Table 2.

Human dietary interventions that tested the effect of soy on the human gut microbiota

Study product	References	Subject number/description	Microbiota alterations	Health effects	Comment
Cheonggukjang (fermented soy product)	[109]	60 postmenopausal Korean women	Reduced proportion of phylum Firmicutes	Menopausal symptom relief and reduced blood glucose only in “high beneficial bacteria” product group	Study product was stratified based on fermentation process and product “beneficial bacteria” content. Microbiota effects were related to this, and only presented at phylum level
Black soymilk (instead of pork in diet)	[110]	8 test, 8 control pre-diabetic/obese Taiwanese adults	No changes in alpha- or beta-diversity; increased relative abundance of Butyricicoccus and SCFA producers; lower abundance of Rothia spp.	Reduced oxidative stress and lower levels of glycative stress markers	V3-V4 16S amplicon sequencing limits resolution
Fermented versus unfermented soy milk	[111]	56 test, 56 control healthy Japanese adults with low Bifidobacterium count	Increased abundance of lactobacilli and bifidobacteria, Faecalibacterium in both groups, more pronounced in fermented soy group; increased Clostridiaceae and Enterobacteriaceae in non-fermented group	Higher levels of faecal SCFAs in fermented soy group; improvement in defaecation habits in both groups, achieved earlier in fermented soy group	V1-V2 16S amplicon sequencing was supplemented by targeted qPCR
Commercial fermented soybean beverage	[112]	Lean (10) and obese (9) participants in USA	Increased abundance of Bifidobacteria and Blautia in lean subjects; increased oral abundance of Veillonellaceae in lean subjects; study product significantly increased Fusobacteria in obese participants	Not tested	V4 16S amplicon sequencing
Fermented soy milk (FSM) plus L. casei plus aglycones, versus unfermented soy milk	[113]	30 test, 30 controls in Japan	Lactobacillaceae significantly increased, Bifidobacteriaceae trended upwards, Enterobacteriaceae and Porphyromonadaceae significantly lower in FSM group	Both groups had improved skin condition and significantly increased levels of urinary isoflavones	V1-V2 16S amplicon sequencing
Soy isoflavone concentrate tablet, 80 m/day	[114]	16 menopausal women for 6 months, in Spain	Increased abundance of Lactonifactor longoviformis, Faecalibacterium prausnitzii, Bifidobacterium sp., Ruminococcus sp., isoflavone metabolizers; Clostridium leptum and C. coccoides abundance increased in equol producers	Not tested	PCR-DGGE* and qPCR
Soy bars containing isoflavones	[115]	17 postmenopausal women in USA	Significant increases in Bifidobacterium after soy consumption; Bifidobacterium and Eubacterium were significantly greater in equol vs non-equol producers	Correlations detected between urinary isoflavones and isoflavone metabolites with microbiota	Microbiota was studied by PCR-DGGE* and pyrosequencing of 16S V4 region
Low glycinin soymilk (LGM), conventional soymilk (S) or bovine milk	[116]	64 overweight and obese men in USA	Total bacteria increased in all treatments; Bacteroides-Prevotella increased in LGM; Firmicutes: Bacteroidetes ratio decreased in LGM and S groups; Eubacterium and Clostridium were more abundant in the S group	Not tested	qPCR for total bacterial load and quantitation of Bacteroides-Prevotella, Bifidobacterium, and Lactobacillus; Short-read sequencing of V1-V3 region. Microbiota of all 3 groups separated by beta-diversity analsysi
Non-fermented soybean milk (NFSM) and fermented soybean milk (FSM)	[117]	10 healthy subjects, 21–25 years old in Japan	Bifidobacteria and lactobacilli were more abundant in both groups, Clostridia were less abundant	Not tested	Bacteriological culture on selective media
Non-fermented soybean milk (NFSM) and fermented soybean milk (FSM), cross-over	[118]	28 healthy adults in China	Bifidobacterium spp. and Lactobacillus spp. Increased; higher ratios of Bifidobacterium spp. and Lactobacillus spp. to Clostridium perfringens (P < 0.05)	Not tested	Bacteriological culture on selective media

*DGGE: Denaturing gradient gel electrophoresis