Modern Methods for Delineating Metagenomic Complexity

Afshinnekoo, Ebrahim; Meydan, Cem; Chowdhury, Shanin; Jaroudi, Dyala; Boyer, Collin; Bernstein, Nick; Maritz, Julia M.; Reeves, Darryl; Gandara, Jorge; Chhangawala, Sagar; Ahsanuddin, Sofia; Simmons, Amber; Nessel, Timothy; Sundaresh, Bharathi; Pereira, Elizabeth; Jorgensen, Ellen; Kolokotronis, Sergios‐Orestis; Kirchberger, Nell; Garcia, Isaac; Gandara, David R.; Dhanraj, Sean; Nawrin, Tanzina; Saletore, Yogesh; Alexander, Noah; Vijay, Priyanka; Hénaff, Elizabeth; Zumbo, Paul; Walsh, Michael; O’Mullan, Gregory D.; Tighe, Scott; Dudley, Joel T.; Dunaif, Anya; Ennis, Sean; O'Halloran, Eoghan; Magalhães, Tiago R.; Boone, Braden; Jones, Angela L.; Muth, Theodore R.; Paolantonio, Katie Schneider; Alter, Elizabeth; Schadt, Eric E.; Garbarino, Jeanne; Prill, Robert J.; Carlton, Jane M.; Levy, Shawn; Mason, Christopher E.

doi:10.1016/j.cels.2015.07.007

Cited by 22 publications

(21 citation statements)

References 2 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Macrobial eDNA studies use massive datasets to evaluate low abundance sequences from unseen taxa, thus susceptibility to artifacts such as sample contamination (Lusk 2014), amplification errors (Schnell et al 2015), sequencing errors (Robasky et al 2014), computational artifacts (Rossberg et al 2014), and inaccurate taxonomic assignment (Afshinnekoo et al 2015b), is high. Mendoza et al (2015) provide a useful overview for navigating these challenges.…”

Section: Analysis Of Edna Datamentioning

confidence: 99%

The ecology of environmental DNA and implications for conservation genetics

2015

View full text Add to dashboard Cite

Environmental DNA (eDNA) refers to the genetic material that can be extracted from bulk environmental samples such as soil, water, and even air. The rapidly expanding study of eDNA has generated unprecedented ability to detect species and conduct genetic analyses for conservation, management, and research, particularly in scenarios where collection of whole organisms is impractical or impossible. While the number of studies demonstrating successful eDNA detection has increased rapidly in recent years, less research has explored the ''ecology'' of eDNA-myriad interactions between extraorganismal genetic material and its environment-and its influence on eDNA detection, quantification, analysis, and application to conservation and research. Here, we outline a framework for understanding the ecology of eDNA, including the origin, state, transport, and fate of extraorganismal genetic material. Using this framework, we review and synthesize the findings of eDNA studies from diverse environments, taxa, and fields of study to highlight important concepts and knowledge gaps in eDNA study and application. Additionally, we identify frontiers of conservation-focused eDNA application where we see the most potential for growth, including the use of eDNA for estimating population size, population genetic and genomic analyses via eDNA, inclusion of other indicator biomolecules such as environmental RNA or proteins, automated sample collection and analysis, and consideration of an expanded array of creative environmental samples. We discuss how a more complete understanding of the ecology of eDNA is integral to advancing these frontiers and maximizing the potential of future eDNA applications in conservation and research.

show abstract

Section: Analysis Of Edna Datamentioning

confidence: 99%

The ecology of environmental DNA and implications for conservation genetics

2015

View full text Add to dashboard Cite

show abstract

“…On 25 April 2015, Petit et al (27) posted a preprint to Zenodo demonstrating that there was no evidence for B. anthracis in the data set. On 29 July 2015, a critique was published by Cell Systems along with a response from the original authors offering a correction to their article (28, 29). A second anecdote of using preprints to aid in postpublication peer review surrounds the publishing of a draft tardigrade genome in the Proceedings of the National Academy of Sciences .…”

Section: Microbiology Anecdotesmentioning

confidence: 99%

Preprinting Microbiology

Schloss

2017

mBio

View full text Add to dashboard Cite

The field of microbiology has experienced significant growth due to transformative advances in technology and the influx of scientists driven by a curiosity to understand how microbes sustain myriad biochemical processes that maintain Earth. With this explosion in scientific output, a significant bottleneck has been the ability to rapidly disseminate new knowledge to peers and the public. Preprints have emerged as a tool that a growing number of microbiologists are using to overcome this bottleneck. Posting preprints can help to transparently recruit a more diverse pool of reviewers prior to submitting to a journal for formal peer review. Although the use of preprints is still limited in the biological sciences, early indications are that preprints are a robust tool that can complement and enhance peer-reviewed publications. As publishing moves to embrace advances in Internet technology, there are many opportunities for preprints and peer-reviewed journals to coexist in the same ecosystem.

show abstract

“…Conventional 16S taxon-based approaches to analyzing microbiome data that are routinely used by the larger scientific community rely heavily on known reference genomes and gene datasets, and result in limited information beyond the relative abundances of microbial species that are present in a sample. In addition to this problem, there are several obvious limitations to this approach exemplified by the fact that almost half of the high-quality sequence reads that are derived from microbiome projects cannot be taxonomically classified [82,83].…”

Section: Forensic Microbiome Challenges and Limitationsmentioning

confidence: 99%

“…The temporal variation is not constant, as some samples, such as gut microbiome, are more robust than others. Similarly, the initial works on the environmental microbiomes have a diverse array of collection techniques: the dust from the fans were sampled for the dorm rooms [25]; swabs were taken from the subways and parks of New York [83]; specialized collection plates were used in the examination of the different office studies. No meta-study has addressed any possible changes to the results from these different sampling techniques.…”

Section: Forensic Microbiome Challenges and Limitationsmentioning

confidence: 99%

Integrating the microbiome as a resource in the forensics toolkit

Clarke

Gómez

Singh

et al. 2017

Forensic Science International: Genetics

View full text Add to dashboard Cite

The introduction of DNA fingerprinting to forensic science rapidly expanded the available evidence that could be garnered from a crime scene and used in court cases. Next generation sequencing technologies increased available genetic data that could be used as evidence by orders of magnitude, and as such, significant additional genetic information is now available for use in forensic science. This includes DNA from the bacteria that live in and on humans, known as the human microbiome. Next generation sequencing of the human microbiome demonstrates that its bacterial DNA can be used to uniquely identify an individual, provide information about their life and behavioral patterns, determine the body site where a sample came from, and estimate postmortem intervals. Bacterial samples from the environment and objects can also be leveraged to address similar questions about the individual(s) who interacted with them. However, the applications of this new field in forensic sciences raises concerns on current methods used in sample processing, including sample collection, storage, and the statistical power of published studies. These areas of human microbiome research need to be fully addressed before microbiome data can become a regularly incorporated evidence type and routine procedure of the forensic toolkit. Here, we summarize information on the current status of microbiome research as applies to the forensic field, the mathematical models used to make predictions, and the possible legal and practical difficulties that can limit the application of microbiomes in forensic science.

show abstract

Modern Methods for Delineating Metagenomic Complexity

Cited by 22 publications

References 2 publications

The ecology of environmental DNA and implications for conservation genetics

The ecology of environmental DNA and implications for conservation genetics

Preprinting Microbiology

Integrating the microbiome as a resource in the forensics toolkit

Contact Info

Product

Resources

About