May 25, 2017

A review on the “vine and wine” microbiomes, a fungus that can infect and kill mosquitos through interaction with the gut microbiota, an introduction to the viruses of coral reefs.

General microbiome

The Role of Microbiota and Immunobiotics in Granulopoiesis of Immunocompromised Hosts – Susana Salva – Frontiers in Immunology

Successive range expansion promotes diversity and accelerates evolution in spatially structured microbial populations – Felix Goldschmidt – The ISME Journal

Human gut microbiome

TGF-β in inflammatory bowel disease: a key regulator of immune cells, epithelium, and the intestinal microbiota – Sozaburo Ihara – Journal of Gastroenterology

Review: Towards an Integrative Understanding of Diet–Host–Gut Microbiome Interactions – Mark N Read – Frontiers in Immunology

Review: Genes, emotions and gut microbiota: The next frontier for the gastroenterologist – Arturo Panduro – World Journal of Gastroenterology

Animal experiments

Modulation of the gut microbiota impacts non-alcoholic fatty liver disease: a potential role for bile acids – Aafke WF Janssen – Journal of Lipid Research

Antimicrobial peptides extend lifespan in Drosophila – Gerrit Loch – PLOS ONE

Animal microbiome

Bacterial diversity of cosmopolitan Culex pipiens and invasive Aedes japonicus from Germany – Sina Zotzmann – Parasitology Research

Comparison of Microbiomes between Red Poultry Mite Populations (Dermanyssus gallinae): Predominance of Bartonella-like Bacteria – Jan Hubert – Microbial Ecology

* Insect pathogenic fungus interacts with the gut microbiota to accelerate mosquito mortality – Ge Wei – PNAS

Plant, root, and soil microbiome

Leaf bacterial diversity mediates plant diversity and ecosystem function relationships – Isabelle Laforest-Lapointe – Nature

Alpine soil carbon is vulnerable to rapid microbial decomposition under climate cooling – Linwei Wu – The ISME Journal

Review: From Vineyard Soil to Wine Fermentation: Microbiome Approximations to Explain the “terroir” Concept – Ignacio Belda – Frontiers in Microbiology

Phages and viruses

Differentiation and Structure in Sulfolobus islandicus Rod-Shaped Virus Populations – Maria A Bautista – Viruses

Review: Virus–host interactions and their roles in coral reef health and disease – Rebecca Vega Thurber – Nature Reviews Microbiology

Metabolomics

Inter-individual Recovery of the Microbiota and Metabolome Over Time Following Fecal Microbiota Transplantation in Patients with Recurrent Clostridium difficile Infection – Anna M Seekatz – bioRxiv

Metabolic profiling by gas chromatography-mass spectrometry of energy metabolism in high-fat diet-fed obese mice – Daxesh P Patel – PLOS ONE

Review: Livestock metabolomics and the livestock metabolome: A systematic review – Seyed Ali Goldansaz – PLOS ONE

Techniques

Review: A diverse community to study communities: integration of experiments and mathematical models to study microbial consortia – Antonella Succurro – Journal of Bacteriology

More microbes

Decoding and reprogramming fungal iterative nonribosomal peptide synthetases – Dayu Yu – Nature Communications

Microbes in the news

Companies Pursue Diagnostics that Mine the Microbiome – Andrea Anderson – The Scientist

The fungal microbiome contributes to alcohol-induced liver damage in mice – EurekAlert

May 21, 2017

Events and jobs

FULLY FUNDED POSTDOCTORAL FELLOW POSITION TO STUDY MICROBIOME-BEHAVIOR INTERACTIONS: PORTUGAL

General microbiome

Bioinorganic antimicrobial strategies in the resistance era – Regiel-Futyra et al, Coordination Chemistry Reviews

Biofilm microenvironment induces a widespread adaptive amino-acid fermentation pathway conferring strong fitness advantage in Escherichia coli – Letoffe et al, PLoS Genetics

