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Otagiri T, Sato N, Shiozaki T, Harayama Y, Matsumoto M, Kobayashi K, Asamura H. An optimal skeletal element for DNA testing: Evaluation of DNA quantity and quality from various bone types in routine forensic practice. Leg Med (Tokyo) 2024; 68:102415. [PMID: 38280273 DOI: 10.1016/j.legalmed.2024.102415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/19/2023] [Accepted: 01/18/2024] [Indexed: 01/29/2024]
Abstract
For human identification, the quality and quantity of DNA must be sufficient for amplification and analysis. When DNA extraction from bone tissues and teeth is required, the optimal skeletal elements should be selected as samples for DNA extraction because DNA yield differs among elements. Recently, some studies have reported that a high quantity of high-quality DNA can be extracted from the small cancellous bones of the hands and feet. In this study, we evaluated the effectiveness of small cancellous bones in the human identification of skeletal remains in routine forensic genetic casework. Cancellous bones [phalanges, (meta)carpal bones, and (meta)tarsal bones)] and the cortical bones (femur and petrous bones) and teeth, which have generally been recommended as samples, were collected from the same individuals that needed identifying using DNA analysis in our laboratory. The quantity of DNA from small cancellous bones tended to be higher than that from cortical bones, and the quality from the former was as high as that from the latter. This study showed that in routine forensic casework, the small cancellous bones of the hands and feet should be actively selected as samples for DNA testing.
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Affiliation(s)
- Tomomi Otagiri
- Department of Legal Medicine, Shinshu University School of Medicine, Matsumoto, Nagano 390-8621, Japan.
| | - Noriko Sato
- Department of Legal Medicine, Shinshu University School of Medicine, Matsumoto, Nagano 390-8621, Japan.
| | - Tetsuya Shiozaki
- Department of Legal Medicine, Shinshu University School of Medicine, Matsumoto, Nagano 390-8621, Japan.
| | - Yuta Harayama
- Department of Legal Medicine, Shinshu University School of Medicine, Matsumoto, Nagano 390-8621, Japan.
| | - Momoe Matsumoto
- Department of Legal Medicine, Shinshu University School of Medicine, Matsumoto, Nagano 390-8621, Japan.
| | - Kanya Kobayashi
- Department of Legal Medicine, Shinshu University School of Medicine, Matsumoto, Nagano 390-8621, Japan.
| | - Hideki Asamura
- Department of Legal Medicine, Shinshu University School of Medicine, Matsumoto, Nagano 390-8621, Japan.
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2
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Ķimsis J, Pokšāne A, Kazarina A, Vilcāne A, Petersone‐Gordina E, Zayakin P, Gerhards G, Ranka R. Tracing microbial communities associated with archaeological human samples in Latvia, 7-11th centuries AD. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:383-391. [PMID: 37057308 PMCID: PMC10472514 DOI: 10.1111/1758-2229.13157] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/23/2023] [Indexed: 06/19/2023]
Abstract
In the grave environment, microorganisms are major ecological participants in the successional decomposition of vertebrates and could infiltrate the skeleton/skeletal material during taphonomic processes. The diversity of archaeological skeleton-associated microbial assemblages and the impact of various factors are poorly understood. This study aimed to evaluate the taxonomic microbial composition of archaeological human bone and teeth samples from the 7th to 11th centuries AD from two burial sites in Latvia. Samples were analysed by a shotgun metagenomics-based approach. The results showed a strong presence of the environmental DNA in the samples, and variability in microbial community structure between individual samples. Differences in microbial composition were observed between bone and tooth samples, as well as between different burial sites. Furthermore, the presence of endogenous ancient DNA (aDNA) in tooth samples was detected. Overall, compositions of microbial communities associated with archaeological human remains in Latvia dated 7-11th century AD were influenced by the sample type and burial location. These findings indicate that, while the content of historical DNA in archaeological samples is low, the comparison of archaeological skeleton-associated microbial assemblages across time and space, along with aDNA damage profile analysis, is important and could help to reveal putative ancient microorganisms.
