Category Archives: Human respiratory

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 20, 2015

Posted on by

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 15, 2015

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Human respiratory microbiome

Aging and the microbiome: implications for asthma in the elderly? – Sanjay H Chotirmall, and Conor M Burke – Expert Review of Respiratory Medicine

Human oral microbiome

Code blue: Acinetobacter baumannii, a nosocomial pathogen with a role in the oral cavity –
A.M. Richards – Molecular Oral Microbiology

Inhibitory effect of Lactobacillus salivarius on Streptococcus mutans biofilm formation – C.-C. Wu – Molecular Oral Microbiology

Animal models of microbiome research

Murine Gut Microbiota—Diet Trumps Genes – Jens Walter – Cell Host & Microbe

Animal microbiome

Effects of dietary synbiotic on growth, survival, lactobacillus bacterial count, blood indices and immunity of beluga (Huso huso Linnaeus, 1754) juvenile – R. Akrami – Aquaculture Nutrition

Plant microbiome

Short-term impact of two liquid organic fertilizers on Solanum lycopersicum L. rhizosphere Eubacteria and Archaea diversity – L. Canfora – Applied Soil Ecology

A review on weeds as source of novel plant growth promoting microbes for crop improvement – C. Sarathambal – Journal of Applied and Natural Science

Different mycorrhizal fungal strains determine plant community response to nitrogen and water availability – Laura B. Martínez – Journal of Plant Nutrition and Soil Science

Soil microbiome

Effects of wildfires on flora, fauna and physico-chemical properties of soil-An overview –
Manoj Kumar Jhariy* and Abhishek Raj – Journal of Applied and Natural Science

Cellulolytic potential under environmental changes in microbial communities from grassland litter – Renaud Berlemont – Frontiers in Microbiology

Water microbiome

Insights into environmental controls on microbial communities in a continental serpentinite aquifer using a microcosm-based approach – Melitza Crespo-Medina – Frontiers in Microbiology

Diversity of arsenite oxidizing bacterial communities in arsenic-rich deltaic aquifers in West Bengal, India – Devanita Ghosh – Frontiers in Microbiology

Food microbiology

Isolation and Identification of Lactic Acid Bacteria in Winter Salad (Local Pickle) during Fermentation Using 16S rRNA Gene Sequence Analysis – Mansour Saeedi – Journal of Food Safety

Metagenomics

Going from microbial ecology to genome data and back: studies on a haloalkaliphilic bacterium isolated from Soap Lake, Washington State – Melanie R. Mormile – Frontiers in Microbiology

Bioinformatics

The yearly Database Issue of Nucleic Acids Research is out. Just a selection:
–  rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development – Steven F. Stoddard
–  Update on RefSeq microbial genomes resources – Tatiana Tatusova

Scientific Meeting 2014 “NGS Data after the Gold Rush” Meeting, Norwich, UK – EMBnet.journal. Selection of 2 abstracts:
–  Analyzing RNA-Seq data with RNASeqGUI – Claudia Angelini, Francesco Russo – EMBnet.journal
–  NGS data management and analysis for hundreds of projects: Experiences from Sweden – Ola Spjuth – EMBnet.journal
Microbial Ecology

Perspective: Impact of spatial distribution on the development of mutualism in microbes – Ákos T. Kovács – Frontiers in Microbiology

Bacteria in the news

Cataloguing 10 million human gut microbial genes – Tim Sandle – Pharmamicroresources

Arctic bacteria could make life-saving drugs – Samantha Bresnahan – KSPR

Iron Overload Disease Causes Rapid Growth of Potentially Deadly Bacteria, UCLA Study Finds – Infection Control Today

The Microbiome Diet: Evolving Past Paleo – Raphael Kellman

Is Naya Rivera right about her ‘showering too often’ theory? – Hope Gillette – Voxxi

Science, publishing and career

Want To Be In STEM? Here Are The 10 Best Metro Areas – Hank Campbell – Science 2.0

Gender gap: Women welcome in ‘hard working’ fields, but ‘genius’ fields are male-dominated, study finds – Rachel Feltman – Washington Post

Bik’s Picks

Prolonging lifespan: Researchers create ‘Methuselah fly’ by selecting best cells – Science Daily

Proteins found in the brain may help speed up flu recovery while you sleep – Lydia Ramsey – Popular Science

What the history of dogs tells us about civilization in the Americas – Elahe Izadi – Washington Post

Earth’s magnetic field guides sea turtles home – Julia Rosen – Science News

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January 13, 2015

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Human oral microbiome

The Biofilm Community: Rebels with a Cause – A. Wilson Aruni – Current Oral Health Reports

Human respiratory microbiome

Culture and molecular-based profiles show shifts in bacterial communities of the upper respiratory tract that occur with age – J C Stearns – The ISME Journal

Recombination is a key driver of genomic and phenotypic diversity in a Pseudomonas aeruginosa population during cystic fibrosis infection – Sophie E. Darch – Scientific Reports

Human gut microbiome

Effect of Exclusive Enteral Nutrition on the Microbiota of Children With Newly Diagnosed Crohn’s Disease – Nadeem O. Kaakoush – Clinical and Translational Gastroenterology

The intestinal microbiota: its role in health and disease – Luc Biedermann, Gerhard Rogler – European Journal of Pediatrics

Geographical patterns of the standing and active human gut microbiome in health and IBD – Ateequr Rehman – Gut

Severity of atopic disease inversely correlates with intestinal microbiota diversity and butyrate-producing bacteria – L. Nylund – Allergy

The influence of the microbiota on the immune response to transplantation – Bartman, Caroline – Current Opinion in Organ Transplantation

Animal models of microbiome research

The enduring importance of animal models in understanding periodontal disease – George Hajishengallis – Virulence

Animal microbiome

Similarities and seasonal variations in bacterial communities from the blood of rodents and from their flea vectors – Carmit Cohen – The ISME Journal

Molecular analysis of cecal and tracheal microbiome of heat-stressed broilers supplemented with prebiotic and probiotic – Muhammad U. Sohail – Avian Pathology

