Category Archives: Microbes in the News

May 15, 2017

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General microbiome

Plastics in the North Atlantic garbage patch: A boat-microbe for hitchhikers and plastic degraders – D Didier – Science of the Total Environment

Biodegradation and metabolic fate of levofloxacin via a freshwater green alga, Scenedesmus obliquus in synthetic saline wastewater – JQ Xiong – Algal Research

Ionic liquid-based reagents improve the stability of midterm fecal sample storage – L Hao – Journal of Microbiological Methods

Aerobic vaginitis: no longer a stranger – GGG Donders – Research in Microbiology –

The antibiotic resistome: gene flow in environments, animals and human beings – Y Hu – Frontiers of Medicine

 

Human respiratory microbiome

Neutrophil Extracellular Traps are associated with disease severity and microbiota diversity in Chronic Obstructive Pulmonary Disease – AJ Dicker – Journal of Allergy and Clinical Immunology

Airway Microbial Diversity is Inversely Associated with Mite-Sensitized Rhinitis and Asthma in Early Childhood – CY Chiu – Scientific Reports

Determination of nasal and oropharyngeal microbiomes in a multicenter population-based study – findings from Pretest 1 of the German National Cohort – MK Akmatov – Scientific Reports

Compositionally and functionally distinct sinus microbiota in chronic rhinosinusitis patients have immunological and clinically divergent consequences – EK Cope – Microbiome

 

Animal microbiome

Response of turkeys fed wheat-barley-rye based diets to xylanase supplementation – G González Ortis – Animal Feed Science and Technology

Bifidobacterium CECT 7765 modulates early stress-induced immune, neuroendocrine and behavioral alterations in mice – A Moya Pérez – Brain, Behavior, and Immunity

 

Water and extremophile

UV-Resistant Actinobacteria from High-Altitude Andean Lakes: Isolation, Characterization and Antagonistic Activities – MC Rasuk – Photochemistry and Photobiology

 

Techniques

A Tunable Protein Oscillator Controls Directional Movements In Myxococcus xanthus – M Guzzo – bioRxiv

Uncovering The Drivers Of Animal-Host Microbiotas With Joint Distribution Modeling – JR Bjork – bioRxiv

 

Microbes in news

Hospital superbugs – The Hans India

Market pressures and inadequate production are hampering access to essential antibiotics – EurekAlert

Learning the rules of antibiotics to make old drugs work on new bugs –  D Gitig – ARS Technica

Does Cooking Kill Probiotics? – KDA Traegner – Care2

Research team hopes to reduce size of tsunami using bacteria – The Mainichi

Antibiotic-resistant bacteria predate dinosaurs study reports – J Scalise – Science Recorder

Vexed childhood likely to cause irritable bowel syndrome (IBS) – NewsGram

Study suggests link between imbalanced gut microbiome and systemic sclerosis – UCLA Health

Microbiome leader Professor Borody joins researchers at the China Microbiota Transplantation Conference – MENAFN

How doctors could use viruses to kill drug-resistant bacteria – CTV News

Microbiologists find bugs, bacteria – and poo – lurking inside the UK’s cars – J Watkiss – Cambridge News

#Flint: As Mich. Gov. Snyder Signs $100,000,000 in Aid Into Law, Residents Warned Water Filters Harbor Bacteria – M Judge – The Root

Rutgers Researchers See Paper as a Defense Against Bacteria – J Murtha – Tap Into

Bacteria find clarified – S Silaitoga – The Fiji Times Online

The Filthiest, Most Bacteria Infested Places In Your Kitchen – Sky Valley Chronicle

May 13, 2017

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Events and jobs

Microbiology/Molecular Biology/Wildlife Disease Technician: Wisconsin – USGS – National Wildlife Health Center

Sr. Associate, Quality Control Microbiology – Moderna

Staff Research Associate, Anaerobic Microbiology – UC Berkeley

General microbiome

Perspective: The Microbiome-Mitochondrion Connection: Common Ancestries, Common Mechanisms, Common Goals – Alfredo Franco-Obregón – mSystems

Human gut microbiome

Systemic sclerosis is associated with specific alterations in gastrointestinal microbiota in two independent cohorts – Elizabeth R Volkmann – BMJ Open Gastroenterology

Review: Microbiota: Clostridia protect from gut infections in early life – Irene Vacca – Nature Reviews Microbiology

Animal microbiome

The malleable gut microbiome of juvenile rainbow trout (Oncorhynchus mykiss): Diet-dependent shifts of bacterial community structures – Stéphanie Céline Michl – PLOS ONE

Plant, root, and soil microbiome

Bacterial root microbiome of plants growing in oil sands reclamation covers – Eduardo Kovalski Mitter – Frontiers in Microbiology

Effect of Trichoderma harzianum on maize rhizosphere microbiome and biocontrol of Fusarium Stalk rot – Kandasamy Saravanakumar – Scientific Reports

