Category Archives: General Microbiome

Human microbiome, June 26

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Mass spectrometry on Neanderthal poop – how cool is that? Then, nice article about fecal transplants, the Bristol Stool Chart Mug, role of bacteria in colon cancer, and Mycobacterium tuberculosis as a possible human symbiont.

Gut microbiome

Screen Shot 2014-06-26 at 10.22.55 PMThe Neanderthal Meal: A New Perspective Using Faecal Biomarkers – Ainara Sistiaga – PLOS ONE

“Our gas chromatography-mass spectrometry results from El Salt (Spain), a Middle Palaeolithic site dating to ca. 50,000 yr. BP, represents the oldest positive identification of human faecal matter.”

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I enjoyed reading this article. And not just because they mentioned one of our studies.
Getting to the Bottom of Fecal Transplants – Ricki Lewis – PLOS.org

“(…) babies’ bacteria were quite different at the outset, but by the end of the year, their communities resembled those in the adult digestive tract. And it was published right here at PLOS.”

41C8qjeUK2LWhich led me to the awesome The Bristol Stool Chart Mug – Amazon
Which I then ordered.

 

CRCFusobacterium and Enterobacteriaceae: Important players for CRC? – Emma Allen-Vercoea, Christian Jobin – Immunology Letters

“Not surprisingly, microbial dysbiosis is associated with numerous intestinal disorders including inflammatory bowel diseases (IBD) and colorectal cancer (CRC). In this piece, we will review recent evidence that gut microbial dysbiosis can influence intestinal disease, including colitis and CRC.”

Screen Shot 2014-06-26 at 9.45.42 PMPrevalence and Duration of Asymptomatic Clostridium difficile Carriage among Healthy Subjects in Pittsburgh, Pennsylvania – Alison L. Galdys – Journal of Clinical Microbiology

“The prevalence of C. difficile carriage in this healthy cohort is concordant with prior estimates. C. difficile-colonized individuals may be important reservoirs for C. difficile and may falsely test positive for infections due to C. difficile when evaluated for community-acquired diarrhea caused by other enteric pathogens.”

Blood sugar improves with first gastrointestinal microbiome modulator, NM504 – Science Daily

“The not-yet-named therapeutic, NM504, is the first in a new class of therapies known as GI microbiome modulators. “

Role of humanRole of human gut microbiota metabolism in the anti-inflammatory effect of traditionally used ellagitannin-rich plant materials – Jakub P. Piwowarski – Journal of Ethnopharmacology

“The formation of urolithins was determined by ex vivo incubation of human faecal samples with aqueous extracts from selected plant materials.”

Me and my microbiome – New Scientist

“Now there are claims that a truly villainous bacterium – Mycobacterium tuberculosis, which causes TB – is actually symbiotic and helped us evolve our large brains (see “ Eat meat TB brainy”). “

Eat meat TB brainy – Adrian Williams, Robin Dunbar – New Scientist

“The tuberculosis bacterium co-evolved with humans at least 70,000 years ago, and possibly a great deal earlier. Could chronic TB infections have originally been beneficial to human life? Did the pathogen act as a symbiont, supplying nicotinamide at times of meat deficiency?”

Animal models of human microbiota and disease

Screen Shot 2014-06-26 at 9.47.30 PMIncorporation of therapeutically modified bacteria into gut microbiota inhibits obesity – Zhongyi Chen – Journal of Clinical Investigation

“Here, we demonstrated that administration of engineered NAPE-expressing E. coli Nissle 1917 bacteria in drinking water for 8 weeks reduced the levels of obesity in mice fed a high-fat diet. “

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Non-human microbiome, June 25

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Mongolian Gerbils, soil microbiome affects plant flowering time, soybeans, and seawater viruses.

Mammalian microbiome

Screen shot 2014-06-25 at 01.26PM, Jun 25Helicobacter pylori Induced Gastric Immunopathology Is Associated with Distinct Microbiota Changes in the Large Intestines of Long-Term Infected Mongolian Gerbils – Markus M. Heimesaat – PLOS ONE

“Comprehensive cultural analyses revealed that severe gastric diseases such as atrophic pangastritis and precancerous transformations were accompanied by elevated luminal loads of E. coli and enterococci in the caecum and together with Bacteroides/Prevotella spp. in the colon of H. pylori WT, but not MUT infected gerbils as compared to naïve animals. “

Plant microbiome

Screen shot 2014-06-25 at 01.27PM, Jun 25Changes in the Bacterial Community of Soybean Rhizospheres during Growth in the Field – Akifumi Sugiyama – PLOS ONE

“Pyrosequencing analysis revealed that differences between the bacterial communities of rhizosphere and bulk soils at the phylum level; i.e., Proteobacteria were increased, while Acidobacteria and Firmicutes were decreased in rhizosphere soil during growth. “

Screen shot 2014-06-25 at 06.41PM, Jun 25Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative – Maggie R. Wagner – Ecology Letters

“Here, we tested separately the effects of four naturally occurring soil microbiomes and their constituent soil chemistries on flowering phenology and reproductive fitness of Boechera stricta, a wild relative of Arabidopsis. “

Water microbiology

Screen shot 2014-06-25 at 01.27PM, Jun 25 1Anthropogenic Litter in Urban Freshwater Ecosystems: Distribution and Microbial Interactions – Timothy Hoellein – PLOS ONE

“To assess microbial interactions with AL, we incubated AL and natural substrates in 3 freshwater ecosystems, quantified biofilm metabolism as gross primary production (GPP) and community respiration (CR), and characterized biofilm bacterial community composition via high-throughput sequencing of 16S rRNA genes.”

