December 5, 2015

Two job openings in our lab / UCSF, parasitism in TM6, and colonization of a new island.

Jobs and Events

Two job openings in our lab / UCSF School of Dentistry (San Francisco) for our hyposalivation project: Full time study coordinator and Part time dental assistant (20 hours per week)

3rd Microbiome R&D and Business Collaboration Forum: Europe, 11–12 April 2016, London, United Kingdom

General microbiome

The Hologenome Concept: Helpful or Hollow? – Nancy A. Moran , Daniel B. Sloan – PLOS Biology

Opinion: Cross-Kingdom Similarities in Microbiome Ecology and Biocontrol of Pathogens – Gabriele Berg – Frontiers in Microbiology

Review: Molecular Players Involved in the Interaction Between Beneficial Bacteria and the Immune System – Arancha Hevia – Frontiers in Microbiology

Commentary: Towards biome-specific analysis of meta-omics data – Youssef Darzi – ISME Journal

Human gut microbiome

Insights into the Role of Erysipelotrichaceae in the Human Host – Nadeem O. Kaakoush – Frontier sin Cellular and Infection Microbiology

Review: Interaction of Intestinal Microorganisms with the Human Host in the Framework of Autoimmune Diseases – Borja Sánchez – Frontiers in Immunology

Review: Mechanisms of Microbe–Host Interaction in Crohn’s Disease: Dysbiosis vs. Pathobiont Selection – Ludovica F. Buttó – Frontiers in Immunology

Review: The role of gut microbiota and diet in experimental autoimmune encephalitis and multiple sclerosis – Tatsusada Okuno – Clinical and Experimental Neuroimmunology

Animal and bioreactor models

Identification and Phylogeny of the First T Cell Epitope Identified from a Human Gut Bacteroides Species – Maria Elisa Perez-Muñoz – PLOS ONE

Wheat bran promotes enrichment within the human colonic microbiota of butyrate-producing bacteria that release ferulic acid – Sylvia H Duncan – Environmental Microbiology

Animal microbiome

Composition of the Spruce Budworm (Choristoneura fumiferana) Midgut Microbiota as Affected by Rearing Conditions – Mathieu Landry – PLOS ONE

Plant, root, and soil microbiome

Carbon-fixation rates and associated microbial communities residing in arid and ephemerally wet Antarctic Dry Valley soils – Thomas Niederberger – Frontiers in Microbiology

Forest wildfire and grassland prescribed fire effects on soil biogeochemical processes and microbial communities: Two case studies in the semi-arid Southwest – Lisa M. Fultz – Applied Soil Ecology

Response of the soil microbial community and soil nutrient bioavailability to biomass harvesting and reserve tree retention in northern Minnesota aspen-dominated forests – Tera E. Lewandowski – Applied Soil Ecology

Disease suppression in winter wheat from novel symbiosis with forest fungi – Mary Ridout – Fungal Ecology

Comparative genomics of candidate phylum TM6 suggests that parasitism is
widespread and ancestral in this lineage – Yun Kit Yeoh – Molecular Biology and Evolution

Carbon constrains fungal endophyte assemblages along the timberline – Teng Yang – Environmental Microbiology

Exploring the phenotypic space of non-Saccharomyces wine yeast biodiversity – Debra Rossouw – Food Microbiology

Colonization of new land by arbuscular mycorrhizal fungi – Knud Brian Nielsen – Fungal Ecology

Water and extremophile microbiome

Microbial communities reflect temporal changes in cyanobacterial composition in a shallow ephemeral freshwater lake – Jason Nicholas Woodhouse – ISME Journal

Characterization of Bacterial Communities in Deep-Sea Hydrothermal Vents from Three Oceanic Regions – Tianliang He – Marine Biotechnology

Air microbiome

PhD thesis: Microbial biodiversity of the atmosphere – Ann Maureen Klein – University of Oregon

Built environment microbiome

The biogeography of the Plastisphere: implications for policy – Linda A Amaral-Zettler – Frontiers in Ecology and the Environment

Colonization of new land by arbuscular mycorrhizal fungi – Knud Brian Nielsen – Fungal Ecology

Bioinformatics and metagenomics

COMMET: comparing and combining multiple metagenomic datasets – Nicolas Maillet – ArXiv

MetaScope – Fast and accurate identification of microbes in metagenomic sequencing data – Benjamin Buchfink – ArXiv

hc-OTU: A Fast and Accurate Method for Clustering Operational Taxonomic Unit based on Homopolymer Compaction – Seunghyun Park – ACM Transactions on Computational Biology and Bioinformatics

Functional metagenomic selection of RubisCO from uncultivated bacteria – Vanessa A. Varaljay – Environmental Microbiology

Metagenomic evidence for the presence of phototrophic Gemmatimonadetes bacteria in diverse environments – Yonghui Zeng – Environmental Microbiology Reports

Book Chapter: Metagenomics as a Tool for Enzyme Discovery: Hydrolytic Enzymes from Marine-Related Metagenomes – Ana Popovic – Prokaryotic Systems Biology

Microbes in the news

Superbug known as ‘phantom menace’ on the rise in U.S – Lena H. Sun – Washington Post

Petri dish Art: Holiday deer – Microbe World

The Blob, but smaller: Tasmania’s slime moulds – Ann Jones – ABC Australia
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