The fish intestinal microbiota plays vital roles in host growth and health, and has co-evolved with the host in a mutually positive way (Wang et al., 2018). Intestinal microbiota is primarily affected by host phylogeny (Cornejo-Granados et al., 2017) and partly associated with growth stages, ambient condition and diet (Wang et al., 2018). With the rapid development of the modern aquaculture industry, intestinal microbial dysbiosis, immune deficiency and mass outbreak of diseases (e.g., enteritis and red-skin disease) are frequently appeared in fish because of the accumulation of opportunistic pathogens and/or other viruses under inteansive farming model (Chen et al., 2021). Previous studies have shown that maintaining the intestinal microbial homeostasis will greatly benefit the growth, immunity, and disease resistance in fish (Hoseinifar et al., 2018; Wang et al., 2019; Yang et al., 2019). Thus, exploring useful approaches to maintain the intestinal microbial homeostasis in fish will be conducive to improve the production, and effectively decrease the abuse of antibiotics in aquaculture.

Dietary supplementation of probiotics could modulate intestinal microbiota, improve production performance, immune response and disease resistance in many fish species, such as Asian seabass larvae (Lates calcarifer) (Masduki et al., 2020), grouper (Epinephelus coioides) (Yang et al., 2019), common carp (Cyprinus carpio L.) (Meng et al., 2021), tilapia (Oreochromis niloticus) (Li et al., 2019), snakehead (Channa argus) (Kong et al., 2021), and so on. Recently, probiotics as means of intestinal health maintain and diseases control in aquaculture have been reviewed extensively (Lazado et al., 2015; Hoseinifar et al., 2018; Doan et al., 2020; Teame et al., 2020; Zhang et al., 2020; Simon et al., 2021). The precise mechanism by which the positive performance of probiotics in aquaculture have must be more comprehensive and have not been well studied. So far as we know, one of the most recognized mechanisms is that probiotics can improve fish intestinal homeostasis and health via re-shaping the intestinal microbiota (Dawood et al., 2019; Doan et al., 2020; Simon et al., 2021; Guo et al., 2022). Nevertheless, information pertaining to interactions between host-derived probiotics and intestinal microbiota (including microbial composition and function) are still limited in teleost fish (Kong et al., 2021).

Japanese seabass, Lateolabrax japonicus, is one of the most economically important marine fish in China, and the annual production has reached 195, 246 tons in 2020 (China Fishery and Statistics Yearbook, 2021). Previous study has evaluated the application of five possible host-derived probiotic strains (Bacillus siamensis LF4, Lactococcus petaurid LF3, Micrococcus yunnanensis LD5, Micrococcus aloeverae LC3, Mitsuaria chitosanitabida LD3) in juvenile Japanese seabass (L. japonicus). The results demonstrated that probiotic L. petauri LF3 and B. siamensis LF4 could effectively improve growth performance, innate immunity, antioxidant activity and ammonia tolerance (Yang et al., 2021). To the best of our knowledge, limited information is still available about the impact of host-derived probiotics on intestinal microbiota in Japanese seabass. In this study, therefore, the intestinal microbial community and putative function of juvenile Japanese seabass in response to host-derived probiotic L. petauri LF3 and B. siamensis LF4 were analyzed and characterized by using high-throughput sequencing technology.

The application of probiotics in fish aquaculture has been extensively reported, while limited information is available about the interactions between host-derived probiotics and intestinal microbiota (Kong et al., 2021). In this study, the impact of host-derived probiotic L. petauri LF3 and B. siamensis LF4 on intestinal microbiota in juvenile Japanese seabass were analyzed by using high-throughput sequencing technology. The intestinal microbiota of Japanese seabass (L. japonicus) fed control or probiotic diets shared three dominant phyla (Fusobacteria, Proteobacteria and Firmicutes), which had been also reported as dominant phyla in the intestines of other teleost fish, such as European seabass (Dicentrarchus labrax) (Kokou et al., 2020; Wassef et al., 2020; Serra et al., 2021), Asian seabass (Lates calcarifer) (Apper et al., 2016), grass carp (Ctenopharyngodon idellus) (Shi F. et al., 2021), tilapia (O. niloticus) (Adeoye et al., 2016; Li et al., 2019), orange-spotted grouper (Epinephelus coioides) (Yang et al., 2019), and so on. Overabundances of certain taxa led to intestinal microbiota turning from balance to dysbiosis status, and then threaten host well-being (Li et al., 2019; Yang et al., 2019; Serra et al., 2021). In this study, the relative abundances of Fusobacteria and Proteobacteria were decreased in Japanese seabass fed probiotic diets. In line with the present study, decreased abundances of Fusobacteria and/or Proteobacteria following probiotics application were documented in Asian seabass (L. calcarifer) (Masduki et al., 2020) and orange-spotted grouper (E. coioides) (Yang et al., 2019). Inhibiting opportunistic pathogens Fusobacteria and Proteobacteria overgrowth would create redundant niches, which might benefit the growth of other beneficial microbes (Xun et al., 2019; Tan and Sun, 2020; Shi F. et al., 2021). On the other hand, the supplementation of host-derived probiotics in diet (groups LF3 and LF4) apparently enhanced the relative abundances of Firmicutes, Actinobacteria and Bacteroidetes in this study. Firmicutes and Bacteroidetes have been recorded previously as primarily beneficial phyla in healthy Japanese seabass (L. japonicus) (Wang et al., 2017), European sea bass (D. labrax) (Parma et al., 2019; Rimoldi et al., 2020), common carp (Cyprinus carpio L.) (Meng et al., 2021), and grouper (E. coioides) (Yang et al., 2019). Bacteria of phylum Actinobacteria could produce a wide range of exoenzymes and secondary metabolites (Ventura et al., 2007). In particular, the genus Bifidobacterium, belonging to phylum Actinobacteria, is an important lactic acid producer, which was used as probiotic in aquaculture (Jha et al., 2015). This may illustrate the better growth performance and feed utilization in Japanese seabass fed probiotic L. petauri LF3 and B. siamensis LF4 (Yang et al., 2021).

