Category Archives: Phages and viruses

August 3, 2016

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Saliva and Polycystic Ovary Syndrome, early colonization of honey bees, hospital air metagenomes, analysis tool for viral metagenomes.

Human oral microbiome

The Salivary Microbiome in Polycystic Ovary Syndrome (PCOS) and its Association with Disease-related Parameters: A Pilot Study – Lisa Lindheim – Frontiers in Microbiology

A novel compound to maintain a healthy oral plaque ecology in vitro – Marleen M. Janus – Journal of Oral Microbiology

Human vaginal microbiome

Does the vaginal microbiota plays a role in the development of cervical cancer? – Maria Kyrgiou – Translational Research

Human skin microbiome

Diverse human skin fungal communities in children converge in adulthood – Jay-Hyun Jo – Journal of Investigative Dermatology

Human gut microbiome

A pleiotropic missense variant in SLC39A8 is associated with Crohn’s disease and human gut microbiome composition – Dalin Li – Gastroenterology

Press: Genetic Variant Newly Linked to Crohn’s Disease Also Associated with Altered Gut Microbiome Composition – PR Web

Gut microbiota associated with HIV infection is significantly enriched in bacteria tolerant to oxygen – Grégory Dubourg – BMJ Open Gastroenterology

Review: A clinical update on the significance of the gut microbiota in systemic autoimmunity – Elizabeth C. Rosser – Journal of Autoimmunity

Review: The human gut microbiome of Latin America populations: a landscape to be discovered – Fabien Magne – Current Opinion in Infectious Diseases

Animal microbiome

Early gut colonizers shape parasite susceptibility and microbiota composition in honey bee workers – Ryan S. Schwarz – PNAS

Another pika paper by the same authors (who killed all pika to obtain gut contents – booh): Pika gut may select for rare but diverse environmental bacteria – Huan Li – Frontiers in Microbiology

Review: Bacterial symbiosis in the fish gut and its role in health and metabolism – Goutam Banerjee – Symbiosis

Plant, root, and soil microbiome

Diverse gene functions in a soil mobilome – Wenting Luo – Soil Biology and Biochemistry

Genetic Diversity and Association Characters of Bacteria Isolated from Arbuscular Mycorrhizal Fungal Spore Walls – Gopal Selvakumar – PLOS ONE

Spatio-temporal variation of core and satellite arbuscular mycorrhizal fungus communities in Miscanthus giganteus – Christopher J. Barnes – Frontiers in Microbiology

DGGE: Impacts of Grazing Intensity and Plant Community Composition on Soil Bacterial Community Diversity in a Steppe Grassland – Tong-bao Qu – PLOS ONE

Book chapter: Calling in the Dark: The Role of Volatiles for Communication in the Rhizosphere – Nicole M. van Dam – Deciphering Chemical Language of Plant Communication

Book Chapter: Truffle-Associated Bacteria: Extrapolation from Diversity to Function – Elena Barbieri – True Truffle (Tuber spp.) in the World

Water and extremophile microbiome

Yeasts from sub-Antarctic region: biodiversity, enzymatic activities and their potential as oleaginous microorganisms – A. Martinez – Extremophiles

First report of microorganisms of Caucasus glaciers (Georgia) – Nicoletta Makowska – Biologia

Species sorting along a subsidy gradient alters bacterial community stability – Mario E. Muscarella – Ecology

Air microbiome / Built environment microbiome

Longitudinal Metagenomic Analysis of Hospital Air Identifies Clinically Relevant Microbes – Paula King – PLOS ONE

Bioinformatics

MetLab: An In Silico Experimental Design, Simulation and Analysis Tool for Viral Metagenomics Studies – Martin Norling – PLOS ONE

MetaCoMET: a web platform for discovery and visualization of the core microbiome – Yi Wang – Bioinformatics

More microbiology

Tempo and mode of genome evolution in a 50,000-generation experiment – Olivier Tenaillon – Nature