Divergence across diet, time and populations rules out parallel evolution in the gut microbiomes of Trinidadian guppies – Karen E Sullam – The ISME Journal

Composition and predicted functional ecology of mussel-associated bacteria in Indonesian marine lakes – Daniel F. R. Cleary – Antonie van Leeuwenhoek

Deep down on a Caribbean reef: lower mesophotic depths harbor a specialized coral-endosymbiont community – Pim Bongaerts – Scientific Reports

Soil microbiome

Exploring the dynamics of bacterial community composition in soil: the pan-bacteriome approach – Giovanni Bacci – Antonie van Leeuwenhoek

Role of RNase on microbial community analysis in the rice and wheat plants soil by 16S rDNA-DGGE – Md. Mizanur Rahman – Journal of Crop Science and Biotechnology

Field-based evidence for consistent responses of bacterial communities to copper contamination in two contrasting agricultural soils – Jing Li – Frontiers in Microbiology

Evident bacterial community changes but only slight degradation when polluted with pyrene in a red soil – Gaidi Ren – Frontiers in Microbiology

Soil bacterial and fungal communities respond differently to various isothiocyanates added for biofumigation – Ping Hu – Frontiers in Microbiology

Seasonal dynamics of bacterial and archaeal methanogenic communities in flooded rice fields and effect of drainage – Björn Breidenbach and Ralf Conrad – Frontiers in Microbiology

Biogeography and biophysicochemical traits link N2O emissions, N2O emission potential and microbial communities across New Zealand pasture soils – Sergio E. Morales – Soil Biology and Biochemistry

Formation of iron-rich shelled structures (IRSS) by microbial communities – David C. Fernández-Remolar – Journal of Geophysical Research: Biogeosciences

Effects of alkyl-imidazolium ionic liquid [Omim]Cl on the functional diversity of soil microbial communities – Pengpeng Guo – Environmental Science and Pollution Research

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

Separation of soil microbial community structure by aggregate size to a large extent under agricultural practices during early pedogenesis of a Mollisol – Na Li – Applied Soil Ecology

Microbial community structure of anoxic-oxic-settling-anaerobic sludge reduction process revealed by 454-pyrosequencing – Zhen Zhou – Chemical Engineering Journal

Conservation tillage positively influences the microflora and microfauna in the black soil of Northeast China – Shixiu Zhang – Soil and Tillage Research

Resuscitation of the rare biosphere contributes to pulses of ecosystem activity – Zach Aanderud – Frontiers in Microbiology

Water microbiome

Drinking water microbiology — from measurement to management – Caitlin R Proctor, Frederik Hammes – Current Opinion in Biotechnology

Microbial biogeography of drinking water: patterns in phylogenetic diversity across space and time – Guus Roeselers – Environmental Microbiology

Energy landscapes shape microbial communities in hydrothermal systems on the Arctic Mid-Ocean Ridge – Håkon Dahle – The ISME Journal
http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej2014247a.html

Metagenomics

Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics – Tomàs Llorens-Marès – The ISME Journal

Environmental Metagenomics: The Data Assembly and Data Analysis Perspectives – Vinay Kumar – Journal of The Institution of Engineers (India): Series A

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

Metagenomic Insights into the Effects of Fructo-oligosaccharides (FOS) on the Composition of Fecal Microbiota in Mice – Bingyong Mao – Journal of Agricultural and Food Chemistry

Diagnosis of Neuroinvasive Astrovirus Infection in an Immunocompromised Adult With Encephalitis by Unbiased Next-Generation Sequencing – Samia N. Naccache – Clinical Infectious Diseases

Unbiased Next-Generation Sequencing and New Pathogen Discovery: Undeniable Advantages and Still-Existing Drawbacks – Arianna Calistri and Giorgio Palù – Clinical Infectious Diseases

Identification of diverse circular single-stranded DNA viruses in adult dragonflies and damselflies (Insecta: Odonata) of Arizona and Oklahoma, USA – Anisha Dayaram – Infection, Genetics and Evolution

Metabolomics

Multi -omics and metabolic modelling pipelines: challenges and tools for systems microbiology – Marco Fondi and Pietro Liò – BioRxiv

Techniques

Accounting for uncertainty in DNA sequencing data – Jason A. O’Rawe – Trends in Genetics

More microbes
3D-Printed Microfluidic Device for the Detection of Pathogenic Bacteria Using Size-based Separation in Helical Channel with Trapezoid Cross-Section – Wonjae Lee – Scientific Reports

Microbes in the news

UCSD hires star biologist Rob Knight – Gary Robbins – UT San Diego

Drug developed out of microbiome studies advances in phase I trial – Stephanie M. Lee – SF Gate
and
Second Genome’s gut check uncovers a possible drug for bowel disease – Ron Leuty – San Francisco Business Times

The Megabiome – It’s not micro anymore – Megabiome.net

Are We Really 10% Human and 90% Bacteria? Exploring The Microbiome… (with Jessica Richman and Jonathan Eisen) – Tim Ferriss Show – Four Hour Workweek

Mounting Research Shows Gut-Brain Connection – Traci Pedersen – Psych Central

Microbiota organization influences colorectal cancers – Nicola Garrett – Family Practice News

“MyNewGut”: New project explores role of gut microbiota in preventing diet- and brain-related diseases – News-Medical.net

Joint Pain, From the Gut – David Kohn – The Atlantic

A Lamp Whose Light Comes From Bioluminescent Bacteria – Liz Stinson – Wired.com

Pieter Dorrestein Recognized by Pharmacology Society – Heather Buschman – UC San Diego

Science, publishing and career

Post publication peer review comes of age – Emma Stoye – Chemistry World

What Tech Conferences Need to Stop for Women to Contribute More – Kellyn Pot’Vin-Gorman – LinkedIn

Bik’s Picks

Because our lab is close: Jeepers! New Look at ‘Creeping’ San Andreas Fault
by Becky Oskin – LiveScience
http://www.livescience.com/49435-san-andreas-fault-less-creepy.html

These scientists raised bot fly larvae in their own bodies — on purpose – Rachel Feltman – The Washington Post

Today in Adorable Science: Disney Has Created a L’il Turtle Robot to Draw Doodles in the Sand – Carolyn Cox – The Mary Sue

