Non invasive analysis of metabolic changes following nutrient input into diverse fish species, as investigated by metabolic and microbial profiling approaches
- Subject Areas
- Aquaculture, Fisheries and Fish Science, Biochemistry, Biodiversity, Genomics, Microbiology
- NMR, gut microbiota, metabolic profiling, microbial profiling, fish biodiversity
- © 2014 Asakura et al.
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.
- Cite this article
- 2014. Non invasive analysis of metabolic changes following nutrient input into diverse fish species, as investigated by metabolic and microbial profiling approaches. PeerJ PrePrints 2:e472v2 https://doi.org/10.7287/peerj.preprints.472v2
An NMR-based metabolomic approach in aquatic ecosystems is valuable for studying the environmental effects of pharmaceuticals and other chemicals on fish. This technique has also contributed to new information in numerous research areas, such as basic physiology and development, disease, and water pollution. We evaluated the microbial diversity in various fish species collected from Japan’s coastal waters using next-generation sequencing, followed by evaluation of the effects of feed type on co-metabolic modulations in fish-microbial symbiotic ecosystems in laboratory-scale experiments. Intestinal bacteria of fish in their natural environment were characterized (using 16S rRNA genes) for trophic level using pyrosequencing and noninvasive sampling procedures developed to study the metabolism of intestinal symbiotic ecosystems in fish reared in their environment. Metabolites in feces were compared, and intestinal contents and feed were annotated based on HSQC and TOCSY using SpinAssign and network analysis. Feces were characterized by species and varied greatly depending on the feeding types. In addition, feces samples demonstrated a response to changes in the time series of feeding. The potential of this approach as a non-invasive inspection technique in aquaculture is suggested.
In this second version of the preprint, we have corrected several typographical errors in the main text.
Bacterial species from 42 ﬁsh gut communities classiﬁed into the phylum level. Bar graphs for each library represent the percentage of each phylum. Scientific names of the ﬁsh hosts are listed along the horizontal axis. Habitat and food habits of these fish are described in Table S1.
Microbiota profiles from fish guts evaluated by PCA (n = 41, k = 52, R2X = 0.154, R2Y = 0.114, Q2 = 0.059). (A) PCA score plot based on PC1 and PC2. The numbers on PCA denote the values of species diversity calculated by the Shannon diversity index. (B) PCA score plot based on PC1 and PC4. (C, D, E) PCA loading plots for PC1 (C), PC2 (D), and PC4 (E) of top 12 positives (C, D, E) and negatives (C).
Microbiota profiles from fish guts evaluated by PCA (n = 19, k = 69, R2X = 0.175, R2Y = 0.158, Q2 = 0.018) for comparison between fish eaters and Omnivora. (A) PCA score plot based on PC1 and PC2. Symbols representing individual communities are colored by Fish eater (red) and Omnivora (green). (B) PCA loading plots for PC1.
Supplemental Figure 4. 1H NMR spectra of methanol-soluble fraction from 14 fish feces (a) to (n). (a) to (n) fish are listed in Table S3.
1H-13C HSQC spectra of methanol-soluble component profiles from artificial feed. Peaks were used in Figure 2. Red, amino acid; blue, unsaturated fatty acid; aqua, fatty acid and phospholipid. Peak numbers and annotated metabolites are listed in Supplementary Table S3.
1H-13C HSQC spectra of methanol-soluble component profiles for evaluation of retention capability of water-soluble components in fish feces of Sebastiscus marmoratus. Black and red indicate the fecal samples before and after rinsing with artificial seawater (for 15 min with shaking, 3 times), respectively.
Metabolic and microbial profiles of intestinal contents and feces of 13 species of breeding fish (Table S3). PCA scores plot for microbial profile in feces (n = 22, k = 109, R2X = 0.282, R2Y = 0.241, Q2 = 0.089), microbial profile in intestinal contents (n = 19, k = 65, R2X = 0.219, R2Y = 0.141, Q2 = 0.066), metabolic profile in feces (n = 115, k = 793, R2X = 0.224, R2Y = 0.187, Q2 = 0.138), and metabolic profile in intestinal contents (n = 20, k = 786, R2X = 0.331, R2Y = 0.152, Q2 = 0.251) are shown. Triangle indicates intestinal contents, circle indicates feces. Color indicates the feeding status of breeding fish.
List of fishes for which the sequence analysis was performed
List of methanol-soluble compounds detected in 1H-13C HSQC spectra and annotated by SpinAssign program
Supplemental Table 3. List of fishes that performed the culturing and sampling of feces