Category Archives: Metagenomics & Bioinformatics

September 9, 2015

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Gut virome of Malawian twins, equine grass sickness, and high-throughput microfluidics.

Pregnancy and birth

Significant increase of oral bacteria in the early pregnancy period in Japanese women – Natsumi Fujiwara – Journal of Investigative and Clinical Dentistry

Human gut microbiome

From the Jeff Gordon lab: Gut DNA viromes of Malawian twins discordant for severe acute malnutrition – Alejandro Reyes – PNAS

Research Highlight: Gut microbiota, host genetics and diet interact to affect the risk of developing obesity and the metabolic syndrome – Claire Greenhill – Nature Reviews Endocrinology

Animal microbiome

Understanding Intestinal Microbiota in Equine Grass Sickness: Next Generation Sequencing of Faecal Bacterial DNA – Leng J. – Equine Veterinary Journal

Plant, root, and soil microbiome

Soil organic carbon and microbial communities respond to vineyard management – F. Zehetner – Soil Use and Management

Bioinformatics

Sparse Zero-Sum Games as Stable Functional Feature Selection – Nataliya Sokolovska – PLOS ONE

Techniques

Spatiotemporal microbial single-cell analysis using a high-throughput microfluidics cultivation platform – Alexander Grünberger – Cytometry Part A

Microbes in the news

Twins Study Explores Gut Virome Role in Severe Acute Malnutrition Risk – Genome Web

Study shows characterization of lung micro-organisms could help lung cancer patients – Medical Express

Pediatric antibiotic administration can have long-term effects on child development – BioTechInAsia

10 Mysteries of the Human Microbiome Revealed – Mental Floss

Microbes and art

3D Printed clothing house microorganisms: The wearable gut. An intestine-inspired tutu – with video – Nature Biotechnology

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September 8, 2015

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How Bifidobacterium species digest human milk oligosaccharides, yeast species in floral nectar, and microbes of the cryosphere.

Pregnancy and birth

Comparative transcriptomics reveals key differences in the response to milk oligosaccharides of infant gut-associated bifidobacteria – Daniel Garrido – Scientific Reports

Human oral microbiome

Dental caries-not just holes in teeth! A perspective – William H. Bowen – Molecular Oral Microbiology

Progress in oral personalized medicine: contribution of ‘omics’ – Ingrid Glurich – Journal of Oral Microbiology

Human gut microbiome

Editorial: Modeling the Context-Dependent Associations between the Gut Microbiome, Its Environment, and Host Health – Thomas J. Sharpton – mBio

Review: Gut Microbiota Dysbiosis in Obesity-Linked Metabolic Diseases and Prebiotic Potential of Polyphenol-Rich Extracts – Fernando F. Anhê – Current Obesity Reports

Review: The gut microbiota and host health: a new clinical frontier – Julian R Marchesi – Gut

Animal models

Distinct but Spatially Overlapping Intestinal Niches for Vancomycin-Resistant Enterococcus faecium and Carbapenem-Resistant Klebsiella pneumoniae – Silvia Caballero – PLOS Pathogens

An Overview of Typical Infections of Research Mice: Health Monitoring and Prevention of Infection – James R. Fahey – Current Protocols in Mouse Biology

Editorial: The bug eye bandits – Yvonne Bordon – Nature Reviews Immunology

Plant, root, and soil microbiome

Species coexistence in simple microbial communities: unravelling the phenotypic landscape of co-occurring Metschnikowia species in floral nectar – María I. Pozo – Environmental Microbiology

Unveiling the metabolic potential of two soil-derived microbial consortia selected on wheat straw – Diego Javier Jiménez – Scientific Reports

Crop rotation of flooded rice with upland maize impacts the resident and active methanogenic microbial community – Björn Breidenbach – Environmental Microbiology

Water microbiome

Methane and microbial dynamics in the Gulf of Mexico water column – Chrisoulla Rakowski – Frontiers in Marine Science

Transformation of Organic Matter by Microbial Community in Sediments of Lake Baikal under Experimental Thermobaric Conditions of Protocatagenesis – Olga N. Pavlova – Geomicrobiology Journal

Extremophiles

Metagenomic analysis reveals that modern microbialites and polar microbial mats have similar taxonomic and functional potential – Richard A. White III – Frontiers in Microbiology

Review: Microbial ecology of the cryosphere: sea ice and glacial habitats – Antje Boetius – Nature Reviews Microbiology

Metagenomics and bioinformatics

ConStrains identifies microbial strains in metagenomic datasets – Chengwei Luo – Nature Biotechnology

Review: High-throughput bacterial functional genomics in the sequencing era – Andrew N Gray – Current Opinion in Microbiology

Techniques

Uniform and accurate single-cell sequencing based on emulsion whole-genome amplification – Yusi Fu – PNAS

Microbes in the news

Seal fur and Arctic bacteria leach toxic mercury into waters – Joshua Sokol – New Scientist

Time to Give Up Showers and Spray Yourself With a Coating of Live Bacteria –
Madeleine Davies – Jezebel

A Look Inside the Lunch Boxes of Diet & Exercise Researchers – Ann Marie Awad – WRKF

Poo transplants can eliminate two superbugs from the gut: mice study – Eliza Berlage – The Conversation

Genetic Factors Drive Roles of Gut Bacteria in Diabetes and Obesity – News Wise

Bik’s Picks

Mercury offloaded in Northern elephant seal hair affects coastal seawater surrounding rookery – Jennifer M. Cossaboon – PNAS

