Events and jobs
Post-doc in High-Throughput Metagenomics – University of Cambridge
Microbes in the news
Before you head out to the beach this weekend, check bacteria levels – ABC News
Oil-Munching Bacteria Helped Clean Up the Deepwater Horizon Oil Spill – Cynthia Wallentine, Invisiverse
Bacteria Hysteria
Here’s What the Gross Bacteria on Your Expired Makeup Really Looks Like – Erin Reimel, Glamour Magazine
General microbiome
The microbiome in hematopoietic stem cell transplant recipients and cancer patients: Opportunities for clinical advances that reduce infection – AY Koh – PLoS Pathogens
Research Highlight: New insights into the BAT–liver–gut axis – A Morris – Nature Reviews
Biodiversity and ecosystem function: making sense of numerous species interactions in multi-species communities – C Brophy – Ecology
Obstruction of pilus retraction stimulates bacterial surface sensing – CK Ellison – bioRxiv
Human gut microbiome
Hospital association of the gut microbiota mobilome in preterm infants – A Ravi – Pediatric Research
Human respiratory microbiome
Maturation of the Infant Respiratory Microbiota, Environmental Drivers and Health Consequences: A Prospective Cohort Study – AATM Bosch – Am J Respir Crit Care Med.
Review: Perna canaliculus and the Intestinal Microbiome – ET Saltzman – Marine Drugs
Animal microbiome
Host-specific associations affect the microbiome of Philornis downsi, an introduced parasite to the Galápagos Islands – MY Ben – Molecular Ecology
Comparative genome analysis of the Flavobacteriales bacterium strain UJ101, isolated from the gut of Atergatis reticulatus – JA Yang – Journal of Microbiology
Plant, root and soil microbiome
Ammonia oxidizer populations vary with nitrogen cycling across a tropical montane mean annual temperature gradient – S Pierre – Ecology
Bacterial periphytic communities related to mercury methylation within aquatic plant roots from a temperate freshwater lake (South-Western France) – S Gentès – Environ Sci Pollut Res Int.
Consistently inconsistent drivers of microbial diversity and abundance at macroecological scales – JN Hendershot – Ecology
Living cover crops have immediate impacts on soil microbial community structure and function – DM Finney – Journal of Soil and Water Conservation
Draft Genome Sequence of Pseudomonas koreensis CI12, a Bacillus cereus “Hitchhiker” from the Soybean Rhizosphere – GL Lozano – Genome Announcements
Colonization and Maize Growth Promotion Induced by Phosphate Solubilizing Bacterial Isolates – Y Li – International Journal of Molecular Sciences
Biogeography and ecological diversity patterns of rare and abundant bacteria in oil-contaminated soils – S Jiao – Molecular Ecology
Water microbiome and extremophiles
Organohalide respiration with chlorinated ethenes under low pH conditions – Y Yang – Environmental Science & Technology
Microbes in news
These Cleaning Bots Can Zap Bacteria Out of Your Water Supply in Minutes – D Nield – Science Alert
Four strains of bacteria work together to produce pigment for food and cosmetics industry – ML Martialay – Phys.org
Texas: Fecal bacteria levels at Gulf beaches ahead of Fourth of July holiday weekend – K Bradshaw – mySA
Gut microbiome’s link to the brain – S Downing – Nine.com
Breast Milk Bacteria are Important for Establishing Infant Gut Microbiome – S Parmar – Medical News Bulletin
Fig Enzyme could Help to fight Infection and Heal Wounds – DN Gameiro – Labiotech.eu
Gut Health: The Next Mega-Trend in Health and Wellness – H Schieber – Researchci
I spent three days as a hunter-gatherer to see if it would improve my gut health – T Spector – Medical Xpress
Altering gut bacteria pathways may stimulate fat tissue to prevent obesity – Medical Xpress
The broiler chicken intestine – an apt target for proteomic studies – E O’Reilly – BMC Blog Network
A few gut microbiome reviews, apparently a simple bacterial community in bullet ants, circadian rhythm of rhizosphere bacterial communities, and you might want to think twice before you step into the ocean for a swim this summer.
