Monthly Archives: July 2014

Microbiome digest, July 31

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A snapshot of the human microbiome, a robot helping the Knight lab process samples (I want one!), and finally something that does NOT involve the microbiome.

Human microbiome general

SnapShot: The Human Microbiome – Antonio González – Cell

“This SnapShot presents several aspects of the human microbiome, including the characterization of the microbial species populating different body sites, the distribution of microbes across different geographic locations, and how the microbiome can be altered by a physiological process, exemplified by pregnancy.”

 

Animal models of microbiome

Symbiotic Bacterial Metabolites Regulate Gastrointestinal Barrier Function via the Xenobiotic Sensor PXR and Toll-like Receptor 4 – Madhukumar Venkatesh – Immunity

“Here we showed that microbial-specific indoles regulated intestinal barrier function through the xenobiotic sensor, pregnane X receptor (PXR).”

Bacterial Sensor Nod2 Prevents Inflammation of the Small Intestine by Restricting the Expansion of the Commensal Bacteroides vulgatus – Deepshika Ramanan – Immunity

“Here, we identified several abnormalities in the small-intestinal epithelium of Nod2−/− mice including inflammatory gene expression and goblet cell dysfunction, which were associated with excess interferon-γ production by intraepithelial lymphocytes and Myd88 activity.”

Effect of virgin and refined olive oil consumption on gut microbiota. Comparison to butter – M. Hidalgo – Food Research International

“Evolution of symbiont population in feces was studied using culture-dependent and culture-independent methods. In the latter, the V3 region of 16S rDNA was amplified and separated by Denaturing Gradient Gel Electrophoresis; followed by sequencing of the most representative bands. “

Animal gut microbiome

Longitudinal shifts in bacterial diversity and fermentation pattern in the rumen of steers grazing wheat pasture – D.W. Pitta – Anaerobe

“Rumen samples were collected on days 14, 28, 56 and 76, separated into solid and liquid fractions and analyzed for bacterial diversity using 16S pyrotag technology. “

Metabolomics

The cross talk between microbiota and the immune system: metabolites take center stage – Hagit Shapiro – Current Opinion in Immunology

“While most attention has focused on the innate recognition of immune-stimulatory bacterial molecules, such as cell wall components and nucleic acids, we emphasize here the impact of diet-dependent microbial metabolites on the development and function of the immune system.”

Bioinformatics tools

eSNaPD: A Versatile, Web-Based Bioinformatics Platform for Surveying and Mining Natural Product Biosynthetic Diversity from Metagenomes – Boojala Vijay B. Reddy – Chemistry & Biology

“Environmental Surveyor of Natural Product Diversity (eSNaPD) is a web-based bioinformatics and data aggregation platform that aids in the discovery of gene clusters encoding both novel natural products and new congeners of medicinally relevant natural products using (meta)genomic sequence data. “

RAMICS: trainable, high-speed and biologically relevant alignment of high-throughput sequencing reads to coding DNA – Imogen A. Wright and Simon A. Travers

“To facilitate such analyses, we have developed a novel tool, RAMICS, that is tailored to mapping large numbers of sequence reads to short lengths (<10 000 bp) of coding DNA”

Computational integration of genomic traits into 16S rDNA microbiota sequencing studies – Alexander Keller – Gene

“Here, we show in a proof-of-concept that computational approaches are able to retain functional information about microbial communities assessed through 16S rDNA (meta)barcoding by referring to reference genomes.”

Viruses and helminths

How helminths go viral – Rick M Maizels1, William C Gause

“On pages 573 and 578 of this issue, Reese et al. (3) and Osborne et al. (4), respectively, provide fine detail on how helminth worms can substantially enhance and reactivate viral infection, with major health implications for tropical medicine.”

Helminth infection reactivates latent γ-herpesvirus via cytokine competition at a viral promoter – T. A. Reese – Science

“We found that helminth infection, characterized by the induction of the cytokine interleukin-4 (IL-4) and the activation of the transcription factor Stat6, reactivated murine γ-herpesvirus infection in vivo.”

Virus-helminth coinfection reveals a microbiota-independent mechanism of immunomodulation – Lisa C. Osborne – Science

“Helminth coinfection resulted in impaired antiviral immunity and was associated with changes in the microbiota and STAT6-dependent helminth-induced alternative activation of macrophages. “

More Microbiology

Larger Mammalian Body Size Leads to Lower Retroviral Activity – Aris Katzourakis – PLOS Pathogens

“Body size explains 37% of the variance in ERV integration rate over the last 10 million years, controlling for the effect of confounding due to other life history traits. “

Microbes in the news

Researcher: Bacteria Ate Some Gulf Spill Toxins, but Worst Remain – Sandy Smith – EHS Today

“In two new studies conducted in a deep sea plume, Assistant Professor Olivia Mason found a species of bacteria called Colwellia likely consumed gaseous hydrocarbons and perhaps benzene, toluene, ethylbenzene and xylene compounds that were released as part of the oil spill. “

Baxter breaks out – Hal Hodson – New Scientist
http://www.sciencedirect.com/science/article/pii/S0262407914614342

“Baxter is even turning its grippers to lab work. Correll is working with UCB’s Rob Knight to teach Baxter the job of preparing faeces samples for research.”

