Category Archives: Events and jobs

July 30, 2016

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Honey bee gut microbiome altered by pesticides, colobine primates, sulfur vents, bioaerosol, failed microbiome spore transplant trial.

Events

London Microbiome Workshop – September 7th 2016, Royal College of Physicians, London

Pregnancy and birth

Antibiotic perturbation of the preterm infant gut microbiome and resistome – Andrew J. Gasparrini – Gut Microbes

Multisite microbiome

Acquisition of a high diversity of bacteria during Hajj pilgrimage, including Acinetobacter baumannii with blaOXA-72, and Escherichia coli with blaNDM-5 carbapenemases – Thongpan Leangapichart – Antimicrobial Agents and Chemotherapy

Human gut microbiome

Limited prolonged effects of rifaximin treatment on irritable bowel syndrome-related differences in the fecal microbiome and metabolome – Natalia Zeber-Lubecka –
Gut Microbes

Altered gut microbiota in Rett syndrome – Francesco Strati – Microbiome

Animal experiments

Honey bee gut microbiome is altered by in-hive pesticide exposures – Madhavi Kakumanu – Frontiers in Microbiology

Animal microbiome

The antibiotic resistome of swine manure is significantly altered by association with the Musca domestica larvae gut microbiome – Hang Wang – The ISME Journal

Using the gut microbiota as a novel tool for examining colobine primate GI health – Katherine R. Amato – Global Ecology and Conservation

Plant, root, and soil microbiome

Bioprospecting metagenomics of a microbial community on cotton degradation: mining for new glycoside hydrolases – Guoxiu Zhang – Journal of Biotechnology

Dramatic Increases of Soil Microbial Functional Gene Diversity at the Treeline Ecotone of Changbai Mountain – Congcong Shen – Frontiers in Microbiology

Review: Plant litter decomposition: drivers insight to the ecological process – Gaurav Mishra – European Journal of Biological Research

Water and extremophile microbiome

Transcriptional control in marine copiotrophic and oligotrophic bacteria with streamlined genomes – Matthew T. Cottrell – Applied and Environmental Microbiology

Distribution and niche separation of planktonic microbial communities in the water columns from the surface to the hadal waters of the Japan Trench under the eutrophic ocean – Takuro Nunoura – Frontiers in Microbiology

Diversity and Composition of Bacterial Community in Soils and Lake Sediments from an Arctic Lake Area – Neng Fei Wang – Frontiers in Microbiology

Characterization of Chemosynthetic Microbial Mats Associated with Intertidal Hydrothermal Sulfur Vents in White Point, San Pedro, CA, USA – Priscilla J. Miranda – Frontiers in Microbiology

Hydrogen limitation and syntrophic growth among natural assemblages of thermophilic methanogens at deep-sea hydrothermal vents – Begüm D. Topçuoğlu – Frontiers in Microbiology

Review: Halophiles: Champions of Environmental Adaptations and Their Industrial Applications – Rachana Singh – Current Biological Engineering (WTF: $63.00)

Review: An overview of siderophores for iron acquisition in microorganisms living in the extreme – Luis O. De Serrano – BioMetals

Air microbiome

Review: Approach of molecular methods for the detection and monitoring of microbial communities in bioaerosols: A review – Keunje Yoo – Journal of Environmental Sciences

Oil reservoir microbiome

Species divergence vs functional convergence characterizes crude oil microbial community assembly – Yong Nie – Frontiers in Microbiology

Metagenomics

Editorial: From Genes to Species: Novel Insights from Metagenomics – Eamonn P. Culligan – Frontiers in Microbiology

Sequencing techniques

Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinIONTM sequencing – Minh Duc Cao – GigaScience

Microbes in the news

Poop Pill’s Surprise Failure Shows That the Microbiome is Still a Mystery – Ryan Cross – MIT Technology Review
Gut check: Seres Therapeutics shares plunge after microbiome drug fails in trial – CNBC
Seres Therapeutics Announces Interim Results from SER-109 Phase 2 ECOSPOR Study in Multiply Recurrent Clostridium Difficile Infection – Seres

I, microbe: Book Review of “I Contain Multitudes” by Ed Yong – Silvia Bulgheresi – Nature Microbiology
Hot off the press: Interview with Ed Yong – Andrew Jermy – Nature Microbiology

Teasing out the microbiome of the Kansas prairie. One teaspoonful of soil holds DNA of tens of thousands of microbial species – EurekAlert
Teasing out the microbiome of the Kansas prairie. One teaspoonful of soil holds DNA of tens of thousands of microbial species – Science Daily

Parasitic infection may have spoiled zebrafish experiments.Common contaminant may change shoaling behaviour, a proxy for stress and anxiety in behavioural studies. – Petra Szilagyi – Nature
What Does Your Poop Say About Your Evolution, and Other Ecological Connections to the Microbiome – Jens Hegg – PLOS Blogs

Powerful new bacteria discovered in Cookeville hot tub – Daily News Journal

Could a new CREAM fight off superbugs? Scientists develop lotion which stops bacteria getting into wounds – Madlen Davies – Daily Mail

There’s Nothing Green About Jill Stein’s Vaccine Stance – Emily Willingham – Forbes

Your soap and toothpaste could be messing with your microbiome – Alison Moodie – The Guardian

Anthrax sickens 13 in western Siberia, and a thawed-out reindeer corpse may be to blame – Ben Guarino – Washington Post

Bik’s not-microbiology Picks

Khloe Kardashian’s Vagina Oil Is a Bad Idea. Koko is telling her young female followers to moisturize their ‘vaginal lining’ with Vitamin E. Definitely do not do this– Samantha Allen – The Daily Beast

The Physicians Committee Releases Seven Dietary Guidelines for a Healthy Microbiota
The Key to Optimal Gut Health? Eat 50 to 55 Grams of Daily Fiber – PCRM

 

July 26, 2016

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The last common ancestor, pika gut microbiome, fire-fighting chemicals and soil microbiome, improved Illumina-compatible 18S rRNA primers.

