Category Archives: Extremophiles

June 10, 2015

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Another load of microbiome reviews, historical responses of microbes to mercury in soil layers, and different pictures of microbial diversity using culture or molecular techniques.

Microbiome of pregnancy and health

Review: Lungs, Microbes and the Developing Neonate – Warner B.B., Hamvas A. – Neonatology

Review: Placentophagy: therapeutic miracle or myth? – Cynthia W. Coyle – Archives of Women’s Mental Health

Review: Preterm delivery and intimacy during pregnancy: interaction between oral, vaginal and intestinal microbiomes – Herrera Morban DA – Medwave

Human gut microbiome

Review: Monitoring host responses to the gut microbiota – Joshua S Lichtman, Justin L Sonnenburg and Joshua E Elias – The ISME Journal

Review: Intestinal Fucose as a Mediator of Host–Microbe Symbiosis – Joseph M. Pickard and Alexander V. Chervonsky – The Journal of Immunology

Review: Novel players in coeliac disease pathogenesis: role of the gut microbiota – Elena F. Verdu – Nature Reviews Gastroenterology & Hepatology

Review: Gut Microbiome-Brain Communications Regulate Host Physiology and Behavior – Sun Hye Lee and Claire B. de La Serre – Journal of Nutritional Health & Food Science

Review: Biliary Mucosal Barrier and Microbiome – Verdier J – Viszeralmedizin

Review: From Next-Generation Sequencing to Systematic Modeling of the Gut Microbiome – Boyang Ji and Jens Nielsen – Frontiers in Microbiology

Animal and other models of microbiome research

Bioimage analysis of Shigella infection reveals targeting of colonic crypts – Ellen T. Arena – PNAS

Animal microbiome

Filamentous fungi isolated from the fur microbiota of callitrichids kept in captivity in Brazil – de Freitas RA – J Zoo Wildl Med

Plant root and soil microbiome

Microbial response to simulated global change is phylogenetically conserved and linked with functional potential – Anthony S Amend – The ISME Journal

Microbial and biochemical basis of a Fusarium wilt-suppressive soil – Jae-Yul Cha – The ISME Journal

Microbial DNA records historical delivery of anthropogenic mercury – Alexandre J Poulain – The ISME Journal

Riverbed methanotrophy sustained by high carbon conversion efficiency – Mark Trimmer – The ISME Journal

Culture-Dependent and -Independent Methods Capture Different Microbial Community Fractions in Hydrocarbon-Contaminated Soils – Franck O. P. Stefani – PLOS ONE

Crop monoculture rather than agriculture reduces the spatial turnover of soil bacterial communities at a regional scale – Eva L. M. Figuerola – Environmental Microbiology

Bacteria and fungi associated with isoprene consumption in soil – Christopher M. Gray – Elementa-Science of the Anthropocene

Microbial rRNA:rRNA gene ratios may be unexpectedly low due to extracellular DNA preservation in soils – Glade Dlott – Journal of Microbiological Methods

Differences in microbial community composition between injection and production water samples of water flooding petroleum reservoirs – P. K. Gao – Biogeosciences

Commentary: Scrambled and not-so-tiny genomes of fungal endosymbionts – Chih-Horng Kuo – PNAS

Water microbiome

Sampling the Sea Surface Microlayer – Michael Cunliffe, Oliver Wurl – Springer Protocols
Built environment microbiome

Book chapter: Bacteria and Fungi in Green Roof Ecosystems – Krista L. McGuire – Green Roof Ecosystems

Extremophile microbiome

Application of artificial neural networks as a tool for moisture prediction in microbially colonized halite in the Atacama Desert – K. Wierzchos – Journal of Geophysical Research – Biogeosciences

Bioreactor microbiology

Methanobacterium Dominates Biocathodic Archaeal Communities in Methanogenic Microbial Electrolysis Cells – Michael Siegert – ACS Sustainable Chemistry & Engineering

Metagenomics and bioinformatics

ProDeGe: a computational protocol for fully automated decontamination of genomes – Kristin Tennessen – The ISME Journal

RNeXML: a package for reading and writing richly annotated phylogenetic, character, and trait data in R – Carl Boettiger – arXiv

PrimerView: high-throughput primer design and visualization – Damien M. O’Halloran – Source Code for Biology and Medicine

Techniques

Whole genome capture of vector-borne pathogens from mixed DNA samples: a case study of Borrelia burgdorferi – Giovanna Carpi – BMC Genomics

Cultivation of Environmental Bacterial Communities as Multispecies Biofilms – Marc A. Demeter – Springer Protocols Handbook

Microbes in the news

Brits will swab surfers’ butts to understand antibiotic-resistant bacteria – Alexandra Ossola – Popular Science

You’ve been invaded – by your Microbiome! Video with Rob Knight – UCSD TV

Understanding the nasal microbiome – American Microbiome Institute

How gut bacteria affects your health: What we know, what we don’t – Emily Kaiser – MPR News

The Secrets of Ocular Microbiomes – Mark B. Abelson – Review of Ophthalmology

Nice graphics: To the Phyllosphere and Beyond! – Ben Wolfe – Lucky Peach

Meanwhile in the Future: When Antibiotics Stop Working – Rose Eveleth – Gizmodo

Obesity and Microbiota: What’s Hype, What’s Helpful? – Jeannette Y. Wick – HCP Live

Science, publishing, and career

Nobel Prize Winner Tim Hunt Shocks Journalists With Sexist Comments – Cat Ferguson – BuzzFeed Science

Career coaching for scientists – Joanne Kamens – Nature Biotechnology

Intel Capital Creates $125M Fund for Women-, Minority-led Startups – Deborah Gage – Wall Street Journal

