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Abstract Background Childhood undernutrition is a major global health challenge with devastating lifelong consequences. Linear growth stunting due to undernutrition has been linked to poor health outcomes, and mothers who experience growth stunting in childhood are more likely to give birth to stunted children later in life. Based on these findings, we hypothesized that intergenerational colonization of mice with microbiota from human donors with undernutrition may recapitulate certain immune and growth changes observed in this disorder. Results To test this hypothesis, we developed a gnotobiotic murine model of undernutrition using microbiota from human infants with healthy or stunted growth trajectories. Intergenerational colonization with microbiota derived from children with growth stunting lead to less linear growth and the development of immune features of undernutrition and enteropathy, including intestinal villus blunting, lower liver IGF-1 and accumulation of intraepithelial lymphocytes and plasma cells in the small intestine. In contrast, colonization after weaning lead to fewer host phenotypic changes between these distinct microbial communities. Conclusions These results are broadly consistent with previous findings demonstrating that exposure of the immune system to microbial products during the weaning phase is a critical determinant of later life immune function. Overall, our results suggest intergenerational colonization with human microbiota samples is a useful approach with which to investigate microbiota-dependent changes in growth and immunity in early life. Murine models that capture the intergenerational and multifactorial nature of undernutrition are critical to understanding the underlying biology of this disorder. Video Abstract

Background: Childhood undernutrition is a major global health challenge with devastating lifelong consequences. Linear growth stunting due to undernutrition has been linked to poor health outcomes, and mothers who experience growth stunting in childhood are more likely to give birth to stunted children later in life. Based on these findings, we hypothesized that intergenerational colonization of mice with microbiota from human donors with undernutrition may recapitulate certain immune and growth changes observed in this disorder. Results: To test this hypothesis, we developed a gnotobiotic murine model of undernutrition using microbiota from human infants with healthy or stunted growth trajectories. Intergenerational colonization with microbiota derived from children with growth stunting lead to less linear growth and the development of immune features of undernutrition and enteropathy, including intestinal villus blunting, lower liver IGF-1 and accumulation of intraepithelial lymphocytes and plasma cells in the small intestine. In contrast, colonization after weaning lead to fewer host phenotypic changes between these distinct microbial communities. Conclusions: These results are broadly consistent with previous findings demonstrating that exposure of the immune system to microbial products during the weaning phase is a critical determinant of later life immune function. Overall, our results suggest intergenerational colonization with human microbiota samples is a useful approach with which to investigate microbiota-dependent changes in growth and immunity in early life. Murine models that capture the intergenerational and multifactorial nature of undernutrition are critical to understanding the underlying biology of this disorder. 7T5ZN13mtZ1d8dLkaKDJxv Video Abstract [ABSTRACT FROM AUTHOR]

Antibiotic resistance genes (ARGs) are prevalent in the infant gut microbiota and make up the intestinal resistome, representing a community ARG reservoir. This study focuses on the dynamics and persistence of ARGs in the early gut microbiota, and the effect of early exposures therein. We leveraged 2,328 stool metagenomes from 475 children in the HELMi cohort and the available parental samples to study the diversity, dynamics, and intra-familial sharing of the resistome during the first two years of life. We found higher within-family similarity of the gut resistome composition and ARG load in infant-mother pairs, and between spouses, but not in father-infant pairs. Early gut microbiota composition and development correlated with the ARG load; Bacteroides correlated positively and Bifidobacterium negatively with the load, reflecting the typical resistance levels in these taxa. Caesarean delivered infants harbored lower ARG loads, partly reflecting the scarcity of Bacteroides compared to vaginally delivered. Exposure to intrapartum or post-natal antibiotics showed only modest associations with the ARG load and composition, mainly before 12 months. Our results indicate that the resistome is strongly driven by the normal development of the microbiota in early life, and suggest importance of longer evolution of ARGs over effects of recent antibiotic exposure.

Objective: The effects of sanitation and hygiene interventions on the gut microbiome and enteric pathogen burden are not well understood. We measured the association between free chlorine residue (FCR) levels in drinking water, microbiome composition, and stool enteric pathogens in infants and young children in Haiti. Methods: FCR levels were measured in household drinking water and enteric pathogen burden was evaluated using multiplex RT-PCR of stool among 131 children from one month to five years of age living in Mirebalais, Haiti. Microbiome profiling was performed using metagenomic sequencing. Results: Most individuals lived in households with undetectable FCR measured in the drinking water (112/131, 86%). Detection of enteric pathogen DNA in stool was common and did not correlate with household water FCR. The infant microbiome in households with detectable FCR demonstrated reduced richness (fewer total number of species, P = 0.04 Kruskall–Wallis test) and less diversity by Inverse Simpson measures (P = 0.05) than households with undetectable FCR. Infants in households with a detectable FCR were more likely to have abundant Bifidobacterium. Using in vitro susceptibility testing, we found that some Bifidobacterium species were resistant to chlorine. Conclusions: FCR in household drinking water did not correlate with enteric pathogen burden in our study.

Background: Maternal diet during pregnancy may play a role in infant health outcomes via the maternal microbiota. We assessed the association of the maternal diet index for the Mediterranean area (MDI-med) with infant gut microbiota at 1 month of life. Methods: The MAMI study is a longitudinal birth cohort in the Mediterranean area. In this work, a cross-sectional study, including 120 mother–infant dyads with available maternal diet and infant microbiota at 1-month-old data, was undertaken. The MDI developed in the US (MDI-US) was adapted for the MAMI cohort (MDI-med). Stratification based on extreme values resulted (22 in the "lower" MDI-med group and 23 in the "upper" group from the mean). Relative microbial abundances and alpha (microbial richness and diversity indexes) and beta diversity (Bray–Curtis distance matrix) were compared between the groups. Results: Higher maternal daily vegetable intake and lower red meat intake were the characteristics of the "upper" MDI-med group. Significantly lower microbial diversity (Shannon and InvSimpson index (p = 0.01)), but no changes in richness (Chao1 index) nor in beta-diversity, using Bray–Curtis distance, were observed in the "upper" group, compared to the "lower" MDI-med group. A higher relative abundance of the Bifidobacterium genus (Actinomycetota phylum) was associated with maternal daily vegetable and yogurt intake. Conclusion: Reduced infant microbial diversity at 1 month of age was associated with "upper" MDI-med scores. Higher maternal intakes of vegetables and yogurt were associated with higher relative abundances of the Bifidobacterium genus in the infant gut. Further studies are needed to understand the link between pregnancy diet, infant microbiota, and health outcomes. [ABSTRACT FROM AUTHOR]

