Integrated transcriptomic and microbiota analyses reveal growth-related intestinal responses to feeding strategies in Nibea coibor

Abstract

Feeding strategies critically influence intestinal homeostasis in farmed fish, however, their underlying regulatory mechanisms remain poorly understood. Nibea coibor, a fish species with local characteristics in Zhanjiang (Guangdong Province, China), was chosen as the experimental model for studying feeding strategies. This study employed integrated multi-omics analyses to systematically dissect the multidimensional regulatory networks of four different feeding strategies on intestinal morphology, transcriptome, and microbiota in Nibea coibor. Feeding strategies reshaped gut microbiota composition and significantly altered gene expression. Compared with daytime feeding (DF), continuous fasting (CF) induced villus atrophy and goblet cell loss, disrupted microbial homeostasis (Vibrio, Actinomyces, Photobacterium, and Akkermansia upregulation), and triggered transcriptional reprogramming (pfkfb4, pla2g12b, rptor, and pecam1 downregulation; col1a upregulation). In contrast, intermittent fasting (IF, two-day fasting/one-day feeding) achieved optimal intestinal health with the highest goblet cell density, villus height, and microbial diversity, suggesting microbiota-mediated gut plasticity and adaptation. Nighttime feeding (NF) elicited minor downregulation of energy metabolism genes without causing significant morphological or microbial alterations, indicating limited short-term circadian effects. Finally, the PLS-PM model delineated the cascade regulatory relationships linking gut microbiota, transcriptome, and intestinal morphology. These findings highlight intermittent fasting as a promising strategy to sustain intestinal homeostasis through microbiota-host synergy, while underscoring the risks of prolonged fasting-induced metabolic and barrier dysfunction. This work provides valuable insights for refining feeding protocols in marine fish aquaculture, especially N. coibor.

Keywords

Nibea coibor / Feeding strategies / Intestinal homeostasis / Microbiota / PLS-PM

References

[1]  Macêdo ÉSD, Almeida OCD, Lucena JEC, Torres MBADM, Bicudo ÁJDA. Combined effects of dietary starch:protein ratios and short cycles of fasting/refeeding on nile tilapia growth and liver health. Aquaculture Res. 2021;52(3):1139–49.

[2] Alterovitz G, Xiang M, Mohan M, Ramoni MF. GO pad: the gene ontology partition database. Nucleic Acids Res, 2007, 35: D322-327.

[3] Argüello-Guevara W, Apolinario W, Bohórquez-Cruz M, Reinoso S, Rodríguez S, Sonnenholzner S. Effects of intermittent feeding on water quality, skin parasites, feed consumption, and growth performance of juvenile longfin yellowtail Seriola rivoliana (Valenciennes, 1833). Aquacult Res, 2018, 49(11): 3586-3594.

[4] 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;37:1. https://doi.org/10.1038/s41587-019-0209-9.

[5] Chen CC, Lin CY, Lu HY, Liou CH, Ho YN, Huang CW, et al. Transcriptomics and gut microbiome analysis of the edible herb Bidens pilosa as a functional feed additive to promote growth and metabolism in tilapia (Oreochromis spp.). BMC Genomics. 2024;25(1):785. https://doi.org/10.1186/s12864-024-10674-8.

[6] Chen X, Yi H, Liu S, Zhang Y, Su Y, Liu X, Bi S, Lai H, Zeng Z, Li G. Promotion of pellet-feed feeding in mandarin fish (Siniperca chuatsi) by Bdellovibrio bacteriovorus is influenced by immune and intestinal flora. Aquaculture, 2021, 542: 736864.

[7] Chen YY, Wu XY, Lai JS, Liu Y, Song MJ, Li FY, Gong Q. Comprehensive transcriptome analysis reveals the effect of feeding rhythm on the immunity and metabolism of Acipenser dabryanus. Fish Shellfish Immunol, 2022, 122: 276-287.

[8] Dai T, Rosario SR, Katsuta E, Sawant Dessai A, Paterson EJ, Novickis AT, Cortes Gomez E, Zhu B, Liu S, Wang H, Abrams SI, Seshadri M, Bshara W, Dasgupta S. Hypoxic activation of PFKFB4 in breast tumor microenvironment shapes metabolic and cellular plasticity to accentuate metastatic competence. Cell Rep, 2022, 41(10): 111756.

