Category Archives: Human oral

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 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 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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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 30, 2015

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Metabolomics and gut colonization of gnotobiotic mice, metabolomics of mice treated with antibiotics, inter-individual and temporal variation in human oral microbiotas, and several papers on microbes in agricultural-use soil.

Events

Free Cell Press webinar on Microbiome, Antibiotics and Human Disease: July 28th – Cell Press

Microbiome of pregnancy and birth

Book chapter: The Effect of Diet and Probiotics on the Human Gut Microbiome – Lorenzo Morelli – Metabolic Syndrome and Complications of Pregnancy

Human oral microbiome

Inter-Individual Differences in the Oral Bacteriome Are Greater than Intra-Day Fluctuations in Individuals – Yukuto Sato – PLOS ONE

Oral microflora of supragingival and subgingival biofilms in Algerian healthy adults – Sara Ziouani – African Journal of Microbiology Research

Human respiratory microbiome

Airway bacteria and respiratory symptoms are common in ambulatory HIV-positive UK adults – Camus Nimmo – European Respiratory Journal

Oral application of lactic acid bacteria following treatment with antibiotics inhibits allergic airway inflammation – Qiuxiang Zhang – Journal of Applied Microbiology

Human vaginal microbiome

Soluble Immune Mediators and Vaginal Bacteria Impact Innate Genital Mucosal Antimicrobial Activity in Young Women – Rebecca Pellett Madan – American Journal of Reproductive Immunology

Human gut microbiome

Fetal programming of overweight through the microbiome: boys are disproportionately affected – A. L. Kozyrskyj – Journal of Developmental Origins of Health and Disease

Impact of fluoroquinolones on human microbiota. Focus on the emergence of antibiotic resistance – Victoire de Lastours – Future Microbiology

Animal models

Metabolome progression during early gut microbial colonization of gnotobiotic mice – Angela Marcobal – Scientific Reports

Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment – Yael R. Nobel – Nature Communications

Altered Interactions between the Gut Microbiome and Colonic Mucosa Precede Polyposis in APCMin/+ Mice – Joshua S. Son – PLOS ONE

Animal microbiome

Review: The use of probiotics in aquaculture – Ngo Van Hai – Journal of Applied Microbiology

Thesis: Roles of the symbiotic microbial communities associated with sponge hosts in the nitrogen and phosphorus cycles – Russell T Hill – University of Maryland

Master Thesis: Arsenic Exposure Alters the Microbiome of Larval Zebrafish: A Metagenomic Analysis – Dylan A. Dahan – Bard Digital Commons

Discovery of a novel circular DNA virus in the Forbes sea star, Asterias forbesi – Elizabeth Fahsbender – Archives of Virology

Sexual transmission of beneficial microbes – Chad C. Smith – Trends in Ecology & Evolution

Plant, root, and soil microbiome

Rhizosphere bacteria and fungi associated with plant growth in soils of three replanted apple orchards – Ingrid H. Franke-Whittle – Plant and Soil

Microbial population dynamics in response to Pectobacterium atrosepticum infection in potato tubers – Viia Kõiv – Scientific Reports

Maternal effects on tree phenotypes: considering the microbiome – Maria Vivas – Trends in Plant Science

Bacterial population and biodegradation potential in chronically crude oil-contaminated marine sediments are strongly linked to temperature – Rafael Bargiela – Scientific Reports

Soil Microbial Communities are Shaped by Plant-Driven Changes in Resource Availability During Secondary Succession – Lauren C. Cline – Ecology

Warmer temperature accelerates methane emissions from the Zoige wetland on the Tibetan Plateau without changing methanogenic community composition – Mengmeng Cui – Scientific Reports

Water microbiome

Constitutive presence of antibiotic resistance genes within the bacterial community of a large subalpine lake – Andrea Di Cesare – Molecular Ecology

Draft Genome Sequences of Leviviridae RNA Phages EC and MB Recovered from San Francisco Wastewater – Alexander L. Greninger – Genome Announcements

Seasonal Dynamics of Marine Microbial Community in the South Sea of Korea – Sung-Suk Suh – PLOS ONE

Built environment / water treatment microbiology

Comparative metagenomics reveals microbial community differentiation in a biological heap leaching system – Qi Hu – Research in Microbiology

