Category Archives: Food Microbiology

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 15, 2015

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Microbiome of pregnancy and birth

The Gut Microbiota Composition in Dichorionic Triplet Sets Suggests a Role for Host Genetic Factors – Kiera Murphy – PLOS ONE

Human oral microbiome

Periodontitis and Porphyromonas gingivalis in Preclinical Stage of Arthritis Patients – Motomu Hashimoto – PLOS ONE

Investigation of Salivary Function and Oral Microbiota of Radiation Caries-Free People with Nasopharyngeal Carcinoma – Jingyang Zhang – PLOS ONE

Human respiratory microbiome

Impact of the CFTR-Potentiator Ivacaftor on Airway Microbiota in Cystic Fibrosis Patients Carrying A G551D Mutation – Cédric Bernarde – PLOS ONE

An Observational Study Examining the Relationship between Respiratory Symptoms, Airway Inflammation and Bacteriology in Children with Severe Neurodisability – Ruth E. Trinick – PLOS ONE

Sinonasal Microbiome Sampling: A Comparison of Techniques – Ahmed Bassiouni – PLOS ONE

Animal models of microbiome research

Robust Vaginal Colonization of Macaques with a Novel Vaginally Disintegrating Tablet Containing a Live Biotherapeutic Product to Prevent HIV Infection in Women– Laurel A. Lagenaur – PLOS ONE

Animal microbiome

Not exactly microbiome but nice: Detection of Mitochondrial COII DNA Sequences in Ant Guts as a Method for Assessing Termite Predation by Ants – Tom M. Fayle – PLOS ONE

Soil microbiome

Forensic Biology: Fungi Identify the Geographic Origin of Dust Samples – PLOS ONE

The Impact of Resource Availability on Bacterial Resistance to Phages in Soil – Pedro Gómez – PLOS ONE

Water microbiome

Redox-Specialized Bacterioplankton Metacommunity in a Temperate Estuary – Peeter Laas – PLOS ONE

Food microbiology

Cheese’omics: Overview of a Surface-Ripened Cheese Community Functioning by Meta-Omics Analyses – Eric Dugat-Bony – PLOS ONE

More microbiology

Sackler Colloquium: Reproduction, symbiosis, and the eukaryotic cell – Peter Godfrey-Smith – PNAS USA

Alternating Antibiotics Render Resistant Bacteria Beatable – Lauren Richardson – PLOS Biology

Microbes in the news

University doctoral candidate Joanna Adadevoh researches bacterial microbe groundwater purification – Anna Pollard – Cavalier Daily

13 min video: Connecting the Microbiome and Antibiotics to Obesity – Eric Topol talks to Martin Blaser

Probiotics might be like a DJ in a club: In the gut, one key probiotic helps by orchestrating others – Melissa Healy – Los Angeles Times

Microbiology and art

Extremophiles on Display: A new American Museum of Natural History exhibit highlights the incredible range of conditions under which life on Earth survives – Ashley P. Taylor – The Scientist

Science, publishing, and career

AMA: Peer review process and retractions in scientific publishing – Ivan Oransky and Charon Pierson – Reddit/science

Opinion: Senior Scientists Should Be Writing – Three reasons why authorship matters, even—perhaps especially—to established scholars – Jens P. Goetze and Jens F. Rehfeld – The Scientist

Bik’s Picks

Scientists unveil sex-linked control of genes – Stanford Medicine

Distinct metabolomic signatures are associated with longevity in humans – Susan Cheng – Nature Communications

Female Chimps – The Possible Inventors Of Spears – Kurt Cottrell – MidDay Daily

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April 10, 2015

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Pregnancy and birth microbiome

Maternal fucosyltransferase 2 status affects the gut bifidobacterial communities of breastfed infants – Zachery T Lewis – Microbiome

The Infant Nasopharyngeal Microbiome Impacts Severity of Lower Respiratory Infection and Risk of Asthma Development – Shu Mei Teo – Cell Host & Microbe

Mid-trimester amniotic fluid pro-inflammatory biomarkers predict the risk of spontaneous preterm delivery in twins: a retrospective cohort study – S M Lee – Journal of Perinatology

