Category Archives: General Microbiome

January 7, 2015

Posted on by

Human skin microbiome

Commensal–dendritic-cell interaction specifies a unique protective skin immune signature – Shruti Naik – Nature

Human gut microbiome

Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism – Fiona Cuskin – Nature

Animal models of microbiome research

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile – Charlie G. Buffie – Nature

Animal microbiome

Antibiotics in ingested human blood affect the mosquito microbiota and capacity to transmit malaria – Mathilde Gendrin – Nature Communications

The putative functional ecology and distribution of archaeal communities in sponges, sediment and seawater in a coral reef environment – Ana R. M. Polónia – Molecular Ecology

Plant microbiome

Plant-Plant-Microbe Mechanisms Involved in Soil-Borne Disease Suppression on a Maize and Pepper Intercropping System – Min Yang – PLOS ONE

Water microbiome

Adapt or Die on the Highway To Hell: Metagenomic Insights into Altered Genomes of Firmicutes from the Deep Biosphere – Brandon Briggs, Frederick Colwell – AGU Fall Meeting San Francisco

Biodiversity hot spot on a hot spot: novel extremophile diversity in Hawaiian fumaroles – Kate Wall – Microbiology Open

Bioinformatics

Binpairs: Utilization of Illumina Paired-End Information for Improving Efficiency of Taxonomic Binning of Metagenomic Sequences – Anirban Dutta – PLOS ONE

Probiotics

Isolation and Characterization of Faecalibacterium prausnitzii from Calves and Piglets – Carla Foditsch – PLOS ONE

Antibiotics

A new antibiotic kills pathogens without detectable resistance – Losee L. Ling – Nature

Phages and viruses

Impact of Spontaneous Prophage Induction on the Fitness of Bacterial Populations and Host-Microbe Interactions – Arun M. Nanda – Journal of Bacteriology

More microbes

The Rebirth of Culture in Microbiology through the Example of Culturomics To Study Human Gut Microbiota – Jean-Christophe Lagier – Clinical Microbiology Reviews

Current and Past Strategies for Bacterial Culture in Clinical Microbiology – Jean-Christophe Lagier – Clinical Microbiology Reviews

Microbes in the news

How bacteria control their size – Diana Lutz – Washington University in St. Louis

Nestlé Health Science Invests $65M in Microbiome Therapy Startup – Drug Discovery and Development
Deep bacteria may evolve even without passing genes on – Colin Barras – New Scientist

Enough with the cleaning – it’s time we stopped giving bacteria such a hard time – Emer Sexton – Irish Examiner

Skin microbes trigger specific immune responses – Science Daily

Beer, bread yeast-eating bacteria aid human health – Science Daily

Science, publishing, career

Outreach: Speak up for science – Virginia Gewin – Nature

Science at risk as young researchers increasingly denied research grants – Phys.org

Science, in the Words of Alan Alda – Jessica Lahey – The Atlantic

University or University of Life? Neither provides workers with necessary people skills – Science Daily

English Is the Language of Science. That’s lousy luck for scientists in most of the world – Boer Deng – Slate.com

Bik’s Picks

Forget the selfish gene: Evolution of life is driven by the selfish ribosome, research suggests – Science Daily

Search for the First True Alien Earth Heats Up – Mike Wall – Space.com

[hr]

January 5, 2015

Posted on by

Happy New Year!

Human oral microbiome

Salivaomics – David T.W. Wong – The Journal of the American Dental Association

Human respiratory microbiome

The Bergen COPD microbiome study (MicroCOPD): rationale, design, and initial experiences – Rune Grønseth – European Clinical Respiratory Journal

Human skin microbiome

Interactions between host factors and the skin microbiome – Adam SanMiguel, Elizabeth A. Grice – Cellular and Molecular Life Sciences

Molecular Characterization of the Skin Fungal Microbiota in Patients with Seborrheic Dermatitis – Akiomi Tanaka – Clinical & Experimental Dermatology Research

Human gut microbiome

Microbiota-Mediated Inflammation and Antimicrobial Defense in the Intestine – Silvia Caballero and Eric G. Pamer – Annual Review of Immunology

* Role of the intestinal microbiota and fecal transplantation in inflammatory bowel diseases – Jie Liang – Journal of Digestive Diseases

