Plant-Derived Phytobiotics as Emerging Alternatives to Antibiotics Against Foodborne Pathogens

Abstract

Growing consumer awareness of clean labels is driving demand for preservative-free products yet concerns about foodborne pathogens and microbiological safety remain significant. Plant-derived compounds with bioactive properties—phytobiotics—have emerged as promising alternatives or complements to conventional antimicrobial agents. This review discusses phytobiotics, including essential oils, polyphenols, alkaloids, and organosulfur compounds, highlighting their structural diversity and antimicrobial potential. Phytobiotics combat foodborne pathogens by disrupting cell structures, inhibiting biofilms and quorum sensing, and interfering with genetic and protein synthesis. Importantly, some phytobiotics exhibit synergistic effects when combined with antibiotics or other natural agents, enhancing overall antimicrobial efficacy. The impact of phytobiotics on the microbiota of food products and the gastrointestinal tract is also addressed, with attention to both beneficial modulation and possible unintended effects. Practical applications in food preservation and supplementation are analyzed, as well as challenges related to composition variability, stability, and interactions with food matrices. Nevertheless, modern technologies such as nanoencapsulation, complexation with polysaccharides, and advanced extraction methods are being developed to address these challenges and enhance the stability and bioavailability of phytobiotics. Continued investment in research and innovation is essential to fully harness the potential of phytobiotics in ensuring safe, natural, and sustainable food systems.

1. Introduction

Phytobiotics, also referred to as phytochemicals or phytogenics, constitute a diverse group of plant-derived compounds that have attracted considerable scientific interest as natural alternatives to synthetic antibiotic growth promoters, particularly in the fields of animal husbandry and aquaculture. These compounds are derived from a variety of plants, including vegetables, fruits, herbs, legumes, and essential oils, and are rich in bioactive molecules such as polysaccharides, flavonoids, alkaloids, carotenoids, and phenolic compounds. Phytobiotics exhibit a number of beneficial properties, including antimicrobial, antioxidant, anti-inflammatory, and immunomodulatory effects that help improve animal health and performance. In animal production, phytobiotics have shown potential to reduce the reliance on synthetic antibiotics, thereby mitigating the risk of antibiotic resistance. In addition, their antioxidant abilities help reduce oxidative stress, and their anti-inflammatory properties promote a reduction in inflammation, which has a positive impact on animal health and growth performance. Owing to their immune system impact, phytobiotics can modulate the immune response of organisms by activating relevant genes, which increases animals’ resistance to diseases. They also improve the composition and function of the intestinal microbiota, promoting better absorption of nutrients, higher feed efficiency, and better weight gain. In poultry, fish, and swine farming, phytobiotics are a promising alternative to antibiotics, especially after the ban on their use in the swine industry, where they not only support health but also increase animal productivity by eliminating the risk of developing resistance. Phytobiotics can be utilized in various forms, including solid, dried, ground, or as extracts, either in crude or concentrated form [1,2,3].

Beyond their application in animal production, phytobiotics are increasingly studied as natural preservatives in food systems. Because of their antimicrobial properties and efficacy against various pathogens, phytobiotics have recently gained attention as an alternative to synthetic preservatives in food protection. They have been shown to be effective against a variety of bacteria, fungi, and viruses, helping to extend the shelf life of food products and ensure food safety [1,2,4,5]. Moreover, they do not cause resistance, thus making them a safe and sustainable solution compared to traditional antibiotics. This is particularly important considering the increase in food-borne infections caused by antibiotic-resistant microorganisms observed in recent years, which poses a serious public health challenge. Among the most common pathogens found in food are Campylobacter spp., Salmonella spp., Escherichia coli, and Listeria monocytogenes. These bacteria are not only widespread in the food chain but also often show resistance to key classes of antibiotics. For example, Campylobacter spp. show resistance to quinolones and macrolides, Salmonella spp. to quinolones and cephalosporins, while E. coli often has resistance mechanisms to β-lactams. Also of particular concern is the multidrug resistance of L. monocytogenes, which limits the options for effective treatment of infections caused by this pathogen [6,7,8,9]. The situation is further complicated by the emergence of new pathogens, such as Aliarcobacter spp., Aeromonas spp., and Cronobacter spp., which are also showing increasing resistance to antimicrobials [7]. Conventional methods of combating these microorganisms, based on antibiotic therapy, are becoming increasingly ineffective, increasing the need to seek alternative antimicrobial strategies. In this context, phytobiotics, as natural substances of plant origin with documented antimicrobial activity, are a promising alternative. Many bioactive compounds present in plants, such as phenols, flavonoids, alkaloids, and essential oils, have been shown to have the ability to inhibit the growth of foodborne pathogens, including antibiotic-resistant strains [10]. Their mechanisms of action include damaging bacterial cell membranes, disrupting cellular metabolism, and inhibiting protein synthesis, making them effective agents for promoting food safety and consumer health in the face of the growing problem of antibiotic resistance [3].

2. The Major Classes of Phytobiotics

Phytobiotics represent a diverse group of plant-derived compounds with significant potential in nutrition. The division into several classes reflects their diverse chemical structure and biological activity (

Table 1. The main classes of phytobiotics.

Compound Group	Examples	Key Properties	Main Sources
Phenolic compounds	Flavonoids, phenolic acids, stilbens, and lignans	Antimicrobial, antioxidant, and anti-inflammatory	Herbs, spices, fruits, and vegetables [1,2,11]
Terpenes	Mono- and sesquiterpenes	Antimicrobial, antioxidant, and flavoring agents	Essential oils and oleoresins [2,11]
Organosulfur compounds	Allicin and glucosinolates	Antimicrobial, antioxidant, and anti-inflammatory	Garlic, onions, and cruciferous vegetables [2,12]
Alkaloids	Berberine and quinine	Antimicrobial and anti-inflammatory	Various medicinal plants [1,12]
Phytosterols	Beta-sitosterol and campesterol	Cholesterol-lowering and anti-inflammatory	Vegetable oils, nuts, and seeds [12]
Saponins	Diosgenin and ginsenosides	Antimicrobial, immune-modulating, and cholesterol-lowering	Legumes, soybeans, quinoa, and ginseng [2]
Polysaccharides	Beta-glucans and arabinogalactans	Immune-stimulating and prebiotic	Mushrooms, oats, and barley [13]

).

2.1. Phenolic Compounds

Phenolic compounds represent one of the most abundant and significant groups of plant secondary metabolites, characterized by the presence of at least one hydroxyl group directly attached to an aromatic ring. These compounds play a vital role in plant physiology, participating in defense mechanisms, responses to environmental stresses (e.g., UV protection), and interactions between plants and pathogens. These compounds protect plants from herbivorous insects, fungi, and nematodes that attack root zones. They are involved in processes such as cell wall thickening, hormone production, and seed germination. They also contribute to the color, taste, and aroma of plant parts, such as fruits and flowers. With their diverse chemical structures and varying degrees of polymerization, phenolic compounds exhibit a wide range of biological activities, including antioxidant, anti-inflammatory, and antimicrobial activities. They are widely distributed throughout the plant kingdom and constitute an essential component of the human diet, occurring in vegetables, fruits, cereals, herbs, and fermented products [14,15,16]. Phenolic compounds are typically classified into simple and polyphenolic compounds (Figure 1) [14].

2.1.1. Simple Phenolic Compounds

Class of phenolic compounds, which contain one phenol unit (or its derivative). They have a general C6 backbone representation—a benzene ring with one or more hydroxyl (-OH) groups directly attached to it. Simple phenolic compounds are found in a variety of plant-based foods, including fruits, vegetables, legumes, cereals, seeds, and beverages such as coffee, tea, and wine [17]. These include simple phenols—the simplest forms of phenolic compounds, belonging to hydroxyphenols, dihydroxybenzenes (e.g., resorcinol, catechol, and hydroquinone), dihydroxyphenols or trihydroxybenzenes (e.g., hydroxyquinol, pyrogallol, and phloroglucinol).

Simple phenolic compounds also include carboxylic acid-containing phenols, known as phenolic acids. Phenolic acids include two main subgroups: hydroxybenzoic acids, with a general structure of the C6-C1 type (e.g., gallic acid, p-hydroxybenzoic acid, protocatechuic acid), and hydroxycinnamic acids, which have a C6-C3 skeleton (e.g., caffeic acid, synapic acid, ferulic acid, p-coumaric acid, cinnamic acid) [14]. Phenolic acids are widely distributed among plants such as fruits, vegetables, spices, and grains and are also present in beverages such as coffee and tea. In plants, these compounds play a role in defense against pathogens and environmental stress. These phytochemicals are known for their beneficial effects on human health, including their antioxidant, antibacterial, antiviral, and anti-inflammatory properties, as well as anti-cancer, anti-atherogenic, and cardioprotective properties [18].

According to some classifications, simple phenolic compounds also include coumarins, based on the presence of an aromatic structure with a hydroxyl group. These compounds are widely distributed in the vascular bundles of plants and exhibit activity against herbivores. Coumarins are a group of broad-spectrum compounds that have applications in pharmacology, the food industry, and agriculture and exhibit a range of biological activities [19]. Frequently mentioned chemical compounds in this group are umbelliferone and scopoletin. Another representative of coumarins is 7-hydroxycoumarin, which is found in coriander, carrots, and garden angelica. A subgroup of coumarins, called furanocoumarins, is found in plants of the Apiaceae family, such as psoraline, which exhibits antifungal properties and phytotoxicity [20].

2.1.2. Polyphenols

These are natural plant compounds that contain two or more hydroxyl groups attached to aromatic rings. Polyphenols can be further subdivided into four main groups: flavonoids, stilbenes, tannins, and lignans [14]. Polyphenols play an important biological role in plants, exhibiting a broad spectrum of protective, structural, regulatory, and signaling functions. In their capacity as powerful antioxidants, they participate in neutralizing reactive oxygen species formed under abiotic stress conditions, such as UV radiation, temperature fluctuations, drought, or the presence of heavy metals. Simultaneously, they protect plants from biotic stress by acting as antimicrobial compounds against bacteria, fungi, and viruses and as repellents against insects and herbivores. Polyphenols affect the structural integrity of plants by participating in the construction of cell walls and regulate key physiological processes such as seed germination and plant growth and development, enabling them to adapt to changing environmental conditions. They also play an important role in ecological interactions—attracting pollinators and seed dispersers by imparting color to flowers and fruits, while repelling herbivores through their bitter taste and toxicity. Some of them exhibit allelopathic effects, inhibiting the growth of competing plant species. Moreover, polyphenols participate in the transmission of cellular signals and activation of defense mechanisms, and their biosynthesis is an adaptive response of plants to changing environmental conditions, promoting the storage of carbon compounds during periods of limited nitrogen availability or slowed growth. Polyphenols are attributed with numerous health-promoting properties, primarily due to their potent antioxidant activity. Polyphenols exhibit a broad spectrum of biological activities. They protect cells from oxidative stress, modulate inflammatory processes, support cardiovascular function, and inhibit the growth of cancer cells. They interact with the intestinal microbiome, supporting its balance, and exhibit antimicrobial activity against bacteria, fungi, and viruses, helping to strengthen the body’s defense mechanisms [3,21,22,23,24,25].

The largest and most structurally diverse group of phenolic compounds comprises flavonoids. These encompass subclasses such as flavonols (e.g., quercetin, kaempferol, myricetin), flavones (e.g., apigenin, luteolin, chrysin), flavanones (e.g., naringin, hesperetin), flavanols (e.g., catechin, epicatechin, epigallocatechin), isoflavones (e.g., genistein, daidzein), and anthocyanins (e.g., paonidin, delphinidin, cyanidin). Flavonoids, commonly found in various plant organs, play an important role in imparting color and fragrance to flowers and fruits, promoting pollination and seed dispersal. They participate in plant defense mechanisms against biotic and abiotic stresses, acting as natural UV filters, signaling molecules, phytoalexins, detoxifying, and antimicrobial compounds. They also support resistance to drought, frost, and heat stress [26].

Stilbenes (1,2-diphenylethylene) are characterized by a C6-C2-C6 backbone. These compounds are produced by plants as secondary metabolites that play a protective role under stress conditions and against pathogens, bacterial and fungal growth. The most well-known representative of this group is resveratrol, particularly recognized for its antioxidant and anti-inflammatory properties. It occurs naturally, among others, in grapes, red wine, peanuts, blueberries, cranberries, chocolate, and tomatoes. Other representatives of this group include gnetol, pterostilbene, piceatannol, polydatin, oxyresveratrol, isorhapontin, astringin, and amurensin H [27].

