Category Archives: Metabolomics

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

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

Human skin microbiome

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

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

Human gut microbiome

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

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

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

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

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

Microbiome models

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

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

Soil, plant root, and rock microbiome

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

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

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

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

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

Water microbiome

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

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

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

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

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

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

Extremophile microbiome

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

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

Bioreactor microbiome

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

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

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

Viruses and phages

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

Metagenomics and bioinformatics

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

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

Metabolomics

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

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

Techniques

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

Microbes in the news

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

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

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

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

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

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

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

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

Microbiome and money

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

Science, publishing, and career

Scientists Who Cheat – The Editorial Board – New York Times

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

Bik’s Picks

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

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

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

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May 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

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

General microbiome

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

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

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

Human oral microbiome

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

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

Human gut microbiome

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

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

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

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

Human urogenital microbiome

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

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

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

Plant and soil microbiome

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

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

Water microbiome

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

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

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

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

Extremophile microbiome

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

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

Built environment microbiome

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

Bioreactor microbiology

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

Metagenomics

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

Metabolomics

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

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

Functional foods

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

Viruses and phages

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

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

More microbiology

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

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

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

Microbes in the news

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

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

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

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

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

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

Microbes and money

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

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

Science, publishing, and career

(Satire) The Allium Top Tips For Scientists and Engineers – The Allium
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May 13, 2015

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General human microbiome

Commentary: Our unique microbial identity – Jack A Gilbert – Genome Biology

Human oral microbiome

Oral Microbiota Shift after 12-Week Supplementation with Lactobacillus reuteri DSM 17938 and PTA 5289; A Randomized Control Trial – Nelly Romani Vestman – PLOS ONE

L-Arginine Destabilizes Oral Multi-Species Biofilm Communities Developed in Human Saliva – Ethan Kolderman – PLOS ONE

Human gut microbiome

Ecological and evolutionary adaptations shape the gut microbiome of BaAka African rainforest hunter-gatherers – Andres Gomez – BioRxiv

Gut Microbial Dysbiosis May Predict Diarrhea and Fatigue in Patients Undergoing Pelvic Cancer Radiotherapy: A Pilot Study – Aiping Wang – PLOS ONE

Animal models

Ability of the gut microbiota to produce PUFA-derived bacterial metabolites: Proof of concept in germ-free versus conventionalized mice – Céline Druart – Molecular Nutrition & Food Research

Response of the Rumen Microbiota of Sika Deer (Cervus nippon) Fed Different Concentrations of Tannin Rich Plants – Zhipeng Li – PLOS ONE

Plant root and soil microbiome

Influence of Edaphic, Climatic, and Agronomic Factors on the Composition and Abundance of Nitrifying Microorganisms in the Rhizosphere of Commercial Olive Crops – Joan Caliz – PLOS ONE

CRISPRs

CRISPR Diversity in E. coli Isolates from Australian Animals, Humans and Environmental Waters – Maxim S. Sheludchenko – PLOS ONE

Metabolomics, proteomics

Catching the tip of the iceberg – Evaluation of sample preparation protocols for metaproteomic studies of the rumen microbiota – Simon Deusch and Jana Seifert – Proteomics

Other microbial science

Treating cancer with infection: A review on bacterial cancer therapy – Shirley Wong and Roderick A. Slavcev – Letters in Applied Microbiology

The spatial profiles and metabolic capabilities of microbial populations impact the growth of antibiotic-resistant mutants – Karishma S. Kaushik – Interface

Microbes in the news

Microbiome Fingerprints: Researchers identify people by the unique combinations of microbes found in and on their bodies – Kate Yandell – The Scientist

Gut bacteria help turn animals into fossils – David Shultz – Science Magazine

Microbiome, Immune Therapies, Biologics Showcased at DDW – Caroline Helwick – Medscape

Scientists at work: studying indoor microbial ecology means sampling in public restrooms – Erica Hartmann – The Conversation

The Link Between Obesity, the Microbiome, and Neurologic Function – Alan R. Jacobs – Medscape

