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11 pages, 2646 KiB

Open AccessArticle

Bacterial Infection Disrupts the Intestinal Bacterial Community and Facilitates the Enrichment of Pathogenic Bacteria in the Intestines of Penaeus vannamei

by Renjun Zhou, Shaoping Weng and Jianguo He

Microorganisms 2025, 13(4), 864; https://doi.org/10.3390/microorganisms13040864 - 10 Apr 2025

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Abstract

Pathogenic infections can reshape the intestinal microbiota of aquatic animals, thereby impacting their health status. In this study, we aimed to investigate whether Vibrio parahaemolyticus infection induces dysbiosis in the intestinal bacterial community of Penaeus vannamei and to assess the associated ecological risks. [...] Read more.

Pathogenic infections can reshape the intestinal microbiota of aquatic animals, thereby impacting their health status. In this study, we aimed to investigate whether Vibrio parahaemolyticus infection induces dysbiosis in the intestinal bacterial community of Penaeus vannamei and to assess the associated ecological risks. Our findings revealed the deterministic processes in intestinal bacterial community assembly during bacterial infections, indicating that host selection, i.e., host immune response post-infection, has a significant influence on intestinal microbes. More importantly, we found that bacterial infection reshaped the intestinal community by reducing the relative abundance of probiotic Ruegeria species (e.g., R. atlantica, R. lacuscaerulensis, R. conchae, R. profundi, R. arenilitoris, R. pomeroyi) and increasing the relative abundance of Vibrio species (V. harveyi, V. sinaloensis, V. coralliilyticus, and V. brasiliensis). Significant negative correlations were observed between the relative abundance of these Ruegeria species and the relative abundance of Vibrio species. Moreover, the control P. vannamei contained a substantially higher number of keystone species belonging to Ruegeria in the bacterial community network, whereas bacterial infection individuals had few or no keystone species belonging to Ruegeria, with keystone species belonging to Vibrio becoming more prominent. Thus, the significant increase in Vibrio species abundance in the P. vannamei intestine following bacterial infection was associated with the marked reduction in Ruegeria species. Our findings will provide valuable insights into the complex interactions among bacterial infection, intestinal microbiota, and host health, and they provide guidance for the development of probiotics in promoting the healthy culture of P. vannamei. Full article

(This article belongs to the Special Issue Aquatic Microorganisms and Their Application in Aquaculture)

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22 pages, 6843 KiB

Open AccessArticle

Variation of Microorganisms and Water Quality, and Their Impacts on the Production of Penaeus vannamei in Small-Scale Greenhouse Ponds

by Siyu Wu, Haochang Su, Lei Su, Yucheng Cao, Guoliang Wen, Yu Xu, Bin Shen, Shanshan Wu, Yuting Su and Xiaojuan Hu

Microorganisms 2025, 13(3), 546; https://doi.org/10.3390/microorganisms13030546 - 27 Feb 2025

Cited by 1 | Viewed by 655

Abstract

To study the factors affecting Penaeus vannamei production in small-scale greenhouse ponds, four ponds in Jiangmen, Guangdong Province, China were selected. This study investigated the variation in the characteristics of bacterial communities and pathogens in pond water and shrimp intestines, as well as [...] Read more.

To study the factors affecting Penaeus vannamei production in small-scale greenhouse ponds, four ponds in Jiangmen, Guangdong Province, China were selected. This study investigated the variation in the characteristics of bacterial communities and pathogens in pond water and shrimp intestines, as well as water quality factors during the culture stage. Multivariate linear regression equations were used to analyse the potential factors affecting production. The nitrite concentration reached its peak in the mid-culture stage, with a maximum of 16.3 mg·L⁻¹, whereas total nitrogen and salinity were highest in the late culture stage, reaching 48.4 mg·L⁻¹ and 26, respectively. The dominant bacteria in the pond water were Marivita and Rhodobacteraceae, whereas in the shrimp intestines, they were Bacillus and Candidatus Bacilloplasma. The nitrifying bacteria in the pond water were dominated by Nitrosomonas and Nitrobacter. Pathogens detected in the pond water included acute hepatopancreatic necrosis disease (AHPND), Enterocytozoon hepatopenaei (EHP), and white spot syndrome virus (WSSV). The counts of EHP and the relative abundance of Ardenticatenales_norank and Marivita in the pond were the main factors affecting the shrimp production (p < 0.01). This study indicates that establishing optimal bacterial communities, such as Marivita, Nitrobacter, and Rhodobacteraceae, and controlling the counts of EHP and AHPND pathogens is crucial for regulating the pond environment and enhancing production. Full article

(This article belongs to the Special Issue Aquatic Microorganisms and Their Application in Aquaculture)