Press: Still changing after all these years. Long-term evolution experiment looks at genetic changes in bacteria: Richard Lenski – Science Daily

Review: Survival of the Fittest: How Bacterial Pathogens Utilize Bile To Enhance Infection – Jeticia R. Sistrunk – Clinical Microbiology Reviews

Book: Infective Endocarditis. Epidemiology, Diagnosis, Imaging, Therapy, and Prevention – Editors: Gilbert Habib – Springer

Élie Metchnikoff (1845–1916): celebrating 100 years of cellular immunology and beyond – David M. Underhill – Nature Reviews Immunology

Microbes in the news

Understanding diverse microbial communities: An interview with A. Murat Eren (Meren) – Kelle Freel – The Molecular Ecologist

Back from vacation? Your gut bacteria picked up souvenirs, too – Meredith Knight – Genetic Literacy Project

Evelo, Mayo Clinic team up to use bacteria for cancer immunotherapies – Ben Adams – Fierce Biotech

Plop into Canada’s first poop-themed dessert café next month – Heather Dockray – Mashable
Poop Dessert Cafe to open in Koreatown.Toronto is poised to get its first poop-themed café, set to open in August – The Star
First poo-themed dessert cafe set to open in Canada – Rachael Revesz – The Independent

Council agrees to trial of microbiology treatment – Lici Beveridge – Hattiesburg American

Opinion: Goals and possibilities in microbiology – Andrea Taboada – The Independent Florida Alligator

How Do Microbes Build Resistance to Metals? – Contagion

Bacteria Needed To Save Coral Reef – The Munich Eye

WATCH: Pac-Man Faithfully Recreated with Microbes – Nathaniel Scharping – Discover Magazine

 

August 2, 2016

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Microbial mercury in Antarctic sea ice, bacteria and magnetic field, and what is living in your showerhead.

Events and jobs

Microbiomes of the Built Environment – Meeting #3  (will also be web-casted) – Monday October 17, 2016, at UC Irvine, CA

Postdoctoral position in microbial physiology/environmental microbiology, self-healing concrete, Aarhus University Denmark – Science Careers

General microbiome

Philosophical Transactions of the Royal Society B themed issue: ‘From DNA barcodes to biomes’
A new way to contemplate Darwin’s tangled bank: how DNA barcodes are reconnecting biodiversity science and biomonitoring – Mehrdad Hajibabaei
Dissecting host-associated communities with DNA barcodes – Christopher C. M. Baker
Scaling up discovery of hidden diversity in fungi: impacts of barcoding approaches – Rebecca Yahr
Insect symbionts in food webs – Ailsa H. C. McLean

Pregnancy and birth

Review: The mode of delivery affects the diversity and colonization pattern of the gut microbiota during the first year of infants’ life: a systematic review – Erigene Rutayisire – BMC Gastroenterology

Human (and animal) oral microbiome

Review: Gene Sequence Analyses of the Healthy Oral Microbiome in Humans and Companion Animals: A Comparative Review – Eric M. Davis – Journal of Veterinary Dentistry

Human respiratory microbiome

Association between Staphylococcus aureus nasal carriage and disease phenotype in patients affected by systemic lupus erythematosus – Fabrizio Conti – Arthritis Research & Therapy

Human gut microbiome

Alterations in the Fecal Microbiota of Patients with HIV-1 Infection: An Observational Study in A Chinese Population – Zongxin Ling – Scientific Reports

Animal experiments

Chronic Repression of mTOR Complex 2 Induces Changes in the Gut Microbiota of Diet-induced Obese Mice – Mi-Ja Jung – Scientific Reports

Plant, root, and soil microbiome

Environmental metabarcoding reveals contrasting microbial communities at two poplar phytomanagement sites – Julie Foulon – Science of the Total Environment

Coupling among Microbial Communities, Biogeochemistry, and Mineralogy across Biogeochemical Facies – James C. Stegen – Scientific Reports

