Category Archives: Science – Career – Publishing

August 18, 2015

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New paper from our lab about human microbiota during pregnancy, association between obesity and cervical microflora, Argentina soil metagenomes, proteomics library, and microbiology during mozzarella cheese making.

Events and conferences

ECCMID: 26th European Congress of Clinical Microbiology and Infectious Diseases: April 2016, Istanbul, Turkey

General microbiome

Review: Fulfilling the Promise of Microbiomics to Revolutionize Medicine – Traci L Testerman – J Microbiol Exp

Review: Cross-kingdom similarities in microbiome functions – Rodrigo Mendes – ISME Journal

Pregnancy and birth microbiome

From our lab: Temporal and spatial variation of the human microbiota during pregnancy – Daniel B. DiGiulio – PNAS

Maternal group B Streptococcus and the infant gut microbiota – A. E. Cassidy-Bushrow – Journal of Developmental Origins of Health and Disease

The stool microbiota of insulin resistant women with recent gestational diabetes, a high risk group for type 2 diabetes – Marina Fugmann – Scientific Reports

Human reproductive tract microbiome

Relationship of Specific Bacteria in the Cervical and Vaginal Microbiotas With Cervicitis – Linda M. Gorgos – Sexually Transmitted Diseases

Changes in vaginal microbiota following antimicrobial and probiotic therapy – Jean M. Macklaim – Microbial Ecology in Health and Disease

Association between obesity and cervical microflora dominated by Lactobacillus iners in Korean women – Hea Young Oh – Journal of Clinical Microbiology

Distribution of human papillomavirus (HPV) genotypes and bacterial vaginosis presence in cervical samples from Paraguayan indigenous – Pamela Mongelos – International Journal of Infectious Diseases

The most common isolated microorganisms and its clinical manifestation in hospitalised women suffering from urogenital diseases in Latvia – Anatolijs Naumčiks – International Journal of Reproduction, Contraception, Obstetrics and Gynecology

Human respiratory microbiome

Conference abstract: Profiling of lung microbial communities in lung cancer and chronic obstructive pulmonary disease patients – Yanhong Liu – Cancer Research

Human oral microbiome

Conference abstract: 16S rRNA saliva analysis unveils differences in the head and neck squamous cell carcinoma microbiome before and after surgical resection – Rafael E. Guerrero-Preston – Cancer Research

Human gut microbiome

Variable alterations of the microbiota, without metabolic or immunological change, following faecal microbiota transplantation in patients with chronic pouchitis – J. Landy – Scientific Reports

Review: Systematic Review of the Relation Between Intestinal Microbiota and Toll-Like Receptors in the Metabolic Syndrome: What Do We Know So Far? – José Pedro Portela-Cidade – GE Portuguese Journal of Gastroenterology

Review: Commensal Microbiome Promotes Resistance to Local and Systemic Infections – Nan Zhang – Chinese Medical Journal

Animal microbiome

High diversity of viable bacteria isolated from lymph nodes of slaughter pigs and its possible impacts for food safety – Evelyne Mann – Journal of Applied Microbiology

Geographic patterns in the bacterial microbiome of the glassy-winged sharpshooter, Homalodisca vitripennis (Hemiptera: Cicadellidae) – E. W. Welch – Symbiosis

Plant, root, and soil microbiome

Using direct amplification and next-generation sequencing technology to explore foliar endophyte communities in experimentally inoculated western white pines – Lorinda S. Bullington – Fungal Ecology

Maize lines with different nitrogen use efficiency select bacterial communities with different β-glucosidase-encoding genes and glucosidase activity in the rhizosphere – Shamina I. Pathan – Biology and Fertility of Soils

Fire severity shapes plant colonization effects on bacterial community structure, microbial biomass, and soil enzyme activity in secondary succession of a burned forest – Joseph E. Knelman – Soil Biology and Biochemistry

Diversity of hydrolases from hydrothermal vent sediments of the Levante Bay, Vulcano Island (Aeolian archipelago) identified by activity-based metagenomics and biochemical characterization of new esterases and an arabinopyranosidase – Antonio Placido – Applied Microbiology and Biotechnology

Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe – Jonathan W. Leff – PNAS

Soil Metagenomes from Different Pristine Environments of Northwest Argentina – Christina B. McCarthy – Genome Announcements

Relationships between the density and activity of microbial communities possessing arylsulfatase activity and soil sulfate dynamics during the decomposition of plant residues in soil – Séverine Piutti – European Journal of Soil Biology

Food microbiology

Microbial changes of natural milk cultures for mozzarella cheese during repeated propagation cycles – Angela Guidone – LWT – Food Science and Technology

No paper, just abstract, no pathogens appear to have been found: Culture-independent Pathogenic Bacterial Communities in Bottled Mineral Water – Hamdy A. Hassan – Renewable Energy & Sustainable Development

A diagnosis of the microbiological quality of dehydrated bee-pollen produced in Brazil – Adriane Alexandre Machado De-Melo – Letters in Applied Microbiology

Metagenomics and bioinformatics

HipMer: An Extreme-Scale De Novo Genome Assembler – Evangelos Georganas

Functional metagenomic discovery of bacterial effectors in the human microbiome and isolation of commendamide, a GPCR G2A/132 agonist – Louis J. Cohen – PNAS

Proteomics and metabolomics

The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity – Samuel H. Payne – Scientific Data

Monitoring microbial metabolites using an inductively coupled resonance circuit – Daniil Karnaushenko – Scientific Reports

Extremophiles

Biotechnological applications of extremophiles, extremozymes and extremolytes – Noura Raddadi – Applied Microbiology and Biotechnology

Microbes in the news

Mothers facing C-sections look to vaginal ‘seeding’ to boost their babies’ health – Aimee Molloy – The Guardian

Bacterial community in pregnant women linked to preterm birth, study finds – Erin Digitale – Stanford Medicine
Stanford preterm birth study counters Detroit findings – Karen Bouffard – The Detroit News
Microbe Mix May Play Role In Preterm Birth Risk – Rob Stein – NPR

Biologist investigates how gene-swapping bacteria evade antibiotics – University of Texas at Dallas – EurekAlert

Methane and Climate Change: Arctic Bacteria Might Eat Methane? – Nature World News

How beneficial bacteria protect intestinal cells – Quinn Eastman – Emory News Center

Researchers Identify Metaproteomic Differences between Obese, Non-Obese Individuals – Adam Bonislawski – Genomeweb

How does Cincinnati Children’s Hospital use the microbiome to study lupus? A look inside with Diana Taft – Megan McGrath – DNA Genotek

Science, publishing, and career

A Scientific Look at Bad Science – Bourree Lam – The Atlantic

Bik’s Picks

Photos: Ancient Flowering Plant May Have Lived with Dinosaurs – Live Science

First-Ever Salamander in Amber Found in Caribbean – Richard Farrell – Discovery

Nasa awards $200,000 grant to a research project aimed at turning astronaut poo into food – Independent

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August 17, 2015

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Gut microbiota composition is associated with stool consistency, sequencing the lung microbiome, and the importance of purses as fomites.

