Major Depressive Disorder (MDD) is a prevalent and debilitating mood disorder characterized by persistent low mood and anhedonia [1]. As of the latest estimates, depression affects over 250 million people worldwide, leading to a societal and economic burden [2]. The etiology of depression is multifaceted and encompasses genetic, environmental, and neurobiological determinants. Among these, chronic stress represents a pervasive environmental factor, notorious for its propensity to trigger and exacerbate depressive symptoms [Kendler et al., 2005]. However, the pathophysiology of MDD is not yet completely understood.

The gut microbiota, a dynamic and highly diverse microbial community residing in the gastrointestinal tract (GIT), has recently emerged as a prominent player in shaping brain function and behavior [Cryan et al., 2019]. Alterations in the gut microbiota composition, also known as dysbiosis, have been associated with various neurological and psychiatric disorders, including MDD [5]. Such alterations have also been described in animal models of prolonged depressive state, such as the Chronic Unpredictable Mild Stress (CUMS) model [6]. However, the intricate mechanisms by which the gut microbiota influences the brain are not fully elucidated.

Short-Chain Fatty Acids (SCFA), microbial metabolites derived from dietary fiber fermentation, serve as key mediators of the microbiome-gut-brain axis [7]. Their essential role in preserving gut homeostasis encompasses influences on intestinal epithelium integrity, energy metabolism, mucosal immunity, and inflammatory regulation [7]. Beyond their local effects, SCFAs exhibit systemic influence by reaching other tissues following absorption into the bloodstream [8]. Notably, their ability to cross the blood-brain barrier enables a potential activation of receptors within the brain, emphasizing their capacity to participate in intricate signaling pathways [9]. SCFAs have been linked to neuroimmune modulation and influence brain function and behavior, potentially playing a role in depression [10]. The three main SCFAs in the gut lumen - butyrate, acetate and propionate - are decreased in individuals with MDD, indicating a possible involvement of these metabolites in the etiology of the disease [11], [12], [13], [14]. This depletion of SCFAs was similarly observed in the CUMS model [15].

In particular, SCFAs are increasingly recognized for their involvement in epigenetic alterations, including Histone Deacetylases (HDACs) and histone modifications, which play a pivotal role in the regulation of gene expression [16]. Epigenetic modifications are integral to understanding how environmental factors, such as chronic stress, affect the brain [17]. Notably, epigenetic mechanisms have been linked to changes in gene expression patterns and are associated with the pathophysiology of depression [18]. Epigenetic regulation acts as a mediator for the dysregulation of stress response systems, dysfunction in monoamine neurotransmitters, and neuroinflammation in MDD and other stress-related disorders in animal models [19].

Histones are important components of chromatin, orchestrating the folding of DNA into nucleosome structures composed of histones H2A, H2B, H3, and H4 [20]. The modification of histones, an important epigenetic pathway, assumes a critical role in the regulation of gene replication, transcription, and DNA damage repair [20]. Specifically, histone acetylation is generally associated with active gene transcription, while its counterpart, deacetylation, correlates with transcriptional inhibition. The status of histone acetylation (ac) is regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs), which exhibit opposing roles [21]. Additionally, histone trimethylation (me3) on lysine (K) residuals emerges as a versatile regulator of gene transcription, capable of promoting or inhibiting transcription under distinct conditions [22]. Notably, SCFAs are recognized as HDAC inhibitors [23]; however, their precise role in modulating epigenetic processes in the brain is still not completely understood.

The relevance of specific brain regions such as the hippocampus, prefrontal cortex, and parietal cortex in the context of Depressive Disorder is well-established. These brain regions play crucial roles in mood regulation [24], [25], [26], and alterations in these areas are closely associated with depressive disorders, indicating their intricate involvement in the manifestation of depressive symptoms. The investigation of various histone modifications and HDACs across these brain regions, particularly under stress conditions and in response to specific interventions for MDD [27], [28], [29], [30], provides valuable insights into potential mechanisms underlying new potential interventions, such as the oral supplementation of SCFAs. This study aims to investigate the relationship between chronic stress, alterations in the gut microbiome, epigenetic modifications in these specified brain regions, and their combined impact on depressive-like behaviors.