151
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Maile AE, Inoue CG, Barksdale LE, Carter DO. Toward a universal equation to estimate postmortem interval. Forensic Sci Int 2017; 272:150-153. [DOI: 10.1016/j.forsciint.2017.01.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 01/09/2017] [Accepted: 01/10/2017] [Indexed: 10/20/2022]
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152
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Dabbs GR, Bytheway JA, Connor M. Comparing the Scoring of Human Decomposition from Digital Images to Scoring Using On-site Observations. J Forensic Sci 2017; 62:1292-1296. [DOI: 10.1111/1556-4029.13409] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 11/09/2016] [Accepted: 11/09/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Gretchen R. Dabbs
- Anthropology; Southern Illinois University; 1000 Faner DrMail Code 4502 Carbondale IL 62901
| | | | - Melissa Connor
- Social and Behavioral Sciences; Mesa State University; 1100 North Ave Grand Junction CO 81506
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153
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Pechal JL, Schmidt CJ, Jordan HR, Benbow ME. Frozen: Thawing and Its Effect on the Postmortem Microbiome in Two Pediatric Cases . J Forensic Sci 2017; 62:1399-1405. [PMID: 28120409 DOI: 10.1111/1556-4029.13419] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 11/15/2016] [Accepted: 12/01/2016] [Indexed: 12/18/2022]
Abstract
Previous postmortem microbiome studies have focused on characterizing taxa turnover during an undisturbed decomposition process. How coexisting conditions (e.g., frozen, buried, burned) affect the human microbiome at the time of discovery is less well understood. Microbiome data were collected from two pediatric cases at the Wayne County Medical Examiner in Michigan. The bodies were found frozen, hidden in a freezer for an extended time. Microbial communities were sampled from six external anatomic locations at three time points during the thawing process, prior to autopsy. The 16S rRNA V4 gene amplicon region was sequenced using high-throughput sequencing (Illumina MiSeq). Microbial diversity increased, and there was a distinct shift in microbial community structure and abundance throughout the thawing process. Overall, these data demonstrate that the postmortem human microbiome changes during the thawing process, and have important forensic implications when bodies have been substantially altered, modified, and concealed after death.
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Affiliation(s)
- Jennifer L Pechal
- Department of Entomology, Michigan State University, 243 Natural Science Building, East Lansing, MI
| | - Carl J Schmidt
- Wayne County Medical Examiner's Office and Department of Pathology, University of Michigan, 1300 E. Warren Avenue, Detroit, MI
| | - Heather R Jordan
- Department of Biological Sciences, Mississippi State University, 295 Lee Blvd., Mississippi State University, MS
| | - M Eric Benbow
- Department of Entomology; Department of Osteopathic Medical Specialties; and Ecology, Evolutionary Biology and Behavior, Michigan State University, 243 Natural Science Building, East Lansing, MI
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154
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Tomberlin JK, Crippen TL, Tarone AM, Chaudhury MFB, Singh B, Cammack JA, Meisel RP. A Review of Bacterial Interactions With Blow Flies (Diptera: Calliphoridae) of Medical, Veterinary, and Forensic Importance. Ann Entomol Soc Am 2017; 110:19-36. [DOI: 10.1093/aesa/saw086] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
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155
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Johnson HR, Trinidad DD, Guzman S, Khan Z, Parziale JV, DeBruyn JM, Lents NH. A Machine Learning Approach for Using the Postmortem Skin Microbiome to Estimate the Postmortem Interval. PLoS One 2016; 11:e0167370. [PMID: 28005908 PMCID: PMC5179130 DOI: 10.1371/journal.pone.0167370] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 11/12/2016] [Indexed: 02/06/2023] Open
Abstract
Research on the human microbiome, the microbiota that live in, on, and around the human person, has revolutionized our understanding of the complex interactions between microbial life and human health and disease. The microbiome may also provide a valuable tool in forensic death investigations by helping to reveal the postmortem interval (PMI) of a decedent that is discovered after an unknown amount of time since death. Current methods of estimating PMI for cadavers discovered in uncontrolled, unstudied environments have substantial limitations, some of which may be overcome through the use of microbial indicators. In this project, we sampled the microbiomes of decomposing human cadavers, focusing on the skin microbiota found in the nasal and ear canals. We then developed several models of statistical regression to establish an algorithm for predicting the PMI of microbial samples. We found that the complete data set, rather than a curated list of indicator species, was preferred for training the regressor. We further found that genus and family, rather than species, are the most informative taxonomic levels. Finally, we developed a k-nearest- neighbor regressor, tuned with the entire data set from all nasal and ear samples, that predicts the PMI of unknown samples with an average error of ±55 accumulated degree days (ADD). This study outlines a machine learning approach for the use of necrobiome data in the prediction of the PMI and thereby provides a successful proof-of- concept that skin microbiota is a promising tool in forensic death investigations.
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Affiliation(s)
- Hunter R. Johnson
- Department of Mathematics and Computer Science, John Jay College, The City University of New York, New York, NY, United States of America 10019
| | - Donovan D. Trinidad
- Department of Sciences, John Jay College, The City University of New York, New York, NY, United States of America 10019
| | - Stephania Guzman
- Department of Sciences, John Jay College, The City University of New York, New York, NY, United States of America 10019
| | - Zenab Khan
- Department of Mathematics and Computer Science, John Jay College, The City University of New York, New York, NY, United States of America 10019
- Department of Sciences, John Jay College, The City University of New York, New York, NY, United States of America 10019
| | - James V. Parziale
- Department of Sciences, John Jay College, The City University of New York, New York, NY, United States of America 10019
| | - Jennifer M. DeBruyn
- Department of Biosystems Engineering & Soil Science, University of Tennessee, Knoxville, TN, United States of America, 37996
| | - Nathan H. Lents
- Department of Sciences, John Jay College, The City University of New York, New York, NY, United States of America 10019
- * E-mail:
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156
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Young JM, Austin JJ, Weyrich LS. Soil DNA metabarcoding and high-throughput sequencing as a forensic tool: considerations, potential limitations and recommendations. FEMS Microbiol Ecol 2016; 93:fiw207. [DOI: 10.1093/femsec/fiw207] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/14/2016] [Accepted: 10/06/2016] [Indexed: 11/14/2022] Open
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157
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Wang J, Du X, Zhang Y, Li T, Liao X. Effect of Substrate on Identification of Microbial Communities in Poultry Carcass Composting and Microorganisms Associated with Poultry Carcass Decomposition. J Agric Food Chem 2016; 64:6838-6847. [PMID: 27548371 DOI: 10.1021/acs.jafc.6b02442] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Three composting systems, which consisted of different ratios of chicken manure, sawdust, and poultry carcasses, were used to investigate the effect of substrate on the identification of microbial communities and microorganisms associated with poultry carcass decomposition by characterizing the microbial communities and physicochemical parameters. The physicochemical and Miseq Illumina sequencing results showed the composition of substrate had a significant effect on the identification and metabolic capabilities of microbial communities in decomposting process. Poultry carcasses might be the potential driver for the identification of bacterial communities in poultry carcass composting, whereas the initial C/N ratio may mainly contribute to the diversity of fungal communities and the similar dominant microbial communities in treatments. Poultry carcasses and initial C/N ratio could respectively affect the composition and abundance of microorganisms associated with the decomposition of poultry carcasses. Understanding the potential composting driver could allow development of an efficient carcass degradation system.
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Affiliation(s)
- Jie Wang
- Department of Bioengineering, College of Food Science, and ‡Department of Animal Production, College of Animal Science, South China Agricultural University , Guangzhou 510642, People's Republic of China
| | - Xueqing Du
- Department of Bioengineering, College of Food Science, and ‡Department of Animal Production, College of Animal Science, South China Agricultural University , Guangzhou 510642, People's Republic of China
| | - Yitao Zhang
- Department of Bioengineering, College of Food Science, and ‡Department of Animal Production, College of Animal Science, South China Agricultural University , Guangzhou 510642, People's Republic of China
| | - Ting Li
- Department of Bioengineering, College of Food Science, and ‡Department of Animal Production, College of Animal Science, South China Agricultural University , Guangzhou 510642, People's Republic of China
| | - Xindi Liao
- Department of Bioengineering, College of Food Science, and ‡Department of Animal Production, College of Animal Science, South China Agricultural University , Guangzhou 510642, People's Republic of China
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158
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Javan GT, Finley SJ, Can I, Wilkinson JE, Hanson JD, Tarone AM. Human Thanatomicrobiome Succession and Time Since Death. Sci Rep 2016; 6:29598. [PMID: 27412051 DOI: 10.1038/srep29598] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 06/22/2016] [Indexed: 12/16/2022] Open
Abstract
The thanatomicrobiome (thanatos, Greek for death) is a relatively new term and is the study of the microbes colonizing the internal organs and orifices after death. Recent scientific breakthroughs in an initial study of the thanatomicrobiome have revealed that a majority of the microbes within the human body are the obligate anaerobes, Clostridium spp., in the internal postmortem microbial communities. We hypothesized that time-dependent changes in the thanatomicrobiome within internal organs can estimate the time of death as a human body decays. Here we report a cross-sectional study of the sampling of 27 human corpses from criminal cases with postmortem intervals between 3.5–240 hours. The impetus for examining microbial communities in different internal organs is to address the paucity of empirical data on thanatomicrobiomic succession caused by the limited access to these organs prior to death and a dearth of knowledge regarding the movement of microbes within remains. Our sequencing results of 16S rRNA gene amplicons of 27 postmortem samples from cadavers demonstrated statistically significant time-, organ-, and sex-dependent changes. These results suggest that comprehensive knowledge of the number and abundance of each organ’s signature microorganisms could be useful to forensic microbiologists as a new source of data for estimating postmortem interval.