Akron Man Found Pooping on Cars Revealed as Subject of Beard Study (fake, and will only flash for 10? sec, but fun)

Bik’s Picks

Over 40% of Honeybee Colonies Died in Year, USDA Says – Tennille Tracy – Wall Street Journal

Chicken Embryos With Dinosaur Snouts Created in Lab – Charles Q. Choi – Live Science

Bill Nye Wants Your Help to Build His ‘Revolutionary’ Solar Spacecraft – Nolan Feeney – Time
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May 7, 2015

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Events

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

Pregnancy and birth microbiome

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

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

Human respiratory microbiome

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

Human gut microbiome

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

Plant root and soil microbiome

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

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

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

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

Built environment microbiome

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

Extremophiles

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

Phages and viruses

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

Microbial Ecology

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

Metagenomics and bioinformatics

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

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

Metabolomics

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

Microbes in the news

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

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

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

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

Microbiome Portrait Experiment for High School Students – Tufts

Bacteria redefine reinforced concrete – RSC Advances Blog

Possible role of gut bacteria in autism – Science Daily

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

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

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

Microbes and money

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

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

Science, publishing, and career

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

Bik’s Picks

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

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

Samantha Cristoforetti: 5 Memorable Moments From the Italian Astronaut’s Time in Space – Alyssa Newcomb – ABC News
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May 6, 2015

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Human oral microbiome

The Impact of Various Time Intervals on the Supragingival Plaque Dynamic Core Microbiome – Wen-xin Jiang – PLOS ONE

Dental and Microbiological Risk Factors for Hospital-Acquired Pneumonia in Non-Ventilated Older Patients – Victoria C. Ewan – PLOS ONE

Human gut microbiome

Unraveling the Influence of Gut Microbes on the Mind – M.J. Friedrich – JAMA

Gut Microbiota and Colorectal Cancer – Yu Y.-N. – Gastrointestinal Tumors

Gut Microbiota and Hepatocellular Carcinoma – Tao X – Gastrointestinal Tumors

Editorial: Gut microbiota and inflammation in chronic kidney disease patients – Denise Mafra – Clinical Kidney Journal

Animal models

Chronic Trichuris muris Infection in C57BL/6 Mice Causes Significant Changes in Host Microbiota and Metabolome: Effects Reversed by Pathogen Clearance – Ashley Houlden – PLOS ONE

Animal microbiome

Bacterial Diversity Associated with Cinachyra cavernosa and Haliclona pigmentifera, Cohabiting Sponges in the Coral Reef Ecosystem of Gulf of Mannar, Southeast Coast of India – C. Jasmin – PLOS ONE

Plant microbiome

Shifts in Symbiotic Endophyte Communities of a Foundational Salt Marsh Grass following Oil Exposure from the Deepwater Horizon Oil Spill – Demetra Kandalepas – PLOS ONE

Endophytic and Epiphytic Microbes as “Sources” of Bioactive Agents – David J. Newman and Gordon M. Cragg – Frontiers in Chemistry

Review: Pivotal roles of phyllosphere microorganisms at the interface between plant functioning and atmospheric trace gas dynamics – Françoise Bringel – Frontiers in Microbiology

Soil and sediment microbiome

Metabolic Activity and Functional Diversity Changes in Sediment Prokaryotic Communities Organically Enriched with Mussel Biodeposits – Thomas Pollet – PLOS ONE

Impacts of dimethyl phthalate on the bacterial community and functions in black soils – Zhi-Gang Wang – Frontiers in Microbiology

Aquatic / Extremophile microbiome

Benthic microbial communities of coastal terrestrial and ice shelf Antarctic meltwater ponds – Stephen D. Archer – Frontiers in Microbiology

Microbial food web components, bulk metabolism, and single-cell physiology of piconeuston in surface microlayers of high-altitude lakes – Hugo Sarmento – Frontiers in Microbiology

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

Bioreactor microbiome

Bacterial Pathogens and Community Composition in Advanced Sewage Treatment Systems Revealed by Metagenomics Analysis Based on High-Throughput Sequencing – Xin Lu – PLOS ONE

