Category Archives: Metagenomics & Bioinformatics

April 21, 2015

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I don’t always eat steak, but when I do, I will put some garlic on it.

Conferences

WAO Symposium on Food Allergy and the Microbiome – December 2015 – Miami, FL, USA

Call for papers: Interactions of the Human Microbiome and Immune System in Health Resilience and Disease Pathogenesis – Journal of Immunology Research

Microbiome of pregnancy and birth

Impact of human milk bacteria and oligosaccharides on neonatal gut microbiota establishment and gut health – Ted Jost – Nutrition Reviews

Human oral microbiome

Editorial on “The oral microbiome in an ecological perspective: More than just a sum of microbes” – Egija Zaura and Alex Mira – Frontiers in Cellular and Infection Microbiology

Human respiratory microbiome

Rapid detection of emerging pathogens and the loss of microbial diversity associated with severe lung disease in cystic fibrosis – William G. Flight – Journal of Clinical Microbiology

Review behind a thick paywall: The pediatric microbiome and the lung – Michael Tracy – Current Opinion in Pediatrics

Review: Lung Microbiomes: New Frontiers? – Kathryn DeRiemer – American Journal of Respiratory and Critical Care Medicine

Review: A systematic review and meta-analysis of probiotics for the treatment of allergic rhinitis – Alexander E. Zajac – International Forum of Allergy & Rhinology

Human gut microbiome

Ménage-à-trois of bariatric surgery, bile acids and the gut microbiome – Rajendra Raghow – World Journal of Diabetes

Gut Microbiome Compositional and Functional Differences between Tumor and Non-tumor Adjacent Tissues from Cohorts from the US and Spain – Gut Microbes

Review: No Vacancy: How Beneficial Microbes Cooperate with Immunity To Provide Colonization Resistance to Pathogens – Martina Sassone-Corsi and Manuela Raffatellu – The Journal of Immunology

Review on chronic kidney disease: Altered intestinal microbial flora and impaired epithelial barrier structure and function in CKD: the nature, mechanisms, consequences and potential treatment – Nosratola D. Vaziri – Nephrology Dialysis Transplantation

Review: The Role of Microbial Amino Acid Metabolism in Host Metabolism – Evelien P. J. G. Neis – Nutrients

Review: Linking Smoking, Coffee, Urate, and Parkinson’s Disease – A Role for Gut Microbiota? – Filip Scheperjans – Journal of Parkinson’s Disease

Animal and other models of microbiome research

Have some garlic with your steak: Dietary allicin reduces transformation of L-carnitine to TMAO through impact on gut microbiota – Wei-Kai Wu – Journal of Functional Foods

Innate Lymphoid Cells Control Early Colonization Resistance against Intestinal Pathogens through ID2-Dependent Regulation of the Microbiota – Xiaohuan Guo – Immunity

Effect of donor animal species and their feeding on the composition of the microbial community establishing in a rumen simulation – M. Witzig – Journal of Applied Microbiology

Impact of a novel protein meal on the gastrointestinal microbiota and host transcriptome of larval zebrafish Danio rerio – Eugene Rurangwa – Frontiers in Physiology

Animal microbiome

Shit happens: Shifts in the gut microbiome observed in wildlife (Giraffa camelopardalis, Antidorcas marsupialis) fecal samples exposed to natural weather conditions: lessons from time series analyses using next generation sequencing for application in field studies – Sebastian Menke – Methods in Ecology and Evolution

Caste-Specific Differences in Hindgut Microbial Communities of Honey Bees (Apis mellifera) – Karen M. Kapheim – PLOS ONE

Molecular Survey of Bacterial Communities Associated with Bacterial Chondronecrosis with Osteomyelitis (BCO) in Broilers – Tieshan Jiang – PLOS ONE

Plant root and soil microbiome

Bacterial diversity amplifies nutrient-based plant–soil feedbacks – Simone Weidner – Functional Ecology

Non-random species loss in bacterial communities reduces antifungal volatile production –
W. H. Gera Hol – Ecology

Application of a new purification method of West-Kazakhstan chestnut soil microbiota DNA for metagenomic analysis – N. Kh. Sergaliev – Eurasian Soil Science

Physiological profiles of microbial communities in mine soils afforested with different tree species – Marcin Chodak – Ecological Engineering

Microbial lipid and amino sugar responses to long-term simulated global environmental changes in a California annual grassland – Chao Liang – Frontiers in Microbiology

Water microbiome

Seasonal diversity and dynamics of haptophytes in the Skagerrak, Norway, explored by high-throughput sequencing – Elianne Sirnæs Egge – Molecular Ecology

Extremophiles

Relationship between phylogenetic and nutritional diversity in Arctic (Kandalaksha Bay) seawater planktonic bacteria – Chiara Pesciaroli – Annals of Microbiology

Geochemical Characteristics and Microbial Community Composition in Toxic Metal-Rich Sediments Contaminated with Au-Ag Mine Tailings – Man Jae Kwon – Journal of Hazardous Materials

Uranium isotopes fingerprint biotic reduction – Malgorzata Stylo – PNAS

Bioreactor microbiome

Metaproteomics of complex microbial communities in biogas plants – Robert Heyer – Microbial Biotechnology

Similar PAH Fate in Anaerobic Digesters Inoculated with Three Microbial Communities Accumulating Either Volatile Fatty Acids or Methane – Florence Braun – PLOS ONE

Reactor performance and methanogenic archaea species in thermophilic anaerobic co-digestion of waste activated sludge mixed with food wastewater – Hyun Min Jang – Chemical Engineering Journal

Functional food microbiology

A proposed framework for an appropriate evaluation scheme for microorganisms as novel foods with a health claim in Europe – Sylvie Miquel – Microbial Cell Factories

Metagenomics and bioinformatics

CoMeta: Classification of Metagenomes Using k-mers – Jolanta Kawulok, Sebastian Deorowicz – PLOS ONE

Large-scale contamination of microbial isolate genomes by Illumina PhiX control – Supratim Mukherjee – Standards in Genomic Sciences

NGS-eval: NGS Error analysis and novel sequence VAriant detection tooL – Ali May – Nucleic Acids Research

Mini review: The Turbulent Network Dynamics of Microbial Evolution and the Statistical Tree of Life – Eugene V. Koonin – Journal of Molecular Evolution

Not really metagenomics but of interest: Ecological overlap and horizontal gene transfer in Staphylococcus aureus and Staphylococcus epidermidis – Guillaume Méric – Genome Biology and Evolution

Haven’t we microbiologists already been doing this for years?
Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform – Shadi Shokralla – Scientific Reports

Techniques

Method Optimization for Fecal Sample Collection and Fecal DNA Extraction – Conny Mathay – Biopreservation and Biobanking

Microbes in the news

Housing characteristics and microbial communities in homes of asthmatic children – Elisabeth Bik – MicroBEnet

OCHS science experiment finds space a hospitable place for bacteria – Cindy Nevitt – Press of Atlantic City

Uranium isotopes carry the fingerprint of ancient bacterial activity – Phys.org

Immune cells support good gut bacteria in fight against harmful bacteria – University of Chicago

Q&A: What Is Listeria? Bacteria Found in Blue Bell Ice Cream – Mary Clare Jalonick – ABC News

Grant will help University of Minnesota study antibiotic-resistant bacteria – Star Tribune

Science, publishing, and career

Mya Breitbart awarded the 2015 STEM Woman of the Year – University of South Florida

Bik’s Picks

Fast imaging of live organisms with sculpted light sheets – Aleksander K. Chmielewski – Scientific Reports

Cheesy, metallic, sweet: 170-year-old champagne is clue to winemaking’s past – Allie Wilkinson – Nature

New Evidence of Prehistoric Trade With Asia Found at Bering Land Bridge Site – Huffington Post
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April 16, 2015