Impact of disinfection on drinking water biofilm bacterial community – Zilong Mi – Journal of Environmental Sciences

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 – The Journal of Hospital Infection

A review of melanized (black) fungal contamination in pharmaceutical products – incidence, drug recall and control measures – Rajendran Vijayakumar – Journal of Applied Microbiology

Bioinformatics and metagenomics

BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS – Bruno Fosso – BMC Bioinformatics

Challenges and opportunities in understanding microbial communities with metagenome assembly (accompanied by IPython Notebook tutorial) – Adina Howe – Frontiers in Microbiology

Metabolomics

Human Urinary Composition Controls Antibacterial Activity of Siderocalin – Robin R. Shields-Cutler – The Journal of Biological Chemistry

Human Urine Decreases Function and Expression of Type 1 Pili in Uropathogenic Escherichia coli – Sarah E. Greene – mBio

New techniques

To Celebrate Marriage Equality, Illumina to Release “BiSeq” Genome Sequencer – The Allium

More microbiology

More than the sum of its parts – Julia Fahrenkamp-Uppenbrink – Science

Ecological communities by design – James K. Fredrickson – Science

The bacterial pangenome as a new tool for analyzing pathogenic bacteria – Laetitia Rouli – New Microbes and New Infections

Microbes in the news

Antibiotics and the Gut Microbiome: Antibiotics given to infant mice may have long-term effects on the animals’ metabolism and gut microbiota – Anna Azvolinsky – The Scientist

Study: Breast milk helps babies develop immunity-boosting gut bacteria – Deena Shanker – Quartz

Your Diet May Be Causing Your Urinary Tract Infections – Mandy Oaklander – Time

uBiome and OpenBiome Partner for Microbiome Study in FMT Patients – Study will provide new insights on mechanics of fecal microbiota transplantation in C. difficile patients – uBiome

Passive Aggressive: Drosophila microbiota influence behavior – Julie Wolf – mBioSphere

Soil water, microbes influence carbon in world’s coldest desert, study finds – Phys.org

Invisible You: Art and Microbiology at the Eden Project – Microbe Post

Science, publishing, and career

The Myth of the Academic Lottery – Kelly J. Baker – Chronicle Vitae

Bik’s Picks

I saw this last night and it was so pretty: Venus and Jupiter to Put on ‘Best Backyard Sky Show of 2015’ – Alyssa Newcomb – ABC News

Say hello to the centipede from hell – Rachel Feltman – Washington Post

California governor signs strict law requiring vaccinations for most kids – Liz Szabo – USA Today

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June 25, 2015

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Vitamin B12 modulates skin microbiome transcription, viruses in fluvial systems, and a webserver for annotation of gut microbiome genes.

Human skin microbiome

Vitamin B12 modulates the transcriptome of the skin microbiota in acne pathogenesis – Dezhi Kang – Science Translational Medicine

Human oral microbiome

Review: Shaping the oral mycobiota: interactions of opportunistic fungi with oral bacteria and the host – H Xu – Current Opinion in Microbiology

Human gut microbiome

Virulence genes are a signature of the microbiome in the colorectal tumor microenvironment – Michael B. Burns – Genome Medicine

Randomised clinical trial: gut microbiome biomarkers are associated with clinical response to a low FODMAP diet in children with the irritable bowel syndrome – B. P. Chumpitazi – Alimentary Pharmacology & Therapeutics

Review: Host-microbiome interactions in health and disease – Liam O’Mahony – Clinical Liver Disease

 

Review: Regulation of intestinal TH17 and Treg cells by gut microbiota – Takeshi Tanoue – Inflammation and Regeneration

Review: Gut microbial short-chain fatty acids in host defense and immune regulation – Hiroshi Ohno – Inflammation and Regeneration

Review: Gut Microbiota-derived Outer Membrane Vesicles: Under-recognized Major Players in Health and Disease? – Maurizio Muraca – Discovery Magazine

Review: The Interplay between the Microbiota and Enterohemorrhagic Escherichia coli – Reed Pifer – ASM Microbiology Spectrum

Plant, root, and soil microbiome

An in-depth analysis of actinobacterial communities shows their high diversity in grassland soils along a gradient of mixed heavy metal contamination – Tomáš Větrovský – Biology and Fertility of Soils