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Affiliation(s)
- Jānis Ķimsis
- Latvian Biomedical Research and Study CentreLaboratory of molecular microbiologyRigaLatvia
| | - Alise Pokšāne
- Latvian Biomedical Research and Study CentreLaboratory of molecular microbiologyRigaLatvia
| | - Alisa Kazarina
- Latvian Biomedical Research and Study CentreLaboratory of molecular microbiologyRigaLatvia
| | | | | | - Pawel Zayakin
- Latvian Biomedical Research and Study CentreLaboratory of molecular microbiologyRigaLatvia
| | | | - Renate Ranka
- Latvian Biomedical Research and Study CentreLaboratory of molecular microbiologyRigaLatvia
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3
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Flocco CG, Methner A, Burkart F, Geppert A, Overmann J. Touching the (almost) untouchable: a minimally invasive workflow for microbiological and biomolecular analyses of cultural heritage objects. Front Microbiol 2023; 14:1197837. [PMID: 37601377 PMCID: PMC10435870 DOI: 10.3389/fmicb.2023.1197837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/27/2023] [Indexed: 08/22/2023] Open
Abstract
Microbiological and biomolecular approaches to cultural heritage research have expanded the established research horizon from the prevalent focus on the cultural objects' conservation and human health protection to the relatively recent applications to provenance inquiry and assessment of environmental impacts in a global context of a changing climate. Standard microbiology and molecular biology methods developed for other materials, specimens, and contexts could, in principle, be applied to cultural heritage research. However, given certain characteristics common to several heritage objects-such as uniqueness, fragility, high value, and restricted access, tailored approaches are required. In addition, samples of heritage objects may yield low microbial biomass, rendering them highly susceptible to cross-contamination. Therefore, dedicated methodology addressing these limitations and operational hurdles is needed. Here, we review the main experimental challenges and propose a standardized workflow to study the microbiome of cultural heritage objects, illustrated by the exploration of bacterial taxa. The methodology was developed targeting the challenging side of the spectrum of cultural heritage objects, such as the delicate written record, while retaining flexibility to adapt and/or upscale it to heritage artifacts of a more robust constitution or larger dimensions. We hope this tailored review and workflow will facilitate the interdisciplinary inquiry and interactions among the cultural heritage research community.
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Affiliation(s)
- Cecilia G. Flocco
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ- German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Anika Methner
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ- German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Franziska Burkart
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ- German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Alicia Geppert
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ- German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Jörg Overmann
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ- German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
- Microbiology, Technical University of Braunschweig, Braunschweig, Germany
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4
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Geweely NS. New frontiers review of some recent conservation techniques of organic and inorganic archaeological artefacts against microbial deterioration. Front Microbiol 2023; 14:1146582. [PMID: 37007519 PMCID: PMC10060858 DOI: 10.3389/fmicb.2023.1146582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 02/13/2023] [Indexed: 03/18/2023] Open
Abstract
The information on the advances and technology of some recent conservation methods (2020–2023) of organic and inorganic archaeological objects against microbial deterioration is recorded. An outline of comparative new protective methods for conserving plant-origin organic artefacts {Fibers (manuscripts, textile) and wood}, animal-origin organic artefacts (painting, parchment and mummies) and inorganic stone artefacts were investigated. The work not only contributes to the development of safe revolutionary ways for more efficient safe conservation of items of historical and cultural worth but also serves as a significant diagnostic signature for detecting the sorts of microbial identification and incidents in antiques. Biological technologies (environmentally friendly green biocides) are the most used recent, efficient and safe strategy acceptable as alternatives to stop microbial deterioration and prevent any potential interactions between the biological agent and the artefacts. Also, a synergistic effect of combining natural biocides with mechanical cleaning or chemical treatments was suggested. The recommended exploration techniques should be considered for future applications.
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5
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Liu R, Zhang K, Li H, Sun Q, Wei X, Li H, Zhang S, Fan S, Wang Z. Dissecting the microbial community structure of internal organs during the early postmortem period in a murine corpse model. BMC Microbiol 2023; 23:38. [PMID: 36765295 PMCID: PMC9912631 DOI: 10.1186/s12866-023-02786-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 02/01/2023] [Indexed: 02/12/2023] Open
Abstract
BACKGROUND Microorganisms distribute and proliferate both inside and outside the body, which are the main mediators of decomposition after death. However, limited information is available on the postmortem microbiota changes of extraintestinal body sites in the early decomposition stage of mammalian corpses. RESULTS This study investigated microbial composition variations among different organs and the relationship between microbial communities and time since death over 1 day of decomposition in male C57BL/6 J mice by 16S rRNA sequencing. During 1 day of decomposition, Agrobacterium, Prevotella, Bacillus, and Turicibacter were regarded as time-relevant genera in internal organs at different timepoints. Pathways associated with lipid, amino acid, carbohydrate and terpenoid and polyketide metabolism were significantly enriched at 8 h than that at 0.5 or 4 h. The microbiome compositions and postmortem metabolic pathways differed by time since death, and more importantly, these alterations were organ specific. CONCLUSION The dominant microbes differed by organ, while they tended toward similarity as decomposition progressed. The observed thanatomicrobiome variation by body site provides new knowledge into decomposition ecology and forensic microbiology. Additionally, the microbes detected at 0.5 h in internal organs may inform a new direction for organ transplantation.
