Foodomics and Microbiological Risk Assessment of Food

Bruno Tilocca, Nicola Costanzo, and Paola Roncada, Department of Health Science, University “Magna Græcia” of Catanzaro,
Catanzaro, Italy
© 2020 Elsevier Inc. All rights reserved.

Microbiological Risk Assessment of Food 1

MRA Assessment in the “Pre-omics” Era 3
Omics Technologies in the MRA of Food 3
Genomics 4
Transcriptomics 4
Proteomics 4
Metabolomics 4
Bioinformatic Data Analysis 5
Integration of Omics Disciplines in Food Science: The Foodomics Approach 5
References 6

Microbiological Risk Assessment of Food

Microbiological risk assessment (MRA) of food is an important tool employed by both food industries and administrative bodies to
ensure food safety and delineate adequate management practices (Martinovic and Nisic, 2019; Notermans et al., 2002). The primary
objective of the microbiological risk assessment in food is the definition of the likelihood of a food-born pathogen to provoke
illness in humans following the consumption of a given food product. When applicable, MRA aims at defining whether a minimal
amount has to be consumed until being considered as health-threatening for consumers (Forsythe, 2007; Martinovic and Nisic,
2019). Moreover, MRA attempts to investigate and identify strategies (e.g. throughout the “farm to fork” chain) to decrease the level
of health risk (i.e. risk mitigation) by reducing the food-borne disease incidence and/or by reducing the severity of the potential
disease (Forsythe, 2007).
Foodborne pathogens are microorganisms (both prokaryotic and eukaryotic) featured by a varied affinity for diverse food prod-
ucts and characteristic incubation periods (Forsythe, 2008; Giacometti and Josic, 2013). Table 1 lists the most common food-borne
pathogen along with their microbiological features.
Pathogenic bacteria such as Escherichia coli, Salmonella spp., Campylobacter spp. and some Bacillus strains colonization repre-
sent the greatest issue for fresh products (Forsythe, 2008; Giacometti and Josic, 2013). On the other hand, foodborne pathogens
such as Listeria monocytogenes and some fungal strains are the major concern for processed and long-term storage foods (Forsythe,
2007, 2008). Viruses and prions are also important infective agents and, especially in the food of animal origin, represent an impor-
tant threat for the consumers health (Bari and Yeasmin, 2018; Bhunia, 2008; Gaso-Sokac et al., 2010). Foodborne viruses such as
rotavirus, norovirus and hepatitis-A virus are responsible for severe enteric diseases characterized by gastroenteric symptoms often
associated with the insurgence of secondary complications (Bhunia, 2008; D’Agostino and Cook, 2015; Giacometti and Josic,
2013). Consumption of meat contaminated with misfolded prion proteins is among the major routes for the transmission of Trans-
missible Spongiform Encephalopathies (TSE) (Holznagel et al., 2015). Here, the transmission via food is facilitated by the great
resistance of the infective protein to heat and the protease activity resulting in an ease of transmission of the disease among animals
and between animals to humans (Holznagel et al., 2015).
Virulence factors of foodborne pathogens are diverse as well as the etiopathogenetic mechanisms undertaken, eliciting a wide
spectrum of disorders and symptoms (Forsythe, 2008; Giacometti and Josic, 2013). These represent an important burden for the
health system and, in the case of acute infections, are related to an increased mortality ratio especially among elderly and immu-
nocompromized consumers (Forsythe, 2007, 2008). Besides the common virulence factors, many microorganisms produce
extracellular polymeric substances (mainly glycoproteins and polysaccharides) facilitating their adhesion to abiotic surfaces
and/or attachment to the surface of other microorganisms. This results in the formation of the biofilm that confers protection
against the most commonly adopted antimicrobial practices (e.g. UV radiation, desiccation, osmotic shock, pH change) other
than enabling bacteria to persist to cleaners, sanitizers and antimicrobial treatments (Bridier et al., 2011; Flemming and Wing-
ender, 2010).
Depending on the poisoning way, foodborne pathogens are distinguished either as infective or toxigenic agents (Forsythe, 2008).
The former class includes highly invasive microorganisms capable of an active replication within the gastrointestinal tract and even-
tual dissemination at a systemic level in the host body (e.g. Salmonella spp., Escherichia coli, Campylobacter jejuni etc) (Forsythe, 2007,
2008). The second class of pathogens includes the microorganisms that provoke food poisoning by means of toxins. The toxins may
be either endotoxins (i.e. structural component of the pathogen cell) or exotoxins (i.e. secondary metabolites products excreted out
of the pathogen cell) (Forsythe, 2008; Freimoser et al., 2019; Richard, 2007). Toxigenic agents such as Clostridium botulinum,
Bacillus cereus, Fusarium spp. and Aspergillus spp. and are capable of toxins production during the intestinal transition and/or