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January 9, 2015

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Human respiratory microbiome

The microbiome in asthma – Yvonne J. Huang – Journal of Allergy and Clinical Immunology

Human gut microbiome

Review: Crosstalk between the microbiome and cancer cells by quorum sensing peptides – Evelien Wynendaele – Peptides

Review: Integrated multi-scale strategies to investigate nutritional compounds and their effect on the gut microbiota – Christophe Lacroix – Current Opinion in Biotechnology

Quiz for CME credits: The gut microbiota and inflammatory noncommunicable diseases: Associations and potentials for gut microbiota therapies – Journal of Allergy and Clinical Immunology

Animal models of microbiome research

Microbiota Controls the Homeostasis of Glial Cells in the Gut Lamina Propria – Panagiotis S. Kabouridis – Neuron

Plant microbiome

Influence of cyanobacterial inoculation on the culturable microbiome and growth of rice – Himani Priya – Microbiological Research

Bioinformatics

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

Metagenomics

Three Novel Virophage Genomes Discovered from Yellowstone Lake Metagenomes – Jinglie Zhou – Journal of Virology

One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly – Sergey Koren, Adam M Phillippy – Current Opinion in Microbiology

Metabolomics

Molecular details of a starch utilization pathway in the human gut symbiont Eubacterium rectale – Darrell W. Cockburn – Molecular Microbiology

Review: Food, Immunity, and the Microbiome – Herbert Tilg, Alexander R. Moschen – Gastroenterology

Modelling the effect of undigested dietary carbohydrate on the health and function of the large bowel – Douglas Rosendale – Bioactive Carbohydrates and Dietary Fibre

More microbes

Comparative genomic analysis of Helicobacter pylori from Malaysia identifies three distinct lineages suggestive of differential evolution – Narender Kumar – Nucleic Acids Research

Microbes in the news

Within the Soil – David Relman and Ed Yong comment on the Nature teixobactin paper – Genome Web

New Antibiotic Stirs Hope Against Resistant Bacteria – Denise Grady – New York Times

A New Antibiotic Found in Dirt Can Kill Drug-Resistant Bacteria – Brian Handwerk – Smithsonian

Commensal Defense: Beneficial gut bacteria have evolved resistance to antimicrobial peptides that hosts release to fight pathogens – Kate Yandell – The Scientist

Can Microbes in the Gut Influence the Brain? January 15, 2015, at 3:00 p.m. ET, live webcast with Christopher Lowry and Sarkis Mazmanian – Lindsay Borthwick – Live Science

Gut bacteria, prebiotics and the link between helping stress, anxiety and depression – Clio Korn – The Independent

Science, publishing, career

Men (on the Internet) don’t believe sexism is a problem in science, even when they see evidence – Rachel Feltman – Washington Post

Bik’s Picks

Why scientists guessed wrong on this year’s flu vaccine, and why it could happen again – Brady Dennis – Washington Post

How to age gracefully? Ask a bowhead whale – Will Dunham – Reuters.com

Do Mars Rover Photos Show Potential Signs of Ancient Life? – Johnny Bontemps – Space.com

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January 6, 2015

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Human gut microbiome

The involvement of gut microbiota in inflammatory bowel disease pathogenesis: potential for therapy – Giovanni Cammarota – Pharmacology & Therapeutics

Studies on Modulation of Gut Microbiota by Wine Polyphenols: From Isolated Cultures to Omic Approaches – Montserrat Dueñas – Antioxidants

Human respiratory microbiome

Cost-effective pooling of DNA from nasopharyngeal swab samples for large-scale detection of bacteria by real-time PCR – Sophie Edouard – Journal of Clinical Microbiology

Animal models of microbiome research

Effects of dietary mono- and multiprobiotic strains on growth performance, gut bacteria and body composition of Javanese carp (Puntius gonionotus, Bleeker 1850) – S.K. Allameh – Aquaculture Nutrition

Animal microbiome

Harlequin ladybird: Detection and decay rates of prey and prey symbionts in the gut of a predator through metagenomics – Débora P. Paula – Molecular Ecology Resources

Protist microbiome

Cytologic and Genetic Characteristics of Endobiotic Bacteria and Kleptoplasts of Virgulinella fragilis (Foraminifera) – Masashi Tsuchiya – The Journal of Eukaryotic Microbiology

Plant microbiome

Synergists and antagonists in the rhizosphere modulate microbial communities and growth of Quercus robur L. – Fuensanta Caravaca – Soil Biology and Biochemistry

Soil microbiome

Examination of biotic and abiotic controls of soil bacterial diversity under perennial shrubs in xeric soils – Naama Berg – CATENA

Two Metagenomes from Late Pleistocene Northeast Siberian Permafrost – Kirill Krivushin – Genome Announcements

Extractable N and microbial community structure respond to grassland restoration regardless of historical context and soil composition – Sara Jo M. Dickens – AoB Plants

Methane dynamics in an alpine fen: A field based study on methanogenic and methanotrophic microbial communities – Alessandro G. Franchini – FEMS Microbiology Ecology

Microbial community composition and functions are resilient to metal pollution along two forest soil gradients – Hamed Azarbad – FEMS Microbial Ecology

Effect of biostimulation, temperature and salinity on respiration activities and bacterial community composition in an oil polluted desert soil – Raeid M.M. Abed – International Biodeterioration & Biodegradation

High-throughput sequencing shows inconsistent results with a microscope-based analysis of the soil prokaryotic community – Masayuki Ushio – Soil Biology and Biochemistry

Water microbiome

Oil-derived marine aggregates – hot spots of polysaccharide degradation by specialized bacterial communities – Carol Arnosti – Deep Sea Research Part II: Topical Studies in Oceanography

Bioreactor and wastewater microbiomes

Overall functional gene diversity of microbial communities in three full-scale activated sludge bioreactors – Yu Xia – Applied Microbiology and Biotechnology

Metatranscriptomic analysis of lignocellulolytic microbial communities involved in high-solids decomposition of rice straw – Christopher W Simmons – Biotechnology for Biofuels

