Category Archives: Human respiratory

July 29, 2015

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Pack hunting by soil amoeba, microbiota of meconium and uterus, transcriptomics of oral phages, no differences in antibiotic resistance gene content in organic or regular pigs, and effects of IBD associated microbes on mouse physiology.

General microbiome

Editorial: News Feature: Microbes on the mind – Helen H. Shen – PNAS

Microbiome of pregnancy and birth

Note: just one sample was PCR positive: First-Pass Meconium Samples from Healthy Term Vaginally-Delivered Neonates: An Analysis of the Microbiota – Richard Hansen – PLOS ONE

Understanding the Biologic Therapies of Probiotics, Prebiotics, and Synbiotics: Exploring Current Evidence for Use in Premature Infants for the Prevention of Necrotizing Enterocolitis – Asmerom, Mussie – Journal of Perinatal & Neonatal Nursing

Human oral microbiome

Transcriptome analysis of bacteriophage communities in periodontal health and disease – Tasha M. Santiago-Rodriguez – BMC Genomics

Human respiratory microbiome

Paired analysis of the microbiota of surface mucus and whole-tissue specimens in patients with chronic rhinosinusitis – Raymond J.T. Kim – International Forum of Allergy & Rhinology

Human genital microbiome

Characterisation of the human uterine microbiome in non-pregnant women through deep sequencing of the 16S rRNA gene – Hans Verstaelen – PeerJ

Human skin microbiome

Review: Regulation of T cell immunity in atopic dermatitis by microbes: the Yin and Yang of cutaneous inflammation – Tilo Biedermann – Frontiers in Immunology

Human gut microbiome

Ruminococcal cellulosomes: molecular Lego to deconstruct microcrystalline cellulose in human gut – Gurvan Michel – Environmental Microbiology

Influence of galacto-oligosaccharide mixture (B-GOS) on gut microbiota, immune parameters and metabonomics in elderly persons – Jelena Vulevic – British Journal of Nutrition

Review: Microbiome influences on allergy in mice and humans – Benjamin J Marsland – Current Opinion in Immunology

Editorial: Gut microbiota: Microbiota and neuroimmune signalling—Metchnikoff to microglia – John F. Cryan & Timothy G. Dinan

Review: A Survey on the Developmental Intestinal Microbiota Research in China: the history, funding, and frontiers of gut bacteria – Hui Min Chen – Journal of Digestive Diseases

Editorial: Stool microbiome changes in VEGF-TKI-induced diarrhoea – Nature Reviews Urology

Models of microbiome research

Microorganisms linked to inflammatory bowel disease-associated dysbiosis differentially impact host physiology in gnotobiotic mice – Thomas W Hoffmann – ISME Journal

The Role of Curcumin in Modulating Colonic Microbiota During Colitis and Colon Cancer Prevention – Rita-Marie McFadden – Inflammatory Bowel Diseases

Intestinal microbiota of mice influences resistance to Staphylococcus aureus pneumonia –
Stefanie Gauguet – Infection and Immunity

Oral Administration of P. gingivalis Induces Dysbiosis of Gut Microbiota and Impaired Barrier Function Leading to Dissemination of Enterobacteria to the Liver – Mayuka Nakajima – PLOS ONE

Fecal microbiota transplantation and bacterial consortium transplantation have comparable effects on the re-establishment of mucosal barrier function in mice with intestinal dysbiosis – Ming Li – Frontiers in Microbiology

Symbiotic maple saps minimize disruption of the mice intestinal microbiota after oral antibiotic administration – Riadh Hammami – International Journal of Food Sciences and Nutrition

Animal microbiome

Characterization of Antibiotic Resistance Gene Abundance and Microbiota Composition in Feces of Organic and Conventional Pigs from Four EU Countries – Lenka Gerzova – PLOS ONE

Symbiotic bacteria enable olive fly larvae to overcome host defences – Michael Ben-Yosef – Royal Society Open Science

Plant, root, and soil microbiome

Not sure where to file this one under, but pretty cool: Pack hunting by a common soil amoeba on nematodes – Stefan Geisen – Environmental Microbiology

Anaerobic degradation pathway of the novel chiral insecticide Paichongding and its impact on bacterial communities in soils – Zhiqiang Cai – Journal of Agricultural and Food Chemistry

Metagenomics and bioinformatics

Exploiting topic modeling to boost metagenomic reads binning – Ruichang Zhang – BMC Bioinformatics

Metabolomics and Proteomics

Effects of Dietary Different Doses of Copper and High Fructose Feeding on Rat Fecal Metabolome – Xiaoli Wei – Journal of Proteome Research

Science, publishing, and career

Let’s Make Gender Diversity in Data Science a Priority Right from the Start – Francine D. Berman – PLOS Biology

Microbes in the news

What are ‘eye crusties’ made of? uBiome asking for participants to use their eye kit

Bacteria Hysteria

Germaphobes look away! Your gym bag might contain high levels of bacteria usually found in faeces – Irish Examiner

Bik’s Picks

A Skeleton, a Catholic Relic, and a Mystery About American Origins – Adrienne Lafrance – The Atlantic

The confounding case of the missing carbon – Michael Casey – CBS News

Washington Is Finally Getting What It Deserves As It Sinks Into The Sea – Kate Sheppard – Huffington Post

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July 28, 2015

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A review of the human hand microbiome, microbiome and anxiety in mouse models, diabetes, bacteria in thrombolites, how plants recruits microbial symbionts, towards a standard in microbial genome annotation, and an article about the lab of Jill Banfield.