UTHealth’s Kevin Morano, microbiologist receives prestigious teaching honor by Minnie Stevens Piper Foundation – EurekAlert

Bik’s Picks

Caffeine acts through neuronal adenosine A2A receptors to prevent mood and memory dysfunction triggered by chronic stress – Manuella P. Kaster – PNAS

Chimps dig palm wine, new study finds: And in case you were wondering, the apes did occasionally get tipsy – Amina Khan – Los Angeles Times

This new Google-backed app will identify a bird just from a photo – Quartz

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June 8, 2015

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General microbiome

Minireview: The brain’s Geppetto—microbes as puppeteers of neural function and behaviour? – Roman M. Stilling – Journal of NeuroVirology

Thesis: Novel computational approaches to investigate microbial diversity – Qingpeng Zhang – Michigan State University

Microbiome of pregnancy and birth

Distinctive Intestinal Lactobacillus Communities in Six-Month-Old Infants From Rural Malawi and South-Western Finland – Aakko, Juhani – Journal of Pediatric Gastroenterology & Nutrition

Antenatal Microbiome: Potential Contributor to Fetal Programming and Establishment of the Microbiome in Offspring – Michelle L. Wright, Angela R. Starkweather – Nursing Research

Review: Should Abnormal Vaginal Flora in 2 nd Trimester of Pregnancy be Treated to Prevent Preterm Labor – Gunjan Kumari, Anjali Tempe – Journal of Medical Sciences

Human oral microbiome

The oral mucosal and salivary microbial community of Behcet’s syndrome and recurrent aphthous stomatitis – Noha Seoudi – Journal of Oral Microbiology

Human gut microbiome

Review: Unraveling the environmental and genetic interactions in atherosclerosis: Central role of the gut microbiota – Elin Org – Atherosclerosis

Review: The Effects of Diet and the Microbiome on Reproduction and Longevity: A Comparative Review Across 5 Continents – Stephanie N. Chilton – Nutrition and Food Sciences

Animal models of microbiome research

Lack of Vitamin D Receptor Causes Dysbiosis and Changes the Functions of the Murine Intestinal Microbiome – Dapeng Jin – Clinical Therapeutics

Animal microbiome

Acromyrmex leaf-cutting ants have simple gut microbiota with nitrogen-fixing potential – Panagiotis Sapountzis – Applied and Environmental Microbiology

Anemone: Response of bacterial colonization in Nematostella vectensis to development, environment and biogeography – Benedikt Mortzfeld – Environmental Microbiology

Plant root and soil microbiome

Responses of bacterial communities in seagrass sediments to polycyclic aromatic hydrocarbon-induced stress – Juan Ling – Ecotoxicology

Analyses of microbial biomass and community diversity in kiwifruit orchard soils of different planting ages – Qingxia Fu – Acta Ecologica Sinica

The effects of the presence of Bt-transgenic oilseed rape in wild mustard populations on the rhizosphere nematode and microbial communities – Yongbo Liu – Science of The Total Environment

Long-term conservation tillage influences the soil microbial community and its contribution to soil CO2 emissions in a Mollisol in Northeast China – Shuxia Jia – Journal of Soils and Sediments

Microbial communities inhabiting oil-contaminated soils from two major oilfields in Northern China: Implications for active petroleum-degrading capacity – Weimin Sun – Journal of Microbiology

Differential degradation of polycyclic aromatic hydrocarbon mixtures by indigenous microbial assemblages in soil – Przemyslaw Sawulski – Letters in Applied Microbiology

A novel salt-tolerant chitobiosidase discovered by genetic screening of a metagenomic library derived from chitin-amended agricultural soil – Mariana Silvia Cretoiu – Applied Microbiology and Biotechnology

Book chapter: Irrigation with Treated Wastewater: Potential Impacts on Microbial Function and Diversity in Agricultural Soils – Ana Rita Lopes – The Handbook of Environmental Chemistry 2015

Water microbiome

Response of bacteria and meiofauna to iron oxide colloids in sediments of freshwater microcosms – Sebastian Höss – Environmental Toxicology and Chemistry

Response of rare, common and abundant bacterioplankton to anthropogenic perturbations in a Mediterranean coastal site – Federico Baltar – FEMS Microbiology Ecology

Book Chapter: Marine Litter as Habitat and Dispersal Vector – Tim Kiessling – Marine Anthropogenic Litter

Thesis: Metagenomic profiling of microbial metal interaction in Red Sea deep-anoxic brine pools – Hanna, Mina Magdy Abdelsayed – American University in Cairo

Built environment microbiome

Microbial community composition of a household sand filter used for arsenic, iron, and manganese removal from groundwater in Vietnam – Katja Sonja Nitzsche – Chemosphere

The role of bacterial communities and carbon dioxide on the corrosion of steel – K.M. Usher – Corrosion Science

Extremophile microbiome

Review: Metagenomics of extreme environments – DA Cowan – Current Opinion in Microbiology

Food microbiology

Review: The impact of climate change on existing and emerging microbial threats across the food chain: An island of Ireland perspective – Linda D. Stewart – Trends in Food Science & Technology

Review: Microbial decontamination of food by electron beam irradiation – Hsiang-Mei Lung – Trends in Food Science & Technology

Bioreactor microbiome

Bioreactor microbial ecosystems for thiocyanate and cyanide degradation unraveled with genome-resolved metagenomics – Rose S. Kantor – Environmental Microbiology

Bioinformatics and metagenomics

CCLasso: Correlation Inference for Compositional Data through Lasso – Huaying Fang – Bioinformatics

GAML: genome assembly by maximum likelihood: combination of diverse sequencing datasets into a single assembly – Vladimír Boža – Algorithms for Molecular Biology

Effects of library size variance, sparsity, and compositionality on the analysis of microbiome data – Sophie J Weiss – PeerJ