Screen shot 2014-06-25 at 01.28PM, Jun 25Comparison of Deep-Water Viromes from the Atlantic Ocean and the Mediterranean Sea – Christian Winter – PLOS ONE

“The identifiable richness and relative abundance in both viromes were dominated by archaeal and bacterial viruses accounting for 92.3% of the relative abundance in the Atlantic Ocean and for 83.6% in the Mediterranean Sea. “

Screen shot 2014-06-25 at 01.28PM, Jun 25 1The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing – Patrick J. Keeling – PLOS Biology

“The MMETSP relies primarily on cultured organisms, and this introduces a different set of biases, most obviously, favoring organisms that are photosynthetic. “

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Human microbiome, June 25

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Detailed analysis on strain level of oral microbiome and immune cell in term and preterm labor.

Oral microbiome

Screen Shot 2014-06-25 at 10.26.27 PMOligotyping analysis of the human oral microbiome – A. Murat Eren – PNAS

“We used a computational approach that relies on information theory to reanalyze the human oral microbiome. This analysis revealed organisms differing by as little as a single rRNA nucleotide, with dramatically different distributions across habitats or individuals.”

Pregnancy and birth

Screen Shot 2014-06-25 at 10.27.47 PMReview: Immune cells in term and preterm labor – Nardhy Gomez-Lopez – Cellular and Molecular Immunology

“Here, we summarize the role of innate and adaptive immune cells in the physiological or pathological activation of labor. “

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General microbiology and science, June 24

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Metabolomics, metagenomics, phages in the human gut, arsenic poisoning in China, and a big award for Dengue research.

Metabolomics

Metaproteomics: Extracting and Mining Proteome Information to Characterize Metabolic Activities in Microbial Communities – Paul E. Abraham – Current Protocols in Bioinformatics

“In this article, we provide an overview of current bioinformatic approaches and software implementations in metaproteome studies in order to highlight the key considerations needed for successful implementation of this powerful community-biology tool. “

Review: The human volatilome: volatile organic compounds (VOCs) in exhaled breath, skin emanations, urine, feces and saliva – Anton Amann – Journal of Breath Research

“Fecal volatiles have been implicated in differentiating certain infectious bowel diseases such as Clostridium difficile, Campylobacter, Salmonella and Cholera. They have also been used to differentiate other non-infectious conditions such as irritable bowel syndrome and inflammatory bowel disease.”

Metagenomics and DNA structure

Sequencing the Strange Communities: Taking on Metagenomics – Aaron Krol – Bio-IT World

““Communities are made up of organisms that interact,” says Jonathan Eisen, a professor at the School of Medicine and the College of Biological Sciences at the University of California, Davis. “They’re not made up of short reads of Illumina sequences. And we need to stitch those together into organisms in order to make useful predictions, and interpretation of experimental data.””

Gene positioning and genome function – Nidhi Vishnoi, Jie Yao – Frontiers in Biology

” In this review, we discuss some recent findings as well as experimental tools to investigate subnuclear gene positioning and to explore its implications in genome functions.”

Phages and viruses

Classification and quantification of bacteriophage taxa in human gut metagenomes – Alison S Waller – ISME Journal 

“Using taxon-specific marker genes, we identified and monitored 20 viral taxa in 252 human gut metagenomic samples, mostly at the level of genera. “

Techniques

Enzymatic Treatment of Specimens before DNA Extraction Directly Influences Molecular Detection of Infectious Agents – Pablo Goldschmidt – PLOS ONE

“The goal of the present work was to assess the efficiency of enzymatic pretreatments on infectious agents to make DNA available for further extraction and amplification.”

Dengue

Sustainable Sciences Institute (SSI) Awarded $1 Million to Battle Growing Threat to Global Public Health: Mosquito-borne Dengue Virus – PR Web

“SSI, a San Francisco nonprofit founded by Eva Harris, UC Berkeley Professor of Infectious Disease and Vaccinology and former MacArthur “Genius” award winner, has worked to minimize the threat of potentially fatal Dengue disease for 15 years. With the latest award of $1 million dollars, Harris and other SSI investigators will be able to extend their reach and speed up their efforts.”

Infection and host response

Early MicroRNA Expression Profile as a Prognostic Biomarker for the Development of Pelvic Inflammatory Disease in a Mouse Model of Chlamydial Genital Infection – Laxmi Yeruva – mBio

“To determine if chemokine and cytokine production within 24 h of infection is associated with the outcome of pathology, levels of 15 chemokines and cytokines were measured. “

Immunity to gastrointestinal nematodes: mechanisms and myths – Richard K. Grencis – Immunological Reviews

“This review aims to discuss the recent discoveries in both host protection and immunoregulation against gastrointestinal nematodes, placing the data in context of the specific life cycles imposed by the different parasites studied and the future challenges of considering the mucosal/immune axis to encompass host, parasite, and microbiome in its widest sense.”

