Category Archives: Food Microbiology

February 3, 2015

Posted on by

Pregnancy and birth

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

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

Human oral microbiome

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

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

Human respiratory microbiome

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

Human gut microbiome

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

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

Animal microbiome

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

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

Plant microbiome

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

Soil microbiome

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

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

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

Water microbiome

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

Microbiome of the built environment

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

Bioreactor microbiome

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

Food microbiology

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

Techniques

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

Bioinformatics, metagenomics

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

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

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

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

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

Book: Biocode: The New Age of Genomics

Phages and viruses

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

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

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

Microbes in the news

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

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

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

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

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

Teaching phylogenetics with DUPLO – Erik Pelve – The Third Domain

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

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

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

Science, publishing, and career

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

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

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

Bik’s Picks

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

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

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

[hr]

January 28, 2015

Posted on by

I will be traveling to visit family in the upcoming week, so there might not be a post every day. But I will do my best to keep y’all up to date with the microbiome literature. In today’s installment, there are articles about skin microbiome around abscesses, misclassifications of bacteria in Genbank, archaea and rice plant roots. Also, if you like chicken wings with Campylobacter, you should have put some sauce on it.

General microbiome

Crystal Ball: Human microbiota: ‘The philosophers have only interpreted the world in various ways. The point, however, is to change it’ – Harald Brüssow – Microbial Biotechnology

Human skin microbiome

The cutaneous microbiome in out-patients presenting acutely with skin abscesses – James M. Horton – Journal of Infectious Diseases

Animal and other models for microbiome research

In Vitro Investigation of the Effect of Oral Bacteria in the Surface Oxidation of Dental Implants – Sathyanarayanan Sridhar – Clinical Implant Dentistry and Related Research

Lentinula edodes-Derived Polysaccharide Alters the Spatial Structure of Gut Microbiota in Mice – Xiaofei Xu – PLOS ONE

Animal microbiome

New Light on the Systematics of Fungi Associated with Attine Ant Gardens and the Description of Escovopsis kreiselii sp. nov. – Lucas A. Meirelles – PLOS ONE

Plant microbiome

Characterization of the cultivable bacterial populations associated with field grown Brassica napus L.: an evaluation of sampling and isolation protocols– Sarah Croes – Environmental Microbiology

Colonization of rice roots with methanogenic archaea controls photosynthesis-derived methane emission – Judith Pump – Environmental Microbiology

Soil and rock microbiome

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

Water microbiome

Disentangling seasonal bacterioplankton population dynamics by high-frequency sampling– Markus V. Lindh – Environmental Microbiology

Combined effects of zooplankton grazing and dispersal on the diversity and assembly mechanisms of bacterial metacommunities – Mercè Berga – Environmental Microbiology

Review: Marine Snow: A Brief Historical Sketch – Mary Silver – Limnology and Oceanography Bulletin

Food microbiology

Just in time for the Superbowl: The Antimicrobial Effect of Spice-Based Marinades against Campylobacter jejuni on Contaminated Fresh Broiler Wings – Gintarė Zakarienė – Journal of Food Science

Metagenomics

Strategies to Avoid Wrongly Labelled Genomes Using as Example the Detected Wrong Taxonomic Affiliation for Aeromonas Genomes in the GenBank Database – Roxana Beaz-Hidalgo – PLOS ONE

Metabolomics

Dominant components of the Thoroughbred metabolome characterised by 1H-nuclear magnetic resonance spectroscopy: A metabolite atlas of common biofluids – E. E. Escalona – Equine Veterinary Journal

New Techniques

DNA sequencing using ​polymerase substrate-binding kinetics – Michael John Robert Previte – Nature Communications

Single cell biotechnology to shed a light on biological ‘dark matter’ in nature – Wei E. Huang – Microbial Biotechnology

Ecology

Natural Variation in Preparation for Nutrient Depletion Reveals a Cost–Benefit Tradeoff – Jue Wang – PLOS Biology

Review: Is successional research nearing its climax? New approaches for understanding dynamic communities – Scott J. Meiners – Functional Ecology

Editorial: Beyond borders: investigating microbiome interactivity and diversity for advanced biocontrol technologies – Gabriele Berg – Microbial Biotechnology