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16 pages, 5262 KiB

Open AccessArticle

Effects of Eucalyptus Essential Oil on Growth, Immunological Indicators, Disease Resistance, Intestinal Morphology and Gut Microbiota in Trachinotus ovatus

by Ziyang Lin, Shengzhe An, Chuanpeng Zhou, Yaqi Chen, Zhenchuang Gao, Juan Feng, Heizhao Lin, Pengwei Xun and Wei Yu

Microorganisms 2025, 13(3), 537; https://doi.org/10.3390/microorganisms13030537 - 27 Feb 2025

Viewed by 555

Abstract

Essential oils serve as potential additives that can enhance immune respons and disease resistance and regulate the gut microbiota of fish. Here, this research aims to identify the impacts of eucalyptus essential oil (EEO) on growth, liver antioxidative and immune parameters, resistance to [...] Read more.

Essential oils serve as potential additives that can enhance immune respons and disease resistance and regulate the gut microbiota of fish. Here, this research aims to identify the impacts of eucalyptus essential oil (EEO) on growth, liver antioxidative and immune parameters, resistance to Streptococcus iniae, intestinal morphology and gut microbiota in Trachinotus ovatus. All fish (initial weight: 26.87 ± 0.30 g) were randomly allocated to 12 floating cages (2.0 × 2.0 × 2.0 m³) with each cage containing 100 fish and fed for 30 days. Four diets were manufactured with the supplementation of varying levels of EEO (control and 5.0, 10.0, and 15.0 mL/kg) and were named CG, EEO1, EEO2 and EEO3, respectively. The results showed that EEO1 and EEO2 diets significantly increased WGR, thickness of the intestinal muscle layer, and the ratio of villus height to crypt depth (V/C), while decreasing the intestinal crypt depth of T. ovatus (p < 0.05). Significantly increased activities of SOD and CAT and significantly reduced MDA levels were present in the EEO1 and/or EEO2 groups (p < 0.05). Moreover, the mRNA levels of nrf2, HO-1, GSH-Px, SOD, C4 and GR genes were significantly upregulated and the expression of keap1 and HSP70 genes were significantly downregulated within the EEO1 and EEO2 groups (p < 0.05). After challenge with S. iniae B240703 for 24 h, the bacterial load for five organs in the EEO2 group was less than that in the CG group (p < 0.05). In addition, the fish fed EEO1 and/or EEO2 diets had significantly lower abundances of pathogenic bacteria (Proteobacteria, Planctomycetota, Burkholderia-Caballeronia-Paraburkholderia, Pseudomonas and Blastopirellula) and a higher beneficial bacteria proportion (Firmicutes) than those fed the CG diets (p < 0.05). In conclusion, a moderate dietary m EO level (5.0~10.0 mL/kg) improved the growth and gut morphology, promoted liver immune response, enhanced resistance to S. iniae and modulated the gut microbiota of T. ovatus. Full article

(This article belongs to the Special Issue Aquatic Microorganisms and Their Application in Aquaculture)

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21 pages, 4999 KiB

Open AccessArticle

Relations Between Core Taxa and Metabolic Characteristics of Bacterial Communities in Litopenaeus vannamei Ponds and Their Probiotic Potential

by Qiong Zhao, Ke Zhou, Fengfeng Zhang, Yu Wang, Jun Hao, Fengxing Xie and Qian Yang

Microorganisms 2025, 13(2), 466; https://doi.org/10.3390/microorganisms13020466 - 19 Feb 2025

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Abstract

Microorganisms play a crucial role in purifying aquaculture water bodies. However, there is limited understanding regarding the core species of bacterial communities in aquaculture ponds and their metabolic functions. Using 16S rRNA gene sequencing technology, network analysis, and Biolog EcoPlates, we identified keystone [...] Read more.

Microorganisms play a crucial role in purifying aquaculture water bodies. However, there is limited understanding regarding the core species of bacterial communities in aquaculture ponds and their metabolic functions. Using 16S rRNA gene sequencing technology, network analysis, and Biolog EcoPlates, we identified keystone and core taxa of bacterial communities in Litopenaeus vannamei ponds and investigated their correlations with their community’s carbon source utilization abilities based on Biolog EcoPlates. We found that keystone and core taxa in bacterial communities were significantly correlated with the carbon source utilization abilities of bacterial communities. The positively correlated core taxa include (1) Bacillus, Flavobacterium, Brevibacillus, and Paenibacillus, which are used as probiotics in aquaculture, and (2) Candidatus Aquiluna, Dechloromonas, Sulfurifustis, Terrimicrobium, Alsobacter, and Gemmobacter, which have been reported to play a role in nitrogen removal. Furthermore, the positively correlated Tropicimonas (Rhodobacterales: Rhodobacteraceae) in aquaculture has not yet been applied. By nitrogen degradation experiments in aquaculture wastewater, we confirmed the synergistic relationship between the genera Tropicimonas and Bacillus. The co-introduction of Tropicimonas sediminicola SDUM182003 and Priestia aryabhattai HG1802 or Bacillus subtilis XQ1804 into the aquaculture tailwater reduced the time required for the removal rates of nitrite nitrogen and nitrate nitrogen to reach over 90% by 24–48 h. Our research reveals the correlation between core taxa and community carbon source utilization, indicating that the core taxa of bacterial communities play a crucial role in the metabolic functions of the community, and offering a reference for exploring new bacterial genera with probiotic potential. Full article