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159
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160
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Crooks ER, Bulling MT, Barnes KM. Microbial effects on the development of forensically important blow fly species. Forensic Sci Int 2016; 266:185-190. [PMID: 27289434 DOI: 10.1016/j.forsciint.2016.05.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 05/23/2016] [Accepted: 05/29/2016] [Indexed: 11/17/2022]
Abstract
Colonisation times and development rates of specific blow fly species are used to estimate the minimum Post Mortem Interval (mPMI). The presence or absence of bacteria on a corpse can potentially affect the development and survival of blow fly larvae. Therefore an understanding of microbial-insect interactions is important for improving the interpretation of mPMI estimations. In this study, the effect of two bacteria (Escherichia coli and Staphylococcus aureus) on the growth rate and survival of three forensically important blow fly species (Lucilia sericata, Calliphora vicina and Calliphora vomitoria) was investigated. Sterile larvae were raised in a controlled environment (16:8h day: night light cycle, 23:21°C day: night temperature cycle and a constant 35% relative humidity) on four artificial diets prepared with 100μl of 10(5) CFU bacterial solutions as follows: (1) E. coli, (2) S. aureus, (3) a 50:50 E. coli:S. aureus mix and (4) a sterile bacteria-free control diet. Daily measurements (length, width and weight) were taken from first instar larvae through to the emergence of adult flies. Survival rates were also determined at pupation and adult emergence. Results indicate that bacteria were not essential for the development of any of the blow fly species. However, larval growth rates were affected by bacterial diet, with effects differing between blow fly species. Peak larval weights also varied according to species-diet combination; C. vomitoria had the largest weight on E. coli and mixed diets, C. vicina had the largest weight on S. aureus diets, and treatment had no significant effect on the peak larval weight of L. sericata. These results indicate the potential for the bacteria that larvae are exposed to during development on a corpse to alter both developmental rates and larval weight in some blow fly species.
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Affiliation(s)
- Esther R Crooks
- Department of Natural Sciences, University of Derby, Kedleston Road DE22 1HE, UK
| | - Mark T Bulling
- Department of Natural Sciences, University of Derby, Kedleston Road DE22 1HE, UK
| | - Kate M Barnes
- Department of Natural Sciences, University of Derby, Kedleston Road DE22 1HE, UK.
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161
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Liu W, Longnecker M, Tarone AM, Tomberlin JK. Responses of Lucilia sericata (Diptera: Calliphoridae) to compounds from microbial decomposition of larval resources. Anim Behav 2016; 115:217-25. [DOI: 10.1016/j.anbehav.2016.03.022] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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162
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Guo J, Fu X, Liao H, Hu Z, Long L, Yan W, Ding Y, Zha L, Guo Y, Yan J, Chang Y, Cai J. Potential use of bacterial community succession for estimating post-mortem interval as revealed by high-throughput sequencing. Sci Rep 2016; 6:24197. [PMID: 27052375 PMCID: PMC4823735 DOI: 10.1038/srep24197] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 03/23/2016] [Indexed: 02/07/2023] Open
Abstract
Decomposition is a complex process involving the interaction of both biotic and abiotic factors. Microbes play a critical role in the process of carrion decomposition. In this study, we analysed bacterial communities from live rats and rat remains decomposed under natural conditions, or excluding sarcosaphagous insect interference, in China using Illumina MiSeq sequencing of 16S rRNA gene amplicons. A total of 1,394,842 high-quality sequences and 1,938 singleton operational taxonomic units were obtained. Bacterial communities showed notable variation in relative abundance and became more similar to each other across body sites during the decomposition process. As decomposition progressed, Proteobacteria (mostly Gammaproteobacteria) became the predominant phylum in both the buccal cavity and rectum, while Firmicutes and Bacteroidetes in the mouth and rectum, respectively, gradually decreased. In particular, the arrival and oviposition of sarcosaphagous insects had no obvious influence on bacterial taxa composition, but accelerated the loss of biomass. In contrast to the rectum, the microbial community structure in the buccal cavity of live rats differed considerably from that of rats immediately after death. Although this research indicates that bacterial communities can be used as a “microbial clock” for the estimation of post-mortem interval, further work is required to better understand this concept.
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Affiliation(s)
- Juanjuan Guo
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan 410013, China
| | - Xiaoliang Fu
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan 410013, China
| | - Huidan Liao
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan 410013, China
| | - Zhenyu Hu
- Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, China
| | - Lingling Long
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan 410013, China
| | - Weitao Yan
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan 410013, China
| | - Yanjun Ding
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan 410013, China
| | - Lagabaiyila Zha
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan 410013, China
| | - Yadong Guo
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan 410013, China
| | - Jie Yan
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan 410013, China
| | - Yunfeng Chang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan 410013, China
| | - Jifeng Cai
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan 410013, China
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163
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Finley SJ, Pechal JL, Benbow ME, Robertson BK, Javan GT. Microbial Signatures of Cadaver Gravesoil During Decomposition. Microb Ecol 2016; 71:524-529. [PMID: 26748499 DOI: 10.1007/s00248-015-0725-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 12/27/2015] [Indexed: 06/05/2023]
Abstract
Genomic studies have estimated there are approximately 10(3)-10(6) bacterial species per gram of soil. The microbial species found in soil associated with decomposing human remains (gravesoil) have been investigated and recognized as potential molecular determinants for estimates of time since death. The nascent era of high-throughput amplicon sequencing of the conserved 16S ribosomal RNA (rRNA) gene region of gravesoil microbes is allowing research to expand beyond more subjective empirical methods used in forensic microbiology. The goal of the present study was to evaluate microbial communities and identify taxonomic signatures associated with the gravesoil human cadavers. Using 16S rRNA gene amplicon-based sequencing, soil microbial communities were surveyed from 18 cadavers placed on the surface or buried that were allowed to decompose over a range of decomposition time periods (3-303 days). Surface soil microbial communities showed a decreasing trend in taxon richness, diversity, and evenness over decomposition, while buried cadaver-soil microbial communities demonstrated increasing taxon richness, consistent diversity, and decreasing evenness. The results show that ubiquitous Proteobacteria was confirmed as the most abundant phylum in all gravesoil samples. Surface cadaver-soil communities demonstrated a decrease in Acidobacteria and an increase in Firmicutes relative abundance over decomposition, while buried soil communities were consistent in their community composition throughout decomposition. Better understanding of microbial community structure and its shifts over time may be important for advancing general knowledge of decomposition soil ecology and its potential use during forensic investigations.
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Affiliation(s)
- Sheree J Finley
- Ph.D. Program in Microbiology, Department of Biological Sciences, Alabama State University, Montgomery, AL, 36104, USA
| | - Jennifer L Pechal
- Department of Entomology, Michigan State University, East Lansing, MI, 48824, USA
| | - M Eric Benbow
- Department of Entomology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Osteopathic Medical Specialties, Michigan State University, East Lansing, MI, 48824, USA
| | - B K Robertson
- Ph.D. Program in Microbiology, Department of Biological Sciences, Alabama State University, Montgomery, AL, 36104, USA
| | - Gulnaz T Javan
- Forensic Science Program, Physical Sciences Department, Alabama State University, 915 S. Jackson St., Hatch Hall Building Room 251, Montgomery, AL, 36104, USA.
