In silico detection of a candidate disease-associated microorganism in metagenomic data from otter clams (Lutraria rhynchaena Reeve, 1854) affected by swollen siphon disease

Phuong Thanh Nguyen; Thi Phuong Oanh Kim; Thi Nguyen Binh Le

doi:10.33988/auvfd.1927232

In silico detection of a candidate disease-associated microorganism in metagenomic data from otter clams (Lutraria rhynchaena Reeve, 1854) affected by swollen siphon disease

Abstract

Swollen siphon disease causes substantial mortality and economic losses in farmed snout otter clams (Lutraria rhynchaena) in Vietnam, yet its causative agent remains unknown. In this study, we performed metagenomic assembly and reconstructed metagenome-assembled genomes (MAGs) from available shotgun sequencing data of diseased siphon tissues. Assembly with metaSPAdes, viral identification with the geNomad pipeline, and genome binning with SemiBin yielded 219,737 contigs and four MAGs. Taxonomic profiling of assembled contigs revealed a bacteria-dominated metagenome (77%), primarily composed of Pseudomonadota, and an order-of-magnitude more annotations than previously reported. Caudoviricetes (~90%), a class of tailed bacteriophages, overwhelmingly dominated the viral contigs suggesting involvement of bacterial hosts associated with Caudoviricetes such as Vibrio spp., in disease etiology. Among the recovered MAGs, only one quality-sufficient MAG (bin 3; completeness 65.21%) was obtained and taxonomically assigned to the family Simkaniaceae (order Chlamydiales). Despite its partial genomic recovery, bin_3 encoded a near-complete type III secretion system and other intracellular lifestyle-associated features, including 247 putative virulence-associated genes. Our findings identify the Simkaniaceae-related bacterium as a candidate disease-associated microorganism. We hypothesize that it may compromise host immunity and facilitate opportunistic Vibrio infection, although this association is correlative and remains to be evaluated. Future experimental validation is needed to assess causality and inform disease prevention strategies

Keywords

Project Number

Project grant number 106.05-2020.20 from Vietnam National Foundation for Science and Technology Development (NAFOSTED)

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Details

Primary Language

English

Subjects

Veterinary Microbiology

Journal Section

Research Article

Authors

Phuong Thanh Nguyen
0000-0002-1451-1317
Vietnam

Thi Phuong Oanh Kim This is me
0000-0003-3877-2375
Vietnam

Thi Nguyen Binh Le ^*
0000-0002-7748-8628
Vietnam

Early Pub Date

September 18, 2026

Publication Date

October 1, 2026

Submission Date

April 16, 2026

Acceptance Date

August 26, 2026

Published in Issue

Year 2026 Volume: 73 Number: 4

DOI

https://doi.org/10.33988/auvfd.1927232

IZ

https://izlik.org/JA39WY23JN

Cite

RIS / Bibtex

APA

Nguyen, P. T., Kim, T. P. O., & Le, T. N. B. (2026). In silico detection of a candidate disease-associated microorganism in metagenomic data from otter clams (Lutraria rhynchaena Reeve, 1854) affected by swollen siphon disease. Ankara Üniversitesi Veteriner Fakültesi Dergisi, 73(4), 468-481. https://doi.org/10.33988/auvfd.1927232

AMA

1.Nguyen PT, Kim TPO, Le TNB. In silico detection of a candidate disease-associated microorganism in metagenomic data from otter clams (Lutraria rhynchaena Reeve, 1854) affected by swollen siphon disease. Ankara Univ Vet Fak Derg. 2026;73(4):468-481. doi:10.33988/auvfd.1927232

Chicago

Nguyen, Phuong Thanh, Thi Phuong Oanh Kim, and Thi Nguyen Binh Le. 2026. “In Silico Detection of a Candidate Disease-Associated Microorganism in Metagenomic Data from Otter Clams (Lutraria Rhynchaena Reeve, 1854) Affected by Swollen Siphon Disease”. Ankara Üniversitesi Veteriner Fakültesi Dergisi 73 (4): 468-81. https://doi.org/10.33988/auvfd.1927232.

EndNote

Nguyen PT, Kim TPO, Le TNB (October 1, 2026) In silico detection of a candidate disease-associated microorganism in metagenomic data from otter clams (Lutraria rhynchaena Reeve, 1854) affected by swollen siphon disease. Ankara Üniversitesi Veteriner Fakültesi Dergisi 73 4 468–481.

IEEE

[1]P. T. Nguyen, T. P. O. Kim, and T. N. B. Le, “In silico detection of a candidate disease-associated microorganism in metagenomic data from otter clams (Lutraria rhynchaena Reeve, 1854) affected by swollen siphon disease”, Ankara Univ Vet Fak Derg, vol. 73, no. 4, pp. 468–481, Oct. 2026, doi: 10.33988/auvfd.1927232.

ISNAD

Nguyen, Phuong Thanh - Kim, Thi Phuong Oanh - Le, Thi Nguyen Binh. “In Silico Detection of a Candidate Disease-Associated Microorganism in Metagenomic Data from Otter Clams (Lutraria Rhynchaena Reeve, 1854) Affected by Swollen Siphon Disease”. Ankara Üniversitesi Veteriner Fakültesi Dergisi 73/4 (October 1, 2026): 468-481. https://doi.org/10.33988/auvfd.1927232.

JAMA

1.Nguyen PT, Kim TPO, Le TNB. In silico detection of a candidate disease-associated microorganism in metagenomic data from otter clams (Lutraria rhynchaena Reeve, 1854) affected by swollen siphon disease. Ankara Univ Vet Fak Derg. 2026;73:468–481.

MLA

Nguyen, Phuong Thanh, et al. “In Silico Detection of a Candidate Disease-Associated Microorganism in Metagenomic Data from Otter Clams (Lutraria Rhynchaena Reeve, 1854) Affected by Swollen Siphon Disease”. Ankara Üniversitesi Veteriner Fakültesi Dergisi, vol. 73, no. 4, Oct. 2026, pp. 468-81, doi:10.33988/auvfd.1927232.

Vancouver

1.Phuong Thanh Nguyen, Thi Phuong Oanh Kim, Thi Nguyen Binh Le. In silico detection of a candidate disease-associated microorganism in metagenomic data from otter clams (Lutraria rhynchaena Reeve, 1854) affected by swollen siphon disease. Ankara Univ Vet Fak Derg. 2026 Oct. 1;73(4):468-81. doi:10.33988/auvfd.1927232