Review: Identification of Viruses and Viroids by Next-Generation Sequencing and Homology-Dependent and Homology-Independent Algorithms – Qingfa Wu – Annual Reviews Phytopathology

Metabolomics

Mapping microbial response metabolomes for induced natural product discovery – Dagmara K. Derewacz – ACS Chemical Biology
http://pubs.acs.org/doi/abs/10.1021/acschembio.5b00001

Techniques

Analysis of microsamples of human faeces: a non-invasive approach to study the bioavailability of fat-soluble bioactive compounds – E. Hernandez-Alvarez – European Journal of Nutrition

Microbes in the news

Say hello to your little friends: Making sense of gut bacteria – Wency Leung – Globe and Mail

Surfers help science in fight against antibiotic resistant bacteria with their poop – Luigi Lugmayer – i4u

Effects of zinc oxide on intestinal microbiota – All About Feed

Video: Waxworm Bacteria Could Recycle Plastic Trash – NBC News

Is That Water Hot Enough to Kill Germs? – C. Claiborne Ray – New York Times

Gut bacteria play a vital role to your health – Sharon Ní Chonchuir – Irish Examiner

New microscope technique could speed identification of deadly bacteria – EurekAlert

Science, publishing, and career

Better advice for ‘Bothered’ – Science Careers Staff – Science Magazine

Retractions and High Profile Journals – Peter Edmonds

Bik’s Picks

Black Hole Hunters – Dennis Overbye – New York Times

Everything You Need to Know About Bill Nye’s Crazy Experimental Spaceship – Jack Linshi – Time

Under the Sea: Google Views for World Oceans Day – Patrick J. Kiger – Discovery

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June 6, 2015

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A new paper on the microbiome of the human nose, several gut microbiome reviews,  microbiomes of soils and extreme environments, microbiome models and a cool poster about defining OTU. Happy Saturday!

Human oral microbiome

Antimicrobial Effect of a Single Dose of Amoxicillin on the Oral Microbiota – Cecilia Larsson Wexell – Clinical Implant Dentistry and Related Research

Human respiratory microbiome

Staphylococcus aureus and the ecology of the nasal microbiome – Cindy M. Liu – Science Advances

Human gut microbiome

Review: Interactions between Diet, Bile Acid Metabolism, Gut Microbiota, and Inflammatory Bowel Diseases – Devkota S – Digestive Diseases

Review: Gut Microbiota, Cirrhosis, and Alcohol Regulate Bile Acid Metabolism in the Gut – Ridlon J.M – Digestive Diseases

Review: Relationship between Obesity, Gut Microbiome and Hepatocellular Carcinoma Development – Hara E. – Digestive Diseases

Animal models of microbiome research

Absence of the intestinal microbiota exacerbates hepatobiliary disease in a murine model of primary sclerosing cholangitis – James H. Tabibian – Hepatology

Effects of dietary fat profile on gut permeability and microbiota and their relationships with metabolic changes in mice – Yan Y. Lam – Obesity

Animal microbiome

Gut-Associated Bacteria of Dendroctonus valens and their Involvement in Verbenone Production – Letian Xu – Microbial Ecology

Feeding of β-1,3/1,6-glucan increases the diversity of the intestinal microflora of carp (Cyprinus carpio) – V. Jung-Schroers – Aquaculture Nutrition

Changes in coral reef communities across a natural gradient in seawater pH – Hannah C. Barkley – Science Advances

Plant root, soil and sediment microbiome

Symbiosis with an endobacterium increases the fitness of a mycorrhizal fungus, raising its bioenergetic potential – Alessandra Salvioli – ISME Journal

Bacterial Diversity in Bentonites, Engineered Barrier for Deep Geological Disposal of Radioactive Wastes – Margarita Lopez-Fernandez – Microbial Ecology

Is Planktonic Diversity Well Recorded in Sedimentary DNA? Toward the Reconstruction of Past Protistan Diversity – Eric Capo – Microbial Ecology

Water microbiome

Phytoplankton community structure in relation to vertical stratification along a north-south gradient in the Northeast Atlantic Ocean – Kristina D. A. Mojica – Limnology and Oceanography

Extremophile microbiome

Supratidal Extremophiles—Cyanobacterial Diversity in the Rock Pools of the Croatian Adria – Maria Brandes – Microbial Ecology

Pyrosequencing-Based Assessment of the Microbial Community Structure of Pastoruri Glacier Area (Huascarán National Park, Perú), a Natural Extreme Acidic Environment – Elena González-Toril – Microbial Ecology

Metagenomics and bioinformatics

Bioinformatic Amplicon Read Processing Strategies Strongly Affect Eukaryotic Diversity and the Taxonomic Composition of Communities – Markus Majaneva

Microbiome models, on computers and in lab dishes, see progress – Jop de Vrieze – Nature Medicine

Don’t miss this cool poster: OTU robustness, reproducibility and ecological consistency in the demarcation of operational taxonomic units – Thomas SB Schmidt

Microbes in the news

Nasal Microbiome Study Examines Influence of Host Genetics, Types of Bacterial Communities – Genome Web

The fastest-growing biome on Earth is in our homes. Forget your kids and pets. Your house’s biodiversity hotspots shelter tons of microorganisms – Mary Jo DiLonardo

Socialising Baboons and Gut Microbes – deSciphered: summarising research with simple graphics

Exploring the Link Between Gut Microbes and Diabetes – Betul Hatipoglu

Kaiser Permanente Fresno uses ‘zapper’ to get rid of deadly bacteria – ABC30

This Man Believes Mushrooms Can Solve Virtually All of Humanity’s Problems: next probiotic? – Munchies

Bik’s Picks

Eating placenta ‘does not benefit health’: There is no scientific evidence that eating the placenta after childbirth can protect women against depression and boost energy, US research suggests –  – BBC News

Ancient Shark Fossil Found in Texas – Deborah Grace – Pioneer News

Video: Robots Falling Down at DARPA Robotics Challenge – IEEE Spectrum – Youtube

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Another June 1, 2015

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Here’s the second update of today, completing the backlog because of my travels. 

