gabriella mason-buck · walking petri dish – “more microbe than human!” 10 x more bacterial...
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Microbiome
▪ Microbial communities that colonise the body
▪ Walking petri dish –“more microbe than human!”
▪ 10 x more bacterial cells than human cells
▪ More recent studies have reduced this estimate to 3:1 or 1:1
▪ Human DNA contains viral parasites
Artistic rendering of the human microbiome.
The Why Files
Metagenomics
▪ The study of all organisms present in a specific environment:
▪ Influence
▪ Combined function
▪ ‘Meta’ (µεΤα) – the ability to go beyond ordinary limitations
▪ ‘Genomic’ - total hereditary material within an organism
▪ omics - the study of every aspect of a given area
DNA Intelligence
‘There is a need to ‘precisely identify and characterise microbes that have
played a role in war, terrorism, and crime events, thus contributing to
discovering the source of the microbes and the party responsible for their use’
Handelsman et al 2007
Forensic Metagenomics
▪ Bioterrorism/Biocrime
▪ Postmortem Interval (PMI)
▪ Human Identification
▪ Cause of death
▪ Animal ID
▪ Body fluid and body site ID
▪ Geolocation
Methods
▪ Initially (specific approaches):
▪ 16S rRNA -Bacteria and Archaea
▪ 18S rRNA – Eukaryotes
▪ trnL intron – Plants
▪ ITS rDNA – Fungi
▪ Now (shotgun approach):
▪ Reliant on bioinformatic analysis to identify sequences
Background
▪ Studies have suggested that urban environments and mass transit systems have geospatially distinct metagenomic profiles
▪ Approximately 55% of the World’s population live in urban areas
Aims
The International Metagenomics and Metadesign of Subways and Urban Biomes (MetaSUB) Consortium aims:
▪ To create geospatial metagenomic and forensic genetic maps
▪ To identify and track antimicrobial resistance markers (AMRs) in the urban built environment
▪ To identify novel biosynthetic gene clusters (BGCs) for drug discovery
http://content.tfl.gov.uk/standard-tube-map.pdf
Global City Sampling Day
21st June 2017
London sampling strategy:
▪ Number of stations: 272
▪ Sampling areas:
▪ Ticket machine
▪ Handrail or elevator button
▪ Bench on the platform
Method
DNA Extraction
Library Preparation
Massively Parallel Sequencing
Bioinformatic Analysis
Data Visualisation
4,424 taxa identified
61 core species (>95% of samples)
1,145 sub-core species (>70% of samples)
2,466 peripheral species (<25% of samples)
10,928 novel predicted viral
species~50% of data unclassified
91.4% prediction accuracy of sample to city
3,741 samples
58 cities Key Findings
General Findings
▪ Most taxa from human skin and airways - Cutibacterium acnes most abundant species
▪ Increasing distance from the equator is associated with a decrease in taxonomic diversity –estimated loss of 6.9672 species for each degree of latitude away from the equator
▪ Samples from Europe and East Asia are the most distinct
▪ We are still identifying new taxa everyday!
Phylum
Actinobacteria
Firmicutes
Proteobacteria
49%51%Gram Negative
Gram Positive
Commensal80%
20%
Not Commensal
84%
16% Forms biofilms
No biofilms
59%41%
Viral host
Not a viral host
London Waterloo
▪ Estimated 147, 574 daily passengers
▪ Interchange for 4 tube lines and national rail services
▪ Close to key tourist attractions such as the London Eye
Data Visualisation:MetaGenScope
*Reads Per Kilobase of transcript per Million mapped reads
*
Abundance of Common Organisms – London Waterloo (Ticket Machine)
Challenges and Considerations
▪ ‘Kitome’
▪ Methodology
▪ Replicates
▪ Controls
▪ Data analysis▪ Software
▪ Computational capacity
Find out more…
JOIN METASUB‘Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance’
www.metasub.org
@metasub
Acknowledgements
Special thanks to the King’s Forensics team
PhD Supervisors:Prof. Denise Syndercombe Court Dr David Ballard
MRes Forensic Science students:Rebecca SmithYe Jee Roh
Chris Mason, MetaSUB Consortium members, sponsors and funding bodies
Sampling Volunteers
In wine there is wisdom, In beer there is freedom, In water there is bacteria.
- Benjamin Franklin
Thank You!