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September 6, 2015

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General microbiome

Recurrent antibiotic exposure may promote cancer formation – Another step in understanding the role of the human microbiota? – Ben Boursi – European Journal of Cancer

Pregnancy and birth microbiome

Clinical chorioamnionitis at term VI: acute chorioamnionitis and funisitis according to the presence or absence of microorganisms and inflammation in the amniotic cavity – Roberto Romero – Journal of Perinatal Medicine

Pregnancy-related changes in the maternal gut microbiota are dependent upon the mother’s periconceptional diet – Wajiha Gohir – Gut Microbes

Potential NICU Environmental Influences on the Neonate’s Microbiome: A Systematic Review – Hartz, Lacey E. – Advances in Neonatal Care

Human oral microbiome

Analysis of the Microbiota of Black Stain in the Primary Dentition – Yue Li – PLOS ONE

Human gut microbiome

Furry pets modulate gut microbiota composition in infants at risk for allergic disease –
Merja Nermes – The Journal of Allergy and Clinical Immunology

Gut microbiome in Chronic Kidney Disease – Maria R. Wing – Experimental Physiology

Editorial: Microbial growth dynamics and human disease – Julia A. Segre – Science

Animal microbiome

Review: Heterogeneity of the gut microbiome in mice: guidelines for optimizing experimental design – Debby Laukens – FEMS Microbiology Reviews

454 Pyrosequencing-based assessment of bacterial diversity and community structure in termite guts, mounds and surrounding soils – Huxley M. Makonde – Springer Plus

Fish: Study of the microbiome of the intestine of the Comephorus dybowski korotneff, 1904 – N. L. Bel’kova – Ecology

Plant, root, and soil microbiome

An analysis of Pseudomonas genomic diversity in take-all infected wheat fields reveals the lasting impact of wheat cultivars on the soil microbiota – T.H. Mauchline – Environmental Microbiology

Selection of biological indicators appropriate for European soil monitoring – D. Stone – Applied Soil Ecology

Effects of silver nanoparticles on soil microorganisms and maize biomass are linked in the rhizosphere – Wouter Sillen – Soil Biology and Biochemistry

Arbuscular mycorrhiza symbiosis in viticulture: a review – Sophie Trouvelot – Agronomy for Sustainable Development

Soil particle size fractions harbour distinct microbial communities and differ in potential for microbial mineralisation of organic pollutants – Michael Hemkemeyer – Soil Biology and Biochemistry

Differential responses of total and active soil microbial communities to long-term experimental N deposition – Zachary B. Freedman – Soil Biology and Biochemistry

Environmental changes affect the assembly of soil bacterial community primarily by mediating stochastic processes – Ximei Zhang – Global Change

Built environment microbiome

Thesis: The building science of office surfaces: implications for microbial community succession – Mahnaz Zare – University of Toronto

Microbial Ecology

Dynamics of an experimental microbial invasion – Francisco Acosta – PNAS

Click to access 1505204112.full.pdf

Bioinformatics

metaModules identifies key functional subnetworks in microbiome-related disease – Ali May – Bioinformatics

ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data – Jane Hawkey – BMC Genomics

WiseScaffolder: an algorithm for the semi-automatic scaffolding of Next Generation Sequencing data – Gregory K. Farrant – BMC Bioinformatics

Inferring microbial interaction network from microbiome data using RMN algorithm
Kun-Nan Tsai – BMC Systems Biology
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September 5, 2015

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Events

The Individual Microbe: Single-cell Analysis and Agent-based Modeling – ASM conference – March 18-20, 2016, Washington DC, USA

R workshop for microbial ecology – Pat Schloss – Nov 2-4, 2015, Detroit – No link but can email Pat at: pschloss@umich.edu

General microbiome

Privacy-Preserving Microbiome Analysis Using Secure Computation – Justin Wagner – BioRxiv

Pregnancy and birth microbiome

Phylogenetic and Metabolic Tracking of Gut Microbiota during Perinatal Development – Federica Del Chierico – PLOS ONE

Human oral microbiome

The Effect of Fixed Orthodontic Appliances and Fluoride Mouthwash on the Oral Microbiome of Adolescents – A Randomized Controlled Clinical Trial – Jessica E. Koopman – PLOS ONE

Review: Oral Paleomicrobiology: study of the ancient oral microbiome – Namrata Dagli

Human gut microbiome

The effect of dietary resistant starch type 2 on the microbiota and markers of gut inflammation in rural Malawi children – M. Isabel Ordiz – Microbiome

Gastrointestinal Microbiome Modulator Improves Glucose Tolerance in Overweight and Obese Subjects: A Randomized Controlled Pilot Trial – Candida J. Rebello – Journal of Diabetes and its Complications

Faecal proteomics: A tool to investigate dysbiosis and inflammation in patients with cystic fibrosis – Griet Debyser – Journal of Cystic Fibrosis

Review: Pathways and functions of gut microbiota metabolism impacting host physiology – Smitha Krishnan – Current Opinion in Biotechnology

Review: Microbiome in Inflammatory Arthritis and Human Rheumatic Diseases – Jose U. Scher – Arthritis & Rheumatology

Review: The human microbiome: opportunities and challenges for clinical care – G. B. Rogers – Internal Medicine Journal

Human respiratory microbiome (see also gut microbiome above)

MRSA Colonization and the Nasal Microbiome in Adults at High Risk for Colonization and Infection – Mary T. Bessesen – Journal of Infection