Reference Module in Food Sciences https://doi.org/10.1016/B978-0-08-100596-5.22833-3 1

2 Foodomics and Microbiological Risk Assessment of Food

Table 1 Foodborne pathogens commonly isolated from food

Pathogen Food product Incubation period Duration of illness

C. jejuni Fruits & vegetables 3–5 days 2–10 days

Milk, cheese, dairy products
Raw chicken and Turkey
Salmonella spp. Raw poultry meat 16–72 h 2–7 days
Raw pork meat
Eggs
Shell fish
Fruits & vegetables
Milk, cheese, dairy products
Cereals, grains, legumes and nuts
Herbs and spices
S. aureus Raw chicken, pork, beef 2–4 h 24–48 h
Fruits & vegetables
Milk, cheese, dairy products
Cereals, grains, legumes and nuts
Herbs and spices
L. monocytogenes Milk, cheese, dairy products 3–70 days Variable
Fruits & vegetables
Red meat
Cereals, grains, legumes and nuts
C. perfrigens Raw pork and chicken 6–24 h 2–14 days
Milk, cheese, dairy products
Herbs and spices
C. botulinum Raw seafood and food products 6–24 h 2–14 days
Raw pork and chicken
Fruits & vegetables
Cereals, grains, legumes and nuts
Herbs and spices
B. cereus Cooked meat 8–12 h 1–2 days
Fruits & vegetables
Milk, cheese, dairy products
Ice cream
Raw seafood and food products
Fruits & vegetables
Cereals, grains, legumes and nuts
Herbs and spices
Y. enterocolitica Raw pork 3–7 days 1–3 weeks
Fruits & vegetables
Milk, cheese, dairy products
Raw seafood and food products
Hepatitis-A virus Raw pork 3–60 days 2–4 weeks
Fruits & vegetables
Milk, cheese, dairy products
Raw seafood and food products
Shighella spp. Fruits & vegetables 16–72 h 2–7 days
Milk, cheese, dairy products
Raw seafood and food products
Cereals, grains, legumes and nuts
E. coli Raw beef, pork, poultry 16–120 h 2–12 days
Fruits & vegetables
Milk, cheese, dairy products
Raw seafood and food products
Cereals, grains, legumes and nuts
Eromonas hydrophila Fruits and vegetables – 1–7 days
Mycotoxin producing fungi Meat 3–7 days Variable
(Aspergillus spp., Fusarium spp., Penicillum spp.) Fruits & vegetables
Milk, cheese, dairy products
Cereals, grains, legumes and nuts
Herbs and spices
Vibrio spp. Raw seafood and food products – –
G. lamblia Water – –
Raw seafood and food products
Fruits & vegetables
Algae Raw seafood and food products – –
 Foodomics and Microbiological Risk Assessment of Food 3

directly in the food during its production and storage (Forsythe, 2008; Freimoser et al., 2019; Tilocca et al., 2019). Toxins may lead
to acute symptoms but are more prone to chronic long-term effects such as teratogenicity, hepatotoxicity, nephrotoxicity and immu-
notoxicity, most likely due to the accumulation of toxins over time (Giacometti et al., 2013; Martinovic et al., 2016).

