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Microorganisms
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Beneficial Microorganisms in Aquaculture
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Beneficial Microorganisms in Aquaculture

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Veterinary Microbiology".

Deadline for manuscript submissions: closed (31 August 2024) | Viewed by 10874

Special Issue Editors

Dr. Jovanka Lukić

E-Mail Website
Guest Editor
Laboratory for Molecular Microbiology (LMM), Institute of Molecular Genetics and Genetic Engineering (IMGGE), University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia
Interests: microorganisms as modulators of fish performance in aquaculture
Dr. Uroš Ljubobratović

E-Mail Website
Guest Editor
Research Centre of Aquaculture and Fisheries, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, H-5540 Szarvas, Hungary
Interests: intensive fish culture; fish reproduction; larviculture

Special Issue Information

Dear Colleagues,

This Special Issue seeks to uncover the role of microorganisms in the maintenance of health and welfare of cultured aquatic species, including animals and plants. Aside from in vivo studies, we welcome research using in vitro/ex vivo systems to study microorganism–host interactions in accordance with the 3Rs. Advanced lab-based methods, including cell lines, fish explant cultures, simulated in vitro digestion, etc., can substantially reduce the use of animals, at least in the initial screening or selection phases of research. We aim to provide a unique overview of the in vitro methods used to test the interaction between microbes and aquatic organisms. Furthermore, modifications of the nutritive value of feeds and live food (e.g., brine shrimp and rotifers), as well as the microbial composition of live food using microorganisms are of special interest. This may be particularly relevant for larval fish, which have incompletely developed digestive and immunological systems, making them vulnerable to microbial overgrowth and feed digestibility issues. We invite researchers to share innovative and applicative ex vivo and in vivo results that are relevant to the topic. The interpretation of the data should be based on thorough statistical analysis. Bioinformatics and machine learning methods would be highly appreciated. We additionally welcome review articles giving a systematic overview of microbiota compositions in different species at different life stages, etc. A systematized presentation of the existing knowledge about microbiota is necessary, considering the growing amount of information resulting from rapidly progressing microbiota sequencing methods.

Dr. Jovanka Lukić
Dr. Uroš Ljubobratović
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • microbiota
  • aquaculture
  • fish
  • growth stages
  • indoor rearing
  • feed digestion
  • infection

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Related Special Issue

Published Papers (7 papers)