Review: Cystic fibrosis lung microbiome: Opportunities to reconsider management of airway infection – Lindsay J. Caverly – Pediatric Pulmonology

Human other sites

In silico analyses of metagenomes from human atherosclerotic plaque samples – Suparna Mitra – Microbiome

Microbiome models

Distinct Shifts in Microbiota Composition during Drosophila Aging Impair Intestinal Function and Drive Mortality – Rebecca I. Clark – Cell Reports

Perspective: Metabolic labeling puts the microbiome under the microscope – Graham J Britton & Jeremiah J Faith – Nature Medicine

Animal microbiome

The composition of the zebrafish intestinal microbial community varies across development – W Zac Stephens – ISME Journal

Shifts in the Midgut/Pyloric Microbiota Composition within a Honey Bee Apiary throughout a Season – Jane Ludvigsen – Microbes and Environments

The genome of Aiptasia, a sea anemone model for coral symbiosis – Sebastian Baumgarten – PNAS

Special Issue: The Mammalian Microbiome and Its Importance in Laboratory Animal Research – André Bleich and James G. Fox – ILAR Journal

Plant, root, and soil microbiome

Predicting Ecological Roles in the Rhizosphere Using Metabolome and Transportome Modeling – Peter E. Larsen – PLOS ONE

Microbiome change by symbiotic invasion in lichens – Wedin Mats – Environmental Microbiology

Plant-associated microbiomes in arid lands: diversity, ecology and biotechnological potential – Asma Soussi – Plant and Soil

Geological connectivity drives microbial community structure and connectivity in polar, terrestrial ecosystems – Belinda C. Ferrari – Environmental Microbiology

Water microbiome

Anthropogenic activities drive the microbial community and its function in urban river sediment – Xu Zhang – Journal of Soils and Sediments

Built environment microbiome

Bacterial Communities and Midgut Microbiota Associated with Mosquito Populations from Waste Tires in East-Central Illinois – Chang-Hyun Kim – Journal of Medical Entomology

Hospital’s Hidden Environmental Hazards: Probing the Microbiome – BioScience

Pyrosequencing analysis of bacterial communities in biofilms from different pipe materials in a city drinking water distribution system of East China – Hongxing Ren – Applied Microbiology and Biotechnology

Food microbiology

The genomics of microbial domestication in the fermented food environment –
John G Gibbons – Current Opinion in Genetics & Development

Bioinformatics

Functional Basis of Microorganism Classification – Chengsheng Zhu – PLOS Computational Biology

ReproPhylo: An Environment for Reproducible Phylogenomics – Amir Szitenberg – PLOS Computational Biology

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities – Dongwan D. Kang – PeerJ

More Microbiology

Evolution of coexistence in a crowded microplate well – J. Arjan G. M. de Visser – PNAS

The rpb2 gene represents a viable alternative molecular marker for the analysis of environmental fungal communities – Tomáš Větrovský – Molecular Ecology Resources

Microbes in the news

Microbial diversity insights are often strongly biased – Suffield Times
Small advances: understanding the microbiome – Amanda Smith – ABC Australia

Science, publishing and career

When science fails a scientist – Kim Hunter-Schaedle – Science

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September 1, 2015

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General microbiome

Perspective: Better together: engineering and application of microbial symbioses – Stephanie G Hays – Current Opinion in Biotechnology

Pregnancy and birth

Maternal use of probiotics during pregnancy and effects on their offspring’s health in an unselected population – Nicole Rutten – European Journal of Pediatrics

Impact of maternal bifidobacteria and the mode of delivery on Bifidobacterium microbiota in infants – S. Sirilun – Beneficial Microbes

Human Milk Oligosaccharides in Premature Infants: Absorption, Excretion and Influence on the Intestinal Microbiota – Mark A. Underwood – Pediatric Research

The influence of impact delivery mode, lactation time, infant gender, maternal age and rural or urban life on total number of Lactobacillus in breast milk Isfahan – Iran – Mansoureh Taghizadeh – Advanced Biomedical Research

Review: Maternal Microbiome and Pregnancy Outcomes That Impact Infant Health: A Review – Anne L Dunlop – Advances in Neonatal Care

Human gut microbiome

Characterization of the gut microbiota of Kawasaki disease patients by metagenomic analysis – Akiko Kinumaki – Frontiers in Microbiology

Review: Microbiome Disturbances and Autism Spectrum Disorders – Cheryl S. Rosenfeld – Drug Metabolism & Disposition

Review: Investigation of Host–Gut Microbiota Modulation of Therapeutic Outcome – Lian Yee Yip – Drug Metabolism & Disposition

Perspective: Could gut microbiota protect against sclerosing cholangitis? – Hanns-Ulrich Marschall – Hepatology

Models of microbiome research

Probiotic Bifidobacterium longum alters gut luminal metabolism through modification of the gut microbial community – Hirosuke Sugahara – Scientific Reports

Microbial community profiles of the colon from steers differing in feed efficiency – Phillip R Myer – Springer Plus

Distinct Shifts in Microbiota Composition during Drosophila Aging Impair Intestinal Function and Drive Mortality – Rebecca I. Clark – Cell Reports

Impact of Fishmeal Replacement in Diets for Gilthead Sea Bream (Sparus aurata) on the Gastrointestinal Microbiota Determined by Pyrosequencing the 16S rRNA Gene – G. Estruch – PLOS ONE

