Category Archives: Science – Career – Publishing

Microbiome digest, October 24, 2014

Posted on by

Microbiome of placentas, infant respiratory microbiome, metabolomics, mutipartite genomes, microbes in the news, and some weekend picks.
Human microbiome general

Microbiome/microbiota and allergies – Yuzaburo Inoue, Naoki Shimojo – Seminars in Immunopathology

“In this review, we summarize the recent findings regarding the importance of the microbiome/microbiota in the development of allergic diseases and also the results of interventional studies using probiotics or prebiotics to prevent allergies.”

Pregnancy and birth

Term and preterm labour are associated with distinct microbial community structures in placental membranes which are independent of mode of delivery – Ronan M. Doyle – Placenta

“In this study, 16S rDNA pyrosequencing was used to identify bacteria in placental membranes. Caesarean sections and vaginal deliveries at term were found to harbour common genera”

Early Respiratory Microbiota Composition Determines Bacterial Succession Patterns and Respiratory Health in Children – Giske Biesbroek – Am J Respir Crit Care Med.

“Upper respiratory microbiota profiles of 60 healthy children at the ages of 1.5, 6, 12 and 24 months were characterized by 16S-based pyrosequencing”

From the “old NEC” to the “new NECs” – Melania Puddu – Journal of Pediatric and Neonatal Individualized Medicine

“This review describes in detail the new NECs especially those which affect preterm infants: contagion or lymphocytosis associated, transfusion associated and cow’s milk allergy associated.”

Metagenomics

The effects of variable sample biomass on comparative metagenomics – Meghan Chafee – Environmental Microbiology

“We investigated the interacting effects of DNA input and library amplification by PCR on comparative metagenomic analysis using dilutions of a single complex template from an Arabidopsis-associated microbial community.”

Metabolomics 

The nexus of syntrophy-associated microbiota in anaerobic digestion revealed by long-term enrichment and community survey – Takashi Narihiro – Environmental Microbiology

“16S pyrotag analysis revealed core populations of known syntrophs (six clades) and methanogens (nine clades) associated with acid degradation, and evidence for substrate- and/or inoculum-dependent specificity in syntrophic partnerships.”

In Vitro Fermentation of Lactulose by Human Gut Bacteria – Bingyong Mao – Journal of Agricultural and Food Chemistry

“This study aimed to identify lactulose-metabolizing bacteria in the human gut, using in-silico and traditional culture methods. “

Epigenomic regulation of host–microbiota interactions – Theresa Alenghat, David Artis – Trends in Immunology

“We review recent advances in understanding the interplay between the microbiota and mammalian epigenomic pathways, and highlight emerging findings that implicate a central role for histone deacetylases (HDACs) in orchestrating host–microbiota interactions.”

More microbiology

Examination of Prokaryotic Multipartite Genome Evolution through Experimental Genome Reduction – George C. diCenzo – PLOS Genetics

“To gain insight into the role and evolutionary history of these replicons, we have ‘reversed evolution’ by constructing a S. meliloti strain consisting solely of the chromosome and lacking the pSymB chromid and pSymA megaplasmid.”

Microbes in the news

How An Antibiotic Gene Jumped All Over The Tree of Life – Ed Yong – National Geographic

“Metcalf showed that it has also jumped from bacteria into every other major branch of life. It’s in animals, plants, fungi, archaea, and even some viruses.”

Research investigates bacteria on banknotes – Harper Adams University

“This study investigates how easy it is for bacteria and pathogens to survive on currency and whether the material the notes are made of, has an effect on the transfer.”

How millennials will save us all – Jennifer Block – Quartz

“Millennials get a bad rap for loading up on debt, mooching off their parents, and hiding behind technology. But there’s one problem that they may be particularly suited to tackling: our shrinking microbiome.“

Bik’s Picks

World’s Most Asked Questions: How Much Water Should I Drink a Day? – SciShow – Youtube

“People ask Google everything under the sun. One of the most commonly searched questions in the world is “How much water should I drink a day?” SciShow has the answer!”

Ten Simple Rules for Writing a PLOS Ten Simple Rules Article – Harriet Dashnow – PLOS Computational Biology

“This search left us wanting, until we discovered the PLOS Ten Simple Rules collection. We have found them to be a series of concise articles that capture the professional zeitgeist of being a scientist in an approachable manner.”

Satire: Ambitious New High-Speed Rail Plan Will Fly Americans To Japan To Use Their Trains – The Onion

“The transit system that the U.S. has needed for so long is now just a 7,000-mile plane journey to Tokyo’s Narita International Airport and a brief passage through Japanese customs away,” Obama continued.”

Microbiome Digest, October 20, 2014

Posted on by

Oral core microbiome, symbionts in crabs, sponges, and Drosophila, metabolites in dolphin’s breath, and retraction of a paper favored by Dr. Oz.

Pregnancy and birth

NEC in Twin Pregnancies: Incidence and Outcomes – Sathyaprasad C Burjonrappa, Brian Shea, Diya Goorah – Journal of Neonatal Surgery

“There is a remarkable higher incidence of NEC amongst twins. Abnormal colonization of the gastrointestinal tract appears to be an immediate postpartum event.”

Human oral microbiome

Intraindividual variation in core microbiota in peri-implantitis and periodontitis – Noriko Maruyama – Scientific Reports

“To improve our knowledge of the different communities of complex oral microbiota, we compared the microbial features between peri-implantitis and periodontitis in 20 patients with both diseases. “

Antimicrobial Effect of Lemongrass Oil against Oral Malodor Microorganisms and the Pilot Study of Safety and Efficacy of Lemongrass Mouthrinse on Oral Malodor – Panitta Satthanakul – Journal of Applied Microbiology

“Antimicrobial activity of LG mouthrinse was examined against common odorigenic microorganisms using broth microdilution assay and the disc diffusion method. A randomized double-blind clinical study was performed in 20 healthy volunteers.”

Animal microbiome

Molecular evidence of digestion and absorption of epibiotic bacterial community by deep-sea crab Shinkaia crosnieri – Tomo-o Watsuji – ISME Journal

“A phylogenetic analysis showed that many of the bacterial 16S ribosomal RNA gene sequences obtained from the intestine were closely related to the sequences of the epibionts, thus they were probably derived from the epibionts.”

* In vivo function and comparative genomic analyses of the Drosophila gut microbiota identify candidate symbiosis factors – Peter D. Newell – Frontiers in Microbiology

“We compared microbiota isolates with con-specific or closely related bacterial species isolated from non-fly environments. “

* Two distinct microbial communities revealed in the sponge Cinachyrella – Marie L. Cuvelier – Frontiers in Microbiology

“Sponges of the genus Cinachyrella are common in Caribbean and Floridian reefs and their archaeal and bacterial microbiomes were explored here using 16S rDNA tag pyrosequencing.”