Special Issue: Faecal transplantation and infectious diseases practitioners – D. Raoult – Clinical Microbiology and Infection

Human Clostridium difficile infection: Inhibition of NHE3 and microbiota profile – Melinda A Engevik – American Journal of Physiology – Gastrointestinal and Liver Physiology

Gut Fungal Microbiota: The Yin and Yang of Inflammatory Bowel Disease –
Richard, Mathias L. – Inflammatory Bowel Diseases

Gut-Microbiota and Mental Health: Current and Future Perspectives –
Ajit Kumar Thakur – Journal of Pharmacology & Clinical Toxicology

Microbiota, Biofilms and Helicobacter Pylori in the Diseases of Gastroduodenal Zone – G.Sh. Isaeva , V.B. Ziatdinov – Kazan Medical Journal

Prebiotic intake reduces the waking cortisol response and alters emotional bias in healthy volunteers – Kristin Schmidt – Psychopharmacology

The Human Microbiome, Ecological Ontology, and the Challenges of Community – Gregory W. Schneider and Russell Winslow – Perspectives in Biology and Medicine

Microbiome of pregnancy and birth

* Temporal dynamics of the very premature infant gut dominant microbiota – Fabien Aujoulat – BMC Biology

The Preterm Placental Microbiome Varies in Association with Excess Maternal Gestational Weight Gain – Kathleen M. Antony – American Journal of Obstetrics and Gynecology

* Study in 2 million children: Cesarean Section and Chronic Immune Disorders – Astrid Sevelsted – Pediatrics

Animal models

Directed shift of vaginal microbiota induced by vaginal application of sucrose gel in rhesus macaques – Kai-tao Hu – International Journal of Infectious Diseases

Investigating the long-term effect of subchronic phencyclidine-treatment on novel object recognition and the association between the gut microbiota and behavior in this animal model of schizophrenia – B. Pyndt Jørgensen – Physiology & Behavior

Red Ginseng and Semen Coicis can improve the structure of gut microbiota and relieve the symptoms of ulcerative colitis – Mingzhang Guo – Journal of Ethnopharmacology

Animal microbiome

Stability of the Gorilla Microbiome Despite SIV Infection – Andrew H. Moeller – Molecular Ecology

Antiviral immunity of Anopheles gambiae is highly compartmentalized, with distinct roles for RNA interference and gut microbiota – Guillaume Carissimo – PNAS USA

* Microbiota shifts in the surface mucopolysaccharide layer of corals transferred from natural to aquaria settings – Zoe A. Pratte – Journal of Invertebrate Pathology

Sponging up metals: Bacteria associated with the marine sponge Spongia officinalis – Cléa Bauvais – Marine Environment Research

Plant microbiome

Host identity is a dominant driver of mycorrhizal fungal community composition during ecosystem development – Laura B. Martínez-García – New Phytologist

* A Model to Explain Plant Growth Promotion Traits: A Multivariate Analysis of 2,211 Bacterial Isolates – Pedro Beschoren da Costa – PLOS ONE

The application of Arabidopsis thaliana in studying tripartite interactions among plants, beneficial fungal endophytes and biotrophic plant-parasitic nematodes – Alfonso Martinuz – Planta

Differences in thallus chemistry are related to species-specific effects of biocrust-forming lichens on soil nutrients and microbial communities – Manuel Delgado-Baquerizo – Functional Ecology

Halotolerant PGPRs Prevent Major Shifts in Indigenous Microbial Community Structure Under Salinity Stress – Nidhi Bharti – Microbial Ecology

Promoting effect of Fusarium oxysporum [f.sp. strigae] on abundance of nitrifying prokaryotes in a maize rhizosphere across soil types – Mary K. Musyoki – Biological Control

Preferential allocation, physio-evolutionary feedbacks, and the stability and environmental patterns of mutualism between plants and their root symbionts – James D. Bever – New Phytologist

Fungi in the future: interannual variation and effects of atmospheric change on arbuscular mycorrhizal fungal communities – T. E. Anne Cotton – New Phytologist

Soil and sediment microbiome

Prevalence of Antibiotic Resistance Genes and Bacterial Pathogens in Long-Term Manured Greenhouse Soils As Revealed by Metagenomic Survey – Hua Fang – Environmental Science & Technology