Water and extremophile microbiome

Characterisation of Arctic Bacterial Communities in the Air above Svalbard – Lewis Cuthbertson – Biology

Diversity of bacteria and archaea from two shallow marine hydrothermal vents from Vulcano Island – Garabed Antranikian – Extremophiles

Unique and highly variable bacterial communities inhabiting the surface microlayer of an oligotrophic lake – Mylène Hugoni – Aquatic Microbial Ecology

Distribution and activity of benthic bacteria in four lakes in the Bory Tucholskie National Park (Poland) – Łukasz Kubera – Aquatic Microbial Ecology

Role of EPS, Dispersant and Nutrients on the Microbial Response and MOS Formation in the Subarctic Northeast Atlantic – Laura Duran Suja – Frontiers in Microbiology

Food microbiology

Impact of a Microbial Cocktail Used as a Starter Culture on Cocoa Fermentation and Chocolate Flavor – Igor Magalhães da Veiga Moreir – Molecules

Techniques

Harnessing the power of digital droplet PCR to conduct real-world microbial competitions – Helen A. Murphy – Molecular Ecology Resources

Microbes in the news

Lung microbiome – Sally Robertson – News-Medical.Net

Resistant Starch from Potatoes Offers Benefits to Gut Microbiome? – Michael Crane – Nutritional Outlook

Visualizing the Microbiome through Handmade Embroidery – Clara Rodríguez Fernández – labiotech

Microbes on the market

‘Imagine being able to edit the microbiome’ – TechAccel talks animal nutrition targeted innovation – Aerin Einstein-Curtis – Feed Navigator

Science, publishing, and career

Weill Cornell Aims For ‘Precision Metagenomics’ With Quantitative Computing – Neil Versel – GenomeWeb

May 12, 2017

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Highlighted articles today bring some interesting news about bacteria. in the first one study of Lebreton et al. shed light on the evolutionary history of pathogens, which evolved nearly indestructible properties and have become leading causes of modern antibiotic-resistant infections in hospitals. In the second highlighted article Schnettger et al. discover a natural mechanism by which our cells kill the bacterium responsible for tuberculosis (TB)  – without the use of antibiotics, meaning that even antibiotic-resistant
strains could be eliminated.

Events and jobs

Postdoctoral researcher – nitrogen-fixing bacteria and cereals

Postdoctoral Research Fellowship in Marine Phycology

General microbiome

Global Phylogenetic Analysis Of Escherichia coli And Plasmids Carrying The mcr-1 Gene Indicates Bacterial Diversity But Plasmid Restriction – Sebastien Matamoros – bioRxiv

Predictive compound accumulation rules yield a broad-spectrum antibiotic – Michelle F. Richter – Nature

Tracing the Enterococci from Paleozoic Origins to the Hospital – François Lebreton – Cell

The Threat of Antimicrobial Resistance on the Human Microbiome – Lauren Brinkac- Microbial Ecology

Evolutionary Biology Needs Wild Microbiomes – Sarah M. Hird – Frontiers in Microbiology

Pregnancy and early life

Association Between Breast Milk Bacterial Communities and Establishment and Development of the Infant Gut Microbiome – Pia S. Pannaraj – JAMA Pediatr

Oral microbiome

The Antibacterial Effect of Additional Photodynamic Therapy in Failed Endodontically Treated Teeth: A Pilot Study – Mohammad Asnaashari – Journal of Lasers in Medical Science

Microbiota Analysis of Biofilms on Experimental Abutments Mimicking Dental Implants: An in Vivo Model – Berta Cortés-Acha – Journal of Periodontology

Human vaginal microbiome

Comparison of the vaginal environment in rhesus and cynomolgus macaques pre- and post-lactobacillus colonization – Gregory J. Daggett Jr – Journal of Medical Primatology

Human nearly-sterile sites (blood, organs, brain)

Active Trachoma Cases In The Solomon Islands Have Varied Polymicrobial Community Structures But Do Not Associate With Individual Non-Chlamydial Pathogens Of The Eye – Robert Butcher – bioRxiv

Human gut microbiome

Gut Microbiome Function Predicts Response to Anti-integrin Biologic Therapy in Inflammatory Bowel Diseases – Ashwin N. Ananthakrishnan – Cell Host & Microbiome

Current challenges in the treatment of severe Clostridium difficile infection: early treatment potential of fecal microbiota transplantation – Yvette H. van Beurden –
Therapeutic Advances in Gastroenterology

Review: Food additives, contaminants and other minor components: effects on human gut microbiota—a review – Paula Roca-Saavedra – Journal of Physiology and Biochemistry

Emulating Host-Microbiome Ecosystem of Human Gastrointestinal Tract in Vitro – Gun-Seok Park – Stem Cell Reviews and Reports