Techniques

Protocols for Metagenomic Library Generation and Analysis in Petroleum Hydrocarbon Microbe Systems – Stephanie M. Moormann – Springer Protocols Handbooks 2014

Science, publishing and career

Assessing Research Productivity: A new way of evaluating academics’ research output using easily obtained data – Ushma S. Neill – The Scientist

How many scientific papers are not original? – Michael Lesk – PNAS USA

Know Your PIO: Scientists and public information officers share several common goals. Here’s how to collaborate effectively – Tracy Vence – The Scientist

Microbes in the news

Signs of mother’s diet, birth delivery mode in human milk microbiome – EA Quinn – Genetic Literacy Project

Celebrate your fat – it’s fighting off infection – Clare Wilson – New Scientist

Common cold really is triggered by chilly weather, Yale scientists find – Sarah Knapton – The Telegraph

Picturing Infection: whole-animal, light-based imaging of infected small mammals – Kelly Rae Chi – The Scientist

Bik’s Picks

New evidence on the origin of carnivorous plants – Thomas J. Givnish – PNAS USA

Inching toward the 3D genome – Elizabeth Pennisi – Science

Chopsticks or spoon: The impact of eating methods on eating rate and glycemic response in healthy adults – Lijuan Sun – Physiology & Behavior

Anti-Vaxxers Are Idolizing the Amish, Inexplicably – Olga Khazan – The Atlantic

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December 23, 2014

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Microbiome publications are definitely not taking a winter break, so here is your holiday update. Merry Christmas to those who celebrate!

Human oral microbiome

Serum IgG Antibody Levels to Periodontal Microbiota Are Associated with Incident Alzheimer Disease – James M. Noble – PLOS ONE

Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle – Xuesong He – PNAS USA

Pyrosequencing of supra- and subgingival biofilms from inflamed peri-implant
and periodontal sites – Simone Schaumann – BMC Oral Health

Human respiratory microbiome

The Microbial Community of the Cystic Fibrosis Airway Is Disrupted in Early Life – Julie Renwick – PLOS ONE

Human gut or general microbiome
Effects of bowel cleansing on the intestinal microbiota – Jonna Jalanka – Gut

The Microbiome of Aging and Age-Related Disease – 2014 Meeting Abstracts

Microbial community pattern detection in human body habitats via ensemble clustering framework – Peng Yang – ArXiv.org

Cancer and the microbiome: potential applications as new tumor biomarker – Khan Shahanavaj – Expert Review of Anticancer Therapy

Influence of Intestinal Microbiota on Body Weight Gain: a Narrative Review of the Literature – Camila S. Cardinelli – Obesity Surgery

Animal models of microbiome research

Host genetics and diet, but not immunoglobulin A expression, converge to shape
compositional features of the gut microbiome in an advanced intercross population
of mice – Larry J Leamy – Genome Biology

Animal microbiome

Microbiomes, plausible players or not in alteration of host behaviour – David G. Biron – Frontiers in Microbiology

The Howler Monkey as a Model for Exploring Host-Gut Microbiota Interactions in Primates – Katherine R. Amato, Nicoletta Righini – Howler Monkeys

The Gut Microbiota Appears to Compensate for Seasonal Diet Variation in the Wild Black Howler Monkey (Alouatta pigra) – Katherine R. Amato – Microbial Ecology

Application of the Human Intestinal Tract Chip to the non-human primate gut microbiota – T.D.J. Bello González – Beneficial Microbes

Effects of dietary supplementation of a commercial prebiotic Previda® on survival, growth, immune responses and gut microbiota of Pacific white shrimp, Litopenaeus vannamei – J.D. Anuta – Aquaculture Nutrition

Metagenomic-Based Study of the Phylogenetic and Functional Gene Diversity in Galápagos Land and Marine Iguanas – Pei-Ying Hong – Microbial Ecology

Plant microbiome

The plant microbiome at work – Klaus Schlaeppi and Davide Bulgarelli – Molecular Plant-Microbe Interactions

Tree communities rapidly alter soil microbial resistance and resilience to drought – David Rivest – Functional Ecology

The Sesquiterpene Biosynthesis and Vessel-Occlusion Formation in Stems of Aquilaria sinensis (Lour.) Gilg Trees Induced by Wounding Treatments without Variation of Microbial Communities – Zheng Zhang – International Journal of Molecular Sciences

Analysis of microbial taxonomical groups present in maize stalks suppressive to colonization by toxigenic Fusarium spp.: A strategy for the identification of potential antagonists – Jürgen Köhl – Biological Control

Soil and sediment microbiome

Diversity, Distribution and Hydrocarbon Biodegradation Capabilities of Microbial Communities in Oil-Contaminated Cyanobacterial Mats from a Constructed Wetland – Raeid M. M. Abed – PLOS ONE

Do climate factors govern soil microbial community composition and biomass at a regional scale? – L. Ma – Biogeosciences Discuss

Water microbiome

Early succession of micro-periphyton communities in kelp bed and barren ground ecological systems – Roberto A. Uribe – Marine Ecology

Greater temporal changes of sediment microbial community than its waterborne counterpart in Tengchong hot springs, Yunnan Province, China – Shang Wang – Scientific Reports

Effects of warming on microbial communities in the coastal waters of temperate and subtropical zones in the Northern Hemisphere, with a focus on Gammaproteobacteria
Dao Thi Anh Tuyet – Journal of Oceanography

Colonization in the photic zone and subsequent changes during sinking determines bacterial community composition in marine snow – Stefan Thiele – Applied and Environmental Microbiology

Diversity, Distribution and Hydrocarbon Biodegradation Capabilities of Microbial Communities in Oil-Contaminated Cyanobacterial Mats from a Constructed Wetland
Raeid M. M. Abed – PLOS ONE

Bioreactor microbiology

Comparative analysis of microbial community of novel lactic acid fermentation inoculated with different undefined mixed cultures – Shaobo Liang – Bioresource Technology

A framework for establishing predictive relationships between specific bacterial 16S rRNA sequence abundances and biotransformation rates – Damian E. Helbling – Water Research

Metagenomics

Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India – Johan Bengtsson-Palme – Frontiers in Microbiology

