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Bacterial Population in Intestines of the Black Tiger Shrimp (Penaeus monodon) under Different Growth Stages
Open accessAbstract
Intestinal bacterial communities in aquaculture have been drawn to attention due to potential benefit to their hosts. To identify core intestinal bacteria in the black tiger shrimp (Penaeus monodon), bacterial populations of disease-free shrimp were characterized from intestines of four developmental stages (15-day-old post larvae (PL15), 1- (J1), 2- (J2), and 3-month-old (J3) juveniles) using pyrosequencing, real-time PCR and denaturing gradient gel electrophoresis (DGGE) approaches. A total of 25,121 pyrosequencing reads (reading length = 442±24 bases) were obtained, which were categorized by barcode for PL15 (7,045 sequences), J1 (3,055 sequences), J2 (13,130 sequences) and J3 (1,890 sequences). Bacteria in the phyla Bacteroides, Firmicutes and Proteobacteria were found in intestines at all four growth stages. There were 88, 14, 27, and 20 bacterial genera associated with the intestinal tract of PL15, J1, J2 and J3, respectively. Pyrosequencing analysis revealed that Proteobacteria (class Gammaproteobacteria) was a dominant bacteria group with a relative abundance of 89% for PL15 and 99% for J1, J2 and J3. Real-time PCR assay also confirmed that Gammaproteobacteria had the highest relative abundance in intestines from all growth stages. Intestinal bacterial communities from the three juvenile stages were more similar to each other than that of the PL shrimp based on PCA analyses of pyrosequencing results and their DGGE profiles. This study provides descriptive bacterial communities associated to the black tiger shrimp intestines during these growth development stages in rearing facilities.
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“Bacterial communities specifically associated with the egg samples (Fig. 5B) were dominated by Pseudomonas, Acinetobacter and Labrenzia, 3 genera found in marine environments (Fournier & Richet, 2006; Palleroni, 2015; Raj Sharma et al., 2019) and which had already been studied during the development of L. vannamei and P. monodon (Rungrassamee et al., 2013; Wang et al., 2020a; Wang et al., 2020b).”
From Potential lineage transmission within the active microbiota of the eggs and the nauplii of the shrimp Litopenaeus stylirostris : possible influence of the rearing water and more (2021) · cites this paper as Rungrassamee et al., 2013
In the citing paper
“These classes have been identified in larvae of the Pacific white shrimp (Litopenaeus vannamei) at early developmental stage (Pangastuti et al., 2009; Zheng et al., 2017) but also in the intestines of adult black tiger shrimps (Penaeus monodon) (Rungrassamee et al., 2013).”
From Potential lineage transmission within the active microbiota of the eggs and the nauplii of the shrimp Litopenaeus stylirostris : possible influence of the rearing water and more (2021) · cites this paper as Rungrassamee et al., 2013
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Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., Lesniewski, R. A., Oakley, B. B., Parks, D. H., Robinson, C. J., et al. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.01541-09 · Cited by 21,481 · cited 1×
“The sequence data was processed using Mothur software to remove low quality sequences [69].”
MethodNaive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
Wang, Q., Garrity, G. M., Tiedje, J. M., & Cole, J. R. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.00062-07 · Cited by 20,145 · cited 2×
“When sequences were classified into taxonomic ranks using the Ribosomal Database Project (RDP) Bayesian classifier with a confidence threshold of 80% [40], phylum distribution of bacteria in intestines at four growth stages varied from 3 to 6 phyla.”
MethodUCHIME improves sensitivity and speed of chimera detection
Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C., & Knight, R. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr381 · Cited by 15,114
Muyzer, G., de Waal, E. C., & Uitterlinden, A. G. (1993) · Applied and Environmental Microbiology · doi:10.1128/aem.59.3.695-700.1993 · Cited by 11,490 · cited 1×
“PCR-DGGE profiles of intestine samples from four shrimp stages were performed according as previously described with some modifications [20,75,76].”
MethodGenome sequencing in microfabricated high-density picolitre reactors
Margulies, M., Egholm, M., Altman, W. E., Attiya, S., Bader, J. S., Bemben, L. A., Berka, J., Braverman, M. S., Chen, Y.-J., Chen, Z., et al. (2005) · Nature · doi:10.1038/nature03959 · Cited by 7,693 · cited 1×
“To provide comprehensive coverage of bacterial communities, a highthroughput pyrosequencing method has been employed to obtain a higher number of sequence-reads [23].”
MethodHost-Bacterial Mutualism in the Human Intestine
Bäckhed, F., Ley, R. E., Sonnenburg, J. L., Peterson, D. A., & Gordon, J. I. (2005) · Science · doi:10.1126/science.1104816 · Cited by 5,277
Lauber, C. L., Hamady, M., Knight, R., & Fierer, N. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.00335-09 · Cited by 4,063 · cited 1×
“The method has recently gained popularity for an in-depth characterization of various microbial communities such as those in the human [24,25,26], fermented food [27], soil [28,29,30,31], extreme environments [32], the deep marine biosphere [33,34], wastewater treatment bioreactors, [35] and plant biospheres [36,37].”