Tailored immunity at mucosae – Yasmine Belkaid – Immunological Reviews

“This issue of Immunological Reviews presents articles from investigators involved in the exploration of the mechanisms by which mucosal barrier sites induce and control innate and adaptive immune responses.”

Detection of bacteria in blood and other sites

Rapid Detection of Enterobacteriaceae Producing Extended Spectrum Beta-Lactamases Directly From Positive Blood Cultures by Matrix-Assisted Laser-Desorption-Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF-MS) – Marina Oviaño – Clinical Microbiology and Infection

“In the assay, 141 blood cultures were tested, 13 out of them were real bacteremias and 128 corresponded to blood culture bottles seeded with bacterial clinical isolates. Bacteremias were analyzed by MALDI-TOF after a positive growth result and the 128 remaining blood cultures 24 hours after the bacterial seeding. “

General microbiology and ecology

The quest for a unified view of bacterial land colonization – Hao Wu – ISME Journal

“Here, we perform comprehensive analyses based on a large variety of bacteria by integrating taxonomic, phylogenetic and metagenomic data, in the quest for a unified view that elucidates genomic, evolutionary and ecological dynamics of the marine progenitors in adapting to nonaquatic environments. “

Lateral transfer of eukaryotic ribosomal RNA genes: an emerging concern for molecular ecology of microbial eukaryotes – Akinori Yabuki – ISME Journal

“Two distinct sequences of the 18S rRNA gene were detected from a clonal culture of the stramenopile, Ciliophrys infusionum. One was clearly derived from Ciliophrys, but the other gene originated from a perkinsid alveolate.”

Arsenic metabolism

Arsenic Pollution Sows Despair in Chinese Cancer Village (slideshow)- Yahoo News

“Xiong Demin could not have foreseen that the mine he worked at for 32 years would leave his home village poisoned and hundreds of residents, including himself and his wife, stricken with cancer.”

Dr. Bik’s Picks – Evolution Edition

Molecular Phylogeny, Biogeography, and Habitat Preference Evolution of Marsupials – Kieren J. Mitchell – Molecular Biology and Evolution

“We use 101 mitochondrial genomes and data from 26 nuclear loci to reconstruct a dated phylogeny including 97% of extant genera and 58% of modern marsupial species”

Parallel sites implicate functional convergence of the hearing gene prestin among echolocating mammals – Zhen Liu – Molecular Biology and Evolution

“By functional assays, we show that a key parameter of prestin function, 1/α, is increased in all echolocating mammals and that the N7T parallel substitution accounted for this functional convergence. Moreover, another parameter, V1/2, was shifted toward the depolarization direction in a toothed whale, the bottlenose dolphin (Tursiops truncatus) and a constant-frequency bat, Stoliczka’s trident bat (Aselliscus stoliczkanus). “

Evolutionary developmental transcriptomics reveals a gene network module regulating interspecific diversity in plant leaf shape – Yasunori Ichihashi – PNAS

“Utilizing the natural variation in leaf morphology between tomato and two related wild species, we identified a gene network module that leads to a dynamic rewiring of interactions in the whole leaf developmental gene regulatory network. “

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General microbiology and science, June 23

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Amplification of 18S rRNA genes, metabolomics, phages, and the scientific way to cut a cake.

Bacteria are everywhere

This article is citing a study that was published in 1992, not sure why they reporting about it now, but here it is:
Earpieces can multiply bacteria 11 times in ear – Tribune

“Besides concerns about deafness, there are also issues regarding use of earpieces and bacteria. A study which measured bacteria levels on audio headsets provided on commercial airline flights entitled “Changes in the microbial flora of airline headset devices after their use,” published in the journal, The Laryngoscope, brings interesting conclusions. “

Anti-bacterial bag-for-life could prevent rise in food poisoning when 5p plastic bag charge comes into force – Independent UK

“Paul Morris, the managing director, said: “Multi-use bags which can carry raw meat one week and vegetables or clothing the next is a concern of many industry experts; this bag provides a solution to the problem.””

Amplification and sequencing techniques 

Investigating Microbial Eukaryotic Diversity from a Global Census: Insights from a Comparison of Pyrotag and Full-Length Sequences of 18S rRNA Genes – Alle A. Y. Lie – Applied and Environmental Microbiology

“Operational taxonomic units (OTUs) derived from full-length (Sanger sequencing) and pyrotag (454 sequencing of the V9 hypervariable region) sequences of 18S rRNA genes from 10 global samples were analyzed in order to compare the resulting protistan community structures and species richness. “

Targeted and Highly Multiplexed Detection of Microorganisms by Employing an Ensemble of Molecular Probes – Weihong Xu – Applied and Environmental Microbiology

“To profile the microbial diversity in environmental and clinical samples, we have devised and employed molecular probe technology, which detects and identifies bacteria that do and do not grow in culture.”

