3.1. Phenolic Compounds of Extracts Obtained from the Peels and Seeds of Different Papaya Varieties
Table 1 presents the total phenolic compounds (mg GAE/100 g dry sample) extracted from different papaya varieties.
The mean total phenolic content (TPC) in the papaya peel ranged from 374.01 to 511.09 mg GAE/100 g dry weight. No significant differences (
p ≥ 0.05) were found in TPC among the different papaya varieties for the peel. In contrast, the mean TPC of the seeds varied significantly among varieties, ranging from 229.61 to 1029.24 mg GAE/100 g dry weight (
p ≤ 0.05). The seeds of the Maradol variety had a TPC of 1029.24 mg GAE/100 g dry weight, which was much higher than the TPC of any of the other varieties tested (
Table 1).
Significant differences in total phenolic content (TPC) were observed between by-products within the same variety. In the Maradol variety, the TPC was significantly higher in the seeds (1029.24 mg GAE/100 g) than in the peel (467.85 mg GAE/100 g). Conversely, in the Tainung variety, the peel had a significantly higher TPC (511.09 mg GAE/100 g) than the seeds (229.61 mg GAE/100 g).
In similar studies, papaya by-products have been reported to contain high phenolic concentrations. Their phenolic content is sensitive to variety, ripening stage, and extraction method; for peels, values typically fall around ~200–900 mg GAE/100 g dry weight under conventional ethanolic extraction and can exceed 1500 mg/100 g when phenolic-enriching or fractionation protocols are used [
12]. For seeds, the literature values under conventional or optimized ethanolic extractions commonly range from ~250 to ~600 mg GAE/100 g dry weight [
13], and increases with ripening have been observed [
31]. In line with these trends, process-optimization studies demonstrate that extraction parameters markedly modulate seed TPC, underscoring the joint influence of methodological factors and developmental stage.
The results of the identification and relative abundance of bioactive compounds in the papaya extracts, derived from HPLC-ESI-QTOF analysis, are presented in
Table 2 and
Table 3.
Table 2 systematically categorizes the identified constituents. Included for each entry are their respective retention times (Rt) and the characteristic fragments acquired during MSn mass spectrometry experiments.
Identification (
Table 2) and relative abundance (
Table 3) of bioactive compounds by HPLC-ESI-QTOF in papaya by-products (peel vs. seed, and between varieties) reveal several interesting patterns. First, phenolic compounds (peaks 1–7) show a notably higher relative abundance in seed extracts compared to peel extracts for many peaks, whereas acids (peaks 8, 9, 10) and flavonoids (peaks 11, 12) show mixed results. While the by-product factor (seed vs. peel) was significant for most analytes (
Pb < 0.001), the variety factor was not (
Pe > 0.05). This indicates conserved individual-peak profiles across varieties despite differences in total phenolics.
This compositional data supports the TPC results, where seeds of certain varieties (e.g., Maradol) had much higher total phenolic content than peels, consistent with seeds being a richer source of individual phenolics and flavonoids. Several literature reports align with these findings. A recent work by Alonso et al. [
43] evaluated the phenolic profile of papaya by-products (including seeds and peel) using HPLC-MS/MS and reported that seeds generally contained higher levels of phenolic compounds compared to the peel extracts. Similarly, Robles-Apodaca et al. [
13] optimized extraction from papaya seeds and showed that seed extracts under optimized conditions are enriched in phenolics and flavonoids, contributing to high antioxidant activity.
These observations (
Table 2 and
Table 3) suggest that the seed represents a major reservoir of phenolic compounds in papaya by-products, particularly in certain varieties. In addition, the identification of compounds such as caffeoylquinic acid derivatives (peak 7), isorhamnetin dihexoside (peak 11), and quercetin-3-O-rutinoside (peak 12) provides a more detailed understanding of the chemical composition of papaya by-products, allowing discrimination not only at the level of total phenolics but also among specific phenolic and flavonoid subclasses. Detection of caffeoylquinic acid derivatives and quercetin glycosides (including quercetin-3-O-rutinoside) aligns with prior papaya by-product profiles [
5,
44]; isorhamnetin glycosides have been reported in papaya tissues (leaves), supporting their occurrence within the species, although tissue-specific confirmation in peel and seed warrants verification [
45].