Lean rats gained more body weight than obese ones from a high-fibre diet – Shaoting Li – British Journal of Nutrition

Microbiota RORgulates intestinal suppressor T cells – Ahmed N. Hegazy – Science

Review: Heterogeneity of the gut microbiome in mice: guidelines for optimizing experimental design – Debby Laukens – FEMS Microbiology Reviews

Animal microbiome

Temporal variation selects for diet–microbe co-metabolic traits in the gut of Gorilla spp – Andres Gomez – The ISME Journal

Domestication and cereal feeding developed domestic pig-type intestinal microbiota in animals of suidae – Kazunari Ushida – Animal Science Journal

Rapid Change of Microbiota Diversity in the Gut but Not the Hepatopancreas During Gonadal Development of the New Shrimp Model Neocaridina denticulata – Man Kit Cheung – Marine Biotechnology

Plant, root, and soil microbiome

The Effect of Long-Term Continuous Cropping of Black Pepper on Soil Bacterial Communities as Determined by 454 Pyrosequencing – Wu Xiong – PLOS ONE

A metagenomic window into carbon metabolism at 3 km depth in Precambrian continental crust – Cara Magnabosco – The ISME Journal

A review: What is the spermosphere and how can it be studied? – Séverine Schiltz – Journal of Applied Microbiology

Metagenomics and bioinformatics

glmgraph: An R Package for Variable Selection and Predictive Modeling of Structured Genomic Data – Li Chen – Bioinformatics

Discovery of phosphonic acid natural products by mining the genomes of 10,000 actinomycetes – Kou-San Ju – PNAS

Techniques

Mass Spectrometry-based PhyloProteomics (MSPP): A novel microbial typing Method – Andreas Erich Zautner – Scientific Reports

Microbes and art

Made of Bacteria, This Living Type Morphs Into New Letterforms: Ori Elisar’s project Living Language blurs the lines between designer and mad scientist with his Hebrew symbols grown in petridishes – Meg Miller – FastcoDesign

Microbes in the news

Unusual throat (and mouth) germs linked to schizophrenia, says two new studies – Amy Ellis Nutt – Washington Post

Some Sexually Transmitted Microbes Might Be Good for You – Marissa Fessenden – Smithsonian

How Does Your Microbiome Grow? The reproduction rates of the bacteria in one’s gut may be a good indicator of health or disease – Health Canal

How Do We Build Our Microbiomes? Exhibition “The Secret World Inside You” opens November 7 – American Museum of Natural History

New Yeast And Bacterial Starters Developed For Truly Wild European Wines – Eurasia Review

Bacteria Hysteria

Are your kid’s backpacks a magnet for bacteria? – Anna Zook – WJHL.com

Bik’s Picks

Acoustic shadows help gleaning bats find prey, but may be defeated by prey acoustic camouflage on rough surfaces – Elizabeth L Clare – eLIFE
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August 30, 2015

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Pregnancy and birth

Fecal Microbial Community Structure Is Stable over Time and Related to Variation in Macronutrient and Micronutrient Intake in Lactating Women – Janae M Carrothers – The Journal of Nutrition

Human oral microbiome

Comparison between Clinical Aspects and Salivary Microbial Profile of Children with and without Early Childhood Caries: A Preliminary Study – Neves AB – Journal of Clinical Pediatric Dentistry

Human gut microbiome

Systematic review: microbial dysbiosis and nonalcoholic fatty liver disease – A. Wieland – Alimentary Pharmacology & Therapeutics

Animal and bioreactor models

Effect of Bifidobacterium thermophilum RBL67 and fructo-oligosaccharides on the gut microbiota in Göttingen minipigs – Sabine A. Tanner – British Journal of Nutrition

Interactions between Drosophila and its natural yeast symbionts—Is Saccharomyces cerevisiae a good model for studying the fly-yeast relationship? – Don Hoang – PeerJ

Differential responses of gut microbiota to the same prebiotic formula in oligotrophic and eutrophic batch fermentation systems – Wenmin Long – Scientific Reports

Animal microbiome

Structure of Manila Clam (Ruditapes philippinarum) Microbiota at the Organ Scale in Contrasting Sets of Individuals – Guillaume Meisterhans – Invertebrate Microbiology

Plant, root, and soil microbiome

Microbiome change by symbiotic invasion in lichens – Wedin Mats – Environmental Microbiology

Comparison of soil microbial communities inhabiting vineyards and native sclerophyllous forests in central Chile – Luis E. Castañeda – Ecology and Evolution

Diversity and distribution of bacterial community in the coastal sediments of Bohai Bay, China – Liping Wang – Acta Oceanologica Sinica

The impact on the soil microbial community and enzyme activity of two earthworm species during the bioremediation of pentachlorophenol-contaminated soils – Zhong Lin – Journal of Hazardous Materials

Water microbiome

Terrestrial origin of bacterial communities in complex boreal freshwater networks – Clara Ruiz-González – Ecology Letters

How are microbial and detrital sources partitioned among and within gastropods species at East Pacific Rise hydrothermal vents? – Sylvie M. Gaudro – Marine Ecology

Extremophile microbiome

Geological connectivity drives microbial community structure and connectivity in polar, terrestrial ecosystems – Belinda C. Ferrari – Environmental Microbiology

Adaptation strategies of endolithic chlorophototrophs to survive the hyperarid and extreme solar radiation environment of the Atacama Desert – Jacek Wierzchos – Frontiers in Microbiology