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Affiliation(s)
- Ruina Liu
- grid.43169.390000 0001 0599 1243College of Forensic Medicine, Xi’an Jiaotong University, Xi’an, 710061 China
| | - Kai Zhang
- grid.43169.390000 0001 0599 1243College of Forensic Medicine, Xi’an Jiaotong University, Xi’an, 710061 China
| | - Huan Li
- grid.452910.bXi’an Mental Health Center Hospital, Xi’an, 710061 China
| | - Qinru Sun
- grid.43169.390000 0001 0599 1243College of Forensic Medicine, Xi’an Jiaotong University, Xi’an, 710061 China
| | - Xin Wei
- grid.43169.390000 0001 0599 1243College of Forensic Medicine, Xi’an Jiaotong University, Xi’an, 710061 China
| | - Huiyu Li
- grid.43169.390000 0001 0599 1243College of Forensic Medicine, Xi’an Jiaotong University, Xi’an, 710061 China
| | - Siruo Zhang
- grid.440288.20000 0004 1758 0451Department of Clinical Laboratory, Shaanxi Provincial People’s Hospital, Shaanxi Xi’an, 710068 People’s Republic of China ,grid.43169.390000 0001 0599 1243Department of Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University, Shaanxi Xi’an, 710061 People’s Republic of China
| | - Shuanliang Fan
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China.
| | - Zhenyuan Wang
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China.
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6
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Postmortem Skeletal Microbial Community Composition and Function in Buried Human Remains. mSystems 2022; 7:e0004122. [PMID: 35353006 PMCID: PMC9040591 DOI: 10.1128/msystems.00041-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bones and teeth can provide a lasting resource to identify human remains following decomposition. Bone can support dynamic communities of micro- and macroscopic scavengers and incidental taxa, which influence the preservation of bone over time. Previously we identified key microbial taxa associated with survivability of DNA in bones of surface-decomposed human remains, observing high intra- and interindividual variation. Here we characterized the postmortem bone microbiome of skeletal remains in a multi-individual burial to better understand subsurface bone colonization and preservation. To understand microbial community origins and assembly, 16S rRNA amplicon sequences from 256 bone and 27 soil samples were compared to bone from individuals who decomposed on the ground surface, and human gut sequences from the American Gut Project. Untargeted metabolomics was applied to a subset of 41 bone samples from buried remains to examine potential microbe–metabolite interactions and infer differences related to community functionality. Results show that postmortem bone microbial communities are distinct from those of the oxic surface soils and the human gut. Microbial communities from surface-deposited bone and shallow buried bone were more similar to those from soils, while bones recovered from saturated areas deeper in the grave showed increased similarity with human gut samples with higher representation of anaerobic taxa, suggesting that the depositional environment affected the established bone microbiome. Correlations between metabolites and microbes indicate that phosphate solubilization is likely an important mechanism of microbially mediated skeletal degradation. This research expands our knowledge of microbial bone colonizers, including colonizers important in a burial environment. IMPORTANCE Understanding the microbes that colonize and degrade bone has important implications for preservation of skeletal elements and identification of unknown human remains. Current research on the postmortem bone microbiome is limited and largely focuses on archaeological or marine contexts. Our research expands our understanding of bone microbiomes in buried remains by characterizing the taxonomic and metabolic diversity of microbes that are colonizing bone after a 4-year postmortem burial interval and examines the potential impact of microbial colonization on human skeletal DNA preservation. Our results indicate that the postmortem bone microbiome is distinct from the human gut and soil. Evidence from combined metabolomic and amplicon sequencing analysis suggests that Pseudomonas and phosphate solubilization likely play a role in skeletal degradation. This work provides important insight into the types and activities of microbes controlling the preservation of buried skeletal remains.