Water and extremophile microbiome

Microbial mercury methylation in Antarctic sea ice – Caitlin M. Gionfriddo – Nature Microbiology

Press: Antarctic sea ice may be a source of mercury in southern ocean fish and birds – Phys.org

Magnetic properties of iron minerals produced by natural iron- and manganese-reducing groundwater bacteria – Alexandra Abrajevitch – Geophysical Journal International

Press: Bacteria Preserve Record of Earth’s Magnetic Fields – EOS

Evidence of small-scale spatial structuring of phytoplankton alpha- and beta-diversity in the open ocean – Erik Askov Mousing – Journal of Ecology

Food microbiology

Bacterial microbiota compositions of naturally fermented milk are shaped by both geographic origin and sample type – Z. Zhong – Journal of Dairy Science

Viruses and phages

The Double-Stranded DNA Virosphere as a Modular Hierarchical Network of Gene Sharing – Jaime Iranzo – mBio

Bioinformatics and metagenomics/metabolomics

Updated version: GutCyc: a Multi-Study Collection of Human Gut Microbiome Metabolic Models – Aria S. Hahn – bioRxiv

Microbes in the news

Is your gut making you sick?. New research suggests that the range and quantity of microbes that live in our guts could have a powerful effect on a range of conditions including depression, MS and obesity – Ann Robinson – The Guardian

How purple bacteria could help save amphibians in the Rockies : A Colorado researcher is using boreal toads’ microbiomes to help them ward off a deadly fungus – Krista Langlois – High Country News

A short and weird story: Bacteria Filled Water Almost Sends ‘Naked and Afraid’ Contestant Home – Natalie D’Alacio – Yahoo News

Your Showerhead Is Crammed Full of Bacteria That Scientists Want to Study – Kate Lunau – Motherboard

If You Had Really Good Eyesight, Could You See a Single Bacterium? – Julie Taylor – uBiomeBlog

Letter: The microbiologist who didn’t wash his hands after urinating – Peter Dawson – The Guardian

Women more likely to die from bacterial blood infection – Adrian O’Dowd – OnMedica

Sham Poo Washes Out. A bacterial pill that tried to duplicate the benefits of a fecal transplant has failed a clinical trial. What does that mean for the microbiome field? – Ed Yong – The Atlantic

Science, publishing, and career

Not “Pulling up the Ladder”: Women Who Organize Conference Symposia Provide Greater Opportunities for Women to Speak at Conservation Conferences – Stephanie Sardelis – PLOS ONE

In Australia: Stella Count: Women write twice as many books as men, but receive less than half the reviews – Daisy Dumas – Daily Life

 

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 25, 2016

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Increased accuracy in microbiome studies, the traveling microbiome, Vibrios on microplastics, and microbes in infant formula.

Human respiratory microbiome

Immune Response and Mortality Risk Relate to Distinct Lung Microbiomes in HIV-Pneumonia Patients – Meera K Shenoy – American Journal of Respiratory and Critical Care Medicine

Human gut microbiome

Biliary Microbiota, Gallstone Disease and Infection with Opisthorchis felineus – Irina V. Saltykova – PLOS Neglected Tropical Diseases

Opinion: Current Knowledge and Future Research Directions on Fecal Bacterial Patterns and Their Association with Asthma – Shantelle Claassen-Weitz – Frontiers in Microbiology

Review: Gut microbiota in autoimmunity: potential for clinical applications – Donghyun Kim – Archives of Pharmacal Research

Review: The Traveling Microbiome – Mark S. Riddle – Current Infectious Disease Reports

Plant, root, and soil microbiome

Browsing by an invasive herbivore promotes development of plant and soil communities during primary succession – Peter J. Bellingham – Journal of Ecology

Review: “Omics” Tools for Better Understanding the Plant–Endophyte Interactions –
Sanjana Kaul – Frontiers in Plant Science

