Category Archives: Phages and viruses

February 4, 2015

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Animal models of microbiome research

Age-related immune clearance of hepatitis B virus infection requires the establishment of gut microbiota – Han-Hsuan Chou – PNAS

Microbiome–metabolome analysis reveals unhealthy alterations in the composition and metabolism of ruminal microbiota with increasing dietary grain in a goat model – Sheng-Yong Mao – Environmental Microbiology

Animal microbiome

Effects of the Diet on the Microbiota of the Red Palm Weevil (Coleoptera: Dryophthoridae) – Matteo Montagna – PLOS ONE

Plant microbiome

Editorial: Evolving insights to understanding mycorrhizas – Ian A. Dickie – New Phytologist

Soil and sediment microbiome

Changes in microbial communities in coastal sediments along natural CO2 gradients at a volcanic vent in Papua New Guinea – Felix F. Raulf – Environmental Microbiology

Cyanobacteria drive community composition and functionality in rock–soil interface communities – Angel Valverde – Molecular Ecology

Water microbiome

Key respiratory genes elucidate bacterial community respiration in a seasonally anoxic estuary – Erin M. Eggleston – Environmental Microbiology

DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity – Matthieu Leray and Nancy Knowlton – PNAS USA

Bioinformatics

Phylogenomics with paralogs – Marc Hellmuth – PNAS USA

16S Classifier: A Tool for Fast and Accurate Taxonomic Classification of 16S rRNA Hypervariable Regions in Metagenomic Datasets – Nikhil Chaudhary – PLOS ONE

DNA extraction and sequencing techniques

Microbial Community Composition and Diversity via 16S rRNA Gene Amplicons: Evaluating the Illumina Platform – Lucas Sinclair – PLOS ONE

Comparison of Eleven Methods for Genomic DNA Extraction Suitable for Large-Scale Whole-Genome Genotyping and Long-Term DNA Banking Using Blood Samples – Androniki Psifidi – PLOS ONE

Metabolomics

Faecal metabolite profiling identifies medium-chain fatty acids as discriminating compounds in IBD – Vicky De Preter – Gut

Probiotics

Review: The effects of consuming probiotic-fermented milk on the immune system: A review of scientific evidence – Lourdes Santiago-López – International Journal of Dairy Technology

Microbes in the News

Aquarium Microbiome Project – Shedd Aquarium

Video: Aquarium Microbiome Project – YouTube

A plea to stop ignoring microbial ecosystem effects of antimicrobial agents – Jonathan Eisen – MicroBEnet

Why you should embrace bacteria – Jody Berger – Deseret News

Infant Microbiota Influenced By Mother’s Birth Delivery, Gestation Period – Chris Weller – Medical Daily

Birth method, gestation duration may alter infants’ gut microbiota and influence later health – ASM

A warm (surprise!) welcome to the microbiome community – Alexandra Carmichael – uBiome

A Bacteria That Hasn’t Had To Evolve In More Than Two Billion Years – George Dvorsky – io9.com

Bik’s Picks

Cigarette Butt Decomposition and Associated Chemical Changes Assessed by 13C CPMAS NMR – Giuliano Bonanomi – PLOS ONE

What’s Up With That: Why Do Cats Love Boxes So Much? – Bryan Gardiner – Wired.com

Satire: Genome Study Finds Gene For Believing Genome Studies – The Allium

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February 3, 2015

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Pregnancy and birth

Dynamics of Infant Gut Microbiota Are Influenced by Delivery Mode and Gestational Duration and Are Associated with Subsequent Adiposity – Shaillay Dogra – mBio

Antimicrobial Protein and Peptide Concentrations and Activity in Human Breast Milk Consumed by Preterm Infants at Risk of Late-Onset Neonatal Sepsis – Stephanie Trend – PLOS ONE

Human oral microbiome

Dental plaque development on a hydroxyapatite disk in young adults observed by using a barcoded pyrosequencing approach – Toru Takeshita – Scientific Reports

Subgingival microbiota in health compared to periodontitis and the influence of smoking – A Camelo-Castillo – Frontiers in Microbiology

Human respiratory microbiome

Comparison of Microbiomes from Different Niches of Upper and Lower Airways in Children and Adolescents with Cystic Fibrosis – Sébastien Boutin – PLOS ONE

Human gut microbiome

The networks of human gut microbe–metabolite associations are different between health and irritable bowel syndrome – Vijay Shankar – The ISME Journal

Review: New insight into the gut microbiome through metagenomics – Boyang Ji, Jens Nielsen – Advances in Genomics and Genetics

Animal microbiome

Examining the diversity of microbes in a deep-sea coral community impacted by the Deepwater Horizon oil spill – R.L. Simister – Deep Sea Research Part II: Topical Studies in Oceanography

Comparative Analysis of the Intestinal Bacterial and RNA Viral Communities from Sentinel Birds Placed on Selected Broiler Chicken Farms – J. Michael Day – PLOS ONE

Plant microbiome

Review: Microbial interactions in the rhizosphere: beneficial influences of plant growth-promoting rhizobacteria on nutrient acquisition process. A review – Youry Pii – Biology and Fertility of Soils

Soil microbiome

Changes in microbial properties and community composition in acid soils receiving wastewater from concentrated animal farming operations – Xiaoyan Ma – Applied Soil Ecology

Fine root decomposition, nutrient mobilization and fungal communities in a pine forest ecosystem – Ang Li – Soil Biology and Biochemistry

Experimental site and season over-control the effect of Pinus halepensis in microbiological properties of soils under semiarid and dry conditions – J. Hedo – Journal of Arid Environments

Water microbiome

Methane oxidation pathways and associated methanotrophic communities in the water column of a tropical lake – Prosper K. Zigah – Limnology and Oceanography

Microbiome of the built environment

Pyrosequencing analysis of roof-harvested rainwater and river water used for domestic purposes in Luthengele village in the Eastern Cape Province of South Africa – Lizyben Chidamba, Lise Korsten – Environmental Monitoring and Assessment

Bioreactor microbiome

Exploring the microbiota dynamics related to vegetable biomasses degradation and study of lignocellulose-degrading bacteria for industrial biotechnological application – Valeria Ventorino – Scientific Reports

Food microbiology

Monitoring of the microbiota of fermented sausages by culture independent rRNA-based approaches – Anna Greppi – International Journal of Food Microbiology

Techniques

PCR-Activated Cell Sorting for Cultivation-Free Enrichment and Sequencing of Rare Microbes – Shaun W. Lim – PLOS ONE

Bioinformatics, metagenomics

Metagenomic Profiling of Known and Unknown Microbes with MicrobeGPS – Martin S. Lindner, Bernhard Y. Renard – PLOS ONE

In peer-review: Advantages of distributed and parallel algorithms that leverage Cloud Computing platforms for large-scale genome assembly – Priti Kumari – F1000Research

SFA-SPA: a suffix array based short peptide assembler for metagenomic data – Youngik Yang – Bioinformatics

A RESTful API for Accessing Microbial Community Data for MG-RAST – Andreas Wilke – PLOS Computational BIology

Review: New insight into the gut microbiome through metagenomics – Boyang Ji, Jens Nielsen – Advances in Genomics and Genetics

Book: Biocode: The New Age of Genomics

Phages and viruses

Rising to the challenge: accelerated pace of discovery transforms marine virology – Jennifer R. Brum & Matthew B. Sullivan – Nature Reviews Microbiology

A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes – Joshua S Weitz – ISME Journal

The Search for Therapeutic Bacteriophages Uncovers One New Subfamily and Two New Genera of Pseudomonas-Infecting Myoviridae – Marine Henry – PLOS ONE

Microbes in the news

The Roots of Health – Episode 18: Microbiome Research & Applications with Dr. Embriette Hyde – Part 1 – WebTalkRadio

The Human Microbiome and Media Confusion – Science in the News – Harvard

Let’s Explore the World of Human Microbiome – Jason Carr – Wired Cosmos

Hospital Microbiome Project – Brent Stephens / Daniel Smith – Hospital Microbiome

Root of Lethal Bacterial Infection, Iron Overload Disease Link Identified – Jacquelyn Gray – HCP Live

Teaching phylogenetics with DUPLO – Erik Pelve – The Third Domain

How Can We Protect Mars From Earth, While Searching For Life? – Elizabeth Howell – AstroBio

Grape seed flour’s metabolic benefits linked to gut changes: Study – Stephen Daniells – NutraIngredients

Sell Your Poop For $13000 A Year And Help Save Lives: Here’s How You Can Do It – Jim Algar – TechTimes

Science, publishing, and career

From Scotland to Brazil: Making the decision (twice) – Julie Gould – Nature Jobs Blog

Los Alamos National Laboratory researcher gets 5 years in prison – Brooks Hays – UPI

A Future Segregated by Science? – Charles M. Blow – New York Times

Bik’s Picks

Walking on ice takes more than brains: ‘Mini-brain’ in spinal cord aids in balance – Science Daily

Surveying the Genomic Landscape of Modern Mammals
– Ricki Lewis – PLOS Blogs

Talking science with a doc, Hawkeye Pierce (with Alan Alda) – Sally Pollack – Burlington Free Press

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February 2, 2015

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The etiology of dental caries, viruses as commensals, genitalia-associated microbes in insects, and pizza metabolomics.