Animal experiments 

A Rab20-Dependent Membrane Trafficking Pathway Controls M. tuberculosis Replication by Regulating Phagosome Spaciousness and Integrity – Laura Schnettger – Cell host & Microbiome

Cooperating Commensals Restore Colonization Resistance to Vancomycin-Resistant Enterococcus faecium – Silvia Caballero – Cell Host & Microbe

Animal microbiome

Characterization of the juvenile green turtle (Chelonia mydas) microbiome throughout an ontogenetic shift from pelagic to neritic habitats – James T. Price – PLoS ONE

A Meta-Transcriptomics Survey Reveals Changes in the Microbiota of the Chinese Mitten Crab Eriocheir sinensis Infected with Hepatopancreatic Necrosis Disease – Huaishun Shen – Frontiers in Microbiology

Plant, root, and soil microbiome

Modifying And Reacting To The Environmental pH Drives Bacterial Interactions – Christoph Ratzke – bioRxiv

Differential responses of soil bacteria, fungi, archaea and protists to plant species richness and plant functional group identity – Sigrid Dassen – Molecular Ecology

Analysis of the bacterial strains using Biolog plates in the contaminated soil from Riyadh community – Fahad Abdullah M. Al-Dhabaan – Saudi Journal of Biological Sciences

Biosurfactant-producing microorganism Pseudomonas sp. SB assists the phytoremediation of DDT-contaminated soil by two grass species – Beibei Wang – Chemosphere

Water and extremophile microbiome 

Molecular Diversity of Sea Spray Aerosol Particles: Impact of Ocean Biology on Particle Composition and Hygroscopicity – Richard E. Cochran – Chem, Cell Press

The novel bacterial phylum Calditrichaeota is diverse, widespread and abundant in marine sediments and has the capacity to degrade detrital proteins – Ian P. G. Marshall – Environmental Microbiology Reports

Single-cell genomics reveals pyrrolysine-encoding potential in members of uncultivated archaeal candidate division MSBL1 – Yue Guan – Environmental Microbiology Reports

The Paradox Of Constant Oceanic Plastic Debris: Evidence For Evolved Microbial Biodegradation? – Ricard Sole – bioRxiv

Copper Pollution Increases the Resistance of Soil Archaeal Community to Changes in Water Regime – Jing LiYu-Rong Liu – Microbial Ecology

Spatiotemporal analysis of microbial community dynamics during seasonal stratification events in a freshwater lake (Grand Lake, OK, USA) – Jessica M. Morrison – PLoS ONE

Nitrotoga is selected over Nitrospira in newly assembled biofilm communities from a tap water source community at increased nitrite loading – Marta Kinnunen – Environmental Microbiology

Unveiling microbial interactions in stratified mat communities from a warm saline shallow pond – Aurélien Saghaï – Environmental Micorbiology

Probiotics / prebiotics

Genotypic and phenotypic diversity of Lactobacillus rhamnosus clinical isolates, their comparison with strain GG and their recognition by complement system – Eija Nissilä – PLoS ONE

Bioinformatics

A Bayesian taxonomic classification method for 16S rRNA gene sequences with improved species-level accuracy – Xiang Gao – BMC Bioinformatics

gCoda: Conditional Dependence Network Inference for Compositional Data – Huaying Fang – Journal of Computational Biology

Effect of Lactobacillus rhamnosus HN001 and Bifidobacterium longum BB536 on the healthy gut microbiota composition at phyla and species level: A preliminary study – Marco Toscano – World Journal of Gastroenterology

Biotechnology

Review:Cyanobacterial metabolites as a source of sunscreens and moisturizers: a comparison with current synthetic compounds – Peyman Derikvand – European Journal of Phycology

Microbes in the news

Dramatic cooperation between two infectious bacteria revealed – Medicalxpress.com

Study finds bacteria in marine sponge produce toxic flame retardant-like compounds – Phys.org

Scientists Find Molecular ‘Key’ to Killing Hearty Bacteria – Extremetech.com

How our gut bacteria affect cancer risk and response to treatment – Theconversation.com

16S sequencing reveals differences between microbiomes in eyes, throat – Healio.com

Cosmetic Companies Now Develop Skin Care Products That Contain Live Bacteria To Treat Several Skin Problems – Sciencetimes.com

 

May 11, 2017

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Gram-negative gut bacteria and Toll-like receptor 4 linked to stimulation of cerebral cavernous malformations, suppression of a single gene by the microbiota promotes T cell survival in mice, quorum sensing negatively regulates toxin production in insect-associated bacteria and may facilitate stable colonization.

