Table 3.

Methodological characteristics of articles reviewed.

Study	Study design	Trial duration	Sample size calculation	Intervention	Additional instructions provided for participants whilst enrolled in trial	Wash-out-period prior to commencing trial	Technique used to assess microbiota composition in feces	Methods used to report changes in microbiota composition/species
Fernandez-Raudales et al.39	Randomized double blinded, 3-arm trial	3 months	NM	Bovine milk	Avoid dietary supplements and antibiotics Inform investigators if became ill during the course of study Avoid fluid milk other than provided by study	One-week washout period. Provided a list of food products to avoid including soy products	Technique 1: qPCR	Bacterial abundance reported in log10 copy number per gram of dry feces
							Technique 2: 16s rRNA sequencing using bTEFAP Region: V1-V3 Pipeline:.NET and # C Database: customed NCBI	Diversity measures: richness (ACE, Chao1) Changes in OTU
Link-Amster et al.40	Randomized controlled, 2-arm trial	3 weeks	NM	Fermented milk (yogurt)	No specific additional instructions for participants were reported	Two-week washout period in which all fresh fermented dairy products were excluded	Culture dependant techniques Enterobacteria were cultured on Drigalski agar Lactobacilli were cultured on MRS agar Bifidobacteria were cultured on Eugon agar	Bacterial counts were reported in CFU/g feces
Odamaki et al.41	Randomized controlled open, 3-arm parallel trial	19 days	Samples size was not based on power calculation; aimed to enroll maximum numbers due to the lack of previous data	Yogurt	The participants were prohibited to consume oligosaccharides, probiotics, dietary fibers, other yogurt, and alcohol	a seven-day pre-observation period was followed where all participants were instructed to follow their ordinary diet	16s rRNA Region: V3-V4 Pipeline: not mentioned Database: Greengenes	Diversity measures: alpha and beta-diversity Relative abundance of bacterial genera
Odamaki et al.42	Randomized open, 2-arm parallel trial	12 weeks	NM	Yogurt	No specific additional instructions for participants were reported	All participants were instructed to participate in a run-in period in which they did not ingest yogurt until notification of their screening results.	qPCR	Bacterial numbers reported in CFU/g wet weight feces
Yilmaz et al.43	Randomized controlled open-label, 2-arm trial	4 weeks	NM	Kefir	No specific additional instructions for participants were reported	No information on wash-out period reported	qPCR	Bacterial numbers reported in CFU/g
Beaumount et al.44	Randomized controlled double-blind, 3-arm parallel trial	5 weeks	Powered to detect changes in SCFA	Casein powder	No specific additional instructions for participants were reported	Two weeks run-in-period where participants we instructed to consume normal protein diet corresponding to their habitual energy intake	16s rRNA Region: V3-V4 Pipeline: QIIME and Mothur Database: not mentioned	Diversity measures: alpha and beta diversity
Reimer et al.45	Randomized controlled, double-blind, 4-arm study	12 weeks	The study was powered to detect change in body composition	Whey bar	Participants were advised to maintain their habitual diet and current level of activity	No information on wash-out period reported	16 s rRNA Region: V3-V4 Pipeline: not mentioned Database: not mentioned	Relative abundance Diversity measures: alpha and beta diversity
Bendtsen et al.46	Randomized controlled, 2-arm parallel trial	24 weeks	Powered to detect difference in weight loss and fecal fat excretion	Quantity of dairy consumed	No specific additional instructions for participants were reported	No information on wash-out period reported	16s rDNA Region: V3+ V4 Pipeline: QIIME Database: Greengenes	Relative abundance Diversity measures: alpha and beta diversity

bTEFAP: bacterial tag-encoded FLX amplicon pyrosequencing; ACE: abundance-based coverage estimator; OUT: operational taxonomic unit; qPCR: quantitative polymerase chain reaction; NM: not mentioned.