Category Archives: Microbes and the market

December 29, 2017

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It’s a bit quiet towards the end of the year, but not without highlights. Could we fight antibiotic resistance by targeting mild infections using alternative drugs? Do we want to correct our own genes using CRISPR and what’s the future for penicillin?

Jobs

Associate Professor – Microbiology – Dental College -chennai

General microbiology

Efficient Hydrogen-Dependent Carbon Dioxide Reduction by Escherichia coli – Magali Roger et al. – Current Biology

Press: Bacteria under pressure run reaction in reverse to sequester carbon – John Timmer – Ars Technica

The Role of Type VI Secretion System Effectors in Target Cell Lysis and Subsequent Horizontal Gene Transfer – Peter David Ringel et al. – Cell Reports

Press: Predatory Bacteria Acquire Drug Resistance Directly from Rivals – Genetic Engineering & Biotechnology News

* Alternative therapeutics for self-limiting infections—An indirect approach to the antibiotic resistance challenge – Kristofer Wollein Waldetoft and Sam P. Brown – PLoS Biology

Author interview: Alternatives to Antibiotics: Why managing mild maladies matters – Beth Baker – PLoS Research News

Animal experiments

Under control: how a dietary additive can restore the gut microbiome and proteomic profile, and improve disease resilience in a marine teleostean fish fed vegetable diets – María Carla Piazzon et al. – Microbiome

Animal microbiome

Mosquito vector-associated microbiota: Metabarcoding bacteria and eukaryotic symbionts across habitat types in Thailand endemic for dengue and other arthropod-borne diseases – Panpim Thongsripong et al. – Ecology and Evolution

Plant, root and soil microbiome

Rhizosphere-associated Alcaligenes and Bacillus strains that induce resistance against blast and sheath blight diseases, enhance plant growth and improve mineral content in rice – Kaleem U. Kakar et al. – Journal of Applied Microbiology

Microbes in the news

A week of holiday junk food could derail your gut microbiome—but there’s hope – Claire Maldarelli – Popular Science

Microbiota and Cancer – Andrea S. Blevins Prime – Cancer Therapy Advisor

Maternal Antibiotic Exposure Affects Infant Fecal Microbiota Following Vaginal Delivery – Jessica Martin – Infectious Disease Advisor

Microbe expert claims we should wash them ‘AT LEAST’ once a week at a high temperature to avoid dust mites and bacteria – Unity Blott – Daily Mail

* CORRECTING THE GENES – Santanu Chakraborty – Bangalore Mirror

Govt study finds faecal bacteria in 97 percent ‘filtered’ water jars in Dhaka – Bdnews24

* 200 million lives saved – but prognosis for penicillin is not healthy – Harry Ridgewell and Angela Long (collaborator) – Wiki Tribune

Microbes on the market

Report on sale: Human Microbiome Therapeutics Market is expected to Witness a CAGR of 14.19 % Till 2022 including Key Players: Rebiotix, Seres Therapeutics – Craig Francis – Social Articles Tracking & PR news.com

Report on sale: Microbiome Drugs Market by Production, Capacity Utilization Rate, Ex-Factory Price, Revenue, Cost, Gross and Gross Margin Analysis – Amit Pawar – Social Articles Tracking & PR news.com

 

December 23, 2017

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Events and jobs
Assistant Professor of Environmental Microbiology (Tenure-Track) – George Mason University – Fairfax, Virginia, USA
The George Mason University, Department of Environmental Science and Policy (ESP) is seeking an enthusiastic and energetic individual for a Tenure-Track Assistant Professor position in Molecular Environmental Microbiology to supplement existing departmental strengths in applied ecology, aquatic ecology, one health and conservation. This is a full-time, tenure-track position to begin August 2018.

Manager, QC Microbiology – Catalent Pharma Solutions, Inc. – Madison, Wisconsin, USA

Post-Doc – Microbiology & Immunology – Cornell University – Ithaca, NY, USA

Biological Sciences Full-Time Instructor (Microbiology Emphasis) – West Valley-Mission Community College District – Saratoga, CA, USA

General microbiome
Review: Building conventions for unconventional lymphocytes. – Lesley Pasman – Immunological Reviews (from September, but not posted before)

Pregnancy and early life
Gut microbiome in gestational diabetes: a cross-sectional study of mothers and offspring 5 years postpartum – Sayyid Hasan – AOGS

Multi-site human microbiome
Review: The role of microbial amyloid in neurodegeneration. – Robert P Friedland – Plos Pathogens

Human respiratory microbiome
Review: Airway microbiome research: a modern perspective on surveillance cultures? – Damien Roux – Annals Of Translational Medicine

Human skin microbiome
Review: Over a Decade of recA and tly Gene Sequence Typing of the Skin Bacterium Propionibacterium acnes: What Have We Learnt? – Andrew McDowell – Microorganisms

Human oral microbiome
Ecological Balance of Oral Microbiota is Required to Maintain Oral Mesenchymal Stem Cell Homeostasis. – Yingying Su – Stem Cells (Dayton, Ohio)

Shift in the Subgingival Microbiome following Scaling and Root Planing in Generalized Aggressive Periodontitis. – Guojing Liu – Journal Of Clinical Periodontology

Human gut microbiome
Quinones are growth factors for the human gut microbiota. – Kathrin Fenn – Microbiome

Opinion: Microbiome-Germline Interactions and Their Transgenerational Implications. – Michael Elgart – Bioessays : News And Reviews In Molecular, Cellular And Developmental Biology

Review: Modeling metabolism of the human gut microbiome – Stefanía Magnúsdóttir – Current Opinion in Biotechnology

Microbial ecology
Opinion: Engineering microbial communities using thermodynamic principles and electrical interfaces. – Christian Zerfaß – Current Opinion In Biotechnology

Animal experiments
Age-dependent alterations of glucose clearance and homeostasis are temporally separated and modulated by dietary fat. – Mads T F Damgaard – The Journal Of Nutritional Biochemistry

Shift of hindgut microbiota and microbial short chain fatty acids profiles in dairy calves from birth to pre-weaning. – Yang Song – FEMS Microbiology Ecology

Impact of genistein on the gut microbiome of humanized mice and its role in breast tumor inhibition. – Bidisha Paul – Plos One

Tomato Powder Inhibits Hepatic Steatosis and Inflammation Potentially Through Restoring SIRT1 Activity and Adiponectin Function Independent of Carotenoid Cleavage Enzymes in Mice. – Cheng-Chung Li – Molecular Nutrition & Food Research

Faecal microRNAs: indicators of imbalance at the host-microbe interface? – G M Moloney – Beneficial Microbes

