Category Archives: Extremophiles

July 21, 2015

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Microbiome of a dead pig in the snow, two papers on oral microbiome in HIV infection, sweetener consumption and microbiome, proteomics of preterm infant colonization, sequencing platform and primer choices, and including microbial ecology in Pre-med programs.

Microbiology of death

Using Bacterial and Necrophagous Insect Dynamics for Post-Mortem Interval Estimation during Cold Season: Novel Case Study in Romania – Lavinia Iancu – Forensic Science International

Pregnancy and birth / Proteomics

Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant – Brandon Brooks

Human oral microbiome

The Oral Microbiome in HIV-positive Individuals – James O. Kistler – Journal of Medical Microbiology

Exploring salivary microbiota in AIDS patients with different periodontal statuses using 454 GS-FLX Titanium pyrosequencing – Fang Zhang – Frontiers in Cellular and Infection Microbiology

Review: Bacteria and Archaea Paleomicrobiology of the Dental Calculus: a Review – Hong T.T. Huynh – Molecular Oral Microbiology

Human urinary tract microbiome

Review: Intracellular Bacterial Communities: A Potential Etiology for Chronic Lower Urinary Tract Symptoms – Victoria C.S. Scott – Urology

Human gut microbiome

High-intensity sweetener consumption and gut microbiome content and predicted gene function in a cross-sectional study of adults in the United States – Cara L. Frankenfeld – Annals of Epidemiology

Pomegranate extract induces ellagitannin metabolite formation and changes stool microbiota in healthy volunteers – Zhaoping Li – Food & Function

Models of microbiome

Neutrophil gelatinase-associated lipocalin regulates gut microbiota of mice – Katsuya Mori – Journal of Gastroenterology and Hepatology

Effect of Dietary Protein Levels on Composition of Odorous Compounds and Bacterial Ecology in Pig Manure – Sungback Cho – Asian Australas. J. Anim. Sci

Animal microbiome

Shotgun Metagenomic Sequencing Reveals Functional Genes and Microbiome Associated with Bovine Digital Dermatitis – Martin Zinicola – PLOS ONE

Diversity and composition of the bacterial community in Amphioxus feces – Minming Pan – Journal of Basic Microbiology

Isolation, characterization, and antibiotic resistance of Vibrio spp. in sea turtles from Northwestern Mexico – Alan A. Zavala-Norzagaray – Frontiers in Microbiology

Microbial Infections Are Associated with Embryo Mortality in Arctic-Nesting Geese – Cristina M. Hansen – Applied and Environmental Microbiology

An insight into the functional role of thioredoxin reductase, a selenoprotein, in maintaining normal native microbiota in the Gulf Coast tick (Amblyomma maculatum) – K. Budachetri – Insect Molecular Biology

Chemotaxis by natural populations of coral reef bacteria – Jessica Tout – The ISME Journal

Review: Exploring the avian gut microbiota: current trends and future directions – David W. Waite – Frontiers in Microbiology

Plant, root, and soil microbiome

Lactic acid bacteria are endophytic components of durum wheat plant following the whole life cycle from plant to flour – Fabio Minervini – Applied and Environmental Microbiology

Application of mesotrione at different doses in an amended soil: Dissipation and effect on the soil microbial biomass and activity – Eva Pose-Juan – Science of The Total Environment

Plant species richness does not attenuate responses of soil microbial and nematode communities to a flood event – Daniela Wagner – Soil Biology and Biochemistry

Declined soil suppressiveness to Fusarium oxysporum by rhizosphere microflora of cotton in soil sickness – Xiaogang Li – Biology and Fertility of Soils

Water / extremophile microbiome

Diversity of methanogens and sulfate-reducing bacteria in the interfaces of five deep-sea anoxic brines of the Red Sea – Yue Guan – Research in Microbiology

Analysis of virus genomes from glacial environments reveals novel virus groups with unusual host interactions – Christopher M. Bellas – Frontiers in Microbiology

A Paleoarchean coastal hydrothermal field inhabited by diverse microbial communities: the Strelley Pool Formation, Pilbara Craton, Western Australia – K. Sugitani – Geobiology

Predicting the response of the deep-ocean microbiome to geochemical perturbations by hydrothermal vents – Daniel C Reed – The ISME Journal

Waste and bioreactor microbiology

GeoChip-based analysis of microbial community of a combined nitritation-anammox reactor treating anaerobic digestion supernatant – Jian Zhao – Water Research

Arsenic toxicity effects on microbial communities and nutrient cycling in indoor experimental channels mimicking a fluvial system – Baigal-Amar Tuulaikhuu – Aquatic Toxicology

Microbial ecology

Review: Ecological speciation in bacteria: reverse ecology approaches reveal the adaptive part of bacterial cladogenesis – Florent Lassalle – Research in Microbiology

Microbiology and Ecology Are Vitally Important to Premedical Curricula – Val H. Smith – Evolution, Medicine, and Public Health

Bioinformatics and metagenomics
MCaVoH: A toolkit for Mining, Classification and Visualization of Human Microbiota –
Maryum Nisar – Journal of Microbiological Methods

An intriguing new bacterial phylum – Naomi Attar – Nature Reviews Microbiology

Metabolic networks

A biosynthetic pathway for a prominent class of microbiota-derived bile acids – A Sloan Devlin – Nature Chemical Biology

Methanogenic food web in the gut contents of methane-emitting earthworm Eudrilus eugeniae from Brazil – Kristin Schulz – The ISME Journal

Auxotrophy and intra-population complementary in the ‘interactome’ of a cultivated freshwater model community – Sarahi L Garcia – Molecular Ecology

Techniques

Primer and platform effects on 16S rRNA tag sequencing – Julien Tremblay – Frontiers in Microbiology

Microbes in the news

Programming Bacteria to Kill Cancer Cells – Lecia Bushak – Newsweek

Scientists keep finding more evidence that bacteria in your stomach are connected to your mood – Kevin Loria – Business Insider

#BacteriaHysteria: The even grosser cause behind gross smelling feet – Stephanie Bell-Flynt

Bik’s Picks
One Migration from Siberia Peopled the Americas: Study – Discovery

Study: Women With Mild Memory Problem Worsen Faster Than Men – Lauran Neergaard – ABC News

Marijuana helps broken bones heal, says Israeli scientific team – Ruth Schuster – Haaretz

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July 20, 2015

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Transcriptomics in periodontitis, stool consistency, truffles, ginger and pigs, and salt deserts.

Events (repeat posts)

Free Cell Press Webinar: Microbiome, Antibiotics and Human Disease with human microbiome leaders Martin Blaser, Michael Fischbach and Julie Segre – July 28, 2015, noon EST

Multi-omics for Microbiomes Conference, September 14-16, 2015, Three Rivers Convention Center, Kennewick, WA
Human oral microbiome / transcriptomics

Small RNA transcriptome of the oral microbiome during periodontitis progression – Ana E. Duran-Pinedo – Applied and Environmental Microbiology

Human gut microbiome

Solid evidence: Stool consistency as a major confounding factor affecting microbiota composition: an ignored variable? – Jack A Gilbert – Gut

Review [PDF]: Beyond gut microbiota: understanding obesity and type 2 diabetes – Eva Lau – Hormones

Models of microbiome research

Ginger and inulin: Assessment of Fecal Microflora Changes in Pigs Supplemented with Herbal Residue and Prebiotic – Ashis Kumar Samanta – PLOS ONE

Plant, root, and soil microbiome (and extremophiles!)