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164
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Burcham ZM, Hood JA, Pechal JL, Krausz KL, Bose JL, Schmidt CJ, Benbow ME, Jordan HR. Fluorescently labeled bacteria provide insight on post-mortem microbial transmigration. Forensic Sci Int 2016; 264:63-9. [PMID: 27032615 DOI: 10.1016/j.forsciint.2016.03.019] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 02/24/2016] [Accepted: 03/10/2016] [Indexed: 01/08/2023]
Abstract
Microbially mediated mechanisms of human decomposition begin immediately after death, and are a driving force for the conversion of a once living organism to a resource of energy and nutrients. Little is known about post-mortem microbiology in cadavers, particularly the community structure of microflora residing within the cadaver and the dynamics of these communities during decomposition. Recent work suggests these bacterial communities undergo taxa turnover and shifts in community composition throughout the post-mortem interval. In this paper we describe how the microbiome of a living host changes and transmigrates within the body after death thus linking the microbiome of a living individual to post-mortem microbiome changes. These differences in the human post-mortem from the ante-mortem microbiome have demonstrated promise as evidence in death investigations. We investigated the post-mortem structure and function dynamics of Staphylococcus aureus and Clostridium perfringens after intranasal inoculation in the animal model Mus musculus L. (mouse) to identify how transmigration of bacterial species can potentially aid in post-mortem interval estimations. S. aureus was tracked using in vivo and in vitro imaging to determine colonization routes associated with different physiological events of host decomposition, while C. perfringens was tracked using culture-based techniques. Samples were collected at discrete time intervals associated with various physiological events and host decomposition beginning at 1h and ending at 60 days post-mortem. Results suggest that S. aureus reaches its highest concentration at 5-7 days post-mortem then begins to rapidly decrease and is undetectable by culture on day 30. The ability to track these organisms as they move in to once considered sterile space may be useful for sampling during autopsy to aid in determining post-mortem interval range estimations, cause of death, and origins associated with the geographic location of human remains during death investigations.
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Affiliation(s)
- Z M Burcham
- Department of Biological Sciences, Mississippi State University, Starkville, MS, USA.
| | - J A Hood
- Department of Biological Sciences, Mississippi State University, Starkville, MS, USA.
| | - J L Pechal
- Department of Entomology, Michigan State University, East Lansing, MI, USA.
| | - K L Krausz
- Department of Microbiology, Molecular Genetics, and Immunology, University of Kansas Medical Center, Kansas City, KS, USA.
| | - J L Bose
- Department of Microbiology, Molecular Genetics, and Immunology, University of Kansas Medical Center, Kansas City, KS, USA.
| | - C J Schmidt
- Department of Pathology, University of Michigan, MI, USA.
| | - M E Benbow
- Department of Entomology, Michigan State University, East Lansing, MI, USA; Department of Osteopathic Medical Specialties, Michigan State University, East Lansing, MI, USA.
| | - H R Jordan
- Department of Biological Sciences, Mississippi State University, Starkville, MS, USA.
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165
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Dabbs GR, Connor M, Bytheway JA. Interobserver Reliability of the Total Body Score System for Quantifying Human Decomposition. J Forensic Sci 2016; 61:445-451. [DOI: 10.1111/1556-4029.12962] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 03/11/2015] [Accepted: 03/29/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Gretchen R. Dabbs
- Southern Illinois University; Department of Anthropology; 1000 Faner Dr., Mail Code 4502 Carbondale IL 62901
| | - Melissa Connor
- Colorado Mesa University; Forensic Investigation Research Station; 1100 North Avenue Grand Junction CO 81501
| | - Joan A. Bytheway
- Sam Houston State University; Southeast Texas Applied Forensic Science Facility; Box 2296 Huntsville Texas 77341
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166
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Pittner S, Ehrenfellner B, Monticelli FC, Zissler A, Sänger AM, Stoiber W, Steinbacher P. Postmortem muscle protein degradation in humans as a tool for PMI delimitation. Int J Legal Med 2016; 130:1547-1555. [PMID: 26951243 PMCID: PMC5055573 DOI: 10.1007/s00414-016-1349-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 02/22/2016] [Indexed: 01/07/2023]
Abstract
Forensic estimation of time since death relies on diverse approaches, including measurement and comparison of environmental and body core temperature and analysis of insect colonization on a dead body. However, most of the applied methods have practical limitations or provide insufficient results under certain circumstances. Thus, new methods that can easily be implemented into forensic routine work are required to deliver more and discrete information about the postmortem interval (PMI). Following a previous work on skeletal muscle degradation in the porcine model, we analyzed human postmortem skeletal muscle samples of 40 forensic cases by Western blotting and casein zymography. Our results demonstrate predictable protein degradation processes in human muscle that are distinctly associated with temperature and the PMI. We provide information on promising degradation markers for certain periods of time postmortem, which can be useful tools for time since death delimitation. In addition, we discuss external influencing factors such as age, body mass index, sex, and cause of death that need to be considered in future routine application of the method in humans.
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Affiliation(s)
- Stefan Pittner
- Department of Cell Biology, University of Salzburg, Hellbrunnerstr. 34, 5020, Salzburg, Austria.
| | - Bianca Ehrenfellner
- Department of Cell Biology, University of Salzburg, Hellbrunnerstr. 34, 5020, Salzburg, Austria
| | - Fabio C Monticelli
- Department of Forensic Medicine and Forensic Neuropsychiatry, University of Salzburg, Ignaz-Harrer-Straße 79, 5020, Salzburg, Austria
| | - Angela Zissler
- Department of Cell Biology, University of Salzburg, Hellbrunnerstr. 34, 5020, Salzburg, Austria
| | - Alexandra M Sänger
- Department of Cell Biology, University of Salzburg, Hellbrunnerstr. 34, 5020, Salzburg, Austria
| | - Walter Stoiber
- Department of Cell Biology, University of Salzburg, Hellbrunnerstr. 34, 5020, Salzburg, Austria
| | - Peter Steinbacher
- Department of Cell Biology, University of Salzburg, Hellbrunnerstr. 34, 5020, Salzburg, Austria
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167
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McCleskey BC, Dye DW, Davis GG. Review of Postmortem Interval Estimation Using Vitreous Humor: Past, Present, and Future. Acad Forensic Pathol 2016; 6:12-18. [PMID: 31239869 DOI: 10.23907/2016.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 01/08/2016] [Accepted: 02/04/2016] [Indexed: 11/12/2022]
Abstract
For decades, forensic scientists have sought a means of estimating the postmortem interval using laboratory analyses. The best known of these attempts uses a linear regression formula based on the increasing concentration of potassium ions in vitreous humor following death. Like all laboratory analyses, the determination of a potassium concentration is subject to pre-analytical, analytical, and post-analytical errors. Any error is magnified when entered into a regression formula that itself is subject to statistical variation, typically with a 95% confidence interval. Estimating the postmortem interval based solely on the concentration of potassium in vitreous humor proved too simplistic for accurate modeling of the myriad factors that influence postmortem changes. Research continues, using more complicated algorithms involving multivariate ion and chemical analyses and genomic sequencing of the postmortem biome. However refined estimates of the postmortem interval based on laboratory analysis become, sound medical practice will still require the integration of scene findings and information concerning the last time that a given decedent was known to be alive with the results of postmortem examination and laboratory analyses into a medical opinion concerning the postmortem interval.
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Affiliation(s)
| | - Daniel W Dye
- Jefferson County Coroner/Medical Examiner Office, University of Alabama at Birmingham - Pathology
| | - Gregory G Davis
- Jefferson County Coroner/Medical Examiner's Office and University of Alabama at Birmingham- Pathology
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168
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Javan GT, Finley SJ, Abidin Z, Mulle JG. The Thanatomicrobiome: A Missing Piece of the Microbial Puzzle of Death. Front Microbiol 2016; 7:225. [PMID: 26941736 PMCID: PMC4764706 DOI: 10.3389/fmicb.2016.00225] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 02/12/2016] [Indexed: 11/13/2022] Open
Abstract
Death is a universal phenomenon; however, is there "life after death?" This topic has been investigated for centuries but still there are gray areas that have yet to be elucidated. Forensic microbiologists are developing new applications to investigate the dynamic and coordinated changes in microbial activity that occur when a human host dies. There is currently a paucity of explorations of the thanatomicrobiome (thanatos-, Greek for death) and epinecrotic communities (microbial communities residing in and/or moving on the surface of decomposing remains). Ongoing studies can help clarify the structure and function of these postmortem microbiomes. Human microbiome studies have revealed that 75-90% of cells in the body prior to death are microbial. Upon death, putrefaction occurs and is a complicated process encompassing chemical degradation and autolysis of cells. Decomposition also involves the release of contents of the intestines due to enzymes under the effects of abiotic and biotic factors. These factors likely have predictable effects on postmortem microbial communities and can be leveraged for forensic studies. This mini review provides a critical examination of emerging research relating to thanatomicrobiome and epinecrotic communities, how each is studied, and possible strategies of stochastic processes.