[9] Dar SA, Srivastava PP, Varghese T, Gupta S, Gireesh-Babu P, Krishna G. Effects of starvation and refeeding on expression of ghrelin and leptin gene with variations in metabolic parameters in Labeo rohita fingerlings. Aquaculture, 2018, 484: 219-227.

[10] Dawood MAO, Amer AA, Gouda AH, Gewaily MS. Interactive effects of cyclical fasting, refeeding, and dietary protein regimes on the growth performance, blood health, and intestinal histology of Nile tilapia (Oreochromis niloticus). Aquaculture. 2023;573:739620. https://doi.org/10.1016/j.aquaculture.2023.739620.

[11] Drew RE, Rodnick KJ, Settles M, Wacyk J, Churchill E, Powell MS, et al. Effect of starvation on transcriptomes of brain and liver in adult female zebrafish (Danio rerio). Physiol Genomics. 2008;35:283–95. https://doi.org/10.1152/physiolgenomics.90213.2008.

[12] Einen O, Waagan B, Thomassen MS. Starvation prior to slaughter in Atlantic salmon (Salmo salar) - I. Effects on weight loss, body shape, slaughter- and fillet-yield, proximate and fatty acid composition. Aquaculture. 1998;166(1–2):85–104. https://doi.org/10.1016/S0044-8486(98)00279-8.

[13] Falahatkar B, Sharahi AR, Movafagh AN, Moludinia B. Effect of restricted feeding and refeeding on the compensatory growth and serum metabolites of juvenile Siberian sturgeon (Acipenser baerii). Acta Biochim Pol, 2025, 14(72): 14761.

[14] Fan SL, Li HD, Zhao R. Effects of normoxic and hypoxic conditions on the immune response and gut microbiota of Bostrichthys sinensis. Aquaculture. 2020;525:735336. https://doi.org/10.1016/j.aquaculture.2020.735336.

[15] Feng WR, Li JL, Xu YF, Jiang G, Su SY, Zhang ZH, et al. Effects of starvation-refeeding on antioxidant status, metabolic function, and adaptive response in the muscle of Cyprinus carpio. Aquaculture. 2025;602:742372. https://doi.org/10.1016/j.aquaculture.2025.742372.

[16] Flood MJ, Noble C, Kagaya R, Damsgård B, Purser GJ, Tabata M. Examining the daily feeding rhythms of amago Oncorhynchus masou masou using self-feeding systems. Aquaculture. 2011;318:244–7. https://doi.org/10.1016/j.aquaculture.2011.05.007.

[17] Frantz C, Stewart KM, Weaver VM. The extracellular matrix at a glance. J Cell Sci. 2010;123(Pt 24):4195–200.

[18] Fu LL, Cai WJ, Liu HK, Hooft JM, Øverland M, Han D, et al. Effects of 4-octyl itaconate and dimethyl fumarate on growth performance, intestinal microbiota, intestinal and hepatopancreas health of juvenile gibel carp (Carassius gibelio). Aquaculture. 2023;569:739376. https://doi.org/10.1016/j.aquaculture.2023.739376.

[19] Fu Q, Li YQ, Zhao SC, Wang HJ, Zhao CY, Zhang P, et al. Comprehensive identification and expression profiling of immune-related lncRNAs and their target genes in the intestine of turbot (Scophthalmus maximus L.) in response to Vibrio anguillarum infection. Fish Shellfish Immunol. 2022;130:233–43.

[20] Huang YS, Lin ZD, Rong H, Hao ML, Zhu DS, Li SK, et al. Effects of conjugated linoleic acid on growth, body composition, antioxidant status, lipid metabolism and immunity parameters of juvenile Chu's croaker, Nibea coibor. Aquaculture Res. 2017b;49(1):546–56. https://doi.org/10.1111/are.13486.

[21] Huang YS, Lin ZD, Rong H, Hao ML, Zou WG, Li SK, et al. Cloning, tissue distribution, functional characterization and nutritional regulation of Δ6 fatty acyl desaturase in chu's croaker Nibea coibor. Aquaculture. 2017a;479:208–16. https://doi.org/10.1016/j.aquaculture.2017.05.041.

[22] Islam SMM, Rohani MF, Shahjahan M. Probiotic yeast enhances growth performance of Nile tilapia (Oreochromis niloticus) through morphological modifications of intestine. Aquac Rep. 2021;21:100800. https://doi.org/10.1016/j.aqrep.2021.100800.

[23] Kanehisa M, Goto S, Kawashima S, Nakaya A. The KEGG databases at genomenet. Nucleic Acids Res, 2002, 30: 42-46.