Human skin microbiome

The Cutaneous Microbiome in Outpatients Presenting With Acute Skin Abscesses – James M. Horton – Journal of Infectious Diseases

Book chapter: Skin Microbiota and Attractiveness to Mosquitoes – Niels O. Verhulst, Willem Takken – Encyclopedia of Metagenomics

Human gut microbiome

High prevalence of cannabis use among Aka foragers of the Congo Basin and its possible relationship to helminthiasis – Casey J. Roulette – American Journal of Human Biology

Hospitalization Type Predicts Risk of Subsequent Severe Sepsis – Hallie C Prescott – American Journal of Respiratory and Critical Care Medicine

Review: Harnessing the Microbiome to Enhance Cancer Immunotherapy – Michelle H. Nelson – Journal of Immunology Research

Review: The functional impact of the intestinal microbiome on mucosal immunity and systemic autoimmunity – Randy S. Longman – Current Opinion in Rheumatology

Review: The intestinal microbiome in spondyloarthritis – Tejpal Gill – Current Opinion in Rheumatology

Microbiome models

Thesis: Alterations in the Fecal Microbiome of Healthy Horses in Response to Antibiotic Treatment – Rachel Sarah Liepman – Ohio State University

Thesis: Effects of Maternal Dietary Yeast Supplementation on Foal Growth and Microbial
Diversity of the Hindgut in Quarter Horse Mares and Their Offspring – Elizabeth Rebecca Share – Ohio State University

Soil, plant root, and rock microbiome

Fungal invasion of the rhizosphere microbiome – Emilie Chapelle – ISME Journal

Shifts in the phylogenetic structure of arbuscular mycorrhizal fungi in response to experimental nitrogen and carbon dioxide additions – Rebecca C. Mueller – Oecologia

Archean (3.33 Ga) microbe-sediment systems were diverse and flourished in a hydrothermal context – Frances Westall – Geology

Crop rotational diversity enhances belowground communities and functions in an agroecosystem – L. K. Tiemann – Ecology Letters

Evaluation of culture-based techniques and 454 pyrosequencing for the analysis of fungal diversity in potting media and organic fertilizers – Abdullah M. Al-Sadi – Journal of Applied Microbiology

Water microbiome

Aquifer community structure in dependence of lithostratigraphy in groundwater – Andrea Beyer – Environmental Science and Pollution Research

Microbial diversity in the deep-sea sediments of Iheya North and Iheya Ridge, Okinawa Trough – Jian Zhang – Microbiological Research

Urbanisation and earthquake disturbance influence microbial nutrient limitation in streams – Emma R. Moffett – Freshwater Biology

On the use of the serial dilution culture method to enumerate viable phytoplankton in natural communities of plankton subjected to ballast water treatment – John J. Cullen, Hugh L. MacIntyre – Journal of Applied Phycology

Unravelling core microbial metabolisms in the hypersaline microbial mats of Shark Bay using high-throughput metagenomics – Rendy Ruvindy – ISME Journal

Carbon export efficiency and phytoplankton community composition in the Atlantic sector of the Arctic Ocean – Frédéric A. C. Le Moigne – Journal of Geophysical Research – Oceans

Extremophile microbiome

Photoadaptation to the polar night by phytoplankton in a permanently ice-covered Antarctic lake – Morgan-Kiss R. M.- Limnology and Oceanography

Biodegradation: Updating the concepts of control for microbial clean-up in contaminated aquifers – Rainer Udo Meckenstock – Environmental Science & Technology

Bioreactor microbiome

Multi-system Nernst–Michaelis–Menten model applied to bioanodes formed from sewage sludge – Mickaël Rimboud – Bioresource Technology

Community shifts in a well-operating agricultural biogas plant: how process variations are handled by the microbiome – Susanne Theuerl – Applied Microbiology and Biotechnology

Review: Tolerance engineering in bacteria for the production of advanced biofuels and chemicals – Aindrila Mukhopadhyay – Trends in Microbiology

Viruses and phages

When Competing Viruses Unify: Evolution, Conservation, and Plasticity of Genetic Identities – Luis P. Villarreal, Guenther Witzany – Journal of Molecular Evolution

Metagenomics and bioinformatics

Large-scale Machine Learning for Metagenomics Sequence Classification – Kévin Vervier – ArXiv

Review: Metagenomics as a tool for the investigation of uncultured microorganisms – N. V. Ravin – Russian Journal of Genetics

Metabolomics

Metabolic dynamics analysis by massive data integration: application to tsunami-affected field soils in Japan – Tatsuki Ogura – ACS Chemical Biology

Review: Defining the Metabolome: Size, Flux, and Regulation – Nicola Zamboni – Molecular Cell

Techniques

Review: High-Throughput Sequencing Technologies – Jason A. Reuter – Molecular Cell

Microbes in the news

One Week Change In My Microbiome – Richard Sprague – uBiome blog

Unconscious use of ‘medical marijuana? ‘ Hunter-gatherer cannabis use linked to fewer internal parasites – Science Daily

Touchy Feely: Physical contact helps determine who’s present among baboons’ gut bacteria – Kerry Grens – The Scientist

Mysteries of cat, human health revealed through microbiome – Meredith Knight – Genetic Literacy Project

Gut check: Does a hospital stay set patients up for sepsis by disrupting the body’s microbiome? – Kara Gavin – University of Michigan