Prenatal maternal stress (PNMS)—characterized by exposure to stress, anxiety, depression, or intimate partner violence—has been linked to biological alterations in infants, including disruptions to their intestinal microbiota, which have long‐term implications for children's developmental outcomes. Significant research has been done examining the effects of PNMS on the microbiome in animals, but less is known about these effects in human research. The current systematic review aimed to synthesize current findings on the association between PNMS and mother and infant microbiomes. Medline, Embase, PsycInfo, Web of Science, and Eric databases were searched through to February 2022. A total of eight studies (n = 2219 infants, 2202 mothers) were included in the qualitative synthesis. Findings provided promising evidence of the role that PNMS plays in altering the microbial composition, diversity, and gut immunity in mothers and infants. Notably, majority of included studies found that higher PNMS was linked to increases in genera from the phylum Proteobacteria. The factors influencing these effects are explored including nutrition, birth mode, and parenting behaviors. Potential interventions to mitigate the adverse effects of PNMS are discussed, along with recommendations for future studies with longitudinal designs to better understand the appropriate type and timing of interventions needed to promote "healthy" maternal and infant microbial functioning. [ABSTRACT FROM AUTHOR]

Background: Maternal diet during pregnancy may play a role in infant health outcomes via the maternal microbiota. We assessed the association of the maternal diet index for the Mediterranean area (MDI-med) with infant gut microbiota at 1 month of life. Methods: The MAMI study is a longitudinal birth cohort in the Mediterranean area. In this work, a cross-sectional study, including 120 mother–infant dyads with available maternal diet and infant microbiota at 1-month-old data, was undertaken. The MDI developed in the US (MDI-US) was adapted for the MAMI cohort (MDI-med). Stratification based on extreme values resulted (22 in the “lower” MDI-med group and 23 in the “upper” group from the mean). Relative microbial abundances and alpha (microbial richness and diversity indexes) and beta diversity (Bray–Curtis distance matrix) were compared between the groups. Results: Higher maternal daily vegetable intake and lower red meat intake were the characteristics of the “upper” MDI-med group. Significantly lower microbial diversity (Shannon and InvSimpson index (p = 0.01)), but no changes in richness (Chao1 index) nor in beta-diversity, using Bray–Curtis distance, were observed in the “upper” group, compared to the “lower” MDI-med group. A higher relative abundance of the Bifidobacterium genus (Actinomycetota phylum) was associated with maternal daily vegetable and yogurt intake. Conclusion: Reduced infant microbial diversity at 1 month of age was associated with “upper” MDI-med scores. Higher maternal intakes of vegetables and yogurt were associated with higher relative abundances of the Bifidobacterium genus in the infant gut. Further studies are needed to understand the link between pregnancy diet, infant microbiota, and health outcomes.

During pregnancy, changes occur to influence the maternal gut microbiome, and potentially the fetal microbiome. Diet has been shown to impact the gut microbiome. Little research has been conducted examining diet during pregnancy with respect to the gut microbiome. To meet inclusion criteria, dietary analyses must have been conducted as part of the primary aim. The primary outcome was the composition of the gut microbiome (infant or maternal), as assessed using culture-independent sequencing techniques. This review identified seven studies for inclusion, five examining the maternal gut microbiome and two examining the fetal gut microbiome. Microbial data were attained through analysis of stool samples by 16S ribosomal RNA gene-based microbiota assessment. Studies found an association between the maternal diet and gut microbiome. High-fat diets (% fat of total energy), fat-soluble vitamins (mg/d) and fibre (g/d) were the most significant nutrients associated with the gut microbiota composition of both neonates and mothers. High-fat diets were significantly associated with a reduction in microbial diversity. High-fat diets may reduce microbial diversity, while fibre intake may be positively associated with microbial diversity. The results of this review must be interpreted with caution. The number of studies was low, and the risk of observational bias and heterogeneity across the studies must be considered. However, these results show promise for dietary intervention and microbial manipulation in order to favour an increase of health-associated taxa in the gut of the mother and her offspring. [ABSTRACT FROM AUTHOR]

Objectives: The gut microbiome (GM) connects physical and social environments to infant health. Since the infant GM affects immune system development, there is interest in understanding how infants acquire microbes from mothers and other household members. Materials and Methods: As a part of the Cebu Longitudinal Health and Nutrition Survey (CLHNS), we paired fecal samples (proxy for the GM) collected from infants living in Metro Cebu, Philippines at 2 weeks (N = 39) and 6 months (N = 36) with maternal interviews about prenatal household composition. We hypothesized that relationships between prenatal household size and composition and infant GM bacterial diversity (as measured in fecal samples) would vary by infant age, as well as by household member age and sex. We also hypothesized that infant GM bacterial abundances would differ by prenatal household size and composition. Results: Data from 16 S rRNA bacterial gene sequencing show that prenatal household size was the most precise estimator of infant GM bacterial diversity, and that the direction of the association between this variable and infant GM bacterial diversity changed between the two time points. The abundances of bacterial families in the infant GM varied by prenatal household variables. Conclusions: Results highlight the contributions of various household sources to the bacterial diversity of the infant GM, and suggest that prenatal household size is a useful measure for estimating infant GM bacterial diversity in this cohort. Future research should measure the effect of specific sources of household bacterial exposures, including social interactions with caregivers, on the infant GM. [ABSTRACT FROM AUTHOR]

The microbiomes of 83 preterm very-low-birth-weight (VLBW) infants and clinical covariates were analyzed weekly over the course of their initial neonatal intensive care unit (NICU) stay, with infant growth as the primary clinical outcome. Birth weight significantly correlated with increased rate of weight gain in the first 6 weeks of life, while no significant relationship was observed between rate of weight gain and feeding type. Microbial diversity increased with age and was significantly correlated with weight gain and percentage of the mother's own milk. As expected, infants who received antibiotics during their NICU stay had significantly lower alpha diversity than those who did not. Of those in the cohort, 25 were followed into childhood. Alpha diversity significantly increased between NICU discharge and age 2 years and between age 2 years and age 4 years, but the microbial alpha diversity of 4-year-old children was not significantly different from that of mothers. Infants who showed improved length over the course of their NICU stay had significantly more volatile microbial beta diversity results than and a significantly decreased microbial maturity index compared with infants who did not; interestingly, all infants who showed improved length during the NICU stay were delivered by Caesarean section. Microbial beta diversity results were significantly different between the time of the NICU stay and all other time points (for children who were 2 or 4 years old and mothers when their children were 2 or 4 years old). IMPORTANCE Preterm infants are at greater risk of microbial insult than full-term infants, including reduced exposure to maternal vaginal and enteric microbes, higher rates of formula feeding, invasive procedures, and administration of antibiotics and medications that alter gastrointestinal pH. This investigation of the VLBW infant microbiome over the course of the neonatal intensive care unit (NICU) stay, and at ages 2 and 4 years, showed that the only clinical variables associated with significant differences in taxon abundance were weight gain during NICU stay (Klebsiella and Staphylococcus) and antibiotic administration (Streptococcus and Bifidobacterium). At 2 and 4 years of age, the microbiota of these VLBW infants became similar to the mothers' microbiota. The number of microbial taxa shared between the infant or toddler and the mother varied, with least the overlap between infants and mothers. Overall, there was a significant association between the diversity and structure of the microbial community and infant weight and length gain in an at-risk childhood population.

