Neotoma albigula
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA757000 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15601516_1.fastq.gz | Fastqsanger.gz | |||
| SRR15601516_2.fastq.gz | Fastqsanger.gz | |||
| SRR15601517_1.fastq.gz | Fastqsanger.gz | |||
| SRR15601517_2.fastq.gz | Fastqsanger.gz | |||
| SRR15601518_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 124 |
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Project description:Stool metagenomics from Neotoma albigula Raw sequence reads
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Project description:trnL sequences obtained from woodrat fecal samples Raw sequence reads
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Project description:We present the de novo transcriptome sequencing, analysis and microarray development for a vertebrate herbivore, the woodrat (Neotoma spp.). This genus is of ecological and evolutionary interest, especially with respect to ingestion and hepatic metabolism of potentially toxic plant secondary compounds. We generated a liver transcriptome of the desert woodrat (Neotoma lepida) with the Roche 454 platform. The assembled contigs were well annotated using rodent references (99.7% annotation), and biotransformation function was reflected in the gene ontology. The transcriptome was used to develop a custom microarray (eArray, Agilent). To compare the effect of native diet/habitat and phylogenetic similarity, we performed 3 experiments with the Neotoma probes only: one across species with similar habitat niches (N. lepida versus N. bryanti, Palm Springs), one across species with different habitat niches (N. lepida versus N. bryanti, Caspers Wilderness), and one across populations within a species (N. bryant Palm Springs versus Caspers Wilderness). The resulting one-color arrays had high technical and biological quality. Probes designed from the woodrat transcriptome performed significantly better than functionally similar probes from the Norway rat (Rattus norvegicus). Biotransformation processes and functions were highly represented in the results. Comparisons between ecologically similar woodrat species revealed fewer gene expression differences than ecologically different woodrat species. The conspecific comparison had overall fewest differences.
2013-07-30 | GSE43941 | GEO
Project description:Oxalate, broadly found in both dietary and endogenous sources, is a primary constituent in 80% of kidney stones, an affliction that has tripled in prevalence over the last 40 years. Oxalate-degrading bacteria within the gut microbiota can mitigate the effects of oxalate and are negatively correlated with kidney stone formation, but bacteriotherapies involving oxalate-degrading bacteria have met with mixed results. To inform the development of more effective and consistent bacteriotherapies, we sought to quantify the interactions and limits between oxalate and an oxalate-adapted microbiota from the wild mammalian herbivore Neotoma albigula (woodrat), which consumes a high-oxalate diet in the wild. We tracked the microbiota over a variable-oxalate diet ranging from 0.2% to 12%, with the upper limit approximating 10× the level of human consumption. The N. albigula microbiota was capable of degrading ~100% of dietary oxalate regardless of the amount consumed. However, the microbiota exhibited significant changes in diversity dynamically at the operational taxonomic unit (OTU), family, and community levels in accordance with oxalate input. Furthermore, a cohesive microbial network was stimulated by the consumption of oxalate and exhibited some resistance to the effects of prolonged exposure. This study demonstrates that the oxalate-adapted microbiota of N. albigula exhibits a very high level of degradation and tolerance for oxalate. IMPORTANCE The bacteria associated with mammalian hosts exhibit extensive interactions with overall host physiology and contribute significantly to the health of the host. Bacteria are vital to the mitigation of the toxic effects of oxalate specifically as mammals do not possess the enzymes to degrade this compound, which is present in the majority of kidney stones. Contrary to the body of literature on a few oxalate-degrading specialists, our work illustrates that oxalate stimulates a broad but cohesive microbial network in a dose-dependent manner. The unique characteristics of the N. albigula microbiota make it an excellent source for the development of bacteriotherapies to inhibit kidney stone formation. Furthermore, this work successfully demonstrates methods to identify microbial networks responsive to specific toxins, their limits, and important elements such as microbial network cohesivity and architecture. These are necessary steps in the development of targeted bacteriotherapies.