Jobs

Verily (Google-associated) is looking for a Microbiome Research Associate

Pregnancy and birth

Probiotic properties of lactic acid bacteria isolated from human milk – N.A. Reis – Journal of Applied Microbiology

Human oral microbiome

High Throughput Quantitative Method for Assessing Coaggregation among Oral Bacterial Species – Elizabeth Levin-Sparenberg – Letters in Applied Microbiology

Periodontal infectogenomics: systematic review of associations between host genetic variants and subgingival microbial detection – Luigi Nibali – Journal of Clinical Periodontology

Human respiratory microbiome

Upper airway viruses and bacteria and clinical outcomes in children with cough – Kerry-Ann F. O’Grady – Pediatric Pulmonology

Human skin microbiome

Hypothesis: The skin microbiome: Is it affected by UV-induced immune suppression? – Vijaykumar Patra – Frontiers in Microbiology

Human gut microbiome

Gut microbiota-host interactions and juvenile idiopathic arthritis – Miika Arvonen – Pediatric Rheumatology

Designing fecal microbiota transplant trials that account for differences in donor stool efficacy – Scott W. Olesen – bioRxiv

Probiotics and the Microbiome in Celiac Disease: A Randomised Controlled Trial – Joanna Harnett – Evidence-Based Complementary and Alternative Medicine

Review: Links Between the Microbiome and Bone – Christopher J Hernandez – Journal of Bone and Mineral Research

Human vaginal microbiome

More Easily Cultivated Than Identified: Classical Isolation With Molecular Identification of Vaginal Bacteria – Sujatha Srinivasan – The Journal of Infectious Diseases

The Effects of Hormones and Vaginal Microflora on the Glycome of the Female Genital Tract: Cervical-Vaginal Fluid – Bernard J. Moncla – PLOS ONE

Review: New Systems for Studying Intercellular Interactions in Bacterial Vaginosis – Melissa M. Herbst-Kralovetz – The Journal of Infectious Diseases

Animal experiments

Lactulose differently modulates the composition of luminal and mucosal microbiota in C57BL/6J mice – Bingyong Mao – Journal of Agricultural and Food Chemistry

American Ginseng Attenuates Colitis Associated Colon Carcinogenesis in Mice: Impact on Gut Microbiota and Metabolomics – Chong-Zhi Wang – Cancer Prevention Research

Alterations of Gut Microbiota After Roux-en-Y Gastric Bypass and Sleeve Gastrectomy in Sprague-Dawley Rats – Yikai Shao – Obesity Surgery

Animal microbiome

Diet diversity is associated with beta but not alpha diversity of pika gut microbiota – Huan Li – Frontiers in Mcrobiology

The Microbial Signature Provides Insight into the Mechanistic Basis of Coral Success across Reef Habitats – Alejandra Hernandez-Agreda – mBio

Perspective: Hominid superorganisms – Julia A. Segre – Science

Plant, root, and soil microbiome

Long-term response of soil microbial communities to fire and fire-fighting chemicals –
A. Barreiro – Biology and Fertility of Soils

Desert Perennial Shrubs Shape the Microbial-Community Miscellany in Laimosphere and Phyllosphere Space – Varsik Martirosyan – Microbial Ecology

Lichen-associated Fungal Community in Hypogymnia hypotrypa (Parmeliaceae, Ascomycota) Affected by Geographic Distribution and Altitude – Yanyan Wang – Frontiers in Microbiology

Water management impacts rice methylmercury and the soil microbiome – Sarah E. Rothenberg – Science of the Total Environment

Ecological restoration of a copper polluted vineyard: Long-term impact of farmland abandonment on soil bio-chemical properties and microbial communities – Luciano Cavani – Journal of Environmental Management

Review: Soil C and N models that integrate microbial diversity – Benjamin P. Louis – Environmental Chemistry Letters

Water and extremophile microbiome

Genomes of Abundant and Widespread Viruses from the Deep Ocean – Carolina Megumi Mizuno – mBio

Microbial communities associated with Antarctic snow pack and their biogeochemical implications – Runa Antony – Microbiological Research

Novel chytrid lineages dominate fungal sequences in diverse marine and freshwater habitats – André M. Comeau – Scientific Reports

Metabolomics

Review: Gut Microbiota Profiling: Metabolomics Based Approach to Unravel Compounds Affecting Human Health – Pamela Vernocchi – Frontiers in Microbiology

Functional foods

Review: Fermented Foods: Are They Tasty Medicines for Helicobacter pylori Associated Peptic Ulcer and Gastric Cancer? – Mydhily R. B. Nair – Frontiers in Microbiology

Bioinformatics

A novel alignment-free method for detection of lateral genetic transfer based on TF-IDF – Yingnan Cong – Scientific Reports
Exploring lateral genetic transfer among microbial genomes using TF-IDF – Yingnan Cong – Scientific Reports

Techniques

Design and Evaluation of Illumina MiSeq Compatible Primers for the 18S rRNA Gene for Improved Characterization of Mixed Microalgal Communities – Ian M. Bradley – Applied and Environmental Microbiology

More microbiology

Are multi-omics enough? – Cristina Vilanova – Nature Microbiology

Review: Bacterial Communities: Interactions to Scale – Reed M. Stubbendieck – Frontiers in Microbiology

The physiology and habitat of the last universal common ancestor – Madeline C. Weiss – Nature Microbiology

Press: Scientists find Luca, a single-cell, bacterium-like organism that is the common ancestor of all life on Earth – Andrew Griffin – Independent
Behold LUCA, the Last Universal Common Ancestor of Life on Earth – Jason Daley – Smithsonian
Our last common ancestor inhaled hydrogen from underwater volcanoes – Robert F. Service – Science
Meet Luca, the Ancestor of All Living Things – Nicholas Wade – New York Times

Microbes in the news

What your gut microbiome may be telling you – Katrina Clarke – The Record

Healthy microbiome supports antibiotic-free production – World Poultry

Charlottesville Lab to Test Microbiology of Local Breweries – NBC29

Nanostructured bacterial film makes new mortar resistant to water uptake – NanoWerk

Bik’s non-microbiology Picks

The Dutchies are still holding the top positions! A century of trends in adult human height – NCD Risk Factor Collaboration (NCD-RisC) – eLIFE

July 22, 2016

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Fungi in human GI tract, antibiotics reduce Alzheimer’s lesions in mouse model, cospeciation of primates and gut microbes, dangerous bacteria after sewer spill.

Jobs

Research scientists to engineer microbiome engineering therapies – Eligo Bioscience

General microbiome

Perspective: Is triclosan harming your microbiome? – Alyson L. Yee – Science

Understanding How Microbiomes Influence the Systems they Inhabit: Insight from Ecosystem Ecology – Ed Hall – bioRxiv

Pregnancy and birth microbiome

Midtrimester Cervicovaginal Microbiota: Identification of Microbial Variations Associated with Puerperal Infection at Term – Akila Subramaniam – American Journal of Perinatology

Human mouth microbiome

Salivary and fecal microbiota and metabolome of celiac children under gluten-free diet – Maria De Angelis – International Journal of Food Microbiology

Human respiratory microbiome

Lung Microbiome in HIV Infection – Homer L. Twigg III – Translational Research

Human vaginal microbiome

Proceedings of the 2015 NIH/NIAID Bacterial Vaginosis Expert Consultation – The Journal of Infectious Diseases

Human gut microbiome

Age and gender affect the composition of fungal population of the human gastrointestinal tract – Francesco Strati – Frontiers in Microbiology

A reduction in the butyrate producing species Roseburia spp. and Faecalibacterium prausnitzii is associated with chronic kidney disease progression – Shuanghong Jiang – Antonie van Leeuwenhoek

Review: An update discussion on the current assessment of the safety of veterinary antimicrobial drug residues in food with regard to their impact on the human intestinal microbiome – Carl E. Cerniglia – Drug Testing and Analysis

