title: The salivary microbiome for differentiating individuals: proof of principle.
abstract: Human identification has played a prominent role in forensic science for the past two decades. Identification based on unique genetic traits is driving the field. However, this may have limitations, for instance, for twins. Moreover, high-throughput sequencing techniques are now available and may provide a high amount of data likely useful in forensic science. This study investigates the potential for bacteria found in the salivary microbiome to be used to differentiate individuals. Two different targets (16S rRNA and rpoB) were chosen to maximise coverage of the salivary microbiome and when combined, they increase the power of differentiation (identification). Paired-end Illumina high-throughput sequencing was used to analyse the bacterial composition of saliva from two different people at four different time points (t = 0 and t = 28 days and then one year later at t = 0 and t = 28 days). Five major phyla dominate the samples: Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes and Fusobacteria. Streptococcus, a Firmicutes, is one of the most abundant aerobic genera found in saliva and targeting Streptococcus rpoB has enabled a deeper characterisation of the different streptococci species, which cannot be differentiated using 16S rRNA alone. We have observed that samples from the same person group together regardless of time of sampling. The results indicate that it is possible to distinguish two people using the bacterial microbiota present in their saliva.
authors.affiliation: School of Criminal Justice, University of Lausanne, Lausanne, Switzerland.
authors.forename: Sarah L
authors.initials: SL
authors.lastname: Leake
authors.affiliation: Swiss Institute of Bioinformatics, Vital-IT Group, Lausanne, Switzerland.
authors.forename: Marco
authors.initials: M
authors.lastname: Pagni
authors.affiliation: Swiss Institute of Bioinformatics, Vital-IT Group, Lausanne, Switzerland; Department of Biology, University of Fribourg, Fribourg, Switzerland.
authors.forename: Laurent
authors.initials: L
authors.lastname: Falquet
authors.affiliation: School of Criminal Justice, University of Lausanne, Lausanne, Switzerland.
authors.forename: Franco
authors.initials: F
authors.lastname: Taroni
authors.affiliation: Institute of Microbiology, Lausanne, Switzerland. Electronic address: gilbert.greub@chuv.ch.
authors.forename: Gilbert
authors.initials: G
authors.lastname: Greub
mesh_terms: D000328:Adult; D001419:Bacteria / Q000145:classification* / Q000235:genetics*; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D012321:DNA-Directed RNA Polymerases; D018732:Forensic Anthropology / Q000379:methods*; D005554:Forensic Medicine / Q000379:methods*; D064368:Healthy Volunteers; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D056186:Metagenomics / Q000379:methods*; D064307:Microbiota; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012463:Saliva / Q000382:microbiology*; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D012321:DNA-Directed RNA Polymerases; C105078:RNA polymerase beta subunit
keywords: Forensic science; Human identification; Illumina sequencing; Saliva microbiota