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Human gut microbiome

Alcoholic Liver Disease: The Gut Microbiome and Liver Cross Talk – Phillipp Hartmann – Alcoholism: Clinical and Experimental Research

Animal models of microbiome research

Xylo-oligosaccharides and virginiamycin differentially modulate gut microbial composition in chickens – Mohsen Pourabedin – Microbiome

Taking advantage of quorum sensing – Cláudio Nunes-Alves – Nature Reviews Microbiology

Changes in the colon microbiota and intestinal cytokine gene expression following minimal intestinal surgery – Susan Lapthorne – World Journal of Gastroenterology

Animal microbiome

Insect life history and the evolution of bacterial mutualism – Lee M. Henry – Ecology Letters

Bugs full of viruses – Astrid Gall – Nature Reviews Microbiology

Similar sponge-associated bacteria can be acquired via both vertical and horizontal transmission – Detmer Sipkema – Environmental Microbiology

Transcriptional activity of the giant barrel sponge, Xestospongia muta Holobiont: Molecular Evidence for Metabolic Interchange – Cara L. Fiore – Frontiers in Microbiology

Water microbiome

Shift of anammox bacterial community structure along the Pearl Estuary and the impact of environmental factors – Bingbing Fu – Journal of Geophysical Research

Metatranscriptome analyses indicate resource partitioning between diatoms in the field – Harriet Alexander – PNAS USA

Microbiome of the built environment

Total Concentrations of Virus and Bacteria in Indoor and Outdoor Air – Aaron J. Prussin – Environmental Science and Technology Letters
See also my blog post on MicroBE.net about this paper, with a lively discussion on filters and pore sizes

Food microbiology

Effect of Gamma Irradiation on the Bacteriological and Sensory Analysis of Raw Whole Milk under Refrigeration – Adriana Cristina de Oliveira Silva

Bioreactor microbiology

Disturbance opens recruitment sites for bacterial colonization in activated sludge – David C. Vuono – Environmental Microbiology

Metaproteomics of complex microbial communities in biogas plants – Robert Heyer – Microbial Biotechnology

16S rRNA gene analysis, not metagenomics: Metagenomic analysis for the microbial consortium of anaerobic CO oxidizers – Ying Guo – Microbial Biotechnology

Bioinformatics

Protocol: Bioinformatics and Microarray Data Analysis on the Cloud – Barbara Calabrese, Mario Cannataro – Methods in Molecular Biology

An Ontology-Based GIS for Genomic Data Management of Rumen Microbes – Saber Jelokhani-Niaraki – Genomics & Informatics

Behind a very thick paywall: Application of Meta-Mesh on the analysis of microbial communities from human associated-habitats – Xiaoquan Su – Quantitative Biology

Metagenomics

The metagenomic approach and causality in virology – Silvana Beres Castrignano and Teresa Keico Nagasse-Sugahara – Rev Saúde Pública

Techniques

Use of pressure cycling technology for cell lysis and recovery of bacterial and fungal communities from soil – Emily A. Bruner – BioTechniques

Microbial Ecology

Estimating and Mapping Ecological Processes Influencing Microbial Community Assembly – James C. Stegen – Frontiers in Microbiology

More microbiology

The Infallible Microbial Identification Test: Does It Exist? – Alex van Belkum – Journal of Clinical Microbiology

Microbes in the news

Synthetic Cheese and the Microbiome – Alex A. — MicroBE.net

Total Concentrations of Virus and Bacteria in Indoor and Outdoor Air – Elisabeth Bik – MicroBE.net

A Review of the Oral Microbiome: Orli Reports – Orli Kadoch – uBiome Blog

To fight nasty digestive bugs, scientists set out to build a better gut—using stem cells – Medical Xpress

#BacteriaArePlural The bacteria that steals DNA from its surroundings – Mette Risbråthe – Norwegian University of Life Sciences

#BacteriaHysteria: Germ warfare: Kitchens can harbor hidden bacteria – Katherine Roth – The Pueble Chieftain

Science, publishing, and career

A resource for cell line authentication, annotation and quality control – Mamie Yu – Nature

Science AMA Series: We are Charon Pierson, journal editor and elected member of the Governing Council for the Committee on Publication Ethics (COPE) and Ivan Oransky, co-founder of Retraction Watch. AUA about publication ethics and retractions.

Rule rewrite aims to clean up scientific software – Nature Biotechnology asks peer reviewers to check accessibility of code used in computational studies – Erika Check Hayden – Nature

Bik’s Picks

Response of seafloor ecosystems to abrupt global climate change – Sarah E. Moffitt – PNAS USA

Longread: The Pollen Detective – He’d used science to crack cases from art forgery to bank robbery. But then a murder took place in his own backyard – David Wolman – Medium

This professor measured his fingernail growth for 35 years. The results will amaze you! – Seriously, Science? – Discover

April 11, 2015

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Another new paper on gorilla gut microbiome, reviews on role of microbes in obesity, and finding the microbial equivalent of cockroaches.

Pregnancy and birth microbiome

Pathogenesis of neonatal necrotizing enterocolitis – Joanna C. Lim – Pediatric Surgery International

Human oral microbiome

Differentiation of salivary bacterial profiles of subjects with periodontitis and dental caries – Daniel Belstrøm – Journal of Oral Microbiology

Secretome of gingival epithelium in response to subgingival biofilms – N. Bostanci – Molecular Oral Microbiology

Human gut microbiome

Perspective: Integrating host gene expression and the microbiome to explore disease pathogenesis – Allyson L Byrd and Julia A Segre – Genome Biology

Review: Recent Advances in Characterizing the Gastrointestinal Microbiome in Crohn’s Disease: A Systematic Review – Emily K Wright – Inflammatory Bowel Diseases

Review: Dietary effects on human gut microbiome diversity – Zhenjiang Xu and Rob Knight – British Journal of Nutrition

Review: Obesity and the gastrointestinal microbiota: a review of associations and mechanisms – Catherine Graham – Nutrition Reviews

Review: Gut Microbiome and Obesity: A Plausible Explanation for Obesity – Claudia Sanmiguel – Current Obesity Reports

Animal model microbiome

Distinct Commensals Induce Interleukin-1β via NLRP3 Inflammasome in Inflammatory Monocytes to Promote Intestinal Inflammation in Response to Injury – Sang-Uk Seo – Immunity
Animal microbiome

Gut microbiome composition and metabolomic profiles of wild western lowland gorillas (Gorilla gorilla gorilla) reflect host ecology – Andres Gomez – Molecular Ecology

Soil and plant root microbiome

Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests – Cedar N. Hesse – Frontiers in Microbiology

Parent materials have stronger effects than land use types on microbial biomass, activity and diversity in red soil in subtropical China – Huan Deng – Pedobiologia

Changes in soil microbial functional diversity and biochemical characteristics of tree peony with amendment of sewage sludge compost – Xiangdong Huang – Environmental Science and Pollution Research

16S rRNA study, not metagenomics: Cataloguing the bacterial diversity of the Sundarbans mangrove, India in the light of metagenomics – Pijush Basak – Genomics Data

Relationships among bulk soil physicochemical, biochemical, and microbiological parameters in an organic alfalfa-rice rotation system – Ana R. Lopes – Environmental Science and Pollution Research

Soil microbial responses over 2 years following biochar addition to a north temperate forest – Genevieve L. Noyce – Biology and Fertility of Soils

Water microbiome

Temporal Dynamics of Active Prokaryotic Nitrifiers and Archaeal Communities from River to Sea – Mylène Hugoni – Microbial Ecology

Extremophile microbiome

Finding the microbial equivalent of cockroaches: The impact of gamma radiation on sediment microbial processes – Ashley R. Brown – Applied and Environmental Microbiology

Built environment microbiome

Methods to Assess Human Occupancy and Occupant Activity in Hospital Patient Rooms – Sandra Dedesko – Building and Environment