General microbiome

Lactobacillus plantarum producing a Chlamydia trachomatis antigen induces a specific IgA response after mucosal booster immunization – Katarzyna Kuczkowska – PLoS ONE

Human oral microbiome

The dental calculus metabolome in modern and historic samples – Irina M Velsko – bioRxiv

Insights of the dental calculi microbiome of pre-Columbian inhabitants from Puerto Rico – Tasha M Santiago-Rodriguez – PeerJ

Arginine Improves pH Homeostasis via Metabolism and Microbiome Modulation – M Angelo – Journal of Dental Research

Human gut microbiome

Faecal Microbiota Transplantation for Inflammatory Bowel Disease: A Systematic Review and Meta-analysis – Sudarshan Paramsothy – Journal of Crohn’s and Colitis

Significantly higher faecal counts of the yeasts candida and saccharomyces identified in people with coeliac disease – Joanna Harnett – Gut Pathogens

Research Highlight: Tooling up for microbiota research – Hugh Thomas – Nature Reviews Gastroenterology & Hepatology

Review: The gut microbiota: a key factor in the therapeutic effects of (poly)phenols – Juan Carlos Espín – Biochemical Pharmacology

Animal experiments

* Endothelial TLR4 and the microbiome drive cerebral cavernous malformations – Alan T Tang – Nature

* Microbiota promotes systemic T-cell survival through suppression of an apoptotic factor – Raymond Soto – PNAS

Bifidobacterium adolescentis IM38 ameliorates high-fat diet-induced colitis in mice by inhibiting NF-κB activation and lipopolysaccharide production by gut microbiota – Su-Min Lim – Nutrition Research

Tyrosine kinase inhibitors of Ripk2 attenuate bacterial cell wall-mediated lipolysis, inflammation and dysglycemia – Brittany M Duggan – Scientific Reports

Total fecal microbiota transplantation alleviates high-fat diet-induced steatohepatitis in mice via beneficial regulation of gut microbiota – Da Zhou – Scientific Reports

Animal microbiome

* Quorum Sensing Attenuates Virulence in Sodalis praecaptivus – Shinichiro Enomoto – Cell Host & Microbe

The digestive and defensive basis of carcass utilization by the burying beetle and its microbiota – Heiko Vogel – Nature Communications

Plant, root, and soil microbiome

Antibacterial producing actinomycetes from Extra Andean Patagonia – M S Vela Gurovic – Journal of Arid Environments

High-throughput sequencing reveals bacterial community composition in the rhizosphere of the invasive plant Flaveria bidentis – Z Song – Weed Research

Microbiomes associated with infective stages of root-knot and lesion nematodes in soil – Ahmed Elhady – PLoS ONE

Review: Plant-insect-pathogen interactions: a naturally complex ménage à trois – Flávia P Franco – Current Opinion in Microbiology

Review: CuO and ZnO Nanoparticles Modify Interkingdom Cell Signaling Processes Relevant to Crop Production: A Review – Anne Anderson – Journal of Agricultural and Food Chemistry

The phosphotransferase system gene ptsi in Bacillus cereus regulates expression of soda2 and contributes to colonization of wheat roots – Tantan Gao – Research in Microbiology

Water and extremophile microbiome

Review: Microbial processes driving coral reef organic carbon flow – Cynthia B Silveira – FEMS Microbiology Reviews

Diversity of biocrust-forming cyanobacteria in a semiarid gypsiferous site from Central Spain – Concha Cano-Díaz – bioRxiv

Probiotics/prebiotics

Probiotic Bifidobacterium longum NCC3001 Reduces Depression Scores and Alters Brain Activity: a Pilot Study in Patients With Irritable Bowel Syndrome – Maria Ines Pinto-Sanchez – Gastroenterology

Bioinformatics

dbOTU3: A new implementation of distribution-based OTU calling – Scott W Olesen – PLoS ONE

MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads – Thomas Nordahl Petersen – PLoS ONE

Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes – Sheng-Yong Niu – Briefings on Bioinformatics

Techniques

Review: Imaging mass spectrometry for metabolites: technical progress, multimodal imaging, and biological interactions – Ying-Ning Ho – WIREs Systems Biology and Medicine

Live-Cell Nanoscopy in Antiadhesion Therapy – Joan A Geoghegan – Trends in Microbiology

Low concentration DNA extraction and recovery using a silica solid phase – Constantinos Katevatis – PLoS ONE

More microbes

When more is less: Emergent suppressive interactions in three-drug combinations – Casey Beppler – BMC Microbiology

Effects of stochasticity and division of labor in toxin production on two-strain bacterial competition in Escherichia coli – Benedikt von Bronk – PLoS Biology

Biosynthesis of the antibiotic nonribosomal peptide penicillin in baker’s yeast – Ali R Awan – Nature Communications

Microbes in the news

Cosmetics: The next microbiome frontier – Marc S Reisch – Chemical and Engineering News

A defence mechanism that can trap and kill TB bacteria – Science Daily

Is IBS All In Your Mind? New Study Hints at Close Ties Between the Brain and the Gut – Jessica Wapner – Newsweek

Bacteria art

Scientists ‘paint’ with bacteria, create microbial masterpieces – Tom Ensey – wistv.com

May 10, 2017

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A short digest today, but not without interesting pieces. Largest study yet to demonstrate vertical transfer of bacteria from mother to infant, microbes could orchestrate plant ‘migration’, and many fascinating pieces of news on microbes. How may we make peace with microbes in and around us?

