Taxonomic Composition and Functional Potentials of Gastrointestinal Microbiota in 12 Wild-stranded Cetaceans

Overview

Journal Front Microbiol

Specialty Microbiology

Date 2024 Sep 13

PMID 39268538

Authors

Jie Fan

Hui Kang

Meiqi Lv

Yuhuan Zhai

Yangyang Jia

Zixin Yang

Chengcheng Shi

Changhao Zhou

Lin Diao

Jingsuo Li

Xiaowei Jin

Shanshan Liu

Karsten Kristiansen

Peijun Zhang

Jianwei Chen

Songhai Li

Affiliations

Soon will be listed here.

Abstract

Cetaceans play a crucial role in marine ecosystems; however, research on their gastrointestinal microbiota remains limited due to sampling constraints. In this study, we collected hindgut samples from 12 stranded cetaceans and performed 16S rRNA gene amplicon sequencing to investigate microbial composition and functional potentials. Analysis of ZOTUs profiles revealed that the phyla Firmicutes, Proteobacteria, and Bacteroidetes dominated all hindgut samples. However, unique microbial profiles were observed among different cetacean species, with significant separation of gut microbiota communities according to biological evolutionary lineages. Different genera that contain pathogens were observed distinguishing delphinids from physeteroids/ziphiids. Delphinid samples exhibited higher abundances of , , and , whereas physeteroid and ziphiid samples showed higher abundances of , , and . Functional analysis indicated convergence in the gut microbiota among all cetaceans, with shared bacterial infection pathways across hindgut samples. In addition, a comparison of the gastrointestinal microbial composition between a stranded short-finned pilot whale () and a stranded rough-toothed dolphin () using 16S rRNA gene sequencing revealed distinct microbial community structures and functional capacities. To the best of our knowledge, this study represents the first report on the gastrointestinal microbiota of the pantropical spotted dolphin (), Blainville's beaked whale (), and rough-toothed dolphin, with various comparisons conducted among different cetacean species. Our findings enhance the understanding of microbial composition and diversity in cetacean gastrointestinal microbiota, providing new insights into co-evolution and complex interactions between cetacean microbes and hosts.

Citing Articles

Genetic diversity of single-celled microorganism sp. and its associated gut microbiome in free-ranging marine mammals from North-Western Mediterranean Sea.

Marangi M, Boughattas S Curr Res Microb Sci. 2025; 8:100349.

PMID: 39926158 PMC: 11803257. DOI: 10.1016/j.crmicr.2025.100349.

References

Miller C, Holm H, Horstmann L, George J, Fredricks H, Van Mooy B . Coordinated transformation of the gut microbiome and lipidome of bowhead whales provides novel insights into digestion. ISME J. 2019; 14(3):688-701. PMC: 7031289. DOI: 10.1038/s41396-019-0549-y. View

Ley R, Hamady M, Lozupone C, Turnbaugh P, Ramey R, Bircher J . Evolution of mammals and their gut microbes. Science. 2008; 320(5883):1647-51. PMC: 2649005. DOI: 10.1126/science.1155725. View

Li C, Tan X, Bai J, Xu Q, Liu S, Guo W . A survey of the sperm whale () commensal microbiome. PeerJ. 2019; 7:e7257. PMC: 6612419. DOI: 10.7717/peerj.7257. View

Higgins R . Bacteria and fungi of marine mammals: a review. Can Vet J. 2000; 41(2):105-16. PMC: 1476275. View

Xie F, Jin W, Si H, Yuan Y, Tao Y, Liu J . An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants. Microbiome. 2021; 9(1):137. PMC: 8199421. DOI: 10.1186/s40168-021-01078-x. View

Di Guardo G, Centelleghe C, Mazzariol S . Cetacean Host-Pathogen Interaction(s): Critical Knowledge Gaps. Front Immunol. 2018; 9:2815. PMC: 6279917. DOI: 10.3389/fimmu.2018.02815. View