Historically, Bifidobacterium species were reported as abundant in the breastfed infant gut. However, recent studies in resource-rich countries show an increased abundance of taxa regarded as signatures of dysbiosis. It is unclear whether these differences are the product of genetics, geographic factors, or interventions such as formula feeding, antibiotics, and caesarean section. Fecal pH is strongly associated with Bifidobacterium abundance; thus, pH could be an indicator of its historical abundance. A review of 14 clinical studies published between 1926 and 2017, representing more than 312 healthy breastfed infants, demonstrated a change in fecal pH from 5.0 to 6.5 (adjusted r2 = 0.61). This trend of increasing infant fecal pH over the past century is consistent with current reported discrepancies in Bifidobacterium species abundance in the gut microbiome in resource-rich countries compared to that in historical reports. Our analysis showed that increased fecal pH and abundance of members of the families Enterobacteriaceae, Clostridiaceae, Peptostreptococcaceae, and Veillonellaceae are associated, indicating that loss of highly specialized Bifidobacterium species may result in dysbiosis, the implications of which are not yet fully elucidated. Critical assessment of interventions that restore this ecosystem, measured by key parameters such as ecosystem productivity, gut function, and long-term health, are necessary to understand the magnitude of this change in human biology over the past century.

ABSTRACT Shigella continues to be a major contributor to diarrheal illness and dysentery in children younger than 5 years of age in low- and middle-income countries. Strategies for the prevention of shigellosis have focused on enhancing adaptive immunity. The interaction between Shigella and intrinsic host factors, such as the microbiome, remains unknown. We hypothesized that Shigella infection would impact the developing microbial community in infancy and, conversely, that changes in the gastrointestinal microbiome may predispose infections. To test this hypothesis, we characterized the gastrointestinal microbiota in a longitudinal birth cohort from Malawi that was monitored for Shigella infection using 16S rRNA amplicon sequencing. Children with at least one Shigella quantitative polymerase chain reaction (qPCR) positive sample during the first 2 years of life (cases) were compared to uninfected controls that were matched for sex and age. Overall, the microbial species diversity, as measured by the Shannon diversity index, increased over time, regardless of case status. At early time points, the microbial community was dominated by Bifidobacterium longum and Escherichia/Shigella. A greater abundance of Prevotella 9 and Bifidobacterium kashiwanohense was observed at 2 years of age. While no single species was associated with susceptibility to Shigella infection, significant increases in Lachnospiraceae NK4A136 and Fusicatenibacter saccharivorans were observed following Shigella infection. Both taxa are in the family Lachnospiraceae, which are known short-chain fatty acid producers that may improve gut health. Our findings identified temporal changes in the gastrointestinal microbiota associated with Shigella infection in Malawian children and highlight the need to further elucidate the microbial communities associated with disease susceptibility and resolution. IMPORTANCE Shigella causes more than 180 million cases of diarrhea globally, mostly in children living in poor regions. Infection can lead to severe health impairments that reduce quality of life. There is increasing evidence that disruptions in the gut microbiome early in life can influence susceptibility to illnesses. A delayed or impaired reconstitution of the microbiota following infection can further impact overall health. Aiming to improve our understanding of the interaction between Shigella and the developing infant microbiome, we investigated changes in the gut microbiome of Shigella-infected and uninfected children over the course of their first 2 years of life. We identified species that may be involved in recovery from Shigella infection and in driving the microbiota back to homeostasis. These findings support future studies into the elucidation of the interaction between the microbiota and enteric pathogens in young children and into the identification of potential targets for prevention or treatment.

Attempts to alter intestinal dysbiosis via administration of probiotics have consistently shown that colonization with the administered microbes is transient. This study sought to determine whether provision of an initial course of Bifidobacterium longum subsp. infantis (B. infantis) would lead to persistent colonization of the probiotic organism in breastfed infants. Mothers intending to breastfeed were recruited and provided with lactation support. One group of mothers fed B. infantis EVC001 to their infants from day 7 to day 28 of life (n = 34), and the second group did not administer any probiotic (n = 32). Fecal samples were collected during the first 60 postnatal days in both groups. Fecal samples were assessed by 16S rRNA gene sequencing, quantitative PCR, mass spectrometry, and endotoxin measurement. B. infantis-fed infants had significantly higher populations of fecal Bifidobacteriaceae, in particular B. infantis, while EVC001 was fed, and this difference persisted more than 30 days after EVC001 supplementation ceased. Fecal milk oligosaccharides were significantly lower in B. infantis EVC001-fed infants, demonstrating higher consumption of human milk oligosaccharides by B. infantis EVC001. Concentrations of acetate and lactate were significantly higher and fecal pH was significantly lower in infants fed EVC001, demonstrating alterations in intestinal fermentation. Infants colonized by Bifidobacteriaceae at high levels had 4-fold-lower fecal endotoxin levels, consistent with observed lower levels of Gram-negative Proteobacteria and Bacteroidetes. IMPORTANCE The gut microbiome in early life plays an important role for long-term health and is shaped in large part by diet. Probiotics may contribute to improvements in health, but they have not been shown to alter the community composition of the gut microbiome. Here, we found that breastfed infants could be stably colonized at high levels by provision of B. infantis EVC001, with significant changes to the overall microbiome composition persisting more than a month later, whether the infants were born vaginally or by caesarean section. This observation is consistent with previous studies demonstrating the capacity of this subspecies to utilize human milk glycans as a nutrient and underscores the importance of pairing a probiotic organism with a specific substrate. Colonization by B. infantis EVC001 resulted in significant changes to fecal microbiome composition and was associated with improvements in fecal biochemistry. The combination of human milk and an infant-associated Bifidobacterium sp. shows, for the first time, that durable changes to the human gut microbiome are possible and are associated with improved gut function.

Necrotizing enterocolitis (NEC) is a severe intestinal disease of very preterm infants with mother's own milk (MOM) providing protection, but the contribution of the MOM microbiota to NEC risk has not been explored. Here, we analyze MOM of 110 preterm infants (48 NEC, 62 control) in a cross-sectional study. Breast milk contains viable bacteria, but there is no significant difference in MOM microbiota between NEC and controls. Integrative analysis between MOM microbiota, human milk oligosaccharides (HMOs), and the infant gut microbiota shows positive correlations only between Acinetobacter in the infant gut and Acinetobacter and Staphylococcus in MOM. This study suggests that NEC protection from MOM is not modulated through the MOM microbiota. Thus, "'restoring" the MOM microbiota in donor human milk is unlikely to reduce NEC, and emphasis should instead focus on increasing fresh maternal human milk intake and researching different therapies for NEC prevention., Competing Interests: Declaration of interests L.B. is the UC San Diego Chair of Collaborative Human Milk Research, endowed by the Family Larsson-Rosenquist Foundation (FLRF), Switzerland. L.B. is a co-inventor on patent applications related to the use of HMOs in preventing NEC and other inflammatory diseases. N.D.E. and J.E.B. report grants to their institutions from Prolacta Bioscience US and Danone Early Life Nutrition. N.D.E. declares lecture honoraria donated to charity from Nestlé Nutrition Institute. C.J.S. declares lecture honoraria from Nestlé Nutrition Institute., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

