Abstract The microbiome plays many roles in human health, often through the exclusive lens of clinical interest. The inevitable end point for all living hosts, death, has its own altered microbiome configurations. However, little is understood about the ecology and changes of microbial communities after death, or their potential utility for understanding the health condition of the recently living. Here we reveal distinct postmortem microbiomes of human hosts from a large-scale survey of death cases representing a predominantly urban population, and demonstrated these microbiomes reflected antemortem health conditions within 24–48 hours of death. Our results characterized microbial community structure and predicted function from 188 cases representing a cross-section of an industrial-urban population. We found strong niche differentiation of anatomic habitat and microbial community turnover based on topographical distribution. Microbial community stability was documented up to two days after death. Additionally, we observed a positive relationship between cell motility and time since host death. Interestingly, we discovered evidence that microbial biodiversity is a predictor of antemortem host health condition (e.g., heart disease). These findings improve the understanding of postmortem host microbiota dynamics, and provide a robust dataset to test the postmortem microbiome as a tool for assessing health conditions in living populations.
Deciphering mechanisms that regulate succession on ephemeral resources is critical for elucidating food web dynamics and nutrient recycling. Blow fly (Diptera: Calliphoridae) colonization and utilization of vertebrate carrion serve as a model for such studies, as they are the primary invertebrates that recycle this ephemeral resource. Initial colonization by blow flies often results in heightened attraction and colonization by competing conspecifics and heterospecifics, thereby regulating associated arthropod succession patterns. We examined the response of Cochliomyia macellaria (F.) and Chrysomya rufifacies (Macquart) to conspecific and heterospecific eggs. Because Ch. rufifacies is facultatively predacious and cannabalistic, we hypothesized that adults would recognize the presence of conspecific and heterospecific eggs, thus avoiding potential predation and competition. Using a Y-tube olfactometer, we measured the residence time response of C. macellaria and Ch. rufifacies to conspecific and heterospecific eggs of three different age classes (fresh to 9-h-old). Fly responses to surface-sterilized eggs and to an aqueous solution containing egg-associated microbes were then examined. High-throughput sequencing was used to survey egg-associated bacteria from both species. We report that C. macellaria and Ch. rufifacies exhibit differential responses to eggs of conspecifics and heterospecifics, which appear to be a result of microbial volatile-related odors. These behaviors likely influence predator–prey interactions between species. Preliminary high-throughput sequencing revealed Ch. rufifacies had a similar egg-associated fauna as C. macellaria, which may serve as a form of camouflage, allowing it to colonize and thereby attract C. macellaria, a common prey for its larvae.
The National Research Council issued a report in 2009 that heavily criticized the forensic sciences. The report made several recommendations that if addressed would allow the forensic sciences to develop a stronger scientific foundation. We suggest a roadmap for decomposition ecology and forensic entomology hinging on a framework built on basic research concepts in ecology, evolution, and genetics. Unifying both basic and applied research fields under a common umbrella of terminology and structure would facilitate communication in the field and the production of scientific results. It would also help to identify novel research areas leading to a better understanding of principal underpinnings governing ecosystem structure, function, and evolution while increasing the accuracy of and ability to interpret entomological evidence collected from crime scenes. By following the proposed roadmap, a bridge can be built between basic and applied decomposition ecology research, culminating in science that could withstand the rigors of emerging legal and cultural expectations.
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.
Riparian plant invasions can result in near-monocultures along stream and river systems, prompting management agencies to target invasive species for removal as an ecological restoration strategy. Riparian plant invaders can alter resource conditions in the benthos and drive bottom-up shifts in aquatic biota. However, the influence of management activities on the structure and function of aquatic communities is not well understood. We investigated how removal of a riparian invader, Lonicera maackii (Amur honeysuckle), influenced aquatic macroinvertebrate community functional and taxonomic diversity in a headwater stream. We hypothesized that removal of L. maackii from invaded riparia would result in ( H 1 ) increased aquatic macroinvertebrate abundance, density, and diversity; ( H 2 ) a taxonomic and functional shift in community composition; and, in particular, ( H 3 ) increased functional diversity. Aquatic macroinvertebrates were sampled monthly from autumn 2010 to winter 2013 in headwater stream riffles with a dense riparian L. maackii invasion and those where L. maackii had been experimentally removed. We found macroinvertebrate density was significantly higher in the L. maackii removal reach ( P <0.05) and that macroinvertebrate community structure and functional trait presence was distinct between stream reaches and across seasons ( P <0.05). The removal reach exhibited greater functional richness during spring and summer and had more unique functionally relevant taxa (20% and 85%) compared with the L. maackii reach (5% and 75%) during summer and autumn seasons. Our results suggest bottom-up processes link restoration activities in the riparian corridor and aquatic biota through alterations of functional composition in the benthic community.
Microbial communities have potential evidential utility for forensic applications. However, bioinformatic analysis of high-throughput sequencing data varies widely among laboratories. These differences can potentially affect microbial community composition and downstream analyses. To illustrate the importance of standardizing methodology, we compared analyses of postmortem microbiome samples using several bioinformatic pipelines, varying minimum library size or minimum number of sequences per sample, and sample size. Using the same input sequence data, we found that three open-source bioinformatic pipelines, MG-RAST, mothur, and QIIME2, had significant differences in relative abundance, alpha-diversity, and beta-diversity, despite the same input data. Increasing minimum library size and sample size increased the number of low-abundant and infrequent taxa detected. Our results show that bioinformatic pipeline and parameter choice affect results in important ways. Given the growing potential application of forensic microbiology to the criminal justice system, continued research on standardizing computational methodology will be important for downstream applications.
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