Immunotherapy: Target the Gut in Patients with Multiple Sclerosis – Linda G. Hughes – HCP Live

Q&A With Pavan Bhargava of Johns Hopkins University School of Medicine: Studying the Microbiome in Treatment of Multiple Sclerosis – Adam Hochron – HCP Live

Contact Lenses Can Change the Ocular Microbiome – Amanda B. Keener – The Scientist

Microbiome and money

Synthetic Biologics to Host Microbiome Analyst & Investor Meeting – Market Watch

Science, publishing, and career

Scientists Who Cheat – The Editorial Board – New York Times

Michael LaCour Probably Fabricated a Document About Research Integrity – Jesse Singal – New York Magazine

Bik’s Picks

What’s Old Is New Again: Revolutionary new methods for extracting, purifying, and sequencing ever-more-ancient DNA have opened an unprecedented window into the history of life on Earth – Bob Grant – The Scientist

See The Tiny Origami Robot That’s Going Viral — Folds Itself, Walks, Swims, And Dissolves [Video] – Inquisitr

Quick to laugh or smile? It may be in your genes – Science Daily

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May 28, 2015

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Catching up after a couple of days in Paris…

General microbiome

Metagenomics meets time series analysis: unraveling microbial community dynamics – Karoline Faust – Current Opinion in Microbiology

What’s Bugging you and your Diet? – Bryn L Yeomans and Nicholas T Bello – Journal of Food and Nutritional Disorders

Pregnancy and birth microbiome

Comparison of Bacterial Composition in Blood and Placentas Using Conventional and Molecular Methods – Tingtao Chen – Clinical Microbiology: Open Access

Gut microbiome composition is associated with temperament during early childhood – Lisa M. Christian – Brain, Behavior, and Immunity

Human genital microbiome

Cervical Microbiota in Women with Preterm Prelabor Rupture of Membranes – Marian Kacerovsky – PLOS ONE

Re: The vaginal microbiome, vaginal anti-microbial defence mechanisms and the clinical challenge of reducing infection-related preterm birth – C Griffin – BJOG: An International Journal of Obstetrics & Gynaecology
Author’s reply re: The vaginal microbiome, vaginal anti-microbial defence mechanisms and the clinical challenge of reducing infection-related preterm birth – SS Witkin – BJOG: An International Journal of Obstetrics & Gynaecology

Human gut microbiome

Human seroreactivity to gut microbiota antigens – Benjamin S. Christmann – Journal of Allergy and Clinical Immunology

Models of microbiome research

A Role for Gut Microbiota and the Metabolite-Sensing Receptor GPR43 in a Murine Model of Gout – Angélica T. Vieira – Arthritis & Rheumatology

Tumor Grafting Induces Changes of Gut Microbiota in Athymic Nude Mice in the Presence and Absence of Medicinal Gynostemma Saponins – Lei Chen – PLOS ONE

Dynamic vaginal microbiota in pigtail macaques is associated with menstrual cycle and inflammation (MUC9P.753) – Nichole Klatt – The Journal of Immunology

Animal microbiome

Pyrosequencing Characterization of the Microbiota from Atlantic Intertidal Marine Sponges Reveals High Microbial Diversity and the Lack of Co-Occurrence Patterns – Anoop Alex – PLOS ONE

Characterization of the Bacterial Microflora on the Skin of Boreal toads, Anaxyrus (Bufo) boreas boreas, and Columbia Spotted Frogs, Rana luteiventris, in Grand Teton National Park, Wyoming USA – A.M. Hillis – International Journal of Microbiology Research

Soil microbiome

Niche and metabolic principles explain patterns of diversity and distribution: theory and a case study with soil bacterial communities – Jordan G. Okie – The Royal Society – Proceedings B

Book: The Soils of Antarctica – James G. Bockheim

Thesis: Role of Viruses Infecting Bacteria in Subsurface Sediments and Groundwater – Donald Pan – University of Nebraska-Lincoln

Water microbiome

Interaction and signalling between a cosmopolitan phytoplankton and associated bacteria – S. A. Amin – Nature

Towards a better quantitative assessment of the relevance of deep-sea viruses, Bacteria and Archaea in the functioning of the ocean seafloor – R. Danovaro – Aquatic Microbial Ecology

Bioreactor microbiome

Ecological Media Reveal Community Structure Shifts in a Municipal Wastewater Treatment Train – Bergmann RC – Bioremediation & Biodegradation

Extremophile microbiome

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

Book: The Soils of Antarctica – James G. Bockheim

Techniques

New Perspectives on Microbial Community Distortion after Whole-Genome Amplification – Alexander J. Probst – PLOS ONE

Human Bacterial and Fungal Amplicon Collection and Processing for Sequencing – Julia Oh – Bio-Protocol

Deconstructing the Polymerase Chain Reaction: Understanding and Correcting Bias Associated with Primer Degeneracies and Primer-Template Mismatches – Stefan J. Green – PLOS ONE

Microbial Ecology

Community quorum sensing signalling and quenching: microbial granular biofilm assembly – Chuan Hao Tan – NPJ Biofilms and Microbiomes

Theoretical analysis of the cost of antagonistic activity for aquatic bacteria in oligotrophic environments – Eneas Aguirre-von-Wobeser – Frontiers in Microbiology

More microbiology

Instrumentation: The mystery of the microscope in mud – Brian J. Ford – Nature

Antibiotic alternatives rev up bacterial arms race: From predatory microbes to toxic metals, nature is inspiring new ways to treat infections – Sara Reardon – Nature

Bioinformatics and Metagenomics

obitools: a unix-inspired software package for DNA metabarcoding – Frédéric Boyer – Molecular Ecology Resources

