Category Archives: Built Environment Microbiology

May 15, 2015

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Human skin microbiome

Pilot Study on Novel Skin Care Method by Augmentation with Staphylococcus epidermidis, an Autologous Skin Microbe – A Blinded Randomized Clinical Trial – Yuichi Nodake – Journal of Dermatological Science

Human gut microbiome

Metagenome Sequencing of the Hadza Hunter-Gatherer Gut Microbiota – Simone Rampelli – Current Biology

Deviations in human gut microbiota: a novel diagnostic test for determining dysbiosis in patients with IBS or IBD – C. Casén – Alimentary Pharmacology & Therapeutics

Intestinal Blautia is associated with reduced death from graft-versus-host disease – Robert R. Jenq – Biology of Blood and Marrow Transplantation

Pubmed link only: The coeliac stomach: gastritis in patients with coeliac disease – B. Lebwohl – Alimentary Pharmacology & Therapeutics

DGGE: Schisandra chinensis fruit modulates the gut microbiota composition in association with metabolic markers in obese women : a randomized, double-blind placebo controlled study – Mi-young Song – Nutrition Research

Review: Gut microbes, immunity, and spondyloarthritis – Matthew L. Stoll – Clinical Immunology

Microbiome models

Relationships Between Diet-Related Changes in the Gut Microbiome And Cognitive Flexibility – K.R. Magnusson – Neuroscience

Animal microbiome

Aphids: Genetic characterisation of new host-specialised biotypes and novel associations with bacterial symbionts in the pea aphid complex – Jean Peccoud – Insect Conservation and Diversity

Review: The Multi-Tasking Gut Epithelium of Insects – Jia-Hsin Huang – Insect Biochemistry and Molecular Biology

Plant and soil microbiome

On small soil beetles: Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics – Carmelo Andújar – Molecular Ecology

Changes in soil nutrient content and bacterial community after 12 years of organic amendment application to a vineyard – M. E. Calleja-Cervantes – European Journal of Soil Science

Built Environment microbiology

Self-healing bio-concrete uses bacteria to repair itself – Anthony Cuthbertson – International Business Times

Bioreactor microbiology

Rare taxa have potential to make metabolic contributions in enhanced biological phosphorus removal ecosystems – Christopher E. Lawson – Environmental Microbiology

Bioinformatics

Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods – Jullien M. Flynn -Ecology and Evolution

More microbiology

Editorial: Sifting out virulent bacteria – Naomi Attar – Nature Reviews Microbiology

Review: Dust Devil: The Life and Times of the Fungus That Causes Valley Fever – Eric R. G. Lewis – PLOS Pathogens

Microbes in the news

Decode your kitty’s microbiome – participate in some Cat-izen science – Alexandra Ossola –
Popular science

BacteriaHysteria

Faecal matter on plane tray tables, unwashed blankets… and 80 million bacteria on suitcases: The dirty secrets of air travel revealed – John Hutchinson – Daily Mail

Science, publishing, and career

“Reframing my track record undoubtedly helped. Here’s how I did it.” Accounting for career breaks – Emily Nicholson – Science

Bik’s Picks

Denver Zoo Penguins Go ‘Extinct’ For Endangered Species Day – CBS Denver

A Simple Hand-Grip Test Could Predict Your Risk For Heart Disease And Death – Anna Almendrala – Huffington Post

An astronaut’s surprisingly helpful guide to pooping in space – Elahe Izadi – Washington Post

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May 12, 2015

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Microbiome of pregnancy and birth

Metagenomic Analysis of Milk of Healthy and Mastitis-Suffering Women – Esther Jiménez – Journal of Human Lactation

Human oral microbiome

Abstract: Changes In The Oral Microbiome Of HIV-Infected Individuals May Alter Nitrogen Metabolism And The Enterosalivary Circulation Of Nitrate – Carl D. Koch – Am J Respir Crit Care Med

Human respiratory microbiome

Conference abstracts in Am J Respir Crit Care Med:

Human gut microbiome

Metabolism Links Bacterial Biofilms and Colon Carcinogenesis – Caroline H. Johnson – Cell Metabolism

Review: The gut microbiome: What do we know? – Francisco Guarner – Clinical Liver Disease

Review: A model for the role of gut bacteria in the development of autoimmunity for type 1 diabetes – Austin G. Davis-Richardson – Diabetologia

Functional foods

Review: A breakthrough in probiotics: Clostridium butyricum regulates gut homeostasis and anti-inflammatory response in inflammatory bowel disease – Takanori Kanai – Journal of Gastroenterology

Animal models of microbiome research

Phylum Level Change in the Cecal and Fecal Gut Communities of Rats Fed Diets Containing Different Fermentable Substrates Supports a Role for Nitrogen as a Factor Contributing to Community Structure – Martin Kalmokoff – Nutrients

Animal microbiome

Variation in koala microbiomes within and between individuals: effect of body region and captivity status – Niccoló Alfano – Scientific Reports

Plants and soil microbiome

Minimal genomes of mycoplasma-related endobacteria are plastic and contain host-derived genes for sustained life within Glomeromycota – Mizue Naito – PNAS

Transcriptome diversity among rice root types during asymbiosis and interaction with arbuscular mycorrhizal fungi – Caroline Gutjahr – PNAS
Reintroduction of locally extinct vertebrates impacts arid soil fungal communities –
Laurence J. Clarke – Molecular Ecology

Compartmentalized and contrasted response of ectomycorrhizal and soil fungal communities of Scots pine forests along elevation gradients in France and Spain
Ana Rincón – Environmental Microbiology

Impact of tropical lowland rainforest conversion into rubber and oil palm plantations on soil microbial communities – Valentyna Krashevska – Biology and Fertility of Soils

Masters Thesis: The establishment of apple orchards as temperate forest garden systems and their impact on indigenous bacterial and fungal population abundance in Southern Ontario, Canada – Paul Wartman – University of Guelph, Canada

Review: Plant growth promoting rhizobacteria and sustainable agriculture: A review –
Muhammad Arslan Ashraf – African Journal of Microbiology Research

Water microbiome

Organic and inorganic composition and microbiology of produced waters from Pennsylvania shale gas wells – Denise M. Akob – Applied Geochemistry

Perspective: Using dispersants after oil spills: impacts on the composition and activity of microbial communities – Sara Kleindienst – Nature Reviews Microbiology

Not sure if these are small enough (20-500 um) to be classified as microbes: Metagenetic tools for the census of marine meiofaunal biodiversity: An overview – Laura Carugati – Marine Genomics

Extremophile microbiome

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

Comparison of Archaeal and Bacterial Diversity in Methane Seep Carbonate Nodules and Host Sediments, Eel River Basin and Hydrate Ridge, USA – Olivia U. Mason – Microbial Ecology

Deep-sea hydrothermal vent bacteria related to human pathogenic Vibrio species – Nur A. Hasan – PNAS

Microbial communities of the Lemon Creek Glacier show subtle structural variation yet stable phylogenetic composition over space and time – Cody S. Sheik – Frontiers in Microbiology

Built environment microbiome

Forensic analysis of the microbiome of phones and shoes – Simon Lax – Microbiome

The Actinobacterial Colonization of Etruscan Paintings – Marta Diaz-Herraiz – Scientific Reports

