Category Archives: Bik’s Non-Microbiology Picks

July 9, 2016

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Bacteroidales from homeothermic animals, 136 microbial genomes from the Red Sea, corrosion of concrete sewers, and the microbiology lab in 2050 (still sexist!).

Pregnancy and birth

Integrated network-diversity analyses suggest suppressive effect of Hodgkin’s lymphoma and slightly relieving effect of chemotherapy on human milk microbiome – Zhanshan (Sam) Ma – Scientific Reports

Review: The Microbiome, Antibiotics, and Health of the Pediatric Population – Ravi S Misra- EC Microbiology

Human oral microbiome

Metagenomic Analysis of Sputum Microbiome as a Tool Towards Culture-independent Pathogen Detection of Patients with Ventilator-associated Pneumonia – Qiulong Yan – American Journal of Respiratory and Critical Care Medicine

Human respiratory microbiome

Smoking Cessation and the Microbiome in Induced Sputum Samples from Cigarette Smoking Asthma Patients – Christian Munck – PLOS ONE

Association of sputum microbiota profiles with severity of community-acquired pneumonia in children – Melinda M. Pettigrew – BMC Infectious Diseases

Human gut microbiome

Review: Polysaccharide degradation by the intestinal microbiota and its influence on human health and disease – Darrell W. Cockburn – Journal of Molecular Biology

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

Editorial: A Role for Chemists in Microbiome Research – Courtney C. Aldrich – ACD Infectious Diseases

Animal experiments

Longitudinal analysis of the lung microbiota of cynomolgous macaques during long-term SHIV infection – Alison Morris – Microbiome

Animal microbiome

Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals – Kate L. Ormerod – Microbiome

Biodiversity and Activity of the Gut Microbiota across the Life History of the Insect Herbivore Spodoptera littoralis – Bosheng Chen – Scientific Reports

Long-term effect of heavy-metal pollution on diversity of gastrointestinal microbial community of Bufo raddei – Wenya Zhang – Toxicology Letters

Plants, roots, and soil microbiome

Multiscale assemblage of an ectomycorrhizal fungal community: The influence of host functional traits and soil properties in a 10-ha miombo forest – David Bauman – FEMS Microbiology Ecology

Impact of Soil Salinity on the Structure of the Bacterial Endophytic Community Identified from the Roots of Caliph Medic (Medicago truncatula) – Mahmoud W. Yaish – PLOS ONE

Diversity of fungal endophytes in recent and ancient wheat ancestors Triticum dicoccoides and Aegilops sharonensis – Maya Ofek-Lalzar – FEMS Microbiology Ecology

The effect of bullet removal and vegetation on mobility of Pb in shooting range soils – Abioye O. Fayiga – Chemosphere

Water and extremophile microbiome

A catalogue of 136 microbial draft genomes from Red Sea metagenomes – Mohamed F. Haroon – Scientific Data

A comprehensive method for amplicon-based and metagenomic characterization of viruses, bacteria, and eukaryotes in freshwater samples – Miguel I. Uyaguari-Diaz – Microbiome

Hydrocarbon biodegradation by Arctic sea-ice and sub-ice microbial communities during microcosm experiments, Northwest Passage (Nunavut, Canada) – Marie-Ève Garneau – FEMS Microbiology Ecology

Built environment microbiome

Wastewater Enhanced Microbial Corrosion of Concrete Sewers – Guangming Jiang – Environmental Science & Technology

Bioreactors

The bioleaching potential of a bacterial consortium – Mauricio Latorre – Bioresource Technology

Biofilms

DGGE: Representative sampling of natural biofilms: influence of substratum type on the bacterial and fungal communities structure – Jennifer Hellal – SpringerPlus

Bioinformatics and metagenomics

GUTSS: An Alignment-Free Sequence Comparison Method for Use in Human Intestinal Microbiome and Fecal Microbiota Transplantation Analysis – Mitchell J. Brittnacher – PLOS ONE

Icarus: visualizer for de novo assembly evaluation – Alla Mikheenko – Bioinformatics

deBGA: read alignment with de Bruijn Graph-based seed and extension – Bo Liu – Bioinformatics

ConsPred – a rule-based (re-)annotation framework for prokaryotic genomes – Thomas Weinmaier – Bioinformatics

Proteomics

Review: Metaproteomic data analysis at a glance: advances in computational microbial community proteomics – Expert Review of Proteomics

Bik’s Picks

A typical day working in a laboratory in 2050: Are microbiologists becoming chemists and serene workers? – Daniele Sohier – Current Opinion in Food Science

Napa native on space mission showed early signs of promise – Jonathan Bloom – ABC News

 

 

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 30, 2016

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Mycorrhizal fungi and CO2, pathogen defense in the gut, Mississippi River plume.

Animal experiments

Defensive Mutualism Rescues NADPH Oxidase Inactivation in Gut Infection – Gratiela Pircalabioru – Cell Host & Microbe

Press: Good gut relationships key in defence against pathogens – Medical Xpress

Plant, root, and soil microbiome

Mycorrhizal association as a primary control of the CO2 fertilization effect – César Terrer – Science

Press: Study finds that plant growth responses to high carbon dioxide depend on symbiotic fungi – EurekAlert

Grassland to woodland transitions: Dynamic response of microbial community structure and carbon use patterns – Courtney A. Creamer – Journal of Geophysical Research

The interaction between arbuscular mycorrhizal fungi and endophytic bacteria enhances plant growth of Acacia gerrardii under salt stress – Abeer Hashem – Frontiers in Microbiology

Water and extremophile microbiome

Mississippi River plume enriches microbial diversity in the northern Gulf of Mexico – Olivia U. Mason – Frontiers in Microbiology

Editorial: Anthropogenic impacts on the microbial ecology and function of aquatic environments – Maurizio Labbate – Frontiers in Microbiology