3.2. Antioxidant Activity of Extracts Obtained from the Peels and Seeds of Different Papaya Varieties
The results of antioxidant activity, quantified via the 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging assay and the 2,2′-azinobis-(3-ethylbenzothiazoline)-6-sulfonic acid (ABTS) radical scavenging assay, are presented in mg of Trolox per 100 g of extract in
Table 4.
The mean antioxidant activity, as determined by the DPPH method, in papaya shells ranged from 189.08 to 287.91 mg Trolox/100 g dry weight. For the seeds, the mean values varied between 208.19 and 276.33 mg Trolox/100 g dry weight. No significant differences (p ≥ 0.05) in DPPH antioxidant activity were observed among the different papaya varieties, nor were there significant differences between the two by-products (shell and seeds) within the same variety.
Analysis of the ABTS method results revealed distinct patterns in antioxidant activity across papaya by-products. The mean values for papaya shell ranged from 144.49 to 209.73 mg Trolox/100 g dry weight, with significant differences (
p ≤ 0.05) observed among the different varieties. For the seeds, mean ABTS values varied between 168.10 and 289.96 mg Trolox/100 g dry weight, and significant differences (
p ≤ 0.05) were indeed found among varieties. Notably, the Maradol variety’s seeds (280.96 mg Trolox/100 g) exhibited significantly higher antioxidant activity compared to both the Solo (168.10 mg Trolox/100 g) and Tainung (191.74 mg Trolox/100 g) varieties. The Hawaiian variety (227.02 mg Trolox/100 g) did not show significant differences when compared to other varieties. Furthermore, significant differences in ABTS activity were also observed between the shell and seeds, specifically within the Maradol variety (
Table 4).
These results are consistent with assay chemistry. ABTS detects both hydrophilic and lipophilic antioxidants, while DPPH performs best in non-polar media; as a result, DPPH often under-resolves differences that ABTS can detect in mixed plant matrices like papaya by-products. This helps explain why DPPH showed no significant variety or shell–seed effects, but ABTS did reveal variety effects in seeds [
46,
47].
Consistent with our results, in papaya, Jeon et al. [
31] showed that seed extracts consistently exhibited higher DPPH and ABTS radical scavenging capacities than the pulp/shell at comparable concentrations, and that total phenolics were strongly correlated with antioxidant activity measured by the ABTS method. Similarly, and highlighting cultivar-specific responses, Gaye et al. [
48], using aqueous extracts of three Senegalese cultivars, reported that by DPPH, seeds showed antioxidant activity greater than or equal to that of shells in all cultivars. In contrast, and reinforcing the assay-dependent sensitivity mentioned above, ABTS results were cultivar-dependent: in the first cultivar, seeds outperformed shells; in the second cultivar, shells outperformed seeds; and in the third cultivar, seeds again outperformed peels, underscoring genotype-tissue-assay interactions.
3.3. Antimicrobial Activity of Extracts Obtained from the Shells and Seeds of Different Papaya Varieties
For antimicrobial activity, analyses were performed against bacteria (
Bacillus cereus,
Staphylococcus aureus,
Salmonella choleraesuis,
Listeria innocua, and
Listeria monocytogenes).
Table 5 presents the antibacterial activity results (expressed as % inhibition) of the various papaya extracts (Solo, Hawaiian, Maradol and Tainung) at concentrations of 1000, 700, and 350 mg/L.
The variety of papaya significantly influenced the antimicrobial capacity of the extracts. The Hawaiian variety demonstrated superior inhibitory effects against four of the five bacterial strains tested: Listeria innocua, Listeria monocytogenes, Bacillus cereus, Staphylococcus aureus, and Salmonella choleraesuis. Overall, inhibition percentages ranged from 40.60% to 84.63% against L. innocua, 61.47% to 89.21% against L. monocytogenes, 52.92% to 86.17% against B. cereus, 52.90% to 92.64% against S. aureus, and 66.40% to 94.92% against S. choleraesuis.