* Symbiotic archaea in marine sponges show stability and host specificity in community structure and ammonia oxidation functionality – Fan Zhang – FEMS Microbiology Ecology

“PCR cloning and sequencing of archaeal 16S rRNA and amoA genes showed that the archaeal community composition and structure were different from that in seawater and varied among sponge species. “

Plant microbiome

Reduced dependence of rhizosphere microbiome on plant-derived carbon in 32-year long-term inorganic and organic fertilized soils – Chao Ai – Soil Biology and Biochemistry

“Wheat rhizosphere microbiome was studied by stable isotope probing and pyrosequencing.”

Environmental microbiome

Characterization of bacterial communities associated with seasonal water masses from Tongyoung in South Sea of Korea – Sung-Suk Suh – Ocean Science Journal

“In this study, we adopted a 16S rRNA gene tag-pyrosequencing technique to investigate the bacterial communities associated with two different water masses from Tongyoung in the South Sea of Korea. “

Bacterial community structure of a lab-scale anammox membrane bioreactor – Alejandro Gonzalez-Martinez – Biotechnology Progress

“In this study, next-generation sequencing techniques have been used for the investigation of the bacterial communities of this MBR Anammox for the first time ever. “

Metagenomics & Bioinformatics

GenomePeek: What exactly is that sequencing data? – Katelyn McNair – MicroBEnet

“I wrote the initial version of GenomePeek, and tested it with various data sets using this student’s data. I quickly found that some genes work better than others, and so currently the four genes analyzed are: 16S, recA, rpoB, and groEL.”

Metabolomics

Metabolite Content Profiling of Bottlenose Dolphin Exhaled Breath – Alexander A. Aksenov – Analytical Chemistry

“We have developed a method to reproducibly sample breath from small cetaceans, specifically Atlantic bottlenose dolphins (Tursiops truncatus). “

Proteomics

Symbiosis, Dysbiosis and Rebiosis – the value of metaproteomics in human microbiome monitoring – Lei Mao and Jacqueline Franke – Proteomics

“After a brief review of the history and state-of-the-art of metaproteomics in the field of environmental health research, focus of this perspective article will be put on the role of cross-species joint efforts in symbiosis, dysbiosis and rebiosis of the human gut during human development, pathogenesis and aging.”

More microbiology

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

“This discussion is intended to stimulate discourse about these seemingly different but very similar dormant states.”

* Phylogenomic Reconstruction Indicates Mitochondrial Ancestor Was an Energy Parasite
Zhang Wang, Martin Wu – PLOS ONE

“Using a phylogenomic approach and leveraging on the increased taxonomic sampling of alphaproteobacterial and eukaryotic genomes, we reconstructed the metabolisms of both proto-mitochondria and pre-mitochondria.”

Real-time video imaging as a new and rapid tool for antibiotic susceptibility testing by the disk diffusion method: a paradigm for evaluating resistance to imipenem and identifying extended-spectrum β-lactamases – Stéphanie Le Page – International Journal of Antimicrobial Agents

“..we present here for the first time video movies of the appearance of the diameter of inhibition by the disk diffusion in real-time. “

Microbes in the news

Can Microbes Help Feed the World? – Amy Mayer – BioScience

“To help meet the challenge for food, scientists are using new technologies to better understand the role that soil microbes might play in bolstering agricultural production. “

Dentists Want To See Studies On Pot-Cavity Link – CBS Local

“Patients are experiencing tooth decay, expensive dentist bills and the pain of dealing with it all. The biggest side effect is dry mouth.”

Bik’s Picks

Brain surgery, by robot, through the cheek – Science Daily

“Engineers have developed a surgical robot designed to perform brain surgery by entering through the cheek instead of the skull that can operate on a patient in an MRI scanner. Additionally, the engineers have designed the system so that much of it can be made using 3-D printing in order to keep the price low.”

* Hilarious cartoons on Imgur: Real Scientists vs. Movie Scientists 

* Authors retract green coffee bean diet paper touted by Dr. Oz – Ivan Oransky – Retraction Watch

“Two authors of a 2012 paper sponsored by a company that made grand claims about green coffee bean extract’s abilities to help people lose weight have retracted it. The study was cited by The Dr. Oz Show, and last month it cost the company a $3.5 million settlement with the Feds.”

[hr]

Microbiome digest, October 15, 2014

Posted on by

A seminar this Friday with Pat Schloss, but without HMP girl, aspartame and gut microbiome in a rat model, bacteria in arsenic contaminated soil, and inter-kingdom horizontal gene transfer.

Human oral microbiome

General Immune Status and Oral Microbiology in Patients with Different Forms of Periodontitis and Healthy Control Subjects – Jana Schmidt – PLOS ONE

“Subgingival plaque samples were taken from each individual and immediately cultivated for microbiological examination.”

Pregnancy and birth

* The vaginal microbiome, vaginal anti-microbial defence mechanisms and the clinical challenge of reducing infection-related preterm birth – SS Witkin – BJOG: An International Journal of Obstetrics & Gynaecology

“Ascending bacterial infection is implicated in about 40–50% of preterm births. “

Animal models of microbiome research

* Low-Dose Aspartame Consumption Differentially Affects Gut Microbiota-Host Metabolic Interactions in the Diet-Induced Obese Rat – Marie S. A. Palmnäs – PLOS ONE

“Serum metabolomics analysis revealed aspartame to be rapidly metabolized and to be associated with elevations in the short chain fatty acid propionate, a bacterial end product and highly gluconeogenic substrate, potentially explaining its negative affects on insulin tolerance. “

Effect of dietary supplementation with resveratrol on nutrient digestibility, methanogenesis and ruminal microbial flora in sheep – T. Ma – Journal of Animal Physiology and Animal Nutrition

“Two experiments were conducted to evaluate the effect of resveratrol on methanogenesis and microbial flora in Dorper × thin-tailed Han cross-bred ewes. “

Soil microbiome

Changing precipitation pattern alters soil microbial community response to wet-up under a Mediterranean-type climate – Romain L Barnard – ISME Journal

“Here, we investigated the effects of extending winter rainfall into the normally dry summer period on soil microbial response to a controlled rewetting event”

Surface binding and intracellular uptake of arsenic in bacteria isolated from arsenic contaminated site – Neha Vishnoi, Sonal Dixit, D.P. Singh – Ecological Engineering

“The present study deals with the surface binding and uptake of arsenic (As) in two bacterial strains (Bacillus subtilis and Paenibacillus macerans) isolated from the As contaminated soil.”