Modulation of the fecal microbiota in Sprague-Dawley rats using genetically modified and isogenic corn lines. – Penggao Li – Journal Of Agricultural And Food Chemistry

Sex-dependent impact of Roundup on the rat gut microbiome – Veronica L. Lozano – Toxicology Reports

Effects of garlic-supplemented diet on growth performance and intestinal microbiota of rainbow trout (Oncorhynchus mykiss) – Miray Etyemez Büyükdeveci – Aquaculture

Animal microbiome
Identification and chemical characterization of N acyl-homoserine lactone quorum sensing signals across sponge species and time. – Maya Britstein – FEMS Microbiology Ecology

Reptile-associated Borrelia species in the goanna tick (Bothriocroton undatum) from Sydney, Australia. – Jessica L Panetta – Parasites & Vectors

Multi-Omic Biogeography of the Gastrointestinal Microbiota of a Pre-Weaned Lamb – Antonio Palomba – Proteomes

Identification, comparison and validation of robust rumen microbial biomarkers for methane emissions using diverse Bos Taurus breeds and basal diets – Marc D. Auffret – Frontiers in Microbiology

Plant, root, and soil microbiome
Structure and function of the microbial consortia of activated sludge in typical municipal wastewater treatment plants in winter. – Bo Zhang – Scientific Reports

Key microbial taxa in the rhizosphere of sorghum and sunflower grown in crop rotation. – Tanzelle Oberholster – The Science Of The Total Environment

Metagenomic analysis of soil and freshwater from zoo agricultural area with organic fertilization. – Aylan K Meneghine – Plos One

Field study reveals core plant microbiota and relative importance of their drivers. – Kelly Hamonts – Environmental Microbiology

Enhanced arsenic uptake and polycyclic aromatic hydrocarbon (PAH)-dissipation using Pteris vittata L. and a PAH-degrading bacterium. – Lu Sun – The Science Of The Total Environment

Division of labor during biofilm matrix production – Anna Dragos – bioRxiv

Succession of Fungal and Oomycete Communities in Glyphosate-Killed Wheat Roots – Daniel Schlatter – Phytopathology

Long-term and legacy effects of manure application on soil microbial community composition – Yuting Zhang – Biology and Fertility of Soils

Ammonium nitrogen content is a dominant predictor of bacterial community composition in an acidic forest soil with exogenous nitrogen enrichment – Yanxia Nie – Science of the Total Environment

Water and extremophile microbiome
Consequences of contamination on the interactions between phytoplankton and bacterioplankton. – Goni-Urriza Marisol – Chemosphere

Identification of active denitrifiers by DNA-Stable Isotope Probing and amplicon sequencing reveals Betaproteobacteria as responsible for attenuation of nitrate contamination in a low impacted aquifer. – M Inés Bellini – FEMS Microbiology Ecology

The importance of filamentous cyanobacteria in the development of oxygenic photogranules. – Kim Milferstedt – Scientific Reports

Temperate phages as self-replicating weapons in bacterial competition. – Xiang-Yi Li – Journal Of The Royal Society, Interface (In freshwater metazoan Hydra vulgaris)

The Biogeographical Distribution of Benthic Roseobacter Group Members along a Pacific Transect Is Structured by Nutrient Availability within the Sediments and Primary Production in Different Oceanic Provinces – Marion Pohlner – Frontiers in Microbiology

Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics – Kristin Bergauer – PNAS (From November 2017, not posted before)

Homoacetogenesis in Deep-Sea Chloroflexi, as Inferred by Single-Cell Genomics, Provides a Link to Reductive Dehalogenation in Terrestrial Dehalococcoidetes – Holly L. Sewell – mBio

Seasonal and depth-wise variations in bacterial and archaeal groups in the Arabian Sea oxygen minimum zone – Mandar Bandekar – Deep Sea Research Part II: Topical Studies in Oceanography

Review: Microalgae–bacteria biofilms: a sustainable synergistic approach in remediation of acid mine drainage – Sudharsanam Abinandan – Applied Microbiology and Biotechnology

Built environment
Changes in bacterial and archaeal communities during the concentration of brine at the graduation towers in Ciechocinek spa (Poland) – Agnieszka Kalwasińska – Extremophiles

The Coal Seam Microbiome (CSMB) Reference Set, a lingua franca for the microbial coal-to-methane community – Silas H.W. Vick – International Journal of Coal Geology

Food microbiology
Review: Impact of nanosilver on gut microbiota: a vulnerable link. – Dinesh Kumar Dahiya – Future Microbiology

Probiotics / prebiotics
Effects of fermented soymilk with Lactobacillus casei Shirota on skin condition and the gut microbiota: a randomised clinical pilot trial. – T Nagino – Beneficial Microbes

Effect of tablets containing probiotic candidate strains on gingival inflammation and composition of the salivary microbiome: a randomised controlled trial. – M K Keller – Beneficial Microbes

Phages and viruses
Review: Inflammatory Bowel Disease’s Specific Changes of Enteric Mycobiota and Virome. – Yi Chu – Journal Of Digestive Diseases

Review: Phages of life – the path to pharma. – Amanda Forde – British Journal Of Pharmacology

Bioinformatics
Hybrid-denovo: A de novo OTU-picking pipeline integrating single-end and paired-end 16S sequence tags. – Xianfeng Chen – Gigascience

** 3D molecular cartography using LC-MS facilitated by Optimus and ‘ili software. – Ivan Protsyuk – Nature Protocols **

Non-biological synthetic spike-in controls and the AMPtk software pipeline improve fungal high throughput amplicon sequencing data – Jonathan M Palmer – bioRxiv

Multi-omics integration—a comparison of unsupervised clustering methodologies – Giulia Tini – Briefings in Bioinformatics

Review: Genome-scale metabolic networks in time and space – Ove Øyås – Current Opinion in Systems Biology

Techniques
Flow cytometric fingerprinting for microbial strain discrimination and physiological characterization. – Benjamin Buysschaert – Cytometry. Part A : The Journal Of The International Society For Analytical Cytology

Off-axis electron holography of bacterial cells and magnetic nanoparticles in liquid – Tanya Prozorov – Journal of the Royal Society

Microbes in the news
Higher Numbers of 2 Bacteria Species Found in Sarcoidosis Patients, Study Finds – Janet Stewart – Sarcoidosis News

The Surprising Way Your Brain and Gut Are Connected – Julia Malacoff – Shape

Gut Bacteria May Influence Infant Intelligence – Batya Swift Yasgur – MedScape

What Humans Can Learn About Gut Health From Monkey ‘Huddling’ – Francesca Friday – Observer

