TABLE 1.

Studies in Which Researchers Relate the Early-Life Microbiome With Health Outcomes in Later Childhood and Adulthood

Research Objective	Study Population or Animal Model	Early-Life Factors and Timing of Exposure	Timing of Microbiome Analysis or Intervention	Health Outcome and Timing of Assessment	Summary of Findings	Ref. No.
NEC
To assess microbial dysbiosis before NEC in a systematic review and meta-analysis	Systematic review and meta-analysis of 14 human fecal microbiome studies of NEC	None	Variations in the microbiome before NEC development	NEC at ∼30 wk postconception	Increased proteobacteria and decreased firmicutes and bacteroidetes preceded NEC onset. Antibiotics, diet, and mode of delivery do contribute to microbial dysbiosis associated with NEC. However, causality related to these factors cannot be determined	57
To determine if 1 or more gut bacterial taxa differ between cases of NEC and controls	Prospective human cohort analysis (primary cohort, n = 122; secondary cohorts, n = 44)	None	Variations in the microbiome before NEC development	NEC in very low birth wt infants	Increases in gammaproteobacteria and decreases in negativicutes and clostridia-negativicutes classes over time preceded NEC development	58
To enhance strain-level resolution of NEC-associated pathogens by using deep shotgun metagenomics sequencing	Prospective human cohort analysis (n = 166)	None	Variations in the microbiome before NEC development	NEC in infancy	Variations in the microbiome were detected before NEC development. However, at 17–22 d postpartum, infants with high antibiotic treatment were enriched for E coli. The group later identified uropathogenic E coli as a major risk factor for NEC and associated death	59
To compare the efficacy and safety of enteral probiotic administration in preventing NEC	Systematic review and meta-analysis of 24 randomized or quasi-randomized controlled trials in humans	None	Enteral probiotic supplementation before NEC development	Stage II and stage III NEC in infancy	Enteral probiotic supplementation significantly reduced the incidence of NEC and mortality in infants	60
To assess the intestinal microbiota composition before NEC development in infants who developed NEC and controls	Prospective human cohort analysis (n = 38)	None	Variations in the microbiome before NEC development	NEC in infancy	An average of 7 samples were collected per subject and the temporal changes in microbiome composition were assessed. Throughout early life, before the development of NEC, different microbial populations dominate the gut and are associated with NEC development. In addition, the microbiome compositional progression appears to be associated with the timing of NEC onset	61
To identify microbial and metabolic biomarkers of NEC	Nested case-control design (n = 35)	None	Variations in the microbiome before NEC development	NEC in infancy	Lower α diversity 4–9 d postbirth was associated with NEC development. Microbiomes of subjects tended to cluster according to NEC status. These microbial variations were associated with shifts in urine metabolites, namely alanine and histidine	62
To determine if gut microbiome composition can be used to predict NEC severity	Prospective human cohort analysis (n = 30)	None	Variations in the microbiome before NEC development	NEC in infancy	Variations in the microbiome were not associated with NEC severity. There were also no differences in the microbiome post-NEC compared with controls	63
To assess whether fecal microbiota transplantation is an effective treatment of NEC	Wild-type and Grx1−/− mouse models of NEC	None	Fecal microbiota transplant from 1 to 4 d postbirth	NEC 5 d postbirth	Fecal microbiota transplant from healthy 6–8-wk-old mice to mouse pups conditioned for NEC reduced NEC incidence and severity compared with controls. This was dependent on Grx1. The mechanism of action is potentially through TLR-mediated inflammation and gut permeability	64
To determine if patients at risk for NEC can be identified by their meconium and early postnatal microbiota	Prospective human cohort analysis (n = 33)	Early enteral feeding and breast milk	Variations in meconium microbiome and neonatal microbiome before NEC	NEC in infancy	Clostridium perfringens and Bacteroides dorei were increased in the meconium of infants who developed NEC. C perfringens abundance persisted in neonatal stool samples. The amount of breast milk before NEC and earlier enteral feeding was negatively associated with NEC and associated with increased lactate-producing bacilli	65