Review: Endophytic actinobacteria of medicinal plants: diversity and bioactivity – Patrycja Golinska – Antonie van Leeuwenhoek

Differences in Arbuscular Mycorrhizal Fungal Community Composition in Soils of Three Land Use Types in Subtropical Hilly Area of Southern China – Caihuan Wang – PLOS ONE

Water microbiome

Long-term effects of the antibacterial agent triclosan on marine periphyton communities – K. Martin Eriksson – Environmental Toxicology and Chemistry

Revealing the unexplored fungal communities in deep groundwater of crystalline bedrock fracture zones in Olkiluoto, Finland – Elina Sohlberg – Frontiers in Microbiology

Prevalence of tetracycline resistance genes among multi-drug resistant bacteria from selected water distribution systems in southwestern Nigeria – Ayodele. T. Adesoji – Annals of Clinical Microbiology and Antimicrobials

Functional gene pyrosequencing reveals core proteobacterial denitrifiers in boreal lakes –
Jatta Saarenheimo – Frontiers in Microbiology

Review: Virus ecology of fluvial systems: a blank spot on the map? – Peter Peduzzi – Biological Reviews

Built Environment Microbiome

Microbially influenced corrosion communities associated with fuel-grade ethanol environments – Charles H. D. Williamson – Applied Microbiology and Biotechnology

Metagenomics and bioinformatics

MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome – Stephen Nayfach – Bioinformatics

Review: Biotechnological applications of functional metagenomics in the food and pharmaceutical industries – Laura M. Coughlan – Frontiers in Microbiology

Techniques

Label-free NIR-SERS discrimination and detection of foodborne bacteria by in situ synthesis of Ag colloids – Longyan Chen – Journal of Nanobiotechnology

Microbes in the news

How To Prevent Acne: Vitamin B12, Found In Meat And Dairy, Alters Bacteria And Leads To Pimples – Susan Scutti – Medical Daily

When Gut Bacteria Changes Brain Function: Some researchers believe that the microbiome may play a role in regulating how people think and feel – David Kohn – The Atlantic

Klaus Nielsen, scientist who tried to smuggle contagious bacteria, begins sentencing hearing – CBC News

Squares, triangles, circles: regardless of their form, bacteria can figure out where to split – TU Delft / Kavli Foundation

 

Students Find, Name Bacteriophages in Massive Team Project – Illinois Wesleyan University

BacteriaHysteria

Shocking images reveal how a Glastonbury wristband could ‘harbour 20 TIMES more bacteria than clothes’ – Daily Mail

BlackBerry Ltd May Have Plans To Develop Bacteria-Free Phones – Aman Jain – Value Walk

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June 24, 2015

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Chinese mushroom might help with weight loss (in mice), asthma and the microbiome (also in mice), metabolic networks in the gut, and benefits of resistant starch. Plus: Taylor Swift won’t be doing anymore reviewing for Nature.

Human oral microbiome

Alterations of Bacteroides sp., Neisseria sp., Actinomyces sp., and Streptococcus sp. populations in the oropharyngeal microbiome are associated with liver cirrhosis and pneumonia – Haifeng Lu – BMC Infectious Diseases

Intra-Genomic Heterogeneity in 16S rRNA Genes in Strictly Anaerobic Clinical Isolates from Periodontal Abscesses – Jiazhen Chen – PLOS ONE

Human gut microbiome

Akkermansia muciniphila and improved metabolic health during a dietary intervention in obesity: relationship with gut microbiome richness and ecology – Maria Carlota Dao – Gut

Animal models

Ganoderma lucidum reduces obesity in mice by modulating the composition of the gut microbiota – Chih-Jung Chang – Nature Communications

Evidence that asthma is a developmental origin disease influenced by maternal diet and bacterial metabolites – Alison N. Thorburn – Nature Communications

Characterization of the bacterial gut microbiota of piglets suffering from new neonatal porcine diarrhoea – Marie Louise Hermann-Bank – BMC Veterinary Research

Animal microbiome

Allometry of animal–microbe interactions and global census of animal-associated microbes – Thomas L. Kieft, Karen A. Simmons – Proceedings B

Introduction of Non-Native Pollinators Can Lead to Trans-Continental Movement of Bee-Associated Fungi – Shannon M. Hedtke – PLOS ONE