The role of the microbiome of truffles in aroma formation: a meta-analysis approach -Maryam Vahdatzadeh – Applied and Environmental Microbiology

Bacterial diversity and composition in the fluid of pitcher plants of the genus Nepenthes – Yayoi Takeuchi – Systematic and Applied Microbiology

A snapshot of microbial communities from the Kutch: one of the largest salt deserts in the World – Aanal S. Pandit – Extremophiles

Temporal patterns of prokaryotic abundance, community structure and microbial activity in glacier foreland soils – Katrin Hofmann – Antonie van Leeuwenhoek

Built environment microbiome

Winner of today’s Longest Title Award: Intensive care unit environmental surfaces are contaminated by multidrug-resistant bacteria in biofilms: combined results of conventional culture, pyrosequencing, scanning electron microscopy, and confocal laser microscopy – H. Hu – Journal of Hospital Infection

Waste treatment microbiology

High prevalence of type 41 and high sequence diversity of partial hexon gene of human adenoviruses in municipal raw sewage and activated sludge – Hsion-Wen Kuo – Journal of Applied Microbiology

Acute Gastrointestinal Illness Risks in North Carolina Community Water Systems: A Methodological Comparison – Nicholas B. DeFelice – Environmental Science & Technology

Metagenomics

Phylogenetically typing bacterial strains from partial SNP genotypes observed from direct sequencing of clinical specimen metagenomic data – Jason W. Sahl – Genome Biology

Microbial Ecology

Gene-specific selective sweeps in bacteria and archaea caused by negative frequency-dependent selection – Nobuto Takeuchi – BMC Biology

Techniques

A method to analyze, sort, and retain viability of obligate anaerobic microorganisms from complex microbial communities – Anne W. Thompson – Journal of Microbiological Methods

Use of 16S rRNA gene-targeted group-specific primers for real-time PCR analysis of predominant bacteria in mouse feces – Yun-wen Yang – Applied and Environmental Microbiology

Antibiotics

Prevalence of Parental Misconceptions About Antibiotic Use – Louise Elaine Vaz – Pediatrics

Microbes in the news

Ginger and prebiotic promote good bacteria in pigs – All About Feed

How plants keep bad bacteria out – ZeeNews India

Parental Knowledge About Appropriate Antibiotic Use Still Poor – Diana Phillips – Medscape

Bik’s Picks

Can’t get Kylie out of your head? Blame the shape of your brain – Sam Wong – New Scientist

Seti: Search for alien life receives $100m boost – Clive Cookson – Financial Times

Remembering the Apollo 11 Moon Landing With the Woman Who Made It Happen – Lily Rothman – Time

Endangered dragonflies, raised in captivity over several years, being released – Dispatch Times

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July 16, 2015

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Biomimetic robot models of host-microbiome interactions, an eukaryotic model for astrobiology, how plants use salicylic acid to sculpt their root microbiome, and how to cook Hadza tubers.

Human oral microbiome

TLR4, NOD1 and NOD2 Mediate Immune Recognition of Putative Newly-Identified Periodontal Pathogens – Julie Marchesan – Molecular Oral Microbiology

Human respiratory microbiome

Intraalveolar Catecholamines and the Human Lung Microbiome – Robert P. Dickson – American Journal of Respiratory and Critical Care Medicine

Human gut microbiome

Transforming berberine into its intestine-absorbable form by the gut microbiota – Ru Feng – Scientific Reports

I could not find information about primers or sequencing strategy, no ordination plots: Colonic bacterial composition in Parkinson’s disease – Ali Keshavarzian – Movement Disorders

Review: Role of gut microbiota in the modulation of atherosclerosis-associated immune response – Dmitry A. Chistiakov – Frontiers in Microbiology

Review: Potential role of the intestinal microbiota in programming health and disease – Olivier Goulet – Nutrition Reviews

Review: Microbiota and the gut–brain axis – John Bienenstock – Nutrition Reviews

Review: The Blood-Brain Barrier’s Gut Check – Nga Bien-Ly – Science Translational Medicine

Review: The Microbes inside Us and the Race for Colibactin – Helge B. Bode – Angewandte Chemie International Edition

Animal models

Macaques: Persistent effects of early infant diet and associated microbiota on the juvenile immune system – Nicole Narayan – Gut Microbes

Pigs: Wheat and barley differently affect porcine intestinal microbiota – Eva Weiss – Journal of the Science of Food and Agriculture

Rats: Bacterial Flora Changes in Conjunctiva of Rats with Streptozotocin-Induced Type I Diabetes – Chao Yang – PLOS ONE

Animal microbiome

Fish-like marine chordate: Diversity and composition of the bacterial community in Amphioxus feces – Minming Pan – Journal of Basic Microbiology

Plant, root, and soil microbiome

Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa – Sarah L. Lebeis – Science

Silencing a key gene of the common symbiosis pathway in Nicotiana attenuata specifically impairs arbuscular mycorrhizal infection without influencing the root-associated microbiome or plant growth – Karin Groten – Plant, Cell & Environment

Water microbiome

Microbial communities related to biodegradation of dispersed Macondo oil at low seawater temperature with Norwegian coastal seawater – Odd G. Brakstad – Microbial Biotechnology

Extremophile microbiome

UV-resistant yeasts isolated from a high-altitude volcanic area on the Atacama Desert as eukaryotic models for astrobiology – André A. Pulschen – Microbiology Open

Waste management microbiology

Changes in diversity of cultured bacteria resistant to erythromycin and tetracycline in swine manure during simulated composting and lagoon storage – L. Wang – Letters in Applied Microbiology

Functional foods

Assessing digestibility of Hadza tubers using a dynamic in-vitro model – Stephanie L. Schnorr – American Journal of Physical Anthropology

Bioinformatics

Exploring Host-Microbiome Interactions using an in Silico Model of Biomimetic Robots and Engineered Living Cells – Keith C. Heyde – Scientific Reports

K-Pax2: Bayesian identification of cluster-defining amino acid positions in large sequence datasets – Alberto Pessia – Microbial Genomics

Microbes in the news

Healthy Living: Preterm Birth Disparities: Doctor Dunlop and her team have begun a five year study to examine prenatal stress, diet and a woman’s microbiome on birth outcomes – 9&10 News
Five-year study to examine the gut microbiome of premature infants – Matt Wood – Science Life University of Chicago

Plant defense hormones help sculpt root microbiome – Science Daily

Research finds diversifying your diet may make your gut healthier – Science Codex

Do you smoke? UBiome wants to study your mouthome – Claire Maldarelli – Popular Science

Bik’s Picks

Polar Bears Don’t Go Into Hibernation-Like State in Summer, Researchers Say – James Gorman – New York Times

Finally, Bacon-Flavored Health Food Has Arrived: introducing dulse, a seaweed that tastes like bacon – Elizabeth Palermo – Live Science

Why screams are scary (hint: It’s not because they’re loud) – Eryn Brown – Los Angeles Times

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July 14, 2015

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Antibiotic-induced changes in mouse gut microbiome, the lichen microbiome, and what’s floating in the airplane toilet?

