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Microorganisms
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Dietary Components and Gut Microbes in Fish
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Dietary Components and Gut Microbes in Fish

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

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 12054

Special Issue Editors

Prof. Dr. Shimei Lin

E-Mail Website
Guest Editor
College of Fisheries, Southwest University, Chongqing, China
Interests: protein sources; starch level; functional compounds; liver health; intestinal microbes
Dr. Yongjun Chen

E-Mail Website
Guest Editor
College of Fisheries, Southwest University, Chongqing, China
Interests: carbohydrate utilization; glycolipid metabolism; liver health; feed additives; fish species

Special Issue Information

Dear Colleagues,

The gastrointestinal tract is as one of the major routes of infection in fish. Thus, healthy gut microbiota is essential to promote host health and well-being of fish. The intestinal microbiota of fish is classified as autochthonous when they are able to colonize the host's epithelial surface or are associated with the microvilli, or as allochthonous (associated with digesta or present in the lumen). The gut microbiota of fish is highly sensitive to dietary changes. It is demonstrated that dietary macronutrients, micronutrients, and feed additives (including but not limited to functional glycomic ingredients, probiotics, prebiotics, synbiotics, and immunostimulants) substantially affect the gut microbiota of fish. Furthermore, some information is available on bacterial colonization of the gut enterocyte surface as a result of dietary manipulation, which indicates that changes in indigenous microbial populations may have repercussions on secondary host–microbe interactions.

This Special Issue aims to gather up-to-date research on the effect of dietary components on the gut microbiota and will cover the following topics:

  • Dietary macronutrients on gut microbes
  • Dietary micronutrients on gut microbes
  • Diet shift on gut microbes
  • Functional glycomic ingredients on gut microbes
  • Dietary microecologics on gut microbes
  • Feed immunostimulants on gut microbes

Prof. Dr. Shimei Lin
Dr. Yongjun Chen
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

  • gut microbes
  • feed immunostimulants
  • functional compounds
  • liver health
  • glycolipid metabolism

Published Papers (7 papers)