General microbiology
Mapping quorum sensing onto neural networks to understand collective decision making in heterogeneous microbial communities – Tahir Yusufaly & James Q. Boedicker – ePub in Physical Biology, first in arXiv
Cheating fosters species co-existence in well-mixed bacterial communities – Anne Leinweber, R Fredrik Inglis and Rolf Kümmerli – ISME Journal
One ligand, two regulators and three binding sites: How KDPG controls primary carbon metabolism in Pseudomonas – Rosaria Campilongo et al. – PLoS Genetics
PrePrint: Statistics and simulation of growth of single bacterial cells: illustrations with B. subtilis and E. coli – Johan H. van Heerden et al. – bioRxiv
Performance of electro-spun carbon nanofiber electrodes with conductive poly(3,4-ethylenedioxythiophene) coatings in bioelectrochemical systems – Juan J.L. Guzmana & Meryem O. Pehlivaner Kara et al. – Journal of Power Sources
Press: Bacteria-coated nanofiber electrodes digest pollutants – Blaine Friedlander – Phys.org
Human skin microbiome
Review: Keratinocytes as sensors and central players in the immune defense against Staphylococcus aureus in the skin – Katharina Bitschar et al. – Journal of Dermatological Science
Human gut microbiome
Review: The nutrition-gut microbiome-physiology axis and allergic diseases – Craig McKenzie – Immunological Reviews
16S sequencing and functional analysis of the fecal microbiome during treatment of newly diagnosed pediatric inflammatory bowel disease – Ashton JJ et al. – Medicine (Baltimore)
Review: The Critical Roles of Polysaccharides in Gut Microbial Ecology and Physiology – Nathan T. Porter and Eric C. Martens – Annual Reviews of Microbiology
Review: Gut Microbiota as a Target for Preventive and Therapeutic Intervention against Food Allergy – Rosita Aitoro et al. – Nutrients
Two distinct metacommunities characterize the gut microbiota in Crohn’s disease patients – Qing He & Yuan Gao et al. – GigaScience
Animal experiments
PrePrint: Clostridium difficile colonizes alternative nutrient niches during infection across distinct murine gut microbiomes – Matthew L Jenior et al. – bioRxiv
Animal microbiome
PrePrint: Bacterial community profiles and Vibrio parahaemolyticus abundance in individual oysters and their association with estuarine ecology – Ashley L. Marcinkiewicz et al. – bioRxiv
Diversity and Persistence of the Gut Microbiome of the Giant Neotropical Bullet Ant – Corrie S. Moreau & Benjamin E. R. Rubin – Integrative and Comparative Biology
PrePrint: Gut microbiota in the burying beetle, Nicrophorus vespilloides, provide colonization resistance against larval bacterial pathogens – Yin Wang & Daniel Rozen – bioRxiv
Plant, root and soil microbiome
Effects of habitat constraints on soil microbial community function – Naoise Nunan et al. – Scientific Reports
Diurnal cycling of rhizosphere bacterial communities is associated with shifts in carbon metabolism – Christopher Staley et al. – Microbiome
Biological control of Pythium, Rhizoctonia and Sclerotinia in lettuce: the plant protective activity of the bacterium Paenibacillus alvei K165 is associated with the induction of systemic resistance – G. Fatouros et al. – Plant Pathology
Water and extremophile microbiome
Membrane biofilm communities in full-scale membrane bioreactors are not randomly assembled and consist of a core microbiome – Gerald K. Matar & Samik Bagchi et al. – Water Research
Comparison of two bioinformatics tools used to characterize the microbial diversity and predictive functional attributes of microbial mats from Lake Obersee, Antarctica – Hyunmin Koo et al. – Journal of Microbiological Methods
Built environment
Hospital Building and Healthcare Associated Infections (HAIs) in terms of total contamination data and cases grouped by department/areas – Shadha M. Abbas Al Asadi – Scientific Journal of Medical Research
Microbes in the news
The Bugs That Keep Us Safe – Maria-Luisa Alegre – American Journal of Transplantation
Study on human skin microbiome finds archaea abundance associated with age – Phys.org
The Dust Storm Microbiome – Weismann Institute of Science – Laboratory Equipment
Starbucks’ iced coffee may have fecal bacteria in it — so do all these other things – Donovan Harrell – Miami Herald (BBC investigation)
Bacteria change a liquid’s properties and escape entrapment – Gail Mccormick – Phys.org
Only association: Gut feelings are real: Some people have stomach bacteria that makes them more anxious and stressed, study shows – DailyMail
Elevated bacteria counts found at 4 Island beaches – Rick Kelley – Valley Morning Star
Plasmids: traffickers of antibiotic resistance – Modernising Medical Microbiology – University of Oxford
Microbes on the market
Diabetes: J&J and Seventure Partners launch investment – tg – European Biotechnology
Global Microbiome Drugs Market 2017- Pfizer, Second Genome , Seres Therapeutics, MaaT Pharma, Enterome Bioscience – Nakul Shirke – Daily Hover
Lots of interesting pre-prints in this post that might be worth following! Also a blog post on some cool science art with kombucha, as well as a lot of articles on rhizosphere-microbe interactions.
