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Heatmap of the difference from the minimum Akaike’s information criterion (AIC) (left) between each fitted model for each individual. Dark red shows models that are the best fit; blue are models that differ a lot from minimum AIC. Model fit (right) on the averaged distribution in each species. Colour in bold indicates the “best” fitted model. *Model-species combination that has significantly worse fit
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In this study, we hypothesized that sympatrically grown farmed fish, i.e. fish which experience similar environmental conditions and nutritionally similar diets, would have more convergent gut microbiota. Using a “common garden” approach, we identified the core microbiota and bacterial community structure differences between five fish species farme...
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Citations
... Such low overlap implies that each experimental treatment, i.e. aquafeed, shapes a different gut microbiota structure. Some of the OTUs representing the core microbiota, such as Cutibacterium and Corynebacterium have been detected in previous studies in sea bass (Nikouli et al. , 2021 along with several Gammaproteobacteria (i.e. Pseudomononas ) although the gamma core bacteria detected here belonged to different genera. ...
As aquaculture is nowadays the major fish-food production sector, continuous research is undergoing for aquafeeds that could replace conventional fishmeal in order to enhance its environmental and economic sustainability. Fish gut microorganisms might be involved in nutrient assimilation and thus they are crucial for their hosts’ well-being. In this study the bacterial diversity was investigated by16S rRNA gene metabarcoding in order to investigate changes in midgut (M) and feces (F) microbiota of sea bass Dicentrachus labrax fed with conventional (C) and innovative-low fish meal diet (I), aiming at discovering microbiota that could be associated with the enhancement of host's health and productivity. Our results indicated that Proteobacteria (Pseudomonadota) prevailed in all samples followed by Firmicutes (Bacillota) or Bacteroidota (mostly in feces), while fecal communities were richer. Taxonomic distributions at the operational taxonomic unit level in midgut samples revealed differentially abundant fermentative species that prevailed in individuals fed with the innovative diet. Especially Staphylococcus was more abundant in MI samples implying enhancement from ingredients present only in the innovative diet and implying that this feed shapes rather favorable microbiota, which could support the digestion and good growth performance in aquaculture.
... Among the hydrobionts, there is a significant degree of variation in the dominant members of the gut microbial community. For example, fish communities are rich in Proteobacteria [46], while amphibious communities are dominated by Firmicutes and Bacteroidetes [47]. In the present study, Firmicutes and Proteobacteria were identified as the keystone phyla of the gut microbiome, whereas the phyla Bacteroidetes and Actinobacteria were also abundant. ...
Many amphibian behaviors and physiological functions adapt to daily environmental changes through variations in circadian rhythms. However, these adaptations have yet to be reported in Dybowski’s frog (Rana dybowskii). We aimed to elucidate the dynamic changes in the behavior and gut microbiota of R. dybowskii within a 24 h cycle during their migration to hibernation sites. Thus, we monitored their behavior at 4 h intervals and collected samples for microbiome analysis. We found that the juvenile frogs arrived at hibernation sites earlier than the adults. Among the adults, the male frogs arrived earlier. The richness and diversity of the gut microbiota in the adult R. dybowskii were lowest at 14:00. At 6:00, the differences between the males and females were most significant. At 18:00, there was an increase in the activity of Bacteroides, Coprobacillus, Ruminococcus, and Dorea in the intestinal tracts of the male frogs, whereas in the intestinal tract of the female frogs, there was an increase in the activity of Pseudoramibacter_Eubacterium, Desulfovibrio, Anaerotruncus, and PW3. This indicated diurnal rhythmic variations in the gut microbiota and significant sex-based differences in the microbial activity at different time points. Our findings contribute to the understanding of the circadian rhythm of R. dybowskii and provide crucial insights into improving breeding strategies.
... The fish-microbiome interactions play a vital role in determining the overall health and well-being of farmed fish (de Bruijn et al., 2018;Raulo et al., 2018;Perry et al., 2020;Luan et al., 2023). Numerous studies have examined the fish-associated microbiome throughout various life stages, from juvenile and adult stages along with their dynamics with the rearing environment including factors such as water quality and feed composition (Wang et al., 2018;Krotman et al., 2020;Zeng et al., 2020;Nikouli et al., 2021;Roquigny et al., 2021;Sehnal et al., 2021;Karlsen et al., 2022;Quero et al., 2022;Rabelo-Ruiz et al., 2022). However, so far, little is known about the diversity and function of these microorganisms, particularly in relation to disease occurrence during the earlier rearing stages. ...