Unanticipated geochemical and microbial community structure under seasonal ice cover in a dilute, dimictic Arctic lake – Ursel Schuette – Frontiers in Microbiology

Comparative activity and functional ecology of permafrost soils and lithic niches in a hyper-arid polar desert – Jacqueline Goordial – Environmental Microbiology

Metagenomics and bioinformatics

Bioinformatic Characterization of Mosquito Viromes within the Eastern United States and Puerto Rico: Discovery of Novel Viruses – Kenneth G. Frey – Evolutionary Bioinformatics

Review: Reconstructing single genomes from complex microbial communities – Dongwan D. Kang – it-Information Technology

Review: A history of DNA sequence assembly – Eugene W. Myers Jr – it-Information Technology

Review: Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes – Miklós Bálint – FEMS Microbiology Reviews

Microbes in the news

Stanford undergrads cook up a biotech startup to develop new antibiotics for drug-resistant superbugs – Rosemary Mena-Werth – Stanford News

From the Evolution Conference, talk by Danielle Whittaker: Bacteria give bird its sexy smells – Patrick Monahan – Science

Australia’s Melbourne takes selfie of its microbiome – i4U News

The Microbiome and Bronchiolitis: An Unusual Pairing or Is It? – Lewis First – AAP Gateway

An Ounce of (Water) Prevention: microbial fuel degradation – Katherine Vanover – Fuel Market News

New study shows chronic fatigue isn’t just in your head. It may have to do with your gut – Ariana Eunjung Cha – Washington Post

Resistance to antibiotics and to immune system are interconnected in bacteria – EurekAlert

In times of great famine, microalgae digest themselves. AWI researchers decipher the connection between nutrient availability and algae growth – EurekAlert

Researchers develop effective strategy for disrupting bacterial biofilms – EurekAlert

How a germ catches a virus – Phys.org

Coming Soon: Gut Bacteria That Actually Cure Your Disease: The $34 billion probiotics market includes some dubious products. This crop looks different – Deena Shanker – Bloomberg

TV weatherman retracts story about toxic bacteria at Northwest Florida beaches – The Destin Log

Bik’s non-microbiology Picks

Former Relman lab member: NASA Astronaut Kate Rubins Prepares for First Trip to Space – Alison Thoet – ABC News

107 Nobel laureates sign letter blasting Greenpeace over GMOs – Joel Achenbach – Washington Post

The Academic Hermit – What are you going to do with your tool?: installation as the Frederick G. Novy Collegiate Professor of Microbiome Research at the University of Michigan – Pat Schloss

June 24, 2016

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Placenta samples not distinguishable from controls, gut microbiome in ME/CFS and PKU patients, childhood undernutrition, corals’ microbial sentinels, and plant root traps.

Pregnancy and birth

I was hoping for this study to be done: Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota – Abigail P. Lauder – Microbiome

Systematic review: Treatment of bacterial vaginosis in pregnancy in order to reduce the risk of spontaneous preterm delivery – a clinical recommendation – Thor Haahr – Acta Obstetricia et Gynecologica Scandinavica

Human ear microbiome

The microbiome of otitis media with effusion – Chun Ling Chan – The Laryngoscope

Human gut microbiome

Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome – Ludovic Giloteaux – Microbiome

Phenylketonuria and Gut Microbiota: A Controlled Study Based on Next-Generation Sequencing – Felipe Pinheiro de Oliveira – PLOS ONE

Review: Childhood undernutrition, the gut microbiota, and microbiota-directed therapeutics – Laura V. Blanton – Science

Editorial: Gut microbiota and undernutrition – Caroline Ash – Science

Infection and microbiology

Role of Clinicogenomics in Infectious Disease Diagnostics and Public Health Microbiology – Lars F. Westblade – Journal of Clinical Microbiology

Novel Taxa Associated with Human Fungal Black-Grain Mycetomas: Emarellia grisea gen. nov., sp. nov., and Emarellia paragrisea sp. nov. – Andrew M. Borman – Journal of Clinical Microbiology

Sociomicrobiology and Pathogenic Bacteria – Joao B. Xavier – Microbiology Spectrum

Paleomicrobiology Data: Authentification and Interpretation – Michel Drancourt – Microbiology Spectrum

Animal experiments

Dietary fucoidan modulates the gut microbiota in mice by increasing the abundance of Lactobacillus and Ruminococcaceae – Qingsen Shang – Food & Function

Animal microbiome

Perspective: Corals’ microbial sentinels – Tracy D. Ainsworth – Science

Plant, root, and soil microbiome

Escaping Underground Nets: Extracellular DNases Degrade Plant Extracellular Traps and Contribute to Virulence of the Plant Pathogenic Bacterium Ralstonia solanacearum – Tuan Minh Tran – PLOS Pathogens

Press: An ‘arms race’ raging beneath our plants: A crop’s DNA-laden root trap manages to hold on to only a quarter of its bacterial prisoners. – Amy Middleton – Cosmos Magazine

Responsiveness of soil nitrogen fractions and bacterial communities to afforestation in the Loess Hilly Region (LHR) of China – Chengjie Ren – Scientific Reports

Spatial Shifts in Soil Microbial Activity and Degradation of Pasture Cover Caused by Prolonged Exposure to Cement Dust – Fuensanta Caravaca – Land Degradation & Development

Water and extremophile microbiome

Biogeochemical and 16S rRNA gene sequence evidence supports a novel mode of anaerobic methanotrophy in permanently ice-covered Lake Fryxell, Antarctica – Matthew A. Saxton – Limnology and Oceanography

Food microbiology

The Microbiome and Metabolites in Fermented Pu-erh Tea as Revealed by High-Throughput Sequencing and Quantitative Multiplex Metabolite Analysis – Yongjie Zhang – PLOS ONE