A bloodstream infection by Ruminococcus gnavus in a patient with a gall bladder perforation – Kim et al, Anerobe

Microbial community compositional analysis for membrane bioreactor treating antibiotics containing wastewater – Zhu et al, Chemical Engineering Journal

Thermophilic Moorella thermoautotrophica-immobilized cathode enhanced microbial electrosynthesis of acetate and formate from CO2 – Yu et al, Bioelectrochemistry

Arumberiamorph structure in modern microbial mats: implications for Ediacaran palaeobiology – Kolesnikov et al, Bulletin de la Société Géologique de France

Succession in the petroleum reservoir microbiome through an oil field production lifecycle – Vigneron et al, ISME

Human respiratory microbiome

Population Genomic Analysis of 1,777 Extended-Spectrum Beta-Lactamase-Producing Klebsiella pneumoniae Isolates, Houston, Texas: Unexpected Abundance of Clonal Group 307 – Long et al, Mbio

Human oral microbiome

Pro-resolving mediators in the regulation of periodontal disease – Van Dyke, Molecular Aspects of Medicine

A structure-derived snap-trap mechanism of a multispecific serpin from the dysbiotic human oral microbiome – Goulas et al, Journal of Biological Chemistry

Human gut microbiome

Is frozen fecal microbiota transplantation as effective as fresh fecal microbiota transplantation in patients with recurrent or refractory clostridium difficile infection: a meta-analysis? – Tang et al, Diagnostic Microbiology and Infectious Disease

Weight-loss interventions and gut microbiota changes in overweight and obese patients: a systematic review – Seganfredo et al, Obesity Reviews

 

Dysbiosis of Gut Microbiome and Its Impact on Epigenetic Regulation – Lee et al, Journal of Clinical Epigenetics

Hypoxia and Inactivity Related Physiological Changes (Constipation, Inflammation) Are Not Reflected at the Level of Gut Metabolites and Butyrate Producing Microbial Community: The PlanHab Study – Sket et al, Frontiers in Physiology

Is there a potential role of fecal microbiota transplantation in the treatment of inflammatory bowel disease? – Eun, Intestinal Research

Diet and contaminants: driving the rise to obesity epidemics? – Di Ciaula and Portincasa, Current Medical Chemistry

How to: Establish and run a stool bank – Terveer et al, Clinical Microbiology and Infection

Animal experiments

Transforming growth factor β: a master regulator of the gut microbiota and immune cell interactions – Bauche and Marie, Clinical and Translational Immunology

Aloin, a Component of the Aloe Vera Plant Leaf, Induces Pathological Changes and Modulates the Composition of Microbiota in the Large Intestine of F344/N Male Rats – Boudraeu et al, Toxicology Science

Diabetes-associated microbiota in fa/fa rats is modified by Roux-en-Y gastric bypass – Arora et al, ISME

Absorption and degradation of sulfated polysaccharide from pacific abalone in in vitro and in vivo models – Ai et al, Journal of Functional Foods

Dietary ZnO nanoparticles alters intestinal microbiota and inflammation response in weaned piglets – Xia et al, Oncotarget

Dietary delta-tocotrienol favors abundance and diversity of beneficial microbiomes in obese male mice – Shen et al, FASEB

Bile acid binding resin prevents fat accumulation through intestinal microbiota in high-fat diet-induced obesity in mice – Kusumoto et al, Metabolism

In vitro ability of mastitis causing pathogens to form biofilms – Schonborn et al, Journal of Dairy Research

Dysbiosis of Intestinal Microbiota and Decreased Antimicrobial Peptide Level in Paneth Cells during Hypertriglyceridemia-Related Acute Necrotizing Pancreatitis in Rats – Huang et al, Frontiers in Microbiology

Effects of replacing Leymus chinensis with whole-crop wheat hay on Holstein bull apparent digestibility, plasma parameters, rumen fermentation, and microbiota – Niu et al, Scientific Reports