Objective: The effects of sanitation and hygiene interventions on the gut microbiome and enteric pathogen burden are not well understood. We measured the association between free chlorine residue (FCR) levels in drinking water, microbiome composition, and stool enteric pathogens in infants and young children in Haiti., Methods: FCR levels were measured in household drinking water and enteric pathogen burden was evaluated using multiplex RT-PCR of stool among 131 children from one month to five years of age living in Mirebalais, Haiti. Microbiome profiling was performed using metagenomic sequencing., Results: Most individuals lived in households with undetectable FCR measured in the drinking water (112/131, 86%). Detection of enteric pathogen DNA in stool was common and did not correlate with household water FCR. The infant microbiome in households with detectable FCR demonstrated reduced richness (fewer total number of species, P = 0.04 Kruskall-Wallis test) and less diversity by Inverse Simpson measures (P = 0.05) than households with undetectable FCR. Infants in households with a detectable FCR were more likely to have abundant Bifidobacterium. Using in vitro susceptibility testing, we found that some Bifidobacterium species were resistant to chlorine., Conclusions: FCR in household drinking water did not correlate with enteric pathogen burden in our study., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

A major challenge in working with longitudinal data when studying some temporal process is the fact that differences in pace and dynamics might overshadow similarities between processes. In the case of longitudinal microbiome data, this may hinder efforts to characterize common temporal trends across individuals or to harness temporal information to better understand the link between the microbiome and the host. One possible solution to this challenge lies in the field of "temporal alignment" – an approach for optimally aligning longitudinal samples obtained from processes that may vary in pace. In this work we investigate the use of alignment-based analysis in the microbiome domain, focusing on microbiome data from infants in their first years of life. Our analyses center around two main use-cases: First, using the overall alignment score as a measure of the similarity between microbiome developmental trajectories, and showing that this measure can capture biological differences between individuals. Second, using the specific matching obtained between pairs of samples in the alignment to highlight changes in pace and temporal dynamics, showing that it can be utilized to predict the age of infants based on their microbiome and to uncover developmental delays. Combined, our findings serve as a proof-of-concept for the use of temporal alignment as an important and beneficial tool in future longitudinal microbiome studies. [ABSTRACT FROM AUTHOR]

Infancy is a critical life stage for the establishment of the gut microbiome. Human milk contains a unique microbial ecosystem that serves as a continuous source of commensal bacteria for the infant. However, the origin of the human milk microbiota, how it is influenced by breastfeeding exclusivity, and its role in infant gut microbiota assembly are not clear. To interrogate these questions, we examined the relationships among fecal, oral, breast skin, and human milk microbiota of 33 exclusively breastfeeding (EBF) and mixed-feeding (MF; human milk + infant formula) mother–infant pairs at 6 weeks postpartum. Here, we show that MF infants have a significantly more diverse oral microbiome comprised of lower relative abundances of Streptococcus and Gemella and higher abundances of Veillonella. Using both SourceTracker2 and FEAST, we demonstrate breast skin and infant saliva as the principal contributing sources to the human milk microbiota. Of the sampled sites, human milk and maternal stool were predicted to contribute the largest fraction to the infant fecal microbiome, but the majority of the community was estimated to arise from unknown sources. Lastly, we identified twenty-one significant co-occurrence relationships between bacteria in human milk and on other maternal and infant body sites. These results demonstrate several unique microbial interrelationships between breastfeeding dyads, providing insight into potential mechanisms of microbial assembly in early life. [ABSTRACT FROM AUTHOR]

A major challenge in working with longitudinal data when studying some temporal process is the fact that differences in pace and dynamics might overshadow similarities between processes. In the case of longitudinal microbiome data, this may hinder efforts to characterize common temporal trends across individuals or to harness temporal information to better understand the link between the microbiome and the host. One possible solution to this challenge lies in the field of “temporal alignment” – an approach for optimally aligning longitudinal samples obtained from processes that may vary in pace. In this work we investigate the use of alignment-based analysis in the microbiome domain, focusing on microbiome data from infants in their first years of life. Our analyses center around two main use-cases: First, using the overall alignment score as a measure of the similarity between microbiome developmental trajectories, and showing that this measure can capture biological differences between individuals. Second, using the specific matching obtained between pairs of samples in the alignment to highlight changes in pace and temporal dynamics, showing that it can be utilized to predict the age of infants based on their microbiome and to uncover developmental delays. Combined, our findings serve as a proof-of-concept for the use of temporal alignment as an important and beneficial tool in future longitudinal microbiome studies.

Human milk oligosaccharides (HMOs) are a family of glycans found in breastmilk with over 200 identified structures. Despite being t​​he third-largest solid component in breastmilk, HMOs are indigestible by infants, and they serve as food for the infant gut bacteria. Most research thus far has focused on Bifidobacterium species that harbor many glycoside hydrolases (GHs) tailored to break the carbon bonds in HMO molecules. However, there are additional microbes in the infant gut, such as Bacteroides species, with increasing evidence that they, too, are able to break-down HMOs. To study the unbiased impact of breastfeeding on the infant gut microbiome, we need to investigate the underlying mechanisms of HMO utilization by all members of the infant gut. Here, we developed an optimized system for isolating Bacteroides strains from infant stool samples. We then examined the HMO utilization capacity of multiple Bacteroides isolates by performing growth curves on six common HMOs (2'-FL, DFL, 3'-SL, 6'-SL, LNT, LNnT). Isolates often displayed similar growth characteristics on similarly-structured HMOs, like sialylated or fucosylated sugars. We identified variation in HMO utilization across multiple strains of the same species, and chose to focus here on a Bacteroides dorei isolate that was able to utilize the test HMOs. We performed RNA sequencing on B. dorei cultures, comparing the transcriptional profile in minimal media supplemented with glucose or HMOs. We showed that B. dorei employs an extensive metabolic response to HMOs. Surprisingly, there was no clear up-regulation for most GH families previously known to break-down HMOs, possibly because they were almost exclusively described in Bifidobacterium species. Instead, B. dorei exhibits a generalized response to HMOs, markedly up-regulating several shared GH families across all conditions. Within each GH family, B. dorei displays a consistent pattern of up-regulation of some genes with down-regulation of the others. This response pattern to HMOs has yet to be described in other commensals of the infant gut. Our work highlights the importance of expanding the HMO-microbiome studies beyond Bifidobacterium species, sheds light on the differences across Bacteroides strains in terms of HMO utilization, and paves the way to understanding the mechanisms enabling Bacteroides HMO utilization. [ABSTRACT FROM AUTHOR]