Human respiratory microbiome

Common Cell Shape Evolution of Two Nasopharyngeal Pathogens – Frédéric J. Veyrier – PLOS Genetics

Human gut microbiome

Trimethylamine-N -oxide: A Novel Biomarker for the Identification of Inflammatory Bowel Disease – Aze Wilson – Digestive Diseases and Sciences

Review: Roles of commensal microbiota in pancreas homeostasis and pancreatic pathologies – Camila Leal-Lopes – Journal of Diabetes Research

Animal models of microbiome research

Antibiotic-Induced Alterations of the Murine Gut Microbiota and Subsequent Effects on Colonization Resistance against Clostridium difficile – Alyxandria M. Schubert – mBio

Animal microbiome

The Apis mellifera Filamentous Virus Genome – Laurent Gauthier – Viruses

Concentrations of viable oil-degrading microorganisms are increased in feces from Calanus finmarchicus feeding in petroleum oil dispersions – Ingvild Fladvad Størdal – Marine Pollution Bulletin

Editorial: Microbial symbiosis of marine sessile hosts- diversity and function – Suhelen Egan – Frontiers in Microbiology

Plant, root, and soil microbiome

Analyzing the antagonistic potential of the lichen microbiome against pathogens by bridging metagenomic with culture studies – Tomislav Cernava – Frontiers in Microbiology

Indigenous trees restore soil microbial biomass at faster rates than exotic species – Chun Li – Plant and Soil

MSc Thesis: Tree Islands of Fertility Structure Bacterial Community Assembly and Functional Genes Contributing to Ecosystem Processes – Tayte Paul Campbell – Brigham Young University

Rhizosphere microbiome selection by Epichloë endophytes of Festuca arundinacea – Elizabeth Lewis Roberts – Plant and Soil

Responses of soil microbial communities and enzyme activities to nitrogen and phosphorus additions in Chinese fir plantations of subtropical China – W. Y. Dong – Biogeosciences Discussions

Water microbiome

Ubiquitous healthy diatoms in the deep sea confirm deep carbon injection by the biological pump – S. Agusti – Nature Communications

Extremophile microbiome

Characterization of the Bacterial and Sulphate Reducing Community in the Alkaline and Constantly Cold Water of the Closed Kotalahti Mine – Malin Bomberg – Minerals

Co-occurrence patterns in aquatic bacterial communities across changing permafrost landscapes – J. Comte – Biogeosciences Discussions

Built environment and waste microbiome

Meta-genomic analysis of toilet waste from long distance flights; a step towards global surveillance of infectious diseases and antimicrobial resistance – Thomas Nordahl Petersen- Scientific Reports

Development of antibiotic resistance genes in microbial communities during long-term operation of anaerobic reactors in the treatment of pharmaceutical wastewater – Sevcan Aydin – Water Research

One-Time Addition of Nano-TiO2 Triggers Short-Term Responses in Benthic Bacterial Communities in Artificial Streams – Alexandra Ozaki – Microbial Ecology

Characterization of microbial community structure during continuous anaerobic digestion of straw and cow manure – Li Sun – Microbial Biotechnology

Characterization of the microbial community structure and the physicochemical properties of produced water and seawater from the Hibernia oil production platform – C. William Yeung – Environmental Science and Pollution Research

Archaea

The distribution, diversity, and importance of 16S rRNA gene introns in the order Thermoproteales – Zackary J. Jay – Biology Direct

Bioinformatics

Estimating beta diversity for under-sampled communities using the variably weighted Odum dissimilarity index and OTUshuff – Daniel K. Manter – Bioinformatics

Swarm v2: highly-scalable and high-resolution amplicon clustering – Frederic Mahe – PeerJ

Cutting edge: Anatomy of BioJS, an open source community for the life sciences – Guy Yachdav – eLIFE

Metagenomics

Metagenomic insights into strategies of aerobic and anaerobic carbon and nitrogen transformation in boreal lakes – Sari Peura – Scientific Reports

Metabolic networks, proteomics

A Single Host-Derived Glycan Impacts Key Regulatory Nodes of Symbiont Metabolism in a Coevolved Mutualism – Min Pan – mBIO

Extracellular protein analysis of activated sludge and their functions in wastewater treatment plant by shotgun proteomics – Peng Zhang – Scientific Reports

Techniques

Scaffolding of a bacterial genome using MinION nanopore sequencing – E. Karlsson – Scientific Reports

Microbial Ecology

Biodiversity inhibits parasites: Broad evidence for the dilution effect – David J. Civitello – PNAS

Science, publishing, and career

Big Data: Astronomical or Genomical? Projecting to the year 2025, we compared genomics with three other major generators of Big Data: astronomy, YouTube, and Twitter. – Zachary D. Stephens – PLOS Biology

The Outrage Factor – Then and Now: There’s a lot of outrage about outrage storming around women in science and science journalism at the moment. And fear of causing it, too. – Hilda Bastian – PLOS Blogs

Microbes in the news

Aging in Microbes: bacteria are using every trick in the book to get ahead – Josh Mitteldorf

Bik’s Picks

Everything you need to know about Tuesday’s Pluto encounter – Rachel Feltman – Washington Post

Introducing the Pentaquark: Physicists Prove a New Particle Exists – Tanya Basu – Time

Neighborhood greenspace and health in a large urban center : higher health perception if you live near trees – Omid Kardan – Scientific Reports
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July 9, 2015

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Microbiome in colicky infants, bacterial communities on seaweed, and viral communities in soil.

Events

Altering the Microbiome: Can it Impact Health? Sept 24, 2015. Call for Abstracts- Deadline August 3, 2015

Microbiome of pregnancy and birth

Probiotic Lactobacillus rhamnosus GG therapy and microbiological programming in infantile colic: a randomized, controlled trial – Anna Pärtty – Pediatric Research

Human respiratory microbiome
The Lung Microbiome: New Principles for Respiratory Bacteriology in Health and Disease – Robert P. Dickson – PLOS Pathogens

Human gut microbiome

Interactions between the intestinal microbiota and bile-acids in gallstones patients – Nirit Keren – Environmental Microbiology Reports

Plant, root, and soil microbiome

Continental-scale variation in seaweed host-associated bacterial communities is a function of host condition, not geography – Ezequiel M. Marzinelli – Environmental Microbiology

Ecotoxicological assessment of soil microbial community tolerance to glyphosate – Marco Allegrini – Science of The Total Environment

Dynamics of autochthonous soil viral communities parallels dynamics of host communities under nutrient stimulation – Sharath Srinivasiah – FEMS Microbiology Ecology

Water microbiome

Zonation of bacterioplankton communities along aging upwelled water in the northern Benguela upwelling – Benjamin Bergen – Frontiers in Microbiology