Microbiome of pregnancy and birth

Prevalence of oral Candida in the first year of life – C. Stecksén-Blicks – Mycoses

Cross-colonization of infants with probiotic organisms in a neonatal unit – L. Hickey – Journal of Hospital Infection

Human oral microbiome

Periodontal microbiota and phospholipases: The Oral Infections and Vascular Disease Epidemiology Study (INVEST) – Adrien Boillot – Atherosclerosis

Review: Alterations of the oral microbiota and oral clinical findings in dry mouth – Y. Hayashi – Journal of Oral Biosciences

Human skin and eye microbiome

Review of Human Hand Microbiome Research – Sarah L. Edmonds-Wilson – Journal of Dermatological Research

Correspondence: Harnessing the microbiome in glaucoma and uveitis – Ankur Gupta – Medical Hypotheses

Human respiratory microbiome

High diversity of non-sporulating moulds in respiratory specimens of immunocompromised patients: should all the species be reported when diagnosing invasive aspergillosis? – Dea Garcia-Hermoso – Mycoses

 

Human gut microbiome

The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment – Xuan Zhang – Nature Medicine

A tough pill to swallow (perspective): Ready for Oral Fecal Microbiota Pill in Clinical Practice? – Timothy Nguyen – The Journal for Nurse Practitioners

Review: The human gut microbiota and virome: potential therapeutic implications – Emidio Scarpellini – Digestive and Liver Disease

Review: Intestinal Immunity and Gut Microbiota as Therapeutic Targets for Preventing Atherosclerotic Cardiovascular Diseases – Tomoya Yamashita – Circulation Journal

Microbiome models

Microbiota and host determinants of behavioural phenotype in maternally separated mice – G. De Palma – Nature Communications

Microbiota regulates type 1 diabetes – Michael P Burrows – PNAS

Gut microbiota facilitates dietary heme-induced epithelial hyperproliferation by opening the mucus barrier in colon – Noortje Ijssennagger – PNAS

Intestinal inhibition of Atg7 prevents tumour initiation through a microbiome-influenced immune response and suppresses tumour growth – Jonathan Lévy – Nature Cell Biology

Lactulose increases bacterial diversity and modulates the swine faecal microbiome as revealed by 454-pyrosequencing – Jong Pyo Chae – Animal Feed Science and Technology

Dynamic Metabonomic and Microbiological Response of Rats to Lincomycin Exposure: An Integrated Microbiology and Metabonomics Analysis – Manna Lin – RSC Advances

Green propolis modulates gut microbiota, reduces endotoxemia and expression of TLR4 pathway in mice fed a high-fat diet – Aline Rissetti Roquetto – Food Research International

Changes in the Swine Gut Microbiota in Response to Porcine Epidemic Diarrhea Infection – Hyeon-Woo Koh – Microbes and Environments

Review: Interrelatedness Between Dysbiosis in the Gut Microbiota Due to Immunodeficiency and Disease Penetrance of Colitis – Avijit Ray – Immunology

Animal microbiome

Experimental studies of microbial populations and incidence of zoonotic pathogens in the faeces of red deer (Cervus elaphus) – Sebastian Gnat – Letters in Applied Microbiology

Yeast microbiota of natural cavities of manatees (Trichechus inunguis and T. manatus) in Brazil and its relevance for animal health and management in captivity – José J.C. Sidrim – Canadian Journal of Microbiology

An Efficient Strategy Developed for Next-Generation Sequencing of Endosymbiont Genomes Performed Using Crude DNA Isolated from Host Tissues: A Case Study of Blattabacterium cuenoti Inhabiting the Fat Bodies of Cockroaches – Yukihiro Kinjo – Microbes and Environments

Prokaryotic microbiota in the digestive cavity of the jellyfish Cotylorhiza tuberculata – Sara Cortés-Lara – Systematic and Applied Microbiology

Plant, root, and soil microbiome

Inner workings of thrombolites: spatial gradients of metabolic activity as revealed by metatranscriptome profiling – J. M. Mobberley – Scientific Reports

Changes in fungal community of Scots pine (Pinus sylvestris) needles along a latitudinal gradient in Sweden – Hanna Millberg – Fungal Ecology

Temporal dynamics of plant-soil feedback and root-associated fungal communities over 100 years of invasion by a non-native plant – Nicola J. Day – Journal of Ecology

Fungal colonization of the rooting system of the early land plant Asteroxylon mackiei from the 407-Myr-old Rhynie Chert (Scotland, UK) – Christine Strullu-Derrien – Botanical Journal of the Linnean Society

Alder trees enhance crop productivity and soil microbial biomass in tea plantations – P.E. Mortimer – Applied Soil Ecology

