Ontology highlight
ABSTRACT:
PROVIDER: PRJNA659564 | ENA |
REPOSITORIES: ENA
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Project description:White bass (Morone chrysops) are a popular sportfish throughout the southern United States, and one parent of the commercially successful hybrid striped bass (M. chrysops x M. saxatilis). Currently, white bass are cultured using diets formulated for other carnivorous fish, such as largemouth bass (Micropterus salmoides) or hybrid striped bass and contain a significant percentage of marine fish meal. Since there are no studies regarding the utilization of alternative proteins in this species, we evaluated global gene expression of white bass fed diets in which fish meal was partially or totally replaced by various combinations of soybean meal, poultry by-product meal, canola meal, soy protein concentrate, wheat gluten, or a commercial protein blend (Pro-Cision). Significant differential expressed genes and gene ontology of pairwise comparisons between control diet and each test diet are presented and discussed.
2024-02-14 | GSE220235 | GEO
Project description:Transcriptome analysis to determine the impact of oral exposure (in a sugar meal) to the liquid supernatant (i.e. LB culture media) of Chromobacterium sp. Panama biofilm culture. The biofilm supernatant (i.e. media) was first filtered with a 0.2uM filter to remove all live bacterial cells. It was then mixed with 10% sucrose, and a control sucrose meal was mixed with filtered LB. Mosquitoes were exposed to each sugar meal for 24 hours and then midguts were dissected from 20 adult females per treatment. The entire experiment was performed 4 independent times.
2018-03-31 | GSE109727 | GEO
Project description:Serum samples were taken from four healthy donors before a meal and 3, 5, 7, 9 h after a meal (Supplementary Table S6, Sheet 1). The analysis of the serum peptidome against the HuMiProt90 database showed that the amount of non-human peptides (potentially bacterial peptides) in the bloodstream significantly increased 5 h after a meal (Figure 3D, Supplementary Table S6, Sheet 3). The comparison of these data with the transit time of food in different parts of the gastrointestinal tract suggests that bacterial peptides enter the bloodstream predominantly in the small intestine. At the same time, phyla Proteobacteria, Firmicutes and Actinobacteria are the main contributors to the increase in (potentially) bacterial peptides 5 h after a meal (Supplementary Table S6, Sheets 5 and 6).
2024-06-14 | PXD027618 | Pride
Project description:We compare the transcriptome of gnotobiotic Ae. aegypti generated by contaminating axenic (bacteria-free) larvae with bacterial isolates found in natural mosquito breeding sites. We focused on four bacterial isolates (Lysobacter, Flavobacterium, Paenibacillus and Enterobacteriaceae) and found that different gnotobiotic treatments resulted in massive transcriptomic changes throughout the mosquito development.
2021-12-15 | GSE173472 | GEO
Project description:Pseudomonas alloputida KT2440 (previously misclassified as P. putida KT2440 based on 16S rRNA gene homology) has emerged as an ideal host strain for plan t biomass valorization. However, P. alloputida KT2440 is unable to natively utilize abundant pentose sugars (e.g., xylose and arabinose) in hydrolysate streams, which may account for up to 25% of lignocellulosic biomass. In the last decades, microbes have been engineered to utilize the pentose sugars. However, most of the engineered strains were either slow-growing or displayed phenotypes that could not be replicated. In this work, we successfully isolated five Pseudomonas species with the native capability to utilize glucose, xylose and p-coumarate as a sole carbon source. These isolates were in two clusters; one set of isolates (M2 and M5) and the second set of isolates (BP6 and BP7) showed 85.6% and 96.2% ANI, respectively, to P. alloputida KT24440. BP8 showed 84.6% ANI to P. putida KT2440 and does not belong to any neighboring type strains indicating a new species. Notably, the isolates showed robust growth solely on xylose and higher growth rates (m, 0.36-0.49 h-1) when compared to only known xylose-utilizing Pseudomonas taiwanenesis VLB120 (m, 0.28 h-1) as a control. Unexpectedly, among five isolates, M2 and M5 grew solely on arabinose as well. Comprehensive analysis of genomics, transcriptomics and proteomics revealed the isolates utilize xylose and arabinose via Weimberg pathway (xylD-xylX-xylA) and oxidative pathway (araD-araX-araA), respectively. Furthermore, a preliminary result demonstrated the production of flaviolin solely on xylose and arabinose in the isolate, showing noteworthy potential to be an alternative host for lignocellulosic feedstocks into valuable products. This is the first report on isolating Pseudomonas strains natively capable of utilizing all of the major carbon sources in lignocellulosic biomass, and leading to higher consumption of available substrates and therefore maximizing the product yield.
2023-05-10 | PXD031549 | Pride
Project description:The purpose of this experiment was to study the effects of the bacterial enzyme ACC deaminase on the transcriptional changes within canola seedlings. Seedlings from seeds treated with the plant growth-promoting bacteria Pseudomonas putida UW4 which expresses a high level of ACC deaminase and its ACC deaminase-minus mutant were compared to untreated seedlings along with a transgenic line of canola expressing the ACC deaminase enzyme in the roots. ACC deaminase breaks down 1-aminocyclopropane-1-carboxylic acid, the biosynthetic precursor to the plant hormone ethylene, lowering ethylene levels and improving plant fitness. Plants treated with the ACC deaminase-containing bacteria and transgenic plants expressing ACC deaminase are more tolerant to a variet of stresses and this expression study helps to illuminate the pathways responsible for the growth promotion provided by the beneficial bacteria and the role of the enzyme itself.
2009-03-30 | E-TABM-582 | biostudies-arrayexpress
Project description:In order to investigate the diurnal oscillations of ruminal bacteria, and their responses to the changes in different feeding patterns, we conducted an animal experiment by feeding the sheep ad libitum with a hay-based diet (50% of alfalfa hay and 46% of oats hay) and a grain-based diet (45% of corn meal and 11% of soybean meal) for 30 days, and ruminal fluid samples were collected at six different timepoints from T2 to T22 in one day, and the composition and diversity of the bacterial communities in rumen microbiomes of the sheep in the Grain-diet and Hay-diet groups at different timepoints were analyzed through 16S rRNA sequencing.
2025-01-08 | GSE286149 | GEO
Project description:Exoproteomics of Hopland soil isolates. Metabolic trait to efficiently utilize plant polymers provides the energy-expensive microbial adaptation to survive in low carbon availability soil.
2019-07-01 | MSV000084044 | MassIVE