Category Archives: Infection and transplantation

January 21, 2015

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Today’s digest features the microbiome of chewing gum, infants of stressed-out moms, growing segmented filamentous bacteria, and a YouTube video with Jack Gilbert.

Chewing gum microbiome

Quantification and Qualification of Bacteria Trapped in Chewed Gum – Stefan W. Wessel – PLOS ONE

Human gut microbiome

Review: Gut microbial metabolism and colon cancer: Can manipulations of the microbiota be useful in the management of gastrointestinal health? – Antoaneta Belcheva – BioEssays

Microbiome of pregnancy and birth

Maternal Prenatal Stress is Associated with the Infant Intestinal Microbiota – Maartje A.C. Zijlmans – Psychoneuroendocrinology (which is a nice word for Scrabble or Hangman)

Animal and other models of microbiome research

Growth and host interaction of mouse segmented filamentous bacteria in vitro – Pamela Schnupf – Nature

Signaling between two interacting sensor kinases promotes biofilms and colonization by a bacterial symbiont – Allison N. Norsworthy and Karen L. Visick – Molecular Microbiology

Soil microbiome

Pyrosequencing analysis of a bacterial community associated with lava-formed soil from the Gotjawal forest in Jeju, Korea – Jong-Shik Kim – Microbiology Open

Water microbiome

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

Immunology

Reduced neonatal regulatory T cell response to microbial stimuli associates with subsequent eczema in high-risk infants – Intan H. Ismail – Pediatric Allergy and Immunology

Metagenomics

Biological interpretation of genome-wide association studies using predicted gene functions – Tune H. Pers – Nature Communications

Microbes in the news

YouTube video with Jack Gilbert: Invisible Influence: A Bacterial Guide to Your Health – Argonne OutLoud on YouTube

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

GM microbes created that can’t escape the lab – Engineered bacteria kept in check with a designer diet – Elie Dolgin – Nature

SDSU Hosts the “Year of the Phage” – Jeneene Chatowsky and Michael Price – San Diego State University

Novel IBD microbiome drug advanced to phase 1 trial – Healio

Optibiotix unlocking the mysteries of the human microbiome – Ian Lyall – Proactive Investors

New bacterial ‘language’ discovered: Previously unknown communication pathway – Science Daily

Science, publishing and career

Turning point: Swati Padmaraj – Scott Kraft – Nature

Time management: Seize the moment – Jeffrey M. Perkel – Nature

How to recruit a good bioinformatician – Opiniomics

Science and Art

Micro Masterpiece: The artful science of Tom Deerinck, a micrographer who consistently places in Nikon’s Small World competition – Jef Akst – The Scientist

Bik’s Picks

The Science Behind Deflated Footballs – Erin Blakemore – Smithsonian

Science gets its moment in Obama’s 2015 State of the Union – David Malakoff – Science

The Namer: Carl Linnaeus’s lasting impact on biological science – Kerry Grens – The Scientist

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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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December 23, 2014

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Microbiome publications are definitely not taking a winter break, so here is your holiday update. Merry Christmas to those who celebrate!

Human oral microbiome

Serum IgG Antibody Levels to Periodontal Microbiota Are Associated with Incident Alzheimer Disease – James M. Noble – PLOS ONE

Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle – Xuesong He – PNAS USA

Pyrosequencing of supra- and subgingival biofilms from inflamed peri-implant
and periodontal sites – Simone Schaumann – BMC Oral Health

Human respiratory microbiome

The Microbial Community of the Cystic Fibrosis Airway Is Disrupted in Early Life – Julie Renwick – PLOS ONE

Human gut or general microbiome
Effects of bowel cleansing on the intestinal microbiota – Jonna Jalanka – Gut

The Microbiome of Aging and Age-Related Disease – 2014 Meeting Abstracts

Microbial community pattern detection in human body habitats via ensemble clustering framework – Peng Yang – ArXiv.org

Cancer and the microbiome: potential applications as new tumor biomarker – Khan Shahanavaj – Expert Review of Anticancer Therapy

Influence of Intestinal Microbiota on Body Weight Gain: a Narrative Review of the Literature – Camila S. Cardinelli – Obesity Surgery

