Exploring the Roles of Tuna-Associated Acinetobacter sp. YFT067: Implications for Host Health and Metabolism

Abstract

The gut microbiome and its metabolites are vitally important for host dietary digestion, nutrient absorption, and energy metabolism. Yellowfin tuna (Thunnus albacares), a large warm-blooded fish that sustains continuous high-speed swimming, demonstrates higher energy demands than other fish. However, there are no relevant reports on the functional contribution of specialized gut microbiota to energy homeostasis of tuna. To bridge this knowledge gap, we characterized the function of a new bacterial strain, Acinetobacter seifertii YFT067, derived from the intestine of wild yellowfin tuna. According to whole genome sequencing, YFT067 exhibited the probiotic potential with a high ability in nutrient metabolism. In vitro test demonstrated that YFT067 is tolerant to the simulated gastroenteric juice and strong in adhesion. The six-week zebrafish feeding trial with 10⁸ CFU/g YFT067 strain supplementation significantly enhanced body growth, feed conversion, and digestive enzyme activity of the host as well as the intestinal health, including enhanced goblet cells number and short-chain fatty acids (propionate, butyrate, and valerate) contents. Transcriptomic analysis revealed that the digestive system and metabolism process were significantly up-regulated with fabp, fatp4, mgat3a, acat1, apoa1b, and apoa4a enriched in the fat digestive and absorption pathway and pltp, cetp, and nceh1a enriched in the cholesterol metabolism pathway. These findings indicated A. seifertii YFT067 as a promising probiotic candidate for enhancing tuna farming production through improving metabolic efficiency and intestinal health. Our study provides foundational evidence for developing YFT067-based probiotic formulations to optimize growth performance and cultivation sustainability in tuna aquaculture.

Keywords

Acinetobacter / gut microbiota / lipid absorption / probiotic / Thunnus albacares

References

[1] J. A. Gilbert, M. J. Blaser, J. G. Caporaso, J. K. Jansson, S. V. Lynch, and R. Knight, “Current Understanding of the Human Microbiome,” Nature Medicine 24, no. 4 (2018): 392–400, https://doi.org/10.1038/nm.4517.

[2] K. A. Krautkramer, J. Fan, and F. Bäckhed, “Gut Microbial Metabolites as Multi-Kingdom Intermediates,” Nature Reviews Microbiology 19, no. 2 (2021): 77–94, https://doi.org/10.1038/s41579-020-0438-4.

[3] E. C. Lindsay, N. B. Metcalfe, and M. S. Llewellyn, “The Potential Role of the Gut Microbiota in Shaping Host Energetics and Metabolic Rate,” Journal of Animal Ecology 89, no. 11 (2020): 2415–2426, https://doi.org/10.1111/1365-2656.13327.

[4] E. K. Mallott and K. R. Amato, “Host Specificity of the Gut Microbiome,” Nature Reviews Microbiology 19, no. 10 (2021): 639–653, https://doi.org/10.1038/s41579-021-00562-3.

[5] M. L. Pepke, S. B. Hansen, and M. T. Limborg, “Unraveling Host Regulation of Gut Microbiota Through the Epigenome–Microbiome Axis,” Trends in Microbiology 32, no. 12 (2024): 1229–1240, https://doi.org/10.1016/j.tim.2024.05.006.

[6] H. Van Doan, S. H. Hoseinifar, E. Ringø, et al., “Host-Associated Probiotics: A Key Factor in Sustainable Aquaculture,” Reviews in Fisheries Science & Aquaculture 28, no. 1 (2020): 16–42, https://doi.org/10.1080/23308249.2019.1643288.

[7] X. Y. Ding, C. Y. Wei, Z. Y. Liu, H. L. Yang, F. Han, and Y. Z. Sun, “Autochthonous Bacillus subtilis and Enterococcus faecalis Improved Liver Health, Immune Response, Mucosal Microbiota and Red-Head Disease Resistance of Yellow Drum (Nibea albiflora),” Fish & Shellfish Immunology 134 (2023): 108575, https://doi.org/10.1016/j.fsi.2023.108575.

[8] M. T. El-Saadony, M. Alagawany, A. K. Patra, et al., “The Functionality of Probiotics in Aquaculture: An Overview,” Fish & Shellfish Immunology 117 (2021): 36–52, https://doi.org/10.1016/j.fsi.2021.07.007.

