Acta NaturaeActa NaturaeActa Naturae2075-8251Acta Naturae Ltd2776410.32607/actanaturae.27764Research ArticlesЭкспериментальные статьиResearch ArticleWhole-genome sequencing uncovers metabolic and immune system variations in Propionibacterium freudenreichii isolatesПолное секвенирование генома выявляет вариабельность метаболических и иммунных систем у изолятов Propionibacterium freudenreichiihttps://orcid.org/0009-0002-1139-6162AntipenkoIvan D.АнтипенкоИван Денисович
Russian Federation

Laboratory for Research on Molecular Mechanisms of Longevity, Department of Biology and Biotechnology

факультет биологии и биотехнологии, лаборатория исследований молекулярных механизмов долголетия

iantipenko@hse.ruhttps://orcid.org/0009-0002-0266-0566VenedyukhinaSophia A.ВенедюхинаСофия Александровна
Russian Federation

Laboratory for Research on Molecular Mechanisms of Longevity, Department of Biology and Biotechnology

факультет биологии и биотехнологии, лаборатория исследований молекулярных механизмов долголетия

inbox@sofia.vened.ruhttps://orcid.org/0000-0002-1108-3695SorokinaNinel P.СорокинаНинель Петровна
Russian Federation
n.sorokina@fncps.ruhttps://orcid.org/0000-0001-8251-992XKucherenkoIrina V.КучеренкоИрина Валентиновна
Russian Federation
i.kucherenko@fncps.ruSmirnovaTatiana S.СмирноваТатьяна Сергеевна
Russian Federation
t.smirnova@fncps.ruRogovGregory N.РоговГригорий Новомирович
Russian Federation
g.rogov@fncps.ruShkurnikovMaxim Y.ШкурниковМаксим Юрьевич
Russian Federation

Laboratory for Research on Molecular Mechanisms of Longevity, Department of Biology and Biotechnology

факультет биологии и биотехнологии, лаборатория исследований молекулярных механизмов долголетия

mshkurnikov@hse.ruHSE UniversityНациональный исследовательский университет «Высшая школа экономики»All-Russian Research Institute of Butter and Cheese Making, Branch of the Gorbatov Federal Research Center for Food SystemsВсероссийский научно-исследовательский институт маслоделия и сыроделия – филиал Федерального научного центра пищевых систем им. В.М. Горбатова РАН0412202517472823107202529092025Copyright ©; 2025, Antipenko I.D., Venedyukhina S.A., Sorokina N.P., Kucherenko I.V., Smirnova T.S., Rogov G.N., Shkurnikov M.Y.Copyright ©; 2025, Антипенко И.Д., Венедюхина С.А., Сорокина Н.П., Кучеренко И.В., Смирнова Т.С., Рогов Г.Н., Шкурников М.Ю.2025Antipenko I.D., Venedyukhina S.A., Sorokina N.P., Kucherenko I.V., Smirnova T.S., Rogov G.N., Shkurnikov M.Y.Антипенко И.Д., Венедюхина С.А., Сорокина Н.П., Кучеренко И.В., Смирнова Т.С., Рогов Г.Н., Шкурников М.Ю.https://creativecommons.org/licenses/by/4.0https://actanaturae.ru/2075-8251/article/view/27764

Propionibacterium freudenreichii plays a crucial role in the production of Swiss-type cheeses; however, genomic variability among strains, which affects their technological traits, remains insufficiently explored. In this study, whole-genome sequencing and comparative analysis were performed on five industrial P. freudenreichii strains. Despite their overall high genomic similarity, the strains proved different in gas production and substrate metabolism. Phylogenetic analysis revealed a close relationship between strain FNCPS 828 and P. freudenreichii subsp. shermanii (z-score = 0.99948), with the latter being unable to reduce nitrates but being able to metabolize lactose. The narG gene encoding the nitrate reductase alpha subunit was detected in only one of the five analyzed strains ‒ FNCPS 828 ‒ and in 39% of previously described P. freudenreichii genomes, suggesting its potential as a marker of nitrate-reducing capability. Analysis of 112 genomes showed that the I‒G CRISPR‒Cas system was present in more than 90% of the strains, whereas the type I‒E system was found in approximately 25%. All the five study strains harbored the type I‒G system; strain FNCPS 3 additionally contained a complete type I‒E system with the highest number of CRISPR spacers, some of which matched previously published bacteriophage sequences. The most prevalent anti-phage defense systems included RM I, RM IV, AbiE, PD-T4-6, HEC-06, and ietAS. These findings highlight the genetic diversity of P. freudenreichii strains, which is of great importance in their industrial applications. The identification of narG as a potential marker of nitrate-reducing activity, along with detailed mapping of CRISPR‒Cas systems, boosts opportunities for the rational selection and engineering of starter cultures with tailored metabolic properties and increased resistance to bacteriophages.

Бактерии Propionibacterium freudenreichii играют важную роль в производстве сыров швейцарского типа, однако геномная вариабельность штаммов, влияющая на их технологические свойства, остается недостаточно изученной. Охарактеризованы метаболические и генетические различия промышленных штаммов P. freudenreichii. Сопоставление фенотипических и геномных данных позволяет выявлять маркеры технологически значимых признаков и использовать их для скрининга новых штаммов. Это создает основу для подбора консорциумов с заданными свойствами и разработки заквасочных культур с улучшенными производственными характеристиками. В работе проведено полногеномное секвенирование и сравнительный анализ пяти промышленных штаммов P. freudenreichii. Эти штаммы, несмотря на их высокую геномную идентичность, различались газообразованием и метаболизмом субстратов. Филогенетический анализ показал близость штамма P. freudenreichii FNCPS 828 к подвидy P. freudenreichii subsp. shermanii (z-score = 0.99948), который не способен восстанавливать нитраты, но метаболизирует лактозу. Ген narG, кодирующий альфа-субъединицу нитратредуктазы, идентифицирован только у одного из пяти проанализированных штаммов — FNCPS 828, а также у 39% ранее описанных штаммов P. freudenreichii, что указывает на этот ген как на потенциальный маркер нитратвосстанавливающей активности. Анализ 112 геномов P. freudenreichii выявил систему CRISPR-Cas I-G у 74% штаммов, а тип I-E только примерно у 25%. Все пять изученных штаммов содержали систему типа I-G; у FNCPS 3 также обнаружена полноценная система I-E с наибольшим числом CRISPR-спейсеров, включая соответствовавшие геномам ранее опубликованных бактериофагов. Наиболее распространенные антифаговые системы включали RM I и IV, AbiE, PD-T4-6, HEC-06 и ietAS. Таким образом, выявлено генетическое разнообразие штаммов P. freudenreichii, имеющее значение для их промышленного применения. Обнаружение narG в качестве потенциального маркера восстановления нитратов, а также детальное картирование систем CRISPR-Cas расширяют возможности рационального подбора и инженерной оптимизации заквасочных культур P. freudenreichii с заданными метаболическими свойствами и устойчивостью к бактериофагам.

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