Evolution of gut microbiota composition from birth to 24 weeks in the INFANTMET Cohort

Infant gut microbiota colonization: influence of prenatal and postnatal factors, focusing on diet

Maternal microbiota forms the first infant gut microbial inoculum, and perinatal factors (diet and use of antibiotics during pregnancy) and/or neonatal factors, like intra partum antibiotics, gestational age and mode of delivery, may influence microbial colonization. After birth, when the principal colonization occurs, the microbial diversity increases and converges toward a stable adult-like microbiota by the end of the first 3-5 years of life. However, during the early life, gut microbiota can be disrupted by other postnatal factors like mode of infant feeding, antibiotic usage, and various environmental factors generating a state of dysbiosis. Gut dysbiosis have been reported to increase the risk of necrotizing enterocolitis and some chronic diseases later in life, such as obesity, diabetes, cancer, allergies, and asthma. Therefore, understanding the impact of a correct maternal-to-infant microbial transfer and a good infant early colonization and maturation throughout life would reduce the risk of disease in early and late life. This paper reviews the published evidence on early-life gut microbiota development, as well as the different factors influencing its evolution before, at, and after birth, focusing on diet and nutrition during pregnancy and in the first months of life.

Current Knowledge About the Impact of Maternal and Infant Nutrition on the Development of the Microbiota-Gut-Brain Axis

The prenatal and early postnatal periods are stages during which dynamic changes and the development of the brain and gut microbiota occur, and nutrition is one of the most important modifiable factors that influences this process. Given the bidirectional cross talk between the gut microbiota and the brain through the microbiota-gut-brain axis (MGBA), there is growing interest in evaluating the potential effects of nutritional interventions administered during these critical developmental windows on gut microbiota composition and function and their association with neurodevelopmental outcomes. We review recent preclinical and clinical evidence from animal studies and infant/child populations. Although further research is needed, growing evidence suggests that different functional nutrients affect the establishment and development of the microbiota-gut-brain axis and could have preventive and therapeutic use in the treatment of neuropsychiatric disorders. Therefore, more in-depth knowledge regarding the effect of nutrition on the MGBA during critical developmental windows may enable the prevention of later neurocognitive and behavioral disorders and allow the establishment of individualized nutrition-based programs that can be used from the prenatal to the early and middle stages of life.

Similarities in rotavirus vaccine viral shedding and immune responses in pairs of twins

OBJECTIVES

Intestinal rotavirus (RV) vaccine replication and host immune response are suggested to be affected by several factors, including maternal antibodies, breastfeeding history, and gut microbiome, which are thought to be similar in pairs of twins. The aim of this study was to determine whether viral shedding from the fecal RV vaccine strain Rotarix® (RV1) and IgG and IgA responses to RV show similarity in pairs of twins.

METHODS

Quantitative reverse transcription polymerase chain reaction specific to RV vaccine strain RV1 was used to monitor fecal RV1 viral shedding. RV IgG and IgA titers were measured using an in-house enzyme-linked immunosorbent assay. Fecal RV1 viral shedding and immune responses were compared between twins and singletons with mixed effects and fixed effects models.

RESULTS

A total of 347 stool and 54 blood samples were collected from four pairs of twins and twelve singletons during the observation period. Although the kinetics of fecal RV1 viral shedding and immune responses differed among vaccinated individuals, they appeared to be similar within twin pairs. RV shedding after the first dose (P=0.049) and RV IgG titers during the entire observation period (P=0.015) had a significantly better fit in the fixed effect model that assumed that twins have the same response versus the model that assumed that twins have a different response.

CONCLUSIONS

The similarity of RV vaccine viral replication in intestine and host immune responses in twin pairs was demonstrated using statistical analysis.

Dietary Prebiotic Oligosaccharides and Arachidonate Alter the Fecal Microbiota and Mucosal Lipid Composition of Suckling Pigs

BACKGROUND

Early intestinal development is important to infant vitality, and optimal formula composition can promote gut health.

OBJECTIVES

The objectives were to evaluate the effects of arachidonate (ARA) and/or prebiotic oligosaccharide (PRE) supplementation in formula on the development of the microbial ecosystem and colonic health parameters.

METHODS

Newborn piglets were fed 4 formulas containing ARA [0.5 compared with 2.5% of dietary fatty acids (FAs)] and PRE (0 compared with 8 g/L, containing a 1:1 mixture of galactooligosaccharides and polydextrose) in a 2 x 2 factorial design for 22 d. Fecal samples were collected weekly and analyzed for relative microbial abundance. Intestinal samples were collected on day 22 and analyzed for mucosal FAs, pH, and short-chain FAs (SCFAs).

RESULTS

PRE supplementation significantly increased genera within Bacteroidetes and Firmicutes, including Anaerostipes, Mitsuokella, Prevotella, Clostridium IV, and Bulleidia, and resulted in progressive separation from controls as determined by Principal Coordinates Analysis. Concentrations of SCFA increased from 70.98 to 87.37 mM, with an accompanying reduction in colonic pH. ARA supplementation increased the ARA content of the colonic mucosa from 2.35-5.34% of total FAs. PRE supplementation also altered mucosal FA composition, resulting in increased linoleic acid (11.52-16.33% of total FAs) and ARA (2.35-5.16% of total FAs).

CONCLUSIONS

Prebiotic supplementation during the first 22 d of life altered the gut microbiota of piglets and increased the abundance of specific bacterial genera. These changes correlated with increased SCFA, which may benefit intestinal development. Although dietary ARA did not alter the microbiota, it increased the ARA content of the colonic mucosa, which may support intestinal development and epithelial repair. Prebiotic supplementation also increased unsaturation of FAs in the colonic mucosa. Although the mechanism requires further investigation, it may be related to altered microbial ecology or biohydrogenation of FA.

Overview of the Gut Microbiome

The human gastrointestinal tract is home to trillions of microorganisms-collectively referred to as the gut microbiome-that maintain a symbiotic relationship with their host. This diverse community of microbes grows and changes as we do, with developmental, lifestyle, and environmental factors all shaping microbiome community structure. Increasing evidence suggests this relationship is bidirectional, with the microbiome also influencing host physiological processes. For example, changes in the gut microbiome have been shown to alter neurodevelopment and have lifelong effects on the brain and behavior. Age-related changes in gut microbiome composition have also been linked to inflammatory changes in the brain, perhaps increasing susceptibility to neurological disease. Indeed, associations between gut dysbiosis and many age-related neurological diseases-including Parkinson's disease, Alzheimer's disease, multiple sclerosis, and amyotrophic lateral sclerosis-have been reported. Further, microbiome manipulation in animal models of disease highlights a potential role for the gut microbiome in disease development and progression. Although much remains unknown, these associations open up an exciting new world of therapeutic targets, potentially allowing for improved quality of life for a wide range of patient populations.