[9] M. J. Zorriehzahra, S. T. Delshad, M. Adel, et al., “Probiotics as Beneficial Microbes in Aquaculture: An Update on Their Multiple Modes of Action: A Review,” Veterinary Quarterly 36, no. 4 (2016): 228–241, https://doi.org/10.1080/01652176.2016.1172132.

[10] T. L. Korkea-Aho, J. Heikkinen, K. D. Thompson, A. V. Wright, and B. Austin, “Pseudomonas sp. M174 Inhibits the Fish Pathogen Flavobacterium psychrophilum,” Journal of Applied Microbiology 111, no. 2 (2011): 266–277, https://doi.org/10.1111/j.1365-2672.2011.05044.x.

[11] S. H. Hoseinifar, Y. Z. Sun, and C. M. Caipang, “Short-Chain Fatty Acids as Feed Supplements for Sustainable Aquaculture: An Updated View,” Aquaculture Research 48, no. 4 (2017): 1380–1391, https://doi.org/10.1111/are.13239.

[12] M. A. O. Dawood, N. M. Eweedah, E. M. Moustafa, and E. M. Farahat, “Probiotic Effects of Aspergillus oryzae on the Oxidative Status, Heat Shock Protein, and Immune Related Gene Expression of Nile tilapia (Oreochromis niloticus) Under Hypoxia Challenge,” Aquaculture 520 (2020): 734669, https://doi.org/10.1016/j.aquaculture.2019.734669.

[13] H. Van Doan, C. Lumsangkul, O. U. Ruangwong, et al., “Effects of Host-Associated Probiotic Bacillus altitudinis B61-34b on Growth Performance, Immune Response and Disease Resistance of Nile tilapia (Oreochromis niloticus) Raised Under Biofloc System,” Aquaculture Nutrition 27, no. S1 (2021): 61–72, https://doi.org/10.1111/anu.13410.

[14] W. J. Jang, K. B. Lee, M. H. Jeon, et al., “Characteristics and Biological Control Functions of Bacillus sp. PM8313 as a Host-Associated Probiotic in Red Sea Bream (Pagrus major) Aquaculture,” Animal Nutrition 12 (2023): 20–31, https://doi.org/10.1016/j.aninu.2022.08.011.

[15] H. Van Doan, S. H. Hoseinifar, C. Khanongnuch, et al., “Host-associated Probiotics Boosted Mucosal and Serum Immunity, Disease Resistance and Growth Performance of Nile tilapia (Oreochromis niloticus),” Aquaculture 491 (2018): 94–100, https://doi.org/10.1016/j.aquaculture.2018.03.019.

[16] C. C. Lazado, C. M. A. Caipang, and E. G. Estante, “Prospects of Host-Associated Microorganisms in Fish and Penaeids as Probiotics With Immunomodulatory Functions,” Fish & Shellfish Immunology 45, no. 1 (2015): 2–12, https://doi.org/10.1016/j.fsi.2015.02.02.

[17] A. L. Pribyl, P. Hugenholtz, and M. A. Cooper, “A Decade of Advances in Human Gut Microbiome-Derived Biotherapeutics,” Nature Microbiology 10, no. 2 (2025): 301–312, https://doi.org/10.1038/s41564-024-01896-3.

[18] M. T. Sorbara and E. G. Pamer, “Microbiome-Based Therapeutics,” Nature Reviews Microbiology 20, no. 6 (2022): 365–380, https://doi.org/10.1038/s41579-021-00667-9.

[19] K. M. Wanka, T. Damerau, B. Costas, A. Krueger, C. Schulz, and S. Wuertz, “Isolation and Characterization of Native Probiotics for Fish Farming,” BMC Microbiology 18, no. 1 (2018): 119, https://doi.org/10.1186/s12866-018-1260-2.

[20] B. A. Block, H. Dewar, S. B. Blackwell, et al., “Migratory Movements, Depth Preferences, and Thermal Biology of Atlantic Bluefin Tuna,” Science 293, no. 5533 (2001): 1310–1314, https://doi.org/10.1126/science.1061197.

[21] Y. Zou, D. Wu, L. Wei, et al., “Mucus-Associated Microbiotas Among Different Body Sites of Wild Tuna From the South China Sea,” Frontiers in Marine Science 9 (2023): 1073264, https://doi.org/10.3389/fmars.2022.1073264.

[22] Y. Zou, Y. J. Zhang, D. Wu, et al., “Multi-Omics Analysis Revealed the Differences in Lipid Metabolism of Gut Between Adult and Juvenile Yellowfin Tuna (Thunnus albacares),” Frontiers in Microbiology 14 (2024): 1326247, https://doi.org/10.3389/fmicb.2023.1326247.