Risk for Preterm and Very Preterm Delivery in Women Who Were Born Preterm – Boivin, Ariane – Obstetrics & Gynecology

Human oral microbiome

Clinical and microbiological effects of probiotic lozenges in the treatment of chronic periodontitis: a 1-year follow-up study – Merve Tekce – Journal of Clinical Periodontology

Review: Beyond microbial community composition: Functional activities of the oral microbiome in health and disease – Ana E. Duran-Pinedo, Jorge Frias-Lopez – Microbes and Infection

Human gut microbiome

A randomized controlled trial to test the effect of multispecies probiotics on cognitive reactivity to sad mood – Laura Steenbergen – Brain, Behavior, and Immunity

Fungi inhabiting the healthy human gastrointestinal tract: a diverse and dynamic community – Heather E. Hallen-Adams – Fungal Ecology

Changes in human gut microbiota influenced by probiotic fermented milk ingestion – Tatsuya Unno – Journal of Dairy Science

Fecal Microbiota Transplantation Induces Remission in Patients with Active Ulcerative Colitis in a Randomized, Controlled Trial – Paul Moayyedi – Gastroenterology

Review: The Microbiota and Microbiome in Aging: Potential Implications in Health and Age-Related Diseases – Heidi J. Zapata – Journal of the American Geriatrics Society

Review: Gastric cancer and the microbiome – Nivedita Arora – Asian Pacific Journal of Tropical Disease

Review: The Role of Microbiota on the Gut Immunology – Yang Won Min – Clinical Therapeutics

Animal models of microbiome research

Editorial: Gut Microbiota: The Link to Your Second Brain – Vanessa Ridaura – Cell
Belongs to: Indigenous Bacteria from the Gut Microbiota Regulate Host Serotonin Biosynthesis – Jessica M. Yano – Cell

Inoculation of tannin-degrading bacteria into novel hosts increases performance on tannin-rich diets – Kevin D. Kohl – Environmental Microbiology

Crosstalk between Microbiota-Derived Short-Chain Fatty Acids and Intestinal Epithelial HIF Augments Tissue Barrier Function – Caleb J. Kelly – Cell Host & Microbe

Effect of a new recombinant Aeromonas hydrophila vaccine on the grass carp intestinal microbiota and correlations with immunological responses – Lei Liu – Fish & Shellfish Immunology

Colonization and induction of Th17 cells by segmented filamentous bacteria in the murine intestine – Adam M. Farkas – Journal of Immunological Methods

Animal microbiome

Microbiota and probiotics in canine and feline welfare – Łukasz Grześkowiak – Anaerobe

Isolation and use of beneficial microbiota from the digestive tract of lions-paw scallop Nodipecten subnodosus and winged pearl oyster Pteria sterna in oyster aquaculture – Fernando Abasolo-Pacheco – Aquaculture Research

Perspective: Does the Arthropod Microbiota Impact the Establishment of Vector-Borne Diseases in Mammalian Hosts? – Constance A. M. Finney – PLOS Pathogens

Plant and plant root microbiome

Seagrass biofilm communities at a naturally CO2-rich vent – Christiane Hassenrück – Environmental Microbiology Reports

Preferential Association of Endophytic Bradyrhizobia with Different Rice Cultivars and Its Implications for Rice Endophyte Evolution – Pongdet Piromyou – Applied and Environmental Microbiology

Niche partitioning in arbuscular mycorrhizal communities in temperate grasslands: a lesson from adjacent serpentine and nonserpentine habitats – Petr Kohout – Molecular Ecology

Soil microbiome

Microbial community dynamics during the early stages of plant polymer breakdown in paddy soil – Carl-Eric Wegner andWerner Liesack – Environmental Microbiology

Depth-related responses of soil microbial communities to experimental warming in an alpine meadow on the Qinghai-Tibet Plateau – B. Zhang – European Journal of Soil Science

Red Soils Harbor Diverse Culturable Actinomycetes That Are Promising Sources of Novel Secondary Metabolites – Xiaoxuan Guo – Applied and Environmental Microbiology

Water microbiome

Shifts in the meso- and bathypelagic archaea communities composition during recovery and short-term handling of decompressed deep-sea samples – Violetta La Cono –