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7
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Kaszubinski SF, Receveur JP, Nestle ED, Pechal JL, Benbow ME. Microbial community succession of submerged bones in an aquatic habitat. J Forensic Sci 2022; 67:1565-1578. [PMID: 35349167 DOI: 10.1111/1556-4029.15036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 02/06/2022] [Accepted: 03/08/2022] [Indexed: 01/04/2023]
Abstract
After death, microbes (including bacteria and fungi) colonize carrion from a variety of sources during the decomposition process. The predictable succession of microbes could be useful for forensics, such as postmortem submersion interval estimation (PMSI) for aquatic deaths. However, gaps exist in our understanding of microbial succession on submerged bone, particularly regarding longer-term decomposition (>1 year), fungal composition, and differences between internal and external microbial communities. To further explore this potential forensic tool, we described the postmortem microbial communities (bacteria and fungi) on and within submerged bones using targeted amplicon sequencing. We hypothesized predictable successional patterns of microbial colonization would be detected on the surface and within submerged bones, which would eventually converge to a similar microbial community. To best replicate forensic contexts, we sampled bones from replicate swine (Sus scrofa domesticus) carcasses submerged in a freshwater pond, every three months for nearly two years. Microbial bone (internal vs. external) community structure (taxa abundance and diversity) of bones differed for both bacteria and fungi, but internal and external communities did not converge to a similar structure. PMSI estimation models built with random forest regression of postmortem microbiomes were highly accurate (>80% variation explained in PMSI) and showed promise for forensic purposes. Overall, we provide further evidence that internal and external bone microbial communities submerged in an aquatic habitat are distinct and each community undergoes predictable succession, demonstrating potential utility in forensics for modeling PMSI in unattended deaths and/or cold cases.
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Affiliation(s)
- Sierra F Kaszubinski
- Department of Integrative Biology, Michigan State University, East Lansing, Michigan, USA
| | - Joseph P Receveur
- Department of Entomology, Michigan State University, East Lansing, Michigan, USA.,Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, Michigan, USA
| | - Emily D Nestle
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Jennifer L Pechal
- Department of Entomology, Michigan State University, East Lansing, Michigan, USA
| | - M Eric Benbow
- Department of Entomology, Michigan State University, East Lansing, Michigan, USA.,Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, Michigan, USA.,Department of Osteopathic Medical Specialties, Michigan State University, East Lansing, Michigan, USA
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8
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Balaji A, Sapoval N, Seto C, Leo Elworth R, Fu Y, Nute MG, Savidge T, Segarra S, Treangen TJ. KOMB: K-core based de novo characterization of copy number variation in microbiomes. Comput Struct Biotechnol J 2022; 20:3208-3222. [PMID: 35832621 PMCID: PMC9249589 DOI: 10.1016/j.csbj.2022.06.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 11/29/2022] Open
Abstract
Characterizing metagenomes via kmer-based, database-dependent taxonomic classification has yielded key insights into underlying microbiome dynamics. However, novel approaches are needed to track community dynamics and genomic flux within metagenomes, particularly in response to perturbations. We describe KOMB, a novel method for tracking genome level dynamics within microbiomes. KOMB utilizes K-core decomposition to identify Structural variations (SVs), specifically, population-level Copy Number Variation (CNV) within microbiomes. K-core decomposition partitions the graph into shells containing nodes of induced degree at least K, yielding reduced computational complexity compared to prior approaches. Through validation on a synthetic community, we show that KOMB recovers and profiles repetitive genomic regions in the sample. KOMB is shown to identify functionally-important regions in Human Microbiome Project datasets, and was used to analyze longitudinal data and identify keystone taxa in Fecal Microbiota Transplantation (FMT) samples. In summary, KOMB represents a novel graph-based, taxonomy-oblivious, and reference-free approach for tracking CNV within microbiomes. KOMB is open source and available for download at https://gitlab.com/treangenlab/komb.
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Affiliation(s)
- Advait Balaji
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Nicolae Sapoval
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Charlie Seto
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - R.A. Leo Elworth
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Yilei Fu
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Michael G. Nute
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Tor Savidge
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Santiago Segarra
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, USA
- Corresponding author.
| | - Todd J. Treangen
- Department of Computer Science, Rice University, Houston, TX, USA
- Corresponding author.
