Molecular monitoring of the development of intestinal microbiota in Japanese infants

Exploring Maternal Diet-Epigenetic-Gut Microbiome Crosstalk as an Intervention Strategy to Counter Early Obesity Programming

Alterations in a mother's metabolism and endocrine system, due to unbalanced nutrition, may increase the risk of both metabolic and non-metabolic disorders in the offspring's childhood and adulthood. The risk of obesity in the offspring can be determined by the interplay between maternal nutrition and lifestyle, intrauterine environment, epigenetic modifications, and early postnatal factors. Several studies have indicated that the fetal bowel begins to colonize before birth and that, during birth and nursing, the gut microbiota continues to change. The mother's gut microbiota is primarily transferred to the fetus through maternal nutrition and the environment. In this way, it is able to impact the establishment of the early fetal and neonatal microbiome, resulting in epigenetic signatures that can possibly predispose the offspring to the development of obesity in later life. However, antioxidants and exercise in the mother have been shown to improve the offspring's metabolism, with improvements in leptin, triglycerides, adiponectin, and insulin resistance, as well as in the fetal birth weight through epigenetic mechanisms. Therefore, in this extensive literature review, we aimed to investigate the relationship between maternal diet, epigenetics, and gut microbiota in order to expand on current knowledge and identify novel potential preventative strategies for lowering the risk of obesity in children and adults.

Bifidobacterium pseudocatenulatum NCU-08 ameliorated senescence via modulation of the AMPK/Sirt1 signaling pathway and gut microbiota in mice

Aging is a degenerative disease in which organisms and neurological functions decline. Emerging research has underscored the vital role of the gut microbiota in age-related processes. However, the identification of aging-associated core microbiota remains limited. In this investigation, we isolated a strain of B. pseudocatenulatum NCU-08 from the feces of centenarians and assessed its impact on aging using a mouse model induced by D-gal. Our study revealed the exceptional probiotic attributes of B. pseudocatenulatum NCU-08. Administration of B. pseudocatenulatum NCU-08 significantly ameliorated age-related memory impairment, motor dysfunction, and anxiety-like behaviors in aging mice (p < 0.01). Moreover, tissue staining analysis demonstrated that B. pseudocatenulatum NCU-08 reduced the intensity of SA-β-gal-positive in the hippocampus of aging mice. It also reversed pathological damage and structural abnormalities in brain and intestinal tissue. B. pseudocatenulatum NCU-08 inhibited neuroinflammation induced by TLR4/NF-κB (p < 0.01) and preserved the blood-brain barrier integrity by activating the AMPK/Sirt1 pathway (p < 0.05). Furthermore, it mitigated neuronal apoptosis and oxidative stress by upregulating the PI3K/AKT signaling pathway (p < 0.01) and enhancing the activities of antioxidant enzymes, including GSH-Px (p < 0.01), SOD (p < 0.01), and CAT (p < 0.01). Besides, analysis of 16S rRNA sequencing data demonstrated that treatment with B. pseudocatenulatum NCU-08 restored intestinal microbiota homeostasis after senescence. It enhanced the abundance of beneficial bacteria while suppressing the growth of pathogenic microorganisms. In summary, our study unveiled that this novel strain of B. pseudocatenulatum NCU-08 exerts anti-aging effects through regulating the AMPK/Sirt1 pathway and intestinal microbiota. It holds promise as a functional food for promoting anti-aging effects and offers a novel approach to address aging and associated metabolic disorders.

Various Organ Damages in Rats with Fetal Growth Restriction and Their Slight Attenuation by Bifidobacterium breve Supplementation

Children with fetal growth restriction (FGR) and its resultant low birthweight (LBW) are at a higher risk of developing various health problems later in life, including renal diseases, metabolic syndrome, and sarcopenia. The mechanism through which LBW caused by intrauterine hypoperfusion leads to these health problems has not been properly investigated. Oral supplementation with probiotics is expected to reduce these risks in children. In the present study, rat pups born with FGR-LBW after mild intrauterine hypoperfusion were supplemented with either Bifidobacterium breve (B. breve) or a vehicle from postnatal day 1 (P1) to P21. Splanchnic organs and skeletal muscles were evaluated at six weeks of age. Compared with the sham group, the LBW-vehicle group presented significant changes as follows: overgrowth from infancy to childhood; lighter weight of the liver, kidneys, and gastrocnemius and plantaris muscles; reduced height of villi in the ileum; and increased depth of crypts in the jejunum. Some of these changes were milder in the LBW-B.breve group. In conclusion, this rat model could be useful for investigating the mechanisms of how FGR-LBW leads to future health problems and for developing interventions for these problems. Supplementation with B. breve in early life may modestly attenuate these problems.

Associations of intrapartum antibiotics and growth, atopy, gastrointestinal and sleep outcomes at one year of age

BACKGROUND

Studies investigating neonatal outcomes following intrapartum antibiotic exposure show conflicting results.

METHODS

Data were collected prospectively in pregnancy to 1-year-of-age, from 212 mother-infant pairs. Adjusted multivariable regression models estimated relationships following exposure to intrapartum antibiotics among vaginally-born, full-term infants and outcomes related to growth, atopic disease, gastrointestinal symptoms, and sleep at 1-year.

RESULTS

Intrapartum antibiotic exposure (n = 40) was not associated with mass, ponderal index, BMI z-score (1- year), lean mass index (5-months) or height. Antibiotic exposure in labour ≥4-h was associated with increase in fat mass index at 5-months (β 0.42 [95% CI: 0.03, 0.80], p = 0.03). Intrapartum antibiotic was associated with atopy in the first year (OR: 2.93 [95% CI: 1.34, 6.43], p = 0.007). Antibiotic exposure during intrapartum or day 1-7 was associated with newborn fungal infection requiring antifungal therapy (OR 3.04 [95% CI: 1.14, 8.10], p = 0.026), and number of fungal infections (IRR: 2.90 [95% CI: 1.02, 8.27], p = 0.046).

CONCLUSION

Intrapartum and early life exposure to antibiotics were independently associated with measures of growth, atopy, and fungal infections suggesting that intrapartum and early neonatal antibiotics be used prudently following careful risk-benefit analysis.

IMPACT

This prospective study: Shows a shift in fat mass index at 5 months associated with antibiotic administration ≥4 h in labour; an earlier age than previously reported; Shows atopy reported less frequently among those not exposed to intrapartum antibiotics; Supports earlier research of increased likelihood of fungal infection following exposure to intrapartum or early-life antibiotics; Adds to growing evidence that antibiotics used intrapartum and in early neonatal periods influence longer-term outcomes for infants. Suggests that use of intrapartum and early neonatal antibiotics should be used prudently after careful consideration of risk and benefit.

Association between maternal fermented food consumption and child sleep duration at the age of 3 years: the Japan Environment and Children's Study

Background

Using cohort data from the Japan Environment and Children’s Study (JECS), we previously reported that the risk of sleep deprivation in 1-year-old children was reduced with a higher maternal intake of fermented foods, particularly miso. The present study, which evaluates children from the same cohort at 3 years of age, is a continuation of that work.

Methods

After applying exclusion criteria to 104,062 records in the JECS dataset, we evaluated 64,200 mother-child pairs in which the child was 3 years old. We examined the association of the dietary intake of fermented foods during pregnancy with child sleep duration < 10 h at the age of 3 years.

Results

Multivariable logistic regression analysis with the lowest quartile used as a reference revealed adjusted odds ratios (95% confidence intervals) for the second through fourth quartiles of 0.98 (0.90–1.06), 0.93 (0.85–1.01), and 0.85 (0.78–0.94) for cheese intake.

Conclusions

The consumption of fermented foods during pregnancy is associated with reduced risk of sleep deprivation in 3-year-old children, albeit in a limited way.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12889-022-13805-6.

Effects of Different Feeding Methods on the Structure, Metabolism, and Gas Production of Infant and Toddler Intestinal Flora and Their Mechanisms

In this study, we evaluated the effects of different feeding methods on the characteristics of intestinal flora and gas production in infants and toddlers by using an in vitro simulated intestinal microecology fermentation and organoid model. We found that the feeding method influences intestinal gas and fecal ammonia production in infants and toddlers. Supplementation with milk powder for infants in the late lactation period could promote the proliferation of beneficial bacteria, including Bifidobacteria. Intestinal flora gas production in a culture medium supplemented with fucosyllactose (2′-FL) was significantly lower than that in media containing other carbon sources. In conclusion, 2′-FL may reduce gas production in infant and toddler guts through two mechanisms: first, it cannot be used by harmful intestinal bacteria to produce gas; second, it can inhibit intestinal mucosa colonization by harmful bacteria by regulating the expression of intestinal epithelial pathogenic genes/signaling pathways, thus reducing the proliferation of gas-producing harmful bacteria in the gut.

Bifidobacterium breve during infancy attenuates mobility in low birthweight rats

BACKGROUND

Children with low birthweight (LBW) have a higher risk for developing attention-deficit/hyperactivity disorder, for which no prophylactic measure exists. The gut microbiota in infants with LBW is different from that in infants with normal birthweight and is associated with attention-deficit/hyperactivity disorder. Oral supplementation with Bifidobacterium has several health benefits, such as suppressing inflammation.