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Affiliation(s)
- Gulnaz T. Javan
- Forensic Science Program, Physical Sciences Department, Alabama State UniversityMontgomery, AL, USA
| | - Sheree J. Finley
- Ph.D. Program in Microbiology, Department of Biological Sciences, Alabama State UniversityMontgomery, AL, USA
| | - Zain Abidin
- Forensic Science Program, Physical Sciences Department, Alabama State UniversityMontgomery, AL, USA
| | - Jennifer G. Mulle
- Department of Epidemiology, Rollins School of Public Health, Emory UniversityAtlanta, GA, USA
- Department of Human Genetics, School of Medicine, Emory UniversityAtlanta, GA, USA
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169
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Iancu L, Sahlean T, Purcarea C. Dynamics of Necrophagous Insect and Tissue Bacteria for Postmortem Interval Estimation During the Warm Season in Romania. J Med Entomol 2016; 53:54-66. [PMID: 26487246 DOI: 10.1093/jme/tjv156] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 09/17/2015] [Indexed: 06/05/2023]
Abstract
The estimation of postmortem interval (PMI) is affected by several factors including the cause of death, the place where the body lay after death, and the weather conditions during decomposition. Given the climatic differences among biogeographic locations, the understanding of necrophagous insect species biology and ecology is required when estimating PMI. The current experimental model was developed in Romania during the warm season in an outdoor location. The aim of the study was to identify the necrophagous insect species diversity and dynamics, and to detect the bacterial species present during decomposition in order to determine if their presence or incidence timing could be useful to estimate PMI. The decomposition process of domestic swine carcasses was monitored throughout a 14-wk period (10 July-10 October 2013), along with a daily record of meteorological parameters. The chronological succession of necrophagous entomofauna comprised nine Diptera species, with the dominant presence of Chrysomya albiceps (Wiedemann 1819) (Calliphoridae), while only two Coleoptera species were identified, Dermestes undulatus (L. 1758) and Creophilus maxillosus Brahm 1970. The bacterial diversity and dynamics from the mouth and rectum tissues, and third-instar dipteran larvae were identified using denaturing gradient gel electrophoresis analysis and sequencing of bacterial 16S rRNA gene fragments. Throughout the decomposition process, two main bacterial chronological groups were differentiated, represented by Firmicutes and Gammaproteobacteria. Twenty-six taxa from the rectal cavity and 22 from the mouth cavity were identified, with the dominant phylum in both these cavities corresponding to Firmicutes. The present data strengthen the postmortem entomological and microbial information for the warm season in this temperate-continental area, as well as the role of microbes in carcass decomposition.
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Affiliation(s)
- Lavinia Iancu
- "Grigore Antipa" National Museum of Natural History, 1, Sos. Kiseleff, Bucharest 011341, Romania (; ),
| | - Tiberiu Sahlean
- "Grigore Antipa" National Museum of Natural History, 1, Sos. Kiseleff, Bucharest 011341, Romania (; ), Faculty of Biology, University of Bucharest, Independentei Blvd., 91-95, Bucharest 050095, Romania, and
| | - Cristina Purcarea
- Institute of Biology Bucharest, 296 Splaiul Independentei, Bucharest 060031, Romania
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170
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Walters W, Hyde ER, Berg-Lyons D, Ackermann G, Humphrey G, Parada A, Gilbert JA, Jansson JK, Caporaso JG, Fuhrman JA, Apprill A, Knight R. Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys. mSystems 2016; 1:e00009-15. [PMID: 27822518 DOI: 10.1128/mSystems.00009-15] [Citation(s) in RCA: 892] [Impact Index Per Article: 99.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 11/24/2015] [Indexed: 11/20/2022] Open
Abstract
We continue to uncover a wealth of information connecting microbes in important ways to human and environmental ecology. As our scientific knowledge and technical abilities improve, the tools used for microbiome surveys can be modified to improve the accuracy of our techniques, ensuring that we can continue to identify groundbreaking connections between microbes and the ecosystems they populate, from ice caps to the human body. It is important to confirm that modifications to these tools do not cause new, detrimental biases that would inhibit the field rather than continue to move it forward. We therefore demonstrated that two recently modified primer pairs that target taxonomically discriminatory regions of bacterial and fungal genomic DNA do not introduce new biases when used on a variety of sample types, from soil to human skin. This confirms the utility of these primers for maintaining currently recommended microbiome research techniques as the state of the art. Designing primers for PCR-based taxonomic surveys that amplify a broad range of phylotypes in varied community samples is a difficult challenge, and the comparability of data sets amplified with varied primers requires attention. Here, we examined the performance of modified 16S rRNA gene and internal transcribed spacer (ITS) primers for archaea/bacteria and fungi, respectively, with nonaquatic samples. We moved primer bar codes to the 5′ end, allowing for a range of different 3′ primer pairings, such as the 515f/926r primer pair, which amplifies variable regions 4 and 5 of the 16S rRNA gene. We additionally demonstrated that modifications to the 515f/806r (variable region 4) 16S primer pair, which improves detection of Thaumarchaeota and clade SAR11 in marine samples, do not degrade performance on taxa already amplified effectively by the original primer set. Alterations to the fungal ITS primers did result in differential but overall improved performance compared to the original primers. In both cases, the improved primers should be widely adopted for amplicon studies. IMPORTANCE We continue to uncover a wealth of information connecting microbes in important ways to human and environmental ecology. As our scientific knowledge and technical abilities improve, the tools used for microbiome surveys can be modified to improve the accuracy of our techniques, ensuring that we can continue to identify groundbreaking connections between microbes and the ecosystems they populate, from ice caps to the human body. It is important to confirm that modifications to these tools do not cause new, detrimental biases that would inhibit the field rather than continue to move it forward. We therefore demonstrated that two recently modified primer pairs that target taxonomically discriminatory regions of bacterial and fungal genomic DNA do not introduce new biases when used on a variety of sample types, from soil to human skin. This confirms the utility of these primers for maintaining currently recommended microbiome research techniques as the state of the art.
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171
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Rinaldi A. Biometrics' new identity--measuring more physical and biological traits: Research into the characteristics that are unique to an individual is addressing the need to correctly identify people in a variety of medical, social and security contexts. EMBO Rep 2015; 17:22-6. [PMID: 26666447 DOI: 10.15252/embr.201541677] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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172
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Metcalf JL, Xu ZZ, Weiss S, Lax S, Van Treuren W, Hyde ER, Song SJ, Amir A, Larsen P, Sangwan N, Haarmann D, Humphrey GC, Ackermann G, Thompson LR, Lauber C, Bibat A, Nicholas C, Gebert MJ, Petrosino JF, Reed SC, Gilbert JA, Lynne AM, Bucheli SR, Carter DO, Knight R. Microbial community assembly and metabolic function during mammalian corpse decomposition. Science 2015; 351:158-62. [PMID: 26657285 DOI: 10.1126/science.aad2646] [Citation(s) in RCA: 272] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 11/25/2015] [Indexed: 12/22/2022]
Abstract
Vertebrate corpse decomposition provides an important stage in nutrient cycling in most terrestrial habitats, yet microbially mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand the principles governing microbial community assembly during decomposition of mouse and human corpses on different soil substrates. We find a suite of bacterial and fungal groups that contribute to nitrogen cycling and a reproducible network of decomposers that emerge on predictable time scales. Our results show that this decomposer community is derived primarily from bulk soil, but key decomposers are ubiquitous in low abundance. Soil type was not a dominant factor driving community development, and the process of decomposition is sufficiently reproducible to offer new opportunities for forensic investigations.
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Affiliation(s)
- Jessica L Metcalf
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA. Department of Pediatrics, University of California, San Diego, San Diego, CA 92037, USA.
| | - Zhenjiang Zech Xu
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92037, USA
| | - Sophie Weiss
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80303, USA
| | - Simon Lax
- Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA. Institute for Genomic and Systems Biology, University of Chicago, 900 East 57th Street, Chicago, IL 606037, USA
| | - Will Van Treuren
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Embriette R Hyde
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92037, USA
| | - Se Jin Song
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA. Department of Pediatrics, University of California, San Diego, San Diego, CA 92037, USA
| | - Amnon Amir
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92037, USA
| | - Peter Larsen
- Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA. Biosciences Division, Argonne National Laboratory, South Cass Avenue, Argonne, IL 60439, USA
| | - Naseer Sangwan
- Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA. Biosciences Division, Argonne National Laboratory, South Cass Avenue, Argonne, IL 60439, USA. Department of Surgery, University of Chicago, A27 South Maryland Avenue, Chicago, IL 60637, USA
| | - Daniel Haarmann
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX 77340, USA
| | - Greg C Humphrey
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92037, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92037, USA
| | - Luke R Thompson
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92037, USA
| | - Christian Lauber
- Nestlé Institute of Health Sciences, École Polytechnique Fédérale Lausanne, Bâtiment H, 1015 Lausanne, Switzerland
| | - Alexander Bibat
- BioFrontiers Institute, University of Colorado, Boulder, CO 80303, USA
| | | | - Matthew J Gebert
- BioFrontiers Institute, University of Colorado, Boulder, CO 80303, USA
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sasha C Reed
- U.S. Geological Survey, Southwest Biological Science Center, Moab, UT 84532, USA
| | - Jack A Gilbert
- Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA. Institute for Genomic and Systems Biology, University of Chicago, 900 East 57th Street, Chicago, IL 606037, USA. Biosciences Division, Argonne National Laboratory, South Cass Avenue, Argonne, IL 60439, USA. Department of Surgery, University of Chicago, A27 South Maryland Avenue, Chicago, IL 60637, USA. Marine Biological Laboratory, 7 MBL St, Woods Hole, MA 02543, USA
| | - Aaron M Lynne
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX 77340, USA
| | - Sibyl R Bucheli
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX 77340, USA
| | - David O Carter
- Laboratory of Forensic Taphonomy, Forensic Sciences Unit, Division of Natural Sciences and Mathematics, Chaminade University of Honolulu, Honolulu, HI 96816, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92037, USA. Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA 92037, USA.
