General microbiome and science, June 30

Monday is always a busy day, so lots of papers today. Phages, CRISPRs, antibiotic resistance, probiotics, archaea, biofilms and a Goldilocks planet.

Antibiotics and resistance

Horizontal gene transfer in the human gastrointestinal tract: potential spread of antibiotic resistance genes – JR Huddleston – Infection and Drug Resistance

“This review aims to give an overview of the major horizontal transfer mechanisms and their evolution and then demonstrate the human lower gastrointestinal tract as an environment in which horizontal gene transfer of resistance determinants occurs.”

Screen shot 2014-06-30 at 06.47PM, Jun 30Bacterial persisters: formation, eradication, and experimental systems
Sophie Helaine, Elisabeth Kugelberg – Trends in Microbiology

“Toxin–antitoxin (TA) modules have an important role in the formation of persisters and several studies show that they can form in response to different triggers.”

Screen shot 2014-06-30 at 06.48PM, Jun 30Antibiotic Treatment Suppresses Rotavirus Infection and Enhances Specific Humoral Immunity – Robin Uchiyama – Journal of Infectious Diseases

“Microbiota ablation resulted in reduced rotavirus infection/diarrhea and a more durable rotavirus antibody response, suggesting that antibiotic administration before rotavirus vaccination could raise low seroconversion rates that correlate with the vaccine’s inefficacy in developing regions.”

And:  Antibiotics Help Control Rotavirus Infections and Enhance Antirotaviral Immunity: Are You Serious? – Luther A. Bartelt and Richard L. Guerrant – Journal of Infectious Diseases

“Yes, we must understand intriguing new findings; but no, we are far from serious about widespread use of antimicrobials with routine immunizations.”

Screen shot 2014-06-30 at 06.44PM, Jun 30Transferrin Iron Starvation Therapy for Lethal Bacterial and Fungal Infections – Lin Lin – Journal of Infectious Diseases

“These results provide proof of principle that bacterial infections can be treated in vivo by attacking host targets (ie, trace metal availability) rather than microbial targets.”

Bacterial detection in blood and other sites

Screen shot 2014-06-30 at 06.45PM, Jun 30Identification of pathogens from blood culture bottles in spiked and clinical samples using matrix-assisted laser desorption ionization time-of-flight mass-spectrometry analysis – Simone Konnerth – BMC Research Notes

“MALDI-TOF MS using the SARAMIS database was applied to 37 spiked blood culture samples. Identification rates of spiked samples were as follows: The species level was determined in 16 of 21 (76.2%) Gram negative bacteria and in 11 of 13 (84.6%) Gram positive bacteria. “

Infection and host response

Type I and III Interferon Production in Response to RNA Viruses – Elizabeth Reid and Bryan Charleston – Journal of Interferon & Cytokine Research

“There are now many examples of RNA viruses inducing type I and type III IFNs, and although these IFNs act through different receptors, in many systems studied, they induce a similar spectrum of genes. “

CRISPRs

Screen shot 2014-06-30 at 06.50PM, Jun 30Review: Adapting to new threats: the generation of memory by CRISPR-Cas immune systems – Robert Heler – Molecular Microbiology

“Recent studies have begun to elucidate the genetic requirements for adaptation and have demonstrated that rather than being a stochastic process, the selection of new spacers is influenced by several factors. We review here our current knowledge of the CRISPR adaptation mechanism”

Screen shot 2014-06-30 at 06.53PM, Jun 30The three major types of CRISPR-Cas systems function independently in CRISPR RNA biogenesis in Streptococcus thermophilus – Jason Carte – Molecular Microbiology

“Our findings indicate that multiple CRISPR-Cas systems can function independently in crRNA biogenesis within a given organism – an important consideration in engineering coexisting CRISPR-Cas pathways”

Viruses and phages

Screen shot 2014-06-30 at 06.53PM, Jun 30Exploiting gut bacteriophages for human health – Marion Dalmasso – Trends in Microbiology

“We emphasise the complexity and individuality of the phageome, and the link to the health state of the host. We highlight the practical applications of bacteriophages in medicine and in the food chain.”

Screen shot 2014-06-30 at 06.52PM, Jun 30Environmental bacteriophages : viruses of microbes in aquatic ecosystems – Télesphore Sime – Ngando – Frontiers in Microbiology

“The present chapter sought to review the literature on the diversity and functional roles of viruses of microbes in environmental microbiology, focusing primarily on prokaryotic viruses (i.e. phages) in aquatic ecosystems, which form the bulk of our knowledge in modern environmental viral ecology.”

Archaea

Screen shot 2014-06-30 at 06.55PM, Jun 30Taxonomic database and cut-off value for processing mcrA gene 454 pyrosequencing data by MOTHUR – Sizhong Yang – Journal of Microbiological Methods

“The functional mcrA gene of methanogens can generate phylogeny as congruent as the 16S rRNA gene phylogeny. “

Screen shot 2014-06-30 at 06.59PM, Jun 30Biofilm formation of mucosa-associated methanoarchaeal strains
Corinna Bang – Frontiers in Microbiology

“Here, the ability of three methanoarchaeal strains, Methanobrevibacter smithii and Methanosphaera stadtmanae, which form part of the human gut microbiota, and the Methanosarcina mazei strain Gö1 to grow on different surfaces and form biofilms was investigated.”

