Category Archives: Animal experiments

July 1, 2015

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

Human oral microbiome

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

Human respiratory microbiome

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

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

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

Human gut microbiome

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

Animal models

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

Animal microbiome

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

Plant, root, and soil microbiome

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

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

Water microbiome

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

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

Extremophile microbiome

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

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

Built Environment microbiome

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

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

Bioreactor microbiology

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

Bioinformatics and metagenomics

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

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

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

Microbial Ecology

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

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

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

Microbes in the news

The Sum of Our Parts – Janice Dietert – The Scientist

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

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

Bik’s Picks

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

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

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June 30, 2015

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

Events

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

Microbiome of pregnancy and birth

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

Human oral microbiome

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

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

Human respiratory microbiome

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

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

Human vaginal microbiome

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

Human gut microbiome

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

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

Animal models

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

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

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

Animal microbiome

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

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

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

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

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

Plant, root, and soil microbiome

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

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

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

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

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

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

Water microbiome

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

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

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

Built environment / water treatment microbiology

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

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

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

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

Bioinformatics and metagenomics

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

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

Metabolomics

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

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

New techniques

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

More microbiology

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

Ecological communities by design – James K. Fredrickson – Science

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

Microbes in the news

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

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

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

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

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

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

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

Science, publishing, and career

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

Bik’s Picks

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

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

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

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June 26, 2015

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

General microbiome

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

Pregnancy and birth microbiome

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

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

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

Human skin microbiome

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

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

Human gut microbiome

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

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

Animal models of microbiome research

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

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

Animal microbiome

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

Plant, root, and soil microbiome

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

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

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

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

Water microbiome

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

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

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

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

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

Extremophile microbiome

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

Painting microbiome

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

Food microbiology

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

Metabolic networks

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

Microbes in the news

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

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

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

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

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

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

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

Team Effort – XKCD comics

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

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

Science, publishing, and career

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

Introducing “Research Matters” – Grant McFadden – PLOS Pathogens

Practical policies can combat gender inequality – Douglas Hilton – Nature

Bik’s Picks

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

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

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

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June 24, 2015

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

Human oral microbiome

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

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

Human gut microbiome

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

Animal models

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

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

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

Animal microbiome

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

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

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

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

Plant, root and soil microbiome

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

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

Water microbiome

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

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

Functional foods

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

Metabolic networks and metabolomics

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

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

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

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

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

Microbes in the news

IndieGoGo project: A Probiotic Life: Microbiome Documentary

New colon cancer culprit found in gut microbiome – EurekAlert

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

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

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

Microbiology and art

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

Science, publishing, and career

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

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

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

Bik’s Picks

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

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

America’s Next Top Chef is a Supercomputer From IBM – Liz Stinson – Wired
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June 23, 2015

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Gill structure and microbiome of clownfish (Nemo), the Ocean Sampling Day consortium, and capturing prokaryotic dark matter genomes.

Human respiratory microbiome

The use of Next Generation Sequencing in the diagnosis and typing of respiratory infections – Fiona Thorburn – Journal of Clinical Virology

Effects of Vaccination with 10-Valent Pneumococcal Non-Typeable Haemophilus influenza Protein D Conjugate Vaccine (PHiD-CV) on the Nasopharyngeal Microbiome of Kenyan Toddlers – Leah M. Feazel – PLOS ONE

Human vaginal microbiome

Isolation of Vaginal Lactobacilli and Characterization of Anti-Candida Activity – Carola Parolin – PLOS ONE

Letter: Accuracy of Self-Report of Sexual Activity among Adolescent Girls: Implications for Interpretation of Vaginal Flora Patterns – Christina A. Muzny – mBio

Human gut microbiome

Effects of a Formula Containing Two Types of Prebiotics, Bifidogenic Growth Stimulator and Galacto-oligosaccharide, and Fermented Milk Products on Intestinal Microbiota and Antibody Response to Influenza Vaccine in Elderly Patients: A Randomized Controlled Trial – Nagafuchi S – Pharmaceuticals

Systemic Sclerosis is Associated with a Unique Colonic Microbial Consortium – E. Volkmann – Annals of the Rheumatic Diseases

Review: Influence of the human intestinal microbiome on obesity and metabolic dysfunction – Herbert Tilg and Timon E. Adolph