How to keep your gut healthy over the holidays – Yella Hewings-Martin – Medical News Today

Studies Link Oral Microbiome to Cancers – Pam Harrison – MedPage

Bacteria Found Alive in Earth’s Most Extreme Environments for the First Time Hold Clues to Life on Other Planet – Sydney Pereira – Newsweek

Antibiotic resistance: ‘Sleeping’ bacteria that can survive drug treatment identified – Phys.Org

Bacteria-Basted Supertrees Are Sucking Pollution From Our Waste Sites – James Poulos – Good

Everything you know about toxic shock syndrome is probably wrong – Sara Chodosh – Popular Science

Microbes on the market
Direct-to-consumer DNA and microbiome test launched in Europe – PharmaPhorum

BiomX acquires RondinX to expand microbiome targets for IBD, liver disease – Jonathan Solomon – HealIO

DSM Acquires BioCare Copenhagen to Expand Gut Health Ingredients Portfolio with Probiotics – CISION

Sarcoidosis Industry Overview with Total Market Share and Distribution of Sarcoidosis for 7 MM for 2025 – Miltech

Global Human Microbiome Market Analysis, Share, Production, Growth, Trends and Forecast 2017 to 2022 – Arun P. – GeoPolMonitor

Global Microbiome Therapeutic Market Outlook – Johnson and Johnson, AB-Biotics, Vedanta Biosciences, AbbVie Inc – Kevin Harper – The News Columnist

Bacteria Hysteria
‘This is how the X-Men started’: Internet shocked by astronaut discovery of ‘alien bacteria’ on International Space Station – Sarah K. Burris – RawStory

Science, publishing, and career
Graduate Biomedical Science Education Needs a New Philosophy – Gundula Bosch – mBio

December 20, 2017

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A long but great digest today, with lots of diversity – a few studies of poultry gut microbiome and the effects food/probiotics have, a solid showing for human gut microbiome studies – covering its implications on a range of disorders, some news about biotech companies, studies on plants and from environmental sources, a promising analysis of techniques used for sampling for human gut studies, and my normal dosage of non-microbiology science.  Happy Holidays!

Events and jobs

ON-DEMAND WEBINAR How to Harness the Microbiome: Considerations and Implications of the Microbiome in Preclinical Research with Reproducible Results

Senior Biomedical Scientist (Microbiology) – Matchtech – Essex, England

Staff Research Associate 3, UCLA Department of Microbiology, Immunology and Molecular Genetics

Assistant (10782) – Clinical chemistry, microbiology and immunology – Ghent University

Pregnancy and early life

Early-Life Human Microbiota Associated With Childhood Allergy Promotes the T Helper 17 Axis in Mice – Dagbjort H. Petursdottir – Frontiers in Immunology

[Accepted Manuscript] – The neonatal window of opportunity – early priming for life – Harald Renz -Journal of Allergy and Clinical Immunology

Human oral microbiome

The Microbiome of Potentially Malignant Oral Leukoplakia Exhibits Enrichment for Fusobacterium, Leptotrichia, Campylobacter, and Rothia Species – Abdrazak Amer – Frontiers in Microbiology

Exploring the Association between Alzheimer’s Disease, Oral Health, Microbial Endocrinology and Nutrition – Alice Harding – Frontiers in Aging Neuroscience

Admission to the Intensive Care Unit is Associated With Changes in the Oral Mycobiome – Richard R. Watkins – Journal of Intensive Care Medicine

Human nearly-sterile sites

Metagenomics in pooled plasma, with identification of potential emerging infectious pathogens – Min Xu – Transfusion

Human gut microbiome

** High-resolution profiling of the gut microbiome reveals the extent of Clostridium difficile burden – Ninalynn Daquigan – npj Biofilms and Microbiomes

Unravelling the specificity and mechanism of sialic acid recognition by the gut symbiont Ruminococcus gnavus – C. David Owen – Nature Communication

[Editorial] Is gut microbiome a predictive marker to response to immune checkpoint inhibitors? – Khalil Saleh – Immunotherapy

* Microbiota Modulate Anxiety-Like Behavior and Endocrine Abnormalities in Hypothalamic-Pituitary-Adrenal Axis – Ran Huo – Front. Cell. Infect. Microbiology

Possible role of the gut microbiota–brain axis in the antidepressant effects of (R)-ketamine in a social defeat stress model – Chun Yang – Translational Psychiatry

Microbial antigen encounter during a preweaning interval is critical for tolerance to gut bacteria – Kathryn A. Knoop – Science Immunology

* Stool Donor Body Mass Index Does Not Affect Recipient Weight After a Single Fecal Microbiota Transplantation for C. difficile Infection – Monika Fischer – Clinical Gastroenterology and Hepatology

The role of microbiota in the pathogenesis of schizophrenia and major depressive disorder and the possibility of targeting microbiota as a treatment option – Fengli Lv – Oncotarget

Characterization of the urinary microbiota of elderly women and the effects of type 2 diabetes and urinary tract infections on the microbiota – Fengping Liu – Oncotarget

Animal experiments 

* Food-grade cationic antimicrobial ε-polylysine transiently alters the gut microbial community and predicted metagenome function in CD-1 mice – Xiaomeng You – npj Science of Food

Significant improvement of intestinal microbiota of gibel carp (Carassius auratus gibelio) after traditional Chinese medicine feeding – Zhenbing Wu – Journal of Applied Microbiology

* The gastrointestinal microbiome and its association with the control of pathogens in broiler chicken production: A review – Viviana Clavijo – Poultry Science

Influence of dietary avilamycin on ileal and cecal microbiota in broiler chickens – J-H Choi – Poultry Science

Plant, root, and soil microbiome

* Geometagenomics illuminates the impact of agriculture on the distribution and prevalence of plant viruses at the ecosystem scale – Pauline Bernardo – The ISME Journal

Dispersal alters bacterial diversity and composition in a natural community – Michaeline B N Albright – The ISME Journal

** Genomic features of bacterial adaptation to plants – Asaf Levy – Nature Genetics

Soil Bacterial Community Structure and Co-occurrence Pattern during Vegetation Restoration in Karst Rocky Desertification Area – Liang Xue – Frontiers in Microbiology

First insight into microbial community composition in a phosphogypsum waste heap soil – Sylwia Zielińska – ABP

* Harnessing the microbiomes of Brassica vegetables for health issues – Birgit Wassermann – Scientific Reports

Water and extremophile microbiome 

Microdiversification in genome-streamlined ubiquitous freshwater Actinobacteria – Stefan M Neuenschwander – The ISME Journal