METHODS

We examined the effect of gavage supplementation with Bifidobacterium breve M-16V from postnatal days 1-21 in a rat model of intrauterine hypoperfusion.

RESULTS

The open-field test at 5 weeks of age (equivalent to human pubertal age) showed that rats in the LBW-vehicle group were marginally hyperactive compared with rats in the sham group, while rats in the LBW-B.breve group were significantly hypoactive compared with rats in the LBW-vehicle group. The gut microbiota in the LBW-vehicle group exhibited a profile significantly different from that in the sham group, whereas the gut microbiota in the LBW-B.breve group did not exhibit a significant difference from that in the sham group. Anatomical/histological evaluation at 6 weeks of age demonstrated that the brain weight and the cerebral areas on coronal sections were reduced in the LBW groups compared with the sham group. Probiotic supplementation did not ameliorate these morphological brain anomalies in LBW animals. The percentage of Iba-1⁺ cells in the brain was not different among the LBW-B.breve, LBW-vehicle, and sham groups.

CONCLUSION

Bifidobacterium breve supplementation during early life is suggested to have the potential to help children with LBW attenuate hypermobility in adolescence.

Therapeutic Potential of a Novel Bifidobacterium Identified Through Microbiome Profiling of RA Patients With Different RF Levels

The potential therapeutic effects of probiotic bacteria in rheumatoid arthritis (RA) remain controversial. Thus, this study aimed to discover potential therapeutic bacteria based on the relationship between the gut microbiome and rheumatoid factor (RF) in RA. Bacterial genomic DNA was extracted from the fecal samples of 93 RA patients and 16 healthy subjects. Microbiota profiling was conducted through 16S rRNA sequencing and bioinformatics analyses. The effects of Bifidobacterium strains on human peripheral blood mononuclear cells and collagen-induced arthritis (CIA) mice were assessed. Significant differences in gut microbiota composition were observed in patients with different RF levels. The relative abundance of Bifidobacterium and Collinsella was lower in RF-high than in RF-low and RF-negative RA patients, while the relative abundance of Clostridium of Ruminococcaceae family was higher in RF-high than in RF-low and RF-negative patients. Among 10 differentially abundant Bifidobacterium, B. longum RAPO exhibited the strongest ability to inhibit IL-17 secretion. Oral administration of B. longum RAPO in CIA mice, obese CIA, and humanized avatar model significantly reduced RA incidence, arthritis score, inflammation, bone damage, cartilage damage, Th17 cells, and inflammatory cytokine secretion. Additionally, B. longum RAPO significantly inhibited Th17 cells and Th17-related genes—IL-17A, IRF4, RORC, IL-21, and IL-23R—in the PBMCs of rheumatoid arthritis patients. Our findings suggest that B. longum RAPO may alleviate RA by inhibiting the production of IL-17 and other proinflammatory mediators. The safety and efficacy of B. longum RAPO in patients with RA and other autoimmune disorders merit further investigation.

Building Robust Assemblages of Bacteria in the Human Gut in Early Life

The neonatal body provides a range of potential habitats, such as the gut, for microbes. These sites eventually harbor microbial communities (microbiotas). A "complete" (adult) gut microbiota is not acquired by the neonate immediately after birth. Rather, the exclusive, milk-based nutrition of the infant encourages the assemblage of a gut microbiota of low diversity, usually dominated by bifidobacterial species. The maternal fecal microbiota is an important source of bacterial species that colonize the gut of infants, at least in the short-term. However, development of the microbiota is influenced by the use of human milk (breast feeding), infant formula, preterm delivery of infants, caesarean delivery, antibiotic administration, family details and other environmental factors. Following the introduction of weaning (complementary) foods, the gut microbiota develops in complexity due to the availability of a diversity of plant glycans in fruits and vegetables. These glycans provide growth substrates for the bacterial families (such as members of the Ruminococcaceae and Lachnospiraceae) that, in due course, will dominate the gut microbiota of the adult. Although current data are often fragmentary and observational, it can be concluded that the nutrition that a child receives in early life is likely to impinge not only on the development of the microbiota at that time but also on the subsequent lifelong, functional relationships between the microbiota and the human host. The purpose of this review, therefore, is to discuss the importance of promoting the assemblage of functionally robust gut microbiotas at appropriate times in early life.

Newborn-oriented and environmental factors for newborns' skin barrier functions

AIM

This study aimed to examine newborn-oriented and environmental factors of newborn skin barrier functions.

METHODS

This was a retrospective secondary analysis of 227 newborns from a previous study. Newborn skin barrier functions were measured on the fourth day after birth via the following parameters: stratum corneum hydration, transepidermal water loss, skin pH, and sebum secretion. Skin barrier functions were measured at four body sites; their averaged values were used for the analysis. The associations among skin barrier functions, newborn-oriented factors, and environmental factors were evaluated. Multiple regression analysis was performed using a forced entry method, and independent variables for which p-values were <.05 in Student's t test, analysis of variance, and Pearson's correlation analysis were included.

RESULTS

A total of 211 participants were analyzed. The mean ± standard deviation values of stratum corneum hydration, transepidermal water loss, skin pH, and sebum secretion were 28.58 ± 8.40 and 7.28 ± 2.02 g/m² /h, 5.77 ± 0.53, and 23.59 ± 15.89 μg/cm² , respectively. Newborn-oriented factors (gestational days, weight, amount of vernix, and parity) and environmental factors (birth season) were significantly associated with one or more skin barrier functions.

CONCLUSIONS

Newborn-oriented (including labor- and delivery-related) and environmental factors were associated with the skin barrier functions. The newborn maturity level, newborn sex, environmental temperature, and humidity may affect skin barrier functions in newborns. Further studies should focus on the effects of these factors on newborn skin barrier assessments, and develop tailored skincare strategies based on their characteristics.

Milk oligosaccharide-mediated cross-feeding between Enterococcus gallinarum and lactobacilli in the gut microbiota of infant rats

We investigated bacteria that have a nutritional symbiotic relationship with respect to milk oligosaccharides in gut microbiota of suckling rats, with specific reference to sialyllactose (SL) degrading Enterococcus gallinarum. Our next generation sequencing analysis of the colonic contents of 12-day-old suckling rats revealed that almost half of the bacteria in the microbiota belonged to the Lactobacillaceae family. Major Lactobacillus species in the contents were identified as L. johnsonii, L. murinus, and L. reuteri. We then monitored changes in numbers of the above Lactobacillus species, E. gallinarum, and the bacteria belonging to the family Enterobacteriaceae (i.e., enterobacteria) in the colonic contents of infant rats at 7, 12, 21, 28, and 35 days of age by using real-time PCR assays targeting these bacterial groups. The 7-day-old infant rats had a gut microbiota in which enterobacteria were predominant. Such dominance was replaced by L. johnsonii and the concomitant E. gallinarum markedly increased in those of 12 and 21 days of ages. During this period, the number of enterobacteria declined dramatically, but that of L. reuteri surged dramatically. Our separate in vitro experiment showed that supplementation of culture media with SL promoted the growth of L. johnsonii and E. gallinarum, with marked production of lactic acid. These findings revealed possible milk oligosaccharide-mediated cross-feeding between E. gallinarum and L. johnsonii, with the former degrading SL to release lactose to be utilized by the latter.

Effects of the intake of non-live Bifidobacterium bifidum on the faecal IgA of full-term infants: a double-blind, randomised, placebo-controlled study

Bifidobacterium bifidum OLB6378 (OLB6378) was selected as a strain that enhances the production of secretory immunoglobulin A (IgA) in vitro. This ability of non-live OLB6378 has been shown by a clinical trial in preterm infants. In the present study, we examined whether non-live OLB6378 also enhances the production of secretory IgA, even in full-term infants. One hundred full-term infants were allocated to receive formula with (BbF group, 49 infants) or without non-live OLB6378 (PF group, 51 infants). Breastfeeding was prioritised, so infant formula was used for infants with breastfeeding difficulties. The intervention was initiated by five days of age. The faecal IgA concentration and OLB6378 level were determined at one, two, four, and eight weeks of age. Faecal IgA in the BbF group (1.04 ± 0.47 mg/g of faeces, n=45) was significantly higher than that in the PF group (0.85 ± 0.42 mg/g of faeces, n=49) at four weeks of age (p=0.047). OLB6378 was not detected in faeces at any age. This indicated that production of secretory IgA in full-term infants may also be enhanced by non-live OLB6378 intake.

Significance of gut microbiota in alcoholic and non-alcoholic fatty liver diseases

Liver-gut communication is vital in fatty liver diseases, and gut microbes are the key regulators in maintaining liver homeostasis. Chronic alcohol abuse and persistent overnutrition create dysbiosis in gut ecology, which can contribute to fatty liver disease. In this review, we discuss the gut microbial compositional changes that occur in alcoholic and nonalcoholic fatty liver diseases and how this gut microbial dysbiosis and its metabolic products are involved in fatty liver disease pathophysiology. We also summarize the new approaches related to gut microbes that might help in the diagnosis and treatment of fatty liver disease.

Association Between the Mode of Delivery and Infant Gut Microbiota Composition Up to 6 Months of Age: A Systematic Literature Review Considering the Role of Breastfeeding

CONTEXT

Cesarean section (CS), breastfeeding, and geographic location can influence the infant microbiota.

