Author Archives: Tiff

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 16, 2017

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Multiple articles on plant and soil microbiome, along with new BSCs (under “Water and extremophile microbiome) and some new computational methods! And a search for a microbiome core director from my thesis lab, please forward!

Events and jobs
Microbiome Core Director (Research Associate/Research Scientist) – Huttenhower Lab, Harvard T.H. Chan School of Public Health

Microbiology/Majors Biology Professor – College of the Sequoias Community College District in Visalia, CA

Pregnancy and early life
Modeling Metabolic Interactions in a Consortium of the Infant Gut Microbiome – Francisco Pinto – Frontiers in Microbiology

Faecal microbiota transplant in a child with very early onset inflammatory bowel disease – Carlos Sierra Salinas – Anales De Pediatria (Barcelona, Spain : 2003)

Multi-site human microbiome
Review: Gut microbial balance and liver transplantation: alteration, management, and prediction – Xinyao Tian – Frontiers of Medicine

Human respiratory microbiome
Atopobium and Fusobacterium as novel candidates for sarcoidosis-associated microbiota. – Alexandra Zimmermann – The European Respiratory Journal

Associations between infant fungal and bacterial dysbiosis and childhood atopic wheeze in a nonindustrialized setting – Marie-Claire Arrieta – The Journal Of Allergy And Clinical Immunology

Human vaginal microbiome
High rates of bacterial vaginosis and Chlamydia in a low-income, high-population-density community in Cape Town – Katie S. Lennard – South African Journal of Science and Technology

Human gut microbiome
Subspecies in the global human gut microbiome – Paul I Costea – Molecular Systems Biology

Investigation of bioaccessibility of Cu, Fe, Mn, and Zn in market vegetables in the colon using PBET combined with SHIME. – Naiyi Yin – Scientific Reports

Improving regulation of microbiota transplants – Diane Hoffmann – Science

The Human Gut Microbial Metabolome Modulates Fungal Growth via the TOR Signaling Pathway – Carlos García – MSphere

Review: Our Gut Microbiome: The Evolving Inner Self. – Parag Kundu – Cell

Review: The gut microbiota – an emerging risk factor for cardiovascular and cerebrovascular disease – Stefanie Ascher – European Journal of Immunology

Animal experiments
Microbial communities exhibit host-species distinguishability and phylosymbiosis along the length of the gastrointestinal tract – Kevin D. Kohl – Molecular Ecology

Bile acid is a significant host factor shaping the gut microbiome of diet-induced obese mice. – Xiaojiao Zheng – Bmc Biology

Rumen Bacteria Communities and Performances of Fattening Lambs with a Lower or Greater Subacute Ruminal Acidosis Risk – Fei Li – Frontiers in Microbiology: Systems Microbiology

Dietary Antioxidant Micronutrients Alter Mucosal Inflammatory Risk in a Murine Model of Genetic and Microbial Susceptibility  – JF Pierre – The Journal of Nutritional Biochemistry

Dietary stachyose altered the intestinal microbiota profile and improved the intestinal mucosal barrier function of juvenile turbot, Scophthalmus maximus L. – Pei Yang – Aquaculture

Diversity, in-vitro virulence traits and antifungal susceptibility pattern of gastrointestinal yeast flora of healthy poultry, Gallus gallus domesticus. – Supram Hosuru Subramanya – Bmc Microbiology

Animal microbiome
Dispersal limitation promotes the diversification of the mammalian gut microbiota – Andrew H. Moeller – PNAS

Plant, root, and soil microbiome
Multiple new cryptic pathogenic Phytophthora species from Fagaceae forests in Austria, Italy and Portugal – Thomas Jung – IMA Fungus

Soil characteristics determine the rhizobia in association with different species of Mimosa in central Brazil – Raquel de Castro Pires – Plant and Soil

Effects of organochlorine pesticides on plant growth-promoting traits of phosphate-solubilizing rhizobacterium, Paenibacillus sp. IITISM08 – Rupa Rani – Environmental Science and Pollution Research

Duration of continuous cropping with straw return affects the composition and structure of soil bacterial communities in cotton fields – Lei Yang – Canadian Journal of Microbiology

The greater roles of indigenous microorganisms in removing nitrobenzene from sediment compared with the exogenous Phragmites australis and strain JS45 – Xiangqun Chi – Frontiers of Environmental Science & Engineering

Seasonal Variations in Soil and Bacteriological Properties as Affected by Phytogenic Mounds (Nebkhas) of Halocnemum strobilaceum in Lake Manzala, Egypt – Heba K. Issa – Egyptian Journal of Botany

Investigating monsoon and post-monsoon variabilities of bacterioplankton communities in a mangrove ecosystem – Anwesha Ghosh – Environmental Science and Pollution Research

Invasion by Cordgrass Increases Microbial Diversity and Alters Community Composition in a Mangrove Nature Reserve – Min Liu – Frontiers in Microbiology

Effects of temperature, soil substrate, and microbial community on carbon mineralization across three climatically contrasting forest sites – Zuoxin Tang – Ecology and Evolution

Effects of biotic and abiotic factors on soil organic matter mineralization: Experiments and structural modeling analysis – Husen Qiu – European Journal of Soil Biology

Available forms of nutrients and heavy metals control the distribution of microbial phospholipid fatty acids in sediments of the Three Gorges Reservoir, China – Hongyan Sun – Environmental Science and Pollution Research

Temporal diversity dynamics of the arbuscular mycorrhizal fungi of Larrea tridentata (Sesse & Mocino ex DC) Coville in a semi-arid ecosystem – G Hernández-Zamudio – Revista Argentina de Microbiología (Article in Spanish)

Water and extremophile microbiome
Comparative transcriptomics as a guide to natural product discovery and biosynthetic gene cluster functionality – Gregory C. A. Amos – PNAS

Molecular Mechanisms for Microbe Recognition and Defense by the Red Seaweed Laurencia dendroidea. – Louisi Souza de Oliveira – Msphere

Mycobiota of the disused ore mine of Marcinków in Śnieżnik Masiff (western Poland) – Wojciech Pusz – Journal of Mountain Science

Thermophilic bacterial communities inhabiting the microbial mats of “indifferent” and chalybeate (iron-rich) thermal springs: Diversity and biotechnological analysis. – Xue-Ping Wang – Microbiologyopen

Review: The Seagrass Holobiont and Its Microbiome – Kelly Ugarelli – Microorganisms

Built environment
PCR–DGGE Analysis on Microbial Community Structure of Rural Household Biogas Digesters in Qinghai Plateau – Rui Han – Current Microbiology

Deciphering the core fouling-causing microbiota in a membrane bioreactor: Low abundance but important roles – Shaoqing Zhang – ChemoSphere

Increasing tetracycline concentrations on the performance and communities of mixed microalgae-bacteria photo-bioreactors – Yanghui Xiong – Algal Research

Biostimulation of nutrient additions on indigenous microbial community at the stage of nitrogen limitations during composting – Huan Wang – Waste Management

Food microbiology
Mutually stimulating interactions between lactic acid bacteria and Saccharomyces cerevisiae in sourdough fermentation – S. Sieuwerts – LWT – Food Science and Technology

Review: The Mediterranean diet: metabolic and molecular mechanisms – Valeria Tosti – The Journals Of Gerontology. Series A, Biological Sciences And Medical Sciences

Probiotics / prebiotics/ antibiotics
Prebiotic Dietary Fiber and Gut Health: Comparing the in Vitro Fermentations of Beta-Glucan, Inulin and Xylooligosaccharide – Justin L Carlson – Nutrients

Review: Finding the needle in the haystack: systematic identification of psychobiotics. – Aisling Bambury – British Journal Of Pharmacology

Comment: Narrowing the spectrum: the new frontier of precision antimicrobials – Alexandra E Paharik – Genome Medicine

Bioinformatics
A Dirichlet-Multinomial Bayes Classifier for Disease Diagnosis with Microbial Compositions. – Xiang Gao – Msphere

Techniques
Amplicon sequencing of the 16S-ITS-23S rRNA operon with long-read technology for improved phylogenetic classification of uncultured prokaryotes – Joran Martijn – bioRxiv

Novel ITS1 Fungal Primers for Characterization of the Mycobiome. – Mykhaylo Usyk – Msphere

Microbes in the news
BIDMC Researchers Use Artificial Intelligence to Identify Bacteria Quickly and Accurately – Beth Israel Deaconess Medical Center

Magnetically Guided Bacteria Move Confidently Within Strong Currents, May Soon Deliver Drugs Inside Body – MedGadget

Is hand sanitizer bad for my microbiome? – Claire Maldarelli – Popular Science

Nanoparticles as a solution against antibiotic resistance? – Science Daily

Microbes on the market 
Light ‘Em Up: S&N’s Device Images Bacteria in Wounds – Nancy Crotti – MDDI

Contemplating Regulatory Frameworks for FMT – Cristi Rosa – Contagion Live

Vedanta Granted Four U.S. Patents for Therapeutics Based on Beneficial Gut Bacteria – Carolina Henriques – IBD News Today

Science, publishing, and career
What’s Responsible for the Retraction Boom? – Adam Marcus – Research Ethics in the Digital Age

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 27, 2017

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Short digest today – with multiple reviews and papers on animal microbiomes, as well as an interesting art project!