Review: Is intestinal inflammation linking dysbiosis to gut barrier dysfunction during liver disease? – Katharina Brandl – Expert Review of Gastroenterology & Hepatology

Review: Microbiome-generated amyloid and potential impact on amyloidogenesis in Alzheimer’s disease (AD) – Yuhai Zhao – Journal of Nature and Science

Animal models

Non Digestible Oligosaccharides Modulate the Gut Microbiota to Control the Development of Leukemia and Associated Cachexia in Mice – Laure B. Bindels – PLOS ONE

Engineering the gut microbiota to treat hyperammonemia – Ting-Chin David Shen – Journal of Clinical Investigation

Animal microbiome

Exposure of clownfish larvae to suspended sediment levels found on the Great Barrier Reef: Impacts on gill structure and microbiome – Sybille Hess – Scientific Reports

Longitudinal analysis reveals characteristically high proportions of bacterial vaginosis-associated bacteria and temporal variability of vaginal microbiota in northern pig-tailed macaques (Macaca leonina) – Lin Zhu – Zoological Research

Review: Giving microbes their due – animal life in a microbially dominant world – Margaret J. McFall-Ngai – The Journal of Experimental Biology

Plant, root and soil microbiome

Context dependency and saturating effects of loss of rare soil microbes on plant productivity – Gera Hol – Frontiers in Plant Science

Genetic Diversity and Functional Traits of Jacq. Associated with Symbiotic Microbial Communities in Caribbean Swamp Forests in Relation to Insular Distribution, Salinity and Flooding – Amadou Bâ – Wetlands

Terminal Restriction Fragment Length Polymorphism Analysis of Soil Bacterial Communities under Different Vegetation Types in Subtropical Area – Zeyan Wu – PLOS ONE

Water microbiome

The ocean sampling day consortium – Anna Kopf and many others – Gigascience

Thesis: Analysis of the Microbial Community Along Three Sites of the Rio Grande by Denaturing Gradient Gel Electrophoresis – Rebeca Imelda Castro – Texas A&M International University

Bioinformatics

On the Origins and Control of Community Types in the Human Microbiome – Travis E. Gibson – ArXiv

Thesis: Exploring microbial community structure and resilience through visualization and analysis of microbial co-occurrence networks – Sarah Isa Esther Perez – University of British Columbia

Metagenomics

Phylogeny and physiology of candidate phylum ‘Atribacteria’ (OP9/JS1) inferred from cultivation-independent genomics – Masaru K Nobu – The ISME Journal

Review: Capturing prokaryotic dark matter genomes – Cyrielle Gasc – Research in Microbiology

Viruses and phages

Large tailed spindle viruses of Archaea: A new way of doing viral business – Rebecca Hochstein – Journal of Virology

Draft Genome Sequences of Marine RNA Viruses SF-1, SF-2, and SF-3 Recovered from San Francisco Wastewater – Alexander L. Greninger – Genome Announcements

Microbial ecology

Backbones of evolutionary history test biodiversity theory for microbes – James P. O’Dwyer – PNAS

Techniques

Effect of DNA Extraction Methods on the Apparent Structure of Yak Rumen Microbial Communities as Revealed by 16S rDNA Sequencing – Ya-Bing Chen – Polish Journal of Microbiology

Microbes in the news

Bacteria may help bats to fight deadly fungus: As white-nose syndrome spreads, researchers are trialling ways to stop colonies from collapsing – Nala Rogers – Nature

This mushroom might alter gut bacteria for the better, study finds – Catherine Woods – PBS Newshour

Can the Bacteria in Your Gut Explain Your Mood? The rich array of microbiota in our intestines can tell us more than you might think – Peter Andrey Smith – New York Times

Urban microbes come out of the shadows: Genomic sequences reveal cities’ teeming masses of bacteria and viruses – Rachel Ehrenberg – Nature

NIH Earmarks $1.5M to Fund Human Microbiome Research Projects – GenomeWeb

Fat, sugar cause bacterial changes that may relate to loss of cognitive function – Oregon State University

Why Would Anyone Get a Fecal Transplant? Watch a Brother and Sister Explain – Maryn McKenna – National Geographic

Bik’s Picks

Astronaut Terry Virts on the Power of Space Photography – Andrew Katz – Time

Dangerous cervical lesions reduced since start of HPV vaccination – Kathryn Doyle – Reuters

This cockroach-inspired robot will scurry right into your nightmares: Crawling soon to a rescue squad near you – Arielle Duhaime-Ross – The Verge

 

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June 22, 2015

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How do human gut microbiomes change after death, microbiome of Gulf of Mexico 1 year after Deepwater Horizon, and mining microbial dark matter.