At the genus level, Japanese seabass fed with Lc. petaurid LF3 and B. siamensis LF4 containing diets showed lower relative abundances of opportunistic pathogens such as Cetobacterium and Plesiomonas, which might be partly contributed to the improvement of growth performance and general health in juvenile Japanese seabass (L. japonicus) (Yang et al., 2021). In line with the present study, previous reports have showed that lower abundances of Cetobacterium and Plesiomonas existed in the intestine of healthier fish and benefited to host health due to cooperative activity among commensal microbes (Miller et al., 2006; Behera et al., 2018; Liu et al., 2021; Zhang et al., 2021). On the other hand, higher abundances of intestinal possible beneficial Christensenellaceae_R-7_group and Lactobacillus in the phylum Firmicutes, which have been reported as beneficial bacteria to improve growth performance, immunity, antioxidant capability and other welfares in aquatic animals (Van Doan et al., 2017; Zheng et al., 2017; Hoseinifar et al., 2018; Wang et al., 2019), were presented in seabass fed with host-derived probiotics, especially with B. siamensis LF4. The genus Lactobacillus can produce high level of lactic acid, and then are able to improve feed efficiency and alleviate metabolic damage by positively modulating gut microbiota (Hoseinifar et al., 2018; Wang et al., 2019). In line with the current study, significantly elevated abundances of beneficial microorganisms have been also reported in probiotic Clostridium butyricum fed tilapia (O. niloticus) (Li et al., 2019) and common carp (C. carpio L.) (Meng et al., 2021). These results evidenced that beneficial microorganisms were usually common members of the normal microbiota in the fish gut, and under certain circumstances, the higher abundances of these microorganisms could be partly responsible for mucosal homeostasis and avoiding disease happen (Hoseinifar et al., 2018; Yu et al., 2021). Interestingly, seabass fed with Lc. petaurid LF3 demonstrated a sharp increase in the relative abundances of Aeromonas, which is a traditionally opportunistic pathogen in the intestines of aquatic animals (Jiravanichpaisal et al., 2009; Zhu et al., 2016; Chen et al., 2021). However, several studies have evidenced that Aeromonas could be use as probiotic and improve growth, immunity, and disease resistance in certain aquatic animals, such as common carp (C. carpio) (Chi et al., 2014), grass carp (Ctenopharyngodon idella) (Hao et al., 2017), Pacific white shrimp (Litopenaeus vannamei) (Hao et al., 2014), and so on. In general, these results illustrated that host-derived Lc. petaurid LF3 and B. siamensis LF4 can positively remodel intestinal microbial composition.

In the present study, the intestinal microbiota of fish fed probiotics L. petauri LF3 and B. siamensis LF4 demonstrated higher species diversity based on alpha diversity data (Chao1, Ace, Shannon and Simpson indices), and more similarity and lower individual differences based on beta diversity data (PCoA, NMDS and UPGMA clustering tree). The results are in line with other researches in snakehead fish (Channa argus) fed with two lactic acid bacteria (Kong et al., 2021), and common carp (C. carpio L.) fed with Clostridium butyricum (Meng et al., 2021). Generally, high intestinal bacterial diversity reflect a well-development of the host, as the increase of commensal microbial diversity and/or species richness might lead to attenuated colonization resistance against invading opportunistic pathogens, which have the potential to cause infection of the intestine (Rimoldi et al., 2020). In the current study, it is worth noting that probiotic L. petauri LF3 and B. siamensis LF4 can improve intestinal microbial diversities and meanwhile reduce individual differences, which might partly explain the previous results that the two probiotic strains facilitated growth performance, immune response, and ammonia tolerance in juvenile Japanese seabass (L. japonicus) (Yang et al., 2021). Similarly, higher and stabler intestinal microbial diversities were detected in probiotics-treated fish with improving growth, immunity and disease resistance (Kong et al., 2021); (Meng et al., 2021).

