Editorial

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2 pages, 165 KiB

Open AccessEditorial

Editorial for the Special Issue: Gut Microorganisms of Aquatic Animals

by Konstantinos Ar. Kormas

Microorganisms 2019, 7(10), 377; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7100377 - 21 Sep 2019

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Abstract

Since the introduction of the term holobiont [...] Full article

(This article belongs to the Special Issue Gut Microorganisms of Aquatic Animals)

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20 pages, 5205 KiB

Open AccessArticle

Antibiotic-Induced Perturbations Are Manifested in the Dominant Intestinal Bacterial Phyla of Atlantic Salmon

by Shruti Gupta, Jorge Fernandes and Viswanath Kiron

Microorganisms 2019, 7(8), 233; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7080233 - 02 Aug 2019

Cited by 39 | Viewed by 4565

Abstract

The intestinal microbiota of certain farmed fish are often exposed to antimicrobial substances, such as antibiotics, that are used to prevent and treat bacterial diseases. Antibiotics that kill or inhibit the growth of harmful microbes can rapidly alter intestinal microbial diversity and composition, [...] Read more.

The intestinal microbiota of certain farmed fish are often exposed to antimicrobial substances, such as antibiotics, that are used to prevent and treat bacterial diseases. Antibiotics that kill or inhibit the growth of harmful microbes can rapidly alter intestinal microbial diversity and composition, with potential effects on the host health. In this study, we have elucidated the impact of two antibiotics, florfenicol and oxolinic acid, by employing a high-throughput 16S rRNA gene amplicon sequencing technique on the distal and mid intestinal microbial communities of Atlantic salmon (Salmo salar). For this, Atlantic salmon were offered diets with or without antibiotics. We then investigated the bacterial communities in the intestinal mucus of the fish. Our results showed that antibiotic exposure shifts the intestinal microbial profile differentially. In addition, the bacterial compositions of the control and antibiotic-fed groups were significantly different. Antibiotic feeding altered the composition and abundance of the dominant bacterial phyla, namely Proteobacteria, Actinobacteria, Firmicutes, Spirochaetes, Bacteroidetes, Tenericutes, and Thermotogae. The bacterial association network analysis also indicated the differential pattern of co-occurrence of bacteria in the three study groups. The results regarding the differences in the structure and association of the intestinal microbiota of Atlantic salmon after florfenicol and oxolinic acid feeding can be employed to attenuate the adverse effects of antibiotic feeding on fish. Full article

(This article belongs to the Special Issue Gut Microorganisms of Aquatic Animals)

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14 pages, 795 KiB

Open AccessArticle

Investigation of the Potential Effects of Host Genetics and Probiotic Treatment on the Gut Bacterial Community Composition of Aquaculture-raised Pacific Whiteleg Shrimp, Litopenaeus vannamei

by Angela Landsman, Benoit St-Pierre, Misael Rosales-Leija, Michael Brown and William Gibbons

Microorganisms 2019, 7(8), 217; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7080217 - 26 Jul 2019

Cited by 15 | Viewed by 4058

Abstract

This study presents the potential effects of the genetic background and use of probiotics on the gut bacterial composition of Pacific whiteleg shrimp (Litopenaeus vannamei) grown in an indoor aquaculture facility. The strains investigated were Shrimp Improvement Systems (SIS, Islamorada, FL, [...] Read more.