Perspective: Plant genotype, microbial recruitment and nutritional security – Jai S. Patel – Frontiers in Plant Science

I don’t always have symbionts, but when I do, I prefer alphaproteobacteria: Endemic Mimosa species from Mexico prefer alphaproteobacterial rhizobial symbionts – Cyril Bontemps – New Phytologist

Conference abstract: Changes in rhizosphere microbiome from halotolerant tomato are correlated with physiological and biochemical parameters of oxidative stress in plants – Radu Liviu Sumalan – Journal of Biotechnology

Review: Root associated bacteria – Friends or enemies? A review – Gabriela Mihalache – Memoirs of the Scientific Sections of the Romanian Academy

Analysing the effect of soil organic matter on bacterial communities using T-RFLP fingerprinting: different methods, different stories? – A. Blaud – Biology and Fertility of Soils

Water microbiome

Phospholipids fatty acids of drinking water reservoir sedimentary microbial community: Structure and function responses to hydrostatic pressure and other physico-chemical properties – Bei-bei Chai – Journal of Environmental Biology

Extremophiles

Review: Microbial communities and primary succession in high altitude mountain environments – Sonia Ciccazzo – Annals of Microbiology

Metagenomics and bioinformatics

FastQFS – A tool for evaluating and filtering paired-end sequencing data generated from high throughput sequencing – Rahul Sharma – Mycological Progress

Toward a standard in structural genome annotation for prokaryotes – H. James Tripp – Standards in Genomic Sciences

Development of Novel Random Network Theory-Based Approaches to Identify Network Interactions among Nitrifying Bacteria – Cindy Shi – SciTech Connect

Microbial Ecology

Socially mediated induction and suppression of antibiosis during bacterial coexistence
Monica I. Abrudan – PNAS

Microbes in the news

About work in the lab of Jill Banfield: At Tiny Scales, a Giant Burst on Tree of Life – Kevin Hartnett – Quanta Magazine

Swan song for antibiotics? Can phage therapy and gene editing fill the gap? – Nicholas Staropoli – Genetic Literacy Project

Metagenomic Study Finds Differences in Oral, Gut Microbiomes of Rheumatoid Arthritis Patients – Genome Web

Your Burger Is Full of Living Things, Even If It’s Vegetarian – Maddie Stone – Gizmodo

Title incorrect, it’s a Yersinia, but different species: A Species Of Bacteria That Causes Bubonic Plague And Other Disease In Salmon May Also Be Able To Treat Cancer – Lecia Bushak – Medical Daily

Bacteria in gut profiling secret to healthy weight – Peta Bee – The Australian

Bacteria to protect Appenzeller cheese from fakes – Anand Chandrasekhar – SwissInfo

Grandparents largely to blame for China’s spiking childhood obesity, Microbiota treatment sees dramatic results in obese children – RJ Whitehead – FoodNavigator

Bik’s Picks

Reception of odors and repellents in mosquitoes – Anandasankar Ray – Current Opinion in Neurobiology

570 Sea Turtle Hatchlings Are Released Into Atlantic Ocean – Getty Images

Everything you need to know about lactose intolerance – with maps! – New Scientist

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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 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 13, 2015

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Trans-sialidases in human gut microbes, microbiome of the dairy cow’s uterus during metritis, and bacteria getting smaller because of ocean warming.

Jobs

Post-doctoral position is available in the laboratory of Lawrence David at Duke University: to help develop high-throughput microfluidic techniques for investigating bacterial interactions and ecology.

Conferences

Microbiome, Antibiotics and Human Disease, with Michael Fishbach, Martin Blaser, and Julie Segre – Cell Press Webinar July 28, 2015

11 speakers, only 1 woman: Meeting the Microbiome – 12 September 2015 – London, UK – CAM conferences

Microbiome of pregnancy and birth

High rates of Double-Stranded RNA Viruses and Mycoplasma hominis in Trichomonas vaginalis Clinical Isolates in South Brazil – Débora da Luz Becker – Infection, Genetics and Evolution

First Trimester Levels of BV-Associated Bacteria and Risk of Miscarriage Among Women Early in Pregnancy – Deborah B. Nelson – Maternal and Child Health Journal

Human oral microbiome

The impact of smoking and previous periodontal disease on peri-implant microbiota and health: a retrospective study up to 7-year follow-up – Quaranta A. – Annali Di Stomatologia

Human respiratory microbiome

Review: The Etiology and Pathogenesis of Chronic Rhinosinusitis: a Review of Current Hypotheses – Kent Lam – Current Allergy and Asthma Reports

Human gut microbiome

Discovery of intramolecular trans-sialidases in human gut microbiota suggests novel mechanisms of mucosal adaptation – Louise E. Tailford – Nature Communications

Viewpoint: Helicobacter pylori: enemy, commensal or, sometimes, friend? –  Michael B Whalen – The Journal of Infection in Developing Countries

Review: Engineering the Microbiome: a Novel Approach to Immunotherapy for Allergic and Immune Diseases – Nan Shen – Current Allergy and Asthma Reports

