Bacterial diet affects the age-dependent decline of associative learning in Caenorhabditis elegans
- Milk Science Research Institute, Megmilk Snow Brand Co. Ltd., Japan
- Group of Nutritional Neuroscience, Neuroscience Institute, Graduate School of Science, Nagoya University, Japan
- Group of Molecular Neurobiology, Neuroscience Institute, Graduate School of Science, Nagoya University, Japan
- Group of Microbial Motility, Department of Biological Science, Division of Natural Science, Graduate school of Science, Nagoya University, Japan
Figures
Figure 1 with 6 supplements
Thermotaxis performance declines with age.
(A) Schematic of thermotaxis assay. Animals were placed at light blue circles on a thermal gradient without food. The pink rectangle indicates the sections around the Tcult. After 1 hr, the number …
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Figure 1—source data 1
Thermotaxis assays with 17 or 23°C center.
- https://cdn.elifesciences.org/articles/81418/elife-81418-fig1-data1-v1.xlsx
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Figure 1—source data 2
Thermotaxis assays at different ages.
- https://cdn.elifesciences.org/articles/81418/elife-81418-fig1-data2-v1.xlsx
Figure 1—figure supplement 1
Survival curve of animals cultivated at different temperatures.
Survival curves of wild-type animals cultivated with E. coli from eggs at the indicated temperatures. N = 4 experiments with 25 animals/experiment (100 animals in total). Statistics: Log-rank test, …
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Figure 1—figure supplement 1—source data 1
Lifespan at different temperatures.
- https://cdn.elifesciences.org/articles/81418/elife-81418-fig1-figsupp1-data1-v1.xlsx
Figure 1—figure supplement 2
Distributions of animals at different ages on the temperature gradient.
The distributions of animals at D1–D5 on the temperature gradient after thermotaxis assays. Animals were cultivated at 23°C and placed at the center of the 17–23°C gradient. Pink rectangles indicate …
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Figure 1—figure supplement 2—source data 1
Distribution of animals on thermotaxis plates at different ages.
- https://cdn.elifesciences.org/articles/81418/elife-81418-fig1-figsupp2-data1-v1.xlsx
Figure 1—figure supplement 3
HT115-fed animals showed thermotaxis decline.
Box plots summarizing thermotaxis performance indices. Animals were cultivated with OP50 until D1 and then with OP50 or HT115 until D5. The number of experiments is shown. Statistics: The mean …
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Figure 1—figure supplement 3—source data 1
Thermotaxis decline of HT115-fed animals.
- https://cdn.elifesciences.org/articles/81418/elife-81418-fig1-figsupp3-data1-v1.xlsx
Figure 1—figure supplement 4
AFD and AIY are alive at D5.
TagRFP of NUJ296 knjIs15[gcy-8Mp::GCaMP6m+gcy-8Mp::tagRFP+ges-1p::tagRFP] and IK1144 njIs26[AIYp::GCaMP3+AIYp::tagRFP+ges-1p::tagRFP] were imaged to visualize AFD and AIY, respectively. (A, C) …
Figure 1—figure supplement 5
E. coli-fed aged animals sense food.
Food recognition assays of D1 in (A) and D5 adults in (B). Animals were pre-conditioned with (well-fed) or without (food-deprived) E. coli and assayed on plates with or without E. coli. Animals’ …
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Figure 1—figure supplement 5—source data 1
Food recognition assays of young and aged animals.
- https://cdn.elifesciences.org/articles/81418/elife-81418-fig1-figsupp5-data1-v1.xlsx
Figure 1—figure supplement 6
Aged E. coli-fed animals perform salt-avoidance behavior irrespective of diet.
(A) Schematic of conditioning of animals. Animals were conditioned in the absence of food with (NaCl) or without (Mock) NaCl. (B) Schematic of salt-avoidance assays. Gradient and quadrant assays …
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Figure 1—figure supplement 6—source data 1
Salt-taxis assays of young and aged animals.
