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18 pages, 4611 KiB

Open AccessArticle

Identification, Characterization, and Epidemiological Analysis of Lactococcus garvieae Fish Isolates Obtained in a Period of Eighteen Years

by Ivo Sirakov, Tanya V. Strateva, Vasil Svetoslavov Boyanov, Petya Orozova, Daniel Yordanov, Nikolina Rusenova, Raina Gergova, Svetoslav G. Dimov, Bilyana Sirakova, Vladimir Radosavljević, Liliya Boyanova and Ivan Mitov

Microorganisms 2025, 13(2), 436; https://doi.org/10.3390/microorganisms13020436 - 17 Feb 2025

Viewed by 841

Abstract

Lactococcosis caused by Lactococcus garvieae is a bacterial infection affecting fish with a considerable economic impact. Recently, L. garvieae has established itself as an opportunistic pathogen in humans. The aim of the current study was to test classical and molecular-biological methods for the [...] Read more.

Lactococcosis caused by Lactococcus garvieae is a bacterial infection affecting fish with a considerable economic impact. Recently, L. garvieae has established itself as an opportunistic pathogen in humans. The aim of the current study was to test classical and molecular-biological methods for the identification of L. garvieae and examine antimicrobial susceptibility and capsule production, an important virulence factor. Additionally, tests for differentiation from closely related species, as well as epidemiological typing, were performed. In a period of 18 years (2002–2019), 24 isolates presumptively identified as L. garvieae were collected from Oncorhynchus mykiss and Salmo salar fish obtained either from retail stores or fish farms. In order to confirm the species, optimized PCR-based protocols were used. As a result, 21 of the tested strains were proved to be L. garvieae (n = 21). The remaining three isolates were Lactococcus lactis, Streptococcus iniae, and Enterococcus faecalis. Epidemiological typing by randomly amplified polymorphic DNA was performed. Except for a single KG+ isolate, all other strains belonged to the European capsular serotype KG−. All L. garvieae isolates showed susceptibility to all tested antibiotics with the exception of clindamycin, which was a diagnostic sign. A thorough optimization of diagnostic methods is essential to determining the etiology of specific infections affecting the personnel at risk in fish farms, the food industry, or within the broader community. Full article

(This article belongs to the Special Issue Host–Bacteria Interactions in Aquaculture Systems, 2nd Edition)

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21 pages, 3606 KiB

Open AccessArticle

Beyond Microbial Variability: Disclosing the Functional Redundancy of the Core Gut Microbiota of Farmed Gilthead Sea Bream from a Bayesian Network Perspective

by Federico Moroni, Fernando Naya-Català, Ahmed Ibrahem Hafez, Ricardo Domingo-Bretón, Beatriz Soriano, Carlos Llorens and Jaume Pérez-Sánchez

Microorganisms 2025, 13(1), 198; https://doi.org/10.3390/microorganisms13010198 - 17 Jan 2025

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Abstract

The significant microbiota variability represents a key feature that makes the full comprehension of the functional interaction between microbiota and the host an ongoing challenge. To overcome this limitation, in this study, fish intestinal microbiota was analyzed through a meta-analysis, identifying the core [...] Read more.

The significant microbiota variability represents a key feature that makes the full comprehension of the functional interaction between microbiota and the host an ongoing challenge. To overcome this limitation, in this study, fish intestinal microbiota was analyzed through a meta-analysis, identifying the core microbiota and constructing stochastic Bayesian network (BN) models with SAMBA. We combined three experiments performed with gilthead sea bream juveniles of the same hatchery batch, reared at the same season/location, and fed with diets enriched on processed animal proteins (PAP) and other alternative ingredients (NOPAP-PP, NOPAP-SCP). Microbiota data analysis disclosed a high individual taxonomic variability, a high functional homogeneity within trials and highlighted the importance of the core microbiota, clustering PAP and NOPAP fish microbiota composition. For both NOPAP and PAP BNs, >99% of the microbiota population were modelled, with a significant proportion of bacteria (55–69%) directly connected with the diet variable. Functional enrichment identified 11 relevant pathways expressed by different taxa across the different BNs, confirming the high metabolic plasticity and taxonomic heterogeneity. Altogether, these results reinforce the comprehension of the functional bacteria–host interactions and in the near future, allow the use of microbiota as a species-specific growth and welfare benchmark of livestock animals, and farmed fish in particular. Full article