General microbiology

Using Resurrected Ancestral Proviral Proteins to Engineer Virus Resistance – Asunción Delgado et al. – Cell Reports

Press: Four-billion-year-old ‘fossil’ protein resurrected in bacteria protects them from viruses – Phys.org

Infant Gut Microbiome

Association Between Breast Milk Bacterial Communities and Establishment and Development of the Infant Gut Microbiome – Pia S. Pannaraj et al. – JAMA Pediatrics

Press: Breastfeeding plays important role in ‘seeding’ infant microbiome with beneficial bacteria – Leigh Hopper – UCLA

Plant, root and soil microbiome

Microbial communities and diazotrophic activity differ in the root-zone of Alamo and Dacotah switchgrass feedstocks – Richard R. Rodrigues et al. – Global Change Biology Bioenergy

Divergent plant–soil feedbacks could alter future elevation ranges and ecosystem dynamics – Michael E. Van Nuland et al. – Nature Ecology and Evolution

Press: Microscopic soil creatures could orchestrate massive tree ‘migrations’ – University of Tennessee at Knoxville – Science Daily

Microbes in the news

Global warming is altering the microbiota of lizards – Brooks Hays – UPI

TOO much exercise causes a leaky gut and increases health risks, research shows (and be especially careful if you work in the military) – Claudia Tanner – Daily Mail

Be wary of the title: Bacteria in Yogurt Cures Depression, Study Shows – Lorie Johnson – CBN News

Anecdotal evidence: Faecal transplants boost mind-gut link – Sarah Wiedersehn – Yahoo News

Bacteria appears to be behind mysterious outbreak in Liberia – Mike Stobbe – ABC News

Scientists Battle Bacteria with Silver and Mucus – Shawn Radcliffe – Healthline News

Verify: Will I contract flesh-eating bacteria at the beach in Texas? – Brandon Jones – KVUE

BACTERIA could mean the end of the pothole: Radical self repairing road can ‘grow’ into cracks – Cecile Borkhataria – Daily Mail

I Survived Flesh-Eating Bacteria—and It Changed My Life Forever – Aimee Copeland – Time

Microbes on the market

Oral enzyme prevents C. difficile infection, VRE colonization – Healio Gastroenterology

May 9, 2017

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Today’s digest is full of exciting papers that look at how climate change is influencing the gut microbiome of lizards, biogeography of bacteria along the Amazon river, lastly how going to the gym might be bad for you.

Human gut microbiome

Preprint : The Landscape Of Type VI Secretion Across Human Gut Microbiomes Reveals Its Role In Community Composition. Verster A. bioRxiv

Ocean, river, and stream microbiome

Disentangling multi‐scale environmental effects on stream microbial communities. Jyrkänkallio‐Mikkola J. Journal of Biogeography

Bacterial biogeography across the Amazon river-ocean continuum  Doherty M. Frontiers in Microbiology

Spatial variation of microbial communities in sediments along the environmental gradients from Xiaoqing River to Laizhou Bay.   Yu SX.  Marine Pollution Bulletin

The impact of long-term water level draw-down on microbial biomass: A comparative study from two peatland sites with different nutrient status Mpamah PA. European Journal of Soil Biology

The metabolic potential of the single cell genomes obtained from the Challenger Deep, Mariana Trench within the Candidate Superphylum Parcubacteria (OD1). León‐Zayas. Environmental Microbiology

Plant, soil, and air microbiome

Postmortem microbial communities in burial soil layers of skeletonized humans. Thomas TB. Journal of Forensic and Legal Medicine

Metagenomic Analysis of Bacterial Communities in the Rhizosphere of Leguminous Crops and Trees. Ahrenhoerster C. The FASEB Journal

Animal gut microbiome

Can fecal samples be used to inform about microbial communities of the equine hindgut? Reed KJ. Journal of Equine Veterinary Science

Normal variation and changes over time in the equine intestinal microbiome Martin EJ. Journal of Equine Veterinary Science

Climate warming reduces gut microbiota diversity in a vertebrate ectotherm. Bestion E. Nature:Ecology and Evolution

Effect of dietary supplementation with Lactobacillus acidophilus D2/CSL (CECT 4529) on caecum microbioma and productive performance in broiler chickens De Cesare A. PLoS One

Biotechnology 

Editorial Petroleum Microbial Biotechnology: Challenges and Prospects Ismail WA.Frontiers in Microbiology

Antibiotic 

Networks of exchanging antibiotic resistance between environmental, commensal, and pathogenic microbes Dantas G- The FASEB Journal