Science and Career

The stressed-out postdoc – Carrie Arnold – Science

“After he defended his dissertation and moved to a new lab for his postdoc, Ian Street hoped his battles with anxiety and depression were over.”

Bik’s Picks

Africa Needs Science, Not Aid – Nkem Khumbah and Melvin P. Foote –  The New York Times

“Scientific and technological advancement will help eradicate poverty and promote homegrown economic development by providing Africa with the tools to address its own challenges and expand its industrial productivity. “

DDT Linked To Obesity In Female Mice Long After Exposure – Hank Campbell – Science 2.0

“A new epidemiology paper in PLOS One doesn’t try to prove that, the authors instead correlate DDT use from generations ago with increased waistlines of today.  DDT exposure may have made you fat, they conclude.”

 

A Lick Of The Tongue Changes This Ice Cream’s Color – Loren Grush – Popular Science

“The result was Xamaleón, which is Spanish for “chameleon.” With a patent pending, Linares is staying tight-lipped on the recipe, but apparently there’s a special ingredient dubbed the “love elixir,” which must be spritzed on the ice cream before it’s eaten. “

 

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Scientists explain mystery of our ‘lemon Moon’ – James Vincent – The Independent

“A new accurate map of the Moon has shown that it bulges slightly at one side and is flattened at the top and bottom – but how did it get this way?”

 

 

 

Microbiome digest, July 30

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Host diet, sex, and the microbiome, smoking cessation, eukaryotic microbes, CRISPRs and my picks.

Gut microbiome

Individual diet has sex-dependent effects on vertebrate gut microbiota – Daniel I. Bolnick – Nature Communications

“Here we show that gut microbiota composition depends on interactions between host diet and sex within populations of wild and laboratory fish, laboratory mice and humans. “

Smoking Cessation Alters Intestinal Microbiota: Insights from Quantitative Investigations on Human Fecal Samples Using FISH – Biedermann L – Inflammatory Bowel Diseases

“As determined by fluorescence in situ hybridization, an independent direct quantitative microbial approach, we could confirm that intestinal microbiota composition in humans is influenced by smoking.”

More microbiology

Diversity of diversity: conceptual and methodological differences in biodiversity estimates of eukaryotic microbes as compared to bacteria – Jean-David Grattepanche – Trends in Microbiology

“High-throughput sequencing tools underestimate the diversity of eukaryotes by removing morphospecies.”

Microbes in the news

A Trip Overseas Could Change The Bugs Living In Your Gut – Bahar Gholipour – Huntington Post

“I was amazed to see how profoundly a single food poisoning event impacted the gut bacteria,” David, who was a researcher at Harvard University at the time of the study, said in a statement.

Researcher Using Next-Generation Sequencing, Other New Methods to Rapidly Identify Pathogens – Joe Montgomery – Kansas State University News Office – Labmanager.com

“Benjamin Hause, an assistant research professor at the Kansas State Veterinary Diagnostic Laboratory at Kansas State University, recently published an article about one of his discoveries, porcine enterovirus G, which is an important find in the United States.”

Antibiotics and resistance

Perturbation of Iron Homeostasis Promotes the Evolution of Antibiotic Resistance – Orsolya Méhi – Molecular Biology and Evolution

“To decipher the underlying molecular mechanisms, we first performed a global transcriptome analysis and demonstrated that the set of genes regulated by Fur change substantially in response to antibiotic treatment. “

Phages, viruses, and CRISPRs

Adaptation in bacterial CRISPR-Cas immunity can be driven by defective phages – Alexander P. Hynes – Nature Communications

“Here we demonstrate that cells can acquire spacers from defective phages at a rate directly proportional to the quantity of replication-deficient phages to which the cells are exposed.”

Dr. Bik’s Picks

Contamination hits cell work: Mycoplasma infestations are widespread and costing laboratories millions of dollars in lost research – Ewen Callaway – Nature

“A total of 11% of the samples were found to contain Mycoplasma DNA at levels indicative of contamination.”

Five daily portions of fruit and vegetables may be enough to lower risk of early death – Science Daily

“Eating five daily portions of fruit and vegetables is associated with a lower risk of death from any cause, particularly from cardiovascular disease, but beyond five portions appears to have no further effect, finds a new study.”

Lands’ End Announces Science-Themed Tees For Girls After Mom’s Letter Goes Viral – Jessica Samakow – The Huffington Post

“My daughter was very confused. Lots of her friends that are girls love science, too. Why were there no cool science shirts for girls?”

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General microbiome and science, July 29

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Bioinformatics tools, metabolomics, antibiotic resistance, biomeme hypothesis and the Kardashian index. Mine is still very low, so I’m good.