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Research

21 pages, 2101 KiB  
Article
Bacillus spp. Isolated from Miang as Potential Probiotics in Nile Tilapia Culture—In Vitro Research
by Chioma Stella Anyairo, Kridsada Unban, Pairote Wongputtisin, Jiraporn Rojtinnakorn, Kalidas Shetty and Chartchai Khanongnuch
Microorganisms 2024, 12(8), 1687; https://doi.org/10.3390/microorganisms12081687 - 16 Aug 2024
Viewed by 927
Abstract
Among 79 Bacillus spp. isolated from Miang, a fermented tea in north Thailand, 17 Bacillus strains were selected with probiotic potential in Nile tilapia culture based on the capabilities of bacteriocin production and associated antimicrobial activities against fish pathogens, Aeromonas hydrophila and Streptococcus [...] Read more.
Among 79 Bacillus spp. isolated from Miang, a fermented tea in north Thailand, 17 Bacillus strains were selected with probiotic potential in Nile tilapia culture based on the capabilities of bacteriocin production and associated antimicrobial activities against fish pathogens, Aeromonas hydrophila and Streptococcus agalactiae. However, only six isolates were selected for further extensive studies based on the strength of their antimicrobial activities and their tolerance against simulated gastrointestinal conditions. The molecular identification by 16S rRNA gene sequence analysis revealed that five isolates, K2.1, K6.1, K7.1, K15.4, and K22.6, were Bacillus tequilensis, and the isolate K29.2 was Bacillus siamensis. B. siamensis K29.2 showed complete susceptibility to antibiotics tested in this study, while B. tequilensis K 15.4 showed moderate resistance to some antibiotics; therefore, both strains were selected as potential probiotic bacteria. B. tequilensis K15.4 and B. siamensis K29.2 were capable of the production and secretion of extracellular protease and polysaccharide degrading enzymes, including cellulase, xylanase, and β-mannanase. The tannin tolerant test also demonstrated their ability to grow on selective agar plates and secrete cellulase and β-mannanase in the presence of hydrolyzable tannin. In addition, in vitro digestion of commercial fish substrate revealed that the extracellular enzymes produced by both strains efficiently reacted with feed protein and polysaccharides. Based on the results from this study, B. siamensis K29.2 was deemed to have the highest potential multifunctional probiotic qualities for application in Nile tilapia culture, while the antibiotic-resistant gene in B. tequilensis K15.4 must be clarified before field application. Full article
(This article belongs to the Special Issue Beneficial Microorganisms in Aquaculture)
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14 pages, 3634 KiB  
Article
Effects of Dietary Bacillus amyloliquefaciens SCAU-070 (Based on a Woody Plant-Based Diet) on Antioxidation, Immune and Intestinal Microbiota of Tilapia (Oreochromis niloticus)
by Qijing Chen, Feng Wu, Xinye Chen, Qiaoting Yang, Biyin Ye, Xiaoyu Chen, Xiaoyong Zhang and Qin Pan
Microorganisms 2024, 12(6), 1049; https://doi.org/10.3390/microorganisms12061049 - 23 May 2024
Viewed by 874
Abstract
This study aimed to explore the effects of Bacillus amyloliquefaciens (BA) as one woody forage addition (as a probiotic, 1 × 107 CFU/g) on tilapia (Oreochromis niloticus). Woody forage is one kind of fishery feed that could significantly enhance the [...] Read more.
This study aimed to explore the effects of Bacillus amyloliquefaciens (BA) as one woody forage addition (as a probiotic, 1 × 107 CFU/g) on tilapia (Oreochromis niloticus). Woody forage is one kind of fishery feed that could significantly enhance the growth, feed utilization, and digestibility of tilapia. At first, tilapia was divided into eight groups and fed with control, control + BA, Moringa oleifera, M. oleifera + BA, Neolamarckia cadamba, N. cadamba + BA, Broussonetia papyrifera, and B. papyrifera + BA diets, respectively. After dieting for 8 weeks, the intestinal morphology of tilapia in the eight groups was observed, and the effects of the B. amyloliquefaciens addition and wordy forage on the intestine functions were analyzed by two-way ANOVA. As no significant negative effects were found on the woody forage on tilapia, the villus height, density and width, and epithelial goblet cells in the posterior intestines of tilapia with BA supplementation were greater than those in the groups without BA supplementation, suggesting B. amyloliquefaciens SCAU-070 could promote the growth and development of tilapia intestinal tracts. Furthermore, it was found that B. amyloliquefaciens SCAU-070 enhanced the antioxidation capacity of tilapia posterior intestine tissue by promoting the activity of superoxide dismutase and content of malondialdehyde. In addition, the result of high-throughput sequencing (16S rDNA) showed that the beneficial bacteria Cetobacterium and Romboutsia in the probiotic groups increased significantly, while the potential pathogenic bacteria Acinetobacter decreased significantly. Full article
(This article belongs to the Special Issue Beneficial Microorganisms in Aquaculture)
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15 pages, 3465 KiB  
Article
Gender Impacted Gut Microbiota and Growth Performance in the Blotched Snakehead (Channa maculata)
by Chang Fang, Fang Zeng, Shijun Chen, Shuisheng Li, Yuting Yang, Wanjing Lin, Yun Liu, Cheng Peng and Huirong Yang
