Bacterial functional prediction tools detect but underestimate metabolic diversity compared to shotgun metagenomics in southwest Florida soils

AbstractKey aspects of microbiome research are accurate identification of taxa followed by the profiling of their functionality. Amplicon profiling based on the 16S ribosomal DNA sequence is a ubiquitous technique to identify and profile the abundances of the various taxa. However, it does not provide information on their encoded functionality. Predictive tools which can accurately extrapolate the functional information of a microbiome based on taxonomic profile composition is essential. At present the applicability of these tools is however limited due to requirement of reference genomes from known species. We present IPCO (Inference of Pathways from Co-variance analysis), a new method of inferring functionality for 16S-based microbiome profiles independent of reference genomes. IPCO utilises the biological co-variance observed between paired taxonomic and functional profiles and co-varies it with the queried dataset. It outperforms other established methods both in terms of sample and feature profile prediction. Validation results confirmed that IPCO can replicate observed biological signals seen within shotgun and metabolite profiles. Comparative analysis of predicted functionality profiles with other popular 16S-based functional prediction tools indicates significantly lower performance with predicted functionality showing little to no correlation with paired shotgun features across samples. IPCO is implemented in R and available from https://github.com/IPCO-Rlibrary/IPCO.

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Occurrence and biogeographic significance of Heliaster (Echinodermata: Asteroidea) from the Pliocene of southwest Florida

Journal of Paleontology ◽

10.1017/s0022336000058960 ◽

1988 ◽

Vol 62 (01) ◽

pp. 126-132 ◽

Cited By ~ 8

Author(s):

Douglas S. Jones ◽

Roger W. Portell

Keyword(s):

Central American ◽

Eastern Pacific ◽

Whole Body ◽

Marine Fauna ◽

Western Atlantic ◽

Southwest Florida ◽

Extant Species ◽

Geologic Record ◽

Central American Isthmus

Whole body asteroid fossils are rare in the geologic record and previously unreported from the Cenozoic of Florida. However, specimens of the extant species,Heliaster microbrachiusXantus, were recently discovered in upper Pliocene deposits. This marks the first reported fossil occurrence of the monogeneric Heliasteridae, a group today confined to the eastern Pacific. This discovery provides further non-molluscan evidence of the close similarities between the Neogene marine fauna of Florida and the modern fauna of the eastern Pacific. The extinction of the heliasters in the western Atlantic is consistent with the pattern of many other marine groups in the region which suffered impoverishment following uplift of the Central American isthmus.

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