Extremophile microbiome

Temporal evolution of bacterial communities associated with the in situ wetland-based remediation of a marine shore porphyry copper tailings deposit – N. Diaby – Science of The Total Environment

 

Bioinformatics

Web Resources for Microbial Data – Qinglan Sun – Genomics, Proteomics & Bioinformatics

The unifrac significance test is sensitive to tree topology – Catherine A. Lozupone – BMC Bioinformatics

Microbes in the news

Researchers discover how bacteria sweet-talk their way into plants – Aarhus University – EurekAlert

Probiotics—for plants: Helpful bacteria promote growth, less fertilizer on crops – Phys.org

Designer microbiome: MIT biologists program common gut bacteria – Eryn Brown – LA Times

Certain species dominate oral microbiome in patients with Sjögren’s syndrome – Healio

Science, publishing, and career

How to fail better (and even succeed!) in the academic job market – Dr. Acclimatrix – Tenure She Wrote

Bik’s Picks

Science reveals how giant pandas survive on a bamboo diet – Karen Kaplan – LA Times

Patients can spot trouble with new dental implants – Lisa Rapaport – Reuters

This jumping, squishy robot looks like a tiny UFO – Rachel Feltman – Washington Post
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July 1, 2015

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I’ve been busy in the lab most of the day, and will be tomorrow, so my apologies for posting at weird hours.

Human oral microbiome

The Influence of Smoking on the Peri-Implant Microbiome – A.A. Tsigarida – Journal of Dental Research

Human respiratory microbiome

Dual Transcriptomic Profiling of Host and Microbiota during Health and Disease in Pediatric Asthma – Marcos Pérez-Losada – PLOS ONE

Commentary: Has the airway microbiome been overlooked in respiratory disease? – Olawale Salami – Genome Medicine

Review: The bacterial microbiota in inflammatory lung diseases – Gary B. Huffnagle – Clinical Immunology

Human gut microbiome

Thematic collection of abstracts: GUT in FOCUS Symposium NOBEL FORUM, Karolinska Institutet, February 2nd 2015 – Microbial Ecology in Health and Disease

Animal models

Long noncoding RNA expression profiles in gut tissues constitute molecular signatures that reflect the types of microbes – Lunxi Liang – Scientific Reports

Animal microbiome

Effects of transport, fasting and anaesthesia on the faecal microbiota of healthy adult horses – A. Schoster – Equine Veterinary Journal

Plant, root, and soil microbiome

Pyridine-type alkaloid composition affects bacterial community composition of floral nectar – Yana Aizenberg-Gershtein – Scientific Reports

Review: Role of plant growth regulators as chemical signals in plant–microbe interactions: a double edged sword – Carla Spence – Current Opinion in Plant Biology

Water microbiome

Investigation of a Large Collection of Pseudomonas aeruginosa Bacteriophages Collected from a Single Environmental Source in Abidjan, Côte d’Ivoire – Christiane Essoh – PLOS ONE

Study in 93 wells (Ha! why not 96?): Natural Bacterial Communities Serve as Quantitative Geochemical Biosensors – Mark B. Smith – mBio

Extremophile microbiome

Arsenic rich Himalayan hot spring metagenomics reveal genetically novel predator–prey genotypes – Naseer Sangwan – Environmental Microbiology Reports

Microbial diversity in shallow-water hydrothermal sediments of Kueishan Island, Taiwan as revealed by pyrosequencing – Li Wang – Journal of Basic Microbiology

Built Environment microbiome

Bacterial Exposures and Associations with Atopy and Asthma in Children – Maria Valkonen – PLOS ONE

Studies for antifungal activity of selected concrete sealers on white cement panels – Rajesh K. Verma – International Journal of Science, Engineering and Technology Research (IJSETR)

Bioreactor microbiology

In vitro characterisation of the fermentation profile and prebiotic capacity of gold-fleshed kiwifruit – P. Blatchford – Beneficial Microbes

Bioinformatics and metagenomics

Constructing a Boolean implication network to study the interactions between environmental factors and OTUs – Congmin Zhu – Quantitative Biology

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes – Donovan H. Parks – Genome Research

The 2015 Nucleic Acids Research annual Web Server Issue: web-based software resources for analysis and visualization of molecular biology data

Microbial Ecology

The Final Countdown? Confusion about the species richness of human gut microbiota – E. Avershina – Beneficial Microbes

Individuality, phenotypic differentiation, dormancy and ‘persistence’ in culturable bacterial systems: commonalities shared by environmental, laboratory, and clinical microbiology – Douglas Kell – F1000 Research

Microbial interspecies interactions: recent findings in syntrophic consortia – Atsushi Kouzuma – Frontiers in Microbiology

Microbes in the news

The Sum of Our Parts – Janice Dietert – The Scientist

Human Microbiome Journal Club: “Disease-specific alterations in the enteric virome in inflammatory bowel disease” [Norman et al, 2015]

Would You Eat Off These Bacteria-Covered Plates? The Petri Dishes – Diana Budds – FastCoDesign

Bik’s Picks

Personal Belief Exemptions to Vaccination in California: A Spatial Analysis – Margaret Carrel – Pediatrics
No Mating Partner? No Problem: This Flatworm Injects Sperm Directly Into Own Head To Reproduce – Jim Algar – Tech Times

Citrus fruit linked with melanoma in preliminary study – Kathryn Doyle – Reuters

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June 29, 2015

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Gut microbiome of children with Schistosoma infections, what happens to the hooves after a cow dies, and microbiomes at extremely dry or hot places.

General microbiome

Only one health, and so many omics – Nives Pećina-Šlaus – Cancer Cell International

Interchange of entire communities: microbial community coalescence – Matthias C. Rillig – Trends in Ecology and Evolution

A Vision for Investigating the Microbiology of Health and Disease – W. Ian Lipkin – The Journal of Infectious Diseases

Collateral sensitivity of antibiotic-resistant microbes – Csaba Pál – Trends in Microbiology

Personalized medicine going precise: from genomics to microbiomics – Sanjay K. Shukla – Trends in Molecular Medicine

Review: Secrets from the microbiome: molecular biology meets microbiology meets histopathology….meets clinical biochemistry – Caroline Young – Annals of Clinical Biochemistry

Human respiratory microbiome

Editorial: Infectious asthma triggers: time to revise the hygiene hypothesis? – Wilmore C. Webley – Trends in Microbiology

Human gut microbiome

Differences in the Faecal Microbiome in Schistosoma haematobium Infected Children vs. Uninfected Children – Gemma Louise Kay – PLOS Neglected Tropical Diseases

Glycan complexity dictates microbial resource allocation in the large intestine – Artur Rogowski – Nature Communications

Review: Intestinal Microbiota, Lipids, and the Pathogenesis of Intestinal Failure–Associated Liver Disease – Way Seah Lee – The Journal of Pediatrics

Review: Influence of gut bacteria on development and progression of non-alcoholic fatty liver disease – Ali Abdul-Hai – World Journal of Hepatology

