Author Archives: TinaS

January 3, 2018

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Today we have a nice event /training in social science techniques organized by NERC in Manchester, Bristol and Edinburgh (UK), few microbiology jobs, an interesting review from Arun T. Nair in “Gut Microbiome”, quite a few papers about Synechococcus in “Water and extremophile microbiome”. Check as well “Microbes on market” where you can read about Google and Microsoft investing in medicine startup DNAnexus.

Events

Social science techniques for natural scientists training funded by NERC, UK

Jobs

Microbiologist – Kent, UK

Scientist/Sr.Scientist – Strain Development, CJM Talent Solutions, San Francisco, US

Associate/Assistant Professor : Miami, Florida, FL, US

General microbiome

Comparison of genomes and proteomes of four whole genome-sequenced Campylobacter jejuni from different phylogenetic backgrounds – Clifford G. Clark – PLOS

Phylogenetic inference of Coxiella burnetii by 16S rRNA gene sequencing – Heather P. McLaughlin -PLOS

The photosynthetic bacteria Rhodobacter capsulatus and Synechocystis sp. PCC 6803 as new hosts for cyclic plant triterpene biosynthesis – Anita Loeschcke -PLOS

Pregnancy and early life

Effect of innate antiviral glycoproteins in breast milk on seroconversion to rotavirus vaccine (Rotarix) in children in Lusaka, Zambia – Katayi Mwila-Kazimbaya – PLOS

Oral microbiome

Frequency and levels of candidate endodontic pathogens in acute apical abscesses as compared to asymptomatic apical periodontitis – Isabela N. Rôças – PLOS

Human vaginal microbiome

Combined oral and topical antimicrobial therapy for male partners of women with bacterial vaginosis: Acceptability, tolerability and impact on the genital microbiota of couples – A pilot study – Erica L. Plummer – PLOS

Candida albicans-derived mannoproteins activate NF-κB in reporter cells expressing TLR4, MD2 and CD14 – Traci Ness – PLOS

Replication-dependent size reduction precedes differentiation in Chlamydia trachomatis – Jennifer K. Lee – Nature Communications

Human gut microbiome

T6SS: The bacterial “fight club” in the host gut – Thibault G. Sana – PLOS Pathogens

Review: Gut Microbiota Dysfunction as Reliable Non-invasive Early Diagnostic Biomarkers in the Pathophysiology of Parkinson’s Disease: A Critical Review – Arun T Nair – Journal of Neurogastroenterology and Motility

Animal experiments

Effect of dietary xylooligosaccharides on intestinal characteristics, gut microbiota, cecal short-chain fatty acids, and plasma immune parameters of laying hens – X M Ding – Poultry Science

Influence of a diet enriched with virgin olive oil or butter on mouse gut microbiota and its correlation to physiological and biochemical parameters related to metabolic syndrome – Isabel Prieto – PLOS

Modulation of the diet and gastrointestinal microbiota normalizes systemic inflammation and β-cell chemokine expression associated with autoimmune diabetes susceptibility – Angela M. Henschel – PLOS

Dietary Lactobacillus acidophilus positively influences growth performance, gut morphology, and gut microbiology in rurally reared chickens  – C Forte – Poultry Science

Animal microbiome

Oral Disease and Microbiota in Free-Roaming Cats – Ana Whyte – Topics in Companion Animal Medicine

Review: Effect of Enterococcus Faecium Strain SF68 on Gastrointestinal Signs and Fecal Microbiome in Cats Administered Amoxicillin-Clavulanate – C. Torres-Henderson – Topics in Companion Animal Medicine

Water and extremophile microbiome

Clade and strain specific contributions of Synechococcus and Prochlorococcus to carbon export in the Sargasso Sea – Francesca De Martini – Limnology and Oceanography

Microbial proteins for organic material degradation in the deep ocean – David L. Kirchman – PNAS

Photosynthetic functions of Synechococcus in the ocean microbiomes of diverse salinity and seasons – Yihwan Kim – PLOS

Potential impact of global climate change on benthic deep-sea microbes – Roberto Danovaro – FEMS Microbiology Letters

Variability in the production of organic ligands, by Synechococcus PCC 7002, under different iron scenarios – Guillermo Samperio-Ramos – Journal of Oceanography

Effect of light on N2 fixation and net nitrogen release of Trichodesmium in a field study – Yangyang Lu – Biogeosciences

Microbial diversity of saline environments: searching for cytotoxic activities – Carolina Díaz-Cárdenas – AMB Express

Aerobic proteobacterial methylotrophs in Movile Cave: genomic and metagenomic analyses – Deepak Kumaresan – BMC Microbiome

Probiotics / prebiotics

Bifidobacteria or Fiber Protects against Diet-Induced Microbiota-Mediated Colonic Mucus Deterioration – Bjoern O. Schroeder – Cell Host and Microbe

Modifying progression of aging and reducing the risk of neurodegenerative diseases by probiotics and synbiotics – Huey Shi Lye – Frontiers In Bioscience

Phages and viruses

Isolation and characterization of a N4-like lytic bacteriophage infecting Vibrio splendidus, a pathogen of fish and bivalves – Pantelis Katharios – PLOS

High human papillomavirus (HPV) prevalence in South African adolescents and young women encourages expanded HPV vaccination campaigns – Zizipho Z. A. Mbulawa – PLOS

Zika virus infection modulates the bacterial diversity associated with Aedes aegypti as revealed by metagenomic analysis – Luis E. M. Villegas – PLOS

Localized Recombination Drives Diversification of Killing Spectra for Phage Derived Syringacins – David Baltrus – bioRxiv

Bioinformatics

Assessment of the cPAS-based BGISEQ-500 platform for metagenomic sequencing – Chao Fang – Giga Science

 

Techniques

Imaging bacteria inside their host by cryo-focused ion beam milling and electron cryotomography – João M Medeiros – Current Opinion in Microbiology

Microbes in the news

Tech company’s lights being used to kill germs in ambulances

Astronauts Identify Mystery Microbes in Space for the 1st Time

Microbes on the market

Seres Therapeutics Inc (MCRB) Holdings Increased by State Street Corp

Microsoft, Google invest in precision medicine startup DNAnexus

Tina’s non-microbiology picks

Synthetic Biology in the Driving Seat of the Bioeconomy – Yensi Flores Bueso – Trends in Biotechnology

Expect exoplanet atmospheres, organs with new functions and fewer traffic jams in 2018

December 12, 2017

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Today we have quite a long Microbiome Digest, with many papers in Human Gut , Water, Plant/Soil Microbiome and Probiotics Sections. Among many interesting papers today, check an essay by Stilianos Louca “Probing the metabolism of microorganisms” and a perspective by Cesar de la Fuente “Neuromicrobiology: how microbes influence the brain “.

Events and jobs

LabTechnician/Microbiology, Kalamazoo, MI 49001

Instructional Associate- Microbiology, Fort Worth, TX

Visiting Professor (Part Time) Microbiology Jacksonville, FL Campus

Assistant Professor in Food Microbiology/Safety, Edinburg, Texas (US)

General microbiome

Probing the metabolism of microorganisms – Stilianos Louca – Science

Pregnancy and early life

Persistence of Supplemented Bifidobacterium longum subsp. infantis EVC001 in Breastfed Infants – Steven A. Frese – mSphere

 

 

Human nearly-sterile sites 

Perspective: Neuromicrobiology: how microbes influence the brain – Cesar de la Fuente-Nunez – ACS Chemical Neuroscience

Assessment of the comparability of CLSI, EUCAST and Stokes antimicrobial susceptibility profiles for Escherichia coli uropathogenic isolates – C O’Halloran – British Journal of Biomedical Science

Human gut microbiome

Gut epithelial vitamin D receptor regulates microbiota-dependent mucosal inflammation by suppressing intestinal epithelial cell apoptosis – Lei He – Endocrinology

The long-term effects of faecal microbiota transplantation for gastrointestinal symptoms and general health in patients with recurrent Clostridium difficile infection – J. Jalanka – Alimentary Pharmacology & Therapeutics

Vitamin A deficiency in mice alters host and gut microbial metabolism leading to altered energy homeostasis – Yuan Tian – The Journal of Nutritional Biochemistry

Changes in the gut microbiota composition and the plasma ghrelin level in patients with Helicobacter pylori-infected patients with eradication therapy – Hidetaka Yanagi – Gut Microbiota

Perspectives: Gut microbiota–derived short-chain fatty acids and kidney diseases – Lingzhi Li –  Drug Design, Development and Therapy

Metabolic retroconversion of trimethylamine N-oxide and the gut microbiota – Lesley Hoyles – bioRxiv

Changes in the gut microbiota composition and the plasma ghrelin level in patients with Helicobacter pylori-infected patients with eradication therapy  – Hidetaka Yanagi – Gut Microbiota

Enteric Microbiome Markers as Early Predictors of Clinical Outcome in Allogeneic Hematopoietic Stem Cell Transplant: Results of a Prospective Study in Adult Patients – Nicasio Mancini – Open Forum Infectious Diseases

The long-term effects of faecal microbiota transplantation for gastrointestinal symptoms and general health in patients with recurrent Clostridium difficile infection – J. Jalanka – Alimentary Pharmacology & Therapeutics