Recurrent patterns of microdiversity in a temperate coastal marine environment – Meghan Chafee – The ISME Journal

Microcystin-LR does not induce alterations to transcriptomic or metabolomic profiles of a model heterotrophic bacterium – Robbie M. Martin – PLOS One

Pre-treatment and inoculum affect the microbial community structure and enhance the biogas reactor performance in a pilot-scale biodigestion of municipal solid waste – Valeria Ventorino – Waste Management

Food microbiology

* Inner Workings: Companies seek food safety using a microbiome approach – Carolyn Beans – PNAS

Phages and viruses

* Temporal dynamics of uncultured viruses: a new dimension in viral diversity – Ksenia Arkhipova – The ISME Journal

Bioinformatics

A confidence interval analysis of sampling effort, sequencing depth, and taxonomic resolution of fungal community ecology in the era of high-throughput sequencing – Ryoko Oono – PLOS One

Techniques

Performance of DNA metabarcoding, standard barcoding, and morphological approach in the identification of host–parasitoid interactions – Martin Šigut – PLOS One

** Successful collection of stool samples for microbiome analyses from a large community-based population of elderly men – Melanie Abrahamson – Contemporary Clinical Trials Communications

Microbes on the market 

BiomX Acquires RondinX to Boost Microbiome Discovery and Development Capabilities

Vanterra Capital Backs BIOHM Health, A Total Microbiome Company

Second Genome Advances Lead, Oral Small Molecule SGM-1019, Toward Clinical Investigation in NASH After Demonstrating Safety and Tolerability in Phase 1 Study

Ed’s non-microbiology picks 

Cannabidiol (CBD) as an Adjunctive Therapy in Schizophrenia: A Multicenter Randomized Controlled Trial – Philip McGuire – The American Journal of Psychiatry

Effects of Legal Access to Cannabis on Scheduled II–V Drug Prescriptions – Sarah S. Stith – JAMDA

Ticks parasitised feathered dinosaurs as revealed by Cretaceous amber assemblages – Enrique Peñalver – Nature Communications

Induced and controlled dietary ketosis as a regulator of obesity and metabolic syndrome pathologies – Madeline K. Gibas – Diabetes & Metabolic Syndrome: Clinical Research & Reviews

The effect of vitamin D supplement on the score and quality of sleep in 20-50 year-old people with sleep disorders compared with control group – Mohammad Shahi Majid – Nutritional Neuroscience

Engineers create plants that glow – MIT

December 19, 2017

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Changes to the oral microbiota are associated with risk factors for oral cancer, the benefits of endophytic bacteria on plants, analysis of biofilms from a worldwide sampling of shower hoses.

Pregnancy and early life

Diversity of vaginal microbiota increases by the time of labor onset – Ekaterina Avershina – Scientific Reports

Human oral microbiome

Alterations in oral bacterial communities are associated with risk factors for oral and oropharyngeal cancer – Daniela Börnigen – Scientific Reports

Oral Microbiota: Microbial Biomarkers of Metabolic Syndrome Independent of Host Genetic Factors – Jiyeon Si – Frontiers in Cellular and Infection Microbiology

Animal experiments

Pre-print: Antenatal microbial colonisation of mammalian gut – Elisa Borghi – bioRxiv

Metagenome Analysis of Bodily Microbiota in a Mouse Model of Alzheimer Disease Using Bacteria-derived Membrane Vesicles in Blood – Jin-Young Park – Experimental Neurobiology

Animal microbiome

Differential Ecological Specificity of Protist and Bacterial Microbiomes across a Set of Termite Species – Lena Waidele – Frontiers in Microbiology

Plant, root, and soil microbiome

Pre-print: The ecological genetics of Pseudomonas syringae residing on the kiwifruit leaf surface – Christina Straub – bioRxiv

Inner Plant Values: Diversity, Colonization and Benefits from Endophytic Bacteria – Hongwei Liu – Frontiers in Microbiology

Frankia diversity in host-plant root nodules is independent of abundance or relative diversity of Frankia in corresponding rhizosphere soils – Seifeddine Ben Tekaya – Applied and Environmental Microbiology

Correlated production and consumption of chloromethane in the Arabidopsis thaliana phyllosphere – Muhammad Farhan Ul Haque – Scientific Reports

Rhizodeposition under drought is controlled by root growth rate and rhizosphere water content – Maire Holz – Plant and Soil

Water and extremophile microbiome

Localized high abundance of Marine group II archaea in the subtropical Pearl River Estuary: implications for their niche adaptation – Wei Xie – Environmental Microbiology

Thermophilic bacterial communities inhabiting the microbial mats of “indifferent” and chalybeate (iron-rich) thermal springs: Diversity and biotechnological analysis – Ramganesh Selvarajan – MicrobiologyOpen

Distribution and phylogeny of anaerobic anammonium-oxidizing (anammox) bacteria in water column of the central Pacific Ocean – Koji Hamasaki – Deap Sea Research Part II: Topical Studies in Oceanography

Built environment

Biofilms in shower hoses – Caitlin R Proctor – Water Research

Phages and viruses

Pre-print: Human Herpes Virus 6 (HHV-6) – Pathogen or Passenger? A pilot study of clinical laboratory data and next generation sequencing – Colin Sharp – bioRxiv

Pre-print: ACI-1 class A beta-lactamase is widespread across human gut microbiomes due to transposons harboured by tailed prophages – Chris M Rands – bioRxiv

Bioinformatics

Pre-print: How, when, and where relic DNA biases estimates of microbial diversity – J T Lennon – bioRxiv

Metabolomics

Plasma microbiome-modulated indole- and phenyl-derived metabolites associate with advanced atherosclerosis and postoperative outcomes – Cori A Cason – Journal of Vascular Surgery

Best-matched internal standard normalization in liquid chromatography-mass spectrometry metabolomics applied to environmental samples – Angela K Boysen – Analytical Chemistry

Techniques

Microfluidics: A new tool for microbial single cell analyses in human microbiome studies – Yuguang Liu – Biomicrofluidics

Pre-print: CLIQ-BID: A method to quantify bacteria-induced damage to eukaryotic cells by automated live-imaging of bright nuclei – Yann Wallez – bioRxiv

Mapping the ecological networks of microbial communities – Yandong Xiao – Nature Communications

More microbes

Pre-print: Molecular insights into Vibrio cholerae’s intra-amoebal host-pathogen interactions – Charles Van der Henst – bioRxiv

Nature to the natural rescue: Silencing microbial chats – Diby Paul – Chemico-Biological Interactions

Microbes in the news

Tracking effects of a food preservative on the gut microbiome – EurekAlert

Microbiome intervention with niacin aids insulin sensitivity – Medical Xpress

Wound scanner shows bacteria glowing if your body is infected – New Scientist

Engineering new cellular scaffolding for bacteria – Celia Henry Arnaud – Chemical & Engineering News

Viruses can transfer genes across the superkingdoms of life – ScienceDaily

Microbes on the market

British Health Technology Company Expanding Into Ten European Countries – PR Newswire

December 13, 2017

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Many interesting articles today: Probiotics can inhibit human colonic smooth muscle contraction in vitro in a dose dependent manner, arsenic exposure early in life alters the gut microbiome and can increase E.coli resistance genes, oral administration of two probiotics in mice has specific effects on gene expression in the small intestine, a detailed investigation of the impacts of T. congolense infection in the tsetse fly, and multiple articles on plant and rhizosphere microbiome volatiles.