Food microbiology

Molecular Analysis of Skin Bacterial Assemblages from Codfish and Pollock after Dry-Salted Fish Production – Natalia Pegoraro

Viruses and phages

Infection of phytoplankton by aerosolized marine viruses – Shlomit Sharoni – PNAS

Archaea

The two-domain tree of life is linked to a new root for the Archaea – Kasie Raymann – PNAS

Review: Archaeal Lineages within the Human Microbiome: Absent, Rare or Elusive?
Hans-Peter Horz – Life

Review: The interplay between nucleoid organization and transcription in archaeal genomes – Eveline Peeters – Nature Reviews Microbiology

Metagenomics and bioinformatics

Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data – Kathrin P. Aßhauer – Bioinformatics

ProtPhylo: identification of protein–phenotype and protein–protein functional associations via phylogenetic profiling – Yiming Cheng – Nucleic Acids Research

IonGAP: integrative bacterial genome analysis for Ion Torrent sequence data – Adrian Baez-Ortega – Bioinformatics

Natural Bacterial Communities Serve as Quantitative Geochemical Biosensors – Mark B. Smith – mBio

Manuscript: Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant – Andreas Bremges

Review: The integration of sequencing and bioinformatics in metagenomics – Firouz Abbasian – Reviews in Environmental Science and Bio/Technology

Book Chapter: Protocols and Methods for the in Silico Reconstruction of the Origin and Evolution of Metabolic Pathways – Luana Presta – Briefs in Molecular Science 2015

Book Chapter: Molecular Screening of Azurin-Like Anticancer Bacteriocins from Human Gut Microflora Using Bioinformatics – Van Duy Nguyen – Advanced Computational Methods for Knowledge Engineering

Other microbial papers of interest

Bacterial Swarms Recruit Cargo Bacteria To Pave the Way in Toxic Environments – Alin Finkelshtein – mBio

Mosaic genome of endobacteria in arbuscular mycorrhizal fungi: Transkingdom gene transfer in an ancient mycoplasma-fungus association – Gloria Torres-Cortés – PNAS

Perspective: Resilience vs. historical contingency in microbial responses to environmental change – Christine V. Hawkes – Ecology Letters

A tortoise–hare pattern seen in adapting structured and unstructured populations suggests a rugged fitness landscape in bacteria – Joshua R. Nahum – PNAS

Microbes in the news
Can The Microbes You Leave Behind Be Used to Identify You? – Ed Yong – National Geographic

Forbidden Data: Wyoming wants to conceal the fact that many of its streams are contaminated by E. coli bacteria – Slate

UGSG looks at microbiology, chemistry of Pa. fracked wells – Bob Downing – Ohio.com

Chinese breast milk discovery strengthens case for probiotics in infant formula: Chr Hansen – By Mark Astley – Dairy Reporter

Researchers find metabolic link between bacterial ‘biofilms’, colon cancer – Medical Xpress

Accessing the Hidden Kingdom: Fungal ITS Reference Sequences – NCBI Insights
#BacteriaHysteria

Germ City: Bacteria thriving at the makeup counter: 30% of used makeup samples in stores contain bacteria – PIX11

Tests found bacteria on popular single-serve coffeemakers – Your Central Valley

Bik’s Picks

De novo synthesis of a sunscreen compound in vertebrates – Andrew R Osborn – eLIFE

Chemical messages in 170-year-old champagne bottles from the Baltic Sea: Revealing tastes from the past – Philippe Jeandet – PNAS

Unraveling ancient Egypt’s animal mummy mystery: Roughly a third of the animal mummies examined were completely empty – Michael E. Miller – Washington Post

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May 7, 2015

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Events

Human Gut Microbiome and Diseases Congress – 25-26 June 2015, Milano, Italy

Pregnancy and birth microbiome

The Canadian Healthy Infant Longitudinal Development (CHILD) birth cohort study: assessment of environmental exposures – Tim K Takaro – Journal of Exposure Science and Environmental Epidemiology

The Impact of Infancy Antibiotic Intake on Childhood Obesity; Review of Studies – Mohammad Reza Vafa – Advances in Obesity, Weight Management & Control

Human respiratory microbiome

The Host Response to the Lung Microbiome in Chronic Obstructive Pulmonary Disease
Marc A Sze – American Journal of Respiratory and Critical Care Medicine

Human gut microbiome

Approaches to studying and manipulating the enteric microbiome to improve autism symptoms – Richard E. Frye – Microbial Ecology in Health and Disease

Plant root and soil microbiome

Heading to the Origins – Rice Microbiome as Functional Extension of the Host – Pablo R. Hardoim – Journal of Rice Research

Inoculation of Phaseolus vulgaris with the nodule-endophyte Agrobacterium sp. 10C2 affects richness and structure of rhizosphere bacterial communities and enhances nodulation and growth – Saif-Allah Chihaoui – submitted paper

Biochar in Co-Contaminated Soil Manipulates Arsenic Solubility and Microbiological Community Structure, and Promotes Organochlorine Degradation – Samuel J. Gregory – PLOS ONE

Microbial quality of soil from the Pampa biome in response to different grazing pressures – Rafael S. Vargas – Genetics and Molecular Biology

Built environment microbiome

Dysbiotic drift: mental health, environmental grey space, and microbiota – Alan C Logan – Journal of Physiological Anthropology

Extremophiles

Sub-Ice Microalgal and Bacterial Communities in Freshwater Lake Baikal, Russia – Maria V. Bashenkhaeva – Microbial Ecology

Phages and viruses

Protist predation can select for bacteria with lowered susceptibility to infection by lytic phages – Anni-Maria Örmälä-Odegrip – BMC Evolutionary Biology

Microbial Ecology

Evolutionary ecology of microorganisms: from the tamed to the wild – Jay T Lennon – PeerJ

Metagenomics and bioinformatics

MyPro: A seamless pipeline for automated prokaryotic genome assembly and annotation – Yu-Chieh Liao – Journal of Microbiological Methods

PrePrint: Infer Metagenomic Abundance and Reveal Homologous Genomes Based on the Structure of Taxonomy Tree – Yu-Qing Qiu – IEEE/ACM Transactions on Computational Biology and Bioinformatics

Metabolomics

Effects of Uremic Toxins from the Gut Microbiota on Bone: A Brief Look at Chronic Kidney Disease – Ana Paula Black – Therapeutic Apheresis and Dialysis

Microbes in the news

Ulcer-causing bacteria induces stomach stem cell growth in mice, researchers find – Stanford Medicine

Newly named bacteria help honey bee larvae thrive – Kim Kaplan – Phys.org

The smell of death: Scientist reveals how 400 compounds mix to create heady mixture of scents as bacteria rips apart rotting flesh – Moheb Costandi – Daily Mail

Eat your vegetables, feed your microbiome – David Charbonneau – EyeViewKamloops

Microbiome Portrait Experiment for High School Students – Tufts

Bacteria redefine reinforced concrete – RSC Advances Blog

Possible role of gut bacteria in autism – Science Daily

Environmental exposures study tracks more than 3,200 Canadian babies – Simon Fraser University

Final Report Summary – TORNADO (Molecular Targets Open for Regulation by the gut flora – New Avenues for improved Diet to Optimize European health) – CORDIS Europa

Measles Vaccination Saves You From More Than Measles – Maggie Fox – NBC News

Microbes and money

‘Gut microbiome’ startup moving to science accelerator, seeks study volunteers: Prince William Science Accelerator – ISOThrive – Inside Nova

