Microbiome digest, August 21, 2014

Ground squirrels, scallops, hypersaline water, and dead bodies.

Postmortem human microbiome

* Microbial communities associated with human decomposition and their potential use as postmortem clocks – Sheree J. Finley – International Journal of Legal Medicine

“the scope of this review is to provide a concise summary of the current progress in the newly emerging field of microbial diversity and the next-generation metagenomic sequencing approaches for assessing these communities in humans and in the soil beneath decomposing human.”

* Effects of Season and Host Physiological State on the Diversity, Density, and Activity of the Arctic Ground Squirrel Cecal Microbiota – Timothy J Stevenson – Applied and Environmental Microbiology

“We examined the seasonal changes of the cecal microbiota of captive arctic ground squirrels (Urocitellus parryii) by measuring microbial diversity and composition, total bacterial density and viability, and short-chain fatty acid concentrations at four sample periods (summer, torpor, interbout arousal, and posthibernation).”

Invertebrate microbiome

* IMMR abstract: Analysis of the scallop microbiota by means of 16S rRNA gene pyrosequencing – Aide Lasa – Frontiers in Microbiology

“In this study, we present the analysis of the microbiota associated to reared scallop gonads before and after spawning by pyrosequencing of the 16S rRNA gene. “

Soil microbiome

Bacterial diversity assessment in soil of an active Brazilian copper mine using high-throughput sequencing of 16S rDNA amplicons – Viviane D. Rodrigues – Antonie van Leeuwenhoek

“In this work, pyrosequencing of the V3 region of the 16S rDNA was used to analyze the bacterial communities in soil samples from a Brazilian copper mine. “

* Impact of long-term N, P, K, and NPK fertilization on the composition and potential functions of the bacterial community in grassland soil – Yao Pan – FEMS Microbiology Ecology

“Here, we applied DNA shotgun metagenomic techniques to investigate the effect of inorganic fertilizers N, P, K, and NPK on the bacterial community composition and potential functions in grassland soils in a 54-year experiment. “

Water microbiome

The Santa Pola saltern as a model for studying the microbiota of hypersaline environments – Antonio Ventosa – Extremophiles

“Multi-pond salterns constitute an excellent model for the study of the microbial diversity and ecology of hypersaline environments, showing a wide range of salt concentrations, from seawater to salt saturation. “

Food microbiology

Book: Microorganisms and Fermentation of Traditional Foods – Ramesh C. Ray, Montet Didier – CRC Press

Fungi

Reconstruction of the original mycoflora in pelleted feed by PCR-SSCP and qPCR – Samart Dorn-In – FEMS Microbiology Letters

“A fungal-specific primer pair ITS1/ITS5.8R was used to amplify fungal DNA; PCR products were processed for the PCR-SSCP method. In the resulting acrylamide gel, more than 85% of DNA bands of ground feeds were preserved after pelleting. “

 

From Dandruff to Deep-Sea Vents: Malassezia-like Fungi Are Ecologically Hyper-diverse – Anthony Amend – PLOS Pathogens

“As the dominant component of the mycobiota on human skin —both healthy and diseased [2] —the genus Malassezia has received a fair amount of attention. “

Microbes in the news

The Birth of Pathogens: How Bacteria Become Deadly – Brian Stallard – Nature World News

“Two new studies have revealed two very different ways bothersome bacteria strains can suddenly become deadly, evolving into difficult-to-rid pathogens that can threaten entire populations.” – belongs to a PNAS paper on Salmonella enterica, and a Nature Communications paper on Group B Streptococcus.

Bacteria colonies removed from Savannah River Site using special vacuum – Meg Mirshak – The Augusta Chronicle

“Scientists studied samples and determined the white, stringy “cobwebs” were made up of a broad variety of bacteria and a few types of microbes.”

ASU experts follow gut reaction in autism treatment study – Arizona State University

“A new study approved by the U.S. Food and Drug Administration and led by Arizona State University will examine a novel treatment – called fecal microbiota transplant (FMT) – for GI problems in children with autism.”

Science and career

Ailing academia needs culture change – Viviane Callier, Nathan L. Vanderford – Science

“The research enterprise has become unsustainable in its current form. Research funding levels/mechanisms, the peer-review process, and the methods of training Ph.D.’s are flawed, and these issues are crippling the pipeline of future, successful academic researchers”

Science Media Beset with Gender Gaps – By Curtis Brainard – Scientific American

“One antidote, summit participants suggested, would be having more reporters abide by the seven-part Finkbeiner Test”

Bik’s Picks

* Why does asparagus make our urine smell? – Claudia Hammond – BBC Future

“After eating asparagus, some people can detect a strange smell, while others claim not to notice a thing. What’s going on?”

Chemically mediated behavior of recruiting corals and fishes: A tipping point that may limit reef recovery – Danielle L. Dixson – Science

“We show that juveniles of both corals and fishes are repelled by chemical cues from fished, seaweed-dominated reefs but attracted to cues from coral-dominated areas where fishing is prohibited. “

Scientists discover how lizards regrow tails – John von Radowitz – The Independent

“Researchers have identified a genetic programme that triggers new tissue growth after a lizard sacrifices its tail to escape a predator.”

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