Lignans are natural compounds belonging to the polyphenol class, found mainly in seeds, grains, fruits, and vegetables, with flaxseed and sesame being particularly rich sources. They are composed of two phenolic units joined by a four-carbon bridge and are formed by dimerization of phenylpropanoid units. In plants, they play a protective role—participating in the formation of lignin, which strengthens cell walls and protects plants from pathogen attack and insect feeding. Lignans exhibit several potential health benefits, acting as antioxidants anti-inflammatory, anticancer, cardioprotective, and antimicrobial compounds. In addition, lignans are phytoestrogens and thus may help regulate hormone levels and alleviate symptoms of menopause. Examples of lignans are secolariciresinol, matairesinol, and pinoresinol [28].

Tannins are a diverse group of polyphenolic compounds commonly found in the plant kingdom, which can be divided into condensed tannins (e.g., proanthocyanidins such as catechin and epicatechin), hydrolyzable tannins (which include gallotannins and ellagitannins, e.g., derivatives of gallic acid), and complex tannins, which are a combination of hydrolyzable and condensed tannin units. Those compounds are found in certain plants and act as deterrents against herbivores by binding salivary proteins, causing an astringent effect in the insects’ oral cavity and disrupting feeding behavior [20].

2.2. Terpenes and Terpenoids

Terpenes are a highly diverse and significant class of secondary metabolites found in plants, primarily as a major component of essential oils. They play a key role in various physiological and ecological functions, including a significant contribution to both biotic and abiotic stress responses [29,30,31]. They function as phytoalexins and allelopathic agents involved in plant defense mechanisms, ecological interactions, and environmental adaptation, mediating responses to pathogens, herbivores, and abiotic stressors such as drought or temperature fluctuations [32,33]. Terpenes are a large group of organic compounds that are classified based on the number of isoprene units they contain (C₅H₈; CH₂=C(CH₃)CH=CH₂). Depending on the number of these units, terpenes are classified as monoterpenes (C₁₀, two isoprene units), sesquiterpenes (C₁₅, three units), diterpenes (C₂₀, four units), sesterterpenes (C₂₅, five units), triterpenes (C₃₀, six units), and tetraterpenes (C₄₀, eight isoprene units) (

Table 2. Classification of terpenes with general structures and examples.

Class	Number of Isoprene Units (C5H8)	General Structural Formula	Examples	References
Monoterpenes and monoterpenoids	2	C10H16	limonene, menthol, geraniol, myrcene, carvone, hinokitiol, linalol, carene, sabinene, camphene, thujene, camphor, borneol, eucalyptol, ascaridole, umbellulone, α-and β-phellandrene, terpinolene, α- and β-pinene, ocimene, zingiberene, terpineol, isopulegol, citral, nerol, thymol, carvacrol, pulegone, verbenone, myrtenol, and isoborneol.	[34,35,36,37]
Sesquiterpenes and sesquiterpenoids	3	C15H24	farnesol, nerolidol, codonolactone, hydroxyisocostic acid, β-bisabolene, britannin, fumagalin, widdrol, zerumbone, β-elemene, guai-2-en-10α-ol, α-copaene, α-humulene, β-caryophyllene, germacrene D, nerolidol, β-cubebene, nootkatone, α-farnesene, lactucin, 11β,13-dihydrolactucin, lactupicrin, aubergenone, ketopelenolide b, and δ-cadinene	[38,39,40]
Diterpenes	4	C20H32	phytol, retinol, retinal, geranylgeraniol, taxol, abietic acid, cembrene, crocetin, sugiol, totarol, taxodone, ferruginol, carnosol, solaneriosides, aphapolins, clerodane, carnosic acid, sahandone, salprzelactones, fischeriabietanes, roscotanes, abscisic acid, and gibberellin	[41]
Triterpenes	6	C30H48	squalene, lanosterol, lupeol, β-amyrin, betulin, oleanol, aksytosterol, and ursolol	[42]
Tetraterpenes	8	C40H64	β-carotene, lycopene, zeaxanthin, astaxanthin, canthaxanthin, capsanthin, zeaxanthin, and lutein	[43]
Polyterpenes	n > 8	(C5H8)n	natural rubber (cis-polyisoprene), gutta-percha, and natural latex	[44]

) [31]. Terpenoids are terpenes modified, for example, by adding an oxygen atom or removing a methyl group.

Monoterpenes and monoterpenoids (C10) are compounds built from two isoprene units and can be divided into acyclic (open-chain), monocyclic (one ring), and bicycle (two linked rings) [45]. While monoterpenes consist solely of carbon and hydrogen atoms (C₁₀H₁₆), monoterpenoids bear additional functional groups—alcohols, ketones, aldehydes, carboxylic acids, or phenolic moieties—that modify volatility, solubility, and bioactivity [34]. Commonly found in essential oils, they contribute strongly to plant aroma and flavor. Although not required for basic plant survival, they serve as defense chemicals (e.g., repelling insects or inhibiting microbial growth) and attract pollinators [45]. When administered to other organisms, they exhibit a broad spectrum of biological activities, including anti-inflammatory (e.g., limonene from citrus peels), antiviral, and antimicrobial effects. Pinene (from pine resin) supports respiratory function and exhibits anti-inflammatory properties.

Another group is sesquiterpenes (C15), which consist of three isoprene units. Oxidation or rearrangement reactions lead to the formation of the corresponding sesquiterpenoids [38]. In plants, sesquiterpenes often act as phytoalexins—substances synthesized in response to pathogen attack—or as antifeedants that deter herbivory. They are abundant in many essential oils (e.g., farnesene, bisabolene). Sesquiterpenes exhibit strong antimicrobial (e.g., farnesol found in rose oil), anti-inflammatory (caryophyllene present in black pepper and cloves or budlei A from burdock leaves), and analgesic activity (e.g., lactucopicrin derived from Lactuca virosa), anticancer effects (e.g., nerolidol), and also cardioprotective (zerumbone from Syringa pinnatifolia), and gastroprotective properties (such as sesquiterpene derivatives from Fabiana imbricata) [39,40,46,47]. Dietary sources of sesquiterpenes include many fruits (apple, orange, strawberry) and spices (ginger, black pepper). Sesquiterpenes found in essential oils of foods were previously described by Durán et al. [40].

Diterpenes (C20) consist of four isoprene units and may be acyclic, monocyclic, bicyclic, tricyclic, or multicyclic. They serve various functions in plants: regulation of growth and development via phytohormones (e.g., abscisic acid and gibberellin), plant defense, and acting as precursors for other important molecules. They exhibit a broad spectrum of activities, including antiviral, antimicrobial, antifungal, anticancer, antidiabetic, cardiovascular protective, immunomodulatory, anti-inflammatory, and tissue regeneration-promoting properties [41,48]. An example of a compound belonging to this group is carnosol, present in rosemary. Natural diterpenoids, their source, and their biological activity were previously described by Liu et al. [41].

Next, triterpenes (C30), formed by six isoprene units, are ubiquitous in plant membranes (as precursors to phytosterols) and participate in signaling pathways that regulate growth, differentiation, and stress responses. Additionally, they function in plant defense, deterring herbivores and inhibiting the growth of pathogenic microorganisms [49]. Triterpenes and triterpenoids exhibit diverse biological properties, including anticancer, antiangiogenic, anti-inflammatory, antiviral, antioxidant, antidiabetic, antihyperlipidemic, antimicrobial, hepatoprotective, cardioprotective, and immune-enhancing activities [50]. Examples of triterpenes include betulin, which comes from birch trees, and oleanol, found in olives.

Tetraterpenes (C40), consisting of eight isoprene units, are predominantly carotenoids and xanthophylls, which function as accessory pigments in photosynthesis—absorbing light and protecting against photooxidative damage. Common tetraterpenes include beta-carotene, lutein, and lycopene [51]. In plants, they quench reactive oxygen species, deter herbivores (through coloration signaling toxicity), and attract pollinators or seed dispersers with bright colors. In human nutrition, carotenoids play a vital role in vision, immune support, and reducing the risk of certain chronic diseases via antioxidant activity [46,48].

Polyterpenes are a group of high molecular weight chemical compounds, consisting of long chains of repeating isoprene units, which may vary widely in structure and function. Natural rubber (polyisoprene) consists of 1500–15,000 isopentenyl units and is produced in the latex of the rubber tree (Hevea brasiliensis). Rubber and related polyterpenes (e.g., gutta-percha from Palaquium gutta, resin from pines) can act as deterrents to herbivores and pathogens, reducing the risk of damage to plants, and have great industrial importance [52,53].

2.3. Organosulfur Compounds (OSCs)

Organosulfur compounds are organic molecules containing carbon-sulfur bonds, prevalent in various plants, particularly in Allium (e.g., garlic, onion) and Brassica (e.g., broccoli, cabbage) vegetables [54,55]. Organosulfur compounds are present in the structure of certain essential amino acids, such as cysteine, cystine, and methionine, which constitute components of proteins, the tripeptide glutathione, as well as vitamins, various enzymes, coenzymes, and hormones [56]. OSCs play a critical role in plant defense mechanisms, exhibiting broad-spectrum antimicrobial activity against bacteria, fungi, and viruses, which enhances plant resistance to pathogens [55]. Organosulfur compounds, such as allicin, exert antibacterial effects by reacting with thiol groups in bacterial enzymes, leading to enzyme inactivation, membrane disruption, and inhibition of bacterial growth, including that of Gram-positive, Gram-negative, and multidrug-resistant strains. Additionally, OSCs interfere with biofilm formation, highlighting their potential application in the development of novel antibiotics and strategies to combat antimicrobial resistance, particularly in food preservation [57]. Moreover, plants such as Petiveria alliacea produce OSCs in response to herbivory, with their production being tightly regulated through feedback inhibition mechanisms, helping plants adapt to biotic stressors [58]. OSC compounds can be classified into several classes based on their chemical structure and biological properties. Alk(en)yl Cysteine Sulfoxides are commonly found in Allium vegetables, such as garlic and onions. Notable examples include S-allyl cysteine and thiosulfinates, including allicin, which inhibit microbial growth. Another group includes sulfur-containing compounds such as diallyl sulfides (mono-, di-, and trisulfides), primarily found in garlic. Vinyldithiins and ajoenes, formed during garlic processing, exhibit significant biological activity, particularly anticancer properties [54]. Next class, glucosinolates, found mainly in Brassica vegetables such as broccoli, kale, and cabbage, are hydrolyzed to form bioactive molecules such as isothiocyanates [59,60]. This group also includes dimethylsulfoniopropionate produced by some land plants and marine algae, serving as an anti-stress molecule and also as a precursor to dimethyl sulfide, a volatile compound involved in climate regulation [61]. Glutathione (GSH), a tripeptide composed of glutamate, cysteine, and glycine, is another sulfur-containing molecule classified within plant OSCs. It plays a crucial role as an antioxidant, protecting cells against oxidative stress and contributing to detoxification processes [62].

2.4. Alkaloids

Alkaloids are a diverse group of nitrogen-containing secondary metabolites that play several crucial roles in plants. Alkaloids can be classified based on their chemical structure, biosynthetic pathway, and natural origin. Within the major classes of alkaloids, there are several groups, each with distinctive structural features and specific biological properties (

Table 3. Classes of plant alkaloids, their sources, and biological properties.

Class	Examples	Sources	Properties
Pyridine	Nicotine, Anabasine, Coniine	Tobacco plants, Anabasis aphylla, Conium maculatum	Stimulant effects, addiction potential, antimicrobial activity
Tropane	Atropine, Scopolamine, Cocaine	Atropa belladonna, Erythroxylum coca, Datura stramonium	Anticholinergic, stimulant properties, antimicrobial activity
Isoquinoline	Morphine, Codeine, Berberine	Opium poppy, Coptis chinensis, Hydrastis canadensis	Analgesic effects, pain relief, antimicrobial
Indole	Vincristine, Vinblastine, Harmaline	Catharanthus roseus, Peganum harmala	Antineoplastic, antimicrobial
Purine	Caffeine, Theobromine, Theophylline	Coffee, tea plants, Theobroma cacao	Stimulant effects, mental alertness, antimicrobial
Imidazole	Pilocarpine, Miconazole	Pilocarpus species	Treatment of glaucoma, parasympathomimetic, antifungal
Steroidal	Solanine, Tomatine, Berberine	Solanaceae family, Berberis vulgaris	Toxic properties, effects on cell membranes, antimicrobial

). Primarily, they serve as a defense mechanism against herbivores, pathogens, and competitors. Their toxic nature helps plants repel insects, animals, and microorganisms. In addition, they act as reservoirs of nitrogen, which is essential for plant growth and development. Some alkaloids act as growth regulators due to their structural similarity to known plant hormones [63,64,65].

