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Diet specific expression profiles_MA1

ABSTRACT: Analysis of wildtype (N2) C. elegans fed different diets: E. coli OP50, E. coli HT115 and Comamonas DA1877 Dietary composition has major effects on physiology. Here we show that developmental rate, reproduction and lifespan are altered in C. elegans fed Comamonas DA1877 relative to those fed a standard E. coli OP50 diet. We identify a set of genes that change in expression in response to this diet, and use the promoter of one of these (acdh-1) as a dietary sensor. Remarkably, the effects on transcription and development occur even when Comamonas DA1877 is diluted with another diet, suggesting that Comamonas DA1877 generates a signal that is sensed by the nematode. Surprisingly, the developmental effect is independent from TOR and insulin signaling. Rather, Comamonas DA1877 affects cyclic gene expression during molting, likely through the nuclear hormone receptor NHR-23. Altogether, our findings indicate that different bacteria elicit various responses via distinct mechanisms, which has implications for diseases such as obesity and the interactions between the human microbiome and intestinal cells. 3 biological replicates for each condition, OP50 is reference sample

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: Lesley MacNeil

PROVIDER: E-GEOD-43954 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Diet specific expression profiles_MA2

Project description:Analysis of wildtype (N2) C. elegans fed different diets: E. coli OP50, Comamonas DA1877, and Diluted Comamonas (1:1000 Comamonas DA1877:E. coli OP50) Dietary composition has major effects on physiology. Here we show that developmental rate, reproduction and lifespan are altered in C. elegans fed Comamonas DA1877 relative to those fed a standard E. coli OP50 diet. We identify a set of genes that change in expression in response to this diet, and use the promoter of one of these (acdh-1) as a dietary sensor. Remarkably, the effects on transcription and development occur even when Comamonas DA1877 is diluted with another diet, suggesting that Comamonas DA1877 generates a signal that is sensed by the nematode. Surprisingly, the developmental effect is independent from TOR and insulin signaling. Rather, Comamonas DA1877 affects cyclic gene expression during molting, likely through the nuclear hormone receptor NHR-23. Altogether, our findings indicate that different bacteria elicit various responses via distinct mechanisms, which has implications for diseases such as obesity and the interactions between the human microbiome and intestinal cells. 3 biological replicates for each condition, OP50 is reference sample

2013-03-28 | E-GEOD-43953 | biostudies-arrayexpress

Diet specific expression profiles_MA1

Project description:Analysis of wildtype (N2) C. elegans fed different diets: E. coli OP50, E. coli HT115 and Comamonas DA1877 Dietary composition has major effects on physiology. Here we show that developmental rate, reproduction and lifespan are altered in C. elegans fed Comamonas DA1877 relative to those fed a standard E. coli OP50 diet. We identify a set of genes that change in expression in response to this diet, and use the promoter of one of these (acdh-1) as a dietary sensor. Remarkably, the effects on transcription and development occur even when Comamonas DA1877 is diluted with another diet, suggesting that Comamonas DA1877 generates a signal that is sensed by the nematode. Surprisingly, the developmental effect is independent from TOR and insulin signaling. Rather, Comamonas DA1877 affects cyclic gene expression during molting, likely through the nuclear hormone receptor NHR-23. Altogether, our findings indicate that different bacteria elicit various responses via distinct mechanisms, which has implications for diseases such as obesity and the interactions between the human microbiome and intestinal cells.

2013-03-28 | GSE43954 | GEO

Diet specific expression profiles_MA2

2013-03-28 | GSE43953 | GEO

Interplay between mitochondria and diet mediates pathogen and stress resistance in C. elegans.

Project description:To understand the impact of a diet on host health, we performed a number of assays with C. elegans reared on OP50 or HT115 E. coli. We observed that HT115 provided a substantial increase in resistance to Liquid Killing and abiotic stresses (e.g., heat shock, oxidative stress). This phenomenon was independent of the worms’ innate immune system. In the absence of any other obvious candidates, we turned to microarray transcriptional profiling to gain an unbiased picture of the differences that result from feeding C. elegans with HT115 instead of OP50. To our surprise, there was a relatively small number of genes differentially expressed between worms fed OP50 and HT115. Amongst them were several mitochondrially-associated genes, suggesting that the relevant difference may involve this organelle. Using a variety of approaches, we determined that worms fed HT115 exhibit increased mitochondrial health than their OP50 counterparts. Furthermore, supplementation of growing OP50 with cobalamin recapitulated virtually all of the HT115 phenotypes.

