homes of CF patients, and high-resolution phylogenetic microbial community profiling.

Events

ASM Microbe 2016, June 16-20, Boston MA. With opening keynote lecture by Bill Gates

SC2: Microbiome: Sorting out the hype from the hope – March 6-11 2016, San Francisco

Probiotics and Prebiotics – June 21-23, Budapest

Pregnancy and birth

Routine Use of Probiotics in Preterm Infants: Longitudinal Impact on the Microbiome and Metabolome – Abdulkadir B. – Neonatology

Human oral microbiome

Isolation of Propionibacterium acnes among the microbiota of primary endodontic infections with and without intraoral communication – Sadia Ambreen Niazi – Clinical Oral Investigations

Human gut microbiome

Deciphering bifidobacterial-mediated metabolic interactions and their impact on gut microbiota by a multi-omics approach – Francesca Turroni – The ISME Journal

Lower Neighborhood Socioeconomic Status Associated with Reduced Diversity of the Colonic Microbiota in Healthy Adults – Gregory E. Miller – PLOS ONE

The features of mucosa-associated microbiota in primary sclerosing cholangitis –
J. Torres – Alimentary Pharmacology & Therapeutics

Review: Physiological Role of Gut Microbiota for Maintaining Human Health – Andoh A. – Digestion

Editorial: You Are What You Feed Your Gut Microbiome – Joseph E. Scherger – Health Affairs

Review: Gastroenvironmental distress: metaphorical antecedents of the gut microbiome – Nitin K Ahuja – Medical Humanities

Review: Fostering of advanced mutualism with gut microbiota by Immunoglobulin A – Duncan B. Sutherland – Immunological Reviews

Models of microbiome research

Drosophila: Preventing Age-Related Decline of Gut Compartmentalization Limits Microbiota Dysbiosis and Extends Lifespan – Hongjie Li – Cell Host & Microbe

Editorial: Microbes without Borders: Decompartmentalization of the Aging Gut – Erin S. Keebaugh – Cell Host & Microbe

Mice (and humans): Intestinal REG3 Lectins Protect against Alcoholic Steatohepatitis by Reducing Mucosa-Associated Microbiota and Preventing Bacterial Translocation – Lirui Wang – Cell Host & Microbe

Editorial: Alcohol Lowers Your (Intestinal) Inhibitions – Namrata Iyer – Cell Host & Microbe

Mice: Daikenchuto (TU-100) shapes gut microbiota architecture and increases the production of ginsenoside metabolite compound K – Takumu Hasebe – Pharmacology Research & Perspectives

Editorial: Microbiota Control of Malaria Transmission – Miguel P. Soares – Trends in Parasitology

Animal microbiome

Beetles: Trophic and Non-Trophic Interactions in a Biodiversity Experiment Assessed by Next-Generation Sequencing – Julia Tiede – PLOS ONE

Plant, root, and soil microbiome

The Metagenome of Utricularia gibba’s Traps: Into the Microbial Input to a Carnivorous Plant – Luis David Alcaraz – PLOS ONE

Enhancement of drought stress tolerance in crops by plant growth promoting rhizobacteria – Sai Shiva Krishna Prasad Vurukonda – Microbiological Research

Actinobacteria from Arid and Desert Habitats: Diversity and Biological Activity –
Fatemeh Mohammadipanah – Frontiers in Microbiology

Organic Fertilization in Traditional Mediterranean Grapevine Orchards Mediates Changes in Soil Microbial Community Structure and Enhances Soil Fertility – Fuensanta García-Orenes – Land Degradation & Development

Effects of plant functional group loss on soil biota and net ecosystem exchange: a plant removal experiment in the Mongolian grassland – Dima Chen – Journal of Ecology

Water microbiome

Plankton networks driving carbon export in the oligotrophic ocean – Lionel Guidi – Nature

Built environment microbiome

Assessment of the Microbial Constituents of the Home Environment of Individuals with Cystic Fibrosis (CF) and Their Association with Lower Airways Infections – Alya Heirali – PLOS ONE

Metabolomics

Microbial metabolomics in open microscale platforms – Layla J. Barkal – Nature Communications

More microbiology

Open for discussion: Bacterial sequences detected in 99 out of 99 serum samples from Ebola patients – Marina Manrique – bioRxiv

Ethanol Production by Selected Intestinal Microorganisms and Lactic Acid Bacteria Growing under Different Nutritional Conditions – Fouad M. F. Elshaghabee – Frontiers in Microbiology

Rapid radiation in bacteria leads to a division of labour – Wook Kim – Nature Communications

Total biosynthesis of opiates by stepwise fermentation using engineered Escherichia coli – Akira Nakagawa – Nature Communications

Bioinformatics and metagenomics

PhyloTags: High-resolution phylogenetic microbial community profiling – Esther Singer – The ISME Journal

Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum – Karthik Anantharaman – PeerJ

Microbes in the news

The Good, the Bad and the Microbiome – Rachel Reisig – University of Minnesota

Unraveling the Mysterious Function of the Microbiome – by Mike Orcutt – MIT Technology Review

