The effects of dairy and dairy derivatives on the gut microbiota: a systematic literature review

Figures & data

Table 1. PICOS criteria for inclusion.

Parameter	Criteria
Population	Human participants, both clinical (diseased e.g. CVD, T2DM) and healthy
Intervention	Bovine/cow’s milk Fermented/cultured dairy Casein/whey isolates Milk protein supplements
Comparator	Other proteins (e.g. soy, meat) Other milk types (sheep, goat, donkey and human) Standard diet No dairy
Outcomes	Gut microbiota composition assessed from faeces

CVD: cardiovascular disease; T2DM: diabetes 2 mellitus.

Figure 1. Prisma flow diagram.

Table 2. Population characteristics.

Study	Country	Sample size enrolled and completed	Female%	Age mean	Population type	Inclusion criteria
Fernandez-Raudales et al.^Citation39	United Sates of America	Enrolled: 81 Completed: 64	0	32	Overweight subjects	(i) No usage of antibiotics; (ii) Non-lactose intolerant;(iii) No smoking;(iv) Non-athlete; (v) Non-vegetarian
Link-Amster et al.^Citation40	Switzerland	Enrolled: 30 Completed: 30	14	47	Healthy	(i) Non-lactose intolerant; (ii) No recent antibiotic treatment; (iii) No vaccination with Salmonella typhi during 5 year period preceding the study
Odamaki et al.^Citation41	Japan	Enrolled: 33 Completed: 31	68	52	Healthy	(i) No vegetarians; (ii) Normal stool frequency
Odamaki et al.^Citation42	Japan	Enrolled: 32 Completed: 32	66	40	Healthy	(i) Consumption of yogurt less than twice a week
Yilmaz et al.^Citation43	Turkey	Enrolled: 45 Completed: 45	49	39	Patients with IBD	(i) No allergies or intolerance to milk; (ii) Alcohol consumption < 20 g/day; (iii) No antibiotic treatment within the last 1 month; (iv) No column or bowel operation history up to 3 months before the start of the study; (v) No infection in proceeding month
Beaumount et al.^Citation44	France	Enrolled: 42 Completed: 38	66	30	Healthy overweight (25< BMI <30)	(i) No GI disease; (ii) No usage of antibiotics during the last 3 months before the intervention; (iii) No dairy intolerance; (iv) No smoking
Reimer et al.^Citation45	Canada	Enrolled: 125 Completed: 96	53	40	Overweight or obese (BMI > 25, age 18–75)	(i) No antibiotics during the past three months; (ii) Body mass <350 Ib; (iii) No major GI surgeries, diabetes, CVD, liver pancreas disease; (iv) No chronic use of antacids or bulk laxative
Bendtsen et al.^Citation46	Denmark	Enrolled: 80 Completed:52	87	44	Overweight subjects	(i) No gastrointestinal diseases; (ii) No dairy food allergies; (iii) No infectious or metabolic diseases; (iv) No use of dietary supplements during the study or 6 months prior to the study; (iv) No use of cholesterol-lowering medicine; (vii) Women could not be pregnant or lactating

BMI: body mass index; CVD: cardiovascular disease; GI: gastrointestinal; IBD: inflammatory bowel disease.

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.^Citation39	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.^Citation40	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.^Citation41	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.^Citation42	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.^Citation43	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.^Citation44	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.^Citation45	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.^Citation46	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.

Table 4. Changes in gut microbiota from feces according to dairy intervention.