Effect of poly-β-hydroxybutyrate on growth, enzyme activity and intestinal microbial community of Chinese mitten crab, Eriocheir sinensis (Milne-Edwards) juveniles – Liying Sui – Aquaculture Research

Small stonefly predators affect microbenthic and meiobenthic communities in stream leaf packs – Nabil Majdi – Freshwater Biology

Plant, root and soil microbiome

Hologenome theory supported by co-occurrence networks of species-specific bacterial communities in siphonous algae (Caulerpa) – T. Aires – FEMS Microbial Ecology

Land Use History Shifts In Situ Fungal and Bacterial Successions following Wheat Straw Input into the Soil – Vincent Tardy – PLOS ONE

Water microbiome

Inefficient microbial production of refractory dissolved organic matter in the ocean – Helena Osterholz – Nature Communications

The Link between Microbial Diversity and Nitrogen Cycling in Marine Sediments Is Modulated by Macrofaunal Bioturbation – Maryam Yazdani Foshtomi – PLOS ONE

Functional foods

Review: Preparation, health benefits and applications of resistant starch—a review – Bilal Ahmad Ashwar – Starch – Stärke

Metabolic networks and metabolomics

Inference of Network Dynamics and Metabolic Interactions in the Gut Microbiome – Steven N. Steinway – PLOS Computational Biology

A genome-wide systems analysis reveals strong link between colorectal cancer and trimethylamine N-oxide (TMAO), a gut microbial metabolite of dietary meat and fat – Rong Xu – BMC Genomics

Application of a hierarchical enzyme classification method reveals the role of gut microbiome in human metabolism – Akram Mohammed – BMC Genomics

Comparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks – Hugo Roume – NPJ Biofilms and Microbiomes

Use of the Analysis of the Volatile Faecal Metabolome in Screening for Colorectal Cancer – Claire A Batty – PLOS ONE

Microbes in the news

IndieGoGo project: A Probiotic Life: Microbiome Documentary

New colon cancer culprit found in gut microbiome – EurekAlert

Mushroom used in Chinese medicine ‘slows weight gain’ – James Gallagher – BBC News

Announcing the uBiome Studies Portal “We’re aiming to launch one new study every week.” – uBiome

What is the role of the gut microbiome in developing Parkinson’s disease? – EurekAlert

Microbiology and art

Artists Reveal the Bacterial Beauty of the Human Microbiome – Shaunacy Ferro – Mental Floss

Science, publishing, and career

A day in the life of a malaria researcher – Lin Lee – BioMedCentral Blogs

Towards an unbiased view of science: Authors at Nature Communications now have the option to choose double-blind peer review – Nature Communications

Satire: Taylor Swift Announces She Will No Longer Review For Nature – The Allium

Bik’s Picks

A Middle Triassic stem-turtle and the evolution of the turtle body plan – Rainer R. Schoch & Hans-Dieter Sues – Nature

Scientists Finally Decide Which Bit of This Weird Animal is the Head – Ed Yong – National Geographic

America’s Next Top Chef is a Supercomputer From IBM – Liz Stinson – Wired
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June 21, 2015

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An upcoming workshop on bioinformatics and microbiome, lots of reviews about the intersection of gut microbiome and the immune system, and viruses in Arctic freshwater.

Events

NIMBioS Investigative Workshop: Computational Advances in Microbiome Research – July 27-28, 2015, University of Tennessee, Knoxville

Human oral microbiome

Salivary microbiota-immune profiling in cirrhosis: Could this be the noninvasive strategy that will revolutionize prognostication in hepatology? – Vishal C. Patel – Hepatology

Human gut microbiome

Metagenomic analysis of microbiome in colon tissue from subjects with inflammatory bowel diseases reveals interplay of viruses and bacteria – Weiwei Wang – Inflammatory Bowel Diseases

Review: Interactions between Innate Immunity, Microbiota, and Probiotics – GianMarco Giorgetti – Journal of Immunology Research

Review: Influence of the microbiome on response to vaccination – Amanda M. Jamieson – Human Vaccines & Immunotherapeutics

Review: How the Intricate Interaction among Toll-Like Receptors, Microbiota, and Intestinal Immunity Can Influence Gastrointestinal Pathology – Simona Frosali – Journal of Immunology Research

