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Microorganisms
Volume 13
Issue 11
10.3390/microorganisms13112452
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This is an early access version, the complete PDF, HTML, and XML versions will be available soon.
Article

Potential Bacterial Biomarkers Associated with Penaeus stylirostris Shrimp Larvae to Infer Holobiont Health and Dysbiosis Across Larvae Stages

by
Nolwenn Callac
1,*,
Carolane Giraud
1,
Valérie Perez
1,2,
Dominique Ansquer
1,
Jean-Sébastien Lam
1,
Viviane Boulo
1,3,
Dominique Pham
1 and
Nelly Wabete
1
1
Ifremer, IRD, Université de la Nouvelle-Calédonie, Université de La Réunion, UMR 9220 ENTROPIE, Nouméa 98800, New Caledonia
2
Ifremer, MASAE Microbiologie Aliment Santé Environnement, 44000 Nantes, France
3
Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, 34090 Montpellier, France
*
Author to whom correspondence should be addressed.
Microorganisms 2025, 13(11), 2452; https://doi.org/10.3390/microorganisms13112452 (registering DOI)
Submission received: 10 July 2025 / Revised: 29 September 2025 / Accepted: 1 October 2025 / Published: 25 October 2025
(This article belongs to the Section Microbiomes)
Versions Notes

Abstract

Microbiota play a pivotal role in holobionts, influencing nutrient intake, growth, and overall health. In this context, microbial dysbiosis of Penaeus stylirostris larvae seem to be associated with huge larval mortalities in hatcheries in New Caledonia. To understand larval dysbiosis establishment, our purpose was to identify bacterial biomarkers, as bioindicators, related to a given larval stage and health condition. To this end, larvae were sampled daily to access their active microbiota through sequencing of the V4 region of the 16S rRNA molecule, while their stage and their health were also observed. We identified three biomarkers strongly related to healthy zoea, and some may act as probiotics or play key roles in larval ontogeny and nutrition. We also found six biomarkers linked to unhealthy zoea and eight related to healthy mysis. Biomarkers were mostly related to diseased shrimps (Lewinella) or healthy shrimps (Cognitishimia, Thalassolituus) or were known to prey on cells (P30B-42), suggesting that the larvae might be battling against detrimental conditions. No biomarker related to unhealthy mysis was identified. Finally, our data showed that bacterial bioindicators could be used as an effective biosurveillance proxy in hatcheries, to monitor larval development, and as an early warning tool to predict rearing outcomes.
Keywords: microbiome; pathobiome; active microbiota; shrimp larvae rearing; biosurveillance microbiome; pathobiome; active microbiota; shrimp larvae rearing; biosurveillance

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MDPI and ACS Style

Callac, N.; Giraud, C.; Perez, V.; Ansquer, D.; Lam, J.-S.; Boulo, V.; Pham, D.; Wabete, N. Potential Bacterial Biomarkers Associated with Penaeus stylirostris Shrimp Larvae to Infer Holobiont Health and Dysbiosis Across Larvae Stages. Microorganisms 2025, 13, 2452. https://doi.org/10.3390/microorganisms13112452

AMA Style

Callac N, Giraud C, Perez V, Ansquer D, Lam J-S, Boulo V, Pham D, Wabete N. Potential Bacterial Biomarkers Associated with Penaeus stylirostris Shrimp Larvae to Infer Holobiont Health and Dysbiosis Across Larvae Stages. Microorganisms. 2025; 13(11):2452. https://doi.org/10.3390/microorganisms13112452

Chicago/Turabian Style

Callac, Nolwenn, Carolane Giraud, Valérie Perez, Dominique Ansquer, Jean-Sébastien Lam, Viviane Boulo, Dominique Pham, and Nelly Wabete. 2025. "Potential Bacterial Biomarkers Associated with Penaeus stylirostris Shrimp Larvae to Infer Holobiont Health and Dysbiosis Across Larvae Stages" Microorganisms 13, no. 11: 2452. https://doi.org/10.3390/microorganisms13112452

APA Style

Callac, N., Giraud, C., Perez, V., Ansquer, D., Lam, J.-S., Boulo, V., Pham, D., & Wabete, N. (2025). Potential Bacterial Biomarkers Associated with Penaeus stylirostris Shrimp Larvae to Infer Holobiont Health and Dysbiosis Across Larvae Stages. Microorganisms, 13(11), 2452. https://doi.org/10.3390/microorganisms13112452

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