Pyrrolidines are alkaloids containing a five-membered ring with one nitrogen atom. An example of this class is prolines, which have important functions in plant metabolism. Pyrrolizidines are alkaloids with a bicyclic structure that contains nitrogen. This group includes, for example, lasiocarpine, known for its toxic properties. Quinolizidines are also characterized by a bicyclic structure with the presence of nitrogen atoms. This group includes compounds such as anabasine, which is used in the pharmaceutical industry and exhibits toxic effects in high concentrations. Tropanes, which include compounds such as atropine and cocaine, are known for their medicinal properties but also for their toxicity when used improperly. Atropine, used in medicine, has the ability to dilate pupils, while cocaine, despite its use in anesthesiology, is an addictive substance. Piperidines are alkaloids containing a six-membered ring with one nitrogen atom. An example of this group is piperine, an alkaloid found in pepper, which has been shown to stimulate the digestive system. Pyridines, such as nicotine, which is derived from the pyridine ring, are one of the more recognizable groups of alkaloids. Nicotine, found in tobacco, acts on the nervous system and is responsible for smoking addiction. Isoquinolines are a group of alkaloids with a complex structure, characterized by significant pharmacological activity. An example from this class is morphine, an alkaloid found in opium, which has strong analgesic but also addictive effects. Indoles are alkaloids that contain an indole ring. Compounds such as strychnine and reserpine are examples from this group, exhibiting a variety of biological activities. Strychnine, known for its neurotoxic properties, acts as a potent nervous system stimulant, while reserpine is used to treat hypertension [64,65,66,67,68].

2.5. Phytosterols

Phytosterols are a family of steroids essential for plant cell membranes, contributing to membrane fluidity and structure [69]. They stabilize biological membranes, ensure proper enzyme activity, and are involved in signal transduction, growth hormone production, and plant response to environmental stress, while also exhibiting significant antimicrobial activity [70,71]. Stigmasterol, one of the best-studied phytosterols, exhibits antimicrobial activity, particularly against certain food spoilage-causing bacteria [72]. Plant extracts rich in phytosterols show strong antimicrobial and antifungal properties, inhibiting the growth of various fungal strains, including Candida and Aspergillus species responsible for human infections [73,74,75]. Their antimicrobial is multifaceted, involving interactions with macromolecules that lead to inactivation and interference with cellular components such as membranes and mitochondria, leading to pathogen death [76].

Phytosterols are categorized into three main types: free sterols, conjugated sterols, and sterol derivatives. Free sterols, such as β-sitosterol, campesterol, and stigmasterol, are abundant phytosterols in plants and crucial for membrane stabilization and metabolic regulation. β-sitosterol is widely used in dietary supplements for its cholesterol-lowering effects. Conjugated sterols are formed by combining sterols with fatty acids, phenolic acids, or sugars, such as sterol esters found in vegetable oils (e.g., canola oil), improving fat quality and bioavailability. Sterol derivatives serve as precursors to various bioactive compounds, including steroidal saponins and brassinosteroids, which are important for plant growth and may have applications in cancer treatment and agriculture [77,78,79].

Phytosterols are also based on chemical structure, particularly the presence of methyl groups in the A ring of the sterol. The first group, 4-desmethyl sterols, lacks a methyl group at the C4 position, with sitosterol as an example, known for its cholesterol-lowering properties. Another group, 4-monomethylsteroids, contains one methyl group at the C4 position, such as 24-monomethylositosterol, which exhibits anti-inflammatory properties. The third group, 4,4′-dimethylsteroids, includes compounds such as avenasterol from oats, known for their antioxidant and anti-inflammatory activities [80].

2.6. Saponins

Saponins are a diverse group of naturally occurring plant glycosides with significant ecological, biological, and pharmacological roles. They are amphipathic molecules composed of a hydrophobic aglycone (triterpenoid or steroid) linked to oligosaccharide moieties. The presence of a hydrophobic aglycone backbone in combination with hydrophilic sugar residues gives them an amphipathic character, which is reflected in their ability to foam and emulsify [81,82]. Saponins play an important role in plant defense, repelling insects and herbivores, and participating in allelopathy by inhibiting the growth of competing species. In addition, they are involved in the regulation of growth and development processes and in ecological interactions, such as plant-microbe or plant-plant relationships, affecting the balance of the ecosystem [83,84,85,86,87]. Saponins also exhibit significant antimicrobial properties, which include activity against pathogenic bacteria, fungi, and protozoa. For example, saponins from Medicago plants show high activity against Gram-positive bacteria, especially against Bacillus and Staphylococcus species, while saponins from quinoa are mainly effective against Gram-negative bacteria such as Salmonella enteritidis and Pseudomonas aeruginosa. The antimicrobial effects are attributed to their ability to interact with and permeabilize cell membranes due to their amphiphilic nature. The antimicrobial action of saponins is primarily due to their ability to disrupt cell membranes. This disruption leads to the leakage of cell contents, ultimately causing cell death [88,89]. The most important classes include triterpenoid saponins and steroidal saponins. Triterpenoid saponins are commonly found in dicotyledonous plants [81,82]. Examples of these compounds include ginsenosides present in ginseng and soy saponins found in soybeans [82,90]. These compounds exhibit numerous biological properties, including anti-inflammatory, anticancer, and immunomodulatory effects. Steroidal saponins predominate in monocotyledonous plants and include, among others, diosgenin extracted from yam (Dioscorea spp.) and timosaponin found in Anemarrhena asphodeloides. They exhibit beneficial pharmacological effects, including supporting cardiovascular function [81,82,91].

2.7. Polysaccharides

Polysaccharides play essential roles in plant physiology, encompassing both structural and functional aspects. As major components of the plant cell wall—such as cellulose, hemicelluloses, and pectins—they ensure cellular integrity and mechanical rigidity. Additionally, they are involved in energy storage (e.g., as starch), contribute to defense mechanisms against pathogens, and participate in processes such as growth, morphogenesis, and responses to environmental stress [92,93,94,95,96]. Moreover, plant polysaccharides exhibit antimicrobial properties through various mechanisms, including the disruption of bacterial cell membranes, which increases membrane permeability and leads to cell death. They can also inhibit pathogen adhesion to host cells, thus preventing infection, and block nutrient transport across bacterial membranes, effectively starving the bacteria. The antimicrobial activity of these polysaccharides is influenced by factors such as their molecular weight, monosaccharide composition, degree of branching, and chemical modifications, with different extraction methods potentially altering their structure and biological activity. Significant antimicrobial activity has been demonstrated, for instance, for polysaccharides from Plantago asiatica L. [97,98].

Based on a structural perspective, plant polysaccharides are classified into several basic types. Cellulose, which is a polymer of glucose linked by β(1→4) glycosidic bonds plays a key structural role, forming fibrils that give rigidity to cell walls [95,99]. Starch, made up of glucose linked by α(1→4) glycosidic bonds, and also α-1,6-glycosidic bonds, is the main form of energy storage in plant cells [95,100]. Hemicelluloses, which include xyloglucans and xylans, are also part of the cell wall, where they interact with cellulose and pectins. Pectins, in turn, are polysaccharides of the cell matrix, which affect the elasticity and permeability of cell walls and participate in cell growth and maturation processes [99].

In summary, phytobiotics are a heterogeneous group of natural compounds, differing primarily in chemical structure and the resulting variations in biological activity. The majority of phytobiotic classes exhibit antimicrobial properties, thus establishing them as promising agents for controlling pathogens in food. Considering the high structural and functional diversity, individual photobiotics have different mechanisms of action against microorganisms.

3. Mechanisms of Action of Phytobiotics Against Foodborne Pathogens

Phytobiotics offer a promising and sustainable alternative to synthetic antibiotics in combating food-borne pathogens. The effectiveness of phytobiotics against microorganisms can be attributed to several mechanisms.

3.1. Disruption of Bacterial Cell Wall Integrity, Membrane Structure, and Biofilm Formation

The first mechanism under discussion involves damage to the bacterial cell membrane by phytobiotics, ultimately leading to cell lysis and death. This mode of action is frequently observed in the case of essential oils and concentrated plant extracts such as thymol, linalool, and menthol. These compounds can disrupt the integrity of the bacterial cell envelope, causing leakage of cellular contents and, consequently, bacterial death [101,102,103]. Phytobiotics interfere with bacterial membranes through various mechanisms, beginning with direct membrane damage. Luteolin, for instance, compromises membrane integrity by inducing oxidative stress and cellular damage in Salmonella enterica and E. coli [104]. A more specific effect involves the alteration of membrane fluidity. For instance, shikimic acid induces significant leakage of potassium ions and nucleotides from Staphylococcus aureus, indicating disruption of membrane integrity and permeability. Furthermore, the study reported changes in membrane potential and a decrease in membrane fluidity [105]. In the same work, Bai and colleagues observed that these mechanisms may overlap, as they also noted interactions with membrane structural components—namely proteins. Cell wall proteins (CWPs) of fungi and yeasts—such as mannoproteins and hydrophobins—are essential for adhesion, pathogenicity, and survival. Phytobiotic interactions with CWPs can disrupt these functions, positioning CWPs as viable targets for antimicrobial strategies. Phytobiotics may interact directly with these proteins or indirectly disrupt their structure, for example, by degrading the polysaccharide scaffold [106]. In Gram-positive bacteria, cell wall proteins are anchored to the peptidoglycan layer via sortase enzymes. Anchored proteins, together with teichoic acids and polysaccharides, play a vital role in bacterial interactions [107]. These structures may serve as molecular targets for phytobiotics. For example, in the study by Isah et al. [108], phytochemical compounds were shown to bind to membrane-associated proteins such as peptide-binding proteins, cell wall surface anchors, pilins, transglycosylases, and penicillin-binding proteins (PDB IDs: 5O79, 7RJJ, 2XTL, 3PHS, 3VMQ, 3VSK) [108]. In most cases, antimicrobial activity via damage to the bacterial cell wall and membranes is particularly evident with the use of essential oils. For instance, components of essential oils such as citronellol alter the surface charge and hydrophobicity of bacterial membranes, leading to membrane disruption and potassium leakage [109]. Essential oils are hydrophobic, a property that facilitates their interaction with bacterial cell walls and membranes, ultimately resulting in structural dysfunction [110]. Phytobiotics have also been shown to interfere with or modify lipopolysaccharides in Gram-negative bacteria and teichoic acids in Gram-positive bacteria, disrupting proper cell wall assembly and increasing bacterial susceptibility to environmental stressors [41,107].

