Microbiome and general science digest, July 11

Most recent results from American gut, a metagenomics pipeline, arsenic toxicity, polio and dengue vaccines, and pregnancy urine metabolomics to predict preterm birth.

Human gut microbiome

American GutAmerican Gut releases latest results and pipeline – Jeff Leach – American Gut

“The latest American Gut results are out and we’re very excited to share them with the American Gut community. We now have sequencing and analysis data from 3,238 participants, and as of today, this data equates to 101 million DNA sequences and 27 gigabytes of sequencing information.”

Screen shot 2014-07-11 at 04.27PM, Jul 11Place of upbringing in early childhood as related to inflammatory bowel diseases in adulthood: a population-based cohort study in Northern Europe – Signe Timm – European Journal of Epidemiology

“This study suggests a protective effect from livestock farm living in early childhood on the occurrence of IBD in adulthood, however only among subjects born after 1952. We speculate that lower microbial diversity is an explanation for the findings.”

Pregnancy and birth

Urinary pretermUrinary metabolic profiles in early pregnancy are associated with preterm birth and fetal growth restriction in the Rhea mother–child cohort study – Léa Maitre – BMC Medicine

“Here we used an exploratory metabolic profiling approach (metabolomics) to investigate the association between birth outcomes and metabolites in maternal urine collected early in pregnancy as part of the prospective mother–child cohort Rhea study. “

Metagenomics

MedusaMetagenomic Data Utilization and Analysis (MEDUSA) and Construction of a Global Gut Microbial Gene Catalogue – Fredrik H. Karlsson, Intawat Nookaew, Jens Nielsen – PLOS Computational Biology

“Here we present the bioinformatics pipeline MEDUSA that facilitates analysis of metagenomic reads at the gene and taxonomic level. We also constructed a global human gut microbial gene catalogue by combining data from 4 studies spanning 3 continents. “

Proteomics

Proteomics Staph aureusGenomics and Proteomics Provide New Insight into the Commensal and Pathogenic Lifestyles of Bovine and Human-associated Staphylococcus epidermidis strains – Kirsi Savijoki – Journal of Proteome Research

“Pilot experimental infection studies indicated that while ATCC12228 was able to infect bovine host, the PM221 strain caused more severe clinical signs. “

Dengue

Demanou DengueEvidence of Dengue Virus Transmission and Factors Associated with the Presence of Anti-Dengue Virus Antibodies in Humans in Three Major Towns in Cameroon – Maurice Demanou – PLOS Neglected Tropical Diseases

“Sera were screened for anti-dengue virus IgG and IgM antibodies. Risk factors of seropositivity were tested using logistic regression methods with random effects.”

Carrasco DenguePredictive Tools for Severe Dengue Conforming to World Health Organization 2009 Criteria – Luis R. Carrasco – PLOS Neglected Tropical Diseases

“Higher risk of severe dengue (SD) was associated with female gender, lower than normal hematocrit level, abdominal distension, vomiting and fever on admission. “

Infection and host response

Screen shot 2014-07-11 at 03.35PM, Jul 11Development of Fatal Intestinal Inflammation in MyD88 Deficient Mice Co-infected with Helminth and Bacterial Enteropathogens – Libo Su – PLOS Neglected Tropical Diseases

“We found that MyD88 knockout mice co-infected with H. polygyrus and C. rodentium developed more severe intestinal inflammation and elevated mortality compared to the wild-type mice.”‘

Screen shot 2014-07-11 at 04.28PM, Jul 11Distinct Lipid A Moieties Contribute to Pathogen-Induced Site-Specific Vascular Inflammation – Connie Slocum – PLOS Pathogens

“our results point to a pivotal role for activation of the non-canonical inflammasome in P. gingivalis infection and demonstrate that P. gingivalis evades immune detection at TLR4 facilitating chronic inflammation in the vasculature. “

Dengue

Dengue vaccine lancetClinical efficacy and safety of a novel tetravalent dengue vaccine in healthy children in Asia: a phase 3, randomised, observer-masked, placebo-controlled trial – Maria Rosario Capeding – The Lancet

“Our findings show that dengue vaccine is efficacious when given as three injections at months 0, 6, and 12 to children aged 2–14 years in endemic areas in Asia, and has a good safety profile. “

Also see comment: Dengue vaccines: dawning at last? – Annelies Wilder-Smith – The Lancet

Poliovirus

Jacob John polioEffect of a single inactivated poliovirus vaccine dose on intestinal immunity against poliovirus in children previously given oral vaccine: an open-label, randomised controlled trial – Jacob John – The Lancet

“The substantial boost in intestinal immunity conferred by a supplementary dose of IPV given to children younger than 5 years who had previously received OPV shows a potential role for this vaccine in immunisation activities to accelerate eradication and prevent outbreaks of poliomyelitis.”

Also see comment: Polio endgame management: focusing on performance with or without inactivated poliovirus vaccine – Kimberly M Thompson – The Lancet

Microbes in the News

Screen shot 2014-07-11 at 04.28PM, Jul 11 1How Gross Is Your Phone? A Motherboard Science Experiment – Jason Koebler – Motherboard

“All I wanted to do was recreate a relatively simple study I had just written about. Instead, I ended up creating something vaguely dangerous, which mortified the director of a local DIY biology lab. Here’s what happens when you perform experiments on your coworkers.”

Arsenic metabolism

Screen shot 2014-07-11 at 04.29PM, Jul 11Lung tumors in mice induced by “whole-life” inorganic arsenic exposure at human-relevant doses – Michael P. Waalkes – Archives of Toxicology

“Breeder male and female CD1 mice were exposed to 0, 50, 500 or 5,000 ppb arsenic (as sodium arsenite) in the drinking water for 3 weeks prior to breeding, during pregnancy and lactation, and after weaning (at week 3) groups of male and female offspring (initial n = 40) were exposed for up to 2 years.”

Dr. Bik’s Picks

Scorpions are master architects, according to new research – Science Daily

“The burrows made by scorpions follow a very sophisticated design, beginning with a short, vertical entrance shaft that flattened out a few centimeters below the surface into a horizontal platform, new research has found.”

Beach Sand Used To Make A Battery That Lasts Three Times Longer – Douglas Main – Popular Science

“Sink your toes into this: Beach sand can be used to make lithium-ion batteries that last three times longer than current models, according to a study published in the journal Scientific Reports.”

World Now “A Safer Place”, thanks to creation of Potential Pandemic Virus – The Allium

“Yes, I get your point that they could potentially kill millions of people and hospitalise millions more, causing untold human suffering and extraordinary economic damage, but think of all the advantages to the creation of these bugs”.

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