journal article·2022-06-10Open access

Identifying a Correlation among Qualitative Non-Numeric Parameters in Natural Fish Microbe Dataset Using Machine Learning

Hideaki Shima, Yuho Sato, Kenji Sakata, Taiga Asakura, Jun Kikuchi

Applied Sciences· Volume 12· Issue 12

Abstract

Recent technical innovations and developments in computer-based technology have enabled bioscience researchers to acquire comprehensive datasets and identify unique parameters within experimental datasets. However, field researchers may face the challenge that datasets exhibit few associations among any measurement results (e.g., from analytical instruments, phenotype observations as well as field environmental data), and may contain non-numerical, qualitative parameters, which make statistical analyses difficult. Here, we propose an advanced analysis scheme that combines two machine learning steps to mine association rules between non-numerical parameters. The aim of this analysis is to identify relationships between variables and enable the visualization of association rules from data of samples collected in the field, which have less correlations between genetic, physical, and non-numerical qualitative parameters. The analysis scheme presented here may increase the potential to identify important characteristics of big datasets.
Source: crossref · Quality: baseline

Research context

OpenAlex topics: Metabolomics and Mass Spectrometry Studies · Identification and Quantification in Food · Hydrological Forecasting Using AI

SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.

Affiliations

RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan

Graduate School of Medical Life Science, Yokohama City University, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan

Graduate School of Bioagriculuture Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan

Funding

Ministry of Agriculture, Forestry and Fisheries

References (44)