Physiological responses of insects to microbial fermentation products: insights from the interactions between Drosophila and acetic acid – Kim et al, Journal of Insect Physiology

Animal microbiome

Molecular detection by analysis of the 16S rRNA gene of fecal coliform bacteria from the two Korean Apodemus species (Apodemus agrarius and A. peninsulae) – Rahman et al, Genetics and Molecular Research

Detection and genetic characterization of Pasteurella multocida from alpaca (Vicugna pacos) pneumonia cases – Rimac et al, Tropical Animal Health and Production

Plant, root, and soil microbiome

Soil depth and crop determinants of bacterial communities under ten biofuel cropping systems – Zhang et al, Soil Biology and Biochemistry

Ground cover and slope exposure effects on micro- and mesobiota in forest soils – Gomez-Brandon et al, Ecological Indicators

Root chemical traits and their roles in belowground biotic interactions – Tsunoda and van Dam, Pedobiologia

Proteomics analysis of Fusarium proliferatum under various initial pH during fumonisin production – Li et al, Journal of Proteomics

Culturable bacterial diversity from the chestnut (Castanea sativa Mill.) phyllosphere and antagonism against the fungi causing the chestnut blight and ink diseases – Valverde et al, AIMS Microbiology

Water and extremophile microbiome

The removal of nitrogen compounds from farming wastewater – The effect of different carbon substrates and different microbial activators – Mankiewicz-Boczek et al, Ecological Engineering

How do physicochemical properties influence the toxicity of silver nanoparticles on freshwater decomposers of plant litter in streams? – Batista et al, Ecotoxicology and Environmental Safety

The heterogeneity of composition and assembly processes of the microbial community between different nutrient loading lake zones in Taihu Lake – Zhao et al, Applied Microbiology and Biotechnology

Towards a sustainable biobased industry – Highlighting the impact of extremophiles – Kruger et al, New Biotechnology

Distribution and genetic diversity of microbial populations in the pilot-scale biofilter for simultaneous removal of ammonia, iron and manganese from real groundwater – Cheng et al, Chemosphere

Pilot plant demonstration of stable and efficient high rate biological nutrient removal with low dissolved oxygen conditions – Keene et al, Water Research

Study on The Removal of Hexavalent Chromium from Contaminated Groundwater using Emulsified Vegetable Oil – Wen et al, Process Safety and Environmental Protection

A Novel Roseosiphophage Isolated from the Oligotrophic South China Sea – Yang et al, Viruses

Oxidative Stickland reactions in an obligate aerobic organism — amino acid catabolism in the Crenarchaeon Sulfolobus solfataricus – Stark et al, FEBS

Microbial Diversity in Extreme Marine Habitats and Their Biomolecules – Poli et al, Microorganisms

Methanogenic community was stable in two contrasting freshwater marshes exposed to elevated atmospheric CO2 – Lin et al, Frontiers in Microbiology

Plant-microbial interactions in agriculture and the use of farming systems to improve diversity and productivity – Ishaq, AIMS Microbiology

Effect of arbuscular mycorrhizal fungi on survival and growth of micropropagated Comanthera mucugensis spp. mucugensis (Eriocaulaceae) – Pereira et al, African Journal of Agricultural Research

Native communities of arbuscular mycorrhizal fungi associated with Capsicum annuum L. respond to soil properties and agronomic management under field conditions – Carballar-Hernandez et al, Agriculture, Ecosystems & Environment

Food microbiology

Microbial cell-free extracts affect the biochemical characteristics and sensorial quality of sourdough bread – Cavallo et al, Food Chemistry

Analysis of the microbiota of refrigerated chopped parsley after treatments with a coating containing enterocin AS-48 or by high-hydrostatic pressure – Burgos et al, Food Research International

Microorganisms Found in MPR and Packaged Produce and Their Detection Methods – Acar and Soyer, Minimally Processed Refridgerated Fruits and Vegetables, Food Engineering Series