... Similarly, there is a significant number of interactions involving the Psychrobacter genus, although the contribution of certain species is less than in symptomatic larvae. These findings, indicate the importance of members of this genus that is not detected in previous studies on S. aurata larvae (Califano et al., 2017;Nikouli et al., 2021). Thus, the role and the establishment of members of this genus in relation to the health status of S. aurata larvae required further investigation and should cover diverse larviculture systems to understand their influence on later larval stages, as well as on the subsequent juvenile and adult stages of the fish. ...
Bacterial community structures and dynamics associated with rotated positioning syndrome in gilthead sea bream (Sparus aurata) larviculture
... The Mediterranean Sea hosts a wide variety of habitats, resulting in a great variability in the abundance, the biomass and the biodiversity of fish communities (Coll et al., 2010) and in fish's body conditions (Ordines et al., 2009;Ferri and Matic-Skoko, 2021). The possibility that the microbiota associated with the body niches of fishes also vary geographically was already investigated in the past without reaching a unanimous conclusion (Ye et al., 2014;Riiser et al., 2019;Nikouli et al., 2020). ...
The gut microbiome holds an important role in the health and homeostasis of fishes. However, despite the large diversity and distribution of this vertebrate group, only the intestinal microbiome of a limited number of freshwater and marine fish species has been well characterized to date. In this study, we characterize the gut mucosal microbial communities of three commercially valuable Scorpaena spp. (n=125) by using a comprehensive comparative dataset including 16S rRNA gene amplicon data from four different locations in the Mediterranean Sea. We report that the geographical origin of the individuals influences the diversity and the composition of the gut microbial communities more than the host’s phylogenetic relatedness in this fish group. Moreover, we observe a positive correlation between the composition of the gut microbiota and the phylogenetic distance between the hosts (i.e. phylosymbiosis). Finally, the core microbiota of each species is described both regionally and across the Mediterranean Sea. Only a few bacterial genera appear to be residents of the scorpionfishes’ gut microbiota across the Mediterranean Sea: Photobacterium, Enterovibrio, Vibrio, Shewanella, Epulopiscium, Clostridium sensu stricto 1 and Rombutsia in S. notata, Clostridium sensu stricto 1, Cetobacterium and Rombutsia in S. porcus, and only Clostridium sensu stricto 1 in S. scrofa. This study highlights the importance of investigating the gut microbiome across a species’ geographical range and it suggests this as a general procedure to better characterize the gut microbial ecology of each fish species.
... In our study, we observed a significant increase in the relative abundance of the Cutibacterium and Shewanella genera in the posterior intestines of fish fed the CVP diet. Cutibacterium has been reported in various fish species [51][52][53][54], with specific species within this genus known to produce vitamins from the B group, including B12 and short-chain fatty acids [55,56]. These short-chain fatty acids play critical roles in maintaining intestinal balance, acting as energy sources, anti-inflammatory agents, and growth promoters [57,58]. ...
The use of functional feeds in aquaculture is currently increasing. This study aimed to assess the combined impact of dietary green microalgae Chlorella fusca and ethanol-inactivated Vibrio proteolyticus DCF12.2 (CVP diet) on thick-lipped grey mullet (Chelon labrosus) juvenile fish. The effects on intestinal microbiota and the transcription of genes related to metabolism, stress, and the immune system were investigated after 90 days of feeding. Additionally, the fish were challenged with Aeromonas hydrophila and polyinosinic–polycytidylic acid (poly I:C) to evaluate the immune response. Microbiota analysis revealed no significant differences in alpha and beta diversity between the anterior and posterior intestinal sections of fish fed the control (CT) and CVP diets. The dominant genera varied between the groups; Pseudomonas and Brevinema were most abundant in the CVP group, whereas Brevinema, Cetobacterium, and Pseudomonas were predominant in the CT group. However, microbial functionality remained unaltered. Gene expression analysis indicated notable changes in hif3α, mhcII, abcb1, mx, and tnfα genes in different fish organs on the CVP diet. In the head kidney, gene expression variations were observed following challenges with A. hydrophila or poly I:C, with higher peak values seen in fish injected with poly I:C. Moreover, c3 mRNA levels were significantly up-regulated in the CVP group 72 h post-A. hydrophila challenge. To conclude, incorporating C. fusca with V. proteolyticus in C. labrosus diet affected the microbial species composition in the intestine while preserving its functionality. In terms of gene expression, the combined diet effectively regulated the transcription of stress and immune-related genes, suggesting potential enhancement of fish resistance against stress and infections.
