Microbial and Antimicrobial Resistance Profiles of Microbiota in Common Carps (Cyprinus carpio) from Aquacultured and Wild Fish Populations

Ružauskas, Modestas; Armalytė, Julija; Lastauskienė, Eglė; Šiugždinienė, Rita; Klimienė, Irena; Mockeliūnas, Raimundas; Bartkienė, Elena

doi:10.3390/ani11040929

Cited by 11 publications

(7 citation statements)

References 28 publications

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“…Alpha and beta diversity are important parameters used to evaluate the structural characteristics of microbiota. In our study, gut microbiota diversity and richness were higher in alpine cold-water reservoirs and inner lakes than in ponds, consistent with other research [ 9 , 11 , 63 , 64 ]. This could be due to larger habitats providing a wider range of diets.…”

Section: Discussionsupporting

confidence: 93%

The impact of culture systems on the gut microbiota and gut metabolome of bighead carp (Hypophthalmichthys nobilis)

et al. 2023

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Background The gut microbiota of fish confers various effects on the host, including health, nutrition, metabolism, feeding behaviour, and immune response. Environment significantly impacts the community structure of fish gut microbiota. However, there is a lack of comprehensive research on the gut microbiota of bighead carp in culture systems. To demonstrate the impact of culture systems on the gut microbiome and metabolome in bighead carp and investigate a potential relationship between fish muscle quality and gut microbiota, we conducted a study using 16S ribosomal ribonucleic acid sequencing, gas chromatography-mass spectrometry, and liquid chromatography-mass spectrometry techniques on bighead carp in three culture systems. Results Our study revealed significant differences in gut microbial communities and metabolic profiles among the three culture systems. We also observed conspicuous changes in muscle structure. The reservoir had higher gut microbiota diversity indices than the pond and lake. We detected significant differences in phyla and genera, such as Fusobacteria, Firmicutes, and Cyanobacteria at the phylum level, Clostridium sensu stricto 1, Macellibacteroides, Blvii28 wastewater sludge group at the genus level. Multivariate statistical models, including principal component analysis and orthogonal projections to latent structures-discriminant analysis, indicated significant differences in the metabolic profiles. Key metabolites were significantly enriched in metabolic pathways involved in "arginine biosynthesis" and "glycine, serine, and threonine metabolism". Variation partitioning analysis revealed that environmental factors, such as pH, ammonium nitrogen, and dissolved oxygen, were the primary drivers of differences in microbial communities. Conclusions Our findings demonstrate that the culture system significantly impacted the gut microbiota of bighead carp, resulting in differences in community structure, abundance, and potential metabolic functions, and altered the host's gut metabolism, especially in pathways related to amino acid metabolism. These differences were influenced substantially by environmental factors. Based on our study, we discussed the potential mechanisms by which gut microbes affect muscle quality. Overall, our study contributes to our understanding of the gut microbiota of bighead carp under different culture systems.

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Section: Discussionsupporting

confidence: 93%

The impact of culture systems on the gut microbiota and gut metabolome of bighead carp (Hypophthalmichthys nobilis)

et al. 2023

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“…In agreement with other freshwater teleosts, the following genera were abundant in many of our samples: Propionibacterium (or Cutibacterium ), Staphylococcus , Clostridium , Flavobacterium , Cetobacterium , Pseudomonas , Romboutsia , Spiroplasma , Vibrio , Aeromonas , and Mycoplasma ( e.g. , Roeselers et al, 2011 ; Gajardo et al, 2016 ; do Vale-Pereira et al, 2017 ; Rimoldi et al, 2019 ; Ruzauskas et al, 2021 ). Although it is hard to predict physiological roles for these microbes, some bacteria of the genera Staphylococcus , Vibrio , and Aeromonas can be opportunistic pathogens, while others have been used as probiotics in fish diets promoting positive immune and growth responses ( Austin et al, 1995 ; Taoka et al, 2006 ; Pieters et al, 2008 ; Abd El-Rhman, Khattab & Shalaby, 2009 ; Korkea-aho et al, 2012 ; Gao et al, 2016 ; Qi et al, 2020 ; Tran et al, 2020 ).…”

Section: Discussionsupporting

confidence: 89%

Loss of gut microbial diversity in the cultured, agastric fish, Mexican pike silverside (Chirostoma estor: Atherinopsidae)