Bioinformatics

STAMP: Statistical analysis of taxonomic and functional profiles – Donovan H. Parks – Bioinformatics

“STAMP is a graphical software package that provides statistical hypothesis tests and exploratory plots for analyzing taxonomic and functional profiles. It supports tests for comparing pairs of samples or samples organized into two or more treatment groups. “

Metabolomics

Comparative metabolomics in primates reveals the effects of diet and gene regulatory variation on metabolic divergence – Ran Blekhman – Scientific Reports

“we performed a comparative study using a combination of gene expression and metabolomic profiling in livers from humans, chimpanzees, and rhesus macaques. We show that dietary differences between species have a strong effect on metabolic concentrations”

Antibiotics and resistance

Emergence of quinolone resistance in the microbiota of hospitalized patients treated or not with a fluoroquinolone – Victoire de Lastours – Journal of Antimicrobial Chemotherapy

“FQs received during hospitalization account for high rates of emergence of resistance to FQs in clinically relevant bacteria from human microbiota, reflecting the important ecological impact of FQs. “

The expression of antibiotic resistance genes in antibiotic-producing bacteria –
Stefanie Mak – Molecular Microbiology

“The expression of these genes needs to occur in a timely manner: either in advance of or concomitantly with biosynthesis. “

Tetracycline modifies competitive interactions in experimental microcosms containing bacteria isolated from freshwater – Alex R. Hall – FEMS Microbiology Ecology

“These results suggest that antibiotics such as tetracycline may have important consequences for interactions among bacterial species, but in our experiments this was because species varied in their capacities for growth in the presence of tetracycline, rather than reduced competition at increasing tetracycline concentrations.”

Microbiology general

Please note that this one is just a hypothesis paper – there is no actual data to support this prediction. It’s very speculative, but discussed a lot on forums and Twitter.
Midichlorians – the biomeme hypothesis: is there a microbial component to religious rituals? – Alexander Y Panchin – Biology Direct

“We predict that next-generation microbiome sequencing of samples obtained from gut or brain tissues of control subjects and subjects with a history of voluntary active participation in certain religious rituals that promote microbial transmission will lead to the discovery of microbes, whose presence has a consistent and positive association with religious behavior. “

Science and publishing

Spotlight falls on top 1% in science – Chris Woolston – Nature

“News that a rarified group of scientists has claimed the lion’s share of publications has set off a social-media discussion about the fairness of the system”

Belongs to:

Estimates of the Continuously Publishing Core in the Scientific Workforce – John P. A. Ioannidis, Kevin W. Boyack, Richard Klavans – PLOS ONE

“However, only 150,608 (<1%) of them have published something in each and every year in this 16-year period (uninterrupted, continuous presence [UCP] in the literature).”

Academia’s seamier side: Lying, cheating and fraud – Fred Barbash – Washington Post

“The seamier side of academia, lying, cheating and occasionally stealing, this is the world revealed by a blog which, by all rights, should be dry and boring, like its name, “Retraction Watch.””

The Kardashian index: a measure of discrepant social media profile for scientists – Neil Hall – Genome Biology – Hat tip: Liz Costello

“if your K-index gets above 5, then it’s time to get off Twitter and write those papers”

 Dr. Bik’s Picks

The influence of emotional facial expressions on gaze-following in grouped and solitary pedestrians – Andrew C. Gallup – Nature Scientific Reports

“We found that pedestrians walking alone were not sensitive to this manipulation, while individuals traveling together in groups did reliably alter their response in relation to emotional cues. “

Timing of circadian genes in mammalian tissues – Anja Korenčič – Nature Scientific Reports

“To study the phase variability of CCGs in mammalian peripheral tissues, we develop a core clock model for mouse liver and adrenal gland based on expression profiles and known cis-regulatory sites.”

Footprint of Deepwater Horizon blowout impact to deep-water coral communities –
Charles R. Fisher – PNAS

“Here we show this was not an isolated incident; at least two other coral communities were also impacted by the spill. “

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Non-human microbiome, July 29

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Microbiomes of chickens with Marek’s disease, fish, fungus-growing termites, ticks, leeches, mosses, soil and acid mine drainage.

Chicken microbiome

Marek’s Disease Virus Influences the Core Gut Microbiome of the Chicken During the Early and Late Phases of Viral Replication – Sudeep Perumbakkam – FEMS Microbiology Ecology

“In this study, dysbiosis induced by MDV on the core gut flora of chicken was assessed using next generation sequence (NGS) analysis. “

Fish microbiome

Dietary differences are reflected on the gut prokaryotic community structure of wild and commercially reared sea bream (Sparus aurata) – Konstantinos A. Kormas – Microbiology Open

“There were distinct prokaryotic communities in the three different fish nutritional treatments, with the bacteria dominating over the Archaea. “

Inter Individual Variations of the Fish Skin Microbiota: Host Genetics Basis of Mutualism? – Sébastien Boutin – PLOS ONE