Events and jobs
Research Opportunities in Molecular Microbiology – Washington University in St. Louis
PhD scholarship in Metagenomics analysis and systems biology – Danmarks Tekniske Universitet
General microbiome
Microbiome yarns: microbial forensics for auditing provenance in global food chains – Timmis et al. – Microbial Biotechnology
Adjuncts and alternatives in the time of antibiotic resistance and in-feed antibiotic bans – Brüssow – Microbial Biotechnology
Human gut microbiome
Bacteria facilitate viral co-infection of mammalian cells and promote genetic recombination – Erickson et al. – bioRXiv
Chemical transformation of xenobiotics by the human gut microbiota – Koppel et al. – Science
Distinct gut microbiome patterns associate with consensus molecular subtypes of colorectal cancer – Purcell et al. – bioRXiv
Animal microbiome
Whole genome sequencing-based detection of antimicrobial resistance and virulence in non-typhoidal Salmonella enterica isolated from wildlife – Thomas et al. – bioRXiv
Plant, root, and soil microbiome
Antagonism between two root-associated beneficial Pseudomonas strains does not affect plant growth promotion and induced resistance against a leaf-chewing herbivore – Pangesti et al. – FEMS Microbiology Ecology
Bioelectrochemical approach for control of methane emission from wetlands – Liu et al. – Bioresource Technology
The biocontrol agent Pseudomonas chlororaphis PA23 primes Brassica napus defenses through distinct gene networks – Duke et al. – BMC Genomics
Delftia rhizosphaerae sp. nov. isolated from the rhizosphere of Cistus ladanifer – Carro et al. – International Journal of Systematic and Evolutionary Microbiology
Synthesis and Secretion of Isoflavones by Field-Grown Soybean – Sugiyama et al. – Plant Cell Physiology
The Variation in the Rhizosphere Microbiome of Cotton with Soil Type, Genotype and Developmental Stage – Qiao et al. – Scientific Reports
Complete Genome Sequence of Bacillus paralicheniformis MDJK30, a Plant Growth -Promoting Rhizobacterium with Antifungal Activity – Wang et al. – Genome Anouncements
Extensive Overlap of Tropical Rainforest Bacterial Endophytes between Soil, Plant Parts, and Plant Species – Haruna et al. – Microbial Ecology
Phytoavailability of Cr in Silene vulgaris: The role of soil, plant genotype and bacterial rhizobiome – García-Gonzalez et al. – Ecotoxicology and Environmental Safety
Water and extremophile microbiome
Sulfolobus islandicus meta-populations in Yellowstone National Park hot springs – Campbell et al. – Environmental Microbiology
Bottled aqua incognita: Microbiota assembly and dissolved organic matter diversity in natural mineral waters – Lesaulnier et al. – bioRXiv
Techniques
Rapid whole genome amplification and sequencing of low cell numbers in a bacteraemia model – Anscombe et al. – bioRXiv
Microbes in the news
Do Probiotics Really Work? – Ferris Jabr – Scientific American
Fungi and bacteria team up in dental plaque – Evans – LabRoots
Scientists spy on the secret inner life of bacteria – Saey – Science News
Biofilms: The eradication has begun – McGill University Health Centre – Science Daily
Bacteria and Mental Health: Gut Bacteria Linked to Bipolar Disorder – Villamil – Medical News Bulletin
The Kombucha Craze Steps into Art and the Science of the Microbiome – Fernández – Labiotech
Microbes on the market
Global Microbiome Drugs Industry Market Research Report 2017 – Medgadget
Effects of weight loss treatment on gut microbiota and serum metabolites, mouse gut microbiota can alter visceral sensitivity, a review discussing the microbiota’s ability to shape the maternal immune system.