(This article belongs to the Special Issue Aquatic Microorganisms and Their Application in Aquaculture)

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32 pages, 24926 KiB

Open AccessArticle

Histopathological and Proteomics Analysis of Shrimp Litopenaeus vannamei Infected with Ecytonucleospora hepatopenaei

by Ping Ni, Yingyao Ma, Bingxin Shi and Mengqiang Wang

Microorganisms 2025, 13(2), 402; https://doi.org/10.3390/microorganisms13020402 - 12 Feb 2025

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Abstract

Ecytonucleospora hepatopenaei (EHP) is a microsporidian pathogen that primarily infects the hepatopancreas of Litopenaeus vannamei. Previous studies on EHP detection primarily focused on histology, in situ hybridization (ISH), and PCR, mainly concentrating on hepatopancreatic infections, with limited research on extra-hepatopancreatic tissues. This [...] Read more.

Ecytonucleospora hepatopenaei (EHP) is a microsporidian pathogen that primarily infects the hepatopancreas of Litopenaeus vannamei. Previous studies on EHP detection primarily focused on histology, in situ hybridization (ISH), and PCR, mainly concentrating on hepatopancreatic infections, with limited research on extra-hepatopancreatic tissues. This study investigates the pathogenic mechanisms of EHP infection in L. vannamei through molecular quantification, histopathology, and proteomics analysis. RT-qPCR was employed to examine the infection differences across various tissues at the molecular level, revealing that the hepatopancreas, stomach, midgut, muscle, gills, and antennal glands are susceptible tissues. Pathological analysis, combining H&E staining, Masson’s trichrome staining, and immunohistochemistry, identified the EHP-targeted sites at the tissue level. Masson’s staining effectively highlighted fibrosis, unveiling the histopathological characteristics of chronic EHP infection, while immunohistochemistry enhanced the specificity of EHP localization. The pathological features of EHP infection were primarily characterized by inflammation, cell degeneration and necrosis, and the accumulation of microsporidia in the cytoplasm. Proteomics analysis was used to interpret the histopathological findings, revealing significant enrichment of pathways related to inflammation, immune regulation, metabolism, and apoptosis regulation. These findings provide new insights into the infection mechanisms and tissue tropism of EHP. Full article

(This article belongs to the Special Issue Aquatic Microorganisms and Their Application in Aquaculture)

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12 pages, 2948 KiB

Open AccessArticle

Highly Pleomorphic Strains of the Vibrio Predator Pseudoalteromonas piscicida and Their Outer Membrane Vesicles: A Scanning Electron Micrographic Study

by Gary P. Richards, Joseph Uknalis and Michael A. Watson

Microorganisms 2025, 13(2), 365; https://doi.org/10.3390/microorganisms13020365 - 7 Feb 2025

Viewed by 747

Abstract

Pseudoalteromonas species are recognized for their probiotic roles in reducing pathogens in aquaculture products by secreting a broad range of antimicrobial compounds. Some species, like P. piscicida, are also predators that attack susceptible prey bacteria, including V. parahaemolyticus, by transferring outer [...] Read more.

Pseudoalteromonas species are recognized for their probiotic roles in reducing pathogens in aquaculture products by secreting a broad range of antimicrobial compounds. Some species, like P. piscicida, are also predators that attack susceptible prey bacteria, including V. parahaemolyticus, by transferring outer membrane vesicles (OMVs) containing digestive compounds to the surface of their prey. These vesicles digest holes in the prey’s cell wall releasing nutrients upon which the Pseudoalteromonas feed. In the present study, scanning electron microscopy was performed on two P. piscicida strains grown in sterile seawater and nutrient-enriched seawater, without the presence of bacterial prey, to determine if the presence of prey or low-nutrient media was required to induce vesicle formation. Micrographs revealed OMV formation and high pleomorphism of P. piscicida in the absence of prey cells and regardless of the nutrient levels of the seawater. Phenotypic characteristics included the presence of (i) vesiculated and non-vesiculated bacteria, (ii) large bulbous OMV versus small OMV, (iii) pilus-like connectors of widely varying lengths to which vesicles were attached, (iv) highly elongated (10 µm long) Pseudoalteromonas cells, and (v) cells that appeared to extend to 50 µm long and to be septating and dividing into short chains and individual cells. The possible contribution of these novel phenotypes to Pseudoalteromonas predation is discussed. Full article