Animal experiments

Antibiotic-induced perturbations in gut microbial diversity influences neuro-inflammation and amyloidosis in a murine model of Alzheimer’s disease – Myles R. Minter – Scientific Reports

Press: Antibiotics weaken Alzheimer’s disease progression through changes in the gut microbiome – EurekAlert
Could antibiotics reduce levels of Alzheimer’s-causing plaques? – Hannah Nichols – MedicalNewsToday

Pathogenic shifts in endogenous microbiota impede tissue regeneration via distinct activation of TAK1/MKK/p38 – Christopher P Arnold – eLIFE

Bacterial community characterization of water and intestine of the shrimp Litopenaeus stylirostris in a biofloc system – Emilie Cardona – BMC Microbiology

Impact of Helminth Infections and Nutritional Constraints on the Small Intestine Microbiota – Isabella M. Cattadori – PLOS ONE

Nutrient Deprivation Affects Salmonella Invasion and Its Interaction with the Gastrointestinal Microbiota – Sophie Yurist-Doutsch – PLOS ONE

Celecoxib alters the intestinal microbiota and metabolome in association with reducing polyp burden – David C. Montrose – Cancer Prevention Research

Review: Interactions between host genetics and gut microbiome in diabetes and metabolic syndrome – Siegfried Ussar – Molecular metabolism

Animal microbiome

Cospeciation of gut microbiota with hominids – Andrew H. Moeller – Science

Press: Primates, Gut Microbes Evolved Together. Symbiotic gut bacteria evolved and diverged along with ape and human lineages, researchers find – Anna Azvolinsky – The Scientist
Microbes in our guts have been with us for millions of years – Ann Gibbons – Science
Your gut bacteria predates appearance of humans, genetic study finds – Naomi Stewart – The Guardian

A snapshot of the microbiome of Amblyomma tuberculatum ticks infesting the gopher tortoise, an endangered species – Khemraj Budachetri – Ticks and Tick-borne Diseases

Do Vertebrate Gut Metagenomes Confer Rapid Ecological Adaptation? –
Antton Alberdi – Trends in Ecology & Evolution

Vaginal microbial communities from synchronized-heifers and cows with reproductive disorders – Candelaria Gonzalez Moreno – Journal of Applied Microbiology

Review: The woodrat gut microbiota as an experimental system for understanding microbial metabolism of dietary toxins – Kevin D. Kohl – Frontiers in Microbiology

Plant, root, and soil microbiome

Plant Identity Exerts Stronger Effect than Fertilization on Soil Arbuscular Mycorrhizal Fungi in a Sown Pasture – Yong Zheng – Microbial Ecology

Beneficial cyanobacteria and eubacteria synergistically enhance bioavailability of soil nutrients and yield of okra – Mallappa Manjunath – Heliyon

Naming Potentially Endangered Parasites: Foliicolous Mycobiota of Dimorphandra wilsonii, a Highly Threatened Brazilian Tree Species– Meiriele da Silva – PLOS ONE

Contribution of the seed microbiome to weed management – D Müller-Stöver – Weed Research

Mycorrhizal associations of trees have different indirect effects on organic matter decomposition – Melanie K. Taylor – Journal of Ecology

Water and extremophile microbiome

Vancomycin resistant enterococci and bacterial community structure following a sewage spill into an aquatic environment – Suzanne Young – Applied and Environmental Microbiology

Press: USF researchers find dangerous bacteria after sewer spills – EurekAlert
USF researchers say they found dangerous bacteria after sewage spill – Anne Lindberg – Saint Peters Blog

Hospital Effluents Are One of Several Sources of Metal, Antibiotic Resistance Genes, and Bacterial Markers Disseminated in Sub-Saharan Urban Rivers – Amandine Laffite – Frontiers in Microbiology

Microbial communities in sediments of Lagos Lagoon, Nigeria: Elucidation of community structure and potential impacts of contamination by municipal and industrial wastes – Chioma C. Obi – Frontiers in Microbiology

Cryoconite pans on Snowball Earth: supraglacial oases for Cryogenian eukaryotes? – P. F. Hoffman – Geobiology

Effects of multiple dimensions of bacterial diversity on functioning, stability and multifunctionality – Fabian Roger – Ecology

Heterotrophic bacteria in Antarctic lacustrine and glacial environments – Johanna Laybourn-Parry – Polar Biology

Microbial diversity and activity in seafloor brine lake sediments (Alaminos Canyon block 601, Gulf of Mexico) – M. Crespo-Medina – Geobiology

Bioinformatics and metagenomics

MetaG: a graph-based metagenomic gene analysis for big DNA data – Linkon Chowdhury – Network Modeling Analysis in Health Informatics and Bioinformatics

DFAST and DAGA: web-based integrated genome annotation tools and resources – Yasuhiro Tanizawa – Bioscience of Microbiota, Food and Health

Genome-centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion – Inka Vanwonterghem – Environmental Microbiology

Microbes in the news

Breast-feeding the Microbiome (Excerpt from his book) – Ed Yong – New Yorker

Janet Jansson Among Nine Authors of Nature Review Article – PNNL

Northern Arizona University professor Bruce Hungate named a fellow of the American Academy of Microbiology – Arizona Business Daily

UF scientists identify seal as source of new strain of bacteria that caused disease in hunter – Sarah Carey – University of Florida

Gut Bacteria May Drive Inflammation in Sepsis, ARDS – Salynn Boyles – MedPageToday

With Rob Knight as keynote speaker: Fermenting Knowledge at Fermentation Festivals (with Kombucha Recipe) – John D. Ivanko – Mother Earth News

Your death microbiome could catch your killer – Anna Williams – New Scientist

Microbes and money

Osel, Inc. Comments on New Study Showing Role of Vaginal Microbiome in Women’s Health – PharmiWeb

Q&A: Indigo’s CEO Reveals the Strategy Behind Its Plant Microbiome Technology – Olivia Vanni – BostInno

Eminent Harvard Geneticist Professor George Church Joins uBiome Advisory Board – Benzinga

Immuron to Cooperate with Leading Australian Universities on Autism Research – Nasdaq

July 20, 2016

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Jobs

Postdoc: Arbuscular mycorrhizal fungi and associated microbiota – Boyce Thompson Institute at Cornell campus (NY) (via ASM)

Pregnancy and birth

Why Don’t All Infants Have Bifidobacteria in Their Stool? – Gerald W. Tannock – Frontiers in Microbiology

Not liking this title: I did not see that coming! It is more than bugs in the bagina – Tamsin Board – Molecular Reproduction and Development

The Probiotics in Pregnancy Study (PiP Study): rationale and design of a double-blind randomised controlled trial to improve maternal health during pregnancy and prevent infant eczema and allergy – Christine Barthow – BMC Pregnancy and Childbirth

Human skin microbiome

Age-related differences in morphological characteristics of residual skin surface components collected from the surface of facial skin of healthy male volunteers – N. E. Chalyk – Skin Research and Technology