Induction of oxidative stress by phytobiotics also contributes to antimicrobial activity by destabilizing bacterial cell membranes. This mechanism involves enhanced production of reactive oxygen species (ROS), leading to damage of membrane lipids and proteins, loss of cytoplasmic membrane potential, and disruption of ATP production [111,112]. Phytobiotics can also cause cytoplasmic content leakage through structural disruption of the cell membrane. Triphenyl sesquineolignans derived from the Illicium genus rupture bacterial membranes, resulting in rapid bactericidal activity [113]. Similarly, isochlorogenic acid C obtained from stevia induces significant leakage of intracellular proteins and potassium ions from E. coli, indicating damage to both the inner and outer membranes [114]. Another mechanism involves interference with the synthesis of the bacterial cell wall or membrane. Phenolic compounds and alkaloids from various plants inhibit the activity of peptidoglycan synthases, thereby preventing proper bacterial cell wall formation [115]. One key target is the MurA enzyme, which catalyzes the first step in peptidoglycan biosynthesis. Inhibition of MurA disrupts the structural integrity of the cell wall, ultimately leading to cell lysis [116,117]. Compounds such as catechin (derived from Uncaria gambir) and allylpyrocatechol (Piper betle) have been shown to bind directly to MurA and inhibit its enzymatic activity, as demonstrated in both in vitro and in silico studies [116,117]. Autolysins—enzymes responsible for controlled degradation of peptidoglycan—may also be targets of phytobiotic modulation. Studies have shown that LytC and LytF autolysins alter their dynamics and subcellular localization in response to environmental cues or the presence of inhibitors, suggesting a potential regulatory effect by phytobiotics [118]. Moreover, certain plant-derived compounds, such as phytobiotics isolated from traditional Chinese medicines, have been shown to inhibit sortase A, the enzyme responsible for anchoring surface proteins to the cell wall in Gram-positive bacteria. Inhibition of this enzyme reduces bacterial adhesion and virulence [119]. Through interference with various components or stages of cell wall synthesis, phytobiotics can weaken the structural integrity of bacterial walls, increase susceptibility to environmental stress, and ultimately lead to bacterial cell death. Phytobiotics may also alter the chemical and functional composition of bacterial cell walls by modifying key components and inhibiting enzymes involved in their biosynthesis. Exposure to these compounds can lead to significant deformation of the cell wall, resulting in changes in cell shape and size. For example, cranberry juice has been shown to modify the morphology of E. coli, affecting the expression of flagellar proteins and reducing the fimbrial structures such as P fimbriae [120]. Similarly, an extract from Pelargonium zonale induced morphological abnormalities in Candida albicans, including cell wall damage and aberrant budding [121]. Phytobiotics also show potential as efflux pump inhibitors. Efflux pumps are often associated with the development of antibiotic resistance in bacteria. These transport systems actively excrete a wide range of antibiotics and other toxic compounds from bacterial cells, reducing intracellular concentrations and diminishing treatment efficacy [122]. Natural compounds may enhance the efficacy of antibiotics by inhibiting efflux pump activity, thereby increasing intracellular antibiotic concentrations [122,123,124,125,126]. For example, the ethyl acetate fraction of pomegranate (Punica granatum) exhibited potent efflux pump inhibitory activity [127]. Flavonoids such as phloretin and naringenin, when combined with existing efflux pump inhibitors, enhanced the antibacterial activity against Pectobacterium brasiliense [128]. However, exposure to phytobiotics may also drive adaptive responses. Under phytobiotic-induced stress conditions, bacteria can adopt filamentous morphology as a survival strategy. This adaptation promotes biofilm formation, which in turn increases resistance to antimicrobial agents [129,130]. Biofilms represent a crucial bacterial adaptation to environmental stressors, including the action of phytobiotics. These structures, composed of bacterial cells embedded in an extracellular matrix, significantly restrict the penetration of antimicrobial agents and thus enhance microbial survival. Certain phytobiotics affect biofilm development. For instance, plant extracts from the genus Inula significantly reduced biofilm biomass and altered colony morphology of Chromobacterium violaceum, indicating disruption of biofilm structural organization [131]. This control over biofilm formation is closely linked to interference with quorum-sensing mechanisms. Selected plant-derived compounds, particularly essential oils and their phytochemical constituents, have been shown to inhibit biofilm formation by blocking intercellular communication or disrupting the synthesis of extracellular substances such as exopolysaccharides and structural proteins [132,133]. Another relevant mechanism is the inhibition of extracellular polymer production, particularly exopolysaccharides (EPS), which are essential for biofilm adhesion and structural stability. Inhibition of EPS biosynthesis weakens biofilm integrity and increases susceptibility to external stressors [134]. Phytobiotics may also prevent bacterial adhesion to surfaces by interacting with adhesins or by altering physicochemical properties of bacterial cells, such as hydrophobicity and aggregation capacity [134,135]. Alterations in cell wall structure and function impair the initial contact between bacterial cells and surfaces, thereby inhibiting early biofilm development. A critical aspect of phytobiotic activity is the modulation of gene expression associated with adhesion, EPS production, and resistance to environmental stressors [136,137]. By targeting regulatory pathways, phytobiotics can influence the transition of bacteria from the planktonic (free-living) to the sessile state necessary for biofilm maturation [136,137]. Phytobiotics influence not only the development and stability of mature biofilms but also the very early stages of their formation, such as the initial adhesion of bacterial cells to surfaces. This initial adhesion phase is critical for subsequent biofilm maturation and the persistence of infection. It has been documented that plant-derived compounds can disrupt the function of bacterial adhesin proteins, which play a key role in the attachment of bacteria to substrates [138]. The structural similarity of certain phytobiotics to signaling molecules, such as acyl-homoserine lactones, enables competitive inhibition of these molecules, thereby impeding biofilm formation [133]. For example, an extract from Adiantum philippense significantly reduced exopolysaccharide production and disrupted biofilm architecture, as confirmed by both in vitro and in silico analyses [138]. This disruption of biofilm architecture is closely linked to interference with bacterial communication systems. Quorum sensing is crucial during the initial stages of biofilm development, as it coordinates adhesion and biofilm formation. Berry fruit extracts and wood-derived terpenes have been shown to reduce quorum sensing activity, resulting in diminished bacterial adhesion and inhibition of biofilm formation [139]. In addition to their effects on membranes and biofilm formation, phytobiotics also interfere with bacterial resistance mechanisms.

3.2. Inhibition of Protein and DNA Synthesis

As previously noted, phytobiotics inhibit bacterial cell wall synthesis; however, their activity extends further into molecular pathways such as protein biosynthesis and DNA replication, ultimately resulting in growth arrest and bacterial cell death. It was observed long ago that extracts from Phytolacca dodecandra contain ribosome-inactivating proteins (RIPs) capable of inactivating the 60S ribosomal subunit, thereby effectively inhibiting translation [140]. Phenolic compounds and plant-derived alkaloids can interact with bacterial ribosomes, disrupting translation by altering the conformation of the ribosomal active site [115]. Beginning with translation, the flavonoid quercetin (found in Calendula officinalis) inhibits peptidyl transferase and peptide deformylase activity, resulting in the arrest of both initiation and maturation of polypeptide chains, as demonstrated in S. aureus [141]. In later translation stages, plant-derived compounds can act analogously to kirromycins by binding elongation factor Tu (EF-Tu) and halting polypeptide elongation [142]. Some plant extracts also affect the expression of key ribosomal proteins, including 30S subunit protein S1 and the GroEL chaperonin (60 kDa), thereby destabilizing the entire translational machinery [143]. With regard to DNA, phytobiotics are capable of inhibiting bacterial genome replication. Plant polyphenols effectively suppress the activity of DNA gyrase, an enzyme critical for DNA replication and transcription [135]. Isothiocyanates, such as sulforaphane and phenethyl isothiocyanate, have demonstrated strong inhibitory effects on DNA synthesis in Bacillus subtilis and E. coli [144]. For example, andrographolide has been shown to inhibit DNA replication in S. aureus and to prevent biofilm formation [145]. Additionally, recently isolated phenolic saccharides from Polygonum cuspidatum were found to block the activity of DNA primase, an enzyme essential for replication initiation [146]. Coumarins such as scopoletin and daphnetin have also been shown to inhibit the GTPase activity of the FtsZ protein, a key factor in bacterial cell division and protein synthesis, thereby disrupting cytokinesis [147]. Furthermore, alcoholic extracts from Achillea millefolium flower heads demonstrated the ability to inhibit protein synthesis in E. coli cells [148].

3.3. Induction of Oxidative Stress

Phytobiotics exert their antibacterial effects, in part, by targeting molecular pathways associated with oxidative stress in microbial cells. They may act directly by inducing oxidative stress through the generation of reactive oxygen species (ROS). For example, leaf extract from Litsea salicifolia has been shown to trigger ROS production in bacterial cells, leading to oxidative damage and cell death [149]. A similar oxidative mechanism is observed for hop-derived phytochemicals, which induce oxidative damage in bacterial cells, contributing to their antimicrobial activity [150]. One of the primary molecular targets of phytobiotics is catalase—an enzyme responsible for decomposing hydrogen peroxide (H₂O₂) into water and oxygen, thereby protecting bacterial cells from the toxic effects of ROS [151,152]. Inhibition of catalase by phytobiotics results in the accumulation of hydrogen peroxide and other ROS within bacterial cells, leading to lipid peroxidation, protein misfolding, and DNA damage. For instance, astragalin, a flavonol glycoside extracted from Gymnocarpium dryopteris, has been shown to inhibit catalase activity [153].

3.4. Disruption of Central Metabolism by Phytobiotics

Phytobiotics also exert antibacterial effects by interfering with the central metabolism of microorganisms. Key bacterial metabolic pathways—such as glycolysis, the tricarboxylic acid (TCA) cycle, and the pentose phosphate pathway—are disrupted by phytobiotics through altered substrate availability and modulation of enzyme activities involved in these processes [148,149]. For instance, changes in pH can influence bacterial metabolism by affecting ATP levels and the NADH/NAD⁺ ratio, both of which are critical for microbial survival [154]. Some phytocompounds directly inhibit ATP synthase. Phenolic constituents of ginger, such as 6-gingerol and 6-shogaol, inhibit ATP synthase activity in E. coli, thereby reducing ATP production [155]. Similarly, resveratrol and piceatannol—polyphenolic phytochemicals—bind to specific inhibitory sites on ATP synthase, enhancing its inhibition [156]. Certain phytobiotics also affect the proton motive force required for ATP synthesis. Extracts from Donella welwitschii have been shown to disrupt the activity of the H⁺-ATPase pump, leading to reduced ATP production in bacterial cells [157]. These findings suggest that phytobiotics can effectively impair bacterial metabolic processes, thereby reducing both microbial growth and pathogenic potential. In the context of phytobiotics, energy spilling (overflow metabolism) is also worth mentioning. This phenomenon leads to inefficient energy utilization by bacteria, resulting in ATP loss that could otherwise be allocated for cell growth and maintenance [158]. Phytobiotics—including plant extracts and bioactive compounds—demonstrate the ability to modulate bacterial metabolism and energy use. For instance, clove essential oil and its active component—eugenol—have been shown to effectively reduce methane production and ammoniacal nitrogen waste in the rumen by inhibiting methanogenic and deaminating bacteria [159]. This activity may promote more efficient energy utilization by minimizing losses associated with methanogenesis and deamination [159,160]. It is important to note that while phytobiotics exhibit antimicrobial activity by inducing oxidative stress, their presence may also trigger resistance mechanisms in microorganisms. Bacterial cells possess redox sensors that detect oxidative stress and activate detoxification pathways. Phytobiotics can influence these sensors, leading to altered gene expression and the activation of defense mechanisms. For instance, redox-responsive transcriptional sensors can oxidize thiol groups in cysteine residues, thereby regulating the transcription of genes involved in detoxification [161]. Moreover, phytobiotics may act at an additional regulatory level by modulating the expression of genes encoding antioxidant enzymes, thereby enhancing bacterial detoxification capacity against ROS [162,163].

A summarized mechanism of action of phytobiotics on pathogenic microorganisms is presented in

Table 4. Mechanisms underlying the antimicrobial action of phytobiotics.

Mechanism Category	Mechanism of Action	References
Disruption of bacterial cell wall integrity, membrane structure, and biofilm formation	Disruption of cell wall and membrane integrity	[101,102,103]
	Alteration of membrane fluidity and membrane potential	[105]
	Targeting cell wall proteins and structural components	[106,107]
	Binding to membrane-associated proteins	[108]
	Interaction with lipopolysaccharides and teichoic acids	[41,107]
	Induction of oxidative stress damaging membranes	[111,112,113,114]
	Interference with membrane synthesis	[115]
	Inhibition of MurA enzyme in peptidoglycan synthesis	[116,117]
	Modulation of autolysins and sortase A	[118,119]
	Modification of bacterial morphology	[120,121]
	Efflux pump inhibition	[122,125,126,128]
	Inhibition of biofilm formation and quorum sensing	[129,130,131]
	Inhibition of EPS production and bacterial adhesion	[134,135]
	Modulation of gene expression linked to biofilm	[136,137]
Inhibition of protein and DNA synthesis	Inhibition of protein synthesis (e.g., ribosomal binding)	[115,140,142]
	Inhibition of DNA replication (e.g., DNA gyrase, primase)	[135,144,145,146]
	Inhibition of bacterial cell division (e.g., FtsZ inhibition)	[147]
	Inhibition of translation-related proteins and factors	[148]
Induction of oxidative stress	ROS induction and catalase inhibition	[149,150,151]
Disruption of central metabolism by phytobiotics	Disruption of central metabolism (glycolysis, TCA, PPP)	[148,149]
	Inhibition of ATP synthase and H+-ATPase activity	[155,156,157]
	Energy spilling and modulation of energy use	[158,159,160]

.