[24] Kar S, Maji N, Sen K, Roy S, Maity A, Ghosh Dastidar S, et al. Reprogramming of glucose metabolism via PFKFB4 is critical in FGF16-driven invasion of breast cancer cells. Biosci Rep. 2023;43(8). https://doi.org/10.1042/BSR20230677.

[25] Kim JJ, Khan WI. Goblet cells and mucins: role in innate defense in enteric infections. Pathogens (Basel, Switzerland). 2013;2(1):55–70.

[26] Köprücü S. Histological and histochemical characterization of the digestive tract of European catfish (Silurus glanis Linnaeus, 1758). Cell Mol Biol. 2016.

[27] Kormas KA, Meziti A, Mente E, Frentzos A. Dietary differences are reflected on the gut prokaryotic community structure of wild and commercially reared sea bream (Sparus aurata). Microbiol Open, 2014, 3(5): 718-728.

[28] Krogdahl A, Bakke-McKellep AM. Fasting and refeeding cause rapid changes in intestinal tissue mass and digestive enzyme capacities of Atlantic salmon (Salmo salar L.). Comparative biochemistry and physiology. Part a, Molecular & Integrative Physiology. 2005;141:450–60. https://doi.org/10.1016/j.cbpb.2005.06.002.

[29] Li TT, Qi MT, Gatesoupe FJ, Tian DC, Jin WH, Li J, et al. Adaptation to fasting in crucian carp (Carassius auratus): gut microbiota and its correlative relationship with immune function. Microb Ecol. 2019;78(1):6–19. https://doi.org/10.1007/s00248-018-1275-0.

[30] Li ZZ, Tran NT, Ji PN, Sun ZQ, Wen XB, Li SK. Effects of prebiotic mixtures on growth performance, intestinal microbiota and immune response in juvenile chu’s croaker, Nibea coibor. Fish Shellfish Immunol. 2019;89:564–73. https://doi.org/10.1016/j.fsi.2019.04.025.

[31] Lin F, Yuan YY, Ye XK, Lv JH, Liu X, Guo HJ, et al. Characterization and role of connective tissue growth factor gene in collagen synthesis in swim bladder of chu's croaker (Nibea coibor). International Journal of Biological Macromolecules. 2023;227:1336–45. https://doi.org/10.1016/j.ijbiomac.2022.12.010.

[32] Lin F, Zhang HR, Yu J, Yu CQ, Chen CY, Sun ZJ, et al. Effects of dietary selenium on growth performance, antioxidative status and tissue selenium deposition of juvenile Chu’s croaker (Nibea coibor). Aquaculture. 2021;536:736439. https://doi.org/10.1016/j.aquaculture.2021.736439.

[33] Liu B, Guo HY, Liu BS, Zhang N, Yang JW, Guo L, et al. Starvation and refeeding influence the growth, biochemical index, intestinal microbiota, and transcriptomic profiles of golden pompano Trachinotus ovatus (Linnaeus 1758). Front Marine Sci. 2022;9:998190. https://doi.org/10.3389/fmars.2022.998190.

[34] Liu JL, Zhong YF, Luo XM, Ma YF, Liu JX, Wang HF. Intermittent fasting reshapes the gut microbiota and metabolome and reduces weight gain more effectively than melatonin in mice. Frontiers in Nutrition. 2021;8:784681. https://doi.org/10.3389/fnut.2021.784681.

[35] Liu XC, Shi HR, He Q, Lin FM, Wang Q, Xiao SQ, et al. Effect of starvation and refeeding on growth, gut microbiota and non-specific immunity in hybrid grouper (Epinephelus fuscoguttatus♀×E. lanceolatus♂). Fish Shellfish Immunol. 2020. https://doi.org/10.1016/j.fsi.2019.11.055.

[36] Long SF, Ding T, Zheng YL, Shao JM, Liu Y, Wang QL. USP5 motivates immunosuppressive microenvironment in multiple myeloma by activating STAT2-PFKFB4-mediated glycolysis. Cancer Immunol Immunother. 2025;74(6):180. https://doi.org/10.1007/s00262-025-04031-1.

[37] Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2. Genome Biol. 2014;15:550. https://doi.org/10.1186/PREACCEPT-8897612761307401.

