Creating a 3D microbial and chemical snapshot of a human habitat

Kapono, Clifford A.; Morton, James T.; Bouslimani, Amina; Melnik, Alexey V.; Orlinsky, Kayla; Knaan, Tal Luzzatto; Garg, Neha; Vázquez-Baeza, Yoshiki; Protsyuk, Ivan; Zhu, Quanyin; Alexandrov, Theodore; Smarr, Larry; Knight, Rob; Dorrestein, Pieter C.

doi:10.1038/s41598-018-21541-4

Cited by 37 publications

(40 citation statements)

References 43 publications

(52 reference statements)

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“…These data show that individual microbiomes can persist into the early postmortem period, which is consistent with the observations of Pechal et al . The current findings also complement recent work demonstrating that antemortem skin microbial communities on humans resembled those of their phones and surfaces (e.g., door knobs, counters, and floors) in home and office environments. All of these results are encouraging for forensic science since they demonstrate that microbial communities on surfaces and objects can be traced back to the people who frequently interact with those objects or surfaces, thus providing a new method to establish associations and identifications.…”

Section: Discussionsupporting

confidence: 92%

“…However, recent developments of metagenomic DNA sequencing technology have allowed microbial communities to be investigated at unprecedented scales (7,8) and detail (9,10). Thus far, there have been two primary forensic applications of this technology: using skin microbial communities as trace evidence to associate individuals with objects and/ or locations (11)(12)(13)(14)(15) and estimating postmortem interval (PMI) (16)(17)(18)(19). Both of these applications are in the early stages of development, but they have already shown great potential.…”

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confidence: 99%

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Trace Evidence Potential in Postmortem Skin Microbiomes: From Death Scene to Morgue

Kodama

Metcalf

et al. 2018

Journal of Forensic Sciences

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Microbes can be used effectively as trace evidence, at least in research settings. However, it is unknown whether skin microbiomes change prior to autopsy and, if so, whether these changes interfere with linking objects to decedents. The current study included microbiomes from 16 scenes of death in the City and County of Honolulu and tested whether objects at the scenes can be linked to individual decedents. Postmortem skin microbiomes were stable during repeated sampling up to 60 h postmortem and were similar to microbiomes of an antemortem population. Objects could be traced to decedents approximately 75% of the time, with smoking pipes and medical devices being especially accurate (100% match), house and car keys being poor (0%), and other objects like phones intermediate (~80%). These results show that microbes from objects at death scenes can be matched to individual decedents, opening up a new method of establishing associations and identifications.

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Section: Discussionsupporting

confidence: 92%

mentioning

confidence: 99%

Trace Evidence Potential in Postmortem Skin Microbiomes: From Death Scene to Morgue

Kodama

Metcalf

et al. 2018

Journal of Forensic Sciences

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“…[27][28][29][30] To look for sunscreen in environmental samples, MASST found matches to the indoor environment or personal objects such as offices, houses, cars, bikes, phones, wallets, keys, mattresses, plants, meat for human consumption, corals, and even in coral reef in remote areas such as Moorea. [31][32][33] While there have been no identifiable toxic effects on humans 34 , these results show that human-made chemicals may be widely distributed without truly understanding the potential long-term impact.…”

Section: ) Can Masst Be Used To Track Sunscreens In Human and Enviromentioning

confidence: 90%

MASST: A Web-based Basic Mass Spectrometry Search Tool for Molecules to Search Public Data