Pregnancy and early life
Review: The unique immunological and microbial aspects of pregnancy – Gil Mor – Nature Reviews Immunology
Human oral microbiome
Review: Microbiome and Microbial Biofilm Profiles of Peri-Implantitis: A Systematic Review – Gloria Inés Lafaurie – Journal of Periodontology
Human gut microbiome
Bifidobacterium-Rich Fecal Donor May Be a Positive Predictor for Successful Fecal Microbiota Transplantation in Patients with Irritable Bowel Syndrome – S Mizuno – Digestion
Microbiota in anorexia nervosa: The triangle between bacterial species, metabolites and psychological tests – Francesca Borgo – PLOS ONE
Animal experiments
Fructo-oligosaccharides and intestinal barrier function in a methionine–choline-deficient mouse model of nonalcoholic steatohepatitis – Kotaro Matsumoto – PLOS ONE
Microbiota regulates visceral pain in the mouse – Pauline Luczynski – eLife
Metagenomic characterization of the effect of feed additives on the gut microbiome and antibiotic resistome of feedlot cattle – Milton Thomas – bioRxiv
Animal microbiome
Combining ‘omics and microscopy to visualize interactions between the Asian citrus psyllid vector and the Huanglongbing pathogen Candidatus Liberibacter asiaticus in the insect gut – Angela Kruse – PLOS ONE
Plant, root, and soil microbiome
Application of struvite alters the antibiotic resistome in soil, rhizosphere, and phyllosphere – Qing-Lin Chen – Environmental Science & Technology
Water and extremophile microbiome
Synergistic hydrolysis of xylan using novel xylanases, β-xylosidases, and an α-l-arabinofuranosidase from Geobacillus thermodenitrificans NG80-2 – Di Huang – Applied Microbiology and Biotechnology
Longitudinal variation of microbial communitiesin benthic biofilms and association with hydrological and physicochemical conditions in glacier-fed streams – Ze Ren – Freshwater Science
Control of Sulfide Production in High Salinity Bakken Shale Oil Reservoirs by Halophilic Bacteria Reducing Nitrate to Nitrite – Biwin A An – Frontiers in Microbiology
Phages and viruses
Viral and Bacterial Communities of Colorectal Cancer – Geoffrey D Hannigan – bioRxiv
Plasmids, Viruses, And Other Circular Elements In Rat Gut – Tue Sparholt Jørgensen – bioRxiv
Bioinformatics
The metagenomic data life-cycle: standards and best practices – Petra ten Hoopen – GigaScience
PhylOligo: a package to identify contaminant or untargeted organism sequences in genome assemblies – Ludovic Mallet – Bioinformatics
Metabolomics
Gut microbiome and serum metabolome alterations in obesity and after weight-loss intervention – Ruixin Liu – Nature Medicine
Integrating Microbiome and Metabolome Data to Understand Infectious Airway Disease – Robert A Quinn – American Journal of Respiratory and Critical Care Medicine
Coupling targeted and untargeted mass spectrometry for metabolome-microbiome-wide association studies of human fecal samples – Alexey V Melnik – Analytical Chemistry
Techniques
Incorporating comparative genomics into the Design-Test-Learn cycle of microbial strain engineering – Maria Sardi – FEMS Yeast Research
Different amplicon targets for sequencing-based studies of fungal diversity – Francesca De Filippis – Applied and Environmental Microbiology
Microbes in the news
Modified viruses deliver death to antibiotic-resistant bacteria – Sara Reardon – Nature
Microbes on the market
EnteroBiotix raises £500k in first round of equity funding – Philip Gates – Insider.co.uk
Microbiotica To Present At Microbiome Drug Development Summit – BioSpace
Bacteria art
MIT Researchers Use Light-Illuminated Bacteria to Make ‘Living’ Pictures – Kristin Fawcett – Mental Floss
The world’s art is under attack—by microbes – Kate Baggaley – Popular Science
Science, publishing, and career
Editorial: Don’t let Europe’s open-science dream drift – Nature
Today’s Microbiome Digest has quite a few articles from water environment. Both articles I would like to highlight are with cyanobacteria as stars. The first one from Anne D. Jungblut reports on Antarctic cynobacteria diversity, while the second one reveals the new freshwater cyanobacterial genome. One more thing to highlight come from news. Exxon Mobil Corps and Sintetic Genomics Inc have announced a new breakthrough with genetically modified algae which was able to convert 40% of CO2 to lipids, up from the previous 15%. Algae are still far away from being able to run the process at commercial scale and replace fossil fuels, but we love algae! Enjoy this summer reading.