Understanding diversity patterns in bacterioplankton communities from a sub-Antarctic peatland – María Victoria Quiroga – Environmental Microbiology Reports

The hidden seasonality of the rare biosphere in coastal marine bacterioplankton – Laura Alonso-Sáez- Environmental Microbiology

Bacterial community dynamics during polysaccharide degradation at contrasting sites in the Southern and Atlantic Oceans – Matthias Wietz – Environmental Microbiology

Extremophile microbiome

Nature special: Permafrost: overview articles and primary research from Nature papers, including role of microbes in permafrost soils

Metagenomic analysis of a high carbon dioxide subsurface microbial community populated by chemolithoautotrophs and bacteria and archaea from candidate phyla
Joanne B. Emerson – Environmental Microbiology

Food microbiology

Batch-to-batch uniformity of bacterial community succession and flavor formation in the fermentation of Zhenjiang aromatic vinegar – Zong-Min Wang – Food Microbiology

Microbial diversity and stability during primary cultivation and subcultivation processes of Tibetan kefir – Wei Gao – International Journal of Food Science & Technology

There is a serious problem with Figure 1: Tetragenococcus koreensis is part of the microbiota in a traditional Italian raw fermented sausage – C. Amadoro – Food Microbiology

Other  papers of interest

Development and utility of the FDA ‘GutProbe’ DNA microarray for identification, genotyping and metagenomic analysis of commercially available probiotics – J.N. Patro – Journal of Applied Microbiology

Increased Biodiversity in the Environment Improves the Humoral Response of Rats
Cinthia Pi – PLOS ONE

Microbes in the news

Bundle Of Joyful Microbes: Mom’s DNA Alters Baby’s Gut Bacteria – Michaeleen Doucleff – NPR Shots

Worms, germs lead to better immune function – Science Daily
http://www.sciencedaily.com/releases/2015/04/150408145242.htm
What does the term microbiome mean? And where did it come from? A bit of a surprise .. – Jonathan Eisen – MicroBEnet

Leading expert on microbiome Rob Knight wins a 2015 Vilcek Prize for Creative Promise in Biomedical Science – PR NewsWire

Congrats: You Are Officially a Superorganism – Max Lugavere – Huffington Post

Genetically-Engineered Bacteria Can Keep Mice From Getting Fat – Sarah Zhang – Gizmodo

Your microbiome may hold keys to cancer treatment – Alexandra Ossola – Popular Science

Cheese: The latest piece of the French paradox puzzle? – Niamh Michail – Food Navigator

#BacteriaHysteria #BacteriaArePlural: How much bacteria is in your kid’s lunchbox? You might be surprised (and grossed out) – Alex Perez – ABC 7online

Science, publishing, and career

Wanted: staff-scientist positions for postdocs – Kendall Powell – Nature

Book review: Speaking of science – Scientific Babel: How Science Was Done Before and After Global English – Lynn K. Nyhart – Science

Gender Disparity in Peer Review? – Andrew Harrison – Publons

Citations are not enough: Academic promotion panels must take into account a scholar’s presence in popular media – London School of Economics and Political Science

Bik’s Picks

Incredible imprinting – ‘are you my mummy?’ – Biodetectives

Sea Turtle Toddlers’ ‘Lost Years’ Spent Swimming, Not Drifting In Seaweed Matts – Rebekah Marcarelli – HNGN.com

New species of ‘terror bird’ discovered – Sid Perkins – Science

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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 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 6, 2015

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Not all human breast milk sold online is 100% human, microbiome of veggies, and a book by Rob Knight.

