Category Archives: Metabolomics

June 29, 2015

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Gut microbiome of children with Schistosoma infections, what happens to the hooves after a cow dies, and microbiomes at extremely dry or hot places.

General microbiome

Only one health, and so many omics – Nives Pećina-Šlaus – Cancer Cell International

Interchange of entire communities: microbial community coalescence – Matthias C. Rillig – Trends in Ecology and Evolution

A Vision for Investigating the Microbiology of Health and Disease – W. Ian Lipkin – The Journal of Infectious Diseases

Collateral sensitivity of antibiotic-resistant microbes – Csaba Pál – Trends in Microbiology

Personalized medicine going precise: from genomics to microbiomics – Sanjay K. Shukla – Trends in Molecular Medicine

Review: Secrets from the microbiome: molecular biology meets microbiology meets histopathology….meets clinical biochemistry – Caroline Young – Annals of Clinical Biochemistry

Human respiratory microbiome

Editorial: Infectious asthma triggers: time to revise the hygiene hypothesis? – Wilmore C. Webley – Trends in Microbiology

Human gut microbiome

Differences in the Faecal Microbiome in Schistosoma haematobium Infected Children vs. Uninfected Children – Gemma Louise Kay – PLOS Neglected Tropical Diseases

Glycan complexity dictates microbial resource allocation in the large intestine – Artur Rogowski – Nature Communications

Review: Intestinal Microbiota, Lipids, and the Pathogenesis of Intestinal Failure–Associated Liver Disease – Way Seah Lee – The Journal of Pediatrics

Review: Influence of gut bacteria on development and progression of non-alcoholic fatty liver disease – Ali Abdul-Hai – World Journal of Hepatology

Animal microbiome

Cockroaches: Aerobic Bacterial Community of American Cockroach Periplaneta americana,a Step toward Finding Suitable Paratransgenesis Candidates – Sanaz Akbari – Journal of Arthropod-Borne Diseases

Hooves from dead cows: Compost biodegradation of recalcitrant hoof keratin by bacteria and fungi – T. Reuter – Journal of Applied Microbiology

Fish: Modulation of the intestinal microbiota and morphology of tilapia, Oreochromis niloticus , following the application of a multi-species probiotic – B . T. Standen – Applied

Jellyfish: Changing company: Composition of bacterial communities associated with
Aurelia aurita changes with compartment, life stage and population – Nancy Weiland-Bräuer – Applied and Environmental Microbiology

Ants: Bacterial community composition and diversity in an ancestral ant fungus symbiosis – Katrin Kellner – FEMS Microbiology Ecology

Review: A new view of the fish gut microbiome: Advances from next-generation sequencing – Mahdi Ghanbari

Plant microbiome

Host–microbe interactions as a driver of acclimation to salinity gradients in brown algal cultures – Simon M Dittami – The ISME Journal

The olive knot disease as a model to study the role of interspecies bacterial communities in plant disease – Roberto Buonaurio – Frontiers in Plant Science

Review: Biotic Interactions in the Rhizosphere: A Diverse Cooperative Enterprise for Plant Productivity – Clelia De-la-Peña – Plant Physiology

Editorial on plants as alternative hosts for human and animal pathogens – Nicola J. Holden – Frontiers in Microbiology

Soil microbiome

Responses of bacterial communities to simulated climate changes in alpine meadow soil of
Qinghai-Tibet plateau – Junpeng Rui – Applied and Environmental Microbiology

Evaluation of bacterial communities by bacteriome analysis targeting 16S rRNA genes and quantitative analysis of ammonia monooxygenase gene in different types of compost – Rika Kitamura – Journal of Bioscience and Bioengineering

Soil conditions and land use intensification effects on soil microbial communities across a range of European field sites – Bruce C. Thomson – Soil Biology and Biochemistry

Impact of urine and the application of the nitrification inhibitor DCD on microbial communities in dairy-grazed pasture soils – Sergio E. Morales – Soil Biology and Biochemistry

Water microbiome

Metagenomic assessment of viral diversity in Lake Matoaka, a temperate, eutrophic freshwater lake in southeastern Virginia, USA – Jasmin C. Green – Aquatic Microbial Ecology