Human milk oligosaccharides (HMOs) are a family of glycans found in breastmilk with over 200 identified structures. Despite being t​​he third-largest solid component in breastmilk, HMOs are indigestible by infants, and they serve as food for the infant gut bacteria. Most research thus far has focused on Bifidobacterium species that harbor many glycoside hydrolases (GHs) tailored to break the carbon bonds in HMO molecules. However, there are additional microbes in the infant gut, such as Bacteroides species, with increasing evidence that they, too, are able to break-down HMOs. To study the unbiased impact of breastfeeding on the infant gut microbiome, we need to investigate the underlying mechanisms of HMO utilization by all members of the infant gut. Here, we developed an optimized system for isolating Bacteroides strains from infant stool samples. We then examined the HMO utilization capacity of multiple Bacteroides isolates by performing growth curves on six common HMOs (2’-FL, DFL, 3’-SL, 6’-SL, LNT, LNnT). Isolates often displayed similar growth characteristics on similarly-structured HMOs, like sialylated or fucosylated sugars. We identified variation in HMO utilization across multiple strains of the same species, and chose to focus here on a Bacteroides dorei isolate that was able to utilize the test HMOs. We performed RNA sequencing on B. dorei cultures, comparing the transcriptional profile in minimal media supplemented with glucose or HMOs. We showed that B. dorei employs an extensive metabolic response to HMOs. Surprisingly, there was no clear up-regulation for most GH families previously known to break-down HMOs, possibly because they were almost exclusively described in Bifidobacterium species. Instead, B. dorei exhibits a generalized response to HMOs, markedly up-regulating several shared GH families across all conditions. Within each GH family, B. dorei displays a consistent pattern of up-regulation of some genes with down-regulation of the others. This response pattern to HMOs has yet to be described in other commensals of the infant gut. Our work highlights the importance of expanding the HMO-microbiome studies beyond Bifidobacterium species, sheds light on the differences across Bacteroides strains in terms of HMO utilization, and paves the way to understanding the mechanisms enabling Bacteroides HMO utilization.

Vertical transmission of maternal microbes is a major route for establishing the gut microbiome in newborns. The impact of perinatal antibiotics on vertical transmission of microbes and antimicrobial resistance is not well understood. Using a metagenomic approach, we analyzed the fecal samples from mothers and vaginally delivered infants from a control group (10 pairs) and a treatment group (10 pairs) receiving perinatal antibiotics. Antibiotic-usage had a significant impact on the main source of inoculum in the gut microbiome of newborns. The control group had significantly more species transmitted from mothers to infants (P =.03) than the antibiotic-treated group. Approximately 72% of the gut microbial population of infants at 3–7 days after birth in the control group was transmitted from their mothers, versus only 25% in the antibiotic-treated group. In conclusion, perinatal antibiotics markedly disturbed vertical transmission and changed the source of gut colonization towards horizontal transfer from the environment to the infants. [ABSTRACT FROM AUTHOR]

Abstract Background From early life, children are exposed to a multitude of environmental exposures, which may be of crucial importance for healthy development. Here, the environmental microbiota may be of particular interest as it represents the interface between environmental factors and the child. As infants in modern societies spend a considerable amount of time indoors, we hypothesize that the indoor bed dust microbiota might be an important factor for the child and for the early colonization of the airway microbiome. To explore this hypothesis, we analyzed the influence of environmental exposures on 577 dust samples from the beds of infants together with 542 airway samples from the Copenhagen Prospective Studies on Asthma in Childhood2010 cohort. Results Both bacterial and fungal community was profiled from the bed dust. Bacterial and fungal diversity in the bed dust was positively correlated with each other. Bacterial bed dust microbiota was influenced by multiple environmental factors, such as type of home (house or apartment), living environment (rural or urban), sex of siblings, and presence of pets (cat and/or dog), whereas fungal bed dust microbiota was majorly influenced by the type of home (house or apartment) and sampling season. We further observed minor correlation between bed dust and airway microbiota compositions among infants. We also analyzed the transfer of microbiota from bed dust to the airway, but we did not find evidence of transfer of individual taxa. Conclusions Current study explores the influence of environmental factors on bed dust microbiota (both bacterial and fungal) and its correlation with airway microbiota (bacterial) in early life using high-throughput sequencing. Our findings demonstrate that bed dust microbiota is influenced by multiple environmental exposures and could represent an interface between environment and child. Video Abstract

Background Milk fat globule membrane (MFGM) and lactoferrin (LF) are human-milk bioactive components demonstrated to support gastrointestinal and immune development. Significantly fewer diarrhea and respiratory-associated adverse events through 18 mo of age were previously reported in healthy term infants fed a cow-milk–based infant formula with an added source of bovine MFGM and bovine LF through 12 mo of age. Objectives The aim was to compare microbiota and metabolite profiles in a subset of study participants. Methods Stool samples were collected at baseline (10–14 d of age) and day 120. Bacterial community profiling was performed via 16S rRNA gene sequencing and alpha and beta diversity were analyzed (QIIME 2). Differentially abundant taxa were determined using linear discriminant analysis effect size (LefSE) and visualized (Metacoder). Untargeted stool metabolites were analyzed (HPLC/MS) and expressed as the fold-change between group means (control to MFGM+LF ratio). Results Alpha diversity increased significantly in both groups from baseline to 4 mo. Subtle group differences in beta diversity were demonstrated at 4 mo (Jaccard distance; R 2 = 0.01, P  = 0.042). Specifically, Bacteroides uniformis and Bacteroides plebeius were more abundant in the MFGM+LF group at 4 mo. Metabolite profile differences for MFGM+LF versus control included lower fecal medium-chain fatty acids, deoxycarnitine, and glycochenodeoxycholate, and some higher fecal carbohydrates and steroids (P  < 0.05). After applying multiple test correction, the differences in stool metabolomics were not significant. Conclusions Addition of bovine MFGM and LF in infant formula was associated with subtle differences in stool microbiome and metabolome by 4 mo of age, including increased prevalence of Bacteroides species. Stool metabolite profiles may be consistent with altered microbial metabolism. This trial was registered at https://clinicaltrials.gov as NCT02274883. [ABSTRACT FROM AUTHOR]

Since the implementation of screening and prophylaxis guidelines for group B streptococcus (GBS) in the early 1990s there has been considerable advancement in scientific knowledge about the gut microbiome and its role in both health and disease processes. Research assessing early influences during the development of the infant gut microbiome has advanced considerably in the last 15 years. It is now widely accepted that early introduction of antibiotics in infancy is associated with increased risk for illness later in life. Research on antibiotic administration to pregnant individuals during labor for GBS colonization and its potential impact on the developing gut microbiome of term infants is now emerging. Despite the growing body of evidence of the negative impact of antibiotics on the gut microbiome, the guidelines for GBS prophylaxis among pregnant individuals have not changed significantly since their inception in the 1990s. This state of the science review examines the association between intrapartum antibiotic administration and alterations in the gut microbiome of term infants born vaginally, specifically in relation to microbial composition; the occurrence of and effect on antibiotic resistance genes in the infant gut; and the factors that may compound or mitigate these effects. [ABSTRACT FROM AUTHOR]

Infancy is a critical life stage for the establishment of the gut microbiome. Human milk contains a unique microbial ecosystem that serves as a continuous source of commensal bacteria for the infant. However, the origin of the human milk microbiota, how it is influenced by breastfeeding exclusivity, and its role in infant gut microbiota assembly are not clear. To interrogate these questions, we examined the relationships among fecal, oral, breast skin, and human milk microbiota of 33 exclusively breastfeeding (EBF) and mixed-feeding (MF; human milk + infant formula) mother–infant pairs at 6 weeks postpartum. Here, we show that MF infants have a significantly more diverse oral microbiome comprised of lower relative abundances of Streptococcus and Gemella and higher abundances of Veillonella. Using both SourceTracker2 and FEAST, we demonstrate breast skin and infant saliva as the principal contributing sources to the human milk microbiota. Of the sampled sites, human milk and maternal stool were predicted to contribute the largest fraction to the infant fecal microbiome, but the majority of the community was estimated to arise from unknown sources. Lastly, we identified twenty-one significant co-occurrence relationships between bacteria in human milk and on other maternal and infant body sites. These results demonstrate several unique microbial interrelationships between breastfeeding dyads, providing insight into potential mechanisms of microbial assembly in early life.