- https://cdn.elifesciences.org/articles/81418/elife-81418-fig1-figsupp6-data1-v1.xlsx
Figure 2 with 1 supplement
Lactic acid bacteria (LAB) screen for thermotaxis in aged animals.
(A) Schematic of the screening procedure. Animals were cultivated at 23°C with E. coli until D1 and transferred to E. coli or LAB plates every day until D5. At D5, animals were subjected to …
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Figure 2—source data 1
Thermotaxis assays of aged animals fed with different lactic acid bacteria.
- https://cdn.elifesciences.org/articles/81418/elife-81418-fig2-data1-v1.xlsx
Figure 2—figure supplement 1
Animals fed heterofermentative lactic acid bacteria (LAB) are not thermophilic.
Animals were cultivated at 23°C and placed at the center of a 20–26°C gradient to examine the thermophilicity. D5 animals with indicated genotypes were cultivated with E. coli or Lb. reuteri from …
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Figure 2—figure supplement 1—source data 1
Thermophilicity of aged animals fed with different lactic acid bacteria.
- https://cdn.elifesciences.org/articles/81418/elife-81418-fig2-figsupp1-data1-v1.xlsx
Figure 3
Lactic acid bacteria (LAB)-fed aged animals learn a new Tcult.
(A, B) The distribution of animals on thermotaxis plates. Pink rectangles indicate the sections around the Tcult. (A) D1 or D5 animals fed indicated bacteria were cultivated at 23°C and placed at …
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Figure 3—source data 1
Thermotaxis assays of aged animals fed with the select lactic acid bacteria.
- https://cdn.elifesciences.org/articles/81418/elife-81418-fig3-data1-v1.xlsx
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Figure 3—source data 2
Temperature shift experiment of aged animals fed with the select lactic acid bacteria.
- https://cdn.elifesciences.org/articles/81418/elife-81418-fig3-data2-v1.xlsx
Figure 4 with 1 supplement
Lactic acid bacteria (LAB) show various effects on lifespan and locomotion.
Animals were fed E. coli until D1 and indicated bacteria after D1. (A) Survival curves of animals fed indicated LAB are shown with control animals fed E. coli. Nematode Growth Medium (NGM) plates …
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Figure 4—source data 1
Lifespan of animals fed with the select lactic acid bacteria.
- https://cdn.elifesciences.org/articles/81418/elife-81418-fig4-data1-v1.xlsx
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Figure 4—source data 2
Thrashing assays of aged animals fed with the select lactic acid bacteria.
- https://cdn.elifesciences.org/articles/81418/elife-81418-fig4-data2-v1.xlsx
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Figure 4—source data 3
Locomotion of aged animals fed with different lactic acid bacteria.
- https://cdn.elifesciences.org/articles/81418/elife-81418-fig4-data3-v1.xlsx
Figure 4—figure supplement 1
Diet affects thermotaxis of aged animals on peptone-free plates.
Box plots summarizing performance indices of animals cultivated on peptone-free Nematode Growth Medium (NGM) plates. D5 animals were cultivated at 23°C with E. coli or Lb. reuteri from D1. The …
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Figure 4—figure supplement 1—source data 1
Thermotaxis assays using peptone-free plates.
- https://cdn.elifesciences.org/articles/81418/elife-81418-fig4-figsupp1-data1-v1.xlsx
Figure 5 with 1 supplement
Bacteria affect thermotaxis of aged animals as nutrition.
Box plots show thermotaxis performance indices of animals fed indicated bacteria and cultivated at 23°C. Aged animals were transferred every day to new plates from D1. The number of experiments is …
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Figure 5—source data 1
The effect of switching bacteria on the thermotaxis behavior of aged animals.
- https://cdn.elifesciences.org/articles/81418/elife-81418-fig5-data1-v1.xlsx
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Figure 5—source data 2
The effect of heat-killed bacteria on the thermotaxis behavior of aged animals.