Events and jobs

Visiting Professor (Part Time) Microbiology  – Chamberlain College of Nursing, Jacksonville, FL Campus

Seminar: The “Bedside to Bench and Back Again” Paradigm in Gut Microbiome Research – Gary D. Wu – University of Chicago

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General microbiome

Review: Hygiene Hypothesis in Asthma Development: Is Hygiene to Blame? – Erik van Tilburg Bernardes – Archives of Medical Research

Human respiratory microbiome

Composition and variation of respiratory microbiota in healthy military personnel – Jun Hang – PLOS One

Human oral microbiome

Periodontitis is associated with significant hepatic fibrosis in patients with non-alcoholic fatty liver disease – William Alazawi – PLOS One

Human gut microbiome

Hypoxia and inactivity related physiological changes precede or take place in absence of significant rearrangements in bacterial community structure: The PlanHab randomized trial pilot study – Robert Šket – PLOS One

*Arsenic exposure and intestinal microbiota in children from Sirajdikhan, Bangladesh – Xiaoxi Dong – PLOS One

Editorial overview: Gastrointestinal: New frontiers in therapeutics for GI diseases and disorders — from microRNAs to novel pharmaceutics, to low FODMAP diets and microbiome – Fievos L Christofi – Current Opinion in Pharmacology

*Inhibition effect of Bifidobacterium longum, Lactobacillus acidophilus, Streptococcus thermophilus and Enterococcus faecalis and their related products on human colonic smooth muscle in vitro – Jing Gong – PLOS One

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Animal experiments

*The distinct effects of orally administered Lactobacillus rhamnosus GG and Lactococcus lactis subsp. lactis C59 on gene expression in the murine small intestine – Chise Suzuki – PLOS One

Diversity of intestinal bacterial lactase gene in antibiotics-induced diarrhea mice treated with Chinese herbs compound Qi Wei Bai Zhu San – Lu He – 3 Biotech

The Impact of Long-Term Intake of Phenolic Compounds-Rich Grape Pomace on Rat Gut Microbiota – Stéphanie Chacar – Journal of Food Science

Preprint: High-dimensional microbiome interactions shape host fitness – Alison L Gould – bioRxiv

Animal microbiome

Comparison of the intestinal mucosal microbiota in dogs siagnosed with idiopathic inflammatory bowel disease and dogs with food-responsive diarrhea before and after treatment – K. Kalenyak – FEMS Microbiology Ecology

*Molecular characterization of tsetse’s proboscis and its response to Trypanosoma congolense infection – Erick O. Awuoche – PLOS Neglected Tropical Diseases

Preprint: Who is the host of the host-associated microbiome? Colony-level dynamics overshadow individual-level characteristics in the fur microbiome of a social mammal, the Egyptian fruit-bat – oren kolodny – BioRxiv

Plant, root, and soil microbiome

Pontibacter brevis sp. nov., isolated from rhizosphere soil of Tamarix ramosissima – Ghenijan Osman – International Journal of Systemic and Evolutionary Microbiology

*Volatiles in the Rhizosphere: Bioprospecting for Sustainable Agriculture and Food Security – Shyamalina Haldar – In: Volatiles and Food Security. Springer

*Characterization of Bacterial Volatiles and Their Impact on Plant Health Under Abiotic Stress – Anukool Vaishnav – In: Volatiles and Food Security. Springer

Dissertation: Plant growth-promoting rhizobacteria (PGPR) mediate interactions between abiotic and biotic stresses in cool- and warm-season grasses – Richard Coy – Auburn University

Endophytic Microorganisms: Promising Candidate as Biofertilizer – Manish Kumar – In: Microorganisms for Green Revolution. Microorganisms for Sustainability, vol 6. Springer

*Bacterial Volatiles in Promotion of Plant Under Biotic Stress – Shekhar Jain – In: Volatiles and Food Security. Springer

*Microbial Volatiles in Defense – Monika – In: Volatiles and Food Security. Springer

*Microbial Volatiles and Plant Defense – Kalaivani K. Nadarajah – In: Volatiles and Food Security. Springer

Wonders of Microbes in Agriculture for Productivity and Sustainability – Rajababu V. Vyas – In: Microorganisms for Green Revolution. Microorganisms for Sustainability, vol 6. Springer

Water and extremophile microbiome

Review: Marine microbiology: Illuminating the importance of nitrite oxidation – Ursual Hofer – Nature Reviews Microbiology

Microbial Ecology

Robustness of a model microbial community emerges from population structure among single cells of a clonal population – Anne W. Thompson – Environmental Microbiology

Resource availability modulates biodiversity-invasion relationships by altering competitive interactions – Tianjie Yang – Environmental Microbiology

Resistome

Action mechanism of naphthofuranquinones against fluconazole-resistant Candida tropicalis strains evidenced by proteomic analysis: The role of increased endogenous ROS – João Batista de Andrade Neto – Microbial Pathogenesis

Evolution of virulence in Enterococcus faecium, a hospital-adapted opportunistic pathogen – Wei Gao – Current Opinion in Microbiology

Surveillance of antibiotic resistance among common Clostridium difficile ribotypes in Hong Kong – Viola C. Y. Chow – Scientific Reports

Food microbiology

Preprint: Copy number variation in fungi and its implications for wine yeast genetic diversity and adaptation – Jacob Steenwyk – bioRxiv

More Microbes

Draft genome sequence of Actinotignum schaalii DSM 15541T: Genetic insights into the lifestyle, cell fitness and virulence – Atteyet F. Yassin – PLOS one

PsrA controls the synthesis of the Pseudomonas aeruginosa quinolone signal via repression of the FadE homolog, PA0506 – Greg Wells – PLOS one

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Phages and viruses

Dissertation: Uncovering the Biological Features of Unknown Viruses Using Shotgun Metagenomic Sequence Data – Daniel Joseph Nasko – University of Delaware