Water microbiome

Effects of ecological engineered oxygenation on the bacterial community structure in an anoxic fjord in western Sweden – Michael Forth – ISME Journal

“We used molecular ecologic methods to study changes in bacterial community structure in response to the oxygenation in the Byfjord. “

Food microbiology

Assessment of the bacterial and fungal diversity in home-made yoghurts of Xinjiang, China by pyrosequencing – Haiyan Xu – Journal of the Science of Food and Agriculture

“The bacterial and fungal community diversity in 22 home-made yoghurt samples was analyzed by pyrosequencing. “

CRISPRs, phages, viruses

In Hopes Of Fixing Faulty Genes, One Scientist Starts With The Basics – Joe Palca – NPR Morning Edition

“That’s certainly true for Jennifer Doudna. She hasn’t won a Nobel Prize, but many are whispering that she’s in line to win one for her work on something called CRISPR/Cas9 — a tool for editing genes.”

Bioinformatics and metagenomics

* Inter-phylum HGT has shaped the metabolism of many mesophilic and anaerobic bacteria – Alejandro Caro-Quintero and Konstantinos T Konstantinidis – ISME Journal

“Here, we devised a novel bioinformatic pipeline, which minimized the effect of over-representation of specific taxa in the available databases and other limitations of homology-based approaches by analyzing genomes in standardized triplets, to quantify gene exchange between bacterial genomes representing different phyla. “

* Origins of major archaeal clades correspond to gene acquisitions from bacteria –
Shijulal Nelson-Sathi – Nature

“To investigate the origin of higher taxa in archaea, we have determined gene distributions and gene phylogenies for the 267,568 protein-coding genes of 134 sequenced archaeal genomes in the context of their homologues from 1,847 reference bacterial genomes.”

Evidence of Carbon Fixation Pathway in a Bacterium from Candidate Phylum SBR1093 Revealed with Genomic Analysis – Zhiping Wang – PLOS ONE

“A phylogenetic analysis based on the 16S rRNA gene reveals that the phylotypes within candidate phylum SBR1093 are primarily clustered into 5 clades with a shallow branching pattern. “

Metagenomic Approach Reveals Variation of Microbes with Arsenic and Antimony Metabolism Genes from Highly Contaminated Soil – Jinming Luo – PLOS ONE

“Metagenomic analysis revealed that microbes from 18 phyla were present in the 5 samples of soil contaminated with high As and Sb.”

More microbiology

* The Phylogeny of Everything, the Origin of Eukaryotes, and the Rules of Taxonomy: Death to Archaea, Bacteria, and Eucarya! Long live Archaebacteria, Eubacteria, Eukaryota, and Prokaryota! – Judge Starling

“The molecular revelation based on orthologous ribosomal RNA sequences that prokaryotes are separable into two basic taxa—archaebacteria and eubacteria, and that these two taxa are approximately equidistant from eukaryotes, prompted Woese et al. (1990) to come up with a tripartite taxonomy of all life forms.”

Adhesion as a weapon in microbial competition – Jonas Schluter – ISME Journal

“We test the predictions of our model using the enteric pathogen Vibrio cholerae, which produces an extracellular matrix important for biofilm formation. “

Microbes in the news:

* Google Hangout on Friday: MicroSeminar: A new way of doing conferences – Pat Schloss

“You will not see HMP Girl, no quotes of specious statistics, no mention of obscure disease, and no venturing into the weeds of bioinformatics. I will be describing unpublished experiments from the lab where we have taken various sources of microorganisms and used them to colonize mice that lack their own microbiota.”

‘Grapes of Wrath’: Stomping out grape disease one vineyard at a time – Phys.org

“A Rochester Institute of Technology scientist and an RIT alumnus are close to completing the genetic blueprint, or microbiome, of grape crown gall tumor disease—the bane of vineyards worldwide. ”

Redefining Human: The Microbiome Documentary Series – Root House Studio – Kickstarter

“We know science documentaries can be painfully boring, so Redefining Human will use a variety of new techniques to turn this complex science into an informative and entertaining documentary series.”

What’s in my microbiome? – Richard Sprague

“To find out what’s in my microbiome now, I bought a $400 kit from the San Francisco company uBiome. “

Science, publishing and career

* Rise of the Rest: The Growing Impact of Non-Elite Journals – Anurag Acharya – Google / Arxiv

“Our analysis indicates that the number of top-1000 papers published in non-elite journals for the representative subject category went from 149 in 1995 to 245 in 2013, a growth of 64%.”

Review rewards – Welcome efforts are being made to recognize academics who give up their time to peer review – Nature Editorial

“A welcome movement is under way to publicly register and recognize the hitherto invisible efforts of referees.”

Overqualified or underqualified? – Carrie Arnold – Science

“As unemployment stretched from weeks into months, Milstein decided that her Ph.D. was working against her. “

 

Satire: Facebook Offers To Freeze Female Employee’s Newborn Children – The Onion

“Women deserve to have the option to postpone motherhood until they feel fully prepared, which is why Facebook will also cover the cryonic facility’s annual maintenance costs for as many years as our employees feel they need. “

Bik’s Picks

360-Degree View of the Tomato – Anna Azvolinsky – The Scientist

“Researchers have sequenced 360 varieties of the tomato plant to create a comprehensive map of the evolution of the fruit from its wild form to the modern varieties. “

Extinct giant kangaroos didn’t hop, they walked – Andy Coghlan – New Scientist

“They had faces like rabbits and some were 2 metres tall. But now it seems that an extinct giant kangaroo didn’t hop – it walked.“

 

Chimpanzees have favorite ‘tool set’ for hunting staple food of army ants – Science Daily

“New research shows that chimpanzees search for the right tools from a key plant species when preparing to ‘ant dip’ — a crafty technique enabling them to feast on army ants without getting bitten. “

[hr]

General microbiology and science, October 14, 2014

Posted on by

A living review of multivariate techniques, spatial organizations of bacterial genomes, and metabolomics of wetlands, pigs, marine bacteria and free-living humans.

Bioinformatics

* A Guide to Statistical Analysis in Microbial Ecology: a community-focused, living review of multivariate data analyses – Pier Luigi Buttigieg – FEMS Microbiology Ecology

“we present the GUide to STatistical Analysis in Microbial Ecology (GUSTA ME): a dynamic, web-based resource providing accessible descriptions of numerous multivariate techniques relevant to microbial ecologists”

Techniques

New approaches to understanding the spatial organization of bacterial genomes – Tung BK Le, Michael T Laub – Current Opinion in Microbiology

“Here, we review the current arsenal of techniques used to query chromosome structure”

Development of Clamping Probe for Rare DNA Detection using Universal Primers – Meyong il Kim – E-FAS Journal

“In this study, we evaluated the efficiency of rare gene detection for two kinds of clamping probes which were successfully utilized for eukaryotic symbiont analysis”

Metabolomics

Microbial community metabolic function in subsurface flow constructed wetlands of different designs – Mark Button – Ecological Engineering

“Microbial community function followed a clear gradient along the flow direction. Metabolic profiles were system specific (horizontal, vertical, and aerated).”