GenoLIB: a database of biological parts derived from a library of common plasmid features – Neil R. Adames – Nucleic Acids Research

PhD Thesis: Scalable Parallel Methods for Analyzing Metagenomics Data at Extreme Scale – Jeffrey A. Daily – Washington State University

Book Chapter: Lessons Learned from Simulated Metagenomic Datasets – Germán Bonilla-Rosso – Encyclopedia of Metagenomics

Review: Discovery of new protein families and functions: new challenges in functional metagenomics for biotechnologies and microbial ecology – Lisa Ufarté – Frontiers in Microbiology

Microbes in the news

The microbial world at our feet – Richard Burn – Society for General Microbiology

‘Bacteria Whisperer’ Bonnie Bassler reveals the secret lives of bacteria in Vancouver – CBC News

Google Ventures: These eight life sciences techs are the most promising – and worthy of investment – Meghana Keshavan – MedCityNews

Fast food versus the African diet, the bacteria battle waged in your gut – Carina Storrs – CNN

Toddler temperament could be influenced by different types of gut bacteria – Science Daily

Is Your Nervous System Being Hacked by Bacteria in Your Gut? – Gaia Vince – Gizmodo

Bacteria appears to help bats fight deadly white-nose syndrome – Mary Beth Griggs – Popular Science

Invisible helpers of the sea: Marine bacteria boost growth of tiny ocean algae – Phys.org

Some like it hot: Extremophile bacteria could be key to solving nuclear problems – Seaes Manchester

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May 22, 2015

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Several special issues this week: Science features results from the Tara ocean plankton biodiversity expedition, Microbes and Infection has a special on the oral microbiome, and Frontiers bundled several papers under the not-so-pretty name The Human Gutome.

General microbiome

The Microbiome and Autoimmune Disease: Report from a Noel R. Rose Colloquium – Jobert G. Barin – Clinical Immunology

New developments providing mechanistic insight into the impact of the microbiota on allergic disease – Kathy D. McCoy – Clinical Immunology

Review: Self or non-self? The multifaceted role of the microbiota in immune-mediated diseases – Martin A. Kriegel – Clinical Immunology

Human oral microbiome

Special issue of Microbes and Infection (7 papers but most have already been posted in this blog). Editorial with links to 7 papers: A New Frontier: Oral Microbes without Borders – Özlem Yilmaz
Extracellular DNA in oral microbial biofilms – Nicholas S. Jakubovics

Not microbiome but cool: The Diet of Three Medieval Individuals from Caravate (Varese, Italy). Combined Results of ICP-MS Analysis of Trace Elements and Phytolith Analysis Conducted on Their Dental Calculus – A. M. B. Lazzati – International Journal of Osteoarchaeology

Human gut microbiome

Frontiers Research Topic (papers have been posted previously in this blog): The Human Gutome: Nutrigenomics of Host-Microbiome Interactions

Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes – Stefanía Magnúsdóttir – Frontiers in Genetics

Model: Anoxic Conditions Promote Species-Specific Mutualism between Gut Microbes In Silico – Almut Heinken – Applied and Environmental Microbiology

Review: Intestinal microbiota and allergic diseases: A systematic review – L.C.F.L. Melli – Allergologia et Immunopathologia

Human urogenital microbiome

Editorial: Cervicovaginal Microbiota: Simple Is Better – Smita Gopinath – Immunity

Cervicovaginal Bacteria Are a Major Modulator of Host Inflammatory Responses in the Female Genital Tract – Melis N. Anahtar – Immunity

The New World of the Urinary Microbiome in Women – Linda Brubaker, Alan J Wolfe – American Journal of Obstetrics and Gynecology

Plant and soil microbiome

Root-associated bacterial endophytes from Ralstonia solanacearum resistant and susceptible tomato cultivars and their pathogen antagonistic effects – Reshmi Upreti and Pious Thomas – Frontiers in Microbiology

Distinct Circular Single-Stranded DNA Viruses Exist in Different Soil Types – Brian Reavy – Applied and Environmental Microbiology

Water microbiome

Special Science issue: Tara Oceans studies plankton at Planetary Scale – P. Bork- Science

pH levels drive bacterial community structure in sediments of the Qiantang River as determined by 454 pyrosequencing – Shuai Liu – Frontiers in Microbiology

Distribution and diversity of fungi in freshwater sediments on a river catchment scale – Jie Liu – Frontiers in Microbiology

Dynamic Succession of Groundwater Functional Microbial Communities in Response to Emulsified Vegetable Oil Amendment during Sustained In Situ U(VI) Reduction
Ping Zhang – Applied and Environmental Microbiology

Extremophile microbiome

Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms – Young-Mo Kim – Frontiers in Microbiology

Abundance and Distribution of Dimethylsulfoniopropionate Degradation Genes and the Corresponding Bacterial Community Structure at Dimethyl Sulfide Hot Spots in the Tropical and Subtropical Pacific Ocean – Yingshun Cui – Applied and Environmental Microbiology

Built environment microbiome

Feasibility study involving the search for natural strains of microorganisms capable of degrading graffiti from heritage materials – Patricia Sanmartín – International Biodeterioration & Biodegradation

Bioreactor microbiology

Next-Generation Pyrosequencing Analysis of Microbial Biofilm Communities on Granular Activated Carbon in Treatment of Oil Sands Process-Affected Water – M. Shahinoor Islam – Applied and Environmental Microbiology

Metagenomics

Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes – Stefanía Magnúsdóttir – Frontiers in Genetics

Metabolomics

Microbial communication leading to the activation of silent fungal secondary metabolite gene clusters – Tina Netzker – Frontiers in Microbiology

Species interactions differ in their genetic robustness – Lon M. Chubiz – Frontiers in Microbiology