Human respiratory microbiome

Metagenome and Metatranscriptome Profiling of Moderate and Severe COPD Sputum in Taiwanese Han Males – Shih-Wei Lee – PLOS ONE

Human gut microbiome

Bacterial and Fungal Microbiota Changes Distinguish C. difficile Infection from Other Forms of Diarrhea: Results of a Prospective Inpatient Study – William Sangster – Frontiers in Microbiology

Effects of Arabinoxylan and Resistant Starch on Intestinal Microbiota and Short-Chain Fatty Acids in Subjects with Metabolic Syndrome: A Randomised Crossover Study – Stine Hald – PLOS ONE

Review: Intestinal microbiota and chronic constipation – Ying Zhao – Springer Plus

Animal experiments

Intestinal Microbiota Promotes Psoriasis-Like Skin Inflammation by Enhancing Th17 Response – Zuzana Zákostelská – PLOS ONE

Animal microbiome

Effects of 16S rDNA sampling on estimates of the number of endosymbiont lineages in sucking lice – Julie M. Allen – PeerJ

Plant, root, and soil microbiome

Patterns of natural fungal community assembly during initial decay of coniferous and broadleaf tree logs – Annemieke van der Wal – Ecosphere

Bioinformatics

CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community – Thomas Richard Connor – bioRxiv

More microbiology

Synchronized cycles of bacterial lysis for in vivo delivery – M. Omar Din – Nature

Press: Self-destructing bacteria are engineered to kill cancer cells – Sally Adee – New Scientist

Microbes in the news

Algae are melting away the Greenland ice sheet. ‘Black and Bloom’ project explores how microorganisms help to determine the pace of Arctic melting – Alexandra Witze – Nature

Science, publishing, and career

Featuring Bik’s Picks! Scientific literature: Information overload – Esther Landhuis – Nature

The unsung heroes of CRISPR. The soaring popularity of gene editing has made celebrities of the principal investigators who pioneered the field — but their graduate students and postdocs are often overlooked – Heidi Ledford – Nature

2016 Raymond and Beverly Sackler Prize in Convergence Research: QnAs with Stephen Quake – Prashant Nair – PNAS

Bik’s Picks

5 Questions: Randall Stafford advocates a plant-based diet – INterview with Randall Stafford – Stanford Medicine

July 16, 2016

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Bacterial translocation in Crohn’s disease, full length sequencing of mouse microbiome, drinking water and IBD, NanoSIMS, and molecular interactions.

Events
Meet your microbes: The surprising world inside you – New Scientist / UNSW Science – August 13, 2016, Kensington, Australia. Speakers: Elisa Hill and Gabrielle Belz.

Pregnancy and birth / vaginal microbiome

Identification of a novel human papillomavirus by metagenomic analysis of vaginal swab samples from pregnant women – Zhijian Liu – Virology Journal

Human skin microbiome

Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare – Kern Rei Chng – Nature Microbiology

Human oral microbiome

Bacterial diversity and community structure of supragingival plaques in adults with dental health or caries revealed by 16S pyrosequencing – Cuicui Xiao – Frontiers in Microbiology

Profile of bacteria colonizing the exposed bone of patients with anti-osteoclastic drug-related osteonecrosis of the jaws – Zaher Jabbour – Canadian Journal of Microbiology

Human respiratory microbiome

Review: The Lung Microbiome in HIV. Getting to the HAART of the Host–Microbe Interface – Leopoldo N. Segal – American Journal of Respiratory and Critical Care Medicine

Human gut microbiome

Environmental Factors Associated with Altered Gut Microbiota in Children with Eczema: A Systematic Review – Carmen W. H. Chan – International Journal of Molecular Sciences

Fecal Microbiota and Diet of Children with Chronic Constipation – Joyce Gomes de Moraes – International Journal of Pediatrics

The predominant site of bacterial translocation across the intestinal mucosal barrier occurs at the advancing disease margin in Crohn’s disease – Rodrick J. Chiodini – Microbiology

Review: May the Force Be With You: The Light and Dark Sides of the Microbiota–Gut–Brain Axis in Neuropsychiatry – Eoin Sherwin – CNS Drugs

Animal experiments

Gut Microbial Alterations Associated With Protection From Autoimmune Uveitis – Yukiko K. Nakamura – Investigative Ophthalmology & Visual Science

Animal microbiome

Isolation of an antimicrobial compound produced by bacteria associated with reef-building corals – PeerJ Preprint

Evidence of a bacterial core in the stored products pest Plodia interpunctella: The influence of different diets – Matteo Montagna – Environmental Microbiology

Analysis of the mouse gut microbiome using full-length 16S rRNA amplicon sequencing – 
Jongoh Shin – Scientific Reports

Comparative phylogenetic analysis of bacterial associates in Pyrrhocoroidea and evidence for ancient and persistent environmental symbiont reacquisition in Largidae (Hemiptera: Heteroptera) – Eric Robert Lucien Gordon – bioRxiv

Plant, root, and soil microbiome

Strong linkage between plant and soil fungal communities along a successional coastal dune system – Alice Roy-Bolduc – FEMS Microbiology Ecology

Biodiversity of green algae covering artificial hard substrate surfaces in a suburban environment: A case study using molecular approaches – Christine Hallmann – Journal of Phycology

Bacterial selection by mycospheres of Atlantic Rainforest mushrooms – Joshua Andrew Halsey – Antonie van Leeuwenhoek

Bacterial Community Structure at the Microscale in Two Different Soils – Rory Michelland – Microbial Ecology

Diversity of Cultivated Fungi Associated with Conventional and Transgenic Sugarcane and the Interaction between Endophytic Trichoderma virens and the Host Plant – Aline Silva Romão-Dumaresq – PLOS ONE

Water and extremophile microbiome

Genomic and transcriptomic resolution of organic matter utilization among deep-sea bacteria in Guaymas Basin hydrothermal plumes – Meng Li – Frontiers in Microbiology

Microbiome profiling of drinking water in relation to incidence of inflammatory bowel disease – Jessica D. Forbes – Canadian Journal of Microbiology

Viruses and phages

The feral swine virome is dominated by single stranded DNA viruses and contains a novel orthopneumovirus which circulates both in feral and domestic swine – Ben M. Hause – Journal of General Virology

Techniques

Review: Tracking microbial interactions with NanoSIMS – Niculina Musat – Current Opinion in Biotechnology

Other microbiology

Review: Decoding molecular interactions in microbial communities – Nicole A. Abreu – FEMS Microbiology Reviews

Functional Comparison of Bacteria from the Human Gut and Closely Related Non-Gut Bacteria Reveals the Importance of Conjugation and a Paucity of Motility and Chemotaxis Functions in the Gut Environment – Dragana Dobrijevic – PLOS ONE

Verification of an automated, digital dispensing platform for at-will broth microdilution antimicrobial susceptibility testing – Kenneth P. Smith – Journal of Clinical Microbiology

Press: Simple method tests hard-to-treat bacteria’s susceptibility to different antibiotics – Science Codex