Metagenomics, metabolomics, and bioinformatics

Expression of heterologous sigma factors enables functional screening of metagenomic and heterologous genomic libraries – Stefan M. Gaida – Nature Communications

TreeSeq, a Fast and Intuitive Tool for Analysis of Whole Genome and Metagenomic Sequence Data – Bastiaan Wintermans – PLOS ONE

Covariation is a poor measure of molecular coevolution – David Talavera – Molecular Biology and Evolution

Review: Data-driven integration of genome-scale regulatory and metabolic network models – Saheed Imam – Frontiers in Microbiology

Archaea

Complex archaea that bridge the gap between prokaryotes and eukaryotes – Anja Spang – Nature

More microbiology papers

The passenger-associated transport repeat promotes virulence factor secretion efficiency and delineates a distinct autotransporter subtype – Matthew Thomas Doyle – Molecular Microbiology

Microbes and art

Intestine-inspired 3D printed fashion will hold glowing bacteria – Chris Baraniuk – New Scientist

Microbes in the news

Who are the bioaerosols in your neighborhood? Find out by entering a chamber … – Jonathan Eisen – MicroBEnet

Exploring bacterial genes: New technique helps uncover useful functions in microbial genomes – University of Delaware

Newly discovered ‘missing link’ shows how humans could evolve from single-celled organisms: A new microbe found a mile and a half below the Atlantic Ocean  – Rachel Feltman – The Washington Post

Treating a bacterial infection with bacteria lowers chances of recurrence – Meryl Lin McKean – Fox4kc

Toxic Gut Bacteria: New Treatment Could Prevent Repeat Infections – Rachael Rettner – Live Science

Researchers produce jet fuel compounds from fungus – Science Daily

Molecular Homing Beacon Redirects Human Antibodies to Fight Pathogenic Bacteria – Heather Buschman – UC San Diego

Bacteria research opens way for new antibiotics: common building block, called the Passenger-associated Transport Repeat (PATR) present in many pathogens – University of Adelaide

Science, publishing, and career

‘Living figures’ make their debut: Published chart integrates data from outside scientists – Dalmeet Singh Chawla – Nature

The trouble with reference rot: Computer scientists are trying to shore up broken links in the scholarly literature – Jeffrey M. Perkel – Nature

The retirement debate: Stay at the bench, or make way for the next generation: When and how to exit research has become a charged issue in science – Megan Scudellari – Nature

Pint-sized DNA sequencer impresses first users: Portable device offers on-the-spot data to fight disease, catalogue species and more – Erika Check Hayden – Nature

Bik’s Picks

Recovering Sea Lions at Marine Center Deliberately Injured By Chlorine, Police Say – Avianne Tan – ABC News

People with Depression and Bipolar Disorder Feel Sadness Differently – Tanya Lewis – Live Science

Feasting on fruits may leave you craving for more – Silvia Fernandez – Pierce Pioneer News

Trouble Falling Asleep? Doctor Says This Trick Will Put You to Sleep in One Minute – Zachary Stieber – The Epoch Times
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May 4, 2015

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Grant opportunities

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

Events

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

General microbiome

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

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

Human oral microbiome

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

Human gut microbiome

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

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

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

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

Animal models

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

Animal microbiome

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

Plant and soil microbiome

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

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

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

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

Water microbiome

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

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

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

Built environment microbiome

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

Bioreactor microbiology

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

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

Phages and viruses

My life with Mu – Ariane Toussaint – Bacteriophage

Fungi

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

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

Antibiotic resistance

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

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

Metagenomics

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

Microbes in the news

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

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

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

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

Science, publishing, and career

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

Follow the Funding – Bob Grant – The Scientist

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

Science and art

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

Bik’s Picks

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

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

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

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May 1, 2015

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A late post today – I was in meetings all day, and had no time to look at the 474 papers in my inbox until late. But let’s catch up!