Human oral microbiome

Solving the etiology of dental caries – Aurea Simón-Soro, Alex Mira – Trends in Microbiology

Human gut microbiome

Expanding the Role of the Virome: Commensalism in the Gut – Ken Cadwell – Journal of Virology

Animal microbiome

Review: Genitalia-associated microbes in insects – Oliver Otti – Insect Science

Plant microbiome

Decrease in diversity and changes in community composition of arbuscular mycorrhizal fungi in roots of apple trees with increasing orchard management intensity across a regional scale – Maarten van Geel – Molecular Ecology

Water microbiome

Microbial diversity and abundance in the Xinjiang Luliang long-term water-flooding petroleum reservoir – Peike Gao – Microbiology Open

Microbiome of the built environment

Impacts of flood damage on airborne bacteria and fungi in homes after the 2013 Colorado Front Range flood – Joanne B Emerson – Environmental Science & Technology

Techniques

Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms – Martial Marbouty – eLife

Microbial Ecology

Mycorrhizal ecology and evolution: the past, the present, and the future – Marcel G. A. van der Heijden – New Phytologist

Biotic interactions boost spatial models of species richness – Heidi K. Mod – Ecography

Metabolomics

Metabolomic applications in nutritional research: a perspective – Aoife O’Gorman and Lorraine Brennan – Journal of the Science of Food and Agriculture

Microbes in the news

Viral Virtuosos: New understanding of noncoding RNAs may solve a long-standing puzzle about how viruses orchestrate lifelong infections – Christopher S. Sullivan – The Scientist

The answer to fewer viruses in human DNA? We stopped biting each other – SBS

Bacteria used to yield pure water and produce hydrogen, the fuel of the future – Jayalakshmi K – IBTimes

Intestinal microbiome research – Rob Levey – New Hampshire Union Leader

The Energy of Life: Extremophiles should not be viewed through an anthropocentric lens – Jeffrey Marlow and Jan Amend – The Scientist

Bacteria May Help Battle Cancer, Study Suggests – Philly.com

Science and art

Gorgeous Photos Made From the Bacteria on Toilet Seats and iPhones – Liz Stinson – Wired.com

Lab Agar Drawings: Chromobacterium violaceum shaped into Biohazard Symbol – MicrobeWorld

Science, publishing, and career

Trust me, I’m a medical researcher – Jennifer Couzin-Frankel – Science

Balancing Privacy versus accuracy in research protocols – Science

Ten Simple Rules for Organizing an Unconference – Aidan Budd – PLOS Computational Biology

Bik’s Picks

‘DivSeek’ aims to mine the genetic treasure in seed bank vaults – Virginia Gewin – Science Magazine

Baby’s genes, not mom’s, may trigger some preterm births – ScienceDaily

Energy and Nutrient Intake From Pizza in the United States – Lisa M. Powell – Pediatrics

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February 1, 2015

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Ah, the revenge of being away from work: my in-box was bursting out of the seams with new papers. Today I am quickly catching up after being offline for just 3 days, and I will skip most formatting to save some time (e.g. I will only do the bare essentials, and won’t add the hyperlinks). Enjoy.

General microbiome

Review? Discovering Emergent Behavior of Host-Microbiome Interactions with Biomimetic Robotics – Keith C. Heyde, Warren C. Ruder – Biophysical Journal
http://www.sciencedirect.com/science/article/pii/S0006349514046268

Book: Microbiome Community Ecology – Muhammad Saleem – Springer Briefs in Ecology
http://link.springer.com/book/10.1007/978-3-319-11665-5

Human oral microbiome

16S rRNA based microarray analysis of ten periodontal bacteria in patients with different forms of periodontitis – Nursen Topcuoglu, Guven Kulekci – Anaerobe
http://www.sciencedirect.com/science/article/pii/S1075996415000128

Human respiratory microbiome

Dynamics of the nasal microbiota in infancy: A prospective cohort study – Moana Mika – Journal of Allergy and Clinical Immunology
http://www.sciencedirect.com/science/article/pii/S0091674914037099

Review: The microbiome of the upper airways: focus on chronic rhinosinusitis – Thanit Chalermwatanachai – World Allergy Organization Journal
http://link.springer.com/article/10.1186/s40413-014-0048-6/fulltext.html

Human skin microbiome

Mapping axillary microbiota responsible for body odours using a culture-independent approach – Myriam Troccaz – Microbiome Journal
http://www.microbiomejournal.com/content/3/1/3/abstract

The shared microbiota of humans and companion animals as evaluated from Staphylococcus carriage sites – Ana M Misic – Microbiome Journal
http://www.microbiomejournal.com/content/3/1/2/abstract

Insights into bacterial colonization of intensive care patients’ skin: the effect of chlorhexidine daily bathing – N. Cassir – European Journal of Clinical Microbiology & Infectious Diseases
http://link.springer.com/article/10.1007/s10096-015-2316-y

Human gut microbiome

(see also Metagenomics) Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species – Sharon Greenblum – Cell
http://www.sciencedirect.com/science/article/pii/S0092867415000136

Gut microbiota composition correlates with changes in body fat content due to weight loss – M. Remely – Beneficial Microbes
http://wageningenacademic.metapress.com/content/ewq1620085607927/#.VM5HCVWJOuY

Genetic Modifier of the Gut Microbiome, GvHD and Bacterial Translocation Following HSCT – Ahmad Rayes – Biology of Blood and Marrow Transplantation
http://www.sciencedirect.com/science/article/pii/S1083879114008350

A Pilot Study of Donor Enteral Human Milk to Modulate the Gut Microbiome in Children Receiving Stem Cell Transplant – Stella M. Davies – Biology of Blood and Marrow Transplantation
http://www.sciencedirect.com/science/article/pii/S1083879114010441

This might be review (no access from my location): Microbiome, peptide autoantibodies, and eating disorders: a missing link between gut and brain – Akio Inui – Nutrition
http://www.sciencedirect.com/science/article/pii/S0899900715000386

Oral Supplementation with L-Glutamine Alters Gut Microbiota of Obese and Overweight Human Adults: A Pilot Study – Alessandra Zanin Zambom de Souza – Nutrition
http://www.sciencedirect.com/science/article/pii/S0899900715000350

Review: Growth Promotion and Gut Microbiota: Insights from Antibiotic Use – Harald Brüssow – Environmental Microbiology
http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.12786/abstract

Hypothesis: An Agent-Based Modeling Framework for Evaluating Hypotheses on Risks for Developing Autism: Effects of the Gut Microbial Environment – Bronson Weston – Medical Hypotheses
http://www.sciencedirect.com/science/article/pii/S0306987715000481

Hypothesis: Gut feelings: A role for the intestinal microbiota in anorexia nervosa? – Susan C. Kleiman – International Journal of Eating Disorders
http://onlinelibrary.wiley.com/doi/10.1002/eat.22394/abstract

Review??? Beyond Model Systems: Super-Resolving the Subcellular Dynamics of Starch Digestion in the Human Gut Microbiome – Krishanthi S. Karunatilaka – Biophysical Journal
http://www.sciencedirect.com/science/article/pii/S0006349514023030

Review: Intestinal Microbiota And Diet in IBS: Causes, Consequences, or Epiphenomena? – Mirjana Rajilić-Stojanović – American Journal of Gastroenterology
http://www.nature.com/ajg/journal/vaop/ncurrent/full/ajg2014427a.html

Review: H. pylori and its modulation of gastrointestinal microbiota – Christian Schulz – Journal of Digestive Diseases
http://onlinelibrary.wiley.com/doi/10.1111/1751-2980.12233/abstract