Metabolomics and mass spectrometry

This one is published by the not-so-trustworthy Omics group, but it sounds interesting:
Optimisation of Sample Preparation for Direct SPME-GC-MS Analysis of Murine and Human Faecal Volatile Organic Compounds for Metabolomic Studies (links to PDF)
– Reade S – Analytical & Bioanalytical Techniques

“We evaluated different aspects of sample preparation when processing murine and human faecal samples through a pipeline involving solid phase micro-extraction (SPME) coupled to gas chromatography-mass spectrometry (GC-MS)”

Shigella reroutes host cell central metabolism to obtain high-flux nutrient supply for vigorous intracellular growth – David Kentner – PNAS

“Here, we show that infected host cells maintain normal central metabolism for energy production and host cell survival. However, Shigella captures the entire host metabolism output and degrades it further to acetate.”

Beyond the Matrix-Assisted Laser Desorption Ionization (MALDI) Biotyping Workflow: in Search of Microorganism-Specific Tryptic Peptides Enabling Discrimination of Subspecies – Maria-Theresia Gekenidis – Applied and Environmental Microbiology

“Here, it is shown that combining tryptic digestion of the acid/organic solvent extracted (classical biotyping preparation) and resolubilized proteins, nano-liquid chromatography (nano-LC), and subsequent identification of the peptides by MALDI-tandem TOF (MALDI-TOF/TOF) mass spectrometry increases the discrimination power to the level of subspecies.”

Phages and viruses

Modeling the Infection Dynamics of Bacteriophages in Enteric Escherichia coli: Estimating the Contribution of Transduction to Antimicrobial Gene Spread –
Victoriya V. Volkova – Applied and Environmental Microbiology

“Using the model and the most liberal assumptions about transduction efficiency and resistance gene frequency, we approximated the upper numerical limits (“worst-case scenario”) of gene transfer through specialized and generalized transduction in E. coli by enteric coliphages when the transduced genetic segment is picked at random. “

Tolerance of a Phage Element by Streptococcus pneumoniae Leads to a Fitness Defect during Colonization – Hilary K. DeBardeleben – Journal of Bacteriology

“Here, we examined a clinical isolate that carries a novel prophage element, designated Spn1, which was detected in both integrated and episomal forms. Surprisingly, both lytic and lysogenic Spn1 genes were expressed under routine growth conditions.”

Comparison of Five Bacteriophages as Models for Viral Aerosol Studies – Nathalie Turgeon – Applied and Environmental Microbiology

“The presence of viruses in collected air samples was detected by culture and quantitative PCR (qPCR). Our results showed that these selected five phages behave differently when aerosolized and sampled. “

Microbial detection in blood and normally sterile sites

Molecular revolution in the diagnosis of microbial brain abscesses – AK Mishra – European Journal of Clinical Microbiology & Infectious Diseases

“This article reviews the applications of the currently available tools for the etiological diagnosis of a brain abscess.”

General microbiology

Nitrogen stress response and stringent response are coupled in Escherichia coli – Daniel R. Brown – Nature Communications

“Here, we show that transcription of relA, a key gene responsible for the synthesis of ppGpp, is activated by NtrC during nitrogen starvation.”

Stenotrophomonas comparative genomics reveals genes and functions that
differentiate beneficial and pathogenic bacteria – Peyman Alavi – BMC Genomics

“We used comparative genomics as well as transcriptomic and physiological approaches to detect significant borders between the Stenotrophomonas strains: the multi-drug resistant pathogenic S. maltophilia and the plant-associated strains S. maltophilia R551-3 and S. rhizophila DSM14405T (both are biocontrol agents)”

Emergence of bacterial vortex explained – Science Daily

“When a bunch of B. subtilis bacteria are confined within a droplet of water, a very strange thing happens. The chaotic motion of individual swimmers spontaneously organizes into a swirling vortex, with bacteria on the outer edge of the droplet moving in one direction while those on the inside move the opposite direction. “

Dr. Bik’s Picks

Screen Shot 2014-06-23 at 11.53.49 PMScientists tie social behavior to activity in specific brain circuit – Stanford University

“The new findings, published June 19 in Cell, may throw light on psychiatric disorders marked by impaired social interaction such as autism, social anxiety, schizophrenia and depression, said the study’s senior author, Karl Deisseroth, MD, PhD, a professor of bioengineering and of psychiatry and behavioral sciences. “

Scientists use X-rays to look at how DNA protects itself from UV light – Science Daily

“The molecular building blocks that make up DNA absorb ultraviolet light so strongly that sunlight should deactivate them — yet it does not. Now scientists have made detailed observations of a ‘relaxation response’ that protects these molecules, and the genetic information they encode, from UV damage.”

Cut your cake and keep it (fresh), too – Eliza Barclay – NPR

““The ordinary method of cutting out a wedge is very faulty,” wrote Sir Francis Galton, a British mathematician, in a 1906 letter to the journal Nature concerning the scientific principles of cake-cutting.”

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Non-human microbiome, June 23

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What happens with all that triclosan we flush down the drain? Also, baby squirrels, tse-tse flies, pot, and Chinese liquor.

Animal microbiome general 

Two very different papers from the same group, but both are finding that Blautia species are host specific.