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Project description:Diet is one of the primary drivers that sculpts the form and function of the mammalian gut microbiota. However, the enormous taxonomic and metabolic diversity held within the gut microbiota makes it difficult to isolate specific diet-microbe interactions. The objective of the current study was to elucidate interactions between the gut microbiota of the mammalian herbivore Neotoma albigula and dietary oxalate, a plant secondary compound (PSC) degraded exclusively by the gut microbiota. We quantified oxalate degradation in N. albigula fed increasing amounts of oxalate over time and tracked the response of the fecal microbiota using high-throughput sequencing. The amount of oxalate degraded in vivo was linearly correlated with the amount of oxalate consumed. The addition of dietary oxalate was found to impact microbial species diversity by increasing the representation of certain taxa, some of which are known to be capable of degrading oxalate (e.g., Oxalobacter spp.). Furthermore, the relative abundances of 117 operational taxonomic units (OTU) exhibited a significant correlation with oxalate consumption. The results of this study indicate that dietary oxalate induces complex interactions within the gut microbiota that include an increase in the relative abundance of a community of bacteria that may contribute either directly or indirectly to oxalate degradation in mammalian herbivores.
| S-EPMC4836426 | biostudies-literature
Project description:We present the de novo transcriptome sequencing, analysis and microarray development for a vertebrate herbivore, the woodrat (Neotoma spp.). This genus is of ecological and evolutionary interest, especially with respect to ingestion and hepatic metabolism of potentially toxic plant secondary compounds. We generated a liver transcriptome of the desert woodrat (Neotoma lepida) with the Roche 454 platform. The assembled contigs were well annotated using rodent references (99.7% annotation), and biotransformation function was reflected in the gene ontology. The transcriptome was used to develop a custom microarray (eArray, Agilent). To compare the effect of native diet/habitat and phylogenetic similarity, we performed 3 experiments with the Neotoma probes only: one across species with similar habitat niches (N. lepida versus N. bryanti, Palm Springs), one across species with different habitat niches (N. lepida versus N. bryanti, Caspers Wilderness), and one across populations within a species (N. bryant Palm Springs versus Caspers Wilderness). The resulting one-color arrays had high technical and biological quality. Probes designed from the woodrat transcriptome performed significantly better than functionally similar probes from the Norway rat (Rattus norvegicus). Biotransformation processes and functions were highly represented in the results. Comparisons between ecologically similar woodrat species revealed fewer gene expression differences than ecologically different woodrat species. The conspecific comparison had overall fewest differences. Gene expression was compared across 3 groups of woodrats: Neotoma lepida (n=4), N. bryanti Palm Springs (n=4), and N. bryanti Caspers Wilderness (n=4). Animals were fed a rabbit chow diet, called control; intake was monitored over 10 days, after which RNA was extracted from hepatic tissue. One-color arrays were performed.
2013-07-30 | E-GEOD-43941 | biostudies-arrayexpress
Project description:Microbiome analysis of Neotoma lepida following fecal transplants
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Project description:The microbiota inhabiting the mammalian gut is a functional organ that provides a number of services for the host. One factor that may regulate the composition and function of gut microbial communities is dietary toxins. Oxalate is a toxic plant secondary compound (PSC) produced in all major taxa of vascular plants and is consumed by a variety of animals. The mammalian herbivore Neotoma albigula is capable of consuming and degrading large quantities of dietary oxalate. We isolated and characterized oxalate-degrading bacteria from the gut contents of wild-caught animals and used high-throughput sequencing to determine the distribution of potential oxalate-degrading taxa along the gastrointestinal tract. Isolates spanned three genera: Lactobacillus, Clostridium, and Enterococcus. Over half of the isolates exhibited significant oxalate degradation in vitro, and all Lactobacillus isolates contained the oxc gene, one of the genes responsible for oxalate degradation. Although diverse potential oxalate-degrading genera were distributed throughout the gastrointestinal tract, they were most concentrated in the foregut, where dietary oxalate first enters the gastrointestinal tract. We hypothesize that unique environmental conditions present in each gut region provide diverse niches that select for particular functional taxa and communities.
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