Skip to main content

Time-dependent post mortem changes in the composition of intestinal bacteria using real-time quantitative PCR


Post mortem or even normal changes during life occurring in major gut bacterial populations are not known. We investigated Bacteroides sp., Bifidobacterium sp., Clostridium leptum, Clostridium coccoides, Streptococcus sp., Lactobacillus sp. and Enterobacteriacaea ratios in 7 fecal samples from healthy volunteers and in 61 autopsies rectum and cecum samples and studied the effect of post mortem time using quantitative real-time PCR. Bacterial ratios in stool samples from volunteers and rectum samples from autopsy cases were similar and did not change significantly up to 5 days post mortem. In cecum, significant post mortem time-dependent differences were observed in ratios of Bacteroides sp. (p = 0.014) and Lactobacillus sp. (p = 0.024). Our results showed that ratios of Bacteroides sp., Bifidobacterium sp., Clostridium leptum, Clostridium coccoides, Streptococcus sp., Lactobacillus sp. and Enterobacteriacaea can be investigated in autopsy rectum samples up to 5 days after death.


Basic knowledge on the composition of intestinal bacterial populations and changes occurring after death is lacking. Even the normal composition of intestinal microbiota in life is not fully known [1]. Only one study exists in which intestinal bacterial populations have been studied in three elderly women after death using PCR and sequencing [2].

Resident micro-organisms living in the intestinal tract influence host’s normal well-being and physiology including gut metabolism and the regulation of epithelial cell growth [3]. Intestinal microbiota functions as a physical barrier against invading pathogens. It has been suggested that gut microbiota may have a role on the development of diseases, e.g. alcoholic liver cirrhosis [4] and atherosclerosis [5]. Detailed bacterial population studies on the intestinal tract have mostly concentrated on fecal samples because they are easy to collect. Intestinal microbiota consists of a large and diverse community containing hundreds of commensal bacterial species [6]. From sequencing libraries of 16S rRNA genes Durban et al. found that two dominant phyla, Firmicutes and Bacteroidetes accounted for nearly 85% of all sequences in stool samples [7]. Compared to these two major phyla, Bifidobacterium genus is present in eight to ten-fold lower numbers [8]. Although Bacteroides sp., Bifidobacterium sp. and bacteria belonging to the Clostridium coccoides–group (cluster XIVa) and Clostridium leptum–group (cluster IV) dominate in colon [9, 10] there is substantial inter- and intra-individual variation in species composition and distribution [7, 11].

This study aimed to investigate ratios of major intestinal bacterial populations in healthy volunteers and in rectum and cecum autopsy samples. Post mortem time-dependent changes were studied in order to see whether autopsy samples can be used for basic research concerning lifetime. Six species: Bacteroides sp. (phylum Bacteroidetes), Clostridium sp. (Firmicutes), Streptococcus sp. (Firmicutes), Lactobacillus sp. (Firmicutes), Bifidobacterium sp. (Actinobacteria) and Enterobactericaea (Proteobacteria) were chosen since they represent the major intestinal bacterial phyla [12].


Study design and results

This study comprises of 61 male cases collected in the Department of Forensic Medicine of the University of Tampere and 7 male volunteers. The selection criteria for the autopsies have been described elsewhere [13]. None of the controls or cases was reported to has been used antibiotics. Deceased had been stored in +4°C within 24 hours after death. Written consent was obtained from the volunteers.

Samples of the autopsy cases were taken from rectum and cecum. All samples were frozen immediately at −80°C until further processing. On the basis of time post mortem the cases were divided into groups: 1–3 days, 4–5 days and >5 days. Demographic characteristics of these groups are shown in the Table 1.

Table 1 Demographic characteristics of the study subjects divided by post mortem time

Fecal samples were weighed to be 150 mg (wet weight). Bacterial DNA was extracted from the samples using Zymo Fecal DNA Kit (Zymo Research Corporation, Irvine, California, USA). The bacterial ratios were determined by RT-qPCR using specific primers and probes (Table 2). The primers and probes for Enterobacteriacaea and Lactobacillus sp. were designed and confirmed by using BLAST ( and Ribosomal Database Project ( Specificity and cross reactivity of the designed primers and probes were tested using bacterial cultures from clinical samples [13]. PCR assays were performed with AbiPrism 7000 HT Sequence Detection System (Taqman, AppliedBiosystems, California, USA) with Taqman Environmental MasterMix. Endogen and DNA-free water was used as a negative control.

Table 2 Used primers and probes

The comparative Ct method (ΔΔCt, ΔCt sample – ΔCt reference sample)[17], was used where mean values from healthy male volunteers were calculated and used as a reference to determine bacterial relative amount in rectum samples. The differences of the Ct values between the bacteria and the universal bacteria measurement (ΔCt) for each sample were calculated; the comparative Ct (ΔΔCt) for sample and reference samples was calculated. To determine relative amounts of bacteria in cecum samples the rectal sample was used as an inner reference.

