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Gut Microbiota in Fish and Shellfish

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A special issue of Fishes (ISSN 2410-3888). This special issue belongs to the section "Welfare, Health and Disease".

Deadline for manuscript submissions: closed (20 December 2022) | Viewed by 31896

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Special Issue Editors

Dr. Dariel Tovar-Ramı́rez

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Guest Editor

Centro de Investigaciones Biológicas del Noroeste SC, La Paz, Mexico
Interests: the effects of probiotics; the effects of prebiotics and symbiotics on metabolism; microbiota and immune response of fish; our methodologies include biochemical and molecular approaches, such as fluorescent enzymology, functional genomics (qRT-PCR), and transcriptomics (NGS and microarrays); microbiome analysis

Dr. Xiaolin Meng

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Guest Editor

College of Fisheries, Henan Normal University, Xinxiang 453007, China
Interests: intestinal microbiota; probiotics; prebiotics; Chinese herbal medicine; environmental stress; pollutants

Dr. Xulu Chang

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Guest Editor

College of Fisheries, Henan Normal University, Xinxiang 453007, China
Interests: gut microbiota; probiotics; environmental pollutants; Cyprinus carpio

Dr. Yafei Duan

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Guest Editor

South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
Interests: environmental stress; aquatic toxicology; pollutants; intestine microbiota; nutritional immunity; multiomics
Special Issues, Collections and Topics in MDPI journals

Dr. Guokun Yang

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Guest Editor

College of Fisheries, Henan Normal University, Xinxiang 453007, China
Interests: gut microbiota; probiotics; endocrinology; metabolism

Special Issue Information

Dear Colleagues,

The gut microbiota of fish and shellfish are known to play a significant role in a number of physiological functions, including immune regulation, nutrition metabolism, development, behavior, and pathogen resistance. Dysfunction of the gut microbiota could induce numerous diseases in fishes and shellfish. In addition, the composition of the gut microbial communities in fishes and shellfish is affected by exogenous and endogenous factors, such as species differences, developmental stage, diet composition, habitat and surrounding environment (e.g., water temperature and salinity), rearing conditions, and, possibly, phylogenetic position. However, compared with mammals, an insufficient amount of research has been conducted on fish and shellfish gut microbes; therefore, I am pleased to invite you to contribute to the Special Issue “Gut Microbiota in Fish and Shellfish” in the journal Fishes.

Dr. Dariel Tovar-Ramı́rez
Dr. Xiaolin Meng
Dr. Xulu Chang
Dr. Yafei Duan
Dr. Guokun Yang
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. Fishes 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 2600 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

intestinal microbes
probiotics
prebiotics
herbal medicine
environmental stress
pollutants
metabolism
immunology
behavior
genetic

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Published Papers (10 papers)

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Research

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11 pages, 1990 KiB

Open AccessArticle

High Abundance of Candidatus Arthromitus in Intestinal Microbiota of Seriolella violacea (Palm Ruff) under Reared Conditions

by Jaime Romero, Natalia Catalán, Carolina Ramírez, Claudio D. Miranda, Marcia Oliva, Héctor Flores, María Soledad Romero and Rodrigo Rojas

Fishes 2023, 8(2), 109; https://doi.org/10.3390/fishes8020109 - 13 Feb 2023

Cited by 2 | Viewed by 2296

Abstract

Intestinal microbiota has been involved in several processes that benefit the host, such as digestion, nutrient metabolism, resistance to pathogens colonization and immune function. In this study, we investigated the diversity, composition and functional prediction of microbiota of reared Seriolella violacea (palm ruff) in the same cohort sampled at different times (7-, 8- and 9-month-old). Microbial community structure analyses, using 16S rRNA amplicon sequencing, revealed that the intestinal microbiota was dominated by the phyla Firmicutes, Proteobacteria, Fusobacteria and Tenericutes. At the genus level, Candidatus Arthromitus was the most abundant in all sampled timepoints, representing in average 78% of the bacterial community (ranging from 18 to 98%), corresponding to segmented filamentous bacteria, which are interesting because they have been associated with the maturation of immune responses in the gut and protecting the host from bacterial infections. The comparisons of the intestinal microbiota among the three groups showed differences in abundance of bacterial taxa and also in alpha diversity indexes (Shannon and Simpson), as well as beta diversity metrics (weighted and unweighted UniFrac). Potential functions of the intestinal microbiota of palm ruff were retrieved using Philipin and Tax4fun and these analyses revealed high levels of genes for sugar metabolism. To our knowledge, this study represents the first description of the intestinal microbiota of S. violacea. Full article