Review: Implication of Gut Microbiota in Nonalcoholic Fatty Liver Disease
Jerome Boursier – PLOS Pathogens
http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1004559

Review: The human gut microbiota with reference to autism spectrum disorder: considering the whole as more than a sum of its parts – Michael C. Toh and Emma Allen-Vercoe – Microbial Ecology in Health and Disease
http://www.microbecolhealthdis.net/index.php/mehd/article/view/26309

Review: The role of gut microbiota in the development of type 1, type 2 diabetes mellitus and obesity – Ningwen Tai – Reviews in Endocrine and Metabolic Disorders
http://link.springer.com/article/10.1007/s11154-015-9309-0

Review: Diet, Gut Microbiome, and Bone Health – Connie M. Weaver – Current Osteoporosis Reports
http://link.springer.com/article/10.1007/s11914-015-0257-0

Review: Immunogenic properties of a probiotic component of the human gastrointestinal tract microbiota – I. A. Fedorova, V. N. Danilenko – Biology Bulletin Reviews
http://link.springer.com/article/10.1134/S2079086414060036

Animal models of microbiome

Intestinal Microbial Dysbiosis and Colonic Epithelial Cell Hyperproliferation by Dietary α-Mangostin is Independent of Mouse Strain – Fabiola Gutierrez-Orozco – Nutrients
http://www.mdpi.com/2072-6643/7/2/764/htm

Polyphenol-rich sorghum brans alter colon microbiota and impact species diversity and species richness after multiple bouts of dextran sodium sulfate-induced colitis
Lauren E. Ritchie – FEMS Microbiology Ecology
http://femsec.oxfordjournals.org/content/early/2015/01/14/femsec.fiv008.abstract

Effects of chronic exposure to environmentally relevant concentrations of waterborne depleted uranium on the digestive tract of zebrafish, Danio rerio – Starrlight Augustine – Journal of Environmental Radioactivity
http://www.sciencedirect.com/science/article/pii/S0265931X15000041

Cross-Differentiation from the CD8 Lineage to CD4 T Cells in the Gut-Associated Microenvironment with a Nonessential Role of Microbiota – Jen Bon Lui – Cell Reports
http://www.sciencedirect.com/science/article/pii/S2211124714011061

Administration of probiotics Lactobacillus rhamnosus GG and Lactobacillus gasseri K7 during pregnancy and lactation changes mouse mesenteric lymph nodes and mammary gland microbiota – P. Treven- Journal of Dairy Science
http://www.sciencedirect.com/science/article/pii/S0022030215000417

Animal microbiome

First insights into the microbial diversity in the omasum and reticulum of bovine using Illumina sequencing – Shuai Peng – Journal of Applied Genetics
http://link.springer.com/article/10.1007/s13353-014-0258-1/fulltext.html

Prepartum and Postpartum Rumen Fluid Microbiomes: Characterization and Correlation with Production Traits in Dairy Cows – Fabio S. Lima – Applied Environmental Microbiology
http://aem.asm.org/content/81/4/1327.abstract

Relationship between honeybee nutrition and their microbial communities – Miriane Acosta Saraiva – Antonie van Leeuwenhoek
http://link.springer.com/article/10.1007/s10482-015-0384-8

Intestinal microbiota and immune related genes in sea cucumber (Apostichopus japonicus) response to dietary β-glucan supplementation – Gang Yang – Biochemical and Biophysical Research Communications
http://www.sciencedirect.com/science/article/pii/S0006291X15001047

Microbiome affects egg carotenoid investment, nestling development and adult oxidative costs of reproduction in Great tits – Staffan Jacob – Functional Ecology
http://onlinelibrary.wiley.com/doi/10.1111/1365-2435.12404/abstract

Review: Dietary fibre and the importance of the gut microbiota in feline nutrition: a review
Kristel Rochus – Nutrition Research Reviews
http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=9534845&fileId=S0954422414000213

Plant microbiome

T Bacterial Communities Associated with Surfaces of Leafy Greens: Shift in Composition and Decrease in Richness over Time – Merete Wiken Dees – Applied Environmental Microbiology
http://aem.asm.org/content/81/4/1530.abstract

Soil, rock, and sediment microbiome

Long-term forest soil warming alters microbial communities in temperate forest soils – Kristen M. DeAngelis – Frontiers in Microbiology
http://journal.frontiersin.org/Journal/10.3389/fmicb.2015.00104/abstract

This one was submitted in June 2013, but just published: Soil microbial community structure and activity in a 100-year-old fertilization and crop rotation experiment – Cancan Zhao – Journal of Plant Ecology
http://jpe.oxfordjournals.org/content/early/2015/01/28/jpe.rtv007.abstract

Interrogation of Chesapeake Bay sediment microbial communities for intrinsic alkane-utilizing potential under anaerobic conditions – Jamie M. Johnson – FEMS Microbiology Ecology
http://femsec.oxfordjournals.org/content/early/2014/12/24/femsec.fiu035.abstract

Short-term effects of soil amendment with meadowfoam seed meal on soil microbial composition and function – Suphannika Intanon – Applied Soil Ecology
http://www.sciencedirect.com/science/article/pii/S0929139315000104

Molecular diversity of arbuscular mycorrhizal fungi at a large-scale antimony mining area in southern China – Yuan Wei – Journal of Environmental Sciences
http://www.sciencedirect.com/science/article/pii/S100107421500008X

Assessing Fungal Community Structure from Mineral Surfaces in Kartchner Caverns Using Multiplexed 454 Pyrosequencing – Michael Joe Vaughan – Microbial Ecology
http://link.springer.com/article/10.1007/s00248-014-0560-9

Effects of increasing precipitation on soil microbial community composition and soil respiration in a temperate desert, Northwestern China – Gang Huang – Soil Biology and Biochemistry
http://www.sciencedirect.com/science/article/pii/S003807171500019X

Review: Microbial ecology of hot desert edaphic systems – Thulani P. Makhalanyane – FEMS Microbiology Reviews
http://femsre.oxfordjournals.org/content/early/2015/01/23/femsre.fuu011.abstract

Water microbiome

Synchronous shifts in dissolved organic carbon bioavailability and bacterial community responses over the course of an upwelling-driven phytoplankton bloom – Emma K. Wear – Limnology and Oceanography
http://onlinelibrary.wiley.com/doi/10.1002/lno.10042/abstract

Comparison of the microbial communities of hot springs waters and the microbial biofilms in the acidic geothermal area of Copahue (Neuquén, Argentina) – María Sofía Urbieta – Extremophiles
http://link.springer.com/article/10.1007/s00792-015-0729-2

Environmental controls on intragroup diversity of the uncultured benthic archaea of the miscellaneous Crenarchaeotal group lineage naturally enriched in anoxic sediments of the White Oak River estuary (North Carolina, USA) – Cassandre Sara Lazar – Environmental Microbiology
http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.12659/abstract

Methane oxidation pathways and associated methanotrophic communities in the water column of a tropical lake – Prosper K. Zigah – – Limnology and Oceanography
http://onlinelibrary.wiley.com/doi/10.1002/lno.10035/abstract

Seasonal assemblages and short-lived blooms in coastal north-west Atlantic Ocean bacterioplankton – Heba El-Swais – Environmental Microbiology
http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.12629/abstract

Environmental rather than spatial factors structure bacterioplankton communities in shallow lakes along a > 6000 km latitudinal gradient in South America – Caroline Souffreau – Environmental Microbiology
http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.12692/abstract

Microbial Contamination of Drinking Water and Human Health from Community Water Systems
Nicholas J. Ashbolt – Current Environmental Health Reports
http://link.springer.com/article/10.1007/s40572-014-0037-5

Book Chapter: Microbial Bioprospecting in Marine Environments – Mariana Lozada, Hebe M. Dionisi – Hb25_Springer Handbook of Marine Biotechnology
http://link.springer.com/chapter/10.1007/978-3-642-53971-8_11

Bioreactor microbiome

Long-term monitoring reveals stable and remarkably similar microbial communities in parallel full-scale biogas reactors digesting energy crops – Rico Lucas – FEMS Microbiology Ecology
http://femsec.oxfordjournals.org/content/early/2015/01/11/femsec.fiv004.abstract