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Research

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19 pages, 3300 KiB  
Article
Unveiling the Probiotic Potential of the Anaerobic Bacterium Cetobacterium sp. nov. C33 for Enhancing Nile Tilapia (Oreochromis niloticus) Cultures
by Mario Andrés Colorado Gómez, Javier Fernando Melo-Bolívar, Ruth Yolanda Ruíz Pardo, Jorge Alberto Rodriguez and Luisa Marcela Villamil
Microorganisms 2023, 11(12), 2922; https://doi.org/10.3390/microorganisms11122922 - 05 Dec 2023
Viewed by 1176
Abstract
The bacterium strain Cetobacterium sp. C33 was isolated from the intestinal microbial content of Nile tilapia (O. niloticus) under anaerobic conditions. Given that Cetobacterium species are recognized as primary constituents of the intestinal microbiota in cultured Nile tilapia by culture-independent [...] Read more.
The bacterium strain Cetobacterium sp. C33 was isolated from the intestinal microbial content of Nile tilapia (O. niloticus) under anaerobic conditions. Given that Cetobacterium species are recognized as primary constituents of the intestinal microbiota in cultured Nile tilapia by culture-independent techniques, the adaptability of the C33 strain to the host gastrointestinal conditions, its antibacterial activity against aquaculture bacterial and its antibiotic susceptibility were assessed. The genome of C33 was sequenced, assembled, annotated, and subjected to functional inference, particularly regarding pinpointed probiotic activities. Furthermore, phylogenomic comparative analyses were performed including closely reported strains/species relatives. Comparative genomics with closely related species disclosed that the isolate is not phylogenetically identical to other Cetobacterium species, displaying an approximately 5% sequence divergence from C. somerae and a 13% sequence divergence from Cetobacterium ceti. It can be distinguished from other species through physiological and biochemical criteria. Whole-genome annotation highlighted that Cetobacterium sp. nov. C33 possesses a set of genes that may contribute to antagonism against competing bacteria and has specific symbiotic adaptations in fish. Additional in vivo experiments should be carried out to verify favorable features, reinforcing its potential as a probiotic bacterium. Full article
(This article belongs to the Special Issue Dietary Components and Gut Microbes in Fish)
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18 pages, 3786 KiB  
Article
Feed Regime Slightly Modifies the Bacterial but Not the Fungal Communities in the Intestinal Mucosal Microbiota of Cobia Fish (Rachycentron canadum)
by Samira Reinoso, María Soledad Gutiérrez, Angélica Reyes-Jara, Magaly Toro, Katherine García, Guillermo Reyes, Wilfrido Argüello-Guevara, Milton Bohórquez-Cruz, Stanislaus Sonnenholzner and Paola Navarrete
Microorganisms 2023, 11(9), 2315; https://doi.org/10.3390/microorganisms11092315 - 14 Sep 2023
Cited by 1 | Viewed by 1583
Abstract
The bacterial community of the intestinal microbiota influences many host functions, and similar effects have been recently reported for the fungal community (mycobiota). Cobia is a tropical fish that has been studied for its potential in marine aquaculture. However, the study of its [...] Read more.
The bacterial community of the intestinal microbiota influences many host functions, and similar effects have been recently reported for the fungal community (mycobiota). Cobia is a tropical fish that has been studied for its potential in marine aquaculture. However, the study of its bacterial community has been underreported and the mycobiota has not been investigated. We analyzed the gut bacterial and fungal profile present in the intestinal mucosa of reared adult cobias fed two diets (frozen fish pieces (FFPs) and formulated feed (FF)) for 4 months by sequencing the 16S rRNA (V3-V4) and internal transcribed spacer-2 (ITS2) regions using Illumina NovaSeq 6000. No significant differences in the alpha diversity of the bacterial community were observed, which was dominated by the phyla Proteobacteria (~96%) and Firmicutes (~1%). Cobia fed FF showed higher abundance of 10 genera, mainly UCG-002 (Family Oscillospiraceae) and Faecalibacterium, compared to cobia fed FFPs, which showed higher abundance of 7 genera, mainly Methylobacterium-Methylorubrum and Cutibacterium. The inferred bacterial functions were related to metabolism, environmental information processing and cellular processes; and no differences were found between diets. In mycobiota, no differences were observed in the diversity and composition of cobia fed the two diets. The mycobiota was dominated by the phyla Ascomycota (~88%) and Basidiomycota (~11%). This is the first study to describe the gut bacterial and fungal communities in cobia reared under captive conditions and fed on different diets and to identify the genus Ascobulus as a new member of the core fish mycobiota. Full article
(This article belongs to the Special Issue Dietary Components and Gut Microbes in Fish)
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12 pages, 3463 KiB  
Article
The Gut Microbiota of Farmed and Wild Brook Trout (Salvelinus fontinalis): Evaluation of Feed-Related Differences Using 16S rRNA Gene Metabarcoding
by Davide Mugetti, Paolo Pastorino, Chiara Beltramo, Tania Audino, Alessandra Arillo, Giuseppe Esposito, Marino Prearo, Marco Bertoli, Elisabetta Pizzul, Elena Bozzetta, Pier Luigi Acutis and Simone Peletto
Microorganisms 2023, 11(7), 1636; https://doi.org/10.3390/microorganisms11071636 - 22 Jun 2023
Viewed by 1976
Abstract
The gut microbiota has become a topic of increasing importance in various fields, including aquaculture. Several fish species have been the subject of investigations concerning the intestinal microbiota, which have compared different variables, including the intestinal portions, the environment, and diet. In this [...] Read more.
The gut microbiota has become a topic of increasing importance in various fields, including aquaculture. Several fish species have been the subject of investigations concerning the intestinal microbiota, which have compared different variables, including the intestinal portions, the environment, and diet. In this study, the microbiota of farmed and wild brook trout (Salvelinus fontinalis) were analyzed, in which the wall and content of the medial portion of the intestine were considered separately. A total of 66 fish (age class 2+) were sampled, of which 46 were wild and 20 were farmed brook trout, in two different years. Microbiota data were obtained using a 16S metabarcoding approach by analyzing the V3–V4 hypervariable regions of the corresponding 16S rRNA. The data showed that the core microbiota of these species consist of Proteobacteria (Alpha- and Gammaproteobacteria), Actinobacteria, Firmicutes (Bacilli and Clostridia), and, only for farmed animals, Fusobacteria. The latter taxon’s presence is likely related to the fishmeal-based diet administered to farmed brook trout. Indeed, alpha and beta diversity analysis showed differences between wild and farmed fish. Finally, statistically significant differences in the microbiota composition were observed between the intestinal walls and contents of wild fish, while no differences were detected in reared animals. Our work represents the first study on the intestinal microbiota of brook trout with respect to both farmed and wild specimens. Future studies might focus on the comparison of our data with those pertaining to other fish species and on the study of other portions of the brook trout intestine. Full article
(This article belongs to the Special Issue Dietary Components and Gut Microbes in Fish)
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29 pages, 7655 KiB  
Article
The Effects of Different Feeding Regimes on Body Composition, Gut Microbial Population, and Susceptibility to Pathogenic Infection in Largemouth Bass
by Yao Zheng, Haojun Zhu, Quanjie Li and Gangchun Xu
Microorganisms 2023, 11(5), 1356; https://doi.org/10.3390/microorganisms11051356 - 22 May 2023
Cited by 2 | Viewed by 1250
Abstract