Ex Vivo Immunomodulatory Effects of Lactobacillus-, Lacticaseibacillus-, and Bifidobacterium-Containing Synbiotics on Human Peripheral Blood Mononuclear Cells and Monocyte-Derived Dendritic Cells in the Context of Grass Pollen Allergy

Sensing of the intestinal microbiota by the host immune system is important to induce protective immune responses. Hence, modification of the gut microbiota might be able to prevent or treat allergies, mediated by proinflammatory Th2 immune responses. The aim was to investigate the ex vivo immunomodulatory effects of the synbiotics Pollagen® and Kallergen®, containing the probiotic bacterial strains Lactobacillus, Lacticaseibacillus and Bifidobacterium, in the context of grass pollen allergy. Peripheral blood mononuclear cells (PBMCs) from grass pollen-allergic patients and healthy controls were stimulated with grass pollen extract (GPE) and synbiotics and Gata3 expression and cytokine secretion analyzed. Monocyte-derived dendritic cells (MoDCs) cells were matured in the presence of GPE and synbiotics, co-cultured with autologous naïve T cells and maturation markers and cytokine secretion analyzed. GPE stimulation of PBMCs from grass pollen-allergic patients resulted in a significant higher production of the Th2 cytokines IL-4, IL-5, IL-9 and IL-13 compared to healthy controls. Gata3+CD4+ T cell induction was independent of the allergic status. The synbiotics promoted IL-10 and IFN-γ secretion and downregulated the GPE-induced Th2-like phenotype. Co-culturing naïve T cells with MoDCs, matured in the presence of GPE and synbiotics, shifted the GPE-induced Th2 cytokine release towards Th1-Th17-promoting conditions in allergic subjects. The investigated synbiotics are effective in downregulating the GPE-induced Th2 immune response in PBMCs from grass pollen-allergic patients as well as in autologous MoDC-T cell stimulation assays. In addition to increased IL-10 release, the data indicates a shift from a Th2- to a more Th1- and Th17-like phenotype.

Old Folks, Bad Boon: Antimicrobial Resistance in the Infant Gut Microbiome

The development of the intestinal microbiome in the neonate starts, mainly, at birth, when the infant receives its founding microbial inoculum from the mother. This microbiome contains genes conferring resistance to antibiotics since these are found in some of the microorganisms present in the intestine. Similarly to microbiota composition, the possession of antibiotic resistance genes is affected by different perinatal factors. Moreover, antibiotics are the most used drugs in early life, and the use of antibiotics in pediatrics covers a wide variety of possibilities and treatment options. The disruption in the early microbiota caused by antibiotics may be of great relevance, not just because it may limit colonization by beneficial microorganisms and increase that of potential pathogens, but also because it may increase the levels of antibiotic resistance genes. The increase in antibiotic-resistant microorganisms is one of the major public health threats that humanity has to face and, therefore, understanding the factors that determine the development of the resistome in early life is of relevance. Recent advancements in sequencing technologies have enabled the study of the microbiota and the resistome at unprecedent levels. These aspects are discussed in this review as well as some potential interventions aimed at reducing the possession of resistance genes.

Effects of vaginal microbiota transfer on the neurodevelopment and microbiome of cesarean-born infants: A blinded randomized controlled trial

The microbiomes of cesarean-born infants differ from vaginally delivered infants and are associated with increased disease risks. Vaginal microbiota transfer (VMT) to newborns may reverse C-section-related microbiome disturbances. Here, we evaluated the effect of VMT by exposing newborns to maternal vaginal fluids and assessing neurodevelopment, as well as the fecal microbiota and metabolome. Sixty-eight cesarean-delivered infants were randomly assigned a VMT or saline gauze intervention immediately after delivery in a triple-blind manner (ChiCTR2000031326). Adverse events were not significantly different between the two groups. Infant neurodevelopment, as measured by the Ages and Stages Questionnaire (ASQ-3) score at 6 months, was significantly higher with VMT than saline. VMT significantly accelerated gut microbiota maturation and regulated levels of certain fecal metabolites and metabolic functions, including carbohydrate, energy, and amino acid metabolisms, within 42 days after birth. Overall, VMT is likely safe and may partially normalize neurodevelopment and the fecal microbiome in cesarean-delivered infants.

A health-promoting role of exclusive breastfeeding on infants through restoring delivery mode-induced gut microbiota perturbations

The establishment of human gut microbiota in early life is closely associated with both short- and long-term infant health. Delivery mode and feeding pattern are two important determinants of infant gut microbiota. In this longitudinal cohort study, we examined the interplay between the delivery mode and feeding pattern on the dynamics of infant gut microbiota from 6 weeks to 6 months post-delivery in 139 infants. We also assessed the relationship between infant respiratory infection susceptibility and gut microbial changes associated with delivery mode and feeding pattern. At 6 weeks postpartum, the composition and structure of gut microbiota of cesarean section-delivered (CSD) infants differed from those of vaginally delivered (VD) infants, with decreased Bacteroides and Escherichia-Shigella and increased Klebsiella, Veillonella, and Enterococcus. At 6 months postpartum, these delivery mode-induced microbial shifts were restored by exclusive breastfeeding, resulting in similar gut microbial profiles between VD and CSD infants who were exclusively breastfed (P = 0.57) and more variable gut microbial profiles between VD and CSD infants who were mixed fed (P < 0.001). We identified that the VD-associated genera were enriched in healthy infants, while the CSD-associated genera were enriched in infants who suffered from respiratory infections. Our findings indicate that exclusive breastfeeding may play a health-promoting role by reducing infant respiratory infection susceptibility through the restoration of gut microbiota perturbations caused by cesarean section.

Determinants of microbial colonization in the premature gut

Abnormal microbial colonization in the gut at an early stage of life affects growth, development, and health, resulting in short- and long-term adverse effects. Microbial colonization patterns of preterm infants differ from those of full-term infants in that preterm babies and their mothers have more complicated prenatal and postnatal medical conditions. Maternal complications, antibiotic exposure, delivery mode, feeding type, and the use of probiotics may significantly shape the gut microbiota of preterm infants at an early stage of life; however, these influences subside with age. Although some factors and processes are difficult to intervene in or avoid, understanding the potential factors and determinants will help in developing timely strategies for a healthy gut microbiota in preterm infants. This review discusses potential determinants of gut microbial colonization in preterm infants and their underlying mechanisms.

Exploring Molecular Interactions between Human Milk Hormone Insulin and Bifidobacteria

Multiple millennia of human evolution have shaped the chemical composition of breast milk toward an optimal human body fluid for nutrition and protection and for shaping the early gut microbiota of newborns. This biological fluid is composed of water, lipids, simple and complex carbohydrates, proteins, immunoglobulins, and hormones. Potential interactions between hormones present in mother's milk and the microbial community of the newborn are a very fascinating yet unexplored topic. In this context, insulin, in addition to being one of the most prevalent hormones in breast milk, is also involved in a metabolic disease that affects many pregnant women, i.e., gestational diabetes mellitus (GDM). Analysis of 3,620 publicly available metagenomic data sets revealed that the bifidobacterial community varies in relation to the different concentrations of this hormone in breast milk of healthy and diabetic mothers. Starting from this assumption, in this study, we explored possible molecular interactions between this hormone and bifidobacterial strains that represent bifidobacterial species commonly occurring in the infant gut using 'omics' approaches. Our findings revealed that insulin modulates the bifidobacterial community by apparently improving the persistence of the Bifidobacterium bifidum taxon in the infant gut environment compared to other typical infant-associated bifidobacterial species. IMPORTANCE Breast milk is a key factor in modulating the infant's intestinal microbiota composition. Even though the interaction between human milk sugars and bifidobacteria has been extensively studied, there are other bioactive compounds in human milk that may influence the gut microbiota, such as hormones. In this article, the molecular interaction of the human milk hormone insulin and the bifidobacterial communities colonizing the human gut in the early stages of life has been explored. This molecular cross talk was assessed using an in vitro gut microbiota model and then analyzed by various omics approaches, allowing the identification of genes associated with bacterial cell adaptation/colonization in the human intestine. Our findings provide insights into the manner by which assembly of the early gut microbiota may be regulated by host factors such as hormones carried by human milk.