A high fat, high choleststerol diet leads to changes in metabolite patterns in pigs – a metabolomic study – Jianghao Sun – Food Chemistry

“Extracts of plasma, fecal and urine samples from pigs fed high fat or basal regular diets for 11 weeks were analyzed using ultra-high performance liquid chromatography with high-resolution mass spectrometry “

Free-living individuals – as in “not in prison”?
An NMR metabolomics approach reveals a combined-biomarkers model in a wine interventional trial with validation in free-living individuals of the PREDIMED study – Rosa Vázquez-Fresno – Metabolomics

A High-Resolution LC-MS-Based Secondary Metabolite Fingerprint Database of Marine Bacteria – Liang Lu – Nature Scientific Reports

“Till now, 1,430 bacterial strains spanning 168 known species collected from different marine environments were cultured and profiled. “

Viruses and phages

Ribonucleotide reductases reveal novel viral diversity and predict biological and ecological features of unknown marine viruses – Eric G. Sakowski – PNAS USA

“We identify ribonucleotide reductase (RNR) genes as superior markers of viral diversity. RNR genes are distributed over a broad range of viruses”

More microbiology

Strength in Diversity – Daniel J. Wolter, Lucas R. Hoffman – Cell Host & Microbe

“In this issue of Cell Host & Microbe, Hammer et al. (2014) show that distinct, slow-growing bacteria have better in vitro and in vivo growth and virulence when cocultured than in isolation. “

The Journal of Infectious Diseases has a special Issue on Polio: The Final Phase of Polio Eradication and Endgame Strategies for the Post-Eradication Era – Journal of Infectious Diseases

Science, publishing, career

Correcting the scientific record: An introduction to retractions – Bonnie Swoger – Scientific American

“Although the system is far from perfect, the retraction process is one of the ways in which the scientific literature corrects itself over time.”

 

Bik’s Picks

When Racism Was a Science – ‘Haunted Files: The Eugenics Record Office’ Recreates a Dark Time in a Laboratory’s Past – Joshua A. Krisch – New York Times

“In its heyday, the office was the premier scientific enterprise at Cold Spring Harbor. There, bigoted scientists applied rudimentary genetics to singling out supposedly superior races and degrading minorities. “

Paul Ryan: Science doesn’t get climate change – Jane C. Timm – MSNBC

“A full 97% of researchers taking a stance on climate change say it’s man-made, as do 97-98% of the most frequently-published climate scientists. But according to Wisconsin Rep. Paul Ryan, they’re all wrong.”

Get fish fry with a side of science at ‘Science of the Supper Club’ this Friday – Lindsay Christians – The Capital Times

“Science is everywhere, even at a Friday night fish fry. That’s the message of a new event this Friday called “Science of Supper Clubs,” part of the four-day Wisconsin Science Festival held at various venues around the state.”

[hr] [hr]

Microbiome digest, October 13, 2014

Posted on by

Preterm infant gut microbiome, fecal transplants, microbes in space, and microbiome of 8 different fish species.

Pregnancy and birth

* Development of the preterm infant gut microbiome: a research priority – Maureen W Groer (Jack Gilbert lab) – Microbiome

“This review provides a synthesis of our understanding of the normal development of the infant gut microbiome and contrasts this with dysbiotic development in the VLBW infant.”

Fluorescence in situ hybridization for identification of microorganisms in acute chorioamnionitis – D. Schmiedel – Clinical Microbiology and Infection

“Using a diagnostic fluorescence in situ hybridization probe panel, we visualized Staphylococcus aureus and Streptococcus mitis group in two cases of acute chorioamnionitis. “

The Role of Mycoplasma and Ureaplasma in Adverse Pregnancy Outcomes – Amy P. Murtha – Obstetrics and Gynecology Clinics of North America

* Impact Of Lifestyle On The Gut Microbiota Of Healthy Infants And Their Mothers – The Aladdin Birth Cohort – Helena Marell Hesla – FEMS Microbiology Ecology

“Samples collected from infants at ages six days, three weeks, two months and six months and from their mothers before and after delivery, respectively, were analyzed using 454-pyrosequencing.”

Human gut microbiome

* Oral, Capsulized, Frozen Fecal Microbiota Transplantation for Relapsing Clostridium difficile Infection – Ilan Youngster – JAMA

“Self-ranked health scores improved significantly on a scale of 1 to 10 from a median of 5  for overall health and 4.5  for gastrointestinal-specific health on the day prior to FMT to 8 after FMT administration for both overall and gastrointestinal health (P = .001).”

* Impact of Experimental Hookworm Infection on the Human Gut Microbiota – Cinzia Cantacessi – Journal of Infectious Diseases

“We used 16S rRNA gene amplification and pyrosequencing to characterize, for the first time to our knowledge, the differences in composition and relative abundance of fecal microbial communities in human subjects prior to and following experimental infection with the blood-feeding intestinal hookworm, Necator americanus. “

Genomics of schizophrenia: time to consider the gut microbiome? – T G Dinan – Molecular Psychiatry

“To date, this vast quantity of DNA has been largely ignored in schizophrenia research.”

Animal microbiome

Comparative study on gastrointestinal microbiota of eight fish species with different feeding habits – Jinjin Li – Journal of Applied Microbiology

“The V1 to V3 regions of 16S rRNA gene were analyzed by highthroughput sequencing (454 platform) to compare the gut microbiota of different fish species. “

Dining local: the microbial diet of a snail that grazes microbial communities is geographically structured – Richard O’Rorke – Environmental Microbiology

“we collected 102 snail fecal samples as a proxy for diet, and 102 matched-leaf samples from four locations. We used Illumina amplicon sequencing to determine bacterial and fungal community composition. “

Bacterial associates of seed-parasitic wasps (Hymenoptera: Megastigmus) – Amber R Paulson – BMC Microbiology

“We characterized the bacterial symbionts of Megastigmus (Hymenoptera: Torymidae), a lineage of seed-parasitic chalcid wasps, with the goal of identifying microbes that might play an important role in aiding development within seeds, including supplementing insect nutrition or manipulating host trees.“

Bioreactor microbiome

Biofouling and Microbial Communities in Membrane Distillation and Reverse Osmosis – Katherine R. Zodrow – Environmental Science & Technology

“Phylogenetic analysis using next-generation sequencing of 16S ribosomal DNA showed significant shifts in the microbial communities. “

Integrated ‘omics analysis for studying the microbial community response to a pH perturbation of a cellulose-degrading bioreactor culture – Amy A Boaro – FEMS Microbiology Ecology

“16S rDNA pyrosequencing results revealed increased alpha diversity in the microbial community after the perturbation, and a persistence of the dominant community members over the duration of the experiment.”

