Yiannis Kourkoutas ^1* Nikolaos Kopsahelis ² Antonios Koutelidakis ³ Andreas Tzakos ⁴

• ¹ Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
• ² Department of Food Science and Technology, Faculty of Environment, Ionian University, Argostoli, Greece
• ³ Department of Food Science and Nutrition, School of Environment, University of the Aegean, Myrina, Greece
• ⁴ Department of Chemistry, University of Ioannina, Greece, Ioannina, Greece

enriched with beneficial microorganisms and bioac�ve compounds, designed to enhance their func�onal proper�es. This objec�ve is a core focus of FOODBIOMES, a Greek Research Infrastructure commited to microbiome applica�ons to transform food systems and drive progress in sustainability and human health.Hence, this special issue focused on exploring the transforma�ve role of microbiome innova�ons in fostering health-promo�ng and sustainable food systems, bringing together cu�ng-edge research on the design and applica�on of microbiome-based solu�ons, including their role in enhancing food func�onality, addressing environmental challenges, and comba�ng health issues, such as gut dysbiosis, aging, an�bio�c resistance, atopic derma��s, and endometri�s. Chen et al. selected two strains of lac�c acid bacteria for fermen�ng bamboo shoots.Lactiplantibacillus plantarum R1 exhibited prominent poten�al probio�c proper�es (including gastrointes�nal condi�on tolerance, adhesion ability, an�microbial ability, and an�bio�c resistance), while the strain Levilactobacillus brevis R2 was able to produce a high content of γ-aminobutyric acid (GABA). The synergis�c inocula�on of both strains during bamboo shoot fermenta�on led to a remarkable increase in GABA content, surpassing that of naturally fermented bamboo shoots by more than 4.5 �mes and outperforming mono-inoculated fermenta�on. Simultaneously, the nitrite content was maintained within the recommended levels (5.96 ± 1.81 mg/kg). Besides, inoculated fermented bamboo shoots exhibited an increased crude fiber content and reduced fat content. Thus, safe and rapid fermenta�on of bamboo shoots may lay the groundwork for the development of func�onal vegetable products enriched with GABA.Gut microbiota dysbiosis has been a serious risk factor for several gastric and systemic diseases. Recently, available preclinical evidence suggests that the probio�c bacteria Lactiplantibacillus plantarums (LP) may influence the aging process via modula�on of the gut microbiota. The review authored by Gupta et al. summarized compelling evidence of LP's poten�al effect on aging hallmarks, such as oxida�ve stress, inflamma�on, DNA methyla�on, and mitochondrial dysfunc�on. In brief, LP cell cons�tuents exerted considerable an�oxidant poten�al, which may reduce ROS levels directly, restored gut microbiota, facilitated a healthy intes�nal milieu and accelerated mul�-channel communica�on via signaling factors, such as SCFA and GABA. Signaling factors further ac�vated the transcrip�on factor Nrf2 and reduced oxida�ve damage. The authors concluded that LP supplementa�on may be an effec�ve approach to managing aging and associated health risks.In an era increasingly defined by the challenge of an�bio�c resistance, the study of Huang et al. offered groundbreaking insights into the an�bacterial proper�es of two dis�nct Lactiplantibacillus plantarum strains (TE0907 and TE1809), hailing from the unique ecosystem of Bufo gargarizans, as it uniquely focused on elucida�ng the intricate components and mechanisms that empower these strains with their notable an�bacterial capabili�es. The research employed a mul�-omics approach, including agar diffusion tests to assess an�bacterial efficacy and adhesion assays with HT-29 cells to understand the preliminary mechanisms. Addi�onally, gas chromatography-mass spectrometry (GC-MS) was used to analyze the produc�on of organic acids and whole-genome sequencing to iden�fy genes linked to the biosynthesis of an�bio�cs and bacteriocin-coding domains. The compara�ve analysis highlighted the excep�onal an�bacterial efficacy of both strains. A pivotal discovery was the synthesis of ace�c acid in both strains, linking its abundance to their an�microbial efficiency.Genomic explora�on uncovered a diverse range of elements involved in the biosynthesis of an�bio�cs, similar to tetracycline and vancomycin, and poten�al regions encoding bacteriocins, including Enterolysin and Plantaricin. The findings underscored the strains' extensive biochemical and enzyma�c armamentarium, offering valuable insights into their role in antagonizing enteric pathogens for poten�al clinical deployment in safeguarding animal gut health, thereby enriching our understanding of the role of probio�c bacteria in the realm of an�microbial interven�ons.Τradi�onal fermented foods have long been recognized for their numerous health benefits along with their poten�al to aid in the treatment of GI disorders. In this vein, the highthroughput sequencing using the Illumina MiSeq pla�orm was employed to inves�gate the microbiome communi�es of rice-based fermented beverages consumed by ethnic tribes in Southern Assam, namely Zeme Naga, Dimasa Kachari, Hmar, Karbi and Tea tribes (Yumnam et