Amillano-Cisneros

Hernández-Rosas

Gómez‐Gil

et al. 2022

PeerJ

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Teleost fish are the most diverse group of extant vertebrates and have varied digestive anatomical structures and strategies, suggesting they also possess an array of different host-microbiota interactions. Differences in fish gut microbiota have been shown to affect host development, the process of gut colonization, and the outcomes of gene-environment or immune system-microbiota interactions. There is generally a lack of studies on the digestive mechanisms and microbiota of agastric short-intestine fish however, meaning that we do not understand how changes in gut microbial diversity might influence the health of these types of fish. To help fill these gaps in knowledge, we decided to study the Mexican pike silverside (Chirostoma estor) which has a simplified alimentary canal (agastric, short-intestine, 0.7 gut relative length) to observe the diversity and metabolic potential of its intestinal microbiota. We characterized gut microbial populations using high-throughput sequencing of the V3 region in bacterial 16S rRNA genes while searching for population shifts resulting associated with fish development in different environments and cultivation methods. Microbiota samples were taken from the digesta, anterior and posterior intestine (the three different intestinal components) of fish that grew wild in a lake, that were cultivated in indoor tanks, or that were raised in outdoor ponds. Gut microbial diversity was significantly higher in wild fish than in cultivated fish, suggesting a loss of diversity when fish are raised in controlled environments. The most abundant phyla observed in these experiments were Firmicutes and Proteobacteria, particularly of the genera Mycoplasma, Staphylococcus, Spiroplasma, and Aeromonas. Of the 14,161 OTUs observed in this experiment, 133 were found in all groups, and 17 of these, belonging to Acinetobacter, Aeromonas, Pseudomonas, and Spiroplasma genera, were found in all samples suggesting the existence of a core C. estor microbiome. Functional metagenomic prediction of bacterial ecological functions using PICRUSt2 suggested that different intestinal components select for functionally distinct microbial populations with variation in pathways related to the metabolism of amino acids, vitamins, cofactors, and energy. Our results provide, for the first time, information on the bacterial populations present in an agastric, short-gut teleost with commercial potential and show that controlled cultivation of this fish reduces the diversity of its intestinal microbiota.

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“…Furthermore, the intestinal microbiota have an important role in the protection against diseases. These functions are assured through bidirectional gut-brain communication (gut–brain axis), which is mediated by hormonal, immune, and neural signals [ 18 ]. According to He et al (2013) [ 19 ], DDGS can modulate the gut microbiota of fish in a host-specific way.…”

Section: Introductionmentioning

confidence: 99%

Evaluation of DDGS as a Low-Cost Feed Ingredient for Common Carp (Cyprinus carpio Linneus) Cultivated in a Semi-Intensive System

Barbacariu

Rîmbu

Dirvariu

et al. 2022

Life

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Distillers dried grains with solubles (DDGS), a coproduct from the ethanol production industry, is successfully used as an ingredient in feeding cattle and pigs due to its relatively high protein and nutrient content and low price compared to cereals. The aim of this study was to establish the optimal DDGS concentration that can be included in the diet of common carp. A seven-week experiment was performed on common carp with an initial weight of 86 g feed with three experimental diets D0 (DDGS 0%), D1 (DDGS 25%) and D2 (DDGS 35%). The chemical composition of DDGS analyzed by Fourier Transform Near-Infrared (FT-NIR) spectroscopy showed a protein content of 27.56% and oil at 6.75%. Diets with DDGS did not produce significant changes in growth parameters, flesh quality, and blood biochemical profile. Regarding the oxidative status in the muscle tissue, D1 and D2 significantly reduced, in a dose-dependent manner, the specific activity of SOD and GSH, while CAT and GPX were left unaffected. In the liver tissue, CAT, GSH, MDA and carbonylated proteins were reduced in the DDGS diets. The microbiological analysis of the intestinal contents revealed a variation in microbial density depending on the diet used. The total number of aerobic germs was between 224.2 × 104 and 69.84 × 106 (D2 > D1 > D0) and the total number of anaerobic germs was between 15.2 × 102 and 28.2 × 102 (D2 > D0 > D1).

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Microbial and Antimicrobial Resistance Profiles of Microbiota in Common Carps (Cyprinus carpio) from Aquacultured and Wild Fish Populations

Cited by 11 publications

References 28 publications

The impact of culture systems on the gut microbiota and gut metabolome of bighead carp (Hypophthalmichthys nobilis)

The impact of culture systems on the gut microbiota and gut metabolome of bighead carp (Hypophthalmichthys nobilis)

Loss of gut microbial diversity in the cultured, agastric fish, Mexican pike silverside (Chirostoma estor: Atherinopsidae)

Evaluation of DDGS as a Low-Cost Feed Ingredient for Common Carp (Cyprinus carpio Linneus) Cultivated in a Semi-Intensive System

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