Events and jobs
Microbiome Research Scientist (BS or MS or PhD) – St. John of God Foundation for Research and Teaching, Barcelona, Spain
Quality Associate Specialist – Merck, Durham, NC, US
Microbiology Manager OR Microbiology Laboratory Manager Opening, Madison, WI, US
General microbiome
A null model for microbial diversification – Timothy J. Straub – PNAS
Pregnancy and early life
Association between breast milk bacterial communities and establishment and development of the infant gut microbiome – JAMA Pediatrics
Human skin microbiome
Topical antimicrobial treatments can elicit shifts to resident skin bacterial communities and reduce colonization by competitors – Adam J. SanMiguel – Antimicrobial Agents and Chemotherapy
Human gut microbiome
Liver transplant modulates gut microbial dysbiosis and cognitive function in cirrhosis – Jasmohan S. Bajaj – Liver Transplatation
How members of the human gut microbiota overcome the sulfation problem posed by glycosaminoglycans – Alan Cartmell – PNAS
Microbiome restoration diet improves digestion, cognition and physical and emotional wellbeing – Kate Lawrence – PLOS
Animal microbiome
The role of adaptive immunity as an ecological filter on the gut microbiota in zebrafish – Keaton Stagaman – The ISME Journal
Plant, root, and soil microbiome
Biofilm formation enables free-living nitrogen-fixing rhizobacteria to fix nitrogen under aerobic conditions – Di Wang – The ISME Journal
Novel antibiotic resistance determinants from agricultural soil exposed to antibiotics widely used in human medicine and animal farming – Calvin Ho-Fung Lau – Applied and Environmental Microbiology
Water and extremophile microbiome
Animal-like prostaglandins in marine microalgae – Valeria Di Dato – The ISME Journal
Niche partitioning of diverse sulfur-oxidizing bacteria at hydrothermal vents – Dimitri V Meier – The ISME Journal
Identification of dimethylamine monooxygenase in marine bacteria reveals a metabolic bottleneck in the methylated amine degradation pathway – Ian Lidbury – The ISME Journal
DNA extraction replicates improve diversity and compositional dissimilarity in metabarcoding of eukaryotes in marine sediments – Anders Lanzén – PLOS
Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters – David M Needham – The ISME Journal
Integrated metabolism in sponge–microbe symbiosis revealed by genome-centered metatranscriptomics – Lucas Moitinho-Silva – The ISME Journal
Spontaneous mutations of a model heterotrophic marine bacterium – Ying Sun – The ISME Journal
Plastid thylakoid architecture optimizes photosynthesis in diatoms – Serena Flori – Nature Communications
Evolutionary radiation of lanthipeptides in marine cyanobacteria – Andres Cubillos-Ruiz – PNAS
Using Captain Scott’s Discovery specimens to unlock the past: has Antarctic cyanobacterial diversity changed over the last 100 years? – Anne D. Jungblut – Proceedings of the Royal Society B
Novel Synechococcus Genomes Reconstructed from Freshwater Reservoirs – Pedro J. Cabello-Yeves – Frontiers in Microbiology
Functional Gene Diversity and Metabolic Potential of the Microbial Community in an Estuary-Shelf Environment – Yu Wang – Frontiers in Microbiology
Atribacteria from the Subseafloor Sedimentary Biosphere Disperse to the Hydrosphere through Submarine Mud Volcanoes – Tatsuhiko Hoshino – Frontiers in Microbiology
Phages and viruses
Effect of acute predation with bacteriophage on intermicrobial aggression by Pseudomonas aeruginosa – Patrick R. Secor
Bioinformatics
The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data – Gerben Menschaert –
Microbes in the news
Zombie bacteria and viruses in melting permafrost are waking up
ExxonMobil and Synthetic Genomics Report Breakthrough in Algae Biofuel Research
Gut microbiome changes linked to numerous biomarkers of type 2 diabetes
Funky tasting beer? Biofilms may be to blame, MSU researchers say
Bacteria in Your Coughs And Sneezes Can Stay Alive in The Air For Up to 45 Minutes
Microbes on the market
This Company Uses the Human Microbiome to Discover New Disease Mechanisms
Today: A few job searches, a lot of microbes in the news (as we all ponder our bread choices), and some articles about microbes in the wild.
Events and jobs
Assistant Professor-Microbiology (Tenure-Track) – The College of New Jersey
Microbiology Technician – Matchtech, England
Microbiology Analyst – Stericycle, Massachusetts
Animal microbiome
Patterns of seasonality and group membership characterize the gut microbiota in a longitudinal study of wild Verreaux’s sifakas (Propithecus verreauxi) – Springer et al, Ecology and Evolution
Water and extremophile microbiome
Undocumented Potential For Primary Productivity In A Globally-Distributed Bacterial Photoautotroph – Graham et al, bioRxiv (pre-print)
Microbes in the news
White or Whole Wheat Bread Study May Shed Light on Diet Failure – Patrick Keeffe, HealthLine
Gene transfer keeps bacteria fit – University of Basel, Phys.org
In dying, blood-starved heart, bacteria injections offer cellular life support – Beth Mole, Ars Technica
New antibiotic effective against drug-resistant bacteria – Rutgers University, Science Daily
Gut microbiome focus: Differences in the gut microbiome between children and adults can mediate the metabolism of arsenic possibly leading to differences in exposure risk, the gut microbiome’s ability to protect against salmonella infection is dependent on the IFNy producing bacteria, the microbiome of insoluble fibre is characterized, and a new in vitro technique to interrogate intestinal transport of microbiota and antigens. Plus an overview of the world data centre for microorganisms, and MicroScope for microbial genome annotation.