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173
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Fu X, Guo J, Zhu Z, Ding Z, Zha L, Cai J. The potential use of fungi community in postmortem interval estimation in China. Forensic Science International: Genetics Supplement Series 2015. [DOI: 10.1016/j.fsigss.2015.09.189] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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174
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Guo J, Liao H, Fu X, Zha L, Liu J, Cai J. Bacterial community succession analysis by next generation sequencing in Changsha city, China. Forensic Science International: Genetics Supplement Series 2015. [DOI: 10.1016/j.fsigss.2015.09.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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175
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Olakanye AO, Thompson T, Ralebitso-Senior TK. Shifts in soil biodiversity—A forensic comparison between Sus scrofa domesticus and vegetation decomposition. Sci Justice 2015; 55:402-7. [DOI: 10.1016/j.scijus.2015.07.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 06/21/2015] [Accepted: 07/06/2015] [Indexed: 11/16/2022]
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176
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Chimutsa M, Olakanye AO, Thompson TJ, Ralebitso-senior TK. Soil fungal community shift evaluation as a potential cadaver decomposition indicator. Forensic Sci Int 2015; 257:155-9. [DOI: 10.1016/j.forsciint.2015.08.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 06/29/2015] [Accepted: 08/08/2015] [Indexed: 11/20/2022]
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177
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Chun LP, Miguel MJ, Junkins EN, Forbes SL, Carter DO. An initial investigation into the ecology of culturable aerobic postmortem bacteria. Sci Justice 2015; 55:394-401. [DOI: 10.1016/j.scijus.2015.07.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 07/17/2015] [Accepted: 07/22/2015] [Indexed: 01/13/2023]
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178
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Iancu L, Carter DO, Junkins EN, Purcarea C. Using bacterial and necrophagous insect dynamics for post-mortem interval estimation during cold season: Novel case study in Romania. Forensic Sci Int 2015. [DOI: 10.1016/j.forsciint.2015.07.024] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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179
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Benbow ME, Pechal JL, Lang JM, Erb R, Wallace JR. The Potential of High-throughput Metagenomic Sequencing of Aquatic Bacterial Communities to Estimate the Postmortem Submersion Interval. J Forensic Sci 2015; 60:1500-10. [DOI: 10.1111/1556-4029.12859] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 11/10/2014] [Accepted: 11/14/2014] [Indexed: 12/29/2022]
Affiliation(s)
- Mark Eric Benbow
- Department of Entomology; Michigan State University; East Lansing MI 48824
| | - Jennifer L. Pechal
- Department of Entomology; Michigan State University; East Lansing MI 48824
| | - Jennifer M. Lang
- Department of Biology; University of Dayton; Dayton OH 45469-2320
| | - Racheal Erb
- Department of Biology; Millersville University; Millersville PA 17551
| | - John R. Wallace
- Department of Biology; Millersville University; Millersville PA 17551
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180
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Finley SJ, Lorenco N, Mulle J, Robertson BK, Javan GT. Assessment of microbial DNA extraction methods of cadaver soil samples for criminal investigations. AUST J FORENSIC SCI 2015. [DOI: 10.1080/00450618.2015.1063690] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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181
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Hauther KA, Cobaugh KL, Jantz LM, Sparer TE, DeBruyn JM. Estimating Time Since Death from Postmortem Human Gut Microbial Communities. J Forensic Sci 2015; 60:1234-40. [PMID: 26096156 DOI: 10.1111/1556-4029.12828] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 09/01/2014] [Accepted: 09/02/2014] [Indexed: 11/29/2022]
Abstract
Postmortem succession of human-associated microbial communities ("human microbiome") has been suggested as a possible method for estimating postmortem interval (PMI) for forensic analyses. Here we evaluate human gut bacterial populations to determine quantifiable, time-dependent changes postmortem. Gut microflora were repeatedly sampled from the proximal large intestine of 12 deceased human individuals as they decayed under environmental conditions. Three intestinal bacterial genera were quantified by quantitative PCR (qPCR) using group-specific primers targeting 16S rRNA genes. Bacteroides and Lactobacillus relative abundances declined exponentially with increasing PMI at rates of Nt=0.977e(-0.0144t) (r2=0.537, p<0.001) and Nt=0.019e(-0.0087t) (r2=0.396, p<0.001), respectively, where Nt is relative abundance at time (t) in cumulative degree hours. Bifidobacterium relative abundances did not change significantly: Nt=0.003e(-0.002t) (r2=0.033, p=0.284). Therefore, Bacteroides and Lactobacillus abundances could be used as quantitative indicators of PMI.
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Affiliation(s)
- Kathleen A Hauther
- Department of Anthropology, 250 South Stadium Hall, University of Tennessee, Knoxville, TN, USA, 37996
| | - Kelly L Cobaugh
- Biosystems Engineering & Soil Science, 2506 EJ Chapman Drive, University of Tennessee, Knoxville, TN, USA, 37996
| | - Lee Meadows Jantz
- Department of Anthropology, 250 South Stadium Hall, University of Tennessee, Knoxville, TN, USA, 37996
| | - Tim E Sparer
- Department of Microbiology, M409 Walters Life Sciences, University of Tennessee, Knoxville, TN, USA, 37996
| | - Jennifer M DeBruyn
- Biosystems Engineering & Soil Science, 2506 EJ Chapman Drive, University of Tennessee, Knoxville, TN, USA, 37996
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182
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Cobaugh KL, Schaeffer SM, DeBruyn JM. Functional and Structural Succession of Soil Microbial Communities below Decomposing Human Cadavers. PLoS One 2015; 10:e0130201. [PMID: 26067226 PMCID: PMC4466320 DOI: 10.1371/journal.pone.0130201] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 05/16/2015] [Indexed: 12/20/2022] Open
Abstract
The ecological succession of microbes during cadaver decomposition has garnered interest in both basic and applied research contexts (e.g. community assembly and dynamics; forensic indicator of time since death). Yet current understanding of microbial ecology during decomposition is almost entirely based on plant litter. We know very little about microbes recycling carcass-derived organic matter despite the unique decomposition processes. Our objective was to quantify the taxonomic and functional succession of microbial populations in soils below decomposing cadavers, testing the hypotheses that a) periods of increased activity during decomposition are associated with particular taxa; and b) human-associated taxa are introduced to soils, but do not persist outside their host. We collected soils from beneath four cadavers throughout decomposition, and analyzed soil chemistry, microbial activity and bacterial community structure. As expected, decomposition resulted in pulses of soil C and nutrients (particularly ammonia) and stimulated microbial activity. There was no change in total bacterial abundances, however we observed distinct changes in both function and community composition. During active decay (7 - 12 days postmortem), respiration and biomass production rates were high: the community was dominated by Proteobacteria (increased from 15.0 to 26.1% relative abundance) and Firmicutes (increased from 1.0 to 29.0%), with reduced Acidobacteria abundances (decreased from 30.4 to 9.8%). Once decay rates slowed (10 - 23 d postmortem), respiration was elevated, but biomass production rates dropped dramatically; this community with low growth efficiency was dominated by Firmicutes (increased to 50.9%) and other anaerobic taxa. Human-associated bacteria, including the obligately anaerobic Bacteroides, were detected at high concentrations in soil throughout decomposition, up to 198 d postmortem. Our results revealed the pattern of functional and compositional succession in soil microbial communities during decomposition of human-derived organic matter, provided insight into decomposition processes, and identified putative predictor populations for time since death estimation.