Water Content Differences Have Stronger Effects than Plant Functional Groups on Soil Bacteria in a Steppe Ecosystem – Ximei Zhang – PLOS ONE
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0115798

A Novel Sister Clade to the Enterobacteria Microviruses (family Microviridae) Identified in Methane Seep Sediments – Sam Bryson – Environmental Microbiology

Dynamics of Plant Nutrients, Utilization and Uptake, and Soil Microbial Community in Crops Under Ambient and Elevated Carbon Dioxide – Shardendu K. Singh – Nutrient Use Efficiency: from Basics to Advances

Water microbiome

Physical controls of variability in North Atlantic phytoplankton communities – Andrew D. Barton – Limnology and Oceanography

Origins and environmental mobility of antibiotic resistance genes, virulence factors, and bacteria in a tidal creek’s watershed – Andrei L. Barkovskii – Journal of Applied Microbiology

Unraveling the interactive effects of climate change and oil contamination on laboratory-simulated estuarine benthic communities – Francisco J. R. C. Coelho – Global Change Biology

The Food Web of Boiling Springs Lake Appears Dominated by the Heterolobosean Tetramitus thermacidophilus Strain BSL – William H.H. Reeder IV – Journal of Eukaryotic Microbiology

Microbiome of digesters and wastewater

Pyrosequencing of mcrA and Archaeal 16S rRNA Genes Reveals Diversity and Substrate Preferences of Methanogen Communities in Anaerobic Digesters – David Wilkins – Applied and Environmental Microbiology

Association of Biodiversity with the Rates of Micropollutant Biotransformations among Full-Scale Wastewater Treatment Plant Communities – David R. Johnson – Applied and Environmental Microbiology

Microbial Community Structure and Diversity in an Integrated System of Anaerobic-Aerobic Reactors and a Constructed Wetland for the Treatment of Tannery Wastewater in Modjo, Ethiopia – Adey Feleke Desta – PLOS ONE

Enhancement of sludge granulation in anaerobic acetogenesis by addition of nitrate and microbial community analysis – Yang Li – Biochemical Engineering Journal

Microbiome of the built environment

* Indoor Fungi: Companions and Contaminants – A. Nevalainen – Indoor Air

Food microbiology

Evaluation of microbial diversity in the pilot-scale beer brewing process by culture-dependent and culture-independent method – M. Takahashi – Journal of Applied Microbiology

Pyrosequencing vs. culture-dependent approaches to analyze lactic acid bacteria associated to chicha, a traditional maize-based fermented beverage from Northwestern Argentina – Patricia Elizaquível – International Journal of Food Microbiology

Metagenomics

Bacterial Phylogenetic Reconstruction from Whole Genomes Is Robust to Recombination but Demographic Inference Is Not – Jessica Hedge, Daniel J. Wilson – mBio

Reply to “Expanding the Conversation on High-Throughput Virome Sequencing Standards To Include Consideration of Microbial Contamination Sources” – Jason T. Ladner – mBio

Metabolomics

Response of Peripheral Rhythms to the Timing of Food Intake – Megumi Hatori, Satchidananda Panda – Methods in Enzymology

Techniques

The near-quantitative sampling of genomic DNA from various food-borne Eubacteria – Peter Irwin – BMC Microbiology

Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system – Patrick D. Schloss preprint

Preparation and Analysis of Metatranscriptomic Libraries in Petroleum Hydrocarbon Microbe Systems – Jarrad T. Hampton-Marcell – Springer Protocols Handbooks

Protocols for Handling, Storing, and Cultivating Oil Sands Tailings Ponds Materials for Microbial and Molecular Biological Study – J. M. Foght – Springer Protocols Handbooks

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples (video) – Yan Wei Lim – JOVE

Microbes in the news

Book: Principals of Microbial Diversity – James W. Brown – ASM Press

Bacteria hold clues to our health – Heather Kelly – CNN

11+ things everyone needs to know about microbes – Jonathan Eisen – MicrobeNet

How to Build a Healthy Microbiome, Before, During, and After Birth – Kelly Brogan – Mercola.com

Mining the microbiome: How the microbes that share our bodies could help prevent cancer – Leigh MacMillan – Vanderbilt-Ingram