A comparison of bacterial community structure in seawater pond with shrimp, crab, and shellfish cultures and in non-cultured pond in Ganyu, Eastern China – LianTai Li – Annals of Microbiology

Extremophile microbiome

Phylogenetic Profiling and Diversity of Bacterial Communities in the Death Valley, an Extreme Habitat in the Atacama Desert – Francine Piubeli – Indian Journal of Microbiology

Review: Uncultivated thermophiles: current status and spotlight on ‘Aigarchaeota’ – Brian P Hedlund – Current Opinion in Microbiology

Food microbiology

Evaluation and identification of poly-microbial biofilms on natural green Gordal table olives – Antonio Benítez-Cabello – Antonie van Leeuwenhoek

Proteomic and high-throughput analysis of protein expression and microbial diversity of microbes from 30- and 300-year pit muds of Chinese Luzhou-flavor liquor – Qi Zheng – Food Research International

Bacterial communities during the process of high-temperature Daqu production of roasted sesame-like flavour liquor – Yao Su – Journal of the Institute of Brewing

Bioreactor microbiology

Sulfate Reducing Bacteria and Mycobacteria Dominate the Biofilm Communities in a Chloraminated Drinking Water Distribution System – Christa Kimloi Gomez-Smith – Environmental Science & Technology

The Microbiota and Abundance of the Class 1 Integron-Integrase Gene in Tropical Sewage Treatment Plant Influent and Activated Sludge – Magna C. Paiva – PLOS ONE

Metabolic networks

Metabolic pathway activity estimation from RNA-Seq data – Yvette Temate-Tiagueu – ISBRA abstracts

Microbes in the news

Volunteers Needed for Human Microbiota Study: prebiotic effects of certain rice bran components @UArkansas

In Defense of Fiber: How Changing Your Diet Changes Your Gut Bacteria – Mandy Oaklander – Time

Undergraduate is first author on study of Lake Matoaka’s metagenome – Joseph McClain – WM.edu

DNA Genotek Inc. announces recipients of gut microbiome grant program – Steamfeed

Indigo-Clean Is New Light Designed For Hospitals That Kills Bacteria – James Maynard – TechTimes

The ‘frightening’ rise of flesh-eating bacteria: Mystery, pain and amputations – Peter Holley – Washington Post

Fatty and sugary foods linked to lower cognitive functions: Mouse data – Nathan Gray – Food Navigator

Investors Think This Company’s Gut Bacteria Are Worth $1.9 Billion – John Tozzi – Bloomberg

What’s new in gastroenterology? Insights from BMC Medicine at #DDW2015 – Alessandro Recchioni- BioMedCentral

Science, publishing, and career

From trainee to tenure-track: ten tips – Tuuli Lappalainen – Genome Biology

What would be a suitable value for the absolute minimum proportion of female speakers at genomics/bioinformatics conferences? – Keith Bradnam? – ACGT blog

Bik’s Picks

Make it count! ‘Leap second’: Why June 30 will have one extra second – Deborah Netburn – LA Times

SpaceX Rocket Explosion Destroys Students’ Science Experiment – Alyssa Newcomb – ABC News

Rats Dream About the Places They Want to Explore – Kiona Smith-Strickland – Discover Magazine
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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 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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June 12, 2015

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Effects of drinking donkey milk, archaea and fungi on humans,  microbiomes of olives, spoilt wine, cold deserts, indoor air, strawberry soil, and more.