[23] E. Gadoin, C. Desnues, E. R. D'Orbcastel, et al., “Fishing for the Microbiome of Tropical Tuna,” Microbial Ecology 86, no. 1 (2023): 742–755, https://doi.org/10.1007/s00248-022-02096-4.

[24] Y. Ni, Y. Zhang, L. Zheng, et al., “Bifidobacterium and Lactobacillus Improve Inflammatory Bowel Disease in Zebrafish of Different Ages by Regulating the Intestinal Mucosal Barrier and Microbiota,” Life Sciences 324 (2023): 121699, https://doi.org/10.1016/j.lfs.2023.121699.

[25] W. J. Jang, S. K. Kim, S. Y. Park, et al., “Effect of Host-Associated Bacillus-Supplemented Artificial Diets on Growth, Survival Rate, and Gene Expression in Early-Stage Eel Larvae (Anguilla japonica),” Fishes 8, no. 5 (2023): 247, https://doi.org/10.3390/fishes8050247.

[26] O. B. Braïek, S. Morandi, P. Cremonesi, S. Smaoui, K. Hani, and T. Ghrairi, “Safety, Potential Biotechnological and Probiotic Properties of Bacteriocinogenic Enterococcus lactis Strains Isolated From Raw Shrimps,” Microbial Pathogenesis 117 (2018): 109–117, https://doi.org/10.1016/j.micpath.2018.02.021.

[27] S. F. Chen, Y. Q. Zhou, Y. R. Chen, and J. Gu, “Fastp: An Ultra-Fast All-In-One FASTQ Preprocessor,” Bioinformatics 34, no. 17 (2018): i884–i890, https://doi.org/10.1093/bioinformatics/bty560.

[28] I. Sanahuja, A. Ruiz, J. P. Firmino, et al., “Debaryomyces hansenii Supplementation in Low Fish Meal Diets Promotes Growth, Modulates Microbiota and Enhances Intestinal Condition in Juvenile Marine Fish,” Journal of Animal Science and Biotechnology 14, no. 1 (2023): 90, https://doi.org/10.1186/s40104-023-00895-4.

[29] E. Bolyen, J. R. Rideout, M. R. Dillon, et al., “Reproducible, Interactive, Scalable and Extensible Microbiome Data Science Using QIIME 2,” Nature Biotechnology 37, no. 8 (2019): 852–857, https://doi.org/10.1038/s41587-019-0209-9.

[30] G. M. Douglas, V. J. Maffei, J. R. Zaneveld, et al., “PICRUSt2 for Prediction of Metagenome Functions,” Nature Biotechnology 38, no. 6 (2020): 685–688, https://doi.org/10.1038/s41587-020-0548-6.

[31] K. J. Livak and T. D. Schmittgen, “Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2^−ΔΔCT Method,” Methods 25, no. 4 (2001): 402–408, https://doi.org/10.1006/meth.2001.1262.

[32] J. J. Minich, C. Power, M. Melanson, et al., “The Southern Bluefin Tuna Mucosal Microbiome Is Influenced by Husbandry Method, Net Pen Location, and Anti-Parasite Treatment,” Frontiers in Microbiology 11 (2020): 2015, https://doi.org/10.3389/fmicb.2020.02015.

[33] E. Gadoin, L. Durand, A. Guillou, et al., “Does the Composition of the Gut Bacteriome Change During the Growth of Tuna?,” Microorganisms 9, no. 6 (2021): 1157, https://doi.org/10.3390/microorganisms9061157.

[34] A. Nemec, L. Krizova, M. Maixnerova, O. Sedo, S. Brisse, and P. G. Higgins, “Acinetobacter seifertii sp. nov., a Member of the Acinetobacter calcoaceticus-Acinetobacter baumannii Complex Isolated From Human Clinical Specimens,” International Journal of Systematic and Evolutionary Microbiology 65, no. Pt_3 (2015): 934–942, https://doi.org/10.1099/ijs.0.000043.

[35] M. Marija, B. Iris, F. Djordje, et al., “Shortening of the Lactobacillus paracasei subsp. Paracasei BGNJ1-64 AggLb Protein Switches Its Activity From Auto-Aggregation to Biofilm Formation,” Frontiers in Microbiology 7 (2016): 1–14, https://doi.org/10.3389/fmicb.2016.01422.