General microbiome

Editorial: Bacteria make us human – Mohsin Ali – The Lancet

Microbiome of pregnancy and birth

Spotlight: Gut bacteria and necrotizing enterocolitis: cause or effect? – Christopher James Stewart – Trends in Microbiology

Editorial Harnessing the Early-Life Microbiota to Protect Children with Cystic Fibrosis – Leopoldo N. Segal and Martin J. Blaser – The Journal of Pediatrics

Human oral microbiome

Review: Dental Chatter: Bacterial Cross-Talk in the Biofilm of the Oral Cavity – Doron Steinberg – Israel Journal of Chemistry

The interaction between Streptococcus spp. and Veillonella tobetsuensis in the early stages of oral biofilm formation – Izumi Mashima – Journal of Bacteriology

Human gut microbiome

Antibiotic treatment of diarrhoea is associated with decreased time to the next diarrhoea episode among young children in Vellore, India – Elizabeth T Rogawski – International Journal of Epidemiology

High throughput sequencing reveals distinct microbial populations within the mucosal and luminal niches in healthy individuals – Yehuda Ringel – Gut Microbes

Gut Microbiota-Mediated Drug-Antibiotic Interactions – Dong-Hyun Kim – Drug Metabolism & Disposition

Humoral Immunity in the Gut Selectively Targets Phenotypically Virulent Attaching-and-Effacing Bacteria for Intraluminal Elimination – Nobuhiko Kamada – Cell Host & Microbe

MicroRNA-193a-3p Reduces Intestinal Inflammation in Response to Microbiota via Down-regulation of Colonic PepT1 – Xin Dai – The Journal of Biological Chemistry

Editorial: Some Reflections on the Microbiome and Obesity – Richard I. Shader – Clinical Therapeutics

Review: Regulation of body fat mass by the gut microbiota: Possible mediation by the brain – Erik Schéle – Peptides

Review: Role of Intestinal Microbiome in Lipid and Glucose Metabolism in Diabetes Mellitus – Casper van Olden – Clinical Therapeutics

Review: Gut microbiome, gut function, and probiotics: Implications for health – Neerja Hajela – Indian Journal of Gastroenterology

Review: Gut microbiota and the development of pediatric diseases – Chun-Yi Lu – Journal of Gastroenterology

Review: Regulation of body fat mass by the gut microbiota: Possible mediation by the brain – Erik Schéle – Peptides

Animal models

Transcriptional Modulation of Intestinal Innate Defense/Inflammation Genes by Preterm Infant Microbiota in a Humanized Gnotobiotic Mouse Model – Lei Lu – PLOS ONE

Pharmaceuticals and personal care products alter the holobiome and development of a medically important mosquito – Marcus J. Pennington – Environmental Pollution

Differences in the faecal microbiome of non-diarrhoeic clinically healthy dogs and cats associated with Giardia duodenalis infection: impact of hookworms and coccidia – Jan Šlapeta – International Journal for Parasitology

Ezetimibe and simvastatin modulate gut microbiota and expression of genes related to cholesterol metabolism – Emilie Catry – Life Sciences

Animal microbiome

Review: Tick microbiome: the force within – Sukanya Narasimhan – Trends in Parasitology

16S rRNA Amplicon Sequencing Demonstrates that Indoor-Reared Bumblebees (Bombus terrestris) Harbor a Core Subset of Bacteria Normally Associated with the Wild Host – Ivan Meeus – PLOS ONE

Plant microbiome

Plant and soil effects on bacterial communities associated with Miscanthus × giganteus rhizosphere and rhizomes – Dongfang Li – GCB Bioenergy

Soil microbiome

Distinct microbial populations are tightly linked to the profile of dissolved iron in the methanic sediments of the Helgoland mud area, North Sea – Oluwatobi Oni – Frontiers in Microbiology

Ecological effects of combined pollution associated with e-waste recycling on the composition and diversity of soil microbial communities – Jun Liu – Environmental Science & Technology

Water microbiome

Differences in organic matter and bacterioplankton between sections of the largest Arctic river: Mosaic or continuum? – Michail I. Gladyshev – Limnology and Oceanography

Extremophile microbiome

Insights from the Metagenome of an Acid Salt Lake: The Role of Biology in an Extreme Depositional Environment – Sarah Stewart Johnson – PLOS ONE