To compare enteral versus parenteral antibiotics in preventing formula-induced NEC lesions in pigs	Piglet model of NEC	Antibiotic-induced	Enteral and parenteral antibiotic treatment (for 5 d post birth)	NEC in preterm piglets	Enteral antibiotics prevented NEC lesions, whereas lesions in piglets that were treated with parenteral antibiotics were increased. Enteral antibiotics decreased bacterial load and abundances of Gram-positive bacteria in the intestine. It is suggested that delayed colonization (particularly with Gram-positive bacteria) may prevent NEC. However, although microbiome variations correlate with NEC, they do not necessarily precede NEC	66
To determine if total parenteral nutrition, before the start of enteral feeding, can prevent NEC-associated gut dysfunction and inflammation	Piglet model of NEC	Enteral and total parenteral nutrition	Variations in the microbiome after feeding methods	NEC in preterm piglets	Enteral feeding increased microbial diversity and the abundance of Clostridium species. Density of C perfringens was associated with NEC severity. Microbiome variations correlate with NEC but do not necessarily precede NEC	67
To identify microbial profiles before NEC diagnosis	Prospective human cohort analysis (n = 369)	None	Variations in the microbiome before NEC diagnosis	NEC in infancy	Identification of 2 fecal microbiota profiles associated with NEC development (C perfringens type A dominant and Klebsiella dominant)	68
To characterize epigenome to microbiome crosstalk at critical neonatal stages of development	Tissue-based (immature enterocytes) and mouse models (dexamethasone or 5-azacytidine to induce epigenetic changes)	Prenatal dexamethasone or 5-azacytidine treatment	Microbiome to epigenome crosstalk in perinatal life	TLR and tight junction-signaling pathways in offspring	Prenatal dexamethasone and azacytidine treatment alters DNA methylation of tight junction and TLR genes and associated inflammatory pathways in fetuses and guts of 2-wk-old offspring. Both prenatal exposures also altered the offspring microbiome. Azacytidine treatment induces global demethylation, suggesting that the pre- and neonatal epigenome influences neonatal microbial colonization	69
Asthma and atopic disease
To analyze the microbiome of infants before atopic disease development at 1 y of age	Nested case-control design (n = 319) and Ovalbumin-challenged mouse models of asthma	None	Variations in the 3-mo-old gut microbiome	Atopy and wheezing at 1 y of age	Four bacterial taxa (Faecalibacterium, Lachnospira, Veillonella, and Rothia) were decreased among infants with atopy and wheezing at 1 y of age. Supplementation of asthma-induced mice with these 4 bacteria ameliorated airway inflammation	4
To analyze the microbiota of infants before asthma development by 4 y of age	Nested case-control design (n = 319)	None	Variations in the 3-mo-old gut microbiome	Asthma by 4 y of age	Decreased Lachnospira/Clostridium neonatale ratio at 3 mo of age was associated with asthma by 4 y of age	5
To characterize the bacterial and fungal microbiomes in neonates before asthma development at 4 y of age	Prospective human cohort analysis (n = 168)	None	Variations in gut microbiome 35 d postbirth	Asthma at 4 y of age	Variations in bacterial and fungal taxa at 35 d postbirth associated with highest relative risk of asthma. Sterile fecal water from the highest-risk group induces CD4+ T-cell dysfunction	70
To characterize the early-life critical window associated with exacerbated allergic airways responses in mice	Ovalbumin-challenged mouse model	Antibiotic-induced	Perinatal (in utero and through weaning)	Asthma induced later in life	Perinatal vancomycin exposure promotes expansion of firmicutes and exacerbates airway inflammation in mice	71
To analyze the effects of perinatal antibiotic treatment on development of hypersensitivity pneumonitis	Th1/Th17-mediated mouse model	Antibiotic-induced	Perinatal antibiotic exposure	Hypersensitivity pneumonitis in adulthood	Perinatal streptomycin promotes expansion of bacteroidetes and results in exaggerated hypersensitivity pneumonitis	72
To characterize the cellular mechanisms associated with diet or microbiota-mediated immune regulation	Wild-type, Gpr43−/−, and HDAC9−/− house dust mite mouse models of AAD; nested case-control design (n = 40)	Maternal acetate or high-fiber diet; maternal serum levels of acetate	Prenatal antibiotic exposure; prenatal acetate exposure	AAD induced in adulthood; coughing and wheeze by 1 y of age	High-fiber diet or acetate feeding of dams in pregnancy prevents robust AAD in adult offspring. Maternal serum levels of acetate were inversely associated with general practitioner visits for coughing and wheezing in the first 12 mo of life	73