Functional foods

Probiotics for Weight Loss: A Systematic Review and Meta-Analysis – Sunmin Parka, Ji-Hyun Baeb – Nutrition Research

Viruses and phages

Badger, mongoose, otter: Fecal virome analysis of three carnivores reveals a novel nodavirus and multiple gemycircularviruses – Nádia Conceição-Neto – Virology Journal

Review: The Virome in Host Health and Disease – Ken Cadwell – Immunity

More microbiology

Editorial: recent discoveries in evolutionary and genomic microbiology – Anton G. Kutikhin and Arseniy E. Yuzhalin – Frontiers in Microbiology

Financial evaluations of antibiotic stewardship programs—a systematic review – Jan-Willem H. Dik – Frontiers in Microbiology

Antagonistic interactions are sufficient to explain self-assemblage of bacterial communities in a homogeneous environment: a computational modeling approach – Román Zapién-Campos – Frontiers in Microbiology

Microbes in the news

What’s Next for the Microbiome? – Jo Handelsman and Elizabeth R. Stulberg – Whitehouse.gov
The White House wants input on the future of microbiome research (by June 15) – Jonathan Eisen – Microbe.net

Ocean’s microbiome has incredible diversity – and human likeness – Colin Barras – New Scientist
Three-year ocean voyage discovered thousands of new, unfamiliar viruses: A study of plankton reveals just how little we know about the ocean – Arielle Duhaime-Ross – The Verge
Scientists Map 5,000 New Ocean Viruses – Carl Zimmer – Quanta Magazine

Help fund koala microbiome study – Andy Fell – Egghead Research at UC Davis

Nurturing a baby’s microbiome, before and after birth – Kate Gammo – Populair Science

Meet the caesarean mums who are ‘seeding their baby’s microbiome’ – Best Daily

Long-gone bacteria blows the whistle on gold deposits – Geology Page

Microbes and money

Why bacteria is becoming big business – Stephen Valdivia – Fortune
Danone’s big bet on tiny bacteria – Erica Fry – Fortune

uBiome Partners with PicnicHealth: Participants diagnosed with Inflammatory Bowel Disease (IBD) will receive a complementary PicnicHealth account as well as a complementary uBiome research kit. – PR Rocket

Science, publishing, and career

(Satire) The Allium Top Tips For Scientists and Engineers – The Allium
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May 21, 2015

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Nature has a special this week about bees, and how to cure appendicitis without surgery.

Human gut microbiome

Survival of Lactobacillus casei strain Shirota in the intestines of healthy Chinese adults – Ran Wang – Microbiology and Immunology

Animal microbiome

Special in Nature: Bees – Michelle Grayson – Nature

Microbiome: The puzzle in a bee’s gut – Alla Katsnelson – Nature

Plant and soil microbes

Optimization of isolation and cultivation of bacterial endophytes through addition of plant extract to nutrient media – N. Eevers – Microbial Biotechnology

Metagenomic Next-Generation Sequencing of Viruses Infecting Grapevines – Johan T. Burger – Plant Pathology

Metagenomics Approaches Based on Virion-Associated Nucleic Acids (VANA): An Innovative Tool for Assessing Without A Priori Viral Diversity of Plants – Denis Filloux – Plant Pathology

Taxonomic diversity of bacterial populations inhabiting gametophytes of Sphagnum mosses from different geographic regions of Russia – A.V. Shcherbakov – Agronomy Research

Biotic interactions mediate soil microbial feedbacks to climate change – Thomas W. Crowther – PNAS

Extremophile microbiology

Halophiles – Shiladitya DasSarma – eLS

Other microbiology papers

157 fungal genomes: Fungal Traits That Drive Ecosystem Dynamics on Land – Kathleen K. Treseder – Microbiology and Molecular Biology Reviews

Spread of tetracycline resistance genes at a conventional dairy farm – Martina Kyselkova – Frontiers in Microbiology

Temperate and lytic bacteriophages programmed to sensitize and kill antibiotic-resistant bacteria – Ido Yosef – PNAS

Microbiology: Taking the bad with the good – Carl T. Bergstrom & Benjamin Kerr – Nature

Counteraction of antibiotic production and degradation stabilizes microbial communities – Eric D. Kelsic – Nature

Microbes in the news

From Germ Theory to the Microbiome: Why Microbes Still Rule Our Lives – Alanna Collen – Huffington Post

The diet of worms: Soil dwellers emerge as climate change heroes in study – Renee Lewis – Al Jazeera

Richman of uBiome: Scientists can accelerate FMT research – Gut Microbiota For Health

Antibiotics resurface as alternative to removing appendix – Gina Colata – New York Times

Video: School Microbiome Art Project: Students quickly draw and discuss some of their thoughts about the microbial world we live in – Kat Gilbert – YouTube

How a Tiny Bacterium Called Wolbachia Could Defeat Dengue – Scott O’Neill – Scientific American

Science, publishing, and career

No more hidden solutions in bioinformatics: Precision medicine cannot advance without full disclosure of how commercial genome sequencing and interpretation software works – Mauno Vihinen – Nature

Publish or perish: Universities should release reports to show what they are doing to tackle misconduct — and funders should help them to do so effectively – Nature

UK universities slow to publish reports of misconduct investigations: Few institutions have followed research integrity guidelines to the letter – Elizabeth Gibney – Nature
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May 19, 2015

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Two papers today on the microbiome of the Giant Panda – it’s not good at digesting bamboo!