[36] K. Arellano-Ayala, F. J. Ascencio-Valle, P. Gutiérrez-González, Y. Estrada-Girón, M. R. Torres-Vitela, and M. E. Macías-Rodríguez, “Hydrophobic and Adhesive Patterns of Lactic Acid Bacteria and Their Antagonism Against Foodborne Pathogens on Tomato Surface (Solanum lycopersicum L.),” Journal of Applied Microbiology 129, no. 4 (2020): 876–891, https://doi.org/10.1111/jam.14672.

[37] J. Isenring, A. Geirnaert, C. Lacroix, and M. J. A. Stevens, “Bistable Auto-Aggregation Phenotype in Lactiplantibacillus plantarum Emerges After Cultivation in In Vitro Colonic Microbiota,” BMC Microbiology 21, no. 1 (2021): 268, https://doi.org/10.1186/s12866-021-02331-x.

[38] S. Jinendiran, S. Boopathi, N. Sivakumar, and G. Selvakumar, “Functional Characterization of Probiotic Potential of Novel Pigmented Bacterial Strains for Aquaculture Applications,” Probiotics and Antimicrobial Proteins 11, no. 1 (2019): 186–197, https://doi.org/10.1007/s12602-017-9353-z.

[39] J. K. Gustafsson and M. E. V. Johansson, “The Role of Goblet Cells and Mucus in Intestinal Homeostasis,” Nature Reviews Gastroenterology & Hepatology 19, no. 12 (2022): 785–803, https://doi.org/10.1038/s41575-022-00675-x.

[40] A. Bunnoy, U. Na-Nakorn, and P. Srisapoome, “Probiotic Effects of a Novel Strain, Acinetobacter KU011TH, on the Growth Performance, Immune Responses, and Resistance Against Aeromonas hydrophila of Bighead Catfish (Clarias Macrocephalus Günther, 1864),” Microorganisms 7, no. 12 (2019): 613, https://doi.org/10.3390/microorganisms7120613.

[41] A. Pastor, G. Federici, E. Bertini, and F. Piemonte, “Analysis of Glutathione: Implication in Redox and Detoxification,” Clinica Chimica Acta 333, no. 1 (2003): 19–39, https://doi.org/10.1016/S0009-8981(03)00200-6.

[42] Y. Zhang, X. Liang, S. He, H. Feng, and L. Li, “Dietary Supplementation of Exogenous Probiotics Affects Growth Performance and Gut Health by Regulating Gut Microbiota in Chinese Perch (Siniperca chuatsi),” Aquaculture 547 (2022): 737405, https://doi.org/10.1016/j.aquaculture.2021.737405.

[43] K. Martinez-Guryn, N. Hubert, K. Frazier, et al., “Small Intestine Microbiota Regulate Host Digestive and Absorptive Adaptive Responses to Dietary Lipids,” Cell Host & Microbe 23, no. 4 (2018): 458–469, https://doi.org/10.1016/j.chom.2018.03.011.

[44] C. Liu, N. Ma, Y. Feng, et al., “From Probiotics to Postbiotics: Concepts and Applications,” Animal Research and One Health 1, no. 1 (2023): 92–114, https://doi.org/10.1002/aro2.7.

[45] H. Zhang, Q. W. Ding, A. R. Wang, et al., “Effects of Dietary Sodium Acetate on Food Intake, Weight Gain, Intestinal Digestive Enzyme Activities, Energy Metabolism and Gut Microbiota in Cultured Fish: Zebrafish as a Model,” Aquaculture 523 (2020): 735188, https://doi.org/10.1016/j.aquaculture.2020.735188.

[46] M. Yousefi, S. M. Hoseini, E. V. Kulikov, E. V. Kharlitskaya, N. V. Petukhov, and N. G. Khomenets, “Dietary Propionate Administration Improves Growth Performance, Hepatic Lipid Deposition, and Intestinal Activity of Digestive Enzymes, Inflammation, Bacterial Population, and Antioxidant Capacity in Rainbow Trout, Oncorhynchus mykiss,” Aquaculture 578 (2023): 740099, https://doi.org/10.1016/j.aquaculture.2023.740099.

[47] X. Li, S. Wang, M. Zhang, and M. Li, “Sodium Butyrate Improves the Growth Performance, Intestinal Immunity, and Ammonia Tolerance of Yellow Catfish Pelteobagrus fulvidraco by Increasing the Relative Abundance of Candidatus_Arthromitus,” Aquaculture 580 (2024): 740359, https://doi.org/10.1016/j.aquaculture.2023.740359.