“we detected Quantitative Trait Loci (QTL) associated with the abundance of specific skin microbiota bacterial strains in brook charr (Salvelinus fontinalis), combining 16S RNA tagged-amplicon 454 pyrosequencing with genetic linkage analysis. “

Arthropod microbiome

Identifying the core microbial community in the gut of fungus-growing termites – Saria Otani – Molecular Ecology

“The objective of our study was to compare the intestinal bacterial communities of five genera (nine species) of fungus-growing termites to establish whether or not an ancestral core microbiota has been maintained and characterizes extant lineages. “

Characterization of the Bacterial Communities of Life Stages of Free Living Lone Star Ticks (Amblyomma americanum) – Amanda Jo Williams-Newkirk – PLOS ONE

“We performed a metagenomic survey of the bacterial communities of questing A. americanum and tested 131 individuals (66 nymphs, 24 males, and 41 females) from five sites in three states. Pyrosequencing was performed with barcoded eubacterial primers targeting variable 16S rRNA gene regions 5–3.”

Leech microbiome

Hitchhiking of host biology by beneficial symbionts enhances transmission –
Brittany M. Ott – Nature Scientific Reports

“we show that the A. veronii population within secretions originates from the host digestive tract and proliferates synchronously with shedding frequency, demonstrating the coupling of partner biology.”

Plant microbiome

Forestry impacts on the hidden fungal biodiversity associated with bryophytes – Marie L. Davey – FEMS Microbiology Ecology

“Shoots of Hylocomium splendens were collected in Picea abies dominated forests of different ages, and their associated fungal communities were surveyed by pyrosequencing of ITS2 amplicons. “

Soil microbiology

Review: Functional soil microbiome: Belowground solutions to an aboveground problem
Venkatachalam Laksmanan – Plant Physiology

“This update addresses the importance of the functional microbiome to identify phenotypes that may provide a sustainable and effective strategy to increase crop yield and food security.”

Microbial Diversity of a Mediterranean Soil and Its Changes after Biotransformed Dry Olive Residue Amendment – Jose A. Siles – PLOS ONE

“Pyrosequencing of the 16S rRNA gene demonstrated that bacterial diversity was dominated by the phyla Proteobacteria, Acidobacteria, and Actinobacteria, while 28S-rRNA gene data revealed that Ascomycota and Basidiomycota accounted for the majority of phyla in the fungal community.”

Water and drainage microbiome

Diversity and spatiotemporal dynamics of bacterial communities: physicochemical and others drivers along an acid mine drainage – A. Volant – FEMS Microbiology Ecology

“biodiversity and spatiotemporal distribution of bacterial communities were characterized using T-RFLP fingerprinting and highthrouput sequencing.”

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Human microbiome, July 29

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Papillomaviruses in human skin, gastric mucosa in cancer patients, breast milk metabolome, microbiome of a human family, and more.

Skin microbiome

Deep sequencing extends the diversity of human papillomaviruses in human skin –
Davit Bzhalava – Nature Scientific Reports

“This deeper sequencing without prior PCR of a pool of 142 whole genome amplified skin lesions identified 23 known HPV types, 3 novel putative HPV types and 4 non-HPV viruses.”

Gastric microbiome

Differences in Gastric Mucosal Microbiota Profiling in Patients with Chronic Gastritis, Intestinal Metaplasia, and Gastric Cancer Using Pyrosequencing Methods – Chang Soo Eun – Helicobacter

“Gastric mucosal biopsy samples were collected from 31 patients during endoscopy. After the extraction of genomic DNA, variable region V5 of the 16S rRNA gene was amplified. PCR products were sequenced using 454 high-throughput sequencer. “

Pregnancy and Birth

Breast milk metabolome characterization in a single phase extraction, multiplatform analytical approach – Alma Villaseñor – Analytical Chemistry

“We conducted this single-phase extraction procedure on a representative pool of BM, and characterized the metabolic composition using LC-QTOF-MS and GC-Q-MS for polar and lipidic metabolites. “

Effects of Bifidobacterial Supplementation to Pregnant Women and Infants in the
Prevention of Allergy Development in Infants and on Fecal Microbiota [PDF]- Tadao Enomoto – Allergology International

“Effects of Bifidobacterial Supplementation to Pregnant Women and Infants in the Prevention of Allergy Development in Infants and on Fecal Microbiota”

Gut microbiome
The dynamics of a family’s gut microbiota reveal variations on a theme – Patrick D Schloss – Microbiome

“Here we study a chronosequence of the gut microbiota found in eight individuals from a family consisting of two parents and six children ranging in age from two months to ten years old.”

