Abstract
In this study, taxonomic classification of intestinal microbiota from healthy Barbour’s seahorses (Hippocampus barbouri) was determined as it plays an important role in host nutrition and immunity. Genomic DNA was extracted from the intestinal mucus samples of eleven Barbour’s seahorses, which were subjected to high-throughput sequencing of bacterial 16 S rRNA genes targeting V3-V4 regions. The results showed that there were 302,891 amplicon sequence reads representing all samples, with 46 total operational taxonomic units (OTU). Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria were the most predominant phyla observed, with 13 classes, 22 orders, 28 families, and 35 genera, respectively. The results also revealed that the most abundant OTUs were affiliated with the genus Shewanella. Findings in this study may shed light on further studies in exploring the potential implications of intestinal microbiota to seahorses in terms of health status, development, growth, and survival. This could also be used as baseline data for preliminary screening of bacterial species as potential probiotics.
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Data Availability
All sequences obtained in this study are available and will be submitted to GenBank at the NCBI.
Abbreviations
- OTU:
-
(Operational Taxonomic Unit) is used to classify closely related organisms by grouping them based on their DNA sequence similarity of a specific taxonomic marker gene (e.g., 16 S rRNA genes)
- DNA:
-
Sequence similarity of a specific taxonomic marker gene (e.g., 16S rRNA genes)
- BFAR:
-
(Bureau of Fisheries and Aquatic Resources) is the government agency responsible for the development, improvement, management, and conservation of the country’s fisheries and aquatic resources. It was reconstituted as a line bureau by virtue of Republic Act No. 8550 (Philippine Fisheries Code of 1998)
- QIIME:
-
(Quantitative Insights into Microbial Ecology) is a bioinformatic pipeline that was created with the goal of analyzing microbial communities that are sampled using marker genes (e.g., 16 or 18 S rRNA genes)
- DNA:
-
(Deoxyribonucleic Acid) is a molecule that carries genetic instructions for the development, functioning, growth, and reproduction of all known organisms
- RNA:
-
(Ribonucleic Acid) plays a versatile role in translating genetic codon information from DNA genomes into functional proteins for living organisms
- MEGA:
-
(Molecular Evolutionary Genetics Analysis) is a computer software used for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, and estimating rates of molecular evolution
References
Amiri-Jami M, Wang H, Kakuda Y, Griffiths MW (2006) Enhancement of polyunsaturated fatty acid production by Tn5 transposon in Shewanella baltica. Biotechnol Lett 28(15):1187–1192. https://doi.org/10.1007/s10529-006-9077-8
Balcázar JL, Pintado J, Planas M (2010) Bacillus galliciensis sp. nov., isolated from faeces of wild seahorses (Hippocampus guttulatus). Int J Syst Evol Microbiol 60:892–895. https://doi.org/10.1099/ijs.0.011817-0
Bolyen E, Rideout JR, Dillon MR et al (2019) Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol 37(9):852–857. https://doi.org/10.1038/s41587-019-0209-9
Butt RL, Volkoff H (2019) Gut microbiota and energy homeostasis in Fish. Front Endocrinol 10:9. https://doi.org/10.3389/fendo.2019.00009
Chakraborty K, Kizhakkekalam VK, Joy M (2021) Macrocyclic polyketides with siderophore mode of action from marine heterotrophic Shewanella algae: prospective anti-infective leads attenuate drug-resistant pathogens. J Appl Microbiol 130:1552–1570. https://doi.org/10.1111/jam