Challenges of metagenomics and single-cell genomics approaches for exploring cyanobacterial diversity – Michelle Davison – Photosynthesis Research

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

Development and validation of an rDNA operon based primer walking strategy applicable to de novo bacterial genome finishing – Alexander W. Eastman and Ze-Chun Yuan – Frontiers in Microbiology

Metabolomics and transcriptomics

Terpene synthases are widely distributed in bacteria – Yuuki Yamada – PNAS USA

Scaling microbial biomass, metabolism and resource supply – Robert L. Sinsabaugh – Biogeochemistry

Metatranscriptomics of N2-fixing cyanobacteria in the Amazon River plume – Jason A Hilton – ISME Journal

Mining Soil Metagenomes to Better Understand the Evolution of Natural Product Structural Diversity: Pentangular Polyphenols as a Case Study – Hahk-Soo Kang and Sean F. Brady – Journal of the American Chemical Society

Molecular details of a starch utilization pathway in the human gut symbiont Eubacterium rectale – Darrell W. Cockburn – Molecular Microbiology

Techniques

Deciphering the Prokaryotic Community and Metabolisms in South African Deep-Mine Biofilms through Antibody Microarrays and Graph Theory – Yolanda Blanco – PLOS ONE

Rapid species-level identification of vaginal and oral lactobacilli using MALDI-TOF MS analysis and 16S rDNA sequencing – Annette Carola Anderson – BMC Microbiology

Probiotics

Probiotic and technological properties of Lactobacillus spp. strains from the human stomach in the search for potential candidates against gastric microbial dysbiosis – Susana Delgado – Frontiers in Microbiology

Phages and viruses

Effectiveness of bacteriophages in the sputum of cystic fibrosis patients – E. Saussereau – Clinical Microbiology and Infection

More Microbiology

Bridging the gap between viable but non-culturable and antibiotic persistent bacteria – Mesrop Ayrapetyan – Trends in Microbiology

Bacterial microcompartments and the modular construction of microbial metabolism – Cheryl A. Kerfeldemail, Onur Erbilgin – Trends in Microbiology

The impact of triclosan on the spread of antibiotic resistance in the environment – Daniel E. Carey – Frontiers in Microbiology

Microbes in the news

At Last, I Meet My Microbes – Katherine Harmon Courage – NPR Shots

This Is Your Microbiome: Katherine Harmon Courage at NPR is taking a tour through her microbiome and that of her husband, mother, and dog, as she recounts in a four-part series – Genome Web

Big Idea 2015: Medicine, Wellbeing, and the Microbiome – Deepak Chopra – LinkedIn

When Threatened By Worms, Bacteria Summon Killer Fungi – Ed Yong – National Geographic

Parkinson’s disease linked to gut bacteria – Tim Sandle – Digital Journal

Bacteria in 550-million-year-old fossils provide new clues about fossil formation – Science Codex

Yellowstone Thermal Pools Colored by Pollution – Patrick J Kiger – Discovery

Floating Toilets That Clean Themselves Grow On A Lake – Nsikan Akpan – NPR Goats and Soda

Bettendorf wrestling coach’s invention tackles germs and bacteria on sporting mats and floors – Dennis Moran – QC Online

People on Craigslist Want to Give You Bacteria for Free – Natalie Kitroeff – BusinessWeek

Science, publishing, career

Patterns of text reuse in a scientific corpus – Daniel T. Citron and Paul Ginsparg – PNAS USA

The Anti-Plagiarism Machine: An analysis of hundreds of thousands of scientific papers finds text re-use is rampant, but it isn’t always malicious – Adrienne Lafrance – The Atlantic

“You Are Welcome Here”: Small Stickers Make a Big Difference for LGBTQ Scientists – Kyle Frischkorn – Scientific American

Science and Art

Incredible Bacteria-Laced Fabric Combines Art, Biology And Fashion – Priscilla Frank – Huffington Post
Bik’s Picks

Evolutionary perspectives on human height variation – Gert Stulp and Louise Barrett – Biological Reviews

What the ‘marshmallow test’ can teach you about your kids – Chuck Hadad – CNN

7 of the Ocean’s Strangest Creatures, Including a Fish With a Flashlight – Matt Simon – Wired

Modern genetics confirm ancient relationship between fins and hands – Science Daily

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December 19, 2014

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Pregnancy and Birth

Lots of abstracts (mostly from the group of Kjersti Aagaard) from the 35th Annual Meeting of the Society for Maternal-Fetal Medicine — The Pregnancy Meeting in the American Journal of Obstetrics and Gynecology

13: Association of preterm birth with alterations in the microbiome and linkage to host mtDNA variants – Kjersti Aagaard

57: Alterations in the intestinal microbiome of infants are associated with breastfeeding practice – Derrick Chu

78: Distinct alterations in the placental microbiome among spontaneous preterm births – Kjersti Aagaard

79: Metagenomics of a population-based prospective cohort reveals no discernable impact of mode of delivery (MOD) on the infant microbiome by 6 weeks of age – Derrick Chu

122: The microbiome of the placenta is altered among subjects with severe chorioamnionitis & spontaneous preterm birth – Amanda Prince

282: Chorioamnionitis induced by intramniotic injection of IL1, LPS or Ureaplasma parvum is associated with an altered microbiome in a primate model of inflammatory preterm birth (PTB) – Amanda Prince

283: Amniotic fluid microbiome community and inflammation in women with second trimester cervical changes – Amanda Roman

342: Poor maternal nutrition is associated with alterations in the maternal and neonatal microbiome communities – Kathleen Antony

650: Characterization of the vaginal microbiome following preterm premature rupture of membranes (PPROM) – Janet Hill

709: Race, latency, and fetal membrane microbiota diversity in preterm premature rupture of membranes – Sarahn Wheeler

Human oral microbiome

* Comparative analysis of the human saliva microbiome from different climate zones: Alaska, Germany, and Africa – Li J – BMC Microbiology

Human respiratory microbiome

* The adult nasopharyngeal microbiome as a determinant of pneumococcal acquisition – Cremers AJ – Microbiome Journal