Environmental microbiome

Effects of Bioavailable Heavy Metal Species, Arsenic, and Acid Drainage from Mine Tailings on a Microbial Community Sampled Along a Pollution Gradient in a Freshwater Ecosystem – Togwell A. Jackson – Geomicrobiology Journal

“Ribosomal ribonucleic acid, fatty acid, and phospholipid analyses, along with assays of CO2 production, denitrification, and enzyme activities, were performed to characterise the microflora; and environmental conditions were defined by various physicochemical analyses, including determination of bioavailable metal species. “

The role of macrobiota in structuring microbial communities along rocky shores – Catherine A Pfister​, Jack A Gilbert, Sean M Gibbons – PeerJ

“At two coastal locations in the northeast Pacific Ocean, we show that microbial composition was significantly different between inert surfaces, the biogenic surfaces that included rocky shore animals and an alga, and the water column plankton.”

Microbes in (simulated) space

The development and succession of microbial communities in 90-day Bioregenerative Life Support Experiment in the Lunar Palace 1 – Yi Sun – 40th COSPAR Scientific Assembly

“In this study, the development and succession of the microbial communities of air, water system, plant system, and key facilities surfaces in Lunar Palace 1 were continuously monitored and analyzed by using plate counting method and molecular biological method during the 90-day experiment.”

The viability of native microbial communities in martian environment (model) – Vorobyova, Elena – 40th COSPAR Scientific Assembly

“It was shown that in simulated conditions close to the parameters of the Martian regolith, the diversity of natural bacterial communities was not decreased, and in some cases the activation of some bacterial populations occurred in situ.”

Food microbiology

Microbial succession and the functional potential during the fermentation of Chinese soy sauce brine – Joanita Sulaiman – Frontiers in Microbiology

“Whole genome shotgun (WGS) method revealed that the fermentation brine was dominated by the bacterial genus Weissella and later dominated by the fungal genus Candida.”

Transcriptomics/metagenomics

Adaptation to environmental factors shapes the organization of regulatory regions in microbial communities – Leyden Fernandez – BMC Genomics

“We have here characterized and analyzed the metaregulome of three different environments, as well as their impact in the adaptation to particular variable physico-chemical conditions. “

Other microbiology

Inverse Correlation Between Helicobacter pylori Colonization and Obesity in a Cohort of Inner City Children – Hanh D. Vo – Helicobacter

“Our findings in a North American cohort are in agreement with studies from Asia and Europe suggesting that H. pylori infection decreases the prevalence of obesity in children.”

Microbes in the news

* Podcast: Your Home, Your Bacteria – Science Friday

“Jack Gilbert… is trying to develop a better understanding of the way people, bacteria, and the environment around them interact, from the kitchen floor to the greater Chicago area.”

Landmark Crohn’s Microbiome Study Yields Important Findings – David Wild – GastroEndoNews

“The association suggests that there is a potential link between the presence of these microbes and the serologic biomarkers, but that needs to be determined in future studies,” said Dr. Xavier, who presented the study at Digestive Disease Week 2014”

Is that how the capsules will look like? Good news: You can take your fecal transplants orally – Rachel Feltman – Washington Post

“In a study published Saturday in the Journal of the American Medical Association, researchers report that the same success rate can be reached by processing the healthy excrement into capsules and administering the pills by mouth.“

Probiotics on the brain: A growing number of scientists now believe that gut bacteria can influence mental health – Elizabeth Gehrman – Boston Globe

“Whenever someone says there’s an impossibility in medicine,” says Williams, “they end up being corrected in a few years.”

Unravelling the link between gut bacteria and horse health – University of Surrey

“Researchers at the University of Surrey, in collaboration with colleagues from Reading and Liverpool universities, have been awarded £100,000 funding by Petplan Charitable Trust… to create a laboratory model of the horse’s hindgut.”

The Second Brain: Gut Bacteria Control Human Behavior to Get the Best Nutrients – David Gutierrez – Epoch Times

“Bacteria within the gut are manipulative,” researcher Carlo Maley, PhD, said. “There is a diversity of interests represented in the microbiome, some aligned with our own dietary goals, and others not.”

Science, publishing, career

Sometimes My Job Seems Like a Secret – Amy Davidson – Speaking Of Research

“You are going to hell.” “You are a horrible person.” “We cannot be friends anymore.”

Sell yourself: Adding substance to your personal statement – Brian Rybarczyk – Science Careers at Science Magazine

“Obtaining feedback on your personal statement (or any piece of writing) can be intimidating, but feedback is essential for creating a polished and readable document.”

Bik’s Picks

Why Orange Juice Tastes Disgusting After You Brush Your Teeth: Finally, an answer – Sarah Fecht – Popular Science

“In a handy video, the American Chemical Society has explained why orange juice (and food in general) tastes like soap after you brush your teeth. “

[hr]

General microbiology and science digest, October 7, 2014

Posted on by

Transmission of Staph aureus in the hospital, a new assembler tool, metabolomics of the human gut microbiome, and a polio virus spill in Belgium.

More Microbes

Absence of Patient-to-Patient Intrahospital Transmission of Staphylococcus aureus as Determined by Whole-Genome Sequencing – S. Wesley Long – mBio

“To identify patient-to-patient intrahospital transmission using high-resolution genetic analysis, we sequenced the genomes of a consecutive set of 398 S. aureus isolates from sterile-site infections. “

Bioinformatics

Improved Assemblies Using a Source-Agnostic Pipeline for MetaGenomic Assembly by Merging (MeGAMerge) of Contigs – Matthew Scholz, Chien-Chi Lo & Patrick S. G. Chain – Nature Scientific Reports

“MeGAMerge consistently outperforms individual assembly methods, producing larger contigs with an increased number of predicted genes, without replication of data. “

Inferring phylogenies of evolving sequences without multiple sequence alignment – Cheong Xin Chan – Nature Scientific Reports

“Here, using simulated sequence sets of various sizes in both nucleotides and amino acids, we systematically assess the accuracy of phylogenetic inference using an alignment-free approach, based on D2 statistics, under different evolutionary scenarios. “

Gut Check: Exploring Your Microbiome – Coursera / University of Colorado Boulder

“Join us on a guided tour of the human gut and its microscopic inhabitants.”

Metabolomics

Modelling the emergent dynamics and major metabolites of the human colonic microbiota – Helen Kettle – Environmental Microbiology

“To reduce the complexity of the system, we divide the bacterial community into 10 bacterial functional groups (BFGs) each distinguished by its substrate preferences, metabolic pathways and its preferred pH range. “

Microbes in the news

* Petri Dish: The third branch of life – David Woodland – Summit Daily

“In addition to being an interesting branch on the tree of life, archaebacteria have turned out to be an incredibly valuable source of new products for science and industry. “

Pharmaceutical Giant GlaxoSmithKline “Accidentally” Released 45 Liters of Concentrated Live Polio Virus in the Environment – Global Research

“As reported to ECDC by Belgian authorities, on 2 September 2014, following a human error, 45 litres of concentrated live polio virus solution were released into the environment by the pharmaceutical company, GlaxoSmithKline (GSK), in Rixensart city, Belgium.”

Science, publishing and career

* Science is innate! (behind a paywall, even at Stanford) – Jack A Gilbert – Genome Biology

“….when I am asked, as I often am, about how my research findings have influenced my day-to-day activities, I like to take a step back and think about what it means to be a scientist.”