More microbiology

Sugar Synthesis from CO2 in Escherichia coli – Niv Antonovsky – Cell

Press: Eating air, making fuel. Scientists engineer bacteria to create sugar from the greenhouse gas carbon dioxide – Science Daily

Not a scientific paper, just a list of links: Web Alert: Synthetic microbial communities: An annotated selection of World Wide Web sites relevant to the topics in environmental microbiology – Lawrence P. Wackett – Environmental Microbiology

Techniques

High stability of faecal microbiome composition in guanidine thiocyanate solution at room temperature and robustness during colonoscopy – Yuichiro Nishimoto – Gut

Microbes in the news

New life form discovered in saliva is linked to human disease – Andy Coghlan – New Scientist

Seagulls Are Carrying a Dangerous Superbug Through the Skies – Maryn McKenna – National Geographic
Beware of Seagulls Carrying This Dangerous Superbug – Laura Lorenzetti – Fortune

Microbes In The Body Affect Success Of Organ Transplants: Study – Katrina Pascual -Tech Times

Scientists just found a compound that kills 98% of a drug-resistant bacteria – Fiona MacDonald – Science Alert

Milken Institute School of Public Health researchers awarded $7 million to study microbiome – Sera Royal – The GW Hatchet

Mycobacterium in olive oil for cancer treatment – EurekAlert

Scientists discover unsuspected bacterial link to bile duct cancer – MedicalXpress

Bik’s completely-not-microbiology Picks

The social dilemma of autonomous vehicles – Jean-François Bonnefon – Science

June 10, 2016

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Volunteers taking ETEC, 3 new E. coli phages, oral microbiomes of cats and dogs, skin microbes in Japanese amphibians, fungi and bacteria in floor dust.

Human oral microbiome

The oral microbiome of patients with axial spondyloarthritis compared to healthy individuals – Jordan E. Bisanz – PeerJ

Human vaginal microbiome

Association of Sexual Debut in Adolescents With Microbiota and Inflammatory Markers – Jespers, Vicky – Obstetrics & Gynecology

Human blood ‘microbiome’

Rapid identification of fungi in culture-negative clinical blood and respiratory samples by DNA sequence analyses – Farida Sidiq – BMC Research Notes

Human gut microbiome

Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment – Mihai Pop – BMC Genomics

Mucosa-Associated Ileal Microbiota in New-Onset Pediatric Crohn’s Disease – Assa, Amit – Inflammatory Bowel Diseases

Three New Escherichia coli Phages from the Human Gut Show Promising Potential for Phage Therapy – Marion Dalmasso – PLOS ONE

“Free living females” sounded… weird. Soluble Corn Fiber Increases Calcium Absorption Associated with Shifts in the Gut Microbiome: A Randomized Dose-Response Trial in Free-Living Pubertal Females – Corrie M Whisner – Journal of Nutrition

Similar Fecal Microbiota Signatures in Patients With Diarrhea-predominant Irritable Bowel Syndrome and Patients With Depression – Yixuan Liu – Clinical Gastroenterology and Hepatology

DGGE: Differences in the Biodiversity of the Fecal Microbiota of Infants With Rotaviral Diarrhea and Healthy Infants – Peng Fei – Jundishapur Journal of Microbiology

Opinion: How Our Other Genome Controls Our Epi-Genome – Antonella Celluzzi – Trends in Microbiology

Review: The role of the gut microbiota in NAFLD – Christopher Leung – Nature Reviews Gastroenterology & Hepatology

Animal microbiome

Diet may influence the oral microbiome composition in cats – Christina J. Adler – Microbiome

Characterising the Canine Oral Microbiome by Direct Sequencing of Reverse-Transcribed rRNA Molecules – James E. McDonald – PLOS ONE

Bacterial microbiomes from vertically-transmitted fungal inocula of the leaf-cutting ant Atta texana – Lucas A. Meirelles – Environmental Microbiology Reports

Defensive insect symbiont leads to cascading extinctions and community collapse – Dirk Sanders – Ecology Letters

Plant, root, and soil microbiome

Subalpine conifers in two different geographic locations host highly similar foliar bacterial endophyte communities – Alyssa A. Carrell – FEMS Microbiology Ecology

Effect of plant growth-promoting bacteria on the growth and fructan production of Agave americana L. – Neyser De La Torre-Ruiz – Brazilian Journal of Microbiology

Composition of the Cutaneous Bacterial Community in Japanese Amphibians: Effects of Captivity, Host Species, and Body Region – Joana Sabino-Pinto – Microbial Ecology

Water and extremophile microbiome

Benthic protists: the under-charted majority – Dominik Forster – FEMS Microbiology Ecology

Methane release from sediment seeps to the atmosphere is counteracted by highly active Methylococcaceae in the water column of deep oligotrophic Lake Constance – Maren Bornemann – FEMS Microbiology Ecology

Review: How mutualisms arise in phytoplankton communities: building eco-evolutionary principles for aquatic microbes – Elena Kazamia – Ecology Letters

Review: All ecosystems potentially host electrogenic bacteria – Nicolas Chabert – Bioelectrochemistry

Pollution and waste and bioreactor microbiology

Arsenic metabolism and toxicity influenced by ferric iron in simulated gastrointestinal tract and the roles of gut microbiota – Haiyan Yu – Environmental Science & Technology

Pyrosequencing analysis of bacterial diversity in soils contaminated long-term with PAHs and heavy metals: Implications to bioremediation – Saranya Kuppusamy – Journal of Hazardous Materials

A strange combination of samples: Deep metagenome and metatranscriptome analyses of microbial communities affiliated with an industrial biogas fermenter, a cow rumen, and elephant feces reveal major differences in carbohydrate hydrolysis strategies – Simon Güllert – Biotechnology for Biofuels