Animal microbiome

Cockroaches: Aerobic Bacterial Community of American Cockroach Periplaneta americana,a Step toward Finding Suitable Paratransgenesis Candidates – Sanaz Akbari – Journal of Arthropod-Borne Diseases

Hooves from dead cows: Compost biodegradation of recalcitrant hoof keratin by bacteria and fungi – T. Reuter – Journal of Applied Microbiology

Fish: Modulation of the intestinal microbiota and morphology of tilapia, Oreochromis niloticus , following the application of a multi-species probiotic – B . T. Standen – Applied

Jellyfish: Changing company: Composition of bacterial communities associated with
Aurelia aurita changes with compartment, life stage and population – Nancy Weiland-Bräuer – Applied and Environmental Microbiology

Ants: Bacterial community composition and diversity in an ancestral ant fungus symbiosis – Katrin Kellner – FEMS Microbiology Ecology

Review: A new view of the fish gut microbiome: Advances from next-generation sequencing – Mahdi Ghanbari

Plant microbiome

Host–microbe interactions as a driver of acclimation to salinity gradients in brown algal cultures – Simon M Dittami – The ISME Journal

The olive knot disease as a model to study the role of interspecies bacterial communities in plant disease – Roberto Buonaurio – Frontiers in Plant Science

Review: Biotic Interactions in the Rhizosphere: A Diverse Cooperative Enterprise for Plant Productivity – Clelia De-la-Peña – Plant Physiology

Editorial on plants as alternative hosts for human and animal pathogens – Nicola J. Holden – Frontiers in Microbiology

Soil microbiome

Responses of bacterial communities to simulated climate changes in alpine meadow soil of
Qinghai-Tibet plateau – Junpeng Rui – Applied and Environmental Microbiology

Evaluation of bacterial communities by bacteriome analysis targeting 16S rRNA genes and quantitative analysis of ammonia monooxygenase gene in different types of compost – Rika Kitamura – Journal of Bioscience and Bioengineering

Soil conditions and land use intensification effects on soil microbial communities across a range of European field sites – Bruce C. Thomson – Soil Biology and Biochemistry

Impact of urine and the application of the nitrification inhibitor DCD on microbial communities in dairy-grazed pasture soils – Sergio E. Morales – Soil Biology and Biochemistry

Water microbiome

Metagenomic assessment of viral diversity in Lake Matoaka, a temperate, eutrophic freshwater lake in southeastern Virginia, USA – Jasmin C. Green – Aquatic Microbial Ecology

A comparison of bacterial community structure in seawater pond with shrimp, crab, and shellfish cultures and in non-cultured pond in Ganyu, Eastern China – LianTai Li – Annals of Microbiology

Extremophile microbiome

Phylogenetic Profiling and Diversity of Bacterial Communities in the Death Valley, an Extreme Habitat in the Atacama Desert – Francine Piubeli – Indian Journal of Microbiology

Review: Uncultivated thermophiles: current status and spotlight on ‘Aigarchaeota’ – Brian P Hedlund – Current Opinion in Microbiology

Food microbiology

Evaluation and identification of poly-microbial biofilms on natural green Gordal table olives – Antonio Benítez-Cabello – Antonie van Leeuwenhoek

Proteomic and high-throughput analysis of protein expression and microbial diversity of microbes from 30- and 300-year pit muds of Chinese Luzhou-flavor liquor – Qi Zheng – Food Research International

Bacterial communities during the process of high-temperature Daqu production of roasted sesame-like flavour liquor – Yao Su – Journal of the Institute of Brewing

Bioreactor microbiology

Sulfate Reducing Bacteria and Mycobacteria Dominate the Biofilm Communities in a Chloraminated Drinking Water Distribution System – Christa Kimloi Gomez-Smith – Environmental Science & Technology

The Microbiota and Abundance of the Class 1 Integron-Integrase Gene in Tropical Sewage Treatment Plant Influent and Activated Sludge – Magna C. Paiva – PLOS ONE

Metabolic networks

Metabolic pathway activity estimation from RNA-Seq data – Yvette Temate-Tiagueu – ISBRA abstracts

Microbes in the news

Volunteers Needed for Human Microbiota Study: prebiotic effects of certain rice bran components @UArkansas

In Defense of Fiber: How Changing Your Diet Changes Your Gut Bacteria – Mandy Oaklander – Time

Undergraduate is first author on study of Lake Matoaka’s metagenome – Joseph McClain – WM.edu

DNA Genotek Inc. announces recipients of gut microbiome grant program – Steamfeed

Indigo-Clean Is New Light Designed For Hospitals That Kills Bacteria – James Maynard – TechTimes

The ‘frightening’ rise of flesh-eating bacteria: Mystery, pain and amputations – Peter Holley – Washington Post

Fatty and sugary foods linked to lower cognitive functions: Mouse data – Nathan Gray – Food Navigator

Investors Think This Company’s Gut Bacteria Are Worth $1.9 Billion – John Tozzi – Bloomberg

What’s new in gastroenterology? Insights from BMC Medicine at #DDW2015 – Alessandro Recchioni- BioMedCentral

Science, publishing, and career

From trainee to tenure-track: ten tips – Tuuli Lappalainen – Genome Biology

What would be a suitable value for the absolute minimum proportion of female speakers at genomics/bioinformatics conferences? – Keith Bradnam? – ACGT blog

Bik’s Picks

Make it count! ‘Leap second’: Why June 30 will have one extra second – Deborah Netburn – LA Times

SpaceX Rocket Explosion Destroys Students’ Science Experiment – Alyssa Newcomb – ABC News

Rats Dream About the Places They Want to Explore – Kiona Smith-Strickland – Discover Magazine
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June 26, 2015

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Antibiotic resistance genes in stool from 3 twin pairs, oasis microbiome helps date palms cope with drought, and mother’s littlest helpers.

General microbiome

Triclosan and prescription antibiotic exposures and enterolactone production in adults – Margaret A. Adgent – Environmental Research

Pregnancy and birth microbiome

Gut resistome development in healthy twin pairs in the first year of life – Aimee M. Moore – Microbiome

Center Variation in Intestinal Microbiota Prior to Late-Onset Sepsis in Preterm Infants – Diana H. Taft – PLOS ONE

Editorial: Mother’s littlest helpers – Katie Hinde – Science

Human skin microbiome

Identification of the skin virome in a boy with widespread human papillomavirus-2-positive warts that completely regressed after administration of tetravalent human papillomavirus vaccine – M.M. Landini – British Journal of Dermatology

Use of 16S rRNA sequencing and quantitative PCR to correlate venous leg ulcer bacterial bioburden dynamics with wound expansion, antibiotic therapy, and healing – Daniel D. Sprockett – Wound Repair and Regeneration

Human gut microbiome

Editorial: Go with your gut: microbiota meet microglia – Kira Irving Mosher – Nature Neuroscience

Review: Metabolism of Chinese Materia Medica in Gut Microbiota and Its Biological Effects – Yan Wang – Chinese Herbal Medicines

Animal models of microbiome research

The role of beneficial bacteria wall elasticity in regulating innate immune response – Viktoria V. Мokrozub – The EPMA Journal

