59 research outputs found
KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples
Minich JJ, Zhu Q, Janssen S, et al. KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples. mSystems. 2018;3(3):e00218-17
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Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads.
As metagenomic studies move to increasing numbers of samples, communities like the human gut may benefit more from the assembly of abundant microbes in many samples, rather than the exhaustive assembly of fewer samples. We term this approach leaderboard metagenome sequencing. To explore protocol optimization for leaderboard metagenomics in real samples, we introduce a benchmark of library prep and sequencing using internal references generated by synthetic long-read technology, allowing us to evaluate high-throughput library preparation methods against gold-standard reference genomes derived from the samples themselves. We introduce a low-cost protocol for high-throughput library preparation and sequencing
A communal catalogue reveals Earth’s multiscale microbial diversity
Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity
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Environmental and biological factors driving mucosal-associated microbial communities in fish: applications to aquaculture and fisheries
The majority of vertebrate species diversity are within fish. Marine fish occupy a diverse array of ecological niches including a wide range of salinity tolerance, oxygen tolerance, temperature, depth, desiccation, and light. Fish also have adapted a range of biological traits including varying trophic level, morphology, swimming performance, and reproduction. The microbiome, the total aggregation of microscopic organisms including fungi, bacteria, archaea, and viruses in a specified environment, has largely been studied in mammals, particularly humans from which many associations to disease and health have been demonstrated. Fish microbiome research has largely focused on the gut environment from freshwater captive populations including farmed carp, tilapia, and catfish with marine studies primarily limited to food fish such as salmon.
The goal of this dissertation was to develop and apply microbiome tools including sampling methods, DNA extraction, and library preparation (16S and WGSS, whole genome shotgun sequencing) which could be deployed to study a wide range of questions surrounding the parameters which influence the fish mucosal microbiome.
With these set of tools, I have asked 1) how do intentional anthropogenic impacts to the water column (organic fertilizer) influence fish gastrointestinal communities, 2) how body sites differ in mucosal communities and changes across environmental gradients, 3) feasibility of developing a model marine fish to use in microbiome experiments to mimic tuna, 4) how the hatchery built environment influences fish mucosal microbiota.
My dissertation can be summarized by several key findings. First, the mucosal environments of fish are highly differentiated in that the gill, skin, and digesta communities from the same species of fish are colonized by a large range of phylogenetically diverse microbes. In a freshwater system, organic inputs do influence the fish gut communities but indirectly through nutrient changes. In a wild marine fish, body sites are impacted by different environmental gradients with external body sites like the gill and skin most influenced by temporally variable environmental conditions including sea water temperature. In both freshwater and marine indoor hatchery systems, the built environment plays a critical role in influencing or being influenced by the fish mucosal microbiome
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