Pregnancy and birth

Cow’s Milk Contamination of Human Milk Purchased via the Internet – Sarah A. Keim – Pediatrics

Review: Milk Bioactives May Manipulate Microbes to Mediate Parent-Offspring Conflict – Cary R. Allen-Blevins – Evolution, Medicine, and Public Health

Food microbiology

Emerging Perspectives on the Natural Microbiome of Fresh Produce Vegetables – Colin R. Jackson – Agriculture

Metabolomics

Link did not work as of now – might work later? The colibactin warhead crosslinks DNA – Crawford – Nature Chemistry

Microbes in the news

Beyond Probiotics: Can You ‘Hack’ Your Microbiome? – Beth Skwarecki – LifeHacker Australia

Glyphosate, Roundup, GMOs and the microbiome part 1: crowdsourcing literature – Jonathan Eisen – The Tree of Life

Book by Rob Knight – Follow Your Gut – The Enormous Impact of Tiny Microbes – TED books

Ice Worm Guts Tell a Story of Partnership – Manon Verchot – Glacier Hub

An Amazonian Tribe May Hold The Secret To Better Gut Health – Anna Almendrala – Huffington Post

Microbes scared to death by virus presence – ScienceDaily

Spotting a molecular warhead for disease in the human gut – Jim Shelton – Yale News

Microbes are partly to blame for Arctic’s melting permafrost – Mary Beth Griggs – Popular Science

That Vagina Yogurt Probably Wasn’t Really Vagina Yogurt, Says Expert – Ben Richmond – Motherboard

MRSA Bacteria Thrives In Cigarette Smoke Environment – Paola Celedonio – Diabetes Insider

Raising money to go the ASM conference: E. coli and Ebola already sold out: Microbiology students sell giant plush microbes – KCCI

Glowing GE bacteria produced from kits ‘illegally’ in New Zealand – Tom Hunt – The Dominion Post

Bik’s Picks

Breast Milk Sold Online May Not Be 100% Human Milk – Cari Nierenberg – LiveScience

Please learn the difference between tortoises and sea turtles, say Florida wildlife officials – Rowena Lindsay – CS Monitor

What Americans Think About Climate Change in Seven Maps – Eric Roston – Bloomberg
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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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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 20, 2015

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General microbiome

Ribosomal RNA, the lens into life – Daniel McDonald, Zhenjiang Xu, Embriette R. Hyde and Rob Knight – RNA

Upcoming event: Cell Symposium: Human Immunity and the Microbiome in Health and Disease – September 27-29, 2015, Montreal, Canada

Human gut microbiome

Review: Firmicutes and Bacteroidetes involved in insulin resistance by mediating levels of glucagon-like peptide 1 – Claire Greenhill – Nature Reviews Endocrinology

Review: The impact of phytochemicals present in the diet on microbial signalling in the human gut – R.R. McCarthy – Journal of Functional Foods

Review: Targeting gut microbiota as a possible therapy for diabetes – Canxia He – Nutrition Research

Human oral microbiome

Guest editorial for special oral microbes edition – Robert Dwayne Lunsford – Microbes and Infection

Animal microbiome

Cattle: Microbial diversity analysis of subclinical mastitis in dairy cattle in Northeast China – Qingyu Jiang – African Journal of Microbiology Research

Worms: The effects of earthworms Eisenia spp. on microbial community are habitat dependent – Anna Koubová – European Journal of Soil Biology

Review: Insect Behaviour and the Microbiome – Zenobia Lewis, Anne Lizé – Current Opinion in Insect Science

Soil, sediments, and plant root microbiome

Carnivory does not change the rhizosphere bacterial community of the plant Drosera intermedia – Manuel Aira – Applied Soil Ecology

Microbial diversity and community respiration in freshwater sediments influenced by artificial light at night – Franz Hölker – Philosophical Transactions B
and
The biological impacts of artificial light at night: the research challenge – Kevin J. Gaston – Philosophical Transactions B

Microbial abundance and community in subsurface flow constructed wetland microcosms: role of plant presence – Qian Wang – Environmental Science and Pollution Research

Analysis of a population of magnetotactic bacteria of the Gulf of Gabès, Tunisia – Nathalie Pradel – Environmental Science and Pollution Research

Review: Linkages of plant-soil feedbacks and underlying invasion mechanisms – Inderjit and James F. Cahill Jr. – AoB Plants

Response of microbial communities to bioturbation by artificially introducing macrobenthos to mudflat sediments for in situ bioremediation in a typical semi-enclosed bay, southeast China – Ying Ma – Marine Pollution Bulletin

Water and snow microbiome

Microbial abundance and community structure in a melting alpine snowpack – Anna Lazzaro – Extremophiles

