Category Archives: Food Microbiology

January 15, 2015

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Human respiratory microbiome

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

Human oral microbiome

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

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

Animal models of microbiome research

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

Animal microbiome

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

Plant microbiome

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

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

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

Soil microbiome

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

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

Water microbiome

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

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

Food microbiology

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

Metagenomics

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

Bioinformatics

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

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

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

Bacteria in the news

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

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

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

The Microbiome Diet: Evolving Past Paleo – Raphael Kellman

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

Science, publishing and career

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

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

Bik’s Picks

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

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

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

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

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January 14, 2015

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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

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December 16, 2014

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Pregnancy and birth

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

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

Human skin and hair microbiome

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

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

Human oral microbiome

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

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

Human respiratory microbiome

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

Human gut microbiome

Shaping the gut microbiome – Linda Koch – Nature Reviews Microbiology

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

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

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

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

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

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

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

Animal and other models of microbiome research

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

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

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

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

Animal microbiome

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

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

 

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

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

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

 

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

Plant microbiome

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

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

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

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

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

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

Soil and sediment microbiome

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

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

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

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

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

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

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

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

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

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

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

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

Water microbiome

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

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

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

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

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

Food microbiology

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

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

Metabolomics

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

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

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

Bioinformatics

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

Techniques

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

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

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

Functional foods

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

More microbiology

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

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

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

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

Microbes in the news

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

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

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

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

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

Bik’s Picks

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

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

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

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

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December 11, 2014

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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

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December 10, 2014

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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

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December 9, 2014

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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

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Microbiome digest, December 8, 2014

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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

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Microbiome digest, December 2, 2014

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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

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Microbiome digest, November 28, 2014

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Human gut microbiome

Effects of Surgical and Dietary Weight Loss Therapy for Obesity on Gut Microbiota Composition and Nutrient Absorption – Antje Damms-Machado – BioMed Research International

Collateral damage from oral ciprofloxacin versus nitrofurantoin in outpatients with urinary tract infections: a culture-free analysis of gut microbiota – Andrew J. Stewardson – Clinical Microbiology and Infection

Potential of fecal microbiota for early-stage detection of colorectal cancer – Georg Zeller – Molecular Systems Biology

Does the microbiota play a role in the pathogenesis of autoimmune diseases? – Mairi H McLean – Gut

The gut microbiota and inflammatory bowel disease – Katsuyoshi Matsuoka and Takanori Kanai – Seminars in Immunopathology

Metagenomic analysis of the gastric microbiota cultivable from a patient 

with gastritis concomitant with Barrett’s esophagus – Andrés Julián Gutiérrez-Escobar – Rev Gastroenterol Peru

Gut microbiota in patients with type 2 diabetes mellitus – Kristine H Allin – European Journal of Endocrinology

Gut brain axis: diet microbiota interactions and implications for modulation of anxiety and depression – Ruth Ann Luna, Jane A Foster

Behçet’s syndrome patients exhibit specific microbiome signature – Clarissa Consolandi – Autoimmunity Reviews

Animal microbiome

Complete genome sequence and comparative genome analysis of Klebsiella oxytoca HKOPL1 isolated from giant panda feces – Jingwei Jiang – BMC Research Notes

Few highly abundant operational taxonomic units dominate within rumen methanogenic archaeal species in New Zealand sheep and cattle – Henning Seedorf – Applied and Environmental Microbiology

Chironomid Microbiome – Malka Halpern, Yigal Senderovich – Microbial Ecology

Plant microbiome

Understanding and engineering beneficial plant–microbe interactions: plant growth promotion in energy crops – Kerrie Farrar – Plant Biotechnology Journal

Soil and sludge microbiome

Global diversity and geography of soil fungi – Leho Tedersoo – Science

Effects of the Biocontrol Agent Aspergillus flavipes on the Soil Microflora and Soil Enzymes in the Rooting Zone of Pepper Plants Infected with Phytophthora capsici – Hui Wang – Journal of Phytopathology

Plant diversity predicts beta but not alpha diversity of soil microbes across grasslands worldwide – Suzanne M. Prober – Ecology Letters

