|
Deep amplicon sequencing
|
• rRNA
|
• Prokaryotic and eukaryotic identification*
|
• Characterization of the healthy human gut microbiome (HMP) [28]
|
• Potentially higher sensitivity
|
• Targeted gene may not be truly universal
|
| | |
• Determination of taxonomic relationships
|
• Ancient gut microbiomes found to be more similar to modern rural than modern cosmopolitan microbiomes [29]
|
• Less expensive as fewer reads are required for taxonomic classification
|
• Primer bias may alter population structure
|
| |
• rpoB
|
• Archaeal and bacterial identification*
|
• Used to divide the species Gardnerella vaginalis into subgroups [30]
|
• rpoB and cpn-60 offer enhanced taxonomic resolution compared to rRNA [31, 32]
|
• Possibility of variable gene copy numbers amongst targeted species
|
| |
• cpn-60
|
• Determination of taxonomic relationships
| | | |
| |
• Viral RNA polymerase (RdRP)
|
• Novel virus discovery
|
• Identified novel families of picornaviruses off the coast of British Columbia [33]
| | |
|
Metagenomics
|
• Shotgun sequencing
|
• Functional and taxonomic characterization
|
• Detection of African swine fever virus-like sequences representing new members of the family Asfariviridae [9]
|
• Recovery of sequences from all microorganisms
|
• Broad specificity might decrease sensitivity
|
| | | |
• Detection of unexpected microbes from stool samples [12]
|
• No a priori knowledge of microorganisms required
|
• Library preparation is relatively labor intensive
|
| |
• Subtraction
|
• Functional and taxonomic characterization
|
• Identified divergent regions in non-coding RNAs in Listeria monocytogenes[34]
|
• Random primers reduce potential for bias
|
• Bioinformatics analysis is more challenging
|
| | | |
• Association of Fusobacterium nucleatum with colorectal carcinoma [35]
| |
• Relatively expensive as more reads are required than for DAS
|
| |
• Virus concentration
|
• Novel virus discovery
|
• Detection of the novel H1N1 influenza from nasopharyngeal swabs [13]
| |
• Approximately 50% of sequences generally have no significant homology to known proteins in databases (dark matter) [36]
|
| | | |
• Detection of a novel rhabdovirus from serum [37]
| | |
| |
• Hybridization capture
|
• Investigation of sequences with very low copy number
|
• Metagenomic analysis of tuberculosis from a mummy [38]
| |
• Increased granularity in population structure determination [39]
|
| | | |
• Investigation of Yersinia pestis from ancient teeth [40]
| | |