Pregnancy and early life
First-trimester vaginal microbiome diversity: A potential indicator of preterm delivery risk – Mohammed Monzoorul Haque – Scientific Reports

Human skin microbiome
Skin Colonization by Staphylococcus aureus Precedes the Clinical Diagnosis of Atopic Dermatitis in Infancy – Patrick Meylan – Journal of Investigative Dermatology

Human nearly-sterile sites
Review: Gut reactions: How the blood-brain barrier connects the microbiome and the brain – Aric F Logsdon – Experimental Biology and Medicine

Human gut microbiome
Analysis of Fusobacterium persistence and antibiotic response in colorectal cancer – Susan Bullman – Science

Animal experiments
Resident Microbiome Disruption with Antibiotics Enhances Virulence of a Colonizing Pathogen – Courtney A. Thomason – Scientific Reports
# Using house finches!

Structure moderation of gut microbiota in liraglutide-treated diabetic male rats – Qian Zhang – Experimental Biology and Medicine

Volatile Oil from Amomi Fructus Attenuates 5-Fluorouracil-Induced Intestinal Mucositis – Ting Zhang – Frontiers in Pharmacology

Animal microbiome
Comparison of the gut microbiota composition between wild and captive sika deer (Cervus nippon hortulorum) from feces by high-throughput sequencing – Yu Guan – AMB Express

Review: The Gastrointestinal Microbiome: A Review – P.C. Barko – Journal of Veterinary Internal Medicine

Plant, root, and soil microbiome
Metagenomic Approach to Identifying Foodborne Pathogens on Chinese cabbage – Daeho Kim – Journal of Microbiology and Biotechnology

Review: Trade, Diplomacy, and Warfare: The Quest for Elite Rhizobia Inoculant Strains – Alice Checcucci – Frontiers in Microbiology

Water and extremophile microbiome
What intrinsic and extrinsic factors explain the stoichiometric diversity of aquatic heterotrophic bacteria? – Casey M Godwin – ISMEJ

Antagonistic bacteria disrupt calcium homeostasis and immobilize algal cells – Prasad Aiyar – Nature Communications

Probiotics / prebiotics / antibiotics
Review: Existing and investigational therapies for the treatment of Clostridium difficile infection: A focus on narrow spectrum, microbiota-sparing agents – H.G. Maxwell-Scott – Médecine et Maladies Infectieuses

Techniques
Book chapter: Computational Approaches on Stoichiometric and Kinetic Modeling for Efficient Strain Design – Mohammad Mazharul Islam – Synthetic Metabolic Pathways

Microbes in the news
Mothers’ gut bacteria could impact future health of children: new findings – Brigid O’Connell – Herald Sun
# Part of the ENvironmental Determinants of Islet Autoimmunity (ENDIA) study

NASA fires E. coli bacteria into space to see if antibiotic resistance increases in zero gravity – Patricia Grannum – Inquisitr

Mouthwash Kills Mouth Bacteria But May Increase Risk For Diabetes – Allan Adamson – Tech Times

Artist’s feces work contributes to gut-busting research – The Japan Times

Alarm on milk with high levels of bacteria – Angela Oketch – Daily Nation
# In Kenya

Potato Bugs, Weeds, and Harmful Bacteria – Terry Mejdrich – Grand Rapids MN Herald Review

Bacteria Hysteria
Here’s Why You Should Never, Ever Share Earbuds with Anyone – Brittany Gibson – Reader’s Digest
# The article itself makes sense, but the title…

November 19, 2017

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A large number of papers overall, but especially in the plant/soil microbiome and animal experiments. For the former, one is from one of the MicrobiomeDigest contributors (in green) – congratulations!

General microbiome
Genome-driven evolutionary game theory helps understand the rise of metabolic interdependencies in microbial communities – Ali R. Zomorrodi – Nature Communications

Pregnancy and early life
Low dietary fiber intake increases Collinsella abundance in the gut microbiota of overweight and obese pregnant women – Luisa F. Gomez-Arango – Gut Microbes

Multi-site human microbiome
The Akkermansia-muciniphila is a gut microbiota signature in psoriasis – LiRong Tan – Experimental Dermatology

Human respiratory microbiome
Airway microbiota across age and disease spectrum in cystic fibrosis – Edith T. Zemanick – European Respiratory Journal

Human skin microbiome
Review: Skin barrier and microbiome in acne – M. A. Rocha – Archives of Dermatological Research

Fungi in the Wound Microbiome – Lindsay Kalan – Advances in Wound Care

Environmental influences on the skin microbiome of humans and cattle in rural Madagascar – Melissa B. Manus – Evolution, Medicine, and Public Health

Human gut microbiome
The Inuit gut microbiome is dynamic over time and shaped by traditional foods –
Geneviève Dubois – Microbiome

Identifying predictive features of Clostridium difficile infection recurrence before, during, and after primary antibiotic treatment – Sepideh Pakpour – Microbiome

Gastrointestinal and Hepatic Disease in Spondyloarthritis – Liron Caplan – Rheumatic Disease Clinics of North America

Review: Gutsy Moves: The Amygdala as a Critical Node in Microbiota to Brain Signaling – Caitlin S. M. Cowan – BioEssays

Review: The Role of the Gut Microbiome in Multiple Sclerosis Risk and Progression: Towards Characterization of the “MS Microbiome” – Anne-Katrin Pröbstel – Neurotherapeutics

Review: The gut–brain interaction in opioid tolerance – Hamid I Akbarali – Current Opinion in Pharmacology

Review: Lipotoxicity and the gut-liver axis in NASH pathogenesis – Fabio Marra – Journal of Hepatology

Review: Evidence of giant viruses of amoebae in the human gut – Philippe Colson -Human Microbiome Journal

Animal experiments
Evaluating the impact of domestication and captivity on the horse gut microbiome – Jessica L. Metcalf – Scientific Reports

Changes of gut microbiota structure and morphology in weaned piglets treated with fresh fermented soybean meal – Zhengjun Xie – World Journal of Microbiology and Biotechnology

Brown rice and retrograded brown rice alleviate inflammatory response in dextran sulfate sodium (DSS)-induced colitis mice – Kemika Praengam – Food and Function

Depletion of Stercobilin in Fecal Matter from a Mouse Model of Autism Spectrum Disorders – Emily R. Sekera – Metabolomics

Comparison of (R)-ketamine and lanicemine on depression-like phenotype and abnormal composition of gut microbiota in a social defeat stress model – Youge Qu – Scientific Reports

Beyond immunity: The Imd pathway as a coordinator of host defense, organismal physiology and behavior – Zongzhao Zhai – Developmental & Comparative Immunology
# This is a review on the Imd pathway in Drosophila, and its influence on their gut microbiome.