(This article belongs to the Special Issue Host–Bacteria Interactions in Aquaculture Systems, 2nd Edition)

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14 pages, 1671 KiB

Open AccessArticle

Association between Turbot (Scophthalmus maximus) Fish Phenotype and the Post-Larval Bacteriome

by Antonio Louvado, Davide A. M. Silva, Vanessa Oliveira, Carolina Castro, Daniel F. R. Cleary and Newton C. M. Gomes

Microorganisms 2024, 12(10), 2014; https://doi.org/10.3390/microorganisms12102014 - 4 Oct 2024

Cited by 1 | Viewed by 889

Abstract

Over the past decade, an increasing number of studies have emphasized the importance of the host microbiome in influencing organismal health and development. Aligned with this understanding, our study aimed to investigate the potential association between the turbot (Scophthalmus maximus) phenotypic [...] Read more.

Over the past decade, an increasing number of studies have emphasized the importance of the host microbiome in influencing organismal health and development. Aligned with this understanding, our study aimed to investigate the potential association between the turbot (Scophthalmus maximus) phenotypic traits and the post-larval bacteriome. Turbot post-larvae were sampled from twenty randomly selected production cycles thirty days after hatching (DAH) across multiple post-larval production batches over a three-month period (April to June). Fish were selectively sampled based on five phenotypic traits, namely, normal, large, small, malformed, and depigmented. Our results showed that small-sized post-larvae had significantly higher bacterial phylogenetic diversity in their bacterial communities than all other phenotypes. A more in-depth compositional analysis also revealed specific associations between certain bacterial taxa and fish phenotypes. For example, the genera Aliivibrio and Sulfitobacter were enriched in small-sized post-larvae, while the family Micrococcaceae were predominantly found in larger post-larvae. Furthermore, genus Exiguobacterium was linked to depigmented larvae, and genus Pantoea was more prevalent in normal post-larvae. These observations underscore the importance of further research to understand the roles of these bacterial taxa in larval growth and phenotypic differentiation. Such insights could contribute to developing microbiome modulation strategies, which may enhance turbot post-larval health and quality and improve larviculture production. Full article

(This article belongs to the Special Issue Host–Bacteria Interactions in Aquaculture Systems, 2nd Edition)

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17 pages, 2929 KiB

Open AccessArticle

Genomic Insights into Edwardsiella ictaluri: Molecular Epidemiology and Antimicrobial Resistance in Striped Catfish (Pangasianodon hypophthalmus) Aquaculture in Vietnam

by Vera Irene Erickson, Tu Thanh Dung, Le Minh Khoi, Yaovi Mahuton Gildas Hounmanou, Tran Minh Phu and Anders Dalsgaard

Microorganisms 2024, 12(6), 1182; https://doi.org/10.3390/microorganisms12061182 - 11 Jun 2024

Cited by 3 | Viewed by 1772

Abstract

Edwardsiella ictaluri is responsible for causing bacillary necrosis (BNP) in striped catfish (Pangasianodon hypophthalmus) in Vietnam. This study offers a comprehensive genomic characterization of E. ictaluri to enhance understanding of the molecular epidemiology, virulence, and antimicrobial resistance. E. ictaluri isolates were [...] Read more.

Edwardsiella ictaluri is responsible for causing bacillary necrosis (BNP) in striped catfish (Pangasianodon hypophthalmus) in Vietnam. This study offers a comprehensive genomic characterization of E. ictaluri to enhance understanding of the molecular epidemiology, virulence, and antimicrobial resistance. E. ictaluri isolates were collected from diseased striped catfish in the Mekong Delta. The species was confirmed through PCR. Antimicrobial susceptibility testing was conducted using minimum inhibitory concentrations for commonly used antimicrobials. Thirty representative isolates were selected for whole genome sequencing to delineate their genomic profiles and phylogeny. All strains belonged to ST-26 and exhibited genetic relatedness, differing by a maximum of 90 single nucleotide polymorphisms. Most isolates carried multiple antimicrobial resistance genes, with the tet(A) gene present in 63% and floR in 77% of the genomes. The ESBL gene, bla_CTX-M-15, was identified in 30% of the genomes. Three plasmid replicon types were identified: IncA, p0111, and IncQ1. The genomes clustered into two clades based on their virulence gene profile, one group with the T3SS genes and one without. The genetic similarity among Vietnamese isolates suggests that disease spread occurs within the Mekong region, underscoring the importance of source tracking, reservoir identification, and implementation of necessary biosecurity measures to mitigate spread of BNP. Full article

