Acknowledgement
The authors would like to thank Molecular Laboratory of Advance Research Facility, IPB University for infrastructure. The opinions, findings and conclusions or recommendations expressed in this publication are that of the authors alone.
References
- Andersen KS, Kirkegaard RH, Karst SM, Albertsen M. Ampvis2: an R package to analyse and visualise 16S rRNA amplicon data [Internet]. bioRxiv. 2018 [cited Apr 1]. https://doi.org/10.1101/299537
- Arnold SH, Price RJ, Brown WD. Histamine formation by bacteria isolated from skipjack tuna, Katsuwonus pelamis. Bull Jpn Soc Sci Fish. 1980;46:991-5. https://doi.org/10.2331/suisan.46.991
- Badan Pusat Statistik [BPS]. Statistik Pendaratan ikan tradisional 2020 [Internet]. 2021 [cited Dec 14]. https://www.bps.go.id/ publication/2021/11/29/653ae786edb185271d56ed54/statistik-pendaratan-ikan-tradisional-2020.html
- Bokulich NA, Kaehler BD, Rideout JR, Dillon M, Bolyen E, Knight R, et al. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature- classifier plugin. Microbiome. 2018;6:90.
- Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019;37:852-7. https://doi.org/10.1038/s41587-019-0209-9
- Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: high-resolution sample inference from illumina amplicon data. Nat Methods. 2016;13:581-3. https://doi.org/10.1038/nmeth.3869
- Carda-Dieguez M, Mira A, Fouz B. Pyrosequencing survey of intestinal microbiota diversity in cultured sea bass (Dicentrarchus labrax) fed functional diets. FEMS Microbiol Ecol. 2014;87:451-9. https://doi.org/10.1111/1574-6941.12236
- Drzewiecka D. Significance and roles of Proteus spp. bacteria in natural environments. Microb Ecol. 2016;72:741-58. https://doi.org/10.1007/s00248-015-0720-6
- Harfan DT, Rousdy DW, Kurniatuhadi R. Effectiveness of Pseudomonas sp. BOT4 in degrading cooking oil using nitrogen source of sodium nitrate and yeast extract. J Protobiont. 2019;8:106-14.
- Hinman A, Du Bois J. A stereoselective synthesis of (-)-tetrodotoxin. J Am Chem Soc. 2003;125:11510-1. https://doi.org/10.1021/ja0368305
- Jandhyala SM, Talukdar R, Subramanyam C, Vuyyuru H, Sasikala M, Reddy DN. Role of the normal gut microbiota. World J Gastroenterol. 2015;21:8787-803. https://doi.org/10.3748/wjg.v21.i29.8787
- Jiang W, Griffanti G, Tamimi F, McKee MD, Nazhat SN. Multiscale structural evolution of citrate-triggered intrafibrillar and interfibrillar mineralization in dense collagen gels. J Struct Biol. 2020;212:107592.
- Jumria A, Prihartini NC, Alfiyah A. Identification and histopathology Flavobacterium columnare on tilapia (Oreochromis niloticus). Samakia J Ilmu Perikan. 2017;8:17-22.
- Kaale LD, Eikevik TM, Rustad T, Nordtvedt TS. Changes in water holding capacity and drip loss of Atlantic salmon (Salmo salar) muscle during superchilled storage. LWT-Food Sci Technol. 2014;55:528-35. https://doi.org/10.1016/j.lwt.2013.10.021
- Kanki M, Yoda T, Tsukamoto T, Baba E. Histidine decarboxylases and their role in accumulation of histamine in tuna and dried saury. Appl Environ Microbiol. 2007;73:1467-73. https://doi.org/10.1128/AEM.01907-06
- Kim BR, Shin J, Guevarra RB, Lee JH, Kim DW, Seol KH, et al. Deciphering diversity indices for a better understanding of microbial communities. J Microbiol Biotechnol. 2017;27:2089-93. https://doi.org/10.4014/jmb.1709.09027
- Lacapa R, Tangke U, Laitupa IW. Study of decline in bottom fish quality of gill net catches at room temperature and cold storage. J Sain Sos Hum. 2021;1:14-25.
- Liu F, Shi HZ, Guo QS, Yu Y, Wang A, Lv F, et al. Effects of astaxanthin and emodin on the growth, stress resistance and disease resistance of yellow catfish (Pelteobagrus fulvidraco). Fish Shellfish Immunol. 2016;51:125-35. https://doi.org/10.1016/j.fsi.2016.02.020
- Lorentzen G, Rosnes JT, Rotabakk BT, Skuland AV, Hansen JS, Ageeva TN. A simulated e-commerce cold chain for fresh cod (Gadus morhua L.) products: applicability of selected TTIs and effects of pre-treatment and packaging. Food Packag Shelf Life. 2022;31:100794.
- Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011;17:10-2. https://doi.org/10.14806/ej.17.1.200
- Meiriza Y, Dewi EN, Rianingsih L. The difference of characteristic milkfish (Chanos chanos Forsk) boneless in difference packaging during frozen storage. J Pengolah Bioteknol Has Perikan. 2016;5:36-43.
- Min D, Doxey AC, Neufeld JD. AXIOME3: automation, extension, and integration of microbial ecology. Gigascience. 2021;10:giab006.
- Norita, Nurilmala M, Abdullah A. Kualitas ikan tongkol abuabu (Thunnus tonggol) pada kondisi penyimpanan berbeda. J Pengolah Has Perikan Indones. 2019;22:490-7.
- Nurilmala M, Abdullah A, Matutina VM, Nurjanah, Yusfiandayani R, Sondita MFA, et al. Chemical, microbiology changes and detection of hdc gene on longtail tuna thunnus tonggol during chilling temperature storage. J Ilmu Teknol Kelaut Tropis. 2019;11:285-96. https://doi.org/10.29244/jitkt.v11i2.23007
- Nurilmala M, Saputri NN, Abdullah A, Nurjanah N, Yusfiandayani R, Sondita MFA. Detection of histamine-producing bacteria on tuna species using histidine decarboxylase (hdc) and 16S rRNA. Squalen Bull Mar Fish Postharvest Biotechnol. 2020;15:131-9. https://doi.org/10.15578/squalen.v15i3.445
- Pianusa AF, Sanger G, Wonggo D. Study of changes in the freshness quality of tuna (Euthynnus Affinis) soaked in seaweed extract (Eucheuma spinosum) and mangrove fruit extract (Sonneratia alba). J Media Teknol Has Perikan. 2015;3:66-74.
- Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590-6. https://doi.org/10.1093/nar/gks1219
- R Core Team. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. 2013. https://www.R-project.org/.
- R Studio Team. RStudio: Integrated Development for R. RStudio, PBC, Boston, MA. 2020. http://www.rstudio.com/.
- Rimoldi S, Gliozheni E, Ascione C, Gini E, Terova G. Effect of a specific composition of short- and medium-chain fatty acid 1-monoglycerides on growth performances and gut microbiota of gilthead sea bream (Sparus aurata). PeerJ. 2018;6:e5355.
- Rimoldi S, Torrecillas S, Montero D, Gini E, Makol A, Valdenegro VV, et al. Assessment of dietary supplementation with galactomannan oligosaccharides and phytogenics on gut microbiota of European sea bass (Dicentrarchus labrax) fed low fishmeal and fish oil based diet. PLOS ONE. 2020;15:e0231494.
- Robert FS. Measurement of biodiversity: richness and evenness. In: Kaper HG, Roberts FS, editors. Mathematics of planet earth: protecting our planet, learning from the past, safeguarding for the future. Cham: Springer; 2019. p. 1-22.
- Rodriguez J, Gallampois CM, Haglund P, Timonen S, Rowe O. Bacterial communities as indicators of environmental pollution by POPs in marine sediments. Environ Pollut. 2021;268:115690.
- Sari RA, Yunianta, Harsojo. The effect of gamma irradiation and freezing storage as an effort to improve food safety on "patin" fish (Pangasius hypoptalmus). J Pangan Agroindustri. 2018;5:1-8.
- Schloss PD. Amplicon sequence variants artificially split bacterial genomes into separate clusters. mSphere. 2021;6: e0019121.
- Shehata HR, Mitterboeck TF, Hanner R. Characterization of the microbiota of commercially traded finfish fillets. Food Res Int. 2020;137:109373. https://doi.org/10.1016/j.foodres.2020.109373
- Siburian ETP, Dewi P, Kariada N. The effect of temperature and storage time on the growth of bacteria and fungi in milkfish. Unnes J Life Sci. 2012;1:101-5.
- Wang J, Fan Y, Yao Z. Isolation of a Lysinibacillus fusiformis strain with tetrodotoxin-producing ability from puffer fish Fugu obscurus and the characterization of this strain. Toxicon. 2010;56:640-3. https://doi.org/10.1016/j.toxicon.2010.05.011
- Willis AD. Rarefaction, alpha diversity, and statistics. Front Microbiol. 2019;10:2407.
- Wiranata K, Widia IW, Sanjaya IPGD. The development of cold chain system on fresh tuna fish (Euthynnus affinis) for fish retailer. J Biosist Tek Pertan. 2017;6:12-21.
- Zhang J, Meng H, Kong X, Cheng X, Ma T, He H, et al. Combined effects of polyethylene and organic contaminant on zebrafish (Danio rerio): accumulation of 9-nitroanthracene, biomarkers and intestinal microbiota. Environ Pollut. 2021;277:116767.
- Zhuang S, Hong H, Zhang L, Luo Y. Spoilage-related microbiota in fish and crustaceans during storage: research progress and future trends. Compr Rev Food Sci Food Saf. 2021;20:252-88. https://doi.org/10.1111/1541-4337.12659