Clements KD, Pasch IB, Moran D, Turner SJ (2007) Clostridia dominate 16S rRNA gene libraries prepared from the hindgut of temperate marine herbivorous fishes. Mar Biol 150:1431–1440. https://doi.org/10.1007/s00227-006-0443-9
Cordero H, Guardiola FA, Tapia-Paniagua ST et al (2015) Modulation of immunity and gut microbiota after dietary administration of alginate encapsulated Shewanella putrefaciens Pdp11 to gilthead seabream (Sparus aurata L). Fish Shellfish Immunol 45:608–618. https://doi.org/10.1016/j.fsi.2015.05.010
Dhanasiri AK, Brunvold L, Brinchmann MF, Korsnes K, Bergh O, Kiron V (2011) Changes in the intestinal microbiota of wild Atlantic cod Gadus morhua L. upon captive rearing. Microb Ecol 61:20–30. https://doi.org/10.1007/s00248-010-9673-y
Egerton S, Culloty S, Whooley J, Stanton C, Ross RP (2018) The gut microbiota of marine fish. Front Microbiol 9:873. https://doi.org/10.3389/fmicb.2018.00873
Etyemez M, Balcázar JL (2015) Bacterial community structure in the intestinal ecosystem of rainbow trout (Oncorhynchus mykiss) as revealed by pyrosequencing-based analysis of 16S rRNA genes. Res Vet Sci 100:8–11. https://doi.org/10.1016/j.rvsc.2015.03.026
Etyemez-Büyükdeveci M, Balcázar JL, Demirkale I, Dikel S (2018) Effects of garlic-supplemented diet on growth performance and intestinal microbiota of rainbow trout (Oncorhynchus mykiss). Aquaculture 486:170–174. https://doi.org/10.1016/j.aquaculture.2017.12.022
Hau HH, Gralnick JA (2007) Ecology and biotechnology of the genus Shewanella. Annu Rev Microbiol 61:237–258. https://doi.org/10.1146/annurev.micro.61.080706.093257
Hovda MB, Fontanillas R, McGurk C, Obach A, Rosnes JT (2012) Seasonal variations in the intestinal microbiota of farmed Atlantic salmon (Salmo salar L). Aquac Res 43:154–159
Huang Q, Sham RC, Deng Y, Mao Y, Wang C, Zhang T, Leung K (2020) Diversity of gut microbiomes in marine fishes is shaped by host-related factors. Mol Ecol 29:5019–5034. https://doi.org/10.1111/mec.15699
Huber I, Spanggaard B, Appel KF, Rossen L, Nielsen T, Gram L (2004) Phylogenetic analysis and in situ identification of the intestinal microbial community of rainbow trout (Oncorhynchus mykiss, Walbaum). J Appl Microbiol 96:117–132. https://doi.org/10.1046/j.1365-2672.2003.02109.x
Ito T, Sekizuka T, Kishi N, Yamashita A, Kuroda M (2019) Conventional culture methods with commercially available media unveil the presence of novel culturable bacteria. Gut Microbes 10(1):77–91. https://doi.org/10.1080/19490976.2018.1491265
Jiang M, Xu M, Ying C, Yin D, Dai P, Yang Y, Ye K, Liu K (2020) The intestinal microbiota of lake anchovy varies according to sex, body size, and local habitat in Taihu Lake, China. Microbiologyopen 9(1):e00955. https://doi.org/10.1002/mbo3.955
Kizhakkekalam VK, Chakraborty K, Joy M (2020) Antibacterial and antioxidant aryl-enclosed macrocyclic polyketide from intertidal macroalgae associated heterotrophic bacterium Shewanella algae. Med Chem Res 29:145–155. https://doi.org/10.1007/s00044-019-02468-5
Lemaire ON, Méjean V, Iobbi-Nivol C (2020) The Shewanella genus: ubiquitous organisms sustaining and preserving aquatic ecosystems. FEMS Microbiol Rev 44:155–170. https://doi.org/10.1093/femsre/fuz031
Leonardo M, Moser D, Barbieri E et al (1999) Shewanella pealeana sp. nov., a member of the microbial community associated with the accessory nidamental gland of the squid Loligo pealei. Int J Syst Bacteriol 49:1341–1351. https://doi.org/10.1099/00207713-49-4-1341
Li H, Lu L, Chen R, Li S, Xu D (2022) Exploring sexual dimorphism in the intestinal microbiota of the Yellow Drum (Nibea albiflora, Sciaenidae). Front Microbiol 12:808285. https://doi.org/10.3389/fmicb.2021.808285
Lozupone C, Knight R (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71(12):8228–8235. https://doi.org/10.1128/aem.71.12.8228-8235.2005