Dietary Fructo-Oligosaccharides Attenuate Early Activation of CD4+ T Cells Which Produce both Th1 and Th2 Cytokines in the Intestinal Lymphoid Tissues of a Murine Food Allergy Model – M. Tsuda – International Archives of Allergy and Immunology

Disorder of gut amino acids metabolism during CKD progression is related with gut microbiota dysbiosis and metagenome change – Yang Liu – Journal of Pharmaceutical and Biomedical Analysis

Animal microbiome
The sponge microbiome project – Lucas Moitinho-Silva – Gigascience

Novel Microbial Diversity and Functional Potential in the Marine Mammal Oral Microbiome – Natasha K. Dudek – Current Biology

Review: Gut Brain Axis and Its Microbiota Regulation in Mammals and Birds – Jan S. Suchodolski- Veterinary Clinics of North America: Exotic Animal Practice

Analysis of Bacterial and Fungal Nucleic Acid in Canine Sterile Granulomatous and Pyogranulomatous Dermatitis and Panniculitis – Fabio B. Rosa – Veterinary Pathology

Developmental and gut-related changes to microbiomes of the cultured juvenile spiny lobster Panulirus ornatus – MC Ooi – FEMS Microbial Ecology
# Pubmed linked since DOI not yet active

Illumina Based Analysis of Bacterial and Fungal Flora in Foreguts and Hindguts of Crucian Carp (Carassius Aumtus) in Retail Markets – Mingyue Wang – Open Journal of Bacteriology

16S rRNA gene amplicon sequencing reveals dominance of Actinobacteria in Rhodnius pallescens compared to Triatoma maculata midgut microbiota in natural populations of vector insects from Colombia – Luisa M. Montoya-Porras – Acta Tropica

Plant, root, and soil microbiome
Exploration, antifungal and antiaflatoxigenic activity of halophilic bacteria communities from saline soils of Howze-Soltan playa in Iran – Samaneh Jafari – Extremophiles

No single driver of biodiversity: divergent responses of multiple taxa across land use types – Jamie R. Wood – Ecosphere

Community evolution increases plant productivity at low diversity – Sofia J. van Moorse – Ecology Letters

Co-Variation of Bacterial and Fungal Communities in Different Sorghum Cultivars and Growth Stages is Soil Dependent – Thiago R. Schlemper – Microbial Ecology

Microbial communities in the native habitats of Agaricus sinodeliciosus from Xinjiang Province revealed by amplicon sequencing – Jiemin Zhou – Scientific Reports

Previous crop and rotation history effects on maize seedling health and associated rhizosphere microbiome – Maria-Soledad Benitez – Scientific Reports

Soil bacterial community response to altered precipitation and temperature regimes in an old field grassland are mediated by plants – A Koyama – FEMS Microbial Ecology
# Pubmed linked since DOI not yet active

The abundance of health-associated bacteria is altered in PAH polluted soils-Implications for health in urban areas? – Anirudra Parajuli – PLoS One

Effect of halotolerant methylotrophs isolated from saline soil rhizosphere on diminution of salt stress in wheat (Triticum aestivum l.) – Dmitry Y. Sharavin – Journal of Agriculture and Environment

Build your own soil: exploring microfluidics to create microbial habitat structures – Kristin Aleklett – ISMEJ

Influence of high-carbon basal fertiliser on the structure and composition of a soil microbial community under tobacco cultivation – Song-tao Zhang – Research in Microbiology

Impacts of environmental factors on the whole microbial communities in the rhizosphere of a metal-tolerant plant: Elsholtzia haichowensis Sun – Songqiang Deng – Environmental Pollution

Contrasting the microbiomes from forest rhizosphere and deeper bulk soil from an Amazon rainforest reserve – Jose Pedro Fonseca – Gene

Microplot long-term experiment reveals strong soil type influence on bacteria composition and its functional diversity – Jarosław Grządziel – Applied Soil Ecology

Bulk soil bacterial community mediated by plant community in Mediterranean ecosystem, Israel – I. Moroenyane – Applied Soil Ecology
# From fellow MicrobiomeDigest contributor!

Thesis: Characterisation of Metagenomic Bougainvillea Soil DNA Through rDNA PCR Amplification – Aruna Ganesan – INTI International University

Book: Endophytes: Crop Productivity and Protection
Book chapter: Endophytes as Contender of Plant Productivity and Protection: An Introduction – Dinesh K. Maheshwari
Book chapter: Beneficial Effects of Bacterial Endophytes on Forest Tree Species – Akshit Puri

Water and extremophile microbiome
Pole-to-Pole Connections: Similarities between Arctic and Antarctic Microbiomes and Their Vulnerability to Environmental Change – Julia Kleinteich – Frontiers in Ecology and Evolution

Microbial pathway for anaerobic 5′-methylthioadenosine metabolism coupled to ethylene formation – Justin A. North – PNAS

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

Mapping the ‘hospital microbiome’ and the spread of antimicrobial resistance and biofilm on the intensive care units from different regions – Khalid Johani – Infection, Disease, and Health

A study of microbial communities on terracotta separator and on biocathode of air breathing microbial fuel cells – Laura Rago – Bioelectrochemistry

Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes – Irena Maus – Biotechnology of Biofuels

Geochemical Influence on Microbial Communities at CO2-Leakage Analog Sites – Baknoon Ham – Frontiers in Microbiology (Extreme Microbiology)

Food microbiology
Evaluation of microbial consortia and chemical changes in spontaneous maize bran fermentation – Marilù Decimo – AMB Express

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

Probiotics / prebiotics / antibiotics
Treatment efficacy of a probiotic preparation for non-alcoholic steatohepatitis: a pilot trial – Elina Manzhalii – Journal of Digestive Diseases

Review: A Meta-Analysis of the Use of Probiotics to Alleviate Depressive Symptoms – Qin Xiang Ng – Journal of Affective Disorders

Review: Identification of probiotic effector molecules: present state and future perspectives – Sarah Lebeer – Current Opinion in Biotechnology

Review: Association between prior antibiotic therapy and subsequent risk of community-acquired infections: a systematic review – Umer Malik – Journal of Antimicrobial Therapy

Phages and viruses
The gut virome of the protochordate model organism, Ciona intestinalis subtype A – Brittany A. Leigh – Virus Research

Bioinformatics and statistical methods
Statistical analysis of co-occurrence patterns in microbial presence-absence datasets – Kumar P. Mainali – PLoS One

A Sequence-Based Mesh Classifier for the Prediction of Protein-Protein Interactions – Edgar D. Coelho – arXiv

Techniques
Analysis of single-cell genome sequences of bacteria and archaea – Robert M. Bowers – Emerging Topics in Life Sciences

A Synthetic Community System for Probing Microbial Interactions Driven by Exometabolites – John L. Chodkowski – mSystems

The inputs of metagenomics in the diagnostic of infectious diseases – G. Durand – Journal des Anti-infectieux

Genome announcements
Complete Genome Sequence of a Novel Nonnodulating Rhizobium Species Isolated from Agave americana L. Rhizosphere – Víctor Manuel Ruíz-Valdiviezo – genome Announcements

Complete Genome Sequence of Bacillus cereus C1L, a Plant Growth-Promoting Rhizobacterium from the Rhizosphere of Formosa Lily in Taiwan – Chien-Jui Huang – genome Announcements

Nocardia rhizosphaerihabitans sp. nov., a novel actinomycete isolated from a coastal soil – Peng Ding – International Journal of Systematic and Evolutionary Microbiology

The genome and microbiome of a dikaryotic fungus (Inocybe terrigena, Inocybaceae) revealed by metagenomics – Mohammad Bahram – PeerJ

*****************************
Microbes in the news
Gut bacteria at young age can contribute to MS disease onset and progression, study suggests – News Medical

Microbes on the market
Patent: Methods for distinguishing inflammatory bowel diseases using microbial community signatures – Wolfgang F. Fricke and James Robert White

Global Microbiome Sequencing Services Market Forecast to 2022 with Key Companies Profile, Supply, Demand, Cost Structure – Maciej Heyman – MilTech

Know about Microbiology Testing Market Posting +11% CAGR By 2022- Newly Invented Strategies, Healthcare Trends, Growth Opportunities, Forecast, & Key Players like Biomerieux S.A., Danaher, Becton, Dickinson and Company, Cepheid, Abbott, Alere, Bio-Rad Laboratories, Hologic, Bruker, F.Hoffmann-La Roche Ltd – MedGadget

November 18, 2017

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Featuring a bioinformatics paper from my former lab mate, as well as multiple, interesting pre-prints! See also a paper on rats in NYC and a study on peer review.