Why I have taken a leave of absence from Science: to protest the abrupt firing of 4 colleagues – Michael Balter – Letter to Science

“Thus it is particularly painful and sad for me to tell you that I will be taking a three-month leave of absence in protest of recent events at Science and within its publishing organization, the American Association for the Advancement of Science (AAAS).
“

Bik’s Picks

Killer whales learn to communicate like dolphins – Science Daily

“…killer whales can engage in cross-species vocal learning: when socialized with bottlenose dolphins, they shifted the sounds they made to more closely match their social partners.”

NASA selects astrobiologists to study life origins and extraterrestrial possibilities – Jim Algar – Tech Times

“NASA announced 5-year grants adding up to nearly $50 million for seven research groups across the U .S. to study life in the universe and its origins, distribution, evolution and future.”

The most passive aggressive acknowledgement ever – BioDataGanache – SciEasterEggs

“The authors in this paper put some serious time in on this sucker, and they wanted to make a statement about it.”

[hr]

General microbiology and science digest, October 6, 2014

Posted on by

Phages to reduce biofilms or monitor virus outbreaks, binning metagenomic reads, lots of microbes in the news. In Bik’s Picks, we have the 2014 Nobel Prize for Medicine and a giant ant nest.

 

More Microbes

Combined Use of Bacteriophage K and a Novel Bacteriophage To Reduce Staphylococcus aureus Biofilm Formation – D. R. Alves – Applied and Environmental Microbiology

“DRA88 was mixed with phage K to produce a high-titer mixture that showed strong lytic activity against a wide range of S. aureus isolates, including representatives of the major international MRSA clones and coagulase-negative Staphylococcus. “

Detection of Pathogenic Viruses in Sewage Provided Early Warnings of Hepatitis A Virus and Norovirus Outbreaks – Maria Hellmér – Applied and Environmental Microbiology

“ In this study, the presence of eight pathogenic viruses (norovirus, astrovirus, rotavirus, adenovirus, Aichi virus, parechovirus, hepatitis A virus [HAV], and hepatitis E virus) was investigated in sewage to explore whether their identification could be used as an early warning of outbreaks. “

Bioinformatics

New software aims to improve sorting the microbiome – The Cherry Creek News

“MaxBin automates the binning of assembled metagenomic scaffolds using an expectation-maximization algorithm after the assembly of metagenomic sequencing reads,” says Singer, a chemist who also holds an appointment with Berkeley Lab’s Earth Sciences Division. “

Microbes in the news

* King’s launches British Gut – King’s College London

“British Gut – the UK’s largest open-source science project to understand the microbial diversity of the human gut – has been launched today by the Department of Twin Research at King’s College London, in collaboration with American Gut.”

Pay attention to your gut bacteria – Charles Wallace – Financial Times

“A number of organisations, such as Mr Leach’s own American Gut project and the commercial venture uBiome, offer an analysis of the bacteria in your gut for about $100. “

Home sweet microbiome – By Scott LaFee – UT San Diego

“The University of Chicago recently published findings from its Home Microbiome Project, which surveyed the domiciles of seven families: 18 people, three dogs and one cat.”

Medical superbugs: Antibiotic-resistant bacteria carried by more than a third of nursing home residents, study – ABC Australia

“Scientists from Monash University swabbed more than a 100 residents from four high-care facilities across the city.”

Special bacteria, 13000 cleaners to clean Dhaka – Rezaul Hoque – BDNews

“This special kind of microorganism will be sprayed on waste dumps. The spray has been developed in Thailand. We have introduced it here in Bangladesh with the aid of a Malaysian company.””

Yogurt bacteria could replace colonoscopies for cancer detection – Billy Steele – EnGadget

“MIT professor Sangeeta Bhatia is working on engineered bacteria that detects colorectal cancer. After the nanoparticles pass through the digestive system, a urine sample shows results on a reactive paper — similar to that of a pregnancy test.”

Science and Publishing

Adjudicating “misbehavior”: how can scientists respond when they don’t get fair credit? –  Janet D. Stemwedel – Scientific American

“Denying someone of fair credit for the contribution they made to a piece of research is not a good thing. But who can you turn to if someone does it to you? “

Twitter’s science stars, the sequel – John Travis – Science

“We listed. You tweeted (often in outrage). We listened (mostly). And now we’re doubling down on our recent list of Twitter’s 50 most popular researchers with a revision that names 100 of the most followed scientists on the social media platform. “

Bik’s Picks

2014 Nobel Prize in Physiology or Medicine: Cells that constitute a positioning system in the brain – Science Daily

“The 2014 Nobel Prize in Physiology or Medicine has been awarded to John O´Keefe, May-Britt Moser and Edvard I. Moser for their discoveries of cells that constitute a positioning system in the brain.”

Concrete Cast of Ant Nest Reveals Huge Underground Metropolis – Lisa Winter – IFL Science

“Through a process that took a few months, researchers made a cast of an anthill by pumping it full of concrete, allowing it to cure and dry, then excavating it out to explore the intricacies of the ant civilization. “

Tall tale: scientists unravel the genetics of human height – Will Dunham – Daily Mail

“Researchers on Sunday unveiled what they called the biggest such study to date, analyzing genome data from more than a quarter million people to identify nearly 700 genetic variants and more than 400 genome regions relating to height.”

[hr]

Microbiome Digest, October 3, 2014

Posted on by

Antibiotics in the first 24 months of life associated with obesity, Giant Pandas are no cul-de-sac, and microbiome and inflammatory disease. And lots of weekend reads!

Pregnancy and birth

Association of Antibiotics in Infancy With Early Childhood Obesity – L. Charles Bailey – JAMA Pediatrics

“Cumulative exposure to antibiotics was associated with later obesity …; this effect was stronger for broad-spectrum antibiotics”

Human gut microbiome

Faecal microbiota composition and host–microbe cross-talk following gastroenteritis and in postinfectious irritable bowel syndrome – Jonna Jalanka-Tuovinen – Gut

“Using a phylogenetic microarray and selected qPCR assays, we analysed differences in the faecal microbiota of 57 subjects from five study groups”

Animal models of microbiome research

Dietary modulation of the microbiome affects autoinflammatory disease – John R. Lukens – Nature

“Here we show that the intestinal microbiota of diseased Pstpip2cmo mice was characterized by an outgrowth of Prevotella. “

Mammal microbiome

Giant pandas are not an evolutionary cul-de-sac: Evidence from multidisciplinary research
Fuwen Wei – Molecular Biology and Evolution

“The latest and most advanced research shows that giant pandas are successful animals highly adapted to a specialized bamboo diet via morphological, ecological and genetic adaptations and co-adaptation of gut microbiota.”

