Microgrids are indispensable components of active energy systems that supply diverse electrical and thermal demands. A microgrid is composed of distributed energy resources (DER) including renewable resources, combined heat and power generation (CHP) and conventional generation resources that rely on fossil fuels. Energy hubs in microgrids facilitate the conversion of different types of energy resources. The coupling among natural gas and electricity distribution networks introduces new challenges to the short-term operation planning of microgrids. In this paper, a two-stage stochastic optimization problem is formulated for the short-term operation planning of microgrids with multiple-energy carrier networks to determine the scheduled energy and reserve capacity. The problem is formulated as a mixed integer linear programming problem in which the objective function is to minimize the expected operation cost in the short-term operation horizon. The uncertainties in the renewable generation including the wind and solar photovoltaic generation, and electrical and thermal demands are captured by introducing scenarios with respective probabilities. The proposed solution framework ensures the reliability and security of energy supply in multiple scenarios. The advantage of capturing the interdependence among the electricity and natural gas systems to promote energy efficiency is presented. Furthermore, the effectiveness of demand response programs to reduce the operation costs and improve the security measures is investigated. The sensitivity of the operation costs to the variation of natural gas flow and congestion in pipelines and energy prices is addressed to highlight the interdependence among natural gas and electricity infrastructure systems. (C) 2018 Elsevier Ltd. All rights reserved.