Human gut microbiome

* The gut microbiota of Colombians differs from that of Americans, Europeans and Asians – Escobar JS – BMC Microbiology

Gut Microbiota: Its Role in Hepatic Encephalopathy – Rahul Rai – Journal of Clinical and Experimental Hepatology

The fungal microbiota of de-novo paediatric inflammatory bowel disease – I. Mukhopadhya – Microbes and Infection

Human vaginal microbiome

Colonization of the upper genital tract by vaginal bacterial species in non-pregnant women  – Caroline M. Mitchell – American Journal of Obstetrics and Gynecology

Transcriptional fingerprints of antigen-presenting cell subsets in the human vaginal mucosa and skin reflect tissue-specific immune microenvironments – Dorothée Duluc – Genome Medicine

Animal models

Microbially Driven TLR5-Dependent Signaling Governs Distal Malignant Progression through Tumor-Promoting Inflammation – Melanie R. Rutkowski – Cancer Cell

Intestinal microbiota diversity and expression of pattern recognition receptors in newly weaned piglets – Xin Tao – Anaerobe

Host genetics and diet, but not immunoglobulin A expression, converge to shape
compositional features of the gut microbiome in an advanced intercross population
of mice – Larry J Leamy – Genome Biology

The effects of Lactobacillus acidophilus as feed supplement on skin mucosal immune parameters, intestinal microbiota, stress resistance and growth performance of black swordtail (Xiphophorus helleri) – Seyed Hossein Hoseinifar – Fish & Shellfish Immunology

Animal microbiome

Investigation of a new acetogen isolated from an enrichment of the tammar wallaby forestomach – Gagen EJ – BMC Microbiology

Metagenomics, bioinformatics

Determining the quality and complexityof next-generation sequencing data without
a reference genome – Seyed Yahya Anvar – Genome Biology

Techniques

Tracking down the sources of experimental contamination in microbiome studies – Sophie Weiss – Genome Biology

More microbiology

Single cell genomics of bacterial pathogens: outlook for infectious disease research – Jeffrey S McLean and Roger S Lasken – Genome Medicine

A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens – Maha R Farhat – Genome Medicine

Environmental enteropathy and malnutrition: do we know enough to intervene? – William A Petri – BMC Medicine

Microbes in the news

Mix of Bacteria in Gut May Depend More on Diet than Genes – Microbiota, Microbiome Change Quickly, UCSF Researchers Find – Jeffrey Norris – UCSF

Protection of the mouse gut by mucus depends on microbes – Phys.org

Life would go on if all bacteria disappeared (but it would totally suck) – Rachel Feltman – Washington Post

New technology using bacteria from dung helps coffee farmers to purify water – Oliver Balch – The Guardian

Science, publishing, career

Dragging scientific publishing into the 21st century – Razib Khan – Genome Biology

Training for peer review: why we need it and how to get there – David Moher – Biome BioMedCentral

Along with the privilege of authorship come important responsibilities – David Moher – BMC Medicine

Crashing the Old Boys’ Science Club – Yamina Berchiche – Live Science

Bik’s Picks

‘People Can Be Afraid of Anything’ – There are plenty of people afraid of whales who will never even see one. How I learned about, and tried to conquer, my own cetaphobia – Kate Horowitz – The Atlantic

Playlist: Science! – NPR/TED staff – NPR

Birds sensed severe storms and fled before tornado outbreak – Science Daily

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December 16, 2014

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Pregnancy and birth

* The establishment of the infant intestinal microbiome is not affected by rotavirus vaccination – Li Ang – Scientific Reports

In pregnant women: Gut Microbiota as an Epigenetic Regulator: Pilot Study Based on Whole-Genome Methylation Analysis – Himanshu Kumar – mBio

Human skin and hair microbiome

* Molecular characterization of the skin fungal microbiome in patients with psoriasis – Akemi Takemoto – The Journal of Dermatology

* Metagenomic analyses of bacteria on human hairs: a qualitative assessment for applications in forensic science – Silvana R Tridico – Investigative Genetics

Human oral microbiome

Oral Streptococci and Nitrite-Mediated Interference of Pseudomonas aeruginosa – Jessica A. Scoffield and Hui Wu – Infection and Immunity

Antimicrobial effect of lemongrass oil against oral malodour micro-organisms and the pilot study of safety and efficacy of lemongrass mouthrinse on oral malodour – P. Satthanakul – Journal of Applied Microbiology

Human respiratory microbiome

The adult nasopharyngeal microbiome as a determinant of pneumococcal acquisition – Amelieke JH Cremers – Microbiome Journal

Human gut microbiome

Shaping the gut microbiome – Linda Koch – Nature Reviews Microbiology

A viral understudy for commensal bacteria – Yvonne Bordon – Nature Reviews Microbiology

* Impacts of infection with different toxigenic Clostridium difficile strains on faecal microbiota in children – Zongxin Ling – Scientific Reports

Gut Microbiota as an Epigenetic Regulator: Pilot Study Based on Whole-Genome Methylation Analysis – Himanshu Kumar – mBio

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

Host Demise as a Beneficial Function of Indigenous Microbiota in Human Hosts – Martin J. Blaser and Glenn F. Webb – mBio

Editorial for special issue of CMI: Faecal transplantation and infectious diseases practitioners – D. Raoult – Clinical Microbiology and Infection

Review: Dysbiotic Events in Gut Microbiota: Impact on Human Health – Serena Schippa and Maria Pia Conte – Nutrients

Animal and other models of microbiome research

A Winogradsky-based culture system shows an association between microbial fermentation and cystic fibrosis exacerbation – Robert A Quinn – ISME Journal

Whole Grain Oats Improve Insulin Sensitivity and Plasma Cholesterol Profile and Modify Gut Microbiota Composition in C57BL/6J Mice – Albert Lihong Zhou – Journal of Nutrition

The Antipsychotic Olanzapine Interacts with the Gut Microbiome to Cause Weight Gain in Mouse – Andrew P. Morgan – PLOS ONE

Genetically identical co-housed pigs as models for dietary studies of gut microbiomes –
Fang Yang – Microbiome Science and Medicine