This study presents the potential effects of the genetic background and use of probiotics on the gut bacterial composition of Pacific whiteleg shrimp (Litopenaeus vannamei) grown in an indoor aquaculture facility. The strains investigated were Shrimp Improvement Systems (SIS, Islamorada, FL, USA), a strain genetically selected for disease resistance, and an Oceanic Institute (OI, Oahu, HI, USA) strain, selected for growth performance. BioWish 3P (BioWish Technologies, Cincinnati, OH, USA) was the selected probiotic. The study consisted of two separate trials, where all shrimp were raised under standard industry conditions and fed the same diet. Shrimp were stocked in 2920 L production tanks at a density of 200/m³ and acclimated for 14 days. After the acclimation period, triplicate tanks were supplemented daily for a duration of 28 days with probiotics, while three other tanks did not receive any treatment (controls). During the 28-day trial period, there was no statistically supported difference (p > 0.05) in either performance or health status as a result of genetic background or probiotic treatment. However, differences in gut bacterial composition, as assessed by high throughput sequencing of amplicons generated from the V1-V3 region of the bacterial 16S rRNA gene, were observed. The relative abundance of five major operational taxonomic units (OTUs) were found to vary significantly across experimental groups (p < 0.05). Notably, operational taxonomic unit (OTU) SD_Shr-00006 was at its highest abundance in d43 SIS samples, with levels greater than d71 samples of the same genetic line or any of the OI shrimp samples. OTUs for SD_Shr-00098 displayed a similar type of profile, but with highest abundance in the OI genetic line and lowest in the SIS shrimp. SD_Shr-00004 showed an opposite profile, with highest abundance in the SIS d71 samples and lowest in the SIS d43 samples. Together, these results suggest that host genetic background can be an important determinant of gut bacterial composition in aquaculture-raised whiteleg shrimp and indicate that development of strategies to manipulate the microbiome of this important seafood will likely need to be customized depending on the genetic line. Full article

(This article belongs to the Special Issue Gut Microorganisms of Aquatic Animals)

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15 pages, 2332 KiB

Open AccessArticle

Insights into the Potential of the Atlantic Cod Gut Microbiome as Biomarker of Oil Contamination in the Marine Environment

by Juline M. Walter, Andrea Bagi and Daniela M. Pampanin

Microorganisms 2019, 7(7), 209; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7070209 - 22 Jul 2019

Cited by 26 | Viewed by 5110

Abstract

Background: Microorganisms are widespread in all environments, including in and on animal bodies. The gut microbiome has an essential influence on fish health, and is affected by several persistent and harmful organic and inorganic contaminants. Considering the shifts in gut microbiota composition observed [...] Read more.

Background: Microorganisms are widespread in all environments, including in and on animal bodies. The gut microbiome has an essential influence on fish health, and is affected by several persistent and harmful organic and inorganic contaminants. Considering the shifts in gut microbiota composition observed in those studies, we hypothesized that certain microbial groups in the gut can serve as indicators of pollution. To test this hypothesis, we explored the possibility of identifying key microbial players that indicate environmental contamination. Methods: Published 16S rRNA gene amplicon sequencing data generated from the gut microbiota of Atlantic cod caught in geographically different Norwegian waters were used for bacterial diversity comparison. Results: Different microbiomes were identified between the northern Norway and southern Norway samples. Several bacterial genera previously identified as polycyclic aromatic hydrocarbon degraders were present only in the samples collected in the southern Norway area, suggesting fish contamination with oil-related compounds. Conclusions: The results contribute to the identification of bacterial taxa present in the Atlantic cod gut that indicate fish exposure to contaminants in the marine environment. Full article

(This article belongs to the Special Issue Gut Microorganisms of Aquatic Animals)

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17 pages, 3901 KiB

Open AccessArticle

Stimulated Growth and Innate Immunity in Brook Charr (Salvelinus fontinalis) Treated with a General Probiotic (Bactocell^®) and Two Endogenous Probiotics That Inhibit Aeromonas salmonicida In Vitro

by Jeff Gauthier, Stéphanie Rouleau-Breton, Steve J. Charette and Nicolas Derome

Microorganisms 2019, 7(7), 193; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7070193 - 06 Jul 2019

Cited by 6 | Viewed by 3496

Abstract

Aeromonas salmonicida subsp. salmonicida is a Gram-negative bacterium causing furunculosis, an opportunistic infection of farmed salmonid fish. Current treatment methods against furunculosis rely heavily on antibiotherapy. However, strains of this opportunistic fish pathogen were found to possess genes that confer resistance to major [...] Read more.

