Gut metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA774344 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16570600_1.fastq.gz | Fastqsanger.gz | |||
| SRR16570600_2.fastq.gz | Fastqsanger.gz | |||
| SRR16570601_1.fastq.gz | Fastqsanger.gz | |||
| SRR16570601_2.fastq.gz | Fastqsanger.gz | |||
| SRR16570602_1.fastq.gz | Fastqsanger.gz |
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Project description:Peripheral blood mononuclear cell (PBMC) gene expression profiling is a low-invasive tool used in human diet intervention studies. In dogs this technique has been used to investigate disease states but not to examine the effect of diet. We tested the hypothesis that diet alters dog systemic immune cell gene expression profiles by comparing PBMC gene expression in dogs fed either a premium kibbled diet or a raw red meat diet for 9 weeks. Our results showed that diet shifted the dogs’ PBMC gene expression profile and these alterations corresponded with changes in plasma IgA levels. This illustrates that PBMC microarrays are a useful tool that may be applied to study the long-term effects of diet on health outcomes for the dog.
2017-09-07 | GSE103529 | GEO
Project description:To investigate the adaptation of Corynebacterium glutamicum to altering oxygen availabilities, we conceived a triple-phase fermentation process that describes a gradual reduction of dissolved oxygen depicting a shift from aerobiosis via microaerobiosis to anaerobiosis. The distinct process phases were clearly bordered by the bacteria’s physiologic response such as reduced growth rate, biomass substrate yield and altered yield of fermentation products. During the process, sequential samples were drawn at six points and analyzed via RNA-sequencing of Illumina TruSeq Stranded mRNA libaries sequenced paired end on an Illumina MiSeq system using 75 nt read length. We found transcriptional alterations of almost 50 % (1421 genes) of the entire protein coding genes and observed an upregulation of fermentative pathways, a rearrangement of respiration and mitigation of the basic cellular mechanisms such as transcription, translation and replication as a transient response related to the installed oxygen dependent process phases.
2018-03-31 | E-MTAB-6602 | biostudies-arrayexpress
Project description:Interventions: Ten subjects receive probiotic product contained 10 million CFU in viable form 3 times a day for 6 months,Ten subjects receive probiotic product contained 10 million CFU in non viable form 3 times a day for 6 months, Ten subjects receive product without probiotic 3 times a day for 6 months;Active Comparator Dietary Supplement,Active Comparator Dietary Supplement,Placebo Comparator Dietary Supplement;probiotic products in viable form,probiotic products in non viable form,Control
Primary outcome(s): reduceing of number of pathogens in gut at 6 months after intervention number of pathogens / Anova
Study Design: Randomized
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Project description:Aging alters gastrointestinal morphology, microbiota, and functionality, and is associated with increased incidence of intestinal disease. The mechanisms that contribute to these changes are poorly described. Gene expression in dogs has been evaluated for a few select genes under pathogenic or varying dietary conditions, but global gene expression profiles of aged versus young adult dogs have not been compared previously. Thus, we used canine microarrays to compare gene expression profiles of colonic epithelial tissue from geriatric and young adult dogs fed 2 different diets. Colon tissue samples were collected from 6 geriatric (12 yr-old) and 6 young adult (1 yr-old) female beagles after being fed one of two diets (animal protein-based versus plant-protein based) for 12 months. RNA samples were hybridized to Affymetrix GeneChip Canine Genome Arrays. Statistical analyses indicated that age had the greatest impact on gene expression, with 212 genes differentially expressed in geriatric dogs. Although not as robust as age, diet affected mRNA abundance of 66 genes. The effect of age was most notable, with increased expression in genes related to inflammation, stress response, cellular metabolism and cell proliferation and decreased expression in genes associated with apoptosis and defense mechanism in senior dogs. The effect of diet on gene expression was not consistent, but appeared to have a greater response in senior dogs. Six geriatric (11.1 yr old) and 6 weanling (8 wk old) female beagles were used. Three dogs of each age were assigned to one of two dietary treatments and fed for 12 months. Diets tested in this experiment were previously shown to manipulate energy metabolism. One diet was an animal-protein based diet (APB) and was composed primarily of highly digestible ingredients and animal-derived protein and fat sources (brewer’s rice, poultry by-product meal, poultry fat) and was formulated to contain 28% protein, 23% fat, and 5% dietary fiber. The other diet was a plant-protein based diet (PPB) and was composed primarily of moderately digestible plant-derived ingredients (corn, soybean meal, wheat middlings, and meat and bone meal) and was formulated to contain 26% protein, 11% fat, and 15% dietary fiber. Although the two diets were very