The Surprising Link Between Gut Bacteria And Anxiety – Carolyn Gregoire – Huffington Post

Stress, Depression, & The Bacteria In Your Gut – Video with Professor John F. Cryan – Richard Zwolinski – PsychCentral

Really shameful overselling the microbiome from the American Society for Microbiology regarding lupus – Jonathan Eisen – The Tree of Life

Gut Microbiome Rebounds After Colonoscopy Bowel Preparation – Lara C. Pullen – Medscape

Elevator buttons at hospitals have more bacteria than the toilets – Nicole Oran – MedCityNews

Can Mars be terraformed with bacteria? The Cyano Knights think so! Scott Sutherland – The Weather Network

Cholera’s Method of Killing Identified – Jim Algar – Tech Times

Science, publishing and career

A Stronger Post-Publication Culture Is Needed for Better Science – Hilda Bastian – PLOS Medicine

Advocating for women in hiring decisions – Dr. Mellivora – Tenure She Wrote

Science and art

Stylish Silk Scarves, Dyed With Bacteria – Liz Stinson – Wired.com

Bik’s Picks

The global distribution of diet breadth in insect herbivores – Matthew L. Forister – PNAS USA

‘Bad luck’ of random mutations plays predominant role in cancer, study shows – Science Daily

Experimental Diet Pill Tricks Body into Thinking It Ate – Bahar Gholipour – Live Science

[hr]

December 30, 2014

Posted on by

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

[hr]

December 26, 2014

Posted on by

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

[hr]

December 23, 2014

Posted on by

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

[hr]

December 18, 2014

Posted on by

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

[hr]

 

 

Microbiome digest, December 8, 2014

Posted on by

Human microbiome general

The human microbiome: opportunities and challenges for clinical care – Geraint B. Rogers – Internal Medicine Journal

Evaluative Profiling of Arsenic Sensing and Regulatory Systems in the Human Microbiome Project Genomes – Raphael D Isokpehi – Microbiology Insights

Human oral microbiome

* High resolution taxonomic profiling of the subgingival microbiome for biomarker discovery and periodontitis diagnosis – Szymon P. Szafranski – Applied and Environmental Microbiology

Human gut microbiome

Crosstalk at the mucosal border: importance of the gut microenvironment in IBS – Lena Öhman – Nature Reviews Gastroenterology & Hepatology

Antimicrobial resistance characteristics and fitness of Gram negative faecal bacteria from volunteers treated with minocycline or amoxicillin – Miranda Kirchner – Frontiers in Microbiology

Decrease in lactobacilli in the intestinal microbiota of celiac children with a gluten-free diet, and selection of potentially probiotic strains – María J. Lorenzo Pisarello – Canadian Journal of Microbiology

Safety assessment of genetically modified rice expressing human serum albumin from urine metabonomics and fecal bacterial profile – Xiaozhe Qi – Food and Chemical Toxicology

Pregnancy and birth microbiome

Placental Microbiome and Its Role in Preterm Birth – Bin Cao – NeoReviews

High A. vaginae and G. vaginalis vaginal loads are associated with preterm birth – Florence Bretelle – Clinical Infectious Diseases

Cesarean Section and Chronic Immune Disorders – Astrid Sevelsted – Pediatrics

Animal and other models of microbiome research

Intestinal epithelial ​MyD88 is a sensor switching host metabolism towards obesity according to nutritional status – Amandine Everard – Nature Communications

Bugs and Food: A Recipe for Cancer? – Christina L. Ohland, Christian Jobin – Cell Metabolism

The current provided by oxygen-reducing microbial cathodes is related to the composition of their bacterial community – Mickaël Rimboud – Bioelectrochemistry

Animal microbiome

The putative functional ecology and distribution of archaeal communities in sponges, sediment and seawater in a coral reef environment – Ana R.M. Polónia – Molecular Ecology

Plant microbiome

* The role of bacteria and mycorrhiza in plant sulfur supply – Jacinta M. Gahan and Achim Schmalenberger – Frontiers in Plant Science

Arctic fungal communities associated with roots of Bistorta vivipara do not respond to the same fine-scale edaphic gradients as the aboveground vegetation – Sunil Mundra – New Phytologist