General microbiome

Review: 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

Review: Mycobiota: Micro-Eukaryotes Inhabiting Our Body as Commensals or
Opportunistic Pathogens – Lisa Rizzetto – Fungal Genomics & Biology

Review: Archaea in and on the Human Body: Health Implications and Future Directions – Mor N. Lurie-Weinberger, Uri Gophna – PLOS Pathogens

Human skin microbiome

Antimicrobial Efficacy of Preservatives used in Skin Care Products on Skin Micro Biota – Chintha Lalitha – International Journal of Science and Research

Review: Beneficial and deleterious bacterial–host interactions in chronic wound pathophysiology – C. Watters – Chronic Wound Care Management and Research

Human gut microbiome

Influence of Proton-Pump Inhibitors on the Luminal Microbiota in the Gastrointestinal Tract – Ayumi Tsuda – Clinical and Translational Gastroenterology

Microbiome models

A host-microbiome interaction mediates the opposing effects of omega-6 and omega-3 fatty acids on metabolic endotoxemia – Kanakaraju Kaliannan – Scientific Reports

In rats: Human, donkey and cow milk differently affects energy efficiency and inflammatory state by modulating mitochondrial function and gut microbiota – Giovanna Trinchese – The Journal of Nutritional Biochemistry

Fish: A multiple endpoint analysis of the effects of chronic exposure to sediment contaminated with Deepwater Horizon oil on juvenile Southern flounder and their associated microbiomes – Nancy J. Brown-Peterson – Aquatic Toxicology

Hops β-acids and zinc bacitracin affect the performance and intestinal microbiota of broilers challenged with Eimeria acervulina and Eimeria tenella – C. Bortoluzzi – Animal Feed Science and Technology

Staphylococcus aureus nasal isolates: The effects of spatial structure, frequency dependence and resistance evolution on the dynamics of toxin-mediated microbial invasions – Ben Libberton – Evolutionary Applications

Animal microbiome

Biodiversity of the Symbiotic Bacteria Associated with Toxic Marine Dinoflagellate Alexandrium tamarense – Xiaoling Zhang – Journal of Biosciences and Medicines

Plant microbiome

Wild trees in the Amazon basin harbor a great diversity of beneficial endosymbiotic fungi: is this evidence of protective mutualism? – Romina Gazis – Fungal Ecology

A Legume Genetic Framework Controls Infection of Nodules by Symbiotic and Endophytic Bacteria – Rafal Zgadzaj – PLOS Genetics

Diversity and spatial distribution of endophytes community composition in noni (Morinda citrifolia L.) – Liu Yang – Journal of Hill Agriculture

Comparisons of microbial abundance and community among different plant species in constructed wetlands in summer – Jian Zhang – Ecological Engineering

Soil (and plant root) microbiome

Impact of cover crop in pre-plant of apple orchards: relationship between crop health, root inhabiting fungi and rhizospheric bacteria – Luisa M. Manici – Journal of Plant Science

Amplicon-based metagenomics identified candidate organisms in soils that caused yield decline in strawberry – Xiangming Xu – Horticulture Research

Positively Frequency-Dependent Interference Competition Maintains Diversity and Pervades a Natural Population of Cooperative Microbes – Olaya Rendueles – Current Biology

A predictive model for microbial counts on beaches where intertidal sand is the primary source – Zhixuan Feng – Marine Pollution Bulletin

Reintroduction of locally extinct vertebrates impacts arid soil fungal communities – Laurence J. Clarke – Molecular Ecology

A simple experimental set-up to disentangle the effects of altered temperature and moisture regimes on soil organisms – Eveline J. Krab – Methods in Ecology and Evolution

Water microbiome

Identifying homogeneity of multivariate dispersions among biofilm-dwelling microbial communities in colonization surveys for marine bioassessment – Guangjian Xu – Ecological Indicators

Bacterial diversity along a 2600 km river continuum – Domenico Savio – Environmental Microbiology

Minireview: Microbial players involved in the decline of filamentous and colonial cyanobacterial blooms with a focus on fungal parasitism – Mélanie Gerphagnon – Environmental Microbiology

Extremophile microbiome

Bacterial diversity of Drass, cold desert in Western Himalaya, and its comparison with Antarctic and Arctic – Puja Gupta – Archives of Microbiology

Built environment microbiome

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

Food microbiology

Potential spoilage yeasts in winery environments: Characterization and proteomic analysis of Trigonopsis cantarellii – Cauré Portugal – International Journal of Food Microbiology

Microbiota and Metabolome of Un-started and Started Greek-type Fermentation of Bella di Cerignola Table Olives – Maria De Angelis – Food Microbiology