Exposure to soil, house dust and decaying plants increases gut microbial diversity and decreases serum immunoglobulin E levels in BALB/c mice – Dongrui Zhou – Environmental Microbiology

Animal microbiome

The gill microbiota of invasive and indigenous Spondylus oysters from the Mediterranean Sea and northern Red Sea – Yahala Rina Roterman – Environmental Microbiology Reports

Plant, root, and soil microbiome

Exercising influence: distinct biotic interactions shape root microbiomes – Sarah Stuart Sloan, Sarah L Lebeis – Current Opinion in Plant Biology

Oasis Desert Farming Selects Environment-Specific Date Palm Root Endophytic Communities and Cultivable Bacteria that Promote Resistance to Drought – Hanene Cherif – Environmental Microbiology Reports

Comprehensive sampling of an isolated dune system demonstrates clear patterns in soil fungal communities across a successional gradient – Alice Roy-Bolduc – Environmental Microbiology Reports

Metagenomic analyses reveal no differences in genes involved in cellulose degradation under different tillage treatments – Maria de Vries – FEMS Microbiology Ecology

Water microbiome

Viral activities and life-cycles in deep subseafloor sediment – Tim Engelhardt – Environmental Microbiology Reports

Waterborne Viruses: A Barrier to Safe Drinking Water – Aimee M. Gall – PLOS Pathogens

Bacterial biogeography in the coastal waters of northern Zhejiang, East China Sea is highly controlled by spatially structured environmental gradients – Kai Wang – Environmental Microbiology

Distribution patterns of bacterioplankton in the oligotrophic south-eastern Mediterranean Sea – Sabine Keuter – FEMS Microbiology Ecology

Mathematical Model of Dynamic Behavior of Microbial Desalination Cells for Simultaneous Wastewater Treatment and Water Desalination – Qingyun Ping – Environmental Science & Technology

Extremophile microbiome

Review: The changing form of Antarctic biodiversity – Steven L. Chown – Nature

Painting microbiome

Amid the possible causes of a very famous foxing: molecular and microscopic insight into Leonardo da Vinci’s self-portrait – Guadalupe Piñar – Environmental Microbiology Reports

Food microbiology

Empirical Model based on Weibull Distribution describing the Destruction Kinetics of Natural Microbiota in Pineapple (Ananas comosus L.) Puree during High-Pressure Processing – Snehasis Chakraborty – International Journal of Food Microbiology

Metabolic networks

Metabolic network modeling of microbial communities – Matthew B. Biggs – Wiley Interdisciplinary Reviews: Systems Biology and Medicine

Microbes in the news

Metropolitan Metagenomics: Mapping the Urban Genome – Catherine Potenski – BioMedCentral Blog

The Problem With David Perlmutter, the Grain Brain Doctor – Alan Levinovitz – NY Magazine

Oregon State University researcher Kathy Magnusson probes the rodent gut – Diane Dietz – Register Guard

Breast Milk Studies May Lead to Better Probiotics, Baby Formula – Tia Ghose – Live Science

Volunteers sweat for science at NC Museum of Natural Sciences – Rose Rimler – News Observer

Fermented Foods Including Yogurt And Sauerkraut May Help Calm Social Anxiety – John McQuaid – Forbes

You May Be on a Paleo Diet, but Is Your Microbiome? How a meat–centric diet can starve your gut bacteria – Erica Sonnenburg – Psychology Today

Team Effort – XKCD comics

Raise a glass to the Black Death: The ravages of the plague led directly to the creation of the pub, historian claims – Hannah Furness – The Telegraph

Should you eat your baby’s placenta? – Laura Sanders – Science News

Science, publishing, and career

Self-correction in science at work: protecting the integrity of science – Bruce Alberts – Science

Introducing “Research Matters” – Grant McFadden – PLOS Pathogens

Practical policies can combat gender inequality – Douglas Hilton – Nature

Bik’s Picks

Crossbreeding Could Help Coral Survive Warming Waters – Sindya N. Bhanoo – New York Times

Home-brewed heroin is near after scientists nail down poppy morphine gene – Rachel Feltman – Washington Post

New rapid diagnostic test detects Ebola virus in minutes – IBN Live

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June 16, 2015

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Human oral microbiome

The cultivable microbiota of primary and secondary infected root canals, their susceptibility to antibiotics and association with the signs and symptoms of infection – M. E. Łysakowska – International Endodontic Journal

DGGE: Profiling of Oral and Nasal Microbiome in Children With Cleft Palate – Min Zhang – The Cleft Palate–Craniofacial Journal

Human gut microbiome

Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates – Doris Vandeputte – Gut

Bacterial Composition of the Human Upper Gastrointestinal Tract Microbiome Is Dynamic and Associated with Genomic Instability in a Barrett’s Esophagus Cohort – Alevtina Gall – PLOS ONE

Alterations in Intestinal Microbiota Correlate with Susceptibility to Type 1 Diabetes – Aimon K. Alkanani – Diabetes

Specific gut microbiota features and metabolic markers in postmenopausal women with obesity – LK Brahe – Nutrition & Diabetes

Inter- and intra-individual variations in seasonal and daily stabilities of the human gut microbiota in Japanese – Takayoshi Hisada – Archives of Microbiology

Editorial: Gut bacteria feed a healthy brain – Denise Waldron – Nature Reviews Microbiology

Review: The gut microbiota of nonalcoholic fatty liver disease: current methods and their interpretation – Niels van Best – Hepatology International

Review: Can we change our microbiome to prevent colorectal cancer development? – Roberta M. Manzat-Saplacan – Acta Oncologica

Human genital microbiome

Penile Microbiota and Female Partner Bacterial Vaginosis in Rakai, Uganda – Cindy M. Liu – mBio

Models of microbiome

In pigs: Neonatal environment exerts a sustained influence on the development of the intestinal microbiota and metabolic phenotype – Claire A Merrifield – ISME Journal

In goats: Postnatal bacterial succession and functional establishment of hindgut in supplemental feeding and grazing goats – J. Z. Jiao – Journal of Animal Science

In termites: Multiple analyses of microbial communities applied to the gut of the wood-feeding termite Reticulitermes flavipes fed on artificial diets – Cédric Tarayre – Symbiosis

Animal microbiome

Sponges: Pyrosequencing revealed shifts of prokaryotic communities between healthy and disease-like tissues of the Red Sea sponge Crella cyathophora – Zhao-Ming Gao – PeerJ

Sponges: Microbial diversity and putative diazotrophy in high and low microbial abundance Mediterranean sponges – Marta Ribes – Applied and Environmental Microbiology

Plant root and soil microbiome

Tree genotype mediates covariance among communities from microbes to lichens and arthropods – Louis J. Lamit – Journal of Ecology

Assessment of microbial communities in mung bean (Vigna radiata) rhizosphere upon exposure to phytotoxic levels of Copper – Murali Sharaff – Journal of Basic Microbiology

Analyzing the antagonistic potential of the lichen microbiome against pathogens by bridging metagenomic with culture studies – Tomislav Cernava – Frontiers in Microbiology

Response of rhizosphere microbial community structure and diversity to heavy metal co-pollution in arable soil – Linjing Deng – Applied Microbiology and Biotechnology