Water and extremophile microbiome

Can the Bacterial Community of a High Arctic Glacier Surface Escape Viral Control? – Sara M. E. Rassne – Frontiers in Microbiology

Analysis of the bacteriorhodopsin-producing haloarchaea reveals a core community that is stable over time in the salt crystallizers of Eilat, Israel – Nikhil Ram-Mohan – Extremophiles

Dangerous hitchhikers? Evidence for potentially pathogenic Vibrio spp. on microplastic particles – Inga V. Kirstein – Marine Environmental Research

Press: Hitching a ride? Deadly bacteria cling on to discarded plastic – Science Focus

Review: Monitoring and managing microbes in aquaculture – Towards a sustainable industry – Mikkel Bentzon-Tilia – Microbial Biotechnology

Food microbiology

Pulque, a Traditional Mexican Alcoholic Fermented Beverage: Historical, Microbiological, and Technical Aspects – Adelfo Escalante – Frontiers in Microbiology

Flow Cytometric and 16S Sequencing Methodologies for Monitoring the Physiological Status of the Microbiome in Powdered Infant Formula Production – Amir H. P. Anvarian – Frontiers in Microbiology

Techniques

Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies – Daryl M Gohl – Nature Biotechnology

A Modified SDS-Based DNA Extraction Method for High Quality Environmental DNA from Seafloor Environments – Vengadesh Perumal Natarajan – Frontiers in Microbiology

More microbiology

A New Genomics-Driven Taxonomy of Bacteria and Archaea: Are We There Yet? – George M. Garrity – Journal of Clinical Microbiology

Microbes in the news

University of Alberta researchers aim to close the ‘fibre gap’ – Clare Clancy – Edmonton Journal

Oil-degrading bacteria to undergo field trials – T. Nandakumar – The Hindu

How we simulated a microscopic ‘wind farm’ – powered by bacteria – Tyler Shendruk – The Conversation

Microrobots Can Carry Out Medical Operations By Copying A Certain Bacteria – Jeanette Walsh – Stock News USA

Could parasite found in cat feces fight ovarian cancer? Scientists identify specific protein which trains the body to kill tumors – Mia De Graaf – Daily Mail

How do bacteria take up vitamins? – Research in Germany

BioFlash podcast: Why Big Pharma is hungry for bacteria – Biz Journals

Science, publishing, and career

Towards a typology of academic peer review styles – Kevin Wang – Urban Geography

Bik’s Non-Microbiology Picks

All the weird things kids have swallowed, in one hospital’s collection – Megan Thielking – STAT news

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 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 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

July 5, 2016

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Circadian rhythm, resistant starch, mock communities, sea turtle microbiome, tea rhizosphere.

General microbiome

Review: The Metronome of Symbiosis: Interactions Between Microbes and the Host Circadian Clock – Elizabeth A. C. Heath-Heckman – Integrative & Comparative Biology

Human oral microbiome

Microbial Ecosystem Analysis in Root Canal Infections Refractory to Endodontic Treatment – Luiz Carlos Feitosa Henriques – Journal of Endodontics

Human gut microbiome

Impact of dietary resistant starch type 4 on human gut microbiota and immunometabolic functions – Bijaya Upadhyaya – Scientific Reports

Press: Essential Science: Taking on metabolic disorders with starch – Tim Sandle – Digital Journal

Editorial: serologic microbial-associated markers to predict Crohn’s disease behaviour – A. G. Fraser – Alimentary Pharmacology & Therapeutics

Review: Microbiota and Liver – Kazumichi Abe – The Liver in Systemic Diseases

Animal experiments

A Role for Timp3 in Microbiota-Driven Hepatic Steatosis and Metabolic Dysfunction – Maria Mavilio – Cell Reports

Animal microbiome

A first insight into the gut microbiota of the sea turtle Caretta caretta – Khaled F. Abdelrhman – Frontiers in Microbiology

News and views: Co-evolution of marine worms and their chemoautotrophic bacterial symbionts: unexpected host switches explained by ecological fitting? – A. Brune – Molecular Ecology

