Comprehensive whole-genome analysis of Streptococcus infantarius strains from Moroccan farmhouse dairy products: Genomic insights into dairy adaptation, safety, and biotechnological potential

IF 5.2 1区农林科学 Q1 FOOD SCIENCE & TECHNOLOGY

International journal of food microbiology Pub Date : 2025-07-22 DOI:10.1016/j.ijfoodmicro.2025.111358

Mouhcine Gardoul , Bahia Rached , Ahlam Mbarki , Mohammed Ajdig , El Mehdi Belouad , Taha Chouati , Oussama Chauiyakh , Lahcen Ouchari , Olivier Harlé , Kosai Al-Nakeeb , Marouane Melloul , Elmostafa El Fahime

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Abstract

Streptococcus infantarius, a lactic acid bacterium prevalent in Moroccan dairy products, holds significant probiotic and biotechnological potential, yet its genomic features remain poorly characterized. This study aims to provide a comprehensive genomic characterization of six S. infantarius isolates (B50–6, B50–7, B51–6, O53–2, T41–8, K85–8) from Moroccan farmhouse dairy products.

Whole-genome sequencing and comparative analysis were conducted using advanced bioinformatics tools to assess their genetic diversity, functional attributes, adaptive mechanisms, probiotic properties, safety profile, and potential applications in food fermentation.

All strains were confirmed as S. infantarius with average nucleotide identity (ANI) >98.2 % and digital DNA-DNA hybridization (dDDH) >85.9 %. Genomes sizes ranging from 1.81 (K85–8) to 1.91 (T41–8) Mb, with GC content ∼37.4 %. Functional profiling identified 1343, 1343, 1345, 1342, 1359 and 1345 proteins with functional assignments; 519, 521, 536, 520, 542 and 502 hypothetical proteins; and 1752, 1754, 1778, 1752, 1781 and 1740 proteins with COG (Clusters of Orthologous Groups) assignments, in B50–6, B50–7, B51–6, O53–2, T41–8 and K85–8, respectively. Gene enrichment analysis highlighted key metabolic pathways and functional categories relevant to dairy adaptation and biotechnological potential. The total number of genes encoding carbohydrate-active enzymes was 45 (B50–6), 45 (B50–7), 48 (B51–6), 45 (O53–2), 48 (T41–8) and 48 (K85–8). Safety assessments identified 13 (K85–8) to 16 (B51–6) virulence-associated genes per strain. However, no antimicrobial resistance genes or plasmids were detected, while the presence of CRISPR-Cas systems was detected in most strains. A total of 88 mobile genetic elements were identified ranging from 9 (B51–6) to 18 (O53–2) per strain. In addition, prophages were detected in all strains with the exception of T41–8 and K85–8. All Strains exhibited diverse biosynthetic gene clusters (BGCs), including RiPP-like, T3PKS and terpene precursor pathways.

These findings position S. infantarius as a relatively stable core genome, metabolically versatile candidate for dairy fermentation, probiotic and biotechnological applications.

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摩洛哥农家乐乳制品中婴儿链球菌菌株的全面全基因组分析：对乳制品适应性、安全性和生物技术潜力的基因组见解

婴儿链球菌是摩洛哥乳制品中普遍存在的一种乳酸菌，具有重要的益生菌和生物技术潜力，但其基因组特征仍然缺乏特征。本研究旨在对来自摩洛哥农家乐乳制品的6株猪链球菌（B50-6、B50-7、B51-6、O53-2、T41-8、K85-8）进行全面的基因组鉴定。利用先进的生物信息学工具进行全基因组测序和比较分析，以评估它们的遗传多样性、功能属性、适应机制、益生菌特性、安全性及其在食品发酵中的潜在应用。所有菌株的平均核苷酸同源性（ANI）为98.2%，数字DNA-DNA杂交（dDDH）为85.9%。基因组大小从1.81 （K85-8）到1.91 (T41-8) Mb不等，GC含量约37.4%。功能分析鉴定了1343、1343、1345、1342、1359和1345蛋白的功能分配；519、521、536、520、542和502种假设的蛋白质；在B50-6、B50-7、B51-6、O53-2、T41-8和K85-8中，分别有1752、1754、1778、1752、1781和1740蛋白具有COG （Clusters of Orthologous Groups）定位。基因富集分析强调了与乳制品适应和生物技术潜力相关的关键代谢途径和功能类别。糖活性酶编码基因总数为45个（B50-6）、45个（B50-7）、48个（B51-6）、45个（O53-2）、48个（T41-8）和48个（K85-8）。安全性评估鉴定出每个菌株13个（K85-8）至16个（B51-6）毒力相关基因。然而，没有检测到抗菌素耐药基因或质粒，而在大多数菌株中检测到CRISPR-Cas系统。共鉴定出88个移动遗传元件，每个菌株有9个（B51-6） ~ 18个（O53-2）。此外，除T41-8和K85-8外，所有菌株均检测到噬菌体。所有菌株都表现出不同的生物合成基因簇（BGCs），包括ripp样途径、T3PKS途径和萜烯前体途径。这些发现表明，猪链球菌是一种相对稳定的核心基因组，在乳制品发酵、益生菌和生物技术应用方面具有代谢多样性。

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来源期刊

International journal of food microbiology 工程技术-食品科技

CiteScore

10.40

自引率

5.60%

发文量

322

审稿时长

65 days

期刊介绍： The International Journal of Food Microbiology publishes papers dealing with all aspects of food microbiology. Articles must present information that is novel, has high impact and interest, and is of high scientific quality. They should provide scientific or technological advancement in the specific field of interest of the journal and enhance its strong international reputation. Preliminary or confirmatory results as well as contributions not strictly related to food microbiology will not be considered for publication.