Wound-healing intestinal bacteria: Like shrubs after a forest fire
Akkermansia + other anaerobic bacteria temporarily bloom – EurekAlert

San Diego Scientists Find Data Brewing In Local Fermentation Culture – David Wagner – KPBS

Bacteria Have Ability to ‘See,’ Eye-Opening Study Finds – Maggie Fox – NBC News

A gut feeling about bacteria: Men are from Mars, women are from Venus – and their gut bacteria is just as different. – The Senior

How Your Gut Affects Your Bones. The surprising new science of how intestinal bacteria control bone strength – Rana Samadfam – Scientific American

Scientists Discover New Bacteria Responsible For Lyme Disease – David Beasly – Huffington Post

Overhyped: Sci-Q: The Science Of Love: The role of the microbiome in romantic attraction

Science, publishing, and career

Improving the peer-review process and editorial quality: key errors escaping the review and editorial process in top scientific journals – Antoni Margalida – PeerJ

Does it take too long to publish research? – Kendall Powell – Nature

The history of publishing delays – Daniel Himmelstein

The sexual misconduct case that has rocked anthropology – Michael Balter – Science
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February 9, 2016

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Human skin metagenome, gout patients, malaria and gut microbes, the secrets of the rhizosphere, and single-stranded DNA phages.

Events

2nd Annual Translational Microbiome Conference – April 20-21 2016, Boston MA

Pregnancy and birth

Longitudinal Prediction of the Infant Gut Microbiome with Dynamic Bayesian Networks – Michael J. McGeachie – Scientific Reports

Review: Gut microbiota and the pathogenesis of necrotizing enterocolitis in preterm neonates – Nadim Cassir – Future Microbiology

Human skin microbiome

Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing – Yu-Chih Tsai – mBio

Human urinary tract microbiome

Male non-gonococcal urethritis: From microbiological etiologies to demographic and clinical features – Shin Ito – International Journal of Urology

Research highlight: Altered gut microbiota in CKD – Jessica K. Edwards – Nature Reviews Nephrology

Human respiratory microbiome

Review: Microbiome, biofilms, and pneumonia in the ICU – Massimiliano Pirrone – Current Opinion in Infectious Diseases

Human gut microbiome

Intestinal Microbiota Distinguish Gout Patients from Healthy Humans – Zhuang Guo – Scientific Reports

Effect of Proton Pump Inhibitors and Antibiotics on the Gut Microbiome of Hospitalised Older Persons – Caoilfhionn O’Donoghue – Journal of Infection

Editorial: A metabolic bridge between microbiota and humans – Kiyoshi Takeda – Nature Reviews Immunology

Review: The Gut Microbiome: Potential Innovations for the Understanding and Treatment of Psychopathology – Matilda E. Nowakowski – Canadian Psychology/Psychologie canadienne

Review: Metabolic modeling with big data and the gut microbiome – Jaeyun Sung – Applied & Translational Genomics

Review: The influence of commensal bacteria on infection with enteric viruses – Stephanie M. Karst – Nature Reviews Microbiology

Review: One more role for the gut: microbiota and blood brain barrier – Laure Michel – Annals of Translational Medicine

Review: Expanding role of gut microbiota in lipid metabolism – Anatole Ghazalpour – Current Opinion in Lipidology

Models of microbiome research

Mice: Composition of the gut microbiota modulates the severity of malaria – Nicolas F. Villarino – PNAS

Mice: Lambda Interferon Restructures the Nasal Microbiome and Increases Susceptibility to Staphylococcus aureus Superinfection – Paul J. Planet – mBio

Dogs: Longitudinal evaluation of the skin microbiome and association with microenvironment and treatment in canine atopic dermatitis – Charles W. Bradley – Journal of Investigative Dermatology

Goats: The effect of helminth infection on the microbial composition and structure of the caprine abomasal microbiome – Robert W. Li – Scientific Reports

More goats: Grain-rich diets altered the colonic fermentation and mucosa-associated bacterial communities and induced mucosal injuries in goats – Huimin Ye – Scientific Reports

Rats: The Colonic Microbiome and Epithelial Transcriptome Are Altered in Rats Fed a High-Protein Diet Compared with a Normal-Protein Diet – Chunlong Mu – The Journal of Nutrition

Rats: Resistant Starch Alters Gut Microbiome and Metabolomics Profiles Concurrent with Amelioration of Chronic Kidney Disease in Rats – Dorothy A. Kieffer – American Journal of Physiology – Renal Physiology
http://ajprenal.physiology.org/content/early/2016/02/01/ajprenal.00513.2015.abstract

Drosophila: From pathogens to microbiota: how Drosophila intestinal stem cells react to gut microbes – Alessandro Bonfini – Developmental & Comparative Immunology

Animal microbiome

Host plant determines the population size of an obligate symbiont Buchnera aphidicola in aphids – Yuan-Chen Zhang – Applied and Environmental Microbiology

Altered Carbohydrates Allocation by Associated Bacteria-fungi Interactions in a Bark Beetle-microbe Symbiosis – Fangyuan Zhou – Scientific Reports