Identifying Keystone Species in the Human Gut Microbiome from Metagenomic Timeseries Using Sparse Linear Regression – Charles K. Fisher – PLOS ONE

“Here we introduce an approach, Learning Interactions from MIcrobial Time Series (LIMITS), that overcomes these obstacles. LIMITS uses sparse linear regression with boostrap aggregation to infer a discrete-time Lotka-Volterra model for microbial dynamics. “

Antivirulence Activity of the Human Gut Metabolome – L. Caetano M. Antunes – mBio

“We found that a secreted molecule produced by clostridia acts as a strong repressor of Salmonella virulence, obliterating expression of the Salmonella pathogenicity island 1 as well as host cell invasion.”

 Metagenomic Identification of a Novel Salt Tolerance Gene from the Human Gut Microbiome Which Encodes a Membrane Protein with Homology to a brp/blh-Family β-Carotene 15,15′-Monooxygenase – Eamonn P. Culligan – PLOS ONE

“Herein, we report the identification and characterisation of a novel stress tolerance gene from the human gut metagenome. The locus, assigned brpA, encodes a membrane protein with homology to a brp/blh-family β-carotene monooxygenase. “

Review: Archaea and the human gut: New beginning of an old story [DOC]- Gaci N – World Journal of Gastroenterology

“Here we provide an updated census of the archaeal diversity associated to human GIT and their possible role in the gut physiology and health.”

 

Animal models of human microbiome and disease

Maternal high protein or prebiotic fiber diets affect maternal milk composition and gut microbiota in rat dams and their offspring – Megan C. Hallam – Obesity

“Fecal microbiota was analyzed in dams at parturition and 2 weeks post-partum and in offspring at 5 and 22 weeks along with cecal digesta at termination.”

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General microbiology and science

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Some new bioinformatic tools,  dengue response and vaccines, and host response and transcriptomics.

Host response and gene expression

Single-cell RNA-seq: advances and future challenges – Antoine-Emmanuel Saliba – Nucleic Acids Research

“Different single-cell RNA-seq protocols have been introduced and are reviewed here—each one with its own strengths and current limitations.”

Corset: enabling differential gene expression analysis for de novo assembled transcriptomes – Nadia M Davidson and Alicia Oshlack – Genome Biology

“Here we present Corset, a method that hierarchically clusters contigs using shared reads and expression, then summarizes read counts to clusters, ready for statistical testing. Using a range of metrics, we demonstrate that Corset out-performs alternative methods.”

Bioinformatics

Suffix tree searcher: exploration of common substrings in large DNA sequence sets
David Minkley – BMC Research Notes

“The program accommodates very large numbers of very large sequences, with aggregate size reaching tens of billions of nucleotides. The program makes use of pre-sorted persistent “building blocks” to reduce the time required to construct new trees.”

SnipViz: a compact and lightweight web site widget for display and dissemination of multiple versions of gene and protein sequences – Daniel Jaschob – BMC Research Notes

“SnipViz is a client-side software tool designed to disseminate multiple versions of related gene and protein sequences on web sites. SnipViz has a space-efficient, interactive, and dynamic interface for navigating, analyzing and visualizing sequence data.”

Dengue

 

Dengue vaccine trial poses public health quandary – Dennis Normile – Science

 

“The vaccine, developed by Sanofi Pasteur, proved safe, had an overall efficacy rate of 56.5%, and reduced cases of severe disease by 88.5%. But it had limited efficacy against dengue 2, one of four dengue virus serotypes in circulation.”

Predictors of hospital stay and mortality in dengue virus infection-experience from Aga Khan University Hospital Pakistan – Muhammad Abdul Khalil – BMC Research Notes

“Increasing age, coagulopathy and acute kidney injury in patients with DVI is associated with increased hospital stay.”

 

 

Science and publishing

A crisis of trust – Pubpeer

“As PubPeer developed, and especially once we enabled anonymous posting, we were shocked at the number of comments pointing out much more fundamental problems in papers, involving very questionable research practices and rather obvious misconduct. “

Dr. Bik’s Picks

Note to Science: The GOP’s Just Not That That Into You – Jeffrey Kluger – Time

“If the Speaker, by his own admission, isn’t qualified to debate climate change, fine, he’s excused from the conversation—and he should be expected not to offer further opinion on the matter. “

The first Science Hack Day in China – Ariel Waldman – BoingBoing

“Over the course of the weekend in a Shanghai incubator space, kids, parents, scientists, artists and technologists joined forces to play with science and prototype ideas. “

Exclusive: Naked Mole Rat Filled With Regret Over Evolutionary Choices – The Allium

“In an exclusive interview with The Allium, the Naked Mole Rat has revealed its regret at some of the evolutionary choices it has made, in particular the whole nakedness and the teeth.”

 

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Non-human microbiome

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Microbiome of sheep, Drosophila on cherries, wild and sugar beets, sauerkraut, sake, and cheese. Sounds like a good meal.
Sheep microbiome

Pros and Cons of Ion-Torrent Next Generation Sequencing versus Terminal Restriction Fragment Length Polymorphism T-RFLP for Studying the Rumen Bacterial Community – Gabriel de la Fuente – PLOS ONE

“We analysed the bacterial diversity in the rumen of defaunated sheep following the introduction of different protozoal populations, using both next generation sequencing (NGS: Ion Torrent PGM) and terminal restriction fragment length polymorphism (T-RFLP).”