Bioinformatics

MPA Portable: a Stand-alone Software Package for Analyzing Metaproteome Samples on the Go – Thilo Muth – Analytical Chemistry

Dissertation: Revealing Microbial Responses to Environmental Dynamics: Developing Methods for Analysis and Visualization of Complex Sequence Datasets – Matthew Kellom – Arizona State University

Preprint: Rarefaction, alpha diversity, and statistics – Amy Willis – bioRxiv

Biotechnology

Review: Electron transport phenomena of electroactive bacteria in microbial fuel cells: a review of Proteus hauseri – I-Son Ng – Bioresources and Bioprocessing

Dissertation: From Biofuels to Natural Products: Microbial Metabolic Engineering for Chemical Production – Nicole E Nozzi -University of California, Davis

Waste and Pollution

Assessment of a novel anti-biofouling microorganism (Bacillus sp. T5) for control of membrane biofouling and its effect on bacterial community structure in membrane bioreactors – Bahar Yavuztürk Gül – Water Science and Technology

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Microbes in the news

New Data: 2 Million Puerto Ricans Risk Water Contamination – Mekela Panditharatne – NRDC

Bacteria development marks new era in cellular design – Phys.org

Feeding Overcrowded Bacteria Increases Antibiotic Susceptibility – Genetic Engineering and Biotechnology News

A Bacterial Role In High Blood Pressure – The Microbiome Speaks – Chuck Dinerstein – American Council on Science and Health

New Microbiome Analysis Tool Resolves Individual Species, Strains – Rachel Lutz – MD Magazine

How honey bee gut bacteria help to digest their pollen-rich diet – EurekaAlert

Microbes on the market

Bio-Rad Inks Supply and Distribution Agreement for Microbiome MDx – genomeweb

Dannon, as a part of DanoneWave Public Benefit Corporation, Announces $50K in Grants for Graduate Studies – Markets Insider

 

December 7, 2017

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Meta-analysis of a collection of gut microbiome studies, characterization of two dandelion viruses, evaluation of an inclusive Research Education Community for engaging undergraduates in scientific research.

General microbiome

Bacterial social interactions and the emergence of community-intrinsic properties – Jonas Stenløkke Madsen – Current Opinion in Microbiology

Pregnancy and early life

Pre-print: Hospitalized premature infants are colonized by related bacterial strains with distinct proteomic profiles – Christopher T Brown – bioRxiv

Human gut microbiome

Gut microbiota in early life and its influence on health and disease: A position paper by the Malaysian Working Group on Gastrointestinal Health – Yeong Yeh Lee – Journal of Paediatrics and Child Health

Animal experiments

Moving beyond microbiome-wide associations to causal microbe identification – Neeraj K Surana – Nature

Plant, root, and soil microbiome

Arbuscular mycorrhizal fungus causes increased condensed tannins concentrations in shoots but decreased in roots of Lotus japonicus L – Zakaria M Solaiman – Rhizosphere

Shifts in soil microbial community, soil enzymes and crop yield under peanut/maize intercropping with reduced nitrogen levels – Jun Chen – Applied Soil Ecology

Multifarious plant growth promotion by an entomopathogenic fungus Lecanicillium psalliotae – C M Senthil Kumar – Microbiological Research

Water and extremophile microbiome

Pre-print: Optogenetics reprogramming of planktonic cells for biofilm formation – Aiguo Xia – bioRxiv

Phages and viruses

Pre-print: Molecular Identification and Characterization of Two Rubber Dandelion Amalgaviruses – Humberto J Debat – bioRxiv

Internalization of a polysialic acid-binding Escherichia coli bacteriophage into eukaryotic neuroblastoma cells – Timo A Lehti – Nature Communications

Bioinformatics

Pre-print: Personalized modeling of the human gut microbiome reveals distinct bile acid deconjugation and biotransformation potential in healthy and IBD individuals – Almut Heinken – bioRxiv

Meta-analysis of gut microbiome studies identifies disease-specific and shared responses – Claire Duvallet – Nature Communications

Techniques

In vitro enteroid-derived three-dimensional tissue model of human small intestinal epithelium with innate immune responses – Ying Chen – PLOS ONE

More microbes

Galectin-3 impacts Cryptococcus neoformans infection through direct antifungal effects – Fausto Almeida – Nature Communications

Microbes in the news

Lemur study highlights role of diet in shaping gut microbiome – Erin Mckenney – Phys.Org

What Bacteria Can Tell Us About Human Evolution – Tara C Smith – Quanta Magazine

Duke launches new microbiome center, reflecting popularity of microbiome studies – Sean Cho – Duke Chronicle

Study shows first extensive and stable microbiome remodeling via B. infantis in infants – Weber Shandwick – EurekAlert

Air-eating bacteria found in Antarctica – Cosmos

The Microbes Making Themselves at Home on the Space Station – Marina Koren – The Atlantic

Microbes on the market

Breakthrough Evidence on Vomaris Bioelectric Technology’s Impact on Wound Biofilm Infection – PR Newswire

Precision Driven Health and Orion Health release Microbiome report – Voxy

Worldwide microbiome drugs market is likely to grow substantially by 2022 – Digital Journal

Science, career, and publishing

How to Keep Students in Science – Howard Hughes Medical Institute

An inclusive Research Education Community (iREC): Impact of the SEA-PHAGES program on research outcomes and student learning – David I Hanauer – PNAS

Pre-print: Assessing the Landscape of U.S. Postdoctoral Salaries – Rodoniki Athanasiadou – bioRxiv

Editorial: Great mentoring is key for the next generation of scientists – Nature

Amy’s non-microbiology picks

Organocalcium-mediated nucleophilic alkylation of benzene – Andrew S S Wilson – Science

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

 

December 2, 2017

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Events and jobs
PhD Student – Developing and validating a computational model of the gut microbiota–mucosa interactions to replace and reduce animal experiments – Birmingham, UK

Assistant/Associate Professor, Microbiology and Immunology – SUNY Upstate Medical University – Syracuse, NY

Microbiology Manager – Cranleigh Scientific – Kent, England

Adjunct Anatomy and Physiology and Microbiology Instructor – City College – Altamonte Springs, FL

Program Manager – Rutgers, The State University of New Jersey

Assistant Professor, Statistics and Microbiology – The University of Manitoba – Winnipeg, Manitoba, Canada

Human respiratory microbiome
Making It Last: Storage Time and Temperature Have Differential Impacts on Metabolite Profiles of Airway Samples from Cystic Fibrosis Patients – Stephen Wandro – MSystems

