Microbiomes of horses, sheep, chicken, plants in Chili, built environment and rocks.

General microbiomes of animals

Viral Metagenomics on Animals as a Tool for the Detection of Zoonoses Prior to Human Infection? – Sarah Temmam – Int J Mol Sci

“In this review, we summarize our current knowledge of viral diversity within such animals (in particular blood-feeding arthropods, wildlife and domestic animals) using metagenomics and present its possible future application for the surveillance of zoonotic and arboviral diseases.”

Horse microbiome

Faecal Microbiome of the Thoroughbred Racehorse and Its Response to Dietary Amylase Supplementation – Proudman C – Equine Veterinary Journal

“Amplicons for the V1-V3 region of the 16S rDNA gene were multiplexed and sequenced on the 454 resulting in ∼25,000 reads per sample. Differences in bacterial community structure were detected by linear discriminant analysis.”

Sheep microbiome

Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome – Weibing Shi – Genome Research

“Deep metagenomic and metatranscriptomic sequencing demonstrated the presence of methanogens both in the highest and lowest methane-producing sheep, with a similar abundance of methanogens and methanogenesis pathway genes in high and low methane emitters. “

Chicken microbiome

Spatial heterogeneity and stability of bacterial community in the gastrointestinal tracts of broiler chickens – J. H. Choi – Poultry Science

“Bacterial communities in the different regions of gastrointestinal tract (GIT) of broiler chickens were analyzed by pyrosequencing approach to understand microbial composition and diversity. “

Squid microbiome

The real threat posed by discover of antibiotic- resistent bacteria found in squid – Robert Lawrence and Patrick Baron, Baltimore – Washington Post

“The Food and Drug Administration can, and should, do more to limit the misuse of antibiotics in the production of food animals, whether terrestrial or aquatic, in order to reduce the risk of accelerating antibiotic resistance.”

Plant microbiome

Bacterial community structure and detection of putative plant growth-promoting rhizobacteria associated with plants grown in Chilean agro-ecosystems and undisturbed ecosystems – Milko A. Jorquera – Biology and Fertility of Soils

“Soil microorganisms with phytase- and 1-aminocyclopropane-1-carboxylate (ACC) deaminase activities are widely studied as plant growth-promoting rhizobacteria (PGPR). Here, we explored the bacterial community structure and occurrence of putative PGPR in plants grown in agro-ecosystems and undisturbed ecosystems from northern, central, and southern Chile.”

Built Environment Microbiome

microBEnet: Lessons Learned from Building an Interdisciplinary Scientific Community in the Online Sphere – Holly M. Bik, David A. Coil, Jonathan A. Eisen – PLOS Biology

“The microbiology of the Built Environment network (microBEnet: http://www.microbe.net/) was formed as an experiment in interdisciplinary community building, with an overarching goal to facilitate and nurture the development of a new research field: the microbiology of the built environment (MBE). “

Water microbiome

Review: Emerging Strategies and Integrated Systems Microbiology Technologies for Biodiscovery of Marine Bioactive Compounds – Javier Rocha-Martin – Marine Drugs

“Recent advances in genomics, metagenomics, proteomics, combinatorial biosynthesis, synthetic biology, screening methods, expression systems, bioinformatics, and the ever increasing availability of sequenced genomes provides us with more opportunities than ever in the discovery of novel bioactive compounds and biocatalysts.”

From community approaches to single-cell genomics: the discovery of ubiquitous hyperhalophilic Bacteroidetes generalists – María Gomariz – ISME Journal

“Here we have characterized the temporal variation during 1 year of the microbiota of five ponds with increasing salinity (from 18% to >40%), by means of CARD-FISH and DGGE.”

Soil and rock microbiome

Mineral Microniches Control the Diversity of Subsurface Microbial Populations – Aaron A. Jones – Geomicrobiology Journal

“These results suggest that adaptations to specific rocks are retained even when the organism is displaced in time and space from an ancestral rock habitat.”

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