The microbial diversity, distribution, and ecology of permafrost in China: a review – Weigang Hu – Extremophiles

Bioreactor microbiology

Illumina MiSeq Sequencing Reveals Diverse Microbial Communities of Activated Sludge Systems Stimulated by Different Aromatics for Indigo Biosynthesis from Indole – Xuwang Zhang – PLOS ONE

Effects of garlic oil, nitrate, saponin and their combinations supplemented to different substrates on in vitro fermentation, ruminal methanogenesis, and abundance and diversity of microbial populations – A.K. Patra – Journal of Applied Microbiology

Food microbiology

Technological implications of reducing nitrate and nitrite levels in dry-fermented sausages: typical microbiota, residual nitrate and nitrite and volatile profile – Xavier F. Hospital – Food Control

Review: New Approaches for Bacteriotherapy: Prebiotics, New-Generation Probiotics, and Synbiotics – Rachna Patel – Clinical Infectious Diseases

Metagenomics and bioinformatics

DIDA: Distributed Indexing Dispatched Alignment – Hamid Mohamadi – PLOS ONE

Hybrid De Novo Genome Assembly Using MiSeq and SOLiD Short Read Data – Tsutomu Ikegami – PLOS ONE

Using populations of human and microbial genomes for organism detection in metagenomes – Sasha K Ames – Genome Research

Metabolomics

Systems biology of host–microbe metabolomics – Almut Heinken and Ines Thiele – Wiley Interdisciplinary Reviews: Systems Biology and Medicine

Microbes in the news

Don’t douche, and other lessons about the vaginal microbiome: Exploring the microscopic world between our legs – Susan Keown – Fred Hutch

Gut bacteria easy scapegoat to explain diseases, but connections hard to prove – Meredith Knight – Genetic Literacy Project

Find Out Just How Bacteria-Infested Houston Street Is During This Weekend of Walking Tours – Jaime Cone – Bedford and Bowery
and
The Artist & The Scientist: Microbial Maps – Festival Walk in New York City with Chris Mason – Jane’s Walk

Video: The Microbiome Project: Hospitals – Bacteria may actually be beneficial to hospitals – Argonne National Laboratory

Freshmen participate in huge research study on tiny viruses – University of Colorado Boulder

uBiome is launching an academic consortium to bring together researchers and industry teams with the hope of accelerating scientific understanding of the microbiome – uBiome

Each vineyard has a unique microbiome – Louise Lerner – Futurity

Science, publishing, and career

Ten Simple (Empirical) Rules for Writing Science – Cody J. Weinberger – PLOS Computational Biology

Honors Thesis: Students’ Knowledge and Opinions Concerning Genetically Modified Organisms: A Survey at University of Colorado Boulder – Connor Folkerth – University of Colorado at Boulder

Sexism in science: Peer editor tells female researchers their study needs a male author – Rachel Feltman – Washington Post

Bik’s Picks

How This Beetle Creates 500 Explosions Per Second In Its Bum – Ed Yong – National Geographic

Evidence that premature girls thrive more than premature boys – Science Daily

House GOP Wants to Eviscerate NASA Earth Sciences in New Budget – Phil Plait – Bad Astronomy – Slate
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April 28, 2015

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

Events

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

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

Human oral microbiome

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

Human gut microbiome

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

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

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

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

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

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

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

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

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

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

Animal models of microbiome research

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

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

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

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

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

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

Animal microbiome

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

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

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

Plant, plant root and soil microbiome

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Water microbiome

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

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

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

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

Extremophile microbiome

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

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

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

Microbiome of the built environment

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

Bioreactor microbiology

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

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

Food microbiology

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

Microbial Ecology

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

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

Techniques

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

Bioinformatics

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

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

Metagenomics

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

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

Metabolomics and proteomics

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

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

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

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

Phages and viruses

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

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

Microbes in the news

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

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

Facts About Our Microbial Menagerie – Infection Control Today

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

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

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

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

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

Microbes and money

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

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

Science, publishing and career

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

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

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

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

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

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

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