To analyze the infant microbiota in association with food sensitization	Nested case-control design (n = 166)	None	Variations in the gut microbiome at 3 mo of age	Food sensitivity at 1 y of age	Decreased α diversity and increased enterobacteriaceae/bacteroidaceae ratio associated with food sensitization to at least 1 food allergen (milk, egg, peanut, soy) at 1 y of age.	74
To analyze the early-life microbiota in association with resolution of cow’s milk allergy	Nested case-control design (n = 226 subjects with milk allergy)	None	Variations in the gut microbiome at 3–6 mo of age	Milk allergy resolution by 8 y of age	Firmicutes and clostridia were enriched in microbiomes of subjects whose milk allergy resolved by 8 y of age. Bacteroidetes and Enterobacter were enriched among those whose milk allergy did not resolve by 8 y of age	75
To investigate age-dependent microbial modulation of iNKTs in mouse models of IBD and asthma	Ovalbumin-challenged mouse model	None	Exposure to maternal gut microbiome at birth	Asthma induced later in life	Neonatal exposure to a conventional microbiota (compared with GF conditions) increased iNKT in the lungs and protected against allergic asthma induced in adulthood. In addition, hypomethylation of CXCL16, driven by the microbiome, was associated with iNKT induction, implicating the microbiome in gene regulation	76
To analyze the role of the early-life lung microbiota in allergen-induced airway inflammation	Mouse model of house dust mite–induced airway inflammation	None	2-wk window of susceptibility (lung microbiome)	Asthma induced later in life	Variations in the lung microbiome (shift from gammaproteobacteria and firmicutes to bacteroidetes) associated with decreased aeroallergen responsiveness and increased Helios− T-regulatory cells. This is mediated by PD-L1. Blockage of PD-L1 in the first 2 wk of life results in enhanced allergic airway inflammation	77
To analyze the nasopharyngeal microbiome in infancy in association with respiratory disease later in life	Prospective human cohort study (n = 234)	None	Variations in the nasopharyngeal microbiome 7–9 wk postbirth	Chronic wheezing at 5–10 y of age	Children who developed chronic wheezing at 5–7 y of age and were atopic by age 2 were twice as likely to have been colonized with asymptomatic Streptococcus	78
To determine if variations in the skin microbiome in early life are associated with atopic dermatitis	Nested case-control design (n = 20)	None	Variations in the skin (antecubital fossa) microbiome at 2 mo of age	Atopic dermatitis at 1 y of age	Colonization of antecubital fossa at 2 mo of age with Staphylococcus was associated with decreased incidence of atopic dermatitis at 1 y of age	79
To analyze associations between neonatal gut Bifidobacterium species and eczema or atopy development in the first year of life	Nested case-control design (n = 117)	Colonization patterns influenced by household pets, number of siblings, and maternal allergic status	Variations in Bifidobacterium species at 1 wk and 3 mo of age	Atopic dermatitis at 1 y of age	Variations in Bifidobacterium species at 1 wk and 3 mo of age were associated with risk of eczema at 1 y of age. However, the microbiome was not analyzed after 3 mo of age	80
To analyze associations between proportions of IgA coating and bacteria bound to IgA in infancy and allergy development later in life	Nested case-control design (n = 48)	None	IgA and total bacterial load measured at 1 wk and 1 y of age	Asthma, allergic rhinoconjunctivitis, allergic urticaria, and eczema by 7 y of age	At 12 mo of age, children with allergic disease (particularly asthma) displayed a lower proportion of IgA bound to fecal bacteria. IgA recognition patterns for the microbiota varied between children with allergies and healthy children at 1 wk of age	81
To analyze fecal microbial diversity and bacterial abundances in the first year of life in association with asthma and allergies later in life	Nested case-control design (n = 47)	None	Microbial diversity at 1 mo of age	Asthma at 7 y of age	Children with asthma displayed lower overall microbial diversity than children without asthma	82
To investigate the infant intestinal microbiota composition in association with maternal prenatal stress and infant health	Nested case-control design (n = 56)	Prenatal stress	Variations in the microbiome at postnatal days 7, 14, 28, 80, and 110	GI symptoms and allergic response by 3 mo of age	Infants exposed to prenatal stress displayed more GI symptoms (38% compared with 22%) and allergic reactions (43% compared with 0%), which were associated with variations in the microbiome. This microbiome was characterized by less lactic acid bacteria and Akkermansia and greater Escherichia, Enterobacter, and Serratia	83
Obesity and metabolism
To analyze if the early-life microbiota composition is associated with childhood BMI and if antibiotic use modifies this association	Nested case-control design from 2 cohorts (Bibo cohort, n = 87; Flora cohort, n = 75)	Antibiotic treatment	Variations in the gut microbiome at 3 mo of age	BMI at 5–6 y	In the 3-mo-old microbiome, relative abundance of streptococci was positively associated with BMI at 5–6 y of age, and relative abundance of bifidobacteria was negatively associated with BMI at 5–6 y of age. Among children with a history of multiple antibiotic courses, the firmicutes phylum was significantly associated with BMI. However, microbiome composition was not measured at any other time point	84
To analyze the impact of diet on the early-life microbiome in a primate model	Primate model (high-fat versus standard diet)	Maternal high-fat diet during pregnancy and breastfeeding	Variations in the offspring microbiome composition	Shifts in microbial metabolic pathways	In this study, a link to a specific health outcome was not established. However, a maternal high-fat diet did alter the microbiome composition of offspring macaques, which persisted in juvenile macaques. Offspring displayed altered metabolic pathways on the basis of maternal diet. Additionally, these functional pathways (amino acid, carbohydrate, and lipid metabolism) correlated with abundances of specific gut bacteria	44
To determine if the placental microbiome varies in association with birth wt	Prospective human cohort analysis (n = 24)	None	Variations in the placental microbiome composition	Birth wt	Low birth wt infants displayed lower gut microbiome richness and variations in the abundances of specific bacterial taxa compared with normal birth wt infants. Lactobacillus percentage was positively correlated with birth wt	24
To analyze the effect of early-life microbial perturbation with antibiotic treatment on host metabolism and adiposity	Mouse model (high-fat versus standard diet)	Antibiotic-induced	LDP exposure from birth through weaning	Body composition in adulthood	Compared with controls and mice exposed to long-term LDP, mice exposed to LDP for 4 or 8 wk after birth displayed elevated caloric intake and faster total mass and fat mass accumulation. The authors also report that the penicillin-selected microbiota can induce metabolic changes when transferred to GF mice	6
To better understand how early-life antibiotic use alters the gut microbiome composition and metabolic development	Mouse model (high fat versus standard diet)	Antibiotic-induced	Pulsed antibiotic treatment completed shortly after weaning	Body composition from 3–6 wk	Early-life pulsed antibiotic treatment accelerates total mass and bone growth. The authors also report that response to high-fat diet is altered depending on the particular antibiotic and number of courses used to perturb the microbiota	85
To analyze the impact of maternal prepregnancy BMI on the infant gut microbiome composition and functional potential	Nested case-control design (n = 39)	Maternal prepregnancy obesity	Variations in infant microbiome composition and function	Infant metabolism at 18 mo of age	Firmicutes were reported enriched in children born to mothers at a normal wt, whereas bacteroidetes were enriched in infants born to women who were obese. In this study, a link to an infant health outcome was not established, but differential microbiome metabolic functions that were based on whether infants were born to mothers at a normal wt or to women who were obese was identified	86
To investigate the effect of cadmium exposure on the early-life gut microbiota and metabolism in adulthood	SPF mouse model	Cadmium exposure 1 wk before parental mating	Variations in the microbiome composition observed at 8 wk and at adulthood (20 wk)	Body composition measured in adulthood	Cadmium exposure in parental mice resulted in increased fat accumulation in male offspring. Alterations in microbiome composition occurred before measurements of body composition. In addition, through microbiota transfer experiments, the group reported that fat accumulation was driven by the cadmium-exposed microbiome	87
To determine if the early-life gut microbiota composition is associated with wt development in early childhood	Nested case-control design (n = 49)	None	Variations in the microbiome composition between 6 and 12 mo of age	BMI measured at 7 y of age	Greater abundance of Staphylococcus aureus in children who were obese in infancy. Greater abundances of bifidobacteria in children at a normal wt in infancy	88