... This finding matches those of previous studies that have identified Proteobacteria and Firmicutes as being the major constituents of the gut microbiota of marine fish [5,6,19,25,[61][62][63][64]. Within the phylum Proteobacteria, Photobacterium (5.6%), Vibrio (4.5%), Alivibrio (3.5%), and Edwardsiella (3.2%) were the most abundant genera found in the fish samples collected in the bay (Fig. 2B). ...
Background
The natural marine environment represents a vast reservoir of antimicrobial resistant bacteria. The wildlife that inhabits this environment plays an important role as the host to these bacteria and in the dissemination of resistance. The relationship between host diet, phylogeny, and trophic level and the microbiome/resistome in marine fish is not fully understood. To further explore this relationship, we utilize shotgun metagenomic sequencing to define the gastrointestinal tract microbiomes of seven different marine vertebrates collected in coastal New England waters.
Results
We identify inter and intraspecies differences in the gut microbiota of these wild marine fish populations. Furthermore, we find an association between antibiotic resistance genes and host dietary guild, which suggests that higher trophic level organisms have a greater abundance of resistance genes. Additionally, we demonstrate that antibiotic resistance gene burden is positively correlated with Proteobacteria abundance in the microbiome. Lastly, we identify dietary signatures within the gut of these fish and find evidence of possible dietary selection for bacteria with specific carbohydrate utilization potential.
Conclusions
This work establishes a link between host lifestyle/dietary guild, and microbiome composition and the abundance of antibiotic resistance genes within the gastrointestinal tract of marine organisms. We expand the current understanding of marine organism-associated microbial communities and their role as reservoirs of antimicrobial resistance genes.
... As it is well known that diet is a very important factor that affects the host's health, hence interaction of microbial species with the host's nutrition becomes a vital study. Nikouli et al. [7] while working on the gut microbiome composition of five sympatrically farmed marine fish reported that the intestinal microbiome species act as a second genome of the animals controlling various vital functions of the body. Further, it is mentioned that the colonization of the fish gut microbiome community depends on both intrinsic and extrinsic factors including feeding habits. ...
The importance of the gut microbiome in the management of various physiological activities including healthy growth and performance of fish and shellfish is now widely considered and being studied in detail for potential applications in aquaculture farming and the future growth of the fish industry. The gut microbiome in all animals including fish is associated with a number of beneficial functions for the host, such as stimulating optimal gastrointestinal development, producing and supplying vitamins to the host, and improving the host's nutrient uptake by providing additional enzymatic activities. Besides nutrient uptake, the gut microbiome is involved in strengthening the immune system and maintaining mucosal tolerance, enhancing the host's resilience against infectious diseases, and the production of anticarcinogenic and anti-inflammatory compounds. Because of its significant role, the gut microbiome is very often considered an "extra organ," as it plays a key role in intestinal development and regulation of other physiological functions. Recent studies suggest that the gut microbiome is involved in energy homeostasis by regulating feeding, digestive and metabolic processes, as well as the immune response. Consequently, deciphering gut microbiome dynamics in cultured fish and shellfish species will play an indispensable role in promoting animal health and aquaculture productivity. It is mentioned that the microbiome community available in the gut tract, particularly in the intestine acts as an innovative source of natural product discovery. The microbial communities that are associated with several marine organisms are the source of natural products with a diverse array of biological activities and as of today, more than 1000 new compounds have been reported from such microbial species. Exploration of such new ingredients from microbial species would create more opportunities for the development of the bio-pharma/aquaculture industries. Considering the important role of the microbiome in the whole life span of fish and shellfish, it is necessary to understand the interaction process between the host and microbial community. However, information pertaining to host-microbiome interaction, particularly at the cellular level, gene expression, metabolic pathways, and immunomodulation mechanisms, the available literature is scanty. It has been reported that there are three ways of interaction involving the host-microbe-environment operates to maintain homeostasis in the fish and shellfish gut i.e. host intrinsic factors, the environment that shapes the gut microbiome composition, and the core microbial community present in the gut system itself has equal influence on the host biology. In the present review, efforts have been made to collect comprehensive information on various aspects of host-microbiome interaction, particularly on the immune system and health maintenance, management of diseases, nutrient uptake, digestion and absorption, gene expression, and metabolism in fish and shellfish.
