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Molecular characterization of gut microbial shift in SD rats after death for 30 days

Archives of Microbiology volume 202, pages 1763–1773 (2020)Cite this article

Abstract

To observe the temporal shifts of the intestinal microbial community structure and diversity in rats for 30 days after death. Rectal swabs were collected from rats before death (BD) and on day 1, 5, 10, 15, 20, 25, and 30 after death (AD). Bacteria genomic DNA was extracted and V3 + V4 regions of 16S rRNA gene were amplified by PCR. The amplicons were sequenced at Illumina MiSeq sequencing platform. The bacterial diversity and richness showed similar results from day 1 to 5 and day 10 to 25 all presenting downtrend, while from day 5 to 10 showed slightly increased. The relative abundance of Firmicutes and Proteobacteria displayed inverse variation in day 1, 5, 10 and that was the former decreased, the latter increased. Bacteroidetes, Spirochaete and TM7 in day 15, 20, 25, 30 was significantly decline comparing with BD. Enterococcus and Proteus displayed reduced trend over day 1, 5, 10 and day 10, 15, 20, 25, respectively, while Sporosarcina showed obvious elevation during day 15, 20, 25. Accordingly, there was a certain correlation between intestinal flora succession and the time of death. The results suggested that intestinal flora may be potential indicator to aid estimation of post-mortem interval (PMI).

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Acknowledgements

The authors would like to thank Shakir Ullah at English Editorial Services. This work was supported by a National Natural Sciences Funding of China (project no: NSFC81730056).

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Affiliations

  1. Department of Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an, 710061, People’s Republic of China

    Huan Li, E. Yang, Siruo Zhang, Jing Zhang, Lu Yuan, Shakir Ullah, Nosheen Mushtaq & Jiru Xu

  2. College of Forensic Medicine, Xi’an Jiaotong University, Xi’an, 710061, People’s Republic of China

    Ruina Liu, Qi Wang & Zhenyuan Wang

  3. Teaching and Research Section of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400016, People’s Republic of China

    Qi Wang

  4. Shaanxi Provincial Centre for Disease Control and Prevention, Xi’an, People’s Republic of China

    Yi Shi & Cuihong An

Authors
  1. Huan Li
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  2. E. Yang
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  3. Siruo Zhang
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  4. Jing Zhang
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  5. Lu Yuan
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  6. Ruina Liu
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  8. Qi Wang
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  9. Nosheen Mushtaq
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  10. Yi Shi
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  12. Zhenyuan Wang
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Contributions

HL, EY, SZ, JZ, contributed equally to the study design, collection of data, development of the sampling, LY, RL, SU, QW analyses, NM, YS, CA, ZW, JX interpretation of results, and preparation of the paper. All authors read and approved the final manuscript.

Corresponding authors

Correspondence to Zhenyuan Wang or Jiru Xu.

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The authors declare that they have no competing interests.

Ethical statement

All animal experiments were approved by the Institutional Animal Use and Care Committee of Xi’an Jiaotong University (No: 2017-388).

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Communicated by Erko Stackebrandt.

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Supplementary file1 (TIF 17158 kb)

Fig. S1 Average temperature (℃) and humidity (%) during rats’ decay over 30 days.

Supplementary file2 (TIF 50656 kb)

Fig. S2 Rarefaction Measure of observed species 16S rRNA gene sequences were used to measure whether the sequence size was sufficient to satisfy the experiment requirement to estimate microbiome richness.

Supplementary file3 (TIF 143464 kb)

Fig. S3 Relative abundance of each sample at phylum level during 30 days decomposition.

Supplementary file4 (RAR 106573 kb)

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Li, H., Yang, E., Zhang, S. et al. Molecular characterization of gut microbial shift in SD rats after death for 30 days. Arch Microbiol 202, 1763–1773 (2020). https://doi.org/10.1007/s00203-020-01889-w

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  • DOI: https://doi.org/10.1007/s00203-020-01889-w

Keywords

  • Death microbiome
  • Post-mortem interval
  • Intestinal flora
  • High-throughput sequencing
  • SD rats