To investigate the effects of early-life factors on the trajectory of gut microbial development and childhood adiposity	Prospective human cohort analysis (n = 75)	Gestational age and delivery mode	Variations in the microbiome before 6 mo of age	Adiposity at 18 mo of age	Infants with high Bifidobacterium and Collinsella at a later age displayed lower adiposity at 18 mo of age. Infants who acquired these taxa at 6 mo showed the lowest adiposity at 18 mo. In addition, acquisition of these bacterial taxa was influenced by length of gestation and delivery mode	89
To analyze the effect of subtherapeutic antibiotic administration on the gut microbiome and host metabolism	Mouse model of antibiotic-induced adiposity	Antibiotic-induced	Variations in the microbiome measured before sacrifice	Body composition measured in adulthood (16–20 wk)	The authors generated a mouse model of adiposity by exposing mice in early life to antibiotics. Variations in microbial composition before adiposity measurement was not assessed. However, the antibiotics did alter the microbiome composition, SCFA metabolism, and hepatic metabolism of fatty acids and lipids	90
To analyze the association between the early-life gut microbiome composition and BMI in childhood	Prospective human cohort analysis (n = 138)	None	Variations in the microbiome composition within the first year of age	BMI SD score between 1 and 3 y of age	Abundance of Bacteroides fragilis at 3 and 26 wk of age is associated with BMI SD score between 1 and 3 y of age. Abundance of Staphylococcus at 3 and 52 wk is inversely associated with BMI SD score between 1 and 3 y	91
Neurodevelopment
To determine if limited nesting stress alters offspring microbiota, corticosterone levels, and intestinal permeability	Rat model of limited nesting stress	Limited nesting stress	Variations in the gut microbiome composition 21 d post birth (at weaning)	Limited nesting stress from postnatal days 2–10	Limited-nesting pups had hypercorticosteronemia, enhanced intestinal permeability, decreased microbial diversity, and variations in specific microbial taxa	92
To determine if maternal high-fat-diet-induced obesity is associated with social behavioral deficits and altered microbiota in the offspring	High-fat diet mouse model	Maternal high-fat diet	Variations in the gut microbiome composition in offspring	Behavior exams on 7–12-wk-old offspring mice	A maternal high-fat diet induces compositional variations in the gut microbiome of offspring mice. Offspring mice of mothers on a high-fat diet cohoused with mice born of mothers raised on a regular diet displayed normal social behavior. In addition, reintroduction of L reuteri (lacking in offspring mice of a mother on a high-fat diet) restored normal social behavior in these mice	93
To determine if cognitive ability is associated with particular infant gut microbiota profiles	Prospective human cohort analysis (n = 89)	Group 2 was more likely to have been breastfed, less likely to have been born by cesarean delivery, and associated with white ethnicity. Having older siblings was associated with increased α diversity	3 groups of subjects were identified on the basis of their 1-y microbiome analysis	Cognitive outcomes at 1 and 2 y of age	Three groups of subjects were identified on the basis of their microbiome. Group 1 displayed high abundance of Faecalibacterium, group 2 displayed high abundance of Bacteroides, and group 3 displayed high abundance of ruminococcaceae. Individual Mullen scales differed between groups. α diversity was negatively associated with individual Mullen scales at 2 y of age (expressive language and visual reception)	94
To determine if maternal prenatal stress alters the microbial intrauterine environment and behavior in offspring	Mouse model of prenatal stress	Prenatal stress	Variations in placental microbiome and fecal microbiome of offspring	Anxiety-like behavior in offspring	Prenatal maternal stress was associated with variations in the microbiome of dams, offspring, and in the placenta. Additionally, prenatal stress is associated with increased IL-1β in the placenta and reduced brain-derived neurotrophic factor in placenta and adult offspring amygdala	7
To determine if probiotic administration in early life modifies maternal separation-induced gut dysfunction	Rat model (stress induced by maternal separation)	Maternal separation in early life (day 4 to day 19)	Variations in microbiome and gut function in offspring	Hypothalamus-pituitary-adrenal axis activity	Increased corticosterone levels and altered colonic mucosal barrier function in maternally separated rat pups. Early-life administration of probiotics (composed of Lactobacillus rhamnosus and Lactobacillus helveticus strains) to rat pups ameliorates these findings and persists to adulthood	95
