# Topics and Trends in Most Cited Aquaculture disease management and microbiota Papers, Class of 2026

*Canonical URL: https://pri.pepkio.com/top-papers/aquaculture-disease-management-and-microbiota/2026*

## What topics and trends defined most-cited Aquaculture disease management and microbiota research in the Class of 2026?

The 2024 aquaculture disease management and microbiota cohort demonstrates a clear shift toward biofloc technology, metagenomics, and multi-omics host-microbiome profiling. While Nile tilapia and Aeromonas hydrophila remain focal models, research increasingly prioritizes functional antioxidant immunity, relative percent survival, and antibiotic resistance gene mitigation over traditional 16S rRNA surveys.

## At a glance

| Fact | Value |
| --- | --- |
| Field | Aquaculture disease management and microbiota |
| Cohort label | Class of 2026 (2024 publications) |
| Papers analyzed | 6,987 |
| Papers ranked | 20 |
| Top topics in ranked papers | Nile tilapia, Biofloc technology, Antibiotic resistance genes (ARGs), Aeromonas hydrophila, Antioxidant response |
| Publication window | Jan 1, 2024 – Dec 31, 2024 |
| Eligibility | Research articles; reviews excluded |
| Citation window | 18 months post-publication |
| 18m citation range | 20–69 |
| Data source | OpenAlex · Retrieved Jun 2026 |
| License | CC BY 4.0 |