Microbial biogeography of permafrost thaw ponds across the changing northern landscape – Jérôme Comte – Ecography

Food microbiology

Microbiota of Minas cheese as influenced by the nisin producer Lactococcus lactis subsp. lactis GLc05 – Luana Martins Perin – International Journal of Food Microbiology

Built Environment microbiology

Microbiome interplay: plants alter microbial abundance and diversity within the built environment – Alexander Mahnert – Frontiers in Microbiology

Bioinformatics

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways – Zachary A. King – PLOS Biology

Microbes in the news

Scientists Send Kombucha to Space in Search for Extraterrestrial Life – Kasandra Brabaw – Space.com

How Fats Influence the Microbiome – Kate Yandell – The Scientist

Fish oil diet modifies gut bacteria to boost health – News Medical

Soupy bacteria clogs Missisquoi Bay: “When it rots, it stinks bad” – Joel Banner Baird – Burlington Free Press

Bacteria Hysteria

Caveat: Sponsored by a make-up company. I cannot find any publication associated with this article either. Out of date make-up can contain lethal bacteria, London Met scientist finds – London Metropolitan University

‘There’s no way of knowing what fungus or bacteria is left on it’: Medical expert slams bizarre website that buys USED make-up from beauty lovers – before selling it again – Catherine Townsend – Daily Mail

Science, publishing, and career

The most important tasks for peer reviewers evaluating a randomized controlled trial are not congruent with the tasks most often requested by journal editors – Anthony Chauvin – BMC Medicine
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August 24, 2015

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Microbiome of death

Soil fungal community shift evaluation as a potential cadaver decomposition indicator –
Monica Chimutsa – Forensic Science International

Pregnancy and birth

Master Thesis – The Association of Necrotizing Enterocolitis with Integrons and Antibiotic Resistance Genes in the Gut Microbiota of Preterm Infants – Eva Lena F. Estensmo – Norwegian University of Life Sciences

Human respiratory microbiome

Regional Isolation Drives Bacterial Diversification within Cystic Fibrosis Lungs – Peter Jorth – Cell Host & Microbe

Quantitative analysis of pathogens in the lower respiratory tract of patients with chronic obstructive pulmonary disease – Huaying Wang – BMC Pulmonary Medicine

Animal microbiome

Evidence-based recommendations on storing and handling specimens for analyses of insect microbiota – Tobin J Hammer – Peer J

Path analyses of cross-sectional and longitudinal data suggest that variability in natural communities of blood-associated parasites is derived from host characteristics and not interspecific interactions – Carmit Cohen – Parasites & Vectors

Plant, root, and soil microbiome

Available nitrogen is the key factor influencing soil microbial functional gene diversity in tropical rainforest – Jing Cong – BMC Microbiology

Disentangling the ‘brown world’ faecal-detritus interaction web: dung beetle effects on soil microbial properties – Eleanor M. Slade – Oikos

Taxon-specific responses of soil microbial communities to different soil priming effects induced by addition of plant residues and their biochars – Peng Su – Journal of Soils and Sediments

Research Highlight: Root recruiting – Mirella Bucci – Nature Chemical Biology

Water microbiome

Habitat and water quality variables as predictors of community composition in an Indonesian coral reef: a multi-taxon study in the Spermonde Archipelago – Ana Rita Moura Polónia – Science of the Total Environment

Waste water microbiology

Persistence of Ebola Virus in Sterilized Wastewater – Kyle Bibby – Environmental Science & Technology Letters

Metagenomics and bioinformatics

MetaObtainer: A Tool for Obtaining Specified Species from Metagenomic Reads of Next-generation Sequencing – Weihua Pan – Interdisciplinary Sciences: Computational Life Sciences

Minimum Information about a Biosynthetic Gene cluster – Marnix H Medema – Nature Chemical Biology

Viruses

A protein domain-based view of the virosphere-host relationship – Aare Abroi – Biochimie

Microbes in the news

Add Lots of Microbes to ‘Me, Myself, and I’ – David Salisbury – Futurity

The Microbiome Is Science’s Hot New Kid – Anand Veeravagu and Tessa Anderman – The Daily Beast

Science Briefs: Topography of spinach leaf shelters bacteria – John Bordsen – Charlotte Observer

Inside N.C. Science: Bugs – and mates – attracted by body odor – Sarah Council – Charlotte Observer

Universal flu vaccine comes closer, scientists say – Michelle Roberts – BBC News

Science, publishing, and career

Here’s what two college doctors say freshman need to know – LaTasha Seliby and Ranit Mishori – Washington Post

Women, minorities still underrepresented in medical specialties – Megan Brooks – Reuters

Bik’s Picks

Japanese Spacecraft Delivers Mice, Booze and More to ISS – Sarah Lewin – NBC News

Biologists Have Spotted the First Wolf Pack in California in 100 Years – Marissa Fessenden – Smithsonian

Get the Bunsen burner out: It’s time to concoct dinner – Nancy Szokan – Washington Post

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August 18, 2015

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New paper from our lab about human microbiota during pregnancy, association between obesity and cervical microflora, Argentina soil metagenomes, proteomics library, and microbiology during mozzarella cheese making.