Review: Antimicrobial Use, Human Gut Microbiota and Clostridium difficile Colonization and Infection – Caroline Vincent – Antibiotics

Animal models

The microbiota regulates type 2 immunity through RORγt+ T cells – Caspar Ohnmacht – Science

Animal microbiome

Uterine microbiota progression from calving until establishment of metritis in dairy cows – Soo Jin Jeon – Applied and Environmental Microbiology

Preening as a Vehicle for Key Bacteria in Hoopoes – Ángela Martínez-García – Microbial Ecology

Variation in the Microbiota of Ixodes ticks with geography, species and sex – Will Van Treuren – Applied and Environmental Microbiology

The Host as Driver of the Microbiota in the Gut and External Environment of Drosophila melanogaster – Adam C-N Wong – Applied and Environmental Microbiology

An Efficient Strategy Developed for Next-Generation Sequencing of Endosymbiont Genomes Performed Using Crude DNA Isolated from Host Tissues: A Case Study of Blattabacterium cuenoti Inhabiting the Fat Bodies of Cockroaches – Yukihiro Kinjo – Microbes and Environments

Arsenophonus and Sodalis symbionts in louse flies: an analogy to the Wigglesworthia and Sodalis system in tsetse flies – Eva Nováková – Applied and Environmental Microbiology

Review: Microbial metagenomics in aquaculture: a potential tool for a deeper insight into the activity – Marcel Martínez-Porchas – Reviews in Aquaculture

Plant, root, and soil microbiome

High-Throughput Sequencing Reveals Drastic Changes in Fungal Communities in the Phyllosphere of Norway Spruce (Picea abies ) Following Invasion of the Spruce Bud Scale (Physokermes piceae ) – Audrius Menkis – Microbial Ecology

Diversity of endophytic and rhizoplane bacterial communities associated with exotic Spartina alterniflora and native mangrove using Illumina amplicon sequencing – Youwei Hong – Canadian Journal of Microbiology

Communities of Cultivable Root Mycobionts of the Seagrass Posidonia oceanica in the Northwest Mediterranean Sea Are Dominated by a Hitherto Undescribed Pleosporalean Dark Septate Endophyte – Martin Vohník – Microbial Ecology

Precipitation modifies the effects of warming and nitrogen addition on soil microbial communities in northern Chinese grasslands – Naili Zhang – Soil Biology and Biochemistry

Long-term responses of plant growth, soil microbial communities and soil enzyme activities to elevated CO2 and neighbouring plants – Baoli Duan – Agricultural and Forest Meteorology

Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils – Christopher R. Penton – Frontiers in Microbiology

Methanotrophic community abundance and composition in plateau soils with different plant species and plantation ways – Yu Dai – Applied Microbiology and Biotechnology

Water microbiome

More, smaller bacteria in response to ocean’s warming? – Xosé Anxelu G. Morán – Proceedings B

Microbial community changes along the active seepage site of one cold seep in the Red Sea – Huiluo Cao – Frontiers in Microbiology

Spatiotemporal dynamics and determinants of planktonic bacterial and microeukaryotic communities in a Chinese subtropical river – Yongming Wang – Applied Microbiology and Biotechnology

Sediment Ammonia-Oxidizing Microorganisms in Two Plateau Freshwater Lakes at Different Trophic States – Yuyin Yang – Microbial Ecology

Detecting nuisance species using NGST: Methodology shortcomings and possible application in ballast water monitoring – Anastasija Zaiko – Marine Environmental Research

A novel bacterial community index to assess stream ecological health – Kelvin E. M. Lau – Freshwater Biology

Bioreactor microbiome

Functional and taxonomic dynamics of an electricity-consuming methane-producing microbial community – Orianna Bretschger – Bioresource Technology

Microbial community distribution and genetic analysis in a sludge active treatment for a complex industrial wastewater: a study using microbiological and molecular analysis and principal component analysis – Giulio Moretti – Annals of Microbiology

Bioinformatics and metagenomics

A reproducible approach to high-throughput biological data acquisition and integration – Daniela Börnigen – PeerJ

MetaBoot: a machine learning framework of taxonomical biomarker discovery for different microbial communities based on metagenomic data – Xiaojun Wang – PeerJ

Good laboratory practice for clinical next-generation sequencing informatics pipelines –
Amy S Gargis – Nature Biotechnology

Transcriptomics, proteomics, and metabolomics

Mining microbial metatranscriptomes for expression of antibiotic resistance genes under natural conditions – Dennis Versluis – Scientific Reports

Fractionation of biogas plant sludge material improves metaproteomic characterization to investigate metabolic activity of microbial communities – Fabian Kohrs – Proteomics

Combining Mass Spectrometric Metabolic Profiling with Genomic Analysis: A Powerful Approach for Discovering Natural Products from Cyanobacteria – Karin Kleigrewe – Journal of Natural Products

Microbial Ecology

Phylogenetic diversity analyses reveal disparity between fungal and bacterial communities during microbial primary succession – Shawn P. Brown – Soil Biology and Biochemistry