Gut Microbiota and Host Juvenile Growth – Martin Schwarzer – Calcified Tissue International

Disruption of the Gut Ecosystem by Antibiotics – Mi Young Yoon – Yonsei Med Journal

Animal experiments 

Removal of the cecum affects intestinal fermentation, enteric bacterial community structure, and acute colitis in mice – Kirsty Brown – Gut Microbes

Influenza A virus subtype H9N2 infection disrupts the composition of intestinal microbiota of chickens – Alexander Yitbarek – FEMS Microbiology Ecology

Comparision of the intestinal musocal microbiota in dogs diagnosed with idiopathic inflamatorz bowel disease and dogs with food/responsive diarrhea before and after treatement – K. Kalenyak – FEMS Microbiology Ecology

Lysine Restriction Affects Feed Intake and Amino Acid Metabolism via Gut Microbiome in Piglets – Yin J – Logo Cellular Physiology and Biochemistry

Animal microbiome

SPM-1-producing Pseudomonas aeruginosa ST277 clone recovered from microbiota of migratory birds – Willames M.B.S.Martins – Diagnostic Microbiology and Infectious Disease

Plant, root, and soil microbiome

Ravibacter arvi gen. nov., sp. nov., isolated from farmland soil during development of new culture techniques – Dhiraj Kumar Chaudhary – International Journal of Systematic and Evolutionary Microbiology

Mangrovitalea sediminis gen. nov., sp. nov., a member of the family Alteromonadaceae isolated from mangrove sediment – Hu Liao – International Journal of Systematic and Evolutionary Microbiology

Prolonged exposure does not increase soil microbial community compositional response to warming along geothermal gradients – Dajana Radujković – FEMS Microbiology Ecology

Plant–soil feedbacks promote negative frequency dependence in the coexistence of two aridland grasses – Y. Anny Chung – Proceedings of the Royal Society B

Draft genome sequence of Bacillus velezensis 2A-2B strain: a rhizospheric inhabitant of Sporobolus airoides (Torr.) Torr., with antifungal activity against root rot causing phytopathogens – Inés Martínez-Raudales – Standards in Genomic Sciences

Rhizosphere Microorganisms: Application of Plant Beneficial Microbes in Biological Control of Weeds – Satyavir S. Sindhu – Microorganisms for Green Revolution

Shifts in bacterial and fungal diversity in a paddy soil faced with phosphorus surplus – Ming Liu – Biology and Fertility of Soils

Water and extremophile microbiome

Strategies and ecological roles of algicidal bacteria – Nils Meyer – FEMS Microbiology Reviews

Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations – Sarahi L. Garcia – ISME Journal

The predictability of a lake phytoplankton community, from hours to years – Mridul K. Thomas – bioRxiv

Oceaniglobus indicus gen. nov., sp. nov., a member of the family Rhodobacteraceae isolated from surface seawater –  Jianyang Li –  International Journal of Systematic and Evolutionary Microbiology

Nitrosopumilus maritimus gen. nov., sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., four marine ammonia-oxidizing archaea of the phylum Thaumarchaeota – Wei Qin – International Journal of Systematic and Evolutionary Microbiology

A new niche for anoxygenic phototrophs as endoliths – Daniel Roush – Applied and Environmental Microbiology

Quantitative Analysis of O2 and Fe2+ Profiles in Gradient Tubes for Cultivation of Microaerophilic Iron(II)-Oxidizing Bacteria – U. Lueder – FEMS Microbiology Ecology

Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota – Lin-Xing Chen –  ISME Journal

Diversity patterns of microbial eukaryotes mirror those of bacteria in Antarctic cryoconite holes – Pacifica Sommers – FEMS Microbiology Ecology

Linking bacterial community structure to advection and environmental impact along a coast-fjord gradient of the Sognefjord, western Norway – Julia E.Storesund – Progress in Oceanography

Bacterial Succession on Sinking Particles in the Ocean’s Interior -Erik A. Pelve – Frontiers in Microbiology

Growth of Nitrosococcus-Related Ammonia Oxidizing Bacteria Coincides with Extremely Low pH Values in Wastewater with High Ammonia Content – Alexandra Fumasoli – Environmental Science & Technolology

Characteristics of Bacterial Communities in Cyanobacteria-Blooming Aquaculture Wastewater Influenced by the Phytoremediation with Water Hyacinth – Qing Zhou – Water

Biodegradation of phenol by cold-adapted bacteria from Antarctic soils – Gillian Li Yin Lee – Polar Biology

Built environment 

Bacterial community evolutions driven by organic matter and powder activated carbon in simultaneous anammox and denitrification (SAD) process – Cheng-Hao Ge – Bioresource Technology

Food microbiology

The Role of Oligosaccharides in Host-Microbial Interactions for Human Health –  Sarah Ross – Journal of Clinical Gastroenterology

Probiotics / prebiotics

An in vivo assessment of the cholesterol-lowering efficacy of Lactobacillus plantarum ECGC 13110402 in normal to mildly hypercholesterolaemic adults – Adele Costabile – PLOS One

Can Probiotics Reduce Diarrhea and Infant Mortality in Africa?: The Project of a Pilot Study – Mario Del Piano – Journal of Clinical Gastroenterology

Searching for the Perfect Homeostasis: Five Strains of Bifidobacterium longum From Centenarians Have a Similar Behavior in the Production of Cytokines –  Stefania Nicola – Journal of Clinical Gastroenterology

In Vitro Inhibition of Klebsiella pneumoniae by Lactobacillus delbrueckii Subsp. delbrueckii LDD01 (DSM 22106): An Innovative Strategy to Possibly Counteract Such Infections in Humans? – Luca Mogna – Journal of Clinical Gastroenterology

Protective Role of Postbiotic Mediators Secreted by Lactobacillus rhamnosus GG Versus Lipopolysaccharide-induced Damage in Human Colonic Smooth Muscle Cells –  Alessia Cicenia – Journal of Clinical Gastroenterology

In Vitro Activity of Lactobacillus fermentum LF5 Against Different Candida Species and Gardnerella vaginalis: A New Perspective to Approach Mixed Vaginal Infections? –  Francesca Deidda- Journal of Clinical Gastroenterology

Probiotics are a good choice in remission of inflammatory bowel diseases: A meta analysis and systematic review – Mahboube Ganji-Arjenaki – Journal of Cellular Physiology

Optimization of the quenching and extraction procedures for a metabolomic analysis of Lactobacillus plantarum – Qin Yang – Analytical Biochemistry

Phages and viruses

Internalization of a polysialic acid-binding Escherichia  colibacteriophage into eukaryotic neuroblastoma cells – Timo A. Leht – Nature Communication

The human respiratory virome after lung transplantation for COPD: A single centre, prospective, longitudinal study – A.B. Mitchell – Respiratory Medicine

Virome Capture Sequencing in Castleman Disease Identifies Associations with Herpesviridae Family Members but No Novel Viruses – Christopher Sheild Nabel – Blood

Bioinformatics

Multiplexed droplet single-cell RNA-sequencing using natural genetic variation – Hyun Min Kang – Nature Biotechnology

CONSTAX: a tool for improved taxonomic resolution of environmental fungal ITS sequences – Kristi Gdanetz – BMC Bioinformatics

Biotechnology

Engineered synthetic scaffolds for organizing proteins within the bacterial cytoplasm – Matthew J Lee – Nature Chemical Biology

Engineering chemical interactions in microbial communities – Douglas J. Kenny – Chemical Society Reviews

Cyclic lipopeptide signature as fingerprinting for the screening of halotolerant Bacillus strains towards microbial enhanced oil recovery – Bárbara C. S. Farias – Applied Microbiology and Biotechnology

Techniques

Low cost, low tech SNP genotyping tools for resource-limited areas: Plague in Madagascar as a model – Cedar L. Mitchell – PLOS Neglected Tropical Diseases

Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation – John Beaulaurier – Nature Biotechnology

Microbes in the news 

Bacteria discovery in Antarctica prompts rethink of humanity’s search for alien life

When Lemur Families Cuddle, They Share Important Gut Bacteria

$3.9 million supports research to turn bacteria into biofuel producers

Bacteria and Art

Meet the Penn students using medical gauze and bacteria to create art for ‘speculative worlds’

December 5, 2017

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Today we have interesting reviews, one about proteomics and human microbiome by C.A. Kolmedar, the other about oral microbiome by L.P.Shaw and the third about human gut virome by L.A. Ogilvie. In Water section you can read the study by V.J. Koles who developed a model that simulates metagenomes and metatranscriptomes for comparison with observations. In section Bioinformatics you can read about new tools MetaLab and ASAR while in non-microbiology pics you can check podcast “Dances with rocks” with A. Denton, geologist and planetary scientist who wants to dance on Mars. Enjoy!