(This article belongs to the Special Issue Aquatic Microorganisms and Their Application in Aquaculture)

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21 pages, 4832 KiB

Open AccessArticle

Development and Application of Lactobacillus plantarum PSCPL13 Probiotics in Olive Flounder (Paralichthys olivaceus) Farming

by Muhammad Aleem Abbas, Hae-Jung Kim, Ga-Yeong Lee, Hae-Yeon Cho, Syed Al Jawad Sayem, Eon-Bee Lee, Seung-Jin Lee and Seung-Chun Park

Microorganisms 2025, 13(1), 61; https://doi.org/10.3390/microorganisms13010061 - 2 Jan 2025

Viewed by 1348

Abstract

Aquaculture has grown significantly, contributing to global food security and sustainability; however, intensified fish farming has increased disease susceptibility and antibiotic resistance. This study assessed the probiotic potential of Lactobacillus plantarum PSCPL13 (hereafter, PSCPL13), isolated from the intestines of Japanese eels, for enhancing [...] Read more.

Aquaculture has grown significantly, contributing to global food security and sustainability; however, intensified fish farming has increased disease susceptibility and antibiotic resistance. This study assessed the probiotic potential of Lactobacillus plantarum PSCPL13 (hereafter, PSCPL13), isolated from the intestines of Japanese eels, for enhancing the health of olive flounder. After screening 16 Lactobacillus isolates, PSCPL13 was selected because of its potential broad-spectrum antibacterial activity against many pathogens, such as Vibrio and Edwardsiella. This strain exhibited high acid and bile salt tolerance, which is crucial for intestinal survival. Molecular characterisation confirmed PSCPL13 to be L. plantarum. It was resistant to all tested antibiotics and exhibited significant enzyme activity. In vivo assays in olive flounder revealed that the body weight and length of the fish were significantly higher, while the prevalence of pathogens was lower in their gut microbiota. Regarding haematological parameters, the treated groups exhibited lower eosinophil counts and higher IgM levels, suggesting enhancement of the immune system. These findings indicate that PSCPL13 is a potential probiotic that can be used in aquaculture for naturally improving fish health, growth and immunity, in addition to combating antibiotic resistance and reducing environmental impacts. These findings not only highlight the potential of PSCPL13 in sustainable aquaculture but also provide a foundation for the development of future probiotics. Full article

(This article belongs to the Special Issue Aquatic Microorganisms and Their Application in Aquaculture)

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19 pages, 7157 KiB

Open AccessArticle

The Bile Acid Metabolism of Intestinal Microorganisms Mediates the Effect of Different Protein Sources on Muscle Protein Deposition in Procambarus clarkii

by Xiaodi Xu, Xiaochuan Zheng, Qunlan Zhou, Cunxin Sun, Aimin Wang, Aimin Zhu, Yuanyuan Zhang and Bo Liu

Microorganisms 2025, 13(1), 11; https://doi.org/10.3390/microorganisms13010011 - 24 Dec 2024

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Abstract

The most economically important trait of the Procambarus clarkii is meat quality. Protein deposition is essential in muscle growth and nutritional quality formation. The effects and potential mechanisms of feed protein sources on crustaceans’ muscle protein deposition have not been elucidated. This study [...] Read more.

The most economically important trait of the Procambarus clarkii is meat quality. Protein deposition is essential in muscle growth and nutritional quality formation. The effects and potential mechanisms of feed protein sources on crustaceans’ muscle protein deposition have not been elucidated. This study established an all-animal protein source (AP) and an all-plant protein source group (PP), with a feeding period of 8 weeks (four replicates per group, 45 individuals per replicate). The results demonstrated that muscle protein deposition, muscle fiber diameter, and hardness were significantly higher in the PP group (p < 0.05). The transcript levels of genes involved in protein synthesis were notably upregulated, while those of protein hydrolysis and negative regulators of myogenesis notably downregulated in PP group (p < 0.05). Furthermore, protein sources shaped differential intestinal microbiota composition and microbial metabolites profiles, as evidenced by a significant decrease in g_Bacteroides (p = 0.030), and a significant increase in taurochenodeoxycholic acid (TCDCA) in PP group (p = 0.027). A significant correlation was further established by Pearson correlation analysis between the g_Bacteroides, TCDCA, and genes involved in the MSTN-mediated protein deposition pathway (p < 0.05). In vitro anaerobic fermentation confirmed the ability of the two groups of intestinal flora to metabolically produce differential TCDCA (p = 0.038). Our results demonstrated that the ‘Bacteroides-TCDCA-MSTN’ axis may mediate the effects of different protein sources on muscle development and protein deposition in P. clarkii, which was anticipated to represent a novel target for the muscle quality modulation in crustaceans. Full article