Events

Tuesday evening: The Microbiome: An Alien Organ Within the Human Body – OMSI Science Pub (18 August 2015), Portland, OR

Human respiratory microbiome

Integrating microbial and host transcriptomics to characterize asthma-associated microbial communities – Eduardo Castro-Nallar – BMC Medical Genomics

Editorial to the Sze article : Outside In: Sequencing the Lung Microbiome – Michael J. Cox – American Journal of Respiratory and Critical Care Medicine

Human gut microbiome

Gut microbiota composition associated with stool consistency – E F Tigchelaar – Gut

Review: The role for gut permeability in the pathogenesis of type 1 diabetes – a solid or leaky concept? – Xia Li – Pediatric Diabetes

Animal microbiome

Buccal swabbing as a non-invasive method to determine bacterial, archaeal, and eukaryotic microbial community structure in the rumen – Sandra Kittelmann – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Olive Husk Compost Improves the Quality of Intensively Cultivated Agricultural Soils – María Teresa Moreno – Land Degradation & Development

Climate Change and Physical Disturbance Manipulations Result in Distinct Biological Soil Crust Communities – Blaire Steven – Applied and Environmental Microbiology

Built environment microbiology

A study to investigate the importance of purses as fomites – Susheela D Biranjia-Hurdoyal – Advanced Biomedical Research

More microbiology

Review: Diagnostics and Discovery in Viral Central Nervous System Infections – Walter Ian Lipkin – Brain Pathology

(Meta)genomics

Getting the genome in shape: the formation of loops, domains and compartments – Britta AM Bouwman – Genome Biology

Microbes in the news

Bug-killing book pages clean murky drinking water: pages can be torn out to filter drinking water – Jonathan Webb – BBC

A geneticist says any new parent should ‘roll their child on floor of the New York subway’ — here’s why – Erin Brodwin – Business Insider

Having your rot on! In your compost pile you will find billions and billions of microbes with a voracious appetite for organic matter – Chuck Martin – Midland Daily News

Bacteria in flowers may boost honeybees’ healthy gut microbes: Honeybees were into probiotics way before they were cool, a new study suggests. – Beth Mole – Science News

The curious meeting of two partners: the squid–vibrio symbiosis – Tim Miyashiro – Society for General Microbiology

Horses: Heaves and Tracheal Microbiomes: Is There a Connection? – Erica Larson – The Horse

What’s on the menu? Bacteria – lots of them – Elisa Ung – North Jersey.com
“menus are usually the most bacteria-laden object on a restaurant table”

Oral bacteria: friends and foes of the mouth – Nikki Natividad – Rappler

TB Traces: The mummy museum in Vác, Hungary, has human remains that helped researchers learn more about the origins of tuberculosis in Europe – The Scientist

Bik’s Picks

The relationship between the season of birth and early-onset food allergies in children –
Kajiyo Tanaka – Pediatric Allergy and Immunology

NASA working on gecko-inspired, sticky-footed robot – Chuck Bednar – Red Orbit

Tour de Turtles: The Race to Save the Turtles and Maybe Humans as Well – Dave Randle – Huffington Post
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August 16, 2015

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So many new papers, that I need to do a Sunday post as well. Human nose microbiota changes during rhinovirus infection. tsrimethylamine and human gut microbiome, gut microbiota in sloths, and effect of timber harvesting on forest soils.

Human oral microbiome

Long-term evaluation of the antimicrobial susceptibility and microbial profile of subgingival biofilms in individuals with aggressive periodontitis – Talita Gomes Baêta Lourenco – Brazilian Journal of Microbiology

The human oral metaproteome reveals potential biomarkers for caries disease – Pedro Belda-Ferre – Proteomics

Human respiratory microbiome

Changes in microbiota during experimental human Rhinovirus infection – J. J. Hofstra – BMC Infectious Disease

Human gut microbiome

The Microbiome and Osteosarcopenic Obesity in Older Individuals in Long-Term Care Facilities – Julia E. Inglis – Current Osteoporosis Reports

Review: Microbiology Meets Big Data: The Case of Gut Microbiota–Derived Trimethylamine – Gwen Falony – Annual Review of Microbiology

Review: Gut microbiota modulate the immune effect against hepatitis B virus infection – D. Xu – European Journal of Clinical Microbiology & Infectious Diseases

Microbiome models

Osteopontin Deficiency Accelerates Spontaneous Colitis in Mice with Disrupted Gut Microbiota and Macrophage Phagocytic Activity – Takahiko Toyonaga – PLOS ONE

Prolonged antibiotic treatment induces a diabetogenic intestinal microbiome that accelerates diabetes in NOD mice – Kirsty Brown – ISME Journal

Prebiotic effects of diet supplemented with the cultivated red seaweed Chondrus crispus or with fructo-oligo-saccharide on host immunity, colonic microbiota and gut microbial metabolites – Jinghua Liu – BMC Complementary and Alternative Medicine

Animal microbiome

Metagenome Sequencing of the Greater Kudu (Tragelaphus strepsiceros) Rumen Microbiome – Anita N. Dube – Genome Announcements

Diet specialization selects for an unusual and simplified gut microbiota in two- and three-toed sloths – Kimberly A. Dill-McFarland – Environmental Microbiology

Microbiome Variation Across Amphibian Skin Regions: Implications for Chytridiomycosis Mitigation Efforts – Arnaud Bataille – Microbial Ecology

Plant, root, and soil microbiome

Molecular screening of microbial communities for candidate indicators of multiple metal impacts in marine sediments from Northern Australia – Alyssa M. Cornall – Environmental Toxicology and Chemistry

Response of Archaeal and Bacterial Soil Communities to Changes Associated with Outdoor Cattle Overwintering – Alica Chroňáková – PLOS ONE

Long-term effects of timber harvesting on hemicellulolytic microbial populations in coniferous forest soils – Hilary T C Leung – ISME Journal

Microbial Community Composition and Extracellular Enzyme Activities Associated with Juncus roemerianus and Spartina alterniflora Vegetated Sediments in Louisiana Saltmarshes – Anthony J. Rietl – Microbial Ecology

Water microbiome

Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time-series and global field samples – Alma Parada – Environmental Microbiology