Regarding the plant part, seed extracts consistently exhibited higher inhibition than shell across all five bacteria, and the by-product main effect was significant (Pb < 0.001). Although inhibition against S. choleraesuis was often high, the most responsive species depended on the variety (e.g., Maradol peaked for L. innocua; Tainung for L. monocytogenes). Overall, S. aureus and L. monocytogenes tended to show high inhibition, whereas B. cereus and L. innocua were more variable, with L. innocua lower in several varieties.
The antimicrobial activity was clearly influenced by extract concentration in both shell and seed extracts. At 1000 mg/L extract, inhibition reached ~91% for L. monocytogenes and remained in the high 70–80 % for the other species, decreasing stepwise at 700 and 350 mg/L (e.g., down to ~48% for L. innocua at 350 mg/L).
Significant interaction effects were detected for variety × by-product (Pe*b) across all five bacteria (p < 0.001). Variety × concentration (Pe*c) was also significant for all five. By-product × concentration (Pb*c) was non-significant only for L. innocua (p = 0.18) but significant for L. monocytogenes, B. cereus, and S. aureus (p < 0.001) and for S. choleraesuis (p = 0.05).
It is likely that the antimicrobial activity of the papaya extracts reflects a multi-compound mode of action, in which phenolic acids (e.g., caffeoylquinic) and flavonol glycosides (quercetin-based) contribute via membrane disruption, enzyme inhibition, and anti-biofilm/quorum-sensing effects [
49,
50,
51]. In parallel, benzyl isothiocyanate (BITC)—formed from benzyl glucosinolate detected in our profile (
Table 3)—shows potent antibacterial activity, notably against
L. monocytogenes and
S. aureus, as evidenced by recent studies in food-relevant systems and mechanistic assays [
52,
53]. Overall, this evidence supports interpreting the observed inhibition as the integrated outcome of multiple bioactives rather than a single dominant constituent.
These results are consistent with reports indicating that papaya by-products possess broad in vitro antibacterial activity, modulated by cultivar, plant part, and extraction conditions. As comparable examples, first, methanolic extracts of cv. Sekaki/Hong Kong seeds strongly suppressed
B. cereus and
Salmonella enterica, illustrating both the higher mean seed activity and solvent dependence [
54]; second, an ethanolic extract of papaya shell reached a minimum inhibitory concentration of ≈1.56 mg/mL against
L. monocytogenes, in the same order of magnitude as the highest dose used here (1000 mg/L) and consistent with ≈90% inhibition at that level [
55]. Broader evaluations of tropical fruit by-product extracts corroborate dose-dependent suppression of
Listeria,
Salmonella,
Bacillus, and
Staphylococcus, reinforcing the main effect of concentration and the significant variety x concentration interaction observed in our study [
56]. Taken together, these findings support and justify the results obtained in the present study, highlighting that both the concentration effect and varietal differences observed here are consistent with previous literature.
3.4. Characterisation of Digestion Extracts
Table 6 shows the evolution of total phenolic compounds (TPCs) and antioxidant capacity (determined by ABTS and DPPH methods) of papaya extracts during in vitro simulated gastrointestinal digestion. The digestion phases analyzed included the initial sample, stomach, small intestine, and colon simulation. For the colon phase, results are presented as a combined value, as no significant effect on phenolic content or antioxidant activity was observed across its distinct stages.
The TPC content of the papaya extract was significantly higher (
p ≤ 0.05) than the control in the initial sample (207.00 mg GAE/L vs. 27.75 mg GAE/L), and this significant difference was maintained through the stomach and small intestine phases (
Table 6). This sustained higher TPC content suggests a notable bioaccessibility and stability of papaya phenolics against gastric acidity and small intestinal enzymatic degradation, indicating their potential availability for absorption in the upper gastrointestinal tract [
57,
58]. In the colon simulation, no significant difference in TPC was observed (81.74 vs. 64.89 mg GAE/L), which may reflect a combination of upper-tract absorption, microbial transformation into non-Folin-reactive products, and the assay’s limited specificity for structurally modified phenolics [
59,
60].