(This article belongs to the Special Issue Gut Microbiota in Fish and Shellfish)

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15 pages, 3234 KiB

Open AccessArticle

Insights into the Relationship between Intestinal Microbiota of the Aquaculture Worm Sipunculus nudus and Surrounding Sediments

by Junwei Li, Suwen Chen, Peng Wu, Changbo Zhu, Ruiping Hu, Ting Li and Yongjian Guo

Fishes 2023, 8(1), 32; https://doi.org/10.3390/fishes8010032 - 3 Jan 2023

Cited by 7 | Viewed by 1912

Abstract

Sipunculus nudus is an important intertidal aquaculture species that can ingest organic matter from the surface sediment and shows a high transportation capacity in sediment. However, little is known about the influence of intertidal aquaculture species on the sediment microbial community and the exchange of microbiota between the intestine and the surrounding sediment. In this study, the microbial communities in the intestine of S. nudus and three kinds of surrounding sediments were analyzed using high-throughput sequencing of the 16S rRNA gene amplicon, and the relationships between different communities were examined. Principal coordinate analysis and ANOSIM/Adonis analysis showed that the microbial communities of worm intestine samples were significantly different from those of surrounding sediments (p < 0.05). Meanwhile, compared with the sediment samples, the microbial α-diversity was significantly lower in the intestinal samples. Although the relative abundances of Proteobacteria and Cyanobacteria were high in all samples, three phyla (Bacteroidetes, Gemmatimonadetes, and Latescibacteria) showed a great difference between the four groups, as the abundances of the three phyla were significantly lower in the intestinal samples. Moreover, several microbial interactions were found between the worm intestine and surrounding sediments. BugBase functional prediction analysis indicated that the oxygen status of the sediment and the intestine was changed by bioturbation by the worm. Therefore, the microenvironment and microbial community in sediment were affected by the activity of S. nudus in the intertidal aquaculture zone. Full article

(This article belongs to the Special Issue Gut Microbiota in Fish and Shellfish)

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10 pages, 1793 KiB

Open AccessCommunication

Characterization of the Gut Microbiota of Mackerel Icefish, Champsocephalus gunnari

by Hokyung Song, Seungyeon Lee, Dong-Won Han and Jin-Hyoung Kim

Fishes 2023, 8(1), 13; https://doi.org/10.3390/fishes8010013 - 26 Dec 2022

Cited by 2 | Viewed by 2308

Abstract

The gut microbiome of Antarctic fish species has rarely been studied due to difficulties in obtaining samples. The mackerel icefish, Champsocephalus gunnari, primary feeds on krill and is one of the key species in the food web of the Southern Ocean. In this study, we characterized the gut microbiota of C. gunnari by sequencing the V3–V4 region of the bacterial 16S rRNA gene based on the Illumina MiSeq sequencing platform. We collected three types of samples: (1) whole intestine, (2) intestinal wall, and (3) intestinal content. The results showed no significant difference in the alpha diversity between different sample types. However, the microbial community composition of intestinal wall samples was distinct from other sample types. The relative abundance of Photobacterium was higher in intestinal content compared with the walls, which could be due to their chitinolytic activity. In contrast, potential pathogens such as Escherichia, Shigella, and Pseudomonas relatively more abundant in the intestinal wall compared with the intestinal contents. Unlike the gut microbiome of other marine fish species, Vibrio and Lactobacillus were nearly absent in the gut microbiome of C. gunnari. Functional gene profile of the gut microbiome predicted by PICRUSt2 showed higher relative abundance of genes related to biodegradation of nutrients in intestinal content. In contrast, the relative abundance of genes related to biosynthesis of important metabolites, such as menaquinols, was higher in intestinal wall. The difference in the microbial community structure of intestinal wall and intestinal content found in our study supports niche separation in the gut environment and emphasizes the importance of collecting intestinal wall samples in addition to intestinal content samples to understand the full picture of gut microbiome. This is the first time that the gut microbiome of mackerel icefish has been characterized using next-generation sequencing. Full article