Plant, root, and soil microbiome

Soil amendments yield persisting effects on the microbial communities—a 7-year study – Catherine L. Reardon – Applied Soil Ecology

Microbial genetic and enzymatic responses to an anthropogenic phosphorus gradient within a subtropical peatland – Elise Morrison – Geoderma

Salinity altered root distribution and increased diversity of bacterial communities in the rhizosphere soil of Jerusalem artichoke – Hui Yan – Scientific Reports

Development of oligonucleotide microarrays for simultaneous multi-species identification of Phellinus tree-pathogenic fungi – Yuh Tzean – Microbial Biotechnology

Dilution reveals how viral lysis and grazing shape microbial communities – Jacob A. Cram – Limnology and Oceanography

Response of Soil Bacterial Community Structure to Land-use Conversion of Natural Forests in Maoershan National Forest Park, China – Fanjuan Meng – Molecular Soil Biology

Editorial: Unlocking the Secrets of the Rhizosphere – Susanne C. Brink – Trends in Plant Science

Spotlight: The soil-borne supremacy – Corné M.J. Pieterse – Trends in Plant Science

Water and pollution microbiome

Temporal and spatial changes of microbial community in an industrial effluent receiving area in Hangzhou Bay – Yan Zhang – Journal of Environmental Sciences

Built environment microbiome

Metagenomic Analysis Indicates Epsilonproteobacteria as a Potential Cause of Microbial Corrosion in Pipelines Injected with Bisulfite – Dongshan An – Frontiers in Microbiology

Viruses and phages

Viral metagenomics: are we missing the giants? – S Halary – Current Opinion in Microbiology

Single-Stranded DNA Phages: From Early Molecular Biology Tools to Recent Revolutions in Environmental Microbiology – Anna J. Székely – FEMS Microbiology Letters

Sequencing techniques

A comparison of rumen microbial profiles in dairy cows as retrieved by 454 Roche and Ion Torrent (PGM) sequencing platforms – Nagaraju Indugu – PeerJ

Bioinformatics and metagenomics

Improved environmental genomes via integration of metagenomic and single-cell assemblies – Daniel R. Mende – Frontiers in Microbiology

PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes – Ivan Gregor- PeerJ

Estimating and comparing microbial diversity in the presence of sequencing errors – Chun-Huo Chiu – PeerJ

Metabolomics

Metabolic modeling with big data and the gut microbiome – Jaeyun Sung – Applied & Translational Genomics

More microbiology

Cyanobacteria use micro-optics to sense light direction – Nils Schuergers – eLIFE

Ultrasensitive Detection of Bacteria by Targeting Abundant Transcripts – Xinhui Wang – Scientific Reports

Microbes in the news

Pill measures gut gas – Swallowable tool may eventually help reveal digestive problems – Sarah Schwartz – Science News

Gut environment could reduce severity of malaria – EurekAlert

Great stockphoto: Hibernation Helpers: Gut microbes may help regulate the metabolic changes a bear experiences before and during hibernation, scientists show – Catherine Offord – The Scientist

The complex marketing of “probiotic” cosmetics – Éva Lagarde – Premium Beauty News

Plants trick bacteria into attacking too soon – Chris Samoray – Science News

Obstructive sleep apnea-induced hypertension linked to gut microbiome – Baylor College of Medicine

Includes Rob Knight. HT: Tomer Altman. Deepak Chopra Convenes 30+ of the World’s Preeminent Thought Leaders, Philosophers, Scientists, Musicians and Artists to Explore Consciousness at a 3-Day Symposium This Fall – PR Newswire

Researchers identify most dangerous strains of often-deadly bacteria – University of Maryland – EurekAlert

Science, publishing, and career

Harvard Medical School students decry lack of diversity – Melissa Baily – STATnews

I make an appearance here: Getting credit for peer review – Sandeep Ravindran – Science

Change the system to halt harassment – Joan Schmelz – Nature

Bik’s Picks

The peptidergic control circuit for sighing – Peng Li – Nature

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February 6, 2016

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Your Saturday morning Microbiome Digest.

Jobs and events

Postdoctoral Associate, Chicago, Illinois – Shedd Aquarium Microbiome Project

Human urinary tract microbiome

The Bladder Is Not Sterile: History and Current Discoveries on the Urinary Microbiome – Krystal Thomas-White – Current Bladder Dysfunction Reports

Human gut microbiome

American Gut: Researchers Launch Open-Access Gut Project – Nancy Averett – BioScience

Animal microbiome

Faecal virome of red foxes from peri-urban areas – Ivana Lojkić – Comparative Immunology, Microbiology and Infectious Diseases

Closely coupled evolutionary history of ecto- and endosymbionts from two distantly-related animal phyla – Judith Zimmermann – Molecular Ecology

Plant, root, and soil microbiome

Impact of soil heat on reassembly of bacterial communities in the rhizosphere microbiome and plant disease suppression – Menno van der Voort – Ecology Letters

Extracellular DNA extraction is a fast, cheap and reliable alternative for multi-taxa surveys based on soil DNA – Lucie Zinger – Soil Biology and Biochemistry