(This article belongs to the Special Issue Aquatic Microorganisms and Their Application in Aquaculture)

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15 pages, 3448 KiB

Open AccessArticle

Impact of Biochar Addition on Biofloc Nitrifying Bacteria and Inorganic Nitrogen Dynamics in an Intensive Aquaculture System of Shrimp

by Wujie Xu, Demin Zhang, Haochang Su, Yu Xu, Xiaojuan Hu, Guoliang Wen and Yucheng Cao

Microorganisms 2024, 12(12), 2581; https://doi.org/10.3390/microorganisms12122581 - 13 Dec 2024

Cited by 2 | Viewed by 860

Abstract

In this study, an eight-week culture trial of Penaeus vannamei juveniles was conducted in commercial intensive systems to compare the impacts of biochar and molasses addition on biofloc nitrifying bacteria and inorganic nitrogen dynamics under limited water exchange conditions. During the trial, the [...] Read more.

In this study, an eight-week culture trial of Penaeus vannamei juveniles was conducted in commercial intensive systems to compare the impacts of biochar and molasses addition on biofloc nitrifying bacteria and inorganic nitrogen dynamics under limited water exchange conditions. During the trial, the biofloc concentration (in terms of VSS and TSS), quantities of total bacteria (TB) and total Vibrio (TV), and ratio of TV/TB in the culture water were lower in the biochar group compared to the molasses group. Metagenomic sequencing analysis revealed that the bacterial community composition of bioflocs showed higher α-diversity and complexity in the biochar group compared to the molasses group. Moreover, the abundance of nitrifying bacterial genera and functional genes in bioflocs was higher in the biochar group compared to the molasses group. Inorganic nitrogen dynamics showed that NH₄⁺-N and NO₂⁻-N were better controlled in the biochar group compared to the molasses group, as reflected by lower peaks of NH₄⁺-N and NO₂⁻-N and higher NO₃⁻-N concentrations. Excellent production performance of shrimp was achieved, which in turn proved the reliable effect of biochar addition on the mediation of inorganic nitrogen transformation through nitrifying bacteria. These results showed that biochar addition could promote biofloc nitrifying bacteria and nitrification to more effectively control harmful nitrogen for shrimp efficient production. This study provides a practical example for the biochar application in biofloc-based systems for intensive aquaculture. Full article

(This article belongs to the Special Issue Aquatic Microorganisms and Their Application in Aquaculture)

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23 pages, 3840 KiB

Open AccessArticle

Longitudinal Microbiome Investigations Reveal Core and Growth-Associated Bacteria During Early Life Stages of Scylla paramamosain

by Yin Fu, Yongxu Cheng, Lingbo Ma and Qicun Zhou

Microorganisms 2024, 12(12), 2457; https://doi.org/10.3390/microorganisms12122457 - 29 Nov 2024

Viewed by 996

Abstract

In animals, growth and development are strongly correlated with the gut microbiota. The gut of the economically important marine crab (Scylla paramamosain) harbors a diverse microbial community, yet its associations with the surrounding environment, growth performance, and developmental stages remain obscure. [...] Read more.

In animals, growth and development are strongly correlated with the gut microbiota. The gut of the economically important marine crab (Scylla paramamosain) harbors a diverse microbial community, yet its associations with the surrounding environment, growth performance, and developmental stages remain obscure. In this study, we first characterized stage-specific microbiomes and shifts in the contributions of live feed and water via SourceTracker. We observed decreased microbial diversity and increased priority effects along zoea stages. Psychobacter was identified as the core genus, whereas Lactobacillus was the hub genus connecting different stages. Second, microbial correlations with various stage-specific growth traits were observed under interventions generating enhanced (probiotic mixture enrichment), normal (control), and reduced (antibiotic treatment) microbiomes. By combining machine learning regression and bioinformatics analysis, we identified four candidate growth performance-associated probiotics belonging to Rhodobacterales, Sulfitobacter, Confluentimicrobium, and Lactobacillus, respectively. Our study interpreted the dynamics and origins of the Scylla paramamosain zoea microbiome and underscored the importance of optimizing potential probiotics to increase growth performance during early life stages in marine invertebrates for effective larviculture. Full article

(This article belongs to the Special Issue Aquatic Microorganisms and Their Application in Aquaculture)

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15 pages, 3734 KiB

Open AccessArticle

Effect of Dietary Astragalus polysaccharides (APS) on the Growth Performance, Antioxidant Responses, Immunological Parameters, and Intestinal Microbiota of Coral Trout (Plectropomus leopardus)

by Xiaoqi Hao, Heizhao Lin, Ziyang Lin, Keng Yang, Jing Hu, Zhenhua Ma and Wei Yu

Microorganisms 2024, 12(10), 1980; https://doi.org/10.3390/microorganisms12101980 - 30 Sep 2024

Cited by 3 | Viewed by 1237

Abstract

The potential effects of Astragalus polysaccharides (APS) were evaluated in coral trout (Plectropomus leopardus). Five APS levels (0%, 0.05%, 0.10%, 0.15%, and 0.20%) were added to the diet of coral trout, and a 56-day growth trial (initial weight 18.62 ± 0.05 [...] Read more.