Microorganisms 2024, 12(5), 871; https://doi.org/10.3390/microorganisms12050871 - 26 Apr 2024
Viewed by 1100
Abstract
The blotched snakehead Channa maculata is an important economical freshwater species in East Asia. However, there has been relatively little research conducted on the correlation between gender and gut microbes. In this study, 36 of 1000 blotched snakeheads were randomly selected for growth [...] Read more.
The blotched snakehead Channa maculata is an important economical freshwater species in East Asia. However, there has been relatively little research conducted on the correlation between gender and gut microbes. In this study, 36 of 1000 blotched snakeheads were randomly selected for growth performance measurement and gut microbiota high-throughput sequencing. Results showed that microbial diversity, composition, and metabolic functions were altered by gender and growth performance except the microbial network. In our study, Proteobacteria were the most abundant phylum, with Fusobacteria showing enrichment in males and Bacteroidetes in females. Notably, phylum Deinococcus-Thermus was identified as a significant biomarker. The Cetobacterium was the most abundant genus-level taxon. Furthermore, gut microbes specializing in the production of gut-healthy substances, such as coenzymes and vitamins, were identified as biomarkers in the fast-growing group. Our investigation highlighted the impact of gender on the composition and abundance of gut microbial biomarkers in both males and females, thereby influencing differential growth performance through the modulation of specific metabolic functions. Full article
(This article belongs to the Special Issue Beneficial Microorganisms in Aquaculture)
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21 pages, 13027 KiB  
Article
Variations and Interseasonal Changes in the Gut Microbial Communities of Seven Wild Fish Species in a Natural Lake with Limited Water Exchange during the Closed Fishing Season
by Yangyang Liang, Zijia Wang, Na Gao, Xiaoxue Qi, Juntao Zeng, Kai Cui, Wenxuan Lu and Shijie Bai
Microorganisms 2024, 12(4), 800; https://doi.org/10.3390/microorganisms12040800 - 16 Apr 2024
Viewed by 1551
Abstract
The gut microbiota of fish is crucial for their growth, development, nutrient uptake, physiological balance, and disease resistance. Yet our knowledge of these microbial communities in wild fish populations in their natural ecosystems is insufficient. This study systematically examined the gut microbial communities [...] Read more.
The gut microbiota of fish is crucial for their growth, development, nutrient uptake, physiological balance, and disease resistance. Yet our knowledge of these microbial communities in wild fish populations in their natural ecosystems is insufficient. This study systematically examined the gut microbial communities of seven wild fish species in Chaohu Lake, a fishing-restricted area with minimal water turnover, across four seasons. We found significant variations in gut microbial community structures among species. Additionally, we observed significant seasonal and regional variations in the gut microbial communities. The Chaohu Lake fish gut microbial communities were predominantly composed of the phyla Firmicutes, Proteobacteria(Gamma), Proteobacteria(Alpha), Actinobacteriota, and Cyanobacteria. At the genus level, Aeromonas, Cetobacterium, Clostridium sensu stricto 1, Romboutsia, and Pseudomonas emerged as the most prevalent. A co-occurrence network analysis revealed that C. auratus, C. carpio, and C. brachygnathus possessed more complex and robust gut microbial networks than H. molitrix, C. alburnus, C. ectenes taihuensis, and A. nobilis. Certain microbial groups, such as Clostridium sensu stricto 1, Romboutsia, and Pseudomonas, were both dominant and keystone in the fish gut microbial network. Our study offers a new approach for studying the wild fish gut microbiota in natural, controlled environments. It offers an in-depth understanding of gut microbial communities in wild fish living in stable, limited water exchange natural environments. Full article
(This article belongs to the Special Issue Beneficial Microorganisms in Aquaculture)
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14 pages, 3067 KiB  
Article
Early-Life Fecal Transplantation from High Muscle Yield Rainbow Trout to Low Muscle Yield Recipients Accelerates Somatic Growth through Respiratory and Mitochondrial Efficiency Modulation
by Guglielmo Raymo, Ali Ali, Ridwan O. Ahmed and Mohamed Salem
Microorganisms 2024, 12(2), 261; https://doi.org/10.3390/microorganisms12020261 - 26 Jan 2024
Cited by 1 | Viewed by 1248
Abstract
Previous studies conducted in our lab revealed microbial assemblages to vary significantly between high (ARS-FY-H) and low fillet yield (ARS-FY-L) genetic lines in adult rainbow trout. We hypothesized that a high ARS-FY-H donor microbiome can accelerate somatic growth in microbiome-depleted rainbow trout larvae [...] Read more.