Events and jobs
Microbiology Technician I – Abbott – Plymouth, Minnesota, United States

Biology, Assistant Professor, Microbiology – College of Saint Benedict/Saint John’s University in Minnesota (3 year term, not tenure track)

PhD Studentship: Microbiome mediated resiliency of freshwater habitat – University of Birmingham

OMRF seeks participants as it launches new sarcoidosis clinic

General microbiome
Ecological Insights from the Evolutionary History of Microbial Innovations –
Mario E Muscarella – bioRxiv

Pregnancy and early life
Mode of delivery and child and adolescent psychological well-being: Evidence from Hong Kong’s “Children of 1997” birth cohort – Cherry Y. Leung – Scientific Reports

Multi-site human microbiome
Body size phenotypes comprehensively assess cardiometabolic risk and refine the association between obesity and gut microbiota – J de la Cuesta-Zuluaga – International Journal of Obesity

Human gut microbiome
Structural and functional differences in gut microbiome composition in patients undergoing haemodialysis or peritoneal dialysis – Vanessa Stadlbauer – Scientific Report

A role for bacterial urease in gut dysbiosis and Crohn’s disease – Josephine Ni – Science Translational Medicine

Animal experiments
Alteration of the intestinal microbiome characterizes preclinical inflammatory arthritis in mice and its modulation attenuates established arthritis – Rebecca Rogier – Scientific Reports

Dietary protein sources differentially affect microbiota, mTOR activity and transcription of mTOR signaling pathways in the small intestine – Soumya K. Kar – PLoS One

Blockade of CB1 cannabinoid receptor alters gut microbiota and attenuates inflammation and diet-induced obesity – Pegah Mehrpouya-Bahrami – Scientific Reports

Wild Microbiome Stems Tumorigenesis in Lab Mice – Cancer Discovery

Dietary chlorogenic acid regulates gut microbiota, serum-free amino acids and colonic serotonin levels in growing pigs – Yi Wu – International Journal of Food Sciences and Nutrition

Plant, root, and soil microbiomeSoil-mediated effects of global change on plant communities depend on plant growth form – Jes Hines – Ecosphere

Built environment
Spatial variation in the parasite communities and genomic structure of urban rats in New York City – L. P. Angley – Zoonoses and Public Health

Food microbiology
Digestion under saliva, simulated gastric and small intestinal conditions and fermentation in vitro of polysaccharides from the flowers of Camellia sinensis induced by human gut microbiota – Dan Chen – Food and Function

Review: Dietary and Endogenous Sphingolipid Metabolism in Chronic Inflammation – Gregory H. Norris – Nutrients

Review: Cardiovascular and Antiobesity Effects of Resveratrol Mediated through the Gut Microbiota – JK Bird – Advances in Nutrition

Review: Yogurt and Cardiometabolic Diseases: A Critical Review of Potential Mechanisms – MA Fernandez – Advances in Nutrition

Phages and viruses
Molecularly barcoded Zika virus libraries to probe in vivo evolutionary dynamics – Matthew T. Aliota – bioRxiv

Bioinformatics
A Bayesian method for detecting pairwise associations in compositional data – Emma Schwager – PLoS Computational Biology
Shout-out to my old lab mate, Emma!

MetQy: an R package to query metabolic functions of genes and genomes – Andrea Martinez-Vernon – bioRxiv

Genome announcements
Streptomyces tritici sp. nov., a novel actinomycete isolated from rhizosphere soil of wheat (Triticum aestivum L.) – Junwei Zhao – International Journal of Systematic and Evolutionary Biology

Rhodococcus psychrotolerans sp. nov., isolated from rhizosphere of Deschampsia antarctica – Leonardo Jose Silva – Antonie van Leeuwenhoek

Thalassotalea coralli sp. nov., isolated from the torch coral Euphyllia glabrescens – Der-Shyan Sheu – International Journal of Systematic and Evolutionary Biology

Microbes in the news
Lab-Grown Synthetic Nanobots May Officially End Antibiotic Resistance – Patrick Caughill – Futurism

Biolive yoghurt can help to lower blood pressure – Colin Fernandez – IOL

Dolphins: The final frontier for new types of bacteria? – Nicoletta Lanese – Scope

10 Things You Should Never Say to Someone With a Chronic Illness—Seriously – Karen Duffy – Health

Bacterium in a beetle makes it a leaf-eater – Science Daily
Paper: Drastic Genome Reduction in an Herbivore’s Pectinolytic Symbiont – Hassan Salem – Cell

How the Immune System Identifies Invading Bacteria – HHMI
Paper: The structural basis of flagellin detection by NAIP5: A strategy to limit pathogen immune evasion – Jeannette L. Tenthorey – Science

Dog owners have lower mortality, study finds – Katie Silver – BBC
No actual mention of microbiome in paper, which is: Dog ownership and the risk of cardiovascular disease and death – a nationwide cohort study – Mwenya Mubanga – Scientific Report

Microbes on the market
Evelo taps Mayo Clinic expertise for therapeutic bacteria programs – Phil Taylor – FierceBiotech

Human Microbiome Market Global Therapeutics, Drugs Review To 2025 – MedGadget

Researchers receive $500,000 grant to study the “microbiome of death” – Matt Wood – ScienceLife

Science, publishing, and career
Reviewer bias in single- versus double-blind peer review – Andrew Tomkins – PNAS

November 10, 2017

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Events and jobs
Postdoctoral Fellow – Institute of Genome Sciences (IGS) with Hotopp Lab – Baltimore, Maryland

Pregnancy and early life
Influence of vitamin D on key bacterial taxa in infant microbiota in the KOALA Birth Cohort Study – Chris E. Talsness – PLoS One

Review: Role of the Human Breast Milk-Associated Microbiota on the Newborns’ Immune System: A Mini Review – Marco Toscano – Frontiers in Microbiology

Review: The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota – Christian Milani – Microbiology and Molecular Biology Reviews

Multi-site human microbiome
Segmented Filamentous Bacteria Provoke Lung Autoimmunity by Inducing Gut-Lung Axis Th17 Cells Expressing Dual TCRs – C. Pierce Bradley – Cell Host and Microbe

Human vaginal microbiome
Genitourinary Syndrome of the Menopause: Vaginal Health and Microbiota – Maria Jesús Cancelo-Hidalgo – Menopause

Human gut microbiome
Review: Microbial biotransformations in the human distal gut – Elisabeth M Bik – British Journal of Pharmacology

Review: The Human Microbiome and Obesity: Moving beyond Associations – Padma Maruvada – Cell Host and Microbe

A Microbiomic Analysis in African Americans with Colonic Lesions Reveals Streptococcus sp.VT162 as a Marker of Neoplastic Transformation – Hassan Brim – Genes

Multiple articles from Frontiers in Immunology:
LC3-Associated Phagocytosis Is Required for Dendritic Cell Inflammatory Cytokine Response to Gut Commensal Yeast Saccharomyces cerevisiae – Dimitra Lamprinaki – Frontiers in Immunology

Immunological and Clinical Effect of Diet Modulation of the Gut Microbiome in Multiple Sclerosis Patients: A Pilot Study – Marina Saresella – Frontiers in Immunology

Review: TH17 Cell and Epithelial Cell Crosstalk during Inflammatory Bowel Disease and Carcinogenesis – Jan Kempski – Frontiers in Immunology

Animal experiments
Difference in the gut microbiome between ovariectomy-induced obesity and diet-induced obesity – S. Choi – Journal of Microbiology and Biotechnology
No link available yet, linked to PubMed.

The effects of starter microbiota and the early life feeding of medium chain triglycerides on the gastric transcriptome profile of 2- or 3-week-old cesarean delivered piglets – Paolo Trevisi – Journal of Animal Science and Biotechnology

Animal microbiome
Prodigiosin, Violacein, and Volatile Organic Compounds Produced by Widespread Cutaneous Bacteria of Amphibians Can Inhibit Two Batrachochytrium Fungal Pathogens – Douglas C. Woodhams – Microbial Ecology

Accessing the Hidden Microbial Diversity of Aphids: an Illustration of How Culture-Dependent Methods Can Be Used to Decipher the Insect Microbiota – Alina S. Grigorescu – Microbial Ecology

Diversity and characterization of bacteria associated with the deep-sea hydrothermal vent crab Austinograea sp. comparing with those of two shallow-water crabs by 16S ribosomal DNA analysis – Na Zhang – PLoS One

Diets Alter the Gut Microbiome of Crocodile Lizards – Hai-Ying Jiang – Frontiers in Microbiology

Plant, root, and soil microbiome
Opinion: Nitrogen limitation of decomposition and decay: how can it occur? – Colin Averill – Global Change Biology

Compatible bacterial mixture, tolerant to desiccation, improves maize plant growth – Dalia Molina-Romero – PLoS One

Effects of root pruning on the physicochemical properties and microbial activities of poplar rhizosphere soil – Da-Wei Jing – PLoS One

Biochar amendment changes temperature sensitivity of soil respiration and composition of microbial communities 3 years after incorporation in an organic carbon-poor dry cropland soil – Junhui Chen – Biology and Fertility of Soils

Book of interest: Endophytes: Biology and Biotechnology – Dinesh K. Maheshwari

Biosynthetic potential of actinomycetes in brown forest soil on the eastern coast of the aegean sea – I. G. Shirokikh – Eurasian Soil Science

Water and extremophile microbiome
Editorial: Deep Carbon in Earth: Early Career Scientist Contributions to the Deep Carbon Observatory – Donato Giovannelli – Frontiers in Earth Science

Spatial variability of marine bacterial and archaeal communities along the particulate matter continuum – Mireia Mestre – Molecular Ecology

Cyanobacteria and Alphaproteobacteria May Facilitate Cooperative Interactions in Niche Communities – Marc W. Van Goethem – Frontiers in Microbiology

Influences of anthropogenic land use on microbial community structure and functional potentials of stream benthic biofilms – Xiaodong Qu – Scientific Reports

Linking Compositional and Functional Predictions to Decipher the Biogeochemical Significance in DFAA Turnover of Abundant Bacterioplankton Lineages in the North Sea – Bernd Wemheuer – Microorganisms

Biohydrogen production at pH below 3.0: Is it possible? – V.T. Mota – Water Research

Groundwater Microbial Communities Along a Generalized Flowpath in Nomhon Area, Qaidam Basin, China – Y Sheng – Ground Water
No link available yet, linked to PubMed.