Jobs

Microbiology Supervisor, Rockville, Maryland

Associate Bioengineer II, Analytical R&D, Warren, NJ

Events

9th Congress of Microbiology and Parasitology Kicks Off in Cuba

General microbiome

Microbially Mediated Electrosynthesis Processes – Mohita Sharma – Microbial Fuell Cell

Development of Suitable Anode Materials for Microbial Fuel Cells – Thi Hiep Han – Microbial Fuel Cell

Progress and Future Direction of Chromosome-Centric Human Proteome Project – Young-Ki Paik – Journal of Proteome Research

Review: Proteomics and the human microbiome: where we are today and where we would like to be – Carolin Adriane Kolmeder – Emerging Topics in Life Sciences

March of the Microbes: Harnessing the Power of the Human Microbiome to Improve Health and Target Disease – Helen Albert – Clinical OMICs

In vitro models of the human microbiota and microbiome – Julie A.K. McDonald – Emerging Topics in Life Sciences

Pregnancy and early life

Development of the Microbiota in Infants and its Role in Maturation of the Gut Mucosa and the Immune System – Cecilia Ximenez – Archives of Medical Research

Human nearly-sterile sites

The Influence of Age and Sex on Ocular Surface Microbiota in Healthy Adults -Xiaofeng Wen – Immunology and Microbiology

Human respiratory microbiome

Pneumococcal vaccine impacts on the population genomics of non-typeable Haemophilus influenzae – David W Cleary – bioRxiv

The nasopharyngeal microbiome – David W. Cleary- Emerging Topics in Life Sciences

The lung microbiome in health and disease – Miriam F Moffatt – Clinical Medicine

New Strategies and Challenges in Lung Proteomics and Metabolomics. An Official American Thoracic Society Workshop Report – Russell P. Bowler – Annals of the American Thoracic Society

Fungal microbiota in chronic airway inflammatory disease and emerging relationships with the host immune response – Irene Zhang – Frontiers in Microbiology

Oral microbiome

Nonleachable Imidazolium-Incorporated Composite for Disruption of Bacterial Clustering, Exopolysaccharide-Matrix Assembly, and Enhanced Biofilm Removal – Geelsu Hwang – ACS Applied Materials & Interfaces

Review: The oral microbiome – Liam P. Shaw – Emerging Topics in Life Sciences

Use of Probiotics and Oral Health – Robert P. Allaker – Current Oral Health Reports

Subgingival Microbiome Colonization and Cytokine Production during Early Dental Implant Healing – Jeffrey B. Payne – mSphere

Human vaginal microbiome

The human female urogenital microbiome: complexity in normality – David A. MacIntyre – Emerging Topics in Life Sciences

Human gut microbiome

Gut microbiome production of short-chain fatty acids and obesity in children – Selvasankar Murugesan – European Journal of Clinical Microbiology & Infectious Diseases

The gut microbiome and hypertension – Pevsner-Fischer – Current Opinion in Nephrology and Hypertension

In vitro models of the human microbiota and microbiome – Julie A.K. McDonald – Emerging Topics in Life Sciences

Culturomics and Amplicon-based Metagenomic Approaches for the Study of Fungal Population in Human Gut Microbiota – Ibrahim Hamad – Scientific Reports

Lymphatic system and gut microbiota affect immunopathology of neuroinflammatory diseases, including multiple sclerosis, neuromyelitis optica and Alzheimer’s disease – Ikuo Tsunoda – Clinical & Experimental Neuroimmunology

Effect of different treatments and alcohol addiction on gut microbiota in minimal hepatic encephalopathy patients – Zan Zuo – Experimental and Therapeutic Medicine

Microbes Tickling Your Tummy: the Importance of the Gut-Brain Axis in Parkinson’s Disease – Paula Perez-Pardo – Current Behavioral Neuroscience Reports

Gancao-Gansui combination impacts gut microbiota diversity and related metabolic functions – Jingao Yu – Journal of Ethnopharmacology

Gut microbiome production of short-chain fatty acids and obesity in children – Selvasankar Murugesan – European Journal of Clinical Microbiology & Infectious Diseases

Gut microbiota in human SLE and a mouse model of lupus – Xin M. Luo – Applied and Environmental Microbiology

The interaction between smoking, alcohol and the gut microbiome – Gabriele Capurso – Best Practice & Research Clinical Gastroenterology

Animal experiments

Lactation-related metabolic mechanism investigated based on mammary gland metabolomics and 4 biofluids’ metabolomics relationships in dairy cows – Hui-Zeng Sun – BMC Genomics

Differences in the gut microbiota of dogs (Canis lupus familiaris) fed a natural diet or a commercial feed revealed by the Illumina MiSeq platform – Junhyung Kim – Gut Pathogens

Chronic glucocorticoid treatment induced circadian clock disorder leads to lipid metabolism and gut microbiota alterations in rats – Tao Wu – Life Sciences

Animal microbiome

Gut microbiota composition is associated with environmental landscape in honey bees – Julia C Jones –  Ecology and Evolution

Microbiota and environmental stress: how pollution affects microbial communities in Manila clams – M. Milan – Aquatic Toxicology

Analysis of the bacterial microbiome in the small octopus, Octopus variabilis, from South Korea to detect the potential risk of foodborne illness and to improve product management – Jin-JaeLee  – Food Research International

Plant, root, and soil microbiome

Studies on mycorrhizal biodiversity in medicinal plant species of Pookode lake area, Wayanad, Kerala, India – Saranya Babu Jayaprakash C.M. – Annals of Plant Sciences

Effects of Iron Amendments on the Speciation of Arsenic in the Rice Rhizosphere after Drainage – Noriko Yamaguchi – Soils

Continuous application of different organic additives can suppress tomato disease by inducing the healthy rhizospheric microbiota through alterations to the bulk soil microflora – Hongjun Liu – Plant and Soil

Seasonal changes in a maize-based polyculture of central Mexico reshape the co-occurrence networks of soil bacterial communities – Eria A. Rebollar – Frontiers in Microbiology

Evolution of microbial communities during electrokinetic treatment of antibiotic-polluted soil – Hongna Li – Ecotoxicology and Environmental Safety

Roles of different active metal-reducing bacteria in arsenic release from arsenic-contaminated paddy soil amended with biochar – Jiang-taoQiao – Journal of Hazardous Materials

Legume crop rotation suppressed nitrifying microbial community in a sugarcane cropping soil – Chanyarat Paungfoo-Lonhienne – Scientific Reports

Responses of soil nutrients and microbial communities to three restoration strategies in a karst area, southwest China – Dejun Li – Journal of Environmental Management

Microbial community structure and soil pH correspond to methane production in Arctic Alaska soils – Robert Wagner – Environmental Microbiology

Water and extremophile microbiome

Ocean biogeochemistry modeled with emergent trait-based genomics – V. J. Coles – Science

Bacterial Community Profiling of Waters from Aquaculture and Non-aquaculture Sites within Taal Lake Ecosystem through 16S rDNA Analysis – Leslie Michelle M. Dalmacio – The Philippine Journal of Health Research and Development

Prokaryotic Community Composition in Arctic Kongsfjorden and Sub-Arctic Northern Bering Sea Sediments as Revealed by 454 Pyrosequencing – Yin-Xin Zeng –  Frontiers in Microbiology

Microbial communities shaped by treatment processes in a drinking water treatment plant and their contribution and threat to drinking water safety – Qi Li – Frontiers in Microbiology

Diversity of microbial communities and quantitative chemodiversity in layers of marine sediment cores from an causeway (Kaichu-Doro) in Okinawa Island, Japan – Taha Soliman – Frontiers in Microbiology

Bacterial Diversity and Biogeochemistry of Two Marine Shallow-Water Hydrothermal Systems off Dominica (Lesser Antilles) – Petra Pop Ristova – Frontiers in Microbiology

Spatially distinct, temporally stable microbial populations mediate biogeochemical cycling at and below the seafloor in hydrothermal vent fluids – Caroline S. Fortunato –  Environmental Microbiology

Functional diversity and redundancy across fish gut, sediment and water bacterial communities – Arthur Escalas – Environmental Microbiology

Built environment

Archaeal and Bacterial Community Structure in an Anaerobic Digestion Reactor (Lagoon Type) Used for Biogas Production at a Pig Farm – Pampillón-González L – Journal of Molecular Microbiology and Biotechnology

Bacterial perspectives on the dissemination of antibiotic resistance genes in domestic wastewater bio-treatment systems: beneficiary to victim – Dong Wu – Applied Microbiology and Biotechnology

Effect of ammonia on the active microbiome and metagenome and from stable full-scale digesters – J.Ruiz-Sánchez – Bioresource Technology

Droplet distribution and airborne bacteria in an experimental shower unit – C.E.Estrada-Perez – Water Research

Food Microbiology

Environmental Microbiota Drives Microbial Succession and Metabolic Profiles during Chinese Liquor Fermentation – Xueshan Wang – Applied and Environmental Microbiology

Shotgun metagenomics and volatilome profile of the microbiota of fermented sausages -Ilario Ferrocino –  Applied and Environmental Microbiology

Probiotics / prebiotics

Bifidobacterium longum 1714 as a translational psychobiotic: modulation of stress, electrophysiology and neurocognition in healthy volunteers – A P Allen  – Translational Psychiatry

Phage and viruses

High HPV16 E6 viral load in the oral cavity is associated with an increased number of bacteria: A preliminary study – Hideo Shigeishi – Biomedical Reports