Soil and sediment microbiome

Impacts of altered precipitation regimes on soil communities and biogeochemistry in arid and semi-arid ecosystems – Uffe N. Nielsen – Global Change Biology

* Effects of tree identity dominate over tree diversity on the soil microbial community structure – Andrea Scheibe – Soil Biology and Biochemistry

Smooth brome invasion increases rare soil bacterial species prevalence, bacterial species richness and evenness – Candace L. Piper – Journal of Ecology

The interactive effects of elevated ozone and wheat cultivars on soil microbial community composition and metabolic diversity – Xuelian Bao – Applied Soil Ecology

Seasonal variations of the composition of microbial biofilms in sandy tidal flats: Focus of fatty acids, pigments and exopolymers – Claire Passarelli – Estuarine, Coastal and Shelf Science

Pharmaceuticals in the environment: Biodegradation and effects on natural microbial communities. A Review – Anna Barra Caracciolo – Journal of Pharmaceutical and Biomedical Analysis

Water microbiome

Successional Change in Microbial Communities of Benthic Phormidium-Dominated Biofilms – Katie A. Brasell – Microbial Ecology

Microbiome of the built environment

Characterizing airborne fungal and bacterial concentrations and emission rates in six occupied children’s classrooms – D. Hospodsky – Indoor Air

Food microbiology

Analysis of the bacterial community in aged and aging pit mud of Chinese Luzhou-flavour liquor by combined PCR-DGGE and quantitative PCR assay – Huipeng Liang – Journal of the Science of Food and Agriculture

Phages and viruses

Emerging methods to study bacteriophage infection at the single-cell level – Vinh T. Dang and Matthew B. Sullivan – Frontiers in Microbiology

Metabolomics

* The Community Ecology of Microbial Molecules – Robert A. Quinn, Theodore Alexandrov – Journal of Chemical Ecology

Ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry for rapid analysis of the metabolites of morroniside produced by human intestinal bacteria – Min Zhao – Journal of Chromatography B

Small-intestinal or colonic microbiota as a potential amino acid source in animals – Werner G. Bergen – Amino Acids

Techniques

Comparative assessment of next-generation sequencing, denaturing gradient gel electrophoresis, clonal restriction fragment length polymorphism and cloning-sequencing as methods for characterizing commercial microbial consortia – A.D. Samarajeewa – Journal of Microbiological Methods

Microbes in the news

Now We Know Some Creepy Things About How Penicillin Destroys Bacteria – Esther Inglis-Arkell – IO9

Arctic bacteria converts mercury – Kristian Sjøgren – ScienceNordic

Should I Eat Greek Yogurt? – Mandy Oaklander – Time

CSU team examines dairy-cattle microorganisms to improve food safety – Kristen Browning-Blas – Bovine Vet Online

Glyphosate used with GMO crops under attack for disrupting microbiome: Science or a gut feeling? – David Warmflash – Genetic Literacy Project

#BacteriaHysteria: Why it’s time to detox your desk: Average worker comes into contact with more than 10 MILLION disease-causing bacteria lurking on their keyboard, phone and mouse – Lizzie Parry – Daily Mail

Bik’s Picks

The Yearbook: Our list of newsmakers this year – Manasi Vaidya & Shraddha Chakradhar – Nature Medicine

Notable advances 2014 – Amanda Keener – Nature Medicine

Let’s face it, for robots, falling down is easy. But how do you teach them to land safely? – Maki Naro – Popular Science

Force-feeding a human to a snake is not science (and is also super dumb) – Rachel Feltman – Washington Post

[hr]

Microbiome digest, December 4, 2014

Posted on by

Human (gut and other) microbiome

* Temporal variability is a personalized feature of the human microbiome – Gilberto E Flores – Genome Biology

The rest of the story: the microbiome and gastrointestinal infections – Jhansi L Leslie, Vincent B Young – Current Opinion in Microbiology

* Gut Microbiota Elicits a Protective Immune Response against Malaria Transmission – Bahtiyar Yilmaz – Cell

Pregnancy and birth

The infant airway microbiome in health and disease impacts later asthma development –
Shu Mei Teo – BioRxiv

Animal models of microbiome research

Dietary Yeasts Reduce Inflammation in Central Nerve System via Microflora – Kazushiro Takata – Annals of Clinical and Translational Neurology