OBJECTIVE

In this systematic review, evidence of the association between mode of delivery and infant gut microbiota up to 6 months of age was evaluated, as was the role of breastfeeding in this association, according to PRISMA guidelines.

DATA SOURCE

The Pubmed, Web of Science, Scopus, Embase, Medical Database, and Open Grey databases were searched.

DATA EXTRACTION

A total of 31 observational studies with ≥2 infant stool collections up to the sixth month of age and a comparison of gut microbiota between CS and vaginal delivery (VD) were included.

DATA ANALYSIS

Infants born by CS had a lower abundance of Bifidobacterium and Bacteroides spp. at almost all points up to age 6 months. Populations of Lactobacillus, Bifidobacterium longum, Bifidobacterium catenulatum, and Escherichia coli were reduced in infants delivered by CS. Infants born by CS and exclusively breastfed had greater similarity with the microbiota of infants born by VD.

CONCLUSIONS

Species of Bifidobacterium and Bacteroides are potentially reduced in infants born by CS. Geographic location influenced bacterial colonization.

SYSTEMATIC REVIEW REGISTRATION

PROSPERO registration no. 42017071285.

Crosstalk between gut microbiome and immunology in the management of ischemic brain injury

Ischemic brain injury is a serious neurological complication, which accrues an immense activation of neuroinflammatory responses. Several lines of research suggested the interconnection of gut microbiota perturbation with the activation of proinflammatory mediators. Intestinal microbial communities also interchange information with the brain through various afferent and efferent channels and microbial by-products. Herein, we discuss the different microelements of gut microbiota and its connection with the host immune system and how change in immune-microbial signatures correlates with the stroke incidence and post-injury neurological sequelae. The activated inflammatory cells increase the production of proinflammatory cytokines, chemokines, proteases and adhesive proteins that are involved in the systemic inflammation, blood brain barrier disruption, gut dysbiosis and aggravation of ischemic brain injury. We suggest that fine-tuning of commensal gut microbiota (eubiosis) may regulate the activation of CNS resident cells like microglial, astrocytes, mast cells and natural killer cells.

Gut microbiota as the key controllers of "healthy" aging of elderly people

Extrinsic factors, such as lifestyle and diet, are shown to be essential in the control of human healthy aging, and thus, longevity. They do so by targeting at least in part the gut microbiome, a collection of commensal microorganisms (microbiota), which colonize the intestinal tract starting after birth, and is established by the age of three. The composition and abundance of individual microbiota appears to continue to change until adulthood, presumably reflecting lifestyle and geographic, racial, and individual differences. Although most of these changes appear to be harmless, a major shift in their composition in the gut (dysbiosis) can trigger harmful local and systemic inflammation. Recent reports indicate that dysbiosis is increased in aging and that the gut microbiota of elderly people is enriched in pro-inflammatory commensals at the expense of beneficial microbes. The clinical consequence of this change remains confusing due to contradictory reports and a high degree of variability of human microbiota and methodologies used. Here, we present the authors’ thoughts that underscore dysbiosis as a primary cause of aging-associated morbidities, and thus, premature death of elderly people. We provide evidence that the dysbiosis triggers a chain of pathological and inflammatory events. Examples include alteration of levels of microbiota-affected metabolites, impaired function and integrity of the gastrointestinal tract, and increased gut leakiness. All of these enhance systemic inflammation, which when associated with aging is termed inflammaging, and result in consequent aging-associated pathologies.

A pregnancy complication-dependent change in SIgA-targeted microbiota during third trimester

Gut microbiota play a crucial role in metabolic dysfunction during gestation, which might be prevented by using probiotics. This study compared the composition of the gut microbiota in healthy and complicated pregnancies, for screening and isolating healthy pregnancy-derived probiotics. According to the principal component analysis of secretory immunoglobulin A (SIgA)-coated microbiota in the gut, third-trimester volunteers can be divided into three groups: AHd (n = 29), GDMd (n = 37), and GHd (n = 25), dominated by asymptomatic healthy donors (62.07%), gestational diabetes mellitus (GDM) donors (40.54%), and gestational hypertension (GH) donors (40%), respectively. There was a significant difference in β-diversity (p < 0.01) and α-diversity (p < 0.05) among the three groups. At the phylum level, the Firmicutes of the GHd group were significantly lower than those of the AHd group (p = 0.039), while Bacteroidetes (p = 0.005) and Proteobacteria (p = 0.002) of the GHd group were more dominant than those of the AHd group. At the genus level, the linear discriminant analysis effect size showed that SIgA-targeted Enterococcus was the dominant taxonomic biomarker of the AHd group, and the GHd group was enriched with Escherichia and Streptococcus. The GDMd and GHd groups had higher faecal calprotectin, serum lipopolysaccharide, zonulin, and GLYCAM-1 levels. We conclude that the occurrence of complications in the third trimester may be related to intestinal barrier injury associated with disorders of the intestinal SIgA-targeted microbiota; gut barrier injury triggers inflammation in pregnant women. SIgA-targeted L. reuteri showed a significant correlation with low inflammatory response and may be a potential probiotic candidate for preventing pregnancy complications.

Human behavior, not race or geography, is the strongest predictor of microbial succession in the gut bacteriome of infants

Colonization of the gastrointestinal tract with microorganisms during infancy represents a critical control point for shaping life-long immune-mediated disease susceptibility. Abnormal colonization or an imbalance of microbes, termed dysbiosis, is implicated in several diseases. Consequently, recent research has aimed at understanding ways to manipulate a dysbiotic microbiome during infancy to resemble a normal, healthy microbiome. However, one of the fundamental issues in microbiome research is characterizing what a "normal" infant microbiome is based on geography, ethnicity and cultural variations. This review provides a comprehensive account of what is currently known about the infant microbiome from a global context. In general, this review shows that the influence of cultural variations in feeding practices, delivery modes and hygiene are the biggest contributors to microbial variability. Despite geography or race, all humans have similar microbial succession during infancy.

Ethnic diversity in infant gut microbiota is apparent before the introduction of complementary diets

The human gut microbiota develops soon after birth and can acquire inter-individual variation upon exposure to intrinsic and environmental cues. However, inter-individual variation has not been comprehensively assessed in a multi-ethnic study. We studied a longitudinal birth cohort of 106 infants of three Asian ethnicities (Chinese, Malay, and Indian) that resided in the same geographical location (Singapore). Specific and temporal influences of ethnicity, mode of delivery, breastfeeding status, gestational age, birthweight, gender, and maternal education on the development of the gut microbiota in the first 2 years of life were studied. Mode of delivery, breastfeeding status, and ethnicity were identified as the main factors influencing the compositional development of the gut microbiota. Effects of delivery mode and breastfeeding status lasted until 6M and 3M, respectively, with the primary impact on the diversity and temporal colonization of the genera Bacteroides and Bifidobacterium. The effect of ethnicity was apparent at 3M post-birth, even before the introduction of weaning (complementary) foods, and remained significant after adjusting for delivery mode and breastfeeding status. Ethnic influences remained significant until 12M in the Indian and Chinese infants. The microbiota of Indian infants was characterized by higher abundances of Bifidobacterium and Lactobacillus, while Chinese infants had higher abundances of Bacteroides and Akkermansia. These findings provide a detailed insight into the specific and temporal influences of early life factors and ethnicity in the development of the human gut microbiota. Trial Registration: Clinicaltrials.gov registration no. NCT01174875.

The Epigenetic Connection Between the Gut Microbiome in Obesity and Diabetes

Metabolic diseases are becoming an alarming health issue due to elevated incidences of these diseases over the past few decades. Various environmental factors are associated with a number of metabolic diseases and often play a crucial role in this process. Amongst the factors, diet is the most important factor that can regulate these diseases via modulation of the gut microbiome. The gut microbiome participates in multiple metabolic processes in the human body and is mainly responsible for regulation of host metabolism. The alterations in function and composition of the gut microbiota have been known to be involved in the pathogenesis of metabolic diseases via induction of epigenetic changes such as DNA methylation, histone modifications and regulation by noncoding RNAs. These induced epigenetic modifications can also be regulated by metabolites produced by the gut microbiota including short-chain fatty acids, folates, biotin and trimethylamine-N-oxide. In addition, studies have elucidated the potential role of these microbial-produced metabolites in the pathophysiology of obesity and diabetes. Hence, this review focuses on the interactions between the gut microbiome and epigenetic processes in the regulation and development of obesity and diabetes, which may have potential as a novel preventive or therapeutic approach for several metabolic and other human diseases.

Bifidobacterium Supplementation of Colostrum and Breast Milk Enhances Weight Gain and Metabolic Responses Associated with Microbiota Establishment in Very-Preterm Infants

Background

Postnatal growth restriction in very-preterm infants (VPIs) may have long-lasting effects. Recent evidence suggests that developmental problems in VPIs are related to abnormalities in intestinal microbial communities.

Objective

To investigate the effect on growth outcomes in VPIs of supplementation with Bifidobacterium along with mother's colostrum and breast milk.

Methods

A randomized controlled study was performed on 35 VPIs, born between 24 and 31 weeks of gestation with birth weights <1,500 g. The patients received either daily Bifidobacterium breve supplementation (Bifid group) or vehicle supplement only (placebo group). Parenteral nutrition was initiated with glucose, amino acids, and fatty acids for all of the infants soon after birth. Each infant received their own mother's colostrum within 24 h of birth, and breast milk on subsequent days. Fecal bacteria, organic acids, pH, bile acids, and plasma fatty acids were analyzed.

Results

Seventeen infants were allocated to the Bifid group and 18 to the placebo group; the birth weights and gestational ages did not differ significantly between the two groups. Compared to the placebo group, the Bifid group showed significantly greater and earlier weight gain by 8 weeks; significantly higher total fecal bacterial counts, including bifidobacteria; higher levels of total fecal short-chain fatty acids and nominally (but not significantly) higher concentrations of plasma n−3 fatty acids; and lower levels of total fecal bile acid.

Conclusions

Bifidobacterial supplementation of maternal colostrum and breast milk yielded the establishment of a beneficial microbiota profile, leading to favorable metabolic responses that appeared to provide improved growth in VPIs.

Independent and Interactive Effects of Habitually Ingesting Fermented Milk Products Containing Lactobacillus casei Strain Shirota and of Engaging in Moderate Habitual Daily Physical Activity on the Intestinal Health of Older People

Infrequent bowel movements decrease the number of beneficial bacteria in the human intestines, thereby potentially increasing the individual's risk of colorectal cancer. The correction of such bowel problems could therefore make an important contribution to improving population health and quality-adjusted lifespan. We examined independent and interactive effects upon the fecal microbiota of two potentially favorable determinants of intestinal motility: the intake frequency of a fermented milk product containing Lactobacillus casei strain Shirota (LcS) and the quantity/quality of habitual physical activity in 338 community-living Japanese aged 65-92 years. Subjects were arbitrarily grouped on the basis of questionnaire estimates of LcS intake (0-2, 3-5, and 6-7 days/week) and pedometer/accelerometer-determined patterns of physical activity [<7000 and ≥7000 steps/day, or <15 and ≥15 min/day of activity at an intensity >3 metabolic equivalents (METs)]. After adjustment for potential confounders, the respective numbers of various beneficial fecal bacteria tended to be larger in more frequent consumers of LcS-containing products, this trend being statistically significant (mostly P < 0.001) for total Lactobacillus, the Lactobacillus casei subgroup, and the Atopobium cluster; in contrast, there were no statistically significant differences in fecal bacterial counts between the physical activity groups. A multivariate-adjusted logistic regression analysis estimated that the risk of infrequent bowel movements (arbitrarily defined as defecating ≤3 days/week) was significantly lower (P < 0.05) in subjects who ingested LcS-containing products 6-7 rather than 0-2 days/week [odds ratio (95% confidence interval) 0.382 (0.149-0.974)] and was also lower in those who took ≥7000 rather than <7000 steps/day [0.441 (0.201-0.971)] or spent ≥15 rather than <15 min/day of physical activity at an intensity >3 METs [0.412 (0.183-0.929)]. The risk of infrequent bowel movements in subjects who combined 6-7 days/week of LcS with ≥7000 steps/day or ≥15 min/day of activity at >3 METs was only a tenth of that for individuals who combined 0-2 days/week of LcS with <7000 steps/day or <15 min/day at >3 METs. These results suggest that elderly individuals can usefully ingest LcS-containing supplements regularly (≥6 days/week) and also engage in moderate habitual physical activity (≥7000 steps/day and/or ≥15 min/day at >3 METs) in order to enhance their gastrointestinal health.

Geographical location specific composition of cultured microbiota and Lactobacillus occurrence in human breast milk in China

Breast milk bacteria play an important role in the early development of the gut microbiota and the immune system. Dominant living bacteria of 89 healthy Chinese women from 11 cities in five regions were analysed by broad-range yeast extract, casitone, and fatty acid and de Man, Rogosa, and Sharpe-based culturing coupled with 16S rRNA sequence and quantitative polymerase chain reaction. Principal coordinate analysis showed that human breast milk samples were classified into three groups, driven by Enterococcus (abundance in group 1, 63.13%), Streptococcus (abundance in group 2, 68.16%) and Staphylococcus (abundance in group 3, 55.17%). The microbiota profile was highly region-specific. Samples from the Northwest and North of China showed higher alpha diversity compared to other regions (p < 0.05). Staphylococcus, Streptococcus, and Enterococcus were the dominant genera in all samples. Lactobacillus had a high occurrence in samples from the Northwest and North, dominated by Lactobacillus reuteri and Lactobacillus gasseri. Samples of mothers with a high postpartum body mass index showed more Staphylococcus and less Lactobacillus and Streptococcus. Staphylococcus was negatively correlated with Lactobacillus and Streptococcus. The mode of delivery also affected the composition of microbiota, even after culture. These findings indicate differences between the North and South, provide effective information for collection of samples in which Lactobacillus is the predominant genus, and lower the detection limit for small amounts of bacteria.

Poor Bifidobacterial Colonization Is Associated with Late Provision of Colostrum and Improved with Probiotic Supplementation in Low Birth Weight Infants

This study aimed to evaluate the association between bifidobacterial colonization in low birth weight infants and perinatal factors, including the timing of initial colostrum and the effect of probiotics on this colonization. In this non-randomized controlled trial, we enrolled 98 low-birth-weight infants from a neonatal intensive care unit (NICU) in Japan. Infants were divided into three groups: group N (no intervention), group H (received non-live bifidobacteria), and group L (received live bifidobacteria). The number of bifidobacteria in the infants’ stools at 1 month of age was measured using real-time polymerase chain reaction (PCR). We divided infants into “rich bifidobacteria” (≥10^4.8 cells/g feces) and “poor bifidobacteria” (<10^4.8 cells/g feces) subgroups. The ratio of “rich bifidobacteria” infants was 20/31, 34/36, and 30/30 in groups N, H, and L, respectively. In group N, the “rich bifidobacteria” group received first colostrum significantly earlier than the “poor bifidobacteria” group (1 day vs. 4 days, P < 0.05). Compared with the N group, both groups H and L had a significantly high proportion of “rich bifidobacteria” infants (P < 0.05). Bifidobacterial colonization was poor in premature infants at 1 month compared with term infants, and the level of colonization was associated with the timing of initial provision of colostrum. Providing probiotics to premature infants can improve bifidobacterial colonization.

Bacterial profile of infant feces associated with lactation infectious breasts

Background

Mastitis is a common complication in lactating women. However, the diversity of intestinal bacteria in infant exclusively fed infectious milk remains uncharacterized. Our colleagues recently established a method based on 16S and 23S rRNA-targeted reverse transcription–quantitative PCR (RT-qPCR) for detecting bacteria.

Materials and methods

In the present study, the bacteria present in 14 samples of milk and infant feces were characterized using the RT-qPCR method, and concentrations of fecal organic acids were measured during the period of breast massage using HPLC.

Results

Streptococcus agalactiae and Str. parasanguinis were detected in milk from mastitis patients, whereas Str. salivarius and Str. thermophilus were the predominant bacteria in milk from engorged breasts. In feces of breastfed infants, Str. salivarius, Str. thermophiles, and Str. parasanguinis were isolated. Levels of lactate were high in fecal samples, whereas the pH of infant feces stabilized during breast massage. The bacterial diversity of milk from lactation infectious breasts was similar to that in feces of infant fed milk from lactation infectious breasts. Streptococcus species isolated from the feces of breastfed infants are related to oral cavity health.

Conclusion

These results suggest that Streptococcus species, which are part of the healthy oral microflora, may play an important role in preserving the intestinal bacterial flora in infants fed infectious milk.

Dual Factors May Be Necessary for Development of Atopic March in Early Infancy

The incidence of atopic diseases, including atopic dermatitis (AD), food allergies, allergic rhinitis, and asthma, has increased in recent decades, and currently affects approximately 20% of the population. Atopic march is the development of AD in infancy and subsequent food allergies, allergic rhinitis, and asthma in later childhood. Patients with infantile eczema may develop typical symptoms of AD, allergic rhinitis, and asthma at certain ages. Some patients' symptoms persist for several years, whereas others may have resolution with aging. Development of these diseases is strongly influenced by the following two factors: skin dysfunction caused by filaggrin mutations and development of colonization of microflora in early infancy. Filaggrin mutations predisposing to asthma, allergic rhinitis, and allergic sensitization, only in the presence of AD, strongly support the role of filaggrin in the pathogenesis of AD and in subsequent progression of the atopic march. Several studies have shown that development of colonization of microflora in early infancy might affect development of allergic disease or food desensitization. Therefore, massive allergen exposure to genetic skin dysfunction in early infancy and an imbalance of microflora might be necessary for development of atopic march.