Nice or nasty: Protein translocation between bacteria and the different forms of response – Daniel Unterweger – PNAS

Editorial: Resource competition: When communities collide – Jason Merritt – eLIFE

Community-level cohesion without cooperation – Mikhail Tikhonov – eLIFE

Microbes in the news

Overselling the Microbiome Award for @nytimes on thumb sucking, nail biting protecting from allergy – Jonathan Eisen – The Tree of Life

Study to explore microbes attached to floating plastic – Holly Ganz – MicroBE.net

Gut reaction: How bacteria in the belly may affect the heart – Harvard Health

You scratch my back… the beneficial (and not so beneficial) relationships between organisms – Andrew Taylor-Robinson – The Conversation

Viruses Have Guided the Path of Human Evolution – Nathaniel Scharping – Discover Magazine

Antarctica: A Center for Climate Change and Microbiology Research – Latin America Herald Tribune

Science, publishing, and career

Where are the female science professors? A personal perspective – Shina Caroline Lynn Kamerlin – F1000Research

Bik’s Picks

Carl Zimmer’s Game Of Genomes: Episode 1 to 5 – STATnews

July 15, 2016

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Symbionts and reproductive oddities, microbiota in a mouse stroke model, the plant holobiont, CRISPR spacer extraction from metagenomes.

General microbiome

Bacterial cell biology outside the streetlight: reproductive oddities displayed by bacteria associated with multicellular eukaryotes – Silvia Bulgheresi – Environmental Microbiology

New book: The Human Microbiota and Chronic Disease: Dysbiosis as a Cause of Human Pathology – Brian Henderson, Luigi Nibali – Wiley

Events

Webinar: The Microbiome and the Environment – July 26 – ACS Publications

Microbiomes of the Built Environment Meeting 2 Webcast Videos and Presentations Now Available! – Jonathan Eisen

Human gut microbiome

Severe Gut Microbiota Dysbiosis Is Associated With Poor Growth in Patients With Short Bowel Syndrome – Hannah G. Piper – Journal of Parenteral & Enteral Nutrition

Review: Corralling Colonic Flagellated Microbiota – Ruth E. Ley – The New England Journal of Medicine

Editorial: Microbiome and mental health in the modern environment – Emily Deans -Journal of Physiological Anthropology

Animal experiments

Microbiota Dysbiosis Controls the Neuroinflammatory Response after Stroke – Vikramjeet Singh – The Journal of Neuroscience

Press: Post-stroke shifts in gut bacteria could cause additional brain injury – Rachel Ehrenberg – Science News
Stroke Alters Gut Microbiome, Impacting Recovery. A bidirectional link between the brain and the gut can improve or worsen brain injury in mice, researchers report – Tanya Lewis – The Scientist

Animal microbiome

Nest Bacterial Environment Affects Microbiome of Hoopoe Eggshells, but Not That of the Uropygial Secretion – Ángela Martínez-García – PLOS ONE

Highly Variable Bacterial Communities Associated with the Octocoral Antillogorgia elisabethae – Veronica Robertson – Microorganisms

Review: Alice in microbes’ land: adaptations and counter-adaptations of vector-borne parasitic protozoa and their hosts – Guy Caljon – FEMS Microbiology Reviews

Plant, root, and soil microbiome

Fires of differing intensities rapidly select distinct soil fungal communities in a Northwest US ponderosa pine forest ecosystem – C. Reazin – Forest Ecology and Management

The enzymatic and physiological response of the microbial community in semiarid soil to carbon compounds from plants – I. F. Torres – European Journal of Soil Science

DGGE: Rhizobacterial Community Structures Associated with Native Plants Grown in Chilean Extreme Environments – Milko A. Jorquera – Microbial Ecology

Review: Plant–microbe partnerships in 2020: The plant holobiont and its interactions determine plant performance. – Birgit Mitter – Microbial Biotechnology

Water and extremophile microbiome

Syntrophic associations from hypersaline soda lakes converting organic acids and alcohols to methane at extremely haloalkaline conditions – Dimitry Y. Sorokin – Environmental Microbiology

Microbialite response to an anthropogenic salinity gradient in Great Salt Lake, Utah – M. R. Lindsay – Geobiology

Chemodenitrification in the cryoecosystem of Lake Vida, Victoria Valley, Antarctica – N. E. Ostrom – GeoBiology

Speciation and ecological success in dimly lit waters: horizontal gene transfer in a green sulfur bacteria bloom unveiled by metagenomic assembly – Tomàs Llorens–Marès – ISME Journal

Metagenomics and bioinformatics

MetaCRAST: Reference-guided extraction of CRISPR spacers from unassembled metagenomes – Abraham G Moller – PeerJ Preprints

Microbes in the news

Yale engineers think our future homes should be designed with microbes in mind – Dyllan Furness – Digital Trends

How to get Funding for your Human Microbiome Startup – Global Engage

 

July 13, 2016

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So many great new papers that it’s hard to choose! Liver quickly clears bacteria from blood, microbiology of death, mobile genes in human microbiomes from Fiji and the USA, Splenda makes fly more hungry, feather degrading bacilli, underwater microscopy, and what is being transferred in a stool transplant.

Events and jobs

Annual Meeting of the Microbial Ecology Division – November 4, 2016, Nijmegen, The Netherlands

Senior/Tenure Track scientists for the Department of Marine Microbiology and Biochemistry – NIOZ The Netherlands

Microbiome of Death

“Biology of Death” Special Issue – Current Biology
Microbiology of death – Jessica L. Metcalf
Also read (non-microbiology but sadly beautiful): Death and the octopus – Florian Maderspacher

Also appropriate in this category is this video protocol: Removal of Exogenous Materials from the Outer Portion of Frozen Cores to Investigate the Ancient Biological Communities Harbored Inside – Robyn A. Barbato – JOVE

Pregnancy and birth

Early Life Antibiotic Exposure and Weight Development in Children – Catherine A. Mbakwa – The Journal of Pediatrics

Preview: Tummy Time: The Infant Microbiota–IgA Connection – Tyler A. Rice – Cell Host & Microbe

Review: The microbiome in early life: implications for health outcomes – Sabrina Tamburini – Nature Medicine

Special issue with abstracts from the 3rd International Congress on Pre- and Probiotics
in Journal of Pediatric Gastroenterology and Nutrition

A Prebiotic Formula Improves the Gastrointestinal Bacterial Flora in Toddlers – Ya-Ling Chen – Gastroenterology Research and Practice

Human blood “microbiome”

Editorial: Fast-Track Clearance of Bacteria from the Liver – Cristina Llorente – Cell Host & Microbe
Dual-Track Clearance of Circulating Bacteria Balances Rapid Restoration of Blood Sterility with Induction of Adaptive Immunity – Steven P. Broadley – Cell Host & Microbe
CRIg Functions as a Macrophage Pattern Recognition Receptor to Directly Bind and Capture Blood-Borne Gram-Positive Bacteria – Zhutian Zeng – Cell Host & Microbe