Insect microbiome

The bacterial communities of Drosophila suzukii collected from undamaged cherries
James Angus Chandler – PeerJ

“Using 16S rDNA PCR and Illumina sequencing, we characterized the bacterial communities of larval and adult D. suzukii collected from undamaged, attached cherries in California, USA. “

Evaluating Insect-Microbiomes at the Plant-Insect Interface – Clare L. Casteel, Allison K. Hansen – Journal of Chemical Ecology

“In this review, we critically evaluate the requirements for insect-associated microbes to develop synergistic relationships with their hosts, and we mechanistically discuss how some of these insect-associated microbes can target or modify host plant defenses.”

Saccharide breakdown and fermentation by the honey bee gut microbiome
Authors – Fredrick J. Lee – Environmental microbiology

“In order to better understand the contribution of the microbial community to food processing in the honey bee, we generated a metatranscriptome of the honey bee gut microbiome.”

Plant microbiome

Differences between the rhizosphere microbiome of Beta vulgaris ssp. maritima – ancestor of all beet crops – and modern sugar beets – Christin Zachow – Frontiers in Microbiology

“Therefore, we studied bacterial rhizosphere communities associated with the wild beet B. vulgaris ssp. maritima grown in their natural habitat soil from coastal drift lines (CS) and modern sugar beets (Beta vulgaris ssp. vulgaris) cultivated in CS and potting soil (PS) under greenhouse conditions.”

Endophytic bacterial community of grapevine leaves influenced by sampling date and phytoplasma infection process – Daniela Bulgari – BMC Microbiology

“Metagenomic DNA was extracted from sterilized leaves and the endophytic bacterial community dynamic and diversity were analyzed by taxon specific real-time PCR, Length-Heterogeneity PCR and genus-specific PCR. “

Water microbiology

Core Functional Traits of Bacterial Communities in the Upper Mississippi River Show Limited Variation in Response to Land Cover – Christopher Staley – Frontiers in Microbiology

“In this study we characterized functional microbial diversity at 11 sites along the Mississippi River in Minnesota using both metagenomic sequencing and functional-inference-based (PICRUSt) approaches.”

Potential drivers of microbial community structure and function in Arctic snow – Lorrie Maccario – Frontiers in Microbiology

“We applied a metagenomic approach to nine snow samples taken over two months during the spring season. Fungi, Bacteroidetes and Proteobacteria were predominant in metagenomic datasets and changes in community structure were apparent throughout the field season.”

Soil microbiology

Nutrient addition dramatically accelerates microbial community succession – Knelman JE – PLOS ONE

“We evaluated soil properties and examined bacterial community composition in plots before and one year after fertilization.”

Food microbiology

Sauerkraut: bacteria making food – S.E. Gould – Lab Rat – Scientific American

“As the bacteria required for sauerkraut fermentation are found on the cabbage leaves, it’s a very easy and healthy dish to produce. All you need is cabbage! “

Indigenous bacteria and fungi drive traditional kimoto sake fermentations
Nicholas A. Bokulich – Applied and Environmental Microbiology

“Results demonstrate a dynamic microbial succession, with koji and early moto fermentations dominated by Bacillus, Staphylococcus, and Aspergillus flavus subsp. oryzae, succeeded by Lactobacillus spp. and Saccharomyces cerevisiae later in the fermentations. “

Microbiota characterization of a Belgian protected designation of origin cheese, Herve cheese, using metagenomic analysis – V. Delcenserie – Journal of Dairy Science

“The aim of the study was to analyze the bacterial microbiota of Herve cheese using classical microbiology and a metagenomic approach based on 16S ribosomal DNA pyrosequencing. “

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Human microbiome, July 28

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Oral microbes balancing their budgets, bacteria see blue, why Obama likes to fist bump, Gardnerella, and oxygen gradients in the gut.

Oral microbiome

Bioinformatic investigation of the cost management strategies of five oral microbes – Keith J. Cross – Molecular Oral Microbiology

“For Porphyromonas gingivalis, Treponema denticola, Tannerella forsythia, Prevotella intermedia, and Streptococcus sanguinis, the outer membrane/extracellular proteins are made up of a much larger percentage of lower average mass amino acids whereas cytoplasmic proteins are made up of a larger proportion of higher average mass amino acid residues.”

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

“A. baumannii can sense blue light through a blue-light sensing using flavin (BLUF) domain protein, BlsA. The resulting conformational change in BlsA leads to changes in gene expression, including virulence genes.”

Skin microbiome

Study: Fist bumps are less germy than handshakes – Kim Painter – USA Today

“Whitworth and a colleague systematically tested the three greetings for a study published Monday in the American Journal of Infection Control.” (article not available yet – MD).