MRA Assessment in the “Pre-omics” Era

In light of the above harmful effects, several efforts have been made since past times to assess the presence of foodborne pathogens in
the edible products (Priyanka et al., 2016). The ideal detection method for foodborne pathogens, like all other diagnostic methods, is
featured by high specificity and sensitivity. It should be rapid (minutes to hours to obtain a reliable result), easy to perform (no special
skills required) and cost-effective, enabling its spread to all food products (Priyanka et al., 2016). Traditional approaches in food
microbiology risk assessment rely on the survey of the finished food products by means of growing, in pure culture, the microorgan-
isms known to be responsible for food spoilage and/or the insurgence of foodborne disease outbreaks (Hirvonen et al., 2012; Tan
et al., 2014). Nevertheless, the microbiological culture of each foodborne pathogen is rather time-consuming and resulted soon
impracticable in a routine laboratory. To overcome this issue, specific microbial groups and microbial species were conventionally
designed as “indicator” of foodborne pathogen contaminated food and/or improperly treated food product (Fakruddin et al.,
2013; Ramamurthy et al., 2014). Eventual presence of the indicator microorganisms might be numerically evaluated to provide
a measure of the microbial risk and a rough clue of the food quality (Fakruddin et al., 2013; Priyanka et al., 2016; Ramamurthy
et al., 2014). However, this approach suffers from a reduced accuracy and reproducibility due to the intrinsic biases of the employed
method (e.g. bacterial cultivability) other than lacking to consider the uneven distribution of the foodborne pathogens both in spatial
and quantitative terms (Priyanka et al., 2016). Indeed, the reduced abundance of the target pathogen in the food product, or within the
sampled portion, makes its culture inefficient for accurate detection, underestimating the microbiological risk.
The use of immunoassays guarantees faster results in a more reproducible and cost-effective manner when compared to culture-
based techniques (Leach et al., 2010; Priyanka et al., 2016). Among antibody-based methods, ELISA is certainly the most adopted
one while assessing the microbiological risk of food. Here, the antibody-antigen binding affinity is exploited to detect and reveal the
eventual presence of the pathogen; thus, the purity and specificity of the antibody employed are of paramount importance for the
result of the microbiological survey. Antigenically related species (e.g. Brucella abortus, Yersinia enterocolitica, Escherichia coli
O157:H7) may give rise to cross-reactions, resulting in a lack of sensitivity and specificity of the test and/or yield of false-
positive results (Leach et al., 2010).
Analogously to immunoassays, PCR-based methods are also a good alternative to culture-based methods providing results as
fast as 30 min and, when appropriate primer and probes sequences are employed, a clear distinction of microorganisms up to strain
level can be achieved. In addition, the detection limit of the method might be as low as femtograms resulting in a great practicability
in both industrial control plans and food safety laboratories (Palka-Santini et al., 2009; Priyanka et al., 2016; Radhika et al., 2014).
Nevertheless, the protocols for cell lysis and nucleic acid extraction have shown variable efficacy depending on the microbiological
and morphological properties of the target microorganisms, as well as the variable number of copies of the target DNA affect the fair
identification and quantitation of the foodborne pathogens (Tröscher-Mußotter et al., 2019). Moreover, acknowledged the high
sensitivity of this methods, it has been reported that even a low number of exogenous molecules inhibiting or competing with
the DNA amplification might lead to affected results or even a failure of the pathogen detection. Contrarywise, contamination
with DNA fragments can also result in the provision of false-positive information (Leach et al., 2010; Priyanka et al., 2016). It is
therefore crucial the choice of highly specific primers/probe sequences along with an optimized protocol of DNA extraction and
amplification.

Omics Technologies in the MRA of Food

The technological progress of the last two decades has marked a profound change in the methods and techniques adopted for the
microbiological identification and characterization, providing a powerful tool capable of addressing the challenges occurred with
the use of the so-called “pre-omics technologies”. Omics technologies such as genomics, transcriptomics, proteomics and metab-
olomics enable a comprehensive understanding of the microorganism’s behavior in the diverse environments (i.e. food matrices),
clarify how their biology is shaped by the various technological processes and/or the compresence of other microorganisms, besides
enabling the “unbiased” identification and quantitation of microorganisms, including eventual foodborne pathogens (Cifuentes,
2012; León et al., 2018; Martinovic and Nisic, 2019). Nevertheless, setting up an omics-based investigation is rather complex and
the integration of multiple omics discipline is required for a comprehensive depiction of the MRA and suggest adequate interven-
tion strategies (León et al., 2018).
While performing an omics-based investigation of any food product, the first key step is represented by the sampling strategy. It
varies depending on the food product (e.g. texture, size etc.) and must take into account the uneven distribution of the microor-
ganisms over the space (León et al., 2018; Tilocca et al., 2020). As a general rule, the sampled portion should be representative
of the whole food product and must, ideally, consider all the microbial biodiversity harbored (Tilocca et al., 2020). Importantly,
the sampling procedure must also consider the natural variability occurring between different batches of the same food product;
thus, an adequate number of biological replicates have to be preventively estimated.
4 Foodomics and Microbiological Risk Assessment of Food