2019-02-21 | GSE97678 | GEO

RNA-seq Analysis of wildtype (N2) C. elegans at the L4 stage on diets from the laboratory environment and natural environment

Project description:We analyzed RNA-seq data from C. elegans on six bacterial diets, 3 E. coli diets (OP50, HT115, HB101) found in the laboratory setting and 3 found in C. elegans natural environment (Methylobacterium, Xanthomonas, Sphingomonas). We compared gene expression between L4 worms on the OP50 diet to the other 5 bacterial diets. We found that diet influences many gene expression changes, leading to genes being both up regulated and down regulated in a diet-dependent manner.

2020-11-12 | GSE152794 | GEO

Caenorhabditis elegans N2: Control vs. Lysinibacillus sphaericus-fed

Project description:Transcriptional profiling of Caenorhabditis elegans comparing control E. coli OP50-fed C. elegans with L. sphaericus-fed C. elegans

2014-04-01 | GSE54682 | GEO

Caenorhabditis elegans N2: Control vs. Lysinibacillus sphaericus-fed

Project description:Transcriptional profiling of Caenorhabditis elegans comparing control E. coli OP50-fed C. elegans with L. sphaericus-fed C. elegans Two-condition experiment, E. coli OP50-fed C. elegans vs. L. sphaericus-fed C. elegans

2014-04-01 | E-GEOD-54682 | biostudies-arrayexpress

C. elegans gene expression in response to Salmonella enterica infection and recovery by Tetracycline treatment

Project description:(Part 1) Gene expression profiles of C. elegans in response to a 120 hour S. enterica infection. Synchronized larval stage 1 (L1) animals were exposed to S. enterica SL1344 for 36, 72, 96, or 120 hours. As an uninfected control, synchronized L1 animals were exposed to E. coli OP50 for 36 hours. (Part 2) Gene expression profiles of C. elegans in response to Tetracycline-mediated recovery from 72 hour and 96 hour S. enterica infections. Synchronized L1 animals were exposed to S. enterica SL1344 for 72 hours and then shifted to E. coli HT115 plus Tetracycline plates for 24 hours to resolve the infection. Synchronized L1 animals were exposed to S. enterica SL1344 for 96 hours and then shifted to E. coli HT115 plus Tetracycline plates for 24 hours to resolve the infection. Samples include 36 hours on OP50 (36hOP), 36 hours on SL1344 (36hSL), 72 hours on SL1344 (72hSL), 96 hours on SL1344 (96hSL), 120 hours on SL1344 (120hSL), 72 hours on SL1344 plus 24 hours on HT115-Tet (96hHT), 96 hours on SL1344 plus 24 hours on HT115-Tet (120hHT). Duplicate biological samples were included for each timepoint. 14 total samples. Agilent C. elegans expression microarray (GPL14144).

2014-07-26 | E-GEOD-54212 | biostudies-arrayexpress

C. elegans gene expression in response to Salmonella enterica infection and recovery by Tetracycline treatment

2014-07-26 | GSE54212 | GEO

Characterization of the genes that were regulated by feeding with CBM 588

Project description:In the present study, we investigated the effect of CBM 588 on lifespan and multiple-stress resistance using Caenorhabditis elegans as a model animal. When adult C. elegans were fed a standard diet of Escherichia coli OP50 or CBM 588, the lifespan of the animals fed CBM 588 was significantly longer than that of animals fed OP50. Moreover, the worms fed CBM 588 were more resistant to certain stressors, including infections with pathogenic bacteria, UV irradiation, and the metal stressor Cu2+. CBM 588 failed to extend the lifespan of the daf-2/IR, daf-16/FOXO and skn-1/Nrf2 mutants. Transcriptional profiling comparing CBM 588-fed and control-fed animals suggested that DAF-16-dependent class II genes were regulated by CBM 588. In conclusion, CBM 588 extends the lifespan of C. elegans probably through regulation of the insulin/IGF-1 signaling (IIS) pathway and the Nrf2 transcription factor, and CBM 588 improves resistance to several stressors in C. elegans.

2018-12-01 | GSE123163 | GEO

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