Microbiology Technologist OR Microbiology Medical Technologist – Orlando Florida
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Conference: Current concepts in chronic inflammatory diseases: Interactions between microbes, cellular metabolism, and inflammation – Holger Garn – Allergy and Clinical Immunology
Characterisation of Roseomonas mucosa isolated from the root canal of an infected tooth – Nina Diesendorf – BMC Research Notes
* Interindividual variability of soil arsenic metabolism by human gut microbiota using SHIME model – Naiyi Yin – Chemosphere
* Inter-individual differences determine the outcome of wheat bran colonization by the human gut microbiome – Kim De Paepe – Environmental Microbiology
Review: Microbiota Therapy for Clostridium difficile and Antibiotic Resistant Enteric Infections – Brittany Lewis – Annual Review of Microbiology
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* Enhancement of IFNγ Production by Distinct Commensals Ameliorates Salmonella-Induced Disease – Sophie Thiemann – Cell Host and Microbe
Efficacy of antibiotic treatment of implant-associated Staphylococcus aureus infections with moxifloxacin, flucloxacillin, rifampin, and combination therapy: an animal study – Felix Greimel – Drug Design, Development and Therapy
The scales of the zebrafish: host–microbiota interactions from proteins to populations – Adam Burns – Current Opinion in Microbiology
IL-17 Receptor A Maintains and Protects the Skin Barrier To Prevent Allergic Skin Inflammation – Achilleas Floudas – The Journal of Immunology
Irf4-dependent CD103+CD11b+ dendritic cells and the intestinal microbiome regulate monocyte and macrophage activation and intestinal peristalsis in postoperative ileus – Judith-Mira Pohl – Gut
Effect of three lactobacilli with strain-specific activities on the growth performance, faecal microbiota and ileum mucosa proteomics of piglets – Yating Su – Journal of Animal Science and Biotechnology
Characterization of the regulation of a plant polysaccharide utilization operon and its role in biofilm formation in Bacillus subtilis – Cameron Habib – PLOSone
Grazing of leaf-associated Cercomonads (Protists: Rhizaria: Cercozoa) structures bacterial community composition and function – Sebastian Flues – Environmental Microbiology
Green alder (Alnus viridis) encroachment shapes microbial communities in subalpine soils and impacts its bacterial or fungal symbionts differently – G Schwob – Environmental Microbiology
The role of organic acids on microbial deterioration in the Radix pseudostellariae rhizosphere under continuous monoculture regimes – Hongmiao Wu – Scientific Reports
Specificity traits consistent with legume-rhizobia coevolution displayed by Ensifer meliloti rhizosphere colonization – María Eugenia Salas – Environmental Microbiology
Cascading influence of inorganic nitrogen sources on DOM production, composition, lability and microbial community structure in the open ocean – SJ Goldberg – Environmental Microbiology
Functional diversity and redundancy across fish gut, sediment, and water bacterial communities – Arthur Escalas – Environmental Microbiology
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Preprint: Bacteria defend against phages through type IV pilus glycosylation – Hanjeong Harvey- bioRxiv
Dissecting the human microbiome with single-cell genomics – Andrew Tolonen – Genome Medicine
* A human intestinal M-cell-like model for investigating particle, antigen and microorganism translocation – Ana Beloqui – Nature Protocols
* World data centre for microorganisms: an information infrastructure to explore and utilize preserved microbial strains worldwide – Linhuan Wu – Nucleic Acids Research
* MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes – David Vallenet – Nucleic Acids Research
Bacteriocin Gene-Trait matching across the complete Lactobacillus Pan-genome – Fergus Collins – Scientific Reports
Screening and characterization of a novel thermostable lipase with detergent-additive potential from the metagenomic library of a mangrove soil – Leli Tang – Gene
Preprint: Phenotypic consequences of RNA polymerase dysregulation in Escherichia coli – Paramita Sarkar – bioRxiv
Preprint: Campylobacter jejuni transcriptome changes during loss of culturability in water – Christina Bronowski – bioRxiv
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You Are What You Eat, And What You Eat Is Millions of Microbes – Kyle Frischkorn – Smithsonian.com
John Bartlett’s Take on Critical Infectious Disease Topics: Part 3 – John Bartlett – Medscape
Placental Microbiome – Sally Robertson – Life Sciences News
Light-activated bacteria protect rats from heart attacks – Michael Price – Science
These light-eating bacteria could one day help us survive heart attacks – Alessandra Potenza – The Verge
Scientists image molecular machinery never before seen in bacteria – Brooke Hays – UPI
Still quite a few articles on rhizosphere, and antibiotic resistance remains a hot topic, both in the literature and media. How about a Micro-lympics?