Effects of dietary supplementation of modified zinc oxide on growth performance, nutrient digestibility, blood profiles, fecal microbial shedding and fecal score in weanling pigs –

Jin Ho Cho – Animal Science Journal

Bioinformatics

ITScan: a web-based analysis tool for Internal Transcribed Spacer (ITS) sequences – Milene Ferro – BMC Research Notes

Next generation sequencing reads comparison with an alignment-free distance – Emanuel Weitschek – BMC Research Notes

Microbes in the news

Go Ahead, Use the Restroom – Nicholas Bakalar – New York Times

Trusting your gut, and the importance of your microbiome: Words on Wellness – Daniel Neides – Cleveland.com

Microbiome component fights malaria – Bradley J. Fikes – UT San Diego

Gut Microbes May Play a Role in AS – Diana Swift – MedPageToday

Science, publishing, and career

Getting Credit for Data – Eric Martens and Jennifer Lin – PLOS Blogs

What do young scientists want? – Beryl Lieff Benderly – Science Careers

Why Don’t More Minority Students Seek Careers In STEM Fields? – David Orenstein – RedOrbit

Bik’s Picks

Revealed: 100 safety breaches at UK labs handling potentially deadly diseases – Ian Sample – The Guardian

Why DNA pioneer James Watson just sold his Nobel Prize for $4.1 million – Susannah Locke – Vox.com

The Corrupting Power of Cancer – Lauren Richardson – PLOS Blogs

Is The Food Babe A Fearmonger? Scientists Are Speaking Out – Maria Godoy – NPR The Salt

[hr]

Microbiome digest, December 2, 2014

Posted on by

General microbiome

Microbiome, holobiont and the net of life – Emiliano Salvucci – Critical Reviews in Microbiology

Pregnancy and birth

Infectious Causes of Necrotizing Enterocolitis – Sarah A. Coggins – Clinics in Perinatology

Human oral microbiome

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

Oral Microbiota in Crevices Around Dental Implants: Profiling of Oral Biofilm – Takuichi Sato – Interface Oral Health Science

Human respiratory microbiome

* Temporal profiling of the bacterial and fungal communities in ΔF508 adult cystic fibrosis sputum – Andrew Nelson – PeerJ Preprint

Human gut microbiome

* Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production – Gary D Wu – Gut

Microbiome of death

* Initial insights into bacterial succession during human decomposition – Embriette R. Hyde – International Journal of Legal Medicine

Animal and other models of microbiome research

Natural killer T cells play a necessary role in modulating of immune-mediated liver injury by gut microbiota – Jianing Chen – Scientific Reports

Effect of stoned olive pomace on rumen microbial communities and polyunsaturated fatty acids biohydrogenation: an in vitro study – Grazia Pallara – BMC Veterinary Research

Successional changes in the chicken cecal microbiome during 42 days of growth are independent of organic acid feed additives – Brian B Oakley – BMC Veterinary Research

Animal microbiome

The role of host phylogeny varies in shaping microbial diversity in the hindguts of lower termites – Vera Tai – Applied and Environmental Microbiology

Plant microbiome

Relocation, high-latitude warming and host genetic identity shape the foliar fungal microbiome of poplars – Miklós Bálint – Molecular Ecology

Soil and sediment microbiome

Distribution of sediment bacterial and archaeal communities in plateau freshwater lakes – Jingxu Zhang – Applied Microbiology and Biotechnology

Effects of Phragmites invasion on soil microbial activity and structure in a brackish marsh – Keunyea Song – Plant and Soil

Water microbiome

* High temporal and spatial diversity in marine RNA viruses implies that they have an important role in mortality and structuring plankton communities – Julia A. Gustavsen – Frontiers in Microbiology

Impact of atmospheric deposition on the metabolism of coastal microbial communities

Sandra Martínez-García – Estuarine, Coastal and Shelf Science

Assessment of Bacterial and Archaeal Community Structure in Swine Wastewater Treatment Processes – Marcio Luis Busi Da Silva – Microbial Ecology

Food microbiology

Evaluation of microbial diversity in the pilot-scale beer brewing process by culture-dependent and culture-independent method – Masayuki Takahashi- Journal of Applied Microbiology