Biofilms (see also Archaea above and Probiotics below)

Screen shot 2014-06-30 at 07.02PM, Jun 30Development of an in vitro periodontal biofilm model for assessing antimicrobial and host modulatory effects of bioactive molecules
Emma Millhouse – BMC Oral Health

Multi-species biofilms were either treated with either molecule, or alternatively epithelial cells were treated with these prior to biofilm co-culture. Biofilm composition was evaluated and inflammatory responses quantified at a transcriptional and protein level.

Probiotics

Screen shot 2014-06-30 at 06.43PM, Jun 30Review: Enumeration of probiotic strains: Review of culture-dependent and alternative techniques to quantify viable bacteria – Catherine Davis – Journal of Microbiological Methods

“Consensus on an operational definition of viability and systematic efforts to validate these alternative techniques ultimately will strengthen the accuracy and reliability of probiotic strain enumeration.”

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

“We analyzed 64 L. salivarius strains and found that two, K35 and K43, significantly inhibited S. mutans biofilm formation with inhibitory activities more pronounced than those of Lactobacillus rhamnosus GG (LGG), a prototypical probiotic that shows anti-caries activity.

General taxonomy and phylogeny

Screen shot 2014-06-30 at 07.04PM, Jun 30Considering external information to improve the phylogenetic comparison of microbial communities: a new approach based on constrained Double Principal Coordinates Analysis (cDPCoA) – S Dray – Molecular Ecology Resources

“In this work, we extend DPCoA to integrate the information of external variables measured on communities. The constrained Double Principal Coordinates Analysis (cDPCoA) is able to enforce a priori classifications to retrieve subtle differences and(or) remove the effect of confounding factors. “

Screen shot 2014-06-30 at 06.43PM, Jun 30Understanding molecular identification and polyphasic taxonomic approaches for genetic relatedness and phylogenetic relationships of microorganisms – Surajit Das – Journal of Microbiological Methods

“In this regard, a polyphasic taxonomic approach is advantageous because it exploits simultaneously both conventional as well as molecular identification techniques.”

Metabolomics

Screen shot 2014-06-30 at 07.01PM, Jun 30Nutrient sharing in the microbial world – Erica C. Seth and Michiko E. Taga – Frontiers in Microbiology

“Cofactor cross-feeding can contribute to both the health and nutrition of a host organism, the virulence and persistence of pathogens, and the composition and function of environmental communities. “

Metagenomics

Combination of Metagenomics and Culture Based Methods to Study the Interaction Between Ochratoxin A and Gut Microbiota – Mingzhang Guo – Toxicological Sciences

“Changes in functional genes of gut microbiota including signal transduction, carbohydrate transport, transposase, amino acid transport system and mismatch repair were observed.”

Chromosomal organization

NuChart-II: a graph-based approach for the analysis and interpretation of Hi-C data (PDF) – Fabio Tordini – Proceedings of the CIBB 2014

“NuChart-II is a highly optimized implementation of a previous prototype package developed in R, in which the graph-based representation of Hi-C data was tested, but that also showed inevitable problems of scalability while working genome-wide on large datasets.”

Science and education

Screen shot 2014-06-30 at 06.58PM, Jun 30Starting small: using microbiology to foster scientific literacy
Amy F. Savage, Brooke A. Jude – Trends in Microbiology

“In order to achieve scientific literacy for all students, Bard College recently implemented Citizen Science, a common January course for all first-year students. Structured around the question ‘how do we reduce the global burden of disease?’, this course uses microbiological tools to develop an understanding of potential answers.”

 

Dr. Bik’s Picks

Screen Shot 2014-07-01 at 12.06.17 AMBird brains: Public asked to look out for clever rooks – Victoria Gill – BBC News

“The British Trust for Ornithology (BTO) is asking the public to take part in a national survey of bird intelligence. From 1 July, the charity is asking people to submit video clips or descriptions of the behaviour or rooks – some of our cleverest garden birds.”

Screen Shot 2014-07-01 at 12.06.52 AMPotentially habitable Earth-like planet discovered; May have similar temperatures to our planet – Science Daily

“A potentially habitable Earth-like planet that is only 16 light years away has been discovered. The “super-Earth” planet, GJ 832 c, takes 16 days to orbit its red-dwarf star, GJ 832, and has a mass at least five times that of Earth.”

Screen Shot 2014-07-01 at 12.07.35 AMStudy Implicates Smog In Autism And Schizophrenia – Science 2.0

“A recent paper found that exposure to air pollution early in life produces harmful changes in the brains of mice, including an enlargement of part of the brain that is seen in humans who have autism and schizophrenia, and that led them to conclude that smog causes autism.”

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