Bioreactor microbiology

Bacterial communities in haloalkaliphilic sulfate-reducing bioreactors under different electron donors revealed by 16S rRNA MiSeq sequencing – Jiemin Zhou – Journal of Hazardous Materials

Microbial Ecology

Antimicrobial Resistance: The Major Contribution of Poor Governance and Corruption to This Growing Problem – Peter Collignon – PLOS ONE

Local–global overlap in diversity informs mechanisms of bacterial biogeography – Joshua A Livermore and Stuart E Jones – The ISME Journal

Metagenomics and bioinformatics

Inference of Markovian Properties of Molecular Sequences from NGS Data and Applications to Comparative Genomics – Jie Ren – ArXiv

Techniques

Normalization of environmental metagenomic DNA enhances the discovery of under-represented microbial community members – J.-B. Ramond – Letters in Applied Microbiology

Estimating Protistan Diversity using High-throughput Sequencing – Sarah K. Hu – Journal of Eukaryotic Microbiology

Microbes in the news

Connecting Indoor Microbiome Studies with Indoor Chemistry – Jonathan Eisen – MicroBE.net

Smart Sewers Will Reveal What’s in Cambridge Citizens’ Guts – Elie Dolgin – IEEE Spectrum

Microbes disprove long-held assumption that all organisms share a common vocabulary – Science Daily

Scientists study mystery of Lake Erie toxic bacteria – Detroit Free Press

Jessica Cofield puts degrees in microbiology to good use – Crystal Garrett – Sun Journal

MRSA Bacteria From Borrowed Makeup Brush Paralyzes 27-Year-Old Woman – Lecia Bushak – Medical Daily

Science, publishing, and career

Virginia student earns admission to all eight Ivy League schools, and others – T. Rees Shapiro – Washington Post

China’s medical research integrity questioned – The Lancet

The seven sins of peer review – Technologist

Bik’s Picks

Review: Innovations in Health Value and Functional Food Development of Quinoa (Chenopodium quinoa Willd.) – Brittany L. Graf – Comprehensive Reviews in Food Science and Food Safety

In Hawaii, Chickens Gone Wild – Kenneth Chang – New York Times

Komodo dragon named Smaug gets a leg up from a new prosthetic – Rachel Feltman – Washington Post

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April 9, 2015

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Events and conferences

3rd Microbiome R&D and Business Collaboration Forum: USA – 10-11 September 2015, San Diego

Symposium ‘Women & Their Microbes’, Amsterdam, The Netherlands, May 8, 2015 in Micropia

Human gut microbiome

Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease – Xochitl C Morgan – Genome Biology

Animal models of microbiome research

High-grain feeding causes strong shifts in ruminal epithelial bacterial community and expression of Toll-like receptor genes in goats – Jun-hua Liu – Frontiers in Microbiology

Site-specific programming of the host epithelial transcriptome by the gut microbiota – Felix Sommer – Genome Biology

Animal microbiome

Bats: Bacteria Isolated from Bats Inhibit the Growth of Pseudogymnoascus destructans, the Causative Agent of White-Nose Syndrome – Joseph R. Hoyt – PLOS ONE

Plant microbiome

Interactions of Methylotrophs with Plants and Other Heterotrophic Bacteria – Hiroyuki Iguchi – Microorganisms

Soil and sediment microbiome

Effects of 100 years wastewater irrigation on resistance genes, class 1 integrons and IncP-1 plasmids in Mexican soil – Sven Jechalke – Frontiers in Microbiology

Microbial methane formation in deep aquifers of a coal-bearing sedimentary basin, Germany – Friederike Gründger – Frontiers in Microbiology

Farm management, not soil microbial diversity, controls nutrient loss from smallholder tropical agriculture – Stephen A. Wood – Frontiers in Microbiology

Water microbiome

Viruses and bacteria in floodplain lakes along a major Amazon tributary respond to distance to the Amazon River – Rafael M. Almeida – Frontiers in Microbiology

Extremophile microbiome

Permafrost thawing in organic Arctic soils accelerated by ground heat production – Jørgen Hollesen – Nature Climate Change
See also:
Bacteria warm up permafrost – Nature

Alternative lifestyle: The processes that allow life to thrive in deep-sea vents are happening all around us – Nick Higgs – New Scientist

Bacterial community structure across environmental gradients in permafrost thaw ponds: methanotroph-rich ecosystems – Sophie Crevecoeur – Frontiers in Microbiology

Influence of Martian regolith analogs on the activity and growth of methanogenic archaea, with special regard to long-term desiccation – Janosch Schirmack – Frontiers in Microbiology

Diversity and role of plasmids in adaptation of bacteria inhabiting the Lubin copper mine in Poland, an environment rich in heavy metals – Lukasz Dziewit – Frontiers in Microbiology

Active Microbial Communities Inhabit Sulphate-Methane Interphase in Deep Bedrock Fracture Fluids in Olkiluoto, Finland – Malin Bomberg – BioMed Research International

Food microbiology

Review: Recent trends in non-invasive in situ techniques to monitor bacterial colonies in solid (model) food – María M. Lobete – Frontiers in Microbiology

Bioreactor and wastewater microbiome

Bacteriophages as indicators of human and animal faecal contamination in raw and treated wastewaters from Tunisia – M. Yahya – Journal of Applied Microbiology

Microbial Ecology

Taking advantage of quorum sensing – Cláudio Nunes-Alves – Nature Reviews Microbiology

Metagenomics and bioinformatics

Phylogenomics and systematics in Pseudomonas – Margarita Gomila – Frontiers in Microbiology

Kraken: ultrafast metagenomic sequence classification using exact alignments – Derrick E Wood and Steven L Salzberg (HT: Tomer Altman)

Metabolomics

Exometabolomics and MSI: deconstructing how cells interact to transform their small molecule environment – Leslie P Silva – Current Opinion in Biotechnology

 

Microbes in the news

Life below Antarctic ice survives on ancient forests – Catherine Brahic – New Scientist

Eden Project’s ‘Human Biome’ is a gross, musical microbe showcase – Katie Collins – Wired

Company provides easy access to microbiome data – Mark Niu – CCTV America

 

Gates Foundation Issues Call for Application for Round 15 of Grand Challenges Initiative  – Philanthropy News Digest

Changes in Lung Microbiota May Help Predict Cystic Fibrosis Pulmonary Exacerbations – Patricia Silva – Cystic Fibrosis News today

Body maps reveal the bacteria and chemicals lurking on skin – Meera Senthilingam – CNN

 

Gut Bacteria May Be Associated with Parkinson’s Phenotype – Neurology Advisor

Microbes Engineered to Prevent Obesity – Katherine Bourzac – Technology Review
Cornell Researchers Identify Gut Microbes that May Help Some People Remain Thin; Findings Could Result in Clinical Laboratory Tests to Analyze the Microbiomes of Individuals – Dark Daily

Silver linings: a personal memoir about Hurricane Katrina and fungal volatiles
Joan W. Bennett – Frontiers in Microbiology

 

Sequencing the intestinal microbiome to target therapies: Vanni Bucci looking for probiotic cocktails – Bryan Goodchild and Ellie Castano – University of Massachusetts Medical School Communications

Bacteria inhibit bat-killing fungus, could combat white-nose syndrome – Tim Stephens – University of California Santa Cruz

Turtle phage therapy might help develop alternative to antibiotic treatments for humans, Queensland researchers say – Nance Haxton – ABC Australia

9 Types Of Bacteria You Didn’t Know You’re Sharing Your House With – Esther Inglis-Arkell

 

Science, publishing, and career

Chris Butler: Wants to snuggle up to bacteria – BMJ Observations

‘Plagiarism, fraud, and predatory publishing’ are polluting science, says bioethicist Arthur Caplan – Susan Perry – MinnPost