Diversity of Synechococcus at the Martha’s Vineyard Coastal Observatory: Insights from Culture Isolations, Clone Libraries, and Flow Cytometry – Kristen R. Hunter-Cevera – Microbial Ecology

Built environment microbiome

The Effectiveness of Three Home Products in Cleaning and Disinfection of S. aureus and E. coli on Home Environmental Surfaces – Nancy Goodyear – Journal of Applied Microbiology

Geochemical influences and mercury methylation of a dental wastewater microbiome – Asha Rani – Scientific Reports

Metagenomics

Research Highlights: An encrypted growth signature – Naomi Attar – Nature Reviews Microbiology

Archaea / Metabolomics

Untargeted metabolomics studies employing NMR and LC–MS reveal metabolic coupling between Nanoarcheum equitans and its archaeal host Ignicoccus hospitalis – Timothy Hamerly – Metabolomics

Microbes in the news

Toxoplasma parasite’s greedy appetite may be its downfall – University of Melbourne – EurekAlert

Let’s hope the stock photo was not related to the techniques used in this study:
Computerized ‘fishing expedition’ hooks 12,500 virus genomes – Brooks Hays – UPI

New Beach Act aims for faster results on bacteria tests – Dan Radel – APP.com

Swedish infant infects four others with resistant bacteria – New Straits Times

What’s lurking in your lungs? Surprising findings emerge from U-M microbiome research – Health Canal

Science, publishing, and career

Fixing the Leaky Bucket: What Tech Companies Must Do to Retain Their Best Female Talent – Belle Beth Cooper – Huffington Post

Bik’s Picks

Here’s How To Call The International Space Station – Gizmodo

Playing Tetris for 3 minutes could reduce your worst cravings – IBN Live

Teenagers are making themselves DIY braces and it is horrifying – Amy Willis – Metro.co.uk

How the internet of things is having an impact in Africa – HTXT Africa

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August 15, 2015

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Here is your Saturday edition of the Digest. Four papers today about Arctic water and soil microbes, oral bacteria in placentas, using hand microbiomes to identify human ethnicities, and machine learning classifiers give insights in bacterial vaginosis.

Pregnancy and birth microbiome

Oral bacteria in placental tissues: Increased molecular detection in pregnant periodontitis patients – Vanessa Blanc – Oral Diseases

Human skin microbiome

Hand bacteria as an identifier: a biometric evaluation – Amanda B. Holbert – Network Modeling Analysis in Health Informatics and Bioinformatics

Minireview: From Head to Toe: Mapping Fungi across Human Skin – Tim Sandle – EC Microbiology

Human respiratory microbiome

Impact of cigarette smoking on the middle meatus microbiome in health and chronic rhinosinusitis – Vijay R. Ramakrishnan – International Forum of Allergy & Rhinology

Human gut microbiome

Metagenomic Analysis of Crohn’s Disease Patients Identifies Changes in the Virome and Microbiome Related to Disease Status and Therapy, and Detects Potential Interactions and Biomarkers – Pérez-Brocal, Vicente – Inflammatory Bowel Diseases

Animal models

SIV-infection-driven changes of pattern recognition receptor expression in mesenteric lymph nodes and gut microbiota dysbiosis – Tiffany W. Glavan – Journal of Medical Primatology

Plant, root, and soil microbiome

Diazotrophic bacilli isolated from the sunflower rhizosphere and the potential of Bacillus mycoides B38V as biofertiliser – A. Ambrosini – Annals of Applied Biology

Relationships between Oak powdery mildew incidence and severity and commensal fungi – E. T. Topalidou – Forest Pathology

The core microbiome bonds the Alpine bog vegetation to a transkingdom metacommunity – Anastasia Bragina – Molecular Ecology

Warming reduces the cover and diversity of biocrust-forming mosses and lichens, and increases the physiological stress of soil microbial communities in a semi-arid Pinus halepensis plantation – Fernando T. Maestre – Frontiers in Microbiology

Microbial Mineral Colonization Across a Subsurface Redox Transition Zone – Brandon Converse – Frontiers in Microbiology

Mutabilis in mutabili: Spatiotemporal dynamics of a truffle colony in soil – Milan Gryndler – Soil Biology and Biochemistry

Water microbiome

Bacterioplankton community shifts associated with epipelagic and mesopelagic waters in the Southern Ocean – Zheng Yu – Scientific Reports

Microbial diversity in a submarine carbonate edifice from the serpentinizing hydrothermal system of the Prony Bay (New Caledonia) over a 6-year period – Anne Poste – Frontiers in Microbiology

Extremophile microbiome: Arctic edition

Microbial activity is not always limited by nitrogen in Arctic tundra soils – Caroline Melle – Soil Biology and Biochemistry

Arctic soil microbial diversity in a changing world – Aimeric Blaud – Research in Microbiology

Temporal and spatial influences incur reconfiguration of Arctic heathland soil bacterial community structure – Richard Hill – Environmental Microbiology

Diversity of planktonic microorganisms in the Arctic Ocean – Carlos Pedrós-Alió – Progress in Oceanography

Waste treatment microbiology

Shotgun metaproteomic profiling of biomimetic anaerobic digestion processes treating sewage sludge – Ariane Bize – Proteomics

Bioinformatics

Machine learning classifiers provide insight into the relationship between microbial communities and bacterial vaginosis – Daniel Beck – BioData Mining

AmpliSAS: a web server for multilocus genotyping using next-generation amplicon sequencing data – Alvaro Sebastian – Molecular Ecology Resources

Science, publishing, and career

My alma mater, Utrecht University was again voted as the best Dutch university! Academic Ranking of World Universities 2015 – Shanghai Ranking

Microbes in the news

The Microbial Discovery Box: a hands-on activity for science teachers – ASM

Young scientists dreaming big: internship presentation competitions – Uganda Virus Research Institute

Infectious Diseases Like It Hot: How Climate Change Helps Cholera and Salmonella Outbreaks – Marlene Cimons – Think Progress

Before an Animal Disease Becomes a Human Epidemic – Cari Romm – The Atlantic

The dangers of eating snakes: Gauteng pastor encouraged his congregation to eat hair and snakes.

Bik’s Picks

Air Problem Is Worse Than You Think – James Fallows – The Atlantic

Georgia court weighs destiny of 18 captured beluga whales – Rich McKay – Reuters

Los Angeles Throws 96M Balls At California’s Drought Problem – Science Daily

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August 13, 2015

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Fecal microbiota transplants also work with frozen stool, rhizobacterial communities on red pepper plants, effect of vaginal ring contraceptives, and the cilantro microbiome.

