Category Archives: Bik’s Non-Microbiology Picks

January 19, 2015

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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

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January 16, 2015

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(edited: MicrobiomeNews has been around for a year, but I had not seen it until today)

I just found out about MicrobiomeNews, run by MoBio Laboratories. It seems to cover the same articles I have been blogging about.

So here is a question for you, dear readers: Should I stop running this blog MicrobiomeDigest and let MoBio do the work? With only ~100 visitors a day, I am not sure if my efforts (3-4 hours a day) are worth it. After a couple of months of growth, I seem to have reached a plateau, and it is just not serving the large audience I had hoped to attract.

Any suggestions for improvement or increasing the visibility of my blog are very welcome, at eliesbik * stanford dot edu!  But, at least today, here is a new installment.

Pregnancy and birth

Prematurity and Perinatal Antibiotics: A Tale of Two Factors Influencing Development of the Neonatal Gut Microbiota – Daniel B. DiGiulio – The Journal of Pediatrics

Intestinal dysbiosis: an emerging cause of pregnancy complications? – Dongxin Zhang – Medical Hypotheses

Human gut microbiome

The role of the gut microbiome in the healthy adult status – Valeria D’Argenio, Francesco Salvatore – Clinica Chimica Acta

What’s One Phosphate between Friends (and Foe)? – Charles L. Bevins, Andreas J. Bäumler – Cell Host & Microbe

Acarbose treatment affects the serum levels of inflammatory cytokines and the gut content of bifidobacteria in Chinese patients with type 2 diabetes mellitus – Benli Su – Journal of Diabetes

Human urine microbiome

Search for Microorganisms in Men with Urologic Chronic Pelvic Pain Syndrome: A Culture-Independent Analysis in the MAPP Research Network – J. Curtis Nickel – The Journal of Urology

Animal models of microbiome research

Commensal microbes and interferon-λ determine persistence of enteric murine norovirus infection – Megan T. Baldridge – Science

Interferon-λ cures persistent murine norovirus infection in the absence of adaptive immunity – Timothy J. Nice – Science

Adult Hippocampal Neurogenesis is Regulated by the Microbiome – Ebere S. Ogbonnaya – Biological Psychiatry

Animal microbiome

Sweet talking your partner – Christina Tobin Kåhrström – Nature Reviews Microbiology

Soil microbiome

Metagenomic Sequence of saline desert Microbiota from Wild Ass Sanctuary, Little Rann of Kutch, Gujarat, India – Patel Rajesh – Genomics Data

Phages and viruses

Temperate bacteriophages collected by outer membrane vesicles in Komagataeibacter intermedius – Alla Kharina – Journal of Basic Microbiology

Polintons: a hotbed of eukaryotic virus, transposon and plasmid evolution – Mart Krupovic & Eugene V. Koonin – Nature Reviews Microbiology

Archaea

Rooting the Domain Archaea by Phylogenomic Analysis Supports the Foundation of the New Kingdom Proteoarchaeota – Céline Petitjean – Genome Biology and Evolution

Metagenomics

What is a resistance gene? Ranking risk in resistomes – José L. Martínez – Nature Reviews Microbiology

Metabolomics

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

Metabolic dependence of phytoplankton species richness – A. M. Segura – Global Ecology and Biogeography

Microbes in the news

How The Body Maintains A Healthy Balance Of ‘Friendly’ Gut Bacteria – Carolyn Gregoire – Huffington Post

Cracked! Researchers Nearing Completion of Genetic Map of Grapevine Disease – James Duren – Snooth.com

A. vaginae, G. vaginalis linked to preterm birth, miscarriage – Healio

3Bar Biologics developing beneficial bacteria for farmers’ fields – Carrie Ghose – BizJournals

Brain Food: The Human Microbiome (podcast with Greg Caporaso) – Bonnie Stevens – KNAU Northern Arizona University

Analyzing the Gut Microbiome to Help Detect Colorectal Cancer – National Cancer Institute

The Human Microbiome: Biomedical Implications and Birth of a Market – Overview – Research and Markets

New tech keeps bacteria from sticking to surfaces – Krishna Ramanujan – R&D Magazine

Your Phone Contains Personal Contacts… And Lots of Bacteria – Jenna Iacurci – Nature World News

Science, publishing and career

By a former student in our lab: Protecting genetic privacy may be bad for your health – Akshay Maheshwari – SF Gate

A European postdoc for the family – Michelle Gabriele Sandrian – Science

Expectations of brilliance underlie gender distributions across academic disciplines – Sarah-Jane Leslie – Science

Bik’s Picks

What’s the Secret to Getting Kids to Eat Veggies? Let Them Play First! – Shannon Hall – Live Science

HiRISE camera spots long-lost space probe on Mars – Science Daily

Satire: Epidemiologists Warn of Emerging Deadly Pandemic of Selfie-sticks – The Allium

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January 15, 2015

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Human respiratory microbiome