Bik’s Picks

Hair Regrowth Discovery Suggests Skin Cells Communicate Like Bacteria – Dina Fine Maron – Scientific American

Genome sequencing mountain gorillas reveals the genetic impact of inbreeding – Aylwyn Scally – The Conversation

Gem lover donates $13M for Smithsonian’s science education – Brett Zongker  – Washington Post

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April 8, 2015

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Events

#UMassMedChat on the microbiome is Thursday at 11:30 a.m.- UMass Center for Microbiome Research to answer questions on gut health

Microbes in the City: Mapping the Urban Genome, Friday, June 19, 2015 – The New York Academy of Sciences

Human respiratory microbiome

Analysis of microbiota in stable patients with chronic obstructive pulmonary disease – Estefania Aguirre – APMIS

Human gut microbiome

Site-specific programming of the host epithelial transcriptome by the gut microbiota – Felix Sommer – Genome Biology

Animal microbiome

Horses and pigs: Lactobacillus ruminis strains cluster according to their mammalian gut source – Michelle M O’ Donnell1 – BMC Microbiology

Turkeys: Rye Affects Bacterial Translocation, Intestinal Viscosity, Microbiota Composition and Bone Mineralization in Turkey Poults – Guillermo Tellez – PLOS ONE

Amphibians: Larval exposure to polychlorinated biphenyl 126 (PCB-126) causes persistent alteration of the amphibian gut microbiota – Kevin D. Kohl – Environmental Toxicology and Chemistry

Tsetse fly: Paternal transmission of a secondary symbiont during mating in the viviparous tsetse fly – Linda De Vooght – Molecular Biology and Evolution

Squid and Vibrio fisheri: Signaling between two interacting sensor kinases promotes biofilms and colonization by a bacterial symbiont – Allison N. Norsworthy and Karen L. Visick – Molecular Microbiology
Sponges: Phylogenetic diversity of sulphate-reducing Desulfovibrio associated with three South China Sea sponges – D. Zhang – Letters in Applied Microbiology

Plant root and soil microbiome

Plant diversity increases soil microbial activity and soil carbon storage – Markus Lange – Nature Communications

Phylogenetic relatedness determined between antibiotic resistance and 16S rRNA
genes in actinobacteria – Marketa Sagova-Mareckova – BMC Microbiology

Water microbiome

Functional Gene Composition, Diversity and Redundancy in Microbial Stream Biofilm Communities – Andrew Dopheide – PLOS ONE

Metabolomics

Distributing a metabolic pathway among a microbial consortium enhances production of natural products – Kang Zhou – Nature Biotechnology

Metabolite-sensing receptors ​GPR43 and ​GPR109A facilitate dietary fibre-induced gut homeostasis through regulation of the inflammasome – Laurence Macia – Nature Communications

Molecular Signatures of Nicotinoid-Pathogen Synergy in the Termite Gut – Ruchira Sen – PLOS ONE

Unique Honey Bee (Apis mellifera) Hive Component-Based Communities as Detected by a Hybrid of Phospholipid Fatty-Acid and Fatty-Acid Methyl Ester Analyses – Kirk J. Grubbs – PLOS ONE

Bioinformatics

A Robust ANOVA Approach to Estimating A Phylogeny from Multiple Genes – Ximing Xu – Molecular Biology and Evolution

More microbiology papers

Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe – Gemma L. Kay – Nature Communications

Microbes in the news

Beneficial bacteria – Ella Nonni – The Cornell Daily Sun

Mapping All The Chemicals And Tiny Bacteria Living On Our Skin – Adele Peters – FastCoExist

uBiome and HelloFlo are teaming up to explore how the vaginal microbiome changes during pregnancy and postpartum

Video: Gut Microbiome and Its Role in Allergy and Asthma – Christine Cole Johnson – JSPRQ.com

Colorado startup’s microbiome-modulating drug could improve metformin tolerability – Meghana Keshavan – MedCityNews

Race to stamp out animal plague begins – Ewen Callaway – Nature

Science, publishing, and career

The future of the postdoc: There is a growing number of postdocs and few places in academia for them to go. But change could be on the way – Kendall Powell – Nature

Opinion: Addressing systemic problems in the biomedical research enterprise – Bruce Alberts – PNAS USA

History: Women at the edge of science – Jennifer Rampling – Nature

Bik’s Picks

Efficacy of Commercial Weight-Loss Programs: An Updated Systematic Review
Kimberly A. Gudzune – Annals of Internal Medicine

Ecology: Recovering the potential of coral reefs – Nicholas K. Dulvy & Holly K. Kindsvater – Nature
Complex organic molecules discovered in infant star system: Hints that building blocks of chemistry of life are universal – Science Daily

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April 7, 2015

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Lots of abstracts today that were published in the FASEB Journal. Although not clearly marked, these appear to be abstracts from an ASBMB meeting held in March 2015 in Boston, called “The Human Microbiome“. None of these have a link to a PDF.

Course: Frontiers in Host-Microbe Interactions – August 2015

Pregnancy and birth microbiome

The FASEB Journal Abstracts:

Review: Normal flora and bacterial vaginosis in pregnancy: an overview – Mathys Jacobus Redelinghuys – Critical Reviews in Microbiology

Review: The Infant Gut Microbiome: Evidence for Obesity Risk and Dietary Intervention – Petya T. Koleva – Nutrients

Human skin microbiome

The diversity and host interactions of Propionibacterium acnes bacteriophages on human skin – Jared Liu – The ISME Journal

Human oral microbiome

The Repertoire of Archaea Cultivated from Severe Periodontitis – Hong T. T. Huynh – PLOS ONE

Review: Filifactor alocis – a new emerging periodontal pathogen – A. Wilson Aruni – Microbes and Infection

Human gut microbiome

The FASEB Journal Abstracts:

Autism spectrum disorders and intestinal microbiota – Maria De Angelis – Gut Microbes

Review: Impacts of Gut Bacteria on Human Health and Diseases – Yu-Jie Zhang – International Journal of Molecular Sciences

Animal models of microbiome research

The FASEB Journal Abstracts:

Leaky intestine and impaired microbiome in an amyotrophic lateral sclerosis mouse model – Shaoping Wu – Physiological Reports

Metabolomic Modeling To Monitor Host Responsiveness to Gut Microbiota Manipulation in the BTBRT+tf/j Mouse – Matthias S. Klein – Journal of Proteome Research

Animal microbiome

The FASEB Journal Abstract: The Extraordinary Evolution of the Great Ape Microbiome
Howard Ochman

Pigs: How host gender affects the bacterial community in pig feces and its correlation to skatole production – Zhenjin Zhou – Annals of Microbiology

Pigs: Analysis of swine fecal microbiota at various growth stages – Jungman Kim – Archives of Microbiology

Fish / Review: Disinfection of teleost eggs: a review – Evelien De Swaef – Reviews in Aquaculture

Ticks: Concordance of bacterial communities of two tick species and blood of their shared rodent host – Evelyn C. Rynkiewicz – Molecular Ecology

Soil microbiome

Over 150 Years of Long-Term Fertilization Alters Spatial Scaling of Microbial Biodiversity – Yuting Liang – mBio

Analysis of Bacterial and Archaeal Communities along a High-Molecular-Weight Polyacrylamide Transportation Pipeline System in an Oil Field – Cai-Yun Li – International Journal of Molecular Sciences

Effects of Functionalized and Raw Multi-Walled Carbon Nanotubes on Soil Bacterial Community Composition – Dorsaf Kerfahi – PLOS ONE

Review: Effective role of indigenous microorganisms for sustainable environment – Baduru Lakshman Kumar and D. V. R. Sai Gopal – 3 Biotech

Water microbiome

Size-fractionated diversity of eukaryotic microbial communities in the Eastern Tropical North Pacific oxygen minimum zone – M.T. Duret – FEMS Microbial Ecology