Kullback Leibler divergence in complete bacterial and phage genomes – Sajia Akhter – PeerJ

Review: The human gut virome: form and function – Lesley A. Ogilvie – Emerging Topics in Life Sciences

Deep sequencing reveals high bacterial diversity and phylogenetic novelty in pit mud from Luzhou Laojiao cellars for Chinese strong-flavor Baijiu – Mao-KeLiu – Food Research International

Bioinformatics

Accurate Determination of Bacterial Abundances in Human Metagenomes Using Full-length 16S Sequencing Reads – Fanny Perraudeau – bioRxiv

MetaLab: an automated pipeline for metaproteomic data analysis – Kai Cheng – Microbiome

ASAR: visual analysis of metagenomes in R – Askarbek Orakov – Bioinformatics

Bacteria & Biofuels

Metabolome analysis reveals a role for glyceraldehyde 3-phosphate dehydrogenase in the inhibition of C. thermocellum by ethanol – Liang Tian – Biotechnology for Biofuels

Biophotovoltaics: Conversion of Light Energy to Bioelectricity Through Photosynthetic Microbial Fuel Cell Technology – Rashmi Chandra – Microbial Fuel Cell

Techniques

Electron microscopy reveals unique nano forms of bacterial spores – Sumanta Ghosh – bioRxiv

Continuous and High-throughput Electromechanical Lysis of Bacterial Pathogens using Ion Concentration Polarization – Minseok Kim – Analytical Chemistry

Microbes in the news

A New Antibiotic Weakness—Drugs Themselves Help Bacteria Survive

Exercise Changes Gut Microbial Composition Independent of Diet, Study Shows

Bacteria and obesity: Reviewing the connection between gut bacteria, obesity, and diet

Bacteria & Art

Bacteria Collection of Icons Vector Illustration

Tina’s non microbiology picks

PODCAST: This Scientist Wants To Dance On Mars (And She Just Might Make That Happen)

How to Review a Manuscript

December 4, 2017

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Today we have many interesting articles,  Marangoni A. evaluates  antifungal properties of Spirulina platensis against  Candida species; J. de Gunzburg  reports on gut microbiome  protection from antibiotics; E. Uhlig writes about removal of Escherichia coli from “ready‐to‐eat” salads .. while in my personal non microbiological pics you can read the study from A.Carter about women’s visibility in academic seminars. Apparently women ask fewer questions than men. Enjoy your winter read.

Events and jobs

Microbiology Professor, College of the Sequoias, San Jose

Postdoctoral Fellow, EMBL,Hinxton, United Kingdom

General microbiome

Review: Multidrug resistant (or antimicrobial-resistant) pathogens – alternatives to new antibiotics? – Anne-Sophie Brunel – Swiss Medical Weekly

Petri dish versus Winogradsky column: a longue durée perspective on purity and diversity in microbiology, 1880s-1980s – Grote M – History and Philosophy of the Life Sciences

Pregnancy and early life

32-week premature rupture of membranes caused by oropharyngeal microbiota – Alberto Hidalgo-Chicharro – Microbiology Society

Bacteriological and Immunological Profiling of Meconium and Fecal Samples from Preterm Infants: A Two-Year Follow-Up Study – Marta Gómez – Nutrients

Human respiratory microbiome

IL-17 and TNF-α Are Key Mediators of Moraxella catarrhalis Triggered Exacerbation of Allergic Airway Inflammation – Safa Alnahas – Frontiers in Immunology

Oral microbiome

Gingivitis and plaque prevention using three commercially available dentifrices: A comparative clinical and microbiological randomized control parallel study – Ramprasad Reddy – International Journal of Pharmaceutical Investigation

Human vaginal microbiome

In vitro activity of Spirulina platensis water extract against different Candida species isolated from vulvo-vaginal candidiasis cases – Antonella Marangoni – PLOS One

Characterization of a New Ezakiella Isolated From the Human Vagina: Genome Sequence and Description of Ezakiella Massiliensis Sp. Nov – K Diop – Current Microbiology

Newly Isolated Lactobacilli Strains From Algerian Human Vaginal Microbiota: Lactobacillus Fermentum Strains Relevant Probiotic’s Candidates – Liza Ouarabi – Probiotics and Antimicrobial Proteins

Human nearly-sterile sites

A comprehensive analysis of breast cancer microbiota and host gene expression – Kevin J. Thompson – PLOS One

Human gut microbiome

Aging Gut Microbiota at the Cross-Road between Nutrition, Physical Frailty, and Sarcopenia: Is There a Gut–Muscle Axis? – Andrea Ticinesi – Nutrients

Adipose Tissue Metabolism and Cancer Progression: Novel Insights from Gut Microbiota? – Benedicte F. Jordan – Current Pathobiology Reports

Protection of the human gut microbiome from antibiotics – Jean de Gunzburg – The Journal of Infectious Diseases

Gut microbiota and colorectal cancer: insights into pathogenesis for novel therapeutic strategies – Yongbo Kang – Zeitschrift für Gastroenterologie

Genomic Analysis of a Pathogenic Bacterium, Paeniclostridium sordellii CBA7122 Containing the Highest Number of rRNA Operons, Isolated from a Human Stool Sample – Joon Yong Kim – Frontiers in Pharmacology

Cellular senescence in gastrointestinal diseases: from pathogenesis to therapeutics – Frey N – Nature Reviews Gastroenterology

Gut Symbiont Bacteroides fragilis Secretes a Eukaryotic-Like Ubiquitin Protein That Mediates Intraspecies Antagonism – Chatzidaki-Livanis M – mBio

Reduction in Gut Microbial Diversity as a Mechanism of Action of Exclusive Enteral Nutrition – Kaakoush NO – The American Journal of Gastroenterology

Adipose Tissue Metabolism and Cancer Progression: Novel Insights from Gut Microbiota? – Jordan BF – Current Pathobiology Reports

Review: A review of metabolic potential of human gut microbiome in human nutrition – Yadav M – Archives of Microbiology

Animal experiments 

Colonization with Escherichia coli EC 25 protects neonatal rats from necrotizing enterocolitis – Debi M. Thomas – PLOS One

Animal microbiome

Bamboo Specialists From Two Mammalian Orders (Primates, Carnivora) Share a High Number of Low-Abundance Gut Microbe – EA McKenney – Microbial Ecology

Plant, root, and soil microbiome

Organic Amendments in a Long-Term Field Trial-Consequences for the Bulk Soil Bacterial Community as Revealed by Network Analysis – CAO Schmid – Microbial Ecology

Distinctive Soil Archaeal Communities in Different Variants of Tropical Equatorial Forest – D Kerfahi – Microbial Ecology

Water and extremophile microbiome 

Comparative Analyses of Methanogenic and Methanotrophic Communities Between Two Different Water Regimes in Controlled Wetlands on the Qinghai-Tibetan Plateau, China – Hongpeng Cui – Current Microbiology

Built environment

Microbial Insight into a Pilot-Scale Enhanced Two-Stage High-Solid Anaerobic Digestion System Treating Waste Activated Sludge – Jing Wu – International Journal of Environmental Research and Public Health

Food microbiology

Effects of household washing on bacterial load and removal of Escherichia coli from lettuce and “ready-to-eat” salads – Elisabeth Uhlig – Food Science & Nutrition

Organic food and the impact on human health – Hurtado-Barroso S – Critical Reviews in Food Science and Nutrition

Probiotics / prebiotics

Probiotics Ingestion Does Not Directly Affect Thyroid Hormonal Parameters in Hypothyroid Patients on Levothyroxine Treatment – Giorgia Spaggiari – Frontiers in Endocronology

Characterization of probiotic potential of Bacillus species isolated from a traditional brine pickle – Ragul K – Journal of Food Science and Technology

 

Bioinformatics

Microbiome Datasets Are Compositional: And This Is Not Optional – Gregory B. Gloor – Frontiers in Microbiology

A meta-proteomics approach to study the interspecies interactions affecting microbial biofilm development in a model community – Herschend J – Scientific Reports

A 16S rRNA gene sequencing and analysis protocol for the Illumina MiniSeq platform – Monica Pichler – bioRxiv

Techniques

Exploration of Microbial Communities Using the Thermo Scientific Varioskan LUX Multimode Reader and the Invitrogen EVOS FL Cell Imaging System – Anna Hiltunen – BioTechniques

Application of hierarchical oligonucleotide primer extension (HOPE) to assess relative abundances of ammonia- and nitrite-oxidizing bacteria – Giantommaso Scarascia – BMC Microbiology

Microbes in the news

Microorganisms on your scalp, ears and elbows can be turned into music

Microbes on the market

With $1M in funding, Phase Genomics looks to crack genetic codes and discover unknown bacteria

Tina’s non microbiological pics

Women’s visibility in academic seminars: women ask fewer questions than men

 

November 23, 2017

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Today we have pretty much diverse Microbiome Digest particularly in the section of General microbiome. Interesting papers on E coli as a model organism for metabolic engineering, influence of exercise on our gut microbiota and influence of antibiotics on genetic diversity of honeybee gut microbiota. Enjoy reading these and many many more articles and news about microbes.