Another crucial step in the omics-based analysis is represented by the design of an optimal sample preparation protocol that
“clean” the sample out of the wide array of molecules interfering with the downstream processes expected by any of the above-
mentioned omics disciplines. In this view, the sample preparation protocol is strictly dependent by the physicochemical composi-
tion of the studied food product and point to prevent the loss of the microbial fraction along with the undesired molecules (Seifert
et al., 2013). When applicable, sample homogenization is generally the starting point followed by the administration of buffers and
chemicals compatible with the subsequent analytical steps (León et al., 2018; Putignani and Dallapiccola, 2016).
Sampling and sample preparation steps are common to all omics disciplines and, once yielded the microbial fraction in a “clean”
version, it is subjected to different procedures typical of each omics discipline.

Genomics
Genomics (or metagenomics when referred to microbial communities) investigation aims to provide accurate identification of the
pathogens and commensals microorganisms up to strain level (Bergholz et al., 2014). Moreover, it elucidates the potential virulence
and antibiotic resistance traits of the microorganisms(s), other than providing precious information on the origin and transmission
of foodborne diseases (Bergholz et al., 2014; Giacometti and Josic, 2013; León et al., 2018).
The microbial fraction is subjected to a first step of DNA extraction. It can be accomplished by means of “manual” in house proto-
cols, but the use of commercial kits is to date preferred, acknowledged the high standardization and reproducibility rate ensured,
other than enabling analysis in a time-effective manner (Tilocca et al., 2020). Regardless the approach employed, extracted DNA is
subsequently sequenced by means of next-generation sequencing (NGS) platforms, among which 454 Roche pyrosequencing,
SOLiD, and Illumina sequencing by synthesis are the most frequently adopted ones. Sequencing results are released as raw files
that are finally subjected to the bioinformatic data analysis to yield the genome(s) sequences (Thomas et al., 2014).

Transcriptomics
Transcriptomics is an emerging discipline aimed at providing information about gene dynamics. It is intended as the definition of
the genetic elements activated by given microorganisms at the condition of sampling, out of the whole genetic potential. Analo-
gously to genomics, advanced transcriptomics technology is based on the sequencing by means of NGS platforms. Nevertheless,
the target of the sequencing technology is the cDNA obtained by the reverse transcription of the microbial RNA. As for genomics
studies, RNA extraction might be accomplished by means of lab-assembled protocols or through the use of commercial kits.
Extracted RNA is then retrotranscribed into cDNA prior to being subjected to the NGS protocols and bioinformatic data analysis
as expected for the genomic DNA (Wang et al., 2009).

Proteomics
Acknowledged the great importance of genomics and transcriptomics, these technologies are not capable of providing information
on the effective metabolic function being performed by given microorganisms. Genomics and transcriptomics refer to the potential
and active genetic elements respectively but do not take into account the endogenous regulatory mechanisms such as mRNA degra-
dation (total or partial), allosteric changes in mRNA, variable rate of protein translation and possible post-translational modifica-
tion. In this view, proteomics provides the most realistic picture of the ongoing functional array for each microorganism or
microbial community (Andjelkovic et al., 2017; Andjelkovic and Josic, 2018).
General bottom-up proteomics analysis of the food-derived microbial fraction expects a first extraction and purification of the
protein array. Unlike nucleic acid extraction, no commercial kits have been so far validated for a standardized and reproducible
extraction of the proteins; thus, lab-assembled protocols must be optimized with the aim to maximize the protein recovery and
reduce interference arising by other endogenous molecules such as lipids, waxes and nucleic acids (Andjelkovic and Josic,
2018). Extracted proteins are then subjected to denaturation, reduction and alkylation. Denaturation is commonly accomplished
by using physical (heat), chemicals (e.g. SDS) or a combination of both methods. Reduction of the intra- and inter-molecular inter-
actions occurs via the addition of DTT whereas the alkylation (carbamidomethylation) prevent the restoration of the reduced S-
bonds. Linearized proteins are finally digested to peptides through incubation with sequence-specific proteases (typically trypsin)
before being purified and measured at the mass spectrometer. Results are released as raw files that are subjected to bioinformatics
data analysis to yield the sequences of the measured proteins (Ferranti et al., 2016).