Human gut microbiome

Estimating Time Since Death from Postmortem Human Gut Microbial Communities – Kathleen A. Hauther – Journal of Forensic Sciences

16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice – Alan W. Walker – Microbiome Journal

Review: Peripheral aetiopathogenic drivers and mediators of Parkinson’s disease and co-morbidities: role of gastrointestinal microbiota – Sylvia M. Dobbs – Journal of NeuroVirology

Animal models

The effects of xylo-oligosaccharides on performance and microbiota in broiler chickens – De Maesschalck C – Applied and Environmental Microbiology

A comparison of faecal microbial populations of South African Windsnyer-type indigenous pigs (SAWIP) and Large White x Landrace (LW x LR) crosses fed diets containing ensiled maize cobs – Arnold T. Kanengoni – FEMS Microbiology Letters

Plant, root, and soil microbiome

Illumina-based analysis the microbial diversity associated with Thalassia hemprichii in Xincun Bay, South China Sea – Yu-Feng Jiang – Ecotoxicology

Methanotrophic and methanogenic communities in Swiss alpine fens dominated by Carex rostrata and Eriophorum angustifolium – Simrita Cheema – Applied and Environmental Microbiology

Antibacterial effect of the Trichoderma viride fungi on soil microbiome during PAH’s biodegradation – Zuzanna Szczepaniak – International Biodeterioration & Biodegradation

Water microbiome

Microbial community composition, functions and activities in the Gulf of Mexico, one
year after the Deepwater Horizon accident – Etienne Yergeau – Applied and Environmental Microbiology

Metagenomics and Bioinformatics

Compact graphical representation of phylogenetic data and metadata with GraPhlAn – Francesco Asnicar – PeerJ

Techniques

Design and application of a synthetic DNA standard for real-time PCR analysis of microbial communities in a biogas digester – T. May – Applied Microbiology and Biotechnology

Optimizing a PCR protocol for cpn60-based microbiome profiling of samples variously contaminated with host genomic DNA – Lisa A Johnson – BMC Research Notes

Microbes in the news

Mining the microbial dark matter: Microbiologists are finding new ways to explore the vast universe of unknown microbes in the hunt for antibiotics – Corie Lok – Nature

Legumes control infection of nodules by both symbiotic and endophytic bacteria – Aarhus University

Correlation does not mean causation: Yogurt’s Probiotics Can Help Boost Your Socialization Skills – Daily Times Gazette

Teenager killed by plague in rural northern Colorado – Daniel Wallis – Reuters

Recent Built Environment Microbiology papers, June 21 edition – Elisabeth M Bik – MicroBE.net

Science, publishing, and career

Cold E-mails and Hot Coffee: Take action on your career – Albert Chen et al. – Science

Reset your brain: A bit of self-reflection can propel scientists into a career beyond the lab – Christopher Taylor – Nature

Enough talk. There are ways we can help women in science now – Athene Donald – The Guardian

Bik’s Picks

Neanderthal hybrid suggests modern humans bred with them much later than thought – Rachel Feltman – Washington Post

What Pope Francis and scientists have in common when they look at the natural world – Chris Mooney – Washington Post

Musicians don’t just hear in tune, they also see in tune – Science Daily
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June 21, 2015

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

Events

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

Human oral microbiome

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

Human gut microbiome

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

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

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

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

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

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

Animal models

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

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

Animal microbiome

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

Plant microbiome

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

Plant root, soil, and sediment microbiome

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

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

Water microbiome

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

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

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

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

Microbes in the news

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

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

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

Science, publishing and career

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

Bik’s Picks

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

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

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

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

Pregnancy and birth microbiome

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

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

Human respiratory microbiome

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

Human skin microbiome

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

Human oral microbiome

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

Human gut microbiome

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

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

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

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

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

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

Animal models

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

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

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

Animal microbiome

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

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

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

Plant microbiome

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

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

Plant root and soil microbiome

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

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

Built environment microbiome

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

Food microbiology

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

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

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

Metagenomics and bioinformatics

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

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

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

Techiques

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

Microbes in the news

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

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

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

Science, publishing, and career

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

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

Bik’s Picks

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

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

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

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June 18, 2015

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Microbial diversity in Cystic Fibrosis, eating corn starch with your red meat might help prevent colon cancer, and fungal microbiome signatures in children with IBD.