UBiome Seeks Academic Partnerships with the Launch of the uBiome Academic Consortium – WDRB

Science, publishing, and career

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

Bik’s Picks

Listen To These Eerie ‘X-Files’ Sounds Recorded At The Edge Of Space – Macrina Cooper-White – Huffington Post

Finding That Babies Born at 22 Weeks Can Survive Could Change Abortion Debate – Lucy Westcott – Newsweek

Samantha Cristoforetti: 5 Memorable Moments From the Italian Astronaut’s Time in Space – Alyssa Newcomb – ABC News
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May 4, 2015

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Grant opportunities

Newborn and Infant Gut Health – Application deadline : May 13, 2015 – Bill & Melinda Gates Foundation

Events

Free Webinar: The Human Microbiome: Beyond the Gut – May 5, 2:30 pm ET – The Scientist

General microbiome

Review: Sequencing and beyond: integrating molecular ‘omics’ for microbial community profiling – Eric A. Franzosa – Nature Reviews Microbiology

Reproductive Parasitism: Maternally Inherited Symbionts in a Biparental World
Gregory D.D. Hurst and Crystal L. Frost – Cold Spring Harbor Perspectives in Biology

Human oral microbiome

Editorial: Defining functional signatures of dysbiosis in periodontitis progression
Gary P Wang – Genome Medicine
belongs to:
Functional signatures of oral dysbiosis during periodontitis progression revealed by microbial metatranscriptome analysis – Susan Yost – Genome Medicine

Human gut microbiome

Intestinal dysbiosis in children with short bowel syndrome is associated with impaired outcome – Helene Engstrand Lilja – Microbiome

Intestinal Microbiota Signatures Associated With Histological Liver Steatosis in Pediatric-Onset Intestinal Failure – Katri Korpela – Journal of Parenteral & Enteral Nutrition

Differences of the Fecal Microflora With Clostridium difficile Therapies – Thomas J. Louie – Clinical Infectious Diseases

Review: The human gut resistome – Willem van Schaik – Philosophical Transactions B

Animal models

The intestinal microbiota influences Campylobacter jejuni colonization and extra-intestinal dissemination in mice – Jason L. O’Loughlin – Applied and Environmental Microbiology

Animal microbiome

Fish: Selection in the host structures the microbiota associated with developing cod larvae (Gadus morhua) – Ingrid Bakke – Environental Microbiology

Plant and soil microbiome

Crustose coralline algal species host distinct bacterial assemblages on their surfaces – Jennifer M Sneed – The ISME Journal

Influence of plant communities and soil properties during natural vegetation restoration on arbuscular mycorrhizal fungal communities in a karst region – Yueming Liang – Ecological Engineering

Contrasting spatial patterns and ecological attributes of soil bacterial and archaeal taxa across a landscape – Florentin Constancias – Microbiology Open

Predictable communities of soil bacteria in relation to nutrient concentration and successional stage, in a laboratory culture experiment – Woojin Song – Environmental Microbiology

Water microbiome

Accumulation of Clinically Relevant Antibiotic Resistant Genes, Bacterial load and Metals from a Freshwater Lake Sediments in Central Europe – Naresh Devarajan – Environmental Science & Technology

Effects of Heavy Metal and Nutrients on Benthic Microbial Communities in Freshwater Sediment of Poyang Lake (China) – Cho Yu – Journal of Residuals Science & Technology

Review: Stream microbial diversity responds to environmental changes: Review and synthesis of existing research – Lydia Zeglin – Frontiers in Microbiology

Built environment microbiome

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

Bioreactor microbiology

Bacterial community structure in treated sewage sludge with mesophilic and thermophilic anaerobic digestion – Hana Stiborova – Folia Microbiologica

Performance and microbial community dynamics in bioaugmented aerated filter reactor treating with coking wastewater – Shengnan Shi – Bioresource Technology

Phages and viruses

My life with Mu – Ariane Toussaint – Bacteriophage

Fungi

Fungal artificial chromosomes for mining of the fungal secondary metabolome – Jin Woo Bok – BMC Genomics

Review: The Human Mycobiome – Patrick C. Seed – Cold Spring Harbor Perspectives in Medicine

Antibiotic resistance

Antibiotic resistance genes in the environment: prioritizing risks – Johan Bengtsson-Palme & D. G. Joakim Larsson – Nature Reviews Microbiology

Review: The human gut resistome – Willem van Schaik – Philosophical Transactions B

Metagenomics

Under-detection of endospore-forming Firmicutes in metagenomic data – Sevasti Filippidou – Computational and Structural Biotechnology Journal

Microbes in the news

Each Vineyard Has a Unique Microbiome – University of Chicago – The Epoch Times

Viruses: You’ve heard the bad; here’s the good – American Society for Microbiology – Science Daily

Silver turns bacteria into deadly zombies – Emily Conover – Science Magazine

Rare plague outbreak in Colorado linked to pit bull, CDC says – CNN Wire

Science, publishing, and career

A time limit on postdoctoral contracts: The French experience – Elisabeth Pain – Science Careers

Follow the Funding – Bob Grant – The Scientist

Women Scientists Share Their Awful Stories Of Sexism In Publishing – Cat Ferguson – BuzzFeed Science

Science and art

The Microbiome Votes: I mixed my microbiome with the candidates and asked them to vote – Exploring the Invisible

Bik’s Picks

Horribly bleak study sees ‘empty landscape’ as large herbivores vanish at startling rate – Fred Barbash and Justin Wm. Moyer – Washington Post

Here’s How Coffee Cups in Space Could Help Save Lives on Earth – Helen Regan – Time

Why Hawaiians are protesting construction of the world’s second-largest telescope – Joseph Stromberg – Vox.com

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April 30, 2015

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General human microbiome

Microbiome Analysis: Trends in Cancer Epidemiology, Challenges and Opportunities – Elizabeth F. Hebert – International Journal of Cancer Research and Molecular Mechanisms

Human respiratory microbiome

Still under embargo/technical difficulties: Swine Farming Is a Risk Factor for Infection With and High Prevalence of Carriage of Multidrug-Resistant Staphylococcus aureus – Shylo E. Wardyn – Clinical Infectious Diseases

The Culturome of the Human Nose Habitats Reveals Individual Bacterial Fingerprint Patterns – Ursula Kaspar – Environmental Microbiome

Human gut microbiome

Determining the Long-term Effect of Antibiotic Administration on the Human Normal Intestinal Microbiota Using Culture and Pyrosequencing Methods – Mamun-Ur Rashid – Clinical Infectious Diseases

Animal models of microbiome research

Modulation of growth performances, survival, digestive enzyme activities and intestinal microbiota in common carp (Cyprinus carpio) larvae using short chain fructooligosaccharide – Seyed Hossein Hoseinifar – Aquaculture Research

Plant microbiome

Simulation of the evolution of the legume-rhizobia symbiosis under the conditions of ecological instability – N. I. Vorobyov – Russian Journal of Genetics: Applied Research

Review: Plant-associated fungal communities in the light of meta’omics – Derek Peršoh – Fungal Diversity

Water microbiome

Editorial : Roles and mechanisms of parasitism in aquatic microbial communities – Télesphore Sime-Ngando – Frontiers in Microbiology