Animal models of microbiome research

Host genetics and diet, but not immunoglobulin A expression, converge to shape
compositional features of the gut microbiome in an advanced intercross population
of mice – Larry J Leamy – Genome Biology

Animal microbiome

Microbiomes, plausible players or not in alteration of host behaviour – David G. Biron – Frontiers in Microbiology

The Howler Monkey as a Model for Exploring Host-Gut Microbiota Interactions in Primates – Katherine R. Amato, Nicoletta Righini – Howler Monkeys

The Gut Microbiota Appears to Compensate for Seasonal Diet Variation in the Wild Black Howler Monkey (Alouatta pigra) – Katherine R. Amato – Microbial Ecology

Application of the Human Intestinal Tract Chip to the non-human primate gut microbiota – T.D.J. Bello González – Beneficial Microbes

Effects of dietary supplementation of a commercial prebiotic Previda® on survival, growth, immune responses and gut microbiota of Pacific white shrimp, Litopenaeus vannamei – J.D. Anuta – Aquaculture Nutrition

Metagenomic-Based Study of the Phylogenetic and Functional Gene Diversity in Galápagos Land and Marine Iguanas – Pei-Ying Hong – Microbial Ecology

Plant microbiome

The plant microbiome at work – Klaus Schlaeppi and Davide Bulgarelli – Molecular Plant-Microbe Interactions

Tree communities rapidly alter soil microbial resistance and resilience to drought – David Rivest – Functional Ecology

The Sesquiterpene Biosynthesis and Vessel-Occlusion Formation in Stems of Aquilaria sinensis (Lour.) Gilg Trees Induced by Wounding Treatments without Variation of Microbial Communities – Zheng Zhang – International Journal of Molecular Sciences

Analysis of microbial taxonomical groups present in maize stalks suppressive to colonization by toxigenic Fusarium spp.: A strategy for the identification of potential antagonists – Jürgen Köhl – Biological Control

Soil and sediment microbiome

Diversity, Distribution and Hydrocarbon Biodegradation Capabilities of Microbial Communities in Oil-Contaminated Cyanobacterial Mats from a Constructed Wetland – Raeid M. M. Abed – PLOS ONE

Do climate factors govern soil microbial community composition and biomass at a regional scale? – L. Ma – Biogeosciences Discuss

Water microbiome

Early succession of micro-periphyton communities in kelp bed and barren ground ecological systems – Roberto A. Uribe – Marine Ecology

Greater temporal changes of sediment microbial community than its waterborne counterpart in Tengchong hot springs, Yunnan Province, China – Shang Wang – Scientific Reports

Effects of warming on microbial communities in the coastal waters of temperate and subtropical zones in the Northern Hemisphere, with a focus on Gammaproteobacteria
Dao Thi Anh Tuyet – Journal of Oceanography

Colonization in the photic zone and subsequent changes during sinking determines bacterial community composition in marine snow – Stefan Thiele – Applied and Environmental Microbiology

Diversity, Distribution and Hydrocarbon Biodegradation Capabilities of Microbial Communities in Oil-Contaminated Cyanobacterial Mats from a Constructed Wetland
Raeid M. M. Abed – PLOS ONE

Bioreactor microbiology

Comparative analysis of microbial community of novel lactic acid fermentation inoculated with different undefined mixed cultures – Shaobo Liang – Bioresource Technology

A framework for establishing predictive relationships between specific bacterial 16S rRNA sequence abundances and biotransformation rates – Damian E. Helbling – Water Research

Metagenomics

Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India – Johan Bengtsson-Palme – Frontiers in Microbiology

Challenges of metagenomics and single-cell genomics approaches for exploring cyanobacterial diversity – Michelle Davison – Photosynthesis Research

Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms – Martial Marbouty – eLIFE

Development and validation of an rDNA operon based primer walking strategy applicable to de novo bacterial genome finishing – Alexander W. Eastman and Ze-Chun Yuan – Frontiers in Microbiology