Water and extremophile microbiome

Metagenomic Analysis Reveals Symbiotic Relationship among Bacteria in Microcystis-Dominated Community – Meili Xie – Frontiers in Microbiology

Metagenomic Analysis of Virioplankton of the Subtropical Jiulong River Estuary, China – Lanlan Cai – MDPI Viruses

Hydrocarbon pollutants shape bacterial community assembly of harbor sediments – Marta Barbato – Marine Pollution Bulletin

Thesis: The Impact of Temperature, pH and Environmental Heterogeneity on Prokaryotic
Diversity in Yellowstone National Park Thermal Springs – Xiaoben Jiang – The University of New Mexico

Drinking water and waste microbiome

Archaeal community in a human-disturbed watershed in southeast China: diversity, distribution, and responses to environmental changes – Anyi Hu – Applied Microbiology and Biotechnology

Comparison of Particle-Associated Bacteria from a Drinking Water Treatment Plant and Distribution Reservoirs with Different Water Sources – G. Liu – Scientific Reports

Biostimulation of metal-resistant microbial consortium to remove zinc from contaminated environments – Isis E. Mejias Carpio – Science of the Total Environment

Review: Biological Stability of Drinking Water: Controlling Factors, Methods, and Challenges – Emmanuelle I. Prest – Frontiers in Microbiology

Built environment microbiome / microbes in space

Growth of 48 built environment bacterial isolates on board the International Space Station (ISS) – David A Coil – PeerJ

The Last Possible Outposts for Life on Mars – Davila Alfonso F. – Astrobiology

Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy – Stefano Campanaro – Biotechnology for Biofuels

Bioinformatics and metagenomics

TruSPAdes: barcode assembly of TruSeq synthetic long reads – Anton Bankevich – Nature Methods

Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies – Tom O. Delmont – PeerJ

Thesis: A Case Study Tested Framework for Multivariate Analyses of Microbiomes: Software for Microbial Community Comparisons – Eric M. Spaulding – University of Montana – Missoula
Metabolomics

Twin metabolomics: The key to unlocking complex phenotypes in nutrition research – Rebecca Barron – Nutrition Research

Increasing metagenomic resolution of microbiome interactions through functional phylogenomics and bacterial sub-communities – Angélica Cibrián-Jaramillo – Frontiers in Genetics

Microbes in the news

Buffalo Wild Wings Hit By Norovirus Investigation Before Super Bowl Binge – Venessa Wong – BuzzFeed

Explainer: what is the gut microbiota and how does it affect mind and body? – Senaka Ranadheera – The Conversation

Not all statements are true: Microbial miracle workers – Jay Keche – Indiana Daily Student

Science, publishing, and career

Gaming Metrics conference (Feb 4-5, UC Davis) about science misconduct, fake journals, and citation games – Storify Day 1 by Jonathan Eisen
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February 5, 2016

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Just a quick new Digest in the lunch break at the #GamingMetrics conference at UC Davis. Here is a Storify from Day 1 (yesterday) by Jonathan Eisen – more to follow soon.

Pregnancy and birth

Microbial transmission from mothers with obesity or diabetes to infants: an innovative opportunity to interrupt a vicious cycle – Taylor K. Soderborg – Diabetologia

Human urinary tract microbiome

16S rRNA gene-based metagenomic analysis reveals differences in bacteria-derived extracellular vesicles in the urine of pregnant and non-pregnant women – Jae Young Yoo – Experimental & Molecular Medicine

Human gut microbiome

Fungal microbiota dysbiosis in IBD – Harry Sokol – Gut

Animal models of microbiome research

Oxygen Affects Gut Bacterial Colonization and Metabolic Activities in a Gnotobiotic Cockroach Model – Dorothee Tegtmeier – Applied and Environmental Microbiology

Deterministic Assembly of Complex Bacterial Communities in Guts of Germ-Free Cockroaches – Aram Mikaelyan – Applied and Environmental Microbiology

Associations of microbiota and toll-like receptor signaling pathway in esophageal adenocarcinoma – Ali H. Zaidi – BMC Cancer

Comparison of fecal microbiota between German Holstein dairy cows with and without left-sided displacement of the abomasum – Eun-Sik Song – Journal of Clinical Microbiology

Animal microbiome

The Gut Microbiota Modulates Energy Metabolism in the Hibernating Brown Bear Ursus arctos – Felix Sommer – Cell Reports

Plant, root, and soil microbiome

Microbial Diversity in Soil, Sand Dune and Rock Substrates of the Thar Monsoon Desert, India – Subramanya Rao – Indian Journal of Microbiology

Microbial communities play important roles in modulating paddy soil fertility
Xuesong Luo – Scientific Reports

Diversity of archaeal and bacterial communities on exfoliated sandstone from Portchester Castle (UK) – Elisabetta Zanardini – International Biodeterioration & Biodegradation

Distance from the sea as a driving force of microbial communities under water potential stresses in litters of two typical Mediterranean plant species – Anne Marie Farnet Da Silva – Geoderma