Monitoring the impact of bioaugmentation with a PAH-degrading strain on different soil microbiomes using pyrosequencing – S. Festa – FEMS Microbiology Ecology

Built environment microbiome

Fungal and bacterial growth in floor dust at elevated relative humidity levels – Karen C. Dannemiller – Indoor Air

Bioinformatics and statistics

An Introduction to Programming for Bioscientists: A Python-Based Primer – Berk Ekmekci – PLOS Computational Biology

Ten Simple Rules for Effective Statistical Practice – Robert E. Kass – PLOS Computational Biology

Bipartite Graphs for Visualization Analysis of Microbiome Data – Karel Sedlar – Evolutionary Bioinformatics

Techniques

The source of SYBR green master mix determines outcome of nucleic acid amplification reactions – Jianxin Yang – BMC Research Notes

More microbiology

Ancestral Tryptophan Synthase Reveals Functional Sophistication of Primordial Enzyme Complexes – Florian Busch – Cell Chemical Biology

Press: Ancient enzyme resurrected from the ancestor of all bacteria – Conor Gearin – New Scientist
Bacteria perfected protein complexes more than 3.5 billion years ago – Science Daily

Microbes in the news

Tufts microbiologist Cecilia A. Silva-Valenzuela, Ph.D., named Pew Latin American Fellow
Silva-Valenzuela, in Andrew Camilli’s lab, will investigate novel approaches to prevent cholera outbreaks – EurekAlert

Bio-statistician Albert Parker with MSU’s Center for Biofilm Engineering earns top EPA award – Amanda Eggert – Montana State University

Video series with James Hamblin – The Atlantic
Should You Map Your Microbiome? A visit to uBiome
Your Probiotics Aren’t Doing Anything (Yet)
You Probably Don’t Need to Shower – James Hamblin – The Atlantic

Banking on stool despite an uncertain future – Tina Amirtha – Science

Science, publishing, and career

In effort to understand continuing racial disparities, NIH to test for bias in study sections – Jeffrey Mervis – Science

Triplicated paper with multiplicated cells and images – Leonid Schneider – For Better Science
Author denies accusations of blatant duplication – Shannon Palus – Retraction Watch

Bik’s Picks (it’s not microbiology, but pretty cool)

RhizoTubes as a new tool for high throughput imaging of plant root development and architecture: test, comparison with pot grown plants and validation – Christian Jeudy – Plant Methods

June 3, 2016

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Microbes around a methane seep that look like ancient ruins, microbial metabolites protecting intestinal stem cells, and human-derived microbes in a Mars-like simulator.

Jobs and events

For everyone anxious to see the videos of the Stanford Bioinformatics for the Microbiome Symposium (including me!), please be patient. The AV team is working hard to generate videos for each individual talk, but that will take some time. Check in at this blog under the “Jobs and Events” header where I will post them once they are ready.

Assistant Professor in the Department of Biology – Macalester College, St. Paul, MN

Human vaginal microbiome

Predictive value of the composition of the vaginal microbiota in bacterial vaginosis, a dynamic study to identify recurrence-related flora – Bingbing Xiao – Scientific Reports

Human gut microbiome

Review: Reframing the Teenage Wasteland: Adolescent Microbiota-Gut-Brain Axis – Karen-Anne McVey Neufeld – The Canadian Journal of Psychiatry
Editorial to their own paper (?): Stress and the Microbiota-Gut-Brain Axis. An Evolving Concept in Psychiatry – John F. Cryan – The Canadian Journal of Psychiatry

Review: Emerging evidence of the role of gut microbiota in the development of allergic diseases – Kotryna Simonyte Sjödin – Current Opinion Allergy Clinical Immunology

Review: Microbiota and pathogen ‘pas de deux’: setting up and breaking down barriers to intestinal infection – Elizabeth S. McKenney – Pathogens and Disease

Review: Linking Gut Microbiota and Inflammation to Obesity and Insulin Resistance – M. J. A. Saad – Physiology

Research Highlight: Sensing gene–microbiota signals in IBD – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

Editorial: Probiotics and microbiota composition – Mary Ellen Sanders – BMC Medicine

Animal / tissue culture experiments

The Colonic Crypt Protects Stem Cells from Microbiota-Derived Metabolites – Gerard E. Kaiko – Cell

Press: Gut microbes’ metabolite dampens proliferation of intestinal stem cells – Science Daily

Animal microbiome

Unfortunately no reference to our recent paper,  which included dolphin blowhole samples: Isolation of culturable aerobic bacteria and evidence of Kerstersia gyiorum from the blowhole of captive Yangtze finless porpoises – Xiaoling Wan – Antonie van Leeuwenhoek

Plants, roots, and soil microbiome

Seeing is believing: cell biology at the plant–microbe interface: report from the 36th New Phytologist Symposium – Mike Deeks – New Phytologist

Bacteria with Phosphate Solubilizing Capacity Alter Mycorrhizal Fungal Growth Both Inside and Outside the Root and in the Presence of Native Microbial Communities – Yuli Marcela Ordoñez – PLOS ONE

Water and extremophile microbiome

Exhumed hydrocarbon-seep authigenic carbonates from Zakynthos island (Greece): Concretions not archaeological remains – Julian E Andrews – Marine and Petroleum Geology

Press:
Ancient Civilization of Microbes, Not Greeks, Built ‘Lost City’ – Henry Fountain – The New York Times
The lost (microbe) colony: bacteria make underwater ‘ruins’ off Greek island – Alan Yuhas – The Guardian
This “Lost Underwater City” Was Actually Made by Microbes. Though these formations may not be evidence of a lost city, they show off some intriguing chemistry – Danny Lewis – Smithsonian
Microfungal oasis in an oligotrophic desert: diversity patterns and community structure in three freshwater systems of Cuatro Ciénegas, Mexico – Patricia Velez – PeerJ