Pregnancy and birth microbiome

Maternal group B Streptococcus and the infant gut microbiota – A. E. Cassidy-Bushrow – Journal of Developmental Origins of Health and Disease

Not a microbiome paper, but of interest: Cesarean Section Delivery is not a Risk Factor for Development of IBD: A Population-based Analysis – Charles N. Bernstein – Clinical Gastroenterology and Hepatology

Human gut microbiome

Faecal microbiota transplant for recurrent Clostridium difficile infection using long-term frozen stool is effective: clinical efficacy and bacterial viability data – S. P. Costello – Alimentary Pharmacology & Therapeutics

Review: Colonization Resistance of the Gut Microbiota against Clostridium difficile – Ana Elena Pérez-Cobas – Antibiotics

Review: Microbiome and Asthma: What Have Experimental Models Already Taught Us?
R. Bonamichi-Santos – Journal of Immunology Research

Human reproductive microbiome

Effects of a One Year Reusable Contraceptive Vaginal Ring on Vaginal Microflora and the Risk of Vaginal Infection: An Open-Label Prospective Evaluation – Yongmei Huang – PLOS ONE

Animal models

Lessons from the Drosophila microbiota – Emma L Walton – Biomedical Journal

Studying host-microbiota interactions in Drosophila melanogaster – Jean Kanellopoulos – Biomedical Journal

Impact of Selection for Digestive Efficiency on Microbiota Composition in the Chicken –
Sandrine Mignon-Grasteau – PLOS ONE

Animal microbiome

Deep insights into carbohydrate metabolism in the rumen of mehsani buffalo at different diet treatments – Nidhi R. Parmar – Genomics Data

Metagenomics: Microbiome analyses of pacific white shrimp (Litopenaeus Vannamei) collected from disparate geographical locations – Arun S. Seetharam – Genomics Data

Classifying the bacterial gut microbiota of termites and cockroaches: a curated phylogenetic reference database (DictDb) – Aram Mikaelyan – Systematic and Applied Microbiology

Plant, root, and soil microbiome

Rhizobacterial Communities and Red Pepper (Capsicum annum) Yield under Different Cropping Systems – Byung Kwon Jung – International Journal of Agriculture & Biology

Soil Microbial Community Structure and Metabolic Activity of Pinus elliottii Plantations across Different Stand Ages in a Subtropical Area – Zeyan Wu – PLOS ONE

Microbiomes and potential metabolic pathways of pristine and anthropized Brazilian mangroves – Vanessa L.R. Nogueira – Regional Studies in Marine Science

Phylogenetic Characterization and Community Diversity of Hydrocarbon-Utilizing
Bacteria in Soil Microcosms Enriched with Aromatic Hydrocarbons – Ola Olapade A – Bioremediation & Biodegradation

Review: The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes – Pablo R. Hardoim – Microbiology and Molecular Biology Reviews

Water microbiome

Ecological connectivity shapes quasispecies structure of RNA viruses in an Antarctic lake – A. López-Bueno – Molecular Ecology

Causes and consequences of habitat fragmentation in river networks – Matthew R. Fuller – Annals of the New York Academy of Sciences

Capability of the natural microbial community in a river water ecosystem to degrade the drug naproxen – Paola Grenni – Environmental Science and Pollution Research

Food microbiology

Cilantro microbiome before and after nonselective pre-enrichment for Salmonella using 16S rRNA and metagenomic sequencing – Karen G. Jarvis – BMC Microbiology

Changes in the microbial communities of air-packaged and vacuum-packaged common carp (Cyprinus carpio) stored at 4 °C – Yuemei Zhang – Food Microbiology

Metagenomics

An Overview of Genome Organization and How We Got There: from FISH to Hi-C – James Fraser – Microbiology and Molecular Biology Reviews

Microbes in the news

Statistical Advances Help Unlock Mysteries of the Human Microbiome – Infection Control Today

Seeking samples from FIV positive kitties – Holly Ganz – MicroBEnet

NOFA Says ‘Heal the Climate, Heal Ourselves’ – EcoRI news

Guest Post — The Emergent Microbiome: A Revolution for the Life Sciences – Part II, 2015 Patent Trends – Jessica Miles and Anthony D Sabatelli – JDsupra

A Genetically Modified Yeast Turns Sugar Into Painkillers: Stanford scientists have engineered a strain of yeast that can produce opiates on its own – Adam Hoffman – Smithsonian

Science, publishing, and career

What is the future of Science? This guy might know! Podcast with Francis Collins, NIH Director – Michael DL Johnson – Black Science Blog

Bik’s Picks

Longer-term outcome in the prevention of psychotic disorders by the Vienna omega-3 study – G. Paul Amminger – Nature Communications

Music as an aid for postoperative recovery in adults: a systematic review and meta-analysis – Jenny Hole – The Lancet

How can ants tell each other apart? Why, with their crazy refined sense of smell. – Elahe Izadi – Washington Post

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August 12, 2015

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Drug metabolism by gut microbiota, nature vs. nurture in inbred strains of mice, gnotobiotic Drosophila, bat virome, and influence of protist predation on marine microbiomes.

General microbiome

Short-chain fatty acids in control of body weight and insulin sensitivity – Emanuel E. Canfora – Nature Reviews Endocrinology

Pregnancy and birth microbiome

Streptococcal Diversity of Human Milk and Comparison of Different Methods for the Taxonomic Identification of Streptococci – Virginia Martín – Journal of Human Lactation

Human gut microbiome

Editorial: Drug Metabolism by the Host and Gut Microbiota: A Partnership or Rivalry?
Hollie I Swanson – Drug Metabolism and Disposition
Review: Mechanisms of How the Intestinal Microbiota Alters the Effects of Drugs and Bile Acids – Curtis D. Klaassen – Drug Metabolism and Disposition

Comparison of the gut microbiota composition between obese and non-obese individuals in a Japanese population, as analyzed by terminal restriction fragment length polymorphism and next-generation sequencing – Chika Kasai – BMC Gastroenterology

Animal and other models

Microbiota in 110 diverse inbred strains of mice: Genetic and environmental control of host-gut microbiota interactions – Elin Org – Genome Research

Co-culturing Escherichia coli O157:H7 with a non-pathogenic E. coli strain increases toxin production and virulence in a germ-free mouse model – Kakolie Goswami – Infection and Immunity

Ovariectomy results in differential shifts in gut microbiota in low versus high aerobic capacity rats – Kimberly A. Cox-York – Physiological Reports

Studying host-microbiota mutualism in Drosophila: Harnessing the power of gnotobiotic flies – Dali Ma – Biomedical Journal