Human skin microbiome

What if scalp flora was involved in sensitive scalp onset? – A. Guichard – International Journal of Cosmetic Science

Human gut microbiome

Mobile genes in the human microbiome are structured from global to individual scales – I. L. Brito – Nature

Press: Microbiome ‘social network’ revealed by gene swaps
Movement of genes across and between microorganism species could influence humans’ susceptibility to disease – Peter Andrey Smith – Nature News

Fecal Transplants: What Is Being Transferred? – Diana P. Bojanova – PLOS Biology

Press: Poo transplants transfer much more than bacteria. Viruses, fungi – even sloughed colon cells – may affect how well a faecal transplant works – Belinda Smith – Cosmos

Animal experiments

Sucralose Promotes Food Intake through NPY and a Neuronal Fasting Response – Qiao-Ping Wang – Cell Metabolism

Press: Artificial sweeteners trick flies into thinking they’re starving – Lindzi Wessel – STAT News

Investigation into Host Selection of the Cecal Acetogen Population in Rabbits after Weaning – Chunlei Yang – PLOS ONE

Animal microbiome

Genome evolution in the obligate but environmentally active luminous symbionts of flashlight fish – Tory A. Hendry – Genome Biology and Evolution

Deep divergence and rapid evolutionary rates in gut-associated Acetobacteraceae of ants – Bryan P. Brown – BMC Microbiology

Feather-degrading bacilli in the plumage of wild birds: Prevalence and relation to feather wear – Cody M. Kent – The Auk Ornithological Advances

Press: Feather-munching bacteria damage wild bird plumage – EurekAlert

Multi-scale ecological filters shape the crayfish microbiome – James Skelton – PeerJ Preprint

Plant, root, and soil microbiome

Rapid response of arbuscular mycorrhizal fungal communities to short-term fertilization in an alpine grassland on the Qinghai-Tibet Plateau – Xingjia Xiang – PeerJ

High-throughput sequencing of 16S rRNA Gene Reveals Substantial Bacterial Diversity on the Municipal Dumpsite – Kilaza Samson Mwaikono – BMC Microbiology

Temporal and Spatial Variation of Soil Bacteria Richness, Composition, and Function in a Neotropical Rainforest – Stephanie N Kivlin – PLOS ONE

Land use intensification in the humid tropics increased both alpha and beta diversity of soil bacteria – Teotonio Soares de Carvalho = Ecology

The role of arbuscular mycorrhizal fungi in plant uptake, fractions, and speciation of antimony – Yuan Wei – Applied Soil Ecology

Review: Bidirectional Interaction between Phyllospheric Microbiotas and Plant Volatile Emissions – Gerard Farré-Armengol – Trends in Plant Science

Water microbiome

Underwater microscopy for in situ studies of benthic ecosystems – Andrew D. Mullen – Nature Communications

Press: Underwater microscope provides new views of ocean-floor sea creatures in their natural setting – Jules Jaffe – The Conversation

Identifying the key taxonomic categories that characterize microbial community diversity using full-scale classification: a case study of microbial community in the sediments of Hangzhou Bay – Tianjiao Dai – FEMS Microbiology Ecology

Novel acsF gene primers revealed a diverse phototrophic bacterial population including Gemmatimonadetes in the Lake Taihu – Yili Huang – Applied and Environmental Microbiology

Allelopathic interactions involving benthic phototrophic microorganisms – Joey L. Allen – Environmental Microbiology Reports

Metagenomics and bioinformatics

Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond – Satoshi Hiraoka – Microbes and Environments

Metabolites

Research Highlight: Keeping microbial metabolites at bay – Andrea Du Toit – Nature Reviews Microbiology

Techniques

New Primers for Discovering Fungal Diversity Using Nuclear Large Ribosomal DNA – Asma Asemaninejad – PLOS ONE

Not sure what is new here, but: Multiplex amplicon sequencing for microbe identification in community-based culture collections – Jaderson Silveira Leite Armanhi – Scientific Reports

Applying CRISPR–Cas9 tools to identify and characterize transcriptional enhancers – Rui Lopes – Nature Reviews Molecular Cell Biology

Phages and viruses

Perspective: Piggyback-the-Winner in host-associated microbial communities – Cynthia B Silveira – NPJ Biofilms

Microbes in the news

Fill Your House With Microbes and Live With an Animal, Say Yale Researchers – Drake Baer

Unfortunately, no update from his DIY stool transplant with Hadza feces: The Human Microbiome as Road Kill in the Age of the Anthropocene – Jeff Leach – Human Food Project

Studies find that manipulating gut microbes may reverse the negative effect of a high fat – EurekAlert

Archaea: Breakthrough in Reconstruction of Warm Climate Phases – Marine Technology News

Alarming Antibiotic-Resistant Superbug Discovered In NYer’s Bacteria Sample – Miranda Katz – Gothamist

How bacteria can help prospectors find oil – Fram Dinshaw – The Chronicle Herald

With link to video: Tiny ‘racetracks’ show how bacteria get organized – EurekAlert

Microbes and Money

uBiome and University of Oxford Investigate the Relationship Between the Human Microbiome and Personality – PR web

Commercializing the Microbiome: No Guts, No Glory – Michael Darcy – DRG

Evelo and Epiva Merge to Become a Leading Immuno-Microbiome Platform Company – BioSpace

Merck to open new Cambridge facility for microbiome research this year – Boston Business Journal

Science, publishing, and career

How Australia fails mid-career scientists – Catherine Osborne – ABC Australia

How President Obama could really lead on open access – Michael Eisen – it is NOT junk

Where are all the award winning women scientists? – Tenure, she wrote

Bik’s Picks

Organ delivery by 1,000 drones – Michael Francisco – Nature Biotechnology

 

July 11, 2016

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Poor oral health associated with decreased chance of developing IBD, thumb-sucking associated with decreased chance of developing atopic sensitization, and the core actinobacteriome of rice plants.

Jobs

Senior Scientist intestinal health – Wageningen UR Livestock Research, The Netherlands

Human oral microbiome (sort of)

Inverse Association Between Poor Oral Health and Inflammatory Bowel Diseases – Weiyao Yin – Clinical Gastroenterology and Hepatology

Thumb-Sucking, Nail-Biting, and Atopic Sensitization, Asthma, and Hay Fever – Stephanie J. Lynch – Pediatrics

Human respiratory microbiome

Review: Airway Microbiota and the Implications of Dysbiosis in Asthma – Juliana Durack – Current Allergy and Asthma Reports

Review: Understanding the role of the microbiome in chronic obstructive pulmonary disease: principles, challenges, and future directions – Yvonne J. Huang – Translational Research

Human gut microbiome

Review: Communicating systems in the body: how microbiota and microglia cooperate – Daniel Erny – Immunology

Review: Microbiota at the crossroads of autoimmunity – Oded Shamriz – Autoimmunity Reviews

Animal and bioreactor experiments

Dietary silver nanoparticles can disturb the gut microbiota in mice – Sybille van den Brule – Particle and Fibre Toxicology