Counting the Countless: Bacterial Quantification by Targeting rRNA Molecules to Explore the Human Gut Microbiota in Health and Disease

Over the past decade, the advent of next-generation-sequencing tools has revolutionized our approach to understanding the human gut microbiota. However, numerical data on the gut bacterial groups-particularly low-cell-count microbiota, such as indigenous pathobionts, that are otherwise important components of the microbiota-are relatively limited and disparate. As a result, the comprehensive quantitative structure of the human gut microbiota still needs to be fully defined and standardized. With the aim of filling this knowledge gap, we have established a highly sensitive quantitative analytical system that is based on reverse transcription-quantitative PCR and targets microbial rRNA molecules. The system has already been validated in the precise, sensitive, and absolute quantification of more than 70 target bacterial groups belonging to various human gut bacterial clades, including predominant obligate and facultative anaerobes. The system demonstrates sensitivity several hundred times greater than that of other rRNA-gene-targeting methods. It is thus an efficient and valuable tool for exhaustive analysis of gut microbiota over a wide dynamic range. Using this system, we have to date quantified the gut microbiota of about 2,000 healthy Japanese subjects ranging in age from 1 day to over 80 years. By integrating and analyzing this large database, we came across several novel and interesting features of the gut microbiota, which we discuss here. For instance, we demonstrated for the first time that the fecal counts of not only the predominant bacterial groups but also those at lower cell counts conform to a logarithmically normal distribution. In addition, we revealed several interesting quantitative differences in the gut microbiota of people from different age groups and countries and with different diseases. Because of its high analytic sensitivity, the system has also been applied successfully to other body niches, such as in characterizing the vaginal microbiota, detecting septicemia, and monitoring bacterial translocation. Here, we present a quantitative perspective on the human gut microbiota and review some of the novel microbial insights revealed by employing this promising analytical approach.

Gut microbiome and aging: Physiological and mechanistic insights

The development of human gut microbiota begins as soon as the neonate leaves the protective environment of the uterus (or maybe in-utero) and is exposed to innumerable microorganisms from the mother as well as the surrounding environment. Concurrently, the host responses to these microbes during early life manifest during the development of an otherwise hitherto immature immune system. The human gut microbiome, which comprises an extremely diverse and complex community of microorganisms inhabiting the intestinal tract, keeps on fluctuating during different stages of life. While these deviations are largely natural, inevitable and benign, recent studies show that unsolicited perturbations in gut microbiota configuration could have strong impact on several features of host health and disease. Our microbiota undergoes the most prominent deviations during infancy and old age and, interestingly, our immune health is also in its weakest and most unstable state during these two critical stages of life, indicating that our microbiota and health develop and age hand-in-hand. However, the mechanisms underlying these interactions are only now beginning to be revealed. The present review summarizes the evidences related to the age-associated changes in intestinal microbiota and vice-versa, mechanisms involved in this bi-directional relationship, and the prospective for development of microbiota-based interventions such as probiotics for healthy aging.

Our gut microbiota: a long walk to homeostasis

The microbiome of the human gastrointestinal tract (GIT) consists of billions of bacteria, fungi and viruses, of which bacteria play the most important role in nutrition, immune development, production of vitamins and maintaining a well-balanced (homeostatic) microbial population. Many papers have been published on the microbiota in the human GIT, but little is known about the first group of bacteria that colonises an infant. The intestinal tract of an unborn is, despite general belief, not sterile, but contains bacteria that have been transferred from the mother. This opens a new research field and may change our understanding about the role bacteria play in early life, the selection of strains with probiotic properties and the treatment of diseases related to bacterial infections. Differences in bacterial populations isolated from meconia may provide answers to the prevention of certain forms of diabetes. More research is now focusing on the effect that a genetically diverse group, versus a much simpler microbial population, may have on the development of a homeostatic gut microbiome. The effect different bacterial species have on the gut-associated lymphoid tissue and cascade of immune responses has been well researched, but we still fail in identifying the ideal group of intestinal bacteria and if we do, it will certainly not be possible to maintain homeostasis with so many challenges the gut faces. Changes in diet, antibiotics, food preservatives and stress are some of the factors we would like to control, but more than often fail to do so. The physiology and genetics of the GIT changes with age and so the microbiome. This review summarises factors involved in the regulation of a gut microbiome.

Oral Administration of the Probiotic Strain Escherichia coli Nissle 1917 Reduces Susceptibility to Neuroinflammation and Repairs Experimental Autoimmune Encephalomyelitis-Induced Intestinal Barrier Dysfunction

Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system (CNS) with an increasing incidence in developed countries. Recent reports suggest that modulation of the gut microbiota might be one promising therapy for MS. Here, we investigated whether the probiotic Escherichia coli strain Nissle 1917 (ECN) could modulate the outcome of experimental autoimmune encephalomyelitis (EAE), a murine model of MS. We evidenced that daily oral treatment with ECN, but not with the archetypal K12 E. coli strain MG1655, reduced the severity of EAE induced by immunization with the MOG_35-55 peptide. This beneficial effect was associated with a decreased secretion of inflammatory cytokines and an increased production of the anti-inflammatory cytokine IL-10 by autoreactive CD4 T cells, both in peripheral lymph nodes and CNS. Interestingly, ECN-treated mice exhibited increased numbers of MOG-specific CD4⁺ T cells in the periphery contrasting with severely reduced numbers in the CNS, suggesting that ECN might affect T cell migration from the periphery to the CNS through a modulation of their activation and/or differentiation. In addition, we demonstrated that EAE is associated with a profound defect in the intestinal barrier function and that treatment with ECN, but not with MG1655, repaired intestinal permeability dysfunction. Collectively, our data reveal that EAE induces a disruption of the intestinal homeostasis and that ECN protects from disease and restores the intestinal barrier function.

Evolution of gut Bifidobacterium population in healthy Japanese infants over the first three years of life: a quantitative assessment

Bifidobacteria are important members of human gut microbiota; however, quantitative data on their early-life dynamics is limited. Here, using a sensitive reverse transcription-qPCR approach, we demonstrate the carriage of eight signature infant-associated Bifidobacterium species (B. longum, B. breve, B. bifidum, B. catenulatum group, B. infantis, B. adolescentis, B. angulatum and B. dentium) in 76 healthy full-term vaginally-born infants from first day to three years of life. About 21% babies carry bifidobacteria at first day of life (6.2 ± 1.9 log₁₀ cells/g feces); and this carriage increases to 64% (8.0 ± 2.2), 79% (8.5 ± 2.1), 97% (9.3 ± 1.8), 99% (9.6 ± 1.6), and 100% (9.7 ± 0.9) at age 7 days, 1, 3 and 6 months, and 3 years, respectively. B. longum, B. breve, B. catenulatum group and B. bifidum are among the earliest and abundant bifidobacterial clades. Interestingly, infants starting formula-feed as early as first week of life have higher bifidobacterial carriage compared to exclusively breast-fed counterparts. Bifidobacteria demonstrate an antagonistic correlation with enterobacteria and enterococci. Further analyses also reveal a relatively lower/ delayed bifidobacterial carriage in cesarean-born babies. The study presents a quantitative perspective of the early-life gut Bifidobacterium colonization and shows how factors such as birth and feeding modes could influence this acquisition even in healthy infants.

The effects of the Lactobacillus casei strain on obesity in children: a pilot study

There are few data regarding the role of probiotics as a dietary intervention in the management of obesity in children. An open prospective examination was conducted to clarify the effects of Lactobacillus casei strain Shirota (LcS)-containing beverages in obese children. We compared the intestinal microbiota and organic acid levels between 12 obese (average age, 10.8 years; body mass index (BMI) Z score, 2.7±1.7) and 22 control children(average age, 8.5 years; BMI Z score, 0.1±0.7), and pre- and post-intervention in the obese children. The obese group underwent diet and exercise therapy for 6 months and then were given an LcS beverage daily for another 6 months and the body weight and serological markers were monitored. Significant reductions in the faecal concentrations of Bifidobacterium (obese group, 7.9±1.5 vs non-obese group, 9.8±0.5 Log10cells/g; P<0.01) along with a significant decline in the Bacteroides fragilis group, Atopobium cluster and Lactobacillus gasseri subgroup, and acetic acid (obese group, 45.1±16.9 vs non-obese group, 57.9±17.6 μmol/g; P<0.05) were observed in the obese group at baseline. A significant decline in body weight (-2.9±4.6%; P<0.05) and an elevation in the high density lipoprotein cholesterol level (+11.1±17.6%; P<0.05) were observed 6 months after ingestion of the LcS beverage compared to baseline. Furthermore, a significant increase in the faecal concentration of Bifidobacterium (7.0±1.2 before ingestion vs 9.1±1.2 Log10cells/g after ingestion; P<0.01) and an apparent increase in the acetic acid concentration (7.0±1.2 before ingestion vs 9.1±1.2 Log10cells/g after ingestion; P<0.01) were observed 6 months after ingestion. LcS contributed to weight loss while also improving the lipid metabolism in obese children via a significant increase in the faecal Bifidobacterium numbers and the acetic acid concentration.

