Monthly Archives: December 2014

December 30, 2014

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Human oral microbiome

Mucosal Microbiome in Patients with Recurrent Aphthous Stomatitis – K. Hijazi – Journal of Dental Research

Human respiratory microbiome

Impact of saline irrigation and topical corticosteroids on the postsurgical sinonasal microbiota – Cindy M. Liu – International Forum of Allergy & Rhinology

Human gut microbiome

The Gastrointestinal Microbiota and Colorectal Cancer – Temitope O. Keku – American Journal of Physiology – Gastrointestinal and Liver Physiology

The Impact of Diet and Lifestyle on Gut Microbiota and Human Health – Michael A. Conlon and Anthony R. Bird – Nutrients

Understanding How Commensal Obligate Anaerobic Bacteria Regulate Immune Functions in the Large Intestine – Eva Maier – Nutrients

Animal microbiome
Symbiotic bacteria contribute to increasing the population size of a freshwater crustacean, Daphnia magna – Saranya Peerakietkhajorn – Environmental Microbiology Reports

Antibiotic activity and microbial community of the temperate sponge, Haliclona sp. – A. Hoppers – Journal of Applied Microbiology

Plant microbiome

Secondary successional trajectories of structural and catabolic bacterial communities in oil polluted soil planted with hybrid poplar – Shinjini Mukherjee – Molecular Ecology

Fungal Endophytes of Alpinia officinarum Rhizomes: Insights on Diversity and Variation across Growth Years, Growth Sites, and the Inner Active Chemical Concentration – Li Shubin – PLOS ONE

Endophytic microbial community in two transgenic maize genotypes and in their
near-isogenic non-transgenic maize genotype – Débora Alves Ferreira da Silva – BMC Microbiology

Soil, sediment, sludge, litter microbiome

Site properties have a stronger influence than fire severity on ectomycorrhizal fungi and associated N-cycling bacteria in regenerating post-beetle-killed lodgepole pine forests – Nabla M. Kennedy – Folia Microbiologica

Influence of Azo Dye Concentration on Activated Sludge Bacterial Community in the Presence of Functionalized Polyurethane Foam – Hong Lu – Applied Biochemistry and Biotechnology

The Potential of Antibiotic Alternatives for Enriching Beneficial Microbiota in Litter – Adriana A. Pedroso – SOJ Microbiology & Infectious Diseases

Water microbiome

Bacterial Community Composition in Three Freshwater Reservoirs of Different Alkalinity and Trophic Status – Marc Llirós – PLOS ONE

Bioinformatics
* Programming tools: Adventures with R – A guide to the popular, free statistics and visualization software that gives scientists control of their own data analysis – Sylvia Tippmann – Nature

Metabolomics, Proteomics

Symbiosis, dysbiosis, and rebiosis — The value of metaproteomics in human microbiome monitoring – Lei Mao and Jacqueline Franke – Proteomics

Viruses and Phages

Virus evolution towards limited dependence on the non-essential functions of the host: the bacteriophage SPP1 case – Virginija Cvirkaite-Krupovic – Journal of Virology

Microbial Ecology

Review: Metacommunity organisation, spatial extent and dispersal in aquatic systems: patterns, processes and prospects – Jani Heino – Freshwater Biology

Microbes in the news

Is the Bacteria in Our Gut the Key to Our Health? (Podcast with Ed Yong, Jack Gilbert, Jonathan Eisen, Margaret McFall-Ngai starts at 9 min) – To The Point – Barbara Bogaev – KCRW

9 Amazing and Gross Things Scientists Discovered About Microbes This Year – Greg Miller – Wired.com

The Right Chemistry: Exposure to bacteria can help keep us healthy – Joe Schwarcz – Montreal Gazette

Scientists Discover How Mouth Microbes Cause Gum Disease – Randall Mayes – Design & Trend

Microbiologists cultivate “microbial dark matter” – Eric Hopton – RedOrbit

Science, Publishing, and Career

Open Access 2014: A Year that Data Cracked Through Secrecy and Myth – Hilda Bastian- PLOS Blogs