The fate of oxytetracycline in two-phase and single-phase anaerobic cattle manure digesters and its effects on microbial communities – Çağrı Akyol – Journal of Chemical Technology and Biotechnology
http://onlinelibrary.wiley.com/doi/10.1002/jctb.4649/abstract

Identification of the microbial community composition and structure of coal-mine wastewater treatment plants – Qiao Ma – Microbiological Research
http://www.sciencedirect.com/science/article/pii/S0944501315000105

New steady-state microbial community compositions and process performances in
biogas reactors induced by temperature disturbances – Gang Luo – Biotechnology for Biofuels

Click to access s13068-014-0182-y.pdf

Archaea

Diversity of Methane-Cycling Archaea in Hydrothermal Sediment Investigated by General and Group-Specific PCR Primers – Mark A. Lever and Andreas P. Teske – Applied Environmental Microbiology
http://aem.asm.org/content/81/4/1426.abstract

Ecophysiology of uncultivated marine euryarchaea is linked to particulate organic matter – WIlliam D Orsi – ISME Journal
http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej2014260a.html

Bioinformatics

Integrating Multi-omic features exploiting Chromosome Conformation Capture data – Ivan Merelli – Frontiers in Genetics
http://journal.frontiersin.org/Journal/10.3389/fgene.2015.00040/abstract

Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach – Philippe Rocca-Serra – Database
http://database.oxfordjournals.org/content/2015/bau132.full

Koonkie: An Automated Software Tool for Processing Environmental
Sequence Information using Hadoop – Dongjae Kim – ASE360
http://www.ase360.org/bitstream/handle/123456789/164/P9.pdf?sequence=1&isAllowed=y

MetAmp: combining amplicon data from multiple markers for OTU analysis – Ilya Y. Zhbannikov,, James A. Foster – Bioinformatics

Click to access bioinformatics.btv049.full.pdf

MetaAB – A Novel Abundance-Based Binning Approach for Metagenomic Sequences
Van-Vinh Le – Nature of Computation and Communication
Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering
http://link.springer.com/chapter/10.1007/978-3-319-15392-6_13

NCBI BLAST+ integrated into Galaxy – Peter J. A. Cock – BioRxiv

Click to access 014043.full.pdf

Metagenomics

Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species – Sharon Greenblum – Cell
http://www.sciencedirect.com/science/article/pii/S0092867415000136

Integrated metagenomics and network analysis of soil microbial community of the forest timberline – Junjun Ding – Scientific Reports
http://www.nature.com/srep/2015/150123/srep07994/full/srep07994.html

Book Chapter: Marine Sponge Metagenomics – Valliappan Karuppiah, Zhiyong Li – Hb25_Springer Handbook of Marine Biotechnology
http://link.springer.com/chapter/10.1007/978-3-642-53971-8_17

Ecological and genetic interactions between cyanobacteria and viruses in a low-O2 mat community inferred through metagenomics and metatranscriptomics – Alexander A. Voorhies – Environmental Microbiology
http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.12756/abstract

Metagenomic analysis reveals adaptations to a cold adapted lifestyle in a low temperature acid mine drainage stream – Maria Liljeqvist – FEMS Microbiology Ecology
http://femsec.oxfordjournals.org/content/early/2015/01/27/femsec.fiv011.abstract

Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes – Manuel Kleiner – BMC Genomics

Click to access s12864-014-1207-4.pdf

First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking – Yuji Sekiguchi – PeerJ
https://peerj.com/articles/740/

The effects of variable sample biomass on comparative metagenomics – Meghan Chafee – Environmental Microbiology
http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.12668/abstract

Review: Functional genomic and metagenomic approaches to understanding gut microbiota–animal mutualism – Sang Sun Yoon – Current Opinion in Microbiology
http://www.sciencedirect.com/science/article/pii/S1369527415000089

Book Chapter: Marine Metagenome and Supporting Technology – Tetsushi Mori – Hb25_Springer Handbook of Marine Biotechnology
http://link.springer.com/chapter/10.1007/978-3-642-53971-8_19

Transcriptomics, metabolomics

Metatranscriptomic Analyses of Plant Cell Wall Polysaccharide Degradation by Microorganisms in the Cow Rumen – Xin Dai – Applied Environmental Microbiology
http://aem.asm.org/content/81/4/1375.abstract

Genomic Potential for Polysaccharide Deconstruction in Bacteria – Renaud Berlemont and Adam C. Martiny – Applied Environmental Microbiology
http://aem.asm.org/content/81/4/1513.abstract

Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor – Masaru K Nobu – ISME Journal
http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej2014256a.html

Perturbations of tyrosine metabolism promote the indolepyruvate pathway via tryptophan in host and microbiome – Ilya Gertsman – Molecular Genetics and Metabolism
http://www.sciencedirect.com/science/article/pii/S109671921500027X

Gut Symbionts from Distinct Hosts Exhibit Genotoxic Activity via Divergent Colibactin Biosynthesis Pathways – Philipp Engel – Applied Environmental Microbiology
http://aem.asm.org/content/81/4/1502.abstract

Transcriptome analyses to investigate symbiotic relationships between marine – Sergio Balzano – Frontiers in Microbiology
http://journal.frontiersin.org/Journal/10.3389/fmicb.2015.00098/abstract

Perturbations of tyrosine metabolism promote the indolepyruvate pathway via tryptophan in host and microbiome – Ilya Gertsman – Molecular Genetics and Metabolism
http://www.sciencedirect.com/science/article/pii/S109671921500027X

Human metabolic, mineral, and microbiota fluctuations across daily nutritional intake visualized by a data-driven approach – Takuma Misawa – Journal of Proteome Research
http://pubs.acs.org/doi/abs/10.1021/pr501194k

Review: Prospects and challenges for fungal metatranscriptomics of complex communities – Cheryl R. Kuske – Fungal Ecology

Microbial Ecology

Disturbance opens recruitment sites for bacterial colonization – David Vuono – BioRxiv
http://biorxiv.org/content/early/2015/01/27/014456

Review: High-throughput DNA barcoding for ecological network studies – Hirokazu Toju – Population Ecology
http://link.springer.com/article/10.1007/s10144-014-0472-z

Book Chapter: For Three Billion Years, Microorganisms Were the Only Inhabitants of the Earth
Jean-Claude Bertrand – Environmental Microbiology: Fundamentals and Applications
http://link.springer.com/chapter/10.1007/978-94-017-9118-2_4

Book Chapter: Microbiome Ecosystem Ecology: Unseen Majority in an Anthropogenic Ecosystem- Muhammad Saleem – Microbiome Community Ecology
http://link.springer.com/chapter/10.1007/978-3-319-11665-5_1

More microbes

Introduction to a special issue of PLOS Pathogens: The Importance of Pathogen Load – Aubrey J. Cunnington – PLOS Pathogens
http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1004563

Microbes in the news

Satire: Secret Microbiome Forensic Study Reveals DeflateGate Culprit – Megabiome.net

Secret microbiome forensic study reveals #deflategate culprit

Among gut microbes, strains, not just species, matter – MedicalXpress
http://medicalxpress.com/news/2015-01-gut-microbes-strains-species.html

Analysis Highlights Strain Diversity in Gut Microbiome – GenomeWeb
https://www.genomeweb.com/genetic-research/analysis-highlights-strain-diversity-gut-microbiome

Jonathan Eisen and Jessica Richman on the Microbiome – Kevin Bonham – Scientific American
http://blogs.scientificamerican.com/food-matters/2015/01/30/jonathan-eisen-and-jessica-richman-on-the-microbiome/

Part-Time Pooping: A New Way to Make an Extra $13,000 a Year – Everyday Health
http://www.everydayhealth.com/columns/daily-checkup/part-time-pooping-new-way-make-extra-money-year/

OpenBiome will pay for poo – Helen Clark – GizMag
http://www.gizmag.com/openbiome-fecal-transplant/35845/

January 2015 Update on American Gut, British Gut and Australian Gut Human Microbiome Projects – IBS Impact
https://ibsimpact.wordpress.com/2015/01/30/january-2015-update-on-american-gut-british-gut-and-australian-gut-human-microbiome-projects/

The Microbiome – New Research On Inflammatory Bowel Disease May Foreshadow Autism? – Teresa Conrick – Age of Autism
http://www.ageofautism.com/2015/01/the-microbiome-new-research-on-inflammatory-bowel-disease-may-foreshadow-autism.html