Ontogenesis of the Gut Microbiota Composition in Healthy, Full-Term, Vaginally Born and Breast-Fed Infants over the First 3 Years of Life: A Quantitative Bird's-Eye View

Early-life intestinal microbiota development is crucial for host’s long-term health and is influenced by many factors including gestational age, birth and feeding modes, birth environment, ethnic/geographical background, etc. However, ‘quantitative’ data on the actual population levels of gut bacterial communities when these influences are controlled for is relatively rare. Herein, we demonstrate a quantitative perspective of microbiota development in natural and healthy milieus, i.e., in healthy, full-term, vaginally born and breast-fed infants (n = 19) born at same clinic. Fecal microbiota at age 1 and 7 days, 1, 3, and 6 months and 3 years is quantified using highly sensitive reverse-transcription-quantitative-PCR assays targeting bacterial rRNA molecules. At day 1, we detect one or more bacteria in all (100%) of the babies, wherein the microbiota is composed mainly of enterobacteria (35%), Bacteroides fragilis group (23%), enterococci (18%), staphylococci (13%), and bifidobacteria (9%). Altogether, facultative anaerobes predominate during first few weeks whereafter obligate anaerobes including bifidobacteria, B. fragilis group, Clostridium coccoides group, and Clostridium leptum subgroup gradually start prevailing. At 3 years, the composition is represented almost entirely (99%) by obligate anaerobes including C. leptum subgroup (34%), bifidobacteria (22%), B. fragilis group (21%), C. coccoides group (17%), Atopobium cluster (4%), and Prevotella (1%). The overall obligate/facultative proportion is 32/68, 37/63, 54/46, 70/30, 64/36, and 99/1% at 1 and 7 days, 1, 3, and 6 months and 3 years, respectively. However, interestingly, considerable individual-specific variations in the obligate/facultative ratios as well as in the proportions of Firmicutes, Bacteroides, Actinobacteria, and Proteobacteria communities are seen among these babies. This disparity even within this highly homogenous cohort manifests the magnitude of diverse patterns of gut microbiota configuration and hence underpins the importance of considering not only the gestational age, birth, and feeding modes, and ethnic/geographical background but also other potential outstanding factors when investigating the elements shaping the early microbiota development. In summary, the data demonstrate a quantitative bird’s-eye view of the ontogenesis of early-life gut microbiota in typically natural and healthy milieus and should be informative and facilitative for future studies exploring various aspects of the human gut microbiota.

Maternal inheritance of bifidobacterial communities and bifidophages in infants through vertical transmission

BACKGROUND

The correct establishment of the human gut microbiota represents a crucial development that commences at birth. Different hypotheses propose that the infant gut microbiota is derived from, among other sources, the mother's fecal/vaginal microbiota and human milk.

RESULTS

The composition of bifidobacterial communities of 25 mother-infant pairs was investigated based on an internal transcribed spacer (ITS) approach, combined with cultivation-mediated and genomic analyses. We identified bifidobacterial strains/communities that are shared between mothers and their corresponding newborns. Notably, genomic analyses together with growth profiling assays revealed that bifidobacterial strains that had been isolated from human milk are genetically adapted to utilize human milk glycans. In addition, we identified particular bacteriophages specific of bifidobacterial species that are common in the viromes of mother and corresponding child.

CONCLUSIONS

This study highlights the transmission of bifidobacterial communities from the mother to her child and implies human milk as a potential vehicle to facilitate this acquisition. Furthermore, these data represent the first example of maternal inheritance of bifidobacterial phages, also known as bifidophages in infants following a vertical transmission route.

Age-Related Changes in the Composition of Gut Bifidobacterium Species

Bifidobacteria are one of the major components in human microbiota that are suggested to function in maintaining human health. The colonization and cell number of Bifidobacterium species in human intestine vary with ageing. However, sequential changes of Bifidobacterium species ranging from newborns to centenarians remain unresolved. Here, we investigated the gut compositional changes of Bifidobacterium species over a wide range of ages. Faecal samples of 441 healthy Japanese subjects between the ages of 0 and 104 years were analysed using real-time PCR with species-specific primers. B. longum group was widely detected from newborns to centenarians, with the highest detection rate. B. breve was detected in approximately 70% of children under 3 years old. B. adolescentis and B. catenulatum groups were predominant after weaning. B. bifidum was detected at almost all ages. The detection rate of B. dentium was higher in the elderly than in other ages. B. animalis ssp. lactis was detected in 11.4% of the subjects and their ages were restricted. B. gallinarum goup was detected in only nine subjects, while B. minimum and B. mongoliense were undetected at any age. The presence of certain Bifidobacterium groups was associated with significantly higher numbers of other Bifidobacterium species/subspecies. Inter-species correlations were found among each species, exception for B. animalis ssp. lactis. These results revealed the patterns and transition points with respect to compositional changes of Bifidobacterium species that occur with ageing, and the findings indicate that there may be symbiotic associations between some of these species in the gut microbiota.

Gut dysbiosis following C-section instigates higher colonisation of toxigenic Clostridium perfringens in infants

Herein we investigated the intestinal carriage of α-toxigenic and enterotoxigenic Clostridium perfringens during infancy, focusing on its association with other gut microbes and mode of delivery and feeding. Faecal samples from 89 healthy term infants were collected at age 7 days, 1 month, 3 months, 6 months and 3 years. C. perfringens was quantified by qPCR; other gut bacteria were quantified by reverse-transcription-qPCR. Alpha-toxigenic C. perfringens was detected in 3.4% infants at day 7 but was present in 35-40% infants at subsequent time-points, with counts ranging from 10³-10⁷ cells/g faeces. Enterotoxigenic C. perfringens remained undetected at day 7 but was detected in 1.1, 4.5, 10.1 and 4.5% infants at 1 month, 3 months, 6 months and 3 years, respectively. Intriguingly, infants carrying α-toxigenic C. perfringens had lower levels of Bacteroides fragilis group, bifidobacteria, lactobacilli and organic acids as compared to non-carriers. Further analyses revealed that, compared to vaginally-born infants, caesarean-born infants had higher carriage of C. perfringens and lower levels of B. fragilis group, bifidobacteria, lactobacilli and faecal organic acids during first 6 months. Compared to formula-fed infants, breast-fed infants were slightly less often colonised with C. perfringens; and within caesarean-born infants, breast-fed infants had slightly lower levels of C. perfringens and higher levels of B. fragilis group, bifidobacteria, and lactobacilli than formula-fed infants. This study demonstrates the quantitative dynamics of toxigenic C. perfringens colonisation in infants during the early years of life. Caesarean-born infants acquire a somewhat perturbed microbiota, and breast-feeding might be helpful in ameliorating this dysbiosis. Higher carriage of toxigenic C. perfringens in healthy infants is intriguing and warrants further investigation of its sources and clinical significance in infants, particularly the caesarean-born who may represent a potential reservoir of this opportunistic pathogen and might be more prone to associated illnesses.

Association between Yogurt Consumption and Intestinal Microbiota in Healthy Young Adults Differs by Host Gender

Human intestinal microbiota are influenced by various factors viz. diet, environment, age, gender, geographical, and socioeconomic situation, etc. among which diet has the most profound impact. However, studies investigating this impact have mostly included subjects from diverse geographic/socioeconomic backgrounds and hence the precise effects of dietary factors on gut microbiota composition remain largely confounded. Herein, with an aim to evaluate the association between dietary habits, specifically yogurt consumption, and the gut microbiota in healthy young adults sharing similar age, lifestyle routine, geographical setting, etc., we conducted a cross-sectional study wherein 293 collegiate freshmen answered a questionnaire about their frequency of yogurt consumption over the last 2 months and provided stool specimens for microbiota analysis. Fecal microbiota were analyzed by highly sensitive reverse-transcription-quantitative-PCR assays targeting bacterial 16S rRNA molecules. Fecal organic acids were measured by HPLC. Overall, the gut microbiota were predominated (97.1 ± 8.6%) by Clostridium coccoides group, Clostridium leptum subgroup, Bacteroides fragilis group, Bifidobacterium and Atopobium cluster. Interestingly, after adjusting the data for yogurt consumption, females were found to have higher total bacterial (P = 0.013) and Bifidobacterium (P = 0.046) count and fecal pH (P = 0.007) and lower fecal concentration of total organic acids (P = 0.030), succinic acid (P = 0.007) and formic acid (P = 0.046) as compared to males. Altogether, yogurt consumption showed positive linear association with Lactobacillus and Lactobacillus gasseri subgroup in both male and female subjects; however, several gender-specific disparities were also detected in this yogurt-microbiota association. Yogurt consumption demonstrated a negative association with L. sakei subgroup, Enterobacteriaceae and Staphylococcus in males but shared a positive association with L. casei subgroup and succinic acid in female subjects. The study manifests the association between yogurt consumption and gut microbiota in a healthy homogeneous cohort and show how this association can differ by host gender. The findings should be helpful for prospective studies investigating the diet–microbiome interaction in human health and disease.

Lipid-based Nutrient Supplements Do Not Affect Gut Bifidobacterium Microbiota in Malawian Infants: A Randomized Trial

OBJECTIVES

The aim of the study was to assess the effect of nutritional supplementation with lipid-based nutrient supplements (LNS) and corn-soy blend flour on Bifidobacterium and Staphylococcus aureus gut microbiota composition in Malawian infants. In addition, the microbiota changes over time were characterized in the study infants.

METHODS

Healthy 6-month-old Malawian infants were randomly assigned to 1 of 4 intervention schemes for a 6-month period. Infants in the control group were not provided with any supplementary food. Infants in other 3 groups received either micronutrient-fortified corn-soy blend, micronutrient-fortified LNS with milk protein base, or micronutrient-fortified LNS with soy protein base between 6 and 12 months of age. Fecal bifidobacteria and S aureus gut microbiota at 6 and 12 months of age were analyzed by quantitative real-time polymerase chain reaction method.

RESULTS

There was no difference in change in bacterial prevalence or counts between the intervention groups during the 6-month study period. When looking at the total study population, higher counts of total bacteria (P = 0.028), Bifidobacterium genus (P = 0.027), B catenulatum (P = 0.031), and lower counts of B infantis (P < 0.001), B lactis (P < 0.001), B longum (P < 0.001), and S aureus (P < 0.001) were detected in the children's stools at 12 months rather than at 6 months of age.