3.5. Synergism Between Phytobiotics and Other Compounds

When discussing the mechanisms of phytobiotic action, it is also important to highlight their synergistic effects, particularly in combination with antibiotics. The aforementioned mechanisms—such as disruption of cell wall or membrane integrity—often enhance bacterial susceptibility, making these structures more accessible to antibiotics, which frequently target them. Combining phytobiotics with antibiotics can enhance therapeutic efficacy or allow for reduced antibiotic dosages. A strong synergistic effect has been demonstrated, for instance, between berberine and antibiotics such as penicillin and erythromycin [101,106]. Furthermore, indole-based phytochemicals, including camalexin and brassinin, have been studied for their inhibitory effects on the AcrB efflux pump in Escherichia coli. Camalexin, in particular, significantly reduced the minimum inhibitory concentration (MIC) of antibiotics, confirming its potential as an antibiotic potentiator [125]. Extracts from plants such as Phyllanthus emblica and Allium sativum have shown synergistic effects with antibiotics such as ciprofloxacin and tetracycline, improving their efficacy against multidrug-resistant bacteria [162,163]. This is especially significant in the context of rising infections caused by multidrug-resistant pathogens. Similar synergistic effects have been observed with essential oils and plant extracts from Syzygium aromaticum, Zingiber officinale, and Curcuma longa, which increased the susceptibility of Pseudomonas aeruginosa to chloroquine by inhibiting efflux pump activity [164]. Likewise, essential oil and extracts from Pilgerodendron uviferum effectively inhibited the NorA efflux pump in Staphylococcus aureus, thereby supporting antibiotic action [126]. Propolis is another example of a natural compound with potent synergistic potential; when combined with antibiotics such as ciprofloxacin, erythromycin, and gentamicin, it significantly enhanced their activity against S. aureus, mainly through inhibition of efflux pumps [165]. The synergistic potential of phytobiotics can also be analyzed in the context of their combinations with other phytochemicals. Cooperative interactions between compounds have been observed in antimicrobial applications; for example, a combination of flavonoids and ellagitannins from Cistus salviifolius extract significantly lowered the MIC against S. aureus [166]. It is essential to emphasize that mechanisms such as membrane disruption or oxidative stress induction represent only a fraction of the biological effects exerted by phytobiotics. Due to their multifaceted nature and ability to target numerous cellular processes simultaneously, phytobiotics exhibit significant therapeutic synergy [165,166]. Their multi-target actions enhance the efficacy of combination therapies by modulating various signaling pathways [167].

In summary, all of the mechanisms described above—such as damage to bacterial membranes or increased oxidative stress—constitute only part of the broader spectrum of phytobiotic activity. Beyond their antimicrobial effects, phytobiotics possess a range of additional health-promoting properties, including strong antioxidant activity, reduction of oxidative stress and inflammation, and modulation of immune responses [2,12]. Their ability to simultaneously influence multiple biological targets makes phytobiotics powerful enhancers of therapeutic synergy [167,168], while their regulatory effects on cellular pathways further improve the efficacy of combination therapies. Owing to these pleiotropic properties, phytobiotics represent a highly promising and versatile area of research, both as standalone agents and in synergistic applications.

4. Impact of Phytobiotics on Microbiota of Food and the Intestine

When discussing the effects of phytobiotics on foodborne pathogens, it is essential to consider the interactions between phytobiotics and food microbiota, as well as their influence on the gut microbiome.

4.1. Impact on Food-Associated Microbiota

Maintaining a balance between beneficial microorganisms (e.g., Lactobacillus and Bifidobacterium) and pathogens (e.g., Salmonella, Listeria, E. coli) is critical for gut and overall health. A stable gut microbiota protects the host from pathogens by competing for nutrients and attachment sites on the intestinal epithelium, producing antimicrobial compounds, and modulating the immune system. Diet is one of the most important modulators of the composition and function of the microbiota [169].

Crucially, the relationship between phytobiotics and the gut microbiota is bidirectional. On one hand, the presence of specific bacterial strains influences the degradation, absorption, and bioactivation of phytobiotics. On the other hand, phytobiotics themselves modulate the composition of the gut microbiota. This reciprocal interaction can yield significant health benefits, as the resulting metabolites often display strong bioactivity and promote the restoration or maintenance of microbial balance in the gut. Flavonoid-associated metabolic processes have been shown to exhibit both prebiotic (supporting beneficial bacteria) and antimicrobial (suppressing undesirable microbes) characteristics. For example, in vitro cultures supplemented with flavonoids demonstrated enhanced growth of Bifidobacterium, Lactobacillus, and Enterococcus species, alongside inhibition of Clostridium and Bacteroides [170]. Moreover, certain specific bacterial species, including Eubacterium ramulus and Clostridium orbiscindens, participate in flavonoid metabolism, breaking them down into smaller metabolites [171,172]. Additionally, the aglycone form of quercetin (i.e., lacking sugar residues) has been shown to dose-dependently inhibit the growth of various gut bacteria—including Bacteroides galacturonicus, Lactobacillus, Escherichia coli, Enterococcus caccae, and Ruminococcus gauvreauii [173]. Other flavonoids also exhibit antimicrobial activity against foodborne pathogens and are therefore employed as natural preservatives in the food industry [174]. For instance, proanthocyanidins from cranberries inhibit biofilm formation by Pseudomonas aeruginosa [175].

4.2. Impact on Gut Microbiota

Polyphenols also act as prebiotic-like compounds. Because they are not fully digested in the small intestine, they reach the colon, where they are degraded by the microbiota into simpler phenols and acids, which in turn stimulate the growth of fiber-fermenting beneficial bacteria [176,177]. It is important to note that the gut microbiota itself metabolizes flavonoids into active compounds—such as phenolic acids and dihydroflavonols—which can inhibit pathogens or exert anti-inflammatory effects in the gut [178]. Thus, a bidirectional interaction exists: polyphenols shape the microbiota, and the microbiota transforms polyphenols, enhancing their bioavailability and bioactivity [76]. In vitro studies have demonstrated that anthocyanins—such as those derived from raspberries, purple potatoes, black rice, or malvidin-3-glucoside from grapes—have a significant impact on the growth of intestinal bacteria. Specifically, these compounds have been shown to stimulate the proliferation of Bifidobacterium spp. and Lactobacillus spp., while concurrently inhibiting the growth of potentially pathogenic bacteria such as Staphylococcus aureus and Salmonella enterica sv. Typhimurium during in vitro fermentation experiments [179].

Simultaneously, specific bacterial species have been shown to catalyze the degradation of anthocyanins. For example, Eubacterium ramulus and Clostridium saccharogumia participate in the deglycosylation of cyanidin-3-glucoside—one of the principal anthocyanins—by removing glycosidic residues [180]. The metabolites derived from anthocyanin degradation can further modulate the microbiota. In an animal model, administration of a black raspberry extract rich in anthocyanins restored the abundance of beneficial bacterial species such as Eubacterium rectale, Faecalibacterium prausnitzii, and Lactobacillus spp., while reducing the overgrowth of pro-inflammatory sulfate-reducing Desulfovibrio spp. and Enterococcus spp. in mice [181]. Significant shifts in the overall gut microbiota composition have also been observed: raspberry anthocyanins altered the proportions of dominant bacterial phyla by increasing the relative abundance of Firmicutes (including Clostridium spp.) and reducing Bacteroidetes (e.g., Barnesiella spp.) [182].

Moreover, an eight-week supplementation with anthocyanins combined with prebiotic fiber in adults led to beneficial alterations in microbiota composition, marked by an increase in Bacteroidetes and a decrease in Firmicutes and Actinobacteria [183]. It is important to highlight that some compounds known primarily for their immunomodulatory effects—such as urolithins—are in fact metabolites produced by the gut microbiota. Urolithins (including several distinct forms) are derived from ellagic acid; for example, ellagitannins are metabolized in humans primarily into urolithin A and urolithin B [184]. Additionally, urolithins C and D have also been detected in the gastrointestinal tract, indicating that gut bacteria convert ellagic acid into a range of structurally diverse metabolites [185]. This bioconversion occurs mainly in the lower gastrointestinal tract (colon) and is dependent on the presence of a functional gut microbiota. Studies have shown that in individuals consuming ellagitannin-rich extracts from walnuts or pomegranates, bacterial genera such as Bacteroides, Prevotella, and Ruminococcus dominate the gut microbiota. Furthermore, there is a correlation between the abundance of the Coriobacteriaceae family and the production of urolithins, as well as a concurrent reduction in blood cholesterol levels [186]. Interestingly, different microbial species produce distinct urolithins. For example, Bifidobacterium and Clostridium have been identified as capable of metabolizing pomegranate ellagitannins, with species-specific pathways leading to the formation of different urolithin profiles [187]. Animal model studies have also demonstrated that dietary supplementation with astaxanthin can alter the composition of the gut microbiota. Astaxanthin is a carotenoid responsible for the red pigmentation in certain algae, fish, and crustaceans [188]. Administration of astaxanthin to mice at a dose of 50 mg/kg significantly modified the relative abundance of major bacterial phyla—increasing Bacteroidetes and decreasing Proteobacteria—as well as affecting composition at lower taxonomic levels [189]. Furthermore, in Helicobacter pylori-infected mice, a higher daily dose of astaxanthin (200 mg/kg body weight) reduced gastric colonization by the pathogen, alleviated mucosal inflammation, and decreased the release of pro-inflammatory cytokines associated with H. pylori infection [190]. These findings support the selective action of phytobiotics in modulating both beneficial and pathogenic gut microorganisms. Tannins may act synergistically with probiotic bacteria. Certain Lactobacillus strains have been shown to tolerate higher concentrations of tannins due to the presence of tannase enzymes, which allow them to utilize tannins as a source of carbon and energy [191]. This enables dietary tannins to favor tannase-positive probiotics, thereby limiting the growth of competing pathogenic species in the gut. However, the dosage is critical—excessive tannin intake can have antinutritional effects and overly suppress the microbiota. Thus, beneficial outcomes are typically observed at moderate intake levels [177,192]. Although essential oils are best known for their potent antibacterial and antifungal activities, they also exert selective effects on the gut microbiome. For instance, orange essential oil—rich in d-limonene and terpenes—more strongly inhibited the growth of enterotoxigenic Escherichia coli than that of beneficial Lactobacillus strains [193]. While pathogenic strains showed clear inhibition, Lactobacillus rhamnosus remained relatively unaffected—MIC for E. coli was several times lower than that for lactic acid bacteria (LAB) [193]. A similar selectivity has been reported for oregano and thyme essential oils, which contain phenolic compounds such as carvacrol and thymol. These oils markedly suppressed Clostridium perfringens, Salmonella, and E. coli in vitro, with only moderate effects on Lactobacillus spp. [119]. As essential oils act primarily by disrupting microbial cell membranes, depolarizing membrane potential, and inducing leakage of intracellular contents, they tend to be more effective against Gram-positive bacteria. This is due to the more permeable peptidoglycan layer of Gram-positive cells compared to the outer membrane of Gram-negatives. However, phenol-rich oils—such as those containing thymol—can also overcome the Gram-negative barrier by incorporating into the lipid bilayer and increasing membrane fluidity [191,193]. Importantly, when used at moderate doses, essential oils do not sterilize the gut but selectively reduce problematic microbial populations, allowing beneficial fiber-fermenting bacteria to thrive. Moreover, some components of essential oils may actually support probiotic bacteria. For example, low concentrations of limonene—the main terpenoid in citrus oil—do not inhibit and may even stimulate the growth of Lactobacillus [194]. There is a hypothesis that minor constituents of complex essential oils may exert a protective effect on beneficial microbes, while major phenolic components selectively target pathogens. The final outcome is an enhancement of the gut’s natural microbial barrier [193]. In summary, essential oils represent promising phytobiotics that contribute to maintaining microbial balance in the gastrointestinal tract.