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9
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Haarkötter C, Saiz M, Gálvez X, Medina-Lozano MI, Álvarez JC, Lorente JA. Usefulness of Microbiome for Forensic Geolocation: A Review. Life (Basel) 2021; 11:life11121322. [PMID: 34947853 PMCID: PMC8707258 DOI: 10.3390/life11121322] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 11/26/2021] [Accepted: 11/27/2021] [Indexed: 11/16/2022] Open
Abstract
Forensic microbiomics is a promising tool for crime investigation. Geolocation, which connects an individual to a certain place or location by microbiota, has been fairly well studied in the literature, and several applications have been found. The aim of this review is to highlight the main findings in this field, including the current sample storage, DNA extraction, sequencing and data analysis techniques that are being used, and its potential applications in human trafficking and ancient DNA studies. Second, the challenges and limitations of forensic microbiomics and geolocation are emphasised, providing recommendations for the establishment of this tool in the forensic science community.
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10
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Deel H, Emmons AL, Kiely J, Damann FE, Carter DO, Lynne A, Knight R, Xu ZZ, Bucheli S, Metcalf JL. A Pilot Study of Microbial Succession in Human Rib Skeletal Remains during Terrestrial Decomposition. mSphere 2021; 6:e0045521. [PMID: 34259562 PMCID: PMC8386422 DOI: 10.1128/msphere.00455-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 06/21/2021] [Indexed: 11/20/2022] Open
Abstract
The bones of decomposing vertebrates are colonized by a succession of diverse microbial communities. If this succession is similar across individuals, microbes may provide clues about the postmortem interval (PMI) during forensic investigations in which human skeletal remains are discovered. Here, we characterize the human bone microbial decomposer community to determine whether microbial succession is a marker for PMI. Six human donor subjects were placed outdoors to decompose on the soil surface at the Southeast Texas Applied Forensic Science facility. To also assess the effect of seasons, three decedents were placed each in the spring and summer. Once ribs were exposed through natural decomposition, a rib was collected from each body for eight time points at 3 weeks apart. We discovered a core bone decomposer microbiome dominated by taxa in the phylum Proteobacteria and evidence that these bone-invading microbes are likely sourced from the surrounding decomposition environment, including skin of the cadaver and soils. Additionally, we found significant overall differences in bone microbial community composition between seasons. Finally, we used the microbial community data to develop random forest models that predict PMI with an accuracy of approximately ±34 days over a 1- to 9-month time frame of decomposition. Typically, anthropologists provide PMI estimates based on qualitative information, giving PMI errors ranging from several months to years. Previous work has focused on only the characterization of the bone microbiome decomposer community, and this is the first known data-driven, quantitative PMI estimate of terrestrially decomposed human skeletal remains using microbial abundance information. IMPORTANCE Microbes are known to facilitate vertebrate decomposition, and they can do so in a repeatable, predictable manner. The succession of microbes in the skin and associated soil can be used to predict time since death during the first few weeks of decomposition. However, when remains are discovered after months or years, often the only evidence are skeletal remains. To determine if microbial succession in bone would be useful for estimating time since death after several months, human subjects were placed to decompose in the spring and summer seasons. Ribs were collected after 1 to 9 months of decomposition, and the bone microbial communities were characterized. Analysis revealed a core bone decomposer microbial community with some differences in microbial assembly occurring between seasons. These data provided time since death estimates of approximately ±34 days over 9 months. This may provide forensic investigators with a tool for estimating time since death of skeletal remains, for which there are few current methods.