- https://cdn.elifesciences.org/articles/81418/elife-81418-fig5-data2-v1.xlsx
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Figure 5—source data 3
The effect of mixed bacteria on the thermotaxis behavior of aged animals.
- https://cdn.elifesciences.org/articles/81418/elife-81418-fig5-data3-v1.xlsx
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Figure 5—source data 4
The effect of bacterial smell on the thermotaxis behavior of aged animals.
- https://cdn.elifesciences.org/articles/81418/elife-81418-fig5-data4-v1.xlsx
Figure 5—figure supplement 1
Animals ingest E.coli and Lb. reuteri.
Representative images show fluorescently labeled bacteria in the intestine of C. elegans. Animals were cultivated with FICT-labeled E. coli, Lb. reuteri, or the mixture of fluorescently labeled and …
Figure 6 with 1 supplement
Lactobacilli in a clade are associated with high thermotaxis performance of aged animals.
Phylogenetic tree of lactic acid bacteria (LAB) based on 16S rRNA is shown with fermentation mode, and heatmap of performance indices of aged animals fed indicated LAB from D1. Bootstrap values are …
Figure 6—figure supplement 1
Images of Gram-stained bacteria.
Images of Gram-stained E. coli and select lactic acid bacteria (LAB). E. coli and LAB are Gram-negative and -positive, respectively. Scale bar: 10 µm.
Figure 7 with 1 supplement
daf-16 is involved in the effect of Lb. reuteri on thermotaxis in aged animals.
(A) Box plots summarizing thermotaxis performance indices of animals with indicated genotypes in the different diet and age conditions. Animals were cultivated at 23°C with E. coli or Lb. reuteri …
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Figure 7—source data 1
Thermotaxis of kmo-1, nkat-1, and daf-16 mutants.
- https://cdn.elifesciences.org/articles/81418/elife-81418-fig7-data1-v1.xlsx
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Figure 7—source data 2
Distributions of daf-16 mutants on thermotaxis plates.
- https://cdn.elifesciences.org/articles/81418/elife-81418-fig7-data2-v1.xlsx
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Figure 7—source data 3
Lifespan of daf-16 mutants fed with E. coli or Lb. reuteri.
- https://cdn.elifesciences.org/articles/81418/elife-81418-fig7-data3-v1.xlsx
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Figure 7—source data 4
Thermotaix of daf-2 mutants.
- https://cdn.elifesciences.org/articles/81418/elife-81418-fig7-data4-v1.xlsx
Figure 7—figure supplement 1
Lactic acid bacteria (LAB)-fed animals are not dietary restricted.
(A) Expression of pha-4 transcripts in aged animals fed indicated LAB relative to aged animals fed E. coli. (B) Box plots summarizing thermotaxis indices of wild type and eat-2 mutant animals …
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Figure 7—figure supplement 1—source data 1
pha-4 expression of aged animals fed with the select lactic acid bacteria.
- https://cdn.elifesciences.org/articles/81418/elife-81418-fig7-figsupp1-data1-v1.xlsx
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Figure 7—figure supplement 1—source data 2
Thermotaxis assays of eat-2 mutants.
- https://cdn.elifesciences.org/articles/81418/elife-81418-fig7-figsupp1-data2-v1.xlsx
Figure 8 with 1 supplement
daf-16 b isoform functions in neurons to maintain high thermotaxis ability in aged animals fed Lb. reuteri.
(A) Schematic of daf-16 locus with representative isoforms based on WormBase (https://wormbase.org). Black boxes and black lines indicate exons and introns, respectively. Arrows indicate 3′UTR. …
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Figure 8—source data 1
The effect of different daf-16 alleles on the thermotaxis behavior.
