Caister Academic Press

Food Microbiology

Recommended reading:   Climate Change and Microbial Ecology | Polymerase Chain Reaction | SUMOylation and Ubiquitination
A review of Food Microbiology.

Food Microbiology

Adapted from Pina M. Fratamico and Darrell O. Bayles in Foodborne Pathogens: Microbiology and Molecular Biology
Food Microbiology: Microbiological analysis is important to determine the safety and quality of food. For many years, detection and identification of microorganisms in foods, animal feces, and environmental samples have relied on cultural techniques regarded as the "gold standard". Conventional methods are labor intensive, time consuming, and costly, and advances in these methods have been limited to the development of instruments such as the Stomacher or Pulsifier for sample processing, improved liquid and selective/differential agar media, instruments for plating and counting bacteria, and identification test kits. More recently, advances in biotechnology have led to the development of "rapid methods" that minimize manipulation, provide results in less time, and reduce cost. Rapid methods generally include immuno-based and DNA-based assays. Immunological or antibody-based assays include enzyme linked-immunosorbent assays (ELISA) and immunochromatographic or "dipstick" assays. Genetic methods include the polymerase chain reaction (PCR), DNA hybridization, and DNA microarrays, also known as GeneChips.

There is a zero tolerance policy for Listeria monocytogenes in ready-to-eat products and for Escherichia coli O157:H7 in non-intact fresh beef products; thus, appropriate methods must have the ability to detect one colony forming unit in the sample being analyzed after enrichment culturing. Regardless of the technology employed, food analysis remains a challenging task Problems that complicate pathogen detection include: (1) non-uniform distribution of pathogens in the food, thus the sample analyzed may not be representative of the entire lot; (2) low level of the target pathogen compared to that of the indigenous microbiota, which may be present at levels as high as 108 CFU/g in raw products; (3) heterogeneity of food matrices and food components interfering with growth or detection of the target organism; and (4) inability to recover injured target organisms using selective enrichment media.

One of the exciting developments in food microbiology has been the availability and application of molecular analyses that have allowed scientists to address microbial food safety questions beyond merely determining whether particular pathogens are in a food. Such global analyses are allowing scientists to ask deeper questions regarding food-borne pathogens and are currently leading the way to ascertaining the genes, proteins, networks, and cellular mechanisms that determine the persistence of strains in foods and other environments, determine why certain strains are more commonly isolated from foods, and determine why certain strains are more pathogenic. Such molecular tools are also making it possible to more fully determine the microflora present in foods along with pathogens, and to assess the effect that the food microbiota has on the death, survival, and pathogenicity of food borne pathogens. As the application of molecular analyses improves our understanding of the responses of pathogens to foods and food environments, we anticipate that the information will lead to the development of more specific detection tests, will lead to the enhancement of current interventions, and will lead to the development of new interventions.


The genus Clostridium represents a heterogeneous group of anaerobic spore-forming bacteria, comprising prominent toxin-producing species, such as C. difficile, C. botulinum, C. tetani and C. perfringens, in addition to well-known non-pathogens like solventogenic C. acetobutylicum. In the last decade several clostridial genomes have been deciphered and post-genomic studies are currently underway. The advent of newly developed, genetic manipulation tools have permitted functional-based and systems biology analyses of several clostridial strains. Research in this area is at a very exciting stage.
Suggested reading: Clostridia: Molecular Biology in the Post-genomic Era

Salmonella enterica

Secreted proteins are of major importance for the pathogenesis of infectious diseases caused by the facultative intracellular gastrointestinal pathogen Salmonella enterica. A remarkable large number of fimbrial and non-fimbrial adhesins are present in Salmonella and mediate biofilm formation as well as the intimate contact to host cells. The host cell invasion and intracellular proliferation are two hallmarks of Salmonella pathogenesis. Salmonella deploys two type III secretion systems (T3SS) to translocate complex cocktails of effector proteins. Effectors translocated by the Salmonella Pathogenicity Island 1 (SPI1)-T3SS mainly act on the host cell actin cytoskeleton resulting in the invasion of non-phagocytic cells. After entry, Salmonella resides in the so-called Salmonella-containing vacuole, from which translocation of a second set of effector proteins by the SPI2-T3SS initiated. The function of the SPI2-T3SS results intracellular replication and the modification of host cell vesicular traffic involving microtubules. Although classical exotoxins are not known as major virulence determinants of Salmonella, recent data suggest a role of toxins encoded by the Salmonella virulence plasmid. The concerted action of various secreted proteins allows Salmonella to breach multiple barriers of host defense resulting in systemic infection and be development of a carrier state in some infected individuals.
Suggested reading: Bacterial Secreted Proteins   Pili and Flagella