Sulfur-containing compounds found in Allium vegetables—such as garlic, onion, and leek—have long been valued for their antiseptic properties. When garlic is crushed, the enzyme alliinase converts alliin into allicin, a potent sulfur-containing compound with bactericidal activity. Garlic also provides other bioactive sulfur compounds such as sulfoxides, disulfides (e.g., diallyl disulfide), and soluble fructans (inulin, fructooligosaccharides) with known prebiotic properties [195]. This unique combination allows garlic to modulate the microbiome through multiple mechanisms. First, allicin and related sulfur compounds inhibit the growth of various intestinal pathogens. Garlic has demonstrated bactericidal effects against E. coli, Salmonella, Helicobacter pylori, C. perfringens, S. aureus, and C. albicans [196,197]. The mechanism involves the reactive –S(O)– groups in these compounds, which interact with bacterial enzymes (e.g., oxidoreductases, proteases), oxidize thiol groups in active sites, and disrupt bacterial metabolism. Second, moderate garlic intake may promote the growth of beneficial bacteria such as Lactobacillus and Bifidobacterium, due to its content of fermentable fructans that serve as a carbon source [195]. In vitro experiments have shown that adding powdered garlic to fermentation media increases bifidobacterial counts while simultaneously suppressing the growth of Clostridium and Enterobacteriaceae [198].

Furthermore, sulfur metabolites from garlic have been shown to exert anti-inflammatory effects and support the integrity of the intestinal barrier [199]. In animal models, garlic supplementation reduced intestinal permeability, commonly referred to as “leaky gut” [200]. All of the aforementioned examples confirm the beneficial effects of phytobiotics on the gut microbiota. Consequently, phytobiotics have been considered as part of dietary interventions aimed at treating, alleviating, or preventing diseases associated with gut dysbiosis. For instance, an anti-inflammatory diet for inflammatory bowel disease was developed and tested in a clinical study involving 40 patients. This diet included, among other things, large amounts of fruits and vegetables, thus providing a rich source of natural phytochemicals while excluding pro-inflammatory foods [201]. Clinical improvement was observed in more than half of the participants, including symptom relief and enhanced quality of life. Although it remains unclear which specific dietary component played the most critical role, it is evident that the phytobiotic-rich diet led to modulation of the gut microbiota. In addition to their antioxidant properties, the anti-inflammatory effects of phytobiotics should also be emphasized in the context of gut microbiota interactions. Curcumin (from turmeric), boswellic acid (from Boswellia), quercetin (from onion), rosmarinic acid (from rosemary), berberine (from Coptis), catechin (from green tea), and shogaol (from ginger) are all well-documented phytochemicals with established anti-inflammatory activities [202,203]. When discussing diseases associated with gut dysbiosis, it is also essential to mention colorectal cancer—a major contemporary health concern. Disruptions in the intestinal microbial consortium, or the presence of an aberrant microbiota, may contribute to carcinogenesis among various other factors [204]. Many phytochemicals exhibit both anticancer and anti-inflammatory effects on colorectal cancer cells [205]. Notably, these same plant-derived compounds also influence gut microbial ecology, and such changes can occur rapidly—within just a few days of adopting a phytochemical-rich diet [206]. Similarly, polyphenol-rich extracts from sources such as green tea, honey, paprika, blackcurrant, raspberry, cinnamon, and peppermint have demonstrated inhibitory effects against H. pylori—a bacterium linked not only to gastric ulcers but also to an elevated risk of colorectal cancer [207].

Phytobiotics exert their effects by modulating key inflammatory signaling pathways such as NF-κB, MAPK, STAT, and Nrf2—central regulators of the host inflammatory response. These compounds reduce the production of pro-inflammatory cytokines (e.g., interleukins, TNF-α) and mediators such as nitric oxide and prostaglandin E2, thereby suppressing inflammation [203,208,209]. Well-known phytobiotics such as curcumin also inhibit Toll-like receptor 4 (TLR4) and NOD-like receptors (nucleotide-binding oligomerization domain), both of which are involved in initiating innate inflammatory responses [210]. In addition, certain phytobiotics and their synergistic combinations enhance the organism’s antioxidant potential, which further supports their anti-inflammatory effects. Phytobiotics indirectly activate antioxidant signaling pathways to reduce oxidative stress, protecting cells from inflammation-associated damage [211,212,213,214,215]. Moreover, some phytobiotics contribute to maintaining intestinal barrier integrity—a critical factor in preventing chronic inflammation. For example, resveratrol activates the Nrf2/HO-1 signaling pathway, leading to increased expression of tight junction proteins such as ZO-1 and occludin, which reinforce epithelial structure and limit antigen and endotoxin translocation into systemic circulation [216]. Similarly, naringenin exerts protective effects on the intestinal barrier by modulating the MLCK pathway, resulting in reduced production of pro-inflammatory cytokines and improved expression of tight junction proteins [217]. These effects are particularly relevant in the context of intestinal barrier dysfunction observed in inflammatory bowel disease and other chronic conditions.

Gut microorganisms are known for their dualistic nature: while they function as essential intestinal symbionts, they also play a key role in the production and preservation of fermented foods. At the same time, effective microbial control during fermentation and storage is necessary to suppress the growth of pathogenic bacteria. In this context, natural phytobiotics—either inherently present in raw materials or added as spices or extracts—can significantly influence the microbiome of fermented foods, improving microbial safety, extending shelf life, and often shaping the sensory profile of the final product. One example is plant-based fermented foods such as vegetable pickles. In addition to the primary vegetable substrate, various herbs and spices—such as dill, garlic, horseradish, oak leaves, bay leaves, blackcurrant leaves, and chili peppers—are added. These not only contribute to the characteristic flavor of the product but also serve a molecular function by preventing spoilage. For instance, the traditional addition of garlic and horseradish to pickled cucumbers is a well-established method for preventing softening and mold formation. This effect is attributed to phytochemicals such as allicin and mustard oils (from horseradish), which inhibit the growth of molds and unwanted aerobic bacteria on the surface of the ferment. Bay leaves and allspice, often added to vegetable ferments, release eugenol and other essential oils that enhance microbiological stability—such as reducing surface mold growth in pickled cucumbers. In kimchi, garlic has been shown to linearly increase the initial diversity of fermentative microbiota (mainly Lactobacillus and Leuconostoc) in a dose-dependent manner. Higher garlic levels (2–4%) led to earlier and more sustained dominance of LAB, resulting in faster acidification and more effective suppression of undesirable bacteria [218]. Garlic not only accelerated the onset of lactic fermentation but also enhanced metabolite profiles, with increased levels of lactic and acetic acids and elevated production of desirable flavor compounds such as amino acids and esters. Moreover, garlic can serve as a source of autochthonous LAB strains and provides allicin, which selectively eliminates competing microorganisms [161]. Ginger, another common spice in fermented foods, contains phenolic compounds such as gingerol and shogaol with bacteriostatic properties. In kimchi, ginger contributes to the inhibition of L. monocytogenes and Staphylococcus spp. [219].

These findings highlight the multifaceted role of phytobiotics in fermented foods—not only as flavoring agents but also as modulators of microbial dynamics. Through selective inhibition of spoilage and pathogenic bacteria and enhancement of beneficial fermentative species, phytobiotics contribute to both the safety and sensory quality of the final product. Their incorporation into fermentation processes, whether traditional or controlled, represents a natural and effective strategy for microbiome optimization in food systems.

5. Phytobiotics in Practical Applications

The growing interest in phytobiotics stems from their natural origin and their broad-spectrum antimicrobial efficacy, targeting both food spoilage microorganisms and foodborne pathogens. They offer a promising alternative to synthetic preservatives, the use of which is increasingly restricted due to potential side effects—such as allergic reactions or carcinogenicity associated with certain chemical additives—and negative consumer perception [220]. Unlike their applications in animal production—where phytobiotics are primarily used as feed additives to improve gut health or growth performance—their role in food preservation focuses on direct antimicrobial effects, shelf-life extension, and maintaining sensory quality.

Plant extracts can be incorporated into foods in various forms, including powders, pastes, liquids, and other delivery formats [221,222]. Beyond their antimicrobial activity, these natural substances offer additional benefits such as improvement of flavor and color. Some extracts, such as those derived from the genus Hippophae—a small shrub that produces orange-colored berries—are rich in vitamins and other nutrients, making them suitable for boosting the nutritional value of food products [221].

Phytobiotics exhibit potent antimicrobial activity against a broad range of foodborne pathogens and spoilage microorganisms (

Table 5. Selected examples of antimicrobial activity of phytobiotics.

Pathogens Tested	Phytobiotic	MIC Value	References
Salmonella spp.	Mustard allyl isothiocyanate	60–100 ppm	[230]
	Ilex paraguariensis (Yerba Mate)	0.78–6.25 mg/mL	[231]
	Olive leaf extract	35.313 mg/mL	[232]
	Psidium guajava (Goiabeira Vermelha)	1.8–2.4 mg/mL	[233]
	Curcumin, carvacrol, and styrax liquidus	125.0 µg/mL for carvacrol, 132.5 µg/mL for curcumin, 31.3 mg/mL for styrax liquidus	[234]
	Aloe secundiflora leaf ethyl acetate, Aloe rabaiensis leaf methanolic, and Aloe rabaiensis leaf ethyl acetate extracts	0.3906 mg/mL	[235]
	Finger root, clove, lemongrass, cardamom	0.049 to 0.781 µL/mL	[236]
E. coli	Fibrauretine	2.5–5 mg/mL	[237]
	Olive leaf extract	41.083 mg/mL	[232]
	Curcuma longa	40 mg/mL	[238]
	Zanthoxylum armatum	40 mg/mL	[238]
	Azadirachta indica	20 mg/mL	[238]
	Thyme essential oil	2 μg/L	[239]
Campylobacter spp.	Gallic acid	15.63 to 250 μg/mL	[240]
	Allyl isothiocyanate	0.63 to 5 ppm	[241]
	Carvacrol	0.06 mg/mL	[242]
	Grape seed extract	20 mg/L	[243]
	Chinese leek extracts	2.0 mg/mL	[244]
Listeria monocytogenes	Rhodomyrtus tomentosa ethanolic extract	16-32 μg/mL	[245]
	Olive leaf extract	37.055 mg/mL	[232]
	Beetroot extract	20 mg/mL	[246]
	Trans-cinnamaldehyde	0.90 mM	[247]
	Carvacrol	0.75 mM	[247]
	Thymol	0.60 mM	[247]

). For example, extracts from Punica granatum and Phyllanthus emblica have demonstrated both bacteriostatic and bactericidal activity against S. aureus and E. coli, making them effective agents in reducing microbial contamination in food products [223]. Moreover, essential oils and plant extracts possess antifungal properties, which are particularly important for controlling molds that produce mycotoxins [5,224]. Phytobiotics have been successfully applied in various food systems, including salads, marinated fish, and meat products [225,226,227]. A wide range of foodborne pathogens are susceptible to phytobiotics, with Bacillus cereus being among the best-documented examples. This Gram-positive bacterium is highly sensitive to many plant-derived extracts. For instance, clove aqueous extract inhibits B. cereus at an MIC of 0.315% [228]. Similarly, sumac extracts have shown exceptional efficacy against Bacillus spp., including B. cereus, with MIC values ranging from 0.25 to 0.32% [229].

Another Gram-positive pathogen, Staphylococcus aureus, is also susceptible to numerous phytobiotics. Extracts from rosemary, clove, and thyme have demonstrated strong antibacterial effects against this species [228], while pomegranate peel extract has likewise exhibited significant antimicrobial activity [248]. Moreover, punicalagin, specifically extracted from pomegranate, exhibits potent antimicrobial activity by interfering with iron homeostasis and inducing SOS responses, leading to DNA damage and growth inhibition of S. aureus [249]. Phenyllactic acid effectively inhibits the growth of this bacterium in both planktonic and biofilm states, and its antimicrobial activity also persists in dairy products [250]. In addition, essential oils of oregano and thyme have shown strong bactericidal activity against antibiotic-resistant and biofilm-forming strains of S. aureus, making them particularly promising for extending food shelf life [251].

Among Gram-negative bacteria, Escherichia coli—particularly pathogenic strains such as E. coli O157:H7—is of particular concern. Ethanol extracts from hibiscus, rosemary, clove, and thyme have been shown to effectively inhibit E. coli growth [228], with rosemary extract displaying notable efficacy against the O157:H7 strain [252]. Ethanolic extracts of pomegranate (Punica granatum) and Indian gooseberry (Phyllanthus emblica) showed strong bacteriostatic and bactericidal properties against E. coli, with MIC values of 2.5 mg/mL and MBC of 5 mg/mL [223]. In addition, the ethyl acetate fraction of the extract from Patrinia scabiosaefolia showed high antimicrobial activity, suggesting its potential in food preservation [253]. Essential oils from thyme, cinnamon, garlic, and oregano showed strong antimicrobial activity against many food pathogens, including E. coli O157:H7. Phenols and aldehydes are mainly responsible for their activity [254].