Pre- and probiotics

Recent developments in prebiotics to selectively impact beneficial microbes and promote intestinal health – Robert A. Rastall , Glenn R. Gibson – Current Opinion in Biotechnology

* The domestication of the probiotic bacterium Lactobacillus acidophilus – Matthew J. Bull – Scientific Reports

Microbes in the news

Mining industry could benefit from Wheatbelt discovery of salt and acid tolerant bacteria – Lucinda Jose – ABC Australia

Science, publishing, and career

The never-ending Ph.D. – By Adam Ruben – Science Careers

Clueless Reporter from the Mirror Bases Story on Withdrawn OMICS Publishing Group Article – Jeffrey Beall – ScholaryOA

The Next Enlightenment: Sharing Science With the World – Marietta DiChristina – Huffington Post

Bik’s Picks

Actor Alan Alda Challenges Scientists to Explain ‘What is Sleep?’ – Laura Geggel – LiveScience

Ability to consume alcohol may have shaped primate evolution – Sarah C. P. Williams – Science News

#Shirtgate inspires a Kickstarter for shirts covered in (science) ladies – Rachel Feltman – Washington Post

[hr]

Microbiome digest, November 21, 2014

Posted on by

Microbiome general

Rare biosphere exploration using high-throughput sequencing: research progress and perspectives – Aibin Zhan, Hugh J. MacIsaac – Conservation Genetics

Human oral microbiome

Polymicrobial synergy and dysbiosis in inflammatory disease – Richard J. Lamonta, George Hajishengallis – Trends in Molecular Medicine

Human skin microbiome

* Dialogue between skin microbiota and immunity – Yasmine Belkaid, Julia A. Segre – Science

Human respiratory microbiome

Asthma 2014: from monoclonals to the microbiome – Peter G Gibson, Paul S Foster – The Lancet Respiratory Medicine

Human gut microbiome

Development of Fecal Microbiota Transplantation Suitable for Mainstream Medicine – Alexander Khoruts – Clinical Gastroenterology and Hepatology

The role of the gut and microbes in the pathogenesis of spondyloarthritis – Mark Asquith – Best Practice & Research Clinical Rheumatology

From lifetime to evolution: timescales of human gut microbiota adaptation – Sara Quercia – Frontiers in Microbiology

Animal and other models of microbiome research

Development of aminoglycoside and β-lactamase resistance among intestinal microbiota of swine treated with lincomycin, chlortetracycline, and amoxicillin – Jian Sun – Frontiers in Microbiology

Model systems to analyze the role of miRNAs and commensal microflora in bovine mucosal immune system development – Guanxiang Liang – Molecular Immunology

Gut Microbial Colonization Orchestrates TLR2 Expression, Signaling and Epithelial Proliferation in the Small Intestinal Mucosa – Nives Hörmann – PLOS ONE

The effects of elevated CO2 concentration on competitive interaction between aceticlastic and syntrophic methanogenesis in a model microbial consortium – Souichiro Kato – Frontiers in Microbiology

Animal microbiome

Aerobic cloacal and pharyngeal bacterial flora in six species of free-living birds – J. Stenkat – Journal of Applied Microbiology

Plant microbiome

Expanding genomics of mycorrhizal symbiosis – Alan Kuo – Frontiers in Microbiology

Soil and sediment microbiome

* Impact of interspecific interactions on antimicrobial activity among soil bacteria – Olaf Tyc – Frontiers in Microbiology

* Application of ancient DNA to the reconstruction of past microbial assemblages and for the detection of toxic cyanobacteria in subtropical freshwater ecosystems – Gabriela Martínez de la Escalera – Molecular Ecology

Characterisation of the soil microbial community of cultivated and uncultivated vertisol in Australia under several management regimes – Karuna Shrestha – Agriculture, Ecosystems & Environment

Wastewater reuse in irrigation: A microbiological perspective on implications in soil fertility and human and environmental health – Cristina Becerra-Castro – Environment International

Kotuikan Formation assemblage: a diverse organic-walled microbiota in the Mesoproterozoic Anabar succession, northern Siberia – Natalya G. Vorob’eva – Precambrian Research

Water microbiome

Diurnal expression of SAR11 proteorhodopsin and 16S rRNA genes in coastal North Atlantic waters – Raphaël Lami, David L. Kirchman – Aquatic Microbial Ecology

