Effect of sample type and the use of high or low fishmeal diets on bacterial communities in the gastrointestinal tract of Penaeus monodon

Noble, T. H.; Truong, H. H.; Rombenso, A.; Simon, C. J.; Wade, N. M.; Wynne, J. W.

doi:10.1007/s00253-020-11052-6

Environmental biotechnology
Published: 11 January 2021

Effect of sample type and the use of high or low fishmeal diets on bacterial communities in the gastrointestinal tract of Penaeus monodon

T. H. Noble¹,
H. H. Truong²,
A. Rombenso²,
C. J. Simon¹,
N. M. Wade¹ &
J. W. Wynne³

Applied Microbiology and Biotechnology volume 105, pages 1301–1313 (2021)Cite this article

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Abstract

In shrimp aquaculture, manufactured diets that include various supplements and alternative fishmeal ingredients are increasingly being used and their effect on the gastrointestinal (GI) microbiota studied. However, dietary effects on different shrimp GI samples are not known. We investigated how a high (HFM) or low (LFM) fishmeal diet affects bacterial communities from different sample types collected from Penaeus monodon gastrointestinal tract. Bacterial communities of the stomach, intestine tissue and intestine digesta were assessed using 16s rRNA gene sequencing. The feed pellets were also assessed as a potential source of bacteria in the GI tract. Results showed substantial differences in bacterial communities between the two diets as well as between the different sample types. Within the shrimp GI samples, stomach and digesta communities were most impacted by diet, while the community observed in the intestine tissue was less affected. Proteobacteria, Firmicutes and Bacteroidetes were the main phyla observed in shrimp samples, with enrichment of Bacteroidetes and Firmicutes in the LFM fed shrimp. The feed pellets were dominated by Firmicutes and were largely dissimilar to the shrimp samples. Several key taxa were shared however between the feed pellets and shrimp GI samples, particularly in the LFM fed shrimp, indicating the pellets may be a significant source of bacteria observed in shrimp GI samples. In summary, both diet and sample type influenced the bacterial communities characterised from the shrimp GI tract. Thus, it is important to consider the sample type collected from the GI tract when investigating dietary impacts on gut bacterial communities in shrimp.

Key points

• Shrimp gastrointestinal communities are influenced by diet and sample type.

• The low fishmeal diet enriched bacteria that aid in polysaccharide metabolism.

• Feed pellets can be a source of bacteria-detected gastrointestinal tract of shrimp.

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Data availability

Raw data is available through the SRA database under accession number SUB7809378.

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Acknowledgements

We thank David Blyth, Natalie Habilay, Dean Musson, Isaak Kadel and Emmerson West for preparation and maintenance of the experiment and Barney Hines and Nicholas Bourne for proximate sample analyses. We also thank Andrew Bissett for bioinformatic advice and Joel Slinger for reading and providing feedback on the manuscript.

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This study was funded through a collaborative alliance between the Commonwealth Scientific and Industrial Research Organisation and Ridley Corporation.

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CSIRO Agriculture and Food, Queensland Bioscience Precinct, St Lucia, 4072, Australia
T. H. Noble, C. J. Simon & N. M. Wade
CSIRO Agriculture and Food, Bribie Island Research Centre, Woorim, 4507, Australia
H. H. Truong & A. Rombenso
CSIRO Agriculture and Food, Castray Esplanade, Hobart, 7004, Australia
J. W. Wynne

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T. H. Noble
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H. H. Truong
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A. Rombenso
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C. J. Simon
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N. M. Wade
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J. W. Wynne
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THN, JWW and NMW conceived and designed sampling design. HHT, AR and CJS conceived and designed experimental diets. THN and HHT analysed data. THN wrote the manuscript. All authors critically reviewed and approved the manuscript.

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Noble, T.H., Truong, H.H., Rombenso, A. et al. Effect of sample type and the use of high or low fishmeal diets on bacterial communities in the gastrointestinal tract of Penaeus monodon. Appl Microbiol Biotechnol 105, 1301–1313 (2021). https://doi.org/10.1007/s00253-020-11052-6

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Received: 26 July 2020
Revised: 30 November 2020
Accepted: 09 December 2020
Published: 11 January 2021
Issue Date: February 2021
DOI: https://doi.org/10.1007/s00253-020-11052-6

Keywords

Gut microbiota
Bacterial community
Penaeus monodon
Diet
Low fishmeal

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