Bik’s Picks

Watch raindrops make asteroid-like collisions (slo-mo video) – Popular Science

An ‘Otter-This-World’ Christmas! – Total cuteness courtesy of the Monterey Bay Aquarium – Susan C. Schena – Patch.com

Go Outside Tonight and Take a Look at Comet Lovejoy in the Sky – Dan Van Winkle – The Mary Sue

46 Important Things Science Taught Us In 2014 – It was a big year for robot penguins, snake penises, and space exploration. Sadly not all at the same time – Kelly Oakes – BuzzFeed

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December 28, 2014

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Human oral microbiome

Periodontitis: from microbial immune subversion to systemic inflammation – George Hajishengallis – Nature Reviews Immunology

Microbiology of Oral Biofilm-Dependent Diseases: Have We Made Significant Progress to Understand and Treat These Diseases? – Ana Paula Vieira Colombo – Current Oral Health Reports

Human skin microbiome

Dynamics of the surgical microbiota along the cardiothoracic surgery pathway – Sara Romano-Bertrand – Frontiers in Microbiology

Human gut microbiome

Decreased Bacterial Diversity Characterizes the Altered Gut Microbiota in Patients With Psoriatic Arthritis, Resembling Dysbiosis in Inflammatory Bowel Disease – Jose U. Scher – Arthritis & Rheumatology

Insights Into the Role of the Microbiome in Obesity and Type 2 Diabetes – Annick V. Hartstra – Diabetes Care

* The gut microbiota and its role in the development of allergic disease: a wider perspective – C. E. West – Clinical & Experimental Allergy

The power in numbers: Gut microbiota in Parkinson’s disease – Joaquin A. Vizcarra – Movement Disorders

Childhood Obesity: A Role for Gut Microbiota? – Marina Sanchez – Int. J. Environ. Res. Public Health

Animal models of microbiome

Impact of the gut microbiota on rodent models of human disease – Axel Kornerup Hansen – World Journal of Gastroenterology

Dynamics and Establishment of Clostridium difficile Infection in the Murine Gastrointestinal Tract – Mark J. Koenigsknecht – Infection and Immunity

Alteration of the fecal microbiota and serum metabolite profiles in dogs with idiopathic inflammatory bowel disease – Yasushi Minamoto – Gut Microbes

Intermittent hypoxia alters gut microbiota diversity in a mouse model of sleep apnoea
Isabel Moreno-Indias – European Respiratory Journal

Bioreactor models

Lead toxicity to the performance, viability, and community composition of activated sludge microorganisms – Husen Zhang – Environmental Science & Technology

Animal microbiome

Diet strongly influences the gut microbiota of surgeonfishes – Sou Miyake – Molecular Ecology

Plant microbiome

21st century agriculture: integration of plant microbiomes for improved crop production and food security – Angela Sessitsch and Birgit Mitter – Microbial Biotechnology

Soil microbiome

Vertical distribution of the soil microbiota along a successional gradient in a glacier forefield – Thomas Rime – Molecular Ecology

Changes in the composition and diversity of bacterial communities 13 years after soil reclamation of abandoned mine land in eastern China – Yuanyuan Li – Ecological Research

Nitrogen cycling processes and microbial community composition in bed sediments in the Yukon River at Pilot Station – Deborah A. Repert – Journal of Geophysical Research: Biogeosciences

Clay minerals and metal oxides strongly influence the structure of alkane-degrading microbial communities during soil maturation – Annelie Steinbach – ISME Journal

Different vegetable crop rotations affect soil microbial communities and soilborne diseases of potato and onion: literature review and a long-term field evaluation – PJ Wright – New Zealand Journal of Crop and Horticultural Science

Water microbiome

* Biogeography and ecology of the rare and abundant microbial lineages in deep-sea – Rika E. Anderson – FEMS Microbiology Ecology

Comparative metagenomic and metatranscriptomic analyses of microbial communities in acid mine drainage – Lin-xing Chen – ISME Journal