MyD88 Signaling Regulates Steady-State Migration of Intestinal CD103+ Dendritic Cells Independently of TNF-α and the Gut Microbiota – Karin Hägerbrand – The Journal of Immunology

Animal microbiome

Deciphering the bat virome catalog to better understand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases – Zhiqiang Wu – ISME Journal

Plant, root, and soil microbiome

Host promiscuity in symbiont associations can influence exotic legume establishment and colonization of novel ranges – Metha M. Klock – Diversity and Distributions

Temporal and spatial influences incur reconfiguration of Arctic heathland soil bacterial community structure – Richard Hill – Environmental Microbiology

Water microbiome

Marine bacterial community structure resilience to changes in protist predation under phytoplankton bloom conditions – Federico Baltar – ISME Journal

Waste and water treatment microbiology

The activated sludge ecosystem contains a core community of abundant organisms – Aaron M Saunders – ISME Journal

Core-satellite populations and seasonality of water meter biofilms in a metropolitan drinking water distribution system – Fangqiong Ling – ISME Journal

More microbes

Levels and limits in artificial selection of communities – Manuel Blouin – Ecology Letters

Editorial: Origin of the Yeast Whole-Genome Duplication – Kenneth H. Wolfe – PLOS Biology
Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker’s Yeast Lineage – Marina Marcet-Houben – PLOS Biology

Microbes in the news

Global Human Microbiome Market: Asia is expected to show high growth rates by 2020 – MedGadget

Things I Tell My Mom: Five ways for you to participate in science – Cathy Seiler – Ahwatukee Foothills News

Why making and taking fermented drinks is becoming popular again – John McKenna – The Irish Times

Protein Goes Green: Can Algae Become The Next Soy? – Jessie Rack – NPR

Cultured Coffee offers the flavor of poop-brewed coffee without the crap – TJ Dietsch – Geek

Making kefir at home is easy, healthy – Kit Waskom Pollard – Baltimore Sun

‘Genomic Archaeology’ Reveals That Lager Yeast Was Born More Than Once – Andrea Alfano -Tech Times

Researchers resurrect extinct virus to use for gene therapy: Evolutionary ancestors remade based on current viruses – Ars Technica

Science, publishing, and career

Make Peer Review Public: How to make science faster and more robust – Adam Marcus and Ivan Oransky – Slate

Despite concerted effort, barriers to women in science remain – Jennifer Ann Thomson – The Conversation

Outreach: Primary School outreach – inspiring young minds with science – Mariya Lobanovska – SGM

Physics: She did it all: Val Gibson enjoys the autobiography of Mary K. Gaillard, the first female physics professor at Berkeley – Val Gibson – Nature

Bik’s Picks

Octopus Genome Offers Insights Into One Of Ocean’s Cleverest Oddballs – Nell Greenfieldboyce – NPR

Meteor time! How to watch the big Perseid shower – Paul Rogers – San Jose Mercury News

MIT tackling more serious science: they program beer-delivering robots – ZME Science

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August 11, 2015

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Several reviews on human gut microbiome, two papers on coral microbiome, gut microbiota of wild mice, ancient sea microbes found in gold mine stalactites, and an update on the tree of life.

Microbiome of Death

Not a microbiota paper, but cannot leave out: A Longitudinal Study on Human Outdoor Decomposition in Central Texas – Joanna K. Suckling – Journal of Forensic Sciences

Human gut microbiome

Anti-tumour Necrosis Factor Treatment with Adalimumab Induces Changes in the Microbiota of Crohn’s Disease – David Busquets – Journal of Crohn’s and Colitis

Reduced Levels of D-dimer and Changes in Gut Microbiota Composition after Probiotic Intervention in HIV-infected Individuals on Stable ART – Birgitte Stiksrud – Journal of Acquired Immune Deficiency Syndromes

The human gut microbiome as a transporter of antibiotic resistance genes between continents – Johan Bengtsson-Palme – Antimicrobial Agents and Chemotherapy

Review: The gut microbiota in human energy homeostasis and obesity – Michael Rosenbaum – Trends in Endocrinology & Metabolism

Review: Understanding probiotics’ role in allergic children: the clue of gut microbiota profiling – Pamela Vernocchi – Current Opinion in Allergy and Clinical Immunology

Editorial: The Role of Bacteria in Necrotizing Enterocolitis: Understanding the Forest for the Trees – McElroy S.J – Neonatology

Review: Implications of microbiota and bile acid in liver injury and regeneration – Hui-Xin Liu – Journal of Hepatology

Animal and bioreactor models

Metagenomic Analysis of Antibiotic Resistance Genes in Dairy Cow Feces following Therapeutic Administration of Third Generation Cephalosporin – Lindsey Chambers – PLOS ONE

Increased Butyrate Production During Long-Term Fermentation of In Vitro-Digested High Amylose Cornstarch Residues with Human Feces – Li Li – Journal of Food Science

Bacterial diversity in bovine rumen by metagenomic 16S rDNA sequencing and scanning electron microscopy – Raphael Barbetta de Jesus – Acta Scientiarum

Animal microbiome

The Gut Microbiota of Wild Mice – Laura Weldon – PLOS ONE

Necrotizing Enterocolitis in Preterm Pigs Is Associated with Increased Density of Intestinal Mucosa-Associated Bacteria Including Clostridium perfringens – Støy A.C.F. – Neonatology

Cecal drop reflects the chickens’ cecal microbiome, fecal drop does not – J. Pauwels – Journal of Microbiological Methods

Evidence for host specificity among dominant bacterial symbionts in temperate gorgonian corals – Marie La Rivière – Coral Reefs

Identification of Candidate Coral Pathogens on White Band Disease-Infected Staghorn Coral – Sarah A. Gignoux-Wolfsohn – PLOS ONE

Bacteria detected in the honeybee parasitic mite Varroa destructor collected from beehive winter debris – J. Hubert – Journal of Applied Microbiology

Plant, root, and soil microbiome

Remediation of diesel-contaminated soil using in situ chemical oxidation (ISCO) and the effects of common oxidants on the indigenous microbial community: a comparison study – Ku-Fan Chen – Journal of Applied Microbiology

Rhizosphere bacterial communities of dominant steppe plants shift in response to a gradient of simulated nitrogen deposition – An Yang – Frontiers in Microbiology

Diversity and Distribution of Archaea in the Mangrove Sediment of Sundarbans – Anish Bhattacharyya – Archaea

Seasonal effect and anthropogenic impact on the composition of the active bacterial community in Mediterranean orchard soil – Sammy Frenk – FEMS Microbial Ecology

Effects of biochar on copper immobilization and soil microbial communities in a metal-contaminated soil – Sebastián Meier – Journal of Soils and Sediments

