The Characteristics of Intestinal Bacterial Community in Three Omnivorous Fishes and Their Interaction with Microbiota from Habitats

Abstract

Artificial fishery habitats have been extensively used for fishery resource protection and water habitat restoration, and they could attract a large number of omnivorous fishes to gather together. This study intended to reveal the relationship between bacterial communities in the habitats (water and sediment) and intestines of omnivorous fishes (Oreochromis mossambicus, Toxabramis houdemeri and Hemiculter leucisculus). Therefore, we investigated the bacterial communities of samples collected from intestines, water, and sediments in artificial fishery habitats via 16S rRNA metabarcoding high-throughput sequencing technology. The results showed that there were significant differences in the composition, core indicators, diversity and prediction functions in water, sediments, and intestinal microbial communities of the three omnivorous fish. The microbial diversities were significantly higher in habitats than in intestines. The analysis of similarity (ANOSIM) and nonmetric multidimensional scaling (NMDS) results indicated that the intestine microbial communities (T. houdemeri and H. leucisculus) were more similar to the water microbiota, but the intestine microbial communities (O. mossambicus) were more similar to the sediments. Source tracking analysis also confirmed that the contribution of habitat characteristics to omnivorous fish intestinal microorganisms was different; the sediment had a greater contribution than water to the intestinal microbiota of O. mossambicus, which was consistent with their benthic habit. Moreover, the functional prediction results showed that there were unique core indicators and functions between the bacterial community of habitats and intestines. Altogether, these results can enhance our understanding of the bacterial composition and functions about omnivorous fish intestines and their living with habitats, which have provided new information for the ecological benefits of artificial fishery habitats from the perspective of bacterial ecology and contributed to apply artificial fishery habitats in more rivers.

Vertical habitat preferences shape the fish gut microbiota in a shallow lake

“…Understanding and deciphering the ecological succession of fish gut microbiota are helpful to host metabolism, health, and environmental adaptation ( Ghanbari et al, 2015 ; Robinson et al, 2018 ), and therefore has become a central theme of gut ecology ( Xiao et al, 2021 ). Our study revealed that the fish gut microbiota exhibited significant intra-group coherence and inter-group divergence, which was consistent with the results of previous studies ( Bi et al, 2021 ; Yang et al, 2022 ). However, unsupervised machine learning results failed to differentiate from fish gut microbiota at the species level, but instead identified an optimal clustering pattern at k = 2, suggesting that other factors beyond host species may influence the composition of fish gut microbes ( Figure 4A ).…”

“…Due to its status as an urban extensive aquaculture lake, the water body has become eutrophic ( Xia et al, 2022 ), resulting in a dominance of Cyanobacteria within the water microbiota. Consistent with other studies on the gut microbiota of freshwater fish, Proteobacteria and Firmicutes were found to be the dominant phyla in their guts ( Bi et al, 2021 ; Duan et al, 2021 ) ( Figure 2A ). The sediments microbiota exhibited the highest α-diversity in all sampling groups ( Supplementary Figure S2 ), predominantly composed of Proteobacteria.…”

“…Fish gut microbiota play an important role in ecosystem microbial diversity ( Xiao et al, 2021 ), affecting various aspects of the host, such as metabolism, feeding behavior, and immune response ( Cresci and Bawden, 2015 ). Similar to mammals, the gut microbiota of fish can also be considered an important organ responsible for some key physiological functions that contribute to the health maintenance of the host ( Bi et al, 2021 ). However, the mechanism governing aquatic fish gut microbiomes may be utterly different from those of terrestrial mammals ( De Schryver and Vadstein, 2014 ).…”

Microbial Communities Associated with the Intestinal Tract of Grey Mullets from a Mediterranean Aquatic Environment

“…culture of grey mullets Mugilidae species is considered a priority within the current strategies of sustainable European aquaculture [21]. To the authors' knowledge, various studies were made on the gut microbiota of cultured [41] and wild mullets [23,31] and the present study has provided more information on the biodiversity of this ecosystem and their biotechnological potential. Previous studies on Mediterranean grey mullets had showed some interesting biotechnologically traits of intestinal cultivable bacteria as a source of bioactive compounds with immunological and bioremediation functions [42].…”

“…Earlier studies reported the composition and the predicted functions of the associated gut microbiota on Mugil cephalus of different ages from Northwest Pacific marine envi-ronments [30], from Chinese coastal marine areas [31] and on Mediterranean wild thick-lipped grey mullets (Chelon labrosus, Risso 1827) [23]. However, the intestinal microbiota of wild grey mullets from Mediterranean aquatic environments still deserve more explora-tions and remains an important topics of scientific interest.…”