Events and jobs

PhD in Soil Microbiology, Teagasc Johnstown Castle, UK

PhD Fellowship in Molecular Microbiology, Copenhagen, Denmark

Postdoctoral Research Associate – Bacterial Evolutionary Genomics, Missoula, MT, US

Postdoctoral researchers – (Lemon Lab), Cambridge MA, US

Associate Professor/Professor in Microbiology, Nottingham, UK

General microbiome

The Immunomodulatory Drug Glatiramer Acetate is Also an Effective Antimicrobial Agent that Kills Gram-negative Bacteria – Stig Hill Christiansen – Scientific Reports

Temperate phages as self-replicating weapons in bacterial competition – Xiang-Yi Li – bioRxiv

Complete Genome Sequences of Seven Vibrio cholerae Phages Isolated in China – Sudhakar G. Bhandare – Genome Announcements

Survival of microbes in Earth’s stratosphere – Priya Das Sarma – Current Opinion in Microbiology

Review: Cable Bacteria Take a New Breath Using Long-Distance Electricity – Filip J.R. Meysman – Trends in Microbiology

Characterization of the CrbS/R Two-Component System in Pseudomonas fluorescens Reveals a New Set of Genes under Its Control and a DNA Motif Required for CrbR-Mediated Transcriptional Activation – Edgardo Sepulveda – Frontiers in Microbiology

The effect of the 2015 Earthquake on the bacterial community compositions in water in Nepal – Sital R. Uprety – Frontiers in Microbiology

Rokubacteria: genomic giants among the uncultured bacterial phyla – Eric D. Becraft – Frontiers in Microbiology

A communal catalogue reveals Earth’s multiscale microbial diversity – Luke R. Thompson – Nature

Pregnancy and early life

Microbial Mechanistic Insight into the Role of Inulin in Improving Maternal Health in a Pregnant Sow Model – Pan Zhou – Frontiers in Microbiology

Human respiratory microbiome

A practical molecular identification of nonfermenting Gram-negative bacteria from cystic fibrosis – Carolina Paulino da CostaCapizzani – Brazilian Journal of Microbiology

Oral microbiome

Over-the-counter mouthwash use and risk of pre-diabetes/diabetes – Kaumudi J.Joshipura – Nitric Oxide

Profiling of Oral Microbiota in Early Childhood Caries Using Single-Molecule Real-Time Sequencing – Yuan Wang – Frontiers in Microbiology

Exploring the association between Alzheimer’s disease, oral health, microbial endocrinology and nutrition – Alice Harding – Frontiers in Aging Neuroscience

Oral microbiomes from hunter-gatherers and traditional farmers reveal shifts in commensal balance and pathogen load linked to diet – Florent Lassalle – Molecular Ecology

Human skin microbiome

Evaluation of short exposure times of antimicrobial wound solutions against microbial biofilms: from in vitro to in vivo – K Johani – Journal of Antimicrobial Chemotherapy

Human gut microbiome

Review: Influence of microbiota on intestinal immune system in ulcerative colitis and its intervention – Sailong Zhang – Frontiers in Immunology

Exercise Alters Gut Microbiota Composition and Function in Lean and Obese Humans – Allen, Jacob M – Medicine & Science in Sports & Exercise

The Kynurenine Pathway As a Novel Link between Allergy and the Gut Microbiome – Aaron P. Van der Leek – Frontiers in Immunology

The gut microbiota: A new potential driving force in liver cirrhosis and hepatocellular carcinoma – Marco Sanduzzi Zamparelli – United European Gastroenterology Journal

Animal experiments 

Aged Gut Microbiota Contributes to Systemical Inflammaging after Transfer to Germ-Free Mice – Floris Fransen – Frontiers in Immunology

Animal microbiome

Species-specific signatures of the microbiome from Camponotus and Colobopsis ants across developmental stages – Manuela Oliveira Ramalho – PLOS One

Spontaneous body contractions are modulated by the microbiome of Hydra – Andrea P. Murillo-Rincon – Sceintific Reports

Age-related differences in the respiratory microbiota of chickens – Laura Glendinning – PLOS One

A potential new species of porcine Actinobacillus defined by multi-locus sequence analysis – C. Turni – Animal Production Science

Prevalence survey of Toxoplasma gondii in hearts from Western Australian sows – K. Hodgson – Animal Production Science

Antibiotics reduce genetic diversity of core species in the honeybee gut microbiome – Kasie Raymann –  Molecular Ecology

Plant, root, and soil microbiome

Rhizosphere Microbiome Recruited from a Suppressive Compost Improves Plant Fitness and Increases Protection against Vascular Wilt Pathogens of Tomato – Anastasis Antoniou – Frontiers in Plant Science

Exogenous nitrogen addition reduces the temperature sensitivity of microbial respiration without altering the microbial community composition – Hui Wei – Frontiers in Microbiology

Parallelized, aerobic, single carbon-source enrichments from different natural environments contain divergent microbial communities – Theodore M. Flynn – Frontiers in Microbiology

The effect of Lobelia dortmanna L. on the structure and bacterial activity of the rhizosphere – KatarzynaLewicka-Rataj – Aquatic Botany

Illumina-Based Analysis of Endophytic and Rhizosphere Bacterial Diversity of the Coastal Halophyte Messerschmidia sibirica – Xue-Ying Tian – Frontiers in Microbiology

Functionality of Root-Associated Bacteria along a Salt Marsh Primary Succession – Miao Wang – Frontiers in Microbiology

An Integrated Insight into the Relationship between Soil Microbial Community and Tobacco Bacterial Wilt Disease – Hongwu Yang – Frontiers in Microbiology

Water and extremophile microbiome

Deep ocean prokaryotic communities are remarkably malleable when facing long-term starvation – Marta Sebastián – Environmental Microbiology

Interrogating marine virus-host interactions and elemental transfer with BONCAT and nanoSIMS-based methods – Alexis L. Pasulka – Environmental Microbiology

Increased Denitrification Rates Associated with Shifts in Prokaryotic Community Composition Caused by Varying Hydrologic Connectivity – Abigail Tomasek – Frontiers in Microbiology

Chapter 4.1 – The Biota of Intermittent Rivers and Ephemeral Streams: Prokaryotes, Fungi, and Protozoans – Anna M. Romaní – Intermittent Rivers and Ephemeral Streams

Fungal diversity in deep-sea sediments of a hydrothermal vent system in the Southwest Indian Ridge – Wei Xu – Deep Sea Research Part I

Environmental factors shape water microbial community structure and function in shrimp cultural enclosure ecosystems – Dongwei Hou – Frontiers in Microbiology

Taxonomic and Functional Differences between Microbial Communities in Qinghai Lake and Its Input Streams – Ze Ren – Frontiers in Microbiology

Microbial Diversity and Community Structure of Sulfate-Reducing and Sulfur-Oxidizing Bacteria in Sediment Cores from the East China Sea – Yu Zhang – Frontiers in Microbiology
Stratified Bacterial and Archaeal Community in Mangrove and Intertidal Wetland Mudflats Revealed by High Throughput 16S rRNA Gene Sequencing – Zhichao Zhou – Frontiers in Microbiology

 

Food microbiology

Novel insights into microbial community dynamics during the fermentation of Central European ice wine – Mária Bučková – International Journal of Food Microbiology

Diversity within Italian Cheesemaking Brine-Associated Bacterial Communities Evidenced by Massive Parallel 16S rRNA Gene Tag Sequencing – Marilena Marino – Frontiers in Microbiology

Probiotics / prebiotics

Lactobacillus acidophilus Metabolizes Dietary Plant Glucosides and Externalizes Their Bioactive Phytochemicals – Mia C. Theilmann – mBio

Phages and viruses

Bacteriophage Transcytosis Provides a Mechanism To Cross Epithelial Cell Layers – Sophie Nguyen – mBio

MVP: a microbe–phage interaction database  – Na L. Gao – Nucleic Acids Research

Biotechnology

Enrichment of lignocellulose-degrading microbial communities from natural and engineered methanogenic environments – Emine Gozde Ozbayram – Applied Microbiology and Biotechnology

Escherichia coli as a model organism for systems metabolic engineering – Paul A.Adamczyk – Current Opinion in System Biology

Bioinformatics

Review: Computational Approaches for Integrative Analysis of the Metabolome and Microbiome – Jasmine Chong – Metabolites

Techniques

Nucleic acid purification from plants, animals and microbes in under 30 seconds – Yiping Zou – PLOS Biology

Lighting Van Leeuwenhoek’s samples – Lesley A. Robertson – FEMS Microbiology Letters

Analysis of Microbiome Data in the Presence of Excess Zeros – Abhishek Kaul – Frontiers in Microbiology

Stripping flow cytometry: How many detectors do we need for bacterial identification? – Peter Rubbens – Cytometry

Microbes in the news 

Plague Bacteria Entered Europe During Neolithic Age, Genetic Analysis Finds 

How the Immune System Identifies Invading Bacteria

Scientists Program Remote-Controlled Nanobots to Kill Cancer

Microbes on the market 

Qualitative Report on Human Microbiome Market 

Microbes and art

Superbugs And Rockets Side By Side At Science Museum

 

 