The Effect of Human Milk Oligosaccharides and Bifidobacterium longum subspecies infantis Bi-26 on Simulated Infant Gut Microbiome and Metabolites

Human milk oligosaccharides (HMOs) shape the developing infant gut microbiota. In this study, a semi-continuous colon simulator was used to evaluate the effect of 2 HMOs-2'-fucosyllactose (2'-FL) and 3-fucosyllactose (3-FL)-on the composition of infant faecal microbiota and microbial metabolites. The simulations were performed with and without a probiotic Bifidobacterium longum subspecies infantis Bi-26 (Bi-26) and compared with a control that lacked an additional carbon source. The treatments with HMOs decreased α-diversity and increased Bifidobacterium species versus the control, but the Bifidobacterium species differed between simulations. The levels of acetic acid and the sum of all short-chain fatty acids (SCFAs) trended toward an increase with 2'-FL, as did lactic acid with 2'-FL and 3-FL, compared with control. A clear correlation was seen between the consumption of HMOs and the increase in SCFAs (-0.72) and SCFAs + lactic acid (-0.77), whereas the correlation between HMO consumption and higher total bifidobacterial numbers was moderate (-0.46). Bi-26 decreased propionic acid levels with 2'-FL. In conclusion, whereas infant faecal microbiota varied between infant donors, the addition of 2'-FL and 3-FL, alone or in combination, increased the relative abundance and numbers Bifidobacterium species in the semi-continuous colon simulation model, correlating with the production of microbial metabolites. These findings may suggest that HMOs and probiotics benefit the developing infant gut microbiota.

Exploring the Relationship between the Gut Microbiota and Ageing: A Possible Age Modulator

The gut microbiota (GM) has been the subject of intense research in recent years. Therefore, numerous factors affecting its composition have been thoroughly examined, and with them, their function and role in the individual's systems. The gut microbiota's taxonomical composition dramatically impacts older adults' health status. In this regard, it could either extend their life expectancy via the modulation of metabolic processes and the immune system or, in the case of dysbiosis, predispose them to age-related diseases, including bowel inflammatory and musculoskeletal diseases and metabolic and neurological disorders. In general, the microbiome of the elderly tends to present taxonomic and functional changes, which can function as a target to modulate the microbiota and improve the health of this population. The GM of centenarians is unique, with the faculty-promoting metabolic pathways capable of preventing and counteracting the different processes associated with age-related diseases. The molecular mechanisms by which the microbiota can exhibit anti-ageing properties are mainly based on anti-inflammatory and antioxidant actions. This review focuses on analysing the current knowledge of gut microbiota characteristics and modifiers, its relationship with ageing, and the GM-modulating approaches to increase life expectancy.

Gut Microbiome-Brain Alliance: A Landscape View into Mental and Gastrointestinal Health and Disorders

Gut microbiota includes a vast collection of microorganisms residing within the gastrointestinal tract. It is broadly recognized that the gut and brain are in constant bidirectional communication, of which gut microbiota and its metabolic production are a major component, and form the so-called gut microbiome-brain axis. Disturbances of microbiota homeostasis caused by imbalance in their functional composition and metabolic activities, known as dysbiosis, cause dysregulation of these pathways and trigger changes in the blood-brain barrier permeability, thereby causing pathological malfunctions, including neurological and functional gastrointestinal disorders. In turn, the brain can affect the structure and function of gut microbiota through the autonomic nervous system by regulating gut motility, intestinal transit and secretion, and gut permeability. Here, we examine data from the CAS Content Collection, the largest collection of published scientific information, and analyze the publication landscape of recent research. We review the advances in knowledge related to the human gut microbiome, its complexity and functionality, its communication with the central nervous system, and the effect of the gut microbiome-brain axis on mental and gut health. We discuss correlations between gut microbiota composition and various diseases, specifically gastrointestinal and mental disorders. We also explore gut microbiota metabolites with regard to their impact on the brain and gut function and associated diseases. Finally, we assess clinical applications of gut-microbiota-related substances and metabolites with their development pipelines. We hope this review can serve as a useful resource in understanding the current knowledge on this emerging field in an effort to further solving of the remaining challenges and fulfilling its potential.

Maternal vaginal microbiome composition does not affect development of the infant gut microbiome in early life

Birth mode has been implicated as a major factor influencing neonatal gut microbiome development, and it has been assumed that lack of exposure to the maternal vaginal microbiome is responsible for gut dysbiosis among caesarean-delivered infants. Consequently, practices to correct dysbiotic gut microbiomes, such as vaginal seeding, have arisen while the effect of the maternal vaginal microbiome on that of the infant gut remains unknown. We conducted a longitudinal, prospective cohort study of 621 Canadian pregnant women and their newborn infants and collected pre-delivery maternal vaginal swabs and infant stool samples at 10-days and 3-months of life. Using cpn60-based amplicon sequencing, we defined vaginal and stool microbiome profiles and evaluated the effect of maternal vaginal microbiome composition and various clinical variables on the development of the infant stool microbiome. Infant stool microbiomes showed significant differences in composition by delivery mode at 10-days postpartum; however, this effect could not be explained by maternal vaginal microbiome composition and was vastly reduced by 3 months. Vaginal microbiome clusters were distributed across infant stool clusters in proportion to their frequency in the overall maternal population, indicating independence of the two communities. Intrapartum antibiotic administration was identified as a confounder of infant stool microbiome differences and was associated with lower abundances of Escherichia coli, Bacteroides vulgatus, Bifidobacterium longum and Parabacteroides distasonis. Our findings demonstrate that maternal vaginal microbiome composition at delivery does not affect infant stool microbiome composition and development, suggesting that practices to amend infant stool microbiome composition focus factors other than maternal vaginal microbes.

Programmed and environmental determinants driving neonatal mucosal immune development

The mucosal immune system of neonates goes through successive, non-redundant phases that support the developmental needs of the infant and ultimately establish immune homeostasis. These phases are informed by environmental cues, including dietary and microbial stimuli, but also evolutionary developmental programming that functions independently of external stimuli. The immune response to exogenous stimuli is tightly regulated during early life; thresholds are set within this neonatal "window of opportunity" that govern how the immune system will respond to diet, the microbiota, and pathogenic microorganisms in the future. Thus, changes in early-life exposure, such as breastfeeding or environmental and microbial stimuli, influence immunological and metabolic homeostasis and the risk of developing diseases such as asthma/allergy and obesity.

Development of the Anaerobic Microbiome in the Infant Gut

Ninety-five percent of gut microbiota are anaerobes and vary according to age and diet. Complex carbohydrates in human milk enhance the growth of Bifidobacterium and Bacteroides in the first year. Complex carbohydrates in solid foods enhance the growth of Bacteroides and Clostridium in the second year. Short-chain fatty acids produced by Akkermansia and Faecalibacterium may reduce obesity, diabetes and IBD.

