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Microbial communities

Spoilage organisms in meat processing plants

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So far, research has mainly focussed on pathogens that are transmitted through food. Much less attention has been paid to spoilage organisms, which are just as important for the food industry. Prof. Dr Michael Gänzle, University of Alberta, is researching microbial communities in meat-processing plants - with new findings that are important for a more sustainable, safer and more reliable food supply for people.

A dish with bacterial swabs is analyzed

Meat products are good sources of nutrients for human consumption but also provide nutrients for bacterial growth, leading to safety and deterioration concerns. Microbial spoilage is a major cause of food waste. In 2019, 77.4 million tonnes of pork, poultry, beef or mutton were discarded and wasted along the food supply chain, including harvesting, processing, storage, shipping, retail display, and customer handling. Specifically, 20% of this waste occurred during the stages of processing and packaging. Global supply chains rely on a long shelf life of products to allow international or even intercontinental distribution. In addition to concerns related to food safety and the contamination of food with pathogens, the food industry is thus concerned about spoilage microbes and their impact on food spoilage. Our current research aims to characterize microbial communities in food processing plants and their contribution to meat spoilage.

How microbes introduced into the processing facility and spoil meat?

Microbial spoilage depends on the contamination of food from raw materials or from microbial communities residing in food processing facilities, often as bacterial biofilms. Prior to slaughter, muscle tissue is essentially sterile. During slaughtering and dressing, meat is contaminated by microorganisms originating from the air, water, workers and the processing environment. Spoilage microbes in fresh meat and meat products typically originate from the processing environment rather than from animals or humans. Common meat spoiling microbes include the psychrotrophic Pseudomonas, Acinetobacter, Staphylococcus, Psychrobacter, lactic acid bacteria, Enterobacteriaceae and clostridia. Depending on the storage conditions, those microorganisms produce enzymes that break down carbohydrates, proteins, lipids, resulting in the development of off-odors, slime production, and discoloration. The microbial communities in facilities that process different commodities, e.g. dairy, produce, or ready-to-eat products, show substantial overlap, again emphasising that the (refrigerated) processing facilities rather than the respective raw materials are a primary source of spoilage microbes.

A Case study: persistent spoilage microbes in a meat processing facility

We are currently working on the characterization of microbial communities in an Albertan meat processing facility, aiming to determine the overlap between isolates from food contact and non-food contact sites at the production facility, meat at the time of processing and at the end of the 3 month vacuum-packaged shelf life. Most past studies on microbial communities in meat processing facilities relied on culture-independent methods and achieved a genus level identification only. We employed a high-throughput culture-based approach to achieve strain-level identification of microbes by genome sequencing. This offers a unique view on the composition of microbial communities at the strain level and allow for an in-depth characterization of physiological and biochemical characteristics of isolates. Genome sequencing has been achieved by Oxford Nanopore platform. By sequencing 96 strains at a time, the platform provides medium-quality genomes to achieve species-level taxonomy information; strain-level identification requires re-sequencing with higher coverage to obtain strain level identification. To date, we have obtained over 2000 isolates from 116 sampling sites during two visits of the meat processing facility, more than 1000 of these are genome-sequenced.

Diversity and Persistence of spoilage microbes

The concept of bacterial strains is interpreted differently, depending on the context. In food micro biology, isolates that were obtained from the same processing facilities in several visits that are several months apart have been considered the same strain when their genomes differ by fewer than 10 – 20 nucleotides. Microbial persistence has been mainly studied among food pathogens, particularly Listeria monocytogenes, which has been shown to persist in some facilities for a period of up to 17 years. Only limited information is available, however, in relation to the persistence of spoilage microbes. Filling this gap is imperative because most foodborne pathogens including Listeria typically have only a limited capability to form biofilms. However, Listeria integrate into biofilms that are formed by persistent spoilage microbes which thus protect the pathogens against routine sanitization measures.

The strains collected in this study revealed a large diversity of microbes, including representatives of most microbes that are relevant for meat spoilage. Strains of Pseudomonas spp. were most frequently isolated; this species is for its proficiency to form biofilm at refrigeration temperature. Whole genome sequencing revealed that microbes on meat originate from the processing facility and persist despite sanitization. Genomic analyses demonstrated that Carnobacterium maltaromaticum persisted over a period of 6 months across sampling sites and time; moreover, the isolates from meat samples are indistinguishable from isolates obtained from floor drains in the carcass cooler room. These floor drains thus appear to serve as a niche for Carnobacterium, which permanently resides there to re-contaminate meat after cleaning and sanitation cycles. A second hot-spot for microbial strains that were also identified on fresh meat and meat after 3 month of storage were post-sanitation samples from packaging equipment. Other spoilage microbes such as Rahnella and Serratia, originated from food-contact and non-food contact environments in the fabrication and packaging area. This underscores the necessity for a site-specific cleaning and sanitization strategies.

Biofilm formation and Microbial interactions

The ability of bacteria to form biofilms contributes to their persistence within the processing facility and thus increases the risk of products spoilage but also may allow pathogenic microbes, particularly L. monocytogenes to persist. In meat processing facilities, the operation temperature is usually maintained at around 4°C. Most literature data on biofilm formation, however, grow single-species or dual-species biofilms at temperatures of 10°C or higher. We have reconstituted microbial communities from 10 sampling sites to determine their ability to form biofilms on food-graded stainless steel coupons at 4°C and 25°C. The biofilm communities consisted of up to 12 different bacterial strains, few of which dominated the biofilm communities with others persisting with low abundance. The multi-species communities formed denser biofilms at 4°C than at 25°C. These isolates have adapted to the low-temperature that is maintained in processing environments and during distribution and storage of the products. Carnobacterium and Enterobacteriaceae, which are predominant in spoiled vacuum-packaged meats, synergistically co-exist with other species from genera such as Pseudomonas, Flavobacterium and Brochothrix.

Research for a Sustainable, Safe and Secure Food Supply

Research has predominantly been directed towards foodborne pathogens while spoilage microorganisms, which are of equal concern to the food industry, have received much less attention. However, in food processing environments, pathogens and spoilage microbes coexist and interact synergistically or antagonistically, leading to complex challenges. Improved control of food spoilage and reduced food waste also contributes to a more sustainable food system. Extending the shelf life of food products also increases the affordability of food, thereby enhancing access to high quality and nutritious food by food-insecure populations. An improved understanding and control of microbial communities in food processing facilities is thus deeply consequential for current efforts to achieve a more sustainable, safe and secure food supply. Is the food industry on the right path? Current food processing equipment documents that the food industry operates at a remarkably high standard of hygienic design. However, the microbial communities in about 40% of food processing facilities still include L. monocytogenes: Much work remains to be done, both by academia and by industry.

Prof. Dr. Michael Gänzle

Prof. Dr. Michael Gänzle


Shaelyn Xu and Michael G. Gänzle
University of Alberta, Dept. of Agricultural Food and Nutritional Science,
Edmonton, Alberta, Canada.