Two standard curves were used to determine the total amount of bacteria. Tenfold dilution series of between 33 ng/ml and 0.00033 ng/ml from E. coli genomic DNA (ATCC 35401–5) as well as between 109 and 105 colony forming units (CFU) per milliliter from E .coli (ATCC 25922) were applied. The amount of CFU or bacterial DNA in the sample was calculated using values from universal measurement and the equation y = slope log (X) + intercept [18].

Statistical analyses were performed with Kruskal-Wallis median test with PASW Statistical Software, version 18 (SPSS Ltd, Quarry Bay, Hong Kong). If P-value was less than 0.05 (considered significant) pairwise Post Hoc comparisons using Mann–Whitney U-test were done.

Median values of different bacteria in the stool of healthy controls and in post mortem rectum samples showed no statistically significant changes over post mortem time (Figure 1). In cecum, significant post mortem time-dependent differences were observed over the groups in the relative amounts of Bacteroides sp. (p = 0.014) and Lactobacillus sp. (p = 0.024, Table 3). There were significantly more Bacteroides sp. (p = 0.012) and less Lactobacillus sp. (p = 0.015) already in 4–5 days. Statistically significant differences in the total amount of bacterial DNA were seen in healthy volunteers and autopsy rectum samples (p = 0.044, Table 4). In autopsy rectum, the amount of bacterial DNA remained quite stable with time elapsing post mortem except for a high increase observed after day 5 post mortem (p = 0.023). A slightly higher total amount of bacterial DNA (measured as a wet weight) in stool samples donated by the volunteers compared to autopsy rectum samples might be due to lower water concentration in stool compared to rectum without changes in bacterial ratios [19]. Inter-individual variation was great at all time points and in all bacterial measurements.

Figure 1
figure 1

Relative amounts (n-fold difference) of measured bacteria ( Bacteroides sp., C. leptum , C. coccoides, Bifidobacterium sp., Enterobactericaea , Streptococcus sp. and Lactobacillus sp.) in fecal samples of controls and rectum of autopsy cases. Individual values are presented as boxes, median values with horizontal lines. Comparisons over the groups were calculated using non-parametric Kruskal-Wallis test.

Table 3 The relative amounts (n-fold difference) of measured bacteria in cecum samples compared to rectum samples over post mortem time
Table 4 The total amount of bacterial DNA in fecal samples


This study showed that relative amounts of major intestinal bacteria in rectum of autopsy cases were similar to stool donated by volunteers and remained quite stable over post mortem time up to 5 days, after which the total amount of bacteria started to increase. In contrast, in cecum significant post mortem time-dependent differences were observed as increase in ratio of strictly anaerobic Bacteroides sp. and decrease of facultative Lactobacillus sp. due to hypoxia after death. In cecum there is accumulation of undigested nutrients and metabolites produced by bacteria after death, which may be conducive to anaerobic bacterial growth. This study showed that autopsy rectum samples can be used to evaluate major intestinal bacterial populations concerning lifetime up to 5 days after death.


  1. Peterson J, Garges S, Giovanni M, McInnes P, Wang L, Schloss JA, Bonazzi V, McEwen JE, Wetterstrand KA, Deal C, Baker CC, Di Francesco V, Howcroft TK, Karp RW, Lunsford RD, Wellington CR, Belachew T, Wright M, Giblin C, David H, Mills M, Salomon R, Mullins C, Akolkar B, Begg L, Davis C, Grandison L, Humble M, Khalsa J, Little AR: The NIH human microbiome project. Genome Res. 2009, 19: 2317-2323.

    Article  PubMed Central  PubMed  Google Scholar 

  2. Hayashi H, Takahashi R, Nishi T, Sakamoto M, Benno Y: Molecular analysis of jejunal, ileal, caecal and recto-sigmoidal human colonic microbiota using 16S rRNA gene libraries and terminal restriction fragment length polymorphism. J Med Microbiol. 2005, 54: 1093-1101. 10.1099/jmm.0.45935-0.

    Article  CAS  PubMed  Google Scholar 

  3. Morris JA, Harrison LM, Biswas J, Telford DR: Transient bacteraemia: a possible cause of sudden life threatening events. Med Hypotheses. 2007, 69: 1032-1039. 10.1016/j.mehy.2007.02.039.

    Article  CAS  PubMed  Google Scholar 

  4. Chen Y, Yang F, Lu H, Wang B, Chen Y, Lei D, Wang Y, Zhu B, Li L: Characterization of fecal microbial communities in patients with liver cirrhosis. Hepatology. 2011, 54: 562-572. 10.1002/hep.24423.

    Article  PubMed  Google Scholar 

  5. Rosenfeld ME, Campbell LA: Pathogens and atherosclerosis: Update on the potential contribution of multiple infectious organisms to the pathogenesis of atherosclerosis. Thromb Haemost. 2011, 106: 858-867. 10.1160/TH11-06-0392.

    Article  CAS  PubMed  Google Scholar 

  6. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman D: Diversity of the human intestinal microbial flora. Science. 2005, 308: 1635-1638. 10.1126/science.1110591.