The potential effects of Astragalus polysaccharides (APS) were evaluated in coral trout (Plectropomus leopardus). Five APS levels (0%, 0.05%, 0.10%, 0.15%, and 0.20%) were added to the diet of coral trout, and a 56-day growth trial (initial weight 18.62 ± 0.05 g) was conducted. Dietary APS enhanced growth performance, with the highest improvement observed in fish fed the 0.15% APS diet. This concentration also enhanced the antioxidant capacity and immunomodulation of the fish by regulating the expression of genes associated with antioxidant enzymes and immune responses. Intestinal microbiota analysis revealed that APS supplementation significantly increased the Chao1 index and relative abundance of beneficial bacteria (Firmicutes and Bacillus). A high level of APS (0.20%) did not provide additional benefits for growth and health compared to a moderate level (0.15%). These findings indicate that an optimal APS dose promotes growth, enhances antioxidant activity, supports immune function, and improves intestinal microbiota in coral trout. Based on a cubic regression analysis of the specific growth rate, the optimal APS level for the maximal growth of coral trout was determined to be 0.1455%. Full article

(This article belongs to the Special Issue Aquatic Microorganisms and Their Application in Aquaculture)

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13 pages, 1388 KiB

Open AccessArticle

Microeukaryotes Associated with Freshwater Mussels in Rivers of the Southeastern United States

by Akacia K. Halliday-Isaac and Colin R. Jackson

Microorganisms 2024, 12(9), 1835; https://doi.org/10.3390/microorganisms12091835 - 5 Sep 2024

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Abstract

Microeukaryotes are a diverse and often overlooked group of microbes that are important in food webs and other ecological linkages. Little is known about microeukaryotes associated with aquatic invertebrates, although filter feeders such as mussels are likely to take in and potentially retain [...] Read more.

Microeukaryotes are a diverse and often overlooked group of microbes that are important in food webs and other ecological linkages. Little is known about microeukaryotes associated with aquatic invertebrates, although filter feeders such as mussels are likely to take in and potentially retain microeukaryotes in their gut while feeding. Microeukaryotes such as apicomplexans have been reported in marine mussel species, but no studies have examined the presence of these microorganisms in freshwater mussels or how they relate to mussel host species or environmental conditions. In this study, microbial community DNA was extracted from the gut tissue of over 300 freshwater mussels, representing 22 species collected from rivers in the southeastern USA. Microeukaryote DNA was detected using PCR amplification, followed by the sequencing of positive amplicons. Microeukaryotes were found in 167 individual mussels (53%) of those tested. Amplicons included dinoflagellates/algae that differed between mussel species and are likely food sources that were distinct from those found in water and sediment samples analyzed concurrently. A total of 5% of the positive amplicons were non-photosynthetic alveolates that could represent parasitic microeukaryotes. Understanding the distribution of microeukaryotes in the freshwater mussel gut microbiome could further our understanding of the ongoing decline of mussel populations. Full article

(This article belongs to the Special Issue Aquatic Microorganisms and Their Application in Aquaculture)

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21 pages, 5963 KiB

Open AccessArticle

Host Gut-Derived Probiotic, Exiguobacterium acetylicum G1-33, Improves Growth, Immunity, and Resistance to Vibrio harveyi in Hybrid Grouper (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂)

by Mingqing Zhang, Yuwei Feng, Zhongxuan Zhong, Qianping Du, Wei Yu, Jinhui Wu, Xiaolin Huang, Zhong Huang, Guangting Xie and Hu Shu

Microorganisms 2024, 12(8), 1688; https://doi.org/10.3390/microorganisms12081688 - 16 Aug 2024

Cited by 2 | Viewed by 1136

Abstract

Several exogenous probiotics are applicable in fish culture; however, challenges in isolation and verification have hindered the full utilization of numerous host probiotics. Therefore, this study aimed to apply the host probiotic Exiguobacterium acetylicum G1-33 to hybrid grouper (Epinephelus fuscoguttatus ♀ × [...] Read more.