Current understanding of antibiotic-associated dysbiosis and approaches for its management

Increased exposure to antibiotics during early childhood increases the risk of antibiotic-associated dysbiosis, which is associated with reduced diversity of gut microbial species and abundance of certain taxa, disruption of host immunity, and the emergence of antibiotic-resistant microbes. The disruption of gut microbiota and host immunity in early life is linked to the development of immune-related and metabolic disorders later in life. Antibiotic administration in populations predisposed to gut microbiota dysbiosis, such as newborns, obese children, and children with allergic rhinitis and recurrent infections; changes microbial composition and diversity; exacerbating dysbiosis and resulting in negative health outcomes. Antibiotic-associated diarrhea (AAD), Clostridiodes difficile-associated diarrhea (CDAD), and Helicobacter pylori infection are all short-term consequences of antibiotic treatment that persist from a few weeks to months. Changes in gut microbiota, which persist even 2 years after antibiotic exposure, and the development of obesity, allergies, and asthma are among the long-term consequences. Probiotic bacteria and dietary supplements can potentially prevent or reverse antibiotic-associated gut microbiota dysbiosis. Probiotics have been demonstrated in clinical studies to help prevent AAD and, to a lesser extent, CDAD, as well as to improve H pylori eradication rates. In the Indian setting, probiotics (Saccharomyces boulardii and Bacillus clausii) have been shown to reduce the duration and frequency of acute diarrhea in children. Antibiotics may exaggerate the consequences of gut microbiota dysbiosis in vulnerable populations already affected by the condition. Therefore, prudent use of antibiotics among neonates and young children is critical to prevent the detrimental effects on gut health.

No Evidence of a Genetic Causal Relationship between Ankylosing Spondylitis and Gut Microbiota: A Two-Sample Mendelian Randomization Study

Objective: Ankylosing spondylitis (AS) is associated with a variety of gut microbiotas. We aim to analyze the causal relationship between the two at the genetic level. Methods: Mendelian randomization (MR) is a type of instrumental variables (IVs) analysis; MR follows the Mendelian genetic rule of "parental alleles are randomly assigned to offspring" and takes genetic variation as IVs to infer the causal association between exposure factors and study outcome in observational studies. Genome-wide association study (GWAS) summary data of AS were from the FinnGen consortium, and the gut microbiota (Bacteroides, Streptococcus, Proteobacteria, Lachnospiraceae) were from the MiBioGen consortium. The TwoSampleMR and MRPRESSO packages of the R were used to perform a two-sample MR study. Random-effects inverse variance weighted (IVW) was the main analysis method, and MR Egger, weighted median, simple mode, and weighted mode were used as supplementary methods. We examined heterogeneity and horizontal pleiotropy, and examined whether the analysis results were influenced by a single SNP. We applied radial variants of the IVW and MR-Egger model for the improved visualization of the causal estimate. We further examined the causal relationship between AS and gut microbiota, and the robustness of the analysis results. Finally, we performed maximum likelihood, penalized weighted median, and IVW (fixed effects) to further identify the potential causal association. Results: The random-effects IVW results showed that Bacteroides (p = 0.965, OR 95% confidence interval [CI] = 0.990 [0.621-1.579]), Streptococcus (p = 0.591, OR 95% CI = 1.120 [0.741-1.692]), Proteobacteria (p = 0.522, OR 95% CI = 1.160 [0.737-1.826]), and Lachnospiraceae (p = 0.717, OR 95% CI = 1.073 [0.732-1.574]) have no genetic causal relationship with AS. There was no heterogeneity, horizontal pleiotropy or outliers, and results were normally distributed. The MR analysis results were not driven by a single SNP. Conclusions: This study showed that Bacteroides, Streptococcus, Proteobacteria and Lachnospiraceae, four common gut microbiotas associated with AS, had no causal relationship with AS at the genetic level. This study makes a positive contribution to the genetics of AS, but the insufficient number of gut microbiota included is a limitation.

Exposure to polyethylene microplastics alters immature gut microbiome in an infant in vitro gut model

Infants are characterized by an immaturity of the gut ecosystem and a high exposure to microplastics (MPs) through diet, dust and suckling. However, the bidirectional interactions between MPs and the immature infant intestinal microbiota remain unknown. Our study aims to investigate the impact of chronic exposure to polyethylene (PE) MPs on the gut microbiota and intestinal barrier of infants, using the new Toddler mucosal Artificial Colon coupled with a co-culture of epithelial and mucus-secreting cells. Gut microbiota composition was determined by 16S metabarcoding and microbial activities were evaluated by gas, short chain fatty acid and volatolomics analyses. Gut barrier integrity was assessed via evaluation of intestinal permeability, inflammation and mucus synthesis. Exposure to PE MPs induced gut microbial shifts increasing α-diversity and abundance of potentially harmful pathobionts, such as Dethiosulfovibrionaceae and Enterobacteriaceae. Those changes were associated to butyrate production decrease and major changes in volatile organic compounds profiles. In contrast, no significant impact of PE MPs on the gut barrier, as mediated by microbial metabolites, was reported. For the first time, this study indicates that ingestion of PE MPs can induce perturbations in the gut microbiome of infants. Next step would be to further investigate the potential vector effect of MPs.

The influence of maternal factors on the neonatal microbiome and health

The human microbiome plays an essential role in human health. However, the influence of maternal factors on the neonatal microbiome remains obscure. Herein, our observations suggest that the neonatal buccal microbiome is similar to the maternal buccal microbiome, but the neonatal gastrointestinal microbiome develops a unique composition at an early stage. The low complexity of the neonatal buccal microbiome is a hallmark of maternal and neonatal health, but that of the neonatal gastrointestinal microbiome is associated with maternal inflammation-related metabolites. Microbial infections in the maternal reproductive tract universally impact the complexity of the neonatal microbiomes, and the body site is most important in modulating the composition of the neonatal microbiomes. Additionally, maternal lipids attenuated the adverse influence of several maternal factors on the neonatal microbiomes. Finally, admission of neonates to the newborn intensive care unit is associated with sub-optimal states of the maternal buccal and rectal microbiomes and maternal health.

Critical windows of early-life microbiota disruption on behaviour, neuroimmune function, and neurodevelopment

Numerous studies have emphasised the importance of the gut microbiota during early life and its role in modulating neurodevelopment and behaviour. Epidemiological studies have shown that early-life antibiotic exposure can increase an individual's risk of developing immune and metabolic diseases. Moreover, preclinical studies have shown that long-term antibiotic-induced microbial disruption in early life can have enduring effects on physiology, brain function and behaviour. However, these studies have not investigated the impact of targeted antibiotic-induced microbiota depletion during critical developmental windows and how this may be related to neurodevelopmental outcomes. Here, we addressed this gap by administering a broad-spectrum oral antibiotic cocktail (ampicillin, gentamicin, vancomycin, and imipenem) to mice during one of three putative critical windows: the postnatal (PN; P2-9), pre-weaning (PreWean; P12-18), or post-weaning (Wean; P21-27) developmental periods and assessed the effects on physiology and behaviour in later life. Our results demonstrate that targeted microbiota disruption during early life has enduring effects into adolescence on the structure and function of the caecal microbiome, especially for antibiotic exposure during the weaning period. Further, we show that microbial disruption in early life selectively alters circulating immune cells and modifies neurophysiology in adolescence, including altered myelin-related gene expression in the prefrontal cortex and altered microglial morphology in the basolateral amygdala. We also observed sex and time-dependent effects of microbiota depletion on anxiety-related behavioural outcomes in adolescence and adulthood. Antibiotic-induced microbial disruption had limited and subtle effects on social behaviour and did not have any significant effects on depressive-like behaviour, short-term working, or recognition memory. Overall, this study highlights the importance of the gut microbiota during critical windows of development and the subtle but long-term effects that microbiota-targeted perturbations can have on brain physiology and behaviour.