Human skin microbiome
Effects of cosmetics on the skin microbiome of facial cheeks with different hydration levels. – Silvia Esmeralda Pérez-Topete – Microbiology Open

Propionibacterium acnes induces autophagy in keratinocytes: involvement of multiple mechanisms. – Klára Megyeri – The Journal Of Investigative Dermatology

Human oral microbiome
A comparative study of the oral microbiome compositions of healthy postmenopausal, premenopausal, and prepubertal Nigerian females, using 16s rrna metagenomics methods. – K C Anukam – Nigerian Journal Of Clinical Practice

Oral Microbiome Composition Reflects Prospective Risk for Esophageal Cancers – Brandilyn A. Peters – Cancer Research

Review: Microbial colonization of the periodontal pocket and its significance for periodontal therapy. – Andrea Mombelli – Periodontology 2000

Review: Resilience of the Oral Microbiota in Health: Mechanisms That Prevent Dysbiosis. – B T Rosier – Journal Of Dental Research

Human gut microbiome
Specific substrate-driven changes in human faecal microbiota composition contrast with functional redundancy in short-chain fatty acid production. – Nicole Reichardt – The Isme Journal

A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients – Andrew Brantley Hall – Genome Medicine

Characteristics of Fecal Microbiota in Pediatric Crohn’s Disease and Their Dynamic Changes During Infliximab Therapy. – Yizhong Wang – Journal Of Crohn’S & Colitis

Antibiotic Resistome in a large-scale healthy human gut microbiota deciphered by metagenomic and network analyses. – Jie Feng – Environmental Microbiology

Involvement of shared mucosal-associated microbiota in the duodenum and rectum in diarrhea-predominant irritable bowel syndrome. – Gangping Li – Journal Of Gastroenterology And Hepatology

Review: Are the decrease in circulating anti-α1,3-Gal IgG and the lower content of galactosyl transferase A1 in the microbiota of patients with multiple sclerosis a novel environmental risk factor for the disease? – Emmanuel Montassier – Molecular Immunology

Review: Combined therapies to treat complex diseases: The role of the gut microbiota in multiple sclerosis. – Laura Calvo-Barreiro – Autoimmunity Reviews

Review: Computational profiling of the gut–brain axis: microflora dysbiosis insights to neurological disorders – Nikolas Dovrolis – Briefings in Bioinformatics

Animal experiments
IL-17 is a protection effector against the adherent-invasive Escherichia coli in murine colitis. – Hai-Jia Zhang – Molecular Immunology

Changes in gut microbiota during development of compulsive checking and locomotor sensitization induced by chronic treatment with the dopamine agonist quinpirole. – Tony D Jung – Behavioural Pharmacology

Potential Impact of Metabolic and Gut Microbial Response to Pregnancy and Lactation in Lean and Diet-Induced Obese Rats on Offspring Obesity Risk. – Heather A Paul – Molecular Nutrition & Food Research

Clostridium butyricum exerts a neuroprotective effect in a mouse model of traumatic brain injury via the gut-brain axis. – H Li – Neurogastroenterology And Motility : The Official Journal Of The European Gastrointestinal Motility Society

Impacts of diarrhea on the immune system, intestinal environment, and expression of PGRPs in New Zealand rabbits – Yang Chen – PeerJ

Animal microbiome
Multi-level comparisons of cloacal, skin, feather and nest-associated microbiota suggest considerable influence of horizontal acquisition on the microbiota assembly of sympatric woodlarks and skylarks. – H Pieter J van Veelen – Microbiome

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

Production and biotechnological potentialities of extracellular polymeric substances from sponge-associated Antarctic bacteria – Consolazione Caruso – Applied and Environmental Microbiology

Review: Wild gut microbiota protect from disease. – Francesca S Gazzaniga – Cell Research

Plant, root, and soil microbiome
Symbionts protect aphids from parasitic wasps by attenuating herbivore-induced plant volatiles. – Enric Frago – Nature Communications

Microbial decomposition is highly sensitive to leaf litter emersion in a permanent temperate stream. – Juanita Mora-Gómez – The Science Of The Total Environment

Influence of fertilizers and rice cultivation methods on the abundance and diversity of phyllosphere microbiome. – Shobit Thapa – Journal Of Basic Microbiology

Antibiotic-resistant bacteria in the guts of insects feeding on plants: prospects for discovering plant-derived antibiotics. – Katarzyna Ignasiak – Bmc Microbiology

Bacterial endosymbionts influence host sexuality and reveal reproductive genes of early divergent fungi – Stephen J. Mondo – Nature Communications

Organic amendments shift the phosphorus-correlated microbial co-occurrence pattern in the peanut rhizosphere network during long-term fertilization regimes – Yan Chen – Applied Soil Ecology

The interactive effects of arbuscular mycorrhiza and plant growth-promoting rhizobacteria synergistically enhance host plant defences against pathogens – Alejandro Pérez-de-Luque – Scientific Reports

The impact of post-fire salvage logging on microbial nitrogen cyclers in Mediterranean forest soil – Lily Pereg – Science of the Total Environment

Review: Yeast population of the Kindo Peninsula lichens – A. V. Kachalkin – Microbiology

Review: Bacterial Endophyte Colonization and Distribution within Plants – Shyam L. Kandel – Microorganisms

Review: Emerging Microbial Biocontrol Strategies for Plant Pathogens – Sharifah Farhana Syed Ab Rahman – Plant Science

Water and extremophile microbiome
Microbial life on a sand grain: from bulk sediment to single grains. – David Probandt – The Isme Journal

Tracking active groundwater microbes with D2 O labeling to understand their ecosystem function. – Martin Taubert – Environmental Microbiology

Variability of the composition of the microbial community of the deep subsurface thermal aquifer in Western Siberia – V. V. Kadnikov – Microbiology

Cyanobacterial community structure in hot water springs of Indian North-Western Himalayas: A morphological, molecular and ecological approach – Yadvinder Singh – Algal Research

Built environment
Polar solar panels: Arctic and Antarctic microbiomes display similar taxonomic profiles. – Kristie Tanner – Environmental Microbiology Reports

Microorganisms of low-temperature heavy oil reservoirs (Russia) and their possible application for enhanced oil recovery – T. N. Nazina – Microbiology

Food microbiology
Review: Cereal fiber, fruit fiber, and type 2 diabetes: Explaining the paradox. – Karen M Davison – Journal Of Diabetes And Its Complications

Probiotics / prebiotics
Exploring the Impact of Food on the Gut Ecosystem Based on the Combination of Machine Learning and Network Visualization. – Hideaki Shima – Nutrients