## Rankings

| Rank | Title | Authors | Corresponding authors | Affiliation | Journal | 18m citations | DOI |
| ---: | --- | --- | --- | --- | --- | ---: | --- |
| 1 | Combined exposure of emamectin benzoate and microplastics induces tight junction disorder, immune disorder and inflammation in carp midgut via lysosome/ROS/ferroptosis pathway | Xu Shi, Tong Xu, Meichen Gao, Yanju Bi, Jiaqi Wang, Yilin Yin, Shiwen Xu | Tong Xu, Shiwen Xu | Northeast Agricultural University, China | Water Research | 69 | 10.1016/j.watres.2024.121660 |
| 2 | Probiotics reshape the coral microbiome in situ without detectable off-target effects in the surrounding environment | Nathalia Delgadillo-Ordoñez, Neus Garcias-Bonet, Inês Raimundo, Francisca C García, Helena Villela, Eslam O Osman, Erika P Santoro, Joao Curdia, Joao G D Rosado, Pedro Cardoso, Ahmed Alsaggaf, Adam Barno, Chakkiath Paul Antony, Carolina Bocanegra, Michael L Berumen, Christian R Voolstra, Francesca Benzoni, Susana Carvalho, Raquel S Peixoto | Raquel S. Peixoto | King Abdullah University of Science and Technology, Saudi Arabia | Communications Biology | 46 | 10.1038/s42003-024-06135-3 |
| 3 | Tissue Accumulation and Biotransformation of 6PPD-Quinone in Adult Zebrafish and Its Effects on the Intestinal Microbial Community | Xiao-Liang Liao, Zhi-Feng Chen, Qian-Yi Liu, Jia-Ming Zhou, Wen-Xi Cai, Yujie Wang, Zongwei Cai | Zhifeng Chen, Zongwei Cai | Guangdong University of Technology, China | Environmental Science & Technology | 36 | 10.1021/acs.est.4c01409 |
| 4 | Effects of chronic cold stress and thermal stress on growth performance, hepatic apoptosis, oxidative stress, immune response and gut microbiota of juvenile hybrid sturgeon (Acipenser baerii ♀ × A. schrenkii ♂) | Tianyu Liu, Ling Li, Yanchao Yang, Jiarou Li, Xutong Yang, Lei Li, Ziyao Zheng, Boyu Yang, Peiyu Zhang, Haiyan Liu | Tianyu Liu, Peiyu Zhang, Haiyan Liu | Hebei Normal University, China | Fish & Shellfish Immunology | 34 | 10.1016/j.fsi.2024.110078 |
| 5 | Deciphering the gut microbiome of grass carp through multi-omics approach | Ming Li, Hui Liang, Hongwei Yang, Qianwen Ding, Rui Xia, Jie Chen, Wenhao Zhou, Yalin Yang, Zhen Zhang, Yuanyuan Yao, Chao Ran, Zhigang Zhou | Chao Ran, Zhigang Zhou | Chinese Academy of Agricultural Sciences, China | Microbiome | 31 | 10.1186/s40168-023-01715-7 |
| 6 | TLRs signaling pathway regulation, antibacterial and apoptotic activity of largemouth bass ECSIT during Edwardsiella piscicida infection | Xiangyu Pi, Dong Yan, Yang Xu, Mingzhu Pan, Zisheng Wang, Mingxian Chang, Zhitao Qi | Mingxian Chang, Zhitao Qi | Yancheng Institute of Technology, China | Aquaculture | 31 | 10.1016/j.aquaculture.2024.741615 |
| 7 | Transcriptome profiling of triploid Crassostrea gigas gills indicates the host immune mechanism against bacterial infection | Xiumei Liu, Weijun Wang, Haitao Zhao, Yongjie Wang, Liming Jiang, Enshuo Zhang, Yanwei Feng, Xumin Wang, Jiangyong Qu, Jianmin Yang, Zan Li | Zan Li | Yantai University, China | Comparative Biochemistry and Physiology Part D Genomics and Proteomics | 31 | 10.1016/j.cbd.2024.101392 |
| 8 | The major role of glucocorticoid receptor (GR) in astaxanthin alleviates immune stress in Channa argus lymphocyte | Xiaotian Niu, Chuang Sun, Lei Zhao, Xiu‐Mei Chen, Guiqin Wang, Muyang Li | Guiqin Wang, Muyang Li | Jilin Agricultural University, China | Aquaculture | 29 | 10.1016/j.aquaculture.2024.740637 |
| 9 | The intestinal microbiome and Cetobacterium somerae inhibit viral infection through TLR2-type I IFN signaling axis in zebrafish | Hui Liang, Ming Li, Jie Chen, Wenhao Zhou, Dongmei Xia, Qianwen Ding, Yalin Yang, Zhen Zhang, Chao Ran, Zhigang Zhou | Chao Ran, Zhigang Zhou | Chinese Academy of Agricultural Sciences, China | Microbiome | 28 | 10.1186/s40168-024-01958-y |
| 10 | Efficacy of nutritional selenium nanoparticles on growth performance, immune response, antioxidant capacity, expression of growth and immune-related genes, and post-stress recovery in juvenile Sobaity seabream (Sparidentex hasta) | Seyed Eisa Abdollahi-Mousavi, Saeed Keyvanshokooh, Mansour Torfi Mozanzadeh, Ahmad Ghasemi | Saeed Keyvanshokooh, Mansour Torfi Mozanzadeh | Khorramshahr University of Marine Science and Technology, Iran | Fish & Shellfish Immunology | 25 | 10.1016/j.fsi.2024.109452 |