Immunomodulatory effects of complex probiotics on the immuno-suppressed mice induced by cyclophosphamide

Introduction

Previous studies have reported the beneficial effects of Bifidobacterium animalis subsp. lactis XLTG11, Lacticaseibacillus casei Zhang, and Lactiplantibacillus plantarum P8, respectively. However, studies on the immunomodulatory enhancing effects of three complex probiotics have not been conducted. The aim of our study is to investigate the immunomodulatory effects of complex probiotics effect on the immunosuppressed mice induced by cyclophosphamide (CTX).

Methods

An immunocompromised mouse model was established by intraperitoneal injection of cyclophosphamide, which was gavage of different doses of complex probiotics and levamisole hydrochloride. The splenic and thymic indices, intestinal barrier, leukocyte and lymphocyte counts, percentage of splenic lymphocyte subpopulations, cytokine levels, and gut microbiota were determined.

Results

Results showed that the complex probiotics significantly elevated the spleen and thymus indices, increased the villi and crypt depth and the goblet cells. The leukocyte and lymphocyte counts and the percentage of splenic lymphocyte subpopulations in the CTX-treated mice were significantly elevated by the complex probiotics. In addition, the cytokines (IL-6, IL-10, IL-1β, and IFN-γ) were significantly increased after complex probiotic treatment. The complex probiotics restored the gut microbiota structure to the pattern of the control group by reducing the ratio of Firmicutes/Bacteroidetes and enhancing the relative abundances of specific microbiota that produced short-chain fatty acids.

Discussion

This study provides theoretical support for the immunity-enhancing function of the complex probiotics as well as a pharmacological basis for its further development and utilization.

Different gut microbiota in U.S. formula-fed infants consuming a meat vs. dairy-based complementary foods: A randomized controlled trial

Objective

This project aimed to evaluate the impact of meat- vs. dairy-based complementary foods on gut microbiota and whether it relates to growth.

Design

Full-term, formula-fed infants were recruited from the metro Denver area (Colorado, US) and randomized to a meat- or dairy-based complementary diet from 5 to 12 months of age. Infant's length and weight were measured, and stool samples were collected at 5, 10, and 12 months for 16S rRNA gene sequencing and short-chain fatty acids (SCFAs) quantification.

Results

Sixty-four infants completed the dietary intervention (n = 32/group). Weight-for-age Z (WAZ) scores increased in both groups and length-for-age Z scores (LAZ) increased in the meat group only, which led to a significant group-by-time interaction (P = 0.02) of weight-for-length Z (WLZ) score. Microbiota composition (Beta-diversity) differed between groups at 12 months (weighted PERMANOVA P = 0.01) and had a group-by-time interaction of P = 0.09. Microbial community richness (Chao1) increased in the meat group only. Genus Akkermansia had a significant group-by-time interaction and increased in the dairy group and decreased in the meat group. A significant fold change of butyric acid from 5 to 12 months was found in the meat group (+1.75, P = 0.011) but not in the dairy group. Regression analysis showed that Chao1 had a negative association with WLZ and WAZ. Several genera also had significant associations with all growth Z scores.

Conclusion

Complementary feeding not only impacts infant growth but also affects gut microbiota maturation. Complementary food choices can affect both the gut microbiota diversity and structures and these changes in gut microbiota are associated with infant growth.

Microcosm experiment to test bacterial responses to perfluorooctanoate exposure

The impact of perfluoroalkyl and polyfluoroalkyl substances on microbial communities is challenging to investigate in situ because of the complexity and dynamics of natural ecosystems. In the present study, four microcosms were established to explore the impact of perfluorooctanoate (PFOA) on bacterial communities in riverine and marine settings. PFOA distribution between the aqueous and sedimentary phases fluctuated in both PFOA-amended and unamended control systems. PFOA was more rapidly partitioned into the sediment in marine than in riverine microcosms. Differences in iron concentration and salinity may influence PFOA exchange between water and sediment. In marine microcosms, the alpha diversity of bacterial communities was significantly correlated to PFOA concentration. PFOA tended to correlate more strongly with bacterial community composition in water than in sediment. At the whole system level, Lefse's analysis indicated Algoriphagus halophilus as biomarkers for PFOA exposure in both riverine and marine systems, and the family Flavobacteriaceae were also more abundant in the exposed systems. In terms of temporal variation (comparison between three time points in the systems), metastat analysis showed great variability of potential PFOA-sensitive bacteria at the genus level. As such, most PFOA-sensitive genera were transitory and variable and existed for a short term in different systems (river, sea, blank, and experiment) and phases. Compared with other PFOA-sensitive genera, we suggest that further research is carried out to explore the use of Limnobacter as a bioindicator for temporal monitoring of PFOA pollution.

Development of the gut microbiota during early life in premature and term infants

BACKGROUND

The gastrointestinal (GI) microbiota has been linked to health consequences throughout life, from early life illnesses (e.g. sepsis and necrotising enterocolitis) to lifelong chronic conditions such as obesity and inflammatory bowel disease. It has also been observed that events in early life can lead to shifts in the microbiota, with some of these changes having been documented to persist into adulthood. A particularly extreme example of a divergent early GI microbiota occurs in premature neonates, who display a very different GI community to term infants. Certain characteristic patterns have been associated with negative health outcomes during the neonatal period, and these patterns may prove to have continual damaging effects if not resolved.

RESULTS

In this study we compared a set of premature infants with a paired set of term infants (n = 37 pairs) at 6 weeks of age and at 2 years of age. In the samples taken at 6 weeks of age we found microbial communities differing in both diversity and specific bacterial groups between the two infant cohorts. We identified clinical factors associated with over-abundance of potentially pathogenic organisms (e.g. Enterobacteriaceae) and reduced abundances of some beneficial organisms (e.g. Bifidobacterium). We contrasted these findings with samples taken at 2 years of age, which indicated that despite a very different initial gut microbiota, the two infant groups converged to a similar, more adult-like state. We identified clinical factors, including both prematurity and delivery method, which remain associated with components of the gut microbiota. Both clinical factors and microbial characteristics are compared to the occurrence of childhood wheeze and eczema, revealing associations between components of the GI microbiota and the development of these allergic conditions.

CONCLUSIONS

The faecal microbiota differs greatly between infants born at term and those born prematurely during early life, yet it converges over time. Despite this, early clinical factors remain significantly associated with the abundance of some bacterial groups at 2 years of age. Given the associations made between health conditions and the microbiota, factors that alter the makeup of the gut microbiota, and potentially its trajectory through life, could have important lifelong consequences.