Events and conferences

ECCMID: 26th European Congress of Clinical Microbiology and Infectious Diseases: April 2016, Istanbul, Turkey

General microbiome

Review: Fulfilling the Promise of Microbiomics to Revolutionize Medicine – Traci L Testerman – J Microbiol Exp

Review: Cross-kingdom similarities in microbiome functions – Rodrigo Mendes – ISME Journal

Pregnancy and birth microbiome

From our lab: Temporal and spatial variation of the human microbiota during pregnancy – Daniel B. DiGiulio – PNAS

Maternal group B Streptococcus and the infant gut microbiota – A. E. Cassidy-Bushrow – Journal of Developmental Origins of Health and Disease

The stool microbiota of insulin resistant women with recent gestational diabetes, a high risk group for type 2 diabetes – Marina Fugmann – Scientific Reports

Human reproductive tract microbiome

Relationship of Specific Bacteria in the Cervical and Vaginal Microbiotas With Cervicitis – Linda M. Gorgos – Sexually Transmitted Diseases

Changes in vaginal microbiota following antimicrobial and probiotic therapy – Jean M. Macklaim – Microbial Ecology in Health and Disease

Association between obesity and cervical microflora dominated by Lactobacillus iners in Korean women – Hea Young Oh – Journal of Clinical Microbiology

Distribution of human papillomavirus (HPV) genotypes and bacterial vaginosis presence in cervical samples from Paraguayan indigenous – Pamela Mongelos – International Journal of Infectious Diseases

The most common isolated microorganisms and its clinical manifestation in hospitalised women suffering from urogenital diseases in Latvia – Anatolijs Naumčiks – International Journal of Reproduction, Contraception, Obstetrics and Gynecology

Human respiratory microbiome

Conference abstract: Profiling of lung microbial communities in lung cancer and chronic obstructive pulmonary disease patients – Yanhong Liu – Cancer Research

Human oral microbiome

Conference abstract: 16S rRNA saliva analysis unveils differences in the head and neck squamous cell carcinoma microbiome before and after surgical resection – Rafael E. Guerrero-Preston – Cancer Research

Human gut microbiome

Variable alterations of the microbiota, without metabolic or immunological change, following faecal microbiota transplantation in patients with chronic pouchitis – J. Landy – Scientific Reports

Review: Systematic Review of the Relation Between Intestinal Microbiota and Toll-Like Receptors in the Metabolic Syndrome: What Do We Know So Far? – José Pedro Portela-Cidade – GE Portuguese Journal of Gastroenterology

Review: Commensal Microbiome Promotes Resistance to Local and Systemic Infections – Nan Zhang – Chinese Medical Journal

Animal microbiome

High diversity of viable bacteria isolated from lymph nodes of slaughter pigs and its possible impacts for food safety – Evelyne Mann – Journal of Applied Microbiology

Geographic patterns in the bacterial microbiome of the glassy-winged sharpshooter, Homalodisca vitripennis (Hemiptera: Cicadellidae) – E. W. Welch – Symbiosis

Plant, root, and soil microbiome

Using direct amplification and next-generation sequencing technology to explore foliar endophyte communities in experimentally inoculated western white pines – Lorinda S. Bullington – Fungal Ecology

Maize lines with different nitrogen use efficiency select bacterial communities with different β-glucosidase-encoding genes and glucosidase activity in the rhizosphere – Shamina I. Pathan – Biology and Fertility of Soils

Fire severity shapes plant colonization effects on bacterial community structure, microbial biomass, and soil enzyme activity in secondary succession of a burned forest – Joseph E. Knelman – Soil Biology and Biochemistry

Diversity of hydrolases from hydrothermal vent sediments of the Levante Bay, Vulcano Island (Aeolian archipelago) identified by activity-based metagenomics and biochemical characterization of new esterases and an arabinopyranosidase – Antonio Placido – Applied Microbiology and Biotechnology

Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe – Jonathan W. Leff – PNAS

Soil Metagenomes from Different Pristine Environments of Northwest Argentina – Christina B. McCarthy – Genome Announcements

Relationships between the density and activity of microbial communities possessing arylsulfatase activity and soil sulfate dynamics during the decomposition of plant residues in soil – Séverine Piutti – European Journal of Soil Biology

Food microbiology

Microbial changes of natural milk cultures for mozzarella cheese during repeated propagation cycles – Angela Guidone – LWT – Food Science and Technology

No paper, just abstract, no pathogens appear to have been found: Culture-independent Pathogenic Bacterial Communities in Bottled Mineral Water – Hamdy A. Hassan – Renewable Energy & Sustainable Development

A diagnosis of the microbiological quality of dehydrated bee-pollen produced in Brazil – Adriane Alexandre Machado De-Melo – Letters in Applied Microbiology

Metagenomics and bioinformatics

HipMer: An Extreme-Scale De Novo Genome Assembler – Evangelos Georganas

Functional metagenomic discovery of bacterial effectors in the human microbiome and isolation of commendamide, a GPCR G2A/132 agonist – Louis J. Cohen – PNAS

Proteomics and metabolomics

The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity – Samuel H. Payne – Scientific Data

Monitoring microbial metabolites using an inductively coupled resonance circuit – Daniil Karnaushenko – Scientific Reports

Extremophiles

Biotechnological applications of extremophiles, extremozymes and extremolytes – Noura Raddadi – Applied Microbiology and Biotechnology

Microbes in the news

Mothers facing C-sections look to vaginal ‘seeding’ to boost their babies’ health – Aimee Molloy – The Guardian

Bacterial community in pregnant women linked to preterm birth, study finds – Erin Digitale – Stanford Medicine
Stanford preterm birth study counters Detroit findings – Karen Bouffard – The Detroit News
Microbe Mix May Play Role In Preterm Birth Risk – Rob Stein – NPR

Biologist investigates how gene-swapping bacteria evade antibiotics – University of Texas at Dallas – EurekAlert

Methane and Climate Change: Arctic Bacteria Might Eat Methane? – Nature World News

How beneficial bacteria protect intestinal cells – Quinn Eastman – Emory News Center

Researchers Identify Metaproteomic Differences between Obese, Non-Obese Individuals – Adam Bonislawski – Genomeweb

How does Cincinnati Children’s Hospital use the microbiome to study lupus? A look inside with Diana Taft – Megan McGrath – DNA Genotek

Science, publishing, and career

A Scientific Look at Bad Science – Bourree Lam – The Atlantic

Bik’s Picks

Photos: Ancient Flowering Plant May Have Lived with Dinosaurs – Live Science

First-Ever Salamander in Amber Found in Caribbean – Richard Farrell – Discovery

Nasa awards $200,000 grant to a research project aimed at turning astronaut poo into food – Independent

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August 14, 2015

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Two papers on detection of bacteria in blood, vaginal microbiome, a discussion on eukaryotes in the human gut, and fungal communities’ resistance and resilience to wild fires. And some extra non-microbial Bik’s Picks for the weekend!

Human blood / infection microbiome

Bacterial Landscape of Bloodstream Infections in Neutropenic Patients via High Throughput Sequencing – Peter Gyarmati – PLOS ONE

16S rRNA Gene Sequence-Based Identification of Bacteria in Automatically Incubated Blood Culture Materials from Tropical Sub-Saharan Africa – Hagen Frickmann – PLOS ONE

Human vaginal microbiome

A Study of the Vaginal Microbiome in Healthy Canadian Women Utilizing cpn60-Based Molecular Profiling Reveals Distinct Gardnerella Subgroup Community State Types – Arianne Y. K. Albert – PLOS ONE

Human gut microbiome

Are Human Intestinal Eukaryotes Beneficial or Commensals? – Julius Lukeš – PLOS Pathogens

Review: Role of the normal gut microbiota – Sai Manasa Jandhyala – World Journal of Gastroenterology

Review: Paleolithic nutrition for metabolic syndrome: systematic review and meta-analysis – Eric W Manheimer – The American Journal of Clinical Nutrition

Animal models

In Mice: Autophagy Protects against Colitis by the Maintenance of Normal Gut Microflora and Secretion of Mucus – Koichiro Tsuboi – Journal of Biological Chemistry

Plant, root, and soil microbiome

Arbuscular mycorrhizal fungal communities show low resistance and high resilience to wildfire disturbance – Xingjia Xiang – Plant and Soil

From lithotroph- to organotroph-dominant: directional shift of microbial community in sulphidic tailings during phytostabilization – Xiaofang Li – Scientific Reports

Water microbiome

A Dissolved Oxygen Threshold for Shifts in Bacterial Community Structure in a Seasonally Hypoxic Estuary – Rachel L. Spietz – PLOS ONE

Techniques

Collection media and delayed freezing effects on microbial composition of human stool – Roberto Flores – Microbiome

Bioinformatics

Sorting out viral dark matter – Denise Waldron – Nature Reviews Microbiology

Manifold Based Optimization for Single-Cell 3D Genome Reconstruction – Jonas Paulsen – PLOS Computational Biology

Other microbiology

Mycobacterium tuberculosis: Genome watch: Looking at Beijing’s skyline – Dorota Jamrozy & Teemu Kallonen – Nature Reviews Microbiology

Microbes in the news

Feeding My Curiosity – And My Microbes – Alanna Collen – uBiome

Crohn’s and Colitis video featuring Laboratory of Will DePaolo

Bik’s Picks – some extra for you for the weekend!

We’ve Used Up Our Annual Supply of Earth’s Resources—And It’s Only August – Maddie Stone – Gizmodo

Drones could be stressing out wildlife, scientists suggest – Chelsea Harvey – Washington Post

Low-fat diets ‘better than cutting carbs’ for weight loss – James Gallagher – BBC News

Google’s Life Sciences division to build a miniature glucose tracker – Mona Lalwani – EnGadget

Why scientists got an alligator to inhale helium – Rachel Feltman – Washington Post

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August 8, 2015

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Lung and oral microbiomes in setting of HIV infection, cell biology of the plant–microbe interface, deep see prokaryotes, bacterial succession during grape fermentation, and correcting amplicon errors with Dada2.

Pregnancy and birth microbiome

Is abnormal vaginal microflora a risk factor for intrauterine fetal growth restriction? – Natalija Vedmedovska – Asian Pacific Journal of Reproduction

Multiple Opportunistic Pathogens, but Not Pre-existing Inflammation, May Be Associated with Necrotizing Enterocolitis – Steven T. Leach – Digestive Diseases and Sciences

Review: Nutrient availability, the microbiome and intestinal transport during pregnancy – Stuart Astbury – Applied Physiology, Nutrition, and Metabolism

Human oral and lung microbiome

Multi-center Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals – James M. Beck – American Journal of Respiratory and Critical Care Medicine

Review: Microbial protection and virulence in periodontal tissue as a function of polymicrobial communities: symbiosis and dysbiosis – Frank A. Roberts and Richard P. Darveau – Periodontology 2000

Needs assessment for emerging oral microbiome knowledge in dental hygiene education – R. Constance Wiener – Journal of Epidemiological Research