Soil chemical properties affect the reaction of forest soil bacteria to drought and rewetting stress – Marcin Chodak – Annals of Microbiology

Cyanobacteria and algae of buried soils and their modern analogues – A. D. Temraleeva – Paleontological Journal

Diversity and efficiency of anthracene-degrading bacteria isolated from a denitrifying activated sludge system treating municipal wastewater – Spyridon Ntougias – International Biodeterioration & Biodegradation

Water microbiome

Profile of bacterial communities in South African mine-water samples using Illumina next-generation sequencing platform – Jitendra Keshri – Applied Microbiology and Biotechnology

Temporal and Vertical Distribution of Bacterioplankton at the Gray’s Reef National Marine Sanctuary – Xinxin Lu – Applied and Environmental Microbiology

Identification of Microorganisms in Hydrocarbon-Contaminated Aquifer Samples by Fluorescence In Situ Hybridization (CARD-FISH) – Schattenhofer Martha – Springer Protocols Handbooks

Food microbiology

Influence of pig rennet on proteolysis, organic acids content and microbiota of Pecorino di Farindola, a traditional Italian ewe’s raw milk cheese – Tofalo Rosanna – Food Chemistry

Bioinformatics

Alternative for USEARCH: VSEARCH: Open and free 64-bit multithreaded tool for processing metagenomic sequences, including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling – Github

svaseq: removing batch effects and other unwanted noise from sequencing data – Jeffrey T. Leek – Nucleic Acids Research

Phages and viruses

Automated classification of tailed bacteriophages according to their neck organization – Anne Lopes – BMC Genomics

Metabolomics

Metabolic fate of neutral human milk oligosaccharides in exclusively breast-fed infants –
Viktoria Dotz – Molecular Nutrition & Food Research
http://onlinelibrary.wiley.com/doi/10.1002/mnfr.201400160/abstract

Transcriptomics

Transcriptome analysis reveals novel regulatory mechanisms in a genome-reduced bacterium – Pavel V. Mazin – Nucleic Acids Research

More microbiology

In vivo treatment of Helicobacter pylori infection with liposomal linolenic acid reduces colonization and ameliorates inflammation – Soracha Thamphiwatana – PNAS USA

Microbes in the news

How bacteria in your gut could be making you fat, allergic, or anxious – Susannah Locke – Vox

Interview with Dan Knights: UMN professor solves problems from ‘gut bugs’ to Rubik’s Cube – Richard Chin – Twin Cities

Artificial Sweeteners May Have Despicable Impacts on Gut Microbes – Sheena Faherty – Scientific American

The Human Microbiome, An Issue of Clinics in Laboratory Medicine – Google eBook

Science and art

It’s a microbial world – protozoa pancakes

Bik’s Picks

Detection of fraudulent addition of bovine whey in Ricotta cheese by iso-electric focusing
– Fabio Fuselli – Journal of Science of Food and Agriculture

DNA survives critical entry into Earth’s atmosphere – Science Daily

Bill Nye: ‘Science is true, whether or not you believe it’ – Brad Wheeler – The Globe and Mail

The Best Gifts of 2014 for Science Geeks – Smithsonian.com

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Microbiome digest, November 24, 2014

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General microbiome

Microbial sequencing to improve individual and population health – Sharon J Peacock and George M Weinstock – Genome Medicine

Human oral microbiome

Shifts in Campylobacter species abundance may reflect general microbial community shifts in periodontitis progression – Karsten Henne – Journal of Oral Microbiology

Human respiratory microbiome

Analysis of the bacterial community in chronic obstructive pulmonary disease sputum samples by denaturing gradient Gel electrophoresis and real-time PCR – Dachang Wu – BMC Pulmonary Medicine

Human gut microbiome

Microbiome and cancer – Naoko Ohtani – Seminars in Immunopathology

The Gut Microbiome and the Brain – Leo Galland – Journal of Medicinal Food

The ELDERMET biobank: Isolation and characterization of the intestinal microbiota from elderly Irish subjects – Lakshminarayanan, Bhuvaneswari

Animal models of microbiome

Hydrogen sulphide protects against NSAID-enteropathy through modulation of bile and the microbiota – Rory W Blackler – British Journal of Pharmacology