This study investigated the effects of dietary commercial feed (n = 50,025 in triplicate, named group PF for soil dike pond, sampling n = 7; n = 15,000 in triplicate, WF for water tank, n = 8), iced fish (n = [...] Read more.
This study investigated the effects of dietary commercial feed (n = 50,025 in triplicate, named group PF for soil dike pond, sampling n = 7; n = 15,000 in triplicate, WF for water tank, n = 8), iced fish (n = 50,025 in triplicate, PI, n = 7), and a combination of both (n = 50,025 in triplicate, PFI, n = 8) on different metabolic parameters of the largemouth bass, Micropterus salmoides (0.67 ± 0.09 g, culture period from June 2017 to July 2018). Throughout the experimental period, different areas of water (including input water of the front, middle of the pond, and from the drain off at the back) and their mixed samples were simultaneously analyzed to find the source of the main infectious bacteria. Various feeding strategies may differentially affect body composition and shape the gut microbiota, but the mode of action has not been determined. Results showed that no significant differences were found in the growth performance except for the product yield using a different culture mode (PFI vs. WF). For muscle composition, the higher ∑SFA, ∑MUFA, ∑n-6PUFA, and 18:3n-3/18:2n-6 levels were detected in largemouth bass fed with iced fish, while enrichment in ∑n-3PUFA and ∑HUFA was detected in largemouth bass fed with commercial feed. For the gut microbiota, Fusobacteria, Proteobacteria, and Firmicutes were the most dominant phyla among all the gut samples. The abundance of Firmicutes and Tenericutes significantly decreased and later increased with iced fish feeding. The relative abundance of species from the Clostridia, Mollicutes, Mycoplasmatales, and families (Clostridiaceae and Mycoplasmataceae) significantly increased in the feed plus iced fish (PFI) group relative to that in the iced fish (PI) group. Pathways of carbohydrate metabolism and the digestive system were enriched in the commercial feed group, whereas infectious bacterial disease resistance-related pathways were enriched in the iced fish group, corresponding to the higher rate of death, fatty liver disease, and frequency and duration of cyanobacteria outbreaks. Feeding with iced fish resulted in more activities in the digestive system and energy metabolism, more efficient fatty acid metabolism, had higher ∑MUFA, and simultaneously had the potential for protection against infectious bacteria from the environment through a change in intestinal microbiota in the pond of largemouth bass culturing. Finally, the difference in feed related to the digestive system may contribute to the significant microbiota branch in the fish gut, and the input and outflow of water affects the intestinal flora in the surrounding water and in the gut, which in turn affects growth and disease resistance. Full article
(This article belongs to the Special Issue Dietary Components and Gut Microbes in Fish)
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16 pages, 3727 KiB  
Article
The Effect of the Microalgae Chlorella vulgaris on the Gut Microbiota of Juvenile Nile Tilapia (Oreochromis niloticus) Is Feeding-Time Dependent
by Zhicheng Huang, Jinyan Gao, Chunyan Peng, Jingjing Song, Zongsheng Xie, Jixin Jia, Haochen Li, Shumiao Zhao, Yunxiang Liang and Bin Gong
Microorganisms 2023, 11(4), 1002; https://doi.org/10.3390/microorganisms11041002 - 12 Apr 2023
Cited by 5 | Viewed by 2245
Abstract
Chlorella vulgaris is one of the most commonly used microalgae in aquaculture feeds. It contains high concentrations of various kinds of nutritional elements that are involved in the physiological regulation of aquaculture animals. However, few studies have been conducted to illustrate their influence [...] Read more.
Chlorella vulgaris is one of the most commonly used microalgae in aquaculture feeds. It contains high concentrations of various kinds of nutritional elements that are involved in the physiological regulation of aquaculture animals. However, few studies have been conducted to illustrate their influence on the gut microbiota in fish. In this work, the gut microbiota of Nile tilapia (Oreochromis niloticus) (average weight is 6.64 g) was analyzed by high-throughput sequencing of the 16S rRNA gene after feeding with 0.5% and 2% C. vulgaris additives in diets for 15 and 30 days (average water temperature was 26 °C). We found that the impact of C. vulgaris on the gut microbiota of Nile tilapia was feeding-time dependent. Only by feeding for 30 days (not 15 days) did the addition of 2% C. vulgaris to diets significantly elevate the alpha diversity (Chao1, Faith pd, Shannon, Simpson, and the number of observed species) of the gut microbiota. Similarly, C. vulgaris exerted a significant effect on the beta diversity (Bray–Curtis similarity) of the gut microbiota after feeding for 30 days (not 15 days). During the 15-day feeding trial, LEfSe analysis showed that Paracoccus, Thiobacillus, Dechloromonas, and Desulfococcus were enriched under 2% C. vulgaris treatment. During the 30-day feeding trial, Afipia, Ochrobactrum, Polymorphum, Albidovulum, Pseudacidovorax, and Thiolamprovum were more abundant in 2% C. vulgaris-treated fish. C. vulgaris promoted the interaction of gut microbiota in juvenile Nile tilapia by increasing the abundance of Reyranella. Moreover, during the feeding time of 15 days, the gut microbes interacted more closely than those during the feeding time of 30 days. This work will be valuable for understanding how C. vulgaris in diets impacts the gut microbiota in fish. Full article
(This article belongs to the Special Issue Dietary Components and Gut Microbes in Fish)
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26 pages, 5673 KiB  
Article
The Development of the Bacterial Community of Brown Trout (Salmo trutta) during Ontogeny
by Katharina Keiz, Sebastian Ulrich, Jasmin Wenderlein, Patrick Keferloher, Anna Wiesinger, Klaus Neuhaus, Ilias Lagkouvardos, Helmut Wedekind and Reinhard K. Straubinger
Microorganisms 2023, 11(1), 211; https://doi.org/10.3390/microorganisms11010211 - 14 Jan 2023
Cited by 2 | Viewed by 1945
Abstract
Brown trout (Salmo trutta) is an important aquaculture species in Germany, but its production faces challenges due to global warming and a high embryo mortality. Climate factors might influence the fish’s bacterial community (BC) and thus increase embryo mortality. Yet, knowledge [...] Read more.
Brown trout (Salmo trutta) is an important aquaculture species in Germany, but its production faces challenges due to global warming and a high embryo mortality. Climate factors might influence the fish’s bacterial community (BC) and thus increase embryo mortality. Yet, knowledge of the physiological BC during ontogeny in general is scarce. In this project, the BC of brown trout has been investigated in a period from unfertilized egg to 95 days post fertilization (dpf) using 16S rRNA gene amplicon sequencing. Developmental changes differed between early and late ontogeny and major differences in BC occurred especially during early developmental stages. Thus, analysis was conducted separately for 0 to 67 dpf and from 67 to 95 dpf. All analyzed stages were sampled in toto to avoid bias due to different sampling methods in different developmental stages. The most abundant phylum in the BC of all developmental stages was Pseudomonadota, while only two families (Comamonadaceae and Moraxellaceae) occurred in all developmental stages. The early developmental stages until 67 dpf displayed greater shifts in their BC regarding bacterial richness, microbial diversity, and taxonomic composition. Thereafter, in the fry stages, the BC seemed to stabilize and changes were moderate. In future studies, a reduction in the sampling time frames during early development, an increase in sampling numbers, and an attempt for biological reproduction in order to characterize the causes of these variations is recommended. Full article
(This article belongs to the Special Issue Dietary Components and Gut Microbes in Fish)
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Review