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A single genus in the gut microbiome reflects host preference and specificity – A Murat Eren – The ISME Journal

“In our dataset of 57 M sequence reads of the V6 region of the 16S ribosomal RNA gene in samples collected from seven host species, we identified 200 high-resolution taxonomic units within Blautia using oligotyping.” (Humans, cows, swine, deer, chickens)

Screen Shot 2014-06-23 at 11.26.18 PMBlautia and Prevotella sequences distinguish human and animal fecal pollution in Brazil surface waters – Amber M. Koskey – Environmental Microbiology Reports

“We used oligotyping to identify Prevotella and Blautia sequences that can distinguish human fecal contamination. Thirty-five of 61 Blautia oligotypes and 13 of 108 Prevotella oligotypes in humans were specific to or highly abundant (i.e. host-preferred) compared to pig, dog, horse, and cow sources.”

Squirrel microbiome

Screen Shot 2014-06-23 at 11.35.26 PMTemporal Dynamics of the Cecal Gut Microbiota of Juvenile Arctic Ground Squirrels: a Strong Litter Effect across the First Active Season – Timothy J. Stevenson – Applied and Environmental Microbiology  (image courtesy of ego-alterego.com)

“We characterized trends in diversity (454 pyrosequencing), density (flow cytometry), viability (flow cytometry), and metabolism (short-chain fatty acid analysis) of the gut microbial community of juvenile arctic ground squirrels across their first active season at weaning and at 4, 6, 8, and 10 weeks postweaning.”

Insect microbiome

Screen Shot 2014-06-23 at 11.20.33 PMAnalysis of Multiple Tsetse Fly Populations in Uganda Reveals Limited Diversity and Species-Specific Gut Microbiota – Emre Aksoy – Applied and Environmental Microbiology

“We used multiple approaches, including deep sequencing of the V4 hypervariable region of the 16S rRNA gene, 16S rRNA gene clone libraries, and bacterium-specific quantitative PCR (qPCR), to investigate the levels and patterns of gut microbial diversity from a total of 151 individuals.”

Screen Shot 2014-06-23 at 11.22.49 PMMicrobial Population Dynamics in the Hemolymph of Manduca sexta Infected with Xenorhabdus nematophila and the Entomopathogenic Nematode Steinernema carpocapsae – Swati Singh – Applied and Environmental Microbiology

“We show that gut microbes translocate into the hemolymph when the nematode penetrates the insect intestine.”

Screen Shot 2014-06-23 at 11.23.22 PMPurine Biosynthesis, Biofilm Formation, and Persistence of an Insect-Microbe Gut Symbiosis – Jiyeun Kate Kim – Applied and Environmental Microbiology

“When we disrupted purN and purT in the Burkholderia symbiont, the ΔpurN and ΔpurT mutants grew normally, and only the ΔpurT mutant failed to form biofilms. “

Plant microbiome

Plant metabolomics for plant chemical responses to belowground community change by climate change – Sangkyu Park – Journal of Plant Biology

“In this review, we will first summarize recent progress in plant metabolomics methodology and subsequently review recent studies of interactions between plants and soil organisms in relation to climate change issues.”

Bioreactor and sewage microbiology

TriclosanThe Impacts of Triclosan on Anaerobic Community Structures, Function, and Antimicrobial Resistance – Patrick J McNamara – Environmental Science & Technology

“Triclosan amendment caused all of the Bacteria and Archaea communities to structurally diverge from that of the control cultures (based on ARISA).”

Screen Shot 2014-06-23 at 11.24.07 PMShifts in the Microbial Community, Nitrifiers and Denitrifiers in the Biofilm in a Full-scale Rotating Biological Contactor – Xingxing Peng – Environmental Science & Technology

“The objective of this study was to investigate the Microbial community shifts of bacteria, especially nitrifiers and denitrifiers, in the biofilm of two rotating biological contactor (RBC) trains with different running times along the plug flowpath”

Soil microbiology

Screen Shot 2014-06-23 at 11.32.29 PMIdentifying qualitative effects of different grazing types on below-ground communities and function in a long-term field experiment – Catriona A Macdonald – Environmental Microbiology

“All functional community measures (functions, biogeochemical cycling genes, network association between different taxa) were more strongly affected by invertebrate grazers than rabbits.”

Screen Shot 2014-06-23 at 11.25.34 PMExtensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi – Robert Riley – PNAS

“To test the adequacy of the white/brown-rot categories, we analyzed 33 fungal genomes. Some species lack PODs, and thus resemble brown-rot fungi, but possess the cellulose-degrading apparatus typical of white-rot fungi. “

Food and other consumables microbiology

Screen Shot 2014-06-23 at 11.33.28 PMIf the pot doesn’t worry you, the bacteria might: Food safety a new frontier for legal pot – Kristen Wyatt – The Republic

“In Washington state, where retail sales are expected to begin the week of July 7, regulations call for samples of all marijuana sold for consumption to clear a “microbiological screening,” whether it’s in edible, smokeable or concentrate form.”

Screen Shot 2014-06-23 at 11.34.50 PMStarter Culture Selection for Making Chinese Sesame-Flavored Liquor Based on Microbial Metabolic Activity in Mixed-Culture Fermentation – Qun Wu – Applied and Environmental Microbiology

“To obtain a suitable starter culture for making Chinese sesame-flavored liquor, the yeast and bacterium community structures were investigated during spontaneous and solid-state fermentations of this type of liquor.”

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General microbiology and science, June 19

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How to store your sputum samples, how LPS gets inserted into the outer membrane, and why pigs have an even number of toes.

