Microbiome surrounding death and decay, The: microbial ecology of food processing, meat spoilage, and human decomposition environments

2021 Summer.Includes bibliographical references.To view the abstract, please see the full text of the document

Considerations and best practices in animal science 16S ribosomal RNA gene sequencing microbiome studies

Microbiome studies in animal science using 16S rRNA gene sequencing have become increasingly common in recent years as sequencing costs continue to fall and bioinformatic tools become more powerful and user-friendly. The combination of molecular biology, microbiology, microbial ecology, computer science, and bioinformatics—in addition to the traditional considerations when conducting an animal science study—makes microbiome studies sometimes intimidating due to the intersection of different fields. The objective of this review is to serve as a jumping-off point for those animal scientists less familiar with 16S rRNA gene sequencing and analyses and to bring up common issues and concerns that arise when planning an animal microbiome study from design through analysis. This review includes an overview of 16S rRNA gene sequencing, its advantages, and its limitations; experimental design considerations such as study design, sample size, sample pooling, and sample locations; wet lab considerations such as field handing, microbial cell lysis, low biomass samples, library preparation, and sequencing controls; and computational considerations such as identification of contamination, accounting for uneven sequencing depth, constructing diversity metrics, assigning taxonomy, differential abundance testing, and, finally, data availability. In addition to general considerations, we highlight some special considerations by species and sample type

Air versus Water Chilling of Chicken: a Pilot Study of Quality, Shelf-Life, Microbial Ecology, and Economics.

The United States' large-scale poultry meat industry is energy and water intensive, and opportunities may exist to improve sustainability during the broiler chilling process. By USDA regulation, after harvest the internal temperature of the chicken must be reduced to 40°F or less within 16 h to inhibit bacterial growth that would otherwise compromise the safety of the product. This step is accomplished most commonly by water immersion chilling in the United States, while air chilling methods dominate other global markets. A comprehensive understanding of the differences between these chilling methods is lacking. Therefore, we assessed the meat quality, shelf-life, microbial ecology, and techno-economic impacts of chilling methods on chicken broilers in a university meat laboratory setting. We discovered that air chilling methods resulted in superior chicken odor and shelf-life, especially prior to 14 days of dark storage. Moreover, we demonstrated that air chilling resulted in a more diverse microbiome that we hypothesize may delay the dominance of the spoilage organism Pseudomonas Finally, a techno-economic analysis highlighted potential economic advantages to air chilling compared to water chilling in facility locations where water costs are a more significant factor than energy costs.IMPORTANCE As the poultry industry works to become more sustainable and to reduce the volume of food waste, it is critical to consider points in the processing system that can be altered to make the process more efficient. In this study, we demonstrate that the method used during chilling (air versus water chilling) influences the final product microbial community, quality, and physiochemistry. Notably, the use of air chilling appears to delay the bloom of Pseudomonas spp. that are the primary spoilers in packaged meat products. By using air chilling to reduce carcass temperatures instead of water chilling, producers may extend the time until spoilage of the products and, depending on the cost of water in the area, may have economic and sustainability advantages. As a next step, a similar experiment should be done in an industrial setting to confirm these results generated in a small-scale university lab facility

Vacuum Packaging Maintains Fresh Characteristics of Previously Frozen Beef Steaks during Simulated Retail Display

The impact of frozen storage on beef steaks prior to the retail setting may result in changes to the quality and safety of the packaged meat. Therefore, the objective of the current study was to evaluate fresh characteristics on previously frozen steaks during a simulated retail display. Steaks were allocated to one of three packaging treatments (MB, MDF, MFS) and stored frozen (−13 °C) for 25 days in the absence of light. After thawing, steaks were stored in a lighted retail case at 3 °C and evaluated for instrumental surface color, pH, purge loss, lipid oxidation, and microbial spoilage organisms throughout the 25-day fresh display period. There was an increase (p p p < 0.05) throughout the entire display for steaks packaged in MFS and MDF. It is evident that barrier properties of MB limiting oxygen exposure of the steak preserved fresh meat characteristics after frozen storage. Results from the current study suggest that vacuum packaging films can aid in retarding detrimental effects caused by frozen storage after placing the steaks in fresh retail conditions

Inclusion of Beef Heart in Ground Beef Patties Alters Quality Characteristics and Consumer Acceptability as Assessed by the Application of Electronic Nose and Tongue Technology

Consumer purchasing of beef is often driven by the trinity of flavor, palatability, and convenience. Currently, beef patties in the United States are manufactured with fat and lean trimmings derived from skeletal muscles. A reduction in total beef supply may require the use of animal by-product utilization such as variety meats to achieve patty formulations. The current study aimed to assess textural, color, and flavor characteristics in addition to volatile compounds through electronic technology, e-nose and e-tongue, of ground beef patties formulated with beef heart. Ground beef patties were manufactured with 0%, 6%, 12%, or 18% beef heart, with the remainder of the meat block being shoulder clod-derived ground beef. Patties (n = 65/batch/treatment) within each batch (n = 3) with each treatment were randomly allocated to cooked color (n = 17/batch/treatment), Allo–Kramer shear force (AKSF; n = 17/batch/treatment), texture profile analysis (TPA; n = 6/batch/treatment), cooking loss (n = 17/batch/treatment), consumer panel (n = 3/batch/treatment), e-nose (n = 1/batch/treatment), and e-tongue (n = 1/batch/treatment) analysis groups. Patties containing beef heart did not require additional cooking time (p = 0.1325) nor exhibit greater cooking loss (p = 0.0803). Additionally, inclusion rates of beef heart increased hardness (p = 0.0030) and chewiness values (p = 0.0316) in TPA, were internally redder (p = 0.0001), and reduced overall liking by consumer panelists (p = 0.0367). Lastly, patties containing beef heart exhibited greater red-to-brown (p = 0.0003) and hue angle (p = 0.0001) values than control patties. The results suggest that beef heart inclusion does alter ground beef quality characteristics and consumer acceptability

Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops.

In October of 2020, in response to the Coronavirus Disease 2019 (COVID-19) pandemic, our team hosted our first fully online workshop teaching the QIIME 2 microbiome bioinformatics platform. We had 75 enrolled participants who joined from at least 25 different countries on 6 continents, and we had 22 instructors on 4 continents. In the 5-day workshop, participants worked hands-on with a cloud-based shared compute cluster that we deployed for this course. The event was well received, and participants provided feedback and suggestions in a postworkshop questionnaire. In January of 2021, we followed this workshop with a second fully online workshop, incorporating lessons from the first. Here, we present details on the technology and protocols that we used to run these workshops, focusing on the first workshop and then introducing changes made for the second workshop. We discuss what worked well, what didn't work well, and what we plan to do differently in future workshops

Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops

In October of 2020, in response to the Coronavirus Disease 2019 (COVID-19) pandemic, our team hosted our first fully online workshop teaching the QIIME 2 microbiome bioinformatics platform. We had 75 enrolled participants who joined from at least 25 different countries on 6 continents, and we had 22 instructors on 4 continents. In the 5-day workshop, participants worked hands-on with a cloud-based shared compute cluster that we deployed for this course. The event was well received, and participants provided feedback and suggestions in a postworkshop questionnaire. In January of 2021, we followed this workshop with a second fully online workshop, incorporating lessons from the first. Here, we present details on the technology and protocols that we used to run these workshops, focusing on the first workshop and then introducing changes made for the second workshop. We discuss what worked well, what didn’t work well, and what we plan to do differently in future workshops.ISSN:1553-734XISSN:1553-735