Microbes in the news

Skin abscesses displayed distinct cutaneous microbiota – Healio

Stress during pregnancy related to infant gut microbiota – HealthCanal

Fatal peanut allergies could be cured by probiotic bacteria, say Australian doctors – Jonathan Pearlman – The Telegraph

UF researcher gets grant to study probiotics’ effects – Jeff Schweers – Gainesville

Science, publishing and career

Not your average technician: Research relies on unsung heroes working behind the scenes — and some of them have rather unusual jobs – Michael Hopkin – Nature

Career counselling: Pick a path – Neil Savage – Nature

Inclusivity: Mentor matters – Nature

FactChecking Science-based Claims – FactCheck.org
http://www.factcheck.org/2015/01/factchecking-science-based-claims/

Bik’s Picks

Did genetic links to modern maladies provide ancient benefits? – Science Daily

Skull discovery suggests location where humans first had sex with Neanderthals – The Guardian

Spiders Spin Electrically Charged Silk To Make It Sticky – Marissa Fessenden – Smithsonian

[hr]

January 20, 2015

Posted on by

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

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

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

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

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

Human respiratory microbiome

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

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

Human gut microbiome

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

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

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

Pregnancy and birth

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

Animal models of microbiome research

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

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

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

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

Animal microbiome

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

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

Plant microbiome

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

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

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

Soil microbiome

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

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

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

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

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

Water microbiome

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

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

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

Microbiome of the built environment

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

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

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

Bioreactor microbiology

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

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

Food microbiology

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

Viruses and phages

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

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

Metagenomics

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

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

Metabolomics

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

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

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

Microbes in the news

Can the Microbiome Mutiny? – Carl Zimmer – National Geographic

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

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

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

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

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

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

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

Science, publishing, and career

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

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

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

Science and art

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

Bik’s Picks

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

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

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

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

[hr]

January 19, 2015

Posted on by

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

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

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

Human oral microbiome

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

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

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

Microbiome of pregnancy and birth

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

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

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

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

Animal models of microbiome research

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

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

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

Animal microbiome

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

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

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

Plant microbiome

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

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

Soil and sediment microbiome

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

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

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

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

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

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

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

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

Water microbiome

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

Microbiome of the built environment

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

Food microbiology

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

Metagenomics

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

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

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

Metabolomics, transcriptomics, and proteomics

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

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

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

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

Bioinformatics

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

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

Amplification and sequencing techniques

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

Probiotics

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

Microbes in the news

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

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

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

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

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

#BacteriaHysteria

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

Science, publishing, and career

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

Bik’s Picks

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

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

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

[hr]

January 15, 2015

Posted on by

Human respiratory microbiome

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

Human oral microbiome

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

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

Animal models of microbiome research

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

Animal microbiome

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

Plant microbiome

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

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

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

Soil microbiome

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

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

Water microbiome

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

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

Food microbiology

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

Metagenomics

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

Bioinformatics

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

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

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

Bacteria in the news

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

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

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

The Microbiome Diet: Evolving Past Paleo – Raphael Kellman

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

Science, publishing and career

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

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

Bik’s Picks

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

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

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

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

[hr]

January 14, 2015

Posted on by

Human gut microbiome

Review: Fusobacterium and Escherichia: models of colorectal cancer driven by microbiota and the utility of microbiota in colorectal cancer screening – Andrea Leung – Expert Review of Gastroenterology & Hepatology

Animal microbiome

Passage of Wolbachia pipientis through Mutant Drosophila melanogaster Induces Phenotypic and Genomic Changes – Irene L. G. Newton and Kathy B. Sheehan – Applied and Environmental Microbiology

Water microbiome

Alternative Fecal Indicators and Their Empirical Relationships with Enteric Viruses, Salmonella enterica, and Pseudomonas aeruginosa in Surface Waters of a Tropical Urban Catchment – L. Liang – Applied and Environmental Microbiology

Genomic and proteomic characterization of “Candidatus Nitrosopelagicus brevis”: An ammonia-oxidizing archaeon from the open ocean – Alyson E. Santoro – PNAS USA

More microbiology

Innate sensing of microbial products promotes wound-induced skin cancer – Esther Hoste – Nature Communications