Techniques in microbiome research

Screen Shot 2014-06-19 at 11.16.59 PMTime between sputum sample collection and storage significantly influences bacterial sequence composition from Cystic Fibrosis respiratory infections – Leah Cuthbertson – Journal of Clinical Microbiology

“Aliquots were stored at room temperature before freezing at -80°C for increasing intervals up to 72 hour period. Samples were treated with propidium monoazide, to distinguish live from dead cells, prior to DNA extraction, and 16S rRNA gene pyrosequencing was used to characterise the bacterial composition.”

General microbiology

Screen Shot 2014-06-19 at 11.26.58 PMStructural basis for outer membrane lipopolysaccharide insertion – Haohao Dong – Nature

“Here we report the first crystal structure of the unique integral membrane LPS translocon LptD–LptE complex….These findings not only help us to understand important aspects of bacterial outer membrane biogenesis, but also have significant potential for the development of novel drugs against multi-drug resistant pathogenic bacteria.”

Immunology

Screen Shot 2014-06-19 at 11.13.17 PMTeaching the immune system “self” respect and tolerance – Lucienne Chatenoud – Science

“Tolerance is what we would like to restore to cure such disabling diseases. Kasagi et al. (2) indicate that it may be possible to teach the immune system to tolerate “self” again.”

Screen Shot 2014-06-19 at 11.15.42 PMIn Vivo–Generated Antigen-Specific Regulatory T Cells Treat Autoimmunity Without Compromising Antibacterial Immune Response – Shimpei Kasagi – Science

“These antigen-specific Treg cells specifically ameliorated autoimmunity without compromising immune responses to bacterial antigen. We have thus successfully generated antigen-specific Treg cells with therapeutic activity toward autoimmunity”

Phages, viruses, CRISPRs

Screen Shot 2014-06-19 at 11.18.44 PMHaloarcula hispanica CRISPR authenticates PAM of a target sequence to prime discriminative adaptation – Ming Li – Nucleic Acids Research

Science and ethics

Cheating common, say Brazil’s students – Jack Grove – Times Higher Education

“Of a sample of 47 papers published last year, 29 showed signs of word-by-word plagiarism, seven contained self-plagiarism, three had “mosaic plagiarism” (otherwise known as “synonym substitution”) and one exhibited signs of collusion.”

Dr. Bik’s Picks

Screen Shot 2014-06-19 at 11.23.10 PMThe Dangers Of Data Mining – Tommaso Dorigo – Science 2.0

“On my first day at the Erice School of Science Journalism this past week I attended a lecture by Alessio Cimarelli, who discussed “When Data Journalism meets Science: a “Hackathon””.”

Screen Shot 2014-06-19 at 11.32.23 PMEvolutionary biology: Why cattle, pigs are even-toed – Science Daily

“During their evolution, the basic limb skeletal structure was significantly modified such that today’s hippopotami have four toes, while the second and fifth toe face backwards in pigs.”

 

U.S. Says 75 Government Scientists Possibly Exposed To Live Anthrax – Reuters – Huffington Post

“The potential exposure occurred after researchers working in a high-level biosecurity laboratory at the agency’s Atlanta campus failed to follow proper procedures to inactivate the bacteria.”

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General microbiology and science, June 18

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Learn about dengue at the World Cup, a deadly lake, 3D structures of genomes, OTUs and tables, musical kids, and why your iPhone headphones are always in a knot.

Dengue

Evaluation of single-round infectious, chimeric dengue type 1 virus as an antigen for dengue functional antibody assays – Atsushi Yamanaka – Vaccine

“In the present study, SRIPs of DENV-1 (D1-SRIPs) were evaluated as an antigen for functional antibody assays.”

An inhibition model of BPTI to unlinked dengue virus NS2B-NS3 protease – Hua Li – FEBS Letters

“BPTI shows strong competitive inhibitory activity (Ki = 6.5 nM) against this unlinked protease, which adopts a closed conformation.”

The role of cell proteins in dengue virus infection – Ma. Isabel Salazar – Journal of Proteomics

“This review focuses on recent reports about cellular proteins involved along the dengue virus replication cycle, in prime cellular targets during the infection of both humans and mosquito hosts and also on the proteomics and other approaches that are being used to reveal the entire orchestration and most significant processes altered during infection.”

Dengue outlook for the World Cup in Brazil – Eduardo Massad – The Lancet Infectious Diseases

Correspondence on: Dengue outlook for the World Cup in Brazil: an early warning model framework driven by real-time seasonal climate forecasts

Arsenic metabolism

43,000 die annually in Bangladesh: Study – The Daily Star

“This rate is 25 percent all over Bangladesh, said Dr Kazi Matin Ahmed, geology professor of Dhaka University. He presented the paper at a seminar titled “Arsenic Activities, Research and Outcomes” organised by the Bangladesh Medical Research Council (BMRC) in its auditorium in the capital yesterday.”

Arsenic speciation in rice-based food for adults with celiac disease – Sandra Munera-Picazo – Food Additives and Contaminants

“…the objective of this study was to analyze the occurrence of arsenic (As) in gluten-free products, basically those rice-based, intended for celiac adult consumers.”