Plant microbiome

Multi-symbiotic systems: functional implications of the coexistence of grass–endophyte and legume–rhizobia symbioses – Pablo A. García Parisi – Oikos

“After five months, we quantified the number of nodules in Trifolium roots, shoot biomass of both plant species, and the contribution of atmospheric nitrogen fixation vs. soil nitrogen uptake to above ground nitrogen in each plant species. “

Microbes in the news

Young companies, big ideas – The 2014 edition of the CNN 10: Startups – CNN

“Her doubts were assuaged when supporters donated $350,000 to help launch her startup, uBiome. Now, two years later, uBiome is exploring an emerging field of human biology while giving users a glimpse into how their bodies work.”

No women, unfortunately! And they did not accept my application to be a judge either. MO BIO Laboratories, Inc. announces Microbiome Awards winners – PR NewsWire

“MO BIO Laboratories, Inc. is proud to announce the winners of the MO BIO Microbiome Awards, which provide young, extraordinary scientists with funding and recognition to carry out scientific work in the field of microbiome research.”

Super-bacteria are growing in space … and we’re the ones breeding them – Meera Senthilingam – CNN

“You might think of space as a germ-free environment, but microbes can be carried to space inside human gut flora as well as in food and water and once up there, can be expelled by humans in their breath.”

There’s a simple way to stop the spread of antibiotic-resistant bacteria – Melinda Mary Pettigrew – Washington Post

“The issue boils down to this: we use too many antibiotics. Studies show that up to half of all antibiotics are prescribed unnecessarily.”

Across Indian zoos, rat pee spreading bacteria, killing big cats: Scientists – Priyangi Agarwal – The Times of India

“The leptospirosis bacteria, found in rodent urine, makes its way into blood samples of zoo animals and causes higher morbidity and mortality, scientists at the Indian Veterinary Research Institute (IVRI) in Bareilly have found. “

Brazil releases ‘good’ mosquitoes to fight dengue fever – BBC

“Brazilian researchers in Rio de Janeiro have released thousands of mosquitoes infected with bacteria that suppress dengue fever. The hope is they will multiply, breed and become the majority of mosquitoes, thus reducing cases of the disease.“

Science, Publishing, and Career

Young, Brilliant and Underfunded – Andy Harris – New York Times

“The bulk of that money goes to researchers who are in many cases esteemed in their fields — but also, in many cases, beyond the age when most scientists make their most important contributions to their fields.”

Why women leave tech: It’s the culture, not because ‘math is hard’ – Kieran Snyder – Fortune

“Stories from 716 women who left tech show that the industry’s culture is the primary culprit, not any issues related to science education.”

Satire: Tips For Working With A Lab Partner – FakeScience

Bik’s Picks

Is this the end of autumn as we know it? – Stephanie Pappas – BBC Earth

“The study of the basic triggers of autumnal leaf changes, never mind the impact of climate change on these, is still in its infancy in part because scientists have traditionally focused their attentions on the seasonal changes in March and April than those later in the year.”

The Incredible Rubber Glove – Olga Khazan – The Atlantic

“Basic protective gear was revolutionary for 19th-century medicine, and health workers trying to stop Ebola are recognizing its importance all over again.”

This Is Why Your Voice Sounds So Frickin’ Weird To You – Macrina Cooper-White – The Huffington Post

“Have you ever listened to a recording of your own voice and thought, “Whoa. Do I really sound like that?” Well, it’s time to face the music. You really do.”

[hr]

General microbiology and science digest, October 2, 2014

Posted on by

Viruses and metagenomics, the soil of Central Park, and sweat eating bacteria.

Ecology

Loops and autonomy promote evolvability of ecosystem networks – Jianxi Luo – Scientific Reports

“To correlate ecosystem structure and evolvability, we adopt the NK model originally from evolutionary biology to generate and assess the ruggedness of fitness landscapes of a wide spectrum of model food webs with gradual variation in the amount of feeding loops and link density. “

Erosion of functional independence early in the evolution of a microbial mutualism
Kristina L. Hillesland – PNAS USA

“We show that as the bacterium Desulfovibrio vulgaris evolved for 1,000 generations in conditions forcing cooperation with the archaeon Methanococcus maripaludis, it lost a key metabolic trait that would be required for it to grow alone in most environments.”

Tree diversity does not always improve resistance of forest ecosystems to drought – Charlotte Grossiord – PNAS USA

“Within our study network of 160 forest stands across Europe, we found that mixed species forests are less exposed to drought stress in some regions only. “

Phages, viruses, and metagenomics

Dynamics of CRISPR Loci in Microevolutionary Process of Yersinia pestis Strains – Maria Paloma S. Barros – PLOS ONE

“This study allowed observing a microevolutionary process in a group of Y. pestis isolated from Brazil. “

Metagenomic approaches for direct and cell culture evaluation of the virological quality of wastewater – Tiong Gim Aw – Journal of Virological Methods

“In this study, NGS and bioinformatics have been employed for the direct detection and characterization of viruses in wastewater and of viruses isolated after cell culture. “

Metagenomics / Bioinformatics

Analysis of the Relationship between Genomic GC Content and Patterns of Base Usage, Codon Usage and Amino Acid Usage in Prokaryotes: Similar GC Content Adopts Similar Compositional Frequencies Regardless of the Phylogenetic Lineages – Hui-Qi Zhou – PLOS ONE

“The GC contents of 2670 prokaryotic genomes that belong to diverse phylogenetic lineages were analyzed in this paper. “

Benchmarking Undedicated Cloud Computing Providers for Analysis of Genomic Datasets
Seyhan Yazar – PLOS ONE

“We benchmarked two established cloud computing services, Amazon Web Services Elastic MapReduce (EMR) on Amazon EC2 instances and Google Compute Engine (GCE), using publicly available genomic datasets”

SDT: A Virus Classification Tool Based on Pairwise Sequence Alignment and Identity Calculation – Brejnev Muhizi Muhire – PLOS ONE

“Here we present Sequence Demarcation Tool (SDT), …that aims to provide a robust and highly reproducible means of objectively using pairwise genetic identity calculations to classify any set of nucleotide or amino acid sequences.”

A two-stage statistical procedure for feature selection and comparison in functional analysis of metagenomes – Naruekamol Pookhao – Bioinformatics

“We propose a two-stage statistical procedure for selecting informative features and identifying differentially abundant features between two or more groups of microbial communities.”

FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus – Emmanuel Prestat – Nucleic Acids Research

“A new functional gene database, FOAM (Functional Ontology Assignments for Metagenomes), was developed to screen environmental metagenomic sequence datasets. “

Microbes in the News

Soil Microbiome of Central Park – Jef Akst – The Scientist

“The soil of New York City’s Central Park is bursting with biodiversity spanning all three domains of life, according to a study published today”

Supporting the “Good” Gut Microbes – Anna Azvolinksy – The Scientist

“During systemic infection, mice kick-start the production of a specific sugar to feed and protect the beneficial bacteria in their guts while fighting pathogenic strains.”