Factors associated with the diversification of the microbial communities within different natural and artificial saline environments – Shilong He – Ecological Engineering

Review: Direct and indirect effects of climate change on soil microbial and soil microbial-plant interactions: What lies ahead? – Aimée T. Classen – Ecosphere

Water microbiome

Deep subsurface mine stalactites trap endemic fissure fluid Archaea, Bacteria, and Nematoda possibly originating from ancient seas – Gaëtan Borgonie – Frontiers in Microbiology

Drivers of the dynamics of diazotrophs and denitrifiers in North Sea bottom waters and sediments – Haoxin Fan – Frontiers in Microbiology

Waste treatment microbiology

Denitrifying capability and community dynamics of glycogen accumulating organisms during sludge granulation in an anaerobic-aerobic sequencing batch reactor – Zhang Bin – Scientific Reports

Proteomics

Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data – Laurence Yang – PNAS

Colonic metaproteomic signatures of active bacteria and the host in obesity – Carolin A. Kolmeder – Proteomics

More microbes

The universal tree of life: an update – Patrick Forterre – Frontiers in Microbiology

How Do Microbial Populations and Communities Function as Model Systems? – Maureen O’Malley – The Quarterly Review of Biology

Impact of space flight on bacterial virulence and antibiotic susceptibility – Peter William Taylor – Infection and Drug Resistance

Microbes in the news

Look Up! There’s an Invisible Zombie Highway Right Above You – Robert Krulwich – National Geographic

uBiome Invites Health Care Providers to Join New Clinical Microbiome Consortium – Global News Wire

Our microbiome: Separating hype from health – Nicholas Staropoli – Genetic Literacy Project

Poop Transplants And Microbiome Makeovers: How We’ll Engineer Our Bacteria To Feel Better – Jessica Leber – FastCoExist

Researchers Offer New Insights Into the Pulmonary Microbiota of Cystic Fibrosis Patients – Patricia Silva – Cystic Fibrosis News Today

Conflict and Co-operation in Bacterial Communities – MicrobePost

Can Your Body’s Bacteria Cause Cancer? – Charis Eng – Cleveland Clinic

British Ministry of Defense released potentially lethal bacteria on London Tube (in 1963), chemically experimented on soldiers – Russell Boyce – RT

Engineered Bacteria Send A Signal When Water Gets Polluted – Tracy Staedter – Discovery

JGI to Grant $1.2 Million to Genomic Technology Projects – Genome Web

Science, publishing, and career

Science: The Story of Me – Morgan Pak – Huffington Post

4 Ways to Help Everyone Find Their Inner Scientist – Imogen Coe – Huffington Post

Tech Women in India’s Startup Boom Reach Out – Gagandeep Kaur – WomensEnews

Bik’s Picks

Magnetosensitive neurons mediate geomagnetic orientation in Caenorhabditis elegans – Andrés Vidal-Gadea – eLIFE

Here’s why coffee makes you poop – Rachel Feltman – Washington Post

Why You’re More Likely To Be Killed By a Bee Than a Bear: Our fear of bear attacks is far greater than the actual risk of being mauled or killed, experts say. – Carrie Arnold – National Geographic

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August 7, 2015

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Viral infections in coral mucus, microbiology of wind-erosion, cable bacteria in fresh-water sediments, viruses in swimming pools, update on ITS2 database, and specialist taxa.

General human microbiome

Review: Social behavior and the microbiome – Elizabeth A Archie – Current Opinion in Behavioral Sciences

Editorial: Germs and joints: the contribution of the human microbiome to rheumatoid arthritis – Geraint B Rogers – Nature Medicine

Microbiome models

In mice: Pancreatic β-Cells Limit Autoimmune Diabetes via an Immunoregulatory Antimicrobial Peptide Expressed under the Influence of the Gut Microbiota – Jia Sun – Immunity

Re: Gut microbiota depletion from early adolescence in mice: Implications for brain and behavior – Zongxin Ling – Brain, Behavior, and Immunity

Animal microbiome

Coral Mucus Is a Hot Spot for Viral Infections – Hanh Nguyen-Kim – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Microbiology of wind-eroded sediments: Current knowledge and future research directions – V. Acosta-Martínez – Aeolian Research

Water microbiome

The “Melosira years” of Lake Baikal: Winter environmental conditions at ice onset predict under-ice algal blooms in spring – Stephen L. Katz – Limnology and Oceanography

Cable Bacteria in Freshwater Sediments – Nils Risgaard-Petersen – Applied and Environmental Microbiology

First detection of Papillomaviruses and Polyomaviruses in swimming pool waters: unrecognized recreational water-related pathogens? – G La Rosa – Journal of Applied Microbiology

Bioinformatics

ITS2 database V: Twice as much – Markus J. Ankenbrand – Molecular Biology and Evolution

Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud – Malachi Griffith – PLOS Computational Biology

Microbial ecology and other microbiology

Microbial ecosystems are dominated by specialist taxa – Mahendra Mariadassou – Ecology Letters

Review: Physiological and Transcriptional Responses of Different Industrial Microbes at Near-Zero Specific Growth Rates – Onur Ercan – Applied and Environmental Microbiology

The United States Culture Collection Network (USCCN): Enhancing Microbial Genomics Research through Living Microbe Culture Collections – Kyria Boundy-Mills – Applied and Environmental Microbiology

A New Strategy for Smoking Cessation: Characterization of a Bacterial Enzyme for the Degradation of Nicotine – Song Xue – Journal of the American Chemical Society

Microbes in the news

Airplane Poop Could Help Track Global Disease Outbreaks – Sarah Zhang – Wired

2 min podcast: Microbes Deep under Seafloor Reflect Ancient Land Origins – Cynthia Graber – Scientific American

This week in Microbiology: Precision Killing: use of antimicrobial peptides to target specific bacteria in the microbiome, and how the intracellular bacterium Wolbachia selectively kills male hosts.

“Happy Days Study” meets the microbiome – Terry Devitt – University of Wisconsin-Madison

Gut Microbiome After Weight-Loss Surgery – Amanda B. Keener – The Scientist

TSRI Chemists Report Nicotine-Chomping Bacteria May Hold Key to Anti-Smoking Therapy – The Scripps Research Institute

Science, publishing, and career

Biology, wet and dry: an interview with Sarah Teichmann – Elisabeth Pain – Science

“Anyone who photographs a bear will get sent home immediately” Don’t mess with the bears – Eli Kintisch – Science

Australia’s remarkable female scientists highlighted in new exhibition in Canberra – Clarissa Thorpe – ABC Australia

Bik’s Picks

Deepwater Horizon, 5 years on – Samantha B. Joye – Science

Devil Tree Threatens the World’s Rarest Zebras – John R. Platt – Scientific American

Facial expressions in horses: EquiFACS: The Equine Facial Action Coding System – Jen Wathan – PLOS ONE

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August 5, 2015

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Microbiome in patients with Irritable Bowel Syndrome, gastric bypass operations induces long-term microbiome changes, environmental enteropathy in a mouse model, respiratory viruses in large families, and microbiology of restaurant grease waste.