Identifying strains that contribute to complex diseases through the study of microbial inheritance – Jeremiah J. Faith – PNAS USA

Long-term phenotypic evolution of bacteria – Germán Plata – Nature

Co-infection alters population dynamics of infectious disease – Hanna Susi – Nature Communications

Ferment in the family tree – Nathaniel J. Dominy – PNAS USA

Infection and Host response

Profiling lymphocyte interactions at the single-cell level by microfluidic cell pairing – Burak Dura – Nature Communications

B-cell repertoire responses to varicella-zoster vaccination in human identical twins
Chen Wang – PNAS USA

Metabolomics

Next-generation sequencing approach for connecting secondary metabolites to biosynthetic gene clusters in fungi – Ralph A. Cacho – Frontiers in Microbiology

The chemistry of negotiation: Rhythmic, glycan-driven acidification in a symbiotic conversation – Julia A. Schwartzman – PNAS USA

Microbes in the news

I love this title! Featuring Margaret McFall-Ngai: Microbiology: Here’s looking at you, squid – Ed Yong – Nature

How Bread, Beer, and Soy Sauce Changed the Human Microbiome – Francie Diep – Popular Science

Early human microbiome studies may aid modern nutrition science – Nathan Gray – Nutraingredients

Understanding the personalities of bacteria – Phys.org

2014: The Year of the Virus – Joan B. Rose – Huffington Post

Have viruses made us smarter? ‘Junk’ virus genes in our DNA may have helped our brain cells evolve – By Victoria Woollaston – Daily Mail

With Vedanta Deal, Johnson & Johnson Marks Big-Pharma Milestone in the Microbiome – Alex Lash – Xconomy

Scientists developing Teflon for bacteria – Amanda Schupak – CBS News

Understanding the personalities of bacteria – Phys.org

#BacteriaHysteria – beautiful, not filthy! Smartphone bacteria ‘prints’ show how filthy your mobile really is – Rob Waugh – Metro

Science, publishing and career

A generation at risk: Young investigators and the future of the biomedical workforce – Ronald J. Daniels – PNAS USA

Work–life balance: Lab life with kids – Kendall Powell – Nature

Bik’s Picks

‘I can haz genomes’: cats claw their way into genetics – Canine dominance bows to tabby chic as cat sequencing takes off – Ewen Callaway – Nature
and
Out of the bag: The preference for either cats or dogs affects science more than you might think– Nature

Geographically varying associations between personality and life satisfaction in the London metropolitan area – Markus Jokela – PNAS USA

Very important science: Watch a chainsaw made with shark teeth slice through salmon – Francie Diep – Popular Science

[hr]

December 16, 2014

Posted on by

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

[hr]

December 11, 2014

Posted on by

The Bay Area is getting drenched with rain right now, and several leaks in our roof kept me busy with buckets and towels, but the power is still on, so here we go:

Human microbiome general

* Review: The demographic determinants of human microbiome health – Sylvie Estrela – Trends in Microbiology

Human oral microbiome

Salivary Mucins Protect Surfaces from Colonization by Cariogenic Bacteria – Erica Shapiro Frenkel – Applied and Environmental Microbiology

Human gut microbiome

* Effects of the gut microbiota on bone mass – Claes Ohlsson, Klara Sjögren – Trends in Endocrinology & Metabolism

Discovery of a Conjugative Megaplasmid in Bifidobacterium breve – Francesca Bottacini – Applied and Environmental Microbiology

Microbiome of pregnancy and birth

Microbiome of the placenta in pre-eclampsia supports the role of bacteria in the multifactorial cause of pre-eclampsia – Ranmalee Amarasekara – Journal of Obstetrics and Gynaecology Research
Animal and bioreactor models

Optimization of a rapid and efficient analytical pipeline for in-depth metaproteome characterization: evaluation on mock microbial mixtures and application to the mouse gut microbiome – Alessandro Tanca – Microbiome

* Microbial shifts in the aging mouse gut – Morgan GI Langille – Microbiome

Development of human colonic microbiota in the computer-controlled dynamic SIMulator of the GastroIntestinal tract SIMGI – Elvira Barroso – LWT – Food Science and Technology