Applications of Kluyveromyces marxianus in Biotechnology – Varela et al, Yeast Diversity in Human Welfare

Mucin- and carbohydrate-stimulated adhesion and subproteome changes of the probiotic bacterium Lactobacillus acidophilus NCFM – Celebioglu et al, Journal of Proteomics

Techniques

Metaproteomics-guided selection of targeted enzymes for bioprospecting of mixed microbial communities – Speda et al, Biotechnology Biofuels

Microbes in the news

Probiotics are popular, but some questions remain – Reading Eagle

May 17, 2017

Today’s digest includes a few studies of the interactions between microbes (and synergy in metabolism and other processes), a filling of human gut microbiology, and interesting insights into probiotics both in animals and humans.  Also, check out my post later in the day reviewing microbiome related talks at BioData World West 2017 (late April)

Events and jobs

Scientist – Microbiomics – ZymoResearch

PhD in microbiology – Université Catholique de Louvain (UCL)

Microbiology Laboratory Technologist – Yukon Hospital Corporation – Whitehorse, YT

General microbiome

Underlying mechanisms for syntrophic metabolism of essential enzyme cofactors in microbial communities – Margaret F Romine – The ISME Journal

Identification of the potentiating mutations and synergistic epistasis that enabled the evolution of inter-species cooperation – Sarah M. Douglas – PLOS ONE

Pregnancy and early life

PrePrint – Gut dysbiosis following C-section instigates higher colonisation of toxigenic Clostridium perfringens in infants – Nagpal R – Benef Microbes

The influence of dietary immunomodulatory factors on development of food allergy in children – Sardecka I – Postepy Dermatol Alergol.

 

Human oral microbiome

The microbiome of site-specific dental plaque of children with different caries status – Richards VP – Infection and Immunity

Human gut microbiome

Healthy gut microbiota can resolve undernutrition – Emmanuel Hermann – HBSN

The Gut Microbiota and Autism Spectrum Disorders – Qinrui Li – Frontiers in Cellular Neuroscience

The ecological community of commensal, symbiotic, and pathogenic gastrointestinal microorganisms – an appraisal – Haque SZ – Dovepress

Comparative Effectiveness of Faecal Microbiota Transplant by Route of Administration – Nathan D. Gundacker – The Journal of Hospital Infection

Fecal microbiota transplantation in recurrent Clostridium difficile infection in a patient with concomitant inflammatory bowel disease – Gravito-Soares M – Rev Esp Enferm Dig

Alterations in intestinal microbiota relate to intestinal failure-associated liver disease and central line infections – Panliang Wang – Journal of Pediatric Surgery

* The Gastric Microbiome and Its Influence on Gastric Carcinogenesis: Current Knowledge and Ongoing Research – Chao Zhang – Hematology/Oncology Clinics of North America

Insights into the role of the intestinal microbiota in colon cancer – Oke S – Therapeutic Advances in Gastroenterology

Gut microbiota changes as a risk factor for obesity – Kvit KB – Wiad Lek.

Animal experiments 

Drosophila melanogaster as a High-Throughput Model for Host–Microbiota Interactions – Mark Trinder – Frontiers in Microbiology

Dietary Chitosan Supplementation Increases Microbial Diversity and Attenuates the Severity of Citrobacter rodentium Infection in Mice – Guiping Guan – Mediators of Inflammation

Changes in the intestinal bacterial community, short-chain fatty acid profile, and intestinal development of preweaned Holstein calves. 2. Effects of gastrointestinal site and age – J.J. Castro – Journal of Dairy Science

The microbiome regulates amygdala-dependent fear recall – Hoban AE – Molecular Psychiatry

Animal microbiome

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

The influence of a probiotic supplementation on memory in quail suggests a role of gut microbiota on cognitive abilities in birds – Severine Parois – Behavioural Brain Research