Early-life microbiota has been linked to the development of chronic inflammatory diseases. It has been hypothesized that maternal vaginal microbiota is an important initial seeding source and therefore might have lifelong effects on disease risk. To understand maternal vaginal microbiota’s role in seeding the child’s microbiota and the extent of delivery mode-dependent transmission, we studied 665 mother–child dyads from the COPSAC2010 cohort. The maternal vaginal microbiota was evaluated twice in the third trimester and compared with the children’s fecal (at 1 week, 1 month, and 1 year of age) and airway microbiota (at 1 week, 1 month, and 3 months). Based on the concept of weighted transfer ratios (WTRs), we have identified bacterial orders for which the WTR displays patterns indicate persistent or transient transfer from the maternal vaginal microbiome, as well as orders that are shared at later time points independent of delivery mode, indicating a common reservoir.

Over the past decade, there has been a growing awareness of the vital role of the microbiome in the function of the immune system. Recently, several studies have demonstrated a relationship between the composition of the microbiome and the vaccine-specific immune response. As a result of these findings, the administration of probiotics has been proposed as a means of boosting vaccine-specific immunity. Early results have so far been highly inconsistent, with little evidence of sustained benefit. To date, a precise determination of the aspects of the microbiome that impact immunity is still lacking, and the mechanisms of action are also unknown. Further investigations into these questions are necessary to effectively manipulate the microbiome for the purpose of boosting immunity and enhancing vaccine-specific responses in infants. In this review, we summarize recent studies aimed at altering the neonatal gut microbiome to enhance vaccine responses and highlight gaps in knowledge and understanding. We also discuss research strategies aimed at filling these gaps and developing potential therapeutic interventions.

SUMMARYHuman milk oligosaccharides (HMOs) are complex, multi-functional glycans present in human breast milk. They represent an intricate mix of heterogeneous structures which reach the infant intestine in an intact form as they resist gastrointestinal digestion. Therefore, they confer a multitude of benefits, directly and/or indirectly, to the developing neonate. Certain bifidobacterial species, being among the earliest gut colonizers of breast-fed infants, have an adapted functional capacity to metabolize various HMO structures. This ability is typically observed in infant-associated bifidobacteria, as opposed to bifidobacteria associated with a mature microbiota. In recent years, information has been gleaned regarding how these infant-associated bifidobacteria as well as certain other taxa are able to assimilate HMOs, including the mechanistic strategies enabling their acquisition and consumption. Additionally, complex metabolic interactions occur between microbes facilitated by HMOs, including the utilization of breakdown products released from HMO degradation. Interest in HMO-mediated changes in microbial composition and function has been the focal point of numerous studies, in recent times fueled by the availability of individual biosynthetic HMOs, some of which are now commonly included in infant formula. In this review, we outline the main HMO assimilatory and catabolic strategies employed by infant-associated bifidobacteria, discuss other taxa that exhibit breast milk glycan degradation capacity, and cover HMO-supported cross-feeding interactions and related metabolites that have been described thus far., Competing Interests: The authors declare no conflict of interest.

Antibiotic resistance genes (ARGs) are prevalent in the infant gut microbiota and make up the intestinal resistome, representing a community ARG reservoir. This study focuses on the dynamics and persistence of ARGs in the early gut microbiota, and the effect of early exposures therein. We leveraged 2,328 stool metagenomes from 475 children in the HELMi cohort and the available parental samples to study the diversity, dynamics, and intra-familial sharing of the resistome during the first two years of life. We found higher within-family similarity of the gut resistome composition and ARG load in infant-mother pairs, and between spouses, but not in father-infant pairs. Early gut microbiota composition and development correlated with the ARG load; Bacteroides correlated positively and Bifidobacterium negatively with the load, reflecting the typical resistance levels in these taxa. Caesarean delivered infants harbored lower ARG loads, partly reflecting the scarcity of Bacteroides compared to vaginally delivered. Exposure to intrapartum or post-natal antibiotics showed only modest associations with the ARG load and composition, mainly before 12 months. Our results indicate that the resistome is strongly driven by the normal development of the microbiota in early life, and suggest importance of longer evolution of ARGs over effects of recent antibiotic exposure.

Human infants are born with sparse microflora in their gastrointestinal tracts. Acquisition of pioneer bacteria and their initial colonisation are affected by a number of factors, including mode of birth, feeding practices, exposure to antibiotics, and environmental conditions. Subsequent diversification and development of the microbiota continues dynamically until it reaches maturity when the infant is around 3 years old. An important window of opportunity to affect the structure of developing microflora is likely to coincide with the weaning period when a gradual transition in diet from milk-based infant feeding to first family-based solid foods occurs. Although the ability of many dietary factors to modulate the composition of gastrointestinal microflora is well established, it is not so well understood in children. Moreover, there are cultural, economic, varying feeding practices, and geographical factors that play roles in the choice of complementary foods in different regions of the world. We provide a review of recent literature on development of infant microflora and how complementary feeding practices from different cultures may affect the infant gut microbiota during early childhood. [ABSTRACT FROM AUTHOR]

ABSTRACT A variety of autoimmune and allergy events are becoming increasingly common, especially in Western countries. Some pieces of research link such conditions with the composition of microbiota during infancy. In this period, the predominant form of nutrition for gut microbiota is oligosaccharides from human milk (HMO). A number of gut-colonizing strains, such as Bifidobacterium and Bacteroides, are able to utilize HMO, but only some Bifidobacterium strains have evolved to digest the specific composition of human oligosaccharides. Differences in the proportions of the two genera that are able to utilize HMO have already been associated with the frequency of allergies and autoimmune diseases in the Finnish and the Russian populations. Our results show that differences in terms of the taxonomic annotation do not explain the reason for the differences in the Bifidobacterium/Bacteroides ratio between the Finnish and the Russian populations. In this paper, we present the results of function-level analysis. Unlike the typical workflow for gene abundance analysis, BiomeScout technology explains the differences in the Bifidobacterium/Bacteroides ratio. Our research shows the differences in the abundances of the two enzymes that are crucial for the utilization of short type 1 oligosaccharides. IMPORTANCE Knowing the limitations of taxonomy-based research, there is an emerging need for the development of higher-resolution techniques. The significance of this research is demonstrated by the novel method used for the analysis of function-level metagenomes. BiomeScout—the presented technology—utilizes proprietary algorithms for the detection of differences between functionalities present in metagenomic samples.