Microbes of the built environment

Indoor bioaerosol dynamics – William W Nazaroff – Indoor Air

Bioinformatics

An improved method to set significance thresholds for β diversity testing in microbial community comparisons – Arda Gülay and Barth F. Smets – Environmental Microbiology

Metabolomics

Reevaluating the hype: Four bacterial metabolites under scrutiny – Esther Eleonore Fröhlich – European Journal of Microbiology and Immunology

Microbes in the news

Discovering microbiology – Nicholas P Money – Oxford University Press

The Microbes in Your Kitchen (Or in your Starbucks mocha) – Kevin Bonham – Scientific American

Science, Publishing, Career

Science is the most ‘future proof’ degree: Engineering and chemistry seen as courses likely to lead to an adaptable career – Laura Clark – Daily Mail

Bik’s Picks

Dr. Oz gets roasted in science journal’s Christmas edition — science roundup extra (video, links) – Susannah L. Bodman – Oregon Live

Science Explains Why The Best BBQ Is Slow Cooked – Patrick Allan – LifeHacker

The Shapes of Snowflakes – CompoundChem

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December 26, 2014

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Pregnancy and birth

* Early Childhood Gut Microbiomes Show Strong Geographic Differences Among Subjects at High Risk for Type 1 Diabetes – Kaisa M. Kemppainen – Diabetes Care

Human skin microbiome

* Spatial variations in the microbial community structure and diversity of the human foot is associated with the production of odorous volatiles – Deborah Stevens – FEMS Microbiology Ecology

Human respiratory microbiome

Microbiota profiling of bronchial fluids of elderly patients with pulmonary carcinoma – Naoko Ishida – Journal of Oral Biosciences

Human gut microbiome

* Microbial culturomics: paradigm shift in the human gut microbiome study – J.-C. Lagier
Clinical Microbiology and Infection

Fecal microbiota transplantation through mid-gut for refractory Crohn’s disease: Safety, feasibility, and efficacy trial results – Bota Cui – Journal of Gastroenterology and Hepatology

Culturomics: a new approach to study the human microbiome – G. Greub – Clinical Microbiology and Infection

The influence of the human microbiome and probiotics on cardiovascular health – Race Ettinger – Gut Microbes

Prolonged use of a proton pump inhibitor reduces microbial diversity: implications for Clostridium difficile susceptibility – Charlie T Seto – Microbiome

Animal microbiome

Use of metagenomic high-throughput sequencing technology and robust bioinformatics to assess the microbiome of cattle, their environments, and beef products to determine the degree of antimicrobial resistance – X. Yang – Meat Science

News in livestock research – use of Omics-technologies to study the microbiota in the gastrointestinal tract of farm animals – Simon Deusch – Computational and Structural Biotechnology Journal

Birds: Bacteria and the evolution of honest signals. The case of ornamental throat feathers in spotless starlings – Magdalena Ruiz-Rodríguez – Functional Ecology

Silverleaf whitefly: Diversity of symbiotic bacteria associated with Bemisia tabaci (Homoptera: Aleyrodidae) in cassava mosaic disease pandemic areas of Tanzania – L.S. Tajebe – Annals of Applied Biology

Physicochemical conditions, metabolites, and community structure of the bacterial microbiota in the gut of wood-feeding cockroaches (Blaberidae: Panesthiinae) – Eugen Bauer – FEMS Microbiology Ecology

Sea urchin larvae decipher the epiphytic bacterial community composition when selecting sites for attachment and metamorphosis – Shaun J. Nielsen – FEMS Microbiology Ecology

Plant microbiome

Land-use intensity and host plant identity interactively shape communities of arbuscular mycorrhizal fungi in roots of grassland plants – Kriszta Vályi – New Phytologist

Temporal patterns of orchid mycorrhizal fungi in meadows and forests as revealed by 454 pyrosequencing – Jane Oja – New Phytologist

Review: Exploring interactions of plant microbiomes – Fernando Dini Andreote – Scienta Agricola