Protocols for Microcosms for Growing Biofilms on Hydrophobic Substrates: A Polyphasic Approach to Study Biodiversity, Metabolic Activity, and Biofilm Architecture – Wolf-Rainer Abraham – Springer Protocols Handbooks 2014

Animal microbiome

Acidobacteria appear to dominate the microbiome of two sympatric Caribbean Sponges and one Zoanthid – Aileen O¿Connor-Sánchez – Biological Research

Plant microbiome

The impact of systemic and copper pesticide applications on the phyllosphere microflora of tomatoes – Andrea R Ottesen – Journal of the Science of Food and Agriculture

Soil and sediment microbiome

Linkages between the soil organic matter fractions and the microbial metabolic functional diversity within a broad-leaved Korean pine forest – Jing Tian – European Journal of Soil Biology

Carbon sequestration is related to mycorrhizal fungal community shifts during long-term succession in boreal forests – Karina E. Clemmensen – New Phytologist

Comparison of bacterial succession in green waste composts amended with inorganic fertiliser and wastewater treatment plant sludge – Sean Storey – Bioresource Technology

Water microbiome

Initial community and environment determine the response of bacterial communities to dispersant and oil contamination – Alice C. Ortmann – Marine Pollution Bulletin

Initial community and environment determine the response of bacterial communities to dispersant and oil contamination – Alice C. Ortmann, YueHan Lu – Marine Pollution Bulletin

Protistan diversity in a permanently stratified meromictic lake (Lake Alatsee, SW Germany) – Andreas Oikonomou – Environmental Microbiology

Exploration of Microbial Diversity of Taptapani (India) Hot Spring Through Molecular Phylogenetic Analysis – Sudip Kumar Sen – Arabian Journal for Science and Engineering

Food microbiology

Selection of Autochthonous Strains as Starter Cultures for Fermented Fish Products – Barbara Speranza – Journal of Food Science

Microbes in the news

Pregnancy Germs: Friend Or Foe? – How The Maternal Microbiome Influences Pregnancy Health – PR NewsWire / March of Dimes

Study Hints Gut Microbiome Plays A Role in Multiple Sclerosis –
Kate O’Rourke – Gastroenterology and Endoscopy News

“The Great Plate Count Anomaly” that is no more – Gemma Reguera – Small Things Considered ASM

Google Science Fair – Bacteria boosting cereal crop yields – Brett Worthington – ABC Net Australia

Guts of obese dogs look similar to those of obese people – Agata Blaszczak-Boxe – Science Magazine

Baby infected in birthing pool died of Legionnaire’s disease – Bahar Gholipour – CBS News

Science, publishing, and career

Scientists Often Skip A Simple Test That Could Verify Their Work – NPR Morning Edition

Study of massive preprint archive hints at the geography of plagiarism – John Bohannon – Science Insider

Bik’s Picks

Deep Neural Networks are Easily Fooled: High Confidence Predictions for Unrecognizable Images – Anh Nguyen – Arxiv

Three-in-one drug cuts body weight by a third – Nsikan Akpan – Science Magazine

Water vapor on Rosetta’s target comet significantly different from that found on Earth – Science Daily

[hr]

December 10, 2014

Posted on by

Food microbiome

The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types – Jenna M. Lang – PeerJ

Human oral microbiome

Subgingival microbial profiles of Sudanese patients with aggressive periodontitis – H. R. Z. Elabdeen – Journal of Periodontal Research

Human bladder microbiome

Interplay between Bladder Microbiota and Urinary Antimicrobial Peptides: Mechanisms for Human Urinary Tract Infection Risk and Symptom Severity – Vanessa Nienhouse – PLOS ONE

Human gut microbiome

Immunomodulatory Properties of Streptococcus and Veillonella Isolates from the Human Small Intestine Microbiota – Bartholomeus van den Bogert – PLOS ONE

Animal models of microbiome research

The Gut Commensal Bacteroides thetaiotaomicron Exacerbates Enteric Infection through Modification of the Metabolic Landscape – Meredith M. Curtis – Cell Host & Microbe

Gut Microbiota-Produced Succinate Promotes C. difficile Infection after Antibiotic Treatment or Motility Disturbance – Jessica A. Ferreyra – Cell Host & Microbe