(This article belongs to the Special Issue Gut Microbiota in Fish and Shellfish)

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19 pages, 4956 KiB

Open AccessArticle

Effects of Dietary Tannic Acid on Growth, Digestion, Immunity and Resistance to Ammonia Stress, and Intestinal Microbial Community in Pacific White Shrimp (Litopenaeus vannamei)

by Han Gong, Zhen Qin, Zhao Chen, Jitao Li, Zhiqiang Chang, Jian Li and Ping Chen

Fishes 2022, 7(6), 327; https://doi.org/10.3390/fishes7060327 - 10 Nov 2022

Cited by 10 | Viewed by 2647

Abstract

Tannic acid (TA) has great potential as a new feed additive. In this study, we investigated the effects of dietary TA on growth, digestion, nonspecific immunity, and resistance to ammonia stress and intestinal microbiota in Litopenaeus vannamei. The shrimp were fed diets containing different levels of TA: 0 mg/kg (TA-0), 200 mg/kg (TA-200), 400 mg/kg (TA-400), and 800 mg/kg (TA-800) for 56 days, followed by acute ammonia stress for 48 h. The results showed that dietary TA increased the survival rate of the TA-800 group. Dietary TA could improve the morphology of the hepatopancreas and intestinal tissues. After feeding different levels of TA for 56 days, the activities of amylase (AMS) and trypsin (Tryp) were increased, but the activity of lipase (LPS) was decreased. The activities of T-AOC, SOD, and PPO were higher in the hepatopancreas of the three TA treatment groups (p < 0.05). When shrimp were exposed to ammonia stress for 48 h, the activity of immune enzymes (LZM, T-AOC and SOD) and the expression levels of immune genes (LZM, proPO and Cu/Zn-SOD) were higher in the three TA treatment groups (p < 0.05). Furthermore, dietary TA also changed the composition of intestinal microflora by increasing the abundance of Planctomycetes, but decreasing the abundance of Bacteroides and Proteobacteria. The abundance of Rhodopirellula, Ruegeria, and Rhodobacter were higher, but that of Paracoccus, Algoriphagus, Cellvibrio, Flavobacteriaceae, and Bacteroides were lower in response to dietary TA. These results revealed that dietary TA had a positive effect on growth and intestinal microbial composition and enhanced the immune response to ammonia stress in shrimp. Therefore, TA can be a potential natural alternative antibiotic substitute for feed additives in shrimp, and the appropriate supplemental dosage is 400–800 mg/kg in the diet. Full article

(This article belongs to the Special Issue Gut Microbiota in Fish and Shellfish)

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14 pages, 3048 KiB

Open AccessFeature PaperArticle

Differential Study of Microbiota in the Gill and Intestine of Silver Carp (Hypophthalmichthys molitrix) from the Algae-Dominated and Hydrophyte-Dominated Areas of Taihu Lake, China