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Affiliation(s)
- Heather Deel
- Program in Cell & Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Alexandra L. Emmons
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Jennifer Kiely
- Department of Biological Sciences, Sam Houston State University, Huntsville, Texas, USA
| | | | - David O. Carter
- Laboratory of Forensic Taphonomy, Forensic Sciences Unit, Chaminade University of Honolulu, Honolulu, Hawaii, USA
- School of Natural Sciences and Mathematics, Chaminade University of Honolulu, Honolulu, Hawaii, USA
| | - Aaron Lynne
- Department of Biological Sciences, Sam Houston State University, Huntsville, Texas, USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Zhenjiang Zech Xu
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Sibyl Bucheli
- Department of Biological Sciences, Sam Houston State University, Huntsville, Texas, USA
| | - Jessica L. Metcalf
- Program in Cell & Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA
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11
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Rossi C, Ruß-Popa G, Mattiangeli V, McDaid F, Hare AJ, Davoudi H, Laleh H, Lorzadeh Z, Khazaeli R, Fathi H, Teasdale MD, A'ali A, Stöllner T, Mashkour M, Daly KG. Exceptional ancient DNA preservation and fibre remains of a Sasanian saltmine sheep mummy in Chehrābād, Iran. Biol Lett 2021; 17:20210222. [PMID: 34256582 PMCID: PMC8278039 DOI: 10.1098/rsbl.2021.0222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/21/2021] [Indexed: 12/29/2022] Open
Abstract
Mummified remains have long attracted interest as a potential source of ancient DNA. However, mummification is a rare process that requires an anhydrous environment to rapidly dehydrate and preserve tissue before complete decomposition occurs. We present the whole-genome sequences (3.94 X) of an approximately 1600-year-old naturally mummified sheep recovered from Chehrābād, a salt mine in northwestern Iran. Comparative analyses of published ancient sequences revealed the remarkable DNA integrity of this mummy. Hallmarks of postmortem damage, fragmentation and hydrolytic deamination are substantially reduced, likely owing to the high salinity of this taphonomic environment. Metagenomic analyses reflect the profound influence of high-salt content on decomposition; its microbial profile is predominated by halophilic archaea and bacteria, possibly contributing to the remarkable preservation of the sample. Applying population genomic analyses, we find clustering of this sheep with Southwest Asian modern breeds, suggesting ancestry continuity. Genotyping of a locus influencing the woolly phenotype showed the presence of an ancestral 'hairy' allele, consistent with hair fibre imaging. This, along with derived alleles associated with the fat-tail phenotype, provides genetic evidence that Sasanian-period Iranians maintained specialized sheep flocks for different uses, with the 'hairy', 'fat-tailed'-genotyped sheep likely kept by the rural community of Chehrābād's miners.
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Affiliation(s)
- Conor Rossi
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, D02 VF25, Ireland
| | - Gabriela Ruß-Popa
- Austrian Academy of Sciences, Austrian Archaeological Institute, Archaeological Sciences, Hollandstraße 11-13, 1020 Vienna, Austria
| | - Valeria Mattiangeli
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, D02 VF25, Ireland
| | - Fionnuala McDaid
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, D02 VF25, Ireland
| | - Andrew J. Hare
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, D02 VF25, Ireland
| | - Hossein Davoudi
- Central Laboratory, Bioarchaeology Laboratory, University of Tehran, 1417634934 Tehran, Iran
| | - Haeedeh Laleh
- Central Laboratory, Bioarchaeology Laboratory, University of Tehran, 1417634934 Tehran, Iran
- Faculty of Humanities, Department of Archaeology, University of Tehran, 1417935840 Tehran, Iran
| | - Zahra Lorzadeh
- Central Laboratory, Bioarchaeology Laboratory, University of Tehran, 1417634934 Tehran, Iran
| | - Roya Khazaeli
- Central Laboratory, Bioarchaeology Laboratory, University of Tehran, 1417634934 Tehran, Iran
| | - Homa Fathi
- Central Laboratory, Bioarchaeology Laboratory, University of Tehran, 1417634934 Tehran, Iran
| | - Matthew D. Teasdale
- McDonald Institute for Archaeological Research, Dept. of Archaeology, University of Cambridge, Cambridge CB2 3ER, UK
| | - Abolfazl A'ali
- Zanjan Cultural Heritage Centre, Archaeological Museum of Zanjan, Emaarate Zolfaghari, Taleghani St., Zanjan, Iran
| | - Thomas Stöllner
- Research Department, Haus der Archäologien, Ruhr University Bochum, Institute for Archaeological Studies and Deutsches Bergbau-Museum Bochum, Am Bergbaumuseum 31, D-44791 Bochum, Germany
| | - Marjan Mashkour
- Central Laboratory, Bioarchaeology Laboratory, University of Tehran, 1417634934 Tehran, Iran
- Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements (AASPE), Muséum national d'Histoire naturelle, Sorbonne Université, CNRS, CP 56, 55 rue Buffon, 75005 Paris, France
| | - Kevin G. Daly
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, D02 VF25, Ireland
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