The microbiome of the upper airways: focus on chronic rhinosinusitis – 7th Space
http://7thspace.com/headlines/503056/the_microbiome_of_the_upper_airways_focus_on_chronic_rhinosinusitis.html

Germ Theory: What You May Not Know About The Bacteria Crawling Around Your Bathroom – Justin Caba – Medical Daily
http://www.medicaldaily.com/pulse/germ-theory-what-you-may-not-know-about-bacteria-crawling-around-your-bathroom-319884

Altered gut microbiota seen in patients with psoriatic arthritis – Healio.com
http://www.healio.com/rheumatology/psoriatic-arthritis/news/online/%7B0dd6068d-11b8-4e05-82f2-7713d4f28749%7D/altered-gut-microbiota-seen-in-patients-with-psoriatic-arthritis

The Human Microbiome: Biomedical Implications and Birth of a Market – Overview – PRNewsWIre
http://www.prnewswire.co.uk/news-releases/the-human-microbiome-biomedical-implications-and-birth-of-a-market—overview-290212581.html

Meet Dr. Armpit, changing body odor with bacteria – Fast Company
http://www.fastcompany.com/3041388/body-week/meet-dr-armpit-changing-body-odor-with-bacteria

Gut bacteria byproduct linked to chronic kidney disease for the first time – Medical Xpress
http://medicalxpress.com/news/2015-01-gut-bacteria-byproduct-linked-chronic.html

Does draft beer give you a worse hangover? We came across people from the beer industry and beer drinkers who claimed the bacteria in those lines contributes to a hangover. – Jace Larson – Click 2 Houston
http://www.click2houston.com/news/does-draft-beer-give-you-a-worse-hangover/31037044

Bik’s Picks

Face blindness predicted by structural differences in the brain, Stanford neuroscientists discover – Leslie Willoughby – Stanford News
http://news.stanford.edu/news/2015/january/face-blind-brain-013015.html

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January 27, 2015

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Human gut microbiome

Dysbiosis of Fungal Microbiota in the Intestinal Mucosa of Patients with Colorectal Adenomas – Chunguang Luan – Scientific Reports

Plant microbiome

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

Nostopeptolide plays a governing role during cellular differentiation of the symbiotic cyanobacterium Nostoc punctiforme – Anton Liaimer – PNAS USA

Air microbiome

Antibiotics, Bacteria, and Antibiotic Resistance Genes: Aerial Transport from Cattle Feed Yards via Particulate Matter – Andrew D. McEachran – Environmental Health Perspectives

Techniques

Review: High-Throughput Metagenomic Technologies for Complex Microbial Community Analysis: Open and Closed Formats – Jizhong Zhou – mBio

Bioinformatics

A library and collection of scripts to work with Illumina paired-end data (for CASAVA 1.7+ pipeline) – Murat Eren – Github

Why now is the time to learn R – David Smith – OpenSource

Other scientific papers of interest

Pan-viral-microRNA screening identifies interferon inhibition as a common function of diverse viruses – Jennifer E. Cox – PNAS USA

Discussion: Mice are not men – H. Shaw Warren – PNAS USA
Reply to Warren et al. and Shay et al.: Commonalities across species do exist and are potentially important – Keizo Takao – PNAS USA

Microbes in the news

Dust From Factory Farms Carries Drugs, Poop Bacteria, and Antibiotic-Resistant Genes Far and Wide – Tom Philpott – Mother Jones

How does your gut garden grow? Feeding your intestinal bacteria in a positive way – Áilín Quinlan – Irish Independent

The expert’s view: Ted Dinan, Professor of Psychiatry at UCC, on microbiome and stool transplants – Irish Independent

Obama proposes sharp increase to fight drug-resistant bacteria – Amy R. Connolly – UPI

Antibiotics for travellers’ diarrhoea – super-bacteria as a souvenir – Päivi Lehtinen – University of Helsinki

Science, publishing, and career

Number of College Students Pursuing Science, Engineering Stagnates – Melissa Korn – Wall Street Journal

Baring it all: Some researchers believe that openness can promote constructive communication and enable science to move forward faster – Rachel Bernstein – Science Careers

Why women are ditching STEM careers-and how to change it – Vivian Giang – FastCompany

Science and art

“Blurred Bands”: 2015 Lab Grammys: 8 nominees for Lab Parody of the Year – Biotechniques.com

Science and Culture: Science on-screen and behind the scenes – Stephen Ornes – PNAS USA

Science And Art Need Each Other, And Here’s Why – Cheryl Eddy – io9.com

Winners of the British Heart Foundation’s annual Reflections of Research competition – Richard P Grant – The Guardian

Bik’s Picks

Science finds a new way to unboil an egg – Michelle Starr – CNET

Asteroid that flew past Earth has moon – Science Daily

The continental divide of 2014 temperature – Thomas Summer – Science News

Blizzard 2015: Science Experiments to Do With Snow – Alyssa Newcomb – ABC News

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January 23, 2015

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Several papers on the effect of functional foods on the microbiome, fecal bacteria of the blue tit, and finding an old vial of bacteria.

Human gut microbiome

Toll-like receptor 5 in obesity: The role of gut microbiota and adipose tissue inflammation – Satu Pekkala – Obesity

Gut microbial and short-chain fatty acid profiles in adults with chronic constipation before and after treatment with lubiprostone – Dae-Wook Kang – Anaerobe

Review: New aspects on the metabolic role of intestinal microbiota in the development of atherosclerosis – Ioannis Drosos – Metabolism

Review: The influence of diet on the gut microbiota and its consequences for health – Joël Doré, Hervé Blottière – Current Opinion in Biotechnology

Animal and other models of microbiome research

Effects of Probiotic Enterococcus faecium NCIMB 11181 Administration on Swine Fecal Microbiota Diversity and Composition using Barcoded Pyrosequencing – Edward Alain B. Pajarillo – Animal Feed Science and Technology

Influences of structures of galactooligosaccharides and fructooligosaccharides on the fermentation in vitro by human intestinal microbiota – Wei Li – Journal of Functional Foods

Differential effects of probiotics, prebiotics, and synbiotics on gut microbiota and gene expression in rats – Gunaranjan Paturi – Journal of Functional Foods

Animal microbiome

Phylogenetic diversity and biological activity of culturable Actinobacteria isolated from freshwater fish gut microbiota – Mansooreh Jami – Microbiological Research

Life history correlates of fecal bacterial species richness in a wild population of the blue tit Cyanistes caeruleus – Clare McW. H. Benskin – Ecology and Evolution

Review (could also be filed under plant microbiome): Is there a role for symbiotic bacteria in plant virus transmission by insects? – Patricia V. Pinheiro – Current Opinion in Insect Science

Plant microbiome

Endophytic fungi from the genus Colletotrichum are abundant in the Phaseolus vulgaris and have high genetic diversity – L.L. Gonzaga – Journal of Applied Microbiology

Bioreactor microbiome

Effect of hygienization treatment on the recovery and/or regrowth of microbial indicators in sewage sludge – M. Pascual-Benito – Journal of Applied Microbiology

Metabolomics and Proteomics

Review: New aspects on the metabolic role of intestinal microbiota in the development of atherosclerosis – Ioannis Drosos – Metabolism

Not in microbes, but of note: Tissue-based map of the human proteome – Mathias Uhlén – Science

Microbial detection general

First Experience of a Multicenter External Quality Assessment of Molecular 16S rRNA Gene Detection in Bone and Joint Infections – Chloé Plouzeau – Journal of Clinical Microbiology

Use of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry for Identification of Molds of the Fusarium Genus – David Triest – Journal of Clinical Microbiology

A combined light sheet fluorescence and differential interference contrast microscope for live imaging of multicellular specimens – R.P. Baker – Journal of Microscopy

Infection and Immunity

Twin study @Stanford: Variation in the Human Immune System Is Largely Driven by Non-Heritable Influences – Petter Brodin – Cell

Hidden costs of infection: Chronic malaria accelerates telomere degradation and senescence in wild birds – M. Asghar – Science

Review: Advances in Laboratory Methods for Detection and Typing of Norovirus – Jan Vinjé – Journal of Clinical Microbiology

Combating the emerging viral infectious diseases – Shibo Jiang, Peter J. Hotez – Microbes and Infection

Phages, viruses, CRISPRs

Transcriptional regulator-mediated activation of adaptation genes triggers CRISPR de novo spacer acquisition – Tao Liu – Nucleic Acids Research