Metabolomics and transcriptomics

Terpene synthases are widely distributed in bacteria – Yuuki Yamada – PNAS USA

Scaling microbial biomass, metabolism and resource supply – Robert L. Sinsabaugh – Biogeochemistry

Metatranscriptomics of N2-fixing cyanobacteria in the Amazon River plume – Jason A Hilton – ISME Journal

Mining Soil Metagenomes to Better Understand the Evolution of Natural Product Structural Diversity: Pentangular Polyphenols as a Case Study – Hahk-Soo Kang and Sean F. Brady – Journal of the American Chemical Society

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

Techniques

Deciphering the Prokaryotic Community and Metabolisms in South African Deep-Mine Biofilms through Antibody Microarrays and Graph Theory – Yolanda Blanco – PLOS ONE

Rapid species-level identification of vaginal and oral lactobacilli using MALDI-TOF MS analysis and 16S rDNA sequencing – Annette Carola Anderson – BMC Microbiology

Probiotics

Probiotic and technological properties of Lactobacillus spp. strains from the human stomach in the search for potential candidates against gastric microbial dysbiosis – Susana Delgado – Frontiers in Microbiology

Phages and viruses

Effectiveness of bacteriophages in the sputum of cystic fibrosis patients – E. Saussereau – Clinical Microbiology and Infection

More Microbiology

Bridging the gap between viable but non-culturable and antibiotic persistent bacteria – Mesrop Ayrapetyan – Trends in Microbiology

Bacterial microcompartments and the modular construction of microbial metabolism – Cheryl A. Kerfeldemail, Onur Erbilgin – Trends in Microbiology

The impact of triclosan on the spread of antibiotic resistance in the environment – Daniel E. Carey – Frontiers in Microbiology

Microbes in the news

At Last, I Meet My Microbes – Katherine Harmon Courage – NPR Shots

This Is Your Microbiome: Katherine Harmon Courage at NPR is taking a tour through her microbiome and that of her husband, mother, and dog, as she recounts in a four-part series – Genome Web

Big Idea 2015: Medicine, Wellbeing, and the Microbiome – Deepak Chopra – LinkedIn

When Threatened By Worms, Bacteria Summon Killer Fungi – Ed Yong – National Geographic

Parkinson’s disease linked to gut bacteria – Tim Sandle – Digital Journal

Bacteria in 550-million-year-old fossils provide new clues about fossil formation – Science Codex

Yellowstone Thermal Pools Colored by Pollution – Patrick J Kiger – Discovery

Floating Toilets That Clean Themselves Grow On A Lake – Nsikan Akpan – NPR Goats and Soda

Bettendorf wrestling coach’s invention tackles germs and bacteria on sporting mats and floors – Dennis Moran – QC Online

People on Craigslist Want to Give You Bacteria for Free – Natalie Kitroeff – BusinessWeek

Science, publishing, career

Patterns of text reuse in a scientific corpus – Daniel T. Citron and Paul Ginsparg – PNAS USA

The Anti-Plagiarism Machine: An analysis of hundreds of thousands of scientific papers finds text re-use is rampant, but it isn’t always malicious – Adrienne Lafrance – The Atlantic

“You Are Welcome Here”: Small Stickers Make a Big Difference for LGBTQ Scientists – Kyle Frischkorn – Scientific American

Science and Art

Incredible Bacteria-Laced Fabric Combines Art, Biology And Fashion – Priscilla Frank – Huffington Post
Bik’s Picks

Evolutionary perspectives on human height variation – Gert Stulp and Louise Barrett – Biological Reviews

What the ‘marshmallow test’ can teach you about your kids – Chuck Hadad – CNN

7 of the Ocean’s Strangest Creatures, Including a Fish With a Flashlight – Matt Simon – Wired

Modern genetics confirm ancient relationship between fins and hands – Science Daily

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December 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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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 5, 2014

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Human oral microbiome

* Noma Affected Children from Niger Have Distinct Oral Microbial Communities Based on High-Throughput Sequencing of 16S rRNA Gene Fragments – Katrine L. Whiteson – PLOS Neglected Tropical Diseases

* Ancient DNA analysis of dental calculus – Laura S. Weyrich – Journal of Human Evolution