- https://cdn.elifesciences.org/articles/81418/elife-81418-fig8-data1-v1.xlsx
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Figure 8—source data 2
Tissue-specific daf-16 rescue of the thermotaxis behavior.
- https://cdn.elifesciences.org/articles/81418/elife-81418-fig8-data2-v1.xlsx
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Figure 8—source data 3
The effect of timing-specific knockdown of daf-16 on the thermotaxis behavior.
- https://cdn.elifesciences.org/articles/81418/elife-81418-fig8-data3-v1.xlsx
Figure 8—figure supplement 1
Auxin and Auxin-Inducible Degron (AID) tag do not affect the thermotaxis.
Box plots summarizing performance indices of the control conditions for AID system. D5 animals were cultivated at 23°C with E. coli or Lb. reuteri from D1. Auxin, TIR1, and AID degron tag by …
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Figure 8—figure supplement 1—source data 1
The effect of daf-16 knockdown using AID on the thermotaxis behavior.
- https://cdn.elifesciences.org/articles/81418/elife-81418-fig8-figsupp1-data1-v1.xlsx
Figure 9 with 2 supplements
Transcriptome analysis on the effect of aging and diet.
(A) Schematic of transcriptome analysis. We carried out RNA sequencing of indicated samples (eight in total). Principal component analysis was carried out using all samples. Differentially expressed …
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Figure 9—source data 1
Thermotaxis assays of proprotein convertase mutants.
- https://cdn.elifesciences.org/articles/81418/elife-81418-fig9-data1-v1.xlsx
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Figure 9—source data 2
List of genes enriched in aged animals fed with different bacteria.
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Figure 9—figure supplement 1
Heatmap for differentially expressed genes.
Heatmap of the one-way hierarchical clustering using Z-score for normalized value based on log2. 4426 genes satisfying fc2 are shown.
Figure 9—figure supplement 2
Principal component analysis of the transcriptome data of the animals of different ages and diet.
Principal component analysis was carried out for the transcriptome data of D1, and D5 animals fed E. coli or lactic acid bacteria (LAB); (Lb. gasseri, Lb. delbrueckii, P. pentosaceus, Lb. reuteri, Lb…
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Figure 9—figure supplement 2—source data 1
Contribution of each gene on PC1.
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Figure 9—figure supplement 2—source data 2
Contribution of each gene on PC2.
- https://cdn.elifesciences.org/articles/81418/elife-81418-fig9-figsupp2-data2-v1.xlsx
Additional files
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Supplementary file 1
Lifespan statistics.
(a) Lifespan statistics for Figure 1—figure supplement 1. (b) Lifespan statistics for Figure 4A. (c) Lifespan statistics for Figure 7C.
- https://cdn.elifesciences.org/articles/81418/elife-81418-supp1-v1.xlsx
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Supplementary file 2
List of LAB strains.
- https://cdn.elifesciences.org/articles/81418/elife-81418-supp2-v1.xlsx
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Supplementary file 3
RNAseq analyses of aged animals fed with different bacteria.
(a) RNAseq data. (b) Top 5% genes positively contributing to PC1. (c) Top 5% genes negaitively contributing to PC1. (d) Gene ontology analysis of top 5% genes positively contributing to PC1. (e) Gene ontology analysis of top 5% genes negatively contributing to PC1. (f) Top 5% genes positively contributing to PC2. (g) Top 5% genes negatively contributing to PC2. (h) Gene ontology analysis of top 5% genes positively contributing to PC2. (i) Gene ontology analysis of top 5% genes negatively contributing to PC2. (j) Genes enriched in E. coli or Homo lactic acid bacteria (LAB)-fed D5. (k) Gene ontology analysis of E. coli or Homo LAB-enriched genes. (l) Genes enriched in Hetero LAB-fed D5. (m) Gene ontology analysis of Hetero LAB-enriched genes.
- https://cdn.elifesciences.org/articles/81418/elife-81418-supp3-v1.xlsx
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Transparent reporting form
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