Diverse arsenic- and iron-cycling microbial communities in arsenic-contaminated aquifers used for drinking water in Bangladesh – Zahid Hassan – FEMS Microbiology Ecology

Metagenomics, proteomics, bioinformatics

Editorial: Microbial Diversity: A Bonanza of Phyla – Laura Eme, W. Ford Doolittle – Current Biology
belongs to study reconstructing Archaea genomes from metagenomic data: Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling – Cindy J. Castelle – Current Biology

Book Chapter: Evaluation of Combined Genome Assemblies: A Case Study with Fungal Genomes – Mostafa M. Abbas – Bioinformatics and Biomedical Engineering

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

Microbes in the news

Quorum-Sensing Molecule Modifies Gut Microbiota – Anna Azvolinsky – The Scientist

Functional Metagenomics Enables First Study of Bacterial Fitness in the Gut Microbiome – Chris Williams – Columbia Systems Biology

How to Study a Complex Microbial World- Part 1: DNA sequencing – Kevin Bonham -Scientific American

How to Study a Complex Microbial World – Part 2: Next Generation Sequencing Technology – Kevin Bonham -Scientific American

Biological oceanography: Life in the deepest depths – Beth N. Orcutt – Nature Geoscience

1h Podcast/article: Say Cheese! Cheese history and science – GastroPod

Jailbreaking yeast could amp up wine’s health benefits, reduce morning-after headaches – Phys.org

29 min podcast: Queen Bee Microbiome (starts at 8 min), Yams, Resistence To Organic Checkoff – PRX Earth Eats

The World’s First €100M Microbiome-focused Venture Fund opened in France – Labiotech

Bioinformatics tool for metagenome analysis – Nancy Ambrosiano – R&D Magazine

Andreessen-Backed uBiome Is Now Doing An Indiegogo Campaign To Check Out Dental Bacteria – Kim-Mai Cutler – TechCrunch

Science, publishing, and career

“Canadian” Open-Access Journal Doesn’t Look Very Canadian – Jeffrey Beall – ScholarlyOA

Science and art

Art project: What Bacteria And Smell Have To Do With Feminism Today – Katherine Brooks – Huffington Post

Bik’s Picks

Morphological Mutations: Lessons from the Cockscomb Major comb variants and their genetic basis – Denis Headon – PLOS GeneticsWhat’s that thing?

How to Google Something You Don’t Know How to Describe – Adrienne Lafrance – The Atlantic

New Breast Milk Products Are on the Rise, but Commercialization Troubles Many – Andrew Pollack – New York Times

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March 18, 2015

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Human skin microbiome

Book (hopefully also covering women’s skin): The Epidermis of Man: Co-existing with Commensals – Eds. Peter J Heidt et al.

Human oral microbiome

Salivary Microbiota Associated with Immunoglobulin A Nephropathy – Maria Piccolo – Microbial Ecology

Human gut microbiome

Review: Gut bacteria in children with autism spectrum disorders: challenges and promise of studying how a complex community influences a complex disease – Rosa Krajmalnik-Brown – Microbial Ecology in Health and Disease

Microbiome of pregnancy and birth

The Perinatal Microbiome and Pregnancy: Moving Beyond the Vaginal Microbiome –
Prince AL – CSH Perspect Med (only NCBI link available as of now)

Association between breastfeeding and intelligence, educational attainment, and income at 30 years of age: a prospective birth cohort study from Brazil – Cesar G Victora – The Lancet

Review: Individualized medicine and the microbiome of the reproductive tract – Andrea G. Braundmeier – Frontiers in Physiology

Animal and other models

The Quorum Sensing Peptides PhrG, CSP and EDF Promote Angiogenesis and Invasion of Breast Cancer Cells In Vitro – Bart De Spiegeleer – PLOS ONE

Registered report of a replication study: Intestinal inflammation targets cancer-inducing activity of the microbiota – Kate Eaton – eLIFE

Ablation of Tumor Necrosis Factor Is Associated with Decreased Inflammation and Alterations of the Microbiota in a Mouse Model of Inflammatory Bowel Disease – Yava L. Jones-Hall – PLOS ONE