Animal microbiome

Changes in the faecal microbiota of mares precede the development of post partum colic – J. S. Weese – Equine Veterinary Journal

Succession and Replacement of Bacterial Populations in the Caecum of Egg Laying Hens over Their Whole Life – Petra Videnska – PLOS ONE

 

* Adult blood-feeding tsetse flies, trypanosomes, microbiota and the fluctuating environment in sub-Saharan Africa – Anne Geiger – ISME Journal

Spatial and Temporal Features of the Growth of a Bacterial Species Colonizing the Zebrafish Gut – Matthew Jemielita – mBio

Functional genomics and microbiome profiling of the Asian longhorned beetle (Anoplophora glabripennis) reveal insights into the digestive physiology and nutritional ecology of wood feeding beetles – Erin D Scully – BMC Genomics

 

Bacteria–bacteria interactions within the microbiota of the ancestral metazoan Hydra contribute to fungal resistance – Sebastian Fraune – ISME Journal

Plant microbiome

Local-scale biogeography and spatiotemporal variability in communities of mycorrhizal fungi – Mohammad Bahram – New Phytologist

Emergence shapes the structure of the seed-microbiota – Matthieu Barret – Applied and Environmental Microbiology

Bacterial communities in the phylloplane of Prunus species – Yeonhwa Jo – Journal of Basic Microbiology

Changes in rhizospheric microbial community structure and function during the natural recovery of abandoned cropland on the Loess Plateau, China – Chao Zhang – Ecological Engineering

Climate-induced die-off affects plant–soil–microbe ecological relationship and functioning – Francisco Lloret – FEMS Microbiology Ecology

Leaf-inhabiting endophytic yeasts are abundant but unevenly distributed in three Ficus species from botanical garden greenhouses in Germany – Michael Jay L. Solis – Mycological Progress

Soil and sediment microbiome

Succession of Bacterial Community Structure and Diversity in Soil along a Chronosequence of Reclamation and Re-Vegetation on Coal Mine Spoils in China – Yuanyuan Li – PLOS ONE

Soil microbial communities identify organic amendments for use during oil sands reclamation – M.L. Béass – Ecological Engineering

Forest canopy structural controls over throughfall affect soil microbial community structure in an epiphyte-laden maritime oak stand – Carl Rosier – Ecohydrology

Pyrosequencing revealed highly microbial phylogenetic diversity in ferromanganese nodules from farmland – Min Hu – Environ Sci Processes Impacts

Seasonal dynamics of bacterial and archaeal methanogenic communities in flooded rice fields and effect of drainage – Björn Breidenbach1 and Ralf Conrad – Frontiers in Microbiology

Variations of Bacterial Community Structure and Composition in Mangrove Sediment at Different Depths in Southeastern Brazil – Lucas William Mendes – Diversity

Invasive dreissenid mussels and benthic algae in Lake Michigan: characterizing effects on sediment bacterial communities – Philip O. Lee – FEMS Microbiology Ecology

Plant assemblage composition and soil P concentration differentially affect communities of AM and total fungi in a semi-arid grassland – Rim Klabi – FEMS Microbiology Ecology

Bacterial and Archaeal Communities in Sediments of the North Chinese Marginal Seas
Jiwen Liu – Microbial Ecology

Microbial community composition and diversity in Caspian Sea sediments – Nagissa Mahmoudi – FEMS Microbiology Ecology

Priming of the decomposition of ageing soil organic matter: concentration dependence and microbial control – Johannes Rousk – Functional Ecology

Influence of spoil type on afforestation success and natural vegetative recolonization on a surface coal mine in Appalachia, United States – Kenton Sena – Restoration Ecology

Water microbiome

Bacterial community responses to a gradient of alkaline mountaintop mine drainage in Central Appalachian streams – Raven L Bier – The ISME Journal

Big answers from small worlds: a user’s guide for protist microcosms as a model system in ecology and evolution – Florian Altermatt – Methods in Ecology and Evolution

Spatial scales of bacterial community diversity at cold seeps (Eastern Mediterranean Sea) – Petra Pop Ristova – ISME Journal

The effects of oil pollution on Antarctic benthic diatom communities over 5 years – R. Polmear – Marine Pollution Bulletin

Bacterial community dynamics in a swine wastewater anaerobic reactor revealed by 16S rDNA gene sequence analysis – An-Chi Liu – Journal of Biotechnology

Food microbiology

Antimicrobial activity of hop extracts against foodborne pathogens for meat applications – B. Kramer – Journal of Applied Microbiology

Molecular and enological characterization of Touriga Nacional non-Saccharomyces yeasts – Andreia Teixeira – Journal of Applied Microbiology

Metabolomics

Intra- and inter-species interactions in microbial communities – Luis R. Comolli – Frontiers in Microbiology

Metabolomic Pattern Analysis after Mediterranean Diet Intervention in a Nondiabetic Population: A 1- and 3-Year Follow-up in the PREDIMED Study – Rosa Vázquez-Fresno – Journal of Proteome Research

A gut microbial metabolite of linoleic acid, 10-hydroxy-cis-12-octadecenoic acid, ameliorates intestinal epithelial barrier impairment partially via GPR40/MEK-ERK pathway – Junki Miyamoto – The Journal of Biological Chemistry

Bioinformatics

IM-TORNADO: A Tool for Comparison of 16S Reads from Paired-End Libraries – Patricio Jeraldo – PLOS ONE

Techniques

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

Remediation of pharmaceuticals and personal care products using an aerobic granular sludge sequencing bioreactor and microbial community profiling using Solexa sequencing technology analysis – Xia Zhao – Bioresource Technology

Predicting Bacterial Community Assemblages Using an Artificial Neural Network Approach – Peter Larsen – Artificial Neural Networks

Functional foods

Systematic review of randomized controlled trials of probiotics, prebiotics, and synbiotics in inflammatory bowel disease – Ghouri YA – Clinical and Experimental Gastroenterology

More microbiology

Life in a World without Microbes – Jack A. Gilbert, Josh D. Neufeld – PLOS Biology

Demystifying Escherichia coli pathovars – Kate S. Baker – Nature Reviews Microbiology