[38] Lu C, Qiao PY, Fu RH, Wang YD, Lu JY, Ling X, et al. Phosphorylation of PFKFB4 by PIM2 promotes anaerobic glycolysis and cell proliferation in endometriosis. Cell Death Dis. 2024;15(7):469. https://doi.org/10.1038/s41419-024-06613-w.

[39] Lu XY, Wei YL, Sun J, Xiao B, Zhang XY, Li WH, et al. A comparative study of three nucleic acid integrity assay systems. Biopreservation and biobanking. 2023;21(6):624–30. https://doi.org/10.1089/bio.2022.0171.

[40] Ma LH, Terrell M, Brown J, Garcia AC, Elshikha A, Morel L. TLR7/TLR8 activation and susceptibility genes synergize to breach gut barrier in a mouse model of lupus. Frontiers in Immunology. 2023;14:1187145. https://doi.org/10.3389/fimmu.2023.1187145.

[41] Mao XZ, Cai T, Olyarchuk JG, Wei LP. Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics, 2005, 21(19): 3787-3793.

[42] McGuckin MA, Lindén SK, Sutton P, Florin TH. Mucin dynamics and enteric pathogens. Nat Rev Microbiol. 2011;9:265–78. https://doi.org/10.1038/nrmicro2538.

[43] Moore AM, Munck C, Sommer MOA, Dantas G. Functional metagenomic investigations of the human intestinal microbiota. Front Microbiol. 2011;1:11002.

[44] Okamura Y, Miyanishi H, Kono T, Hikima JI. Identification and expression of phospholipase A2 genes related to transcriptional control in the interleukin-17A/F1 pathway in the intestines of Japanese medaka Oryzias latipes. Fish Shellfish Immunol Rep. 2021;2:100028. https://doi.org/10.1016/j.fsirep.2021.100028.

[45] Palazzotto E, Weber T. Omics and multi-omics approaches to study the biosynthesis of secondary metabolites in microorganisms. Curr Opin Microbiol. 2018;45:109–16.

[46] Pan YX, Tao JS, Zhou J, Cheng J, Chen YH, Xiang J, et al. Effect of starvation on the antioxidative pathway, autophagy, and mitochondrial function in the intestine of Chinese perch Siniperca chuatsi. Aquaculture. 2022;548:737683. https://doi.org/10.1016/j.aquaculture.2021.737683.

[47] Panaro NJ, Yuen PK, Sakazume T, Fortina P, Kricka LJ, Wilding P. Evaluation of DNA fragment sizing and quantification by the Agilent 2100 bioanalyzer. Clin Chem. 2000;46:1851–3. https://doi.org/10.1093/clinchem/46.11.1851.

[48] Parris DJ, Morgan MM, Stewart FJ. Feeding Rapidly Alters Microbiome Composition and Gene Transcription in the Clownfish Gut. Applied and Environmental Microbiology. 2019;85(3):e02479–18. https://doi.org/10.1128/AEM.02479-18.

[49] Pérez-Jiménez A, Guedes MJ, Morales AE, Oliva-Teles A. Metabolic responses to short starvation and refeeding in Dicentrarchus labrax: effect of dietary composition. Aquaculture, 2007, 265(1–4): 325-335.

[50] Peter M, Lv HR, Jiang XQ, Liu YL, Hur JW, Esbon M, et al. Effects of starvation on enzyme activities and intestinal microflora composition in loach (Paramisgurnus dabryanus). Aquaculture Reports. 2020;18:100467. https://doi.org/10.1016/j.aqrep.2020.100467.

[51] Pirarat N, Pinpimai K, Endo M, Katagiri T, Ponpornpisit A, Chansue N, Maita M. Modulation of intestinal morphology and immunity in Nile tilapia (Oreochromis niloticus) by Lactobacillus rhamnosus GC. Res Vet Sci, 2011, 91: e92-97.

[52] Qian BY, Xue LY, Huang HL. Liver transcriptome analysis of the large yellow croaker (Larimichthys crocea) during fasting by using RNA-seq. PLoS ONE. 2016;11:e0150240. https://doi.org/10.1371/journal.pone.0150240.

[53] Qin CJ, Gong Q, Wen ZY, Zou YC, Yuan DY, Shao T, Li HT. Comparative analysis of the liver transcriptome of Pelteobagrus vachellii with an alternative feeding time. Comparative Biochemistry and Physiology D-Genomics & Proteomics, 2017, 22: 131-138.