Extreme environment 

Decoupling of microbial carbon, nitrogen, and phosphorus cycling in response to extreme temperature events Mooshammer M. Science Advances

Faecal microbiome 

pH-Mediated Microbial and Metabolic Interactions in Fecal Enrichment Cultures Ilhan ZE. mSpehere

Anemia During Infancy Affects the Fecal Microbiome and Fecal and Serum Metabolomes McClorry S. The FASEB Journal

Microbes in the news

Southern California beaches get bacteria warnings after rain

Monterey County Herald

The Amount Of Bacteria On Gym Equipment Will Make Sure You Never Forget To Wipe Down The Elliptical Again

Bustle

 

May 6, 2017

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Events and jobs

Trainee Microbiology Analyst – Eurofins Lancaster Laboratories

General microbiome

*Review: Optimizing methods and dodging pitfalls in microbiome research – Dorothy Kim – Microbiome

*Book: Dirt Is Good: The Advantage of Germs for Your Child’s Developing Immune System – Jack Gilbert, Rob Knight

Human gut microbiome

*Review: Ménage à trois in the human gut: interactions between host, bacteria and phages – Mohammadali Khan Mirzaei – Nature Reviews Microbiology

Animal microbiome

The functional microbiome of arthropods – Mauro Degli Esposti – PLOS ONE

A comparative study of gut microbiota profiles of earthworms fed in three different substrates – Dianfeng Liu – Symbiosis

Plant, root, and soil microbiome

Breaking continuous potato cropping with legumes improves soil microbial communities, enzyme activities and tuber yield – Shuhao Qin – PLOS ONE

Study on the effect of soil beneficial microorganisms on the growth of kiwifruit – Huihe Li – Biomedical Research

Water and extremophile microbiome

Contribution of different bacterial dispersal sources to lakes: Population and community effects in different seasons – Jérôme Comte – Environmental Microbiology

*Review: The life sulfuric: microbial ecology of sulfur cycling in marine sediments – Kenneth Wasmund – Environmental Microbiology Reports

Fine stratification of microbial communities through a metagenomic profile of
the photic zone – Jose M. Haro-Moreno – bioRxiv

Probiotics / prebiotics

Effect of dietary supplementation with Lactobacillus acidophilus D2/CSL (CECT 4529) on caecum microbioma and productive performance in broiler chickens – Alessandra De Cesare – PLOS ONE

Bioinformatics

BusyBee Web: metagenomic data analysis by bootstrapped supervised binning and annotation – CC Laczny – Nucleic Acids Research

Techniques

*Highlight: How to see more: double hybridization to reveal ecological differentiation among close bacterial relatives – Stefan Bertilsson – Environmental Microbiology

Comparative analysis of the sensitivity of metagenomic sequencing and PCR to detect a biowarfare simulant (Bacillus atrophaeus) in soil samples – Delphine Plaire – PLOS ONE

Microbes in the news

The Invisible Secret That Will Change Your Skin Forever – Rachel Krause – Refinery29

Improve your skin microbiome – Cassie Shortsleeve – Furthermore

Dormant bacteria trapped in ice could be released by climate change – Alayna Treene – Axios

Microbes on the market

Commense Licenses UBC’s Microbiome Therapeutic for Preventing Childhood Asthma – Genetic Engineering & Biotechnology News

Bacteria Hysteria

Why Bacteria Are More Threatening Than Ever – Alice Park – Time

Science, publishing, and career

Infection and Immunity welcomes the new microbiology – Andreas J. Bäumler – Infection and Immunity

May 5, 2017

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A PLoS One paper, with Dr. Bik as one of the co-authors, to characterize human gut microbiome and compare certain taxa against healthy profiles, the relationship between diet, circadian rhythm and gut microbiome, and much more.

Events

Webinar: Interactions between the Mycobiome and Bacteriome: Impact on Health and Disease – Zymo Research

The Real Impact of Rodent Diet on Microbiome and Gut Health Research Webinar Q&A – Taconic

Jobs

PhD position in microbiology – Uppsala Universitet

Microbiology Technician – Pharmaceutical Industry – Runcorn

QC Microbiology/Environmental Control Associate – Yoh’s client – Phoenix

Human multi-site microbiome

Preprint: Microbial Metagenome Of Urinary Tract Infection – Ahmed Moustafa – bioRxiv

Human skin microbiome

Inhibition of fracture healing in the presence of contamination by Staphylococcus aureus: Effects of growth state and immune response – Krystle A. Blanchette et al. – Journal of Orthopaedic Research

Human gut microbiome

Conditional postnatal deletion of the neonatal murine hepatic circadian gene, Npas2, alters the gut microbiome following restricted feeding – Derek S. O’Neil et al. – American Journal of Obstetrics and Gynecology

Press: Study: Alterations to circadian clock change the body’s response to diet – Amy Wallace – UPI