Events

Microbiome R&D and Business Collaboration Forum – September 10-11, 2015, San Diego, USA

European Microbiome Congress 2015 – 18 and 19 November 2015, London, UK

Microbiome of pregnancy and birth

Review: Antibiotics and the developing infant gut microbiota and resistome – Molly K Gibson – Current Opinion in Microbiology

Review: Early Life Experience and Gut Microbiome: The Brain-Gut-Microbiota Signaling System – Cong, Xiaomei – Advances in Neonatal Care

Review: The Prescient Placenta – Christopher Coe – The Scientist

Human respiratory microbiome

Community Surveillance of Respiratory Viruses Among Families in the Utah Better Identification of Germs-Longitudinal Viral Epidemiology (BIG-LoVE) Study –  L. Byington – Clinical Infectious Diseases

Human gut microbiome

Reduction of butyrate- and methane-producing microorganisms in patients with Irritable Bowel Syndrome – Marta Pozuelo – Scientific Reports

Roux-en-Y Gastric Bypass and Vertical Banded Gastroplasty Induce Long-Term Changes on the Human Gut Microbiome Contributing to Fat Mass Regulation – Valentina Tremaroli – Cell Metabolism

Gut-Microbiota-Metabolite Axis in Early Renal Function Decline – Clara Barrios – PLOS ONE

Editorial: Microbiome reflects status of RA and response to therapy – Robert Phillips – Nature Reviews Rheumatology

Microbiome models

Bacterial sensing underlies artificial sweetener-induced growth of gut Lactobacillus – Kristian Daly – Environmental Microbiology

Diet and specific microbial exposure trigger features of environmental enteropathy in a novel murine model – Eric M. Brown – Nature Communications

Animal microbiome

Dominant ectosymbiotic bacteria of cellulolytic protists in the termite gut also have the potential to digest lignocellulose – Masahiro Yuki – Environmental Microbiology

Two gut community enterotypes recur in diverse bumblebee species – Jilian Li- Current Biology

Unique metabolites protect earthworms against plant polyphenols – Manuel Liebeke – Nature Communications

Streptococcus panodentis sp. nov., from the oral cavities of chimpanzees – Masaaki Okamoto – Microbiology and Immunology

Plant, root, and soil microbiome

Fungal root endophytes of Quercus robur subjected to flooding – H. Kwaśna – Forest Pathology

Land Use and Precipitation Affect Organic and Microbial Carbon Stocks and the Specific Metabolic Quotient in Soils of Eleven Ecosystems of Mt. Kilimanjaro, Tanzania – Holger Pabst – Land Degradation & Development

The Phytophthora species assemblage and diversity in riparian alder ecosystems of western Oregon, USA – Laura Lee Sims – Mycologia

Bacterial community structures as a diagnostic tool for watershed quality assessment – Luigimaria Borruso – Research in Microbiology

Water microbiome

Planktonic and sedimentary bacterial diversity of Lake Sayram in summer – Lei Fang – Microbiology Open

Waste and bioreactor microbiome

Reactor performance and microbial community dynamics during anaerobic co-digestion of municipal wastewater sludge with restaurant grease waste at steady state and overloading stages – Vahid Razaviarani – Bioresource Technology

Arsenic toxicity effects on microbial communities and nutrient cycling in indoor experimental channels mimicking a fluvial system – Baigal-Amar Tuulaikhuu – Aquatic Toxicology

Metagenomics and bioinformatics

Xander: employing a novel method for efficient gene-targeted metagenomic assembly – Qiong Wang – Microbiome

Metabolomics

Symposium report: Olfaction in the Kidney: ‘Smelling’ gut microbial metabolites – Niranjana Natarajan and Jennifer L. Pluznick – Experimental Physiology

Microbial Ecology

Clustering in community structure across replicate ecosystems following a long-term bacterial evolution experiment – Hasan Celiker & Jeff Gore – Nature Communications

Microbes in the news

Interview with Peter DiLaura, CEO of Second Genome: Data Mining The Microbiome Toward A Cure For Inflammatory Disease – Peter High – Forbes

Weight loss surgery benefits for gut microbiome last at least a decade – MedicalXpress

Extreme weight loss surgery works, but is it thanks to the knife—or the microbes? – Mitch Leslie – Science

A Belated Look at New York’s Cooling Towers, Prime Suspect in Legionnaires’ Outbreak – Winnie Hu and Noah Remnick – NY Times

Amid Legionnaires’ Fears, City Proposes New Cooling Tower Rules – Mara Gay and Corinne Ramey – Wall Street Journal
Randomised clinical study: Aspergillus niger-derived enzyme digests gluten in the stomach of healthy volunteers – B. N. Salden – Alimentary Pharmacology & Therapeutics

Study: Citrus Greening Bacterium Gives Vector Unexpected Boost – Paul Rusnak – Growing Produce

Team identifies mutations that allow bacteria to resist antibiotics – Phys.org

Africa is within reach of being declared a polio free region – The Conversation

Viruses Thrive In Big Families, In Sickness and In Health – University of Utah

Science, career, and publishing

Where Next for Genetics and Genomics? – Chris Tyler-Smith – PLOS Biology

Tech Women Triumph: $30k Funding In A Day, Success Under Pressure, True Leaders Inspire – Leo King – Forbes

#ilooklikeanengineer wants to challenge your ideas about who can be a scientist – Susan Svrluga – Washington Post

#FieldWorkFail: Gluing Yourself to a Live Crocodile and Other Mistakes: Scientists share the gross, scary, and often hilarious reality of doing experiments in the wild – Robinson Meyer – The Atlantic

9 Scientists Told Us What Scares Them The Most – Kelly Oakes – BuzzFeed

Bik’s Picks

Jack the Ripper’s final victim set to be exhumed following new theory on the killer’s identity – Doug Bolton – Independent

Scientists unearth earthworm’s ability to digest plant toxins – LiveMint

Are monarch butterflies really being massacred? A new study says it’s a lot more complicated than it seems – Sarah Kaplan – Washington Post

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August 4, 2015

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Diet-induced metabolic changes, rhythmicity of mouse gut microbiome, the microbiome of Lake Michigan, and chicken skin virome.