[54] Qin CJ, Xu J, Gong Q, Wen ZY, Liu Y, Shi QC. Feeding time changed the diurnal composition of intestinal microbiota in Pelteobagrus fulvidraco. J Oceanol Limnol, 2024, 42(6): 2034-2044.

[55] Qu ZQ, Yuan B, Li RJ, Ba XB, Zhuang ZJ, Yi X, et al. Integrated omics analysis reveals the effect of feeding scarcity on the lipid metabolism and apoptosis in Nibea coibor. Aquaculture. 2025;596:741905. https://doi.org/10.1016/j.aquaculture.2024.741905.

[56] 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 Research. 2012;41(D1):D590–6. https://doi.org/10.1093/nar/gks1219.

[57] Roberts RD, Lapworth C, Barker RJ. Effect of starvation on the growth and survival of post-larval abalone (Haliotis iris). Aquaculture, 2001, 200(3–4): 323-338.

[58] Rong H, Zhang HR, Ning LJ, Wu K, Limbu SM, Shi QC, et al. The transforming growth factor beta (TGF-β/Smads) pathway regulates collagen synthesis and deposition in swim bladder of Chu’s croaker (Nibea coibor) stimulated by proline. Aquaculture. 2022;558:738360. https://doi.org/10.1016/j.aquaculture.2022.738360.

[59] Rubio VC, Sánchez-Vázquez FJ, Madrid JA. Nocturnal feeding reduces sea bass (Dicentrarchus labrax, L.) pellet-catching ability. Aquaculture. 2003;220:697–705. https://doi.org/10.1016/S0044-8486(02)00616-6.

[60] Sakyi ME, Cai J, Tang JF, Abarike ED, Xia LQ, Li PF, et al. Effects of starvation and subsequent re-feeding on intestinal microbiota, and metabolic responses in Nile tilapia, Oreochromis niloticus. Aquaculture Reports. 2020;17:100370. https://doi.org/10.1016/j.aqrep.2020.100370.

[61] Silva WDSE, Hisano H, Mattioli CC, Torres IFA, Paes-Leme FDO, Luz RK. Effects of cyclical short-term fasting and refeeding on juvenile Lophiosilurus alexandri, a carnivorous Neotropical catfish. Aquaculture. 2019;505:12–7. https://doi.org/10.1016/j.aquaculture.2019.02.047.

[62] Standen BT, Peggs DL, Rawling MD, Foey A, Davies SJ, Santos GA, et al. Dietary administration of a commercial mixed-species probiotic improves growth performance and modulates the intestinal immunity of tilapia, Oreochromis niloticus. Fish & Shellfish Immunology. 2016;49:427–35. https://doi.org/10.1016/j.fsi.2015.11.037.

[63] Stella L, Santopaolo F, Gasbarrini A, Pompili M, Ponziani FR. Viral hepatitis and hepatocellular carcinoma: from molecular pathways to the role of clinical surveillance and antiviral treatment. World J Gastroenterol, 2022, 28: 2251-2281.

[64] Su YQ, Liu XG, Yi HD, Bi S, Chen XL, Lai H, et al. Effects of starvation and refeeding on growth, biochemical composition, enzyme activities and intestine structure of lined seahorses. Hippocampus Erectus Aquaculture. 2021;548:737733. https://doi.org/10.1016/j.aquaculture.2021.737733.

[65] Sun P, Bao PB, Tang BJ. Transcriptome analysis and discovery of genes involved in immune pathways in large yellow croaker (Larimichthys crocea) under high stocking density stress. Fish & Shellfish Immunology. 2017;68:332–40. https://doi.org/10.1016/j.fsi.2017.07.013.

[66] Sun SM, Su YL, Yu H, Ge XP, Zhang CF. Starvation affects the intestinal microbiota structure and the expression of inflammatory-related genes of the juvenile blunt snout bream, Megalobrama amblycephala. Aquaculture. 2020;517:734764. https://doi.org/10.1016/j.aquaculture.2019.734764.

[67] Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010;28:511–5. https://doi.org/10.1038/nbt.1621.

[68] Tremaroli V, Bäckhed F. Functional interactions between the gut microbiota and host metabolism. Nature. 2012;71(7415):242–9.

[69] Uengwetwanit T, Uawisetwathana U, Arayamethakorn S, Khudet J, Chaiyapechara S, Karoonuthaisiri N, Rungrassamee W. Multi-omics analysis to examine microbiota, host gene expression and metabolites in the intestine of black tiger shrimp (Penaeus monodon) with different growth performance. PeerJ, 2020, 8e9646

[70] Wagner CE, McIntyre PB, Buels KS, Gilbert DM, Michel E. Diet predicts intestine length in Lake Tanganyika’s cichlid fishes. Functional Ecology. 2009.