Campylobacter jejuni is an important cause of human food-borne gastroenteritis that frequently colonizes poultry and contaminates their products. The high incidence of clinical disease associated with this bacterium, its low infective dose in humans and its potentially serious sequelae confirm its importance as a major public health hazard. Despite the medical and economic importance of C. jejuni infection, fundamental aspects of the patho-physiology of colonization and infection remain poorly understood. Here, we present an overview of protein secretion in C. jejuni and discuss the contribution of protein secretion systems to the pathogenesis and lifestyle of this bacterium. Both Sec dependent and TAT secretion systems are present. Of the protein secretion pathways that are widely disseminated among Gram-negative bacteria, only the type V (autotransporter) and a plasmid-encoded type IV-secretion system have been reported in C. jejuni. A type II-like system involved in natural competence, a functional flagella export apparatus and an uncharacterized system mediating cytolethal distending toxin secretion are also discussed.
Suggested reading: Bacterial Secreted Proteins

Listeria monocytogenes

As a monoderm prokaryote, protein secretion systems in Listeria monocytogenes are distinct from those encounter in diderm bacteria, still they remain the gates for expressing protein functions outside the intracellular bacterial cell compartment. Despite the fact that protein secretion is a key factor in virulence of a pathogen, fewer studies have been dedicated to pathogenic Gram-positive bacteria compared to Gram-negative bacteria and L. monocytogenes is no exception. Among the six protein secretion systems identified in L. monocytogenes, only proteins putatively translocated via the Sec pathway are indisputably involved in bacterial virulence. The 16 secreted virulence effectors characterised to date are either (i) associated with the cytoplasmic membrane, i.e. as integral membrane proteins or lipoproteins, (ii) associated with the cell wall, i.e. covalently in a sortase-dependent manner or via cell-wall binding domains, or (iii) released in the extracellular milieu. Identification of several candidates as putative secreted virulence factors as well as the availability in the near future of large amount of Listeria genomic data from different sequencing projects are the promess of very exciting time in the field of listerial protein secretion and should provide further insights on how L. monocytogenes interacts with its biotic or abiotic surroundings.
Suggested reading: Bacterial Secreted Proteins

Vibrio cholerae

The Gram-negative bacterium Vibrio cholerae produces both surface-exposed and secreted factors essential for both its survival and growth in the environment and for induction of the diarrheal disease cholera. Surface-exposed factors include three different Type IV pili that mediate persistence in the intestine as well as surface colonization in the environment. In addition, these pili contribute to the evolution of the pathogen by serving as phage receptors or as a structure essential for DNA uptake. Secreted factors associated with disease include the major virulence factor Cholera Toxin (CT) that is responsible for the severe diarrhea associated with cholera disease. Additional secreted toxins, including hemolysin, hemagglutinin/protease, MARTXVc, and Type III and Type VI effectors, have also been found to function in virulence and may significantly contribute to disease of non-CT producing non-O1/non-O139 strains. Export of some virulence factors is interconnected through signal pathways and secretion machineries with other secreted enzymes such as chitinases that are important for survival in the environment. Thus, V. cholerae seems to have efficiently evolved to adapt to both intestinal and aquatic environments and utilizes secreted factors to modulate the environment to promote its own growth, survival, and dissemination.
Suggested reading: Bacterial Secreted Proteins   Vibrio cholerae: Genomics and Molecular Biology


The aspergilli are a fascinating group of fungi exhibiting immense ecological and metabolic diversity. These include notorious pathogens such as Aspergillus flavus, which produces aflatoxin, one of the most potent, naturally occurring, compounds known to man.
Suggested reading: Aspergillus: Molecular Biology and Genomics

Microbial toxins

Toxins are important virulence determinants responsible for microbial pathogenicity and/or evasion of the host immune response.
Suggested reading: Microbial Toxins: Current Research and Future Trends

Food Microbiology Resources

Foodborne Pathogens: Microbiology and Molecular Biology
Bacillus cereus
Emerging foodborne pathogens
Listeria monocytogenes
Staphylococcus aureus
Vibrio spp.
Yersinia enterocolitica
Foodborne pathogens
Current Issues in Molecular Biology

Further reading