Review: The Interaction among Microbiota, Immunity, and Genetic and Dietary Factors Is the Condicio Sine Qua Non Celiac Disease Can Develop – D. Pagliari – Journal of Immunology Research

Review: Molecular methods for studying methanogens of the human gastrointestinal tract: current status and future directions – Prem Prashant Chaudhary – Applied Microbiology and Biotechnology

Animal models

Alterations of the Murine Gut Microbiome with Age and Allergic Airway Disease – Marius Vital – Journal of Immunology Research

DGGE: Alteration of the Microbiota and Virulence Gene Expression in E. coli O157:H7 in Pig Ligated Intestine with and without AE Lesions – Bianfang Liu – PLOS ONE

Animal microbiome

The coral immune response facilitates protection against microbes during tissue regeneration – Jeroen A. J. M. van de Water – Molecular Ecology

Plant microbiome

DGGE: Endophytic bacterial diversity in the phyllosphere of Amazon Paullinia cupana associated with asymptomatic and symptomatic anthracnose – Andréa Cristina Bogas – Springer Plus

Plant root, soil, and sediment microbiome

Successional and seasonal variations in soil and litter microbial community structure and function during tropical postagricultural forest regeneration: a multiyear study – A. Peyton Smith – Global Change Biology

Oil Biodegradation and Oil-degrading Microbial Populations in Marsh Sediments Impacted by Oil from the Deepwater Horizon Well Blowout – Ronald M Atlas – Environmental Science & Technology

Water microbiome

Biodiversity and distribution of polar freshwater DNA viruses – Daniel Aguirre de Cárcer – Science Advances

Baseline Assessment of Mesophotic Reefs of the Vitória-Trindade Seamount Chain Based on Water Quality, Microbial Diversity, Benthic Cover and Fish Biomass Data – Pedro M. Meirelles – PLOS ONE

Vertical Distribution of Bacterial Community Diversity and Water Quality during the Reservoir Thermal Stratification – Hai-Han Zhang – International Journal of Environmental Research and Public Health

Occurrence of Enterococcus species with virulence markers in an urban flow-influenced tropical recreational beach – Asmat Ahmad – Marine Pollution Bulletin

Microbes in the news

International Team Profiles DNA Viruses in Arctic Freshwater Lakes – Genome Web

Why is my hangover so bad? It’s not just the booze giving you a hangover – it’s the microbes in your stomach – Tim Spector

Israel Bets On Recycled Water To Meet Its Growing Thirst – Emily Harris – NPR

Science, publishing and career

Distraction Coefficients of Females in Biomedical Research Laboratories – Chi R. Ality – Significance

Bik’s Picks

Stanford researcher declares that the sixth mass extinction is here – Rob Jordan – Stanford University

A Periodic Diet that Mimics Fasting Promotes Multi-System Regeneration, Enhanced Cognitive Performance, and Healthspan – Sebastian Brandhorst – Cell Metabolism

Eating up to 100 g of chocolate daily linked to lowered heart disease and stroke risk – BMJ’s Heart
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June 20, 2015

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Catching up after spending all day in the lab on Friday, and all day working on figures and text today…. Here’s your weekend digest, with the microbiome of sport schools, phasing of Illumina sequencing, and happy endings for preterm infants.

Pregnancy and birth microbiome

Preterm infant gut colonization in the Neonatal ICU and Complete Restoration two years later – Laura Moles – Clinical Microbiology and Infection

Clostridium butyricum strains and dysbiosis linked to necrotizing enterocolitis in preterm neonates – Nadim Cassir – Clinical Infectious Diseases

Human respiratory microbiome

The microbiome of the human lower airways: a next generation sequencing perspective – Velma T. E. Aho – World Allergy Organization Journal

Human skin microbiome

Poster: Noma disease: 10 years of research in the quest of a microbial etiology – P François – Antimicrobial Resistance and Infection Control

Human oral microbiome

Oral Mucositis in Pediatric Acute Lymphoblastic Leukemia Patients: Evaluation of Microbiological and Hematological Factors – Regina Maria Holanda de Mendonça – Pediatric Hematology-Oncology

Human gut microbiome

Composition and temporal stability of the gut microbiota in older persons – Ian B Jeffery – The ISME Journal