Picoplankton and nanoplankton variability in an Antarctic shallow coastal zone (Admiralty Bay) during the austral summer of 2010/2011 – Mariana Vanzan – Polar Biology

Relationships between Microbial Compositions and Hydrochemical Factors in Nitrate Contaminated Groundwater of Hun River Alluvial Proluvial Fan, China – A.X. Zhou – Journal of Agricultural Science and Technology

Extremophile microbiome

Picoplankton and nanoplankton variability in an Antarctic shallow coastal zone (Admiralty Bay) during the austral summer of 2010/2011 – Mariana Vanzan – Polar Biology

Microbiome of the built environment

Screening of bacteria and concrete compatible protection materials – Yusuf Çağatay Erşan – Construction and Building Materials

Bioreactor microbiology

Metal Oxide Nanoparticles Induce Minimal Phenotypic Changes in a Model Colon Gut Microbiota – Alicia A Taylor – Environmental Engineering Science

Metagenomics

Genome mining: Prediction of lipopeptides and polyketides from Bacillus and related Firmicutes – Gajender Aleti – Computational and Structural Biotechnology Journal

Book: VIRONOMICS: The Study of Viral Genomics in Human Cancer and Disease – Dirk P. Dittmer – Next Generation Sequencing in Cancer Research, Volume 2

Microbes in the news

An Atlas of the Bacteria and Fungi We Breathe Every Day – Neel V. Patel – Wired

Deadly Gut Bacteria Infections Peak in Spring – Rachael Rettner – Live Science

Study finds swine farming is a risk factor for drug-resistant staph infections – University of Iowa

Turning to Bacteria to Fight the Effects of Climate Change – Esther Ngumbi – Scientific American

Are We Less “Gutsy” Than we Used to Be? New Clues about the Evolution of the Human Microbiome from Research in Apes – Sharon Greenblum – Food Insight

How Fluid Flow Affects Bacteria – Science 2.0

Four Exceptional Contributions to the Advancement of Clinical Microbiology and Infectious Diseases Recognised at ECCMID – Select Science

Microbiome Hypome (articles that overstate microbiome importance)

The Cure for Brain Diseases Is in Your Gut – David Perlmutter – The Daily Beast

Microbes and money

Irish Microbiome Research Institute Partners With San-Francisco Based Second Genome On Bowel Disease Research – IBD News Today

Bik’s Picks

Low Sunlight Increases Pancreatic Cancer Risk; Why It’s Important To Get Enough Vitamin D – Justin Caba – Medical Daily

Bat Wings Harbor Special Sensory Cells – Stephanie Pappas – Live Science

Sea Lion Pup Waddling Around San Francisco’s Marina District Safely Captured – KPIX / KCBS

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April 28, 2015

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Wow, this was a busy day with about 700 new articles for y’all to screen. Here we go:

Events

May 7th Webinar: George Weinstock Ph.D., will present “The Human Microbiome: Impact on Health and Disease.”

May 13th Webcast at 11am EDT – “Innovations in the microbiome” with Annick Mercenier and Enea Rezzonico – Nature Publishing Group

Human oral microbiome

Periodontal disease in a remote Asian population: association between clinical and microbiological parameters – Christine Kvarnvik – Journal of Investigative and Clinical Dentistry

Human gut microbiome

Comparison of the gut microbiota of people in France and Saudi Arabia – M. Yasir – Nutrition and Diabetes

Fecal microbiota characteristics of patients with colorectal adenoma detected by screening: A population-based study – James J. Goedert – EBioMedicine

Review: Archaea associated with human surfaces: not to be underestimated – Corinna Bang , Ruth A. Schmitz – FEMS Microbiology Reviews

Review: Keeping bugs in check: The mucus layer as a critical component in maintaining intestinal homeostasis – Martin Faderl – IUBMB Life

Review: A day in the life of the meta-organism: diurnal rhythms of the intestinal microbiome and its host – Christoph A Thaiss – Gut Microbes

Review: Effect of Helicobacter pylori Infection on the Composition of Gastric Microbiota in the Development of Gastric Cancer – Cao L. · Yu J. – GastroIntestinal Tumors

Review: Immunogenetic control of the Intestinal Microbiota – Eric Marietta – Immunology

Review: Type 2 diabetes and gut microbiome: at the intersection of known and unknown – Smitha Upadhyaya – Gut Microbes

Review: Host-Microbiota Interactions in the Intestine – Elson C.O. – Digestive Diseases

Review: Control of commensal microbiota by the adaptive immune system – Husen Zhang – Gut Microbes

Animal models of microbiome research

Effects of low dietary protein on the metabolites and microbial communities in the caecal digesta of piglets – Zhen Luo – Archives of Animal Nutrition

Perturbation of the intestinal microbiota of mice infected with Cryptosporidium parvum – Refaat Ras – International Journal of Parasitology

Host litter-associated gut dynamics affect Escherichia coli abundance and adhesion genotype in rats – Michaela D. J. Blyton – Environmental Microbiology Reports

Regulation by gut commensal bacteria of carcinoembryonic antigen-related cell adhesion molecule expression in the intestinal epithelium – Yasuaki Kitamura – Genes to Cells

Bacteria-Mediated Effects of Antibiotics on Daphnia Nutrition – Elena Gorokhova – Environmental Science & Technology

Role of intestinal microbiota in the generation of polyphenol-derived phenolic acid mediated attenuation of Alzheimer’s disease β-amyloid oligomerization – Dongjie Wang – Molecular Nutrition & Food Research

Animal microbiome

Bacterial symbiont sharing in Megalomyrmex social parasites and their fungus-growing ant hosts – Joanito Liberti – Molecular Ecology

Microbial and sponge loops modify fish production in phase-shifting coral reefs – Cynthia B. Silveira – Environmental Microbiology

Coral symbiotic algae calcify ex hospite in partnership with bacteria – Jörg C. Frommlet – PNAS USA

Plant, plant root and soil microbiome

Yeast nitrogen utilization in the phyllosphere during plant lifespan under regulation of autophagy – Kosuke Shiraishi – Scientific Reports

Role of root microbiota in plant productivity – Andrzej Tkacz and Philip Poole – Journal of Experimental Botany

Seasonal variation of bacterial endophytes in urban trees – Shu Yi Shen – Frontiers in Microbiology

Plant polysaccharides initiate underground crosstalk with bacilli by inducing synthesis of the immunogenic lipopeptide surfactin – Delphine Debois – Environmental Microbiology Reports

Banana leaf and glucose mineralization and soil organic matter in microhabitats of banana plantations under long-term pesticide use – Elena Blume – Environmental Toxicology and Chemistry

Whole-genome comparative analysis of virulence genes unveils similarities and differences between endophytes and other symbiotic bacteria – Sebastian Lòpez-Fernàndez – Frontiers in Microbiology

Decreases in soil moisture and organic matter quality suppress microbial decomposition following a boreal forest fire – Sandra R. Holden – Soil Biology and Biochemistry

Soil bacterial community response to sulfadiazine in the soil–root zone – Rüdiger Reichel – Journal of Plant Nutrition and Soil Science

Three-dimensional structure and cyanobacterial activity within a desert biological soil crust – Hagai Raanan – Environmental Microbiology

Contrasting spatial patterns and ecological attributes of soil bacterial and archaeal taxa across a landscape – Florentin Constancias – Microbiology Open