Editorial: Stopping superbugs, maintaining the microbiota – Victor Nizet – Science Translational Medicine

Biofilm Formation As a Response to Ecological Competition – Nuno M. Oliveria – PLOS Biology

Pawnobiome: Manipulation of the Hologenome Within One Host Generation and Beyond – Jameson D. Voss – Frontiers in Microbiology

Functional foods

Review: Towards microbial fermentation metabolites as markers for health benefits of prebiotics – Kristin A. Verbeke – Nutrition Research Reviews

Techniques

Blocking primers reduce co-amplification of plant DNA when studying bacterial endophyte communities – Brett E. Arenz – Journal of Microbiological Methods

Microbes in the news

The role of the microbiota in preventing allergies – Medical Xpress

World’s largest steel company to use rabbit gut microbe to cut emissions – Emma Hartley – The Guardian

Paw Prints: Streptococcus bacteria a part of natural flora of cats and dogs – Niki Laviolette – Tribune Star

“I’m treating my son’s autism… with someone else’s faeces” – Liam Quinn – Daily Mail
This celebrity reckons autism can be treated with a poo transplant: is he right? – Clair Weaver – AWW

Navy Researchers Identify Bacteria in Human Serum – Christian Kotanen – Science DOD
surface enhanced Raman scattering (SERS) spectroscopy

Why you can’t just eat one french fry (or donut or slice of pizza) – Katherine Ellen Foley – SBS.com

Genetically Modified Bacteria Could Change Future Drug Treatments – Brandi – Clapway

Scientists at Brown University using federal grant to study mysterious fungus killing bats – The Sun Chronicle

Stop Kissing And Cuddling Chicken To Stop Salmonella Outbreak: CDC – Jill Arce – Tech Times

Bik’s Picks

New Horizons Science Update: Pluto Is The Biggest One Of All – Nadia Drake – National Geographic

Your last chance to see ‘Manhattanhenge’ sunset is tonight – Amanda Schallert – NJ.com

What’s in a name? For newborns, maybe fewer medical errors – Tara Haelle – MS News
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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 8, 2015

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Just a short post today. PLOS ONE has a paper about burn victims and gut microbiome, in which both humans as well as mice were studied, but I really disliked the mouse experiments, where mice were deliberately burned (by shaving them and dipping them in near-boiling water). As a scientist, I realize that animal experiments can be useful, but I very much dislike animal studies that involve deliberate burns, enormous tumors, and parabiosis. I hope that these types of experiments can soon be replaced by more animal-friendly versions.

In other news: a bacterium on satellite survived entry into the Earth’s atmosphere. How cool is that?

Human respiratory microbiome

Dysbiosis of upper respiratory tract microbiota in elderly pneumonia patients – Wouter A A de Steenhuijsen Piters – The ISME Journal

Human/animal model gut microbiome

I really dislike the mouse part of this paper: Burn Injury Alters the Intestinal Microbiome and Increases Gut Permeability and Bacterial Translocation – Zachary M. Earley – PLOS ONE

Animal microbiome

Diet shapes the gut microbiome of pigs during nursing and weaning – Steven A. Frese – Microbiome

Plant, root, and soil microbiome

Editorial: Symbiosis: Receptive to infection – Sharon R. Long – Nature

Receptor-mediated exopolysaccharide perception controls bacterial infection – Y. Kawaharada – Nature

Water microbiome

Genomics and Ecophysiology of Heterotrophic Nitrogen-Fixing Bacteria Isolated from Estuarine Surface Water – Mikkel Bentzon-Tilia – mBio

More microbiology

Eye-like ocelloids are built from different endosymbiotically acquired components –
Gregory S. Gavelis – Nature

Spore-Forming Thermophilic Bacterium within Artificial Meteorite Survives Entry into the Earth’s Atmosphere on FOTON-M4 Satellite Landing Module – Alexander Slobodkin – PLOS ONE

Microbes in the news

Justin and Erica Sonnenburg: The Gut Connection – The Insight

Together bacteria invade antibiotic landscapes – Phys.org

Now You Can Buy Shampoo and Cleanser That Promote the Growth of “Good” Bacteria – L.V. Anderson – Slate

Just How Gross Is It to Leave Your Toothbrush In The Bathroom? – Lindsay Colameo – Allure

Science, publishing, and career

Postdocs will be getting a raise – Justin Kiggins – The Spectroscope
and
Will Obama’s revamp of the overtime rules mean postdocs are paid more? – Drugmonkey

Bik’s Picks

Shark selfies: Shark Files: Baited Cameras to Count World Sharks – Lori Cuthbert – Discovery

Scientists Discover a ‘Complex Cocktail of Many Chemicals’ in Snail Venom That Could Treat Cancer, Pain and Addiction – Liz Klimas – The Blaze

These Plastic Chemicals May Be Just As Dangerous As What They Replace – Justin Worland – Time

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July 7, 2015

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A personal perspective on microbiome research, phenotypic heterogeneity in microorganisms, ruling out viruses as causes for necrotizing enterocolitis, and Robert Edgar’s USEARCH.