Targeted metatranscriptomics of compost-derived consortia reveals a GH11 exerting an unusual exo-1,4-β-xylanase activity – Bruno L. Mello – Biotechnology for Biofuels

Environmental factors shaping the archaeal community structure and ether lipid distribution in a subtropic river and estuary, China – Wenting Guo – Applied Microbiology and Biotechnology

Built environment
The Nosocomial Risk of Bacterial Contamination of Surgical Wards at Saint Francis Hospital in Katete District of Zambia – Frank Mtonga – ARC Journal of Clinical Case Reports

Food microbiology
Preventive effects of a probiotic mixture in an ovalbumin-induced food allergy model – HS Shin -Journal of Microbiology and Biotechnology
No link available yet, linked to PubMed.

Digestion under saliva, simulated gastric and small intestinal conditions and fermentation in vitro by human intestinal microbiota of polysaccharides from Fuzhuan brick tea – Guijie Chen – Food Chemistry

Phages and viruses
Several book chapters from Bacteriophage Therapy:
Book Section: Methods for Bacteriophage Preservation – Małgorzata B. Łobocka
Interaction of Bacteriophages with Mammalian Cells – Zuzanna Kaźmierczak

Perspective: The Intra-Dependence of Viruses and the Holobiont – Juris A. Grasis – Frontiers in Immunology

Bioinformatics
Metagenome sequence clustering with hash-based canopies – Mohammad Arifur Rahman – Journal of Bioinformatics and Computational Biology

Book: UNIT 1E.14 Computational Methods for Human Microbiome Analysis – Matthieu J. Miossec – Current Protocols in Microbiology

Microbes in the news
Enhanced understanding of the microbiome is helping medicine – The Economist

Microbes on the market
Seres Therapeutics to Participate in Three Upcoming November Conferences – Business Wire

Global Microbiome Sequencing Services Market Outlook 2017 Growth, Trends, Forecasts 2022 – Samuel – Talk Daily News

Space travel changes gut bacteria in mice – Science Nordic

New model reveals possibility of pumping antibiotics into bacteria – Phys Org
Paper: New free-exchange model of EmrE transport – Anne E. Robinson – PNAS

EPA approves bacteria-infected insects to kill mosquitoes – Bonnie Burton – CNET

Bacteria Hysteria
Deadly bacterial infections could be coming from your kitchen sink PLUGHOLE – Matt Atherton – Express

Science, publishing, and career
The GOP tax bill could be a disaster for PhD students – Jen Kirby – Vox

October 29, 2017

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Multiple reviews and a great deal on plant, soil, and root microbiomes.

General microbiome
Quantifying the strength of quorum sensing crosstalk within microbial communities – Kalinga Pavan T. Silva – PLoS Computational Biology

An Important Role for Purifying Selection in Archaeal Genome Evolution – Zhe Lyu – MSystems

Review: Functional Genomics of Host–Microbiome Interactions in Humans – Francesca Luca – Trends in Genetics

Review: Pharmacological efficacy/toxicity of drugs: A Comprehensive update about the dynamic interplay of microbes – J.A. Gimenez-Bastida – Journal of Pharmaceutical Sciences

Pregnancy and early life
Editorial: Another reason to favor exclusive breastfeeding: microbiome resilience – Alessio Fasano – Jornal de Pediatria
Paper referred: Breastfeeding increases microbial community resilience – Isabel I.Carvalho-Ramos – Jornal de Pediatria

Review: Glycan Utilization and Cross-Feeding Activities by Bifidobacteria – Francesca Turroni – Trends in Microbiology

Human respiratory microbiome
Review: Lung epithelium: barrier immunity to inhaled fungi and driver of fungal-associated allergic asthma – Darin L Wiesner – Current Opinion in Microbiology

Human oral microbiome
Review: Oral Tolerance Development and Maintenance – Erik Wambre – Immunology and Allergy Clinics of North America

Human skin microbiome
Review: Evidence-based update on rosacea comorbidities and their common physiologic pathways – Anna D. Holmes – Journal of the American Academy of Dermatology

Human gut microbiome
Gut microbiome composition in lean patients with NASH is associated with liver damage independent from caloric intake: a prospective pilot study – Sebastião Mauro Bezerra Duarte – Nutrition, Metabolism and Cardiovascular Diseases

Review: Gut microbiota and obesity: Concepts relevant to clinical care – Maria Carlota Dao – European Journal of Internal Medicine

Animal experiments
Effect of yeast supplementation on digestibility, fecal microbiota and serum endotoxin levels in non-exercising and exercising horses – A.A.O. Gobesso – Livestock Science

Ethanol extract of Atractylodis macrocephalae Rhizoma ameliorates insulin resistance and gut microbiota in type 2 diabetic db/db mice – Wen-You Zhang – Journal of Functional Foods

Supplementation of pancreatic digestive enzymes alters the composition of intestinal microbiota in mice – Hiroki Nishiyama – Biochemical and Biophysical Research Communications

Plant, root, and soil microbiome
Potential for plant biocontrol activity of isolated Pseudomonas aeruginosa and Bacillus stratosphericus strains against bacterial pathogens acting through both induced plant resistance and direct antagonism – Kaliannan Durairaj – FEMS Microbiology Letters

Biofilm formation is determinant in tomato rhizosphere colonization by Bacillus velezensis FZB42 – Ameen Al-Ali – Environmental Science and Pollution Research

Immobilization of Lead Migrating from Contaminated Soil in Rhizosphere Soil of Barley (Hordeum vulgare L.) and Hairy Vetch (Vicia villosa) Using Hydroxyapatite – Masahiko Katoh – International Journal of Environmental Research and Public Health

Enhancement of 14C-phenanthrene mineralisation in the presence of plant-root biomass in PAH-NAPL amended soil – Gabriela M.Vázquez-Cuevas – International Biodeterioration & Biodegradation

Impact of fomesafen on the soil microbial communities in soybean fields in Northeastern China – XH Wu – Ecotoxicology and Environmental Safety
DOI not available yet.

Continuum of root–fungal symbioses for plant nutrition – Marcel G. A. van der Heijden – PNAS

Rolling a mycobiome down a hill: endophytes in the Taiwanese Cloud Forest – Daniel Thomas – bioRxiv

Water and extremophile microbiome
Antimicrobial properties and the influence of temperature on secondary metabolite production in cold environment soil fungi – Yogabaanu Ulaganathan – Polar Science

Microbial diversity from chlorophyll maximum, oxygen minimum and bottom zones in the southwestern Atlantic Ocean – Renata Medina-Silva – Journal of Marine Systems

Microbial communities in biological denitrification system using methanol as carbon source for treatment of reverse osmosis concentrate from coking wastewater – Enchao Li – Journal of Water Reuse and Desalination

Review: Periodic survey by metagenomic analysis on the marine microbial communities in an enclosed bay locating at Sanriku coast off northern Japan in the Pacific Ocean – Shugo Watabe – The JSFS 85th Anniversary-Commemorative International Symposium

Review: Synthesizing redox biogeochemistry at aquatic interfaces – Maximilian Peter Lau – Limnologica – Ecology and Management of Inland Waters

Review: The role of operating parameters and oxidative damage mechanisms of Advanced Chemical Oxidation Processes in the combat against antibiotic-resistant bacteria and resistance genes present in urban wastewater – I. Michael-Kordatou – Water Research