Microbiome of pregnancy and birth

Bacterial community structure associated with elective cesarean section versus vaginal delivery in Chinese newborns – Liu D, et al. – J Pediatr Gastroenterol Nutr

The microbiota at multiple body sites during pregnancy in a rural Tanzanian population and the effects of Moringa supplemented probiotic yogurt – Jordan E. Bisanz – Applied and Environmental Microbiology

Review: Gut microbiome and immunity: possible role in sudden infant death syndrome (SIDS) – Paul N. Goldwater – Frontiers in Immunology

Human oral microbiome

Microbiome Profiles in Periodontitis in Relation to Host and Disease Characteristics
Bo-Young Hong – PLOS ONE

Review: The human saliva proteome: overview and emerging methods for characterization
Timothy J. Griffin – SPIE Proceedings

Human gut microbiome

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

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

Gut Microbial Succession Follows Acute Secretory Diarrhea in Humans – Lawrence A. David – mBio

Food Fight: Our gut microbes are no fans of junk food – Laura Beil – Science News

Human vaginal microbiome

Review: Antimicrobial and immune modulatory effects of lactic acid and short chain fatty acids produced by vaginal microbiota associated with eubiosis and bacterial vaginosis – Muriel Aldunate – Frontiers in Physiology

Microbiome models

Composition and function of the undernourished neonatal mouse intestinal microbiome – Geoffrey A. Preidis – The Journal of Nutritional Biochemistry

Maternal microbiota regulate glucocorticoids levels and placental development in mice – Maha Al-Asmakh – Endocrine Abstracts

Different Dynamic Patterns of β-Lactams, Quinolones, Glycopeptides and Macrolides on Mouse Gut Microbial Diversity – Jia Yin – PLOS ONE

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

Physiological variability in volatile organic compounds (VOCs) in exhaled breath and released from faeces due to nutrition- and somatic growth in a standardized caprine animal model – Sina Fischer – Journal of Breath Research

Animal microbiome

The Bamboo-Eating Giant Panda Harbors a Carnivore-Like Gut Microbiota, with Excessive Seasonal Variations – Zhengsheng Xue – mBio

The evolution of the gut microbiota in the giant and the red pandas – Ying Li – Scientific Reports

Patterns of Gut Bacterial Colonization in Three Primate Species – Erin A. McKenney – PLOS ONE

Skin bacteria provide early protection for newly metamorphosed southern leopard frogs (Rana sphenocephala) against the frog-killing fungus, Batrachochytrium dendrobatidis
Whitney M. Holden – Biological Conservation

Plant and Soil microbiome

Bacterial and Fungal Communities in a Degraded Ombrotrophic Peatland Undergoing Natural and Managed Re-Vegetation – David R. Elliott – PLOS ONE

Response of soil, leaf endosphere and phyllosphere bacterial communities to elevated CO2 and soil temperature in a rice paddy – Gaidi Ren – Plant and Soil

Patterns in Species Persistence and Biomass Production in Soil Microcosms Recovering from a Disturbance Reject a Neutral Hypothesis for Bacterial Community Assembly
Fen-Guo Zhang – PLOS ONE

Time-dependent effect of graphene on the structure, abundance and function of the soil bacterial community – Wenjie Ren – Journal of Hazardous Materials

Patterns in Wetland Microbial Community Composition and Functional Gene Repertoire Associated with Methane Emissions – Shaomei He – mBio

Nano titania aided clustering and adhesion of beneficial bacteria to plant roots to enhance crop growth and stress management – G. M. Palmqvist – Scientific Reports

Review: Future challenges and perspectives for applying microbial biotechnology in sustainable agriculture based on a better understanding of plant-microbiome interactions – J. M. Barea – Journal of soil science and plant nutrition

Water microbiome

The influence of land-use, nutrients, and geography on microbial communities and fecal indicator abundance at Lake Michigan beaches – Danielle D. Cloutier – Applied and Environmental Microbiology

Microbial responses to changes in flow status in temporary headwater streams: a cross-system comparison – Catherine M. Febria – Frontiers in Microbiology

Built environment microbiome

Distribution and population structure characteristics of microorganisms in urban sewage system – Yanchen Liu – Applied Microbiology and Biotechnology

Extremophile microbiome

Microbial Community in High Arsenic Shallow Groundwater Aquifers in Hetao Basin of Inner Mongolia, China – Ping Li – PLOS ONE

Microbial diversity in engineered haloalkaline environments shaped by shared geochemical drivers observed in natural analogues – Talitha C. Santini – Applied and Environmental Microbiology

Metagenomic characterization of biodiversity in the extremely arid desert soils of Kazakhstan – O. V. Kutovaya – Eurasian Soil Science

Archaeal Communities in a Heterogeneous Hypersaline-Alkaline Soil – Yendi E. Navarro-Noya – Archaea

Food microbiology

An Integrated Metagenomics/Metaproteomics Investigation of the Microbial Communities and Enzymes in Solid-state Fermentation of Pu-erh tea – Ming Zhao – Scientific Reports

Review: Foodomics in microbiological investigations – Yong-Jiang Xu – Current Opinion in Food Science

Metagenomics and Bioinformatics

Review: Metagenomics: Tools and Insights for Analyzing Next-Generation Sequencing Data Derived from Biodiversity Studies – Anastasis Oulas – Bioinformatics and Biology Insights

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

Divergence thresholds and divergent biodiversity estimates: can metabarcoding reliably describe zooplankton communities? – Emily A. Brown – Ecology and Evolution

Sharing is caring – Claudio Nunes-Alves – Nature Reviews Microbiology

Microbes in the news

Kitty Kickstarter: See the Microbes That Live in Your Cat – Becky Oskin – Live Science

Eden unveils The Human Microbiome this week – West Briton

Bodyguards for precious seeds—without chemical mace – Phys.org

Panda poop reveals they’re bad at digesting bamboo – Laura Geggel – CBS News

Giant Panda Microbiome Ill-Suited for Bamboo Diet, Study Finds – Genome Web

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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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