Modelling Longitudinal Metabonomics and Microbiota Interactions in C57BL/6 mice fed a high fat diet – Ivan Montoliu – Analytical Chemistry

High-fiber and high-protein diets shape different gut microbial communities, which ecologically behave similarly under stress conditions, as shown in a gastrointestinal simulator – Massimo Marzorati – Molecular Nutrition & Food Research

Plant, root, and soil microbiome

Plant and insect microbial symbionts alter the outcome of plant-herbivore-parasitoid interactions: implications for invaded, agricultural and natural systems – Alison E Bennett – Journal of Ecology

Influences of plant type on bacterial and archaeal communities in constructed wetland treating polluted river water – Yan Long – Environmental Science and Pollution Research

Illumina-based analysis of core actinobacteriome in roots, stems, and grains of rice – Wenfeng Wang – Microbiological Research

Water microbiome

Comparative metagenome of a stream impacted by the urbanization phenomenon – Julliane Dutra Medeiros – Brazilian Journal of Microbiology

Drinking water systems

A modified weighted mixture model for the interpretation of spatial and temporal changes in the microbial communities in drinking water reservoirs using compositional phospholipid fatty acid data – I. Stanimirova – Talanta

Bioinformatics

An automated system for evaluation of the potential functionome: MAPLE version 2.1.0 – Hideto Takami – DNA Research

Microbes in the news

You Can Contract Fatal Bacteria Just By Sniffing – Angela Chen – Gizmodo
Deadly bug strikes in a day – New pathway discovered for bacteria – EurekAlert

Tiny bacteria-powered ‘windfarm’ for your phone? – Science Daily
Scientists show how bacteria can power micro-machines – Indiana Express

Antibiotic resistance discovered in the guts of ancient mummies – Andy Coghlan – New Scientist

Antibiotic-resistant bacteria have been around for centuries – Karen Graham – Digital Journal

Seres initiates first clinical trial of synthetic microbiome therapy for C. difficile – Healio

July 6, 2016

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Two microbiology jobs, a Nature special on intestinal gut microbiota, coral dark spot syndrome, extremophiles from Yellowstone springs, and sugar-coating the envelope.

Jobs

Assembly Biosciences in San Francisco is looking for a Bioinformatics Scientist for supporting their microbiome programs. Contact Jared Kaleck at Klein Hersh for more info.

Nature Microbiology is looking for an Associate Editor, based in New York or London.

Events

4th Annual International Raising Clostridium difficile Awareness Conference and Health EXPO – September 20, 2016 – Atlanta

Human skin microbiome

Normal Skin Microbiota is Altered in Pre-clinical Hidradenitis Suppurativa – Hans Christian Ring – Acta Dermato-venereologica

The cutaneous microbiome and aspects of skin antimicrobial defense system resist acute treatment with topical skin cleansers – Aimee M. Two – Journal of Investigative Dermatology

Review: Bacterial and Viral Infections in Atopic Dermatitis: a Comprehensive Review – Peck Y. Ong – Clinical Reviews in Allergy & Immunology

Human urinary tract microbiome

Review: The urinary microbiota: a paradigm shift for bladder disorders? – Linda Brubaker – Current Opinion in Obstetrics & Gynecology

Human vaginal microbiome

Analysis of the Vaginal Microbiome by Next-Generation Sequencing and Evaluation of its Performance as a Clinical Diagnostic Tool in Vaginitis – Ki Ho Hong – Annals of Laboratory Medicine

Human gut microbiome

Fecal microbiota transplantation for recurrent Clostridium difficile infection in hematopoietic stem cell transplant recipients – B.J. Webb – Transplant Infectious Disease

The Esophageal Microbiome in Eosinophilic Esophagitis – Evan S. Dellon – Gastroenterology

Trimethylamine-N-oxide (TMAO) response to animal source foods varies among healthy young men and is influenced by their gut microbiota composition: a randomized controlled trial – Clara E. Cho – Molecular Nutrition & Food Research

Review: The Role of Gut Microflora and the Cholinergic Anti-inflammatory Neuroendocrine System in Diabetes Mellitus – Parth J. Parekh – Frontiers in Endocrinology

Review: Bifidobacteria and Their Role as Members of the Human Gut Microbiota – Amy O’Callaghan – Frontiers in Microbiology

Review: Navigating the Microbial Basis of Inflammatory Bowel Diseases: Seeing the Light at the End of the Tunnel – Laura E. Raffals – Gut and Liver

Animal and in vitro experiments

Composition of Gut Microbiota Influences Resistance of Newly Hatched Chickens to Salmonella Enteritidis Infection – Karolina Varmuzova – Frontiers in Microbiology

Pterostilbene-induced changes in gut microbiota composition in relation to obesity – Usune Etxeberria – Molecular Nutrition & Food Research

An Integrated Multi-Omics Approach Reveals the Effects of Supplementing Grass or Grass Hay with Vitamin E on the Rumen Microbiome and Its Function – Alejandro Belanche – Frontiers in Microbiology

Enterocyte-Associated Microbiome of the Hadza Hunter-Gatherers – Silvia Turroni – Frontiers in Microbiology

Animal microbiome

Composition and Functional Characterization of Microbiome Associated with Mucus of the Coral Fungia echinata Collected from Andaman Sea – Jhasketan Badhai – Frontiers in Microbiology

Epimicrobiota Associated with the Decay and Recovery of Orbicella Corals Exhibiting Dark Spot Syndrome – Julie L. Meyer – Frontiers in Microbiology

Plant, root, and soil microbiome

Temperature mediates continental-scale diversity of microbes in forest soils – Jizhong Zhou – Nature Communications

Molecular biosignatures reveal common benthic microbial sources of organic matter in ooids and grapestones from Pigeon Cay, The Bahamas – S. S. O’Reilly – Geobiology

Availability and function of arbuscular mycorrhizal and ectomycorrhizal fungi during revegetation of dewatered reservoirs left after dam removal – Andrew M. Cortese – Restoration Ecology

A metagenomic-based survey of microbial (de)halogenation potential in a German forest soil – Pascal Weigold – Scientific Reports

Limited recovery of soil microbial activity after transient exposure to gasoline vapors – Jakub J. Modrzyński – Environmental Pollution

Petroleum hydrocarbon contamination, plant identity and arbuscular mycorrhizal fungal community determine assemblages of the AMF spore-associated microbes – Bachir Iffis – Environmental Microbiology

Water and extremophile microbiome

Linking internal and external bacterial community control gives mechanistic framework for pelagic virus-to-bacteria ratios – Selina Våge – Environmental Microbiology

The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. I. Microbial Diversity Based on 16S rRNA Gene Amplicons and Metagenomic Sequencing – Vera Thiel – Frontiers in Microbiology

Genomics-informed isolation and characterization of a symbiotic Nanoarchaeota system from a terrestrial geothermal environment – Louie Wurch – Nature Communications