[71] Wang H, Zhou HX, Jiang H, Hu YT, Li T, Duan GQ. Effect of Starvation on the Serum Physiology, Transcriptome and intestinal microbiota of juvenile largemouth bass (Micropterus salmoides). Aquaculture Research. 2024;2024(1):8961174. https://doi.org/10.1155/2024/8961174.

[72] Wang WZ, Huang JS, Zhang JD, Wang ZL, Li HJ, Amenyogbe E, et al. Effects of hypoxia stress on the intestinal microflora of juvenile of cobia (Rachycentron canadum). Aquaculture. 2021;536:736419. https://doi.org/10.1016/j.aquaculture.2021.736419.

[73] Wei ZL, Zhuang YT, Liu XT, Zou DY, Mai KS, Sun ZZ, et al. Leucine promotes protein synthesis of juvenile white shrimp Litopenaeus vannamei through TOR signaling pathway. Aquaculture. 2023;564:739060. https://doi.org/10.1016/j.aquaculture.2022.739060.

[74] Xia JH, Lin G, Fu GH, Wan ZY, Lee M, Wang L, et al. The intestinal microbiome of fish under starvation. BMC Genomics. 2014;15:266. https://doi.org/10.1186/1471-2164-15-266.

[75] Xie YP, Zhao HF, Lin S, Wang XL, Liu YF, Xie BY. Suppression of certain intestinal microbiota metabolites may lead to gestational diabetes in mice fed a high-fat diet. Frontiers in Microbiology. 2024;15:1473441. https://doi.org/10.3389/fmicb.2024.1473441.

[76] Xie YD, Zhao YF, Shi L, Li W, Chen K, Li M, et al. Gut epithelial TSC1/mTOR controls RIPK3-dependent necroptosis in intestinal inflammation and cancer. J Clin Invest. 2020;130(4):2111–28. https://doi.org/10.1172/JCI133264.

[77] Xu YK, Huang ZW, Zhang BL, Yu CY, Li LS, Li XD, et al. Intestinal bacterial community composition of juvenile Chinese mitten crab Eriocheir sinensis under different feeding times in lab conditions. Sci Rep. 2022;12(1):22206. https://doi.org/10.1038/s41598-022-26785-9.

[78] Ye Q, Gao C, Xiao HR, Ruan SC, Wang YJ, Li XN, et al. Feeding behavior, gut microbiota, and transcriptome analysis reveal individual growth differences in the sea urchin Strongylocentrotus intermedius. Biology. 2024;13:705. https://doi.org/10.3390/biology13090705.

[79] Young MD, Wakefield MJ, Smyth GK, Oshlack A. Gene ontology analysis for RNA-SEQ: accounting for selection bias. Genome Biol. 2010;11:R14. https://doi.org/10.1186/gb-2010-11-2-r14.

[80] Yu WN, Dai WF, Tao Z, Xiong JB. Characterizing the compositional and functional structures of intestinal microflora between healthy and diseased Litopenaeus vannamei. J Fish China, 2018, 42: 399-409

[81] Zhang JJ, Yang HL, Yan YY, Zhang CX, Ye JD, Sun YZ. Effects of fish origin probiotics on growth performance, immune response and intestinal health of shrimp (Litopenaeus vannamei) fed diets with fish meal partially replaced by soybean meal. Aquaculture Nutrition. 2020;26(4):1255–65. https://doi.org/10.1111/anu.13081.

[82] Zhou YF, Gu SW, Li J, Ji P, Zhang YJ, Wu CC, et al. Complete genome analysis of highly pathogenic non-O1/O139 Vibrio cholerae isolated from Macrobrachium rosenbergii reveals pathogenicity and antibiotic resistance-related genes. Front Vet Sci. 2022;9:882885. https://doi.org/10.3389/fvets.2022.882885.

[83] Zou WG, Lin ZD, Huang YS, Limbu SM, Rong H, Yu CQ, et al. Effect of dietary vitamin C on growth performance, body composition and biochemical parameters of juvenile chu's croaker (Nibea coibor). Aquaculture Nutrition. 2019;26. https://doi.org/10.1111/anu.12967.

RIGHTS & PERMISSIONS

The Author(s)