by Dan Zhou, Ting Zhang, Long Ren, Di-An Fang and Dong-Po Xu

Fishes 2022, 7(6), 304; https://doi.org/10.3390/fishes7060304 - 25 Oct 2022

Cited by 5 | Viewed by 2478

Abstract

Both fish gills and guts can support lots of microbiota that play important roles in the health and growth of hosts. Although the microbiota of silver carp has been widely studied, the data on microbial variation according to fish tissues and local habitats are lacking. In this study, the microbes in the guts and gills of silver carp (Hypophthalmichthys molitrix) from the hydrophyte-dominated region (zone H) and the algae-dominated region (zone A) of Taihu Lake in autumn were analyzed. Proteobacteria, Cyanobacteria, and Firmicutes were the dominant bacteria in silver carp. The microbial diversity was higher in the gills than that in the intestines, and higher in fish from zone H than that from zone A. Beta diversity analysis revealed significant differences in microbial community structures between gill and guts, and between fish from the two habitats. Gills had a higher abundance of phyla Actinobacteria, Bacteroidetes, and Deinococcus-Thermus, and a lower abundance of verrucomicrobia than the intestine. Both tissues possessed indicator taxa, while many indicator taxa in the gill were conditional pathogens. Compared to fish from zone H, fish from zone A had more abundant Cyanobacteria, and less abundant Proteobacteria and Bacteroidetes. PICRUSt2 analysis revealed that fish microbial functions were mainly associated with metabolism, replication, repair, folding, sorting, and degradation. These results showed that the microbial community of silver carp from Taihu Lake varied according to tissues and habitats. Full article

(This article belongs to the Special Issue Gut Microbiota in Fish and Shellfish)

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17 pages, 1451 KiB

Open AccessEditor’s ChoiceArticle

First Evaluation of Associated Gut Microbiota in Wild Thick-Lipped Grey Mullets (Chelon labrosus, Risso 1827)

by Jorge García-Márquez, Isabel M. Cerezo, Félix L. Figueroa, Roberto Teófilo Abdala-Díaz and Salvador Arijo

Fishes 2022, 7(4), 209; https://doi.org/10.3390/fishes7040209 - 19 Aug 2022

Cited by 6 | Viewed by 2387

Abstract

This study aimed to characterize the intestinal microbiota of wild thick-lipped grey mullets (Chelon labrosus) and explore its potential functionality on the host. Intestinal contents of anterior and posterior sections from wild fish were collected and DNA was extracted. Subsequently, the V3–V4 regions of 16S rRNA were sequenced using the Illumina technology and results were analyzed by bioinformatics pipeline. The functional profile of the microbial community was analyzed using PICRUSt software. Shannon and Simpson diversity indices were significantly higher in the posterior section of wild specimens. The overall taxonomic composition suggests a certain homogeneity in the anterior section of the intestine and heterogeneity in the posterior section. Due to this, no statistical differences were detected at any level among both intestinal sections. Predicted functions of intestinal microbiota showed the most abundant were those related to amino acid metabolism, carbohydrate metabolism, energy metabolism, membrane transport, and cell replication and repair. Furthermore, the analysis revealed microbial functional genes related to the elimination of environmental toxins. Full article

(This article belongs to the Special Issue Gut Microbiota in Fish and Shellfish)

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17 pages, 7242 KiB

Open AccessArticle

Microbial Community Structure and Metabolic Characteristics of Intestine and Gills of Dwarf-Form Populations of Sthenoteuthis oualaniensis in South China Sea

by Xiaojuan Hu, Haochang Su, Peng Zhang, Zuozhi Chen, Yu Xu, Wujie Xu, Jie Li, Guoliang Wen and Yucheng Cao