Aeromonas salmonicida subsp. salmonicida is a Gram-negative bacterium causing furunculosis, an opportunistic infection of farmed salmonid fish. Current treatment methods against furunculosis rely heavily on antibiotherapy. However, strains of this opportunistic fish pathogen were found to possess genes that confer resistance to major antibiotics including those used to cure furunculosis. Therefore, dispensing bacterial symbionts as probiotics to susceptible hosts appears to be a promising alternative. Here, we present the genomic characterization and in vivo safety assessment of two brook charr (Salvelinus fontinalis) bacterial symbionts that inhibited A. salmonicida subsp. salmonicida growth in vitro (Pseudomonas fluorescens ML11A and Aeromonas sobria TM18) as well as a commercialized probiotic, Pediococcus acidilactici MA18/5M (Bactocell^®). The genomic sequences of ML11A and TM18 obtained by whole-genome shotgun sequencing lack key virulence factor genes found in related pathogenic strains. Their genomic sequences are also devoid of genes involved in the inactivation (or target modification of) several key antimicrobial compounds used in salmonid aquaculture. Finally, when administered daily to live brook charr fingerlings, ML11A, TM18 and Bactocell^® helped improve several physiological condition metrics such as mean body weight, Fulton’s condition factor and blood plasma lysozyme activity (an indicator for innate immune activity). Full article

(This article belongs to the Special Issue Gut Microorganisms of Aquatic Animals)

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14 pages, 1469 KiB

Open AccessArticle

Impact of Aquaculture Practices on Intestinal Bacterial Profiles of Pacific Whiteleg Shrimp Litopenaeus vannamei

by Angela Landsman, Benoit St-Pierre, Misael Rosales-Leija, Michael Brown and William Gibbons

Microorganisms 2019, 7(4), 93; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7040093 - 30 Mar 2019

Cited by 35 | Viewed by 6680

Abstract

Considering the crucial role of the gut microbiome in animal health and nutrition, solutions to shrimp aquaculture challenges, such as improving disease resistance and optimizing growth on lower cost feeds, may lie in manipulation of their microbial symbionts. However, achieving this goal will [...] Read more.

Considering the crucial role of the gut microbiome in animal health and nutrition, solutions to shrimp aquaculture challenges, such as improving disease resistance and optimizing growth on lower cost feeds, may lie in manipulation of their microbial symbionts. However, achieving this goal will require a deeper understanding of shrimp microbial communities and how their composition is influenced by diet formulation, environmental conditions, and host factors. In this context, the current study investigated the intestinal bacterial communities of the Pacific whiteleg shrimp (Litopenaeus vannamei—the most widely aquaculture-farmed shrimp worldwide) reared in indoor aquaculture facilities and outdoor pond systems. While samples showed very consistent intestinal bacterial community profiles within each production system, major differences were uncovered between the two practices. Indeed, bacteria affiliated with Rhodobacteraceae (Proteobacteria) and Actinobacteria were significantly more abundant in indoor samples (84.4% vs. 5.1%; 3.0% vs. 0.06%, respectively), while Vibrionaceae (Proteobacteria), Firmicutes, Fusobacteria and Cyanobacteria were predominant in pond samples (0.03% vs. 44.8%; 0.7% vs. 36.0%; 0.0% vs. 7.9%; 0.001% vs. 1.6%, respectively). Accordingly, the abundance of 11 of the 12 most prominent Operational Taxonomic Units (OTUs) were found to be statistically different between the two production environments. Together, these results indicate that aquaculture practices greatly influence the intestinal bacterial profile of the whiteleg shrimp, and further suggest that bacterial communities of this economically important crustacean could be effectively manipulated using diet composition or environmental conditions. Full article

(This article belongs to the Special Issue Gut Microorganisms of Aquatic Animals)

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12 pages, 1619 KiB

Open AccessArticle

Gut Bacterial Communities in Geographically Distant Populations of Farmed Sea Bream (Sparus aurata) and Sea Bass (Dicentrarchus labrax)

by Eleni Nikouli, Alexandra Meziti, Efthimia Antonopoulou, Eleni Mente and Konstantinos A. Kormas

Microorganisms 2018, 6(3), 92; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms6030092 - 01 Sep 2018

Cited by 37 | Viewed by 5909

Abstract

This study investigated the profile of the autochthonous gut bacterial communities in adult individuals of Sparus aurata and Dicentrarchus labrax reared in sea cages in five distantly located aquaculture farms in Greece and determine the impact of geographic location on them in order [...] Read more.