ABSTRACT The microbiomes of 83 preterm very-low-birth-weight (VLBW) infants and clinical covariates were analyzed weekly over the course of their initial neonatal intensive care unit (NICU) stay, with infant growth as the primary clinical outcome. Birth weight significantly correlated with increased rate of weight gain in the first 6 weeks of life, while no significant relationship was observed between rate of weight gain and feeding type. Microbial diversity increased with age and was significantly correlated with weight gain and percentage of the mother’s own milk. As expected, infants who received antibiotics during their NICU stay had significantly lower alpha diversity than those who did not. Of those in the cohort, 25 were followed into childhood. Alpha diversity significantly increased between NICU discharge and age 2 years and between age 2 years and age 4 years, but the microbial alpha diversity of 4-year-old children was not significantly different from that of mothers. Infants who showed improved length over the course of their NICU stay had significantly more volatile microbial beta diversity results than and a significantly decreased microbial maturity index compared with infants who did not; interestingly, all infants who showed improved length during the NICU stay were delivered by Caesarean section. Microbial beta diversity results were significantly different between the time of the NICU stay and all other time points (for children who were 2 or 4 years old and mothers when their children were 2 or 4 years old). IMPORTANCE Preterm infants are at greater risk of microbial insult than full-term infants, including reduced exposure to maternal vaginal and enteric microbes, higher rates of formula feeding, invasive procedures, and administration of antibiotics and medications that alter gastrointestinal pH. This investigation of the VLBW infant microbiome over the course of the neonatal intensive care unit (NICU) stay, and at ages 2 and 4 years, showed that the only clinical variables associated with significant differences in taxon abundance were weight gain during NICU stay (Klebsiella and Staphylococcus) and antibiotic administration (Streptococcus and Bifidobacterium). At 2 and 4 years of age, the microbiota of these VLBW infants became similar to the mothers’ microbiota. The number of microbial taxa shared between the infant or toddler and the mother varied, with least the overlap between infants and mothers. Overall, there was a significant association between the diversity and structure of the microbial community and infant weight and length gain in an at-risk childhood population. Author Video: An author video summary of this article is available.

Numerous studies suggest that infants delivered by cesarean section are at a greater risk of non-communicable diseases than their vaginal counterparts. In particular, epidemiological studies have linked Cesarean delivery with increased rates of asthma, allergies, autoimmune disorders, and obesity. Mode of delivery has also been associated with differences in the infant microbiome. It has been suggested that these differences are attributable to the “bacterial baptism” of vaginal birth, which is bypassed in cesarean deliveries, and that the abnormal establishment of the early-life microbiome is the mediator of later-life adverse outcomes observed in cesarean delivered infants. This has led to the increasingly popular practice of “vaginal seeding”: the iatrogenic transfer of vaginal microbiota to the neonate to promote establishment of a “normal” infant microbiome. In this review, we summarize and critically appraise the current evidence for a causal association between Cesarean delivery and neonatal dysbiosis. We suggest that, while Cesarean delivery is certainly associated with alterations in the infant microbiome, the lack of exposure to vaginal microbiota is unlikely to be a major contributing factor. Instead, it is likely that indication for Cesarean delivery, intrapartum antibiotic administration, absence of labor, differences in breastfeeding behaviors, maternal obesity, and gestational age are major drivers of the Cesarean delivery microbial phenotype. We, therefore, call into question the rationale for “vaginal seeding” and support calls for the halting of this practice until robust evidence of need, efficacy, and safety is available.

ABSTRACT Historically, Bifidobacterium species were reported as abundant in the breastfed infant gut. However, recent studies in resource-rich countries show an increased abundance of taxa regarded as signatures of dysbiosis. It is unclear whether these differences are the product of genetics, geographic factors, or interventions such as formula feeding, antibiotics, and caesarean section. Fecal pH is strongly associated with Bifidobacterium abundance; thus, pH could be an indicator of its historical abundance. A review of 14 clinical studies published between 1926 and 2017, representing more than 312 healthy breastfed infants, demonstrated a change in fecal pH from 5.0 to 6.5 (adjusted r2 = 0.61). This trend of increasing infant fecal pH over the past century is consistent with current reported discrepancies in Bifidobacterium species abundance in the gut microbiome in resource-rich countries compared to that in historical reports. Our analysis showed that increased fecal pH and abundance of members of the families Enterobacteriaceae, Clostridiaceae, Peptostreptococcaceae, and Veillonellaceae are associated, indicating that loss of highly specialized Bifidobacterium species may result in dysbiosis, the implications of which are not yet fully elucidated. Critical assessment of interventions that restore this ecosystem, measured by key parameters such as ecosystem productivity, gut function, and long-term health, are necessary to understand the magnitude of this change in human biology over the past century.

ABSTRACT Attempts to alter intestinal dysbiosis via administration of probiotics have consistently shown that colonization with the administered microbes is transient. This study sought to determine whether provision of an initial course of Bifidobacterium longum subsp. infantis (B. infantis) would lead to persistent colonization of the probiotic organism in breastfed infants. Mothers intending to breastfeed were recruited and provided with lactation support. One group of mothers fed B. infantis EVC001 to their infants from day 7 to day 28 of life (n = 34), and the second group did not administer any probiotic (n = 32). Fecal samples were collected during the first 60 postnatal days in both groups. Fecal samples were assessed by 16S rRNA gene sequencing, quantitative PCR, mass spectrometry, and endotoxin measurement. B. infantis-fed infants had significantly higher populations of fecal Bifidobacteriaceae, in particular B. infantis, while EVC001 was fed, and this difference persisted more than 30 days after EVC001 supplementation ceased. Fecal milk oligosaccharides were significantly lower in B. infantis EVC001-fed infants, demonstrating higher consumption of human milk oligosaccharides by B. infantis EVC001. Concentrations of acetate and lactate were significantly higher and fecal pH was significantly lower in infants fed EVC001, demonstrating alterations in intestinal fermentation. Infants colonized by Bifidobacteriaceae at high levels had 4-fold-lower fecal endotoxin levels, consistent with observed lower levels of Gram-negative Proteobacteria and Bacteroidetes. IMPORTANCE The gut microbiome in early life plays an important role for long-term health and is shaped in large part by diet. Probiotics may contribute to improvements in health, but they have not been shown to alter the community composition of the gut microbiome. Here, we found that breastfed infants could be stably colonized at high levels by provision of B. infantis EVC001, with significant changes to the overall microbiome composition persisting more than a month later, whether the infants were born vaginally or by caesarean section. This observation is consistent with previous studies demonstrating the capacity of this subspecies to utilize human milk glycans as a nutrient and underscores the importance of pairing a probiotic organism with a specific substrate. Colonization by B. infantis EVC001 resulted in significant changes to fecal microbiome composition and was associated with improvements in fecal biochemistry. The combination of human milk and an infant-associated Bifidobacterium sp. shows, for the first time, that durable changes to the human gut microbiome are possible and are associated with improved gut function.