Functional foods

Probiotic BIFICO cocktail ameliorates Helicobacter pylori induced gastritis – Hong-Jing Yu – World Journal of Gastroenterology

Review: Prebiotics, gut microbiota and metabolic risks: Unveiling the relationship – Adeela Yasmin – Journal of Functional Foods

Review: Current evidence on the use of probiotics in liver diseases – Norberto C. Chávez-Tapia – Journal of Functional Foods

Metagenomics 

Review: Methylotrophs in natural habitats: current insights through metagenomics – Ludmila Chistoserdova – Applied Microbiology and Biotechnology

Metabolomics

Editorial: Microbial metabolite triggers antimicrobial defense – Sky W. Brubaker, Denise M. Monack – Science

Microbes in the news

Soil microbial community variation correlates most strongly with plant species identity – AOB blog

Pew Names 22 Top Scientists as Scholars in the Biomedical Sciences: topics range from microbiome, to mosquito’s preferences – Pew Trusts
and: Microbiology professor becomes UC Merced’s first Pew scholar: Clarissa Nobile receives award for biofilm research – UC Merced

2015 ISCB Overton Prize Awarded to Curtis Huttenhower – Christiana N. Fogg, Diane E. Kovats – PLOS Computational Biology

“Genes in Space” Student Finalists Announced: Tarun Srinivasan, of Houston, TX, plans to examine effects on the gut microbiome of spending time on the ISS – Ricki Lewis – PLOS Blogs

Method reveals what bacteria sense in their surroundings – Leila Gray – UW Health Sciences NewsBeat

“ticks had a microbiome rich in pathogens, including Bartonella”: Ticks’ Migration Linked to Changes in Disease Prevalence – Jacquelyn Gray – HCP Live

Like “kopi luwak” coffee, just bigger: Elephant poop coffee, Thailand’s new delicacy – Doug Powell – BarfBlog

New Tool To Monitor Harmful Bacteria: Scientists offer more accurate health risk prediction model to better inform beach closure decisions – Rosenstiel School of Marine & Atmospheric Science

#EULAR2015: First gut microbiota alterations described in systemic sclerosis patients – Karen Blum – PM360online

Some good information here about bacteria in our gut: Six myths about digestion that just won’t die – ITClips

How does Swiss cheese gets its holes?: by carbon-dioxide-burping microbe Propionibacterium freudenreichii – Nicola Twilly – New Yorker

Product candidate to target specific elimination of Streptococcus mutans may alter oral microbiome to provide long-lasting benefits – Dentistry iQ

Fungus among us, but what kind? Typing error spawns retraction for mushroom paper – Retraction Watch

Science, publishing, and career

Business decisions: stories about the entrepreneurial learning curve – Jeffrey Mervis – Science

Bik’s Picks

Polar bear caught eating dolphins and freezing the leftovers – Penny Sarchet – New Scientist

There’s A Link Between Cat Ownership And Schizophrenia – Leigh Weingus – Huffington Post

“Advice to interns: work hard and make your mark.” New planet discovered by 15-year-old intern – Monica Sarkar – CNN

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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 2, 2015

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General human microbiome

The human microbiome in hematopoiesis and hematological disorders – Veronica E. Manzo and Ami S. Bhatt – Blood

Special issue of Microbial Ecology in Health and Disease: Editorial: We all need friends – Jørgen Valeur

Early Factors Leading to Later Obesity: Interactions of the Microbiome, Epigenome, and Nutrition – Lilly Chang, Josef Neu – Current Problems in Pediatric and Adolescent Health Care

Microbiome of pregnancy and birth

Opportunities to assess factors contributing to the development of the intestinal microbiota in infants living in developing countries – Dennis Lang – Microbial Ecology in Health and Disease

Review: Factors affecting infant gut microbiota and possible consequences for health
Merete Eggesbø – Microbial Ecology in Health and Disease

Human gut microbiome

Draft Genome Sequences of 24 Microbial Strains Assembled from Direct Sequencing from 4 Stool Samples – Patricio Jeraldo – Genome Announcements

Book Chapter: Physiology of Digestion and Absorption: The Functional Interdependence Between Food and the Gut – Stephen J. D. O’Keefe – The Principles and Practice of Nutritional Support