different in terms of ingredient and chemical composition, both were formulated to meet or exceed all nutrient requirements for canine growth according to the Association of American Feed Control Officials. Young dogs were fed ad libitum to allow for adequate growth, while geriatric dogs were fed to maintain baseline BW throughout the experiment. To produce the desired metabolic effects, the PPB diet was formulated to contain a lower caloric density (APB = 5.38 kcal/g; PPB = 4.75 kcal/g) and have a lower nutrient digestibility than the APB diet. Thus, dogs fed the PPB diet needed to consume a greater (P<0.05) quantity of food (237 g/d; 1123 kcal/d) than dogs fed the APB diet (166 g/d; 893 kcal/d) to grow (young) or maintain BW (geriatrics). Even though metabolic indices were altered, mean BW among dietary treatments was not different at any time over the course of the study for young or geriatric dogs. After 12 months on experiment, animals were fasted for 12 hr and then given a lethal dose (130 mg/kg BW) of sodium pentobarbital (Euthasol, Virbac Corp., Fort Worth, TX) intravenously into the left forearm. Death was confirmed by lack of respiration and a corneal reflex, and absence of a heartbeat detected with a stethoscope placed under the left elbow. Colon samples were collected immediately after death was confirmed, flash frozen using liquid nitrogen, and stored at -80oC. Frozen samples were placed in RNAlater-ICE until epithelial layer could be scraped off and used for microarray analysis.
2010-08-01 | E-GEOD-20557 | biostudies-arrayexpress
Project description:The liver is the central organ in the regulation of nutrient metabolism, xenobiotic metabolism, and detoxification. Aging leads to a marked change in liver structure and function, characterized by a decline in weight, blood flow, regeneration rate, and detoxification. However, the mechanisms that contribute to these changes are poorly described. Global gene expression profiles of aged versus young adult dogs have not been compared previously. Thus, we used canine microarrays to compare gene expression profiles of liver tissue from geriatric and young adult dogs fed 2 different diets. Liver tissue samples were collected from 6 geriatric (12 yr-old) and 6 young adult (1 yr-old) female beagles after being fed one of two diets (animal protein-based versus plant-protein based) for 12 months. RNA samples were hybridized to Affymetrix GeneChip Canine Genome Arrays. Statistical analyses indicated that age had the greatest impact on gene expression, with 234 gene transcripts differentially expressed in geriatric dogs. Although not as robust as age, diet affected mRNA abundance of 137 gene transcripts. The effect of age was most notable, with increased expression in genes related to inflammation, oxidative stress, and glycolysis and decreased expression in genes associated with regeneration, xenobiotic metabolism, and cholesterol trafficking in senior dogs. The effect of diet on gene expression was not consistent, but led to more changes in young adult dogs. Six geriatric (11.1 yr old) and 6 weanling (8 wk old) female beagles were used. Three dogs of each age were assigned to one of two dietary treatments and fed for 12 months. Diets tested in this experiment were previously shown to manipulate energy metabolism. One diet was an animal-protein based diet (APB) and was composed primarily of highly digestible ingredients and animal-derived protein and fat sources (brewer’s rice, poultry by-product meal, poultry fat) and was formulated to contain 28% protein, 23% fat, and 5% dietary fiber. The other diet was a plant-protein based diet (PPB) and was composed primarily of moderately digestible plant-derived ingredients (corn, soybean meal, wheat middlings, and meat and bone meal) and was formulated to contain 26% protein, 11% fat, and 15% dietary fiber. Although the two diets were very different in terms of ingredient and chemical composition, both were formulated to meet or exceed all nutrient requirements for canine growth according to the Association of American Feed Control Officials. Young dogs were fed ad libitum to allow for adequate growth, while geriatric dogs were fed to maintain baseline BW throughout the experiment. To produce the desired metabolic effects, the PPB diet was formulated to contain a lower caloric density (APB = 5.38 kcal/g; PPB = 4.75 kcal/g) and have a lower nutrient digestibility than the APB diet. Thus, dogs fed the PPB diet needed to consume a greater (P<0.05) quantity of food (237 g/d; 1123 kcal/d) than dogs fed the APB diet (166 g/d; 893 kcal/d) to grow (young) or maintain BW (geriatrics). Even though metabolic indices were altered, mean BW among dietary treatments was not different at any time over the course of the study for young or geriatric dogs. After 12 months on experiment, animals were fasted for 12 hr and then given a lethal dose (130 mg/kg BW) of sodium pentobarbital (Euthasol, Virbac Corp., Fort Worth, TX) intravenously into the left forearm. Death was confirmed by lack of respiration and a corneal reflex, and absence of a heartbeat detected with a stethoscope placed under the left elbow. Liver samples were collected immediately after death was confirmed, flash frozen using liquid nitrogen, and stored at -80oC until further analysis.