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

Human oral microbiome

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

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

Animal models of microbiome research

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

Animal microbiome

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

Plant microbiome

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

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

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

Soil microbiome

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

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

Water microbiome

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

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

Food microbiology

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

Metagenomics

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

Bioinformatics

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

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

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

Bacteria in the news

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

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

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

The Microbiome Diet: Evolving Past Paleo – Raphael Kellman

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

Science, publishing and career

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

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

Bik’s Picks

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

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

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

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

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January 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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January 13, 2015

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Human oral microbiome

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

Human respiratory microbiome

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

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

Human gut microbiome

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

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

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

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

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

Animal models of microbiome research

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

Animal microbiome

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

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

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

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

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

Soil microbiome

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Water microbiome

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

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

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

Metagenomics

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

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

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

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

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

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

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

Metabolomics

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

Techniques

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

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

Microbes in the news

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

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

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

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

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

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

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

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

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

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

Science, publishing and career

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

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

Bik’s Picks

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

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

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

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January 12, 2015

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Microbiome of pregnancy and birth

Milk- and solid-feeding practices and daycare attendance are associated with differences in bacterial diversity, predominant communities, and metabolic and immune function of the infant gut microbiome – Amanda L. Thompson – Frontiers in Cellular and Infection Microbiology

Human oral microbiome

Combinations of bacterial species associated with symptomatic endodontic infections in a Chinese population – Z Qi – International Endodontic Journal

Human gut microbiome
Inferred metagenomic comparison of mucosal and fecal microbiota from individuals undergoing routine screening colonoscopy reveals similar differences observed during active inflammation – Mei San Tang – Gut Microbes

Intestinal microbiota in metabolic diseases: From bacterial community structure and functions to species of pathophysiological relevance – Thomas Clavel – Gut Microbes

Editorial: a simple faecal preparation protocol for faecal microbiota transplantation – C. R. Kelly – Alimentary Pharmacology & Therapeutics

Human skin microbiome

Microbiology of diabetic foot infections: from Louis Pasteur to ‘crime scene investigation’ – Anne Spichler – BMC Medicine

Human urinary tract microbiome

The human urine virome in association with urinary tract infections – Tasha M. Santiago-Rodriguez – Frontiers in Microbiology

Animal microbiome

Normal bacterial conjunctival flora in the Huacaya alpaca (Vicugna pacos) – Goedele Storms – Veterinary Ophthalmology

Replicating phages in the epidermal mucosa of the eel (Anguilla anguilla) – Miguel Carda Diéguez – Frontiers in Microbiology

Functional phylotyping approach for assessing intraspecific diversity of Ruminococcus albus within the rumen microbiome – Inna Rozman Grinberg – FEMS Microbiology Letters

Master Thesis: Predominant fecal microbiota of captive adult cheetahs housed in European zoos: a cross-sectional study – Niloufar Majdzadeh – Ghent University

Plant microbiome

Plant–microbe interactions: Microbiome remote control – Christopher Surridge – Nature Plants

Impact of plant development on the rhizobacterial population of Arachis hypogaea: a multifactorial analysis – Shyamalina Haldar and Sanghamitra Sengupta

Pyrosequencing Reveals Fungal Communities in the Rhizosphere of Xinjiang Jujube – Peng Liu – BioMed Research International

Soil, sediment, sludge microbiome

Delineating bacterial community structure of polluted soil samples collected from cancer prone belt of Punjab, India – Gagandeep Kaur – 3 Biotech

Nitrogen and methanogen community composition within and among three Sphagnum dominated peatlands in Scandinavia – Magalí Martí – Soil Biology and Biochemistry

Detailed investigation of the microbial community in foaming activated sludge reveals novel foam formers – Feng Guo – Nature Scientific Reports

Long-term experimental warming alters community composition of ascomycetes in Alaskan moist and dry arctic tundra – Tatiana A. Semenova – Molecular Ecology

Microbial community composition of transiently wetted Antarctic Dry Valley soils – Thomas D. Neiderberger – Frontiers in Microbiology

Water microbiome

Ecogenomics reveals metals and land-use pressures on microbial communities in the waterways of a megacity – Gourvendu Saxena – Environmental Science & Technology

An association network analysis among microeukaryotes and bacterioplankton reveals algal bloom dynamics – Shangjin Tan – Journal of Phycology

Phages and viruses

(also see above) The human urine virome in association with urinary tract infections – Tasha M. Santiago-Rodriguez – Frontiers in Microbiology

TRIM28 Represses Transcription of Endogenous Retroviruses in Neural Progenitor Cells – Liana Fasching – Cell Reports

Probiotics

Systematic discovery of probiotics – Samuel C Forster & Trevor D Lawley – Nature Biotechnology

Microbes in the News

Prebiotics: Yeast Is Healthy, And So Are Bacteria That Help Us Break Down Bread And Beer – Science 2.0

Stop Killing the Good Guys! Protect Your Child’s Microbiome From Antibiotic Overuse – Aviva Romm – Huffington Post

Mounting research tightens gut microbial connection with the brain – MedicalXpress
http://medicalxpress.com/news/2015-01-mounting-tightens-gut-microbial-brain.html

Intestinal bacteria study uses Zingerman’s bread – Lea Giotto – The Michigan Daily

Are We Ruled by Our Microbiome? – Qiagen

Could Gut Microbes Help Us Treat Brain Disorders? – Kavli Foundation – Labmanager