Bacterial communities of oceanic sea star (Asteroidea: Echinodermata) larvae – Madeline R. Galac – Marine Biology

Gut bacteria differentially affect egg production in the anautogenous mosquito Aedes aegypti and facultatively autogenous mosquito Aedes atropalpus (Diptera: Culicidae) – Kerri L. Coon – Parasites & Vectors

Review: Better with your parasites? Lessons for behavioural ecology from evolved dependence and conditionally helpful parasites – Kelly L. Weinersmith – Animal Behaviour

Plant, root, and soil microbiome

Response of soil properties and microbial communities to agriculture: Implications for primary productivity and soil health indicators – Pankaj Trivedi – Frontiers in Plant Science

Variations of rhizosphere bacterial communities in tea (Camellia sinensis L.) continuous cropping soil by high-throughput pyrosequencing approach – Yanchun Li – Journal of Applied Microbiology

Water and extremophile microbiome

Oil sands tailings ponds harbour a small core prokaryotic microbiome and diverse accessory communities – S.L. Wilson – Journal of Biotechnology

The Ocean Microbiome: Metabolic Engine of the Marine Carbon Cycle – Elizabeth B. Kujawinski – Microbe

Biofilms

Relevant for Cystic Fibrosis: Temperate phages both mediate and drive adaptive evolution in pathogen biofilms – Emily V. Davies – PNAS

Press: Tiny viruses speed-up evolution of bacteria causing infections in cystic fibrosis patients – News Medical

Techniques

Droplet barcoding for massively parallel single-molecule deep sequencing –
Freeman Lan – Nature Communications

Transcriptomics

Comparative transcriptomics across the prokaryotic tree of life – Ofir Cohen – Nucleic Acids Research

Bioinformatics and metagenomics

PhyloToAST: Bioinformatics tools for species-level analysis and visualization of complex microbial datasets – Shareef M. Dabdoub – Scientific Reports

Optimization of 16S amplicon analysis using mock communities: implications for
estimating community diversity – Andrew Krohn – PeerJ

Benchmarking of methods for identification of antimicrobial resistance genes in bacterial whole genome data – Philip T. L. C. Clausen – Journal of Antimicrobial Chemotherapy

A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies – Shalabh Thakur – BMC Bioinformatics

Editorial: Nucleic Acids Research annual Web Server Issue in 2016 – Nucleic Acids Research

July 2, 2016

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Colonic transit time, innovations in artificial gut systems, and how the majority of the human gut microbiome members can be cultured.

Human respiratory microbiome

Nasopharyngeal microbiota composition of children is related to the frequency of upper respiratory infection and acute sinusitis – Clark A. Santee – Microbiome

Metagenomics Study of Viral Pathogens in Undiagnosed Respiratory Specimens
and Identification of Human Enteroviruses at a Thailand Hospital – Yanfei Zhou – American Journal of Tropical Medicine and Hygiene

Review: The respiratory microbiome of HIV-infected individuals – MB Lawani – Expert Review of Anti-infective Therapy

Review: A tale of two sites: how inflammation can reshape the microbiomes of the gut and lungs – Brittan S. Scales – Journal of Leukocyte Biology

Human gut microbiome

Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut – Henrik M. Roager – Nature Microbiology

Behind the paper: How we got captivated by colonic transit time – Henrik Munch Roager – Nature Microbiology Community

Datafying microbes: Malnutrition at the intersection of genomics and global health – Amber Benezra – BioSocieties

Several reviews in the July issue of Therapeutic Advances in Gastroenterology:
The interplay between the microbiome and the adaptive immune response in cancer development – Edda Russo
The intestinal microbiome, barrier function, and immune system in inflammatory bowel disease: a tripartite pathophysiological circuit with implications for new therapeutic directions – Stephen M. Vindigni
Role of the gut microbiota in health and chronic gastrointestinal disease: understanding a hidden metabolic organ – Caitriona M. Guinane
Novel perspectives on therapeutic modulation of the gut microbiota – Justin L. McCarville