Built environment
The influence of the internal microbiome on the materials used for construction of the transmission natural gas pipelines in the Lodz Province – Agnieszka Staniszewska – E3S Web of Conferences

Application and microbial ecology of psychrotrophs in domestic wastewater treatment at low temperature – Zhenzhen Xu – Chemosphere

Food microbiology
Review: Virgin olive oil yeasts: A review – Ciafardini Gino – Food Microbiology

Effect of vacuum and modified atmosphere packaging on the microbiological, chemical and sensory properties of tropical red drum (Sciaenops ocellatus) fillets stored at 4 °C – Adèle Silbande – International Journal of Food Microbiology

The microbiota of eight species of dehydrated edible seaweeds from North West Spain – Ana del Olmo – Food Microbiology

Microbiological, chemical and sensory spoilage analysis of raw Atlantic cod (Gadus morhua) stored under modified atmospheres – L. Kuuliala – Food Microbiology

Probiotics / prebiotics / antibiotics
Improvement of lactic acid bacteria viability in acid conditions employing agroindustrial co-products as prebiotic on alginate ionotropic gel matrix co-encapsulation – Victor Serrano-Casas – Journal of Functional Foods

Hospital antimicrobial stewardship: the way forward – Céline Pulcinia – The Lancet

Phages and viruses
How do bacteriophages promote antibiotic resistance in the environment? – José Luis Balcázar – Clinical Microbiology and Infection

Predicting virus emergence amid evolutionary noise – Jemma L. Geoghegan – Open Biology

Bioinformatics
A comparison of bioinformatic approaches for 16S rRNA gene profiling of food bacterial microbiota – Francesca De Filippis – International Journal of Food Microbiology

Techniques
A semi-quantitative method for point-of-care assessments of specific pathogenic bioaerosols using a portable microfluidics-based device – Qi Liu – Journal of Aerosol Science

Machine-assisted cultivation and analysis of biofilms – Silla H. Hansen – bioRxiv

Review: Next-generation sequencing applications in clinical bacteriology – Yair Motro – Biomolecular Detection and Quantification

Genome Announcements
Nitrincola alkalilacustris sp. nov. and Nitrincola schmidtii sp. nov., alkaliphilic bacteria isolated from soda pans, and emended description of the genus Nitrincola – Andrea K. Borsodi – International Journal of Systematic and Evolutionary Microbiology

Paenibacillus solanacearum sp. nov., isolated from rhizosphere soil of a tomato plant – Hayoung Cho – International Journal of Systematic and Evolutionary Microbiology

Paenibacillus nebraskensis sp. nov., isolated from the root surface of field-grown maize – Peter Kämpfer – International Journal of Systematic and Evolutionary Microbiology

Nioella aestuarii sp. nov., of the family Rhodobacteraceae, isolated from tidal flat – In-Tae Cha – International Journal of Systematic and Evolutionary Microbiology

Microbes in the news
Puerto Rico reports 76 cases of deadly bacteria caused by tainted water – CNN Wire – KFOR

Microbes on the market
Global Human Microbiome Market Size and Forecast to 2021 – medGadget

Ritter Pharmaceuticals, Inc. (RTTR) Upgraded to Buy by Zacks Investment Research – Sebastian Weber – The Ledge Gazette

October 28, 2017

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A huge Saturday digest (150+ alerts), with many articles in the gut and animal microbiome.

Events and jobs
Postdoctoral researcher in Human Microbiome-Immune System Interactions – University of Luxembourg

Microbiome in Sexual, Maternal and Child Health Symposium – November 29, 2017

Pregnancy and early life
Gut microbiome in gestational diabetes: A Cross-sectional study of mothers and offspring 5 years post-partum – Sayyid Hasan – Acta Obstetricia et Gynecologica Scandivanica

The Influence of Proton Pump Inhibitors on the Fecal Microbiome of Infants with Gastroesophageal Reflux-A Prospective Longitudinal Interventional Study –
Christoph Castellani – Frontiers in Cellular and Infection Microbiology

Gut microbiome of mothers delivering prematurely shows reduced diversity and lower relative abundance of Bifidobacterium and Streptococcus – Cecilie Dahl – PLoS One

2 articles on iron supplements in the American Journal of Nutrition:
Review: Effects of iron fortification and supplementation on the gut microbiome and diarrhea in infants and children: a review – Daniela Paganini – American Journal of Clinical Nutrition

Review: Excess iron intake as a factor in growth, infections, and development of infants and young children – Bo Lönnerdal – American Journal of Clinical Nutrition

Human skin microbiome
RNase 7 participates in cutaneous innate control of Corynebacterium amycolatum – Stephanie Walter – Scientific Reports

FKBP12-Dependent Inhibition of Calcineurin Mediates Immunosuppressive Antifungal Drug Action in Malassezia – Giuseppe Ianiri – mBio

Human oral microbiome
Changes in periodontal and microbial parameters after the space maintainers application – M Aydinbelge – Nigerian Journal of Clinical Practice

Microbiome associated with dentures malodour – Shai Yitzhaki – Journal of Breath Research

Human gut microbiome
Gut microbiomes of mobile predators vary with landscape context and species identity – Julia Tiede – Ecology and Evolution

Distinct Microbial Communities Trigger Colitis Development upon Intestinal Barrier Damage via Innate or Adaptive Immune Cells – Urmi Roy – Cell Reports

Bile salt hydrolase-mediated inhibitory effect of Bacteroides ovatus on growth of Clostridium difficile – Soobin Yoon – Journal of Microbiology

Small-molecule inhibitors directly target CARD9 and mimic its protective variant in inflammatory bowel disease – Elizaveta S. Leshchiner – PNAS

Guiding longitudinal sampling in IBD cohorts – Yoshiki Vázquez-Baeza – Gut
Paper referenced: A microbial signature for Crohn’s disease – Victoria Pascal – Gut

Distinctive Gut Microbiota Is Associated with Diarrheagenic Escherichia coli Infections in Chilean Children – Pablo Gallardo – Frontiers in Cellular and Infection Microbiology

Gut Microbiota Perturbations in Reactive Arthritis and Post-Infectious Spondyloarthritis – Julia Manasson – Arthritis and Rheumatology

Severe intestinal dysbiosis is prevalent in primary Sjögren’s syndrome and is associated with systemic disease activity – Thomas Mandl – Arthritis Research and Therapy

Review: Salmonella enterica Serovar Typhimurium Strategies for Host Adaptation – Christopher J. Anderson – Frontiers in Microbiology

Review: Visceral Congestion in Heart Failure: Right Ventricular Dysfunction, Splanchnic Hemodynamics, and the Intestinal Microenvironment – Vincenzo B. Polsinelli – Current Heart Failure Reports

Review: Gut Microbiota Contribute to Age-Related Changes in Skeletal Muscle Size, Composition, and Function: Biological Basis for a Gut-Muscle Axis – Gregory J. Grosicki – Calcified Tissue International

Animal experiments
Multi-omics Comparative Analysis Reveals Multiple Layers of Host Signaling Pathway Regulation by the Gut Microbiota – Nathan P. Manes – MSystems

The yeast form of the fungus Candida albicans promotes persistence in the gut of gnotobiotic mice – Lena Böhm – PLoS Pathogens

Clinical Effect of IRT-5 Probiotics on Immune Modulation of Autoimmunity or Alloimmunity in the Eye – Jaeyoung Kim – Nutrients

Periodontal pathogenic bacteria, Aggregatibacter actinomycetemcomitans affect non-alcoholic fatty liver disease by altering gut microbiota and glucose metabolism – Rina Komazaki – Scientific Reports

β-Glucans in food modify colonic microflora by inducing antimicrobial protein, calprotectin, in a Dectin-1-induced-IL-17F-dependent manner – T Kamiya – Mucosal Immunology

Microbiome-driven allergic lung inflammation is ameliorated by short-chain fatty acids – A Cait – Mucosal Immunology

Effects of direct-fed microorganisms and enzyme blend co-administration on intestinal bacteria in broilers fed diets with or without antibiotics – T E Askelson – Poultry Science

16S rDNA analysis of the effect of fecal microbiota transplantation on pulmonary and intestinal flora – Tianhao Liu – 3 Biotech

Adaptation to Chronic Nutritional Stress Leads to Reduced Dependence on Microbiota in Drosophila melanogaster – Berra Erkosar – mBio

Characterization of fecal fat composition and gut derived fecal microbiota in high-fat diet fed rats following intervention with chito-oligosaccharide and resistant starch complexes – Wenting Shang – Food and Function