Opinion: Back to the future of soil metagenomics – Joseph Nesme – Frontiers in Microbiology

Waste and water treatment

Occurrence and enrichment of ‘bacterial sherpas’: climb to sustainability in wastewater treatment – M. Arnaldos – Water Science & Technology

Metagenomics

Comprehensive Genomic Analyses of the OM43 Clade, Including a Novel Species from the Red Sea, Indicate Ecotype Differentiation among Marine Methylotrophs – Francy Jimenez-Infante – Applied and Environmental Micro

Microbial Ecology

Model-based media selection to minimize the cost of metabolic cooperation in microbial eco-systems – Mattia Zampieri – Bioinformatics

Microbes in the news

Savvy bacteria parents distribute damage unevenly among their children – Cara Giaimo – Atlas Obscura

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February 2, 2016, second edition

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Updated status of the microbial census, bacteria in the nasopharynx, deodorant and armpit microbiome, lichen microbiome, fungi on decomposing forest materials, and metagenomics cover the amplicon gaps. So many papers I had to do a second installment today!

Events and jobs

Microbiology and bioinformatics positions at Whole Biome in San Francisco. Wearing hoodies encouraged.

General microbiome

The status of the microbial census: an update – Patrick D Schloss – BioRxiv

Getting the hologenome concept right: An eco-evolutionary framework for hosts and their microbiomes – Kevin R Theis – BioRxiv

Human oral microbiome

Interactions between Streptococcus oralis, Actinomyces oris, and Candida albicans in the development of multispecies oral microbial biofilms on salivary pellicle – Indira M.G. Cavalcanti – Molecular Oral Microbiology

Human respiratory microbiome

Unraveling the Molecular Mechanisms Underlying the Nasopharyngeal Bacterial Community Structure – Wouter A. A. de Steenhuijsen Piters – mBio 

Human skin microbiome

The effect of habitual and experimental antiperspirant and deodorant product use on the armpit microbiome – Julie Urban – PeerJ

Skin microbiome surveys are strongly influenced by experimental design – Jacquelyn S. Meisel – Journal of Investigative Dermatology

Unique features of a global human ectoparasite identified through sequencing of the bed bug genome – Joshua B. Benoit – Nature Communications

Human vaginal microbiome

Hormonal Contraceptive Effects on the Vaginal Milieu: Microbiota and Immunity – Jessica Tarleton – Current Obstetrics and Gynecology Reports

Human gut microbiome

Sex differences in the gut microbiome–brain axis across the lifespan – Eldin Jašarević – Philosophical Transactions of the Royal Society B

Very poor English and presentation, does not look peer reviewed: Preliminary analysis showed country-specific gut resistome based on 1267 feces samples – Zhenyu Yang – Gene

Confusing study design and interpretations: Gut Microbiota Linked to Sexual Preference and HIV Infection – Marc Noguera-Julian – EBioMedicine

Sequence-based methods for detecting and evaluating the human gut mycobiome – M.J. Suhr – Letters in Applied Microbiology

Review: Microbiota and arthritis: correlations or cause? – Bravo-Blas, Alberto – Current Opinion in Rheumatology

Perspective: Gut microbiota in 2015: Prevotella in the gut: choose carefully – Ruth E. Ley – Nature Reviews Gastroenterology & Hepatology

Editorial: PPIs alter gut microbiota composition – Nature Reviews Gastroenterology & Hepatology

Review: Samples and techniques highlighting the links between obesity and microbiota –
Emmanouil Angelakis – Microbial Pathogenesis

Animal models of microbiome

Bidirectional interactions between indomethacin and the murine intestinal microbiota – Xue Liang – eLife

 

Mixed feelings about this study that killed turtles to look at effect of probiotics on their shells: Dietary Probiotics Affect Gastrointestinal Microbiota, Histological Structure and Shell Mineralization in Turtles – Mateusz Rawski – PLOS ONE

Animal microbiome

The Role of the Microbial Environment in Drosophila Post-Embryonic Development –
Maura Strigini – Developmental & Comparative Immunology

Plant, root, and soil microbiome

Review about lichen bacterial microbiome: Understanding microbial multi-species symbioses – Ines A. Aschenbrenner – Frontiers in Microbiology

Dead fungal mycelium in forest soil represents a decomposition hotspot and a habitat for a specific microbial community – Vendula Brabcová – New Phytologist

Litter decomposition, residue chemistry and microbial community structure under two subtropical forest plantations: A reciprocal litter transplant study –
Zongming He – Applied Soil Ecology

Disentangling nematode-bacteria interactions using a modular soil model system and biochemical markers – Michael Ackermann – Nematology

Using native trees and cacti to improve soil potential nitrogen fixation during long-term restoration of arid lands – Nguyen E. Lopez-Lozano – Plant and Soil

Warming and nitrogen deposition are interactive in shaping surface soil microbial communities near the alpine timberline zone on the eastern Qinghai–Tibet Plateau, southwestern China – Qinli Xiong – Applied Soil Ecology