General microbiome

Antibiotics, microbiota and health: are there dangers hiding in plain sight? – A. Clinton White Jr – Current Opinion in Infectious Diseases

Short Course in the Microbiome: Meeting Dispatch – Kimberly Falana – Journal of Circulating Biomarkers

Pregnancy and birth microbiome

Influence of Intrapartum Antibiotic Prophylaxis for Group B Streptococcus on Gut Microbiota in the First Month of Life – Corvaglia, Luigi – Journal of Pediatric Gastroenterology and Nutrition

Human gut microbiome

Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome – Saeed Shoaie – Cell Metabolism

Effect of daily intake of pomegranate juice on fecal microbiota and feces metabolites from healthy volunteers – Juana I. Mosele – Molecular Nutrition & Food Research

Gut microbiota richness promotes its stability upon increased dietary fiber intake in healthy adults – Julien Tap – Environmental Microbiology

Review: The intestinal microbiome and health – Susan Tuddenham – Current Opinion in Infectious Diseases

Review: Trimethylamine N-Oxide From Gut Microbiota in Chronic Kidney Disease Patients: Focus on Diet – Cristiane Moraes – Journal of Renal Nutrition

Review: Gut permeability, its interaction with gut microflora and effects on metabolic health are mediated by the lymphatics system, liver and bile acid – Cuong D Tran – Future Medicine

Microbiome models

Rhythmicity of the intestinal microbiota is regulated by gender and the host circadian clock – Xue Liang – PNAS

Viability of gut microbes as a complementary earthworm biomarker of metal exposure – Shin Woong Kim – Ecological Indicators

Adaptation of the human aryl hydrocarbon receptor to sense microbiota-derived indoles – Troy D. Hubbard – Scientific Reports

Which games are growing bacterial populations playing? – Xiang-Yi Li – Interface

Animal microbiome

Chicken skin virome analyzed by high-throughput sequencing shows a composition highly different from human skin – Caroline Denesvre – Virus Genes

Variations in microbiota of culex (melanoconion) ocossa and culex (culex) declarator across periurban and rural environments – M Nelson Starkey – Honors Thesis – Andrews University

Plasmids from the gut microbiome of cabbage root fly larvae encode SaxA that catalyzes the conversion of the plant toxin 2-phenylethyl isothiocyanate – Cornelia U. Welte – Environmental Microbiology

Plant, root, and soil microbiome

Successional Trajectories of Rhizosphere Bacterial Communities over Consecutive Seasons
Shengjing Shi – mBio

Compositional differences in simulated root exudates elicit a limited functional and compositional response in soil microbial communities – Michael S. Strickland – Frontiers in Microbiology

Changes in soil microbial community functionality and structure in a metal-polluted site: The effect of digestate and fly ash applications – M. Garcia-Sánchez – Journal of Environmental Management

Metatranscriptome analysis reveals host-microbiome interactions in traps of carnivorous Genlisea species – Hieu X. Cao – Frontiers in Microbiology

Microbial composition alters the response of litter decomposition to environmental change – Kristin L. Matulich – Ecology

Plant community richness and microbial interactions structure bacterial communities in soil – Daniel C. Schlatter – Ecology

Plant diversity effects on soil microbial functions and enzymes are stronger than warming in a grassland experiment – Katja Steinauer – Ecology

Persistence of the dominant soil phylum Acidobacteria by trace gas scavenging – Chris Greening – PNAS

Review: Current overview on the study of bacteria in the rhizosphere by modern molecular techniques: a mini‒review – L. Lagos – Journal of soil science and plant nutrition

Review: Harnessing phytomicrobiome signaling for rhizosphere microbiome engineering – Liliana Quiza – Frontiers in Plant Science

Water microbiome

The quality of organic matter shapes the functional biogeography of bacterioplankton across boreal freshwater ecosystems – Clara Ruiz-González – Global Ecology and Biogeography

Dissimilatory Arsenate Reduction and In Situ Microbial Activities and Diversity in Arsenic-rich Groundwater of Chianan Plain, Southwestern Taiwan – Suvendu Das – Microbial Ecology

Freshwater ice as habitat: Partitioning of phytoplankton- and bacteria between ice and water in central European reservoirs – R.M.L. McKay – Environmental Microbiology Reports

Urban microbial ecology of a freshwater estuary of Lake Michigan – Jenny C. Fisher – Elementa

Review: Bacterial microcompartments: widespread prokaryotic organelles for isolation and optimization of metabolic pathways – Thomas A. Bobik – Molecular Microbiology

Metagenomics and bioinformatics

SuRankCo: supervised ranking of contigs in de novo assemblies – Mathias Kuhring – BMC Bioinformatics

More microbe research

Species-wide whole genome sequencing reveals historical global spread and recent local persistence in Shigella flexneri – Thomas R Conno – eLIFE

The Cipher Code of Simple Sequence Repeats in “Vampire Pathogens” – Geng Zou – Scientific Reports

Analysis of IS6110 insertion sites provide a glimpse into genome evolution of Mycobacterium tuberculosis – Tanmoy Roychowdhury – Scientific Reports

Protein synthesis by ribosomes with tethered subunits – Cédric Orelle – Nature

Long-term social dynamics drive loss of function in pathogenic bacteria – Sandra Breum Andersen – PNAS

New approaches to understanding the immune response to vaccination and infection –
David Furman – Vaccine

Microbes in the news

Would You Wear a Face Mask Made From Bacteria? – Jenna Rosenstein – Allure

Times-Picayune asks – Did a moldy building kill 4 New Orleans Professors – Jonathan Eisen – MicroBEnet

How the bugs in your gut keep you healthy – Keri Wiginton – Chicago Tribune

Scientists successfully breed symbiotic bacteria in mosquitoes to control dengue fever – ZeeNews India

Weight-Loss Surgery Changes Gut Bacteria – Rachael Rettner – Live Science

Volcanic bacteria take minimalist approach to survival – Otago University

Science, publishing, and career

Achieving Speaker Gender Equity at the American Society for Microbiology General Meeting – Arturo Casadevall – mBio

Bik’s Picks

This one was striking: Lightning strike as a possible cause of mortality of Australian sea lions, Neophoca cinerea – Peter D. Shaughnessy – Marine Mammal Science

Chilly at Work? Office Formula Was Devised for Men – Pam Belluck – New York Times
Belongs to: Energy consumption in buildings and female thermal demand – Boris Kingma & Wouter van Marken Lichtenbelt – Nature Climate Change

This Map Shows How New Yorkers View The Rest Of The United States. Finally, proof! – Carly Ledbetter – Huffington Post

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