 

November 2, 2017

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Second day of November we have quite a few job offers, nice set of microbiome news, two reviews in “gut microbiome” sector. Two (personal) highlights today would be the Thomas J. Browning’s  paper about phytoplankon nutrient co-limitation and Luke R. Thompson’s paper about The Earth Microbiome Project. Enjoy…

Events and jobs

Research Technician, University of York, UK

Postdoctoral Researcher – Molecular Microbiologist, University of Oxford, Oxford, UK

Bioinformatics Postdoc, Max Planck Institute for Infection Biology, Berlin, Germany

Microbiology Postdoctoral Scholar,  The University of California, Berkeley, California, US

Bioinformatics Analyst, Ares Genetics GmbH, Vienna, Austria

Assistant Professor of Microbiology, The University of Alabama in Huntsville, Huntsville, Alabama, US

Tenure-track Assistant Professor of Microbiology, Miami University, Miami, Ohio, US

Tenure Track Assistant Professor in Microbiology, The University of British Columbia, Vancouver,  Canada

General microbiome

Impaired competence in flagellar mutants of Bacillus subtilis is connected to the regulatory network governed by DegU – Theresa Hoelscher – bioRxiv

Gene network analysis identifies a central post-transcriptional regulator of cellular stress survival – Matthew Z. Tien – bioRxiv

Detection of cytosolic Shigella flexneri via a C-terminal triple-arginine motif of GBP1 inhibits actin-based motility – Anthony Piro – bioRxiv

Inter-species population dynamics enhance microbial horizontal gene transfer and spread of antibiotic resistance – Robert M Cooper – eLIFE

A communal catalogue reveals Earth’s multiscale microbial diversity – Luke R. Thompson – Nature

Human gut microbiome

Rapid Assessment of Microbiota Changes in Individuals with Autism Spectrum Disorder Using Bacteria-derived Membrane Vesicles in Urine – Yunjin Lee – Experimental Neurobiology

Review: Dietary and microbial metabolites in the regulation of host immunity – Jun Kunisawa – frontiers in Microbiology

Review: Gut microbiota as a potential target of metabolic syndrome: the role of probiotics and prebiotics – Mingqian He – Cell & Bioscience

Progression of Parkinson’s disease is associated with gut dysbiosis: Two-year follow-up study – Tomomi Minato – PLOS One

Animal experiments

Rapid regrowth and detection of microbial contaminants in equine fecal microbiome samples – Kalie F. Beckers – PLOS One

Cecal Microbiota in Broilers Fed with Prebiotics – Dany Mesa – Frontiers in Genetics

Commensal Lactobacillus Controls Immune Tolerance during Acute Liver Injury in Mice – Nobuhiro Nakamoto – Cell Reports

Food restriction followed by refeeding with a casein- or whey-based diet differentially affects the gut microbiota of pre-pubertal male rats – Majdi Masarwi – The Journal of Nutritional Biochemistry

Animal microbiome 
Evidence for a conserved microbiota across the different developmental stages of Plodia interpunctella – Valeria Mereghetti -Insect Science

Plant, root, and soil microbiome

Stable isotope informed genome-resolved metagenomics reveals that Saccharibacteria utilize microbially processed plant derived carbon – Evan P. Starr – bioRxiv

Water and extremophile microbiome 

Analysis of bacterial communities and characterization of antimicrobial strains from cave microbiota – Muhammad Yasir – Brazilian Journal of Microbiology

Highly divergent 16S rRNA sequences in ribosomal operons of Scytonema hyalinum (Cyanobacteria) – Jeffrey R. Johansen – PLOS One

Study of Microbial diversity in Ganga river water sample by the use of Metagenomics technique – Jamilah Ali Ahmed Zaed – Journal of Pharmacognosy and Phytochemistry

Niche specialization of bacteria in permanently ice-covered lakes of the McMurdo Dry Valleys, Antarctica – Miye Kwon – Environmental Microbiology

Influence of bicarbonate on the abundance of microbial communities capable of reducing U(VI) in groundwater – Dianxin Li – RSC Advances

Monitoring microbial responses to ocean deoxygenation in a model oxygen minimum zone – Steven J. Hallam – Scientific Data

Synechococcus plasticity under environmental changes – Cristiana Callieri – FEMS Microbiology Letters

Nutrient co-limitation at the boundary of an oceanic gyre – Thomas J. Browning -Nature

Evaluation of different 16S rRNA gene V regions for exploring bacterial diversity in a eutrophic freshwater lake – Junyi Zhang – Science of The Total Environment

Microbial community structures and functions of wastewater treatment systems in plateau and cold regions – Dexin Fang – Bioresource Technology

Adaptability as the key to success for the ubiquitous marine nitrite oxidizer Nitrococcus — Jessika Füssel – Science Advances

Food microbiology

Characterization of Enterococcal Community Isolated from an Artisan Istrian Raw Milk Cheese: Biotechnological and Safety Aspects – Mirna Mrkonjic Fuka – Food Technology and Biotechnology

Probiotics / prebiotics
Lactobacillus reuteri suppresses E. coli O157:H7 in bovine ruminal fluid: Toward a pre-slaughter strategy to improve food safety? – Yolande Bertin – PLOS One

Bioinformatics

MetaCherchant: analyzing genomic context of antibiotic resistance genes in gut microbiota – Evgenii I Olekhnovich – Bioinformatics

Techniques

Quantification of diverse virus populations in the environment using the polony method – Nava Baran – Nature Microbiology

Microbes in the news 

Microbiome Link with Colorectal Cancer Drug Toxicity Points to Predictive Tests and Prevention – Genetic Engineering and Biotechnology News

Gut bacteria composition could predict toxicity of chemotherapy drugs in cancer patients – News Medical

Versatile marine bacteria could be an influence on global warming, scientists discover – Science Daily

By 2100, climate change could alter key microbial interactions in the ocean  – Phys Org

Microbes on the market 

Symbiotix Biotherapies Receives $5 Million in Institutional Financing to Advance its Development of Molecular Therapeutics that Modulate Regulatory T Cell Activity

Tina’s (non)microbiology picks 

Concept Inventory Development Reveals Common Student Misconceptions about Microbiology – Amy G. Briggs – Journal of Microbiology & Biology Education

Announcing the winner of this year’s ‘Dance Your Ph.D.’ contest – John Bohannon – Science

 

October 2, 2017

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This Monday we have quite short digest with interesting review from K. Rosenthal about microbial single cell analysis,  T. K. Hattenrath-Lehmann tells us about microbes associated with harmful algal blooms while G. Chen demonstrates mutualistic interaction between bacteria in anaerobic mixed culture. Enjoy your reading.

Events and jobs

Tenure Track Faculty Position in Microbial Systems/Synthetic Biology, Chestnut Hill, Massachusetts

General microbiome

Review: Beyond the bulk: disclosing the life of single microbial cells  – Katrin Rosenthal – FEMS Microbiology Reviews

Metagenomic assessment of the interplay between the environment and the genetic diversification of Acinetobacter – Marc Garcia-Garcera – Environmental Microbiology

Mutualistic interaction between dichloromethane- and chloromethane-degrading bacteria in an anaerobic mixed culture – Gao Chen – Environmental Microbiology

Human skin microbiome

Antisepsis of the skin before spinal surgery with povidone iodine-alcohol followed by chlorhexidine gluconate-alcohol versus povidone iodine-alcohol applied twice for the prevention of contamination of the wound by bacteria – S. Patrick – The Bone & Joint Journal

Human nearly-sterile sites 

Microbiota regulates bone marrow mesenchymal stem cell lineage differentiation and immunomodulation – E Xiao – Stem Cell Research & Therapy

Human gut microbiome

Sulphate-reducing bacteria from ulcerative colitis patients induce apoptosis of gastrointestinal epithelial cells – Cláudia Mara Lara Melo Coutinho –  Microbial Pathogenesis

Animal experiments

Changes in the microbiota cause genetically modified Anopheles to spread in a population – Andrew Pike – Science

Plant, root, and soil microbiome

Impact of spatial organization on a novel auxotrophic interaction among soil microbes – Xue Jiang – bioRxiv

Novel archaeal thermostable cellulases from an oil reservoir metagenome – Anna Lewin – AMB Express

Periodically spilled-oil input as a trigger to stimulate the development of hydrocarbon-degrading consortia in a beach ecosystem – Kai Zhang – Scientific Reports

Water and extremophile microbiome 

Identification of unique microbiomes associated with harmful algal blooms caused by Alexandrium fundyense and Dinophysis acuminata -Theresa K.Hattenrath-Lehmann – Harmful Algae

Metagenomic insights into zooplankton-associated bacterial communities – Daniele De Corte – Environmental Microbiology

Strong impact of anthropogenic contamination on the co-occurrence patterns of a riverine microbial community – Anyi Hu – Environmental Microbiology

Microbial Diversity in a Hypersaline Sulfate Lake: A Terrestrial Analog of Ancient Mars – Alexandra Pontefract – Frontiers in Microbiology

Bioinformatics

SAMSA2: A standalone metatranscriptome analysis pipeline – Samuel T. Westreich – bioRxiv