Built environment microbiome

Microbial succession in an inflated lunar/Mars analog habitat during a 30-day human occupation – Teresa Mayer – Microbiome

In Situ Microbial Community Succession on Mild Steel in Estuarine and Marine Environments: Exploring the Role of Iron-Oxidizing Bacteria – Joyce M. McBeth – Frontiers in Microbiology

Ecology and bioinformatics

Applications of species accumulation curves in large-scale biological data analysis – Chao Deng – Quantitative Biology

Microbes in the news

See beautiful gif below: Educate Your Immune System. Our bodies are confused by this 21st-century world – Moises Velasquez-Manoff – NY Times

Will Microbes Save Agriculture? Experts Aim To Find Out – Geoffrey Mohan – Sci Tech Today

Alzheimer’s May Defend Against Microbes – Paul Rodgers – Forbes

Methane-producing microbes in California rocks – Science Daily

Science, publishing, and career

Science launches the 2016 ‘Dance Your Ph.D.’ contest – John Bohannon – Science Magazine

Let’s talk about preprint servers – Emilie Marcus – Crosstalk Cell

Bik’s Picks

A New Origin Story for Dogs. The first domesticated animals may have been tamed twice – Ed Yong – The Atlantic

The meteoritic origin of Tutankhamun’s iron dagger blade – Daniela Comelli – Meteoritics & Planetary Science

05valasquez-manoff-superJumbo.gif

Gif by Santtu Mustonen, New York Times

 

May 21, 2016

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Helminths positively associated with allergy, baboon vaginal microbiome, nitrogen fixation in poplar trees, boreal lakes as analogues for the Archaean ocean, and PERMANOVA-S as alternative for weighted Unifrac.

Events

2016 Society for Industrial Microbiology and Biotechnology (SIMB) Annual Meeting and Exhibition – July 24-30, New Orleans, LA

General
Editorial overview: Remapping the body of the world: Exploring interactions at the interface of microbial ecology, biological engineering and information science – Steven J. Hallam – Current Opinion in Microbiology

Human oral microbiome

Quantitative molecular detection of 19 major pathogens in the interdental biofilm of periodontally healthy young adults – Florence Carrouel – Frontiers in Microbiology

Species level core oral bacteriome identified by 16S rRNA pyrosequencing in a healthy young Arab population – Nezar Noor Al-hebshi – Journal of Oral Microbiology

Review: Metagenomic Insights into Transferable Antibiotic Resistance in Oral Bacteria – S. Sukumar – Journal of Dental Research

Human gut microbiome

Helminths are positively associated with atopy and wheeze in Ugandan fishing communities: results from a cross-sectional survey – E. L. Webb – Allergy

Stool frequency is associated with gut microbiota composition – Fatemeh Hadizadeh – Gut

The gut-adherent microbiota of PSC–IBD is distinct to that of IBD – Mohammed Nabil Quraishi – Gut

Mucosal adherent bacterial dysbiosis in patients with colorectal adenomas– Yingying Lu – Scientific Reports

Haloferax massiliensis sp. nov., the first human-associated halophilic archaea – Saber Khelaifia – New Microbes and New Infections

Review: The influence of commensal and pathogenic gut microbiota on prion disease pathogenesis – David S. Donaldson – Journal of General Virology

Animal experiments

Effect of Dietary Fibers on Cecal Microbiota and Intestinal Tumorigenesis in Azoxymethane Treated A/J Min/+ Mice – Birgitte Moen – PLOS ONE

Food-grade antimicrobial ɛ-polylysine transiently perturbs the structure of the murine gut microbiome – Xiaomeng You – The FASEB Journal

Animal microbiome

Baboon vaginal microbial flora – Jael A. Obiero – Journal of Medical Primatology

Diversity and fluctuation in ciliate protozoan population in the rumen of cattle – Arfan Abrar – Animal Science Journal

Dietary-driven variation effects on the symbiotic flagellate protist communities of the subterranean termite Reticulitermes grassei Clément – S. Duarte – Journal of Applied Entomology

Plant, root, and soil microbiome

Variable Nitrogen Fixation in Wild Populus – Sharon L. Doty – PLOS ONE

Press: Bacteria in branches naturally fertilize trees – Michelle Ma – University of Washington

Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database – Andrew Bissett – GigaScience

Conference abstract: Microbial communities associated with the biotransformation potential of insensitive explosives in surface soils – F. Crocker – 2016 SIMB Annual Meeting and Exhibition

Water and extremophile microbiome

Millions of Boreal Shield Lakes can be used to Probe the Evolution of Archaean Ocean Life – Sherry Schiff – bioRxiv

Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution – Beatriz Díez – PLOS ONE

Diversity and Activity of Communities Inhabiting Plastic Debris in the North Pacific Gyre – Jessica A. Bryant – mSystems

Biogeography of sulfur-oxidizing Acidithiobacillus populations in extremely acidic cave biofilms – Daniel S Jones – ISME Journal

Biogeography and environmental genomics of the Roseobacter-affiliated pelagic CHAB-I-5 lineage – Sara Billerbeck – Nature Microbiology

Drinking water, waste and pollution microbiology

Integrative microbial community analysis reveals full-scale enhanced biological phosphorus removal under tropical conditions – Yingyu Law – Scientific Reports

Conference abstract: Microbial survival in drinking water systems – A. Pinto – 2016 SIMB Annual Meeting and Exhibition

Bioinformatics

PERMANOVA-S: Association test for microbial community composition that accommodates confounders and multiple distances – Zheng-Zheng Tang – Bioinformatics