Sweat-Eating Bacteria: Acne Miracle Cure? – Discovery News

“A new, small study has shown that applying a topical creme containing the bacteria leads to healthier skin and could be used to treat acne and promote healing in wounds.”

Women in Science

* Sexism in Science – sbhatnagar3 – Phylogenomics Blogspot

“Please don’t treat these seminars as a fashion show. It distracts the people away from your work”.”

Bik’s Picks

Behavior of bats at wind turbines – Paul. M. Cryan – PNAS USA

“Bats are dying in unprecedented numbers at wind turbines, but causes of their susceptibility are unknown. “

Flexible energetics of cheetah hunting strategies provide resistance against kleptoparasitism – David M. Scantlebury – Science

“We show that daily energy expenditure (DEE) of cheetahs was similar to size-based predictions and positively related to distance traveled.”

Previously unseen details of seafloor exposed in new map – Science Daily

“Twice as accurate as the previous version, the new map features a much more vivid picture of seafloor structures, including thousands of previously uncharted mountains.”

[hr]

General microbiology and science, September 29, 2014

Posted on by

Metabolomics, metagenomics, OTU binning, DNA extraction for metagenomics, RNAseq, life without water, microbes and art, and Bik’s Picks.

Metabolomics

A Peptide-Based Method for 13C Metabolic Flux Analysis in Microbial Communities – Amit Ghosh – PLOS Computational Biology

“Here we propose a new type of 13C MFA that infers fluxes based on peptide labeling, instead of amino acid labeling. “

Metabolic fingerprint of dimethyl sulfone (DMSO2) in microbial-mammalian co-metabolism – Xuan He and Carolyn Marie Slupsky – Journal of Proteome Research

“Here, we review a metabolic pathway that integrates the microbial catabolism of methionine with mammalian metabolism of methanethiol (MT), dimethyl sulfide (DMS) and dimethyl sulfoxide (DMSO)”

Metagenomics

Metagenomic epidemiology: a new frontier – Stephen S Francis, Lee W Riley – Journal of Epidemiology and Community Health

“In this commentary we hope to briefly summarise studies into the bacterial and viral microbiome and how this shifting paradigm affects epidemiology.“

Phages and viruses

Viral attack exacerbates the susceptibility of a bloom-forming alga to ocean acidification – Shanwen Chen – Global Change Biology

“..when the harmful bloom alga Phaeocystis globosa is infected with viruses under future ocean conditions, its photosynthetic performance further decreased and cells became more susceptible to stressful light levels..”

Ecology / Bioinformatics

Limits to robustness and reproducibility in the demarcation of operational taxonomic units – Thomas S. B. Schmidt – Environmental Microbiology

“Using a global data set of 887 870 bacterial 16S rRNA gene sequences, we objectively quantified biases introduced by several widely employed sequence clustering algorithms. “

Techniques

* DNA extraction protocols cause differences in 16S rRNA amplicon sequencing efficiency but not in community profile composition or structure – Benjamin E. R. Rubin – MicrobiologyOpen

“While bacterial community composition recovered using Illumina 16S rRNA amplicon sequencing was not detectably biased by any method, the quantity of bacterial DNA varied drastically, reducing the number of samples that could be amplified and sequenced. “

Protocols for metagenomic DNA extraction and Illumina amplicon library preparation for faecal and swab samples – A.-T. E. Vo1 and J. A. Jedlicka – Molecular Ecology Resources

“We developed and tested a novel metagenomic DNA extraction approach using solid phase reversible immobilization (SPRI) beads on Western Bluebird (Sialia mexicana) samples stored in RNAlater.”

Caught in the act: RNA-Seq provides novel insights into mRNA degradation – Jan Gerwig and Jörg Stülke – Molecular Microbiology

“In Molecular Microbiology, Liu et al. (2014) have analysed RNA processing by polynucleotide phosphorylase, the major 3′–5′ exonuclease in Bacillus subtilis.”

3D genome reconstruction from chromosomal contacts – Annick Lesne – Nature Methods

“We propose a two-step algorithm, ShRec3D, and assess its accuracy using both in silico data and human genome-wide 3C (Hi-C) data.”

More microbiology

Multiplication of microbes below 0.690 water activity: implications for terrestrial and extraterrestrial life – Andrew Stevenson – Environmental Microbiology

“We discuss water activity in relation to the limits of Earth’s present-day biosphere; the possibility of microbial multiplication by utilizing water from thin, aqueous films or non-liquid sources;”

Microbes in the News

Scientists sniffing out the Western allergy epidemic – BBC News

“Both families gamely agreed to provide bacterial swabs of their skin, guts and even their homes in the hope they might offer clues about why they suffer from allergies.”

Study looks at bacteria on a plane – CNN Wire

“A study by Auburn University looked at how long two potentially deadly bacteria, e-coli and MRSA, can live on airline surfaces. They checked things like toilet handles, tray tables and seat pockets.”

Bacteria in wine may bring health benefits – LiveScience – Agata Blaszczak Boxe

“In the study, researchers in Spain isolated 11 strains of bacteria from wine, including strains of Lactobacillus, which are also found in yogurt, as well as Oenococcus and Pediococcus bacteria, which are associated with the wine-making process.”

A gut feeling: Bacteria like that found in yoghurt may have helped shape our personalities and made us who we are – Alex Finnis – Daily Mail UK

“Bacteria in our stomachs can affect our brain chemistry, scientists have discovered – which means eating yoghurt could help us be happier.

Science and Art

Should Silicon Valley Hire Microbes? – Glenn McDonald – Discovery

“It’s an art installation slated to launch October 21 at San Francisco’s Modernism Gallery. The event will feature the official certification of approximately 100 billion bacteria in areas including product development and finance. “

Octopus bacteria lights up this installation – Liat Clark – Wired UK

“A designer has harvested bacteria from an octopus to create a bioluminescent installation that lights up when it is moved.”

Photographer Immerses His Film in Live Bacteria for Years to Create Unique Portraits – Gannon Burgett – PetaPixel

“Over the course of a few weeks, months or years, the microbes destabilize and eat away at the silver halide particles in the emulsion.”

Bik’s Picks

Dolphins are attracted to magnets: Add dolphins to the list of magnetosensitive animals, French researchers say – Science Daily

“Dolphins are indeed sensitive to magnetic stimuli, as they behave differently when swimming near magnetized objects.”

Science explains why volcanoes are erupting all over the place right now – Robin Wylie – Washington Post

“The Earth seems to have been smoking a lot recently. Volcanoes are erupting in Iceland, Hawaii, Indonesia, Ecuador and Mexico right now. “

Scientists find tiny, poisonous new mystery frog – Andrew Griffin – Independent

“Scientists have discovered a new species of poison dart frog, small enough to fit on a fingernail but still bearing the toxic poison that gives the frogs their name.”

[hr]