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Affiliation(s)
- Kelly L. Cobaugh
- Department of Biosystems Engineering & Soil Science, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Sean M. Schaeffer
- Department of Biosystems Engineering & Soil Science, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Jennifer M. DeBruyn
- Department of Biosystems Engineering & Soil Science, University of Tennessee, Knoxville, Tennessee, United States of America
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183
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Pittner S, Monticelli FC, Pfisterer A, Zissler A, Sänger AM, Stoiber W, Steinbacher P. Postmortem degradation of skeletal muscle proteins: a novel approach to determine the time since death. Int J Legal Med 2015; 130:421-31. [PMID: 26041514 DOI: 10.1007/s00414-015-1210-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 05/26/2015] [Indexed: 11/30/2022]
Abstract
Estimating the time since death is a very important aspect in forensic sciences which is pursued by a variety of methods. The most precise method to determine the postmortem interval (PMI) is the temperature method which is based on the decrease of the body core temperature from 37 °C. However, this method is only useful in the early postmortem phase (~0-36 h). The aim of the present work is to develop an accurate method for PMI determination beyond this present limit. For this purpose, we used sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), Western blotting, and casein zymography to analyze the time course of degradation of selected proteins and calpain activity in porcine biceps femoris muscle until 240 h postmortem (hpm). Our results demonstrate that titin, nebulin, desmin, cardiac troponin T, and SERCA1 degraded in a regular and predictable fashion in all samples investigated. Similarly, both the native calpain 1 and calpain 2 bands disintegrate into two bands subsequently. This degradation behavior identifies muscular proteins and enzymes as promising substrates for future molecular-based PMI determination technologies.
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Affiliation(s)
- Stefan Pittner
- Department of Cell Biology, University of Salzburg, Hellbrunnerstr. 34, 5020, Salzburg, Austria
| | - Fabio C Monticelli
- Department of Forensic Medicine and Forensic Neuropsychiatry, University of Salzburg, Ignaz-Harrer-Straße 79, 5020, Salzburg, Austria
| | - Alexander Pfisterer
- Department of Cell Biology, University of Salzburg, Hellbrunnerstr. 34, 5020, Salzburg, Austria
| | - Angela Zissler
- Department of Cell Biology, University of Salzburg, Hellbrunnerstr. 34, 5020, Salzburg, Austria
| | - Alexandra M Sänger
- Department of Cell Biology, University of Salzburg, Hellbrunnerstr. 34, 5020, Salzburg, Austria
| | - Walter Stoiber
- Department of Cell Biology, University of Salzburg, Hellbrunnerstr. 34, 5020, Salzburg, Austria
| | - Peter Steinbacher
- Department of Cell Biology, University of Salzburg, Hellbrunnerstr. 34, 5020, Salzburg, Austria.
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184
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Weiss S, Carter DO, Metcalf JL, Knight R. Carcass mass has little influence on the structure of gravesoil microbial communities. Int J Legal Med 2015; 130:253-63. [DOI: 10.1007/s00414-015-1206-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 05/18/2015] [Indexed: 10/23/2022]
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185
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Smith MB, Rocha AM, Smillie CS, Olesen SW, Paradis C, Wu L, Campbell JH, Fortney JL, Mehlhorn TL, Lowe KA, Earles JE, Phillips J, Techtmann SM, Joyner DC, Elias DA, Bailey KL, Hurt RA, Preheim SP, Sanders MC, Yang J, Mueller MA, Brooks S, Watson DB, Zhang P, He Z, Dubinsky EA, Adams PD, Arkin AP, Fields MW, Zhou J, Alm EJ, Hazen TC. Natural bacterial communities serve as quantitative geochemical biosensors. mBio 2015. [PMID: 25968645 DOI: 10.1128/mbio.00326-15.editor] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023] Open
Abstract
UNLABELLED Biological sensors can be engineered to measure a wide range of environmental conditions. Here we show that statistical analysis of DNA from natural microbial communities can be used to accurately identify environmental contaminants, including uranium and nitrate at a nuclear waste site. In addition to contamination, sequence data from the 16S rRNA gene alone can quantitatively predict a rich catalogue of 26 geochemical features collected from 93 wells with highly differing geochemistry characteristics. We extend this approach to identify sites contaminated with hydrocarbons from the Deepwater Horizon oil spill, finding that altered bacterial communities encode a memory of prior contamination, even after the contaminants themselves have been fully degraded. We show that the bacterial strains that are most useful for detecting oil and uranium are known to interact with these substrates, indicating that this statistical approach uncovers ecologically meaningful interactions consistent with previous experimental observations. Future efforts should focus on evaluating the geographical generalizability of these associations. Taken as a whole, these results indicate that ubiquitous, natural bacterial communities can be used as in situ environmental sensors that respond to and capture perturbations caused by human impacts. These in situ biosensors rely on environmental selection rather than directed engineering, and so this approach could be rapidly deployed and scaled as sequencing technology continues to become faster, simpler, and less expensive. IMPORTANCE Here we show that DNA from natural bacterial communities can be used as a quantitative biosensor to accurately distinguish unpolluted sites from those contaminated with uranium, nitrate, or oil. These results indicate that bacterial communities can be used as environmental sensors that respond to and capture perturbations caused by human impacts.
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Affiliation(s)
- Mark B Smith
- Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Andrea M Rocha
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Chris S Smillie
- Computational and Systems Biology Initiative, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Scott W Olesen
- Biological Engineering Department, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Charles Paradis
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, Tennessee, USA
| | - Liyou Wu
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
| | | | - Julian L Fortney
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Tonia L Mehlhorn
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Kenneth A Lowe
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Jennifer E Earles
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Jana Phillips
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Steve M Techtmann
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Dominique C Joyner
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Dwayne A Elias
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Kathryn L Bailey
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Richard A Hurt
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Sarah P Preheim
- Biological Engineering Department, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Matthew C Sanders
- Biological Engineering Department, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Joy Yang
- Computational and Systems Biology Initiative, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Marcella A Mueller
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Scott Brooks
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - David B Watson
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Ping Zhang
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Zhili He
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Eric A Dubinsky
- Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | | | - Matthew W Fields
- Department of Microbiology & Immunology, Montana State University, Bozeman, Montana, USA
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
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186
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Smith MB, Rocha AM, Smillie CS, Olesen SW, Paradis C, Wu L, Campbell JH, Fortney JL, Mehlhorn TL, Lowe KA, Earles JE, Phillips J, Techtmann SM, Joyner DC, Elias DA, Bailey KL, Hurt RA Jr, Preheim SP, Sanders MC, Yang J, Mueller MA, Brooks S, Watson DB, Zhang P, He Z, Dubinsky EA, Adams PD, Arkin AP, Fields MW, Zhou J, Alm EJ, Hazen TC. Natural bacterial communities serve as quantitative geochemical biosensors. mBio 2015; 6:e00326-15. [PMID: 25968645 DOI: 10.1128/mBio.00326-15] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Biological sensors can be engineered to measure a wide range of environmental conditions. Here we show that statistical analysis of DNA from natural microbial communities can be used to accurately identify environmental contaminants, including uranium and nitrate at a nuclear waste site. In addition to contamination, sequence data from the 16S rRNA gene alone can quantitatively predict a rich catalogue of 26 geochemical features collected from 93 wells with highly differing geochemistry characteristics. We extend this approach to identify sites contaminated with hydrocarbons from the Deepwater Horizon oil spill, finding that altered bacterial communities encode a memory of prior contamination, even after the contaminants themselves have been fully degraded. We show that the bacterial strains that are most useful for detecting oil and uranium are known to interact with these substrates, indicating that this statistical approach uncovers ecologically meaningful interactions consistent with previous experimental observations. Future efforts should focus on evaluating the geographical generalizability of these associations. Taken as a whole, these results indicate that ubiquitous, natural bacterial communities can be used as in situ environmental sensors that respond to and capture perturbations caused by human impacts. These in situ biosensors rely on environmental selection rather than directed engineering, and so this approach could be rapidly deployed and scaled as sequencing technology continues to become faster, simpler, and less expensive. Here we show that DNA from natural bacterial communities can be used as a quantitative biosensor to accurately distinguish unpolluted sites from those contaminated with uranium, nitrate, or oil. These results indicate that bacterial communities can be used as environmental sensors that respond to and capture perturbations caused by human impacts.
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187
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Rillig MC, Rolff J, Tietjen B, Wehner J, Andrade-Linares DR. Community priming--effects of sequential stressors on microbial assemblages. FEMS Microbiol Ecol 2015; 91:fiv040. [PMID: 25873462 DOI: 10.1093/femsec/fiv040] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/31/2015] [Indexed: 11/12/2022] Open
Abstract
Microbes in nature are exposed to complex environmental stressors which challenge their functioning or survival. Priming is the improved reaction of an organism to an environmental stressor following a preceding, often milder stress event. This phenomenon, also known as cross-protection, predictive response strategy or acquired stress resistance, is becoming an increasingly well-established research topic in microbiology, which has so far been examined from the perspective of a single organism or population. However, microbes in nature occur as part of communities; thus it is timely to highlight the need to also include this level beyond the individual species in studies of priming effects. We here introduce a conceptual framework for such studies at the level of the microbial assemblage and also chart a way forward for empirical and theoretical study. We illustrate some of the elements of our framework with a simple simulation model. Given the dynamic habitat of many microbes, incorporating priming is important for a more complete understanding of microbial community responses to stress.
