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Characterization of the core gut microbiota of Nile tilapia (Oreochromis niloticus): indication of a putative novel Cetobacterium species and analysis of its potential function on nutrition

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Abstract

The genus Cetobacterium has been considered a dominant group of gut bacteria in many freshwater fish, and members of this genus contribute to anaerobic metabolism. Because of its significant place in the gut of freshwater fish, many studies on Cetobacterium were performed. Those studies mostly focused on the temporal and spatial changes of its abundance in fish intestine, which were affected by food or other environmental conditions. However, only a few studies isolated strains from genus Cetobacterium and reported their characteristics. In the present study, we performed 16S rRNA sequencing of the intestinal mucosa of Nile tilapia (Oreochromis niloticus) and found that Cetobacterium sp. existed widely in the foregut, midgut and hindgut mucosa, and a strain of Cetobacterium was successfully isolated from the gut of tilapia. We sequenced its whole genome and predicted it to be a novel candidate species of Cetobacterium sp. and named it NK01. The size of its genome was 3,095,946 bp, with a guanine + cytosine content of 28.8%. Among the identified genes, 2855 were predicted to be coding DNA sequences, 84 were tRNA and 34 were rRNA. We found that NK01 produced amino acids, including leucine, isoleucine, valine, glycine, alanine, phenylalanine and proline. Strain NK01 could use starch, sucrose, maltose, glucose, and mannose and synthesize and utilize glycogen. INV, GPI, malQ, malZ, sacA, scrK, glgC, glgA and glk, which were related to carbohydrate metabolism, were detected. yiaY and adhE, which oxidize ethanol to acetaldehyde and participate in a variety of metabolic pathways, were also present in the genome. No coding genes directly involved in acetate or butyrate production were detected. NK01 could also catabolize a variety of vitamins, and all genes involved in folate synthesis were detected, including folP, folC, folA and eutT, which converted vitamin B12s into vitamin B12 coenzyme. Here, we investigated the draft genome and in vitro function of Cetobacterium isolated from the intestinal tract of Nile tilapia. The results provided a preliminary understanding of the core microbiota of fish gut.

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Data Availability

The Whole Genome Shotgun project and 16S rRNA gene sequence have been deposited at DDBJ/ENA/GenBank under the accession JANIBO000000000 and OP060691. respectively.

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Funding

This work was financially supported by the following grants: National Natural Science Foundation of China (32102818), funds from China Agriculture Research System of MOF and MARA (CARS-46), and Guangdong Provincial Key R&D Program (2021B0202020001).

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  1. Miao Wang, Gang Chen and Maixin Lu have contributed equally to this work.

Authors and Affiliations

  1. Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China

    Ziyue Zhang & Gang Chen

  2. Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture and Rural Affairs, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, 510380, China

    Ziyue Zhang, Zijian Fan, Mengmeng Yi, Zhigang Liu, Xiaoli Ke, Fengying Gao, Jianmeng Cao, Miao Wang & Maixin Lu

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  1. Ziyue Zhang
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Contributions

All authors contributed to the study conception and design. Material preparation and data collection were performed by Zijian Fan, Mengmeng Yi and Fengying Gao. Formal analysis was performed by Xiaoli Ke, Zhigang Liu and Jianmeng Cao. The first draft of the manuscript was written by Ziyue Zhang. Miao Wang, Maixin Lu and Gang Chen supervised the study, contributed to text preparation and revised the manuscript. All authors read and approved the final manuscript.

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Correspondence to Miao Wang, Gang Chen or Maixin Lu.

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Ethical statement

All experiments were conducted in conformity with the Ethical Committee for Animal Experiments of Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, China, and according to the guidelines of the Animal Welfare Council of China.

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Communicated by Erko Stackebrandt.

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Zhang, Z., Fan, Z., Yi, M. et al. Characterization of the core gut microbiota of Nile tilapia (Oreochromis niloticus): indication of a putative novel Cetobacterium species and analysis of its potential function on nutrition. Arch Microbiol 204, 690 (2022). https://doi.org/10.1007/s00203-022-03301-1

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