Metabolomics
Metabolomics aims to target the overall array of microbial metabolites, enabling their link back to the ongoing biological processes
and integrating the proteomics information (Bayram and Göklrmakll, 2018). Similarly, to proteomes and transcriptomes, metab-
olomes are highly dynamic over the time and their study might provide precious information on the metabolic status of food-
associated microorganisms under diverse circumstances, e.g. in response to industrial processes and/or sanitizing procedures
(Cifuentes, 2012; León et al., 2018). Analogously to proteomics, metabolomics studies make use of the high-sensitive mass spec-
trometers, even though metabolites analysis by means of nuclear magnetic resonance is also common.
 Foodomics and Microbiological Risk Assessment of Food 5

Bioinformatic Data Analysis

The progress in the field of NGS and mass spectrometry have strongly benefitted the investigations performed through the
use of omics sciences. Nevertheless, it also resulted in the production of an enormous amount of data, which treatment
and integration require strong computational efforts and skilled personnel (León et al., 2018). A steadily increasing number
of software and algorithms is nowadays available to help researchers dealing with this huge amount of data and extrapolate
as much information as possible, especially by integrating the complementary omics disciplines (García-Alcalde et al., 2011;
Valdés et al., 2017). Following the application of different criteria and statistics thresholds, bioinformatic tools enable taxo-
nomic and putative functional annotation of the genomic/transcriptomic sequences as well as the functional annotation
and ontology to the protein sequences. In addition, networking of all this heterogeneous information is being supported
to help researchers understanding and drawing a comprehensive depiction of the microbial behavior; thus, suggest inter-
vention strategy aimed to ensure food safety and/or quality (León et al., 2018; Putignani and Dallapiccola, 2016). Never-
theless, the difficulty (sometimes lack) of obtaining complete strain-specific genomes represent a big issue, especially for
transcriptomics and proteomics investigations whose bioinformatics data analysis is, to date, completely dependent on
the quality and availability of genome sequences to be used as a reference (León et al., 2018). Anyhow, the number of
complete reference genomes is rapidly increasing and research to prevent the total dependency of proteomics from the
genomics sequence availability is currently ongoing.

Integration of Omics Disciplines in Food Science: The Foodomics Approach

Integration of the “classical” omics sciences with other novel omics-based disciplines such as nutrigenomics, nutritranscriptom-
ics, nutriproteomics, nutrimetabolomics and epigenomics is the constitutive characteristic of foodomics, an emerging concept
aiming at investigating the heterogeneous array of compounds of any food product, including the associated biological systems,
and its relation with the host body (Bayram and Göklrmakll, 2018; Cifuentes, 2012; Giacometti and Josic, 2013; León et al.,
2018). In this view, the foodomics investigation covers all facets of the food science ranging from matters of traditional concern
such as food safety, quality and traceability to the newest frontiers of food sciences like nutraceutical properties of food compo-
nents and design of functional diets to positively stimulate the human gut microbiota (Putignani and Dallapiccola, 2016). With
regard to the food safety assessment, foodomics make use of genomics to assess the eventual presence of any foodborne pathogen
by targeting its genome or selected strain-specific sequences (e.g. 16S rRNA gene for prokaryotes). Alternatively, the search for
foodborne pathogens might also be performed by targeting the genetic elements of virulence and/or antibiotic resistance, but
less accurate taxonomical information is yielded with the latter approach (Allard et al., 2018; Kim et al., 2018). The contribute
of transcriptomics while assessing food safety is mostly related to the comparative evaluation of the gene expression profile of
foodborne pathogens, and how it changes in response to adverse treatment (e.g. thermal treatment of food, use of disinfectants
etc.). Recent studies have also made use of transcriptomics to assess the metabolic pathway leading to mycotoxin production and
evaluate plausible counterbalancing measures. In addition, comparative studies between pathogenic and non-pathogenic strains
of Listeria strains have been performed, underlining significant differences in their expression profile (Fox et al., 2011; León et al.,
2018; Wurtzel et al., 2012).
Proteomics-based information oriented to food safety is also of extreme importance. In this view, the use of MALDI Biotyper
enables rapid and unbiased detection of the microorganisms, along with the discrimination among taxonomically related
strains (Andjelkovic and Josic, 2018). A further contribute provided by proteomics in food MRA relies on the ability to
identify prototypical proteins of foodborne pathogens, other than the possibility to target bacterial and fungal toxins produc-
tion. Moreover, the detection of post-translational modification and bioactive peptides is of paramount importance for the
detection of allergenic proteins; a filed having a steadily increasing interest in the context of preserving the consumer’s health
(Andjelkovic et al., 2017).
Analogously to the other omics sciences, also metabolomics provides an important contribution to food safety especially
in what concerns the detection of toxin contamination of food and the toxin contamination surveillance throughout the
whole production process (Bayram and Göklrmakll, 2018). Microbial safety of food is only one of the several aspects
of food science and further contributes/information are provided by this and the other disciplines, especially when consid-
ered as a unique integrated approach. Moreover, the integrative approach gives further robustness to the single disciplines
by supporting/validating their data and expanding the knowledge provided. On the other hand, integration of multi-omics
technologies has to face several technical challenges, the major of which is the reduced annotation of the biological data-
bases. Availability of a complete and exhaustively annotated reference database would greatly benefit the omics data inte-
gration both within the individual investigation but also among investigations from diverse laboratories. This would also
facilitate and speed up the complex process of biological interpretation of the results (Ebbels and Cavill, 2009; Rajasun-
daram and Selbig, 2016). Due to these challenges, a limited number of integrative multi-omics studies have been so far
performed. Nevertheless, big efforts are being performed in this context and we are confident in a breakthrough in the
near future.
6 Foodomics and Microbiological Risk Assessment of Food