Wang

Vargas

et al. 2019

Preprint

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Correspondence:We introduce a web-enabled small-molecule mass spectrometry (MS) search engine. To date, no tool can query all the public small-molecule tandem MS data in metabolomics repositories, greatly limiting the utility of these resources in clinical, environmental and natural product applications. Therefore, we introduce a Mass Spectrometry Search Tool (MASST) (https://proteosafe-extensions.ucsd.edu/masst/), that enables the discovery of molecular relationships among accessible public metabolomics and natural product tandem mass spectrometry data (MS/MS).The ability to discover related sequences of proteins or genes in publicly accessible sequence data using Basic Local Alignment Search Tool (BLAST), connected to public sequence data repositories through a web interface (WebBLAST, https://blast.ncbi.nlm.nih.gov/Blast.cgi), was introduced in the 1990s. 1 It has garnered more than 138,159 citations according to Google Scholar, placing it among the most widely used bioinformatics tools. WebBLAST enabled detection of the number of sequences in public repositories related to a given query, the organisms in which those sequences occur, and the evolutionary and inferred functional relationships among related sequences. It therefore permitted a broad community to answer simple but scientifically compelling questions such as: Is a protein or DNA sequence common or rare? How is this sequence distributed among different kinds of organisms? What other sequences are related to this sequence (evolutionary variants, or new mutations, or synthetic constructs)? In the early days of making DNA or protein sequence data publicly available, the "metadata" (e.g., contextual information about the sample, population and location the sequence came from, and technical information about how it was produced) in the public repositories was limited and no standards existed. This is a situation similar to the current status of much of the mass spectrometry data in the public domain. However, when publicly deposited data has metadata available, such as organism, location of sampling, host phenotypes such as diseases, etc., it becomes possible to start building higherlevel hypotheses regarding the evolutionary, ecological or functional relationships among these DNA, RNA or protein sequences. The development of the ability to search data with added context continues to have profound impacts on fields including medicine, chemistry, genetics, molecular biology, genomics, microbiology, and ecology.Algorithms developed for mass spectrometry data, including molecular networking 2 and fragmentation trees 3 , enable similarity searches, while powerful metabolomics analysis software infrastructures, such as MS-DIAL 4 , MetaboAnalyst 5 , XCMS Online 6 , HMDB 7 , some of which have been available for over a decade, focus on annotation of MS/MS spectra or finding statistical relationships between molecular features. However, none of the existing tools enable searching against public data in repositories. Finding the distribution of specific data of i...

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“…[5]) or on building surfaces ( e.g. [6][7][8]). In targeted metabolomics studies, researchers focus on a list of molecules of interest, usually known to be hazardous to human health.…”

Section: Introductionmentioning

confidence: 99%

“…Detected molecules include microbial products, but also compounds being leached by building surfaces (plasticizers, paint constituents…), cleaning products, and molecules deposited by building occupants themselves ( e.g. beauty products, food derivatives) [7][8]. Such results can provide valuable information into a building’s usage and its occupants’ behavior.…”

Section: Introductionmentioning

confidence: 99%

Characterization of the workplace chemical exposome using untargeted LC-MS/MS: a case study

McCall

Anderson

Fogle

et al. 2019

Preprint

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Western people now spend close to 90% of their time indoors, one-quarter of which occurs at their place of employment. As such, interactions between employees and the workplace built environment have significant potential impact on employee health and safety. However, the range of workers’ daily chemical exposures is still poorly understood. Likewise, the influence of workers themselves and of worker behavior on the chemical composition of the workplace is still unknown. In this case study, we used untargeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) to compare the chemical signatures of three different types of workplaces: scientific research buildings, office buildings, and one mixed-purpose building. Our results identified differential signatures of public building surfaces based on building purpose, sampling location and surface materials. Overall, these results are helping define the influence of human behavior on the workplace chemical environment and identify the chemical hazards to which people are exposed throughout their workday.HighlightsImplementation of untargeted liquid chromatography-tandem mass spectrometry to study workplace chemical exposures.Shared chemical signatures were identified based on building purpose.Differential chemical signatures were identified based on surface material and sampling location.Annotated molecules include pharmaceuticals, illicit drugs, food chemicals, constituents of paints and stains, and cleaning products.

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Creating a 3D microbial and chemical snapshot of a human habitat

Cited by 37 publications

References 43 publications

Trace Evidence Potential in Postmortem Skin Microbiomes: From Death Scene to Morgue

Trace Evidence Potential in Postmortem Skin Microbiomes: From Death Scene to Morgue

MASST: A Web-based Basic Mass Spectrometry Search Tool for Molecules to Search Public Data

Characterization of the workplace chemical exposome using untargeted LC-MS/MS: a case study

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