Microbial 16S gene-based composition of a sorghum cropped rhizosphere soil under different fertilization managements – Anna Lavecchia – Biology and Fertility of Soils

Non-symbiotic Bradyrhizobium ecotypes dominate North American forest soils – David VanInsberghe – The ISME Journal

Deforestation fosters bacterial diversity and the cyanobacterial community responsible for carbon fixation processes under semiarid climate: a metaproteomics study – Felipe Bastida – Applied Soil Ecology

Soil pH effects on the interactions between dissolved zinc, non-nano- and nano-ZnO with soil bacterial communities – Daniel S. Read – Environmental Science and Pollution Research

Functional diversity of soil microbial communities under Scots pine, Norway spruce, silver birch and mixed boreal forests – Chodak Marcin – Pedobiologia

Water microbiome

Metabolic cascades in marine microbial communities – Andreas F. Haas and Forest Rohwer – PNAS USA

A Rickettsiales Symbiont of Amoebae with Ancient Features – Frederik Schulz – Environmental Microbiology

Bacterial communities of Beijing surface waters as revealed by 454 pyrosequencing of the 16S rRNA gene – Yu-Mei Wei – Environmental Science and Pollution Research

Cyanobacterial dynamics in shallow Lake Apopka (Florida, U.S.A.) before and after the shift from a macrophyte-dominated to a phytoplankton-dominated state – Matthew N. Waters – Freshwater Biology

Extremophile microbiome

Open Access: Metabolic and trophic interactions modulate methane production by Arctic peat microbiota in response to warming – Alexander Tøsdal Tveit – PNAS USA

Organic nitrogen cycling microbial communities are abundant in a dry Australian agricultural soil – Lori A. Phillips – Soil Biology and Biochemistry

Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystem – Karen Andrade – The ISME Journal

Microbiome of the built environment

From Lab to Field: The Influence of Urban Landscapes on the Invasive Potential of Wolbachia in Brazilian Aedes aegypti Mosquitoes – Heverton Leandro Carneiro Dutra – PLOS Neglected Tropical Diseases

Bioreactor microbiology

Deciphering Cyanide-Degrading Potential of Bacterial Community Associated with the Coking Wastewater Treatment Plant with a Novel Draft Genome – Zhiping Wang – Microbial Ecology

Seasonal Patterns in Microbial Community Composition in Denitrifying Bioreactors Treating Subsurface Agricultural Drainage – Matthew D. Porter – Microbial Ecology

Food microbiology

Analysis of Bacterial Diversity During Acetic Acid Fermentation of Tianjin Duliu Aged Vinegar by 454 Pyrosequencing – Qian Peng – Current Microbiology

Microbial Ecology

Field experimental evidence that stochastic processes predominate in the initial assembly of bacterial communities – Yi-Qi Hao – Environmental Microbiology

Effect of audible sound in form of music on microbial growth and production of certain important metabolites – Niral Sarvaiya, Vijay Kothari – Microbiology

Techniques

Optimized DNA extraction and metagenomic sequencing of airborne microbial communities – Wenjun Jiang – Nature Protocols
http://www.nature.com/nprot/journal/v10/n5/full/nprot.2015.046.html

Bioinformatics

phylogeo: an R package for geographic analysis and visualization of microbiome data –
Zachary Charlop-Powers and Sean F. Brady – Bioinformatics

PhD thesis: Statistical models for large-scale comparative metagenome analysis – Kathrin Petra Aßhauer – Georg-August-Universität Göttingen

Metagenomics

Prokaryotic genes in eukaryotic genome sequences: when to infer horizontal gene transfer and when to suspect an actual microbe – Irena I. Artamonova – Environmental Microbiology

Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes – Bing Li – The ISME Journal

Metabolomics and proteomics

Review: Microbial metaproteomics for characterizing the range of metabolic functions and activities of human gut microbiota – Weili Xiong – Proteomics

Fate of microbial metabolites of dietary polyphenols in rats: is the brain their target destination? – Mattia Gasperotti – ACS Chemical Neuroscience

Novel Systems Modeling Methodology in Comparative Microbial Metabolomics: Identifying Key Enzymes and Metabolites Implicated in Autism Spectrum Disorders – Colin Heberling – International Journal of Molecular Sciences

Navigating through metaproteomics data: A logbook of database searching –
Thilo Muth – Proteomics

Phages and viruses

Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity – Welkin H Pope – eLIFE

Linking environmental prokaryotic viruses and their host through CRISPRs
– Laura Sanguino – FEMS Microbiology Ecology

Microbes in the news

The Healthy Birth: Dyad or Triad? Exploring Birth and the Microbiome – Anne Estes – Science & Sensibility

Designing a Hospital to Better Fight Infection (about the Hospital Microbiome Project) – Robert Lee Hotz – Wall Street Journal
and
WSJ article on the Hospital Microbiome Project – Elisabeth Bik – MicroBEnet

Facts About Our Microbial Menagerie – Infection Control Today

Don’t Trust The Goats; Their Ticks Could Make You Sick – Poncie Rutsch – NPR

Tiny Creatures: The World of Microbes – Anne M. Estes – Mostly Microbes

Time-lapse movie of growth and death in bacterial communities – David Esteban – Experiment.com

Altered saliva shows increased risk for hospitalization in patients with cirrhosis, hepatic encephalopathy – Healio

An arms race of microbial proportions: A war between bacteria and bacteriophages is being fought at the genetic level – Jason Tetro – Popular Science

Microbes and money

uBiome Launches Clinical Laboratory: launch of their CLIA-regulated clinical laboratory to provide clinical tests based on its unique microbial assays – Globe News Wire

New report sheds light on the Global human microbiome market – size, share, segments analysis and outlook to 2020 – Whatech.com

Science, publishing and career

Five Non-Academic Careers for which Ph.D. Holders are Uniquely Qualified… – Colin White – Nature Careers

Study: Peer Review Predicts Success – Ruth Williams – The Scientist

Discussion paper: Appearance and Gender Bias in Academia – Tali Regev – Tel Aviv University

Bik’s Picks
Source of Antarctica’s Eerie ‘Bleeding Glacier’ Found – Becky Oskin – Live Science

Video: Watch an Algae Cell Turn Itself Inside Out – Douglas Main – NewsWeek

How do you find a Burmese python in the Everglades? – Michael Casey – CBS News

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April 27, 2015

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Events:

Life Science Sunset Mixer and Protocols Hackathon – ZappyLab – Berkeley, CA – Thursday April 30 5:30 pm PDT

Microbiome webinar: can diet can modify GI bacteria? – May 6, 2015 at 1:00pm ET – American Society for Nutrition’s Nutritional Science Council

Microbiome of pregnancy and birth

The neonatal gut harbours distinct bifidobacterial strains – Eoin Barrett – Arch Dis Child Fetal Neonatal Ed

Doctoral thesis: Early Life Intestinal Microbiota in Health and in Atopic Eczema – Lotta Nylund – Turku, Finland

In mice: Cross-fostering immediately after birth induces a permanent microbiota shift that is shaped by the nursing mother – Joseph G Daft – Microbiome

Human gut microbiome

Gut microbiota trajectory in pediatric patients undergoing hematopoietic SCT – E Biagi – Bone Marrow Transplantation