References

Allard, M.W., Bell, R., Ferreira, C.M., Gonzalez-Escalona, N., Hoffmann, M., Muruvanda, T., et al., 2018. Genomics of foodborne pathogens for microbial food safety. Curr. Opin.
Biotechnol. 49, 224–229. https://doi.org/10.1016/j.copbio.2017.11.002.
Andjelkovic, U., Gajdosik, M.S., Gaso-Sokac, D., Martinovic, T., Josic, D., 2017. Foodomics and food safety: where we are. Food Technol. Biotechnol. 55, 290–307. https://doi.org/
10.17113/ftb.55.03.17.5044.
Andjelkovic, U., Josic, D., 2018. Mass spectrometry based proteomics as foodomics tool in research and assurance of food quality and safety. Trends Food Sci. Technol. 77, 100–
119. https://doi.org/10.1016/j.tifs.2018.04.008.
Bari, M.L., Yeasmin, S., 2018. Foodborne diseases and responsible agents. In: Food Safety and Preservation. https://doi.org/10.1016/b978-0-12-814956-0.00008-1.
Bayram, M., Göklrmakll, Ç., 2018. Horizon scanning: how will metabolomics applications transform food science, bioengineering, and medical innovation in the current era of
foodomics? OMICS 22, 177–183. https://doi.org/10.1089/omi.2017.0203.
Bergholz, T.M., Moreno Switt, A.I., Wiedmann, M., 2014. Omics approaches in food safety: fulfilling the promise? Trends Microbiol. 22, 275–281. https://doi.org/10.1016/
j.tim.2014.01.006.
Bhunia, A.K., 2008. Foodborne Microbial Pathogens: Mechanisms and Pathogenesis. https://doi.org/10.1007/978-0-387-74537-4.
Bridier, A., Briandet, R., Thomas, V., Dubois-Brissonnet, F., 2011. Resistance of bacterial biofilms to disinfectants: a review. Biofouling 27, 1017–1032. https://doi.org/10.1080/
08927014.2011.626899.
Cifuentes, A., 2012. Food analysis: present, future, and foodomics. ISRN Anal. Chem. 2012, 801607. https://doi.org/10.5402/2012/801607.
D’Agostino, M., Cook, N., 2015. Foodborne pathogens. In: Encyclopedia of Food and Health. https://doi.org/10.1016/B978-0-12-384947-2.00326-3.
Ebbels, T.M.D., Cavill, R., 2009. Bioinformatic methods in NMR-based metabolic profiling. Prog. Nucl. Magn. Reson. Spectrosc. 55, 361–374. https://doi.org/10.1016/
j.pnmrs.2009.07.003.
Fakruddin, M., Mannan, K.S.B., Andrews, S., 2013. Viable but nonculturable bacteria: food safety and public health perspective. ISRN Microbiol. 2013, 703813. https://doi.org/
10.1155/2013/703813.
Ferranti, P., Roncada, P., Scaloni, A., 2016. Foodomics – novel insights in food and nutrition domains. J. Proteom. 147, 1–2. https://doi.org/10.1016/j.jprot.2016.07.016.
Flemming, H.C., Wingender, J., 2010. The biofilm matrix. Nat. Rev. Microbiol. 8, 623–633. https://doi.org/10.1038/nrmicro2415.
Forsythe, S.J., 2007. The Microbiology of Safe Food. https://doi.org/10.1002/9780470999431.
Forsythe, S.J., 2008. The Microbiological Risk Assessment of Food. John Wiley & Sons.
Fox, E.M., Leonard, N., Jordan, K., 2011. Physiological and transcriptional characterization of persistent and nonpersistent Listeria monocytogenes isolates. Appl. Environ. Microbiol.
77, 6559–6569. https://doi.org/10.1128/AEM.05529-11.
Freimoser, F.M., Rueda-Mejia, M.P., Tilocca, B., Migheli, Q., 2019. Biocontrol yeasts: mechanisms and applications. World J. Microbiol. Biotechnol. 35, 154. https://doi.org/
10.1007/s11274-019-2728-4.
García-Alcalde, F., García-López, F., Dopazo, J., Conesa, A., 2011. Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data. Bioinformatics
27, 137–139. https://doi.org/10.1093/bioinformatics/btq594.
Gaso-Sokac, D., Kovac, S., Josic, D., 2010. Application of proteomics in food technology and food biotechnology: process development, quality control and product safety. Food
Technol. Biotechnol. 48, 284–295.
Giacometti, J., Josic, D., 2013. Foodomics in microbial safety. Trac. Trends Anal. Chem. 52, 16–22. https://doi.org/10.1016/j.trac.2013.09.003.
Giacometti, J., Tomljanovic, A.B., Josic, D., 2013. Application of proteomics and metabolomics for investigation of food toxins. Food Res. Int. 54, 1042–1051. https://doi.org/
10.1016/j.foodres.2012.10.019.
Hirvonen, J.J., Siitonen, A., Kaukoranta, S.S., 2012. Usability and performance of CHROMagar STEC medium in detection of Shiga toxin-producing Escherichia coli strains. J. Clin.
Microbiol. 50, 3586–3590. https://doi.org/10.1128/JCM.01754-12.
Holznagel, E., Yutzy, B., Kruip, C., Bierke, P., Schulz-Schaeffer, W., Löwer, J., 2015. Foodborne-transmitted prions from the brain of cows with bovine spongiform encephalopathy
ascend in afferent neurons to the simian central nervous system and spread to tonsils and spleen at a late stage of the incubation period. J. Infect. Dis. 212, 1459–1468.
https://doi.org/10.1093/infdis/jiv232.
Kim, D., Hong, S., Kim, Y.T., Ryu, S., Kim, H.B., Lee, J.H., 2018. Metagenomic approach to identifying foodborne pathogens on Chinese cabbage. J. Microbiol. Biotechnol. 28, 227–
235. https://doi.org/10.4014/jmb.1710.10021.
Leach, K.M., Stroot, J.M., Lim, D.V., 2010. Same-day detection of escherichia coli O157:H7 from spinach by using electrochemiluminescent and cytometric bead array biosensors.
Appl. Environ. Microbiol. 76, 8044–8052. https://doi.org/10.1128/AEM.01990-10.
León, C., Cifuentes, A., Valdés, A., 2018. Foodomics applications. In: Comprehensive Analytical Chemistry. https://doi.org/10.1016/bs.coac.2018.06.008.
Martinovic, A., Nisic, A., 2019. Novel strategies and tools for microbial risk assessment of foods of animal origin. In: IOP Conference Series: Earth and Environmental Science.
https://doi.org/10.1088/1755-1315/333/1/012012.
Martinovic, T., Andjelkovic, U., Gajdosik, M.S., Resetar, D., Josic, D., 2016. Foodborne pathogens and their toxins. J. Proteom. 147, 226–235. https://doi.org/10.1016/
j.jprot.2016.04.029.
Notermans, S., Barendsz, A.W., Rombouts, F., 2002. The evolution of microbiological risk assessment. In: Microbiological Risk Assessment in Food Processing. https://doi.org/
10.1533/9781855736689.5.
Palka-Santini, M., Cleven, B.E., Eichinger, L., Krönke, M., Krut, O., 2009. Large scale multiplex PCR improves pathogen detection by DNA microarrays. BMC Microbiol. 9, 1. https://
doi.org/10.1186/1471-2180-9-1.
Priyanka, B., Patil, R.K., Dwarakanath, S., 2016. A review on detection methods used for foodborne pathogens. Indian J. Med. Res. 144, 327–338. https://doi.org/10.4103/0971-