To determine if early-life stress alters the gut-brain axis	Rat model (stress induced by maternal separation)	Maternal separation in early life	Variations in microbiome composition in rat pups	Symptoms of psychiatric disorders and irritable bowel syndrome	Increased plasma corticosterone and increased tumor necrosis factor-α and interferon-γ. Also, the microbiome composition varied in the maternally separated group compared with the rats that were not maternally separated	96
To examine the effects of prenatal and early-life exposure to propionic acid and LPS on offspring gut microbial metabolism, locomotor activity, and anxiety-like behavior	Rat model	None	Pre- and postnatal LPS or propionic acid exposure	Behavior traits in offspring	Prenatal propionic acid increased anxiety-like behavior in male and female adolescent offspring. Postnatal propionic acid increased anxiety-like behavior in female offspring only. Prenatal propionic acid and LPS induced developmental delays (including delays in eye opening)	97
To determine if colonization by gut microbiota in early life impacts brain development and adult behavior	GF and SPF mouse models	None	Offspring of previously GF mice colonized with SPF microbiota	Behavior in adulthood	Adult colonized offspring displayed similar behaviors compared with SPF mice. These mice spent less time exploring the open arms in the maze (less locomotor activity). Additionally, colonized mice expressed less synaptophysin and PSD-95 in the striatum compared with GF mice, suggesting the microbiome is involved in programming brain development	98
To determine if a maternal high-fat-diet-altered microbiome can modify offspring behavior	Mouse model colonized with maternal high-fat-diet-shaped microbiota	Maternal high-fat diet	Female mice transplanted with high-fat diet microbiome	Behavior traits in offspring	Female mice were transplanted with a high-fat-diet- or control low-fat-diet-associated gut microbiome. Offspring of these mice displayed altered behavior in a sex-dependent manner. Offspring mice displayed less stress after maternal separation. Male offspring displayed decreased exploratory and cognitive behaviors, which is indicative of increased anxiety. Female mice displayed increases in adiposity and body wt	99
To analyze the microbial and molecular mechanisms that underlie the gut-brain axis	GF and conventionally raised mouse models	None	GF mice colonized after weaning	Neuronal activity in the amygdala	Absence of a microbiota in early life results in differential gene expression, exon usage, RNA editing, and upstream gene regulation in the amygdala. This was similar to mice who were raised GF for their entire lives but varied when compared with conventionalized mice	100
To examine whether variations in the vaginal microbiome are associated with varied offspring programming	Mouse model of prenatal stress	Prenatal stress	Variations in the maternal vaginal and neonatal gut microbiome	Metabolic and neurologic programming and in offspring	Lactobacillus abundance is decreased in the vaginal microbiome and in neonates born to dams exposed to early prenatal stress. Other bacterial population abundances also varied in offspring exposed to early prenatal stress. Early prenatal stress altered metabolic profiles and amino acid availability in the brain	101
Immune-mediated diseases (IBD, T1D, etc)
To investigate age-dependent microbial modulation of iNKTs in mouse models of IBD and asthma	Mouse model of oxazolone-induced colitis	None	SPF-colonization during pregnancy lead to SPF-colonized offspring	Colitis induced later in life	Neonatal exposure to a conventional microbiota compared with GF conditions protected mice from oxazolone-induced colitis	76
To determine if and how early-life exposure to antibiotics changes susceptibility to IBD	Mouse model DSS-induced colitis	Antibiotic-induced	LDP after weaning	Colitis induced later in life	LDP-treated mice displayed transient gut microbial compositional alterations, including eradication of segmented filamentous bacteria. In addition, after DSS-induced colitis, LDP mice displayed reduced colitis symptoms, Il-17 expression, and ileal Th17 differentiation compared with mice exposed to metronidazole, enrofloxacin, and controls. Finally, the authors report penicillin’s effects are dependent on eradiation of segmented filamentous bacteria, implicating the microbiome as the mediator between this early life exposure and colitis development	102