Leaf-litter-associated fungi and bacteria along temporal and environmental gradients in boreal streams – Jenny Bergfur, Carina Sundberg – Aquatic Microbial Ecology

Seasonal variation in marine-snow-associated and ambient-water prokaryotic communities in the northern Adriatic Sea – Jana Vojvoda – Aquatic Microbial Ecology

Microbial eukaryote diversity in the marine oxygen minimum zone off northern Chile – Darren J. Parris – Frontiers in Microbiology

* Resolving the abundance and air-sea fluxes of airborne microorganisms in the North Atlantic Ocean – Eva Mayol – Frontiers in Microbiology

Microbial contributions to coupled arsenic and sulfur cycling in the acid-sulfide hot spring Champagne Pool, New Zealand – Katrin Hug – Frontiers in Microbiology

Food microbiology

* Unpasteurised commercial boza as a source of microbial diversity – Andrea Osimani – International Journal of Food Microbiology

Metabolomics

* Prediction and quantification of bioactive microbiota metabolites in the mouse gut –
Gautham V. Sridharan – Nature Communications

An isotope-labeled chemical derivatization method for the quantitation of short-chain fatty acids in human feces by liquid chromatography–tandem mass spectrometry – Jun Han – Analytica Chimica Acta

Metagenomics / Bioinformatics

Key roles for freshwater Actinobacteria revealed by deep metagenomic sequencing – Rohit Ghai – Molecular Ecology

* BiomeNet: A Bayesian Model for Inference of Metabolic Divergence among Microbial Communities – Mahdi Shafiei – PLOS Computational Biology

Phylogeny and phylogeography of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships – Maggie C. Y. Lau – Frontiers in Microbiology

Techniques

Microbial Contamination in Next Generation Sequencing: Implications for Sequence-Based Analysis of Clinical Samples – Michael J. Strong – PLOS Pathogens

Comparing High-throughput Platforms for Sequencing the V4 Region of SSU-rDNA in Environmental Microbial Eukaryotic Diversity Surveys – Frédéric Mahé – Journal of Eukaryotic Microbiology

More microbiology papers

The Red Queen Model of Recombination Hotspots Evolution in the Light of Archaic and Modern Human Genomes – Yann Lesecque – PLOS Genetics

Association between Footwear Use and Neglected Tropical Diseases: A Systematic Review and Meta-Analysis – Sara Tomczyk – PLOS Neglected Tropical Diseases

Impact of wash cycle time, temperature and detergent formulation on the hygiene effectiveness of domestic laundering – M. Honisch – Journal of Applied Microbiology

Microbes in the news

Contaminated samples point the finger at the wrong suspects – Dalmeet Chawla – Imperial College London

Analyzing COPD Patients’ Sputum And Microbiota Composition Might Improve Treatment – Isaura Santos – Lung Disease News

Willy Burgdorfer, Who Found Bacteria That Cause Lyme Disease, Is Dead at 89 – William Yardley – The New York Times

Plants talk to each other using an internet of fungus – Nic Fleming – BBC

Bacteria on Russian ‘sex satellite’ survive reentry – Alec Luhn – The Guardian

Body’s bacteria may keep our brains healthy – Elizabeth Pennisi – Science Magazine

Hand dryers ‘splatter’ users with bacteria, scientists warn – Sarah Knapton – Telegraph UK

Unique sense of ‘touch’ gives a prolific bacterium its ability to infect anything – Morgan Kelly – Princeton

Science, publishing and career

Gates Foundation announces world’s strongest policy on open access research – Richard Van Noorden – Nature News Blog

Bogus Journal Accepts Profanity-Laced Anti-Spam Paper – Jeffrey Beal – Scholarly Open Access

* Sh*t My Reviewers Say – Collecting the finest real specimens of reviewer comments since 1456

Ten Simple Rules to Achieve Conference Speaker Gender Balance – Jennifer L. Martin – PLOS ONE

Bik’s Picks

Shedding light on skin color – Ann Gibbons – Science

Flashback Friday: Does garlic protect against vampires? An experimental study – Seriously Science – Discover Magazine

The Secret Life of Passwords – Ian Urbina – New York Times

[hr]