2011-01-01 | E-GEOD-22945 | biostudies-arrayexpress
Project description:Mechanisms contributing to age-related cognitive decline are poorly defined. Thus, we used canine microarrays to compare gene expression profiles of brain tissue from geriatric and young adult dogs. Cerebral cortex samples were collected from 6 geriatric (12 yr-old) and 6 young adult (1 yr-old) female beagles after being fed one of two diets (animal protein-based versus plant-protein based) for 12 months. RNA samples were hybridized to Affymetrix GeneChip Canine Genome Arrays. Statistical analyses indicated that the age had the greatest impact on gene expression, with 963 transcripts differentially expressed in geriatric dogs. Although not as robust as age, diet affected mRNA abundance of 140 transcripts. As demonstrated in aged rodents and humans, geriatric dogs had increased expression of genes associated with inflammation, stress response, and calcium homeostasis and decreased expression of genes associated with neuropeptide signaling and synaptic transmission. In addition to its existing strengths, availability of gene sequence information and commercial microarrays make the canine a powerful model for studying the effects of aging on cognitive function. Keywords: age; diet Six geriatric (11.1 yr old) and 6 weanling (8 wk old) female beagles were used. Three dogs of each age were assigned to one of two dietary treatments and fed for 12 months. Diets tested in this experiment were previously shown to manipulate energy metabolism. One diet was an animal-protein based diet (APB) and was composed primarily of highly digestible ingredients and animal-derived protein and fat sources (brewer’s rice, poultry by-product meal, poultry fat) and was formulated to contain 28% protein, 23% fat, and 5% dietary fiber. The other diet was a plant-protein based diet (PPB) and was composed primarily of moderately digestible plant-derived ingredients (corn, soybean meal, wheat middlings, and meat and bone meal) and was formulated to contain 26% protein, 11% fat, and 15% dietary fiber. Although the two diets were very different in terms of ingredient and chemical composition, both were formulated to meet or exceed all nutrient requirements for canine growth according to the Association of American Feed Control Officials. Young dogs were fed ad libitum to allow for adequate growth, while geriatric dogs were fed to maintain baseline BW throughout the experiment. To produce the desired metabolic effects, the PPB diet was formulated to contain a lower caloric density (APB = 5.38 kcal/g; PPB = 4.75 kcal/g) and have a lower nutrient digestibility than the APB diet. Thus, dogs fed the PPB diet needed to consume a greater (P<0.05) quantity of food (237 g/d; 1123 kcal/d) than dogs fed the APB diet (166 g/d; 893 kcal/d) to grow (young) or maintain BW (geriatrics). Even though metabolic indices were altered, mean BW among dietary treatments was not different at any time over the course of the study for young or geriatric dogs. After 12 months on experiment, animals were fasted for 12 hr and then given a lethal dose (130 mg/kg BW) of sodium pentobarbital (Euthasol, Virbac Corp., Fort Worth, TX) intravenously into the left forearm. Death was confirmed by lack of respiration and a corneal reflex, and absence of a heartbeat detected with a stethoscope placed under the left elbow. Cerebral cortex samples were collected immediately after death was confirmed, flash frozen using liquid nitrogen, and stored at -80oC until further analysis.