To explore the influence of gut dysbiosis in the progression of T1D	NOD mouse model	Antibiotic-induced	Antibiotic treatment in early life (conception until 40 wk postnatal)	Spontaneous diabetes later in life	Antibiotics were administered to NOD mice from conception until 40 wk postnatal development. Treatment with antibiotics increased incidence of T1D in male mice. Antibiotic treatment also resulted in near ablation of the gut microbiome at 8 wk of age, which may partially explain the increased T1D incidence in male mice	103
To determine if exposure to prenatal antibiotics can protect offspring from T1D	NOD mouse model	Antibiotic-induced	Prenatal antibiotic treatment induced variations in offspring and maternal microbiomes	Spontaneous diabetes later in life	Prenatal neomycin and vancomycin treatment resulted in differential shifts in the offspring and maternal microbiomes. Offspring treated prenatally with neomycin were protected from T1D development, whereas offspring treated prenatally with vancomycin displayed accelerated T1D development. The antibiotic treatment also resulted in altered immune profiles, such as increased T-cell–mediated inflammation in mice treated with vancomycin and altered antigen-presenting cell phenotypes in mice treated with neomycin	104
To determine the impact of targeting Gram-negative gut bacteria at various time points in early life on T1D development	NOD mouse model	Antibiotic-induced	Prenatal antibiotic treatment induced variations in offspring microbiome	Spontaneous diabetes later in life	Pregnant, NOD mice treated with an antibiotic mixture (neomycin, polymyxin B, and streptomycin) were protected from T1D compared with mice treated postnatally. Microbiota transfer from these mice to untreated mice resulted in protection from T1D	105
To compare the effects of pulsed therapeutic antibiotics or continuous low-dose antibiotics in early life on T1D development	NOD mouse model	Antibiotic-induced	Pulsed antibiotic treatment induced variations in 6-wk-old microbiome	Spontaneous diabetes later in life	Pulsed postnatal treatment with tylosin altered the mouse microbiome and accelerated T1D development compared with mice treated with subtherapeutic penicillin from pregnancy to week 12	106
To analyze the association between the infant gut microbiome and T1D development	Prospective human cohort analysis (n = 33)	None	Variations in the microbiome before diagnosis with T1D	T1D diagnosis at ∼3 y of age	T1D disease state was distinguishable by the gut microbiome composition. Seroconverted subjects diagnosed with T1D displayed a marked decrease in α diversity before diagnosis when compared with seroconverted subjects not diagnosed with T1D and nonseroconverted subjects	107
To analyze the effect of peripartum cefoperazone administration on the maternal and offspring microbiota and IBD in the offspring	SPF IL-10 knock-out mouse model combined with DSS-induced colitis	Antibiotic-induced	Peripartum antibiotic treatment induced gut dysbiosis in offspring that persists to adulthood	Spontaneous colitis later in life	Peripartum exposure to cefoperazone increases risk of spontaneous colitis in offspring. Antibiotics also contribute to immune skewing and promote gut dysbiosis that persists to adulthood. Additionally, as demonstrated by fecal transplant to GF IL-10 knock-out dams, immune skewing is mediated by the antibiotic-induced dysbiosis	108
To analyze the impact of a maternal high-fiber diet on T-regulatory cell differentiation in the offspring	SPF GPR41−/− mouse model	Maternal high-fiber diet during pregnancy and breastfeeding	Increased plasma SCFAs	Increased thymic and peripheral T-regulatory cells	Compared with offspring from maternal mice fed a normal diet, high-fiber diet during pregnancy and breastfeeding resulted in increased plasma SCFAs in the offspring. These offspring also displayed higher frequencies of thymic and peripheral T-regulatory cells, which may be prompted by increased SCFA levels	46

AAD, allergic airways disease; CD4+, cluster of differentiation 4; CXCL16, chemokine ligand 16; DSS, dextran sodium sulfate; GI, gastrointestinal; GPR41, G protein–coupled receptor 41; GPR43, G protein–coupled receptor 43; Grx1, Glutaredoxin-1; HDAC9, histone deacetylase 9; IgA, immunoglobulin A; IL-1β, interleukin 1 beta; IL-10, interleukin 10; IL-17, interleukin 17; iNKT, invariant natural killer T cell; LPS, lipopolysaccharide; NOD, nonobese diabetic; PD-L1, programmed death ligand-1; PSD-95, postsynaptic density protein 95; Ref., reference; Th1, T-helper 1; Th17, T-helper 17; TLR, Toll-like receptor; T1D, type 1 diabetes.