Genetic ablation of Cyp8b1 preserves host metabolic function by repressing steatohepatitis and altering gut microbiota composition – Jay V Patankar – American Journal of Physiology – Endocrinology and Metabolism

Effects of a probiotic (SLAB51™) on clinical and histologic variables and microbiota of cats with chronic constipation/megacolon: a pilot study – G. Rossi – Beneficial Microbes

Bacteriocin biosynthesis contributes to the anti-inflammatory capacities of probiotic Lactobacillus plantarum – X. Yin – Beneficial Microbes

Animal microbiome
Large-scale cultivation of the bumblebee gut microbiota reveals an underestimated bacterial species diversity capable of pathogen inhibition – Jessy Praet – Environmental Microbiology

Bacterial community of a spider, Marpiss magister (Salticidae) – Lihua Zhang – 3 Biotech

Fecal bacterial communities of wild-captured and stranded green turtles (Chelonia mydas) on the Great Barrier Reef – S Shamim – FEMS Microbiology Ecology

RECRUITMENT AND ESTABLISHMENT OF THE GUT MICROBIOME IN ARCTIC SHOREBIRDS – Kirsten Frond – FEMS Microbiology Ecology

The gorgonian coral Eunicella labiata hosts a distinct prokaryotic consortium amenable to cultivation – Tina Keller-Costa – FEMS Microbiology Ecology

Inheritance and Establishment of Gut Microbiota in Chickens – Jinmei Ding – Frontiers in Microbiology

Diversity and Transmission of Gut Bacteria in Atta and Acromyrmex Leaf-Cutting Ants during Development – Mariya Zhukova – Frontiers in Microbiology

Seawater transfer alters the intestinal microbiota profiles of Atlantic salmon (Salmo salar L.) – Carola E. Dehler – Scientific Reports

Plant, root, and soil microbiome
Characterizing endophytic competence and plant growth promotion of bacterial endophytes inhabiting the seed endosphere of Rice – Denver I. Walitang – BMC Microbiology

Pseudomonas syringae pv. syringae B728a Regulates Multiple Stages of Plant Colonization via the Bacteriophytochrome BphP1 – Regina McGrane – mBio

The Sphagnome Project: enabling ecological and evolutionary insights through a genus-level sequencing project – David J. Weston – New Phytologist

Bacterial Synergism in Lignocellulose Biomass Degradation – Complementary Roles of Degraders As Influenced by Complexity of the Carbon Source – Larisa Cortes-Tolalpa – Frontiers in Microbiology

Modulation of the efficiency of trace metal phytoremediation by Sedum plumbizincicola by microbial community structure and function – Jinyu Hou – Plant and Soil

Water and extremophile microbiome
Microbial community differentiation between active and inactive sulfide chimneys of the Kolumbo submarine volcano, Hellenic Volcanic Arc – Christos A. Christakis – Extremophiles

Variability in carbon uptake and (re)cycling in Antarctic cryptoendolithic microbial ecosystems demonstrated through radiocarbon analysis of organic biomarkers – A. L. Brady – GE Biology

High reactivity of deep biota under anthropogenic CO2 injection into basalt – Rosalia Trias – Nature Communications

Editorial: Marine microbiome as source of natural products – Fernando de la Calle – Microbial Biotechnology

Elucidating the impact of microbial community biodiversity on pharmaceutical biotransformation during wastewater treatment – Lauren B. Stadler – Microbial Biotechnology

Magnetite production and transformation in the methanogenic consortia from coastal riverine sediments – Shiling Zheng – Journal of Microbiology

Opportunistic Pathogens and Microbial Communities and Their Associations with Sediment Physical Parameters in Drinking Water Storage Tank Sediments – Ke Qin – Pathogens

Review: Methods of ammonia removal in anaerobic digestion: a review – Niclas Krakat – Water Science and Technology

Response of marine bacteria to oil contamination and to high pressure and low temperature deep sea conditions – Hanna Fasca – Microbiology Open

Built environment
The York Gospels: a 1000-year biological palimpsest – Matthew D. Teasdale – Royal Society Open Science (sequencing of parchment)

Conductive properties of methanogenic biofilms – Cheng Li – Bioelectrochemistry

Pulse electromagnetic fields enhance extracellular electron transfer in magnetic bioelectrochemical systems – Huihui Zhou – Biotechnology for Biofuels

Microbes in space
Microbial biodiversity assessment of the European Space Agency’s ExoMars 2016 mission – Kaisa Koskinen – Microbiome

Food microbiology
Safety assessment of transgenic canola RF3 with bar and barstar gene on Sprague-Dawley (SD) rats by 90-day feeding test – Tianqi Lang – Regulatory Toxicology and Pharmacology

Review: The role of wine and food polyphenols in oral health – Adelaida Esteban-Fernández – Trends in Food Science & Technology

Review: The agri-food chain and antimicrobial resistance: A review – John A. Hudson – Trends in Food Science & Technology

Review: Food derived anti-adhesive components against bacterial adhesion: Current progresses and future perspectives – Xiaohong Sun – Trends in Food Science & Technology

Probiotics / prebiotics / antibiotics
Effect of a yoghurt drink containing Lactobacillus strains on bacterial vaginosis in women – a double-blind, randomised, controlled clinical pilot trial – C. Laue – Beneficial Microbes

Bifidobacterium longum BB536 alleviated upper respiratory illnesses and modulated gut microbiota profiles in Malaysian pre-school children – A.S.-Y. Lau – Beneficial Microbes

Prebiotics for the prevention of allergies: A systematic review and meta-analysis of randomized controlled trials – C. Cuello-Garcia – Clinical and Experimental Allergy

Review: Metronidazole: an update on metabolism, structure-cytotoxicity and resistance mechanisms – Simon A Dingsdag – Journal of Antimicrobial Chemotherapy

Selective Proteomic Analysis of Antibiotic-Tolerant Cellular Subpopulations in Pseudomonas aeruginosa Biofilms – Brett M. Babin – mBio

Phages and viruses
Diel cycling and long-term persistence of viruses in the ocean’s euphotic zone – Frank O. Aylward – PNAS

Bioinformatics
MegaGTA: a sensitive and accurate metagenomic gene-targeted assembler using iterative de Bruijn graphs – Dinghua Li – BMC Bioinformatics

EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies – Alex L. Mitchell – Nucleic Acids Research

Techniques
A novel baiting microcosm approach used to identify the bacterial community associated with Penicillium bilaii hyphae in soil – Behnoushsadat Ghodsalavi – PLoS One

New Genomes
Bacillus kwashiorkori sp. nov., a new bacterial species isolated from a malnourished child using culturomics – El hadji Seck – Microbiology Open

Genome Sequence of Geobacillus stearothermophilus DSM 458, an Antimicrobial-Producing Thermophilic Bacterium, Isolated from a Sugar Beet Factory – Kevin Egan – Genome Announcements

Microbes in the news
Doctors warn new parents: Step away from the vaginal fluid swabs – Beth Mole – ARS Technica

New study details bacteria’s ‘sense of touch’ – Brooks Hays – UPI
Paper: Obstruction of pilus retraction stimulates bacterial surface sensing – Courtney K. Ellison – Science

T-Cell Enzyme Uses Deadly Multipronged Attack on Bacteria – GEN News
Paper: Granzyme B Disrupts Central Metabolism and Protein Synthesis in Bacteria to Promote an Immune Cell Death Program – Farokh Dotiwala – Cell

Gut bacteria could determine whether you develop PTSD – Sian Bradley – Wired (Paper from July 19)

Gut bacteria bolster disease research in labs – UNC Health Care

The Next Big Performance Enhancing Drug: Bacteria From Elite Athletes’ Guts? – Peter Audrey Smith – Men’s Journal

Microbes on the market
French Biotech’s Crohn’s Candidate Glides Through Phase I – Alex Dale – Lab Biotech

Enterome’s EB8018, a First-in-class Drug Candidate Targeting Crohn’s Disease, Successfully Completes Phase I Study in Healthy Volunteers – Enterome – Cision (same as above link, more detail)

October 12, 2017

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Interesting papers from every category (especially in “Animal studies, animal microbiome”), and many on molecular mechanisms. Many of the alerts are from books (specifically on yeasts and soil/plant communities) listed below, so be sure to check their table of contents out!