2008-08-05 | E-GEOD-12328 | biostudies-arrayexpress
Project description:In order to genetically determine the essential components of electron flow during respiration of sulfate by the anaerobe Desulfovibrio desulfuricans G20, a growth mode independent of sulfate is needed. However, a mutant of the G20 strain, I2, lacking the abundant type-1 tetraheme cytochrome c3 (TpI-c3), was found to be altered in growth with sulfate. Here we report that I2 does not reduce sulfate with electrons from pyruvate. In contrast, in the absence of sulfate, fermentative growth of I2 on pyruvate actually yielded slightly greater cellular protein than G20. When provided lactate with sulfate or when fermenting pyruvate, I2 produced more hydrogen and accumulated little if any succinate. G20 grows by fumarate dismutation and accumulates the theoretical 2:1 ratio of the end products, succinate and acetate, respectively. In contrast, I2 did not grow on fumarate alone. We inferred that TpI-c3 might be required for transfer of electrons to the membrane-bound fumarate reductase or for establishing a redox environment needed to trigger synthesis of the enzymes for succinate production. Microarray and proteomic analyses of gene and protein expression in I2 compared with G20 were consistent with increases in those enzymes predicted to be necessary for the generation of end products measured. These results support a role for the periplasmic TpI-c3 in electron flow from pyruvate to sulfate and in establishing conditions for enzyme production for fumarate dismutation. In addition, evidence for the simultaneous operation of respiratory electron flow and substrate-level phosphorylation was obtained from end product analysis.
2010-04-25 | GSE21287 | GEO
Project description:Aging animals display a decline in a multitude of physical and physiological functions, including muscle function and strength. Muscle gene expression in dogs has been evaluated for a few select genes under pathogenic or varying dietary conditions, but global gene expression profiles of aged animals has not been performed. Because the mechanisms contributing to age-related decline in muscle function are poorly defined, we used canine microarrays to compare gene expression profiles of muscle tissue from geriatric and young adult dogs. Skeletal muscle (biceps femoris) samples were collected from 6 geriatric (12 yr-old) and 6 young adult (1 yr-old) female beagles after being fed one of two diets (animal protein-based versus plant-protein based) for 12 months. RNA samples were hybridized to Affymetrix GeneChip Canine Genome Arrays. Statistical analyses indicated that age had the greatest impact on gene expression, with 262 genes differentially expressed in geriatric dogs. Although not as robust as age, diet affected mRNA abundance of 22 genes. The effect of age was most notable in genes related to metabolism, cell cycle and cell development, and transcription function, with all of these functional groups being predominantly down-regulated in older animals. The effect of diet on gene expression was mostly limited to the geriatric animals, but interactions between age and diet do not allow for a clear-cut pattern of gene expression to be observed. Keywords: age; diet Six geriatric (11.1 yr old) and 6 weanling (8 wk old) female beagles were used. Three dogs of each age were assigned to one of two dietary treatments and fed for 12 months. Diets tested in this experiment were previously shown to manipulate energy metabolism. One diet was an animal-protein based diet (APB) and was composed primarily of highly digestible ingredients and animal-derived protein and fat sources (brewerâs rice, poultry by-product meal, poultry fat) and was formulated to contain 28% protein, 23% fat, and 5% dietary fiber. The other diet was a plant-protein based diet (PPB) and was composed primarily of moderately digestible plant-derived ingredients (corn, soybean meal, wheat middlings, and meat and bone meal) and was formulated to contain 26% protein, 11% fat, and 15% dietary fiber. Although the two diets were very different in terms of ingredient and chemical composition, both were formulated to meet or exceed all nutrient requirements for canine growth according to the Association of American Feed Control Officials. Young dogs were fed ad libitum to allow for adequate growth, while geriatric dogs were fed to maintain baseline BW throughout the experiment. To produce the desired metabolic effects, the PPB diet was formulated to contain a lower caloric density (APB = 5.38 kcal/g; PPB = 4.75 kcal/g) and have a lower nutrient digestibility than the APB diet. Thus, dogs fed the PPB diet needed to consume a greater (P<0.05) quantity of food (237 g/d; 1123 kcal/d) than dogs fed the APB diet (166 g/d; 893 kcal/d) to grow (young) or maintain BW (geriatrics). Even though metabolic indices were altered, mean BW among dietary treatments was not different at any time over the course of the study for young or geriatric dogs. After 12 months on experiment, animals were fasted for 12 hr and then given a lethal dose (130 mg/kg BW) of sodium pentobarbital (Euthasol, Virbac Corp., Fort Worth, TX) intravenously into the left forearm. Death was confirmed by lack of respiration and a corneal reflex, and absence of a heartbeat detected with a stethoscope placed under the left elbow. Skeletal muscle samples were collected immediately after death was confirmed, flash frozen using liquid nitrogen, and stored at -80oC until further analysis.
2010-05-22 | E-GEOD-12502 | biostudies-arrayexpress