Seawater mesocosm experiments in the Arctic uncover differential transfer of marine bacteria to aerosols – Camilla Fahlgren – Environmental Microbiology Reports

Book: Microbiology of the Everglades Ecosystem – CRC Press

Extremophile microbiome

Physiochemical control of bacterial and protist community composition and diversity in Antarctic sea ice – Anders Torstensson – Environmental Microbiology

Whole-Genome Shotgun Sequence of the Keratinolytic Bacterium Lysobacter sp. A03, Isolated from the Antarctic Environment – Jamile Queiroz Pereira – Genome Announcements

Food microbiome

Microbial Ecology of Watery Kimchi – Kyu Hang Kyung – Journal of Food Science

Bioreactor and biofilter microbiome

Characterization of the microbial community structure and nitrosamine-reducing isolates in drinking water biofilters – Wanfeng Wang – Science of the Total Environment

Metagenomics, Metabolomics, and Transcriptomics

The FASEB Journal Abstracts:

Proficiency testing for bacterial whole genome sequencing: an end-user survey of current capabilities, requirements and priorities – Jacob Moran-Gilad – BMC Infectious Diseases

Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis – Yuzhen Ye, Haixu Tang – ArXiv

Single-cell genomics-based analysis of virus–host interactions in marine surface bacterioplankton – Jessica M Labonté – The ISME Journal

Applying meta-pathway analyses through metagenomics to identify the functional properties of the major bacterial communities of a single spontaneous cocoa bean fermentation process sample – Koen Illeghems – Food Microbiology

Size-fraction partitioning of community gene transcription and nitrogen metabolism in a marine oxygen minimum zone – Sangita Ganesh – The ISME Journal

Transcriptomic evidence for microbial sulfur cycling in the eastern tropical North Pacific oxygen minimum zone – Molly Carolan and J Michael Beman – Frontiers in Microbiology

Review: Progress and Challenges in Developing Metabolic Footprints from Diet in Human Gut Microbial Cometabolism – Linda C Duffy – Journal of Nutrition

Microbial Ecology

Bacterial adaptation to sublethal antibiotic gradients can change the ecological properties of multitrophic microbial communities – Ville-Petri Friman – Proceedings B

Local–global overlap in diversity informs mechanisms of bacterial biogeography – Joshua A Livermore – The ISME Journal

Techniques

Assessing the performance of the Oxford Nanopore Technologies MinION – T. Laver – Biomolecular Detection and Quantification

Next-generation sequencing data analysis on cloud computing – Taesoo Kwon – Genes & Genomics

Microbes in the news

It’s a microbe’s world…we’re just living and dying in it – Margaret Leigh Sinrod – SciTechNow

May deadline: 2015 MO BIO Microbiome Awards – MoBIO

After cancer diagnosis, MIT student 3-D prints tumor, has microbiome analyzed – Nidhi Subbaraman – BetaBoston

Most of the text appears stolen from an article by Lita Proctor:  Human Microbiome: Quiz – Target Health

Video: Why Your Beard Is Disgusting – Discovery News

Episode 4 of The Microbiome Podcast: What’s hot in the microbiome field with Kristina Campbell – American Microbiome Institute

Solving the complex problem of recurrent C. diff with a simple solution: 
Physician scientists are using fecal transplants to break the deadly cycle of a killer infection – Bryan Goodchild and Ellie Castano – University of Massachusetts Medical School

Gut Bacteria May Influence Parkinson’s Risk, Phenotype – Pauline Anderson – Medscape

Summing up: Bassis et al.’s take on the influence of the URT on other human-associated biogeographies – Fiona Whelan – Human Microbiome Journal Club:

Under the microscope, strong-swimming swamp bacteria spontaneously organize into crystals – Phys.org

Science, publishing, and career

Female peers in small work groups enhance women’s motivation, verbal participation, and career aspirations in engineering – Nilanjana Dasgupta – PNAS USA

Bik’s Picks

How California can survive the drought — State is not in complete control – Danielle Venton – Nature

The Brontosaurus Is Back, Baby – Rich Juzwiak – Gawker

Endangered Tortoises Feasting on Invasive Plants – Richard Farrell – Discovery
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April 3, 2015

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Check out today’s #PLOSBuzzFeed on Twitter for some Friday fun.

Human general microbiome

Only 10 microbes are designated by the International Agency for Cancer Research (IACR) as carcinogenic to humans (Review): Cancer and the microbiota – Wendy S. Garrett – Science

Microbiome of pregnancy and birth

Administration of a multistrain probiotic product (VSL#3) to women in the perinatal period differentially affects breast milk beneficial microbiota in relation to mode of delivery – Paola Mastromarino – Pharmacological Research

Conference abstract: Preterm Infant Gut Microbiome and Weight at 36 Weeks Corrected Gestational Age – Diana Taft – The FASEB Journal

Still in press: Should Infants Cry Over Spilled Milk? Fecal Glycomics as an Indicator of a Healthy Infant Gut Microbiome – Steven A Frese – Journal of Pediatric Gastroenterology & Nutrition

Human respiratory microbiome

Conference abstract: Correlative Changes in Macrophage Polarization and Pulmonary Microbiota in Lung Transplant Recipients – E. Bernasconi – The Journal of Heart and Lung Transplantation

Harder to breathe (Review): The changing face of asthma and its relation with microbes – Chris S. Earl – Trends in Microbiology

Human gut microbiome / functional foods

Metabolic and physiologic effects from consuming a hunter-gatherer (Paleolithic)-type diet in type 2 diabetes – U Masharani – European Journal of Clinical Nutrition

Findings from a Randomized Controlled Trial of Fecal Transplantation for Patients with Ulcerative Colitis – Noortje G. Rossen – Gastroenterology

Correlation between gut microbiota composition and parasitic infection of pre-adolescence in Malaysia – Chun-Wie Chong – Journal of Microbiology, Immunology and Infection

Fit to the bone (review): The intestinal microbiome and skeletal fitness: connecting bugs and bones – Julia F. Charles – Clinical Immunology

Poster abstract: Effect of Prebiotic Fiber Intake on Adiposity and Inflammation in Overweight and Obese Children: Assessing the Role of the Gut Microbiota – Alissa C. Nicolucci – Canadian Journal of Diabetes

Animal models of microbiome

Poster abstract: Parallel Improvement in Body Weight, Glycemia, and Intestinal Permeability but not Body Fat with Prebiotic- and Antibiotic-Induced Gut Microbiota Modification – Marc Bomhof – Canadian Journal of Diabetes

Animal microbiome

Drosophila: The Impact of Host Diet on Wolbachia Titer in Drosophila – Laura R. Serbus – PLOS Pathogens

Soil and compost microbiome

Soil plots in Burgundy (but no vineyards!): Mapping and determinism of soil microbial community distribution across an agricultural landscape – Florentin Constancias – MicrobiologyOpen

Molecular profile of microbiota of Finnish commercial compost suppressive against Pythium disease on cucumber plants – D. Yu – Applied Soil Ecology

Wildfire effects on the properties and microbial community structure of organic horizon soils in the New Jersey Pinelands – Robyn A. Mikita-Barbato – Soil Biology and Biochemistry

Extremophile microbiome (see also “Microbes in the news” below)

Microbial dwarves in the mines: Use of Phosphate Solubilizing Bacteria to Leach Rare Earth Elements from Monazite-Bearing Ore – Doyun Shin – Minerals

Food microbiology

This study smells: Microbiological spoilage and volatiles production of gutted European sea bass stored under air and commercial modified atmosphere package at 2oC – Foteini F. Parlapani – Food Microbiology

Viable cells differentiation improves microbial dynamics study of fermented milks – Davide Porcellato – International Dairy Journal

Wine electrophoresis? Inactivation of wine associated microbiota by continuous pulsed electric field treatments – Lucía González-Arenzana – Innovative Food Science & Emerging Technologies