Translational Development of Microbiome-Based Therapeutics: Kinetics of E. coli Nissle and Engineered Strains in Humans and Nonhuman Primates. – Caroline Kurtz – Clinical And Translational Science

Phages and viruses
Distribution and Inferred Evolutionary Characteristics of a Chimeric ssDNA Virus Associated with Intertidal Marine Isopods – Kalia S. I. Bistolas – Viruses

Microbial Ecology
Recipient-Biased Competition for an Intracellularly Generated Cross-Fed Nutrient Is Required for Coexistence of Microbial Mutualists – Alexandra L. McCully – mBio

Review: Cell-cell recognition and social networking in bacteria. – Vera Troselj – Environmental Microbiology

Bioinformatics
Functional sequencing read annotation for high precision microbiome analysis. – Chengsheng Zhu – Nucleic Acids Research

Reader reaction on the fast small-sample kernel independence test for microbiome community-level association analysis. – Bin Guo – Biometrics

Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes – Bhavya Papudeshi – BMC Genomics

Resources and tools for the high-throughput, multi-omic study of intestinal microbiota – Aitor Blanco-Míguez – Briefings in Bioinformatics

Techniques
Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics – Zijuan Lai – Nature Methods

Brief guide to the analysis, interpretation and presentation of microbiota data. – Stefan Zalewski – Archives Of Disease In Childhood. Education And Practice Edition

Optimized fluorescent proteins for the rhizosphere-associated bacterium Bacillus mycoides with endophytic and biocontrol agent potential. – Yanglei Yi – Environmental Microbiology Reports

Genome Announcements
Complete Genome Sequence of Bacillus altitudinis P-10, a Potential Bioprotectant against Xanthomonas oryzae pv. oryzae, Isolated from Rice Rhizosphere in Java, Indonesia. – Anto Budiharjo – Genome Announcements

Mrakia arctica sp. nov., a new psychrophilic yeast isolated from an ice island in the Canadian High Arctic – Masaharu Tsuji – Mycoscience

Microbes in the news
New research provides insights into the skin microbiome – EurekAlert

Lab notes: The vaginal microbiome can predict whether a woman is going to have a premature baby – Scroll.in
Paper link: First-trimester vaginal microbiome diversity: A potential indicator of preterm delivery risk  (posted Nov 27, 2017)

How Bacteria Help Regulate Blood Pressure – Veronique Greenwood – Quanta Magazine

Gut Bacteria Predict Responses, Survival Time to PD-1 Cancer Immunotherapy – Bryant Furlow – Modern Medicine Network

Synthetic Glycolipids As A New Class Of Antimicrobials To Down-Regulate Cell Wall Functions – Narayanaswamy Jayaraman – Science Trends

The microbiological art of making a better sausage – Phys.Org

Will microbial protein replace meat on the table? – Digital Journal – Tim Sandle

New 3-D printed materials harness the power of bacteria – Maria Temming – Science News

Scientists Have Expanded the Genetic Code in Bacteria – Brad Jones – Futurism

Microbes on the market
Qiagen Joins French Biotech to Build the Next Generation of Microbiome Technology – Alex Dale – European Biotech News

DuPont and Ireland’s APC venture forward in microbiome-inspired pact – Will Chu – Nutra Ingredients

Rebiotix Announces Expansion of Phase 1 Trial of the Company’s Oral Capsule Microbiota Product, RBX7455, Following Successful Completion of Initial Study Arms – Markets Insider

Science, publishing, and career
Five ways to fix statistics – Jeff Leek – Nature

Tiffany’s non-microbiology picks
An Open Letter to the Senate Concerning H.R.1 and the Graduate Student Tax Provision – Alana Van Dervort
# A letter (that you can sign) against one part of the bill that passed this morning

November 29, 2017

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Short digest today with many popular news articles, including an article on the bacteria found on the international space station!

Events and jobs

QC Supervisor, Microbiology – Organogenesis, Canton MA, USA

Assistant/Associate Professor of Microbiology – Icahn School of Medicine at Mount Sinai, NYC, New York, USA

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  • Microbe physiology and metabolism

Metagenomics-guided analysis of microbial chemolithoautotrophic phosphite oxidation yields evidence of a seventh natural CO2 fixation pathway – Isreal Figueroa – PNAS

Preprint: RodZ promotes MreB polymer formation and curvature localization to determine the cylindrical uniformity of E. coli shape – Randy Morgenstein – bioRxiv

  • Human respiratory microbiome

Preprint: Modelling the effects of bacterial cell state and spatial location on tuberculosis treatment: Insights from a hybrid multiscale cellular automaton model – Ruth Bowness -bioRxiv

  • Human gut microbiome

The triune of intestinal microbiome, genetics and inflammatory status and its impact on lower gastrointestinal anastomosis healing – Jou Lee – The FEBS Journal

Review: Interindividual variability in gut microbiota and host response to dietary interventions – Genelle Healey – Nutrition Reviews

Quercetin metabolism by fecal microbiota from healthy elderly human subjects – Motoi Tamura – PLoS One

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  • Animal experiments

Preservation of three-dimensional spatial structure in the gut microbiome – Yuko Hasegawa – PLoS One

  • Animal microbiome

Staphylococcus aureus (LA-MRSA) within a pig herd – Anna Irene Vedel Sorensen – PLoS One

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  • Microbes in the news

Bacteria found on International Space Station may be alien in origin, says cosmonaut – Andrew Griffin – Independent

Treatment of abnormal vaginal microbiota prior to embryo transfer may improve reproductive outcomes –  Medical Life Sciences News

Changes in microbiome due to antibiotic exposure may increase risk for inflammatory bowel disease – Medical Life Sciences News

Around 30 jobs created at University of Southampton for £26 million biofilm research project – Aaron Shaw – Daily Echo

Connection between Microbiome and Tissue Contractions Critical for Healthy Bowel Functions – Anamika P – The Global Health News

Scientists Use CRISPR to Turn E.Coli Bacteria into a Microscopic Tape Recorder – Kyree Leary – Futurism

Deep ocean bacteria discovered to play large role in carbon capture – Science Daily

A patient’s legacy: Researchers work to make phage therapy less of a long shot – Eric Boodman – STAT

  • Microbes on the market

Microbiome therapeutics market insights shared in detailed report By focusing on Top Companies like LLC; Seres Therapeutics; ENTEROME Bioscience; MaaT Pharma; Rebiotix, Inc.; Ritter Pharmaceuticals; Second Genome, Inc.; and OpenBiome – medGadget

Biomillenia Leverages QIAGEN Bioinformatics in Microbiome-on-a-Chip Discovery of Unculturable Microbes – Business Wire

 

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