Events and jobs
Biomedical Scientist – microbiology – Edinburgh, Scotland – Matchtech

Technician (Microbiology) – Birmingham, Alabama – LabCorp

Instructor in Microbiology – Corvallis, OR – Oregon State University

Senior Hospital Scientist Microbiology – Tamworth, New South Wales, Australia – NSW Health Pathology

Unlocking the Microbiome – November 15, London, UK – Microbiology Society

General microbiome
The P/N (Positive-to-Negative Links) Ratio in Complex Networks-A Promising In Silico Biomarker for Detecting Changes Occurring in the Human Microbiome – Zhanshan (Sam) Ma – Microbial Ecology

Dysbiosis and Its Discontents – Katarzyna B. Hooks – mBio

Book: Yeasts in Natural Ecosystems: Ecology – Andrey Yurkov, María I. Pozo
Contains multiple articles of interest.

Pregnancy and early life
Transfer and Persistence of a Multi-Drug Resistance Plasmid in situ of the Infant Gut Microbiota in the Absence of Antibiotic Treatment – Heidi Gumpert – Frontiers in Microbiology

Cesarean Section, Formula Feeding, and Infant Antibiotic Exposure: Separate and Combined Impacts on Gut Microbial Changes in Later Infancy – Farzana Yasmin – Frontiers in Pediatrics

Multi-site human microbiome
Oral Lactobacillus Counts Predict Weight Gain Susceptibility: A 6-Year Follow-Up Study – J.A. Rosing – Obesity Facts

Review: Nutritional habits, risk, and progression of Parkinson disease – Roberto Erro – Journal of Neurology

Review: From Osteoimmunology to Osteomicrobiology: How the Microbiota and the Immune System Regulate Bone – Emory Hsu – Calcified Tissue International

Human respiratory microbiome
Review: Role of microbiota on lung homeostasis and diseases – Jian Wang – Science China Life Sciences

Human gut microbiome
Molecular Mechanism by which Prominent Human Gut Bacteroidetes Utilize Mixed-Linkage Beta-Glucans, Major Health-Promoting Cereal Polysaccharides – Kazune Tamura – Cell Reports

Reciprocal Prioritization to Dietary Glycans by Gut Bacteria in a Competitive Environment Promotes Stable Coexistence – Yunus E. Tuncil – mBio

The gut microbiome in atherosclerotic cardiovascular disease – Zhuye Jie – Nature Communications

Cytotoxic and regulatory roles of mucosal-associated invariant T cells in type 1 diabetes – Ophélie Rouxel – Nature Immunology

Review: How diet can impact gut microbiota to promote or endanger health – Benoit Chassaing – Current Opinion in Gastroenterology

Review: Management of inflammatory bowel disease-related anaemia and iron deficiency with specific reference to the role of intravenous iron in current practice – Jürgen Stein – Expert Opinion on Pharmacotherapy

Review: Bile acid-microbiota crosstalk in gastrointestinal inflammation and carcinogenesis – Wei Jia – Nature Reviews Gastroenterology and Hepatology

Review: Environmental triggers in IBD: a review of progress and evidence – Ashwin N. Ananthakrishnan – Nature Reviews Gastroenterology and Hepatology

Animal experiments
Spatial organization of a model 15-member human gut microbiota established in gnotobiotic mice – Jessica L. Mark Welch – PNAS

Potential role of intratumor bacteria in mediating tumor resistance to the chemotherapeutic drug gemcitabine – Leore T. Geller – Science

Increased weight gain by C-section: Functional significance of the primordial microbiome – Keith A. Martinez II – Science Advances

Epicutaneous Tolerance Induction to a Bystander Antigen Abrogates Colitis and Ileitis in Mice – David Dunkin – Inflammatory Bowel Diseases

Dietary fatty acids control the species of N-acyl-phosphatidylethanolamines synthesized by therapeutically modified bacteria in the intestinal tract – Noura S Dosoky – ACS Infectious Diseases

In Vitro Response of Rumen Microbiota to the Antimethanogenic Red Macroalga Asparagopsis taxiformis – Lorenna Machado – Microbial Ecology

Host effects on microbiota community assembly – Kathrin Näpflin – Journal of Animal Ecology
In bumblebees!

Animal microbiome
Comprehensive skin microbiome analysis reveals the uniqueness of human-associated microbial communities among the class Mammalia – Ashley Anne Ross – bioRxiv

Extensive Core Microbiome in Drone-Captured Whale Blow Supports a Framework for Health Monitoring – Amy Apprill – mSystems
Drones were involved.

The Microbiome of Seriola lalandi of Wild and Aquaculture Origin Reveals Differences in Composition and Potential Function – Carolina Ramirez – Frontiers in Microbiology

A Novel Lactobacilli-Based Teat Disinfectant for Improving Bacterial Communities in the Milks of Cow Teats with Subclinical Mastitis – Jie Yu – Frontiers in Microbiology

Amplicon sequencing of bacterial microbiota in abortion material from cattle – Sara Vidal – Veterinary Research

Plant, root, and soil microbiome
Book: Soil Biological Communities and Ecosystem Resilience – Editors Martin Lukac, Paola Grenni, Mauro Gamboni
Multiple articles of interest.

Linking nitrogen load to the structure and function of wetland soil and rhizosphere microbial communities – Eric R. Hester – bioRxiv

Template Preparation Affects 16S rRNA High-Throughput Sequencing Analysis of Phyllosphere Microbial Communities – Xiaoyan Tian – Frontiers in Plant Science

Biocontrol of Bacterial Leaf Blight of Rice and Profiling of Secondary Metabolites Produced by Rhizospheric Pseudomonas aeruginosa BRp3 – Sumera Yasmin – Frontiers in Microbiology

Integration of multi-omics techniques and physiological phenotyping within a holistic phenomics approach to study senescence in model and crop plants – Dominik K Großkinsky – Experimental Botany

Gaining Insight into Plant Responses to Beneficial and Pathogenic Microorganisms Using Metabolomic and Transcriptomic Approaches – Fernando Matías Romero – Metabolic Engineering for Bioactive Compounds

Water and extremophile microbiome
Globally Important Haptophyte Algae Use Exogenous Pyrimidine Compounds More Efficiently than Thiamin – Magdalena A. Gutowskaa – mBio

Fungal community dynamics during a marine dinoflagellate (Noctiluca scintillans) bloom – Jing-YunSun – Marine Environmental Research

Built environment
Biodegradation of tetracycline antibiotics in A/O moving-bed biofilm reactor systems – Han-Yu Chen – Bioprocess and Biosystems Engineering

Food microbiology
Interindividual Variability in Metabolism of [6]-Shogaol by Gut Microbiota – Pei Wang – Journal of Agricultural and Food Chemistry

Microbial technology
Programmed Assembly of Pressure Sensors Using Pattern-Forming Bacteria – Yangxiaolu Cao – Nature Biotechnology
Press: Three words: Synthetic gene circuit. Self-assembling bacteria build pressure sensor – Andrew Silver – The Register

Probiotics / prebiotics / antibiotics
Non-digestible oligosaccharides directly regulate host kinome to modulate host inflammatory responses without alterations in the gut microbiota – Richard Y. Wu – Microbiome

Review: Antibiotics and specialized metabolites from the human microbiota – Walaa K. Mousa – Natural Product Reports

Phages and viruses
Moderate-Throughput Identification and Comparison of Campylobacter-Infecting Bacteriophages – Tylor J. Johnson – bioRxiv

Review: Innate Viral Receptor Signaling Determines Type 1 Diabetes Onset – Zachary J. Morse – Frontiers in Endocrinology

Bioinformatics
A Massively Parallel Sequence Similarity Search for Metagenomic Sequencing Data – Masanori Kakuta – International Journal of Molecular Sciences

Microbes in the news
Hibernating ribosomes help bacteria survive – Saint Louis University – Science Daily
Paper: The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus – Donna Matzov – Nature Communications

A century-old vaccine vial sheds light on one of medicine’s enduring mysteries – Helen Branswell – STAT News

Predatory bacteria-the quest for a new class of antibiotics – Phys.org

Mind the Gut: Copenhagen Exhibition Explores Bacteria and Feelings – Clara Rodríguez Fernández – Labiotech.eu

Gut Love: Bacteria, Love and Immunology Intersect at Esther Klein Gallery Exhibit – PRWeb

How mouldy mushrooms and frog spawn have been turned into art on Spring Bank – Amgus Young – Hull Daily Mail

Microbes on the market
Kaleido Biosciences and CoreBiome Partner to Accelerate Microbiome Therapeutic Development – Business Wire

Tiffany’s non-microbiology picks
The rise and fall and rise again of 23andMe – Erika Check Hayden – Nature

The future of DNA sequencing – Eric D. Green – Nature