This study investigated the profile of the autochthonous gut bacterial communities in adult individuals of Sparus aurata and Dicentrarchus labrax reared in sea cages in five distantly located aquaculture farms in Greece and determine the impact of geographic location on them in order to detect the core gut microbiota of these commercially important fish species. Data analyses resulted in no significant geographic impact in the gut microbial communities within the two host species, while strong similarities between them were also present. Our survey revealed the existence of a core gut microbiota within and between the two host species independent of diet and geographic location consisting of the Delftia, Pseudomonas, Pelomonas, Propionibacterium, and Atopostipes genera. Full article

(This article belongs to the Special Issue Gut Microorganisms of Aquatic Animals)

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6 pages, 1258 KiB

Open AccessCommunication

Microbial Community and Potential Pathogen Shifts Along an Ornamental Fish Supply Chain

by Linda A. Amaral-Zettler, Victor Schmidt and Katherine F. Smith

Microorganisms 2018, 6(3), 91; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms6030091 - 25 Aug 2018

Cited by 6 | Viewed by 4628

Abstract

There is broad interest in disease spread through the pet trade, but empirical research on hosts and pathogens in transit along actual trade routes is notably absent. Using next-generation DNA sequencing, and partnering with the ornamental fish industry, we tracked shifts in microbial [...] Read more.

There is broad interest in disease spread through the pet trade, but empirical research on hosts and pathogens in transit along actual trade routes is notably absent. Using next-generation DNA sequencing, and partnering with the ornamental fish industry, we tracked shifts in microbial community and potential pathogen structure associated with Sailfin Tang (Zebrasoma desjardinii) along the United States (U.S.) leg of an international supply chain. We observed striking changes in microbial diversity and composition of potential pathogens, including increased dominance of vibrios of fishes in transit. Our pilot findings suggest that high investment in fishes early in the supply chain may not matter to their long-term health depending on end destination conditions. Full article

(This article belongs to the Special Issue Gut Microorganisms of Aquatic Animals)

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16 pages, 1879 KiB

Open AccessArticle

Exploring the Impact of the Biofloc Rearing System and an Oral WSSV Challenge on the Intestinal Bacteriome of Litopenaeus vannamei

by Mariana R. Pilotto, André N. A. Goncalves, Felipe N. Vieira, Walter Q. Seifert, Evelyne Bachère, Rafael D. Rosa and Luciane M. Perazzolo

Microorganisms 2018, 6(3), 83; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms6030083 - 08 Aug 2018

Cited by 44 | Viewed by 10152

Abstract

We provide a global overview of the intestinal bacteriome of Litopenaeus vannamei in two rearing systems and after an oral challenge by the White spot syndrome virus (WSSV). By using a high-throughput 16S rRNA gene sequencing technology, we identified and compared the composition [...] Read more.

We provide a global overview of the intestinal bacteriome of Litopenaeus vannamei in two rearing systems and after an oral challenge by the White spot syndrome virus (WSSV). By using a high-throughput 16S rRNA gene sequencing technology, we identified and compared the composition and abundance of bacterial communities from the midgut of shrimp reared in the super-intensive biofloc technology (BFT) and clear seawater system (CWS). The predominant bacterial group belonged to the phylum Proteobacteria, followed by the phyla Bacteroidetes, Actinobacteria, and Firmicutes. Within Proteobacteria, the family Vibrionaceae, which includes opportunistic shrimp pathogens, was more abundant in CWS than in BFT-reared shrimp. Whereas the families Rhodobacteraceae and Enterobacteriaceae accounted for almost 20% of the bacterial communities of shrimp cultured in BFT, they corresponded to less than 3% in CWS-reared animals. Interestingly, the WSSV challenge dramatically changed the bacterial communities in terms of composition and abundance in comparison to its related unchallenged group. Proteobacteria remained the dominant phylum. Vibrionaceae was the most affected in BFT-reared shrimp (from 11.35 to 20.80%). By contrast, in CWS-reared animals the abundance of this family decreased from 68.23 to 23.38%. Our results provide new evidence on the influence of both abiotic and biotic factors on the gut bacteriome of aquatic species of commercial interest. Full article

(This article belongs to the Special Issue Gut Microorganisms of Aquatic Animals)

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