(This article belongs to the Special Issue Host–Bacteria Interactions in Aquaculture Systems, 2nd Edition)

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16 pages, 2272 KiB

Open AccessArticle

Early Succession of Community Structures and Biotic Interactions of Gut Microbes in Eriocheir sinensis Megalopa after Desalination

by Wenlei Xue, Hao Wu, Xinyu Wu, Nannan Li, Ximei Nie and Tianheng Gao

Microorganisms 2024, 12(3), 560; https://doi.org/10.3390/microorganisms12030560 - 11 Mar 2024

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Abstract

As an enduring Chinese freshwater aquaculture product, the Eriocheir sinensis has a high economic value and is characterized by a catadromous life style that undergoes seawater–freshwater migration. However, little is known about their gut microbial status as they move from saltwater to freshwater [...] Read more.

As an enduring Chinese freshwater aquaculture product, the Eriocheir sinensis has a high economic value and is characterized by a catadromous life style that undergoes seawater–freshwater migration. However, little is known about their gut microbial status as they move from saltwater to freshwater acclimatization. Here, we sampled and cultivated Eriocheir sinensis megalopa from three aquaculture desalination ponds and investigated their gut microbiota diversity, community structures and biotic interactions from megalopa stage to the first juvenile stage after desalination for 9 days. Our results revealed that during the transition from megalopa to the first juvenile in Eriocheir sinensis, a significant change in gut microbial composition was observed (for instance, changes in relative abundance of dominant phyla), which was, however, not influenced by different sampling sites. The species diversity (such as the richness) of the gut microbiota showed a hump-shaped pattern along the succession. However, the compositional differences of the gut microbes showed constantly increasing patterns during the succession after freshwater adaption for all three sampling sites. Further co-occurrence analysis also showed that the complexity of the ecological networks in gut microbes was significantly enhanced during the development, such as increasing numbers of network links, connectivity and modularity, and was confirmed by decreasing average path length and proportions of negative links. Taken together, the differences in community structures and biological interactions of gut microorganisms were more pronounced in Eriocheir sinensis megalopa during desalination than in diversity and species compositions. This implies that the gut microbes of Eriocheir sinensis megalopa would become more robust and adaptive during the developmental process. Full article

(This article belongs to the Special Issue Host–Bacteria Interactions in Aquaculture Systems, 2nd Edition)

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24 pages, 4400 KiB

Open AccessArticle

Effect of Food Amounts on Larval Performance, Bacteriome and Molecular Immunologic Development during First-Feeding Culture of European Eel

by Kasun Anuruddha Bandara, Sebastian Nikitas Politis, Sune Riis Sørensen, Elisa Benini, Jonna Tomkiewicz and Olav Vadstein

Microorganisms 2024, 12(2), 355; https://doi.org/10.3390/microorganisms12020355 - 8 Feb 2024

Viewed by 1536

Abstract

Production of European eel offspring has become a reality, but liquid diets during larval culture hold new challenges. This study focused on increasing food amounts without compromising well-being or healthy larvae-bacteria interactions. First-feeding larvae were fed two food amounts (Low = 0.5 mL [...] Read more.

Production of European eel offspring has become a reality, but liquid diets during larval culture hold new challenges. This study focused on increasing food amounts without compromising well-being or healthy larvae-bacteria interactions. First-feeding larvae were fed two food amounts (Low = 0.5 mL food/L water vs. High = 1.5 mL food/L water) until 30 days post-hatch (dph). Results indicated that ~75% of larvae ingested the diet in both treatments, but upregulation of a stress/repair-related gene (hsp90) on 25 and 30 dph indicated nutritional inadequacy. Larvae fed a High amount of food were 3.68% bigger, while larvae in the Low-food group showed 45.2% lower gut fullness and upregulated expression of the gene encoding the “hunger hormone” ghrelin (ghrl), indicating signs of starvation. The High-food group larvae exhibited a healthier bacteriome with a higher abundance of potentially beneficial orders (Lactobacillales and Bacillales), whereas the Low-food group showed more potentially harmful orders (Vibrionales, Rhodobacterales, and Alteromonadales). While survival was initially lower in the High-food group, both treatments had comparable survival by the end of the experiment. In conclusion, feeding European eel larvae with High food amounts seemed beneficial, supported by increased gut fullness, reduced ghrl expression (no starvation), enhanced growth, and the presence of a healthier bacteriome. Full article