Review: With a little help from my enteric microbial friends – Ben Berkhout – Frontiers in Medicine

Editorial: AI-2 to the rescue against antibiotic-induced intestinal dysbiosis? – Zhongke Sun – Trends in Microbiology

Microbiome models

Evidence from Animal Models: Is a Restricted or Conventional Intestinal Microbiota Composition Predisposing to Risk for High-LET Radiation Injury? – Irene Maier – Radiation Research

Rumen Microbiome from Steers Differing in Feed Efficiency – Phillip R. Myer – PLOS ONE

Changes in the composition of intestinal fungi and their role in mice with dextran sulfate sodium-induced colitis – Xinyun Qiu – Scientific Reports

Microbiota prevents cholesterol loss from the body by regulating host gene expression in mice – Chun-Yan Zhong – Scientific Reports

Animal microbiome

Early-life establishment of the swine gut microbiome and impact on host phenotypes – Núria Mach – Environmental Microbiology Reports

Lifestyle Evolution in Cyanobacterial Symbionts of Sponges – Ilia Burgsdorf – mBio

Plant microbiome

Antagonistic interactions between endophytic cultivable bacterial communities isolated from the medicinal plant Echinacea purpurea – Isabel Maida – Environmental Microbiology

Soil microbiome

Distinct soil bacterial communities along a small-scale elevational gradient in alpine tundra – Congcong Shen – Frontiers in Microbiology

Carcass mass has little influence on the structure of gravesoil microbial communities – Sophie Weiss – International Journal of Legal Medicine

Impact of different cropping conditions and tillage practices on the soil fungal abundance of a Phaeozem luvico – Romina P. Gomez – Spanish Journal of Agricultural Research

Biological activity and microbial genetic diversity of bare-fallow and grassland soils – Anna Kot – Acta Agriculturae Scandinavica, Section B — Soil & Plant Science

Masters Thesis: Assessing soil microbial tolerance to salt – Arpita Maheshwari – Lund University

Water microbiome

Microbial metagenomics in the Baltic Sea: Recent advancements and prospects for environmental monitoring – Karolina Ininbergs – AMBIO

Characterizing microbial communities dedicated for conversion of coal to methane in situ and ex situ – Ji Zhang – International Journal of Coal Geology

Dynamics of the bacterial and archaeal communities in the northern South China Sea revealed by 454 pyrosequencing of the 16S rRNA gene – Xia Xiaomin – Deep Sea Research Part II: Topical Studies in Oceanography

Editorial: Microbial symbiosis of marine sessile hosts- diversity and function – Suhelen Egan – Frontiers in Microbiology

Review: Biodiversity, community structure and function of biofilms in stream ecosystems – Katharina Besemer – Research in Microbiology

Built environment microbiome

pecunia non olet? Screening Currency Notes for Microbial Pathogens and Antibiotic Resistance Genes Using a Shotgun Metagenomic Approach – Saakshi Jalali – PLOS ONE

Phages and viruses

Dark matter of the biosphere: The amazing world of bacteriophage diversity – Graham F. Hatfull – Journal of Virology

Bioinformatics and metagenomics

VirSorter: mining viral signal from microbial genomic data – Simon Roux – PeerJ

Denoising DNA deep sequencing data—high-throughput sequencing errors and their correction – David Laehnemann – Briefings in Bioinformatics

FCMM: A comparative metagenomic approach for functional characterization of multiple metagenome samples – Jongin Lee – Journal of Microbiological Methods

PuzzleCluster: A Novel Unsupervised Clustering Algorithm for Binning DNA Fragments in Metagenomics – Current Bioinformatics

Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi – Leho Tedersoo – MycoKeys

ANCOM: Analysis of composition of microbiomes: a novel method for studying microbial composition – Siddhartha Mandal – Microbial Ecology in Health and Disease

Transcriptomics and Metabolomics

MetabNet: an R package for metabolic association analysis of high-resolution metabolomics data – Karan Uppal – Frontiers in Bioengineering and Biotechnology