A systematic review of associations between gut microbiota composition and growth failure in preterm neonates

Growth failure is among the most prevalent and devastating consequences of prematurity. Up to half of all extremely preterm neonates struggle to grow despite modern nutrition practices. Although elegant preclinical models suggest causal roles for the gut microbiome, these insights have not yet translated into biomarkers that identify at-risk neonates or therapies that prevent or treat growth failure. This systematic review aims to identify features of the neonatal gut microbiota that are positively or negatively associated with early postnatal growth. We identified 860 articles, of which 14 were eligible for inclusion. No two studies used the same definitions of growth, ages at stool collection, and statistical methods linking microbiota to metadata. In all, 58 different taxa were associated with growth, with little consensus among studies. Two or more studies reported positive associations with Enterobacteriaceae, Bacteroides, Bifidobacterium, Enterococcus, and Veillonella, and negative associations with Citrobacter, Klebsiella, and Staphylococcus. Streptococcus was positively associated with growth in five studies and negatively associated with growth in three studies. To gain insight into how the various definitions of growth could impact results, we performed an exploratory secondary analysis of 245 longitudinally sampled preterm infant stools, linking microbiota composition to multiple clinically relevant definitions of neonatal growth. Within this cohort, every definition of growth was associated with a different combination of microbiota features. Together, these results suggest that the lack of consensus in defining neonatal growth may limit our capacity to detect consistent, meaningful clinical associations that could be leveraged into improved care for preterm neonates.

Efficacy of Bifidobacterium longum alone or in multi-strain probiotic formulations during early life and beyond

The significance of Bifidobacterium to human health can be appreciated from its early colonization of the neonatal gut, where Bifidobacterium longum represents the most abundant species. While its relative abundance declines with age, it is further reduced in several diseases. Research into the beneficial properties of B. longum has unveiled a range of mechanisms, including the production of bioactive molecules, such as short-chain fatty acids, polysaccharides, and serine protease inhibitors. From its intestinal niche, B. longum can have far-reaching effects in the body influencing immune responses in the lungs and even skin, as well as influencing brain activity. In this review, we present the biological and clinical impacts of this species on a range of human conditions beginning in neonatal life and beyond. The available scientific evidence reveals a strong rationale for continued research and further clinical trials that investigate the ability of B. longum to treat or prevent a range of diseases across the human lifespan.

Maturation of the gut metabolome during the first year of life in humans

The gut microbiota is involved in the production of numerous metabolites that maintain host wellbeing. The assembly of the gut microbiome is highly dynamic, and influenced by many postnatal factors, moreover, little is known about the development of the gut metabolome. We showed that geography has an important influence on the microbiome dynamics in the first year of life based on two independent cohorts from China and Sweden. Major compositional differences since birth were the high relative abundance of Bacteroides in the Swedish cohort and Streptococcus in the Chinese cohort. We analyzed the development of the fecal metabolome in the first year of life in the Chinese cohort. Lipid metabolism, especially acylcarnitines and bile acids, was the most abundant metabolic pathway in the newborn gut. Delivery mode and feeding induced particular differences in the gut metabolome since birth. In contrast to C-section newborns, medium- and long-chain acylcarnitines were abundant at newborn age only in vaginally delivered infants, associated by the presence of bacteria such as Bacteroides vulgatus and Parabacteroides merdae. Our data provide a basis for understanding the maturation of the fecal metabolome and the metabolic role of gut microbiota in infancy.

Microbiota of preterm infant develops over time along with the first teeth eruption

Objective

The temporal growth of the infant microbiome in the early years of life influences short- and long-term infant health. The aim of this longitudinal study was to investigate bacterial dynamics in the microbiome of preterm infants during tooth eruption.

Methods

Saliva samples from normally delivered (n = 24) and preterm infants (n = 31) were collected 30 days after birth and after the eruption of two primary mandibular incisors. Based on Illumina MiSeq Sequencing of the 16S rRNA gene, the dynamic microbial changes of newborns at two-time points were investigated. Meanwhile, the Human Oral Microbiome Database was adopted for assigning taxonomy.

Results

Using alpha and beta diversity analyses, different shift patterns of microbiome structures in preterm and healthy participants and bacterial diversity over time were observed. The relative abundance and shifts trend, along with the two lower primary central incisors eruption, of core oral flora varies in full-term and preterm groups, including Gemella spp., Rothia mucilaginosa, Veillonella atypica, etc. Several microorganisms colonize later in the oral microbiome development of premature babies, such as Gemella spp. In addition to teeth eruption, the growth of the saliva microbiome in preterm infants could be influenced by breastfeeding durations and birth weight.

Conclusion

This study provided insights into how the oral microbiota changes during tooth eruption in preterm infants and how the colonization of the oral cavity with bacteria in preterm infants differs significantly from that in full-term infants.

The Gut Microbiome of Children during the COVID-19 Pandemic

The gut microbiome has been shown to play a critical role in maintaining a healthy state. Dysbiosis of the gut microbiome is involved in modulating disease severity and potentially contributes to long-term outcomes in adults with COVID-19. Due to children having a significantly lower risk of severe illness and limited sample availability, much less is known about the role of the gut microbiome in children with COVID-19. It is well recognized that the developing gut microbiome of children differs from that of adults, but it is unclear if this difference contributes to the different clinical presentations and complications. In this review, we discuss the current knowledge of the gut microbiome in children with COVID-19, with gut microbiome dysbiosis being found in pediatric COVID-19 but specific taxa change often differing from those described in adults. Additionally, we discuss possible mechanisms of how the gut microbiome may mediate the presentation and complications of COVID-19 in children and the potential role for microbial therapeutics.

Development of the infant gut microbiome predicts temperament across the first year of life

Perturbations to the gut microbiome are implicated in altered neurodevelopmental trajectories that may shape life span risk for emotion dysregulation and affective disorders. However, the sensitive periods during which the microbiome may influence neurodevelopment remain understudied. We investigated relationships between gut microbiome composition across infancy and temperament at 12 months of age. In 67 infants, we examined if gut microbiome composition assessed at 1-3 weeks, 2, 6, and 12 months of age was associated with temperament at age 12 months. Stool samples were sequenced using the 16S Illumina MiSeq platform. Temperament was assessed using the Infant Behavior Questionnaire-Revised (IBQ-R). Beta diversity at age 1-3 weeks was associated with surgency/extraversion at age 12 months. Bifidobacterium and Lachnospiraceae abundance at 1-3 weeks of age was positively associated with surgency/extraversion at age 12 months. Klebsiella abundance at 1-3 weeks was negatively associated with surgency/extraversion at 12 months. Concurrent composition was associated with negative affectivity at 12 months, including a positive association with Ruminococcus-1 and a negative association with Lactobacillus. Our findings support a relationship between gut microbiome composition and infant temperament. While exploratory due to the small sample size, these results point to early and late infancy as sensitive periods during which the gut microbiome may exert effects on neurodevelopment.

Potential Benefit of Probiotic E. Coli Nissle in Term Neonates

BACKGROUND

 Probiotics are often viewed as an immunity enhancing agent. The objective of this study was to investigate whether oral administration of Escherichia coli Nissle 1917 reduces the number of infections, their duration, and severity in the first 24 months after parturition in healthy neonates.

SUBJECTS AND METHODS

 This prospective, confirmatory, randomised, double-blind, placebo-controlled study enrolled 567 healthy neonates from four German and two Polish sites. Neonates received 10e8 viable E. coli Nissle (n=283) or placebo (n=284) daily in the first week and every second day in week 2 and 3. After 6 and 12 months, the subjects received additional instillations on ten subsequent days. The overall efficacy was assessed by the number of infections per observation period.

RESULTS

 Incidence rates of infection, infection duration and severity showed no statistically significant difference between groups after 24 months. Post-hoc analyses, however, revealed a short-term benefit of E. coli Nissle four weeks after treatment start which became less pronounced after eight weeks. E. coli Nissle was safe and well tolerated.

CONCLUSIONS

 A long-term effect after colonising the healthy neonate´s gut with E. coli Nissle to protect against infections could not be shown. Additional studies are needed to confirm a transitory, yet clinically significant role of probiotics in the first four weeks after parturition.

