MetaBar - a tool for consistent contextual data acquisition and standards compliant submission

Background: Environmental sequence datasets are increasing at an exponential rate; however, the vast majority of them lack appropriate descriptors like sampling location, time and depth/altitude: generally referred to as metadata or contextual data. The consistent capture and structured submission of these data is crucial for integrated data analysis and ecosystems modeling. The application MetaBar has been developed, to support consistent contextual data acquisition. Results: MetaBar is a spreadsheet and web-based software tool designed to assist users in the consistent acquisition, electronic storage, and submission of contextual data associated to their samples. A preconfigured Microsoft Excel spreadsheet is used to initiate structured contextual data storage in the field or laboratory. Each sample is given a unique identifier and at any stage the sheets can be uploaded to the MetaBar database server. To label samples, identifiers can be printed as barcodes. An intuitive web interface provides quick access to the contextual data in the MetaBar database as well as user and project management capabilities. Export functions facilitate contextual and sequence data submission to the International Nucleotide Sequence Database Collaboration (INSDC), comprising of the DNA DataBase of Japan (DDBJ), the European Molecular Biology Laboratory database (EMBL) and GenBank. MetaBar requests and stores contextual data in compliance to the Genomic Standards Consortium specifications. The MetaBar open source code base for local installation is available under the GNU General Public License version 3 (GNU GPL3). Conclusion: The MetaBar software supports the typical workflow from data acquisition and field-sampling to contextual data enriched sequence submission to an INSDC database. The integration with the megx.net marine Ecological Genomics database and portal facilitates georeferenced data integration and metadata-based comparisons of sampling sites as well as interactive data visualization. The ample export functionalities and the INSDC submission support enable exchange of data across disciplines and safeguarding contextual data

Biocuration: Distilling data into knowledge

Data, including information generated from them by processing and analysis, are an asset with measurable value. The assets that biological research funding produces are the data generated, the information derived from these data, and, ultimately, the discoveries and knowledge these lead to. From the time when Henry Oldenburg published the first scientific journal in 1665 (Proceedings of the Royal Society) to the founding of the United States National Library of Medicine in 1879 to the present, there has been a sustained drive to improve how researchers can record and discover what is known. Researchers' experimental work builds upon years and (collectively) billions of dollars' worth of earlier work. Today, researchers are generating data at ever-faster rates because of advances in instrumentation and technology, coupled with decreases in production costs. Unfortunately, the ability of researchers to manage and disseminate their results has not kept pace, so their work cannot achieve its maximal impact. Strides have recently been made, but more awareness is needed of the essential role that biological data resources, including biocuration, play in maintaining and linking this ever-growing flood of data and information. The aim of this paper is to describe the nature of data as an asset, the role biocurators play in increasing its value, and consistent, practical means to measure effectiveness that can guide planning and justify costs in biological research information resources' development and management

Dynamics of Symbiont Abundance in Bathymodiolin Deep-sea Symbioses

Deep-sea hydrothermal vents and cold seeps are widespread throughout the world's oceans and represent `oases of life' in a dark and hostile environment. These chemosynthetic habitats are often dominated by mussels of the genus Bathymodiolus. The bivalves harbor bacterial symbionts in their gills that use methane and reduced inorganic compounds such as sulfide and hydrogen as energy sources for chemosynthetic primary production. It is well known that the spatial and temporal gradients of these energy sources can be extremely steep at vents and seeps, and some studies have shown that differences in energy source availability affect symbiont abundance in Bathymodiolus mussels. However, in-depth analyses of physico-chemical gradients and their effect on symbiont abundance are lacking. One of the basic requirements for these analyses is a reliable quantification method for the symbionts. The goal of my thesis was therefore to develop an accurate and efficient protocol for determining symbiont abundance in bathymodiolin mussels

The Gut Microbiome In Healthy And Severely Malnourished Humans

Human large intestine is home to tens of trillions of microbes belonging to all three do- mains of life. The functions encoded by the genes in this community: microbiome) include processing and production of macro- and micronutrients. Much remains unknown about the factors that determine the assembly of the gut microbial community starting at birth, and if disruptions in the assembly of this `microbial metabolic organ\u27 early in life result in physiologic and metabolic deficits later in life. The central goal of my thesis was to char- acterize development of the gut microbiome early in life, with a focus on describing the relationship between the microbiome and nutritional status. My thesis consists of three parts. Because the degree of temporal variation in the gut microbiome in children and adults in healthy and diseased state was not well described, I began by using metagenomic methods and a variety of computational and statistical tools to characterize the proportional representation of bacterial phylotypes and gene functions in the fecal communities of seven healthy adult USA monozygotic twin pairs sampled over a four-month period. I found that the fecal microbiota and microbiome are stable within each co-twin even in the face of ecologic invasion with a popular commercial fermented diary product. I then compared the fecal microbiota and microbiome in 524 healthy infants, children and adults living in three different countries with distinct cultural traditions: USA, Malawi and Amazon region of Venezuela). I found that interpersonal variation in babies is significantly greater than between adults, and that the microbiota evolves towards an adult configuration during the first three years of life in all three populations sampled. In addi- tion, distinct patterns of functional maturation were observed which involved microbial genes encoding enzymes that participate in the biosynthesis of several vitamins. Finally, I characterized assembly of gut microbiomes in a cohort of Malawian twins concordant for healthy status and twins discordant for severe forms of malnutrition: kwashiorkor or ma- rasmus). Twins were sampled during their first three years of life, including before, during and after treatment with a peanut butter-based ready-to-use therapeutic food: RUTF). In the case of the discordant twins, both co-twins were treated with RUTF. My comparative metagenomic analyses revealed notable differences in the responses to RUTF in kwashi- orkor versus healthy co-twins