Regionally Distinct Alterations in the Composition of the Gut Microbiota in Rats with Streptozotocin-Induced Diabetes – Roland Wirth – PLOS ONE

Animal microbiome

Environmentally Determined Differences in the Murine Lung Microbiota and Their Relation to Alveolar Architecture – Yeojun Yun – PLOS ONE

Bacteria and Methanogens Differ along the Gastrointestinal Tract of Chinese Roe Deer (Capreolus pygargus) – Zhipeng Li – PLOS ONE

Transcriptomic Immune Response of the Cotton Stainer Dysdercus fasciatus to Experimental Elimination of Vitamin-Supplementing Intestinal Symbionts – Eugen Bauer – PLOS ONE

Metabolomics

Stool Phospholipid Signature is Altered by Diet and Tumors – Julie M. Davies – PLOS ONE

Pathogens’ Exploitation of the Intestinal Food Web
Tu Anh Pham N., Trevor D. Lawley – Cell Host & Microbe

Could resistant starch be the redeemer of dietary carbohydrate? – M Denise Robertson – Practical Diabetes

A New Insight into the Physiological Role of Bile Salt Hydrolase among Intestinal Bacteria from the Genus Bifidobacterium – Piotr Jarocki – PLOS ONE

Metagenomics

Maths on microbes: adding microbial ecophysiology to metagenomics – Wilfred F. M. Röling – Microbial Biotechnology

Functional optimization of gene clusters by combinatorial design and assembly – Michael J Smanski – Nature Biotechnology

More microbiology

Microbiology: Ditch the term pathogen – Arturo Casadevall & Liise-anne Pirofski – Nature

New sequencing technique: MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island – Philip M Ashton – Nature Biotechnology

Microbes in the news

NASA ISS On-Orbit Status 5 December 2014: Microbiome Experiment – SpaceRef

Bacteria’s Game of ‘Telephone’ Foils Microbiologists’ Eavesdropping – Kim Krieger – UConnToday

Science, publishing, career

The Point When Science Becomes Publicity – James Hamblin – The Atlantic

No Lovin’ Feeling… for Science Fair – Claire Wapole – Huffington Post

How to cope when things go wrong in academia – Julie Gould – Nature Jobs

Scientific Peer Review Is Broken. We’re Fighting to Fix It With Anonymity – The Founders of PubPeer – Wired.com

Not sure how old this is, but I liked the graph: The illustrated guide to a Ph.D. – Matt Might

Ocean biology: Marine dreams – Chris Woolston – Nature

New postdoc report covers familiar ground – Beryl Lieff Benderly, Jim Austin – Science Careers

Bik’s Picks

Injectable 3-D vaccines could fight cancer, infectious diseases – ScienceDaily

Glittering Nobel Gown Represents Scientist’s Work – Joanne Manaster – Scientific American

This Commuter Bus Runs On Poop- A U.K.-based biogas plant has developed a 40-seater than runs on converted sewage and food waste – Corinne Iozzio – Smithsonian

[hr]

December 9, 2014

Posted on by

Human oral microbiome

* Characterization and comparison of bacterial communities in benign vocal fold lesions – Alissa S Hanshew – Microbiome

Bacterial invasion and persistence: critical events in the pathogenesis of periodontitis? – S. Ji – Journal of Periodontal Research

Human skin microbiome

This took two years to publish, but here it is: Meeting report for the 1st skin microbiota workshop, Boulder, CO October 15-16 2012 – Jack A Gilbert – Standards in Genomic Sciences

Human respiratory microbiome

Assessment of Airway Microbiota and Inflammation in Cystic Fibrosis Using Multiple Sampling Methods – Edith T. Zemanick – Annals of the American Thoracic Society

Human gut microbiome

* Stability of Gut Enterotypes in Korean Monozygotic Twins and Their Association with Biomarkers and Diet – Mi Young Lim – Scientific Reports

* Microbiota organization is a distinct feature of proximal colorectal cancers – Christine M. Dejea – PNAS USA

Review: Crosstalk between intestinal microbiota, adipose tissue and skeletal muscle as an early event in systemic low-grade inflammation and the development of obesity and diabetes – Christian Bleau – Diabetes/Metabolism Research and Reviews

Pathophysiological responses from human gut microbiome – Anindya Roy Chowdhury, Utpal Bakshi – World Journal of Translational Medicine