Soil Microbial Functions After Forest Fires Affected by the Compost Quality – René Guénon – Land Degradation & Development

Vertical Distribution of Soil Denitrifying Communities in a Wet Sclerophyll Forest under Long-Term Repeated Burning – Xian Liu – Microbial Ecology

Metagenome Sequencing Reveals Rhodococcus Dominance in Farpuk Cave, Mizoram, India, an Eastern Himalayan Biodiversity Hot Spot Region – Surajit De Mandal – Genome Announcements

The stability of textile azo dyes in soil and their impact on microbial phospholipid fatty acid profiles – Muhammad Imran – Ecotoxicology and Environmental Safety

Endophyte community composition is associated with dieback occurrence in an invasive tree – Tracey V. Steinrucken – Plant and Soil

Multi-Analytical Approach Reveals Potential Microbial Indicators in Soil for Sugarcane Model Systems – Acacio Aparecido Navarrete – PLOS ONE

Resilience of soil microbial and nematode communities after biofumigant treatment with defatted seed meals – S. Mocali – Industrial Crops and Products

Effect of cassava mill effluent on biological activity of soil microbial community – Etinosa O. Igbinosa – Environmental Monitoring and Assessment

Editorial: An interkingdom partnership – Naomi Attar – Nature Reviews Microbiology

Review: Synergisms between microbial pathogens in plant disease complexes: a growing trend – Jay Ram Lamichhane – Frontiers in Plant Science

Review: Plant Virus Metagenomics: Advances in Virus Discovery – Marilyn J. Roossinck – Phytopathology

Water microbiome

Microbial ecology in a future climate: effects of temperature and moisture on microbial communities of two boreal fens – Krista Peltoniemi – FEMS Microbiology Ecology

A Multi Size-Level Assessment of Benthic Marine Communities in a Coastal Environment: Are They Different Sides of the Same Coin? – Claudia Vannini – PLOS ONE

Manganese-Cycling Microbial Communities Inside Deep-Sea Manganese Nodules – Marco Blöthe – Environmental Science & Technology

Editorial: Deep sequencing of the global oceans – Cláudio Nunes-Alves – Nature Reviews Microbiology

Extremophile microbiome

Microbial diversity of hypersaline environments: a metagenomic approach – Antonio Ventosa – Current Opinion in Microbiology

Application of a Bayesian nonparametric model to derive toxicity estimates based on the response of Antarctic microbial communities to fuel-contaminated soil – Julyan Arbel – Ecology and Evolution

Bioreactor microbiome

Evaluation of surfactants on waste activated sludge fermentation by pyrosequencing analysis – Aijuan Zhou – Bioresource Technology

Impact of the contemporary environment on denitrifying bacterial communities – Sarah K. Hathaway – Ecological Engineering

Food microbiology

Review: Wine microbiome, a dynamic world of microbial interactions – Youzhong Liu

Metagenomics and bioinformatics

Unusual biology across a group comprising more than 15% of domain Bacteria – Christopher T. Brown – Nature

Complete Genome Sequence of the Bacterium Aalborg_AAW-1, Representing a Novel Family within the Candidate Phylum SR1 – Morten Simonsen Dueholm – Genome Announcements

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs – Felipe A. Simão – Bioinformatics

Educating Future Nursing Scientists: Recommendations for Integrating Omics Content in PhD Programs – Yvette P. Conley – Nursing Outlook

Minireview: Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: Towards a systems-level understanding of human microbiomes – Bikel Shirley – Computational and Structural Biotechnology Journal

Metabolomics and Proteomics

In dogs: Consumption of Cooked Navy Bean Powders Modulate the Canine Fecal and Urine Metabolome – M. Forster – Current Metabolomics

Needles in the Blue Sea: Sub-Species Specificity in Targeted Protein Biomarker Analyses Within the Vast Oceanic Microbial Metaproteome – Mak A. Saito – Proteomics

New aminopeptidase from “microbial dark matter” archaeon – Karolina Michalska – The FASEB Journal

Review: Recent Advances in Metabolomics – E. Smith – Current Metabolomics

Microbial Ecology

Transplantability of a circadian clock to a noncircadian organism – Anna H. Chen – Science Advances

Review: Black Queen evolution: the role of leakiness in structuring microbial communities – J. Jeffrey Morris – Trends in Genetics

Techniques

Preferential Amplification of Pathogenic Sequences – Fang Ge – Scientific Reports

Phasing of single DNA molecules by massively parallel barcoding – Erik Borgström – Nature Communications

Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of
SAR11 bacterioplankton – Amy Apprill – Aquatic Microbial Ecology

Microbes in the news

Newfound groups of bacteria are mixing up the tree of life – Robert Sanders – UC Berkeley

Report: Santa Cruz’s river bacteria comes from birds, not people – Samantha Clark – San Jose Mercury News

Shark Tank Product Improves Oral Health, Measuring Levels Of Bacteria That Cause Bad Breath – Samantha Olson – Medical Daily

Manatee County, not the animal: Bacteria Could Clean Manatee Water Supply – Associated Press

Bacteria Could Help Clean Groundwater Contaminated by Uranium Ore Processing, Rutgers Study Finds – Rutgers Today

BacteriaHysteria

How much bacteria is on money in your pocket? – Click2Houston

WHO: 200 disease-causing bacteria may be found in the kitchen – ABC/CBN news

Science, publishing, and career

Science forum: RIPOSTE: a framework for improving the design and analysis of laboratory-based research – Nicholas GD Masca – eLIFE

Dancers in the Dark: Scientific Careers According to a Gender-Blind Model of Promotion –
Ana M. González Ramos – Interdisciplinary Science Reviews

Incidence of Data Duplications in a Randomly Selected Pool of Life Science Publications – Morten P. Oksvold – Science and Engineering Ethics

Five things I learned when my research went viral – Heidi Appel – The Conversation

Bik’s Picks

Foie Gras: The goose genome sequence leads to insights into the evolution of waterfowl and susceptibility to fatty liver – Lizhi Lu – Genome Biology

An estimate of the number of tropical tree species – JW Ferry Slik – PNAS

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June 12, 2015

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Effects of drinking donkey milk, archaea and fungi on humans,  microbiomes of olives, spoilt wine, cold deserts, indoor air, strawberry soil, and more.