[48] R. Safari, S. H. Hoseinifar, and M. Kavandi, “Modulation of Antioxidant Defense and Immune Response in Zebra Fish (Danio rerio) Using Dietary Sodium Propionate,” Fish Physiology and Biochemistry 42, no. 6 (2016): 1733–1739, https://doi.org/10.1007/s10695-016-0253-z.

[49] A. Bedford and J. Gong, “Implications of Butyrate and Its Derivatives for Gut Health and Animal Production,” Animal Nutrition 4, no. 2 (2018): 151–159, https://doi.org/10.1016/j.aninu.2017.08.010.

[50] G. F. A. Jesus, S. A. Pereira, M. S. Owatari, et al., “Protected Forms of Sodium Butyrate Improve the Growth and Health of Nile tilapia Fingerlings During Sexual Reversion,” Aquaculture 499 (2019): 119–127, https://doi.org/10.1016/j.aquaculture.2018.09.027.

[51] G. Terova, N. Díaz, S. Rimoldi, C. Ceccotti, E. Gliozheni, and F. Piferrer, “Effects of Sodium Butyrate Treatment on Histone Modifications and the Expression of Genes Related to Epigenetic Regulatory Mechanisms and Immune Response in European Sea Bass (Dicentrarchus Labrax) Fed a Plant-Based Diet,” PLoS One 11, no. 7 (2016): e0160332, https://doi.org/10.1371/journal.pone.0160332.

[52] S. Y. Gao, X. Y. Zhao, B. Niu, K. Chang, and W. J. Chen, “Dietary Sodium Butyrate Supplementation Attenuates the Detrimental Effects of High-Fat Diets on Growth Performance, Liver Health, and Disease Resistance in Grass Carp,” North American Journal of Aquaculture 84, no. 3 (2022): 392–401, https://doi.org/10.1002/naaq.10250.

[53] Y. Fan, X. Wang, Y. H. Wang, et al., “Effect of Dietary Bacillus licheniformis on Growth, Intestinal Health, and Resistance to Nitrite Stress in Pacific White Shrimp Litopenaeus vannamei,” Aquaculture International 29, no. 6 (2021): 2555–2573, https://doi.org/10.1007/s10499-021-00764-9.

[54] S. M. Innis, “Metabolic Programming of Long-Term Outcomes Due to Fatty Acid Nutrition in Early Life,” Maternal and Child Nutrition 7, no. S2 (2011): 112–123, https://doi.org/10.1111/j.1740-8709.2011.00318.x.

[55] J. P. Otis, E. M. Zeituni, J. H. Thierer, et al., “Zebrafish as a Model for Apolipoprotein Biology: Comprehensive Expression Analysis and a Role for ApoA-IV in Regulating Food Intake,” Disease Models & Mechanisms 8, no. 3 (2015): 295–309, https://doi.org/10.1242/dmm.018754.

[56] X. C. Jiang, “Phospholipid Transfer Protein: Its Impact on Lipoprotein Homeostasis and Atherosclerosis,” Journal of Lipid Research 59, no. 5 (2018): 764–771, https://doi.org/10.1194/jlr.R082503.

[57] B. S. Graham, D. Grubbs, K. Holland, and B. N. Popp, “A Rapid Ontogenetic Shift in the Diet of Juvenile Yellowfin Tuna From Hawaii,” Marine Biology 150, no. 4 (2007): 647–658, https://doi.org/10.1007/s00227-006-0360-y.

[58] A. L. Nadal, W. Ikeda-Ohtsubo, D. Sipkema, et al., “Feed, Microbiota, and Gut Immunity: Using the Zebrafish Model to Understand Fish Health,” Frontiers in Immunology 11 (2020): 114, https://doi.org/10.3389/fimmu.2020.00114.

[59] X. Zhong, J. Li, F. Lu, J. Zhang, and L. Guo, “Application of Zebrafish in the Study of the Gut Microbiome,” Animal Models and Experimental Medicine 5, no. 4 (2022): 323–336, https://doi.org/10.1002/ame2.12227.

[60] Z. Lu, Q. Li, E. Yongo, J. Xiao, and Z. Guo, “Comparative Energy Metabolism in Red and White Muscles of Juvenile Yellowfin Tuna, Thunnus albacore,” Frontiers in Marine Science 12 (2025): 1585044, https://doi.org/10.3389/fmars.2025.1585044.

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