Could This Acid Lake Hold the Elixir of Life for Cancer Patients? – Ryot.org

“The Berkeley Acid Pit is a giant hole filled with arsenic and sulfuric acid, and has a history of causing disturbing deaths… and it’s making its way into the city’s water supply, according to PitWatch.”

Chromosomal Organization

Targeted chromatin capture (T2C): a novel high resolution high throughput method to detect genomic interactions and regulatory elements – Petros Kolovos – Epigenetics &

“We applied T2C on well-known model regions, the mouse beta-globin locus and the human H19/IGF2 locus. In both cases we identified all known chromatin interactions”

A statistical approach for inferring the 3D structure of the genome – Nelle Varoquaux – Bioinformatics

“We propose a novel approach to infer a consensus 3D structure of a genome from Hi-C data. The method incorporates a statistical model of the contact counts, assuming that the counts between two loci follow a Poisson distribution whose intensity decreases with the physical distances between the loci.”

Spatial organization of interphase chromosomes and the role of chromatin fibril dynamics in the positioning of genome elements – E. S. Gushchanskaya – Molecular Biology

“In this review, we discuss the results of these projects, which allow us to explain the functional basis of nucleus multilevel compartmentalization and to identify the principles of high-level chromatin organization. “

Computational ecology

A fast and unbiased procedure to randomize ecological binary matrices with fixed row and column totals – Giovanni Strona – Nature Communications

“A well-known problem in numerical ecology is how to recombine presence-absence matrices without altering row and column totals. “

Consistent, comprehensive and computationally efficient OTU definitions – Jai Ram Rideout – PeerJ PrePrints

“We present a performance-optimized algorithm, subsampled open-reference OTU picking, for assigning marker gene (e.g., 16S rRNA) sequences generated on next-generation sequencing platforms to operational taxonomic units (OTUs) for microbial community analysis.”

 

Bacteria in blood and sterile sites

Rapid and direct MALDI-MS identification of pathogenic bacteria from blood using ionic liquid-modified magnetic nanoparticles (Fe3O4@SiO2) – Mukesh L. Bhaisare – Journal of Materials Chemistry B

“A novel method for pathogenic bacteria identification directly from blood samples using cationic ionic liquid-modified magnetic nanoparticles (CILMS) is reported.”

Metagenomics

GroopM: An automated tool for the recovery of population genomes from related metagenomes – Michael Imelfort – PeerJ PrePrints

“Here we introduce GroopM, an automated binning tool that primarily uses differential coverage to obtain high fidelity population genomes from related metagenomes. “

DNA-dependent RNA polymerase detects hidden giant viruses in published databanks – Vikas Sharma – Genome Biology and Evolution

“To explore the dark matter, we used viral RNAP2 and reconstructed putative ancestral RNAP2, which were significantly superior in detecting distant clades than current sequences, and we revealed two additional unknown mimiviruses, misclassified as an euryarchaeote and a oomycete plant pathogen, and detected unknown putative viral clades”

Metabolomics

Comparative Metabolomics and Structural Characterizations Illuminate Colibactin Pathway-Dependent Small Molecules – Maria I. Vizcaino – Journal of the American Chemical Society

“Here we implemented a comparative metabolomics and targeted structural network analyses approach to identify a catalog of small molecules dependent on the colibactin pathway from the meningitis isolate E. coli IHE3034 and the probiotic E. coli Nissle 1917.”

Scientific writing and publishing

Screen Shot 2014-06-18 at 11.01.34 PMColour blindness: Still too many red–green figures – S. Colby Allred – Nature

“People with red–green colour blindness cannot interpret figures in research papers that use these colours. We call for all journals to provide alternative versions of figures that are more accessible to such individuals.”

Open access: Sharing your data is easier than you think – Stephen Eglen – Nature

“Storing large volumes of raw data is costly, but many items destined for sharing are highly processed and relatively small. “

Dr. Bik’s Picks

The Irish potato famine pathogen Phytophthora infestans originated in central Mexico rather than the Andes – Erica M. Goss – PNAS

“We sequenced four nuclear genes in representative samples from Mexico and the South American Andes. An Andean origin of P. infestans does not receive support from detailed analyses of Andean and Mexican populations. “

Behavioral and Neural Correlates of Executive Functioning in Musicians and Non-Musicians – Jennifer Zuk – PLOS ONE

“Overall, musicians show enhanced performance on several constructs of EF, and musically trained children further show heightened brain activation in traditional EF regions during task-switching.”

There’s a scientific reason your iPhone headphones are always tangled – Fiona MacDonald – Science Alert

“But between 46 centimeters and 150 centimeters (about five feet), the probability of a knot forming rises dramatically.”

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Non-human microbiome, June 12

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Connected plants are better protected against pathogens, bacteria in olives and peanuts, and hormones made by marine phytoplankton.