Human reproductive microbiome

Is abnormal vaginal microflora a risk factor for intrauterine fetal growth restriction? – Natalija Vedmedovska – Asian Pacific Journal of Reproduction

Human gut microbiome

Alterations of mucosal microbiota in the colon of patients with inflammatory bowel disease revealed by real time polymerase chain reaction amplification of 16S ribosomal ribonucleic acid – Jayakanthan Kabeerdoss – Indian J Med Res

An In Vitro Method to Assess Soil Arsenic Metabolism by Human Gut Microbiota: Arsenic Speciation and Distribution – Naiyi Yin – Environmental Science & Technology

Review: Does a low FODMAP diet help IBS? – Drug and Therapeutics Bulletin

Microbiome models

Modulation of intestinal microbiota in mice by kefir administration – Dong-Hyeon Kim – Food Science and Biotechnology

High nutrient availability reduces the diversity and stability of the equine caecal microbiota – Naja C. K. Hansen – Microbial Ecology in Health & Disease

Impact of Dietary Fiber/Starch Ratio in Shaping Cecal Microbiota in Rabbits – YanLi Zhu – Canadian Journal of Microbiology

Animal microbiome

Electrical Retrieval of Living Microorganisms from Cryopreserved Marine Sponges Using a Potential-Controlled Electrode – Sumihiro Koyama – Marine Biotechnology

PhD Thesis: Reproduction, Sex Ratio and Bacterial Communities of the Coffee Berry Borer Hypothenemus Hampei F. (Coleoptera: Curculionidae) – Mariño Cárdenas – Universidad de Puerto Rico

Effect of starch source (corn, oats or wheat) and concentration on fermentation by equine fecal microbiota in vitro – Brittany E. Harlow – Journal of Applied Microbiology

Role of peptidases of the intestinal microflora and prey in temperature adaptations of the digestive system in planktivorous and benthivorous fish – V. V. Kuz’mina – Fish Physiology and Biochemistry

Plant, root, and soil microbiome

Environmental conditions rather than microbial inoculum composition determine the bacterial composition, microbial biomass and enzymatic activity of reconstructed soil microbial communities – Weibing Xun – Soil Biology and Biochemistry

Editorial: Introduction to a Virtual Special Issue on cell biology at the plant–microbe interface – Ralph Panstruga and Hannah Kuhn – New Phytologist

Influence of 34-years of fertilization on bacterial communities in an intensively cultivated black soil in northeast China – Jing Zhou – Soil Biology and Biochemistry

Functional and structural responses of methanogenic microbial communities in Uruguayan soils to intermittent drainage – Yang Ji – Soil Biology and Biochemistry

Effects of pasture management on soil fertility and microbial communities in the semi-arid grasslands of Inner Mongolia – Jun Liu – Journal of Soils and Sediments

Antibiotic resistance differentiates Echinacea purpurea endophytic bacterial communities with respect to plant organs – Alessio Mengoni – Research in Microbiology

Effect of combined microbes on plant tolerance to Zn–Pb contaminations – Anna Ogar – Environmental Science and Pollution Research

From mesophilic to thermophilic digestion: the transitions of anaerobic bacterial, archaeal, and fungal community structures in sludge and manure samples – Weimin Sun – Applied Microbiology and Biotechnology

Water microbiome

Metagenome-based diversity analyses suggest a significant contribution of non-cyanobacterial lineages to carbonate precipitation in modern microbialites – Aurélien Saghaï – Frontiers in Microbiology

Thesis: Geobiological interactions of archaeal populations in acidic and alkaline geothermal springs of Yellowstone National Park, WY, USA – Jacob Preston Beam – Montana State University

Global diversity and biogeography of deep-sea pelagic prokaryotes – Guillem Salazar – ISME Journal

Built environment microbiology

Halophilic microbial communities in deteriorated buildings – Justyna Adamiak – World Journal of Microbiology and Biotechnology

Food microbiology

Insights into the bacterial community and its temporal succession during the fermentation of wine grapes – Hailan Piao – Frontiers in Microbiology

Identification of key microorganisms involved in Douchi fermentation by statistical analysis and their use in an experimental fermentation – Chen Chen – Journal of Applied Microbiology

In vitro fermentation of lupin seeds (Lupinus albus) and broad beans (Vicia faba): dynamic modulation of the intestinal microbiota and metabolomic output – Patricia Gullón – Food & Function

Bioinformatics

DADA2: High resolution sample inference from amplicon data – Benjamin J Callahan

Transcriptomics

Molecular and chemical dialogues in bacteria-protozoa interactions – Chunxu Song – Scientific Reports

Techniques

Methods for Improving Human Gut Microbiome Data by Reducing Variability through Sample Processing and Storage of Stool – Monika A. Gorzelak – PLOS ONE

Microbes in the News

Prestigious Japanese university comes up with cheesecake … made with Gorilla bacteria! – RocketNews

Lambton College research project proves successful in eliminating bacteria in firefighting gear – Lambton College

Where the sausage gets made – Holly Ganz – MicroBEnet

Calgary diseases expert on the importance of studying our guts – The Globe and Mail

Bik’s Picks

Creepers’ peepers: Why animals’ pupils have different shapes – Nicholas St. Fleur – Seattle Times

Venomous frogs discovered during painful scientific mishap: Frogs head-butt enemies with their spines to inject toxic venom – CBC News

ISS Astronauts to Sample Leafy Greens Grown on Space Station – NDTV

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