CONCLUSIONS

The dietary supplementation did not have an effect on the Bifidobacterium and S aureus microbiota composition of the study infants. The fecal bifidobacterial diversity of the infants, however, changed toward a more adult-like microbiota profile within the observed time.

Safety of Bifidobacterium breve (BBG-01) in preterm infants

BACKGROUND

Since 1982, viable cells of Bifidobacterium breve (BBG-01) have been used in pediatric patients for clinical conditions such as intractable infantile diarrhea, preterm status, and pediatric surgery. Although the efficacy of BBG-01 has been widely reported, adverse events related to the use of BBG-01 have been reported in very few cases.

METHODS

In order to trace adverse events seen by 109 doctors in 88 medical institutions where BBG-01 was used, a questionnaire survey of the number of occurrences and details of each case was conducted.

RESULTS

Eighty-six clinicians (70 institutions) responded to the questionnaire (response rate, 78.9%). Number of respondents according to department of diagnosis (no. BBG-01-treated infants) was as follows: pediatrics, 29 respondents (10 938 patients); premature and newborn medicine, 26 (10 677 patients); obstetrics and gynecology, 1 (1212 patients) and pediatric surgery, 22 (169 patients). More than 90% of the total BBG-01-treated patients (23 092 patients) were in the departments of premature and newborn medicine and pediatrics, and BBG-01 had been used mainly in preterm infants and children with intractable diarrhea. Adverse events occurred in two extremely premature infants with functional ileus due to starch aggregates as vehicle, and in two surgical neonates with bacteremia caused by B. breve genetically identical to BBG-01, and no serious adverse events with poor outcome were reported.

CONCLUSION

Adverse events related to the use of BBG-01 have an extremely low incidence and are mild in severity, thus ensuring the superior safety of this preparation.

Sensitive Quantitative Analysis of the Meconium Bacterial Microbiota in Healthy Term Infants Born Vaginally or by Cesarean Section

For decades, babies were thought to be born germ-free, but recent evidences suggest that they are already exposed to various bacteria in utero. However, the data on population levels of such pioneer gut bacteria, particularly in context to birth mode, is sparse. We herein aimed to quantify such bacteria from the meconium of 151 healthy term Japanese infants born vaginally or by C-section. Neonatal first meconium was obtained within 24–48 h of delivery; RNA was extracted and subjected to reverse-transcription-quantitative PCR using specific primers for Clostridium coccoides group, C. leptum subgroup, Bacteroides fragilis group, Atopobium cluster, Prevotella, Bifidobacterium, Lactobacillus, Enterococcus, Enterobacteriaceae, Staphylococcus, Enterococcus, Streptococcus, C. perfringens, and C. difficile. We detected several bacterial groups in both vaginally- and cesarean-born infants. B. fragilis group, Enterobacteriaceae, Enterococcus, Streptococcus, and Staphylococcus were detected in more than 50% of infants, with counts ranging from 10⁵ to 10⁸ cells/g sample. About 30–35% samples harbored Bifidobacterium and Lactobacillus (10⁴–10⁵ cells/g); whereas C. coccoides group, C. leptum subgroup and C. perfringens were detected in 10–20% infants (10³–10⁵ cells/g). Compared to vaginally-born babies, cesarean-born babies were significantly less often colonized with Lactobacillus genus (6% vs. 37%; P = 0.01) and Lactobacillus gasseri subgroup (6% vs. 31%; P = 0.04). Overall, seven Lactobacillus subgroups/species, i.e., L. gasseri subgroup, L. ruminis subgroup, L. casei subgroup, L. reuteri subgroup, L. sakei subgroup, L. plantarum subgroup, and L. brevis were detected in the samples from vaginally-born group, whereas only two members, i.e., L. gasseri subgroup and L. brevis were detected in the cesarean group. These data corroborate that several bacterial clades may already be present before birth in term infants’ gut. Further, lower detection rate of lactobacilli in cesarean-born babies suggests that the primary source of lactobacilli in infant gut is mainly from maternal vaginal and–to a lesser extent–anal microbiota during vaginal delivery, and that the colonization by some important Lactobacillus species is delayed in babies delivered via cesarean-section.

A comparison of intestinal microbiota in a population of low-risk infants exposed and not exposed to intrapartum antibiotics: The Baby & Microbiota of the Intestine cohort study protocol

Background

The intestinal microbiota influences metabolic, nutritional, and immunologic processes and has been associated with a broad range of adverse health outcomes including asthma, obesity and Type 2 diabetes. Early life exposures may alter the course of gut microbial colonization leading to differences in metabolic and immune regulation throughout life. Although approximately 50 % of low-risk full-term infants born in Canada are exposed to intrapartum antibiotics, little is known about the influence of this common prophylactic treatment on the developing neonatal intestinal microbiota. The purpose of this study is to describe the intestinal microbiome over the first 3 years of life among healthy, breastfed infants born to women with low-risk pregnancies at full term gestation and to determine if at 1 year of age, the intestinal microbiome of infants exposed to intrapartum antibiotics differs in type and quantity from the infants that are not exposed.

Methods

A prospectively followed cohort of 240 mother-infant pairs will be formed by enrolling eligible pregnant women from midwifery practices in the City of Hamilton and surrounding area in Ontario, Canada. Participants will be followed until the age of 3 years. Women are eligible to participate in the study if they are considered to be low-risk, planning a vaginal birth and able to communicate in English. Women are excluded if they have a multiple pregnancy or a preterm birth. Study questionnaires are completed, anthropometric measures are taken and biological samples are acquired including eight infant stool samples between 3 days and 3 years of age.

Discussion

Our experience to date indicates that midwifery practices and clients are keen to participate in this research. The midwifery client population is likely to have high rates of breastfeeding and low rates of intervention, allowing us to examine the comparative development of the microbiome in a relatively healthy and homogenous population. Results from this study will make an important contribution to the growing understanding of the patterns of intestinal microbiome colonization in the early years of life and may have implications for best practices to support the establishment of the microbiome at birth.

Electronic supplementary material

The online version of this article (doi:10.1186/s12887-016-0724-5) contains supplementary material, which is available to authorized users.

Infant formula with galacto-oligosaccharides (OM55N) stimulates the growth of indigenous bifidobacteria in healthy term infants

The objective of the study was to investigate whether an infant formula supplemented with galacto-oligosaccharides (GOS; OM55N) was able to stimulate the growth of indigenous bifidobacteria and to establish microbiota similar to that of breastfed infants. A randomised, double-blind, placebo-controlled trial was performed using 35 healthy term infants (31-54 days of age; 42±6 days) to determine whether infant formula with 0.3 g/dl GOS (OM55N) stimulated the growth of bifidobacteria in the infants’ guts. At the trial onset and 2 weeks after, the infants’ faecal samples were examined for microbiota composition (bacterial abundance and α-diversity) and faecal characteristics. Among the 35 infants, 5 were withdrawn and 8 were excluded from the final evaluation before breaking the blinding since the indigenous bifidobacteria were not detected at the trial onset. After 2 weeks, the abundance of Bifidobacteriaceae was significantly increased in the GOS feeding group compared to the control (+11.6±24.1% vs -3.9±13.0%; P=0.043). The Shannon index, which accounts for both abundance and evenness of the present species, was significantly decreased with GOS supplementation (-0.1±0.4 vs +0.4±0.4; P=0.014). Faecal characteristics such as pH and organic acids were similar in both groups, with no statistical differences. No adverse side effects related to the formula consumption were reported. Although the concentration of GOS was relatively low, the infant formula with GOS increased the abundance of bifidobacteria and resulted in a reduced α-diversity of the microbiota.

Early-Life Events, Including Mode of Delivery and Type of Feeding, Siblings and Gender, Shape the Developing Gut Microbiota

Colonization of the infant gut is believed to be critically important for a healthy growth as it influences gut maturation, metabolic, immune and brain development in early life. Understanding factors that influence this process is important, since an altered colonization has been associated with a higher risk of diseases later in life. Fecal samples were collected from 108 healthy neonates in the first half year of life. The composition and functionality of the microbiota was characterized by measuring 33 different bacterial taxa by qPCR/RT qPCR, and 8 bacterial metabolites. Information regarding gender, place and mode of birth, presence of siblings or pets; feeding pattern and antibiotic use was collected by using questionnaires. Regression analysis techniques were used to study associations between microbiota parameters and confounding factors over time. Bacterial DNA was detected in most meconium samples, suggesting bacterial exposure occurs in utero. After birth, colonization by species of Bifidobacterium, Lactobacillus and Bacteroides was influenced by mode of delivery, type of feeding and presence of siblings, with differences found at species level and over time. Interestingly, infant-type bifidobacterial species such as B. breve or B. longum subsp infantis were confirmed as early colonizers apparently independent of the factors studied here, while B. animalis subsp. lactis presence was found to be dependent solely on the type of feeding, indicating that it might not be a common infant gut inhabitant. One interesting and rather unexpected confounding factor was gender. This study contributes to our understanding of the composition of the microbiota in early life and the succession process and the evolution of the microbial community as a function of time and events occurring during the first 6 months of life. Our results provide new insights that could be taken into consideration when selecting nutritional supplementation strategies to support the developing infant gut microbiome.