Job openings

Philipps-Universität Marburg and the Max-Planck Institute for Terrestrial Microbiology are looking for 2 postdocs (one experimentalist and one bioinformatician)

General microbiome

Personal perspective: From cell biology to the microbiome: An intentional infinite loop – Wendy S. Garrett – Journal of Cell Biology

Microbiome of pregnancy and birth

Cytomegalovirus and other common enteric viruses are not commonly associated with Necrotizing Enterocolitis – Thomas Skeath – Acta Paediatrica

Viremia during pregnancy and risk of childhood leukemia and lymphomas in the offspring: Nested case-control study – Davit Bzhalava – International Journal of Cancer

Human oral microbiome

The Oral Bacterial Communities of Children with Well-Controlled HIV Infection and without HIV Infection – Brittany E. Goldberg – PLOS ONE

Human respiratory microbiome

Sputum Bacterial and Fungal Dynamics during Exacerbations of Severe COPD – Jin Su – PLOS ONE

Human gut microbiome

Chemotherapy-driven dysbiosis in the intestinal microbiome – E. Montassier – Alimentary Pharmacology & Therapeutics

Animal models of microbiome research

Perilipin-2 Modulates Lipid Absorption and Microbiome Responses in the Mouse Intestine – Daniel N. Frank – PLOS ONE

Animal microbiome

NGS metabarcoding proves successful for quantitative assessment of symbiont abundance: the case of feather mites on birds – J. Diaz-Real

Genetic Structure and Antimicrobial Resistance of Escherichia coli and Cryptic Clades in Birds with Diverse Human Associations – Michaela D. J. Blyton – Applied and Environmental Microbiology

Coral transplantation triggers shift in microbiome and promotion of coral disease associated potential pathogens – Jordan M. Casey – Scientific Reports

Plant, root, and soil microbiome

Metabarcoding Analysis of Fungal Diversity in the Phyllosphere and Carposphere of Olive (Olea europaea) – Ahmed Abdelfattah – PLOS ONE

High carbon use efficiency in soil microbial communities is related to balanced growth, not storage compound synthesis – Paul Dijkstra – Soil Biology and Biochemistry

Earthworms modify microbial community structure and accelerate maize stover decomposition during vermicomposting – Yuxiang Chen – Environmental Science and Pollution Research

Water microbiome

Microbial Communities Associated with Zones of Elevated Magnetic Susceptibility in Hydrocarbon-contaminated Sediments – Carol L. Beaver – Geomicrobiology Journal

Bacterial diversity differences along an epigenic cave stream reveal evidence of community dynamics, succession, and stability – Kathleen Brannen-Donnelly – Frontiers in Microbiology

Firmicutes is an Important Component of Microbial Communities in Water-Injected and Pristine Oil Reservoirs; Western Siberia, Russia – Yulia Frank – Geomicrobiology Journal

Functional interactions among filamentous Epsilonproteobacteria and Bacteroidetes in a deep-sea hydrothermal vent biofilm – Runar Stokke – Environmental Microbiology

Temporal Study of the Microbial Diversity of the North Arm of Great Salt Lake, Utah, U.S. – Swati Almeida-Dalmet – Microorganisms

Diversity of the Sediment Microbial Community in the Aha Watershed (Southwest China) in Response to Acid Mine Drainage Pollution Gradients – Weimin Sun – Applied and Environmental Microbiology

Microbial Transport, Retention, and Inactivation in Streams: A Combined Experimental and Stochastic Modeling Approach – Jennifer D. Drummond – Environmental Science & Technology

Extremophile microbiome

Ribosomal tag pyrosequencing of DNA and RNA reveals ‘rare’ taxa with high protein synthesis potential in the sediment of a hypersaline lake in Western Australia – Pascal Weigold – Geomicrobiology Journal

Microbial Diversity in Engineered Haloalkaline Environments Shaped by Shared Geochemical Drivers Observed in Natural Analogues – Talitha C. Santini – Applied and Environmental Microbiology

Built environment microbiome

A New Perspective on Microbiome and Resource Management in Wastewater Systems – Veera Gnaneswar Gude – Biotechnology & Biomaterials

Microbial Ecology

A functional perspective on phenotypic heterogeneity in microorganisms – Martin Ackermann – Nature Reviews Microbiology

Bioinformatics and statistics

USEARCH: Error filtering, pair assembly, and error correction for next-generation sequencing reads – Robert C. Edgar – Bioinformatics

Assessment and Selection of Competing Models for Zero-Inflated Microbiome Data – Lizhen Xu – PLOS ONE

Metabolomics and metatranscriptomics

Functional metabolomics: from biomarker discovery to metabolome reprogramming – Bo Peng – Protein & Cell

Stool metatranscriptomics: A technical guideline for mRNA stabilisation and isolation – Michael Reck – BMC Genomics

Hydrodynamic chronoamperometry for probing kinetics of anaerobic microbial metabolism – case study of Faecalibacterium prausnitzii – Antonin Prévoteau – Scientific Reports

Techniques

A flexible and economical barcoding approach for highly multiplexed amplicon sequencing of diverse target genes – Craig W. Herbold – Frontiers in Microbiology