Meta-omics uncover temporal regulation of pathways across oral microbiome genera during in vitro sugar metabolism – Anna Edlund – ISME Journal

Review: Enteric short-chain fatty acids: microbial messengers of metabolism, mitochondria, and mind: implications in autism spectrum disorders – Derrick F. MacFabe – Microbial Ecology in Health and Disease

Techniques

Co-extraction of DNA and PLFA from soil samples – Sheridan Brewer – Journal of Microbial Methods

Microbial ecology

Editorial: Flexible gene pools: hard to interpret the diversity often observed in microbial communities – Michael M. Desai – Science

Fine-scale diversity and extensive recombination in a quasisexual bacterial population occupying a broad niche – Michael J. Rosen – Science

Microbes in the news

Good craft beer can be spoiled by bacteria – Phys.org / American Society for Microbiology

Treating Koala STDs May also Quash Their Essential Gut Microbes – Katherine Harmon Courage – Scientific American

New study: Gut bacteria cooperate when life gets tough – EurekAlert

Metabolic activity and health of the skin microbiome – Medical Xpress / American Society for Microbiology

Is our first line of defense sleeping on the job? – Science Daily / American Society for Microbiology

Growing Up In an UnSterile World –The Importance of a Healthy Gut Through the Lifespan – Sarah Lobisco – Dr. Lobisco

Citizen Scientists Send Microbes Into Space – Science 2.0

Methanogens: Earth organisms survive under low-pressure Martian conditions – Science Daily

Why is the H-pylori bacteria developing a liking for Mumbai police? – Santosh Andhale – DNA India

Book review: The great microbial beauty – Vittorio Capozzi – Trends in Microbiology

Science, publishing, and career

Plagiarism is the most common cause of retractions in BioMed Central journals:
Retractions Often Due to Plagiarism: Study – Kerry Grens – The Scientist

Bik’s Picks: not-microbial science

Giant Sawfish Have Virgin Births, Rewrite Biology Textbooks – Charles Q. Choi – Live Science

These newly discovered marsupials basically sex each other to death – Elahe Izadi – Washington Post

Seals Help Scientists Probe Remote Seas – Discovery

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Another June 1, 2015

Posted on by

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 23, 2015

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Human vaginal microbiome

Vaginal Biofilm: Much Ado About Nothing, or a New Therapeutic Challenge? – Jack D. Sobel – Clinical Infectious Diseases

Human respiratory microbiome

Correlation between Either Cupriavidus or Porphyromonas and Primary Pulmonary Tuberculosis Found by Analysing the Microbiota in Patients’ Bronchoalveolar Lavage Fluid – Yuhua Zhou – PLOS ONE

Human gut microbiome

Temporal and technical variability of human gut metagenomes – Anita Y Voigt – Genome Biology

Gut metabolites and bacterial community networks during a pilot intervention study with flaxseeds in healthy adult men – Ilias Lagkouvardos – Molecular Nutrition & Food Research

Fecal Microbiota in Pediatric Inflammatory Bowel Disease and Its Relation to Inflammation – Kaija-Leena Kolho – American Journal of Gastroenterology

The impact of ciprofloxacin and clindamycin administration on Gram-negative bacteria isolated from healthy volunteers and characterizing the resistance genes they harbour – Roderick M. Card – Antimicrobial Agents and Chemotherapy

Review: The Role of the Microbiome in Mental Health: A Psychoneuroimmunologic Perspective – Kelly Brogan – Alternative and Complementary Therapies

Review: Dysbiosis and Immune Dysregulation in Outer Space – Jorge L. Cervantes – International Reviews of Immunology

Models of microbiome research

Effects of two whole-grain barley varieties on caecal SCFA, gut microbiota and plasma inflammatory markers in rats consuming low- and high-fat diets – Yadong Zhong – British Journal of Nutrition

Animal microbiome

Dogs: Characterization of Microbial Dysbiosis and Metabolomic Changes in Dogs with Acute Diarrhea – BC Guard – PLOS ONE

Coral: Productivity links morphology, symbiont specificity and bleaching in the evolution of Caribbean octocoral symbioses – David M Baker – ISME Journal