The Host Genotype and Environment Affect Strain Types of Bifidobacterium longum subsp. longum Inhabiting the Intestinal Tracts of Twins – Min Zhang – Applied and Environmental Microbiology

The Influence of the Gut Microbiome on Obesity, Metabolic Syndrome and Gastrointestinal Disease – Parth J Pareck – Clinical and Translational Gastroenterology

Editorial: About the gut microbiome as a pharmacological target in atherosclerosis – Julia.J. Witjes – European Journal of Pharmacology

Editorial: Diabetes, More on Merde, the Microbiome, and the Dung Beetle – Richard I. Shader – Clinical Therapeutics

Review: Effect of Dietary Resistant Starch on Prevention and Treatment of Obesity-related Diseases and Its Possible Mechanisms – Lei Zhang – Biomedical and Environmental Sciences

Animal models

In pigs: Influence of genotype and feeding strategy on pig performance, plasma concentrations of micro nutrients, immune responses and fecal microbiota composition of growing-finishing pigs in a forage-based system – A.G. Kongsted – Livestock Science

In rats: Prenatal Stress-Induced Alterations in Major Physiological Systems Correlate with Gut Microbiota Composition in Adulthood – Anna V. Golubeva – Psychoneuroendocrinology

In mice: The genetic architecture of NAFLD among inbred strains of mice – Simon T Hui – eLIFE

Animal microbiome

Cows: Ruminal Bacterial Community Composition in Dairy Cows Is Dynamic over the Course of Two Lactations and Correlates with Feed Efficiency – Kelsea A. Jewell – Applied and Environmental Microbiology

Thesis: The earthworm microbiome – Daniel Antony Pass – Cardiff University

Thesis: Gut microbiota of migratory passerines at stopover – William Lewis – University of Southern Mississippi

Plant microbiome

PERN: an EU–Russia initiative for rhizosphere microbial resources – Stéphane Declerck – Trends in Biotechnology

Review: Biological control in the microbiome era: challenges and opportunities – Haissam Jijakli – Biological Control

Plant root and soil microbiome

Impact of plant domestication on rhizosphere microbiome assembly and functions
Juan E. Pérez-Jaramillo – Plant Molecular Biology

16S rRNA-based bacterial community structure is a sensitive indicator of soil respiration activity – Rongxiao Che – Journal of Soils and Sediments

Built environment microbiome

Athletic equipment microbiota are shaped by interactions with human skin – Mariah Wood – Microbiome

Food microbiology

Bacteriophages Isolated from Chicken Meat and the Horizontal Transfer of Antimicrobial Resistance Genes – Amira Shousha – Applied and Environmental Microbiology

Microbiological diversity associated with the spontaneous wet method of coffee fermentation – Suzana Reis Evangelista – International Journal of Food Microbiology

Chemical and microbiological characteristics of traditional homemade fresh goat cheeses from Northern Morocco – Ouiam El Galiou – Small Ruminant Research

Metagenomics and bioinformatics

Microbial bioinformatics for food safety and production – Wynand Alkema – Briefings in Bioinformatics

Niche distribution and influence of environmental parameters in marine microbial communities: a systematic review – Felipe H. Coutinho – Peer J

Ultra-large alignments using phylogeny-aware profiles – Nam-phuong D Nguyen – Genome Biology

Techiques

Phasing amplicon sequencing on Illumina Miseq for robust environmental microbial community analysis – Liyou Wu – BMC Microbiology

Microbes in the news

Medicine’s next frontier: The microbiome – Meg Tirrell – CNBC

Microbes could be key for better yields, stronger plants – Michigan State University – AG Professional

Berkeley balcony collapse: A failure at the intersection of building science and microbiology – Brent Stephens – Microbe.net

Science, publishing, and career

Gender Differences in Physicians’ Financial Ties to Industry: A Study of National Disclosure Data – Susannah L. Rose – PLOS ONE

“If you think it’s rude to ask to look at your co-authors’ data, you’re not doing science” – C. K. Gunsalus and Drummond Rennie – Retraction Watch

Bik’s Picks

An Ant With the Right Coat for 158-Degree Weather – Sindya N. Bhanoo – New York Times

8 million mummified animals, mostly dogs, in catacombs at Egypt site – Greg Botelho – CNN

Blind Americans can now ‘see’ with a device that uses their tongues – Michelle Cortez – Mashable

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