Press: Scientists isolate, culture elusive Yellowstone microbe – Science Daily

Fungal and Prokaryotic Activities in the Marine Subsurface Biosphere at Peru Margin and Canterbury Basin Inferred from RNA-Based Analyses and Microscopy – Maria G. Pachiadaki – Frontiers in Microbiology

Unexpected biodiversity of ciliates in marine samples from below the photic zone – Jean-David Grattepanche – Molecular Ecology

Spatial and temporal variability of aerobic anoxygenic photoheterotrophic bacteria along the east coast of Australia – Jaime Bibiloni-Isaksson – Environmental Microbiology

Bioreactor microbiology

Perspectives for microbial community composition in anaerobic digestion: From abundance and activity to connectivity – Jo De Vrieze – Environmental Microbiology

Other microbiology

Opinion: Sugar Coating the Envelope: Glycoconjugates for Microbe–Host Crosstalk – Hanne L.P. Tytgat – Trends in Microbiology

A Combinatorial Algorithm for Microbial Consortia Synthetic Design – Alice Julien-Laferrière – Scientific Reports

Bioinformatics and metagenomics – viruses and phages

Freshwater Metaviromics and Bacteriophages: A Current Assessment of the State of the Art in Relation to Bioinformatic Challenges – Katherine Bruder – Evolutionary Bioinformatics

Alignment-free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transfer – Guillaume Bernard – Scientific Reports

Microbes in the news

Dear Science: How many germs are actually on a toilet seat — and should I care? – Rachel Feltman and Sarah Kaplan – Washington Post

‘Super bacteria’ discovered in Rio’s waters as Olympics near – Flora Charner – CNN
‘Super Bacteria’ Detected at Rio de Janeiro’s Beaches – Rosalie Chen – Time

Scientists Discover A Sponge Extract In Antarctica, Can Kill ‘SuperBug’ MRSA Bacterium – Science World Report

Training in microbiology, molecular biology concludes – The Tribune

Science, publishing, and career

The past, present and future of the PhD thesis – Nature

Let’s make peer review scientific – Drummond Rennie – Nature

Bik’s Picks

Warning: contains autoplay video with sound and light-flashes that might not be suitable for epileptics. Sneak peek: The ‘Game of Genomes’ is coming – sequencing Carl Zimmer’s genome – STAT News

June 28, 2016

Posted on by

A fundraiser to study the turtle microbiome, multiple sclerosis, generalists inside specialist, and visualizing translational activity.

Events

IndieGoGo campaign: TurtleTracts: Study Microbes to Save Sea Turtles – Aubrey Tauer

Also see this blog post: Sneak Peak at our Sea Turtle Microbiome Initiative – Aubrey Tauer

Pregnancy and birth

Gut bacteria and late-onset neonatal bloodstream infections in preterm infants – Phillip I. Tarr – Seminars in Fetal and Neonatal Medicine

Human respiratory microbiome

Commentary: Mode of delivery to the brave new (microbial) world: a defining moment for the respiratory microbiome? – Georgios D. Kitsios – EBioMedicine

Human gut microbiome

Multiple sclerosis patients have a distinct gut microbiota compared to healthy controls – Jun Chen – Scientific Reports

Press: Link between gut bacteria, MS discovered. MS patients show lower levels of good bacteria – Science Daily

Review: Microbiota as Therapeutic Targets – Xavier R.J. – Digestive Diseases

Animal microbiome
The Generalist Inside the Specialist: Gut Bacterial Communities of Two Insect Species Feeding on Toxic Plants Are Dominated by Enterococcus sp. – Cristina Vilanova – Frontiers in Microbiology

Review: The gut microbiome as a virtual endocrine organ with implications for farm and domestic animal endocrinology – T.F. O’Callaghan – Domestic Animal Endocrinology

Plant, root, and soil microbiome
Systemic enrichment of antifungal traits in the rhizosphere microbiome after pathogen attack – Jan-Hendrik Dudenhöffer – Journal of Ecology

A multi-biological assay approach to assess microbial diversity in arsenic (As) contaminated soils – S.R. Stazi – Geomicrobiology Journal

Effects of two fungicide formulations on microbial and macroinvertebrate leaf decomposition under laboratory conditions – Adria A. Elskus – Environmental Toxicology and Chemistry

Book: Plant, Soil and Microbes – Editors: Khalid Rehman Hakeem, Mohd Sayeed Akhtar – Springer

Water and extremophile microbiome

Metagenomics-Guided Mining of Commercially Useful Biocatalysts from Marine Microorganisms – A.R. Uria – Advances in Food and Nutrition Research

Lessons learned from thirty years of geomicrobiological studies of Río Tinto – Ricardo Amils – Research in Microbiology

Metabolic diversity and adaptive mechanisms of iron- and/or sulfur-oxidizing autotrophic acidophiles in extremely acidic environments – Xian Zhang – Environmental Microbiology Reports

Reconstructing metabolic pathways of hydrocarbon-degrading bacteria from the Deepwater Horizon oil spill – Nina Dombrowski – Nature Microbiology

News and views: Marine microbiology: Community clean up – Rachel Mackelprang – Nature Microbiology

Assessing viral taxonomic composition in benthic marine ecosystems: reliability and efficiency of different bioinformatic tools for viral metagenomic analyses – M. Tangherlini – Scientific Reports

Marine phage genomics: the tip of the iceberg – Blanca Perez Sepulveda – Microbiology Letters

Metabolic networks and proteomics

MetaPro-IQ: a universal metaproteomic approach to studying human and mouse gut microbiota – Xu Zhang – Microbiome

The use of propidium monoazide in conjunction with qPCR and Illumina sequencing to identify and quantify live yeasts and bacteria – Mansak Tantikachornkiata – International Journal of Food Microbiology

Protocol: Constructing and Analyzing Metabolic Flux Models of Microbial Communities – José P. Faria – Springer Protocols

Viruses and phages

Opinion: The Janus-Face of Bacteriophages across Human Body Habitats – Adam Wahida – PLOS Pathogens

Review: Research on the human virome: where are we and what is next – Shimian Zou – Microbiome

Microbial ecology and techniques

Visualizing in situ translational activity for identifying and sorting slow-growing archaeal−bacterial consortia – Roland Hatzenpichler – PNAS

Press: See and sort: Developing novel techniques to visualize uncultured microbial cell activity – Science Daily

High functional diversity stimulates diversification in experimental microbial communities – Alexandre Jousset – Science Advances

Measuring the biodiversity of microbial communities by flow cytometry – Ruben Props – Methods in Ecology and Evolution

Highlight: A timely reminder of technical limitations – James I. Prosser – Microbial Biotechnology

Species-sorting and mass-transfer paradigms control managed natural metacommunities – Susanne Günther – Environmental Microbiology

Microbes in the news

Slimy clumps of bacteria kill thousands. Scientists are fighting back – Usha Lee McFarling – STAT News

Why everyone’s suddenly talking about gut bacteria – Laura Entis – Fortune

Scientists find link between makeup of individual’s microbiome and head and neck cancer – News Medical