Vaginal microbiome

Gardnerella vaginalis Outcompetes 29 Other Bacterial Species Isolated From Patients With Bacterial Vaginosis, Using in an In Vitro Biofilm Formation Model – Patrícia Alvesa – Journal of Infectious Diseases

“Here, we isolated 30 BV-associated species and characterized their virulence, using an in vitro biofilm formation model. “

Long-term Effect of Depot Medroxyprogesterone Acetate on Vaginal Microbiota, Epithelial Thickness and HIV Target Cells – Caroline M. Mitchell – Journal of Infectious Diseases

“Vaginal microbiota of women using DMPA for up to 2 years were cultured. Mucosal immune cell populations were measured by immunohistological staining.”

Gut microbiome

Correlation Between Intraluminal Oxygen Gradient and Radial Partitioning of Intestinal Microbiota in Humans and Mice – L. Albenberg – Gastroenterology

“In humans, 16S rRNA gene analyses revealed an increased proportion of oxygen-tolerant organisms of the Proteobacteria and Actinobacteria phyla associated with the rectal mucosa, compared with the feces, indicating an effect of oxygenation on the microbiota. “

Patients with cystic fibrosis have a high carriage rate of non-toxigenic Clostridium difficile – M. P. Bauer – Clinical Microbiology and Infection

“In this case-control study, we found more carriers among CF patients than controls (47% versus 11%), but most strains carried by CF patients were non-toxigenic (77% versus 17%). “

Animal models of human microbiome and disease

Obese-type Gut Microbiota Induce Neurobehavioral Changes in the Absence of Obesity
Annadora J. Bruce-Keller – Biological Phychiatry

“Sequencing-based phylogenetic analysis confirmed the presence of distinct core microbiota between groups, with alterations in α- and β-diversity, modulation in taxonomic distribution, and statistically significant alterations to metabolically active taxa. “

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Microbiome Digest, July 25

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A year worth of oral/stool samples shows relative stability, antibiotics and preterm infants, reagent contamination, and 42. Have a great weekend!

 

Oral and gut microbiome

Screen Shot 2014-07-25 at 9.45.01 PMHost lifestyle affects human microbiota on daily timescales – Lawrence A David – Genome Biology

“Here, we link over 10,000 longitudinal measurements of human wellness and action to the daily gut and salivary microbiota dynamics of two individuals over the course of one year. These time series show overall microbial communities to be stable for months. However, rare events in each subjects’ life rapidly and broadly impacted microbiota dynamics. “

Pregnancy and Birth

Screen Shot 2014-07-25 at 9.44.20 PMThe impact of postnatal antibiotics on the preterm intestinal microbiome – Majd Dardas – Pediatric Research

“Rectal (fecal) swabs were collected at 10 and 30 d and analyzed by 16S rRNA pyrosequencing. At both time points, we examined the rectal microbiome from infants who received only 2 d of antibiotics and those who received at least 7 d of antibiotics.”

Techniques

Screen Shot 2014-07-25 at 9.45.50 PMReagent contamination can critically impact sequence-based microbiome analyses – Susannah Salter – BioRxiv (preprint)

“In this study we demonstrate that contaminating DNA is ubiquitous in commonly used DNA extraction kits, varies greatly in composition between different kits and kit batches, and that this contamination critically impacts results obtained from samples containing a low microbial biomass. “

Dengue

Speaking about “matter of timing”, seems like this paper came out a bit too late.
Screen Shot 2014-07-25 at 9.46.14 PMDengue and the World Football Cup: A Matter of Timing – Christovam Barcellos, Rachel Lowe – PLOS Neglected Tropical Diseases

“We provide a nationwide risk map, averaging June dengue incidence rates for 2001–2012. The areas along the Amazonian rivers and in the inner portions of southernmost states are actually low-risk areas, while elevated dengue risk is found in the central Brazilian plateau.”

Infection and host response

Don’t forget your towel! Even the issue number, 1004201, contains the “The Answer to the Ultimate Question of Life, the Universe, and Everything”. Perfection.
Screen Shot 2014-07-25 at 9.46.22 PMMicrobial Egress: A Hitchhiker’s Guide to Freedom – Ana Traven, Thomas Naderer – PLOS Pathogens

“The Restaurant at the End of the Infection — Macrophages as Host Cells”
“So Long and Thanks for All the Inflammatory Cell Death”

Dr. Bik’s Picks

crowSmarter than a first-grader? Crows can perform as well as 7- to 10-year-olds on cause-and-effect water displacement tasks

“New research conducted by UC Santa Barbara’s Corina Logan, with her collaborators at the University of Auckland in New Zealand, demonstrates the birds’ intellectual prowess may be more fact than fiction.”

JBC Journal of Biological ChemistryFour billion-year-old chemistry in cells today – Phys.org

“Parts of the primordial soup in which life arose have been maintained in our cells today according to scientists at the University of East Anglia.”

