Table 1.

Characteristics of Studies Investigating Dietary Effects on Microbiome Composition in Infants and Children

Country of Study, Age Range and Number of Participants	Study Design	Method of Diet Assessment	Method of Microbiota Assessment	Outcomes	Citation
Sweden 0-1 y N=98	Cross-sectional	Feeding practices questionnaires assessing BF, FF, MF BF cessation	Metagenomic shotgun sequencing by Illumina HiSeq 2000	BF infants predominate in Bifidobacterium, Lactobacillus, Collinsella, Megasphaera, and Veillonella BF cessation increased Bacteroides, Bilophila, Roseburia, Clostridium, and Anaerostipes Newborn and 4 mo microbiota enriched in genes for HMO degradation 12-mo microbiota enriched in genes for complex sugar and starch degradation; increased B. thetaiotaomicron	27
Denmark 0-3 y n=330	Observational Cohort (SKOT)	FFQ at 9. 18. 36 mos. visits	Targeted qPCR analysis	Weaning decreased Bifidobacterium, Lactobacillus, and increased Enterobacteriaceae, Clostridium spp. and Bacteroides spp.	26
U.S. (North Carolina) 1-4y and adults N=28	Cross-sectional	Children attended daycares adhering to nutritional requirements defined by local state and federal rules and regulations	Microarray targeting V1-V6 16S rRNA & qPCR	Children had less diverse microbiota than adults Actinobacteria, Bacilli, Clostridium cluster IV (Ruminococcaceae), and Bacteroidetes were higher in children than adults	30
Italy and Burkina Faso 1-6 y N=29	Cross-sectional	Italian parents completed a detailed medical, diet, and lifestyle survey Burkina Faso parents provided in-depth interview on children’s diet and a 3-d dietary questionnaire	V5-V6 16S rRNA by 454-pyrosequencing	Firmicutes-to-Bacteroidetes ratio (F:B ratio) was ~6-fold higher in Italian than Burkina Faso children 3 genera involved in utilization plant polysaccharides (Prevotella, Xylanibacter (Bacteroidetes), and Treponema (Spirochaetes) were higher in Burkina Faso children.	28
Australia 2-3 y N=37	Cross-sectional	Australian Child and Adolescent Eating Survey (FFQ) 24 hr recall	V6-V8 16S rRNA by Illumina MiSeq	Dairy intake negatively associated with Bacteroidetes, species richness and diversity, and positively with Erysipelatoclostridium spp. and the F:B ratio Vegetable protein intake positively associated with Lachnospira Soy, pulse, and nut positively associated with Bacteroides xylanisolvens Fruit intake negatively associated with Ruminococcus gnavus	32
U.S. (Illinois) 4-8 y N=22	Cross-sectional	Nutrient intake assessed by 3-day food diaries. Youth and Adolescent (YAQ) FFQ was used for dietary patterns	V3-V4 16S rRNA by Illumina MiSeq	2 dietary patterns were associated with microbial taxa and composition Dietary Pattern 1 (intake of fish, protein foods, refined carbohydrates, vegetables, fruit, juice and sweetened beverages, kid’s meals and snacks and sweets) was linked to higher Bacteroidetes, Bacteroides, and Ruminococcus and lower Bifidobacterium, Prevotella, Blautia and Roseburia. Dietary Pattern 2 (intake of grains, dairy and legumes, nuts and seeds) was associated with higher Cyanobacteria and Phascolarctobacterium and lower Dorea and Eubacterium	31
Philippines - Rural (Baybay) and urban (Ormoc City) 7-9 y N=43	Cross-sectional	Parents/guardians interviewed using FFQ modified from Singapore National Dietary Survey and adapted to dietary habits of Filipino children	V6-V8 16S rRNA by 454 pyro-sequencing	87.5% of Baybay children fell into P-type cluster (defined by Prevotellaceae) and 78.9% of the Ormoc samples were included in the termed BB-type cluster (defined by Bacteroidaceae, Bifidobacteriaceae, Ruminococcaceae, and Lachnospiraceae)	33
Thailand - Rural (Buriam) and urban (Bangkok) 9-10 y N=45	Comparative cross-sectional	7-day dietary records	V1-V2 16S rRNA by Illumina MiSeq	Bangkok children had higher Actinobacteria, Bacteroidales and Selenomadales Buriram children had more Clostridiales, Peptostreptococcaceae and unclassified Ruminococcaceae and higher butyrate and propionate	34
Netherlands 6-9 y N=281	Cross-sectional	Parent-report FFQ	Metagenomic shotgun sequencing by Illumina sequencing	Higher Bacteroidetes and Actinobacteria (Bifidobacterium) in children than adults Negative correlation between high dietary fiber consumption and low plasma insulin levels in children with Bacteroides and Prevotella enterotypes, but not Bifidobacterium enterotype	35
Thailand 8-11 y N=60	Cross-sectional	Self-administered FFQ	qPCR	Vegetables positively correlated with Lactobacillus and Prevotella; Bifidobacterium spp. negatively associated with fish and beef	36
China and Malaysia 7-12 y N=210	Cross-sectional	Singapore Health Promotion Board validated FFQ	qPCR	Geographical-related factors (i.e. diet), rather than ethnicity (i.e. Southern Chinese or Malay children) is a major delineator of microbiome changes Bifidobacterium, and Collinsella positively correlated with refined-sugar enriched foods; Collinsella positively associated with fruits and curry foods	37
Bangladesh 8-13 y N=10 U.S. 12-14 y N=4	Cross-sectional	Not reported	V1-V3 16S rRNA by 454 pyrosequencing	Bangladeshi children had lower Bacteroides and higher Prevotella, Butyrivibrio, and Oscillospira Bangladeshi children consumed non-Western diet low in refined-sugar enriched foods and meat and high in rice, bread, and lentils	38
Egypt (Giza) 13.3-14.5 y N=28 U.S.(Ohio) 10.1-15.7 y N=14	Cross-sectional	Not reported	V4 16S rRNA by Iliumina MiSeq	Egyptian consumed Mediterranean-type diet & American children consumed a Western diet Egyptian children had Prevotella enterotype and American children had Bacteroides enterotype Egyptian children had higher fecal SCFAs, microbial polysaccharide degradation-encoding genes, and polysaccharide-degrading genera	40

Abbreviations: F:B, Firmicutes to Bacteroidetes ratio; BF, breastfed; FF, formula-fed; FFQ, food frequency questionnaire; MF, mixed-fed; SCFA, short chain fatty acids; U.S., United States