Human respiratory microbiome

Editorial: Assessing Airway Microbiota in Cystic Fibrosis: What More Should Be Done? – John J. LiPuma – Journal of Clinical Microbiology

Rapid Detection of Emerging Pathogens and Loss of Microbial Diversity Associated with Severe Lung Disease in Cystic Fibrosis – William G. Flight – Journal of Clinical Microbiology

Human gut microbiome

Fungal Signature in the Gut Microbiota of Pediatric Patients With Inflammatory Bowel Disease – Chehoud, Christel AB – Inflammatory Bowel Diseases

Butyrylated starch intake can prevent red meat-induced O6-methyl-2-deoxyguanosine adducts in human rectal tissue: a randomised clinical trial – Richard K. Le Leu – British Journal of Nutrition

Review: Regulatory immune cells in regulation of intestinal inflammatory response to microbiota – M Sun – Mucosal Immunology

Review: Obesity and the microbiome – Ruchi Mathur – Expert Review of Gastroenterology & Hepatology

Animal models

Rats and mice: Space Environmental Factor Impacts upon Murine Colon Microbiota and Mucosal Homeostasis – Lauren E. Ritchie – PLOS ONE

Plant root and soil microbiome

Prokaryotic Diversity in the Rhizosphere of Organic, Intensive, and Transitional Coffee Farms in Brazil – Adam Collins Caldwell – PLOS ONE

Water microbiome

Standard filtration practices may significantly distort planktonic microbial diversity estimates – Cory C. Padilla – Frontiers in Microbiology

Influence of seawater intrusion on microbial communities in groundwater – Tatsuya Unno – Sciences of the Total Environment

Bioreactor microbiome

Eubacteria and archaea communities in seven mesophile anaerobic digester plants in Germany – Christian Abendroth – Biotechnology for Biofuels

Putative Effect of Aquifer Recharge on the Abundance and Taxonomic Composition of Endemic Microbial Communities – Renee J. Smith – PLOS ONE

Microbes in the news

A peek into our teeming inner world – Clive Cookson – Business Day Live

11 Reasons to Love Bacteria, Fungi and Spores – Karen Emslie – Smithsonian

Inkjet Inks Made of Bioactive Silk Could Yield Smart Bandages, Bacteria-Sensing Surgical Gloves & More – Kim Thurler – Tufts Now

When ‘Kill The TseTse Fly, Kill The Disease’ Doesn’t Work – Rio is studying how different metabolic contributions of the microbiota may facilitate parasite transmission – News Wise

Bik’s Picks

Most kangaroos are lefties, study finds – Deborah Netburn – Los Angeles Times

What Food Can Replace Trans Fats’ Creamy Goodness? – Lexi Pandell – Wired.com

Scientists have used DNA tests to track Africa’s worst elephant poaching spots – Rachel Feltman – Washington Post
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June 16, 2015

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Human oral microbiome

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

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

Human gut microbiome

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

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

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

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

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

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

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

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

Human genital microbiome

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

Models of microbiome

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

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

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

Animal microbiome

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

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

Plant root and soil microbiome

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Water microbiome

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

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

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

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

Extremophile microbiome

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

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

Bioreactor microbiome

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

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

Food microbiology

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

Metagenomics and bioinformatics

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

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

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

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

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

Metabolomics and Proteomics

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

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

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

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

Microbial Ecology

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

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

Techniques

Preferential Amplification of Pathogenic Sequences – Fang Ge – Scientific Reports

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

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

Microbes in the news

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

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

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

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

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

BacteriaHysteria

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

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

Science, publishing, and career

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

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

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

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

Bik’s Picks

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

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

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