Regarding antioxidant capacity, papaya extracts showed higher ABTS than the control in the initial and stomach phases, and a significant difference also appeared in the small intestine, although the control showed the higher absolute value in that phase (0.92 vs. 0.81 mg Trolox/L). In the colon simulation, ABTS remained elevated in papaya relative to the control. Conversely, DPPH showed a significant effect for papaya only during the stomach and small intestine (
Table 6), becoming negligible in the colon, consistent with its lower discriminative power in aqueous/mixed media. Furthermore, during simulated digestion, TPC correlated with DPPH antioxidant activity across different digestion phases, but not with that of ABTS. This assay-dependent difference is consistent with previous reports showing method-specific behavior in foods and during in vitro digestion [
61,
62].
Papaya by-products contain numerous phenolic compounds that trigger a potent radical scavenging response [
5,
12]. Our results from the digestion assay are consistent with digestion studies on tropical fruits. In an in vitro model, antioxidant activity, measured using two complementary assays, increased in some fruits, whereas it remained virtually stable in papaya after digestion, supporting the persistence of activity observed in this study [
63]. Additionally, similar behavior has been reported elsewhere: in passion fruit peel, antioxidant activity remained relatively strong after simulated digestion [
64]. In papaya systems, a study on fermented papaya purée showed increased post-digestion bioaccessibility of phenolics with sustained antioxidant readouts compared with the undigested control [
65].
Table 7 displays the production of short-chain fatty acids (SCFAs) exclusively during the simulated colon phase, which is consistent with their established microbial origin.
The papaya extracts significantly enhanced acetic acid content across all three colon stages. Notably, in the proximal colon, acetic acid in the papaya extract sample (1.43 g/L) was approximately 1.59 times higher than in the control (0.90 g/L). Similarly, in the transverse colon, it was 1.53 g/L, approximately 1.37 times higher than the control (1.11 g/L). Propionic acid also followed this stimulatory trend, being 1.46 times higher (1.85 g/L) in the proximal colon and 1.14 times higher (1.89 g/L) in the transverse colon in the papaya extract digester compared to the control (1.46 g/L and 1.65 g/L, respectively). These increases underscore the potential of papaya by-product extract as a fermentable substrate for the gut microbiota, promoting the production of these key SCFAs beneficial for gut health. In contrast, butyric acid content did not show significant differences between the papaya extract and control at any stage (
Table 7), suggesting the extract’s components preferentially stimulate acetate and propionate-producing bacteria or do not favor butyrate synthesis under these conditions. Other SCFAs (valeric, isovaleric, caproic, isobutyric, and isocaproic acids) were not detected above the 0.01 g/L quantification limit.
Compared to the control group, the papaya phenolic extract favoured acetate and propionate over butyrate under these conditions. This pattern aligns with polyphenol-mediated modulation of microbial fermentation, which often shifts metabolism toward acetate and propionate. By contrast, butyrate responses are context dependent and vary with substrate availability, inoculum composition, pH, and transit time [
66,
67]. Notably, the cited red wine and cocoa trials reported microbiota changes without direct SCFA quantification [
68,
69]; thus, our SCFA pattern aligns with biological plausibility rather than direct external confirmation. Complementary in vitro studies indicate that polyphenols can influence fermentation, promoting the production of acetate and propionate [
70].
The dynamics of key microbial populations are compiled in
Table 8, with initial detectable counts in the small intestine and highest counts consistently in the proximal colon, reflecting the microbial load from the inoculum and subsequent resource utilization. The papaya extract influenced microbial populations variably. Total viable aerobic mesophilic bacteria showed significantly higher counts in the small intestine for the papaya extract group (8.52 log CFU/mL vs. control: 7.48 log CFU/mL), and significantly in the transverse colon (8.64 log CFU/mL vs. control: 8.37 log CFU/mL). Enterobacteriaceae counts also increased significantly in the proximal colon with papaya; as a facultative, heterogeneous group, this rise likely indicates greater resource use rather than a uniformly beneficial shift.
