Project Summary

Investigating Muscle-Specific Bacterial Gene Expression Using Next Generation Sequencing to Improve Shelf Life of High-Value Beef Steaks

Principle Investigator(s):
Colton L. Smith1, Ifigenia Geornaras1, Jessica Metcalf1, Erin Nishimura2, and Mahesh N. Nair1 
Institution(s):
1 Department of Animal Sciences, Colorado State University
2 Department of Biochemistry and Molecular Biology, Colorado State University 
Completion Date:
August 2024
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KEY TAKEAWAYS

  • Microbial growth directly impacts the color stability of both striploin and tenderloin beef steaks during aerobic retail display.   
  • Direct measures of lipid and protein oxidation were not impacted by bacterial growth for either muscle.   
  • The 16S rRNA sequencing analysis demonstrated that Pseudomonas spp. predominated the aerobic spoilage process for both muscles.   
  • Further, microbial gene expression showed changes to microbial function during the display period, and metabolomic analysis showed an increase in select aerobic respiration and amino acid metabolites on inoculated striploin and tenderloin steaks. 

BACKGROUND

About 16% of the total meat produced in North America is lost at the distribution and consumer levels primarily due to spoilage concerns, equating to a per person meat loss of 18.6 kg.  Color/appearance is one of the most important sensory attributes that determine the shelf-life of meat, as consumers discriminate against discolored meat. In fact, consumers’ rejection of discolored beef leads to a $3.73 billion loss each year in the United States.  High-value muscle cuts of beef, such as the longissimus lumborum (LL; striploin) and psoas major (PM; tenderloin), have significantly different shelf-life capabilities. Previous research has indicated that the microbial community composition between color stable LL and color-labile PM muscles is similar. Additionally, previous studies have reported that PM has a different metabolite profile compared to LL, which the bacteria could use as nutrients for growth, explaining some of the differences in the rate of spoilage. However, very little available work has been reported that explains the relationships between microbial growth and color stability.  The shelf-life differences between beef muscles have been well-known for several decades, but limited progress has been made on the intervention techniques to address this issue specifically. Therefore, a clear understanding of the interactions between specific muscles and microbial growth is imperative to creating a more sustainable processing and retailing system and minimizing food waste.  The objective of this study was to use microbial gene expression in tandem with metabolomics, culture-based microbial enumeration, microbial growth kinetics, and biochemical properties of muscles to identify intervention pathways to improve the shelf life of high-value beef steaks during retail display. 

Methodology   
Ten (n = 10) side-paired USDA Select beef striploins (LL) and tenderloins (PM) were collected and aged (2ºC) for 14 days in vacuum packaging. After aging, the whole muscles were decontaminated by immersion into boiling water for 2 min to reduce the existing microflora load on the surface of the loins. The outer surface of the decontaminated muscles was aseptically removed, and the loins were fabricated into 1.27 cm (0.5 inch) thick steaks. Steaks were then randomly assigned to one of two treatment groups, namely, decontaminated control (DCON) or inoculated (INOC). The INOC steaks were surface inoculated (ca. 4 log CFU/cm2) with a 6-isolate mixture of spoilage bacteria containing three Pseudomonas spp. and three lactic acid bacteria (LAB). The steaks were wrapped in oxygen-permeable overwrap film on soaker pad-lined trays and placed into a retail display case for up to 8 days. One steak per treatment per muscle was analyzed daily for instrumental (L* a*, and b*) and subjective color, microbial population levels, meat pH, lipid and protein oxidation, 16S rRNA gene sequencing, metatranscriptomics, and metabolomics. Subjective color scores were assigned by trained panelists and percentage surface discoloration was also quantified by trained panelists. Samples were analyzed for aerobic plate counts (APC; tryptic soy agar), Pseudomonas spp. counts (Pseudomonas plate count agar), and lactic acid bacteria counts (MRS agar). Thiobarbituric acid reactive substances (TBARS) and protein carbonyls were performed to quantify lipid and protein oxidation, respectively. Microbiome (16S rRNA amplicon sequencing) was used to assess the changes in microbial communities during the 8-day retail display period. Metatranscriptomic analysis was performed to analyze the gene expression of bacteria present on INOC steaks, and gas-chromatography mass spectrometry was utilized to determine differences in steak surface metabolomes.  

Findings   
There was a display day x treatment interaction (P < 0.05) for L*, a*, and b* values, lean color scores, percentage surface discoloration, and all three bacterial count types for LL. The percentage discoloration and a* values were similar between treatments until day 5, where DCON was lower (P < 0.05) than INOC LL steaks. For both muscles, all bacterial count types (APC, Pseudomonas spp. counts, and LABC) were lower (P < 0.05)  for DCON compared to INOC steaks. On PM steaks, there was a display day x treatment interaction (P < 0.05) for a* and b* values and percentage discoloration. Percentage  discoloration was similar between treatments for PM steaks until day 4 when INOC PM  steaks were more discolored (P < 0.05), and by day 6, were at 87.1% and 37.3% for INOC and DCON steaks, respectively. There was a display day main effect (P < 0.05) for  TBARS for both LL and PM. Further, alpha diversity decreased (P < 0.05) for both LL and  PM throughout the display period and beta diversity metrics showed changes in bacterial  compositions during the display period. The metabolomic profiles revealed that INOC  steaks had the most differences in the carbohydrate metabolism class of metabolites for  both muscles. Differential gene expression analysis revealed 501 genes were significantly up or down regulated for LL INOC steaks from days 3-6 and 628 microbial genes were differentially expressed (P <0.1) for PM INOC steaks from days 2-5. 

Implications 
The data presented in this study suggest that microbial growth directly impacts the color stability of both LL and PM beef steaks during aerobic retail display. Direct measures of lipid and protein oxidation were not impacted by bacterial growth for either muscle. The 16S rRNA sequencing analysis demonstrated that Pseudomonas spp. predominated the aerobic spoilage process for both muscles. Further, microbial gene expression showed changes to microbial function during the display period, and metabolomic analysis showed an increase in select aerobic respiration and amino acid metabolites on PM and LL INOC steaks.    

ARMS#120525-10