Bacteria could contribute to development of wound-induced skin cancer – EurekAlert

Revenge of the bacteria? Earth Talk – August FreePress

Do viruses make us smarter? – Science Daily

The Doctor Who Championed Hand-Washing And Briefly Saved Lives – Rebecca Davis – NPR Morning Edition

Love your gut – and help your body shift those festive pounds – Kathie Swift – Daily Mail

Science, publishing, career

Life sciences workforce trends evolve with the industry – Kathy L Nugent & Lori Lindburg – Nature Biotechnology

12 Common Mistakes In Empirical Social Science – Fred Phillips – Science 2.0

How The War On Science Affects Us All – Greg Satell – Forbes

Bik’s Picks

Devil is in the detail: Evolution of color in plants and animals – Science Daily’

This cannot be statistically sound: Number Of Large Earthquakes Dropped 60 Percent In 2014 – Science 2.0

Why OCD Is ‘Miserable’: A Science Reporter’s Obsession With Contracting HIV – Shots/Fresh Air – NPR

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January 9, 2015

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Human respiratory microbiome

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

Human gut microbiome

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

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

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

Animal models of microbiome research

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

Plant microbiome

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

Bioinformatics

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

Metagenomics

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

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

Metabolomics

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

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

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

More microbes

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

Microbes in the news

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

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

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

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

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

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

Science, publishing, career

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

Bik’s Picks

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

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

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

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January 8, 2015

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Human gut microbiome

Antimicrobial peptide resistance mediates resilience of prominent gut commensals during inflammation – T. W. Cullen – Science

Review: Ancient human microbiomes – Christina Warinner – Journal of Human Evolution

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

Animal models of microbiome research

Opposite effects of anthelmintic treatment on microbial infection at individual versus population scales – Vanessa O. Ezenwa, Anna E. Jolles – Science

Plant microbiome

Engineering the plant rhizosphere – Yanxia Zhang – Current Opinion in Biotechnology

Soil and sediment microbiome

Use of MALDI-TOF Mass Spectrometry and a Custom Database to Characterize Bacteria Indigenous to a Unique Cave Environment (Kartchner Caverns, AZ, USA) (video) – Lin Zhang – JOVE

Sedimentology and Sequence Stratigraphy of the Late Precambrian Carbonates of the Mbuji-Mayi Supergroup in the Sankuru-Mbuji-Mayi-Lomami-Lovoy Basin (Democratic Republic of the Congo) – Franck Delpomdor – Geology and Resource Potential of the Congo Basin

Soil biology for resilient, healthy soil – R. Michael Lehman – Journal of Soil and Water Conservation

Techniques

Improved pipeline for reducing erroneous identification by 16S rRNA sequences using the Illumina MiSeq platform – Yoon-Seong Jeon – Journal of Microbiology

Microbes in the news

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

What’s lurking in your microbiome? Possibly, a cure for disease – Jon Gertner – FastCompany

Could gut bacteria that help us digest beer and bread fight disease, too? – Phys.org

Delivery Mode Alters Newborn’s First Bacterial Exposure How microbiome develops after birth could affect later-life immunity – Bridget M. Kuehn – Gastroenterology and Endoscopy News

CAMI Hosts Community Challenge for Assessing Metagenomes – Joint Genome Institute

Consumer-Funded Test Finds 11 of 12 Pet Foods Contaminated – James Andrews – Food Safety News

Science, publishing, career

My metamorphosis – Elizabeth A. Marchio – Science

A multi-journal partnership to highlight joint first-authors of manuscripts – M Bishr Omary – Gut

Introductory Comments for the Scientific Ethics Theme – Beth A. Fischer – ASM Journal of Microbiology and Biology Education

Exaggerated science reporting – who’s to blame? – NewsWorks

Bik’s Picks

Monkeys can learn to see themselves in the mirror – Science Daily

Poker program Cepheus is unbeatable, claim scientists – The Guardian

Super-insulated clothing could eliminate need for indoor heating – Lisa Zyga – Phys.org

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January 7, 2015

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Human skin microbiome

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

Human gut microbiome

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

Animal models of microbiome research

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

Animal microbiome

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

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

Plant microbiome

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

Water microbiome

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

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

Bioinformatics

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

Probiotics

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

Antibiotics

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

Phages and viruses

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

More microbes

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

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

Microbes in the news

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

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

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

Skin microbes trigger specific immune responses – Science Daily

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

Science, publishing, career

Outreach: Speak up for science – Virginia Gewin – Nature

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

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

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

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

Bik’s Picks

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

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

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January 6, 2015

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Human gut microbiome

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

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

Human respiratory microbiome

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

Animal models of microbiome research

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

Animal microbiome

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

Protist microbiome

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

Plant microbiome

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

Soil microbiome

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

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

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

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

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

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

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

Water microbiome

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

Bioreactor and wastewater microbiomes

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

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

Techniques

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

Science, publishing and career

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

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

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

Microbes in the news

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

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

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

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

Bik’s Picks

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

Inching toward the 3D genome – Elizabeth Pennisi – Science

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

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

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