16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome – Daniel E. Almonacid and Laurens Kraal et al. (including our Elisabeth Bik) – PLoS One

Press: uBiome Publishes Peer-Reviewed Scientific Paper in PLOS ONE on First Version of Technology for Gut Health Screening Test – PRWeb

Commentary: The microbiota: an underestimated actor in radiation-induced lesions? – Harry Sokol and Timon Erik Adolph – Gut

Animal microbiome

Bacterial microbiota in small brown planthopper populations with different rice viruses – Shuo Li et al. – Journal of Basic Microbiology

Plant, root and soil microbiome

Small mammal activity alters plant community composition and microbial activity in an old-field ecosystem – Leigh C. Moorhead et al. – Ecosphere

Edaphic Conditions, Aboveground Carbon Stocks and Plant Diversity on Nickel Mine Tailings Dump Vegetated with Senegalia polyacantha (Willd.) Seigler & Ebinger – Edeth Mukaro et al. – Land Degradation & Development

Water and extremophile microbiome

Preprint: 290 Metagenome-assembled Genomes from the Mediterranean Sea: a resource for marine microbiology – Benjamin J Tully et al. – bioRxiv

Technology

Development of a multiplex real-time PCR assay for phylogenetic analysis of Uropathogenic Escherichia coli – Mojtaba Hasanpour and Akram Najafi – Journal of Microbiological Methods

New issue of the Journal of Microbiological Methods

Microbes in the news

Zika fight: Bacteria-laden mosquitoes unleashed in Florida to combat virus – Phil Keating – Fox News

Drought-quenching bacteria the future of farming? – Taylor Hartman – Daily Sun

Officials warn swimmers to avoid bacteria-laden parts of Lake Lanier – Ellen Eldridge – The Atlanta Journal-Constitution

Pathogenic bacteria train their defence in lakes and oceans – Phys.org

Cross-sector collaboration needed in fight against antimicrobial resistance – Sara Wyant – Agri-Pulse

Microbes on the market

Taconic Biosciences Expands Microbiome Portfolio – P&T Community

Careers

Microbiology Career Profiles – Market Specialist at Pacific Biosciences with Melissa Smith, PhD – ASM

May 1, 2017

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General microbiome

From Gene Annotation to Function Prediction for Metagenomics – F Sharifi – Protein Function Prediction

*Review: A critical assessment of the “sterile womb” and “in utero colonization” hypotheses: implications for research on the pioneer infant microbiome – ME Perez-Muñoz – Microbiome

Collateral damage during antibiotic treatment of C. difficile infection in the aged host: insights into why recurrent disease happens – JH Shin – Gut Microbes

 

Human oral microbiome

Oral Treponeme Major Surface Protein: Sequence Diversity and Distributions within Periodontal Niches – M You – Molecular Oral Microbiology

 

Human gut microbiome

Reduction in fecal microbiota diversity and short-chain fatty acid producers in Methicillin-resistant Staphylococcus aureus infected individuals as revealed by PacBio single molecule, real-time sequencing technology – J Zhao – European Journal of Clinical Microbiology & Infectious Diseases

Gut Check: The evolution of an educational board game – DA Coil – PLoS Biology

From sensing to shaping microbiota: insights into the role of NOD2 in intestinal homeostasis and progression of Crohn’s Disease – I Balasubramanian – Am. J. Physiol. Gastrointest. Liver Physiol.

Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson’s disease patients – JR Bedorf – Genome Medicine

 

Animal microbiome

Progressive response of large intestinal bacterial community and fermentation to the stepwise decrease of dietary crude protein level in growing pigs – Y Peng – Applied Microbiology and Biotechnology

Repeated inoculation of cattle rumen with bison rumen contents alters the rumen microbiome and improves nitrogen digestibility in cattle – GO Ribeiro – Scientific Reports

Impact and consequences of polyphenols and fructooligosaccharide interplay on gut microbiota in rats – CJ Zheng – Food & Function

 

Plant, root and soil microbiome

Not just browsing: an animal that grazes phyllosphere microbes facilitates community heterogeneity – R O′ Rorke – ISME

Environmental Metabarcoding Reveals Contrasting Belowground and Aboveground Fungal Communities from Poplar at a Hg Phytomanagement Site –  A Durand – Microbial Ecology

Understory Dwarf Bamboo Affects Microbial Community Structures and Soil Properties in a Betula ermanii Forest in Northern Japan – B Kong – Microbes & Environments

Effects of root exudates on denitrifier gene abundance, community structure and activity in a micro-polluted constructed wetland – H Wu – Sci. Total Environ

Contribution of native phosphorous-solubilizing bacteria of acid soils on phosphorous acquisition in peanut (Arachis hypogaea L.) – M Pradhan – Protoplasma

 