Microbes in the news
Breathing in Bacteria – The healthy lung receives microbes from the mouth, a new model suggests – Jenny Rood – The Scientist

Viruses may play unexpected role in inflammatory bowel diseases – Science Daily

Researchers See IBD-related Shifts in Individuals’ Gut Viromes – GenomeWeb

How gut bacteria may affect brain health – ScienceCodex

New microbiome drug candidate licensed by major manufacturer – Healio.com

When the Microbiome Stages a Coup – GenomeWeb

Environment, not genes, plays starring role in human immune variation, study finds – Stanford Medicine

Dirty Mouth? Chewing Gum Removes Millions Of Bacteria, But With One Catch – Philip Ross – International Business Times

We’ve found a strange box at our student microbiology lab… – AwesomeScience – Imgur

Immune system promotes digestive health by fostering community of ‘good’ bacteria – EurekAlert

The New Measles – One of the most infectious viruses on the planet is making a comeback in the United States, and many doctors have never even seen it – Adrienne Lafrance – The Atlantic

Science, publishing, and career

Intel Science Talent Search finalists: 9 of 40 from Bay Area – James Urton and Sharon Noguchi – Mercury News

Should Teachers be Allowed to Touch Students? – Jessica Lahey – The Atlantic

Science and art

100 Years of National Geographic Maps: The Art and Science of Where – Cathy Newman – National Geographic

Kitty Microbiome – Artologica – Etsy

Bik’s Picks

Major breakthrough in reading ancient scrolls – Science Daily

The geometry of their shells keeps turtles from getting stuck on their back – Seriously Science – Discover Magazine

Scottish scientists slow down speed of light – Robert Ferris – CNBC

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January 22, 2015

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The enteric virome is more diverse in patients with Crohn’s Disease and ulcerative colitis, measuring how fecal transplants are portrayed in Canadian media, and bacteria and archaea in sugarcane soils.

Human gut microbiome

Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease – Jason M. Norman – Cell

Media Discourse on the Social Acceptability of Fecal Transplants – Kim H. Chuong – Qualitative Health Research

Perspective: Cancer and the gut microbiota: An unexpected link – Laurence Zitvogel – Science Translational Medicine

Editorial: Bugs, Guts, and Glia: How Microbiota Influence Enteric Gliogenesis and Migration – Meenakshi Rao – Neuron

Animal models

MyD88 Signaling in T Cells Directs IgA-Mediated Control of the Microbiota to Promote Health – Jason L. Kubinak – Cell Host & Microbe

Soil microbiome

Environmental Factors Shaping the Community Structure of Ammonia-Oxidizing Bacteria and Archaea in Sugarcane Field Soil – Kanako Tago – Microbes and Environments

Metabolomics

Global biogeographic sampling of bacterial secondary metabolism – Zachary Charlop-Powers – eLIFE

Ecology

Perspective: The physiology and ecological implications of efficient growth – Benjamin RK Roller and Thomas M Schmidt – ISME Journal

Metagenomics and bioinformatics

Pollux: platform independent error correction of single and mixed genomes – Eric Marinier – BMC Bioinformatics

Microbes in the news

When bacteria-killing viruses take over, it’s bad news for the gut – Tina Hesman Saey – ScienceNews

Immune system promotes digestive health by fostering community of ‘good’ bacteria – NewsWise

Gut microbes may trigger autoimmune disease later in life – PuneMirror

Scientists claim breakthrough in taming genetically modified E.coli bacteria – Joel Achenbach – Washington Post

Have we found alien life? Microbes that eat and breath electricity have forced scientists to reimagine how life works – on this planet and others – Corey S. Powell – Popular Science

Science, publishing, and career

Origin stories of the scientists – Adam Ruben – Science

Bik’s Picks

The Science of Mmm – How food and drink tickle the brain’s pleasure centers – John McQuaid – Slate

Will this put an end to a very old discussion? Is glass a true solid? New research suggests it is – Science Daily

Which state f*cking loves science the most? – Phil Edwards – Vox

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January 20, 2015

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Today we will honor #PenguinAwarenessDay with an older paper, but all others links are brand new. There is the cave microbiome, bacteria in fermented yak milk, and a warning about comparing data obtained in mouse models. Here we go:

Perspective: Where Next for Microbiome Research? – Matthew K. Waldor – PLOS Biology

Review: The Microbiome and Graft Versus Host Disease – Nathan Mathewson, Pavan Reddy – Current Stem Cell Reports

Review: The microbiome mutiny hypothesis: can our microbiome turn against us when we are old or seriously ill? – Lajos Rózsa – Biology Direct

Review: Prevention of Microbial Communities: Novel Approaches Based Natural Products – George D. Mogosanu – Current Pharmaceutical Biotechnology

Human respiratory microbiome

Application of a Neutral Community Model To Assess Structuring of the Human Lung Microbiome – Arvind Venkataraman – mBio

Review (behind paywall, even at Stanford): Immunology, genetics and microbiota in the COPD pathophysiology: potential scope for patient stratification – Rajneesh Malhotra, and Henric Olsson – Expert Review of Respiratory Medicine

Human gut microbiome

Helicobacter pylori infection as a protective factor against multiple sclerosis risk in females – Marzena J Fabis Pedrini – J Neurol Neurosurg Psychiatry

Spatial variation of the colonic microbiota in patients with ulcerative colitis and control volunteers – A Lavelle – Gut

Review: The human gastric microbiota: Is it time to rethink the pathogenesis of stomach diseases? – Gerardo Nardone, Debora Compare – United European Gastroenterology Journal

Pregnancy and birth

Review: Human Milk: Mother Nature’s Prototypical Probiotic Food? – Michelle K McGuire, and Mark A McGuire – Advances in Nutrition

Animal models of microbiome research

Perspective: How informative is the mouse for human gut microbiota research? – Thi Loan Anh Nguyen – Disease Models & Mechanisms

Attenuated portal hypertension in germ-free mice: Function of bacterial flora on the development of mesenteric lymphatic and blood vessels – Sheida Moghadamrad – Hepatology

High-throughput 16S rRNA gene sequencing reveals alterations of mouse intestinal microbiota after radiotherapy – Young Suk Kim – Anaerobe

Antibiotic perturbation: An in vitro culture model to study the dynamics of colonic microbiota in Syrian golden hamsters and their susceptibility to infection with Clostridium difficile – Matthew Miezeiewski – ISME J

Animal microbiome

This is a 2013 article, but I included it to honor today’s #PenguinAwarenessDay:
Interspecific variations in the gastrointestinal microbiota in penguins – Meagan L. Dewar – MicrobiologyOpen

Identification and characterization of carboxyl esterases of gill chamber-associated microbiota in the deep-sea shrimp Rimicaris exoculata using functional metagenomics – María Alcaide – Applied and Environmental Microbiology

Plant microbiome

Structure, variation, and assembly of the root-associated microbiomes of rice – Joseph Edwards – PNAS USA

Rhizosphere microbial community composition affects cadmium and zinc uptake of the metal-hyperaccumulating plant Arabidopsis halleri – E. Marie Muehe – Applied and Environmental Microbiology

Exploring functional contexts of symbiotic sustain within lichen-associated bacteria by comparative omics – Martin Grube – ISME J

Soil microbiome

Profiling microbial communities in manganese remediation systems treating coal mine drainage – Dominique L. Chaput – Applied and Environmental Microbiology

Bacterial succession in paddy soils derived from different parent materials – Rong Sheng – Journal of Soils and Sediments

Main factors controlling microbial community structure and function after reclamation of a tailing pond with aided phytostabilization – R. Zornoza – Geoderma

Oligotyping reveals stronger relationship of organic soil bacterial community structure with N-amendments and soil chemistry in comparison to that of mineral soil at Harvard Forest, MA, USA# – Swathi A. Turlapati – Frontiers in Microbiology

Activity and phylogenetic diversity of sulfate-reducing microorganisms in low-temperature subsurface fluids within the upper oceanic crust – Alberto Robador – Frontiers in Microbiology

Water microbiome

Biogeography of Heterotrophic Flagellate Populations Indicates the Presence of Generalist and Specialist Taxa in the Arctic Ocean – Mary Thaler and Connie Lovejoy – Applied and Environmental Microbiology

The effect of carbon subsidies on marine planktonic niche partitioning and recruitment during biofilm assembly – Chuck Pepe-Ranney, Ed Hall – BioRxiv