Show source-provided references
1. Metagenomics: Application of genomics to uncultured microorganisms10.1128/MMBR.68.4.669-685.2004 ↗
2. Genomic sequencing of uncultured microorganisms from single cells10.1038/nrmicro2857 ↗
3. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes10.1038/nbt.2579 ↗
4. Lifestyle evolution in symbiotic bacteria: Insights from genomics10.1016/S0169-5347(00)01902-9 ↗
5. Getting better with bifidobacteria10.1111/j.1365-2672.2005.02600.x ↗
6. Bacteria and host interactions in the gut epithelial barrier10.1038/nchembio.741 ↗
7. Visualizing Individual and Region-specific Microbial–metabolite Relations by Important Variable Selection Using Machine Learning Approaches10.2751/jcac.18.31 ↗
8. Interactions of intestinal bacteria with components of the intestinal mucus10.3389/fcimb.2017.00387 ↗
9. Gut microbial short-chain fatty acids in host defense and immune regulation10.2492/inflammregen.35.114 ↗
10. Mood and gut feelings10.1016/j.bbi.2009.05.058 ↗
11. Growth and host interaction of mouse segmented filamentous bacteria in vitro10.1038/nature14027 ↗
12. Uptake through glycoprotein 2 of FimH+ bacteria by M cells initiates mucosal immune response10.1038/nature08529 ↗
13. Osaka, T., Moriyama, E., Arai, S., Date, Y., Yagi, J., Kikuchi, J., and Tsuneda, S. (2017). Meta-analysis of fecal microbiota and metabolites in experimental colitic mice during the inflammatory and healing phases. Nutrients, 9.10.3390/nu9121329 ↗
14. Dysbiosis of the gut microbiota in disease
15. Shima, H., Masuda, S., Date, Y., Shino, A., Tsuboi, Y., Kajikawa, M., Inoue, Y., Kanamoto, T., and Kikuchi, J. (2017). Exploring the impact of food on the gut ecosystem based on the combination of machine learning and network visualization. Nutrients, 9.10.3390/nu9121307 ↗
16. Deep learning in omics: A survey and guideline10.1093/bfgp/ely030 ↗
17. Application of market basket analysis for the visualization of transaction data based on human lifestyle and spectroscopic measurements10.1021/acs.analchem.5b04182 ↗
18. Mesiar, R., and Sheikhi, A. (2021). Nonlinear random forest classification, a copula-based approach. Appl. Sci., 11.10.3390/app11157140 ↗
19. MacQueen, J. (July, January 21). Some methods for classification and analysis of multivariate observations. Proceedings of the Fifth Berkeley Symposium on Mathematical Statistics and Probability, Berkeley, CA, USA.
20. Random forests: From early developments to recent advancements10.1080/21642583.2014.956265 ↗
21. Li, W.T., Ma, J., Shende, N., Castaneda, G., Chakladar, J., Tsai, J.C., Apostol, L., Honda, C.O., Xu, J., and Wong, L.M. (2020). Using machine learning of clinical data to diagnose COVID-19. medRxiv.10.1101/2020.06.24.20138859 ↗
22. Fish ecotyping based on machine learning and inferred network analysis of chemical and physical properties10.1038/s41598-021-83194-0 ↗
23. Crop classification of upland fields using Random forest of time-series Landsat 7 ETM+ data10.1016/j.compag.2015.05.001 ↗
24. Support vector machines based on K-means clustering for real-time business intelligence systems
25. The global k-means clustering algorithm10.1016/S0031-3203(02)00060-2 ↗
26. Arthur, D., and Vassilvitskii, S. (2006). k-Means++: The Advantages of Careful Seeding, Stanford University.
27. Random forests10.1023/A:1010933404324 ↗
28. Agrawal, R., and Srikant, R. (1994, January 12–15). Fast algorithms for mining association rules. Proceedings of the 20th International Conference on Very Large Data Bases—VLDB, Santiago de Chile, Chile.
29. Market basket analysis algorithms with mapreduce10.1002/widm.1107 ↗
30. Metabolic sequences of anaerobic fermentation on glucose-based feeding substrates based on correlation analyses of microbial and metabolite profiling10.1021/pr3008682 ↗
31. Enterotypes of the human gut microbiome10.1038/nature09944 ↗
32. Wei, F., Fukuchi, M., Ito, K., Sakata, K., Asakura, T., Date, Y., and Kikuchi, J. (2020). Large-scale evaluation of major soluble macromolecular components of fish muscle from a conventional 1H-NMR spectral database. Molecules, 25.10.3390/molecules25081966 ↗
33. Ikotun, A.M., Almutari, M.S., and Ezugwu, A.E. (2021). K-Means-Based Nature-Inspired Metaheuristic Algorithms for Automatic Data Clustering Problems: Recent Advances and Future Directions. Appl. Sci., 11.10.3390/app112311246 ↗
34. The gut microbiota of marine fish10.3389/fmicb.2018.00873 ↗
35. Phototrophic marine benthic microbiomes: The ecophysiology of these biological entities10.1111/1462-2920.14494 ↗
36. Chitin and chitosan: Functional biopolymers from marine crustaceans10.1007/s10126-005-0097-5 ↗
37. Culturable autochthonous gut bacteria in Atlantic salmon (Salmo salar L.) fed diets with or without chitin. Characterization by 16S rRNA gene sequencing, ability to produce enzymes and In Vitro growth inhibition of four fish pathogens10.1016/j.aquaculture.2011.10.016 ↗
38. Food starch structure impacts gut microbiome composition10.1128/mSphere.00086-18 ↗
39. Food and the gut microbiota in IBD: A critical connection10.1097/MOG.0b013e328354586f ↗
40. Organic osmolytes of amphipods from littoral to hadal zones: Increases with depth in trimethylamine N-oxide, scyllo-inositol and other potential pressure counteractants10.1016/j.dsr.2018.05.008 ↗
41. High contents of trimethylamine oxide correlating with depth in deep-sea teleost fishes, skates, and decapod crustaceans10.2307/1543162 ↗
42. Trimethylamine oxide accumulation in marine animals: Relationship to acylglycerol storagej10.1242/jeb.205.3.297 ↗
43. Trimethylamine oxide content and spoilage potential of New Zealand commercial fish species10.1080/00288330.2016.1250785 ↗
44. The Relationship between Fish Intake and Urinary Trimethylamine-N-Oxide10.1002/mnfr.201900799 ↗