Phytase Modulates Ileal Microbiota and Enhances Growth Performance of the Broiler Chickens – Anna Ptak – PLOS ONE

Intestinal Microbiota Succession and Immunomodulatory Consequences after Introduction of Lactobacillus reuteri I5007 in Neonatal Piglets – Chengli Hou – PLOS ONE

Animal microbiome

Monkeys: Metagenomic analysis of the Rhinopithecus bieti fecal microbiome reveals a broad diversity of bacterial and glycoside hydrolase profiles related to lignocellulose degradation – Bo Xu – BMC Genomics

Frogs: Composition of symbiotic bacteria predicts survival in Panamanian golden frogs infected with a lethal fungus – Matthew H. Becker – Proceedings of the Royal Society B

Cows: Altered Microbiomes in Bovine Digital Dermatitis Lesions, and the Gut as a Pathogen Reservoir – Martin Zinicola – PLOS ONE

Culture based, horses: Occurrence of bacteria and polymorphonuclear leucocytes (PMNLs) in foetal compartments at parturition; relationships with foal and mare health in the peripartum period- E. Hemberg – Theriogenology

Bees: Variation in Honey Bee Gut Microbial Diversity Affected by Ontogenetic Stage, Age and Geographic Location – Zuzana Hroncova – PLOS ONE

Bees: Deep Sequencing and Ecological Characterization of Gut Microbial Communities of Diverse Bumble Bee Species – Haw Chuan Lim – PLOS ONE

Sponges: Molecular investigation of the microbial community associated with the fire sponge, Tedania ignis, in Bermuda – Nicholas J Jouett – PeerJ

Millipedes: Microbial dynamics in food, intestine and fecal pellets of two endemic pill-millipedes (Arthrosphaera: Sphaerotheriida) of the Western Ghats [PDF] – C.N. Ambarish and K.R. Sridhar – Journal of Agricultural Technology

Mosquitoes: RNA shotgun metagenomic sequencing of northern California (USA) mosquitoes uncovers viruses, bacteria, and fungi – James Angus Chandler – Frontiers in Microbiology

Soil and plant root microbiome

Impact of metagenomic DNA extraction procedures on the identifiable endophytic bacterial diversity in Sorghum bicolor (L. Moench) – Mapula Kgomotso Annah Maropola – Journal of Microbiological Methods

Rhizosphere microbial community manipulated by 2 years of consecutive biofertilizer application associated with banana Fusarium wilt disease suppression – Zongzhuan Shen – Biology and Fertility of Soils

The Effect of Phylogenetically Different Bacteria on the Fitness of Pseudomonas fluorescens in Sand Microcosms – Olaf Tyc – PLOS ONE

Organic amendments in avocado crops induce suppressiveness and influence the composition and activity of soil microbial communities – Nuria Bonilla – Applied and Environmental Microbiology

Water microbiome

The biogeography of abundant and rare bacterioplankton in the lakes and reservoirs of China – Lemian Liu – The ISME Journal

Marine Fungi from Deep Subseafloor Sediments: Species richness and Adaptation -Vanessa Rédou – Applied and Environmental Microbiology

Microbial Methane Potential for the South Sumatra Basin Coal: Formation Water Screening and Coal Substrate Bioavailability – Rita Susilawati – Energy Procedia

Site history and edaphic features override the influence of plant species on microbial communities in restored tidal freshwater wetlands – Christine E. Prasse – Applied and Environmental Microbiology

Spatial variability of microbial assemblages associated with a dominant habitat-forming seaweed – Alexandra H. Campbell – Frontiers in Microbiology

Bioreactor microbiome

Dissecting microbial community structure and methane-producing pathways of a full-scale anaerobic reactor digesting activated sludge from wastewater treatment by metagenomic sequencing – Jianhua Guo – Microbial Cell Factories

Anaerobic codigestion of pretreated wheat straw with cattle manure and analysis of the microbial community – Zilin Song – Bioresource Technology

Analysis of Microbial Communities in the Oil Reservoir Subjected to CO2-Flooding by Using Functional Genes as Molecular Biomarkers for Microbial CO2 Sequestration – Jin-Feng Liu – Frontiers in Microbiology