Catchment-scale biogeography of riverine bacterioplankton – Daniel S Read – ISME J

Microbiome of the built environment

Spatio-temporal variability of airborne bacterial communities and their correlation with particulate matter chemical composition across two urban areas – I. Gandolfi – Applied Microbiology and Biotechnology

The community distribution of bacteria and fungi on ancient wall paintings of the Mogao Grottoes – Yantian Ma – Nature Scientific Reports

A long-term study examining the antibacterial effectiveness of Agion silver zeolite technology on door handles within a college campus – B.A. Potter – Letters in Applied Microbiology

Bioreactor microbiology

Groundwater Chemistry Determines the Prokaryotic Community Structure of Waterworks Sand Filters – Christian N. Albers – Environmental Science & Technology

Impact of Organic Load Shock on the Dynamic Transition of Microbial Communities During the Anaerobic Start-up Process – Jie Li – Energy Procedia

Food microbiology

High-throughput sequencing reveals microbial community diversity of Tibetan naturally fermented yak milk – Wenjun Liu – Annals of Microbiology

Viruses and phages

Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome – Bonnie L Hurwitz – ISME J

BSc thesis: Metagenomic study of the human gut virome during the first year of life – David Mayo Muñoz – Universitat Politecnica de Valencia

Metagenomics

Strong spurious transcription likely a cause of DNA insert bias in typical metagenomic clone libraries – Kathy N Lam, Trevor C Charles – BioRXiv

Commentary: Capturing bacterial chromosome conformation – Andrea Du Toit – Nature Reviews Microbiology

Metabolomics

Intestinal Microbiota-Derived Metabolomic Blood Plasma Markers for Prior Radiation Injury – Pilib Ó Broin – International Journal of Radiation Oncology

Investigation of biotechnological potential of sponge-associated bacteria collected in Brazilian coast – O.C.S. Santos – Letters in Applied Microbiology

Review: The Role of Colonic Bacteria in the Metabolism of the Natural Isoflavone Daidzin to Equol – Fatemeh Rafii – Metabolites

Microbes in the news

Can the Microbiome Mutiny? – Carl Zimmer – National Geographic

Fast-Paced Microbiome (about Rob Knight) – Genome Web

Researchers urge caution in studies of mice and microbes – Sarah DeWeerdt – SFARI

Gut microbes trigger autoimmune disease later in life in mice – Science Codex

Ulcer Bacteria Tied to Lower Multiple Sclerosis Risk in Women – HealthDay

Breweries partner with bacteria-detecting Philadelphia start-up – Diane Mastrull – Philly.com

New Species Discovered Beneath Ocean Crust – Robert Perkins – Pressroom USC

Ancient Viruses Gain New Functions in the Brain – Andrea Alfano – Scientific American

Science, publishing, and career

Is it Ph.D. or PhD? And are PhDs who act like MDs a special kind of douchebag? Twitter debates – Chris Seper – MedCityNews

Is the Debate and “Pause” on Experiments That Alter Pathogens with Pandemic Potential Influencing Future Plans of Graduate Students and Postdoctoral Fellows? – Julie K. Pfeiffer – mBio

Don’t be that dude: Handy tips for the male academic – Tenure She Wrote

Science and art

Today in microbes and art: Bioart and Bacteria – The Artwork of Anna Dumitriu – Jonathan Eisen – The Tree of Life

Bik’s Picks

Exercise at depth alters bradycardia and incidence of cardiac anomalies in deep-diving marine mammals – Terrie M. Williams – Nature Communications

What’s Up With That: Birds Bob Their Heads When They Walk – Nick Stockton – Wired

Over 80 percent of Americans support “mandatory labels on foods containing DNA” – Ilya Somin – Washington Post

The Discoloration of the Taj Mahal due to Particulate Carbon and Dust Deposition – M. H. Bergin – Environmental Science & Technology

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January 19, 2015

Posted on by

Thanks for all the encouraging comments here and per email! This blog appears to fill an important niche in the coverage of scientific microbiome research, in a wide range of hosts and environmental sources, so I will continue writing this. But please spread the word – 100 viewers per day is nice, but more is better!

As one of the commenters suggested, I will try to mark Reviews as such, so they are easier to find (or skip).

Here we go with a new post. It’s Monday, so there is a lot to cover.

Human oral microbiome

Herpesvirus in the oral cavity of children with leukaemia and its impact on the oral bacterial community profile – Tacíria M Bezerra – Journal of Clinical Pathology

Bifidobacteria strains isolated from stools of iron deficient infants can efficiently sequester iron – Pamela Vazquez-Gutierrez – BMC Microbiology

Review: Tuning the Brain-Gut Axis in Health and Disease – Rainbo Hultman – Current Stem Cell Reports

Microbiome of pregnancy and birth

Clinical chorioamnionitis at term I: microbiology of the amniotic cavity using cultivation and molecular techniques – Roberto Romero – Journal of Perinatal Medicine

Review: Relationship between periodontal diseases and preterm birth: Recent epidemiological and biological data – Moneet Walia, Navdeep Saini – International Journal of Applied and Basic Medical Research

Review: Viral Infections During Pregnancy – Michelle Silasi – American Journal of Reproductive Immunology

Review: Stress and the Commensal Microbiota: Importance in parturition and infant neurodevelopment – Tamar L. Gur – Frontiers in Psychiatry

Animal models of microbiome research

Commensal microbiota influence systemic autoimmune responses – Jens T Van Praet – The EMBO Journal

Modulation of the Intestinal Microbiota Is Associated with Lower Plasma Cholesterol and Weight Gain in Hamsters Fed Chardonnay Grape Seed Flour – Hyunsook Kim – J. Agric. Food Chem

Dysbiotic bacteria translocate in progressive SIV infection – Z Klase – Mucosal Immunology

Animal microbiome

Comparison of the gut microbiomes of 12 bony fish and 3 shark species – Carrie E. Givens – Marine Ecology Progress Series

Genomes of the rice pest brown planthopper and its endosymbionts reveal complex complementary contributions for host adaptation – Jian Xue – Genome Biology

Review: Towards an integrated understanding of the consequences of fungus domestication on the fungus-growing termite gut microbiota – Michael Poulsen – Environmental Microbiology

Plant microbiome

Primary succession of Bistorta vivipara (L.) Delabre (Polygonaceae) root associated fungi mirrors plant succession in two glacial chronosequences – Marie Davey – Environmental Microbiology

Book: Beneficial Plant-Bacterial Interactions – Bernard R. Glick

Soil and sediment microbiome

Soil Bacterial Communities are Shaped by Temporal and Environmental Filtering: Evidence from a Long-Term Chronosequence – Zachary Freedman and Donald R. Zak – Environmental Microbiology

Abstract: Garlic mustard and its effects on soil microbial communities in a sandy pine forest in central Illinois – Alexander B Faulkner – Proceedings, 19th Central Hardwood Forest Conference; 2014 March

Bacterial community composition at anodes of microbial fuel cells for paddy soils: the effects of soil properties – Ning Wang – Journal of Soils and Sediments

Adaptation of soil microbial community structure and function to chronic metal contamination at an abandoned Pb-Zn mine – Lur Epelde – FEMS Microbiology Ecology

Soil-Borne Microbiome: Linking Diversity to Function – Lucas W. Mendes – Microbial Ecology

Phytoextraction of nickel and rhizosphere microbial communities under mono- or multispecies hyperaccumulator plant cover in a serpentine soil – Marie Rue – Australian Journal of Botany

Methane-derived carbon flow through microbial communities in arctic lake sediments – Ruo He – Environmental Microbiology

Review: Potential applications of soil microbial ecology and next-generation sequencing in criminal investigations – Sheree J. Finley – Applied Soil Ecology

Water microbiome

Book (open access): Subseafloor Biosphere Linked to Hydrothermal Systems
Some chapters of interest:
– Intra-Field Variation of Prokaryotic Communities On and Below the Seafloor in the Back-Arc Hydrothermal System of the Southern Mariana Trough – Shingo Kato
– Microbial Cell Densities, Community Structures, and Growth in the Hydrothermal Plumes of Subduction Hydrothermal Systems – Michinari Sunamura, Katsunori Yanagawa
– Comparative Investigation of Microbial Communities Associated with Hydrothermal Activities in the Okinawa Trough – Ken Takai, Satoshi Nakagawa
– Quantification of Microbial Communities in Hydrothermal Vent Habitats of the Southern Mariana Trough and the Mid-Okinawa Trough – Katsunori Yanagawa

