Title |
A computationally simplistic poly-phasic approach to explore microbial communities from the Yucatan aquifer as a potential sources of novel natural products |
Author |
Marfil-Santana Miguel David1, O’Connor-Sánchez Aileen1, Ramírez-Prado Jorge Humberto1, De los Santos-Briones Cesar1, López- Aguiar2, Lluvia Korynthia2, Rojas-Herrera Rafael3, Lago-Lestón Asunción4, and Prieto-Davó Alejandra2* |
Address |
1Center for Scientific Investigation of Yucatan (CICY), Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida, Yucatán, C.P. 97200, Mexico, 2National Autonomous University of Mexico (UNAM), School of Chemistry, Campus Sisal, Puerto de Abrigo s/n Municipio de Hunucmá, Sisal, Yucatan, C.P. 97356, Mexico, 3School of Chemical Engeneering, Autonomous University of Yucatan (UADY), Periférico Norte Kilometro 33.5, Chuburná de Hidalgo Inn, Mérida, Yucatán, C.P. 97203, Mexico, 4Post Graduate Studies and Research Center of Ensenada (CICESE), Ensenada, Baja California, C.P. 22860, Mexico |
Bibliography |
Journal of Microbiology, 54(11),774-781, 2016,
|
DOI |
10.1007/s12275-016-6092-x
|
Key Words |
natural product discovery, polyketide synthase,
secondary metabolites, Yucatan aquifer, microbial metagenomics |
Abstract |
The need for new antibiotics has sparked a search for the
microbes that might potentially produce them. Current sequencing
technologies allow us to explore the biotechnological
potential of microbial communities in diverse environments
without the need for cultivation, benefitting natural
product discovery in diverse ways. A relatively recent method
to search for the possible production of novel compounds
includes studying the diverse genes belonging to polyketide
synthase pathways (PKS), as these complex enzymes are an
important source of novel therapeutics. In order to explore
the biotechnological potential of the microbial community
from the largest underground aquifer in the world located
in the Yucatan, we used a polyphasic approach in which a
simple, non-computationally intensive method was coupled
with direct amplification of environmental DNA to assess
the diversity and novelty of PKS type I ketosynthase (KS)
domains. Our results suggest that the bioinformatic method
proposed can indeed be used to assess the novelty of KS enzymes;
nevertheless, this in silico study did not identify some
of the KS diversity due to primer bias and stringency criteria
outlined by the metagenomics pipeline. Therefore, additionally
implementing a method involving the direct cloning of
KS domains enhanced our results. Compared to other freshwater environments, the aquifer was characterized by considerably
less diversity in relation to known ketosynthase domains;
however, the metagenome included a family of KS
type I domains phylogenetically related, but not identical, to
those found in the curamycin pathway, as well as an outstanding
number of thiolases. Over all, this first look into the microbial
community found in this large Yucatan aquifer and
other fresh water free living microbial communities highlights
the potential of these previously overlooked environments
as a source of novel natural products. |