Plant microbiome

Towards a holistic understanding of the beneficial interactions across the Populus microbiome – Stéphane Hacquard – New Phytologist

Soil microbiome

Soil Fungal Communities Respond to Grassland Plant Community Richness and Soil Edaphics – Nicholas LeBlanc – Microbial Ecology

Impact of plant species evenness, dominant species identity and spatial arrangement on the structure and functioning of soil microbial communities in a model grassland – L. Massaccesi – Oecologia

Contrasting assembly processes in a bacterial metacommunity along a desiccation gradient – Angel Valverde – Frontiers in Microbiology

 

Water microbiome

Metatranscriptome of marine bacterioplankton during winter time in the North Sea assessed by total RNA sequencing – Anna Kopf – Marine Genomics

Integrated metagenomic and metaproteomic analyses of marine biofilm communities – Dagmar H. Leary – Biofouling: The Journal of Bioadhesion and Biofilm Research

 

Spatial Diversity of Bacterioplankton Communities in Surface Water of Northern South China Sea – Jialin Li – PLOS ONE

* High Genetic Diversity and Novelty in Eukaryotic Plankton Assemblages Inhabiting Saline Lakes in the Qaidam Basin – Jiali Wang – PLOS ONE

Effects of ocean acidification on the biogenic composition of the sea-surface microlayer: Results from a mesocosm study – Luisa Galgani – Journal of Geophysical Research: Oceans

Other (Food, biotechnology)

Microbial Dynamics and Control in Shale Gas Production – Jason Gaspar – Environmental Science & Technology Letters

Dynamics and diversity of microbial community succession in traditional fermentation of Shanxi aged vinegar – Zhiqiang Nie – Food Microbiology

Resilience of Aggregated Microbial Communities Subjected to Drought—Small-Scale Studies – Amélie Barthès – Microbial Ecology

Microbial diversity in sugarcane ethanol production in a Brazilian distillery using a culture-independent method – Ohana Yonara Assis Costa – Journal of Industrial Microbiology & Biotechnology

 

Metagenomics and viromes

Evaluation of viral genome assembly and diversity estimation in deep metagenomes – Daniel Aguirre de Cárcer – BMC Genomics

Niche-dependent genetic diversity in Antarctic metaviromes – Olivier Zablocki – Bacteriophage

Metabolomics

The cross-talk between opportunistic fungi and the mammalian host via microbiota’s metabolism – Luigina Romani – Seminars in Immunopathology

The metabolomics of airway diseases, including COPD, asthma and cystic fibrosis – B. Fatemeh Nobakht M. Gh. – Biomarkers

 

Metabolomics as a tool for diagnosis and monitoring in coeliac disease – Danielle Ryan – Metabolomics

 

Transcriptomics

Single-cell transcriptomics for microbial eukaryotes – Martin Kolisko – Current Biology

Bioinformatic tools

The R package otu2ot for implementing the entropy decomposition of nucleotide variation in sequence data – Alban Ramette and Pier Luigi Buttigieg – Frontiers in Microbiology

Techniques

Introduction to Genetic, Genomic, and System Analyses for Communities – Jack A. Gilbert, Nicole M. Scott – Springer Protocols Handbooks 2014

Microbes in the news

It’s all around us: Three scientists on how the microbiome shapes our world – Plus: Why you shouldn’t give probiotics to your dog – Brooke Borel

Professor’s new book aims to advance microbiome research – Brian McNeill – Phys.org

Book: Metagenomics for Microbiology, 1st Edition – Izard and Rivera – Elsevier

Symbiota Maps Plant Microbiome to Boost Crop Yields – Martin LaMonica – Xconomy

* History Lessons from Bacteria – Cindy Lu – Cell

 

Revolutionizing the interaction between plants and bacteria – Phys.org

Life’s extremists may be an untapped source of antibacterial drugs – David Salisbury – VanderBilt.edu

 

Science, publishing, career

Point of view: How postdocs benefit from building a union – Benjamin Cain

Bik’s Picks

The XKCD guid to the universe’s most bizarre physics – Randall Munroe – Wired.com

Physicists Solve Mystery of Scotch Whisky Rings – Rachel Nuwer – Scientific American

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