... The definition of the core microbiota is based on shared microorganisms among comparable habitats [39], and for this, a large number of replicate samples is needed to overcome the effect of individual variability [40]. Indeed, such prerequisites are achievable under experimental conditions (e.g., Uren Webster et al. [11], Panteli et al. [41]) or in the case of farmed fish populations (e.g., Nikouli et al. [42], Le et al. [43], Nikouli et al. [44]). However, when core microbiota of fish from natural populations are investigated by experimental fishing in the open sea, collecting adequate replicates of specimens of the same age cannot be secured, so scientists must rely on what they catch. ...
... alletteratus, M. surmuletus, S. porcus, S. scrofa, S. canicula, S. cretense, S. cantharus, and U. scaber), there are no available data on gut microbiota and microbiomes to date, while the gut microbiota of D. annularis, D. vulgaris, P. pagrus, and P. erythrinus have been recently investigated by Escalas et al. [47]. Regarding P. pagrus, its gut bacterial microbiota has been studied in a farmed population [44]. The core microbiota of these 12 species consisted of 23 known and two yet-unaffiliated (from the Clostridiaceae and Vibrionaceae families) genera (Table S2). ...
... Despite that each feeding habit and digestive physiology categories did not have similar numbers of fish species, the rather sporadicor, at least, inexplicable with the current data-differences leave the host species effect as the more likely factor for the shaping of the midgut bacterial microbiota; additional data from more species per feeding type category are required in future studies to clarify this issue. Even in co-farmed species reared under the same environmental and dietary conditions, each fish species was found to host its own distinct gut microbiota [44]. However, gut microbiota is susceptible to manipulations at least for experimental or commercial rearing purposes [1]. ...
Fish microbiome science is progressing fast, but it is biased toward farmed or laboratory fish species against natural fish populations, which remain considerably underinvestigated. We analyzed the midgut bacterial microbiota of 45 specimens of 12 fish species collected from the Gyaros Island marine protected area (Aegean Sea, Greece). The species belong to seven taxonomic families and are either herbivores or omnivores. Mucosa midgut bacterial diversity was assessed by amplicon metabarcoding of the 16S rRNA V3–V4 gene region. A total of 854 operational taxonomic units (OTUs) were identified. In each fish species, between 2 and 18 OTUs dominated with cumulative relative abundance ≥ 70%. Most of the dominating bacterial taxa have been reported to occur both in wild and farmed fish populations. The midgut bacterial communities were different among the 12 fish species, except for Pagrus pagrus and Pagellus erythrinus, which belong to the Sparidae family. No differentiation of the midgut bacterial microbiota was found based on feeding habits, i.e., omnivorous vs. carnivorous. Comparing wild and farmed P. pagrus midgut bacterial microbiota revealed considerable variation between them. Our results expand the gut microbiota of wild fish and support the host species effect as the more likely factor shaping intestinal bacterial microbiota.
... piscicida, representing the aetiological agent of pasteurellosis [48], suggesting an opportunistic lifestyle towards the fish host. The Pseudomonas genus was found in the core gut microbiome of 5 sympatrically farmed marine fish species [49] as well as in the core mid-gut microbiota of Mediterranean seabass and seabream [15] whereas Staphylococcus epidermidis represented one of the core OTUs in S. aurata in the Aegean Sea [15]. Pseudomonas members have been often reported in carnivorous teleosts and reported the most abundant shared bacterial species in the gut of S. aurata and D. labrax [50], and have been reported to contribute to teleosts' digestion through the secretion of several digestive enzymes [50 and references therein]. ...