The Human Milk Microbiota Produces Potential Therapeutic Biomolecules and Shapes the Intestinal Microbiota of Infants

Human milk not only provides a perfect balance of nutrients to meet all the needs of the infant in the first months of life but also contains a variety of bacteria that play a key role in tailoring the neonatal faecal microbiome. Microbiome analysis of human milk and infant faeces from mother-breastfed infant pairs was performed by sequencing the V1-V3 region of the 16S rRNA gene using the Illumina MiSeq platform. According to the results, there is a connection in the composition of the microbiome in each mother-breastfed infant pair, supporting the hypothesis that the infant's gut is colonised with bacteria from human milk. MiSeq sequencing also revealed high biodiversity of the human milk microbiome and the infant faecal microbiome, whose composition changes during lactation and infant development, respectively. A total of 28 genetically distinct strains were selected by hierarchical cluster analysis of RAPD-PCR (Random Amplified Polymorphic DNA-Polymerase Chain Reaction) electrophoresis profiles of 100 strains isolated from human milk and identified by 16S RNA sequencing. Since certain cellular molecules may support their use as probiotics, the next focus was to detect (S)-layer proteins, bacteriocins and exopolysaccharides (EPSs) that have potential as therapeutic biomolecules. SDS-PAGE (Sodium Dodecyl-Sulfate Polyacrylamide Gel Electrophoresis) coupled with LC-MS (liquid chromatography-mass spectrometry) analysis revealed that four Levilactobacillus brevis strains expressed S-layer proteins, which were identified for the first time in strains isolated from human milk. The potential biosynthesis of plantaricin was detected in six Lactiplantibacillus plantarum strains by PCR analysis and in vitro antibacterial studies. ¹H NMR (Proton Nuclear Magnetic Resonance) analysis confirmed EPS production in only one strain, Limosilactobacillus fermentum MC1. The overall microbiome analysis suggests that human milk contributes to the establishment of the intestinal microbiota of infants. In addition, it is a promising source of novel Lactobacillus strains expressing specific functional biomolecules.

Diversity and temporal dynamics of breast milk microbiome and its influencing factors in Chinese women during the first 6 months postpartum

Human breast milk (HBM) plays an important role in providing nutrients, beneficial microorganisms and bioactive components for infants, helping maturation of their immune system and gastrointestinal development. Here, we present a study aiming to investigate the diversity and temporal dynamics of the milk microbiome across the first 6 month postpartum in Chinese healthy breastfeeding women, and to investigate to what extent other variables (e.g., sampling location, infant sex, and mode of delivery) might also be related to variations in the human milk microbiome, and the association with maternal diet and nutrients. Fifty-three healthy pregnant women from four cities were recruited from a China Maternal and Infant Health Cohort Study and breast milk samples were collected and analyzed using 16S rRNA metagenomic sequencing. We illustrated the diversity and temporal dynamics during lactation (Adonis p-value = 3e–04). Firmicutes and Proteobacteria were the most abundant phyla, and Streptococcus, Staphylococcus, Serratia, and Corynebacterium were the core genera. Partitioning around medoids clustering identified two major internal clusters of breast milk microbiota. Cluster 1 was dominated by Acinetobacter and Pseudomonas, while Cluster 2 was dominated by Streptococcus and Staphylococcus. Among other environmental variables, sampling location showed significant influence on breast milk microbiome (Adonis p-value = 4e–04), while infant sex (Adonis p-value = 0.33) and mode of delivery (Adonis p-value = 0.19) were less related to variations in the human milk microbiome. Maternal diet such as tuber was significantly correlated with the relative abundance of Neisseria (rho = 0.34, adjusted p-value = 0.01) and Cutibacterium (rho = −0.35, adjusted p-value = 0.01), and nutrients such as carbohydrates were significantly correlated with the relative abundance of Aquabacterium (rho = −0.39, adjusted p-value = 0.0027), and vitamin B12 was significantly correlated with the relative abundance of Coprococcus (rho = 0.40, adjusted p-value = 0.0018), etc. These results illustrated the dynamic changes of composition and diversity during the lactation phases of the Chinese breast milk microbiome and addressed the importance of geographic location on milk microbiota, and associations with maternal diet consumption, which have potential benefits on the establishment and future health of breastfeeding infants.

Gut microbiota plays a role in irritable bowel syndrome by regulating 5-HT metabolism

Irritable bowel syndrome (IBS) is a common chronic functional gastrointestinal disorder. Brain-gut-microbiota axis dysfunction is an important pathogenic factor for IBS, in which neurotransmitters and gut microbes play key roles. The gastrointestinal tract contains large amounts of serotonin (5-hydroxytryptamine, 5-HT), a neurotransmitter that has been strongly linked to IBS-related symptoms. More than 90% of serotonin is synthesized in the gut by enterochromaffin cells (ECs), and certain intestinal flora can affect the occurrence and development of IBS by regulating 5-HT and its metabolism. In this review, we will discuss the role of gut microbiota in IBS by regulating 5-HT.

Cross-sectional observational study protocol: missing microbes in infants born by caesarean section (MiMIC): antenatal antibiotics and mode of delivery

INTRODUCTION

The intestinal microbiome in early life plays a major role in infant health and development. Factors like antibiotic exposure, breast/formula feeding and mode of delivery are known to affect the microbiome. The increasing occurrence of caesarean section (C-section) deliveries and antibiotic exposure warrants further insight into the potential missing microbes in those infants. The study objective is to study the effect of maternal antibiotic administration during pregnancy and/or C-section mode of delivery on the development of the infant's intestinal microbiome until the age of 2 years.

METHODS AND ANALYSIS

A single site, cross-sectional observational study of C-section and vaginally delivered infants being either exposed to maternal antibiotic treatment or not during the third trimester of pregnancy. Throughout the nine visits, stool, urine, saliva, hair, breast milk and vaginal swabs will be collected from either mother and/or infant for microbiome and metabolomic analysis.

ETHICS AND DISSEMINATION

The protocol was approved by the Clinical Research Ethics Committee of the Cork Teaching Hospitals. The trial has been registered at ClinicalTrials.gov.The findings from this study will be disseminated in peer-reviewed journals, during scientific conferences, and directly to the study participants. Sequencing data will be deposited in public databases.

TRIAL REGISTRATION NUMBER

NCT04134819.

A child is not an adult: development of a new in vitro model of the toddler colon

Early life is a critical period where gut ecosystem and functions are being established with significant impact on health. For regulatory, technical, and cost reasons, in vitro gut models can be used as a relevant alternative to in vivo assays. An exhaustive literature review was conducted to adapt the Mucosal Artificial Colon (M-ARCOL) to specific physicochemical (pH, transit time, and nutritional composition of ileal effluents) and microbial parameters from toddlers in the age range of 6 months-3 years, resulting in the Tm-ARCOL. In vitro fermentations were performed to validate this newly developed colonic model compared to in vivo toddler data. Results were also compared to those obtained with the classical adult configuration. Fecal samples from 5 toddlers and 4 adults were used to inoculate bioreactors, and continuous fermentations were performed for 8 days. Gut microbiota structure (lumen and mucus-associated microbiota) and functions (gas and short-chain fatty acids) were monitored. Clearly distinct microbial signatures were obtained between the two in vitro conditions, with lower α-diversity indices and higher abundances of infant-related microbial populations (e.g., Bifidobacteriaceae, Enterobacteriaceae) in toddler versus adult conditions. In accordance with in vivo data, methane was found only in adult bioreactors, while higher percentage of acetate but lower proportions of propionate and butyrate was measured in toddlers compared to adults. This new in vitro model will provide a powerful platform for gut microbiome mechanistic studies in a pediatric context, both in nutritional- (e.g., nutrients, probiotics, prebiotics) and health-related (e.g., drugs, enteric pathogens) studies. KEY POINTS: • Development of a novel in vitro colonic model recapitulating the toddler environment. • Specific toddler versus adult digestive conditions are preserved in vitro. • The new model provides a powerful platform for microbiome mechanistic studies.