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17 pages, 1024 KiB  
Review
Advances in the Effects of Dietary Macronutrients on the Gut Microbiota of Tilapia (Oreochromis spp.)
by Weihao Ou, Zihe Guo, Ying Pan, Kai Huang, Yanqun Ma and Zhibiao Qin
Microorganisms 2024, 12(3), 543; https://doi.org/10.3390/microorganisms12030543 - 08 Mar 2024
Viewed by 646
Abstract
The homeostasis of the intestinal microbiota of fish is beneficial to fish health, while food can affect the intestinal microbiota. Tilapia (Oreochromis spp.) has great economic value and is a good model to use in studying the digestion and absorption of nutrients. [...] Read more.
The homeostasis of the intestinal microbiota of fish is beneficial to fish health, while food can affect the intestinal microbiota. Tilapia (Oreochromis spp.) has great economic value and is a good model to use in studying the digestion and absorption of nutrients. Furthermore, at present, due to a high demand and high price of high-quality feed raw materials, the nutritional composition of aquafeeds has been changing dynamically. There has yet to be a comprehensive review of research conducted on the influences of dietary macronutrients (proteins, lipids, and carbohydrates) on the tilapia intestinal microbiota. Therefore, this review focuses on the effects of dietary macronutrients on the gut microbiota of tilapia. Interestingly, we found that the best growth performance might not represent the best composition or functions of the gut microbiota. Overall, the unscientific addition of macronutrients to feed is harmful to the intestinal microbiota. Therefore, both growth performance and gut microbiota should be considered when evaluating certain macronutrients. It is our hope that this review will aid in regulating the intestinal microbiota of fish through nutritional means, thereby promoting tilapia farming. Full article
(This article belongs to the Special Issue Dietary Components and Gut Microbes in Fish)
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