General microbiome

Review: Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: Towards a systems-level understanding of human microbiomes – Bikel Shirley – Computational and Structural Biotechnology Journal

Review: Mycobiota: Micro-Eukaryotes Inhabiting Our Body as Commensals or
Opportunistic Pathogens – Lisa Rizzetto – Fungal Genomics & Biology

Review: Archaea in and on the Human Body: Health Implications and Future Directions – Mor N. Lurie-Weinberger, Uri Gophna – PLOS Pathogens

Human skin microbiome

Antimicrobial Efficacy of Preservatives used in Skin Care Products on Skin Micro Biota – Chintha Lalitha – International Journal of Science and Research

Review: Beneficial and deleterious bacterial–host interactions in chronic wound pathophysiology – C. Watters – Chronic Wound Care Management and Research

Human gut microbiome

Influence of Proton-Pump Inhibitors on the Luminal Microbiota in the Gastrointestinal Tract – Ayumi Tsuda – Clinical and Translational Gastroenterology

Microbiome models

A host-microbiome interaction mediates the opposing effects of omega-6 and omega-3 fatty acids on metabolic endotoxemia – Kanakaraju Kaliannan – Scientific Reports

In rats: Human, donkey and cow milk differently affects energy efficiency and inflammatory state by modulating mitochondrial function and gut microbiota – Giovanna Trinchese – The Journal of Nutritional Biochemistry

Fish: A multiple endpoint analysis of the effects of chronic exposure to sediment contaminated with Deepwater Horizon oil on juvenile Southern flounder and their associated microbiomes – Nancy J. Brown-Peterson – Aquatic Toxicology

Hops β-acids and zinc bacitracin affect the performance and intestinal microbiota of broilers challenged with Eimeria acervulina and Eimeria tenella – C. Bortoluzzi – Animal Feed Science and Technology

Staphylococcus aureus nasal isolates: The effects of spatial structure, frequency dependence and resistance evolution on the dynamics of toxin-mediated microbial invasions – Ben Libberton – Evolutionary Applications

Animal microbiome

Biodiversity of the Symbiotic Bacteria Associated with Toxic Marine Dinoflagellate Alexandrium tamarense – Xiaoling Zhang – Journal of Biosciences and Medicines

Plant microbiome

Wild trees in the Amazon basin harbor a great diversity of beneficial endosymbiotic fungi: is this evidence of protective mutualism? – Romina Gazis – Fungal Ecology

A Legume Genetic Framework Controls Infection of Nodules by Symbiotic and Endophytic Bacteria – Rafal Zgadzaj – PLOS Genetics

Diversity and spatial distribution of endophytes community composition in noni (Morinda citrifolia L.) – Liu Yang – Journal of Hill Agriculture

Comparisons of microbial abundance and community among different plant species in constructed wetlands in summer – Jian Zhang – Ecological Engineering

Soil (and plant root) microbiome

Impact of cover crop in pre-plant of apple orchards: relationship between crop health, root inhabiting fungi and rhizospheric bacteria – Luisa M. Manici – Journal of Plant Science

Amplicon-based metagenomics identified candidate organisms in soils that caused yield decline in strawberry – Xiangming Xu – Horticulture Research

Positively Frequency-Dependent Interference Competition Maintains Diversity and Pervades a Natural Population of Cooperative Microbes – Olaya Rendueles – Current Biology

A predictive model for microbial counts on beaches where intertidal sand is the primary source – Zhixuan Feng – Marine Pollution Bulletin

Reintroduction of locally extinct vertebrates impacts arid soil fungal communities – Laurence J. Clarke – Molecular Ecology

A simple experimental set-up to disentangle the effects of altered temperature and moisture regimes on soil organisms – Eveline J. Krab – Methods in Ecology and Evolution

Water microbiome

Identifying homogeneity of multivariate dispersions among biofilm-dwelling microbial communities in colonization surveys for marine bioassessment – Guangjian Xu – Ecological Indicators

Bacterial diversity along a 2600 km river continuum – Domenico Savio – Environmental Microbiology

Minireview: Microbial players involved in the decline of filamentous and colonial cyanobacterial blooms with a focus on fungal parasitism – Mélanie Gerphagnon – Environmental Microbiology

Extremophile microbiome

Bacterial diversity of Drass, cold desert in Western Himalaya, and its comparison with Antarctic and Arctic – Puja Gupta – Archives of Microbiology

Built environment microbiome

Indoor air bacterial communities in Hong Kong households assemble independently of occupant skin microbiomes – David Wilkins – Environmental Microbiology

Food microbiology

Potential spoilage yeasts in winery environments: Characterization and proteomic analysis of Trigonopsis cantarellii – Cauré Portugal – International Journal of Food Microbiology

Microbiota and Metabolome of Un-started and Started Greek-type Fermentation of Bella di Cerignola Table Olives – Maria De Angelis – Food Microbiology

Functional foods

Probiotic BIFICO cocktail ameliorates Helicobacter pylori induced gastritis – Hong-Jing Yu – World Journal of Gastroenterology

Review: Prebiotics, gut microbiota and metabolic risks: Unveiling the relationship – Adeela Yasmin – Journal of Functional Foods

Review: Current evidence on the use of probiotics in liver diseases – Norberto C. Chávez-Tapia – Journal of Functional Foods

Metagenomics 

Review: Methylotrophs in natural habitats: current insights through metagenomics – Ludmila Chistoserdova – Applied Microbiology and Biotechnology

Metabolomics

Editorial: Microbial metabolite triggers antimicrobial defense – Sky W. Brubaker, Denise M. Monack – Science

Microbes in the news

Soil microbial community variation correlates most strongly with plant species identity – AOB blog

Pew Names 22 Top Scientists as Scholars in the Biomedical Sciences: topics range from microbiome, to mosquito’s preferences – Pew Trusts
and: Microbiology professor becomes UC Merced’s first Pew scholar: Clarissa Nobile receives award for biofilm research – UC Merced

2015 ISCB Overton Prize Awarded to Curtis Huttenhower – Christiana N. Fogg, Diane E. Kovats – PLOS Computational Biology

“Genes in Space” Student Finalists Announced: Tarun Srinivasan, of Houston, TX, plans to examine effects on the gut microbiome of spending time on the ISS – Ricki Lewis – PLOS Blogs

Method reveals what bacteria sense in their surroundings – Leila Gray – UW Health Sciences NewsBeat

“ticks had a microbiome rich in pathogens, including Bartonella”: Ticks’ Migration Linked to Changes in Disease Prevalence – Jacquelyn Gray – HCP Live

Like “kopi luwak” coffee, just bigger: Elephant poop coffee, Thailand’s new delicacy – Doug Powell – BarfBlog

New Tool To Monitor Harmful Bacteria: Scientists offer more accurate health risk prediction model to better inform beach closure decisions – Rosenstiel School of Marine & Atmospheric Science

#EULAR2015: First gut microbiota alterations described in systemic sclerosis patients – Karen Blum – PM360online

Some good information here about bacteria in our gut: Six myths about digestion that just won’t die – ITClips

How does Swiss cheese gets its holes?: by carbon-dioxide-burping microbe Propionibacterium freudenreichii – Nicola Twilly – New Yorker

Product candidate to target specific elimination of Streptococcus mutans may alter oral microbiome to provide long-lasting benefits – Dentistry iQ

Fungus among us, but what kind? Typing error spawns retraction for mushroom paper – Retraction Watch

Science, publishing, and career

Business decisions: stories about the entrepreneurial learning curve – Jeffrey Mervis – Science

Bik’s Picks

Polar bear caught eating dolphins and freezing the leftovers – Penny Sarchet – New Scientist

There’s A Link Between Cat Ownership And Schizophrenia – Leigh Weingus – Huffington Post

“Advice to interns: work hard and make your mark.” New planet discovered by 15-year-old intern – Monica Sarkar – CNN

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