Salmonella spp., which includes various pathogenic strains, also demonstrates susceptibility to phytobiotics. Pomegranate extracts have been found to effectively inhibit Salmonella growth [248], while rosemary has shown antimicrobial activity against Salmonella eenterica serotypes Enteridis and Typhi [252]. Multiple studies report high sensitivity of S. enterica to a variety of phytobiotics and phytochemicals. For instance, extracts from Quercus infectoria and Phyllanthus emblica—rich in tannins, flavonoids, saponins, and terpenoids—exhibited complete bactericidal effects against drug-resistant S. Typhi and S. Enteritidis serotypes at concentrations of 50 mg/mL and 25 mg/mL, respectively. When combined at lower concentrations (12.5 mg/mL), these extracts showed a strong synergistic effect [255]. A mixture of compounds including thymol, menthol, linalool, trans-anethole, methyl salicylate, 1,8-cineole, and p-cymene has demonstrated strong antimicrobial activity against various Salmonella serotypes, specifically S. Enteritidis and S. Typhimurium [103]. Several phytochemicals have demonstrated the potential to interfere with and prevent the development of various multidrug resistance mechanisms. Naringenin, 5-methoxypsoralen, and licarin A were found to inhibit the AcrAB-TolC efflux pump, a key component in antibiotic resistance in S. enterica [256]. Methanolic extract and essential oil from Nigella sativa (black seed) also exhibited potent activity against resistant S. enterica strains, with the methanolic extract showing lower MIC values and larger inhibition zones compared to the essential oil [257]. Plants such as Adhatoda vasica, Amaranthus hybridus, and Aloe barbadensis have shown high efficacy against multidrug-resistant S. Typhi serotypes [258]. Furthermore, Anacardium occidentale, Artemisia afra, Detarium microcarpum, and Detarium senegalense displayed both antibacterial and antibiofilm activity against S. enterica, with A. afra and D. senegalense being particularly effective [259].

Listeria monocytogenes, notable for its ability to proliferate under refrigeration conditions, also demonstrates sensitivity to phytobiotics. Rosemary extract has been shown to exert strong antimicrobial activity against this microorganism [252], while sumac extract has exhibited bacteriostatic effects [229]. A nanoemulsion of eugenol was found to significantly inhibit biofilm formation and fully eradicate mature biofilms of L. monocytogenes strains (Scott A and AT19115) at both 25 °C and 10 °C. The mode of action involved suppression of cell motility, EPS, and extracellular DNA production, as well as quorum sensing activity [260]. Additionally, extracts from processed cranberry pomace have demonstrated antimicrobial activity against L. monocytogenes, attributed to high levels of phenolic compounds and antioxidant capacity. The observed effects were primarily due to membrane damage and disruption of transmembrane transport [261]. Rosmarinic acid, ascorbic acid, and essential oils from thyme and clove significantly reduced L. monocytogenes growth in artificially contaminated soft cheese over a 4-week period. The mechanism of action included membrane disruption and interference with intracellular processes [262]. L. monocytogenes exhibits susceptibility to various phytobiotics, not only in vitro but also in vivo. Trans-cinnamaldehyde (TC), carvacrol (CR), and thymol improved survival in Galleria mellonella larvae infected with L. monocytogenes, with CR and TC being most effective. Their mechanism involved activation of host genes responsible for antimicrobial peptide production [263]. Methanolic extracts from Allium cepa (onion) and Zingiber officinale (ginger) also demonstrated strong activity against L. monocytogenes, in part by binding and inhibiting the virulence factor listeriolysin O [264]. Dehydrocorydaline, a compound isolated from Corydalis turschaninovii, exhibited potent antibacterial activity at low MIC and MBC values, inhibiting biofilm formation and bacterial motility through disruption of carbohydrate metabolism and cell wall synthesis pathways [265].Extracts from Psoraleae semen (Bogolji) and Sophorae radix (Gosam) showed strong antilisterial properties, with Bogolji being particularly effective. These extracts remained stable under various conditions and exhibited low cytotoxicity [266].

The anaerobic foodborne pathogen C. perfringens is also susceptible to phytobiotic interventions. Ethanolic leaf extract of Eucalyptus globulus showed strong antibacterial activity against antibiotic-resistant C. perfringens type D, with an inhibition zone of 14.6 mm and an MIC of 1500 µg/mL. Notably, the extract also enhanced the efficacy of the antibiotic ceftriaxone [267]. Extracts from Artemisia annua, especially dichloromethane and hexane fractions, exhibited antimicrobial activity against C. perfringens, with MIC values of 185 and 270 µg/mL, respectively. Active compounds identified included ponticaepoxide and chrysosplenol D [268]. Compounds isolated from Humulus lupulus (hops)—such as xanthohumol, lupulone, and humulone—displayed antimicrobial activity against C. perfringens, with MIC and MBC values ranging from 15–107 µg/mL, comparable to standard antibiotics [269]. In another study, 10 aqueous plant extracts—including those from allspice, cardamom, cinnamon, clove, coriander, ginger, and nutmeg—demonstrated efficacy against C. perfringens at effective concentrations ranging from 0.625 to 10 g/kg and exhibited synergistic effects with salt and sodium nitrite [270]. A blend of natural antimicrobial compounds—including maltodextrin, citric acid, sodium citrate, malic acid, and extracts from citrus and olives—significantly reduced the virulence of C. perfringens by restoring intestinal barrier integrity and suppressing the production of pro-inflammatory cytokines [271].

The increasing interest in natural preservatives is largely driven by evolving consumer preferences for “clean-label” products—those free from synthetic additives. Although synthetic preservatives are effective, they are often associated with potential health risks, including risks from long-term consumption and environmental contamination [272]. Social pressure and regulatory measures have led to the withdrawal of some of these additives from the market [273,274]. In this context, phytobiotics align with these consumer expectations, offering safer alternatives with a lower risk of adverse effects and reduced ecological impact [275]. These natural substances, including essential oils, plant extracts, and fermented metabolites, exhibit potent antimicrobial and antioxidant properties and can be used to preserve a wide range of food products [276,277]. However, their application in food technology faces several limitations, such as low chemical stability, susceptibility to oxidation, and potential negative impacts on sensory qualities. These challenges are particularly evident in direct applications to complex food matrices, where interactions with other food components may reduce antimicrobial efficacy. To mitigate these drawbacks, advanced formulation strategies have been developed. Encapsulation techniques—including nanoencapsulation— can protect active compounds, improve their solubility and bioavailability, and enable controlled release, thus enhancing their overall functionality in food preservation systems [5,278]. Phytobiotics can be used in various forms—such as essential oils, plant extracts, or fermented components—for preserving a wide range of food products. Phytobiotics have been successfully applied in the preservation of various food categories. In meat and poultry, their direct addition has been shown to significantly extend shelf life and improve microbiological safety [279,280]. In fresh products such as fruits and vegetables, phytobiotic-based natural preservatives help maintain quality and inhibit pathogen growth [281]. Additionally, phytobiotics serve as excellent stabilizers for edible oils, with plant-derived antioxidants improving oxidative stability while meeting clean-label requirements favored by consumers [282]. An innovative application involves incorporating phytobiotics into packaging systems [279]. For example, pectin-based films enriched with plant extracts have shown selective antibacterial and antioxidant activity, enhancing food shelf life [283]. In meat and seafood preservation, edible coatings and films fortified with phytobiotics significantly reduce oxidative processes and microbial growth in these perishable raw materials [284,285]. Edible coatings and biopolymer films, composed of materials such as cellulose, chitosan, starch, and proteins can be enriched with antimicrobial agents, forming active packaging with dual functionality. These systems not only serve as physical barriers but also facilitate the gradual release of active antimicrobial substances, directly inhibiting microbial growth at the food surface. Chitosan coating with nanoencapsulated savory oil (Satureja), developed by Pabast et al. [286], effectively delayed spoilage of lamb meat by inhibiting the growth of mesophilic bacteria, Pseudomonas spp., and LAB for 20 days at 4 °C [286]. Similarly, active films based on hydroxypropylmethylcellulose containing nanoemulsified oregano oil were shown by Lee et al. [287] to inhibit growth of S. Typhimurium, E. coli, L. monocytogenes, Bacillus cereus and Staphylococcus aureus [287]. Active packaging with phytobiotics also works well in fish and meat products. Surendhiran et al. [288] created chitosan nanofibers with pomegranate oil that reduced fungal growth on bread; in turn, chitosan spray coatings with a nanoemulsion of Ferulago angulata oil reduced the initial number of psychrotrophic and Pseudomonas bacteria on filleted rainbow trout by 3 log₁₀ CFU/g over 16 days of refrigeration, significantly delaying fish spoilage [288].

In addition to chitosan-based systems, starch-based edible coatings enriched with essential oils also offer promising results in preserving fresh produce. These coatings help regulate gas exchange and moisture loss while providing antimicrobial protection, making them suitable for extending the shelf life of fruits and vegetables. Furthermore, encapsulation of phytobiotics in proteins or polysaccharides not only improves their functional properties but also allows for tailored release profiles compatible with specific food types [289]. Several commercial solutions have already emerged, including biopolymer films enhanced with zinc oxide nanoparticles, which simultaneously improve mechanical integrity and antimicrobial action [290]. Natural preservatives such as bacteriocins, lysozyme, and lactoferrin are also gaining traction in industrial formulations due to their broad-spectrum antimicrobial activity [277,291]. Nonetheless, industrial scalability and cost-effectiveness remain significant hurdles. Sustainable extraction methods, including green synthesis and scalable encapsulation techniques, are being explored to meet economic and environmental criteria [289,290].

Finally, the implementation of phytobiotics in food technology must comply with regulatory standards. Comprehensive toxicological and safety assessments are required prior to their approval for use in food products, with particular emphasis on compound stability, migration potential, interactions with food matrices, and long-term effects on human health [292,293]. Moreover, the global regulatory landscape is highly heterogeneous—some countries apply precautionary principles, while others require complete risk assessments. Navigating these frameworks is essential for the successful commercialization and adoption of phytobiotic-based preservation systems [292].

In summary, phytobiotics offer a promising alternative to synthetic food preservatives due to their antimicrobial, antioxidant, and safety properties. Although broader adoption requires overcoming certain technological and sensory challenges, advances in encapsulation methods and standardization of applied research could greatly facilitate the commercialization of these compounds in the food industry [5,278,280].

6. Challenges and Limitations of the Effective Application of Phytobiotics in Combating Foodborne Pathogens

Phytobiotics have emerged as promising alternatives to conventional antibiotics in both human and animal nutrition, particularly in the context of combating antibiotic-resistant foodborne pathogens. Despite their potential, several challenges and limitations hinder their broader application in food systems and therapeutic settings. The commercialization of phytobiotics poses a number of challenges, including the need to ensure their stability and safety of consumption, as well as overcoming barriers related to high production costs, market competition, stringent regulatory requirements, and lack of standardization that may limit their wider use.

One major challenge lies in the intrinsic variability of phytobiotics. Their composition can fluctuate significantly depending on the plant species, the geographical origin, cultivation conditions, harvest time, and processing methods. This variability affects the consistency and predictability of their antimicrobial efficacy. Furthermore, phytobiotics often comprise complex mixtures of bioactive compounds, the individual and synergistic effects of which are not yet fully understood. This complicates both scientific evaluation and regulatory approval.

