Table Info

Table 1.

Different regions sequenced and primers used in amplicon metagenomics in table olives

Processing method	Olive cultivar	Gene	Region/loci	Primers	Sequencing platform	Target microorganisms	Genera	Reference
Natural green	Nocellara Etnea	16S rRNA	V3	Probio_Uni & Probio_Rev	Ion Torrent	Bacteria	Halomonas, Achromobacter, Marinobacter, Serratia, Bradyrhizobium, (former) Lactobacillus, Pediococcus, Hafnia, Enterococcus	Randazzo et al. [39]
Natural green	Aloreña de Málaga	16S rRNA	V2-V3	M13F-27F & M13R-357R	Roche 454	Bacteria	Celerinatantimonas, Pseudomonas, Propionibacterium, Modestobacter, Rhodovibrio, Salinibacter	Medina et al. [42]
Natural green	Nocellara Etnea	16S rRNA	V3	Probio_Uni & Probio_Rev	Illumina	Bacteria	(Former) Lactobacillus, Weissella, Enterobacter, Bacteroides, Faecalibacterium, Klebsiella, Raoultella	Vacalluzzo et al. [40]
Spanish-style & natural green	Manzanilla	16S rRNA	V3-V4	PCR_1 F & PCR_1 R	Illumina	Bacteria	(Former) Lactobacillus, Alkalibacterium, Enterococcus, Serratia, Allidiomarina, Halomonas, Marinobacter, Pseudomonas	Ruiz-Barba et al. [43]
Spanish-style & natural green	Manzanilla		ITS1-ITS2	ITS1_KYO2_F & ITS2_KYO2_R	Illumina	Yeast/Fungi	Saccharomyces, Pichia, Nakazawaea, Candida	Ruiz-Barba et al. [43]
Spanish-style	Hojiblanca	16S rRNA	V3-V4	Pro341F & Pro805R	Illumina	Bacteria	Vibrio, Marinilactibacillus, Lactiplantibacillus, Enterococcus, Secundilactobacillus, Loigolactobacillus, Amphibacillus, Pediococcus, Halolactibacillus, Weissella, Lentilactobacillus	Correa-Galeote et al. [44]
Spanish-style & Greek-style	Halkidiki & Konservolia	16S rRNA	V2-4-8 and V3-7-9	Data not available	Ion Torrent	Bacteria	(Former) Lactobacillus, Pediococcus	Argyri et al. [45]
Spanish-style & Greek-style	Halkidiki & Konservolia		ITS1-ITS2	ITS1F & ITS2R	Ion Torrent	Yeast/Fungi	Pichia, Wickerhamomyces, Brettanomyces, Aureobasidium, Schwanniomyces	Argyri et al. [45]
Greek-style	Bella di Cerignola	16S rRNA	V1-V3	28F & 519R	Roche 454	Bacteria	(Former) Lactobacillus, Hafnia, Methylobacterium, Propionibacterium, Clostridium	De Angelis et al. [46]
Greek-style	Kalamata	16S rRNA	V1-V3	27F & 519 R	Illumina	Bacteria	(Former) Lactobacillus, Leuconostoc, Celerinatantimonas, Propionibacterium, Pseudomonas, Staphylococcus, Enterobacter	Kazou et al. [37]
Greek-style	Kalamata		ITS1-ITS2	ITS1F & ITS2R	Illumina	Yeast/Fungi	Pichia, Saccharomyces, Ogataea, Penicillium, Millerozyma, Engyodontium, Wickeramomyces	Kazou et al. [37]
Greek-style	Nyons	16S rRNA	V3-V4	S-DBact-0341-b-S-17 & S-D-Bact-0785-a-A-21	Illumina	Bacteria	Celerinatantimonas, Photobacterium, Marinobacterium, Halomonas, Iodomarina, Bacillus, Lactococcus, Leuconostoc, Lacticaseibacillus	Penland et al. [10]
Greek-style	Nyons		ITS2	ITS3f & ITS4_Kyo1	Illumina	Yeast/Fungi	Citeromyces, Wickerhamomyces, Zygotorulaspora, Candida, Pichia	Penland et al. [10]
Greek-style	Kalamata	16S rRNA	V3-V4	S-D-Bact-0341- b-S-17 & S-D-Bact-0785-a-A-21	llumina	Bacteria	(Former) Lactobacillus, Pediococcus, Curvibacter, Sphinghomonas, Pannonibacter, Phenylobacterium	Michailidou et al. [38]
Greek-style	Kalamata	18S rRNA	V7-V8	FR1 & FF390	llumina	Yeast/Fungi	Pichia, Brettanomyces, Issatchenkia, Cladosporium, Saccharomyces, Candida	Michailidou et al. [38]
Greek-style & natural green	Taggiasca	26S rRNA	D1	NL4R & LS2-MF	Illumina	Yeast/Fungi	Aureobasidium, Cyteromyces, Wickeramomyces, Debaromyces, Pichia, Alternaria, Cystobasidium, Yamadazyma	Traina et al. [47]
Greek-style & natural green	Cypriot, Kalamata, Picual	16S rRNA	V3-V4	V3 &V4	Illumina	Bacteria	(Former) Lactobacillus, Lactiplantibacillus, Streptococcus, Lactococcus, Pediococcus, Salinivibrio, Weissella, Latilactobacillus, Staphylococcus	Kamilari et al. [48]
Greek-style & natural green	Cypriot, Kalamata, Picual		ITS1	BITS & B58S3	Illumina	Yeast/Fungi	Aspergillus, Botryosphaeria, Meyerozyma, Zygosaccharomyces, Saccharomyces, Geosmithia, Wickeromyces, Candida, Penicillium, Hanseniospora	Kamilari et al. [48]

rRNA: ribosomal RNA

Declarations

Author contributions

FTM: Conceptualization, Validation, Writing—review & editing, Supervision. DL: Investigation, Writing—original draft, Writing—review & editing. Both authors read and approved the submitted version.

Conflicts of interest

The authors declare that they have no conflicts of interest.

Ethical approval

Not applicable.

Consent to participate

Not applicable.

Consent to publication

Not applicable.

Availability of data and materials

Not applicable.

Funding

Not applicable.

Copyright

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