Jobs
Microbiology Technician – Seattle Washington
Events
*Annual Microbiology Retreat µlympics – Indiana University
General microbiology
*Commentary: History of Medicine: Origin of the Term Microbiome and why it Matters – Susan L. Prescott – Human Microbiome Journal
A Stoichioproteomic Analysis of Samples from the Human Microbiome Project – Briana Vecchio-Pagan – Frontiers in Microbiology
Adaptor protein mediates dynamic pump assembly for bacterial metal efflux – Ace George Santiago et al. – PNAS
Press: E. coli bacteria’s defense secret revealed – Bill Steele – Phys.org
Uncharacterized bacterial structures revealed by electron cryotomography – Megan J. Dobro et al. – Journal of Bacteriology
Press: Researchers discover new structures in bacteria, seek to determine function – Phys.org
Microbots decorated with silver nanoparticles kill bacteria in aqueous media – Diana Vilela et al. – Applied Materials and Interfaces
Human gut microbiome
Book chapter: The gut microbiome and inflammatory bowel disease – Maire A. Conrad et al. – Pediatric Inflammatory Bowel Disease (Ed. Petar Mamula et al.)
Quantitative systems pharmacology and the personalized drug-microbiota-diet axis – Ines Thiele et al. – Current Opinion in Systems Biology
Human nearly-sterile sites
Endometrial microbiota—new player in town – Inmaculada Moreno & Jason M. Franasiak – Fertility and Sterility
Contributions of the maternal oral and gut microbiome to placental microbial colonization in overweight and obese pregnant women – Luisa F. Gomez-Arango et al. – Scientific Reports
Plant, root and soil microbiome
Stability and dynamics of enzyme activity patterns in the rice rhizosphere: Effects of plant growth and temperature – Tida Ge et al. – Soil Biology and Biochemistry
Doctoral thesis: Exploring candidate genes and rhizosphere microbiome in relation to iron cycling in Andean potatoes – Hua Xiao – Virginia Tech
Analysis of bacterial communities in rhizosphere soil of continuously cropped healthy and diseased konjac – Jinping Wu et al. – World Journal of Microbiology and Biotechnology
*Fishing bacteria with a nanonet – F. De Cesare et al. – Materials Today
Isolation, identification, characterization, and screening of rhizospheric bacteria for herbicidal activity – Charles Oluwaseun Adetunji et al. – Organic Agriculture
Bacterial communities on wheat grown under long-term conventional tillage and no-till in the Pacific Northwest of the US – Chuntao Yin et al. – Phytobiomes
*Dispersal enhances beta diversity in nectar microbes – Rachel L. Vannette & Tadashi Fukami – Ecology Letters
Temporal dynamics of soil microbial communities below the seedbed under two contrasting tillage regimes – Florine Degrune et al. – Frontiers in Microbiology
Water and extremophile microbiome
Effect of phosphate-solubilizing bacteria on phosphorus dynamics and the bacterial community during composting of sugarcane industry waste – German A. Estrada-Bonilla et al. – Systematic and Applied Microbiology
Colonization habitat controls biomass, composition, and metabolic activity of attached microbial communities in the Columbia River hyporheic corridor – Noah Stern et al. – Applied and Environmental Microbiology
Prokaryote species richness is positively correlated with eukaryote abundance in wastewater treatment biofilms – I.L. Angell et al. – Letters in Applied Microbiology
Built environment
The bacterial composition of ventilation filter dust in Norwegian pre-school nurseries – Anders B Nygaard & Colin Charnock – Indoor and Built Environment
Factors Determining the Biodiversity of Halophilic Microorganisms on Historic Masonry Buildings – Anna Otlewska et al. – Microbes and Environments
Phages and viruses
The pepper virome: natural co-infection of diverse viruses and their quasispecies – Yeonhwa Jo et al. – BMC Genomics
Bioinformatics
A novel method to determine the minimum number of sequences required for reliable microbial community analysis – Jiajia Ni et al. – Journal of Microbiological Methods
*PrePrint: Critical Assessment of Metagenome Interpretation − a benchmark of computational metagenomics software – Alexander Sczyrba et al. – bioRxiv
Microbes in the news
Live antibiotics use bacteria to kill bacteria – Elizabeth Eaton – Science News
Will a New Drug to Fight Antibiotic Resistant Bacteria Really Work? – Shawn Radcliffe – Healthline news
Former Pfizer Scientist Is Resurrecting Projects To Solve The Multidrug Resistant Bacteria Problem – John LaMattina – Forbes
The Algae That Devastated Florida’s Coasts Also Contained 28 Kinds Of Bacteria, Study Finds – Kate Stein – WGCU
Microbes on the market
DoggyBiome: studying the microbiome to improve dog health – AnimalBiome – Backerkit
Science, career and publishing