			Changes in the fecal microbiota in response to the intervention/comparator
			Changes of relative abundance in phylum, genus or species level
	Study	Intervention/comparator	Phylum	Genus	Species	Diversity changes (alpha or beta diversity)
	Fernandez-Raudales et al.^Citation39	Arm 1: Bovine milk, 500 mL/d	^⊘Firmicutes Bacteroidetes ↓ Proteobacteria ↑ ^⊘ Firmicutes/Bacteroidetes	Roseburia ↑ Lactobacillus ↑ Prevotella ↓ Bifidobacterium ↑	NR	ACE ↓ Chao1 ↓
		Arm 2: Low Glycine soymilk, 500 mL/d	Firmicutes ↓ Bacteroidetes ↑ Proteobacteria ↑ Firmicutes/Bacteroidetes ↓	Roseburia ↓ Prevotella ↑	NR	ACE↓ Chao1 ↓
Milk		Arm 3: Conventional soymilk, 500 mL/d	Firmicutes ↓ Bacteroidetes ↑ Proteobacteria ↑ Firmicutes/Bacteroidetes ↓	Roseburia ↓ Prevotella ↑	NR	ACE ↓ Chao1 ↓
Fermented dairy	Link-Amster et al.^Citation40	Arm 1: Fermented milk (yogurt), 3 × 125 g units per day	NR	Lactobacillus ↑ Bifidobacterium ↑	Lactobacillus acidophilus ↑	NA
		Arm 2: No fermented dairy/no placebo	NR	^⊘Lactobacillus ^⊘Bifidobacterium	^⊘Lactobacillus acidophilus	NA
	Odamaki et al.^Citation41	Arm 1: Yogurt provided during two phases of the trial, 200 g/d	NR	^⊘Odoribacter ^⊘Bilophila, Dorea ↓ ^⊘Ruminococcus ^⊘Bifidobacterium	NR	No changes in alpha or beta diversity
		Arm 2: Yogurt provided during one phase of the trial (during the balanced diet phase), 200 g/d	NR	Odoribacter ↓ Bilophila, ↓ Dorea ↓ Ruminococcus ↓ Bifidobacterium ↑	NR	No changes in alpha or beta diversity
		Arm 3: No yogurt during both phases of the trial	NR	Odoribacter ↑ Bilophila, ↑ Dorea ↑ Ruminococcus ↑ Bifidobacterium ↓	NR	No changes in alpha or beta diversity
	Odamaki et al.^Citation42	Arm 1: Yogurt, 160 g/d	NR	NR	Bacteroides fragilis ↓	NA
		Arm 2: UHT milk, 200 mL/d	NR	NR	^⊘Bacteroides fragilis	NA
	Yilmaz et al.^Citation43	Arm 1: Kefir 400 mL/d	NR	Lactobacillus ↑	NR	NA
		Arm 2: No fermented dairy/no placebo	NR	^⊘Lactobacillus	NR	NA
Dairy derivatives	Beaumount et al.^Citation44	Arm 1: Casein powder to provide 15% habitual E intake	NR	NR	NR	No changes in alpha or beta diversity
		Arm 2: Maltodextrin powder to provide 15% habitual E intake	NR	NR	NR	No changes in alpha or beta diversity
		Arm 3: Soy powder to provide 15% habitual E intake	NR	NR	NR	No changes in alpha or beta diversity
	Reimer et al.^Citation45	Arm 1: Whey protein bar (5 g), twice a week	^⊘Actinobacteria	^⊘Bifidobacterium	NR	No changes in alpha or beta diversity
		Arm 2: Prebiotic bar (5 g), twice a week	Actinobacteria ↑	Bifidobacterium ↑	NR	↓alpha diversity (↓ Chao1)
		Arm 3: Whey+prebiotic bar (5 g), twice a week	Actinobacteria ↑	Bifidobacterium ↑	NR	↓alpha diversity
		Arm 4: Control- no bars	^⊘Actinobacteria	^⊘Bifidobacterium	NR	No changes in alpha or beta diversity
Dairy quantity	Bendtsen et al.^Citation46	Arm 1: High dairy (HD)	No significant taxonomic changes in genus phylum level	No significant taxonomic changes in genus level	NR	No changes in alpha or beta diversity
		Arm 2: Low dairy (LD)	No significant taxonomic changes in genus phylum level	Veillonella ↓	NR	No changes in alpha or beta diversity

↑ abundance increased; ↓ abundance decreased; ^⊘Unchanged, NR: not reported in the study, NA: not applicable to the study.

Figure 2. Mechanistic pathways by which dairy and its components may impact the gastrointestinal environment and the gut microbiota composition.

