The biodiesel industry has made crude glycerine a low value and priced “commodity” whose supply has grown rapidly, causing an oversupply; part of the pertinent research in this area has thus been focused on seeking new biotechnological applications for glycerol as carbon source (Fonseca et al,, 2009; Pachauri and He, 2006). The biodiesel industry’s crude glycerine sub-product loses commercial value due to the presence of impurities whose removal implies a high cost; a search has thus been made for microorganisms which directly metabolise to generate eco-innovator and sustainable high added-value compounds; thereby providing biodiesel production with added value. 1,3-propanediol (1,3-PD) production from industrial glycerine with microorganisms from genera such as Klebsiella, Citrobacter and Clostridium is one of the options being evaluated. 1,3-PD production is not found as “commodity” on the market; this diol obtained from crude glycerine by biotechnological means is a growing technology and currently has 80,000 tons per year worldwide production at a cost of US$ 3 to US$ 6 per kilo when produced by chemical route. 1,3-PD has applications as mass consumption substance, as solvent, in formulations for adhesives, laminas, resins, in detergents, cosmetics as moisturiser, such as heavy-duty antifreeze agent and as polytrimethylene terephthalate (PTT) monomer (Zeng and Biebl, 2002). The potential worldwide market for 1,3-PD is US$ 3,500 million dollars: US$ 750 million for applications as monomer in resins, US$ 750 million for mass consumption applications and US$ 2,000 million for industrial applications (Ferguson, 2006). It has been predicted that the potential market (based on its use for PTT production) will be £500 million in 2020 (Paster M et al,., 2003) and £350 million in 2015 (English B et al,., 2006). It is also considered that the actual market is small as the necessary technology is still being developed (Paster M et al, ., 2003). The accelerated increase in the supply of glycerine around the world has begun to be a matter for preoccupation since as biodiesel production increase so does that of natural glycerine and such sub-product is becoming a significant problem with the boom for this biofuel (Hogeendoorn et al,., 2007). For example, glycerine production in Europe could reach 2 million tons this year when trying to fulfil European Parliament directive 2003/30/CE. Colombian biodiesel production for 2010 has been predicted as being around 600,000 tons, generating 60,000 tons of glycerine at 80% concentration, together with fatty acids, water and methanol (Mesa- Dishington, 2008). During the last 15 years, the Universidad Nacional de Colombia’s Instituto de Biotecnologia’s (IBUN) Bioprocesses and Bioprospecting Group has investigated a group of bacteria from the Clostridium genera isolated from Colombian agricultural soils which have shown greater solventogenic ability than Clostridium acetobutylicum ATCC 824, the international reference strain (Montoya et al,., 2000). Such isolates have been biochemically and molecularly characterised, finding that they are closely related to Clostridium butyricum strains but could become constituted as a new specie (Arévalo et al,., 2002; Montoya et al, 2000; Suarez, 2004). It has been found that five of the native Colombian strains were able to produce 1,3-PD from glycerol, having volumetric productivity greater than that of the C. butyricum reference strains, the native IBUN 158B strain obtaining the highest value (Cárdenas et al, 2006). The 1,3-PD production dhaB, dhaB1 and dhaT operon gene sequences have been determined in native Clostridium sp. strains IBUN 13A and IBUN 158B (Montoya, 2009). Environmental and culture medium conditions have been optimised at bank level for 1,3-PD production with industrial carbon and nitrogen sources, showing that the native IBUN 158B strain consumes biodiesel-derived glycerine without prior treatment and produces diol in similar yields (Aragón, 2007; Pérez, 2009) to those from a genetically-modified Clostridium strain reported in the literature (Gonzalez-Pajuelo et al 2005) Investigations are currently being carried out for determining the 1,3-PD operon regulator genes. However, biotechnological processes’ profitability mainly depends on the cost of crude material and the microorganism’s ability to transform glycerol into 1,3-PD. This means that there has been insistence on the search for focalised molecular designs for obtaining the most competitive hyper-producer strain on the market. The present work thus proposes studying the differential expression of genes expressed during 1,3-PD production by using transcriptomics and metabolomics for creating a genetic modification strategy by metabolic simulation. Correlating proteomic and transcriptomic data may lead to gaining real-time access to the metabolic context of the route consisting of enzymes having direct and associated function, with which simulations can be established by analysing the metabolic flow necessary for rationally identifying the most suitable molecular approaches for generating mutants having a booster function.