More microbiology

ppGpp couples transcription to DNA repair in E. coli – Venu Kamarthapu – Science

Press: Factor preserves DNA integrity in bacteria despite assault from antibiotics – Science Daily
Spatial organization shapes the turnover of a bacterial transcriptome – Jeffrey R Moffitt – eLIFE

The Small World Initiative™: An Innovative Crowdsourcing Platform for Antibiotics – Ana Maria Barral – The FASEB Journal

Effects of Dispersal and Initial Diversity on the Composition and Functional Performance of Bacterial Communities – Yinghua Zha – PLOS ONE

Microbes in the news

Featuring my work (but not my quotes): The inner lives of dolphins – Marine mammals carry an unexpected microbial mix – Steve Fyffe – Stanford Medicine Magazine

About Stanley Falkow and Denise Monack: Microbe mentoring: The recipe for success includes independence, a gentle shove and a good stiff drink – Kathy Zonana – Stanford Medicine Magazine

President Obama Awards the National Medals of Science & Technology and Innovation. Stanford Professor of Microbiology Stanley Falkow get his award at 11:30 min in this video.

Students are developing bacteria that eat plastic polluting our oceans. Om nom. – Josh Hrala – Science Alert

A Comprehensive Survey of Preclinical Microbiology Curricula Among US Medical Schools – Dora J. Melber – Clinical Infectious Diseases

University Of California, San Diego Invests $12 Million In Its Own Microbiome Research Efforts! – Vinny – University Herald

Bik’s Picks

Striking Immune Phenotypes in Gene-Targeted Mice Are Driven by a Copy-Number Variant Originating from a Commercially Available C57BL/6 Strain – Vinay S. Mahajan

Press: Immune Defect Detected in Knockout Mice – Tanya Lewis – The Scientist

May 19, 2016

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Two papers on triclosan effects, genome reduction in a common soil bacterium, spatial patterns of ocean microbes, and deep sequencing in unexplained fever cases.

Triclosan and microbiome

Two very different papers about the effect of triclosan on the microbiome:

Crossover Control Study of the Effect of Personal Care Products Containing Triclosan on the Microbiome – Angela C. Poole – mSphere

Antimicrobial in Common Toothpaste Doesn’t Impact Gut, Oral Microbiome – ASM

but:

Triclosan Exposure Is Associated with Rapid Restructuring of the Microbiome in Adult Zebrafish – Christopher A. Gaulke – PLOS ONE

The Case Against Antibacterial Soap Is Getting Stronger – Alexandra Sifferlin – Time

Human oral microbiome

Undergraduate thesis: Exploring a possible correlation between the human oral microbiome and body mass index – Ivy S. McDermot – University of Colorado Boulder

Human gut microbiome

Irritable Bowel Syndrome special in Nature: 
Irritable bowel syndrome – Michelle Grayson
Microbiome: Bacterial broadband – Michael Eisenstein

HIV infection results in metabolic alterations in the gut microbiota different from those induced by other diseases – Sergio Serrano-Villar – Scientific Reports

Review: 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 – Therapeutic Advances in Gastroenterology

Animal experiments

Microbiome-metabolome responses in the cecum and colon of pig to a high resistant starch diet – Yue Sun – Frontiers in Microbiology

Animal microbiome

Characterisation of the bacterial community structures in the intestine of Lampetra morii – Yingying Li – Antonie van Leeuwenhoek

Review: Microbiomes, metagenomics, and primate conservation: New strategies, tools, and applications – R.M. Stumpf – Biological Conservation

Plant, root, and soil microbiome

Genome reduction in an abundant and ubiquitous soil bacterial lineage – Tess Brewer – bioRxiv

Insight into structure dynamics of soil microbiota mediated by the richness of replanted Pseudostellaria heterophylla – Yong-Po Zhao – Scientific Reports

Review: Microbial inoculation of seed for improved crop performance: issues and opportunities – Maureen O’Callaghan – Applied Microbiology and Biotechnology

Water and extremophile microbiome

Distinct Spatial Patterns of SAR11, SAR86, and Actinobacteria Diversity along a Transect in the Ultra-oligotrophic South Pacific Ocean – Nyree J. West – Frontiers in Microbiology

In situ Dynamics of O2, pH, Light, and Photosynthesis in Ikaite Tufa Columns (Ikka Fjord, Greenland)—A Unique Microbial Habitat – Erik C. L. Trampe – Frontiers in Microbiology

Waste and pollution microbiology

Diversity of ammonia-oxidizing bacteria and archaea in response to different aeration rates during cattle manure composting – Lei Yan – Ecological Engineering

Microbes and infection

Deep sequencing approach for investigating infectious agents causing fever – T. N. Susilawati – European Journal of Clinical Microbiology & Infectious Diseases

Metagenomics and bioinformatics

A two-part mixed-effects model for analyzing longitudinal microbiome compositional data – Eric Z. Chen – Bioinformatics

Review: Metagenomics, Metatranscriptomics, and Metabolomics Approaches for Microbiome Analysis – Vanessa Aguiar-Pulido, Wenrui Huang, Victoria Suarez-Ulloa, Trevor Cickovski, Kalai Mathee and Giri Narasimhan – Evolutionary Bioinformatics

More microbiology

Structure of the T4 baseplate and its function in triggering sheath contraction – Nicholas M. I. Taylor – Nature

How viruses infect bacteria: A tale of a tail – EurekAlert

A platform for the discovery of new macrolide antibiotics – Ian B. Seiple – Nature

Microbes in the news

Darwinolide, a New Diterpene Scaffold That Inhibits Methicillin-Resistant Staphylococcus aureus Biofilm from the Antarctic Sponge Dendrilla membranosa – Jacqueline L. von Salm – Organic Letters
University of South Florida Scientists Discover Antarctic Sponge Extract Can Help Kill MRSA – University of South Florida
Arctic Sponge Extract May Be Potent Against MRSA – Xuan Pham – Lab Roots