Previous studies conducted in our lab revealed microbial assemblages to vary significantly between high (ARS-FY-H) and low fillet yield (ARS-FY-L) genetic lines in adult rainbow trout. We hypothesized that a high ARS-FY-H donor microbiome can accelerate somatic growth in microbiome-depleted rainbow trout larvae of the ARS-FY-L line. Germ-depleted larvae of low ARS-FY-L line trout reared in sterile environments were exposed to high- or low-fillet yield-derived microbiomes starting at first feeding for 27 weeks. Despite weight-normalized diets, somatic mass was significantly increased in larvae receiving high fillet yield microbiome cocktails at 27 weeks post-hatch. RNA-seq from fish tails reveals enrichment in NADH dehydrogenase activity, oxygen carrier, hemoglobin complex, gas transport, and respiratory pathways in high fillet yield recolonized larvae. Transcriptome interrogation suggests a relationship between electron transport chain inputs and body weight assimilation, mediated by the gut microbiome. These findings suggest that microbiome payload originating from high fillet yield adult donors primarily accelerates juvenile somatic mass assimilation through respiratory and mitochondrial input modulation. Further microbiome studies are warranted to assess how increasing beneficial microbial taxa could be a basis for formulating appropriate pre-, pro-, or post-biotics in the form of feed additives and lead to fecal transplantation protocols for accelerated feed conversion and fillet yield in aquaculture. Full article
(This article belongs to the Special Issue Beneficial Microorganisms in Aquaculture)
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16 pages, 3686 KiB  
Article
Co-Culturing Microalgae with Roseobacter Clade Bacteria as a Strategy for Vibrionaceae Control in Microalgae-Enriched Artemia
by José Pintado, Patricia Ruiz, Gonzalo Del Olmo and Pavlos Makridis
Microorganisms 2023, 11(11), 2715; https://doi.org/10.3390/microorganisms11112715 - 6 Nov 2023
Cited by 1 | Viewed by 1649
Abstract
Bacterial communities associated with fish larvae are highly influenced by the microbiota of live prey used as feed (rotifers or Artemia), generally dominated by bacterial strains with a low degree of specialization and high growth rates, (e.g., Vibrionaceae), which can be [...] Read more.
Bacterial communities associated with fish larvae are highly influenced by the microbiota of live prey used as feed (rotifers or Artemia), generally dominated by bacterial strains with a low degree of specialization and high growth rates, (e.g., Vibrionaceae), which can be detrimental to larvae. Co-cultivation of microalgae used in the enrichment of Artemia (e.g., Phaeodactylum tricornutum, or Chlorella minutissima) with Vibrio-antagonistic probiotics belonging to the Roseobacter clade bacteria (e.g., Phaeobacter spp. or Ruegeria spp.) was studied. The introduction of the probiotics did not affect microalgae growth or significantly modify the composition of bacterial communities associated with both microalgae, as revealed by DGGE analysis. The inoculation of P. tricornutum with Ruegeria ALR6 allowed the maintenance of the probiotic in the scale-up of the microalgae cultures, both in axenic and non-axenic conditions. Using Ruegeria-inoculated P. tricornutum cultures in the enrichment of Artemia reduced the total Vibrionaceae count in Artemia by 2 Log units, therefore preventing the introduction of opportunistic or pathogenic bacteria to fish larvae fed with them. Full article
(This article belongs to the Special Issue Beneficial Microorganisms in Aquaculture)
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23 pages, 10045 KiB  
Article
Long-Term Application of a Synbiotic Chitosan and Acinetobacter KU011TH Mixture on the Growth Performance, Health Status, and Disease Resistance of Hybrid Catfish (Clarias gariepinus × C. macrocephalus) during Winter
by Pisey Say, Sukkrit Nimikul, Anurak Bunnoy, Uthairat Na-Nakorn and Prapansak Srisapoome
Microorganisms 2023, 11(7), 1807; https://doi.org/10.3390/microorganisms11071807 - 14 Jul 2023
Cited by 2 | Viewed by 1687
Abstract
The effects of potential synbiotic chitosan and Acinetobacter KU011TH mixture on growth performance, immune response, and A. hydrophila resistance were investigated for the first time. The control group was fed a basal diet (A), and group B was given the formula B diet [...] Read more.
The effects of potential synbiotic chitosan and Acinetobacter KU011TH mixture on growth performance, immune response, and A. hydrophila resistance were investigated for the first time. The control group was fed a basal diet (A), and group B was given the formula B diet that was supplemented with chitosan at 20 mL/kg diet via top dressing. The other synbiotic groups, C, D, and E, were top-dressed with the target probiotics at 1 × 108, 1 × 109, and 1 × 1010 CFU/kg diet, respectively, and coated with the same concentration of chitosan. Fish were continuously fed the five different feeds for 16 weeks during winter. At the end of the trial, the growth parameters of the test groups did not significantly differ from those of the control (p > 0.05). All the symbiotic-chitosan treatments significantly increased various hematological and serum immune parameters. Moreover, the expression levels of immune-related genes were strongly elevated in the head kidney and spleen, whereas upregulated expression was observed in the liver and whole blood (p < 0.05). Survival analysis indicated that fish in groups B and C showed significantly higher survival (84.33 ± 2.21 and 79.50 ± 6.34%) than those in groups A, D and E (55.33 ± 8.82%–74.00 ± 6.50) (p < 0.05) after injection with A. hydrophila for 14 days. Full article
(This article belongs to the Special Issue Beneficial Microorganisms in Aquaculture)
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