Fishes 2022, 7(4), 191; https://doi.org/10.3390/fishes7040191 - 4 Aug 2022

Cited by 2 | Viewed by 2122

Abstract

Sthenoteuthis oualaniensis is an important biological resource in the South China Sea. However, the microbiological characteristics of this squid, especially those of the dwarf-form, are poorly understood. This study was conducted to analyze the microbial community structure and metabolic characteristics of the intestinal and gill tissues of dwarf-form populations of S. oualaniensis. The dwarf-form squids of different sexes and gonadal maturities were collected from South China Sea in spring 2020. Results showed that Mycoplasma was the most dominant group of bacteria in the intestinal samples of the females with immature gonads (FN), females at sexual maturity (FY), and males at sexual maturity (MY) and the second-highest relative abundance group in males with immature gonads (MN). The microbial community structure in squid gills differed from that of intestinal flora. The BD1-7 clade was the dominant genus in gill samples of all groups. Furthermore, the microbial community activities in gills were higher than in intestinal groups, especially FYG. The larger dwarf-form populations had microbial communities with more robust utilization of carbon sources, assessed via average well color development (AWCD). Correlation and redundancy analysis determined that AWCD significantly positively correlated with the relative abundance of BD1-7 clade (p < 0.05). The results indicated that the dominant group of bacteria and microbial community structure were different between the intestinal and gill microbial communities in the dwarf-form S. oualaniensis populations of different sexes and maturities. Moreover, the metabolic potential of the gill microbial community was higher than that of the intestinal microbial community in the dwarf-form populations. Full article

(This article belongs to the Special Issue Gut Microbiota in Fish and Shellfish)

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18 pages, 5139 KiB

Open AccessArticle

Potential Role of Gastrointestinal Microbiota in Growth Regulation of Yellowtail Kingfish Seriola lalandi in Different Stocking Densities

by Yan Jiang, Chaoyong Yu, Yongjiang Xu, Xuezhou Liu, Aijun Cui, Bin Wang and Heting Zhou

Fishes 2022, 7(4), 154; https://doi.org/10.3390/fishes7040154 - 28 Jun 2022

Cited by 3 | Viewed by 2205

Abstract

A 90-day study was performed under three different stocking densities, including high density (10,000 fishes/cage), medium density (8000 fishes/cage), and low density (6000 fishes/cage), in a deep-sea net cage for yellowtail kingfish (Seriola lalandi). The physiological characteristics and growth performance were tested, and structural characteristics of the gastrointestinal microbiota were systematically analyzed. The results show that fishes with high density had a lower weight gain rate and a specific growth rate, as well as higher serum cortisol content. The diversity, types and numbers of dominant microbiota with significant differences, and the numbers of shared genera among the different groups all changed. Core genera in the gastrointestinal tract were obtained according to the principles of dominance, commonality, and difference. The changes in the relative abundance of the core genera might be related to the growth and physiological characteristics of the host. The ratio of Firmicutes to Bacteroidetes in the stomach and pyloric caecum, which favors the accumulation of energy by the host from the diet, was higher in the medium-density group than in the other groups. This indicates that the higher density could cause physiological stress and affect growth performance. In order to reduce the resulting growth differences, gastrointestinal microbiota might assist the host in accumulating energy, participating in the energy distribution by adjusting its structure. Based on the growth, physiology, and production practices, the medium density was the appropriate density in this study. This study provides a reference for the improvement of deep-sea culture technology and the promotion of healthy growth through the gastrointestinal microecological regulation of yellowtail kingfish. Full article

(This article belongs to the Special Issue Gut Microbiota in Fish and Shellfish)

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14 pages, 1210 KiB

Open AccessArticle

Incorporation of Fructooligosaccharides in Diets Influence Growth Performance, Digestive Enzyme Activity, and Expression of Intestinal Barrier Function Genes in Tropical Gar (Atractosteus tropicus) Larvae

by Graciela M. Pérez-Jiménez, Emyr Saul Peña-Marín, Claudia I. Maytorena-Verdugo, Cesar Antonio Sepúlveda-Quiroz, Luis Daniel Jiménez-Martínez, Susana De la Rosa-García, Gloria Gertrudys Asencio-Alcudia, Rafael Martínez, Dariel Tovar-Ramírez, Mario A. Galaviz, Talhia Martínez-Burguete, Carlos A. Alvarez-González and Carina Shianya Alvarez-Villagomez