Plant microbes

plant connectedEcological and evolutionary effects of fragmentation on infectious disease dynamics – Jussi Jousimo – Science

“To test the combined effects of ecological and evolutionary forces on host-pathogen systems, we analyzed the spatiotemporal dynamics of a plant (Plantago lanceolata)–fungal pathogen (Podosphaera plantaginis)relationship for 12 years in over 4000 host populations. “

Food microbiology

OliveGiarraffa and Grossa di Spagna naturally fermented table olives: Effect of starter and probiotic cultures on chemical, microbiological and sensory traits – C.L. Randazzo – Food Research International

“Multiplex PCR assay of lactic acid bacteria (LAB) showed that L. casei was detected in all samples, L. pentosus was the dominant species in spontaneous samples and in probiotic inoculated samples”

Screen Shot 2014-06-12 at 9.25.22 PMPeanut fractions boost the growth of Lactobacillus casei that alters the interactions between Campylobacter jejuni and host epithelial cells – Serajus Salaheen – Food Research International

“Our data suggest that peanut fraction induced the growth of L. casei which in turn led to a reduction in the growth of C. jejuni as well as its colonization. “

Water microbes

water hormonesPhytoplankton blooms: An overlooked marine source of natural endocrine disrupting chemicals – Yinhan Gong – Ecotoxicology and Environmental Safety

“Selected phytoplankton isolates are potent secretors of estrogenic and androgenic substances.”

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Human microbiome, June 12

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Today digest features the comparison of the HMP vs MetaHIT extraction protocols, microbiota and food consumption, mites in your skin, and a TIME article with a critical view.

Oral microbiome

Screen Shot 2014-06-12 at 9.59.53 PMGum disease bacteria selectively disarm immune system, study finds – Medical express

“In a new study, University of Pennsylvania researchers show that bacteria responsible for many cases of periodontitis cause this imbalance, known as dysbiosis, with a sophisticated, two-prong manipulation of the human immune system.”

Gut microbiome

yin yangReview: The Yin and Yang of Bacterial Resilience in the Human Gut Microbiota – Molly K. Gibson – Journal of Molecular Biology

“Here we review the mechanisms by which the host modulates the gut community composition during health and disease, and discuss prospects for antibiotic and probiotic therapy for restoration of a healthy intestinal community following disruption.”

obese women fructInulin-type fructans modulate intestinal Bifidobacterium species populations and decrease fecal short-chain fatty acids in obese women – Nuria Salazar – Clinical Nutrition

“ITF consumption selectively modulates Bifidobacterium spp. and decreases fecal SCFA concentration in obese women. ITF could lessen metabolic risk factors associated with higher fecal SCFA concentration in obese individuals.”

Screen Shot 2014-06-12 at 8.36.07 PMGlossary of the Gut Microbiome – Compiled by The American College of Gastroenterology

 

Skin microbiome

Screen Shot 2014-06-12 at 9.44.13 PMThese mites live on your face and come out to have sex at night – Joseph Stromberg – Vox

“Right now, there are thousands of mites on your face. They’re microscopic, but closely related to spiders and ticks. And despite your reaction to hearing this news, there’s absolutely nothing wrong with you.”

Animal models of human microbiome and disease

vitkQuantification of phylloquinone and menaquinones in feces, serum, and food by high-performance liquid chromatography-mass spectrometry – J. Philip Karl – Journal of Chromatography B

“We developed a novel method employing high-performance liquid chromatography-mass spectrometry with atmospheric pressure chemical ionization (LC-APCI-MS) for simultaneous quantification of 11 vitamin K vitamers that can be applied in feces, serum and food.”

Microbial Bioreactors

vegetalBeneficial effects of fermented vegetal beverages on human gastrointestinal microbial ecosystem in a simulator – Fernanda Bianchi – Food Research International

“To monitor the effects on microbial community composition, plate counts on specific growth media and a PCR-DGGE analysis were performed on samples from all colon compartments – ascending, transverse and descending.”

Microbiome conference

Screen Shot 2014-06-12 at 8.42.07 PMKenneth Rainin Foundation’s 2014 Innovations Symposium to Feature Virus Hunters and Gut Explorers – Taming the Microbiome – July 15 – 16, 2014, San Francisco.

“This year’s dynamic keynote speakers each bring a unique perspective on the human microbiome.”

Microbiome in the Press

timeExercise Helps Your Gut Bacteria: Amazing, Overblown, or Plain Incorrect? – Alexandra Sifferlin – Time

“Though he sees great promise in researching the microbiome, Eisen says it irks him when studies are blown out of portion both by scientists and the press.”

Screen Shot 2014-06-12 at 9.56.29 PMHere’s bacteria you ought to be eating – Craig Sailor – The Olympian

“Blake is a big proponent of raw, living fermented foods. The probiotic or friendly bacteria in the food provides nutrients and vitamins. “They also produce digestive enzymes that help us get more out of our food,” she said.”

breadWhite Bread May Encourage Growth Of ‘Good’ Bacteria – Jaleesa Baulkman – University Herald (mentions a study featured here that was recently published in American Chemical Society’s Journal of Agricultural and Food Chemistry.)

“Researchers said their most novel finding was that white bread boosted Lactobacillus, a group of beneficial bacteria. The results were surprising because white bread is a much-maligned food. “

Techniques: DNA extraction from stool

Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis – Agata Wesolowska-Andersen – Microbiome

“We observed significant differences in distribution of bacterial taxa depending on the method. While eukaryotic DNA was most efficiently extracted by the MetaHIT protocol, DNA from bacteria within the Bacteroidetes phylum was most efficiently extracted by the HMP protocol.”

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