Short-term effects of mechanical drainage on fungal and bacterial community structure in a managed grassland soil – B.J. Fay – Applied Soil Ecology

Water and extremophile microbiome

Microbial Communities in Methane- and Short Chain Alkane-Rich Hydrothermal Sediments of Guaymas Basin – Frederick Dowell – Frontiers in Microbiology

Bioreactor and crude oil microbiology

Illumina MiSeq sequencing reveals the key microorganisms involved in partial nitritation followed by simultaneous sludge fermentation, denitrification and anammox process – Bo Wang – Bioresource Technology

Microbial communities of light crude from Nigeria and potential for in situ biodegradation, souring, and corrosion – Okoro Chuma Conlette – Petroleum Science and Technology

Built environment microbiome

Rhinitis, Ocular, Throat and Dermal Symptoms, Headache and Tiredness among Students in Schools from Johor Bahru, Malaysia: Associations with Fungal DNA and Mycotoxins in Classroom Dust – Dan Norbäck – PLOS ONE

Bioinformatics and metagenomics

Metagenomics uncovers gaps in amplicon-based detection of microbial diversity – Emiley A. Eloe-Fadrosh – Nature Microbiology

Development of an Analysis Pipeline Characterizing Multiple Hypervariable Regions of 16S rRNA Using Mock Samples – Jennifer J. Barb – PLOS ONE

Optimization of alignment-based methods for taxonomic binning of metagenomics reads – Magali Jaillard – Bioinformatics

Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes – John A Lees – BioRxiv

Proteomics

Review: Recent development of mass spectrometry and proteomics applications in identification and typing of bacteria – Keding Cheng – Proteomics – Clinical Applications

Microbes in the news

Study shows maternal diet alters the breast milk microbiome and microbial gene content – EurekAlert

Deodorant And Antiperspirant Alter The Skin Microbiome, But Researchers Can’t Be Sure Of Long-Term Effects – Stephanie Castillo – Medical Daily

Beard bacteria could lead to new antibiotics – Matthew Stock – Reuters

Science, publishing, and career

“Those who can, publish. Those who can’t, blog.” Jingmai O’Connor – Current Biology

Chill out about Jingmai O’Connor’s criticism of bloggers – Jeremy Fox – Dynamic Ecology

Paul Knoepfler: Stem cell scientist finds his ‘niche’ in blogging – Karen Weintraub – STAT News

How to (not) write a microbiome grant, part I

How to (not) write a microbiome grant, part II. A deeper dive on preliminary data – David Baltrus – My Chrobial Romance

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February 1, 2016

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Vaginal microbiota transplant, temporal sampling of lung microbiota, skin microbiota of a cute frog, extreme CO2 exposure in soil, and microbial mats.

General human microbiome

Human Microbiota of the Argentine Population- A Pilot Study – Belén Carbonetto – Frontiers in Microbiology

Now officially published: Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host Cells in Humans – Ron Sender – Cell

Pregnancy and birth

Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer – Maria G Dominguez-Bello – Nature Medicine

Chiba study of Mother and Children’s Health (C-MACH): cohort study with omics analyses – Kenichi Sakurai – BMJ Open

Human respiratory microbiome

Prevalence and antimicrobial susceptibility profiles of Staphylococcus aureus nasal carriage among pre-clinical and clinical medical students in a Tanzanian University
Benard Okamo – BMC Research Notes

A case report demonstrating the utility of next generation sequencing in analyzing serial samples from the lung following an infection with influenza A (H7N9) virus –
Yongfeng Hu – Journal of Clinical Virology

Human gut microbiome

Genomic analysis of the human gut microbiome suggests novel enzymes involved in quinone biosynthesis – Dmitry A. Ravcheev – Frontiers in Microbiology

Animal models of microbiome research

Research Highlight: Transgenerational missing taxa – Naomi Attar – Nature Reviews Microbiology

Ingestion of Milk Containing Very Low Concentration of Antimicrobials: Longitudinal Effect on Fecal Microbiota Composition in Preweaned Calves – Richard Van Vleck Pereira – PLOS ONE

Animal microbiome

Molecular evidence of vector-borne pathogens in dogs and cats and their ectoparasites in Algiers, Algeria – Amina Bessas – Comparative Immunology, Microbiology and Infectious Diseases

Manatees: Antifungal Resistance and Virulence Among Candida spp. from Captive Amazonian manatees and West Indian Manatees: Potential Impacts on Animal and Environmental Health – José Júlio Costa Sidrim – EcoHealth

Very cute frog: Assessing Antibacterial Potential of Components of Phyllomedusa distincta Skin and its Associated Dermal Microbiota – Ananda Brito de Assis – Journal of Chemical Ecology

Plant, root, and soil microbiome

Altered carbon turnover processes and microbiomes in soils under long-term extremely high CO2 exposure – Felix Beulig – Nature Microbiology

Precipitation regime drives warming responses of microbial biomass and activity in temperate steppe soils – Weixing Liu- Biology and Fertility of Soils

The diversity of iron reducing bacteria communities in subtropical paddy soils of China – Qi-an Peng – Applied Soil Ecology