This paper is not novel at all: An improved method for bacterial identification through 16S rDNA sequencing using double set of primers: a case study – Amanat Ali – Pak. J. Agri. Sci.,

Microbes in the news

How Bacteria Make This Underground, Awe-Inspiring Cave Shine Gold – Michele Lent Hirsch – Smithsonian

Bacteria in a bottle? AOBiome offers ways to stay clean without traditional soap – Nidhi Subbaraman – The Boston Globe

uBiome to Award Grant of up to $100k for Groundbreaking Microbiome Research – PR Web

Bik’s Picks

NASA Releases Time-Lapse Video Of Mars Rover Opportunity’s Journey: 11 Years In Just 8 Minutes – Jim Algar – Tech Times

Self-Driving ‘Robocabs’ Could Help Curb Global Warming – Wendy Koch – National Geographic

‘Vampires’ keep doctors in the dark for fear of stereotyping: study – Reuters

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July 6, 2015

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Oral microbiomes of dogs and their owners, airway mycobiome in CF patients, memory B cells and antibodies to gut microbiota, and yogurt containing seawater (?).

Human oral microbiome

Comparison of the Oral Microbiomes of Canines and Their Owners Using Next-Generation Sequencing – Changin Oh – PLOS ONE

Systemic immunity shapes the oral microbiome and susceptibility to bisphosphonate-associated osteonecrosis of the jaw – Shirin Kalyan – Journal of Translational Medicine

Review: Oral malodorous gases and oral microbiota: From halitosis to carcinogenesis – Naoko Tanda – Journal of Oral Biosciences

Human respiratory microbiome

A cohort study of the airway mycobiome in adult cystic fibrosis patients: differences in community structure of fungi compared to bacteria reveal predominance of transient fungal elements – Rolf Kramer – Journal of Clinical Microbiology

Review: The role of the local microbial ecosystem in respiratory health and disease – Wouter A. A. de Steenhuijsen Piters – Philosophical Transactions B

Review: The mechanism or mechanisms driving atopic asthma initiation: The infant respiratory microbiome moves to center stage – Patrick G. Holt – Journal of Allergy and Clinical Immunology

Human gut microbiome

Diversification of memory B cells drives the continuous adaptation of secretory antibodies to gut microbiota – Cornelia Lindner – Nature Immunology

Dietary modulation of the gut microbiota – a randomised controlled trial in obese postmenopausal women – Lena K. Brahe – British Journal of Nutrition

Anti-TNF treatment with adalimumab induces changes in the microbiota of Crohn’s disease – Busquets David – Journal of Crohn’s and Colitis

Effects of high doses of vitamin D3 on mucosa-associated gut microbiome vary between regions of the human gastrointestinal tract – Mina Bashir – European Journal of Nutrition

Review: Suppression of inflammation by helminths: a role for the gut microbiota? – Paul Giacomin – Philosophical Transactions B

Review: Immune-microbiota interactions in health and disease – Noah W. Palm – Clinical Immunology

Animal models

Lentinula edodes-derived polysaccharide rejuvenates mice in terms of immune responses and gut microbiota – Xiaofei Xu – Food and Function

Effect of Lactobacillus plantarum FH185 on the Reduction of Adipocyte Size and Gut Microbial Changes in Mice with Diet-induced Obesity – Sun-Young Park – Korean Journal for Food Science of Animal Resources

In vitro probiotic characteristics of Lactobacillus plantarum ZDY 2013 and its modulatory effect on gut microbiota of mice – Renhui Huang – Journal of Dairy Science

Reduced airway microbiota diversity is associated with elevated allergic respiratory inflammation – Wenkai Yu – Annals of Allergy, Asthma & Immunology

The prebiotics 3’Sialyllactose and 6’Sialyllactose diminish stressor-induced anxiety-like behavior and colonic microbiota alterations: evidence for effects on the gut-brain axis – Andrew J. Tarr – Brain, Behavior, and Immunity

Effect of yogurt containing deep sea water on health-related serum parameters and intestinal microbiota in mice – Sun Moon Kang – Journal of Dairy Science

Animal microbiome

In situ identification and quantification of starch-hydrolyzing bacteria attached to barley and corn grain in the rumen of cows fed barley-based diets – Yun Xia – FEMS Microbiology Ecology

Developmental Dynamic Analysis of the Excreted Microbiome of Chickens Using Next-Generation Sequencing – Lim S. – Journal of Molecular Microbiology and Biotechnology

Wolbachia influences the production of octopamine and affects Drosophila male aggression – Chelsie E. Rohscheib – Applied and Environmental Microbiology

Expanding the Entamoeba Universe: New Hosts Yield Novel Ribosomal Lineages – Alison S. Jacob – Journal of Eukaryotic Microbiology

Interactions between multiple helminths and the gut microbiota in wild rodents – Jakub Kreisinger – Philosophical Transactions B

Plant, root, and soil microbiome

The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes – Pablo R. Hardoim – Microbiology and Molecular Biology Reviews