| 11 | Effects of ammonia nitrogen stress on the physiological, biochemical, and metabolic levels of the gill tissue of juvenile four-finger threadfin (Eleutheronema tetradactylum) | Jing-Hui Jin, Eric Amenyogbe, Ye Yang, Zhong-Liang Wang, Yi Lu, Rui-Tao Xie, Eric Kwabena Droepenu, Jian-Sheng Huang | Jiansheng Huang | Guangdong Ocean University, China | Aquatic Toxicology | 24 | 10.1016/j.aquatox.2024.107049 |
| 12 | Metagenomic approach revealed the mobility and co-occurrence of antibiotic resistomes between non-intensive aquaculture environment and human | Li Tian, Guimei Fang, Guijie Li, Liguan Li, Tong Zhang, Yanping Mao | Yanping Mao | Shenzhen University, China | Microbiome | 22 | 10.1186/s40168-024-01824-x |
| 13 | Advancing fish breeding in aquaculture through genome functional annotation | Ian A. Johnston, Matthew Kent, Pierre Boudinot, Mark Looseley, Luca Bargelloni, Sara Faggion, Gabriela Merino, Garth R Ilsley, Julien Bobe, Costas S. Tsigenopoulos, Joseph Robertson, Peter W. Harrison, Paulino Martı́nez, Diego Robledo, Daniel J. Macqueen, Sigbjørn Lien | Ian A. Johnston, Daniel J. Macqueen | Xelect Ltd, United Kingdom | Aquaculture | 22 | 10.1016/j.aquaculture.2024.740589 |
| 14 | Effects of Lactobacillus plantarum and Bacillus subtilis on growth, immunity and intestinal flora of largemouth bass(Micropterus salmoides) | Wangyang Jin, Lihua Jiang, Siling Hu, Aiyi Zhu | Lihua Jiang, Aiyi Zhu | Zhejiang Ocean University, China | Aquaculture | 22 | 10.1016/j.aquaculture.2024.740581 |
| 15 | The coral pathogen Vibrio coralliilyticus uses a T6SS to secrete a group of novel anti-eukaryotic effectors that contribute to virulence | Shir Mass, Hadar Cohen, Ram Podicheti, Douglas B Rusch, Motti Gerlic, Blake Ushijima, Julia C van Kessel, Eran Bosis, Dor Salomon | Shir Mass, Hadar Cohen, Ram Podicheti, Douglas B. Rusch, Motti Gerlic, Blake Ushijima, Julia C. van Kessel, Eran Bosis, Dor Salomon | Tel Aviv University, Israel | PLoS Biology | 22 | 10.1371/journal.pbio.3002734 |
| 16 | Biological control of a parasite: The efficacy of cleaner fish in salmon farming | Ruth Beatriz Mezzalira Pincinato, Atle Øglend, Martin D. Smith, Frank Asche | Ruth Beatriz Mezzalira Pincinato | University of Stavanger, Norway | Ecological Economics | 22 | 10.1016/j.ecolecon.2024.108359 |
| 17 | Control of Vibrio vulnificus proliferation in the Baltic Sea through eutrophication and algal bloom management | David J. Riedinger, Víctor Fernández‐Juárez, Luis F. Delgado, Theodor Sperlea, Christiane Hassenrück, Daniel P. R. Herlemann, Christian Pansch, Marija Kataržytė, Florian Brück, Alwin Ahrens, Marcin Rakowski, Kasia Piwosz, Angela Stevenson, Thorsten B. H. Reusch, Greta Gyraitė, Detlef Schulz-Bull, Heike Benterbusch-Brockmöller, Sandra Kube, Susann Dupke, Anders F. Andersson, Lasse Riemann, Matthias Labrenz | Matthias Labrenz | Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Germany | Communications Earth & Environment | 21 | 10.1038/s43247-024-01410-x |
| 18 | Effect of non-antibiotic factors on conjugative transfer of antibiotic resistance genes in aquaculture water | Chendong Zhao, Bongkotrat Suyamud, Yue Yuan, Shayok Ghosh, Xulin Xu, Jiangyong Hu | Jiangyong Hu | National University of Singapore, Singapore | Journal of Hazardous Materials | 21 | 10.1016/j.jhazmat.2024.136701 |
| 19 | Effects of Nitrite Stress on the Antioxidant, Immunity, Energy Metabolism, and Microbial Community Status in the Intestine of Litopenaeus vannamei | Yafei Duan, Guowei Zhong, Yuxiu Nan, Yukai Yang, Meng Xiao, Hua Li | Yafei Duan | South China Sea Fisheries Research Institute, China | Antioxidants | 21 | 10.3390/antiox13111318 |
| 20 | Guava and Star gooseberry leaf extracts improve growth performance, innate immunity, intestinal microbial community, and disease resistance in Nile tilapia (Oreochromis niloticus) against Aeromonas hydrophila | Manoj Tukaram Kamble, Sage Chaiyapechara, Krishna R. Salin, Phimsucha Bunphimpapha, B. R. Chavan, Ram C. Bhujel, Seema Vijay Medhe, Aikkarach Kettawan, Parunya Thiyajai, Kim D. Thompson, Nopadon Pirarat | Krishna R. Salin, Nopadon Pirarat | Asian Institute of Technology, Thailand | Aquaculture Reports | 20 | 10.1016/j.aqrep.2024.101947 |

## Topic trends

### What Topics Define the Class of 2026?

The 2024 aquaculture disease management and microbiota research landscape is centered on disease prevention, mucosal immunity, and sustainable microbial interventions in key commercial species. Major farmed aquatic species drive research activity, led by Nile tilapia (Oreochromis niloticus) and Pacific white shrimp (Litopenaeus vannamei), alongside common carp and largemouth bass (Micropterus salmoides). Host health assessments heavily rely on key antioxidant and immune biomarkers, including superoxide dismutase, glutathione peroxidase, catalase, lysozyme, alkaline phosphatase, and inflammatory cytokines like TNF-α and IL-1β. A central focus of high-impact studies is combating bacterial pathogens—most notably Aeromonas hydrophila—and mitigating antibiotic resistance genes (ARGs) in aquatic environments. To address these disease challenges without relying on conventional antibiotics, researchers are actively investigating biofloc technology, dietary probiotic strains such as Bacillus subtilis, and mucosal immune modulation. Furthermore, advanced analytical methodologies including 16S rRNA gene sequencing, whole-genome sequencing, metagenomics, metabolomics, and co-occurrence network analysis have become essential tools for resolving host-microbe interactions and hepatopancreas morphological responses under environmental stressors like ammonia toxicity.

*Leading research themes*

### How Did Topics Shift from the Class of 2025 to the Class of 2026?

Comparing the 2023 and 2024 publication cohorts reveals a distinct methodological evolution from basic microbial profiling toward functional multi-omics and ecological disease mitigation strategies. Sustainable aquaculture interventions experienced notable gains: biofloc technology expanded two-fold (from 2 to 4 papers), while quantitative disease challenge metrics like relative percent survival (RPS) emerged strongly with 3 high-impact publications. High-throughput sequencing technologies transitioned toward deeper resolution, with metagenomics and whole-genome sequencing increasing three-fold (from 1 to 3 papers each), supported by rising adoption of multi-omics integration, metabolomics, and microbial co-occurrence network analysis. Functional host health markers such as glutathione peroxidase, superoxide dismutase, and hepatopancreas morphological evaluation also demonstrated increased attention. Conversely, single-marker descriptive studies experienced relative declines: standard 16S rRNA gene sequencing fell (from 3 to 2 papers, 0.67x fold-change), as did traditional lysozyme assays (from 9 to 4 papers, 0.44x fold-change). Primary disease model studies focusing exclusively on Nile tilapia (from 12 to 6 papers, 0.50x) and Aeromonas hydrophila challenge models (from 6 to 4 papers, 0.67x) yielded share to broader host-microbiome and ARG dynamics across diverse aquaculture systems.

*How topics shifted year over year*

## Cite this ranking

```
Pepkio Research Index (PRI). Topics and Trends in Most Cited Aquaculture disease management and microbiota Papers, Class of 2026. https://pri.pepkio.com/top-papers/aquaculture-disease-management-and-microbiota/2026. Accessed 2026-07-24.

Zheng Su, Tinsley Li, Thematic Shifts in Early-High-Impact Cancer Genomics and Diagnostics Research: A Bibliometric and Semantic Analysis. bioRxiv 2026.07.04.736459; doi: https://doi.org/10.64898/2026.07.04.736459
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