Microbes in the news 

Oral sex spreading unstoppable bacteria

 

September 15, 2017

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Events and jobs

 
Assistant or Associate Professor – Microbiology/Infectious Disease, Farmington, US

 
General microbiome

 
Review: Human microbiota in aging and infection: A review – Elisavet Stavropoulou  – Critical Reviews in Food Science and Nutrition

 

Phylogeographic, genomic, and meropenem susceptibility analysis of Burkholderia ubonensis – Erin P. Price – PLOS

 
Pregnancy and early life

 
The relation between cesarean birth and child cognitive development – Cain Polidano – Scientific Reports

 

Simultaneously Monitoring Immune Response and Microbial Infections During Pregnancy through Plasma cfRNA Sequencing – Wenying Pan – Clinical Chemistry

 
Human respiratory microbiome

 
Oral microbiomeTooth Be Told, Genetics Influences Oral Microbiome – Emily R. Davenport – Cell Host & Microbe

 
Host Genetic Control of the Oral Microbiome in Health and Disease – Andres Gomez – Cell Host & Microbe

 

Human nearly-sterile sites 

 

Evaluation of the Bacterial Diversity in the Human Tongue Coating Based on Genus-Specific Primers for 16S rRNA Sequencing – Beili Sun – BioMed Research International

 

Review: Microbiota-Derived Uremic Retention Solutes: Perpetrators of Altered Nonrenal Drug Clearance in Kidney Disease – Alexander J. Prokopienko – Expert Review of Clinical Pharmacology

 

Human gut microbiome

 
Microbial metabolites as mimickers of human molecules – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

 
The intestinal microbiota regulates body composition through NFIL3 and the circadian clock – Yuhao Wang – Science

 
The Landscape of Type VI Secretion across Human Gut Microbiomes Reveals Its Role in Community Composition – Adrian J. Verster – Cell Host & Microbe

 
Butyrate-producing bacteria supplemented in vitro to Crohn’s disease patient microbiota increased butyrate production and enhanced intestinal epithelial barrier integrity – Annelies Geirnaert – Scientific Reports

 
Linking Spatial Structure and Community-Level Biotic Interactions through Cooccurrence and Time Series Modeling of the Human Intestinal Microbiota – Eric J. de Muinck –  mSystems
Review: Microbiota and neurodegenerative diseases – Moira Marizzonip – Current Opinion in Neurology

 
Effect of cytomegalovirus and Epstein–Barr virus replication on intestinal mucosal gene expression and microbiome composition of HIV-infected and uninfected individuals – Gianella Sara – AIDS

 
Systematic Review and Meta-analysis: Fecal Microbiota Transplantation for Treatment of Active Ulcerative Colitis – Narula Neeraj – Inflammatory Bowel Diseases

 
Signatures in the gut microbiota of Japanese infants who developed food allergies in early childhood – Masaru Tanaka – FEMS Microbiology Ecology

 
Quantity and source of dietary protein influence metabolite production by gut microbiota and rectal mucosa gene expression: a randomized, parallel, double-blind trial in overweight humans – Martin Beaumont – The American Journal of Clinical Nutrition
Analysis of Mucosa-Associated Microbiota in Colorectal Cancer – Kehan Xu – Medical Science Monitor

 
Animal experiments 

 
Short-term dietary methionine supplementation affects one-carbon metabolism and DNA methylation in the mouse gut and leads to altered microbiome profiles, barrier function, gene expression and histomorphology – Isabelle R. Miousse – Genes & Nutrition

 
Development of Inflammatory Bowel Disease Is Linked to a Longitudinal Restructuring of the Gut Metagenome in Mice – Thomas Sharpton – mSystems

 
Development of a Stable Lung Microbiome in Healthy Neonatal Mice – Matea Kostric – Microbial Ecology

 

Animal microbiome

 

Seasonal variation in nutrient utilization shapes gut microbiome structure and function in wild giant pandas – Qi Wu  – Proceedings of the Royal Society of London B

 
Plant, root, and soil microbiome

 
Soil microbial community responses to acid exposure and neutralization treatment – Doyun Shin – Journal of Environmental Management

 
Spatial patterns of hypolithic cyanobacterial diversity in Northern Australia –  Keith Christian – Ecology & Evolution

 

Food microbiology

 

Short-Term Intake of a Fructose-, Fat- and Cholesterol-Rich Diet Causes Hepatic Steatosis in Mice: Effect of Antibiotic Treatment – Annette Brandt – Nutrients

 
Overview of craft brewing specificities and potentially associated microbiota – Lindsey Rodhouse – Critical Reviews in Food Science and Nutrition

 

Probiotics / prebiotics
Isolation of probiotic piliated Lactobacillus rhamnosus strains from human faecal microbiota using SpaAantiserum-based colony immunoblotting – Zhen-quan Yang – Journal of Microbiology and Biotechnology

 

Phages and viruses
CRISPR-based Herd Immunity Limits Phage Epidemics in Bacterial Populations – Pavel Payne – bioRxiv

 
Bioinformatics
A comparison of sequencing platforms and bioinformatics pipelines for compositional analysis of the gut microbiome – Imane Allali – BMC Microbiology

 
Minimizing mixing intensity to improve the performance of rice straw anaerobic digestion via enhanced development of microbe-substrate aggregates – Moonkyung Kim – Bioresource Technology

 
Long term effects of cerium dioxide nanoparticles on the nitrogen removal, micro-environment and community dynamics of a sequencing batch biofilm reactor – Yi Xu – Bioresource Technology

 

Microbes in the news 
NIPGR scientists identify bacteria that can devour fungi

 
Are Genes to Blame for Cavity-causing Bacteria?

 
Microbes on the market (news about biotech companies)

 
Newly Launched CoreBiome Touts Microbiome ‘Profiling’ Services

 
Inventor converts waste plastics to fertilizer, fuel

 
Science, publishing, and career

 
The hundred most-cited publications in microbiota of diabetes research: A bibliometric analysis – Jiaxing Tian – Medicine

August 31, 2017

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Today we have a lot of interesting job offers, a lot of news, many papers from Nature’s Scientific Reports and several reviews from Immunological Reviews and to mention each time more and more papers dealing with wastewater treatments. Enjoy your (still) summer microbiome reading.

Events and jobs

Laboratory Manager (Microbiology), Sydney, Australia

Algae Technician, MBD Energy Limited, Townsville 

PhD position: Synthetic Microbiology/Biotechnology, Germany

PhD position (m/f) in the field of microbiota-host interaction in laying hens, Germany

PhD position in the field of microbial ecology of the fowl gastrointestinal tract,  Germany

Post-Doctoral Research Associate, King’s College London , UK

Synthetic Biologist / Geneticist: Ginkgo Bioworks, Boston, MA

General microbiome

Numerous uncharacterized and highly divergent microbes which colonize humans are revealed by circulating cell-free DNA – Mark Kowarsky – PNAS

Maintenance of microbial cooperation mediated by public goods in single and multiple traits scenarios – Özhan Özkaya – Journal of Bacteriology

Pregnancy and early life

The oral microbiome and adverse pregnancy outcomes – Charles M Cobb – International Journal of Women’s Health

Human respiratory microbiome

The nasal microbiota of dairy farmers is more complex than oral microbiota, reflects occupational exposure, and provides competition for staphylococci – Sanjay K. Shukla –  PLOS One

Sphenoid sinus microbiota in pituitary apoplexy: a preliminary study – Gavin J. Humphreys – Pituitary

Oral microbiology

Review: Studying the human oral microbiome: challenges and the evolution of solutions – Angela ML Benn – Australian Dental Journal

Human vaginal microbiome

The human vaginal microbial community – Mario Vaneechoutte – Research in Microbiology

Replication and refinement of a vaginal microbial signature of preterm birth in two racially distinct cohorts of US women – Benjamin J. Callahan – PNAS

Comparison of vaginal microbiota sampling techniques: cytobrush versus swab – Anita Mitra – Scientific Reports

Human nearly-sterile sites 

Dominance of ST131 Escherichia coli carrying blaCTX-M in patients with bloodstream infections caused by cephalosporin-resistant strains in Australia, New Zealand and Singapore: whole genome analysis of isolates from a randomised trial –  Patrick Harris – bioRxiv

Temporal Stability and Composition of the Ocular Surface Microbiome – Jerome Ozkan – Scientific Reports

Human gut microbiome

Review:Interactions between bile salts, gut microbiota, and hepatic innate immunity – Kristin Schubert – Immunological Reviews

Review:Deciphering interactions between the gut microbiota and the immune system via microbial cultivation and minimal microbiomes – Thomas Clavel – Immunological Reviews

Review: Gut microbiota: Role in pathogen colonization, immune responses, and inflammatory disease – Joseph M. Pickard – Immunological Reviews

Gut microbiota and chronic kidney disease: implications for novel mechanistic insights and therapeutic strategies – Wei Pan –  International Urology and Nephrology

Ecophylogenetics Reveals the Evolutionary Associations between Mammals and their Gut Microbiota – Christopher Andrew Gaulke -bioRxiv

Unveiling the gut microbiota composition and functionality associated with constipation through metagenomic analyses – Leonardo Mancabelli –  Scientific Reports