Review: The Brain-Body-Microbial Communities: A Crosstalk and Stress Exchange
Beyond the “Gut hypothesis” – Afifi Ma – Abnormal and Behavioural Psychology

Review: The Role of the Microbial Metabolites Including Tryptophan Catabolites and Short Chain Fatty Acids in the Pathophysiology of Immune-Inflammatory and Neuroimmune Disease – Gerwyn Morris – Molecular Neurobiology

Animal experiments

Relationship between the microbiota in different sections of the gastrointestinal tract, and the body weight of broiler chickens – Geon Goo Han – Springer Plus

The upper respiratory tract microbiome and its potential role in bovine respiratory disease and otitis media – Svetlana F. Lima – Scientific Reports

Review: Farewell to Animal Testing: Innovations on Human Intestinal Microphysiological Systems – Tae Hyun Kang – Micromachines

Plant, root, and soil microbiome

Effects of Short-Term Warming and Altered Precipitation on Soil Microbial Communities in Alpine Grassland of the Tibetan Plateau – Kaoping Zhang – Frontiers in Microbiology

Bacterial diversity in the rhizosphere of two phylogenetically closely related plant species across environmental gradients – Xiaofan Na – Journal of Soils and Sediments

Soil microbial communities of three major Chinese truffles in Southwest China – Yu Fu – Canadian Journal of Microbiology

Review: Ecology of nitrogen fixing, nitrifying and denitrifying microorganisms in tropical forest soils – Silvia Pajares – Frontiers in Microbiology

Water and extremophile microbiome

Metagenomic analysis of microbial community of an Amazonian geothermal spring in Peru – Sujay Paul – Genomics Data

Characterization of microbial mat microbiomes in the modern thrombolite ecosystem of Lake Clifton, Western Australia using shotgun metagenomics – John G. Warden – Frontiers in Microbiology

Built environment microbiome

Microbes in the Water Infrastructure: Underpinning Our Society – Takashi Narihiro – Microbes and Environments

Techniques / Metabolomics

Capturing the diversity of the human gut microbiota through culture-enriched molecular profiling – Jennifer T. Lau – Genome Medicine

A Microbiome DNA Enrichment Method for Next-Generation Sequencing Sample Preparation – Erbay Yigit – Current Protocols in Molecular Biology

Sample preparation optimization in fecal metabolic profiling – Olga Deda – Journal of Chromatography B

Viruses and phages

Survival studies of a temperate and lytic bacteriophage in bovine faeces and slurry – Sepo Nyambe – Journal of Applied Microbiology

Microbes in the news

Conference report: Machine Learning Method Differentiates Between Healthy Male, Female Microbiomes: Topological Data Analysis – UC San Diego

A New Role for Marine Archaea. Researchers discover acetogenesis in archaea, suggesting an important role for these little-studied organisms in generating organic carbon below the seafloor – Catherine Offord – The Scientist

Stop worrying about GMOs; it’s that organic granola bar that could make you sick: Listeria – Henry I. Miller – LA Times

USM marine microbiologist Jay Grimes weighs in on vibrio vulnificus – WDAM

Chesterfield Royal scientists send ripples around the NHS – Andy Done-Johnson – Derbyshire Times

Efficiency in the pathology lab: Friend or Foe; the probiotic power of helminths can prevent Crohn’s Disease – Anouk Gouvras – BioMedCentral blog

Supplement may switch off cravings for high-calorie foods – Stephen Feller – UPI
Cravings for high-calorie foods may be switched off by new food supplement – Kate Wighton – Imperial College London

Science, publishing, and career

“He Thinks He’s Untouchable”: Michael Katze, famous for his studies of Ebola and the flu, ran a lab at the University of Washington where intoxication and sexual harassment went unchecked – Azeen Ghorayshi – Buzzfeed

June 28, 2016

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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