Screen Shot 2014-07-25 at 9.47.50 PMDustup Over Lionfish Science Fair Project – Bob Grant – The Scientist

A former graduate student says he feels slighted by a failure to attribute his contributions to a line of research regarding the salinity tolerances of an invasive species. “I’m not sure what happened, but my main issue is that the national media has presented a story that is sensationalized, and has left me out of the picture.”

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Microbiome digest, July 24

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Introducing the crAssphage, an 84 bp BLAST from the past, archaea in the Savannah, metabolomics of racehorse microbiome, and X-raying headphones.

Human oral microbiome

Proceedings RoyalMolecular analysis of ancient caries – Marc Simón – Proceedings of the Royal Society, Biological Sciences

“An 84 base pair sequence of the Streptococcus mutans virulence factor, known as dextranase, has been obtained from 10 individuals from the Bronze Age to the Modern Era in Europe and from before and after the colonization in America. “

Human gut microbiome

Nature CommunicationsA highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes – Bas E. Dutilh – Nature Communications

“Here we describe the discovery of a previously unidentified bacteriophage present in the majority of published human faecal metagenomes, which we refer to as crAssphage.”

Gut family SchlossThe dynamics of a family’s gut microbiota reveal variations on a theme – Patrick D Schloss – Microbiome

“Using 16S rRNA gene and metagenomic shotgun sequence data, it was possible to distinguish the family from a cohort of normal individuals living in the same geographic region and to differentiate each family member”

Pregnancy and Birth

Screen Shot 2014-07-24 at 05.53PM, Jul 24An unnecessary cut? – Sky Dylan-Robbins – The New Yorker

“The most common operating-room procedure in the United States is the Cesarean section. “

Animal microbiome

Equine Vet JournalCharacterisation of the faecal metabolome and microbiome of Thoroughbred racehorses – C. J. Proudman – Equine Veterinary Journal

“Faecal metabolome was characterised using thermal desorption-gas chromatography-mass spectrometry (TD-GC-MS), with spectral analysis performed using AMDIS and compared against the NIST database. Taxonomic description of the faecal microbiota was achieved using error-corrected 454 pyrosequencing data from 16S rRNA gene amplicons”

Journal of MicrobiologyPyrosequencing-based analysis of fecal microbial communities in three purebred pig lines – Edward Alain B. Pajarillo – Journal of Microbiology

“Taxon-dependent and -independent analyses were performed to evaluate differences in the fecal bacterial communities and to identify bacterial genera that can be used to discriminate breeds, following high-throughput pyrosequencing of 16S rRNA genes. “

Environmental microbiome

Screen Shot 2014-07-24 at 05.55PM, Jul 24Seasonal Effects in a Lake Sediment Archaeal Community of the Brazilian Savanna – Thiago Rodrigues – Archaea

“Here we describe for the first time the diversity of archaeal communities from freshwater lake sediments of the Cerrado in the dry season and in the transition period between the dry and rainy seasons, when the first rains occur. Gene libraries were constructed, using Archaea-specific primers for the 16S rRNA and amoA genes.”

Screen Shot 2014-07-24 at 05.56PM, Jul 24Spatial patterns and links between microbial community composition and function in cyanobacterial mats – Mohammad A. Al-Najjar – Frontiers in Microbiology

“Similar clustering was found when the community composition of the mats’ cyanobacterial layers were compared by automated ribosomal intergenic spacer analysis, indicating a significant link between the microbial community composition and function. “

MicrobeNetNew Joint Initiative from the Knight and Sogin Labs as a Follow-up to the MoBEDAC Initiative – Embriette Hyde

“By the end of the funded period, standard 16S rRNA and ITS (fungal) analysis pipelines will be developed and made available to the MoBe community, 16S rRNA and ITS databases will be markedly improved, QIIME and VAMPS will be tightly integrated into a new database engine called QiiTA to facilitate analysis by all MoBe researchers, and two major training workshops will be offered. “

Dr. Bik’s PicksDNA

DNA mostly ‘junk?’ Only 8.2 percent of human DNA is ‘functional’, study finds – Science Daily

“This figure is very different from one given in 2012, when some scientists involved in the ENCODE (Encyclopedia of DNA Elements) project stated that 80% of our genome has some biochemical function.”

Screen Shot 2014-07-24 at 05.58PM, Jul 24Sex differences in medicine – BeWell – Stanford University

“A man can be diagnosed with the same disease as a woman, and yet the course the disease takes in each could prove very different. And a treatment which works for one gender may prove ineffective for the other. “

corksIs Climate Change Ruining Wine Corks? – Kelly Dickerson – LiveScience

“Many people may only worry about corks when it’s time to pop the Champagne, but some experts are worried about wine cork quality, which has been mysteriously in decline for almost 20 years.“

Headphone x rayDoc X-Rays His Broken Headphones to Fix Them – Bahar Gholipour – LiveScience

“”Closed fracture of a speaker wire within its rubber/plastic sleeve is a rare headphone injury, usually due to a traction trauma,” Skalski wrote in his report of the case.”

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