Conversely, lactic acid bacteria (LAB) were detected only in the colon and exhibited significantly higher counts in the control sample across all colon stages (
Table 8). Similarly, enterococci counts were significantly higher in the control only in the distal colon (4.98 log CFU/mL vs. papaya: 4.97 log CFU/mL). The concurrent rise in total aerobes (small intestine, transverse colon) and Enterobacteriaceae in the proximal colon, together with the significant declines in LAB and enterococci, is consistent with selective inhibition by papaya bioactives. Dietary polyphenols often exert stronger antimicrobial activity against Gram-positive taxa—compatible with the observed LAB/enterococci decreases—while some Gram-negative facultatives tolerate and/or metabolize polyphenol-derived substrates [
71,
72]. In addition, papaya seeds provide benzyl isothiocyanate (BITC), a broad-spectrum antimicrobial with documented potency against Gram-positive bacteria that could reinforce this pattern [
73,
74].
The stage-resolved increases in total viable aerobes (small intestine, transverse colon) and the higher proximal-colon counts align with how phenolic-rich substrates shape gut ecology: phenolics from papaya by-products supply bioactive molecules that are transformed by microbes, supporting growth of facultative and saccharolytic groups in early/upper compartments and sustaining high loads proximally as fermentable inputs are most available there [
75]. Notably, the effect appears to be source-specific and may depend on the polyphenol class, the co-presence of fermentable dietary fibers, and the colon region, with certain polyphenols preferentially favoring acetate production while others more strongly influence butyrate or propionate [
76]. This interpretation is consistent with evidence that tropical fruit-derived phenolics (including papaya peels) are abundant and bioactive, and that polyphenol-rich matrices can remodel communities and fermentation readouts in vitro [
5,
70].
3.5. Multivariate Analysis
Figure 1 displays the Principal Component Analysis (PCA), which projects the samples and variables onto the plane defined by Principal Component 1 (PC1) and Principal Component 2 (PC2). These two components account for a combined 74.98% of the total variance (PC1 at 48.79% and PC2 at 26.19%). PC1 is primarily associated with antimicrobial activity, and it is located on the right side of the plot. This is where varieties like Hawaiian are positioned and seeded, suggesting a higher antimicrobial capacity in their extracts. Moreover, the position of phenolic compounds such as Hidroxybenzoic acid isomer (peak 2), Quercetin-3-Orhamnosyl rutinoside (peak 3), and Zeatin-9-glucoside (peak 6) suggests their potential contribution to the antimicrobial activity observed in these extracts.
On the other hand, PC2 differentiates the samples based on the antioxidant activity, with the variety Maradol showing a positive correlation with this activity. The variety Tainung exhibits a higher concentration of compounds such as Protocatechuicacid-O-hexoside (peak 10), which may be involved in the inhibition of bacterial growth.
The PCA clearly visualized data dispersion, effectively separating the extracts based on two orthogonal bioactivity axes: antimicrobial capacity (PC1) and antioxidant potential (PC2). This statistical separation supports the specialized functional profiles of the papaya by-products. The positive correlation along PC1 between antimicrobial assays and Hawaiian seed extracts provides a strong statistical basis for their superior inhibitory performance, chemically linked to hydroxybenzoic acid isomer and Quercetin-3-O-rhamnosyl rutinoside. Conversely, the differentiation along PC2 highlights the compositional uniqueness of the Maradol variety, which is aligned with high antioxidant activity, confirming its superior antioxidant profile. These results offer a rationale for a nuanced valorization strategy: Hawaiian extracts are the most promising candidates for strong antimicrobial applications, while Maradol extracts are better suited for use as natural antioxidants, a targeted approach central to optimizing the use of these by-products in the food industry.