A key genetic factor for fucosyllactose utilization affects infant gut microbiota development

Recent studies have demonstrated that gut microbiota development influences infants' health and subsequent host physiology. However, the factors shaping the development of the microbiota remain poorly understood, and the mechanisms through which these factors affect gut metabolite profiles have not been extensively investigated. Here we analyse gut microbiota development of 27 infants during the first month of life. We find three distinct clusters that transition towards Bifidobacteriaceae-dominant microbiota. We observe considerable differences in human milk oligosaccharide utilization among infant bifidobacteria. Colonization of fucosyllactose (FL)-utilizing bifidobacteria is associated with altered metabolite profiles and microbiota compositions, which have been previously shown to affect infant health. Genome analysis of infants' bifidobacteria reveals an ABC transporter as a key genetic factor for FL utilization. Thus, the ability of bifidobacteria to utilize FL and the presence of FL in breast milk may affect the development of the gut microbiota in infants, and might ultimately have therapeutic implications.

The factors shaping the development of infants' gut microbiota are poorly understood. Here, the authors show that alterations in gut microbiota development in infants are associated with the presence of bifidobacteria having a gene for utilisation of human milk oligosaccharides.

Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study

BACKGROUND

It has been reported that the composition of human gut microbiota changes with age; however, few studies have used molecular techniques to investigate the long-term, sequential changes in gut microbiota composition. In this study, we investigated the sequential changes in gut microbiota composition in newborn to centenarian Japanese subjects.

RESULTS

Fecal samples from 367 healthy Japanese subjects between the ages of 0 and 104 years were analyzed by high-throughput sequencing of amplicons derived from the V3-V4 region of the 16S rRNA gene. Analysis based on bacterial co-abundance groups (CAGs) defined by Kendall correlations between genera revealed that certain transition types of microbiota were enriched in infants, adults, elderly individuals and both infant and elderly subjects. More positive correlations between the relative abundances of genera were observed in the elderly-associated CAGs compared with the infant- and adult-associated CAGs. Hierarchical Ward's linkage clustering based on the abundance of genera indicated five clusters, with median (interquartile range) ages of 3 (0-35), 33 (24-45), 42 (32-62), 77 (36-84) and 94 (86-98) years. Subjects were predominantly clustered with their matched age; however, some of them fell into mismatched age clusters. Furthermore, clustering based on the proportion of transporters predicted by phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) showed that subjects were divided into two age-related groups, the adult-enriched and infant/elderly-enriched clusters. Notably, all the drug transporters based on Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology groups were found in the infant/elderly-enriched cluster.

CONCLUSION

Our results indicate some patterns and transition points in the compositional changes in gut microbiota with age. In addition, the transporter property prediction results suggest that nutrients in the gut might play an important role in changing the gut microbiota composition with age.

Birth mode-dependent association between pre-pregnancy maternal weight status and the neonatal intestinal microbiome

The intestinal microbiome is a unique ecosystem that influences metabolism in humans. Experimental evidence indicates that intestinal microbiota can transfer an obese phenotype from humans to mice. Since mothers transmit intestinal microbiota to their offspring during labor, we hypothesized that among vaginal deliveries, maternal body mass index is associated with neonatal gut microbiota composition. We report the association of maternal pre-pregnancy body mass index on stool microbiota from 74 neonates, 18 born vaginally (5 to overweight or obese mothers) and 56 by elective C-section (26 to overweight or obese mothers). Compared to neonates delivered vaginally to normal weight mothers, neonates born to overweight or obese mothers had a distinct gut microbiota community structure (weighted UniFrac distance PERMANOVA, p < 0.001), enriched in Bacteroides and depleted in Enterococcus, Acinetobacter, Pseudomonas, and Hydrogenophilus. We show that these microbial signatures are predicted to result in functional differences in metabolic signaling and energy regulation. In contrast, among elective Cesarean deliveries, maternal body mass index was not associated with neonatal gut microbiota community structure (weighted UniFrac distance PERMANOVA, p = 0.628). Our findings indicate that excess maternal pre-pregnancy weight is associated with differences in neonatal acquisition of microbiota during vaginal delivery, but not Cesarean delivery. These differences may translate to altered maintenance of metabolic health in the offspring.

Sensitive quantification of Clostridium perfringens in human feces by quantitative real-time PCR targeting alpha-toxin and enterotoxin genes

BACKGROUND

Clostridium perfringens is a widespread pathogen, but the precise quantification of this subdominant gut microbe remains difficult due to its low fecal count (particularly in asymptomatic subjects) and also due to the presence of abundant polymerase-inhibitory substances in human feces. Also, information on the intestinal carriage of toxigenic C. perfringens strains in healthy subjects is sparse. Therefore, we developed a sensitive quantitative real-time PCR assays for quantification of C. perfringens in human feces by targeting its α-toxin and enterotoxin genes. To validate the assays, we finally observed the occurrence of α-toxigenic and enterotoxigenic C. perfringens in the fecal microbiota of healthy Japanese infants and young adults.

METHODS

The plc-specific qPCR assay was newly validated, while primers for 16S rRNA and cpe genes were retrieved from literature. The assays were validated for specificity and sensitivity in pre-inoculated fecal samples, and were finally applied to quantify C. perfringens in stool samples from apparently healthy infants (n 124) and young adults (n 221).

RESULTS

The qPCR assays were highly specific and sensitive, with a minimum detection limit of 10(3) bacterial cells/g feces. Alpha-toxigenic C. perfringens was detected in 36% infants and 33% adults, with counts ranging widely (10(3)-10(7) bacterial cells/g). Intriguingly, the mean count of α-toxigenic C. perfringens was significantly higher in infants (6.0±1.5 log10 bacterial cells/g), as compared to that in adults (4.8±1.2). Moreover, the prevalence of enterotoxigenic C. perfringens was also found to be significantly higher in infants, as compared to that in adults. The mean enterotoxigenic C. perfringens count was 5.9±1.9 and 4.8±0.8 log10 bacterial cells/g in infants and adults, respectively.

CONCLUSIONS

These data indicate that some healthy infants and young adults carry α-toxigenic and enterotoxigenic C. perfringens at significant levels, and may be predisposed to related diseases. Thus, high fecal carriage of toxigenic C. perfringens in healthy children warrants further investigation on its potential sources and clinical significance in these subjects. In summary, we present a novel qPCR assay for sensitive and accurate quantification of α-toxigenic and enterotoxigenic C. perfringens in human feces, which should facilitate prospective studies of the gut microbiota.

The gut microbiota and its role in the development of allergic disease: a wider perspective

The gut microbiota are critical in the homoeostasis of multiple interconnected host metabolic and immune networks. If early microbial colonization is delayed, the gut-associated lymphoid tissues (GALT) fail to develop, leading to persistent immune dysregulation in mice. Microbial colonization has also been proposed as a major driver for the normal age-related maturation of both Th1 and T regulatory (Treg) pathways that appear important in suppressing early propensity for Th2 allergic responses. There is emerging evidence that resident symbionts induce tolerogenic gut-associated Treg cells and dendritic cells that ensure the preferential growth of symbionts; keeping pathogenic strains in check and constraining proinflammatory Th1, Th2, and Th17 clones. Some effects of symbionts are mediated by short-chain fatty acids, which play a critical role in mucosal integrity and local and systemic metabolic function and stimulate the regulatory immune responses. The homoeostatic IL-10/TGF-β dominated tolerogenic response within the GALT also signals the production of secretory IgA, which have a regulating role in mucosal integrity. Contrary to the 'sterile womb' paradigm, recent studies suggest that maternal microbial transfer to the offspring begins during pregnancy, providing a pioneer microbiome. It is likely that appropriate microbial stimulation both pre- and postnatally is required for optimal Th1 and Treg development to avoid the pathophysiological processes leading to allergy. Disturbed gut colonization patterns have been associated with allergic disease, but whether microbial variation is the cause or effect of these diseases is still under investigation. We are far from understanding what constitutes a 'healthy gut microbiome' that promotes tolerance. This remains a major limitation and might explain some of the inconsistency in human intervention studies with prebiotics and probiotics. Multidisciplinary integrative approaches with researchers working in networks, using harmonized outcomes and methodologies, are needed to advance our understanding in this field.

Differences in folate production by bifidobacteria of different origins

Bifidobacteria are known to produce folate, a vital nutrient for humans. Previous studies have suggested that the ability to produce folate is strain dependent, but further adequate evaluation is needed. In this study, a total of 44 strains, including 12 species and 7 subspecies, of bifidobacteria were investigated for the production of folate during cultivation in medium containing essential levels of folate for growth of the tested strains. An in vitro assay showed that all strains of human-residential bifidobacteria (HRB) were able to produce folate, whereas most strains of non-HRB were not, with the exception of the B. thermophilum and B. longum ssp. suis strains. The differences in the in vivo production of folate by HRB and non-HRB were confirmed using mono-associated mice. The fecal folate concentrations, blood levels of hemoglobin and mean corpuscular volumes were significantly higher in the mice colonized with a folate producer, B. longum subsp. longum, compared with mice colonized with a nonproducer, B. animalis subsp. lactis. Our results confirmed the differences in folate production between HRB and non-HRB strains and suggested the benefit of HRB to hosts from the perspective of potential folate delivery.