Antimicrobial and stimulatory peptides produced by milk protein digestion and lactose facilitates the growth of so-called beneficial bacterial genera such as Lactobacillus and Bifidobacterium. Milk fat and opioid peptides (produced during protein digestion) negatively alter the luminal environment by inducing inflammation and increasing the gastrointestinal transit time, which consequently perturb the gut microbiota composition. Fermented dairy products favor the growth of beneficial bacteria in the gut via the active bacterial cultures and fermentation by-products.

Table

	Record numbers
Total articles from search	6592
Duplicates removed	1499
Remaining records for screening	5093
Title and abstract exclusion
Animal/in vitro studies	118
Studies in children	15
Conference abstracts	11
Studies on other cattle’s product (e.g. donkey, sheep, goat)	68
Studies on human milk	116
Studies on infants and infant formulae	69
Not in English	2
Off topic	4598
Review articles	44
Not RCTs	22
Total ineligible studies	5063
Records available for full text assessment	30
Full text assessment
Full text not available or not in English	5
Comparator not complying with study criteria	14
Wrong study	3
Total ineligible studies	22
Full text included in analysis	8

Fernandez-Raudales D, Hoeflinger JL, Bringe NA, Cox SB, Dowd SE, Miller MJ, Gonzalez de Mejia E. Consumption of different soymilk formulations differentially affects the gut microbiomes of overweight and obese men. Gut Microbes. 2012;3:490–500. doi:10.4161/gmic.21578.

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Link-Amster H, Rochat F, Saudan K, Mignot O, Aeschlimann J. Modulation of a specific humoral immune response and changes in intestinal flora mediated through fermented milk intake. FEMS Immunol Med Microbiol. 1994;10:55–63. doi:10.1111/j.1574-695X.1994.tb00011.x.

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Odamaki T, Kato K, Sugahara H, Xiao J, Abe F, Benno Y. Effect of probiotic yoghurt on animal-based diet-induced change in gut microbiota: an open, randomised, parallel-group study. Benef Microbes. 2016;7:473–484. doi:10.3920/BM2015.0173.

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Odamaki T, Sugahara H, Yonezawa S, Yaeshima T, Iwatsuki K, Tanabe S, Tominaga T, Togashi H, Benno Y, Xiao J-Z. Effect of the oral intake of yogurt containing Bifidobacterium longum BB536 on the cell numbers of enterotoxigenic Bacteroides fragilis in microbiota. Anaerobe. 2012;18:14–18. doi:10.1016/j.anaerobe.2011.11.004.

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Yılmaz İ, Dolar ME, Özpınar H. Effect of administering kefir on the changes in fecal microbiota and symptoms of inflammatory bowel disease: a randomized controlled trial. Turk J Gastroenterol. 2019;30:242. doi:10.5152/tjg.2018.18227.

 PubMed Web of Science ®Google Scholar

Beaumont M, Portune KJ, Steuer N, Lan a, Cerrudo V, Audebert M, Dumont F, Mancano G, Khodorova N, Andriamihaja M. Quantity and source of dietary protein influence metabolite production by gut microbiota and rectal mucosa gene expression: a randomized, parallel, double-blind trial in overweight humans. Am J Clin Nutr. 2017;106:1005–1019. doi:10.3945/ajcn.117.158816.

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Reimer RA, Willis HJ, Tunnicliffe JM, Park H, Madsen KL, Soto‐Vaca a. Inulin‐type fructans and whey protein both modulate appetite but only fructans alter gut microbiota in adults with overweight/obesity: a randomized controlled trial. Mol Nutr Food Res. 2017;61:1700484. doi:10.1002/mnfr.201700484.

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Bendtsen LQ, Blædel T, Holm JB, Lorenzen JK, Mark AB, Kiilerich P, Kristiansen K, Astrup a, Larsen LH. High intake of dairy during energy restriction does not affect energy balance or the intestinal microflora compared with low dairy intake in overweight individuals in a randomized controlled trial. Appl Physiol Nutr Metab. 2018;43:1–10. doi:10.1139/apnm-2017-0234.

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