Edgar R, Flyvbjerg H . Error filtering, pair assembly and error correction for next-generation sequencing reads. Bioinformatics. 2015; 31(21):3476-82. DOI: 10.1093/bioinformatics/btv401. View

Price M, Dehal P, Arkin A . FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One. 2010; 5(3):e9490. PMC: 2835736. DOI: 10.1371/journal.pone.0009490. View

Bai S, Zhang P, Zhang C, Du J, Du X, Zhu C . Comparative Study of the Gut Microbiota Among Four Different Marine Mammals in an Aquarium. Front Microbiol. 2021; 12:769012. PMC: 8567075. DOI: 10.3389/fmicb.2021.769012. View

10.

Waltzek T, Cortes-Hinojosa G, Wellehan Jr J, Gray G . Marine mammal zoonoses: a review of disease manifestations. Zoonoses Public Health. 2012; 59(8):521-35. PMC: 7477081. DOI: 10.1111/j.1863-2378.2012.01492.x. View

11.

Hu J, Chen J, Ma L, Hou Q, Zhang Y, Kong X . Characterizing core microbiota and regulatory functions of the pig gut microbiome. ISME J. 2024; 18(1). PMC: 10873858. DOI: 10.1093/ismejo/wrad037. View

12.

Bik E, Costello E, Switzer A, Callahan B, Holmes S, Wells R . Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea. Nat Commun. 2016; 7:10516. PMC: 4742810. DOI: 10.1038/ncomms10516. View

13.

Zou K, Chen J, Ruan H, Li Z, Guo W, Li M . eDNA metabarcoding as a promising conservation tool for monitoring fish diversity in a coastal wetland of the Pearl River Estuary compared to bottom trawling. Sci Total Environ. 2019; 702:134704. DOI: 10.1016/j.scitotenv.2019.134704. View

14.

Wan X, Li J, Cheng Z, Ao M, Tian R, McLaughlin R . The intestinal microbiome of an Indo-Pacific humpback dolphin (Sousa chinensis) stranded near the Pearl River Estuary, China. Integr Zool. 2020; 16(3):287-299. DOI: 10.1111/1749-4877.12477. View

15.

Zhang Z, Zhu J, Ghenijan O, Chen J, Wang Y, Jiang L . Prokaryotic taxonomy and functional diversity assessment of different sequencing platform in a hyper-arid Gobi soil in Xinjiang Turpan Basin, China. Front Microbiol. 2023; 14:1211915. PMC: 10682777. DOI: 10.3389/fmicb.2023.1211915. View

16.

Yin J, Li Y, Tian Y, Zhou F, Ma J, Xia S . Obese Ningxiang pig-derived microbiota rewires carnitine metabolism to promote muscle fatty acid deposition in lean DLY pigs. Innovation (Camb). 2023; 4(5):100486. PMC: 10448216. DOI: 10.1016/j.xinn.2023.100486. View

17.

Zhang P, Goodman S . Learning from the heaviest ancient whale. Innovation (Camb). 2023; 4(5):100501. PMC: 10477792. DOI: 10.1016/j.xinn.2023.100501. View

18.

Beasley I, Cherel Y, Robinson S, Betty E, Hagihara R, Gales R . Stomach contents of long-finned pilot whales, Globicephala melas mass-stranded in Tasmania. PLoS One. 2019; 14(1):e0206747. PMC: 6331100. DOI: 10.1371/journal.pone.0206747. View

19.

Li X, He L, Luo J, Zheng Y, Zhou Y, Li D . Paeniclostridium sordellii hemorrhagic toxin targets TMPRSS2 to induce colonic epithelial lesions. Nat Commun. 2022; 13(1):4331. PMC: 9321280. DOI: 10.1038/s41467-022-31994-x. View

20.

Liu Y, Chen L, Ma T, Li X, Zheng M, Zhou X . EasyAmplicon: An easy-to-use, open-source, reproducible, and community-based pipeline for amplicon data analysis in microbiome research. Imeta. 2024; 2(1):e83. PMC: 10989771. DOI: 10.1002/imt2.83. View