Plant and soil microbiome

Quantitative assessment of the differential impacts of arbuscular and ectomycorrhiza on soil carbon cycling – Nadejda A. Soudzilovskaia – New Phytologist

Soil pH and biome are both key determinants of soil archaeal community structure –
Binu M. Tripathi – Soil Biology and Biochemistry

Solarization makes a great impact on the abundance and composition of microbial communities in soil – Kazunori Yokoe – Soil Science and Plant Nutrition

The relationship between successional vascular plant assemblages and associated microbial communities on coal mine spoil heaps – G. Woźniak – Community Ecology

Long-term soil transplant simulating climate change with latitude significantly alters microbial temporal turnover – Yuting Liang – ISME Journal

Differential acquisition of amino acid and peptide enantiomers within microbial community groups and its implications for carbon and nitrogen cycling in soil – R.C.I. Broughton – Soil Biology and Biochemistry

Molecular mechanisms underlying the close association between soil Burkholderia and fungi – Nejc Stopnisek – ISME Journal

Water microbiome

Editorial: Computational eco‐systems biology in Tara Oceans: translating data into knowledge – Shinichi Sunagawa – Molecular Systems Biology

Editorial: The making of Tara Oceans: funding blue skies research for our Blue Planet – Eric Karsenti – Molecular Systems Biology

Cross-depth analysis of marine bacterial networks suggests downward propagation of temporal changes – Jacob A Cram – ISME Journal

Air microbiome

Characterization of active and total fungal communities in the atmosphere over the Amazon rainforest – A. M. Womack – Biogeosciences Discuss

Bioreactor microbiology

Palygorskite changes heavy metal bioavailability and microbial functional diversity in sewage sludge composting – Siying Liu – Environmental Technology

Evaluation of System Performance and Microbial Communities of a Bioaugmented Anaerobic Membrane Bioreactor Treating Pharmaceutical Wastewater – Kok Kwang Ng – Water Research

Bioinformatics and Metagenomics

Read Mapping on de Bruijn graph – Antoine Limasset and Pierre Peterlongo – arXiv

NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation – Roie Levy – BMC Bioinformatics

Consortium of the ‘bichlorophyllous’ cyanobacterium Prochlorothrix hollandica and chemoheterotrophic partner bacteria: culture and metagenome based description – Natalia Velichko – Environmental Microbiology Reports

A new approach for detecting fungal and oomycete plant pathogens in next generation sequencing metagenome data utilising electronic probes – Andres Espindola – International Journal of Data Mining and Bioinformatics

Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity – Yan He – Microbiome

Strong spurious transcription likely contributes to DNA insert bias in typical metagenomic clone libraries – Kathy N Lam – Microbiome

Metabolomics

Using community metabolomics as a new approach to discriminate marine microbial particulate organic matter in the western English Channel – Carole A. Llewellyn – Progress in Oceanography

Metabolic potential of fatty acid oxidation and anaerobic respiration by abundant members of Thaumarchaeota and Thermoplasmata in deep anoxic peat – Xueju Lin – ISME Journal

Phages, viruses, CRISPRs

Computational Detection of CRISPR/crRNA Targets – Ambarish Biswas – CRISPR Methods in Molecular Biology

Creation and Analysis of a Virome: Using CRISPR Spacers – Michelle Davison – CRISPR Methods in Molecular Biology

More microbes

Not open access, alas. van Leeuwenhoek microscopes—where are they now? – Lesley A. Robertson – FEMS Microbiology Letters

Microbes in the news

Headline from 2030: Is your space commute making you sick? Microbiomes undergo weird changes in space – Alexandra Ossola – Popular Science

Leaf bacteria fertilize trees, researchers claim – Elizabeth Pennisi – Science

The bugs within us – Hordes of bacteria live inside animals, affecting their health, food choices and mating – Roberta Kwok – Student Science

Report from the 1st Annual Translational Microbiome Conference: Moving from lab to clinic: Microbiome on the move – Taconic Insights

Recent Built Environment Microbiology papers – Elisabeth Bik – MicroBE.net

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May 22, 2015

Posted on by

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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