Probiotics

Aggregation and Adhesion Activity of Lactobacilli Isolated from Fermented Products In Vitro and In Vivo: a Potential Probiotic Strain – S Grigoryan – Probiotics and Antimicrobial Proteins

 

Built environment microbiology

Three-stage anaerobic co-digestion of food waste and horse manure – J Zhang – Scientific Reports

 

Microbes in news

Undeveloped microbiomes make infants more prone to illness – R Saxena – ARS Technica

Being a guinea pig for science can be a long, slow slog – B Jefferson – SCPR

Pharma pollution fuels resistance to antibiotics, bacteria turns super bug – TNN – The Times of India

Cleaning up Iowa’s beaches – E Jordan – The Gazette

Augusta hospital adopts test to help find treatment for some patients quicker – S Turner – Aiken Standard

Only a superweapon can kill superbacteria, and humanity finally found it – W Nicol – Digital Trends

‘Lab in a cell’ helps crack code on chlamydia – R Shore –  Edmonton Journal

 

 

April 28, 2017

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Quite a few interesting articles and news about microbes: are we colonised with bacteria in utero? What is the relevance of cooperative interactions in microbial biotechnological processes? Microbe colonies  in space? Read more in today’s Microbiome Digest..

General microbiome

Variable habitat conditions drive species covariation in the human microbiota – Charles K. Fisher – PLOS

Pregnancy and early life

*Review: The prenatal gut microbiome: are we colonized with bacteria in utero? – R. W. Walker – Pediatric Obesity

Development of the cutaneous microbiome in the preterm infant: A prospective longitudinal study – Mohan Pammi – PLOS
 Human respiratory microbiome

A commensal streptococcus hijacks a Pseudomonas aeruginosa exopolysaccharide to promote biofilm formation – Jessica A. Scoffield – PLOS
Human oral microbiome

A genome-wide association study identifies nucleotide variants at SIGLEC5 and DEFA1A3 as risk loci for periodontitis – Matthias Munz – Human Molecular Genetics

Human nearly-sterile sites 

A case of polymicrobial anaerobic spondylodiscitis due to Parvimonas micra and Fusobacterium nucleatum – Leanne M Cleaver – JMM Case Reports

Human gut microbiome

Small Molecules from Deep within the Gut – Michael Ehrmann – ChemBioChem

Single Delivery of High-Diversity Fecal Microbiota Preparation by Colonoscopy Is Safe and Effective in Increasing Microbial Diversity in Active Ulcerative Colitis – Jacob Vinita – Inflammatory Bowel Diseases

Fecal Microbiota Transplantation for Refractory Clostridium difficile Colitis in Solid Organ Transplant Recipients – R. J. Friedman-Moraco – American Journal of Transplantation

Abundance profiling of specific gene groups using precomputed gut metagenomes yields novel biological hypotheses – Konstantin Yarygin – PLOS
Animal experiments

Neonatal mono-colonization of germ-free mice with Lactobacillus casei enhances casein immunogenicity after oral sensitization to cow’s milk – Matieny Aicha Maiga – Molecular Nutrition & Food Research

Shifts in the Gut Microbiota Composition Due to Depleted Bone Marrow Beta Adrenergic Signaling Are Associated with Suppressed Inflammatory Transcriptional Networks in the Mouse Colon – Tao Yang – Frontiers in Physiology

Animal microbiome

Viral gut metagenomics of sympatric wild and domestic canids, and monitoring of viruses: Insights from an endangered wolf population – Nádia Conceição-Neto – Ecology and Evolution

The environmental and host-associated bacterial microbiota of Arctic seawater-farmed Atlantic salmon with ulcerative disorders – C Karlsen – Journal of Fish Diseases

Plant, root, and soil microbiome

Soil aggregation and associated microbial communities modify the impact of agricultural management on carbon content – Pankaj Trivedi – Environmental Microbiology

In-depth characterization of bacterial and archaeal communities present in the abandoned Kettara pyrrhotite mine tailings (Morocco) – Odile Bruneel –  Extremophiles

Water and extremophile microbiome 

Geochemistry and microbial diversity of cave waters in the gypsum karst aquifers of Emilia Romagna region, Italy – Ilenia M. D’Angeli – Science of The Total Environment
Probiotics / prebiotics

Characterization, identification and application of lactic acid bacteria isolated from Leymus chinensis silage – Qing Zhang – Grassland Science
Biotechnology

*Review: Cooperation in microbial communities and their biotechnological applications – Matteo Cavaliere – Environmental Microbiology

Techniques

MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data – Achal Dhariwal – Nucleic Acid Research

Microbes in the news

Adaptive Phage Therapeutics – Terminally Ill Patient Successfully Treated With Bacteriophage – BioSpace

Research Links Microbiome Makeup To Remission in Pediatric Crohn’s – Gastroenterology & Endoscopy News

NASA Astronauts Are Close to Identifying Unknown Microbe Colonies That Grow in Space – Sciencealert.com