Drying effects on archaeal community composition and methanogenesis in bromeliad tanks – Franziska B. Brandt – FEMS Microbiology Ecology

The effect of psychrotrophic bacteria isolated from the root zone of winter wheat on selected biotic and abiotic factors – Sebastian Wojciech Przemieniecki – Journal of Plant Protection Research

Soil microbiome

Influence of exogenous organic matter on prokaryotic and eukaryotic microbiota in an agricultural soil. A multidisciplinary approach – Daniela Pezzolla – Soil Biology and Biochemistry

Soil bacteria hold the key to root cluster formation – Byron B. Lamont – New Phytologist

Distinct composition signatures of archaeal and bacterial phylotypes in the Wanda Glacier forefield, Antarctic Peninsula – Igor S. Pessi – FEMS Microbiology Ecology

The effect of storage on microbial activity and bacterial community structure of drained and flooded paddy soil – Juan Wang – Journal of Soils and Sediments

Detection and diversity of copper containing nitrite reductase genes (nirK) in prokaryotic and fungal communities of agricultural soils – Andrew Long – FEMS Microbiology Ecology

Archaeal community diversity and abundance changes along a natural salinity gradient in estuarine sediments – Gordon Webster – FEMS Microbiology Ecology

Water microbiome

Molecular analysis of the benthos microbial community in Zavarzin thermal spring (Uzon Caldera, Kamchatka, Russia) – Alexey S Rozanov – BMC Genomics

Food microbiology

Cheese rind microbial communities: diversity, composition and origin – Françoise Irlinger – FEMS Microbiology Letters

Microbiome and immunology

The role of IL-10 in microbiome-associated immune modulation and disease tolerance – Benoît Levast – Cytokine

TL1A regulates TCRγδ+ intraepithelial lymphocytes and gut microbial composition – Peter Tougaard – European Journal of Immunology

Microbiome components with probiotic or other interesting properties

Miniaturized Cultivation of Microbiota for Antimalarial Drug Discovery – Carrie Waterman – Medicinal Research Reviews

Antagonism against fish pathogens by cellular components and verification of probiotic properties in autochthonous bacteria isolated from the gut of an Indian major carp, Catla catla (Hamilton) – Anjan Mukherjee and Koushik Ghosh – Aquaculture Research

Probiotic strains introduced through live feed and rearing water have low colonizing success in developing Atlantic cod larvae – Jorunn Skjermo – Aquaculture

Metabolomics

Introducing the USA Plant, Algae and Microbial Metabolomics Research Coordination Network (PAMM-NET) – Lloyd W. Sumner – Metabolomics

Towards the Fecal Metabolome Derived from Moderate Red Wine Intake – Ana Jiménez-Girón – Metabolites

Bioinformatics

Inconsistent Denoising and Clustering Algorithms for Amplicon Sequence Data – Koskinen Kaisa – Journal of Computational Biology

Microbes in the news

Is 2015 the Year We All Sequence Our Microbiomes?– The Atlantic

Do new natural products lurk in genes of bacteria? – Kevin Stacey-Brown – Futurity

Discovery holds promise for decoding elusive bacteria – Business Standard

Experimental Drugs Target Bacteria’s Social Network – Carl Zimmer – Scientific American

Did Microbes Shape the Human Life Span? – Tia Ghose – LiveScience

Does the Gut Microbiome Play a Role in Autoimmune Disease? – Amy Nett – ChrisKresser.com

Bik’s Picks

To Raise Science Scores, Colleges Look Beyond the Lecture – Richard Perez-Pena – New York Times

Tsunami Science: Advances Since the 2004 Indian Ocean Tragedy – Becky Oskin – Live Science

Rudimentary egg and sperm cells made from stem cells – David Cyranoski – Nature

Who Patented ‘My Favorite Things’? – Robinson Meyer – 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 18, 2014

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Human gut microbiome

* Metagenomic Analysis of Viruses in Feces from Unsolved Outbreaks of Gastroenteritis in Humans – Nicole E. Moore – Journal of Clinical Microbiology