Human gut microbiome

* Gut microbiota are related to Parkinson’s disease and clinical phenotype – Filip Scheperjans – Movement Disorders

The role of the microbiome in immune cell development – Nita H. Salzman – Annals of Allergy, Asthma & Immunology

Ezakiella peruensis gen. nov., sp. nov. isolated from human fecal sample from a coastal traditional community in Peru – Nisha B. Patel – Anaerobe

Microbiome and Immunology

Microbial Programming of Systemic Innate Immunity and Resistance to Infection – Thomas B. Clarke – PLOS Pathogens

Animal models of microbiome research

* (see also Metabolomics) Diet and Feeding Pattern Affect the Diurnal Dynamics of the Gut Microbiome – Amir Zarrinpar – Cell Metabolism

Effects of cyclophosphamide on immune system and gut microbiota in mice – Xiaofei Xu, Xuewu Zhang – Microbiological Research

Gut microbiota and environment in patients with major burns – A preliminary report – Kentaro Shimizu – Burns

Animal microbiome

* The Feline Oral Microbiome: A Provisional 16S rRNA gene based Taxonomy with Full-length Reference Sequences – Floyd E. Dewhirst – Veterinary Microbiology

Diversity and health status specific fluctuations of intrauterine microbial communities in postpartum dairy cows – K. Wagener – Veerinary Microbiology

* Evidence of Polyethylene Biodegradation by Bacterial Strains from the Guts of Plastic-Eating Waxworms – Jun Yang – Environmental Science & Technology

Metabolomics

* Diet and Feeding Pattern Affect the Diurnal Dynamics of the Gut Microbiome – Amir Zarrinpar – Cell Metabolism

A Systematic Computational Analysis of Biosynthetic Gene Cluster Evolution: Lessons for Engineering Biosynthesis – Marnix H. Medema – PLOS Computational Biology

The Evolution of Fungal Metabolic Pathways – Jennifer H. Wisecaver – PLOS Genetics

The microbial degradation of onion flavonol glucosides and their roasting products by the human gut bacteria Eubacterium ramulus and Flavonifractor plautii – Katrin Ulbrich – Food Research International

Desulfovibrio desulfuricans isolates from the gut of a single individual: Structural and biological lipid a characterization – Wei Zhang-Sun – FEBS Letters

Metagenomics

Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies – James F. Denton – PLOS Computational Biology

Microbes in the news

A Worm’s Gut Could Help Dispose of Plastic Trash: Microbes found in the guts of waxworms like to feast on polyethylene – Rachel Nuwer – Smithsonian Magazine

Friendly bacteria are protective against malaria – MedicalXpress

Self-healing Concrete Vanishes Potholes Using Bacteria. Here’s How it Works – Jan Dizon – TechTimes

Wireless Implant Eliminates Bacteria, Then Dissolves – WND

Science, publishing and career

* Ten Simple Rules for Finishing Your PhD – Jacopo Marino – PLOS Computational Biology

Bik’s Picks

Amid Bugs, Hail, Floods and Bacteria, Italian Olives Take a Beating – Elisabetta Povoledo – New York Times

See it, touch it, feel it: Researchers use ultrasound to make invisible 3-D haptic shape that can be seen and felt – Science Daily

Satire: Breaking: James Watson Faked Winning A Nobel Prize – The Allium

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Microbiome digest, November 21, 2014

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Microbiome general

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

Human oral microbiome

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

Human skin microbiome

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

Human respiratory microbiome

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

Human gut microbiome

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

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

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

Animal and other models of microbiome research

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

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

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

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

Animal microbiome

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

Plant microbiome

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

Soil and sediment microbiome

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

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

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

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

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

Water microbiome

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

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

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

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

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

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

Food microbiology

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

Metabolomics

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

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

Metagenomics / Bioinformatics

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

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

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

Techniques

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

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

More microbiology papers

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

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

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

Microbes in the news

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

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

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

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

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

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

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

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

Science, publishing and career

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

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

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

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

Bik’s Picks

Shedding light on skin color – Ann Gibbons – Science

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

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

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