These bacteria are all over your wallet and smartphone
“Due to rising temperatures, we will NOT be accepting boob or sock money.” – Maria Lamagna – MarketWatch

Tampa Bay: Bacteria threatens Bay Area palm trees #Phytoplasma

Panda poop study provides insights into microbiome, reproductive troubles – EurekAlert

Indian gut similar to Bangladeshis, omnivorous animals, claims study
We acquire them from our mothers during birth, pass on to us through the breast milk and live with us till we die – Anuradha Mascarehnas – Indian Express

Science, publishing, and career

Ecology: The sea-otter whisperer – Jane Lubchenco – Nature

Bik’s Picks

MinION in space: Virologist Kate Rubins is set to make history as the first person to sequence DNA in space – Frontline Genomics

With lighting by my husband’s company Xicato: Arts: California on camera. The re-opening of the San Francisco Museum of Modern Art – John Gilbey – Nature

May 12, 2016

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Dandruff, archaeological dental calculus methanogens, extreme longevity, UK twins, and dissemination of human-derived bacteria into the Antarctic microbiome.

Pregnancy and birth microbiome

Early-life gut microbiome composition and milk allergy resolution – Supinda Bunyavanich – Journal of Allergy and Clinical Immunology

Human skin microbiome

Dandruff is associated with the conjoined interactions between host and microorganisms – Zhijue Xu – Scientific Reports

Human oral microbiome

Restricted diversity of dental calculus methanogens over five centuries, France – Hong T. T. Huynh – Scientific Reports

Metabolic and Community Synergy of Oral Bacteria in Colorectal Cancer – Kaitlin J. Flynn – mSphere

Peri-implant and periodontal microbiome diversity in aggressive periodontitis patients: a pilot study – Vanessa Sousa – Clinical Oral Implants Research

Human respiratory microbiome

The nasal microbiota in infants with cystic fibrosis in the first year of life: a prospective cohort study – Moana Mika – The Lancet Respiratory Medicine

Examining changes in bacterial abundance in complex communities using next-generation sequencing is enhanced with quantitative PCR – Joshua R. Stokell – Antonie van Leeuwenhoek

Human gut microbiome

Gut Microbiota and Extreme Longevity – Elena Biagi – Current Biology

Enteral feeding reduces metabolic activity of the intestinal microbiome in Crohn’s disease: an observational study – C Walton – European Journal of Clinical Nutrition

Genetic Determinants of the Gut Microbiome in UK Twins – Julia K. Goodrich – Cell Host & Microbe

Gut microbiota composition and Clostridium difficile infection in hospitalized elderly individuals: a metagenomic study – Christian Milani – Scientific Reports

Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing – Emily Vogtmann – PLOS ONE

Review: Structural and functional changes within the gut microbiota and susceptibility to Clostridium difficile infection – Caná L. Ross – Anaerobe

Preview: What’s LPS Got to Do with It? A Role for Gut LPS Variants in Driving Autoimmune and Allergic Disease – Taylor Feehley – Cell Host & Microbe

Review: Koch’s postulates, microbial dysbiosis and inflammatory bowel disease – Benjamin P. Willing – Clinical Microbiology and Infection

Review: Impact of gut microbiota on diabetes mellitus – G. Blandino – Diabetes & Metabolism

Review: Microbiota and the nitrogen cycle: Implications in the development and progression of CVD and CKD – David Briskey – Nitric Oxide

Review: Impact of microbial derived secondary bile acids on colonization resistance against Clostridium difficile in the gastrointestinal tract – Jenessa A. Winston – Anaerobe

Review: The microbiome-immune-host defense barrier complex (microimmunosome) and developmental programming of noncommunicable diseases – Rodney R. Dietert – Reproductive Toxicology

Animal experiments

A low dose of an organophosphate insecticide causes dysbiosis and sex-dependent responses in the intestinal microbiota of the Japanese quail (Coturnix japonica) – Eduardo Crisol-Martínez – PeerJ

Structural modulation of gut microbiota by chondroitin sulfate and its oligosaccharide – Qingsen Shang – Macromolecules

Administration of probiotic kefir to mice with Clostridium difficile infection exacerbates disease – Jennifer K. Spinler – Anaerobe

Editorial: Immunology: You Remind Me of a Microbe I Know – Ray Soto and June Round – Current Biology

Forum: Human Microbiota-Associated Mice: A Model with Challenges – Marie-Claire Arrieta – Cell Host & Microbe

Plant, root, and soil microbiome

Geography and agronomical practices drive diversification of the epiphytic mycoflora associated with barley and its malt end product in western Canada – Wen Chen – Agriculture, Ecosystems & Environment
http://www.sciencedirect.com/science/article/pii/S0167880916301669

Revisiting the pink-red pigmented basidiomycete mirror yeast of the phyllosphere –
Alec Cobban – MicrobiologyOpen
http://onlinelibrary.wiley.com/doi/10.1002/mbo3.374/abstract

 

Water and extremophile microbiome

Escherichia coli out in the cold: Dissemination of human-derived bacteria into the Antarctic microbiome – Michelle L. Power – Environmental Pollution

Habitat heterogeneity and connectivity shape microbial communities in South American peatlands – Felix Oloo – Scientific Reports

The Egyptian Red Sea coastal microbiome: A study revealing differential microbial responses to diverse anthropogenic pollutants – Ghada A. Mustafa – Environmental Pollution

Conference Highlight: Decoding Microbial “Relationship Statuses” at OSM 2016 – Kelsey Ellis – Bulletin Limnology and Oceanography

Phages and viruses

Genomic Signatures of Emerging Viruses: A New Era of Systems Epidemiology – Angela L. Rasmussen – Cell Host & Microbe