Altered faecal and mucosal microbial composition in post-infectious irritable bowel syndrome patients correlates with mucosal lymphocyte phenotypes and psychological distress – J. Sundin – Alimentary Pharmacology & Therapeutics

Animal models of microbiome research

* The composition of the gut microbiota shapes the colon mucus barrier – Hedvig E Jakobsson – EMBO Reports

Diet Dominates Host Genotype in Shaping the Murine Gut Microbiota – Rachel N. Carmody – Cell Host & Microbe

Animal microbiome

Fish: The Gastrointestinal Phage Communities of the Cultivated Freshwater Fishes – Yang He – FEMS Microbiology Letters

Mussel: Algae Consumption and Nitrate Removal in a Raw Water Transport System by Limnoperna fortunei and its Associated Microorganisms – Ruijian Zhang – Water Environment Research

Plant microbiome

Meeting report: A snapshot of molecular plant–microbe interaction research – Sebastian Wittulsky – New Phytologist

Plant–microbe interactions change along a tallgrass prairie restoration chronosequence – Anna J. Herzberger – Restoration Ecology

Water microbiome

The influence of iron and siderophores on eukaryotic phytoplankton growth rates and community composition in the Ross Sea – Adam B. Kustka – Marine Chemistry

Food microbiology

Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products – Mathieu Almeida – BMC Genomics

Metabolomics

Identification and characterization of intestinal lactobacilli strains capable of degrading immunotoxic peptides present in gluten – R.M. Duar – Journal of Applied Microbiology

Microbes in the news

Behind The Scenes At The Lab That Fingerprints Microbiomes – Katherine Harmon Courage – NPR Shots Health News

Complex genome-microbiome link may influence risk for IBD – Healio

Patients don’t understand risks of unnecessary antibiotics, study shows – Science Daily

The Microbiota Crisis: How the Herbicide Glyphosate is Killing Microbiomes – Martin Michener – Health Impact News

Bik’s Picks

Asian Glow May Indicate Lower Pain Tolerance – Stephani Sutherland – Scientific American

What was the Worst #ScienceFail of 2014? (Op-Ed) – Aaron Huertas – LiveScience

Breakthrough of the year 2014 – Science

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December 17, 2014

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A late digest today – I have been busy writing a paper and cooking for our lab’s annual holiday potluck party tomorrow. But here we go:

Human gut microbiome

Complex host genetics influence the microbiome in inflammatory bowel disease – Dan Knights – Genome Medicine

Microbiota and the human nature: know thyself – Harald Brüssow – Environmental Microbiology

Animal and bioreactor models of microbiome

Simulating distal gut mucosal and luminal communities using packed-column biofilm reactors and an in vitro chemostat model – Julie A.K. McDonald – Journal of Microbiological Methods

A novel method to characterize bacterial communities affected by carbon source and electricity generation in microbial fuel cells using stable isotope probing and Illumina sequencing – Yang Song – Journal of Microbiological Methods

Animal microbiome
Crab: Linking regional variation of epibiotic bacterial diversity and trophic ecology in a new species of Kiwaidae (Decapoda, Anomura) from East Scotia Ridge (Antarctica) hydrothermal vents – Katrin Zwirglmaier – MicrobiologyOpen

Soil microbiome

Minireview: The soil resistome: a critical review on antibiotic resistance origins, ecology and dissemination potential in telluric bacteria – Joseph Nesme and Pascal Simonet – Environmental Microbiology

The soil microbial community predicts the importance of plant traits in plant–soil feedback – Po-Ju Ke – New Phytologist

Metagenomics

Tle distribution and diversity in metagenomic datasets reveal niche specialization – Frank Egan – Environmental Microbiology Reports

Techniques

Application of a single-colony coculture technique to the isolation of unculturable gut bacteria – Yoshiki Tanaka – Microbiology and Immunology