Influence of gut microbiota on neuropsychiatric disorders – María Carmen Cenit – World Journal of Gastroenterology

Fecal microbiota transplantation for Clostridium difficile infection in patients with ileal pouches – Nan Lan – Gastroenterology Report

The Intestinal Microbiome in Infectious Diseases: The Clinical Relevance of a Rapidly Emerging Field – Vanessa C Harris – Open Forum Infectious Diseases

A novel approach for the prediction of species-specific biotransformation of xenobiotic/drug molecules by the human gut microbiota – Ashok K. Sharma – Scientific Reports

Animal experiments

Metagenomic Analysis of Cecal Microbiome Identified Microbiota and Functional Capacities Associated with Feed Efficiency in Landrace Finishing Pigs – Zhen Tan – Frontiers in Microbiology

Characterization of the ecological role of genes mediating acid resistance in Lactobacillus reuteri during colonization of the gastrointestinal tract – Janina A. Krumbeck – Environmental Microbiology

Animal microbiome

High Spatial and Temporal Variations of Microbial Community along the Southern Catfish Gastrointestinal Tract: Insights into Dynamic Food Digestion – Zhimin Zhang – Frontiers in Microbiology

Unraveling the gut microbiome of the long-lived naked mole-rat – Tewodros Debebe – Scientific Reports

Plant, root, and soil microbiome

Effects of cationic surfactant on the bioaccumulation of polycyclic aromatic hydrocarbons in rice and the soil microbial community structure – Ni Ni – RSC Advances

The impact of adsorption on the exposure assessment of Bacillus thuringiensis in the water-sediment system: a mathematical model approach – Stefano Cervelli – Biology and Fertility of Soils

Phylogenetic diversity and antagonistic traits of root and rhizosphere pseudomonads of a bean from Iran for controlling Rhizoctonia solani – Vahid Keshavarz-Tohid – Research in Microbiology

Petroleum Contamination and Plant Identity Influence Soil and Root Microbial Communities While AMF Spores Retrieved from the Same Plants Possess Markedly Different Communities – Bachir Iffis – Frontiers in Microbiology

Taxonomic and functional shifts in the beech rhizosphere microbiome across a natural soil toposequence – Y. Colin – Scientific Reports

Microbial communities with distinct denitrification potential in spruce and beech soils differing in nitrate leaching – Jiří Bárta – Scientific Reports

The rhizospheric microbial community structure and diversity of deciduous and evergreen forests in Taihu Lake area, China – Wei Z – PLOS One

Taxonomic and functional shifts in the beech rhizosphere microbiome across a natural soil toposequence – Y. Colin – Scientific Reports

Water and extremophile microbiome 

Seasonal Succession and Spatial Patterns of Synechococcus Microdiversity in a Salt Marsh Estuary Revealed through 16S rRNA Gene Oligotyping – Katherine R. M. Mackey – Frontiers in Microbiology

Independent Shifts of Abundant and Rare Bacterial Populations across East Antarctica Glacial Foreland – Wenkai Yan – Frontiers in Microbiology

Microbial community structure and diversity within hypersaline Keke Salt Lake environments – Rui Han – Canadian Journal of Microbiology

Cyanobacterial Allelochemicals But Not Cyanobacterial Cells Markedly Reduce Microbial Community Diversity – Filipa Dias – Frontiers in Microbiology

A microfluidics-based in situ chemotaxis assay to study the behaviour of aquatic microbial communities – Bennett S. Lambert –  Nature Microbiology

Anaerobic methanotrophic communities thrive in deep submarine permafrost – Matthias Winkel – bioRxiv

Microbial communities in peatlands along a chronosequence on the Sanjiang Plain, China – Xue Zhou – Scientific Reports

Microbial communities in marine sediments modify success of an invasive macrophyte – Paul E. Gribben – Scientific Reports

Built environment 

Novosphingobium clariflavum sp. nov., isolated from a household product plant –  Xin Zhang – International Journal of Systematic and Evolutionary Microbiology

Probiotics / prebiotics

Bifidobacterium longum W11: an antibiotic-resistant probiotic – Francesco Di Pierro – Nutrafoods

Lactobacillus plantarum LP‑Onlly alters the gut flora and attenuates colitis by inducing microbiome alteration in interleukin‑10 knockout mice – Hongqi Chen – Molecular Medicine Reports

Bacillus As Potential Probiotics: Status, Concerns, and Future Perspectives – Fouad M. F. Elshaghabee – Frontiers in Microbiology

Probiotics administration following sleeve gastrectomy surgery: A randomized double-blind trial – S Sherf-Dagan – International Journal of Obesity

Phages and viruses

Infection with purified Piscine orthoreovirus demonstrates a causal relationship with heart and skeletal muscle inflammation in Atlantic salmon – Øystein Wessel  – PLOS One

HPeV-3 predominated among Parechovirus A positive infants in the summer of 2013-2014 in Queensland, Australia – Donna M. McNeale – bioRxiv

Review: A bacteriophages journey through the human body – Jeremy J. Barr – Immunological Reviews

Mouse hepatitis virus nsp14 exoribonuclease activity is required for resistance to innate immunity – James Brett Case – bioRxiv

Bioinformatics

microPop: Modelling microbial populations and communities in R – Helen Kettle – Methods in Ecology and Evolution

Biotechnology

Biodegradation of mono-, di- and trifluoroacetate by microbial cultures with different origins – Diogo A.M. Alexandrino – New Biotechnology

Metagenomic mining pectinolytic microbes and enzymes from an apple pomace-adapted compost microbial community – Man Zhou – Biotechnology for Biofuels

Wastewater microbiology

Unravelling diversity and metabolic potential of microbial consortia at each stage of leather sewage treatment – Hebin Liang – RSC Advances

Influence of microbial community diversity and function on pollutant removal in ecological wastewater treatment – Yaohui Bai – Applied Microbiology and Biotechnology

Techniques

A Comparison of Methods to Analyze Aquatic Heterotrophic Flagellates of Different Taxonomic Groups – Alexandra Jeuck – Protist

Fast and Simple Tool for the Quantification of Biofilm-Embedded Cells Sub-Populations From Fluorescent Microscopic Images – Mikhail Bogachev – bioRxiv

Microbes in the news 

Gut bacteria that “talk” to human cells may lead to new treatments

Gut Microbiome Differences in REM Sleep Behavior Disorder, Parkinson’s, and Healthy Controls

Scientists Made Music From the Human Microbiome, and It’s Seriously Cool

Over 50% of Bacteria and Viruses inside Human Body are Unknown to Science

August 25, 2017

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Highlight of the day goes to Anna Karenina principle on microbiomes by J.R. Zaneveld as a Perspective in Nature Microbiology: “When healthy our microbiomes look alike, but when stressed each one of us has our own microbial snowflake”.

Events and jobs

Food Microbiology Microscopist II, EMSL Analytical, Inc. ,Cinnaminson, NJ 

Research Associate, University of Bristol – School of Biochemistry

General microbiome

Perspectives: Stress and stability: applying the Anna Karenina principle to animal microbiomes – Jesse R. Zaneveld – Nature Microbiology

Sugar metabolism of the first thermophilic Planctomycetes Thermogutta terrifontis: comparative genomic and transcriptomic approache – Alexander Elcheninov – bioRxiv

Horizontally Acquired Genes Are Often Shared between Closely Related Bacterial Species – Evgeni Bolotin –  Frontiers in Microbiology

Pregnancy and early life

Early gut mycobiota and mother-offspring transfer – Kasper Schei -Microbiome

Oral Microbiology

Genetic influences on the human oral microbiome – Brittany A. Demmitt – BMC Genomics

 

Human gut microbiome

Beyond gut feelings: how the gut microbiota regulates blood pressure – Francine Z. Marques – Nature Reviews Cardiology

Animal microbiome 

Upper and lower respiratory tract microbiota in horses: bacterial communities associated with health and mild asthma (inflammatory airway disease) and effects of dexamethasone – Stephanie L. Bond – BMC Microbiology

Plant, root, and soil microbiome

Transient exposure to oxygen or nitrate reveals ecophysiology of fermentative and sulfate-reducing benthic microbial populations – Zainab Abdulrahman Beiruti – Environmental Microbiology

Water and extremophile microbiome

Prey range and genome evolution of Halobacteriovorax marinus predatory bacteria from an estuary – Brett G. Enos – bioRxiv

Genomic insights into potential interdependencies in microbial hydrocarbon and nutrient cycling in hydrothermal sediments – Nina Dombrowski –  Microbiome

Prey range and genome evolution of Halobacteriovorax marinus predatory bacteria from an estuary – Brett G. Enos – bioRxiv

Bacteria-induced mixing in natural waters – T. Sommer – Geophysical Research Letters

Food microbiology

Unraveling the correlation between microbiota succession and metabolite changes in traditional Shanxi aged vinegar – Zhiqiang Nie – Scientific Reports

Microbes in the news

Space travel microbes turn urine into polymers

Is The Secret To A Healthier Microbiome Hidden In The Hadza Diet?

IBM: Your Computer Can Help Scientists Study Connection Between Body Bacteria and Autoimmune Diseases