MethodMicrobial diversity in the deep sea and the underexplored “rare biosphere”
Sogin, M. L., Morrison, H. G., Huber, J. A., Welch, D. B. M., Huse, S. M., Neal, P. R., Arrieta, J. M., & Herndl, G. J. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0605127103 · Cited by 3,803 · cited 1×
“The method has recently gained popularity for an in-depth characterization of various microbial communities such as those in the human [24,25,26], fermented food [27], soil [28,29,30,31], extreme environments [32], the deep marine biosphere [33,34], wastewater treatment bioreactors, [35] and plant biospheres [36,37].”
MethodTHE POPULATION FREQUENCIES OF SPECIES AND THE ESTIMATION OF POPULATION PARAMETERS
Good, I. J. (1953) · Biometrika · doi:10.1093/biomet/40.3-4.237 · Cited by 3,427 · cited 2×
“The coverage index was calculated by 1– (n/N), where n is the number of phylotypes and N is the total number of sequences [41].”
BackgroundMethodEcological and Evolutionary Forces Shaping Microbial Diversity in the Human Intestine
Ley, R. E., Peterson, D. A., & Gordon, J. I. (2006) · Cell · doi:10.1016/j.cell.2006.02.017 · Cited by 3,358 · cited 2×
“in less harsh condition for bacteria to reside within [60,62], resulting in different intestinal bacterial diversity from the harsher conditions in the juveniles.”
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Understanding the role of the shrimp gut microbiome in health and disease
Holt, C. C., Bass, D., Stentiford, G. D., & van der Giezen, M. (2020) · Journal of Invertebrate Pathology · doi:10.1016/j.jip.2020.107387 · Cited by 368
“Proteobacteria are widespread in aquatic invertebrate gut microbiotas and are often a dominant component of this community in other Crustacea (Hakim, 2015; Holt et al., 2020; Huang, 2014; Meziti, 2010; Rungrassamee, 2013, 2014; Zhang, 2014).”
BackgroundCornejo-Granados, F., Lopez-Zavala, A. A., Gallardo-Becerra, L., Mendoza-Vargas, A., Sánchez, F., Vichido, R., Brieba, L. G., Viana, M. T., Sotelo-Mundo, R. R., & Ochoa-Leyva, A. (2017) · Scientific Reports · doi:10.1038/s41598-017-11805-w · Cited by 302
Rungrassamee, W., Klanchui, A., Maibunkaew, S., Chaiyapechara, S., Jiravanichpaisal, P., & Karoonuthaisiri, N. (2014) · PLoS ONE · doi:10.1371/journal.pone.0091853 · Cited by 288
“DGGE was performed as previously described [29] with slight modifications.”
BackgroundMethodResultInfluentialCardona, E., Gueguen, Y., Magré, K., Lorgeoux, B., Piquemal, D., Pierrat, F., Noguier, F., & Saulnier, D. (2016) · BMC Microbiology · doi:10.1186/s12866-016-0770-z · Cited by 268
Zhang, M., Sun, Y., Chen, K., Yu, N., Zhou, Z., Chen, L., Du, Z., & Li, E. (2014) · Aquaculture · doi:10.1016/j.aquaculture.2014.09.008 · Cited by 230
Metadata
- Authors
- Rungrassamee, W., Klanchui, A., Chaiyapechara, S., Maibunkaew, S., Tangphatsornruang, S., Jiravanichpaisal, P., & Karoonuthaisiri, N.
- Affiliations
- National Center for Genetic Engineering and Biotechnology (TH)
- Corresponding author
- Karoonuthaisiri, Nitsara
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2013-04-05
- Volume
- 8
- Issue
- 4
- Pages
- e60802
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC3618293
- OpenAlex
- W2020616960
- Cited by
- 179
- References
- 77
- Citations by year
- 2026: 4 · 2025: 13 · 2024: 18 · 2023: 17 · 2022: 18 · 2021: 25 · 2020: 19 · 2019: 11 · 2018: 17 · 2017: 13 · 2016: 9 · 2015: 9 · 2014: 4 · 2013: 1
- FWCI
- 4.24
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS ONE (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, other-oa)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Greater South Information System
- Funders
- Thailand Research Fund (TRG5480014)
- Burapha University
- National Center for Genetic Engineering and Biotechnology
- Topics
- Life Sciences › Immunology and Microbiology › Immunology › Aquaculture disease management and microbiota
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Agricultural and Biological Sciences › Aquatic Science › Aquaculture Nutrition and Growth
- Keywords
- Penaeus monodon, intestinal bacterial community, gut microbiota, growth stages, postlarvae, juveniles, Gammaproteobacteria, Bacteroides, Firmicutes, shrimp aquaculture
- MeSH terms
- Animals, Bacteria, DNA, Bacterial, Intestines, Larva, Time Factors, Sequence Analysis, DNA, Aquaculture, Principal Component Analysis, Penaeidae
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