The present study was aimed to improve the phytosterol contents in food commodities. Plant microbe interaction is an efficient and ecofriendly way to induce nutritional or desired contents, plant biochemicals to get improved food crops. The present study addresses the issue of nutritional improvement of food crops to provide healthy food, to the people for global green food security. The plant microbe interactions establish a direct relation with plant throughout its development. This resistance termed as induced systemic resistance (ISR) can be achieved applying non-pathogenic bacterial strains. This phenomenon of ISR has been used to manage barley crop using Acetobacter aceti as a biological inducer. Initially, staple food crops Triticum aestivum (wheat), Cicer arietinum (white chickpea), Cicer arietinum (black chickpea), Hordeum vulgare (barley), Oryza sativa (rice), Zea mays (corn) and Pennisetum glaucum (millet) were screened for their phytosterol contents on the basis of their nutritional quantities e.g. biochemicals, physical texture, vitamin contents. All these staple crops were evaluated through transcriptional analysis of squalene synthase (SS) genes which have a direct relation with increased phytosterol production. Biochemical analyses were performed using standard procedures and it was recorded that food crop varieties exhibit variable levels of pectins, alkaloids, saponins, phenolics, terpenoids, phytosterols and flavonoids. High nutritional and biochemical staple food varieties were screened. Barley (Hordeum vulgare) screened out among other staple food crops showed the maximum amount of phytosterols 0.239 ± 0.04 g/kg and other plant biochemicals which are essential in plant growth. These phytosterols compounds are one of the documented remedies for the treatment of hyperlipidemia. Thus, regular consumption of food with high contents of phytosterols controls lipid absorption most efficiently than other food products. Additionally, its dietary benefits and nutritional facts further support its use as most recommended staple food crop worldwide. Squalene synthase expression analysis including a family of genes i.e. SSA, SS1, SS2 and SS3 was carried out using reverse transcription polymerase chain reaction (RT-PCR) in selected staple food crops yielding elevated expression of the most of these genes. Maximum expression of SSA was recorded in chickpea black 64.3 ± 4.63 ng/5μL, which was closely related to barley and chickpea white with 62.91 ± 4.23 and 60.8 ± 3.98 ng/5μL respectively. Wheat and millet exhibited close expression of SSA gene 54.87 ± 3.86 and 54.79 ± 3.68 ng/5μL respectively. Comparatively, rice showed lesser expression of SSA gene 50.07 ± 3.01 ng/5μL, whereas, corn recorded least expression with 28.92 ± 1.27 ng/5μL. Gene SS1 showed maximum expression in barley along with chickpea black and corn 30.14 ± 1.78, 29.91 ± 1.69 and 29.0 ± 1.03 ng/5μL. SS2 gene recorded its maximum expression in barley 41.7 ± 1.99 ng/5μL, chickpea black 39.8 ± 1.98 ng/5μL and corn 37.9 ± 1.76 ng/5μL. Wheat 37.2 ± 1.69 ng/5μL showed no difference in SS2 gene expression than corn, however, SS2 was significantly less expressive in millet 33.8 ± 1.31 ng/5μL and chickpea white 33.1 ± 1.29 ng/5μL. SS3 gene is mainly responsible for squalene production in wheat 44.21 ± 2.43 ng/5μL. Among other staple food crops barley, 42.84 ± 2.16 ng/5μL and chickpea black 42.39 ± 2.01 ng/5μL recorded a second highest expression of SS3 genes. Following with corn 41.86 ± 1.97 ng/5μL, rice 40.87 ± 1.46 ng/5μL and white chickpea recorded 39.8 ± 1.16 ng/5μL. whereas, millet recorded no SS3 gene expression. Different strains of bacillus i.e. AC1, AC2, AC3…AC8 was analyzed as plant inducers and AC8 was screened out as the best inducer in barley. It induced highest quantities of phtosterols 0.008 ± 0.001 g/kg including other biochemicals (i.e. phenolics, alkaloids and terpenoids). AC8 also showed its maximum activity in SS gene expression analysis. The most expressive gene recorded under AC8 treatment was SSA, which has the maximum role in the up regulation of squalene synthase and phytosterols. SS2 reported second highly induced gene against AC8 treatment. SS3 recorded at third level. SS1 was reported as the least expressive gene. AC8 reported as the most favorable microbial strain which showed the best relationship with barley and reported the maximum genetic expression of SSA. AC7 reported as least significant strain in an expression of gene SS1. The current study revealed that among eight microbial strains AC8 had a maximum potential to increase ascorbic acid, pantothenic acid, pyridoxine, thiamine and riboflavin in barley than other microbial strains. AC8 screened out among other microbial strains on the basis of its high vitamins induction potential. AC3 plus AC6 were reported second in the recorded list although other strains had a chronological reduction in vitamins as AC2 > AC7 > AC4 > AC5 and AC1. Overall temperature variation results revealed that AC8 treated barley showed significant induction of phytosterols 0.009 ± 0.003 g/kg and vitamins at T3 (26.5 ± 1.5 °C). Chromatographic techniques such as preparative thin layer chromatography (PTLC), column chromatography (CC) and gas chromatography mass spectrometry (GCMS) were used to identify bioactive compounds of A. aceti. Identified bioactive compounds were responsible for vitamins and phytosterol induction in barley. A total of 13 bioactive compounds were identified through bioactivity guided assay and were analyzed through principle component analysis. Mainly four chemical compounds i.e., quinolinic acid, pyridoxic acid, p.Aminobenzoate and α-Oxobutanoic acid were evaluated through PCA directly associated with increased vitamin contents. Solvent system chloroform: ethanol (4:1) was used to extract bioactive compounds of A. aceti from its crude metabolites. Selected crops were tested against cholesterol reduction in albino rats. The rats were fed with different selected crops and found that the barley 121.7 ± 6.26 mg/dl reduced maximum blood cholesterol level. The selected crop barley was further treated with eight different bacterial strains to enhance its nutritional values and checked against cholesterol reduction. The AC8 treated barley 119.9 ± 5.19 mg/dl reported a maximum reduction in total cholesterol. Following with AC8 treated barley grown at T3 (26.5 ± 1.5 °C) temperature reported maximum cholesterol reduction with 112.6 ± 4.16 mg/dl. This study on small-scale produced good results in the rhizospheric induction of microbes in barley crop. This association promoted the production of phytosterols, vitamins and other nutrients in barley crop. Such barley crop fortified with nutrients could be used to manage the lipid metabolic syndrome for a healthy life.