Water and extremophile microbiome

Editorial: Systems biology and ecology of microbial mat communities – Martin G. Klotz – Frontiers in Microbiology

Bioreactor microbiology

Microbial communities from 20 different hydrogen-producing reactors studied by 454 pyrosequencing – Claudia Etchebehere – Applied Microbiology and Biotechnology

Impact of Organic Carbon Electron Donors on Microbial Community Development under Iron- and Sulfate-Reducing Conditions – Man Jae Kwon – PLOS ONE

Performance and microbial community variations in thermophilic anaerobic digesters treating OTC medicated cow manure under different operational conditions – Çağrı Akyol – Bioresource Technology

More microbiology

Acanthamoeba and mimivirus interactions: the role of amoebal encystment and the expansion of the ‘Cheshire Cat’ theory – Ludmila Karen dos Santos Silva – Current Opinion in Microbiology

Gene flow in microbial communities could explain unexpected patterns of synonymous variation in the Escherichia coli core genome – Rohan Maddamsetti – Mobile Genetic Elements

Microbes in the news

The Bacterium Disappearing From Our Stomachs – H. pylori is losing its foothold – Chau Tu – Science Friday

The Mycobiome: The largely overlooked resident fungal community plays a critical role in human health and disease – Mahmoud Ghannoum – The Scientist

Opportunities for Nanoscience and Nanotechnology in Studying Microbiomes – Paul S Weiss – ACS Nano

“Seeding” The Newborn’s Microbiome – Can We Do It? Should We Be Doing It? – Anne M. Estes – Science & Sensibility

Icy Worlds and their Analog Sites.Fieldwork on Earth provides insight into life’s potential on icy bodies – Keith Cooper – NASA Astrobiology

Bilingual Exhibition Explores the Human Microbiome – Alexandra Mendoza – La Prensa San Diego

Stalin May Have Studied Mao’s Poop in a Secret Lab – Erin Blakemore – Smithsonian

Mapping the Mouth Microbiome – GenEngNews

CosmosID raises $6M to advance microbiome bioinformatics offering – Nick Paul Taylor – Fierce BiotechIt

Science, publishing, and career

The Scientific 23 with Ed Yong: “Science takes us… to the entire natural world, to space, to molecules – things related to humans but not about us.”

How quality control could save your science. It may not be sexy, but quality assurance is becoming a crucial part of lab life – Monya Baker – Nature
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January 29, 2016

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Prescription drugs and microbiome analyses, antimicrobial targets in sarcoidosis granulomas, host-microbiota interactions in antibiotic-associated diseases, and iridescence in self-organizing biofilms.

General microbiome

Perspective: Prescription drugs obscure microbiome analyses – Suzanne Devkota – Science

Review: The role of microbiota in cancer therapy – Ernesto Perez-Chanona – Current Opinion in Immunology

Human respiratory microbiome

COPD and the microbiome – Manoj J. Mammen – Respirology

Molecular Analysis of Sarcoidosis Granulomas Reveals Antimicrobial Targets – Joseph E Rotsinger – American Journal of Respiratory Cell and Molecular Biology

Human skin microbiome

Review: The microbiome and atopic eczema: More than skin deep – Charlotte L Thomas – Australasian Journal of Dermatology

Human gut microbiome

Gut microbiota and allergic disease in children – Sarah L. Bridgman – Annals of Allergy, Asthma & Immunology

Effects of enteral polymeric diet on gut microbiota in children with Crohn’s disease – Chloé Guinet-Charpentier – Gut

Review: Effect of antibiotics on gut microbiota, glucose metabolism and bodyweight regulation – a review of the literature – Kristian Hallundbæk Mikkelsen – Diabetes, Obesity and Metabolism

Animal models

Effects of dispersal limitation in the face of intense selection via dietary intervention on the faecal microbiota of rats – Heli J. Barron Pastor – Environmental Microbiology Reports

Fecal dysbiosis in miniature dachshunds with inflammatory colorectal polyps –
Hirotaka Igarashi – Research in Veterinary Science

Dietary antigens limit mucosal immunity by inducing regulatory T cells in the small intestine – Kwang Soon Kim – Science

Translocation of microbes and changes of immunocytes in the gut of rapid- and slow-progressor Chinese rhesus macaques infected with SIVmac239 – Lin-Tao Zhang – Immunology

From the Sonnenburg lab: Host-Microbiota Interactions in the Pathogenesis of Antibiotic-Associated Diseases – Joshua S. Lichtman – Cell Reports

Effect of Antimicrobial Consumption and Production Type on Antibacterial Resistance in the Bovine Respiratory and Digestive Tract – Boudewijn Catry – PLOS ONE

Animal microbiome

Symbiotic Bacteria in Gills and Guts of Chinese Mitten Crab (Eriocheir sinensis) Differ from the Free-Living Bacteria in Water – Meiling Zhang – PLOS ONE

Earthworm: Isolation, identification, and characterization of gut microflora of Perionyx excavatus collected from Midnapore, West Bengal – Tanushree Tulsian Samanta – Journal of Basic Microbiology