Stability and safety are critical issues for the application of phytobiotics in the food industry. The stability of phytobiotics is influenced by various factors, including chemical interactions, environmental conditions, microbial contamination, and extraction methods. Phytobiotics are prone to chemical degradation during storage, which can lead to the loss of active components and the formation of inactive or even toxic metabolites. Many phytobiotics are highly susceptible to degradation under food processing and storage conditions, including exposure to heat, light, oxygen, humidity, and variations in pH, which can significantly diminish their bioactivity and shelf life, thereby limiting their practical utility in food systems [294,295]. It has been shown that higher temperatures can accelerate the degradation of active compounds, as observed for diarylheptanoids in Curcuma comosa (at as low as 40 °C) and phenolic compounds in Gynura procumbens [296,297]. Microbial contamination, particularly by pathogenic microorganisms capable of forming biofilms, poses a significant threat by degrading active constituents and generating harmful by-products. Therefore, maintaining strict control measures during preparation, packaging, storage, and transportation is essential to preserve product integrity [298]. Furthermore, extraction and preparation methods significantly affect the stability of phytobiotics. Techniques such as ultrasonic, microwave, and supercritical fluid extraction, although effective in isolating bioactive compounds, can modify the structure and stability of these compounds, potentially resulting in less stable or less bioactive forms [299]. In addition to stability concerns, many phytobiotics suffer from poor bioavailability due to their complex structures and low water solubility. This limits their effectiveness when administered in traditional forms [300]. The bioavailability of phytobiotic compounds—particularly polyphenols and essential oils—is a crucial factor determining their practical effectiveness. The bioavailability of phytobiotics, which refers to the extent and rate at which the active compounds are absorbed and utilized by the body, is influenced by several factors, both intrinsic to the compounds themselves and related to the host and the surrounding environment. One of the primary factors is the chemical structure of the phytobiotics. Whether a compound is hydrophilic or lipophilic significantly affects its solubility in gastrointestinal fluids, which in turn influences its ability to permeate the intestinal epithelial cells and reach systemic circulation. Lipophilic compounds, for example, often require the presence of fats or bile salts for enhanced absorption [301]. Additionally, host-related factors such as age, sex, ethnicity, physiological status, and overall health condition can significantly affect the bioavailability of phytobiotics [302]. For instance, the composition of an individual’s gut microbiota can influence the metabolism and absorption of plant-derived compounds, while gastrointestinal diseases or impaired digestion can limit bioavailability [303]. Considering the interindividual variability in pharmacokinetics and bioavailability, determining the optimal dose of phytobiotics is challenging. Factors such as end-organ dysfunction, interactions with other drugs, and dietary intake can affect the efficacy of phytobiotics, complicating dose optimization [304].

The food matrix in which phytobiotics are consumed also plays a significant role in their bioavailability and functionality. Interactions with food components such as proteins, lipids, fibers, and carbohydrates can either facilitate or hinder the release, solubility, stability, and absorption of phytobiotics, ultimately affecting their efficacy. While some nutrients may enhance the bioavailability of bioactive compounds—for example, dietary fats improving the absorption of lipophilic phytochemicals—others, such as certain polyphenols, may form complexes that impede intestinal uptake. Moreover, these interactions can alter the antimicrobial potency of phytobiotics, impact their sensory properties, or lead to the formation of undesired byproducts, complicating their effective application in food systems [302].

Beyond direct effects on bioavailability, phytobiotics can engage in complex functional interactions within food matrices and biological environments. These interactions can be synergistic, leading to enhanced biological activities such as greater antioxidant or antimicrobial effects, as observed with the combination of polyphenols such as quercetin and resveratrol. Conversely, antagonistic effects may arise when the efficacy of one or more active constituents is diminished by other dietary compounds. Such outcomes depend on the molecular structure, concentration, and environmental context in which these compounds act. Furthermore, functional interactions may modulate metabolic pathways, influence the solubility and cellular uptake of phytobiotics, and affect their systemic clearance, thereby altering their pharmacokinetics and pharmacodynamics [303].

Overall, the complex interplay between phytobiotics, food matrices, and host factors poses a significant challenge in the practical application of phytobiotics, necessitating further research to fully exploit their potential in food formulations.

Concerns also remain regarding the impact of phytobiotics on the gut microbiota. Phytobiotics are recognized for their ability to beneficially modulate the gut microbiome by promoting the proliferation of commensal microbial populations, such as Lactobacillus and Bifidobacterium, while inhibiting the growth and virulence of pathogenic bacteria, thus exerting prebiotic-like effects. These activities not only support gut health but also offer broader systemic benefits, such as improved nutrient absorption, enhanced mucosal immunity, and better metabolic regulation [305]. Regular consumption of phytobiotics has been associated with the prevention and management of various chronic diseases, largely through modulation of gut microbiota composition, reduction of low-grade inflammation, and restoration of metabolic balance [306]. Despite these promising health benefits and the general perception of phytobiotics as safe natural compounds, concerns remain regarding their broader impact on gut microbial communities. While phytobiotics have the potential to inhibit pathogenic bacteria, their effects on commensal and probiotic populations have yet to be fully characterized. Disruption of the gut microbial balance could possibly yield unintended health consequences. It was shown that some phytochemicals, such as pyrrolizidine alkaloids, have been identified as hepatotoxic and potentially carcinogenic, highlighting the need for thorough toxicity assessments. Safety and toxicity profiles of phytobiotics are not yet fully established. Although many are generally recognized as safe, the potential for adverse effects—especially at higher doses or with chronic exposure—necessitates rigorous toxicological assessment [307]. Additionally, differences in individual tolerance, species-specific responses in animals, and the presence of contaminants or adulterants can further complicate safety evaluations. Safety assessments employ in vitro and in vivo methodologies, including high-throughput screening systems, animal model studies, and adherence to international regulatory frameworks such as those established by the European Food Safety Authority (EFSA) [308].

Finally, the economic and regulatory landscape presents substantial barriers to commercialization of phytobiotics. Despite growing interest in natural alternatives to antibiotics, the process of introducing phytobiotics to the market remains a complex and costly endeavor. High expenses are associated with extraction, purification, and standardization processes, which further increase when transitioning from laboratory to industrial-scale production. This is further complicated by the necessity of consistent quality assurance and the variability of the plant material due to environmental factors. Additionally, the financial burden is increased by the extensive requirements for research and development—including efficacy assessments, bioavailability studies, and toxicological evaluations—which are crucial not only for formulation optimization but also to satisfy regulatory requirements. These scientific and economic challenges are compounded by complex regulatory barriers. Phytobiotics intended for food applications must comply with stringent safety and efficacy standards that differ depending on the region. Regulation and quality control of phytobiotics are complex because of their natural origin and the variability of their composition. Ensuring the safety, efficacy, and consistency of phytobiotic products requires stringent testing and standardization, which is currently lacking or undeveloped in many regions [309]. Although organizations such as EFSA provide guidance for botanical additives, existing frameworks often do not provide detailed protocols tailored to the complexity of phytobiotics. The World Health Organization has accepted the use of chromatographic fingerprinting for the qualitative and quantitative evaluation of herbal products [310]. However, the practical application of this strategy is often hindered by the limited availability of simple, rapid, sensitive, and sufficiently validated analytical methods—particularly for assessing the long-term stability of phytoconstituents [311]. This shortfall reduces regulatory confidence and remains a major obstacle to the broader acceptance of phytobiotic products.

7. Key Knowledge Gaps

Although the topic of using phytobiotics against foodborne pathogens has been the subject of a considerable amount of research over the years, there are still some knowledge gaps waiting to be filled. Completing them through targeted research is essential for the effective use of plant-derived phytobiotics against foodborne pathogens. Future research should focus on understanding the mechanisms of action, interactions between phytochemicals, in vivo efficacy, resistance development, standardization, safety, and regulatory challenges to realize the full potential of these natural antimicrobials.

While many studies have reported antimicrobial properties of plant extracts, the specific mechanisms by which these phytochemicals inhibit pathogens remain unclear. For example, antimicrobial activity of various phytochemicals against pathogens such as Salmonella, E. coli, and Listeria has been observed, but the exact biochemical pathways involved in this action need further clarification [312,313]. Also, the potential for pathogens to develop resistance to phytobiotics is not well documented. Long-term studies are required to assess whether long-,term use of these compounds could lead to resistance, similar to that seen with conventional antibiotics [103,313,314]. In addition, the interactions between different phytochemicals in a single plant extract and their combined effects on pathogens are not well explored. Rather, single phytobiotics are being studied, while understanding these interactions might help formulate more effective combinations of phytobiotics [103,262].

Moreover, most of the research on this topic has been conducted in vitro, and there is a significant gap in understanding how these phytobiotics work in vivo, particularly in complex food matrices and in the human body. For example, while some plant extracts have shown promising results in vitro, their efficacy in real food systems and their bioavailability in humans require further research [103,313,315].

Comprehensive studies on the safety and potential toxicity of phytobiotics are limited. To ensure that they are fully safe for human consumption, there is still a need for research aimed at assessing their safety, efficacy, and potential interactions with conventional treatments. Furthermore, knowledge should be supplemented with an understanding of the long-term effects of the consumption of these compounds, especially at higher doses. Evaluating their impact on human health and the microbiome is crucial to establishing guidelines for their inclusion in food systems [313,315].

8. Future and Prospects of Phytobiotics in the Food Industry

Phytobiotics are becoming increasingly important as natural food safety and quality enhancers. However, as outlined in the chapter above, the application potential of phytobiotics in the food industry depends on overcoming a number of technological, economic, and regulatory constraints (

Table 6. Barriers to the effective use of phytobiotics and corresponding mitigation strategies.

Difficulties in the Use of Probiotics	Description	Solutions
Chemical and physical degradation	Susceptible to environmental factors such as light, heat, and pH variations	Use of nanocarriers such as liposomes and phytosomes to enhance stability, ensuring proper storage conditions
Interaction with other components	Multi-component formulations can cause degradation or loss of activity; possible reactions between components lead to degradation or toxic metabolites	Careful formulation and use of advanced delivery systems
Bioavailability issues	Poor solubility and stability lead to low bioavailability	Nanocarrier systems to improve solubility and targeted delivery
Environmental and storage conditions	Susceptible to deterioration during storage	Advanced drug delivery systems to protect from degradation
Microbial contamination	Ensuring stability and pathogenic microorganisms degrading active constituents	Robust quantification and quality control methods
Regulatory and quality control	Ensuring stability and consistency is challenging due to the complex nature	Novel decontamination approaches
Extraction and preparation	Impact of extraction methods on compound stability	Advanced extraction techniques

).

In recent years, new strategies to improve the stability and bioavailability of phytobiotics have been intensively developed, including nanoencapsulation techniques, the formation of complexes with polysaccharides, and the use of modern extraction methods such as supercritical CO₂ extraction or subcritical water extraction. The use of polymeric nanocarriers not only increases the solubility and persistence of bioactive compounds but can also reduce their toxicity and improve their efficacy in biological environments [316]. In the context of enhancing the biological activity of phytobiotics, strategies for combining them with other natural components, such as postbiotics, bacteriocins, or secondary metabolites of probiotic microorganisms, are also important. The interaction of these compounds can lead to synergistic effects, increasing the effectiveness of biocontrol and limiting the growth of pathogens without the need for synthetic preservatives [317]. The need for in-depth research on such interactions is a current and promising direction of scientific development. For this purpose, advanced research methods, such as omics techniques (transcriptomics, proteomics, and metabolomics) and molecular modeling, are increasingly being used to better understand the mechanisms of action of phytobiotics at the cellular and molecular levels. The implementation of phytobiotics on a large scale in the food industry also requires the development of optimal storage conditions and methods to prevent microbial contamination at the production and distribution stages. The use of light-impermeable packaging and the storage of products at low temperatures can significantly extend shelf life and preserve the activity of plant compounds. Simultaneously, it is essential to overcome regulatory and economic barriers to the commercialization of phytobiotics. Research and development investment is crucial, enabling the establishment of efficient and cost-effective extraction and formulation technologies. International regulatory harmonization can contribute to simplifying registration procedures, while cooperation between the public and private sectors can provide the adequate funding needed to develop and implement innovative solutions.

In conclusion, this review highlights the significant potential of plant-derived phytobiotics as natural alternatives to conventional antibiotics for combating foodborne pathogens. Bioactive compounds present in phytobiotics exhibit numerous properties, including antimicrobial, antioxidant, and anti-inflammatory, and recent advances in extraction and formulation technologies have further enhanced their stability and bioavailability. However, the practical implementation of phytobiotics in the food industry requires a multidisciplinary approach. Optimization of processing, storage, and delivery systems is technologically essential to maintain their biological activity throughout the food production chain. In terms of safety, accurate toxicological assessment and standardization of phytobiotic preparations are critical to ensure consumer protection and consistent product quality. In addition, regulatory challenges must be addressed, including the need for a clear regulatory framework, harmonized international standards, and streamlined approval processes for the use of phytobiotics in food products. To fully unlock the benefits of phytobiotics, coordinated efforts between scientists, industry, and regulatory bodies are needed. Investments in research and innovation should focus not only on elucidating mechanisms of action using advanced analytical and omics-based techniques but also on developing cost-effective and scalable production methods. With a strategic, collaborative, and science-based approach, phytobiotics hold great promise for improving food safety, reducing reliance on synthetic preservatives, and supporting sustainable food systems.