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Affiliation(s)
- Matthias C Rillig
- Freie Universität Berlin, Institut für Biologie, Plant Ecology, D-14195 Berlin, Germany Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195 Berlin, Germany
| | - Jens Rolff
- Freie Universität Berlin, Institut für Biologie, Evolutionary Biology, D-14195 Berlin, Germany Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195 Berlin, Germany
| | - Britta Tietjen
- Freie Universität Berlin, Institut für Biologie, Biodiversity/Ecological Modeling, D-14195 Berlin, Germany Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195 Berlin, Germany
| | - Jeannine Wehner
- Freie Universität Berlin, Institut für Biologie, Plant Ecology, D-14195 Berlin, Germany Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195 Berlin, Germany
| | - Diana R Andrade-Linares
- Freie Universität Berlin, Institut für Biologie, Plant Ecology, D-14195 Berlin, Germany Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195 Berlin, Germany
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188
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Damann FE, Williams DE, Layton AC. Potential Use of Bacterial Community Succession in Decaying Human Bone for Estimating Postmortem Interval. J Forensic Sci 2015; 60:844-50. [PMID: 25808627 DOI: 10.1111/1556-4029.12744] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 04/04/2014] [Accepted: 06/14/2014] [Indexed: 11/30/2022]
Abstract
Bacteria are taphonomic agents of human decomposition, potentially useful for estimating postmortem interval (PMI) in late-stage decomposition. Bone samples from 12 individuals and three soil samples were analyzed to assess the effects of decomposition and advancing time on bacterial communities. Results indicated that partially skeletonized remains maintained a presence of bacteria associated with the human gut, whereas bacterial composition of dry skeletal remains maintained a community profile similar to soil communities. Variation in the UniFrac distances was significantly greater between groups than within groups (p < 0.001) for the unweighted metric and not the weighted metric. The members of the bacterial communities were more similar within than between decomposition stages. The oligotrophic environment of bone relative to soft tissue and the physical protection of organic substrates may preclude bacterial blooms during the first years of skeletonization. Therefore, community membership (unweighted) may be better for estimating PMI from skeletonized remains than community structure (weighted).
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Affiliation(s)
- Franklin E Damann
- Department of Defense, National Museum of Health and Medicine, Silver Spring, MD, 20910
| | - Daniel E Williams
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, 37996
| | - Alice C Layton
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, 37996
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189
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Carter DO, Metcalf JL, Bibat A, Knight R. Seasonal variation of postmortem microbial communities. Forensic Sci Med Pathol 2015; 11:202-7. [DOI: 10.1007/s12024-015-9667-7] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/05/2015] [Indexed: 12/01/2022]
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190
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Ushio M, Yamasaki E, Takasu H, Nagano AJ, Fujinaga S, Honjo MN, Ikemoto M, Sakai S, Kudoh H. Microbial communities on flower surfaces act as signatures of pollinator visitation. Sci Rep 2015; 5:8695. [PMID: 25733079 PMCID: PMC4346974 DOI: 10.1038/srep08695] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 02/02/2015] [Indexed: 11/30/2022] Open
Abstract
Microbes are easily dispersed from one place to another, and immigrant microbes might contain information about the environments from which they came. We hypothesized that part of the microbial community on a flower's surface is transferred there from insect body surfaces and that this community can provide information to identify potential pollinator insects of that plant. We collected insect samples from the field, and found that an insect individual harbored an average of 12.2 × 105 microbial cells on its surface. A laboratory experiment showed that the microbial community composition on a flower surface changed after contact with an insect, suggesting that microbes are transferred from the insect to the flower. Comparison of the microbial fingerprint approach and direct visual observation under field condition suggested that the microbial community on a flower surface could to some extent indicate the structure of plant–pollinator interactions. In conclusion, species-specific insect microbial communities specific to insect species can be transferred from an insect body to a flower surface, and these microbes can serve as a “fingerprint” of the insect species, especially for large-bodied insects. Dispersal of microbes is a ubiquitous phenomenon that has unexpected and novel applications in many fields and disciplines.
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Affiliation(s)
- Masayuki Ushio
- Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga 520-2113, Japan
| | - Eri Yamasaki
- 1] Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga 520-2113, Japan [2] Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Hiroyuki Takasu
- 1] Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga 520-2113, Japan [2] Atmosphere and Ocean Research Institute (AORI), The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
| | - Atsushi J Nagano
- 1] Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga 520-2113, Japan [2] PRESTO, Japan Science and Technology Agency, Japan
| | - Shohei Fujinaga
- Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga 520-2113, Japan
| | - Mie N Honjo
- Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga 520-2113, Japan
| | - Mito Ikemoto
- Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga 520-2113, Japan
| | - Shoko Sakai
- Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga 520-2113, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga 520-2113, Japan
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191
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Lax S, Hampton-Marcell JT, Gibbons SM, Colares GB, Smith D, Eisen JA, Gilbert JA. Forensic analysis of the microbiome of phones and shoes. Microbiome 2015; 3:21. [PMID: 25969737 PMCID: PMC4427962 DOI: 10.1186/s40168-015-0082-9] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 04/03/2015] [Indexed: 05/21/2023]
Abstract
BACKGROUND Microbial interaction between human-associated objects and the environments we inhabit may have forensic implications, and the extent to which microbes are shared between individuals inhabiting the same space may be relevant to human health and disease transmission. In this study, two participants sampled the front and back of their cell phones, four different locations on the soles of their shoes, and the floor beneath them every waking hour over a 2-day period. A further 89 participants took individual samples of their shoes and phones at three different scientific conferences. RESULTS Samples taken from different surface types maintained significantly different microbial community structures. The impact of the floor microbial community on that of the shoe environments was strong and immediate, as evidenced by Procrustes analysis of shoe replicates and significant correlation between shoe and floor samples taken at the same time point. Supervised learning was highly effective at determining which participant had taken a given shoe or phone sample, and a Bayesian method was able to determine which participant had taken each shoe sample based entirely on its similarity to the floor samples. Both shoe and phone samples taken by conference participants clustered into distinct groups based on location, though much more so when an unweighted distance metric was used, suggesting sharing of low-abundance microbial taxa between individuals inhabiting the same space. CONCLUSIONS Correlations between microbial community sources and sinks allow for inference of the interactions between humans and their environment.
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Affiliation(s)
- Simon Lax
- />Institute for Genomics and Systems Biology, Biosciences Department, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439 USA
- />Department of Ecology and Evolution, University of Chicago, 1101 E 57th Street, Chicago, IL 60637 USA
| | - Jarrad T Hampton-Marcell
- />Institute for Genomics and Systems Biology, Biosciences Department, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439 USA
| | - Sean M Gibbons
- />Institute for Genomics and Systems Biology, Biosciences Department, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439 USA
- />Graduate Program in Biophysical Sciences, University of Chicago, 5801 South Ellis Avenue, Chicago, USA
| | - Geórgia Barguil Colares
- />Departamento de Biologia, Universidade Federal do Ceará, Avenida da Universidade, 2853 - Benfica, Fortaleza, CE 60440-900 Brazil
| | - Daniel Smith
- />Institute for Genomics and Systems Biology, Biosciences Department, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439 USA
- />Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030 USA
| | - Jonathan A Eisen
- />Department of Evolution and Ecology, University of California, 1544 Newton Ct, Davis, CA USA
- />Department of Medical Microbiology and Immunology, University of California, 1544 Newton Ct, Davis, CA USA
- />UC Davis Genome Center, University of California, 1 Shields Avenue, Davis, CA USA
| | - Jack A Gilbert
- />Institute for Genomics and Systems Biology, Biosciences Department, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439 USA
- />Department of Ecology and Evolution, University of Chicago, 1101 E 57th Street, Chicago, IL 60637 USA
- />Graduate Program in Biophysical Sciences, University of Chicago, 5801 South Ellis Avenue, Chicago, USA
- />Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543 USA
- />College of Environmental and Resource Sciences, Zhejiang University, 38 Zheda Road, Hangzhou, 310058 China
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192
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Olakanye AO, Thompson T, Komang Ralebitso-senior T. Changes to soil bacterial profiles as a result of Sus scrofa domesticus decomposition. Forensic Sci Int 2014; 245:101-6. [DOI: 10.1016/j.forsciint.2014.10.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 07/28/2014] [Accepted: 10/04/2014] [Indexed: 10/24/2022]
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193
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Hyde ER, Haarmann DP, Petrosino JF, Lynne AM, Bucheli SR. Initial insights into bacterial succession during human decomposition. Int J Legal Med 2014; 129:661-71. [DOI: 10.1007/s00414-014-1128-4] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 11/14/2014] [Indexed: 01/21/2023]
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194
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Finley SJ, Benbow ME, Javan GT. Microbial communities associated with human decomposition and their potential use as postmortem clocks. Int J Legal Med 2015; 129:623-32. [DOI: 10.1007/s00414-014-1059-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 07/30/2014] [Indexed: 12/16/2022]
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195
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Can I, Javan GT, Pozhitkov AE, Noble PA. Distinctive thanatomicrobiome signatures found in the blood and internal organs of humans. J Microbiol Methods 2014; 106:1-7. [PMID: 25091187 DOI: 10.1016/j.mimet.2014.07.026] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 07/23/2014] [Accepted: 07/23/2014] [Indexed: 11/26/2022]
Abstract
According to the Human Microbiome Project, 90% of the cells in a healthy adult body are microorganisms. What happens to these cells after human host death, defined here as the thanatomicrobiome (i.e., thanatos-, Greek defn., death), is not clear. To fill the void, we examined the thanatomicrobiome of the spleen, liver, brain, heart and blood of human cadavers. These organs are thought to be devoid of microorganisms in a healthy adult host. We report that the thanatomicrobiome was highly similar among organ tissues from the same cadaver but very different among the cadavers possibly due to differences in the elapsed time since death and/or environmental factors. Isolation of microbial DNA from cadavers is known to be a challenge. We compared the effectiveness of two methods by amplifying the 16S rRNA genes and sequencing the amplicons from four cadavers. Paired comparisons revealed that the conventional DNA extraction method (bead-beating in phenol/chloroform/bead-beating followed by ethanol precipitation) yielded more 16S rRNA amplicons (28 of 30 amplicons) than a second method (repeated cycles of heating/cooling followed by centrifugation to remove cellular debris) (19 of 30 amplicons). Shannon diversity index of the 16S rRNA genes revealed no significant difference by extraction method. The present report provides a proof of principle that the thanatomicrobiome may be an efficient biomarker to study postmortem transformations of cadavers.