(This article belongs to the Special Issue Host–Bacteria Interactions in Aquaculture Systems, 2nd Edition)

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Review

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16 pages, 578 KiB

Open AccessReview

Microbial Interactions in Rearing Systems for Marine Fish Larvae

by Vasiliki Paralika and Pavlos Makridis

Microorganisms 2025, 13(3), 539; https://doi.org/10.3390/microorganisms13030539 - 27 Feb 2025

Viewed by 626

Abstract

This article reviews the scientific literature discussing the microbial interactions between water microbiota, live food microbiota, fish larvae immune system and gut microbiota, and biofilm microbial communities in rearing systems for marine fish larvae. Fish gut microbiota is the first line of defense [...] Read more.

This article reviews the scientific literature discussing the microbial interactions between water microbiota, live food microbiota, fish larvae immune system and gut microbiota, and biofilm microbial communities in rearing systems for marine fish larvae. Fish gut microbiota is the first line of defense against opportunistic pathogens, and marine fish larvae are vulnerable to high mortalities during the first weeks after hatching. The bacterial colonization of fish larvae is a dynamic process influenced by environmental and host-related factors. The bacteria transferred to larvae from the eggs can influence the composition of the gut microbiota in the early stages of fish. Fish larvae ingest free-living microorganisms present in the water, as marine fish larvae drink water for osmoregulation. In marine aquaculture systems, the conventional feeding–rearing protocol consists of zooplankton (rotifers, Artemia, and copepods). These live food organisms are filter-feeders. Once transferred to a new environment, they quickly adopt the microflora of the surrounding water. So, the water microbiota is similar to the microbiota of the live food at the time of ingestion of live food by the larvae. In aquaculture rearing systems, bacterial biofilms may harbor opportunistic pathogenic bacteria and serve as a reservoir for those microbes, which may colonize the water column. The methods applied for the study of fish larvae microbiota were reviewed. Full article

(This article belongs to the Special Issue Host–Bacteria Interactions in Aquaculture Systems, 2nd Edition)

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42 pages, 2146 KiB

Open AccessReview

Aquatic Invertebrate Antimicrobial Peptides in the Fight Against Aquaculture Pathogens

by Tomás Rodrigues, Francisco Antonio Guardiola, Daniela Almeida and Agostinho Antunes

Microorganisms 2025, 13(1), 156; https://doi.org/10.3390/microorganisms13010156 - 14 Jan 2025

Cited by 1 | Viewed by 2068

Abstract

The intensification of aquaculture has escalated disease outbreaks and overuse of antibiotics, driving the global antimicrobial resistance (AMR) crisis. Antimicrobial peptides (AMPs) provide a promising alternative due to their rapid, broad-spectrum activity, low AMR risk, and additional bioactivities, including immunomodulatory, anticancer, and antifouling [...] Read more.

The intensification of aquaculture has escalated disease outbreaks and overuse of antibiotics, driving the global antimicrobial resistance (AMR) crisis. Antimicrobial peptides (AMPs) provide a promising alternative due to their rapid, broad-spectrum activity, low AMR risk, and additional bioactivities, including immunomodulatory, anticancer, and antifouling properties. AMPs derived from aquatic invertebrates, particularly marine-derived, are well-suited for aquaculture, offering enhanced stability in high-salinity environments. This study compiles and analyzes data from AMP databases and over 200 scientific sources, identifying approximately 350 AMPs derived from aquatic invertebrates, mostly cationic and α-helical, across 65 protein families. While in vitro assays highlight their potential, limited in vivo studies hinder practical application. These AMPs could serve as feed additives, therapeutic agents, or in genetic engineering approaches like CRISPR/Cas9-mediated transgenesis to enhance resilience of farmed species. Despite challenges such as stability, ecological impacts, and regulatory hurdles, advancements in peptidomimetics and genetic engineering hold significant promise. Future research should emphasize refining AMP enhancement techniques, expanding their diversity and bioactivity profiles, and prioritizing comprehensive in vivo evaluations. Harnessing the potential of AMPs represents a significant step forward on the path to aquaculture sustainability, reducing antibiotic dependency, and combating AMR, ultimately safeguarding public health and ecosystem resilience. Full article

(This article belongs to the Special Issue Host–Bacteria Interactions in Aquaculture Systems, 2nd Edition)

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