Gilthead seabream is among the most important farmed fish species in the Mediterranean Sea. Several approaches are currently applied to assure a lower impact of diseases and higher productivity, including the exploration of the fish microbiome and its manipulation as a sustainable alternative to improve aquaculture practices. Here, using 16S rRNA gene high-throughput sequencing, we explored the microbiome of farmed seabream to assess similarities and differences among microbial assemblages associated to different tissues and compare them with those in the surrounding environment. Seabream had distinct associated microbiomes according to the tissue and compared to the marine environment. The gut hosted the most diverse microbiome; different sets of dominant ASVs characterized the environmental and fish samples. The similarity between fish and environmental microbiomes was higher in seawater than sediment (up to 7.8 times), and the highest similarity (3.9%) was observed between gill and seawater, suggesting that gills are more closely interacting with the environment. We finally analyzed the potential connections occurring among microbiomes. These connections were relatively low among the host’s tissues and, in particular, between the gut and the others fish-related microbiomes; other tissues, including skin and gills, were found to be the most connected microbiomes. Our results suggest that, in mariculture, seabream microbiomes reflect only partially those in their surrounding environment and that the host is the primary driver shaping the seabream microbiome. These data provide a step forward to understand the role of the microbiome in farmed fish and farming environments, useful to enhance disease control, fish health, and environmental sustainability.
... The "typical" makeup of the fish gut microbiome is composed of core taxa of bacteria predominantly of the phyla Proteobacteria, Firmicutes, Actinobacteria, Fusobacteria, and Bacteroidetes (Cahill, 1990;Gómez and Balcázar, 2008;Roeselers et al., 2011;Ghanbari et al., 2015;Adamovsky et al., 2018). The relative abundance of genera present in the gut microbiome varies greatly between species of fish (Givens et al., 2015;Egerton et al., 2018;Nikouli et al., 2021) and between individuals within a species (Burke et al., 2011). ...
The gut microbiome of fish contains core taxa whose relative abundances are modulated in response to diet, environmental factors, and exposure to toxicogenic chemicals, influencing the health of the host fish. Recent advances in genomics and metabolomics have suggested the potential of microbiome analysis as a biomarker for exposure to toxicogenic compounds. In this 35-day laboratory study, 16S RNA sequencing and multivariate analysis were used to explore changes in the gut microbiome of juvenile Lates calcarifer exposed to dietary sub-lethal doses of three metals: vanadium (20 mg/kg), nickel (480 mg/kg), and iron (470 mg/kg), and to two oils: bunker C heavy fuel oil (HFO) (1% w/w) and Montara, a typical Australian medium crude oil (ACO) (1% w/w). Diversity of the gut microbiome was significantly reduced compared to negative controls in fish exposed to metals, but not petroleum hydrocarbons. The core taxa in the microbiome of negative control fish comprised phyla Proteobacteria (62%), Firmicutes (7%), Planctomycetes (3%), Actinobacteria (2%), Bacteroidetes (1%), and others (25%). Differences in the relative abundances of bacterial phyla of metal-exposed fish were pronounced, with the microbiome of Ni-, V-, and Fe-exposed fish dominated by Proteobacteria (81%), Firmicutes (68%), and Bacteroidetes (48%), respectively. The genus Photobacterium was enriched proportionally to the concentration of polycyclic aromatic hydrocarbons (PAHs) in oil-exposed fish. The probiotic lactic acid bacterium Lactobacillus was significantly reduced in the microbiota of fish exposed to metals. Transcription of cytokines IL-1, IL-10, and TNF-a was significantly upregulated in fish exposed to metals but unchanged in oil-exposed fish compared to negative controls. However, IL-7 was significantly downregulated in fish exposed to V, Ni, Fe, and HFOs. Fish gut microbiome exhibits distinctive changes in response to specific toxicants and shows potential for use as biomarkers of exposure to V, Ni, Fe, and to PAHs present in crude oil.