    Article  PubMed Central  PubMed  Google Scholar 

  7. Durbán A, Abellán JJ, Jiménez-Hernández N, Ponce M, Ponce J, Sala T, D'Auria G, Latorre A, Moya A: Assessing gut microbial diversity from feces and rectal mucosa. Microb Ecol. 2011, 61: 123-133. 10.1007/s00248-010-9738-y.

    Article  PubMed  Google Scholar 

  8. Mariat D, Firmesse O, Levenez F, Guimarăes V, Sokol H, Doré J, Corthier G, Furet JP: The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age. BMC Microbiol. 2009, 9: 123-10.1186/1471-2180-9-123.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  9. Lay C, Sutren M, Rochet V, Saunier K, Dore J, Rigottier-Gois L: Design and validation of 16S rRNA probes to enumerate members of the clostridium leptum subgroup in human faecal microbiota. Environ Microbiol. 2005, 7: 933-946. 10.1111/j.1462-2920.2005.00763.x.

    Article  CAS  PubMed  Google Scholar 

  10. Orrhage K, Nord CE: Bifidobacteria and lactobacilli in human health. Drugs Exp Clin Res. 2000, 26: 95-111.

    CAS  PubMed  Google Scholar 

  11. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, Egholm M, Henrissat B, Heath AC, Knight R, Gordon JI: A core gut microbiome in obese and lean twins. Nature. 2009, 457: 480-484. 10.1038/nature07540.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  12. Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S: Enterotypes of the human gut microbiome. Nature. 2011, 12: 174-180.

    Article  Google Scholar 

  13. Tuomisto S, Karhunen P, Vuento R, Aittoniemi J, Pessi T: Evaluation of post mortem bacterial migration using culturing and real-time quantitative PCR. J Forensic Sci. 2013, 58: 910-916. 10.1111/1556-4029.12124.

    Article  CAS  PubMed  Google Scholar 

  14. Brunk CF, Li J, Avaniss-Aghajani E: Analysis of specific bacteria from environmental samples using a quantitative polymerase chain reaction. Curr Issues Mol Biol. 2002, 4: 13-18.

    CAS  PubMed  Google Scholar 

  15. Furet JP, Firmesse O, Gourmelon M, Bridonneau C, Tap J, Mondot S, Doré J, Corthier G: Comparative assessment of human and farm animal faecal microbiota using real-time quantitative PCR. FEMS Microbiol Ecol. 2009, 68: 351-362. 10.1111/j.1574-6941.2009.00671.x.

    Article  CAS  PubMed  Google Scholar 

  16. Yang S, Lin S, Kelen GD, Quinn TC, Dick JD, Gaydos CA, Rothman RE: Quantitative multiprobe PCR assay for simultaneous detection and identification to species level of bacterial pathogens. J Clin Microbiol. 2002, 40: 3449-3454. 10.1128/JCM.40.9.3449-3454.2002.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  17. Suzuki N, Yoshida A, Nakano Y: Quantitative analysis of multi-species oral biofilms by TaqMan real-time PCR. Clin Med Res. 2005, 3: 176-185. 10.3121/cmr.3.3.176.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  18. Yoshida A, Suzuki N, Nakano Y, Kawada M, Oho T, Koga T: Development of a 5′ nuclease-based real-time PCR assay for quantitative detection of cariogenic dental pathogens streptococcus mutans and streptococcus sobrinus. J Clin Microbiol. 2003, 41: 4438-4441. 10.1128/JCM.41.9.4438-4441.2003.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  19. Geibel JP: Secretion and absorption by colonic crypts. Annu Rev Physiol. 2005, 67: 471-490. 10.1146/annurev.physiol.67.031103.153530.

    Article  CAS  PubMed  Google Scholar 

Download references


The excellent technical assistance from the personnel of the Department of Forensic Medicine, especially Mervi Seppänen, Kari Mänttäri and Olli Penttilä, University of Tampere, Finland is gratefully acknowledged. We also appreciate the participation of the volunteers.


This study was financially supported by the Tampere Graduate Program in Biomedicine and Biotechnology (TGPBB), the Finnish Foundation for Alcohol Studies, the Competitive Research Funding of the Pirkanmaa Hospital District, the European Union 7th Framework Program grant number 201668 for the AtheroRemo Project, the Pirkanmaa Regional Fund of the Finnish Cultural Foundation.

Author information

Authors and Affiliations


Corresponding author

Correspondence to Sari Tuomisto.

Additional information

Competing interests

The authors declare that they have no competing interests.

Authors’ contributions

ST performed experiments and analyses, helped in collection of the autopsy samples and wrote the manuscript. PK was the iniator of the project and group leader and participated in writing the script. TP was the guarantor of the microbiological part of the study, designed the sample collection and experiments, and participated in writing the manuscript. All authors read and approved the final manuscript.

Authors’ original submitted files for images

Below are the links to the authors’ original submitted files for images.

Authors’ original file for figure 1

Rights and permissions

This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Reprints and permissions

About this article

Cite this article

Tuomisto, S., Karhunen, P.J. & Pessi, T. Time-dependent post mortem changes in the composition of intestinal bacteria using real-time quantitative PCR. Gut Pathog 5, 35 (2013).

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: