TABLE 2.

Overview of omics approaches used to assess the impact of biopreservation on food ecosystems and main findings.

Omics approach	Methodological details	Food	Main finding	References
PCR-Denaturing gradient gel electrophoresis/Temporal temperature gradient electrophoresis associated or not with band sequencing	V3 region of 16S rDNA	Cooked and peeled shrimp	Carnobacterium divergens V41 but not Lactococcus piscium CNCM I-4031 used to inoculate shrimp dominated and was associated with reduction of off-flavours	Saraoui et al., 2017
	V3 region of 16S rDNA	Vacuum-packaged beef meat	Bands associated with spoilage bacteria (Pseudomonas, Enterobacteriaceae, Brochothrix. thermosphacta), but not with LAB, disappeared in samples inoculated with Latilactobacillus sakei and Latilactobacillus curvatus bioprotective strains	Zhang et al., 2018
	V3 region of 16S rDNA	Vacuum-packed cooked ham	Predominant spoilage LAB were not detected when the bioprotective Latilactobacillus sakei B-2 strain was used	Hu et al., 2008
	V6–V8 region of 16S rDNA	Beef cuts packaged in nisin-coated plastic bags	Similar diversity in control and nisin-treated samples although differences were observed with plate counts for Brochothrix thermosphacta	Ercolini et al., 2010
DNA sequencing	Pyrosequencing of V3–V4 region of 16S rDNA	Cold-smoked salmon	Different OTU ratios were observed between control and samples inoculated with Lactococcus piscium EU2241 (= CNCM I-4031). No correlation with sensory analysis	Leroi et al., 2015
	Illumina sequencing of V3–V4 region of 16S rDNA	Raw/peeled shrimp	Shewanella baltica significantly inhibited after co-inoculation with Lactiplantibacillus plantarum AB-1 and Lacticaseibacillus casei LC	Li et al., 2019
	Illumina sequencing of V3–V4 region of 16S rDNA	St Nectaire-type cheese	Implantation of an inhibitory consortium whose inhibitory activity toward Escherichia coli O26:H11 depended on indigenous microbiota composition	Frétin et al., 2020
	Illumina sequencing of V3–V4 region of 16S rDNA and of an internal 280 bp fragment of the gyrB gene	Diced cooked ham	Bioprotective activity and implantation of a nisin-producing strain of Lactococcus lactis depended on microbiota composition	Chaillou et al., 2022
	Illumina sequencing of V4 region of 16S rDNA	Fresh filled pasta	Cultures of Lactiplantibacillus plantarum and Lacticaseibacillus paracasei were not dominant but reduced the initial microbiota and gave a competitive advantage to other LAB species	Tabanelli et al., 2020
16S rRNA sequencing	Sequencing of V3–V4 region of 16S rRNA from cDNA	Fermented sausage	Large domination of Lactobacillaceae and reduction of bacterial diversity in samples inoculated with protective Latilactobacillus curvatus strain	Giello et al., 2018
	Sequencing of V3–V4 region of 16S rRNA from cDNA	Beef burgers in nisin-activated packaging	Lower abundance of some taxa in samples with nisin-activated packaging	Ferrocino et al., 2015
Volatilome analysis	Headspace SPME/GC-MS	Cooked and peeled tropical shrimp	Inhibition of Brochothrix thermosphacta by Lactococcus piscium CNCM I-4031 correlated with attenuation of off-odours and diminution of some volatile compounds	Fall et al., 2012
	Headspace SPME/GC-MS	Salmon gravlax	6 protective strains exhibited their own volatilome profiles. Quality improvement was not correlated with implantation of protective culture	Wiernasz et al., 2020
	Headspace SPME/GC-MS	Fresh filled pasta	Lacticaseibacillus rhamnosus and Lacticaseibacillus paracasei influenced the aroma profile with overall acceptability of the product	Tabanelli et al., 2020
	NMR spectroscopy	in vitro	Kinetic analysis of 11 major metabolites involved in the metabolism of Lacticaseibacillus rhamnosus and Lacticaseibacillus plantarum	Ebrahimi et al., 2016
	FTICR-MS	Red wines	No effect on the volatile compounds of a Metschnikowia pulcherrima bioprotective strain. Wines produced from bioprotected or sulphited must had different metabolic signatures	Simonin et al., 2020