A novel universal DNA labeling and amplification system for rapid microarray-based detection of 117 antibiotic resistance genes in Gram-positive bacteria – Christian Strauss – Journal of Microbiological Methods

Microbial Ecology

Microbial biogeography: the end of the ubiquitous dispersal hypothesis? – Christopher J. van der Gast – Environmental Microbiology

Bacteria can mobilize nematode-trapping fungi to kill nematodes – Xin Wang – Nature Communications

Microfluidic single-cell analysis links boundary environments and individual microbial phenotypes – Christian Dusny and Andreas Schmid – Environmental Microbiology

Microbes in the News

Microbiome may have shaped early human populations – Phys.org

Commensal bacteria were critical shapers of early human populations – Phys.org

Microbes played a significant role in human evolution, study says – Chuck Bednar – RedOrbit

The microbes we eat: Study investigates bacteria in different diets – Nathan Gray – NutraIngredients

Researchers source stool samples to study gut bacteria – Nicole Kwan – FOX News

Bacterial biofilms are associated with colon cancer, imaging technique reveals – Science Daily

Do Autoimmune Diseases Begin in the Gut? – Stephen Paget – Medscape

People may inherit ‘gut’ bacteria that cause Crohn’s disease and ulcerative colitis – MedicalXpress

* 2015 will be the year of the Microbiome (and 28 other predictions) – Fortune

#BacteriaHysteria: The hidden dangers lurking in your kitchen: Chopping boards harbour 200% more faecal bacteria than toilet seats and potatoes and leeks can give you food poisoning – Lizzie Parry – Daily Mail Online

Scientists Debate If It’s OK To Make Viruses More Dangerous In The Lab – Nell Greenfieldboyce – NPR Shots Health News

Science, publishing, and career

12 Unimpressed Comments From Peer Reviewers – Kristy Hamilton – IFL Science (for more entertaining quotes in Environmental Microbiology, see here)

Journalists to Catalog Retractions: Staff of the blog Retraction Watch will create a database of papers retracted from the scientific literature – Kerry Grens – The Scientist

Here’s What Happens When Female MIT PhDs Do a Reddit AMA About Computer Science – Lauren Landry – BostInno

How to be a science girl in a Barbie world – Eve Andrews – Grist.org

For Sale: “Your Name Here” in a Prestigious Science Journal – Charles Seife – Scientific American

These Beautiful Women in Science Art Prints Feature Rad As Heck Ladies – Sam Maggs – The Mary Sue

Bik’s Picks

Happy Holidays from the Corals! – Ocean Portal – Smithsonian

Science’s good, bad, ugly year – Tom Siegfried – Science News

Meet Bill Nye, The Anti-Science Guy – Robert Tracinski – The Federalist

10 Cutest Animals in Science in 2014 – Megan Gannon – Live Science

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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

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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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December 12, 2014

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Human oral microbiome

Periodontal microbiology in Latin America – Adolfo Contreras – Periodontology 2000

Current perspective of the impact of smoking on the progression and treatment of periodontitis – Francisco H. Nociti Jr – Periodontology 2000

Effect of periodontal treatment on preterm birth rate: a systematic review of meta-analyses – Néstor J. López, Sergio Uribe and Benjamín Martinez – Periodontology 2000

Pregnancy and birth

* The Infant Microbiome Development: Mom Matters – Noel T. Mueller – Trends in Molecular Medicine

(see also above) Effect of periodontal treatment on preterm birth rate: a systematic review of meta-analyses – Néstor J. López, Sergio Uribe and Benjamín Martinez – Periodontology 2000

Pre- and probiotics, functional foods

Repeated cooking and freezing of whole wheat flour increases resistant starch with beneficial impacts on in vitro fecal fermentation properties – Jennifer A. Arcila, Devin J. Rose – Journal of Functional Foods

Potential of cereal grains and grain legumes in modulating pigs’ intestinal microbiota – A review – Tobias Aumiller – Livestock Science

Significance of Inulin Fructans in the Human Diet – Gertjan Schaafsma and Joanne L. Slavin – Comprehensive Reviews in Food Science and Food Safety