Several exogenous probiotics are applicable in fish culture; however, challenges in isolation and verification have hindered the full utilization of numerous host probiotics. Therefore, this study aimed to apply the host probiotic Exiguobacterium acetylicum G1-33 to hybrid grouper (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂) cultures and explore its mechanism of action. In total, 360 hybrid grouper were divided into four groups, which were fed the following for 60 days: three received commercial feed with varying concentrations of E. acetylicum G1-33 (10⁶, 10⁸, and 10¹⁰ CFU/g), while a control group received commercial feed. The results showed that supplementation with 10⁶ and 10⁸ CFU/g of E. acetylicum G1-33 enhanced gut morphology, upregulated growth-related genes (ghr1, igf-2, s6k1, tor), and promoted growth, with supplementation with 10⁸ CFU/g resulting in the most notable enhancement. However, supplementation with 10¹⁰ CFU/g inhibited growth, possibly because of changes in intestinal morphology. Additionally, supplementation with E. acetylicum G1-33 upregulated the expression of immune-related genes (c3, myd88, Cu/Zn-sod, tlr3, and tnf2) in the liver and head kidney but led to an increase in malondialdehyde content, as well as a decrease in alkaline phosphatase and acid phosphatase activities, in the liver and serum, indicating increased oxidative stress. Moreover, supplementation with 10⁶ and 10⁸ CFU/g E. acetylicum G1-33 enhanced the widespread expression of immune-related genes in the head kidney and liver, respectively, and improved resistance to Vibrio harveyi, whereas supplementation with 10¹⁰ CFU/g weakened this resistance. In conclusion, E. acetylicum G1-33, particularly at 10⁸ CFU/g, emerged as an effective probiotic, optimizing growth performance and immunity in hybrid grouper. This research is pioneering in its application of E. acetylicum in mariculture, potentially broadening the range of probiotic strategies in aquaculture. Full article

(This article belongs to the Special Issue Aquatic Microorganisms and Their Application in Aquaculture)

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13 pages, 1720 KiB

Open AccessArticle

Salmonirosea aquatica gen. nov., sp. nov., a Novel Genus within the Family Spirosomaceae, Was Isolated from Brackish Water in the Republic of Korea

by Kiwoon Baek, Sumin Jang, Jaeduk Goh and Ahyoung Choi

Microorganisms 2024, 12(8), 1671; https://doi.org/10.3390/microorganisms12081671 - 14 Aug 2024

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Abstract

A Gram-stain-negative, obligately aerobic, non-motile, rod-shaped bacterial strain designated SJW1-29^T was isolated from brackish water samples collected from the Seomjin River, Republic of Korea. The purpose of this study was to characterize strain SJW1-29^T and determine its taxonomic position as a [...] Read more.

A Gram-stain-negative, obligately aerobic, non-motile, rod-shaped bacterial strain designated SJW1-29^T was isolated from brackish water samples collected from the Seomjin River, Republic of Korea. The purpose of this study was to characterize strain SJW1-29^T and determine its taxonomic position as a potential new genus within the family Spirosomaceae. The strain grew within the range of 10–30 °C (optimum, 25 °C), pH 5.0–10.0 (optimum, 7.0), and 1–4% NaCl (optimum, 3%). Phylogenetic analysis based on the 16S rRNA gene revealed that strain SJW1-29^T belongs to the family Spirosomaceae and is closely related to Persicitalea jodogahamensis Shu-9-SY12-35C^T (91.3% similarity), Rhabdobacter roseus R491^T (90.6%), and Arundinibacter roseus DMA-K-7a^T (90.0%), while the similarities to strains within the order Cytophagales were lower than 90.0%. The genome is 7.1 Mbp with a G+C content of 50.7 mol%. The use of genome-relatedness indices confirmed that this strain belongs to a new genus. The major polar lipid profile consisted of phosphatidylethanolamine, and MK-7 was the predominant menaquinone. The predominant fatty acids were summed feature 3 (C_16:1 ω7c and/or C_16:1 ω6c), iso-C_15:0, iso-C_17:0 3-OH, and C_16:0, representing more than 80% of the total fatty acids. The phenotypic, chemotaxonomic, genetic, and phylogenetic properties suggest that strain SJW1-29^T represents a novel species within a new genus in the family Spirosomaceae, for which the name Salmonirosea aquatica gen. nov., sp. nov., is proposed. The type strain of Salmonirosea aquatica is SJW1-29^T (=KCTC 72493^T = NBRC 114061^T = FBCC-B16924^T). Full article

(This article belongs to the Special Issue Aquatic Microorganisms and Their Application in Aquaculture)

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22 pages, 7852 KiB

Open AccessArticle

Effects of Dietary Multi-Strain Probiotics on Growth Performance, Antioxidant Status, Immune Response, and Intestinal Microbiota of Hybrid Groupers (Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂)

by Guangting Xie, Xiaoying Chen, Yuwei Feng, Zhide Yu, Qiuqin Lu, Manfeng Li, Ziqi Ye, Heizhao Lin, Wei Yu and Hu Shu

Microorganisms 2024, 12(7), 1358; https://doi.org/10.3390/microorganisms12071358 - 2 Jul 2024

Cited by 5 | Viewed by 2123

Abstract

This study aims to examine the effects of the mixture of Bacillus cereus G1–11 and Exiguobacterium acetylicum G1–33, isolated from the gut of hybrid groupers (Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂), on the host. The hybrid groupers were divided into a [...] Read more.