Summary We assessed the subsistence-related variation of the human gut microbiome at a fine resolution for two of the main dimensions of microbiome variation, age and geography. For this, we investigated the fecal microbiome and metabolome in rural Bassa and urbanized individuals from Nigeria, including infants, and compared data with worldwide populations practicing varying subsistence. Our data highlight specific microbiome traits that are progressively lost with urbanization, such as the dominance of pristine fiber degraders and the low inter-individual variation. For the Bassa, this last feature is the result of their subsistence-related practices favoring microbial dispersal, such as their extensive environmental contact and the usage of untreated waters from the Usuma River. The high degree of microbial dispersal observed in the Bassa meta-community nullifies the differences between infant and adult intestinal ecosystems, suggesting that the infant-type microbiome in Western populations could be the result of microbiome-associated neotenic traits favored by urbanization. [ABSTRACT FROM AUTHOR]

Breast milk is the perfect nutrition for infants, a result of millions of years of evolution. In addition to providing a source of nutrition, breast milk contains a diverse array of microbiota and myriad biologically active components that are thought to guide the infant's developing mucosal immune system. It is believed that bacteria from the mother's intestine may translocate to breast milk and dynamically transfer to the infant. Such interplay between mother and her infant is a key to establishing a healthy infant intestinal microbiome. These intestinal bacteria protect against many respiratory and diarrheal illnesses, but are subject to environmental stresses such as antibiotic use. Orchestrating the development of the microbiota are the human milk oligosaccharides (HMOs), the synthesis of which are partially determined by the maternal genotype. HMOs are thought to play a role in preventing pathogenic bacterial adhesion though multiple mechanisms, while also providing nutrition for the microbiome. Extracellular vesicles (EVs), including exosomes, carry a diverse cargo, including mRNA, miRNA, and cytosolic and membrane-bound proteins, and are readily detectable in human breast milk. Strongly implicated in cell-cell signaling, EVs could therefore may play a further role in the development of the infant microbiome. This review considers the emerging role of breast milk microbiota, bioactive HMOs, and EVs in the establishment of the neonatal microbiome and the consequent potential for modulation of neonatal immune system development. [ABSTRACT FROM AUTHOR]

The human microbiome seeding starts at birth, when pioneer microbes are acquired mainly from the mother. Mode of delivery, antibiotic prophylaxis, and feeding method have been studied as modulators of mother-to-infant microbiome transmission, but other key influencing factors like modern westernized lifestyles with high hygienization, high-calorie diets, and urban settings, compared with non-westernized lifestyles have not been investigated yet. In this study, we explored the mother-infant sharing of characterized and uncharacterized microbiome members via strain-resolved metagenomics in a cohort of Ethiopian mothers and infants, and we compared them with four other cohorts with different lifestyles. The westernized and non-westernized newborns' microbiomes composition overlapped during the first months of life more than later in life, likely reflecting similar initial breast-milk-based diets. Ethiopian and other non-westernized infants shared a smaller fraction of the microbiome with their mothers than did most westernized populations, despite showing a higher microbiome diversity, and uncharacterized species represented a substantial fraction of those shared in the Ethiopian cohort. Moreover, we identified uncharacterized species belonging to the Selenomonadaceae and Prevotellaceae families specifically present and shared only in the Ethiopian cohort, and we showed that a locally produced fermented food, injera, can contribute to the higher diversity observed in the Ethiopian infants' gut with bacteria that are not part of the human microbiome but are acquired through fermented food consumption. Taken together, these findings highlight the fact that lifestyle can impact the gut microbiome composition not only through differences in diet, drug consumption, and environmental factors but also through its effect on mother-infant strain-sharing patterns. • Microbiome sharing is reduced in Ethiopian and non-westernized mother-infant pairs • Some uncharacterized species are present and shared only in the Ethiopian cohort • Locally produced fermented food provides some of these unusual microbiome species • The microbiome is impacted by lifestyle and also through mother-infant strain-sharing patterns Manara et al. investigate how lifestyle affects mother-infant microbiome sharing. Manara et al. show that Ethiopian and other non-westernized infants share a smaller microbiome fraction (mainly uncharacterized species) with their mothers and identify some unusual mother-infant shared species present in locally produced fermented food. [ABSTRACT FROM AUTHOR]

ABSTRACT The gut microbiome becomes shaped in the first days of life and continues to increase its diversity during the first months. Links between the configuration of the infant gut microbiome and infant health are being shown, but a comprehensive strain-level assessment of microbes vertically transmitted from mother to infant is still missing. We collected fecal and breast milk samples from multiple mother-infant pairs during the first year of life and applied shotgun metagenomic sequencing followed by computational strain-level profiling. We observed that several specific strains, including those of Bifidobacterium bifidum, Coprococcus comes, and Ruminococcus bromii, were present in samples from the same mother-infant pair, while being clearly distinct from those carried by other pairs, which is indicative of vertical transmission. We further applied metatranscriptomics to study the in vivo gene expression of vertically transmitted microbes and found that transmitted strains of Bacteroides and Bifidobacterium species were transcriptionally active in the guts of both adult and infant. By combining longitudinal microbiome sampling and newly developed computational tools for strain-level microbiome analysis, we demonstrated that it is possible to track the vertical transmission of microbial strains from mother to infants and to characterize their transcriptional activity. Our work provides the foundation for larger-scale surveys to identify the routes of vertical microbial transmission and its influence on postinfancy microbiome development. IMPORTANCE Early infant exposure is important in the acquisition and ultimate development of a healthy infant microbiome. There is increasing support for the idea that the maternal microbial reservoir is a key route of microbial transmission, and yet much is inferred from the observation of shared species in mother and infant. The presence of common species, per se, does not necessarily equate to vertical transmission, as species exhibit considerable strain heterogeneity. It is therefore imperative to assess whether shared microbes belong to the same genetic variant (i.e., strain) to support the hypothesis of vertical transmission. Here we demonstrate the potential of shotgun metagenomics and strain-level profiling to identify vertical transmission events. Combining these data with metatranscriptomics, we show that it is possible not only to identify and track the fate of microbes in the early infant microbiome but also to investigate the actively transcribing members of the community. These approaches will ultimately provide important insights into the acquisition, development, and community dynamics of the infant microbiome.

Exclusive breastfeeding is recommended for the first six months of life, but many infants receive pumped milk, formula, donor human milk, or other nutritional sources during this critical period. Substantive evidence shows early nutrition influences development of the microbiome and immune system, affecting lifelong health. However, the underlying mechanisms are unclear and the nuances of human milk feeding are rarely considered. This review synthesizes evidence from human studies and model systems to discuss the impact of different nutritional sources on co-development of the gut microbiome, antigen tolerance, and immunity. We highlight two key mechanisms: epigenetics and the so-called "weaning reaction". Collectively, this evidence highlights i) the fundamental role of parents' own milk, fed directly at the breast, as a dynamic and personalized nutrition source that drives developmental programming, and ii) the deficiencies of alternative nutritional sources and priority research areas for improving these alternatives when direct breastfeeding is not possible.