Effects of targeted delivery of propionate to the human colon on appetite regulation, body weight maintenance and adiposity in overweight adults – Edward S Chambers – Gut

Animal models

P47 – A dietary-driven redox modulation of gut microbiome-host interactions: the rescue of epithelial barrier and mucus production during dysbiosis by dietary nitrate – Bárbara Rocha – Free Radical Biology and Medicine

Dietary Pectin–Derived Acidic Oligosaccharides Improve the Pulmonary Bacterial Clearance of Pseudomonas aeruginosa Lung Infection in Mice by Modulating Intestinal Microbiota and Immunity – Henry Bernard – The Journal of Infectious Diseases

Soil microbiome

Response of autochthonous microbiota of diesel polluted soils to land-farming treatments – Gloria Andrea Silva-Castro – Environmental Research

Are there links between responses of soil microbes and ecosystem functioning to elevated CO2, N deposition and warming? A global perspective – Pablo García-Palacios – Global Change Biology

Experimental evaluation of CO2 percolation effects on subsurface soil microbiota –
Patricia Österreicher-Cunha – International Journal of Greenhouse Gas Control

Water microbiome

In situ grazing experiments apply new technology to gain insights into deep-sea microbial food webs – Maria G. Pachiadaki – Deep Sea Research Part II: Topical Studies in Oceanography

Metabolomics

Microbial Urease in Health and Disease – Diego Mora, Stefania Arioli – PLOS Pathogens

Bioinformatics

“Bioinformatics: Introduction and Methods,” a Bilingual Massive Open Online Course (MOOC) as a New Example for Global Bioinformatics Education – Yang Ding – PLOS Computational Biology

Techniques
Effect of Two Different Commercial DNA Extraction Kits on the Bacterial 16S rRNA gene Denaturing Gradient Gel Electrophoresis Profile of Arabian Gelding Feces – Megan L. Shepherd – Journal of Equine Veterinary Science

More microbiology papers

mBio Addresses the Pause in Gain-of-Function (GOF) Experiments Involving Pathogens with Pandemic Potential (PPP) – Arturo Casadevall – mBio

The battle for iron – Andrew E. Armitage, Hal Drakesmith – Science

Bacteriophage exclusion, a new defense system – Rodolphe Barrangou and John van der Oost – The EMBO Journal

Microbes in the news

Poo And You: A Journey Into The Guts Of A Microbiome – Katherine Harmon Courage – NPR Health

The Gut and Arthritis: The Evidence Grows – Nancy Walsh and Diana Swift – MedPageToday

Gross! Apparently Your Bacteria Is What Makes or Breaks a Relationship? – Zahra Barnes – Glamour.com (who knew?)

A Powder Made From Bacteria Waste Could Curb Overeating – Sarah Zhang – Gizmodo

Science, publishing, career

Scientific Elevator Pitches: A number of competitions around the world are challenging young scientists to describe their research in mere minutes – Rina Shaikh-Lesko – The Scientist

More science doctorates, fewer postdoctorate science jobs – Beryl Lieff Benderly – Science Careers

Making science a desirable career – Jessica K. Polka, Kristin A. Krukenberg – Science Magazine

Tips for Talking to Politicians: Members of an American Society for Cell Biology panel urge their colleagues to consider science advocacy – Tracy Vence – The Scientist

What Should High School Students Learn About Science? – Ria Misra – Space io9

Faculty member leads development of webinars that improve science education – Samantha Schwartz – PennState News

In defamation case, PubPeer moves to quash subpoena to unmask anonymous commenters – Kelly Servick – Science Magazine

Scientific American’s Top 10 Science Stories of 2014 – Scientific American

Bik’s Picks

Why whale poo matters – George Monbiot – The Guardian

Introduction to special Science Issue on bird genomes: A flock of genomes – Guojie Zhang – Science

The Darwin Awards: sex differences in idiotic behaviour – Ben Alexander Daniel Lendrem – British Medical Journal

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