Bioreactor microbiome

Characterization of the microbial community structure and nitrosamine-reducing isolates in drinking water biofilters – Wanfeng Wang – Science of the Total Environment

Bioinformatics

PhyloRelief: Explaining Diversity in Metagenomic Datasets by Phylogenetic-Based Feature Weighting – Davide Albanese – PLOS Computational Biology

One of the figures has the Giant Microbes in it! Personalized microbial network inference via co-regularized spectral clustering – Sultan Imangaliyev – Methods

Microbes in the news

“Life at the Limits” shows extremophiles aren’t just bacteria – AMNH exhibit includes live axolotls, nautiluses, and mantis shrimp – John Timmer – Ars Technica

uBiome’s Dental Campaign to Give Portion of Proceeds to Charitable Dental Organization
Partnering with Oral Health America’s Smiles Across America – PR Web

No Bonferroni correction but: Is The Microbiome Correlated with Income? The Answer Will Surprise You – Alexandra Carmichael – uBiome

Cross-posting this week’s contribution for MicroBE.net: Gently down the stream: the microbiome along a river’s course – Elisabeth Bik – MicroBE.net

Cleaning with Bleach May Lead to Childhood Infections – Laura Geggel – Live Science

How the guts of poultry affect performance – Jake Davies – FWI

Cigarette Smoke Makes Superbugs More Aggressive – Heather Buschman – UC San Diego

The Plague Bacteria Found in Flea Samples Near Flagstaff – NAZ Today

Travelers Bringing Drug-Resistant Bacteria to U.S.: Strain of Shigella is easily transmitted and causes tough-to-treat diarrhea, CDC says – WebMD

France bans imports of Puglia vegetables as olive bacteria starts mini trade war – Nicole Winfield – US News

Science, publishing, and career

Hoax-detecting software spots fake papers – John Bohannon – Science

A career is like a love affair – Madeleine Jacobs – Science

Ten Simple Rules to Win a Nobel Prize – Richard J. Roberts – PLOS Computational Biology

Science and art

This is gorgeous: A Sprawling New Cut Paper Bacterium by Rogan Brownby – Christopher Jobson – Colossal

Bik’s Picks

All animal phyla in 35 photos – Melissa Hogenboom – BBC

Shelled Out: 5 Egg-Citing Facts – Laura Geggel – Live Science

My Real-Time Response To Learning What The Rock Eats Every Day – Mallory Ortberg

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April 2, 2015

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Animal models of microbiome research

Dietary fat intake and age influence gut microbiota and colonic inflammation in C57BL/6J mice – Su Jeong Kim – The FASEB Journal

Maternal obesity alters gut microbial ecology in offspring of NOD mice – Meijun Zhu – The FASEB Journal

Metabolite-sensing receptors ​GPR43 and ​GPR109A facilitate dietary fibre-induced gut homeostasis through regulation of the inflammasome – Laurence Macia – Nature Communications

Animal microbiome

Cheetah (not microbiome but could not resist): Dietary Factors Associated with Faecal Consistency and Other Indicators of Gastrointestinal Health in the Captive Cheetah (Acinonyx jubatus) – Katherine M. Whitehouse-Tedd – PLOS ONE

Ants: Genome evolution in an ancient bacteria-ant symbiosis: parallel gene loss among Blochmannia spanning the origin of the ant tribe Camponotini – Laura E. Williams, Jennifer J. Wernegreen – PeerJ

Sponges: Functional gene-based discovery of phenazines from the actinobacteria associated with marine sponges in the South China Sea – Valliappan Karuppiah – Applied Microbiology and Biotechnology

Editorial: Sponge symbionts and the marine P cycle – Albert S Colman – PNAS USA

Soil and plant root communities

Bacterial community of cushion plant Thylacospermum ceaspitosum on elevational gradient in the Himalayan cold desert – Klára Řeháková – Frontiers in Microbiology

Soil microbial functional diversity and biomass as affected by different thinning intensities in a Chinese fir plantation – Xin-Li Chen – Applied Soil Ecology

Impact of organic and conventional peach and apple production practices on soil microbial populations and plant nutrients – Ramesh R. Pokharel, Rick Zimmerman – Organic Agriculture

Impact of preferential methane flow through soil on microbial community composition
Julia Gebert, Mirjam Perner – European Journal of Soil Biology

Characterization of bacterial strains and their impact on plant growth promotion and yield of wheat and microbial populations of soil – Ashok Kumar – African Journal of Agricultural

Metabolomics

Gut Commensal Immunomodulatory Factors: Identification and Structure-Function Studies – Sungwhan Oh – The FASEB Journal

Review: Metagenomics for the discovery of novel biosurfactants of environmental interest from marine ecosystems – Stephen A Jackson – Current Opinion in Biotechnology

Techniques

Modification of a commercial DNA extraction kit for safe and rapid recovery of DNA and RNA simultaneously from soil, without the use of harmful solvents – E. Tournier

Other articles of interest

Dengue: Large-scale recoding of an arbovirus genome to rebalance its insect versus mammalian preference – Sam H. Shen – PNAS USA

Mitochondrial and plastid genome architecture: Reoccurring themes, but significant differences at the extremes – David Roy Smith and Patrick J. Keeling – PNAS USA

Bioinformatics

A standardized, extensible framework for optimizing classification improves marker-gene taxonomic assignments – Nicholas A. Bokulich – PeerJ Preprint

Microbes in the news

I enjoyed reading this: Microbiome Blues in E – Michael Tanner – Clinical Correlations
“You haven’t been squeaky clean since you were bunking with a placenta. “

Drinking water microbiology — from measurement to management – David Coil – MicroBEnet

Movie Night at Bozeman Public Library, April 7th: Bugs with Benefits, an Intro to the Human Microbiome – Bozeman Daily

Do Antibiotics Raise Diabetes Risk via Gut Microbiota? – Liam Davenport – Medscape

About Genome Biology study: Longer DNA fragments reveal rare species diversity – Phys.org

Editorial about mBio study: Soil source for vine bacteria – Nature

Treating the Root Cause of IBS: Small Intestine Bacterial Overgrowth – Maura Henninger – Huffington Post

Origin Sciences Ltd: Newly-Published Data Shows the Effectiveness of OriCol™ for Sampling the Gut Microbiome – BusinessWire

Smart phone diagnosis? Biosensing platform quickly and accurately diagnoses disease and monitors treatment remotely – Science Daily

Science, publishing, and career

Peer review with Elizabeth Marincola (CEO of PLOS) – Royal Society

Fighting Plagiarism In Scientific Papers – Tommaso Dorigo – Science 2.0

Editor’s point of view: Science’s Big Scandal: Even legitimate publishers are faking peer review – Charles Seife – Slate

Stanford Graduate student charged with poisoning labmates’ drinks – Kylie Jue – Stanford Daily

Four simple tools to promote gender balance at conferences – Julie Pfeiffer – The Tree of Life

Bik’s Picks

The human sex ratio from conception to birth – Steven Hecht Orzack – PNAS USA

Failed synchronization of the womb’s clock with mother’s body clock critical in miscarriages – Science Daily

Watch the century’s fastest lunar eclipse Saturday – CBS News

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March 31, 2015

Posted on by

For today’s digest, I screened over 500 papers, and thousands of Tweets for you. Here is my selection:

Pregnancy and birth microbiome

PhD thesis [PDF]: Dynamics of co-existing Escherichia coli lineages in situ of the infant gut – Heidi Kira Gumpert – Technical University of Denmark

Associations between Gut Microbial Colonization in Early Life and Respiratory Outcomes in Cystic Fibrosis – Anne G Hoen – The Journal of Pediatrics

Review: Probiotics for Preterm Infants: A Premature or Overdue Necrotizing Enterocolitis Prevention Strategy? – Sharon Anderson – Neonatal Network

