# Genetic and functional diversity of Streptococcus thermophilus strains isolated from Saint-Nectaire PDO cheese area

Anna Grizon, Sébastien Theil, Cécile Callon, Pauline Gerber, Eric Dugat-Bony, Sandra Helinck, Pascal Bonnarme, Christophe Chassard

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Anna Grizon, Sébastien Theil, Cécile Callon, Pauline Gerber, Eric Dugat-Bony, et al.. Genetic and functional diversity of Streptococcus thermophilus strains isolated from Saint-Nectaire PDO cheese area. First forum on Fermented Foods, May 2023, Lyon, France. hal-04862920

HAL Id: hal-04862920

https://hal.science/hal-04862920v1

Submitted on 3 Jan 2025

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# Genetic and functional diversity of *Streptococcus thermophilus* strains isolated from Saint-Nectaire PDO cheese area

Anna Grizon¹,²,³, Sebastien Theil¹, Cécile Callon¹, Pauline Gerber³, Eric Dugat-Bony², Sandra Helinck², Pascal Bonnarme², Christophe Chassard¹

¹ Université Clermont Auvergne, INRAE, VetAgro Sup, UMR545 Fromages, 20 côte de Reyne, 15000 Aurillac, France ² Université Paris Saclay, INRAE, AgroParisTech, UMR SayFood, F-78850 Thiverval Grignon, France

## INTRODUCTION

PDO cheeses producers from Massif Central (France) mostly use commercial starter cultures for the manufacture of cheeses. The use of commercial starters in cheese production results in the loss of typical characteristics of the products. To strengthen the link with the area and improve sensorial qualities and typicality of cheeses, PDO cheeses producers are interested in the development of specific autochthonous starter cultures. To meet this demand, a first step was to isolate new wild strains from the local producing areas, and investigate the genetic and functional diversity of these strains within these reservoirs. The present study explores the diversity of wild strains of *Streptococcus thermophilus* from natural habitats at a local scale, on Saint-Nectaire cheese-producing PDO area. The comparative analysis of whole genome sequences of 26 wild strains of *Streptococcus thermophilus* were carried out. Important functional properties of the isolates were investigated including milk acidification and proteolytic activities.

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## MATERIALS AND METHODS

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## RESULTS

### Isolation and identification

<table><caption>Table 1: *Streptococcus thermophilus* isolation source</caption><thead><tr><th>Categorie's name</th><th>Isolation source</th><th>Season of isolation</th><th>Number of isolates</th></tr></thead><tbody><tr><td rowspan="3">SN-Isolates</td><td>SN-Farms</td><td>Summer</td><td>7</td></tr><tr><td>SN-Farms</td><td>Winter</td><td>14</td></tr><tr><td>ARILAIT collection</td><td>/</td><td>1</td></tr><tr><td>Commercial strains</td><td>Commercial starters</td><td>/</td><td>4</td></tr></tbody></table>

### Proteolytic activity

Proteolysis is a strategic enzymatic activity for cheese production since it directly impacts texture and flavors of cheeses. Low proteolytic activities and limited functional diversity on this criteria were mainly observed.

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### Genetic diversity

<figure><img src="image_7.png" /><figcaption>Figure 3: Presence-absence matrix for the visualization of isolates pan-genome. Isolates with same colors were isolated on the same farms. Isolates with « H » were isolated in winter.</figcaption></figure>

* Five main clades with obvious differences of accessory genes

* Isolates from winter and summer milks, and isolates from same farms are dispersed in the seven branches: genetic variability of the isolates do not depend of the season of isolation, or of the farms, despite a small isolation area.

4

Replication and repair

Amino acid metabolism

Protein families: metabolism

Poorly characterized

Cellular community - prokaryotes

Unclassified: metabolism

Protein families: genetic information processing

5

Glycan biosynthesis and metabolism

Metabolism of cofactors and vitamins

Cellular community - prokaryotes

rug resistance: antimicrobial

Replication and repair

Amino acid metabolism

nclassified: signaling and cellular processes

Carbohydrate metabolism

Lipid metabolism

Translation

Nucleotide metabolism

6

Protein families: signaling and cellular processes

Infectious disease: bacterial

Signal transduction

Poorly characterized

Carbohydrate metabolism

Unclassified: metabolism

Protein families: genetic information processing

Unclassified: genetic information processing

rug resistance: antimicrobial

<caption>Figure 5: Words clouds representing KEGG class over-represented in each groups formed with the hierarchical clustering (PLS-DA analysis)</caption>

Accessory genes of the :

* **fourth clade** might confer benefits to isolates during the manufacture of cheeses (texture/flavors)

* **fifth clade** are associated with important functional characteristics for cheese-manufacture: acidification, texture and flavors

* **sixth clade** could facilitate survival under stressful environmental conditions such as manufacture of cheeses.

<caption>Figure 4: Hierarchical clustering of accessory genes KEGG annotations</caption>

* Six clades almost identical to those observed in the pan-genome clustering.

* Three clades composed of several isolates (clades 4, 5 and 6) and differentiated by the KEGG functional categories of their accessory genes.

* Clades 1, 2 and 3 are composed of a single isolate and stand out for their large number of accessory genes that are involved in all the functional categories represented above.

## CONCLUSION AND PERSPECTIVES

Wild strains of *Streptococcus thermophilus* could represent a source of genetic and functional diversity and an opportunity to select new for cheese production. This diversity is demonstrated within *Streptococcus thermophiles*, isolated from the same location and is also independent of the season of isolation. A specific technological characterization and safety evaluation of isolates is in process to confirm their technological interest in case of.

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