Review: Characterization of the intestinal microbiota and its interaction with probiotics and health impacts – Carine Nunes de Almada – Applied Microbiology and Biotechnology

Commentary: The Gut Microbiome: A New Frontier for Alcohol Investigation – Gail A. Cresci – Alcoholism: Clinical and Experimental Research

Review: The Microbiome for Gastroenterologists – Amit Dutta – Gastroenterology & Endoscopy News

Animal microbiome

Dynamic Distribution of the Gut Microbiota and the Relationship with Apparent Crude Fiber Digestibility and Growth Stages in Pigs – Qing Niu – Scientific Reports

Rumen: A new family of hybrid virophages from an animal gut metagenome – Natalya Yutin – Biology Direct

Rumen: Exploring the sheep rumen microbiome for carbohydrate-active enzymes – Lucas Dantas Lopes – Antonie van Leeuwenhoek

Fish: Dietary input of microbes and host genetic variation shape among-population differences in stickleback gut microbiota – Chris CR Smith – The ISME Journal

Insects: Characterization of the microbiota in the guts of Triatoma brasiliensis and Triatoma pseudomaculata infected by Trypanosoma cruzi in natural conditions using culture independent methods – Marcia Gumiel – Parasites and Vectors

Plant root and soil microbiome

Link to PDF on Fierer lab website (PNAS link still not working): Continental-scale distributions of dust-associated bacteria and fungi – Albert Barberán – PNAS

Stability and succession of the rhizosphere microbiota depends upon plant type and soil composition – Andrzej Tkacz – The ISME Journal

Forest harvesting reduces the soil metagenomic potential for biomass decomposition – Erick Cardenas – The ISME Journal

Peatland vascular plant functional types affect methane dynamics by altering microbial community structure – Bjorn JM Robroek – Journal of Ecology

Structure and function of rhizosphere and non-rhizosphere soil microbial community respond differently to elevated ozone in field-planted wheat – Zhan Chen – Journal of Environmental Sciences

Review: Plant-microbe Cross-talk in the Rhizosphere: Insight and Biotechnological Potential – Shyamalina Haldar – The Open Microbiology Journal

Water microbiome

Pyrosequencing analysis of microbial communities reveals dominant cosmopolitan phylotypes in deep-sea sediments of the eastern Mediterranean Sea – Paraskevi N. Polymenakou – Research in Microbiology

Characterization of the Relative Importance of Human- and Infrastructure-Associated Bacteria in Graywater: A Case Study – Scott P. Keely – Journal of Applied Microbiology

Extremophiles

Calcite-accumulating large sulfur bacteria of the genus Achromatium in Sippewissett Salt Marsh – Verena Salman – The ISME Journal

Book: Microbial Evolution under Extreme Conditions – Corien Bakermans – Google Books/Nature

Microbiome of the built environment

Evolutionary dynamics of methicillin-resistant Staphylococcus aureus within a healthcare system – Li-Yang Hsu – Genome Biology

Food microbiology

Evolution of microbial counts and chemical and physico-chemical parameters in high-moisture Mozzarella cheese during refrigerated storage – Annamaria Ricciardi – LWT – Food Science and Technology

Phages, viruses, and CRISPRs

CRISPR Immunity Drives Rapid Phage Genome Evolution in Streptococcus thermophilus – David Paez-Espino – mBio

Perspective: Can Plant Viruses Cross the Kingdom Border and Be Pathogenic to Humans?
Fanny Balique – Viruses

Diversity of putative archaeal RNA viruses in metagenomic datasets of a yellowstone acidic hot spring – Hongming Wang – Springer Plus

Metagenomics and Bioinformatics

He’s alive! Elviz – exploration of metagenome assemblies with an interactive visualization tool – Michael Cantor – BMC Bioinformatics

Genome assembly using Nanopore-guided long and error-free DNA reads – Mohammed-Amin Madoui – BMC Genomics

Protocol: Generating Enriched Metagenomes from Active Microorganisms with DNA Stable Isotope Probing – Carolina Grob – Springer Protocols Handbooks 2015

PhD thesis: MetaPathways : a modular pipeline for the analysis of environmental sequence information – Niels William Hanson – University of British Columbia

Metabolomics

Identification of Metabolic Signatures Linked to Anti-Inflammatory Effects of Faecalibacterium prausnitzii – Sylvie Miquel – mBio

MetaboAnalyst 3.0—making metabolomics more meaningful – Jianguo Xia – Nucleic Acids Research

Microbes in the news

Crowd funding: Stayin’ alive: how do microbes help corals recover from bleaching? The roles of bacteria in corals – Laura Núñez-Pons – Experiment.com

Building a better microbiome – Richard A. Marini – Express News

The Truth About C-Sections, Probiotics, and the Bacteria in Your Gut: Dr. Neil Stollman on fecal microbiota transplants

Your make-up could be a breeding ground for bacteria – Kimberley Hibbert – Jamaica Observer

Learning from Earth’s Smallest Ecosystems (Kavli Hangout) – Alan Brown – Live Science

Spoiled rotten: how breweries are trying to spot bad beer through DNA – Josh Lowensohn -The Verge

The Fecal Bacterium You’ll Learn to Love – Jason Tetro – Huffington Post

Pet Talk: Research reveals canine skin microbiome – Your Houston News

Physician-scientist cautions against indiscriminate use of antibiotics – Bob Kustra – Idaho Statesman

Waterproof bacteria inspire special coatings – Tim Sandle – Digital Journal

Metanome changes name to Diversigen – News Medical

Solving Real-World Problems With Unconventional Solutions: Using Bacteria To Heal Wounds – Texas A&M Today

Strike a healthy bacteria balance in your gut – Scott Scanlon – Buffalo News

How Safe is Your Shrimp? – Consumer Reports study finds 60% of frozen shrimp contaminated with bacteria – Food Safety News

Science, publishing, and career

Trove of VA reports reveals research misconduct, medical malpractice – Brendan Borrell – Retraction Watch

Lab Bloopers: Reddit users share the worst mishaps they’ve witnessed while working in the lab – Jenny Rood – The Scientist

Peer review, explained (cartoon) – Academia Obscura

Bik’s Picks

Why pregnant women in Mississippi keep dying – Danielle Paquette – Washington Post

Oil May Have Killed Gulf Dolphins – David Biello – Scientific American

Photos: 7-Year-Old Boy Discovers T. Rex Cousin – Live Science
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April 24, 2015

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Events

MetaSUB: First International Summit of Metagenomics & Metadesign of Subways and Urban Biomes – June 2015 – Christopher Mason – MicroBE.net

Human oral microbiome

Comparison of Bacterial Community Composition of Primary and Persistent Endodontic Infections Using Pyrosequencing – Giorgos N. Tzanetakis – Journal of Endodontics

Total and Specific Bacterial Levels in the Apical Root Canal System of Teeth with Post-treatment Apical Periodontitis – Henrique S. Antunes – Journal of Endodontics

Ability of Human Oral Microbiota to Produce Wine Odorant Aglycones from Odourless Grape Glycosidic Aroma Precursors – Carolina Muñoz-González – Food Chemistry

Human gut microbiome

Ecological effect of ceftazidime/avibactam on the normal human intestinal microbiota – Mamun-Ur Rashid – International Journal of Antimicrobial Agents