Fishes 2022, 7(3), 137; https://doi.org/10.3390/fishes7030137 - 10 Jun 2022

Cited by 10 | Viewed by 2559

Abstract

This study was conducted to investigate the effects of dietary fructooligosaccharides (FOS) on the growth, survival rate, digestive enzyms activity, and the expression of intestinal barrier function genes in tropical gar (Atractosteus tropicus) larvae. A total of 960 larvae (0.030 ± 0.006 g) were fed three diets supplemented with increasing FOS concentrations (2.5, 5, and 7.5 g kg⁻¹) and a control diet for 15 days. Results revealed that a 7.5 g kg⁻¹ FOS supplementation improved weight gain, specific growth rate, and survival rate (p < 0.05). Furthermore, 5 g kg⁻¹ FOS supplementation increased alkaline protease and amylase activities and induced an upregulation of the claudin-17 gene expression (p < 0.05). Meanwhile, the inclusion of 7.5 g kg⁻¹ FOS induced the upregulation of mucin 2 (muc-2), and the tight junction genes zo-2 and claudin-3 (p < 0.05). In addition, 2.5, 5, and 7.5 g kg⁻¹ FOS promoted the downregulation of the claudin-15 gene expression (p < 0.05). At the same time, FOS inclusion did not increase the pro-inflammatory cytokine il-8 expression. We can conclude that 7.5 g kg⁻¹ FOS supplementation improves growth performance, survival rate, and digestive capacity, and could contribute to the reinforcement of the intestinal barrier function of Tropical gar larvae. Full article

(This article belongs to the Special Issue Gut Microbiota in Fish and Shellfish)

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Review

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26 pages, 1520 KiB

Open AccessEditor’s ChoiceReview

Epigenetics and Probiotics Application toward the Modulation of Fish Reproductive Performance

by Md Afsar Ahmed Sumon, Mohammad Habibur Rahman Molla, Israa J. Hakeem, Foysal Ahammad, Ramzi H. Amran, Mamdoh T. Jamal, Mohamed Hosny Gabr, Md. Shafiqul Islam, Md. Tariqul Alam, Christopher L. Brown, Eun-Woo Lee, Mohammed Moulay, Amer H. Asseri, F A Dain Md Opo, Ahad Amer Alsaiari and Md. Tawheed Hasan

Fishes 2022, 7(4), 189; https://doi.org/10.3390/fishes7040189 - 28 Jul 2022

Cited by 10 | Viewed by 7846

Abstract

Fish represent an excellent source of animal protein as well as a biomedical research model as a result of their evolutionary relatedness and similarity with the human genome. Commercial and ornamental fish culture has achieved popularity, but reproductive dysfunctions act as a limiting factor for quality fry production, interfering with the sustainability of the aquaculture industry. Fish reproduction is crucial for any species’ existence, and reproductive performance can potentially be improved through applications of epigenetics and probiotics. Epigenetics is a highly sensitive molecular approach that includes chromatin structure and function alteration, DNA methylation, and modification of non-coding RNA molecules for the transfer of desired information from parents to offspring. DNA methyltransferase improves reproductive cyp11a1, esr2b, and figla gene expression and feminizes zebrafish (Danio rerio). Moreover, epigenetics also contributes to genome stability, environmental plasticity, and embryonic development. However, methylation of specific genes can negatively affect sperm quality, resulting in poor fertilization. Probiotic administration is able to induce responsiveness of incompetent follicles to maturation-inducing hormones and can change oocyte chemical composition during vitellogenic development. The positive role of probiotics on testicular cells is validated by upregulating the transcription levels of leptin, bdnf, and dmrt1 genes facilitating the spermatogenesis. This review not only discusses the effects and mechanism of epigenetics and probiotics for improving fish reproduction, but also presents an overview of the causal factors and current techniques used to eradicate dysfunction. Moreover, key genes and hormones related to fish reproduction along with research gaps and future prospects are also considered. This review provides an overview of necessary information for students, scientists, researchers, and breeders to resolve fish reproduction-related problems to ensure profitable and sustainable aquaculture. Full article

(This article belongs to the Special Issue Gut Microbiota in Fish and Shellfish)

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