Table 1.

Methods and outcomes of clinical studies examining UPFs and the gut microbiome.

References	Gut Microbiome Collection Method and Frequency		Alpha Diversity	Beta Diversity	Microbiome Sequencing Analysis: Bacterial Composition Changes in Relation to UPFs		Composition Changes Related to Specific UPFs
					Increase ↑	Decrease ↓
Atzeni, 2022 [17]	One stool sample collected by volunteers at home and frozen	METHODS	Chao1, Shannon, and Simpson indices analyzed with one-way ANOVA.	Euclidean distance analyzed by PERMANOVA.	16S rRNA analysis of the V4 variable region using Novaseq		No significant differences between bacterial taxa and UPF item categories.
		RESULTS	No significant differences.	No significant differences.	Positive association between Alloprevotella spp. (p = 0.041) and Sutterella spp. (p = 0.116) vs. tertile 2. Positive association between Alloprevotella spp. (p = 0.065), Negativibacillus spp. (p = 0.096), and Prevotella spp. (p = 0.116) vs. tertile 3.
Cuevas-Sierra, 2021 [16]	One fecal sample self-collected by volunteer using OMNIgene. GUT kits from DNA Genotek (Ottawa, ON, Canada)	METHODS	Chao1 and Shannon indices analyzed using a paired non-parametric test.	Bray–Curtis index analyzed using PERMANOVA test.	16S rRNA analysis of the V3–V4 variable regions using MiSeq		Women: dairy and pizza positively correlated with Actinobacteria (p < 0.05), and pizza positively correlated with Bifidobacterium spp. (p < 0.05) Men: meat positively correlated with Bacteroidetes (p < 0.05)
		RESULTS	Men consuming >5 servings/day of UPFs showed lower richness compared to men consuming <3 servings/day (observed p = 0.03, Shannon p = 0.01, Chao1 p = 0.04), yet no differences in women or whole population.	No significant differences.	Whole population: Gemmiger spp. (p < 0.001), Granulicatella spp. (p < 0.001), Parabacteroides spp. (p < 0.001), Shigella spp. (p < 0.001), Bifidobacterium spp. (p < 0.001), Anaerofilum spp. (p = 0.001), Cc_115 spp. (p = 0.007), Oxalobacter spp. (p = 0.008), Collinsella spp. (p = 0.008) Women: Acidaminococcus spp. (p < 0.001), Butyrivibrio spp. (p < 0.001), Gemmiger spp. (p < 0.001), Shigella spp. (p < 0.001), Anaerofilum spp. (p = 0.001), Parabacteroides spp. (p = 0.002), Bifidobacterium spp. (p = 0.006) Men: Granullicatella spp. (p < 0.001), Blautia spp. (p = 0.002)	Whole population: Lachnospira spp. (p = 0.003), Roseburia spp. (p = 0.003) Women: Melainabacter spp. (p = 0.002), Lachnospira spp. (p = 0.003) Men: Anaerostipes spp. (p < 0.001)
Fernandes, 2023 [18]	One fecal sample collected at home; one aliquot was stored in a tube containing 3.5 mL of guanidine for genomic DNA conservation	METHODS	Chao1, Shannon, Simpson, and Observed Species indices analyzed using Pearson’s correlation coefficients.	N/A	16S rRNA analysis of the V2–V4 + V6–V9 (excluding V1 and V5) variable regions using Ion Torrent Personal Genome Machine™		N/A
		RESULTS	No associations between food processing level and alpha diversity.	N/A	Clostridium butyricum, Odoribacter splanchnicus, Barnesiella intestinihominis Alistipes onderdonkii, Alistipes indistinctus,	Ruminococcus sp., [Ruminococcus] gnavus, Bacteroides vulgatus, Bacteroides plebeius
García-Vega, 2020 [19]	One fecal sample self-collected by volunteer at home, refrigerated, and brought to the lab within 12 h	METHODS	Estimates calculated with BiodiversityR 2.11. Shannon and Shannon evenness (Jevenness) indices calculated using Vegan 2.5 and tested with ANOVA.	Estimates calculated with GUniFrac 1.1 and tree-based UniFrac distances tested with PERMANOVA.	16S rRNA analysis of the V4 variable region using MiSeq		OTUs from Oscillospira sp., unclassified Ruminococcaceae, Ruminococcus sp., Lachnospira sp. positively associated with intake of plant-derived food groups, rich in dietary fiber; Bifidobacterium adolescentis associated with plant-derived food groups; bile-tolerant Bilophila sp., Prevotella copri, and the opportunistic pathogen Prevotella melaninogenica were associated with increased intake of animal-derived foods
		RESULTS	Higher in females than males (Shannon, p = 0.046), higher in middle-aged than younger individuals (Shannon, p = 0.012). No significant association between diet quality (including UPF intake) and alpha diversity.	Differences according to participants’ city of origin (p = 0.001), sex (p = 0.001), socioeconomic level (p = 0.024) and BMI (p = 0.002). No significant association between diet quality (including UPF intake) and beta diversity.	Bifidobacterium adolescentis, Prevotella melaninogenica, Subdoligranulum variabile, Veillonella dispar, Ruminococcus sp., Bilophila sp., Oscillospira spp.	Prevotella copri, Clostridium hathewayi, Ruminococcaceae unclassified sp., Gemella sp., Lachnospira sp., Oscillospira spp.

Abbreviations: UPF = ultra-processed food; BMI = body mass index; OTUs = operational taxonomic units; PERMANOVA = permutational multivariate analysis of variance; N/A = not applicable.