Gut microbial communities of American pikas (Ochotona princeps): evidence for phylosymbiosis and adaptations to novel diets – Kevin D. Kohl – Journal of Animal Ecology

This Gut Ain’t Big Enough for Both of Us. Or Is It? Helminth-Microbiota Interactions in Veterinary Species – Peachey LE – Trends in Parasitology

Convergence of gut microbiotas in the adaptive radiations of African cichlid fishes – Baldo L – ISME

Plant, root, and soil microbiome

Divergent extremes but convergent recovery of bacterial and archaeal soil communities to an ongoing subterranean coal mine fire – Sang-Hoon Lee – The ISME Journal

Prokaryotic Communities at Different Depths between Soils with and without Tomato Bacterial Wilt but Pathogen-Present in a Single Greenhouse – Chol Gyu Lee – Microbes and Environments

Water and extremophile microbiome

Annual community patterns are driven by seasonal switching between closely related marine bacteria – Christopher S Ward – The ISME Journal

A bacterial community-based index to assess the ecological status of estuarine and coastal environments – Eva Aylagas – Marine Pollution Bulletin

The impact of wastewater treatment effluent on microbial biomasses and diversities in coastal sediment microcosms of Hangzhou Bay – Yile Tao – Marine Pollution Bulletin

The impact of long-term hydrocarbon exposure on the structure, activity, and biogeochemical functioning of microbial mats – Johanne Aubé – Marine Pollution Bulletin

Changes in microbial community during hydrogen and methane production in two-stage thermophilic anaerobic co-digestion process from biowaste – S. Zahedi – Waste Management

Comparative analysis of microbial diversity in two hot springs of Bakreshwar, West Bengal, India – Chaudhuri B – Genomics Data

Built environment (subways, indoor surfaces)

Characterizing bacterial communities in paper production-troublemakers revealed – Zumsteg A – MicrobiologyOpen

 

Probiotics / prebiotics

Dairy Propionibacteria: Versatile Probiotics – Rabah H – Microorganisms

Contribution of anthocyanin-rich foods in obesity control through gut microbiota interactions – Jamar G – BioFactors

Positive Effect of Probiotics on Constipation in Children: A Systematic Review and Meta-Analysis of Six Randomized Controlled Trials – Huang R – Frontiers in Cellular and Infection Microbiology

Mechanisms of Action of Probiotics and the Gastrointestinal Microbiota on Gut Motility and Constipation – Dimidi E – Advances in Nutrition

Bioinformatics

PrePrint – MetaMeta: Integrating Metagenome Analysis Tools To Improve Taxonomic Profiling – Vitor C. Piro – bioRxiv

Using null models to infer microbial co-occurrence networks – Nora Connor – PLOS ONE

Techniques

Characterization of microbial mixtures by mass spectrometry – Sandrin TR – Mass Spectrometry Reviews

Microbes in the news 

Cork scientists link gut bacteria to anxiety disorders

New tick bacteria in Australia being investigated as possible cause of Lyme disease-type illness

Optical nanofiber ‘hears’ bacteria swim, cancer cells move

Microbes on the market 

BiomX raises $24 million to boost bacteria based drugs

 

Ed’s non-microbiology picks

Breakthrough in delirium research ‘solves 2,500-year-old mystery’

Novel tissue-engineered islet transplant achieves insulin independence in type 1 diabetes – Bioengineering of an Intraabdominal Endocrine Pancreas -David A. Baidal – New England Journal of Medicine

High levels of exercise linked to nine years of less aging (at the cellular level)

Migratory birds bumped off schedule as climate change shifts spring

PrePrint – Using Social Network Analysis to Better Understand Compulsive Exercise Behavior among a Sample of Sorority Members –  Megan S. Patterson – Human Kinetics

Edible insects could play key role in cutting harmful emissions – EurkAlert!

May 15, 2017

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

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 11, 2017

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 6, 2017

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