Wolbachia small noncoding RNAs and their role in cross-kingdom communications – Jaime G. Mayoral – PNAS USA

How the virophage compels the need to readdress the classification of microbes – Didier Raoult – Virology

Microbes in the news

To Get To The Bottom Of Your Microbiome, Start With A Swab Of Poo – Katherine Harmon Courage – NPR Shots Health News

Seth Bordenstein: Expert to give talk on animal microbiome – Arizona State University

Could a bacterial ‘fingerprint’ solve a sexual assault case? – Rachel Feltman – Washington Post

Oil-Dwelling Bacteria Are Highly Social Creatures, Contrary To Previous Belief – Rebekah Marcarelli – Headlines and Global News

Methane Bursts On Mars Could Hint At Previous Life – Joe Palca – NPR

Bik’s Picks

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping – Suhas S.P. Rao – Cell

Shift workers ‘sicker and fatter’ – James Gallagher – BBC News

How to turn 4,000 watts of white light into a 45-meter-wide rainbow – Popular Science

How to Bike Home Your Christmas Tree in 11 Simple Steps – Anna Broadway – City Lab

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December 15, 2014

Posted on by

Pregnancy and birth microbiome

Antibiotics in early life and obesity – Laura M. Cox & Martin J. Blaser – Nature Reviews Endocrinology

Is there a role for probiotics in the prevention of preterm birth? – Siwen Yang – Frontiers in Immunology

Human oral microbiome

A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome – Christina Warinner – Philosophical Transactions of the Royal Society B

Commensal Streptococcus mitis is a unique vector for oral mucosal vaccination – Nada Daifalla- Microbes and Infection

Human respiratory microbiome

Correlation Between Nasal Microbiome Composition and Remote Purulent Skin and Soft-Tissue Infections – Ryan C. Johnson – Infection and Immunity

Human gut microbiome

The fungal microbiota of de-novo paediatric inflammatory bowel disease – I. Mukhopadhya – Microbes and Infection

Microbiome changes in healthy volunteers treated with GSK1322322, a novel antibiotic targeting bacterial peptide deformylase – Seda Arat – Antimicrobial Agents and Chemotherapy

Impact of commensal microbiota on the host pathophysiology: focusing on immunity and inflammation – Hiroshi Ohno – Seminars in Immunopathology
http://link.springer.com/article/10.1007/s00281-014-0472-2

Human vaginal microbiome

Trichomonas vaginalis origins, molecular pathobiology and clinical considerations.
Hirt, Robert P – Current Opinion in Infectious Diseases
http://journals.lww.com/co-infectiousdiseases/Abstract/publishahead/Trichomonas_vaginalis_origins,_molecular.99539.aspx

Animal microbiome

Impact of a Complex Food Microbiota on Energy Metabolism in the Model Organism Caenorhabditis elegans – Elena Zanni – BioMed Research International

Plant microbiome

The bacterial rhizobiome of hyperaccumulators: future perspectives based on omics analysis and advanced microscopy – Giovanna Visioli – Frontiers in Plant Science

Soil microbiome

Effect of 25-year fertilization on soil microbial biomass and community structure in a
continuous corn cropping system – Peng Shi – Archives of Agronomy and Soil Science

Microbial regulation of nitrogen dynamics along the hillslope of a natural forest – Kazuo Isobe – Frontiers in Environmental Science

Ancient and modern environmental DNA – Mikkel Winther Pedersen – Philosophical Transactions of the Royal Society B

Protocols for Investigating the Microbiology of Oil Sands Deposits – Christina Ridley – Springer Protocols Handbooks 2014

Water microbiome

Spatially resolved sampling reveals dynamic microbial communities in rising hydrothermal plumes across a back-arc basin – Cody S Sheik – ISME Journal
http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej2014228a.html

Protocols for Investigating the Microbiology of Coal-Bed-Produced Waters – Amy V. Callaghan – Springer Protocols Handbooks 2014

The shift of microbial population composition accompanying the injected water flowing in the water-flooding petroleum reservoirs – P. K. Gao – BioGeosciences Discussions

Air microbiome

MALDI-TOF mass spectrometry and identification of new bacteria species in air
samples from Makkah, Saudi Arabia – Emmanouil Angelakis – BMC Research Notes

Bioreactor microbiology
Spatial heterogeneity in degradation characteristics and microbial community composition of pesticide biopurification systems – Pieter Verhagen – Journal of Applied Microbiology

Metabolomics

Development of High-Performance Chemical Isotope Labeling LC-MS for Profiling the Human Fecal Metabolome – Wei Xu – Analytical Chemistry
http://pubs.acs.org/doi/abs/10.1021/ac503619q

A straightforward and efficient analytical pipeline for metaproteome characterization – Alessandro Tanca – Microbiome

Microbes in the News

Healthier Soils Will Give Us – and the Planet — a Healthier Century – Robert T. Fraley – Huffington Post

These Crazy Bacteria-Filled Spacesuits May Be What Let Us Survive On Other Planets – Adele Peters – FastCoexist

Parkinson’s Disease Associated With Altered Intestinal Bacteria: Interview with Filip Scheperjans – Medical Research

New Imaging Technique Reveals Bacterial Biofilms in Colon Cancer Patients – Catherine Griffin – Science World Report

450 bacteria on a plastic giraffe vs. 80 million in a kiss is not bad at all! #BacteriaHysteria:
Is your child playing with a germ-infested toy? Here’s how to reduce the risks – Tracy Frank – InForum

Origin Of Eukaryotic Cells Gets A New Hypothesis – Science 2.0

Science, publishing, and career
Retraction Watch is growing, thanks to a $400,000 grant from the MacArthur Foundation – Ivan Oransky – Retraction Watch

Bik’s Picks

The Innovative Chemistry of Tinsel – Francie Diep – Popular Science

The Math And Science Of Latkes – Tania Lombrozo – NPR

Northern white rhino dies at San Diego zoo; only 5 left worldwide – Faith Karimi and Joe Sutton – CNN

Why this computer science professor bakes 1,400 cookies for his students during finals week – John Cook – GeekWire

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