Animal models of microbiome research

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

Animal microbiome

Carpoglyphus lactis (Acari: Astigmata) from various dried fruits differed in associated microorganisms – Jan Hubert – Journal of Applied Microbiology

Bacterial dynamics within the mucus, tissue and skeleton of the coral Porites lutea during different seasons – Jie Li – Scientific Reports

 

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

Plant microbiome

* Removal of floral microbiota reduces floral terpene emissions – Josep Peñuelas – Scientific Reports

Contrasting diversity of epibiotic bacteria and surrounding bacterioplankton of a common submerged macrophyte, Potamogeton crispus, in freshwater lakes – Dan He – FEMS Microbiology Ecology

Review: Sphagnum physiology in the context of changing climate: emergent influences of genomics, modelling and host–microbiome interactions on understanding ecosystem function – David J. Weston – Plant, Cell & Environment

Book: Principles of Plant-Microbe Interactions – Springer

Soil and sediment microbiome

Anthropogenic land use shapes the composition and phylogenetic structure of soil arbuscular mycorrhizal fungal communities – Mari Moora – FEMS Microbiology Ecology

Halophyte plant colonization as a driver of the composition of bacterial communities in salt marshes chronically exposed to oil hydrocarbons – Vanessa Oliveira – FEMS Microbiology Ecology

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

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

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

Primary succession of soil enzyme activity and heterotrophic microbial communities along the chronosequence of Tianshan Mountains No. 1 Glacier, China – Jun Zeng – Antonie van Leeuwenhoek

Water microbiome

Off-site impacts of agricultural composting: role of terrestrially derived organic matter in structuring aquatic microbial communities and their metabolic potential – Thomas Pommier – FEMS Microbiology Ecology

Microbiome of the built environment

* Diversity of Bacterial Communities of Fitness Center Surfaces in a U.S. Metropolitan Area – Nabanita Mukherjee – International Journal of Environmental Research and Public Health

Food microbiology

Potentially probiotic acetic acid bacteria isolation and identification from traditional dairies microbiota – Babak Haghshenas – International Journal of Food Science & Technology

Metagenomics

Microbial community pattern detection in human body habitats via ensemble clustering framework – Peng Yang – BMC Systems Biology

Proteomics and metabolomics

Insights on the human microbiome and its xenobiotic metabolism: what is known about its effects on human physiology? – Tewes Tralau – Expert Opinion on Drug Metabolism & Toxicology

Proteomic tools to decipher microbial community structure and functioning – Florence Arsène-Ploetze – Environmental Science and Pollution Research

Systems-based approaches to unravel multi-species microbial community functioning – Florence Abram – Computational and Structural Biotechnology Journal

Amplification and other techniques

* Multi-template polymerase chain reaction – Elena Kalle – Biomolecular Detection and Quantification

Microfluidic static droplet array for analyzing microbial communication on a population gradient – Heon-Ho Jeong – Lab Chip

More microbiology papers

* Gain-of-function experiments: time for a real debate – W. Paul Duprex (with David Relman) – Nature Reviews Microbiology

Ciprofloxacin mechanism: Emergence of antibiotic resistance from multinucleated bacterial filaments – Julia Bos – PNAS USA

Microbes in the news

The fragrance of flowers depends on the fungi and bacteria that coated – Beta Wired

The Human Microbiome: Getting Personal – Katy Califf – ASM Microbe

Science, publishing, career

Scientists Are Not That Smart – Chad Orzel – New York Magazine

io9 Science Survey: Tell Us About Working With Rodents in the Lab – Annalee Newitz – io9

Best Way for Professors to Get Good Student Evaluations? Be Male – Amanda Marcotte – Slate

Bik’s Picks

Unfortunately sold out, but really cute: DNA Molecule Plush – ThinkGeek

The birth of a dinosaur footprint: Subsurface 3D motion reconstruction and discrete element simulation reveal track ontogeny (with movies) – Peter L. Falkingham – PNAS USA

Billionaire’s New Science Institute Plans “Google Maps” View of Cells – Joshn Fischman – Scientific American

Expanded DNA alphabet wins Science award – Bradley J. Fikes – UT San Diego

[hr]