Review: Preterm infant nutrition, gut bacteria, and necrotizing enterocolitis – Josef Neu –  Current Opinion in Clinical Nutrition & Metabolic Care

Human oral microbiome

Periodontal Therapy Effects on Nitrite Related to Oral Bacteria: A 6-Month Randomized Clinical Trial – Sheila C Cortelli – Journal of Periodontology

Perspective: Mouthguards: Does the indigenous microbiome play a role in maintaining oral health? – Purnima S. Kumar and Matthew R. Mason – Frontiers in Cellular and Infection Microbiology

Human respiratory microbiome

Nasal Inoculation of the Commensal Neisseria lactamica Inhibits Carriage of Neisseria meningitidis by Young Adults: A Controlled Human Infection Study – Alice M. Deasy – Clinical Infectious Diseases

Human skin microbiome

Molecular cartography of the human skin surface in 3D – Amina Bouslimani – PNAS USA

Human gut microbiome

Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection – Alexa Weingarden – Microbiome Journal

Insight into alteration of gut microbiota in Clostridium difficile infection and asymptomatic C. difficile colonization – Zhang Lihua – Anaerobe

Review: The microbiota in inflammatory bowel disease – Donal Sheehan – Journal of Gastroenterology

Review: Promoting Health and Longevity through Diet: From Model Organisms to Humans – Luigi Fontana, Linda Partridge – Cell

Review: TLR4 at the crossroads of nutrients, gut microbiota and metabolic inflammation
Licio A. Velloso – Endocrine Reviews

Review: Cultivating Healthy Growth and Nutrition through the Gut Microbiota – Sathish Subramanian – Cell

Review: The human gut microbiome, a taxonomic conundrum – Senthil Alias Sankar – Systematic and Applied Microbiology

Review: The Role of Infectious Mediators and Gut Microbiome in the Pathogenesis of Celiac Disease – Mohammad Rostami-Nejad – Archives of Iranian Medicine

Review: Exercise and the microbiota – Orla O’Sullivan – Gut Microbes

Animal models of microbiome research

Abnormal Pregnancy Outcomes in Mice Using an Induced Periodontitis Model and the Haematogenous Migration of Fusobacterium nucleatum Sub-Species to the Murine Placenta – Sara Stockham – PLOS ONE

Lactobacillus rhamnosus lowers zebrafish lipid content by changing gut microbiota and host transcription of genes involved in lipid metabolism – Silvia Falcinelli – Scientific Reports

Interactive effects of oligofructose and obesity predisposition on gut hormones and microbiota in diet-induced obese rats – Nina L. Cluny – Obesity

Animal microbiome

Editorial to Baboon microbiome paper: Metagenomics: Social behavior and the microbiome – Jack A Gilbert – eLIFE

More baboons: Development, diet, and dynamism: longitudinal and cross-sectional predictors of gut microbial communities in wild baboons – Tiantian Ren – Environmental Microbiology

Spider monkey: Effect of preservation method on spider monkey (Ateles geoffroyi) fecal microbiota over 8 weeks – Vanessa L. Hale – Journal of Microbiological Methods

Cats: Molecular identification of black-pigmented bacteria from subgingival samples of cats suffering from periodontal disease – L. Pérez-Salcedo – Journal of Small Animal Practice

Desert wool rat: Validating the use of trap-collected feces for studying the gut microbiota of a small mammal (Neotoma lepida) – Journal of Mammalogy

Tortoise: Kinship, inbreeding, and fine-scale spatial structure influence gut microbiota in a hindgut-fermenting tortoise – Michael L. Yuan – Molecular Ecology

Trout: Bacterial community structure in the intestinal ecosystem of rainbow trout (Oncorhynchus mykiss) as revealed by pyrosequencing-based analysis of 16S rRNA genes
Miray Etyemez, José Luis Balcázar – Research in Veterinary Science

Fruit fly: Pyrosequencing reveals a shift in symbiotic bacteria populations across life stages of Bactrocera dorsalis – Awawing A. Andongma – Scientific Reports

Aphids: Bacterial Communities Associated with Host-Adapted Populations of Pea Aphids Revealed by Deep Sequencing of 16S Ribosomal DNA – Jean-Pierre Gauthier – PLOS ONE

Plant microbiome

A metagenome for lacustrine Cladophora (Cladophorales) reveals remarkable diversity of eukaryotic epibionts and genes relevant to materials cycling – Linda E. Graham – Journal of Phycology

Soil and plant root microbiome

A novel pathway producing ​dimethylsulphide in bacteria is widespread in soil environments – O. Carrión – Nature Communications

Metabolic characteristics of microbial communities of Aeolian sandy soils induced by saline water drip irrigation in shelter forests – Z. Jin – European Journal of Soil Science

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

Effects of monoculture and mixed culture of grass and legume forage species on soil microbial community structure under different levels of nitrogen fertilization – Jie Zhao – European Journal of Soil Biology

Soil microbial community variation correlates most strongly with plant species identity, followed by soil chemistry, spatial location and plant genus – Jean H. Burns – AoB Plants

Long-term oil contamination causes similar changes in microbial communities of two distinct soils – Jingqiu Liao – Frontiers in Environmental Science

Soil Microbial Community Structure and Target Organisms under Different Fumigation Treatments – Sadikshya R. Dangi – Applied and Environmental Soil Science

Water microbiome

Carbonate fabrics in the modern microbialites of Pavilion Lake: two suites of microfabrics that reflect variation in microbial community morphology, growth habit, and lithification – C. Harwood Theisen – Geobiology

The Unique Chemistry of Eastern Mediterranean Water Masses Selects for Distinct Microbial Communities by Depth – Stephen M. Techtmann – PLOS ONE

Planktonic eukaryote molecular diversity: discrimination of minerotrophic and ombrotrophic peatland pools in Tierra del Fuego (Argentina) – Enrique Lara – J. Plankton Research

Extremophile microbiome

Ice cover extent drives phytoplankton and bacterial community structure in a large north-temperate lake: implications for a warming climate – B. F. N. Beall – Environmental Microbiology

Marine microbes rapidly adapt to consume ethane, propane, and butane within the dissolved hydrocarbon plume of a natural seep – Stephanie D. Mendes – Journal of Geophysical Research: Oceans

Built environment microbiome

Are microbial communities in green roof substrates comparable to those in post-industrial sites?—a preliminary study – Chloe J. Molineux – Urban Ecosystems

Food microbiology

Some journals just have great titles: Microbial community changes in Makgeolli during brewing – Changhoon Chai – Journal of the Institute of Brewing

Review: Fermented Foods as Experimentally Tractable Microbial Ecosystems – Benjamin E. Wolfe, Rachel J. Dutton – Cell

Metagenomics and bioinformatics

Assessing the limits of restraint-based 3D modeling of genomes and genomic domains
Marie Trussart – Nucleic Acids Research

CRISPR Detection from Short Reads Using Partial Overlap Graphs – Ilan Ben-Bassat, Benny Chor – Research in Computational Molecular Biology

CLARK: fast and accurate classification of metagenomic and genomic sequences using
discriminative k-mers – Rachid Ounit – BMC Genomics

FlowClus: efficiently filtering and denoising pyrosequenced amplicons – John M Gaspar and W Kelley Thomas – BMC Bioinformatics

Review: 16S rRNA gene high-throughput sequencing data mining of microbial diversity and interactions – Feng Ju, Dr. Tong Zhang – Applied Microbiology and Biotechnology

Book Chapter: Single-Cell Sequencing of Microorganisms – Ying Chen – Single Cell Sequencing and Systems Immunology

Metabolomics

Review: Rumen Nutrition Symposium How to use data on the rumen microbiome to improve our understanding of ruminant nutrition – J. L. Firkins and Z. Yu – Journal of Animal Science

