Microbiome digest, October 30, 2014

Bacteriocins in human metagenomic libraries, freezing/thawing effects on community composition, microbiome of preterm neonates, and bacteria in soil.
Multiple-site human microbiome

Diversity and dynamics of bacteriocins from human microbiome – Jinshui Zheng – Environmental Microbiology

“We employed bioinformatic analyses to identify putative bacteriocin sequences in metagenomic sequences obtained from different human body sites. “

Human respiratory microbiome

* Implications of multiple freeze-thawing on respiratory samples for culture-independent analyses – Leah Cuthbertson – Journal of Cystic Fibrosis

“Following each cycle, an aliquot was removed and treated with propidium monoazide (PMA) prior to DNA extraction and 16S rRNA gene pyrosequencing.”

Human gut microbiome

Immune Homeostasis, Dysbiosis and Therapeutic Modulation of the Gut Microbiota – Christine T. Peterson – Clinical & Experimental Immunology

“This review discusses host-microbiota homeostasis, consequences of its perturbation, and the associated challenges in therapeutic developments that lie ahead.”

Microbiome of pregnancy and birth

* Intestinal Microbiota Development in Preterm Neonates and Effect of Perinatal Antibiotics – Silvia Arboleya – The Journal of Pediatrics

“We used 16S ribosomal RNA gene sequence-based microbiota analysis and quantitative polymerase chain reaction to evaluate the establishment of the intestinal microbiota. “

Animal microbiome

Hidden Population Structure and Cross-species Transmission of Whipworms (Trichuris sp.) in Humans and Non-human Primates in Uganda – Ria R. Ghai – PLOS Neglected Tropical Diseases

“We examined the phylogenetic structure of whipworms in a multi-species community of non-human primates and humans in Western Uganda, using both traditional microscopy and molecular methods.”

Soil microbiome

Metagenomic analysis reveals microbial functional redundancies and specificities in a soil under different tillage and crop-management regimes – Renata Carolini Souza – Applied Soil Ecology

“in this study we used a shotgun metagenomic approach to compare different soil…, and crop … managements in a 13-year-old field experiment in southern Brazil. “

Evaluating T-RFLP protocols to sensitively analyze the genetic diversity and community changes of soil alkane degrading bacteria – Julia Giebler – European Journal of Soil Biology

“This study aimed at identifying a reliable, highly resolving fingerprinting method to monitor alkane degrading communities in soil.”

Contrasting land uses in Mediterranean agro-silvo-pastoral systems generated patchy diversity patterns of vascular plants and below-ground microorganisms – Simonetta Bagella – Comptes Rendus Biologies

“Species richness decreased with increasing land use intensity, the Shannon index showed the highest values in grasslands and hay crops.”

Food microbiology

Characterization and use of microbial communities in Doenjang to control the unpleasant odor of Ginkgo epicarp – Sunhyun Park – Food Science and Biotechnology

“Microbes in doenjang were probably responsible for the reduction in the butyric acid content. Microbial communities were analyzed during fermentation.”

Bioreactor microbiology

Thermophilic anaerobic digestion of thermal pretreated sludge: role of microbial community structure and correlation with process performances – M.C. Gagliano – Water Research

“16S rRNA gene clonal analysis and Fluorescence In Situ Hybridization (FISH) analyses allowed us to identify the majority of bacterial and archaeal populations. “

Bioinformatics

Fast dendrogram-based OTU clustering using sequence embedding – Thuy-Diem Nguyen – Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics

“In this paper, we introduce a new hierarchical clustering method called CRiSPy-Embed which aims to produce high-quality clustering results at a low computational cost. “

Focus: a new multilayer graph model for short read analysis and extraction of biologically relevant features – Julia Warnke – Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics

“We present Focus, a new multilayer graph model for short read analysis and extraction of biologically relevant features. “

The UniFrac significance test generates different outputs given semantically equivalent inputs – Jeffrey Long – Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics

“We identify a discrepancy in the UniFrac methodology that causes semantically equivalent inputs to produce different outputs in tests of statistical significance.”

Microbes in the news

SpaceX 4 splashes down, returns bacteria samples to Earth – Josh Barrett – WaayTV

“HudsonAlpha’s Genomic Sciences Lab will be sequencing the genomes of E. coli bacteria that were aboard the ISS. For some reason, bacteria are not as susceptible to antibiotics in space.”

Bik’s Picks

Why Millennials &%#@! Love Science – Alexandra Ossola – The Atlantic

“Today’s young adults see new discoveries both as a source of awe and a means for innovation.”

1,000 Flavors of Banana: the New Science of Food Additives – Annie Gasparro – The Wall Street Journal

“Rather than sourcing the jalapeño or poblano pepper, you can create it with a flavor house, and just apply it over a corn chip,” said Jared Simon, marketing director for Hain Celestial Group Inc. ’s snacks and bakery division, which uses natural flavors for its foods such as Terra vegetable chips.”

Spooky Science: The Sounds of Halloween – Science Buddies – Scientific American

“In this science activity, you will investigate what goes into the composition of a perfect creepy soundtrack. “

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