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Affiliation(s)
- Ismail Can
- Forensic Science Program, Alabama State University, Montgomery, AL 36101, United States.
| | - Gulnaz T Javan
- Forensic Science Program, Alabama State University, Montgomery, AL 36101, United States.
| | - Alexander E Pozhitkov
- Department of Periodontics, University of Washington, Box 3574444, Seattle, WA 98195, United States.
| | - Peter A Noble
- PhD Program in Microbiology, Alabama State University, Montgomery, AL 36101, United States; Department of Periodontics, University of Washington, Box 3574444, Seattle, WA 98195, United States.
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196
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Lauber CL, Metcalf JL, Keepers K, Ackermann G, Carter DO, Knight R. Vertebrate decomposition is accelerated by soil microbes. Appl Environ Microbiol 2014; 80:4920-9. [PMID: 24907317 DOI: 10.1128/AEM.00957-14] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Carrion decomposition is an ecologically important natural phenomenon influenced by a complex set of factors, including temperature, moisture, and the activity of microorganisms, invertebrates, and scavengers. The role of soil microbes as decomposers in this process is essential but not well understood and represents a knowledge gap in carrion ecology. To better define the role and sources of microbes in carrion decomposition, lab-reared mice were decomposed on either (i) soil with an intact microbial community or (ii) soil that was sterilized. We characterized the microbial community (16S rRNA gene for bacteria and archaea, and the 18S rRNA gene for fungi and microbial eukaryotes) for three body sites along with the underlying soil (i.e., gravesoils) at time intervals coinciding with visible changes in carrion morphology. Our results indicate that mice placed on soil with intact microbial communities reach advanced stages of decomposition 2 to 3 times faster than those placed on sterile soil. Microbial communities associated with skin and gravesoils of carrion in stages of active and advanced decay were significantly different between soil types (sterile versus untreated), suggesting that substrates on which carrion decompose may partially determine the microbial decomposer community. However, the source of the decomposer community (soil- versus carcass-associated microbes) was not clear in our data set, suggesting that greater sequencing depth needs to be employed to identify the origin of the decomposer communities in carrion decomposition. Overall, our data show that soil microbial communities have a significant impact on the rate at which carrion decomposes and have important implications for understanding carrion ecology.
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197
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Ozcan S, Kim BJ, Ro G, Kim JH, Bereuter TL, Reiter C, Dimapasoc L, Garrido D, Mills DA, Grimm R, Lebrilla CB, An HJ. Glycosylated proteins preserved over millennia: N-glycan analysis of Tyrolean Iceman, Scythian Princess and Warrior. Sci Rep 2014; 4:4963. [PMID: 24831691 PMCID: PMC4894394 DOI: 10.1038/srep04963] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 04/24/2014] [Indexed: 12/02/2022] Open
Abstract
An improved understanding of glycosylation will provide new insights into many biological processes. In the analysis of oligosaccharides from biological samples, a strict regime is typically followed to ensure sample integrity. However, the fate of glycans that have been exposed to environmental conditions over millennia has not yet been investigated. This is also true for understanding the evolution of the glycosylation machinery in humans as well as in any other biological systems. In this study, we examined the glycosylation of tissue samples derived from four mummies which have been naturally preserved: – the 5,300 year old “Iceman called Oetzi”, found in the Tyrolean Alps; the 2,400 year old “Scythian warrior” and “Scythian Princess”, found in the Altai Mountains; and a 4 year old apartment mummy, found in Vienna/Austria. The number of N-glycans that were identified varied both with the age and the preservation status of the mummies. More glycan structures were discovered in the contemporary sample, as expected, however it is significant that glycan still exists in the ancient tissue samples. This discovery clearly shows that glycans persist for thousands of years, and these samples provide a vital insight into ancient glycosylation, offering us a window into the distant past.
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Affiliation(s)
- Sureyya Ozcan
- 1] Department of Chemistry, University of California, Davis, California 95616, USA [2] Cancer Research Institute & Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Korea [3]
| | - Bum Jin Kim
- 1] Cancer Research Institute & Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Korea [2]
| | - Grace Ro
- Department of Chemistry, University of California, Davis, California 95616, USA
| | - Jae-Han Kim
- Department of Food Nutrition, Chungnam National University, Daejeon, Korea
| | - Thomas L Bereuter
- Institute of Analytical Chemistry, University of Vienna, Vienna, Austria
| | - Christian Reiter
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Lauren Dimapasoc
- Department of Chemistry, University of California, Davis, California 95616, USA
| | | | - David A Mills
- University of California, Davis, California 95616, USA
| | - Rudolf Grimm
- 1] Cancer Research Institute & Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Korea [2] Agilent Technologies Inc., Santa Clara, California 95051, USA [3] Robert Mondavi Institute for Food Science, University of California, Davis, California 95616, USA [4]
| | - Carlito B Lebrilla
- 1] Department of Chemistry, University of California, Davis, California 95616, USA [2] Department of Biochemistry and Molecular Medicine, University of California, Davis, California 95616, USA [3]
| | - Hyun Joo An
- 1] Cancer Research Institute & Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Korea [2]
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198
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Der Sarkissian C, Ermini L, Jónsson H, Alekseev AN, Crubezy E, Shapiro B, Orlando L. Shotgun microbial profiling of fossil remains. Mol Ecol 2014; 23:1780-98. [PMID: 24612293 DOI: 10.1111/mec.12690] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 01/23/2014] [Accepted: 02/02/2014] [Indexed: 01/20/2023]
Abstract
Millions to billions of DNA sequences can now be generated from ancient skeletal remains thanks to the massive throughput of next-generation sequencing platforms. Except in cases of exceptional endogenous DNA preservation, most of the sequences isolated from fossil material do not originate from the specimen of interest, but instead reflect environmental organisms that colonized the specimen after death. Here, we characterize the microbial diversity recovered from seven c. 200- to 13 000-year-old horse bones collected from northern Siberia. We use a robust, taxonomy-based assignment approach to identify the microorganisms present in ancient DNA extracts and quantify their relative abundance. Our results suggest that molecular preservation niches exist within ancient samples that can potentially be used to characterize the environments from which the remains are recovered. In addition, microbial community profiling of the seven specimens revealed site-specific environmental signatures. These microbial communities appear to comprise mainly organisms that colonized the fossils recently. Our approach significantly extends the amount of useful data that can be recovered from ancient specimens using a shotgun sequencing approach. In future, it may be possible to correlate, for example, the accumulation of postmortem DNA damage with the presence and/or abundance of particular microbes.
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Affiliation(s)
- C Der Sarkissian
- Centre for Geogenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen K, 1350, Denmark
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199
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The microbial corpse clock. Nature 2013; 502:413-413. [DOI: 10.1038/502413c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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