Microbes in the news

Modeling microbial metabolism on indoor surfaces – Jack Gilbert – MicroBEnet

Body Maps Expose the Chemical Residue That Coats Our Skin – Marcus Woo – Wired.com
Crazy maps reveal colonies of bacteria and chemicals all over the human body – Kevin Loria – Business Insider
3D Human Skin Maps Aid Study of Relationships Between Molecules, Microbes and Environment – Heather Buschman – UC San Diego

Advancing the understanding of the dental microbiome – Maria Perno Goldie – Dentistry IQ

Who Let the Microbes Out: A Paw Print of Doggy Skin Bacteria – Daniella Lowenberg – PLOS blogs

Antibiotic-resistant bacteria are not match for medieval potion – Alexandra Ossola – Popular Science

Antibiotic-Resistant Bacteria From Texan Cattle Yards Are Now Airborne, Study Finds
Kevin McSpadden – Time

Growing a Baby Microbiome – Kevin Bonham – Scientific American

Poop Transplants Can Treat Severe Infection In Patients – FPJ Bureau – The Free Press Journal

Poo transplants could save thousands – Geoff Egan – Range News
Healthy Microbiome Changes Last After Fecal Transplant in New Research – Elizabeth Gough-Gordon – MPR

With sample collection videos: GoViral – collecting nasal and saliva samples from sick people – Boston Children’s Hospital

Northwestern leads research on effects of long-term stay in space – Peter Kotecki – The Daily Northwestern
Conference paper: Research from the NASA Twins Study and Omics in Support of Mars Missions – NASA Technical Reports

Podcast (1min30): Donate Your Health Data To Medical Science – Cynthia Graber – Scientific American – American Gut, GoViral

You Act What You Eat: How Gut Microbes Modify Our Behavior – Monica Thunder – ResetMe

Meet The Bacteria That Make A Stink In Your Pits – Poncie Rutsch – NPR
Bacterial genetic pathway involved in body odor production discovered – Science Daily

Should Gut Bugs Influence the 2015 Dietary Guidelines? – Cameron Wells – US News

Glowing Tampons Help Detect Sewage Leaks – Gwen Pearson – Wired

Nearly half of hospital uniforms are washed in temperatures too cool to kill bacteria, says DMU research – De Montfort University
Egyptians Brewed Beer in Tel Aviv 5,000 Years Ago – Megan Gannon – Live Science

Conferences

#IHMC2015: 5th International Human Microbiome Congress, March 31-April 2, 2015, Luxembourg (6/23 plenary speakers are women)

The 2nd Microbiome R&D and Business Collaboration Forum Europe, May 07 – 08, 2015, London, UK (10/36 listed speakers are women)

1st Annual Translational Microbiome Conference, 13–14 May 2015, Boston, United States (5/11 speakers are women)

ASM General Meeting, May 30 – June 2, 2015, New Orleans, LA, USA

Symbiomes: Systems Biology of Host-Microbiome Interactions, 5-10 June 2015, Pultusk, Poland (5/17 speakers are women)

The Human Microbiome, 10-12 Jun 2015, EMBL Heidelberg, Germany (8/23 confirmed speakers are women)

Exploring Human Host-Microbiome Interactions in Health and Disease, June 29 – July 1, 2015 , Cambridge, UK (7/17 speakers are women)

Science, publishing, and career

How Articles Get Noticed and Advance the Scientific Conversation – Victoria Costello – PLOS Blogs

Writing a Good Peer Review to Improve Scholarship: What Editors Value and Authors Find Helpful – H. McLaughlin – Social Work Education: The International Journal

Discussion: Mistake index as a surrogate of quality in scientific manuscripts – Antoni Margalida – PNAS USA

What if you could replace performance evaluations with four simple questions? – Jena McGregor – Washington Post

Bik’s Picks

What 60 Minutes Got Right And Wrong On Duke’s Polio Virus Trial Against Glioblastoma – David Kroll – Forbes.com

The Astonishing beauty of Ordinary Sand magnified 250X – Aetherforce

What Elephants and Whales Look Like From Space – Robinson Meyer – The Atlantic

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March 30, 2015

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Microbiome in rhinosinusitis patients, microbes in permafrost, and responses of soil to deforestation.

Meetings
London Microbiome Meeting 2015 (LMM2015), St. Thomas’ Hospital, 28 May 2015

Human respiratory microbiome

Sinus microbiota varies among chronic rhinosinusitis phenotypes and predicts surgical outcome – Vijay R. Ramakrishnan – Journal of Allergy and Clinical Immunology

Animal microbiome

Antimicrobial resistance in faecal samples from buffalo, wildebeest and zebra grazing together with and without cattle in Tanzania – A.A.S. Katakweba – Journal of Applied Microbiology

Soil and plant root microbiome

Soil microbiome responses to the short-term effects of Amazonian deforestation –
Acacio A. Navarrete – Molecular Ecology

Reconstructed metagenomes reveal changes of microbial functional profiling during PAHs degradation along a rice (Oryza sativa) rhizosphere gradient – B. Ma – Journal of Applied Microbiology

Profiling bacterial diversity in a limestone cave of the western Loess Plateau of China – Yucheng Wu – Frontiers in Microbiology

Extremophile microbiome

Structure, mineralogy, and microbial diversity of geothermal spring microbialites associated with a deep oil drilling in Romania – Cristian Coman – Frontiers in Microbiology

Shifts in methanogenic community composition and methane fluxes along the degradation of discontinuous permafrost – Mette M. Svenning – Frontiers in Microbiology

Bioreactor microbiome

Analysis of microbial community composition in a lab-scale membrane distillation bioreactor – Q. Zhang – Journal of Applied Microbiology

Food microbiology

Diffusion of solutes inside bacterial colonies immobilized in model cheese depends on their physicochemical properties: a time-lapse microscopy study – Juliane Floury – Frontiers in Microbiology

Metagenomics

It’s a dirty job — A robust method for the purification and de novo genome assembly of Cryptosporidium from clinical material – Sofia Andersson – Journal of Microbiological Methods

Bioinformatics and statistics

Power and Sample-Size Estimation for Microbiome Studies Using Pairwise Distances and PERMANOVA – Brendan J. Kelly – Bioinformatics

More microbe papers

Review: Tackling antibiotic resistance: the environmental framework – Thomas U. Berendonk – Nature Reviews Microbiology

Microbes in the news

You Should Know: Kristina Campbell and The Intestinal Gardener – DNLee – Scientific American
Link to blog: The Intestinal Gardener – Kristina Campbell

Video of the February VLAB meeting at Stanford: Gut-Feeling — Ventures into the Microbiome – Colleen Cutcliffe – VLAB videos

Chronic Rhinosinusitis Varies By Bacterial Microbiome – Vijay R. Ramakrishnan – Medical Research

Doctors: How gut bacteria affects obesity, diabetes, child health – Jondi Gumz – Santa Cruz Sentinel

The bacteria that could make your blue jeans greener – Michael Keller – Green Biz

Bacteria power up by using magnets as batteries – Catherine Brahic – New Scientist

Antibiotics from the medieval medicine cabinet: Could medieval medicine provide new antibiotics to treat deadly modern infections? – CrowdFunder

Science, publishing and career

These scientists studied journalists covering science. Whoa, meta. – Suzanne Jacobs – Grist

Let’s compare the backgrounds of science writers for Fox and NPR – Boing Boing

Mind the (gender) gap: Kew’s records show fewer than 3% of land plant species published by women – Lauren Gardiner – Kew Royal Botanical Gardens

I’m an engineer, not a cheerleader. Let’s abandon silly rules about gender roles. – Sara Sakowitz – Washington Post

Bik’s Picks

Velvet Worms, Squirting Slime – James Gorman – New York Times

An apple a day may not keep the doctor away, study says – Lindsey Tanner – Big Story AP

Family income, parental education related to brain structure in children, adolescents – Science Daily

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