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Bioinformatic Approach to Investigate Larvae Gut Microbiota Cellulosimicrobium protaetiae via Whole-Genome Analysis

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Abstract

The insect larvae Protaetia brevitarsis seulensis have recently been researched as a nutritious food source and concentrated on their environmental impacts. Therefore, their gut microbiota has been studied to elucidate their effects and roles on the environment. Of the abundance of bacterial genus identified based on the 16S rRNA genes from isolates of the gut of insect larva Protaetia brevitarsis seulensis, six of the prominent genus were identified as Bacillus (40.2%), Cellulosimicrobium (33.5%), Microbacterium (2.8%), Streptomyces (3%), Krasilnikoviella (17.5%), and Isoptericola (3%) and their similarity of 16S rRNA blast changed from 99 to 100%. Cellulosimicrobium protaetiae BI34T showed strong denitrification and cellulose degradation activity. The newly complete genome sequence of BI34T and the genomes of five species was published in the genus Cellulosimicrobium with emphasis on the denitrification and secondary metabolite genes. In order to elucidate the relationship between the strain BI34T and the host insect larva, the whole-genome sequence was analyzed and compared with the genomes of five strains in the same genus, Cellulosimicrobium, loaded from GenBank. Our results revealed the composition of the gut microbiota of the insect larvae and analyzed the genomic data for the new strain to predict its characteristics and to understand the nitrogen metabolism pathway.

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Data Availability

The datasets generated during and/or analyzed during the current study are available from the corresponding author upon reasonable request.

Abbreviations

BGCs:

Biosynthetic gene clusters

CDSs:

Protein coding genes

COG:

Clusters of orthologous groups of proteins

HGAP:

Hierarchical genome assembly process

ncRNA:

Non-coding RNA

NRP:

Non-ribosomal peptide

SMRT:

Single-molecule real time

RAST:

Rapid annotation subsystems technology

rRNA:

Ribosomal RNA

tRNA:

Transfer RNA

T3PKS:

Type III polyketide synthase

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Acknowledgements

This research was supported by grants from the KRIBB Research Initiative in Korea and funded by University of Technology and Education - The University of Danang under project number T2022-06-06.

Author information

Authors and Affiliations

  1. The University of Danang, University of Science and Technology, 54 Nguyen Luong Bang St., Da Nang, 550 000, Vietnam

    Han Le Ho & Luan Tran-Van

  2. The University of Danang, University of Technology and Education, 48 Cao Thang St., Danang, 550 000, Vietnam

    Phan Thi Quy Quyen, Thi Ngoc Thu Tran & Thi Dong Phuong Nguyen

  3. Biological Resource Center, Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, 181 Ipsingil, Jeongeup, 56212, Jeonbuk, Korea

    Song-Gun Kim

  4. University of Science and Technology (UST), 217 Gajeong-ro, Yuseong, Daejeon, 34113, Korea

    Song-Gun Kim & Ling Min Jiang

  5. School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 62 Nanyang Drive, Singapore, 637459, Singapore

    Kit Wayne Chew

  6. Department of Chemical Engineering and Materials Science, Yuan Ze University, Taoyuan, Taiwan

    Kuan Shiong Khoo

  7. Institut Sains Biologi, Fakulti Sains, Universiti Malaya, 50603, Kuala Lumpur, Malaysia

    Sook Sin Chan

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  1. Han Le Ho
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Contributions

HLH and TDPN conceived and designed the study. HLH, LTV, and PTQQ performed the research. HLH, SGK, and LMJ analyzed and validated data. KSK, KWC, and TNTT contributed to new methods and analytical tools. HLH and TDPN wrote the manuscript. KSK, SSC, and KWC reviewed and edited the manuscript. All authors read and approved the manuscript.

Corresponding author

Correspondence to Thi Dong Phuong Nguyen.

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The manuscript does not contain experiments using animals. The manuscript does not contain human studies.

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Genome information for the 16S rRNA, chromosome and plasmid are available under the GenBank/EMBL/DDBJ accession number MK966391, CP052757 and CP052758.

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Le Ho, H., Tran-Van, L., Quyen, P.T.Q. et al. Bioinformatic Approach to Investigate Larvae Gut Microbiota Cellulosimicrobium protaetiae via Whole-Genome Analysis. Mol Biotechnol (2024). https://doi.org/10.1007/s12033-023-00984-9

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