In the present study, compared to the control group, supplementation of host-derived Lc. petaurid LF3 and B. siamensis LF4 led to biomarkers emerging, especially phylum Firmicutes, as selected using LEfSe. In general, phylum Firmicutes is a well recognized class of beneficial microorganisms. Early researches have showed that bacteria (i.e., genus Bacillus, Lactobacillus, Lactococcus, Enterococcus, and Clostridium) in phylum Firmicutes can secretion of various enzymes and decreasing the intestinal pH by producing short-chain fatty acids (Dawood et al., 2019), which can inhibit the proliferation of pathogenic bacteria and improve intestinal microecology of aquatic animals (Hao et al., 2017; Hoseinifar et al., 2018; Dawood et al., 2019; Li et al., 2019; Wang et al., 2019; Yang et al., 2019; Meng et al., 2021). The results of phylum Firmicutes significantly enriched by dietary supplementation of host-derived probiotics again proved that probiotics can increase the beneficial bacteria to achieve the purpose of positively modulating intestinal microbiota of aquatic animals (Hoseinifar et al., 2018; Wang et al., 2019; Yang et al., 2019; Doan et al., 2020; Kong et al., 2021).

The NSTI values (0.19 ± 0.03) for seabass intestinal samples in the present study were in line with those for red swamp crayfish, Procambarus clarkii (0.171 ± 0.023) and pacific white shrimp, Litopenaeus vannamei (0.18 ± 0.02) (Zeng et al., 2017; Chen et al., 2021). It has been validated that PICRUSt 2 could accurately predict the functions of seabass intestinal microbiota (Chen et al., 2021). In this study, the dominated function of Amino acid metabolism, Carbohydrate metabolism and Global and overview maps were accurately predicted using PICRUSt 2, which are associated strongly with seabass digestion and absorption. Unexpectedly, the intestinal microbial functions were stable among all groups, although dietary supplementation with host-derived probiotics remarkably changed the intestinal microbial community. In agreement with the present study, the intestinal microbial functions (including carbrohydrate transport and metabolism, lipid transport and metabolism, and so on) were determined to be almost similar in snakehead fish (C. argus) fed with a basal diet or diets supplemented with 1.0 × 10⁸ CFU/g of host-derived probiotics (L. lacti L19, E. faecalis W24, L. lacti L19 + E. faecalis W24 (Kong et al., 2021). However, these results contradict to previous studies that the change of intestinal microbial composition was associated with function change in aquatic animals, such as zebrafish (Danio rerio) (Shi Y. Y. et al., 2021) and turbot (Scophthalmus maximus) (Guo et al., 2022). Guo et al. (2022) has reported that several pathways related to glycan, lipid and amino acid metabolism upregulated in turbots (S. maximus) fed with probiotic (strain B. coagulans G1902, unspecified source). We hypothesized that this paradox might be caused by the different probiotic species and source, and rearing environment. Additionally, this study supported the hypothesis that when the host is sufficiently healthy, the function of the intestinal microbiota might maintain relative stability rather than emerge significant changes (Fan and Pedersen, 2021).

Host-derived probiotic L. petauri LF3 and B. siamensis LF4 decreased opportunistic pathogenic Fusobacteria, Proteobacteria, and Plesiomonas and apparently increased beneficial Firmicutes, Bacteroidetes, and Lactobacillus in juvenile Japanese seabass (L. japonicus). Dietary supplementation of host-derived probiotic L. petauri LF3 and B. siamensis LF4 significantly improve the intestinal microbial diversities and led to Firmicutes as a significant biomarker emerge. However, the intestinal microbial functions (i.e., amino acid metabolism, carbohydrate metabolism, energy metabolism, etc.) did not alter by host-derived probiotics. These results lay the necessary theoretical basis for the development and application of host-associated probiotics in Japanese seabass.

The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: NCBI [accession: PRJNA759698].

The animal study was reviewed and approved by the Animal Care and Use Committee of Jimei University.

H-LY investigation and original draft.: Z-YL: data analysis and writing. J-TJ: investigation and data analysis. Z-XL: feed preparation and animal trial. J-DY: review and editing. Y-ZS: supervision, project administration, funding acquisition, review and editing. All authors contributed to the article and approved the submitted version.

This work was supported by the National natural science foundation of China (32072990), Science and Technology Major/Special Project of Fujian Province (2021NZ029022), Xiamen Marine and Fisheries Development Fund (19CZP018HJ04) and the China Agriculture Research System (CARS-47-G14).

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.