Book chapter: Women of Science – Laura E. Willis – Viewpoints on Media Effects: Pseudo-reality and Its Influence on Media Consumers (Ed. Carol M. Madere)
PrePrint: An elective course for medical students on innovation and entrepreneurship – Erik Reinertsen et al. – bioRxiv
Jobs and events
Two tenure-track assistant professor or associate professors – Department of Plant and Microbial Biology – College of Biological Sciences, University of Minnesota
Sign up for the webinar by Edward Messick, GENEWIZ – Topic: Metagenomics for Biomarker Discovery: Applications in Precision Medicine – Webinar date and time: June 14, 2017 at 5 PM
General microbiome
Ferrous Iron Efflux Systems in Bacteria – H Pi – Metallomics
Metagenomics of microbial and viral life in terrestrial geothermal environments – A Strazzulli – Reviews in Environmental Science and Bio/Technology
Bacterial Infections in Neonates Following Mupirocin-Based MRSA Decolonization: A Multicenter Cohort Study – R Pierce – Infection Control & Hospital Epidemiology
Human gut microbiome
Interindividual variability of soil arsenic metabolism by human gut microbiota using SHIME model – N Yin – Chemosphere
Report: Daily Changes in Composition and Diversity of the Intestinal Microbiota in Patients with Anorexia Nervosa: A Series of Three Cases – SC Kleiman – European Eating Disorders Review
Animal experiment
A Targeted Metabolomics Analysis Identifies Intestinal Microbiota-Derived Urinary Biomarkers of Colonization Resistance in Antibiotic-Treated Mice – ME Obrenovich – Antimicrobial Agents and Chemotherapy
Animal microbiome
Molecular dialogues with the microbiota: Lessons from the zebrafish intestine – K Guillemin – Mechanisms of Development
Plant, root and soil microbiome
The nodule microbiome; N2-fixing rhizobia do not live alone – P Martínez-Hidalgo – Phytobiomes Journal
Decreased plant productivity resulting from plant group removal experiment constrains soil microbial functional diversity – X Zhang – Global Change Biology
Turnover of carbon and phosphorus in the microbial biomass depending on phosphorus availability – M Spohn – Soil Biology and Biochemistry
Effect of soil preparation techniques on the biochemical properties and microbial communities of a citrus orchard after replanting and conversion into organic management – A Pérez-Piqueres – Applied Soil Ecology
Water microbiome and extremophile
Review: The Vulnerability and Resilience of Reef-Building Corals – HM Putnam – Current Biology
Bacterial and archaeal community structure of pan-Arctic Ocean sediments revealed by pyrosequencing – X Lin – Acta Oceanologica Sinica
Genetic diversity of nitrate reducing bacteria in marine and brackish water nitrifying bacterial consortia generated for activating nitrifying bioreactors in recirculating aquaculture systems – PG Preena – Aquaculture Research
Techniques
Integrated transcriptomic, proteomic and epigenomic analysis of Plasmodium vivax salivary-gland sporozoites – A Jex – bioRxiv
Discrimination of haloarchaeal genera using Raman spectroscopy and robust methods for multivariate data analysis – NE Dina – Journal of Raman Spectroscopy
Metabolomics
Comparative metabolomics in vanilla pod and vanilla bean revealing the biosynthesis of vanillin during the curing process of vanilla – F Gu – AMB Express
Phages
A highly specific phage defense system is a conserved feature of the Vibrio cholerae mobilome – BJ O’ Hara – PLoS Genetics
Built environment microbiome
Warm and wet: robust lipase-producing bacteria from the indoor environment – K Tanner – bioRxiv
Impacts of biostimulation and bioaugmentation on the performance and microbial ecology in methanogenic reactors treating purified terephthalic acid wastewater – M Liu – Water Research
More microbes
Viral Encephalitis of Unknown Cause: Current Perspective and Recent Advances – PGE Kennedy – Viruses
Protozoa and microbiome – SL Burgess – Infection and Immunity
Reciprocal control of motility and biofilm formation by the PdhS2 two-component sensor kinase of Agrobacterium tumefaciens – JE Heindl – bioRxiv
Intercellular communication via the comX-Inducing Peptide (XIP) of Streptococcus mutans – J Kaspar – bioRxiv
Hammondia hammondi has a developmental program in vitro that mirrors its stringent two host life cycle – SL Sokol – bioRxiv
Microbes in news
Engineering ‘good’ bacteria to kill bad ones – The Straits Times
White or wholemeal? It depends on your gut bacteria – A Middleton – Cosmos
Ixcela Announces Partnership with ORACLE TEAM USA to Improve Athletes’ Internal Health and Performance – Business Wire
New Study Finds Gut Bacteria May Inhibit Cancer Drugs – K Lant – Futurism
Therapy could stop superbugs on farms – P Ghosh – BBC News
SHU students travel to present phages research – P Parise – Setonian Online
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