Bacterial and archaeal guilds associated with electrogenesis and methanogenesis in paddy field soil – Bo Lin – Geoderma

Food microbiology

Comparing natural and selected starter cultures in meat and cheese fermentations – Daniela Bassi – Current Opinion in Food Science

Phages and viruses

Perspective: The Next Epidemic — Lessons from Ebola – Bill Gates – The New England Journal of Medicine

Genomic characteristics and environmental distributions of the uncultivated Far-T4 phages – Simon Roux – Frontiers in Microbiology

Isolation of Phages for Phage Therapy: A Comparison of Spot Tests and Efficiency of Plating Analyses for Determination of Host Range and Efficacy – Mohammadali Khan Mirzaei – PLOS ONE

Evaluation of a Viral Microarray Based on Simultaneous Extraction and Amplification of Viral Nucleotide Acid for Detecting Human Herpesviruses and Enteroviruses – Yi Liu – PLOS ONE

Review: Origins and evolution of viruses of eukaryotes: The ultimate modularity – Eugene V. Koonin – Virology

Metagenomics and bioinformatics

Accurate read-based metagenome characterization using a hierarchical suite of unique signatures – Tracey Allen K. Freitas – Nucleic Acid Research

k-mer analysis: Crossing the streams: a framework for streaming analysis of short DNA sequencing reads – Qingpeng Zhang – PeerJ

Essential genome of Pseudomonas aeruginosa in cystic fibrosis sputum – Keith H. Turner – PNAS USA

Hypothesis: Systems modeling approaches for microbial community studies: From metagenomics to inference of the community structure – Mark Hanemaaijer – Frontiers in Microbiology

Metabolomics

Review: Role of Resistant Starch in Improving Gut Health, Adiposity, and Insulin Resistance – Michael J Keenan – Advances in Nutrition

Microbial Degradation of Whole-Grain Complex Carbohydrates and Impact on Short-Chain Fatty Acids and Health – Knud Erik Bach Knudsen – Advances in Nutrition

Microbes in the news

Pet Peeves on 16S rRNA gene sequencing – Noah Fierer – Fierer lab

Can Probiotic Bacteria Save An Endangered Frog? – Ed Yong – National Geographic

New paper examines social effects on the gut microbiome of wild baboons – William G. Gilroy – Notre Dame News

Breast-Feeding Boosts Chances Of Success, Study In Brazil Finds – Rob Stein – NPR

Breast-Feeding May Have Benefits Decades Later – Nicholas Bakalar – New York Times

Lab creates bioinformatics tool for metagenome analysis – Phys.org

Could Man’s Best Friend Be Man’s Best Medicine? – Alexis Blue – University of Arizona

Dog germs may be good for you – Bradley J. Fikes – UT San Diego

The vaginal microbiome changes during and after pregnancy – American Microbiome Institute

Can the bacteria in your bowels increase your cancer risk? – Amy Yurkanin – AL.com

Your microbiome: groundbreaking research about our gut bacteria shows it could be the key to health – Jacqui Gibbons – High 50 Health

From human gut to the smartphone, new health monitoring – Tim Sandle – Digital Journal

Parasite turns shrimp into voracious cannibals – Chris Bunting – University of Leeds

Gut Bacteria, ASD, and Probiotics: Exploring the Relationship – Elizabeth Gough-Gordon – EMPR

New Molecular Tool Assesses Vaginal Microbiome Health, Diagnosis Infections-Fast – ASM

Technology helps unlock secrets of rare bacteria – Phys.org

Stanford researchers unravel secrets of shape-shifting bacteria – Tom Abate and Chris Cesare – Stanford News

Video: Alexander Fleming – Inventor of Penicillin – Scientiflix

Bik’s Picks

Ultrasoundings: monitoring a pregnant dolphin – Bill Van Bonn – Shedd Aquarium

Why are there so many freaking beetles? Science may finally have the answer. – Rachel Feltman – Washington Post

The myopia boom: Short-sightedness is reaching epidemic proportions. Some scientists think they have found a reason why – Elie Dolgin – Nature

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