5916.198677.
Putignani, L., Dallapiccola, B., 2016. Foodomics as part of the host-microbiota-exposome interplay. J. Proteom. 147, 3–20. https://doi.org/10.1016/j.jprot.2016.04.033.
Radhika, M., Saugata, M., Murali, H.S., Batra, H.V., 2014. A novel multiplex PCR for the simultaneous detection of Salmonella enterica and Shigella species. Braz. J. Microbiol. 45,
667–676. https://doi.org/10.1590/S1517-83822014005000041.
Rajasundaram, D., Selbig, J., 2016. More effort - more results: recent advances in integrative “omics” data analysis. Curr. Opin. Plant Biol. 30, 57–61. https://doi.org/10.1016/
j.pbi.2015.12.010.
Ramamurthy, T., Ghosh, A., Pazhani, G.P., Shinoda, S., 2014. Current perspectives on viable but non-culturable (VBNC) pathogenic bacteria. Front. Public Health 2, 103. https://
doi.org/10.3389/fpubh.2014.00103.
Richard, J.L., 2007. Some major mycotoxins and their mycotoxicoses-An overview. Int. J. Food Microbiol. 119, 3–10. https://doi.org/10.1016/j.ijfoodmicro.2007.07.019.
Seifert, J., Herbst, F.A., Halkjær Nielsen, P., Planes, F.J., Jehmlich, N., Ferrer, M., Von Bergen, M., 2013. Bioinformatic progress and applications in metaproteogenomics for
bridging the gap between genomic sequences and metabolic functions in microbial communities. Proteomics 13, 2786–2804. https://doi.org/10.1002/pmic.201200566.
Tan, L.K., Ooi, P.T., Carniel, E., Thong, K.L., 2014. Evaluation of a modified cefsulodin-irgasan-novobiocin agar for isolation of Yersinia spp. PloS One 9, e106329. https://doi.org/
10.1371/journal.pone.0106329.
Thomas, T., Gilbert, J., Meyer, F., 2014. Metagenomics: a guide from sampling to data analysis. In: The Role of Bioinformatics in Agriculture. https://doi.org/10.1201/b16568.
Tilocca, B., Balmas, V., Hassan, Z.U., Jaoua, S., Migheli, Q., 2019. A proteomic investigation of Aspergillus carbonarius exposed to yeast volatilome or to its major component 2-
phenylethanol reveals major shifts in fungal metabolism. Int. J. Food Microbiol. 306, 108265. https://doi.org/10.1016/j.ijfoodmicro.2019.108265.
 Foodomics and Microbiological Risk Assessment of Food 7

Tilocca, B., Costanzo, N., Morittu, V.M., Spina, A.A., Soggiu, A., Britti, D., et al., 2020. Milk microbiota: characterization methods and role in cheese production. J. Proteom. 210,
103534. https://doi.org/10.1016/j.jprot.2019.103534.
Tröscher-Mußotter, J., Tilocca, B., Stefanski, V., Seifert, J., 2019. Analysis of the bacterial and host proteins along and across the porcine gastrointestinal tract. Proteomes 7, 4.
https://doi.org/10.3390/proteomes7010004.
Valdés, A., Cifuentes, A., León, C., 2017. Foodomics evaluation of bioactive compounds in foods. Trac. Trends Anal. Chem. 96, 2–13. https://doi.org/10.1016/j.trac.2017.06.004.
Wang, Z., Gerstein, M., Snyder, M., 2009. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10, 57–63. https://doi.org/10.1038/nrg2484.
Wurtzel, O., Sesto, N., Mellin, J.R., Karunker, I., Edelheit, S., Bécavin, C., et al., 2012. Comparative transcriptomics of pathogenic and non-pathogenic Listeria species. Mol. Syst.
Biol. 8, 583. https://doi.org/10.1038/msb.2012.11.