Maynard CL, Elson CO, Hatton RD, Weaver CT (2012) Reciprocal interactions of the intestinal microbiota and immune system. Nature 489:231–241. https://doi.org/10.1038/nature11551
Ni J, Yan Q, Yu Y, Zhang T (2014) Factors influencing the grass carp gut microbiome and its effect on metabolism. FEMS Microbiol Ecol 87(3):704–714. https://doi.org/10.1111/1574-6941.12256
Org E, Mehrabian M, Parks BW, Shipkova P, Liu X, Drake TA, Lusis AJ (2016) Sex differences and hormonal effects on gut microbiota composition in mice. Gut Microbes 7(4):313–322. https://doi.org/10.1080/19490976.2016.1203502
Ortega RCMH, Tabugo SRM, Martinez JGT, Padasas CS, Balolong MP, Balcázar JL (2021) High-throughput sequencing‐based analysis of bacterial communities associated with Barbour’s seahorses (Hippocampus barbouri) from Surigao del Norte, Philippines. Lett Appl Microbiol 73(3):280–285. https://doi.org/10.1111/lam.13511
Pérez T, Balcázar JL, Ruiz-Zarzuela I, Halaihel N, Vendrell D, de Blas I, Múzquiz JL (2010) Host-microbiota interactions within the fish intestinal ecosystem. Mucosal Immunol 3:355–360. https://doi.org/10.1038/mi.2010.12
Satomi M (2014) The Family Shewanellaceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds) The Prokaryotes. Springer, Berlin, pp 597–625
Straub D, Blackwell N, Langarica-Fuentes A, Peltzer A, Nahnsen S, Kleindienst S (2020) Interpretations of environmental microbial community studies are biased by the selected 16S rRNA (gene) amplicon sequencing pipeline. Front Microbiol 11:550420. https://doi.org/10.3389/fmicb.2020.550420
Tanu, Deobagkar DD, Khandeparker R, Sreepada RA, Sanaye SV, Pawar HB (2011) A study on bacteria associated with the intestinal tract of farmed yellow seahorse, Hippocampus kuda (Bleeker, 1852): characterization and extracellular enzymes. Aqua Res 43:386–394. https://doi.org/10.1111/j.1365-2109.2011.02841.x
Vincent AC, Sadler LM (1995) Faithful pair bonds in wild seahorses, Hippocampus whitei. Anim Behav 50(6):1557–1569. https://doi.org/10.1016/0003-3472(95)80011-5
Xing M, Hou Z, Yuan J, Liu Y, Qu Y, Liu B (2013) Taxonomic and functional metagenomic profiling of gastrointestinal tract microbiome of the farmed adult turbot (Scophthalmus maximus). FEMS Microbiol Ecol 86:432–443. https://doi.org/10.1111/1574-6941.12174
Yoon SH, Ha SM, Kwon S et al (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67:1613–1617. https://doi.org/10.1099/ijsem.0.001755
Acknowledgements
RCMHO acknowledges the DOST-ASTHRDP for the funding of the study and JLB acknowledges the support from the Economy and Knowledge Department of the Catalan Government through Consolidated Research Group (ICRA-ENV 2017 SGR 1124), as well as from the CERCA program.
Funding
This study is funded by DOST under DOST-ASTHRDP scholarship grant to RCMHO.
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RCMHO: Conceptualization, methodology, investigation, formal analysis, visualization, writing - (both original draft and review and editing), funding acquisition. SRMT: Conceptualization, methodology, supervision, funding acquisition. JGTM: Conceptualization, methodology, supervision. CSP: Conceptualization, methodology, investigation, visualization JLB: Methodology, investigation, formal analysis, visualization, supervision, writing - (review and editing).
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Ortega, R.H., Tabugo, S.M., Martinez, J.T. et al. High-throughput sequencing reveals the dominance of Shewanella species in the intestinal microbiota of barbour’s seahorses (Hippocampus barbouri). Biologia 78, 2875–2879 (2023). https://doi.org/10.1007/s11756-023-01423-5
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DOI: https://doi.org/10.1007/s11756-023-01423-5