Manually curated database: Mycobiome: Approaches to analysis of intestinal fungi – Jie Tang – Journal of Immunological Methods

No abstract, behind paywall – Isoflavones and the gut microbiome – Herman Depypere – Maturitas

Animal models of microbiome research

Perturbation of the intestinal microbiota of mice infected with Cryptosporidium parvum – Refaat Ras – International Journal for Parasitology

Dysbiosis and Staphyloccus aureus Colonization Drives Inflammation in Atopic Dermatitis – Tetsuro Kobayashi – Immunity

Animal microbiome

Evaluation of Composition and Individual Variability of Rumen Microbiota in Yaks by 16S rRNA High-throughput Sequencing Technology – Wei Guo – Anaerobe

Diversity and phylogenetic analysis of endosymbiotic bacteria of the date palm root borer Oryctes agamemnon (Coleoptera: Scarabaeidae) – Wael S El-Sayed and Reda A Ibrahim – BMC Microbiology

Review: Genomics of the honey bee microbiome – Nancy A. Moran – Current Opinion in Insect Science

Review: Hologenome theory and the honey bee pathosphere – Ryan S. Schwarz – Current Opinion in Insect Science

Water microbiome

Metagenome-assembled genomes uncover a global brackish microbiome – Luisa W Hugerth – BioRxiv

Built environment microbiome

Review: Hospital-associated microbiota and implications for nosocomial infections – Simon Lax and Jack A Gilbert – Trends in Molecular Medicine

Microbes and immunology

Of mice, macaques and men: scaling of virus dynamics and immune responses – Christian L. Althaus – Frontiers in Microbiology

Extremophiles

Deciphering the microbiota of Tuwa hot spring, India using shotgun metagenomic sequencing approach – Amitsinh Mangrola – Genomics Data

Review: Thermophiles in the genomic era: Biodiversity, science, and applications – M. Sofía Urbieta – Biotechnology Advances

Microbes in the news

Justin and Erica Sonnenburg: Cute Family. And You Should See Their Bacteria –  John Swansburg @thescienceofus @NYMag

Episode 5 of The Microbiome Podcast: Diet and its impact on our microbiota and health with Drs. Erica and Justin Sonnenburg – American Microbiome Institute

The Man Who Drank Cholera and Launched the Yogurt Craze – Ilya Metchnikoff laid the foundation for modern probiotics – Lina Zeldovich- Nautilus

Dirk Gevers, heading the Janssen Human Microbiome Institute – Nature Reviews Drug Discovery

Science, publishing, and career

Big names or big ideas: Do peer-review panels select the best science proposals? – Danielle Li, Leila Agha – Science

Bik’s Picks

When Hubble Stared at Nothing for 100 Hours – Nadia Drake – National Geographic

Neuroscientists Create Illusion of Having Invisible Body – Sci-News

Entire genomes of woolly mammoths mapped: Clues to extinction, possibility of bringing mammoths back – Science Daily

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April 20, 2015

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Happy 4/20! Here is a paper from last June that deserves renewed attention today: 

Understanding Cultivar-Specificity and Soil Determinants of the Cannabis Microbiome – Max E. Winston – PLOS ONE

Human oral microbiome

Review: Ecological Approaches to Oral Biofilms: Control without Killing – Marsh P.D. – Caries Research

Human vaginal microbiome

A multi-platform metabolomics approach identifies novel biomarkers associated with bacterial diversity in the human vagina – Amy McMillan – ArXiv

Comparison of detection methods for vaginal lactobacilli – I. Smidt – Beneficial Microbes

Human gut microbiome

Differences in Gut Microbiota Between Atopic and Healthy Children – Tiina Drell – Current Microbiology

DGGE: Is there interaction between gut microbial profile and cardiovascular risk in chronic kidney disease patients? – Amanda F Barros – Future Medicine

Thesis: Characterization and Investigation of Fungi Inhabiting the Gastrointestinal Tract of Healthy and Diseased Humans – Mallory J Suhr – University of Nebraska-Lincoln

Poster: The MS Microbiome Consortium (MSMC): an academic multi-disciplinary collaborative effort to elucidate the role of the gut microbiota in MS (P2.205)
Ilana Katz Sand – Neurology

Review: Gut microbiota and Ma-Pi 2 macrobiotic diet in the treatment of type 2 diabetes – Francesco Fallucca – World Journal of Diabetes

Animal microbiome

The coral core microbiome identifies rare bacterial taxa as ubiquitous endosymbionts
Tracy D Ainsworth – The ISME Journal

Plant root and soil microbiome

Tree: Genetic Diversity and Functional Traits of Pterocarpus officinalis Jacq. Associated with Symbiotic Microbial Communities in Caribbean Swamp Forests in Relation to Insular Distribution, Salinity and Flooding – Amadou M. Bâ, Elsie Rivera-Ocasio – Wetlands

Plant: Effects of cowpea (Vigna unguiculata) root mucilage on microbial community response and capacity for phenanthrene remediation – Ran Sun – Journal of Environmental Sciences

Effect of conventional and organic orchard floor management practices on enzyme activities and microbial counts in a ‘Cripp’s Pink’/M7 apple orchard – André H Meyer – South African Journal of Plant and Soil

Successional and seasonal variations in soil and litter microbial community structure and function during tropical post-agricultural forest regeneration: A multi-year study
A. Peyton Smith – Global Change Biology

Editorial: Increasing diversity – Andrea Du Toit – Nature Reviews Microbiology

Soils naturally suppressive to banana Fusarium wilt disease harbor unique bacterial communities – Zongzhuan Shen – Plant and Soil

Cropping systems modulate the rate and magnitude of soil microbial autotrophic CO2 fixation in soil – Xiao H. Wu – Frontiers in Microbiology

Cave microbiome
Nutrient input influences fungal community composition and size and can stimulate Mn(II) oxidation in caves – SK Carmichael – Environmental Microbiology Reports

Water microbiome

Temporal and spatial constraints on community assembly during microbial colonization of wood in seawater – Dimitri Kalenitchenko – The ISME Journal

Extremophiles

In situ expression of eukaryotic ice-binding proteins in microbial communities of Arctic and Antarctic sea ice – Christiane Uhlig – The ISME Journal

Metatranscriptomes reveal functional variation in diatom communities from the Antarctic Peninsula – Gareth A Pearson – The ISME Journal

Venn Diagrams galore: Multi-scale variability analysis reveals the importance of spatial distance in shaping Arctic soil microbial functional communities – Yu Shi – Soil Biology and Biochemistry

Microbes of the built environment

Influence of housing characteristics on bacterial and fungal communities in homes of asthmatic children – K. C. Dannemiller – Indoor Air

Microbial diversity in bioaerosol samples causing ODTS compared to reference bioaerosol samples as measured using Illumina sequencing and MALDI-TOF – Anne Mette Madsen – Environmental Research

Molecular characterization of microbial communities and quantification of Mycobacterium immunogenum in metal removal fluids and their associated biofilms
Jianfeng Wu – Environmental Science and Pollution Research

Bioreactor and wastewater microbiology

Microbial Mats as a Biological Treatment Approach for Saline Wastewaters: The Case of Produced Water from Hydraulic Fracturing – Benay Akyon – Environmental Science & Technology

Dynamics and distribution of bacterial and archaeal communities in oil-contaminated temperate coastal mudflat mesocosms – Gbemisola O. Sanni – Environmental Science and Pollution Research