The evolution of bacterial resistance against bacteriophages in the horse chestnut phyllosphere is general across both space and time – Britt Koskella – Philosophical Transactions B

Influence of corn, switchgrass, and prairie cropping systems on soil microbial communities in the upper Midwest of the United States – Ederson da C. Jesus – GCB Bioenergy

Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota –
Eduard Vico Oton – The ISME Journal

Composition of soil microbial communities in the rhizosphere of cucumber cultivars with differing nitrogen acquisition efficiency – Xingang Zhou – Applied Soil Ecology

Differential Decay of Wastewater Bacteria and Change of Microbial Communities in Beach Sand and Seawater Microcosms – Qian Zhang – Environmental Science & Technology

New traceability strategies based on a biological Bar Code by PCR-DGGE using bacterial and yeast communities for determining farming type of peach – Ahmed El Shobaky – Egyptian Journal of Basic and Applied Sciences

Optimization of biostimulant for bioremediation of contaminated coastal sediment by response surface methodology (RSM) and evaluation of microbial diversity by pyrosequencing – Bakthavachallam Subha – Marine Pollution Bulletin

Water microbiome

Metagenomic study of red biofilms from Diamante Lake reveals ancient arsenic bioenergetics in haloarchaea – Nicolás Rascovan – ISME Journal

Viral assemblage composition in Yellowstone acidic hot springs assessed by network analysis – Benjamin Bolduc – The ISME Journal

Built Environment Microbiome

Bacteriological assessment of the hospital environment in two referral hospitals in Yaoundé-Cameroon – Kamga Hortense Gonsu – Pan African Medical Journal

Green spaces and cognitive development in primary schoolchildren – Payam Dadvand – PNAS

Food microbiology

Source Tracking and Succession of Kimchi Lactic Acid Bacteria during Fermentation –
Se Hee Lee – Journal of Food Science

House microbiotas as sources of lactic acid bacteria and yeasts in traditional Italian sourdoughs – Fabio Minervini – Food Microbiology

Proteomics

Estimating the computational limits of detection of microbial non-model organisms – Mathias Kuhring – Proteomics

Antarctic archaea–virus interactions: metaproteome-led analysis of invasion, evasion and adaptation – Bernhard Tschitschko – The ISME Journal

Microbial Ecology

Paleobiological Perspectives on Early Microbial Evolution – Andrew H. Knoll – Cold Spring Harbor Perspectives in Biology

Review: Building the microbiome in health and disease: niche construction and social conflict in bacteria – Luke McNally – Philosophical Transactions B

Hypothesis: Restriction modification systems as engines of diversity – Kim Sneppen – Frontiers in Microbiology

Review: A Replisome’s journey through the bacterial chromosome – Thomas R. Beattie – Frontiers in Microbiology

Bioinformatics and metagenomics

Horizontal gene transfer in an acid mine drainage microbial community – Jiangtao Guo – BMC Genomics

ISQuest: Finding Insertion Sequences in Prokaryotic Sequence Fragment Data – Abhishek Biswas – Bioinformatics

Comparing K-mer based methods for improved classification of 16S sequences – Hilde Vinje – BMC Bioinformatics

Databases for Microbiologists – Igor B. Zhulin – Journal of Bacteriology

Techniques

Here, there, and everywhere: From PCRs to next‐generation sequencing technologies and sequence databases, DNA contaminants creep in from the most unlikely places – Karl Gruber – EMBO Reports

Microbes in the news

Bacteria ‘Fight Club’ could help find new cures for diseases – Alexandra Ossola – Popular Science
Sold on Symbiosis: A love of the ocean lured Nicole Dubilier into science; gutless sea worms and their nurturing bacterial symbionts keep her at the leading edge of marine microbiology – Anna Azvolinsky – The Scientist

Terroir: how fungi, yeasts and bacteria affect the taste of your wine – Max Allen – The Australian

Brookline’s Maya Sekhar wins grand prize at state science fair (work on phages)

Almost half of Americans don’t understand threat of antibiotic resistance – Ginger Skinner – Consumer Reports

The Human Microbiome: do not underestimate microbes! – John Dalton – David Game College

Faecal transplants, diet on trend as society embraces gut health – Hamish Fitzsimmons – ABC.au

Aquarium Microbiome Project – Shedd Aquarium – YouTube

The Microbiology Weekly – Cesar Sanchez

This Bacteria-Slaying Light Fixture Is Perfectly Safe For Humans – Andrew Liszewski – Gizmodo

Researcher finds bacteria in pistachio trees – Angela Simental – Las Cruces Sun

Bacteria-Eating Viruses Could Be New Ally Against Superbugs In A ‘Post-Antibiotic Era’ – Ben Hirschler – Reuters / Huffington Post

Linking the microbiome and colorectal cancer: an author Q+A – Sophie Marchant – BioMedCentral blogs

Bik’s Picks

US Fish & Wildlife struggles to save remaining polar bears – Sam Catherman – News Quench

Professor: Nothing Fishy About Portuguese Man o’ War at Jersey Shore – NBC

Japan And The U.S. Are Going To Have An Actual Giant Robot Battle – Damon Beres – The Huffington Post

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