Techniques

A microfluidics-based in vitro model of the gastrointestinal human–microbe interface – Pranjul Shah – Nature Communications

Effect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elderly adults and infants – Cian J. Hill – Microbiome

Video: Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization – Melis N. Anahtar – JOVE

Microbial Ecology

A Novel Analysis Method for Paired-Sample Microbial Ecology Experiments – Scott W. Olesen – PLOS ONE

More microbiology

Self-driven jamming in growing microbial populations – Morgan Delarue – bioRxiv

Review: Advances in Understanding Bacterial Pathogenesis Gained from Whole-Genome Sequencing and Phylogenetics – Elizabeth Klemm – Cell Host & Microbe

Microbes in the news

Osel, Inc.’s Lead Product LACTIN-V Enters Phase 2b Study to Prevent Recurrence of Bacterial Vaginosis– Digital Journal

Bacteria Battle Can Lead to Dandruff – Jennifer Viegas – Discovery
Bacteria the yin and yang of dandruff, says study – MedicalXpress

New Microbiome Research Tool Offers Potential to Revolutionise Drug Development
– PR Newswire

Experts react to ‘waste of money’ headlines against probiotics – Adi Menayang – NutraIngredients

How scientists are harnessing the ice-making powers of bacteria – Zach St. George – The Week

Researchers Engineer Bacteria to Streamline Biofuel Production Process – IndiaWest

New Microbiome Research Tool Offers Potential to Revolutionise Drug Development – PR Newswire

Twin study finds that gut microbiomes run in families – EurekAlert

From the American Urological Association meeting: Gut Bugs Differ in Chronic Prostatitis. Difference in taxa may aid biomarker, researchers say – MedPageToday

In Infants With Necrotizing Enterocolitis, Gut Dysbiosis Precedes Disease – Julie A. Jacob – JAMA

Science, publishing, and career

Reminder to deposit DNA sequences – Mark Blaxter – Science

Unexpected revelations for study volunteer: What health information do researchers owe the volunteers in their studies – Jennifer Couzin-Frankel – Science

Bik’s Picks

WATCH: What happened to astronaut Scott Kelly’s DNA during his year in space – Carl Zimmer – STAT News

May 11, 2016

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Microbiomes in low-income human habitats, graph mining for sequence datasets, and a PhD Comics video on the microbiome.

Events

The Barcelona Debates on The Human Microbiome – June 30th and July 1st, 2016 – Barcelona

2016 Molecular Genetics of Bacteria and Phages Meeting in Madison, Wisconsin – August 8-12

General microbiome

Book: Microbiota of the Human Body – Implications in Health and Disease – Editor: Andreas Schwiertz – Springer

Human skin microbiome

Analysis of Facial Implants for Bacterial Biofilm Formation Using Scanning Electron Microscopy – Thomas J. Walker – JAMA Facial Plastic Surgery

Human gut microbiome

Interconnected microbiomes and resistomes in low-income human habitats – Erica C. Pehrsson – Nature

Review: The human gut microbiota and its interactive connections to diet – C. Milani – Journal of Human Nutrition and Dietetics

Editorial: The Bugs Within Our Body: The Human Microbiota – DJ Philpott – Clinical Pharmacology & Therapeutics

Plant, root, and soil microbiome

Fate of classical faecal bacterial markers and ampicillin-resistant bacteria in agricultural soils under Mediterranean climate after urban sludge amendment – Clarissa Gondim-Porto – Science of the Total Environment

Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi – Stéphane Hacquard – Nature Communications

Gypsum amendment to rice paddy soil stimulated bacteria involved in sulfur cycling but largely preserved the phylogenetic composition of the total bacterial community – Susanne Wörner – Environmental Microbiology Reports

Built environment microbiome

Interconnected microbiomes and resistomes in low-income human habitats – Erica C. Pehrsson – Nature

Metagenomics and bioinformatics

Graph mining for next generation sequencing: leveraging the assembly graph for biological insights – Julia Warnke-Sommer – BMC Genomics

More microbiology

Phenotypic heterogeneity driven by nutrient limitation promotes growth in fluctuating environments – Frank Schreiber – Nature Microbiology

Microbes in the news

Video: The Hidden World of Microbiomes – PhD Comics

Microbiome Monday: What Are You Made Of? – American Museum of Natural History

How dust from the Sahara fuels poisonous bacteria blooms in the Caribbean – Sarah Kaplan – Washington Post

UGA study finds Saharan dust affects marine bacteria, potential pathogen Vibrio
Vibrio can cause serious illness in humans, other marine organisms – EurekAlert

Thank Me Later: New Planet-Saving Bacteria Eats Switchgrass, Makes Biofuel – Tina Casey – Clean Technica

Game-Changing Bacteria Transmits Tuberculosis Through the Skin – HCP Live

Narrow spectrum antibiotic kills pathogens without killing good bacteria – EurekAlert

Dr Paul Blatchford awarded Emerging Researcher Grant – Press Release: Plant and Food Research

The Eye of a Microbial Camera – Nils Schuergers and Tchern Lenn – Natural History Mag

Science, publishing, and career

There’s a huge gender pay gap for STEM careers — just one year after graduation – Brian Resnick – Vox

Young women in STEM fields earn up to one-third less than men – EurekAlert

Bik’s Non-Microbiology Picks

Coral snakes predict the evolution of mimicry across New World snakes – Alison R. Davis Rabosky – Nature Communications

Meet the scientist debunking every dumb food myth on the internet
For every pseudoscientific blog parroting the latest trend, Yvette d’Entremont has a fact-based response – Diana Duong – Chatelaine

Is it safe to eat a newspaper? A Washington Post columnist is about to find out – Damian Garde – STAT news