Techniques

Flow cytometry as an auxiliary tool for the selection of probiotic bacteria – D. Mudroňová – Beneficial Microbes

Other microbiology papers

Shattering old beliefs: Gram’s stain does not cross the bacterial cytoplasmic membrane – Michael J. Wilhelm – ACS Chemical Biology

Dynamic Clustering in Suspension of Motile Bacteria – Xiao Chen – ArXiv

Microbes in the news

Jessica Richman, CEO of uBiome joins for short Toolmaker Talk about microbiome – Quantified Self Radio

Top 100 Most Influential People, with Martin Blaser – Almudena Bernabea – Time

Video: David Sela, PhD: Probiotics, nutrition & the microbiome – UMass Amherst – YouTube

Can Specks of Dust Help Solve Crimes? – Mandy Oaklander – Time

Bacterial flora of remote tribespeople carries antibiotic resistance genes – Science Daily

In fight against Crohn’s, professor battles bacteria – Scott Goss – USA Today

Are gut bacteria manipulating your mood? – Viviane Richter – Cosmos Magazine

To fight nasty digestive bugs, U-M scientists set out to build a better gut – using stem cells – HealthCanal

Mouth bacteria can tell the status of liver disease – Zee News

How the gut garden affects fat-burning – Sylvia Harral, Michele Stewart – Recorder Online

Maple Syrup Extract May Fight Infection-Causing Bacteria: Study – Joanna Adams – Huffington Post

How Things Work: Phages occupy bacteria to cure infection – Sharon Wu – The Tartan

The Bacteria Will See You Now: How Little Bugs Create Big Problems in Hospitals – Brian Krans – HealthLine

Cytokinins Cannot Be Associated with Plants Only: Being Present in Bacteria, They Also Affect Resistance to TB – Martina Šaradínová

Microbes and art

Video: Anna Dumitriu – “Don’t try this at home” – creating microbial artwork from faecal transplants – YouTube

Now with a Colon and Rectum – but Super Stomach and Tremendous Testicle are cute too. Bladder is on sale! I Heart Guts Plush Organs

Science, publishing, and career

University of Victoria student diving for his master’s – Jeff Bell – Times Colonist (HT: Ed Yong)

Bik’s Picks

Roundup and Risk Assessment – Michael Specter – New Yorker

Vampire Squid Outlast Their Shallower Peers – SindyaN. Bhanoo – New York Times

New species of frog found in Costa Rica looks just like Kermit – Andrea Romano – Mashable

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April 16, 2015

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Human gut microbiome

Alcoholic Liver Disease: The Gut Microbiome and Liver Cross Talk – Phillipp Hartmann – Alcoholism: Clinical and Experimental Research

Animal models of microbiome research

Xylo-oligosaccharides and virginiamycin differentially modulate gut microbial composition in chickens – Mohsen Pourabedin – Microbiome

Taking advantage of quorum sensing – Cláudio Nunes-Alves – Nature Reviews Microbiology

Changes in the colon microbiota and intestinal cytokine gene expression following minimal intestinal surgery – Susan Lapthorne – World Journal of Gastroenterology

Animal microbiome

Insect life history and the evolution of bacterial mutualism – Lee M. Henry – Ecology Letters

Bugs full of viruses – Astrid Gall – Nature Reviews Microbiology

Similar sponge-associated bacteria can be acquired via both vertical and horizontal transmission – Detmer Sipkema – Environmental Microbiology

Transcriptional activity of the giant barrel sponge, Xestospongia muta Holobiont: Molecular Evidence for Metabolic Interchange – Cara L. Fiore – Frontiers in Microbiology

Water microbiome

Shift of anammox bacterial community structure along the Pearl Estuary and the impact of environmental factors – Bingbing Fu – Journal of Geophysical Research

Metatranscriptome analyses indicate resource partitioning between diatoms in the field – Harriet Alexander – PNAS USA

Microbiome of the built environment

Total Concentrations of Virus and Bacteria in Indoor and Outdoor Air – Aaron J. Prussin – Environmental Science and Technology Letters
See also my blog post on MicroBE.net about this paper, with a lively discussion on filters and pore sizes

Food microbiology

Effect of Gamma Irradiation on the Bacteriological and Sensory Analysis of Raw Whole Milk under Refrigeration – Adriana Cristina de Oliveira Silva

Bioreactor microbiology

Disturbance opens recruitment sites for bacterial colonization in activated sludge – David C. Vuono – Environmental Microbiology

Metaproteomics of complex microbial communities in biogas plants – Robert Heyer – Microbial Biotechnology

16S rRNA gene analysis, not metagenomics: Metagenomic analysis for the microbial consortium of anaerobic CO oxidizers – Ying Guo – Microbial Biotechnology

Bioinformatics

Protocol: Bioinformatics and Microarray Data Analysis on the Cloud – Barbara Calabrese, Mario Cannataro – Methods in Molecular Biology

An Ontology-Based GIS for Genomic Data Management of Rumen Microbes – Saber Jelokhani-Niaraki – Genomics & Informatics

Behind a very thick paywall: Application of Meta-Mesh on the analysis of microbial communities from human associated-habitats – Xiaoquan Su – Quantitative Biology

Metagenomics

The metagenomic approach and causality in virology – Silvana Beres Castrignano and Teresa Keico Nagasse-Sugahara – Rev Saúde Pública

Techniques

Use of pressure cycling technology for cell lysis and recovery of bacterial and fungal communities from soil – Emily A. Bruner – BioTechniques

Microbial Ecology

Estimating and Mapping Ecological Processes Influencing Microbial Community Assembly – James C. Stegen – Frontiers in Microbiology

More microbiology

The Infallible Microbial Identification Test: Does It Exist? – Alex van Belkum – Journal of Clinical Microbiology

Microbes in the news

Synthetic Cheese and the Microbiome – Alex A. — MicroBE.net

Total Concentrations of Virus and Bacteria in Indoor and Outdoor Air – Elisabeth Bik – MicroBE.net

A Review of the Oral Microbiome: Orli Reports – Orli Kadoch – uBiome Blog

To fight nasty digestive bugs, scientists set out to build a better gut—using stem cells – Medical Xpress

#BacteriaArePlural The bacteria that steals DNA from its surroundings – Mette Risbråthe – Norwegian University of Life Sciences

#BacteriaHysteria: Germ warfare: Kitchens can harbor hidden bacteria – Katherine Roth – The Pueble Chieftain

Science, publishing, and career

A resource for cell line authentication, annotation and quality control – Mamie Yu – Nature

Science AMA Series: We are Charon Pierson, journal editor and elected member of the Governing Council for the Committee on Publication Ethics (COPE) and Ivan Oransky, co-founder of Retraction Watch. AUA about publication ethics and retractions.

Rule rewrite aims to clean up scientific software – Nature Biotechnology asks peer reviewers to check accessibility of code used in computational studies – Erika Check Hayden – Nature

Bik’s Picks

Response of seafloor ecosystems to abrupt global climate change – Sarah E. Moffitt – PNAS USA

Longread: The Pollen Detective – He’d used science to crack cases from art forgery to bank robbery. But then a murder took place in his own backyard – David Wolman – Medium

This professor measured his fingernail growth for 35 years. The results will amaze you! – Seriously, Science? – Discover