This study aims to examine the effects of the mixture of Bacillus cereus G1–11 and Exiguobacterium acetylicum G1–33, isolated from the gut of hybrid groupers (Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂), on the host. The hybrid groupers were divided into a control (C, without any probiotics), B. cereus (BC, 10¹⁰ cfu/g), E. acetylicum (EA, 10⁸ cfu/g), compound (mix, a 1:1 mixture of B. cereus and E. acetylicum), and positive reference group (P, Lactobacillus acidophilus, 5 × 10⁸ cfu/L). Each group had four replicates, with 30 fish per replicate (53.30 ± 0.50 g), and were fed for 60 days. The results showed that adding probiotics to the feed significantly improved the weight gain, weight growth rate, specific growth rate, and digestive enzyme activities of hybrid groupers compared to the C group. The compound group was the most significant. In addition, composite probiotics added to feed significantly upregulated the expression levels of several growth-related genes in the liver and muscles. The activities of alkaline phosphatase, catalase, glutathione peroxidase, glutathione transferase, lysozyme, and total antioxidant capacity in the serum and liver were significantly influenced through mixed probiotic feeding. Moreover, the expression levels of several immune-related genes in the liver, spleen, and head kidney were significantly enhanced by adding single and mixed probiotics to feed, with the synergy of mixed probiotics being the best. An analysis of the gut microbiota showed that adding composite bacteria enhanced the richness and diversity of the gut microbiota, significantly increasing the relative abundance of potential probiotics (Cetobacterium and Microbacterium) while decreasing the presence of potential pathogens (Mycoplasma). Overall, our findings highlighted the efficacy of mixed probiotics (B. cereus and E. acetylicum) in enhancing growth performance, nutritional value of hybrid grouper feed, antioxidant capacity, immune response, and intestinal health, in finding the best combination of functional feed additives. Full article

(This article belongs to the Special Issue Aquatic Microorganisms and Their Application in Aquaculture)

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Review

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33 pages, 2342 KiB

Open AccessReview

Effects of Microorganisms in Fish Aquaculture from a Sustainable Approach: A Review

by Jesús Mateo Amillano-Cisneros, María Anel Fuentes-Valencia, José Belisario Leyva-Morales, Macario Savín-Amador, Henri Márquez-Pacheco, Pedro de Jesús Bastidas-Bastidas, Lucía Leyva-Camacho, Zamaria Yoselin De la Torre-Espinosa and César Noé Badilla-Medina

Microorganisms 2025, 13(3), 485; https://doi.org/10.3390/microorganisms13030485 - 21 Feb 2025

Cited by 1 | Viewed by 1451

Abstract

Aquaculture is the fastest-growing food production sector. However, it faces significant challenges, including demand from a growing global population, which is estimated to reach 10.4 billion by the year 2100, disease outbreaks, environmental impacts, and the overuse of antibiotics. To address these issues, [...] Read more.

Aquaculture is the fastest-growing food production sector. However, it faces significant challenges, including demand from a growing global population, which is estimated to reach 10.4 billion by the year 2100, disease outbreaks, environmental impacts, and the overuse of antibiotics. To address these issues, sustainable alternatives such as the use of microorganisms (probiotics, bacteriophages, and genetically modified microorganisms) have gained attention. This review examines the effects of these microorganisms on fish aquaculture, focusing on their potential to improve growth, health, and disease resistance while reducing environmental impacts. Probiotics, particularly lactic acid bacteria and yeasts, have been shown to enhance immune responses, digestive enzyme activity, and nutrient absorption in fish. Bacteriophages offer a promising alternative to antibiotics for controlling bacterial pathogens, with studies demonstrating their efficacy in reducing mortality rates in infected fish. Additionally, genetically modified microorganisms (GMMs) have been explored for their ability to produce beneficial compounds, such as enzymes and antimicrobial peptides, which can improve fish health and reduce the need for chemical treatments. Despite their potential, challenges such as regulatory hurdles, public acceptance, and environmental risks must be addressed. This review highlights the importance of further research to optimize the use of microorganisms in aquaculture and underscores their role in promoting sustainable practices. By integrating these biological tools, the aquaculture industry can move towards a more sustainable and environmentally friendly future. Full article

(This article belongs to the Special Issue Aquatic Microorganisms and Their Application in Aquaculture)

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