Microbiome of the built environment

Review: From commensalism to mutualism: integrating the microbial ecology, building science, and indoor air communities to advance research on the indoor microbiome – Brent Stephens – Indoor Air

Food microbiology

Diversity of Lactic Acid Bacteria Isolated from Brazilian Water Buffalo Mozzarella Cheese – Luana Faria Silva – Journal of Food Science

Metagenomics

Metagenome assembly through clustering of next-generation sequencing data using protein sequences – Mikang Sim, Jaebum Kim – Journal of Microbiological Methods

An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data – Xutao Deng – Nucleic Acids Research

Review: Tales from the crypt and coral reef: the successes and challenges of identifying new herpesviruses using metagenomics – Charlotte J. Houldcroft and Judith Breuer – Frontiers in Microbiology

Metabolomics, transcriptomics, and proteomics

Effects of high fructose and salt feeding on systematic metabonome probed via 1H NMR spectroscopy – Yongxia Yang – Magnetic Resonance in Chemistry

Also see above: Adaptation of soil microbial community structure and function to chronic metal contamination at an abandoned Pb-Zn mine – Lur Epelde – FEMS Microbiology Ecology

Isolation and characterization of novel lipases/esterases from a bovine rumen metagenome – Florence Privé – Applied Microbiology and Biotechnology

Review: Proteomics of hosts and pathogens in cystic fibrosis – Karthik Shantharam Kamath – Proteomics – Clinical Applications

Bioinformatics

Book chapter: e-DNA Meta-Barcoding: From NGS Raw Data to Taxonomic Profiling – Fosso Bruno – RNA Bioinformatics / Methods in Molecular Biology

Book chapter: Deciphering Metatranscriptomic Data – Evguenia Kopylova – RNA Bioinformatics / Methods in Molecular Biology

Amplification and sequencing techniques

Quantitative evaluation of bias in PCR amplification and next-generation sequencing derived from metabarcoding samples – Marta Pawluczyk – Analytical and Bioanalytical Chemistry

Probiotics

Consecutive oral administration of Bifidobacterium longum MM-2 improves the defense system against influenza virus infection by enhancing natural killer cell activity in a murine model – Tomohiro Kawahara – Microbiology and Immunology

Microbes in the news

* One Scientist’s Race To Help Microbes Help You – Katherine Harmon Courage – NPR Shots

Researchers reveal link between the microbiome of young mice and later onset of autoimmune disease – News Medical

Podcast: Do Gut Bacteria Tell Us What To Eat? – Beth Anne Austein / The Food Guys – Montana Public Radio

The Fungus in Your Cheese Is Having Weird Sex – Rose Eveleth – Smithsonian.com

Disturbed gut microbiome linked to Parkinson’s disease – News Medical

#BacteriaHysteria

Honoring last week’s Law Enforcement Appreciation Day: Sheriff’s Office gets bacteria cleanse – Richard Goad – Cleveland Banner

Science, publishing, and career

7 Tips for Women at Science Conferences – Hilda Bastian – PLOS Blogs

Bik’s Picks

Do 80% of Americans not know there’s DNA in food? – Ben Lillie blog

Researchers Who Provided Key Evidence For Gluten Sensitivity Have Now Thoroughly Shown That It Doesn’t Exist – Jennifer Welsh – Business Insider

This whale might be old, but it does not look too happy (or it is swimming upside down?)
The Secret To Living 200 Years? Ask A Whale – Paul Rodgers – Forbes.com

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January 16, 2015

Posted on by

(edited: MicrobiomeNews has been around for a year, but I had not seen it until today)

I just found out about MicrobiomeNews, run by MoBio Laboratories. It seems to cover the same articles I have been blogging about.

So here is a question for you, dear readers: Should I stop running this blog MicrobiomeDigest and let MoBio do the work? With only ~100 visitors a day, I am not sure if my efforts (3-4 hours a day) are worth it. After a couple of months of growth, I seem to have reached a plateau, and it is just not serving the large audience I had hoped to attract.

Any suggestions for improvement or increasing the visibility of my blog are very welcome, at eliesbik * stanford dot edu!  But, at least today, here is a new installment.

Pregnancy and birth

Prematurity and Perinatal Antibiotics: A Tale of Two Factors Influencing Development of the Neonatal Gut Microbiota – Daniel B. DiGiulio – The Journal of Pediatrics

Intestinal dysbiosis: an emerging cause of pregnancy complications? – Dongxin Zhang – Medical Hypotheses

Human gut microbiome

The role of the gut microbiome in the healthy adult status – Valeria D’Argenio, Francesco Salvatore – Clinica Chimica Acta

What’s One Phosphate between Friends (and Foe)? – Charles L. Bevins, Andreas J. Bäumler – Cell Host & Microbe

Acarbose treatment affects the serum levels of inflammatory cytokines and the gut content of bifidobacteria in Chinese patients with type 2 diabetes mellitus – Benli Su – Journal of Diabetes

Human urine microbiome

Search for Microorganisms in Men with Urologic Chronic Pelvic Pain Syndrome: A Culture-Independent Analysis in the MAPP Research Network – J. Curtis Nickel – The Journal of Urology

Animal models of microbiome research

Commensal microbes and interferon-λ determine persistence of enteric murine norovirus infection – Megan T. Baldridge – Science

Interferon-λ cures persistent murine norovirus infection in the absence of adaptive immunity – Timothy J. Nice – Science

Adult Hippocampal Neurogenesis is Regulated by the Microbiome – Ebere S. Ogbonnaya – Biological Psychiatry

Animal microbiome

Sweet talking your partner – Christina Tobin Kåhrström – Nature Reviews Microbiology

Soil microbiome

Metagenomic Sequence of saline desert Microbiota from Wild Ass Sanctuary, Little Rann of Kutch, Gujarat, India – Patel Rajesh – Genomics Data

Phages and viruses

Temperate bacteriophages collected by outer membrane vesicles in Komagataeibacter intermedius – Alla Kharina – Journal of Basic Microbiology

Polintons: a hotbed of eukaryotic virus, transposon and plasmid evolution – Mart Krupovic & Eugene V. Koonin – Nature Reviews Microbiology

Archaea

Rooting the Domain Archaea by Phylogenomic Analysis Supports the Foundation of the New Kingdom Proteoarchaeota – Céline Petitjean – Genome Biology and Evolution

Metagenomics

What is a resistance gene? Ranking risk in resistomes – José L. Martínez – Nature Reviews Microbiology

Metabolomics

Intestinal Microbiota-Derived Metabolomic Blood Plasma Markers for Prior Radiation Injury – Pilib Ó Broin – International Journal of Radiation Oncology*Biology*Physics

Metabolic dependence of phytoplankton species richness – A. M. Segura – Global Ecology and Biogeography

Microbes in the news

How The Body Maintains A Healthy Balance Of ‘Friendly’ Gut Bacteria – Carolyn Gregoire – Huffington Post

Cracked! Researchers Nearing Completion of Genetic Map of Grapevine Disease – James Duren – Snooth.com

A. vaginae, G. vaginalis linked to preterm birth, miscarriage – Healio

3Bar Biologics developing beneficial bacteria for farmers’ fields – Carrie Ghose – BizJournals

Brain Food: The Human Microbiome (podcast with Greg Caporaso) – Bonnie Stevens – KNAU Northern Arizona University

Analyzing the Gut Microbiome to Help Detect Colorectal Cancer – National Cancer Institute

The Human Microbiome: Biomedical Implications and Birth of a Market – Overview – Research and Markets

New tech keeps bacteria from sticking to surfaces – Krishna Ramanujan – R&D Magazine

Your Phone Contains Personal Contacts… And Lots of Bacteria – Jenna Iacurci – Nature World News

Science, publishing and career

By a former student in our lab: Protecting genetic privacy may be bad for your health – Akshay Maheshwari – SF Gate

A European postdoc for the family – Michelle Gabriele Sandrian – Science

Expectations of brilliance underlie gender distributions across academic disciplines – Sarah-Jane Leslie – Science

Bik’s Picks

What’s the Secret to Getting Kids to Eat Veggies? Let Them Play First! – Shannon Hall – Live Science

HiRISE camera spots long-lost space probe on Mars – Science Daily

Satire: Epidemiologists Warn of Emerging Deadly Pandemic of Selfie-sticks – The Allium

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