Plant, root, and soil microbiome

Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction – Kiley W Seitz – The ISME Journal

Not a good paper (poor figures and language problems – see my comments on PubPeer), about carnivorous plant: Microbiome and Biocatalytic Bacteria in Monkey Cup (Nepenthes Pitcher) Digestive Fluid – Xin-Yue Chan – Scientific Reports

Microbial diversity drives multifunctionality in terrestrial ecosystems – Manuel Delgado-Baquerizo – Nature Communications

Various fungal communities colonise the functional wood tissues of old grapevines externally free from grapevine trunk disease symptoms – E. Bruez – Australian Journal of Grape and Wine Research

Arbuscular mycorrhizal fungi regulate soil respiration and its response to precipitation change in a semiarid steppe – Bingwei Zhang – Scientific Reports

Sewage sludge addition modifies soil microbial communities and plant performance depending on the sludge stabilization process – Eva Lloret – Applied Soil Ecology

Review: Engineering the Rhizosphere – Yves Dessaux – Trends in Plant Science

Water and extremophile microbiome

Bacterial diversity in the surface sediments of the hypoxic zone near the Changjiang Estuary and in the East China Sea – Qi Ye – Microbiology Open

Ecological succession reveals potential signatures of marine–terrestrial transition in salt marsh fungal communities – Francisco Dini-Andreote – The ISME Journal

Profiling microbial community in a watershed heavily contaminated by an active antimony (Sb) mine in Southwest China – Weimin Sun – Science of The Total Environment

More microbiology

A unique self-organization of bacterial sub-communities creates iridescence in Cellulophaga lytica colony biofilms – Betty Kientz – Scientific Reports

Bioinformatics and metagenomics

Ten Simple Rules for a Bioinformatics Journal Club – Andrew Lonsdale – PLOS Computational Biology

NINJA-OPS: Fast Accurate Marker Gene Alignment Using Concatenated Ribosomes – Gabriel A. Al-Ghalith – PLOS Computational Biology

Microbes in the news

Stop pooping! You’re killing sentient beings! – PZ Myers – Pharyngula

ASM’s Commitment to Interdisciplinary Microbiome Research – American Society for Microbiology

Fermentation Farm wants you to eat better bacteria – Kathleen Luppi – LA Times

This bacteria can live for years in distilled water, and causes abscess, seizures and death: Melioidosis / Burkholderia pseudomallei – Jacinta Bowler – Science Alert

Science, publishing, and career

How to read a scientific paper – Adam Ruben – Science

High rejection rates by journals ‘pointless’– Analysis suggests higher selectivity fails to increase journals’ impact factors – David Matthews – Times Higher Education

How to stop the sexual harassment of women in science: reboot the system – Zuleyka Zevallow – The Conversation

Bik’s Picks

Arthropods of the great indoors: characterizing diversity inside urban and suburban homes – Matthew A Bertone

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January 28, 2016

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Events

2016 Mo Bio Microbiome Awards: provides young, extraordinary scientists with funding and recognition to carry out scientific work in the field of Microbiome research – Deadline May 31, 2016

Live streaming now: Women in Science Summit 2016 #SciWomen16 hosted by the California Academy of Sciences

Human gut microbiome

Metagenomic Approach for Identification of the Pathogens Associated with Diarrhea in Stool Specimens – Yanjiao Zhou – Journal of Clinical Microbiology

Review: Gut microbiota and allergic disease in children – Sarah L. Bridgman – Annals of the Allergy, Asthma & Immunology

Animal models of microbiome research

The microenvironment of injured murine gut elicits a local pro-restitutive microbiota – Ashfaqul Alam – Nature Microbiology

Editorial: Host response: Microbiota prime antiviral response – Julie K. Pfeiffer – Nature Microbiology

Editorial: Winning the Microbial Battle, but Not the War – Hiutung Chu – Cell

Animal microbiome

Apibacter mensalis sp. nov.: a rare member of the bumble bee gut microbiota – Jessy Praet – International Journal of Systematic and Evolutionary Microbiology

Water and extremophile microbiome

Diversity and Biogeography of Bathyal and Abyssal Seafloor Bacteria – Christina Bienhold – PLOS ONE

Built environment microbiome

Comparison of Two Culture Methods for Use in Assessing Microbial Contamination of Duodenoscopes – Michaela A. Gazdik – Journal of Clinical Microbiology

Waste microbiology

Microwave and ultrasound pre-treatments influence microbial community structure and digester performance in anaerobic digestion of waste activated sludge – Maria Westerholm – Applied Microbiology and Biotechnology

Effects of copper particles on a model septic system’s function and microbial community – Alicia A. Taylor – Water Research

Microbes in the news

Poop espionage: Stalin ‘used secret laboratory to analyse Mao’s excrement’– Steven Rosenberg – BBC

Science, publishing, and career

Peer-reviewing Frontiers – Michiel Dijkstra – Frontiers Blog

Faking it: In the face of routine rejection, many scientists must learn to cope with the insidious beast that is impostor syndrome – Chris Woolston – Nature

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