A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome

Age-specific reference genomes of the human gut microbiome can provide higher resolution for metagenomic analyses including taxonomic classification, strain-level genomic investigation and functional characterization. We present the Early-Life Gut Genomes (ELGG) catalog with 32,277 genomes representing 2172 species from 6122 fecal metagenomes collected from children under 3 years old spanning delivery mode, gestational age, feeding pattern, and geography. The ELGG substantially expanded the phylogenetic diversity by 38% over the isolate microbial genomes, and the genomic landscape of the early-life microbiome by increasing recruitment of metagenomic reads to 82.8%. More than 60% of the ELGG species lack an isolate representative. The conspecific genomes of the most abundant species from children differed in gene diversity and functions compared to adults. The ELGG genomes encode over 80 million protein sequences, forming the Early-Life Gut Proteins (ELGP) catalog with over four million protein clusters, 29.5% of which lacked functional annotations. The ELGG and ELGP references provided new insights into the early-life human gut microbiome and will facilitate studies to understand the development and mechanisms of disturbances of the human gut microbiome in early life.

Here the authors present a large-scale resource of the early-life human gut microbiome from children under three years old, which comprises 32,277 metagenome-assembled gut genomes, representing 2172 species, and more than 80 million gut proteins representing >4 million protein clusters, spanning multiple clinical factors including age, delivery mode, gestational age, and feeding patterns.

Exploring the Potential of Human Milk and Formula Milk on Infants’ Gut and Health

Early-life gut microbiota plays a role in determining the health and risk of developing diseases in later life. Various perinatal factors have been shown to contribute to the development and establishment of infant gut microbiota. One of the important factors influencing the infant gut microbial colonization and composition is the mode of infant feeding. While infant formula milk has been designed to resemble human milk as much as possible, the gut microbiome of infants who receive formula milk differs from that of infants who are fed human milk. A diverse microbial population in human milk and the microbes seed the infant gut microbiome. Human milk contains nutritional components that promote infant growth and bioactive components, such as human milk oligosaccharides, lactoferrin, and immunoglobulins, which contribute to immunological development. In an attempt to encourage the formation of a healthy gut microbiome comparable to that of a breastfed infant, manufacturers often supplement infant formula with prebiotics or probiotics, which are known to have a bifidogenic effect and can modulate the immune system. This review aims to elucidate the roles of human milk and formula milk on infants’ gut and health.

Immunomodulatory effects of the Bifidobacterium longum BL-10 on lipopolysaccharide-induced intestinal mucosal immune injury

The intestine is the largest digestive and immune organ in the human body, with an intact intestinal mucosal barrier. Bifidobacterium longum is the specific gut commensals colonized in the human gut for boosting intestinal immunity to defend against intestinal mucosal immune injury. In the LPS-induced intestinal injury model, the Bifidobacterium longum BL-10 was suggested to boost the intestinal immune. Detailly, compared with the LPS-induced mice, the BL10 group significantly reduced intestine (jejunum, ileum, and colon) tissue injury, pro-inflammatory cytokines (TNF-α, IFN-γ, IL-2, IL-6, IL-17, IL-22, and IL-12) levels and myeloperoxidase activities. Moreover, the B. longum BL-10 significantly increased the number of immunocytes (CD4+ T cells, IgA plasma cells) and the expression of tight junction protein (Claudin1 and Occludin). B. longum BL-10 regulated the body's immune function by regulating the Th1/Th2 and Th17/Treg balance, which showed a greater impact on the Th1/Th2 balance. Moreover, the results also showed that B. longum BL-10 significantly down-regulated the intestinal protein expression of TLR4, p-IκB, and NF-κB p65. The B. longum BL-10 increased the relative abundance of the genera, including Lachnospiraceae_NK4A136_group and Clostridia_UCG-014, which were related to declining the levels of intestinal injury. Overall, these results indicated that the B. longum BL-10 had great functionality in reducing LPS-induced intestinal mucosal immune injury.

The Biotics Family: Current Knowledge and Future Perspectives in Metabolic Diseases

Globally, metabolic diseases such as obesity, type 2 diabetes mellitus and non-alcoholic fatty liver disease pose a major public health threat. Many studies have confirmed the causal relationship between risk factors and the etiopathogenesis of these diseases. Despite this, traditional therapeutic management methods such as physical education and diet have proven insufficient. Recently, researchers have focused on other potential pathways for explaining the pathophysiological variability of metabolic diseases, such as the involvement of the intestinal microbiota. An understanding of the relationship between the microbiome and metabolic diseases is a first step towards developing future therapeutic strategies. Currently, much attention is given to the use of biotics family members such as prebiotics (lactolose, soy oligosaccharides, galactooligosaccharides, xylooligosaccharides or inulin) and probiotics (genera Lactobacillus, Bifidobacterium, Lactococcus, Streptococcus or Enterococcus). They can be used both separately and together as synbiotics. Due to their direct influence on the composition of the intestinal microbiota, they have shown favorable results in the evolution of metabolic diseases. The expansion of the research area in the biotics family has led to the discovery of new members, like postbiotics. In the age of personalized medicine, their use as therapeutic options is of great interest to our study.

Neonatal Diet and Gut Microbiome Development After C-Section During the First Three Months After Birth: A Systematic Review

Background

Cesarean section (C-section) delivery imprints fundamentally on the gut microbiota composition with potential health consequences. With the increasing incidence of C-sections worldwide, there is a need for precise characterization of neonatal gut microbiota to understand how to restore microbial imbalance after C-section. After birth, gut microbiota development is shaped by various factors, especially the infant’s diet and antibiotic exposure. Concerning diet, current research has proposed that breastfeeding can restore the characteristic gut microbiome after C-section.

Objectives

In this systematic review, we provide a comprehensive summary of the current literature on the effect of breastfeeding on gut microbiota development after C-section delivery in the first 3 months of life.

Methods

The retrieved data from PubMed, Scopus, and Web of Science were evaluated according to the PICO/PECO strategy. Quality assessment was conducted by the Newcastle–Ottawa Scale.

Results

After critical selection, we identified 14 out of 4,628 studies for the evaluation of the impact of the diet after C-section delivery. The results demonstrate consistent evidence that C-section and affiliated intrapartum antibiotic exposure affect Bacteroidetes abundance and the incapacity of breastfeeding to reverse their reduction. Furthermore, exclusive breastfeeding shows a positive effect on Actinobacteria and Bifidobacteria restoration over the 3 months after birth. None of the included studies detected any significant changes in Lactobacillus abundance in breastfed infants after C-section.

Conclusion

C-section and intrapartum antibiotic exposure influence an infant’s gut microbiota by depletion of Bacteroides, regardless of the infant’s diet in the first 3 months of life. Even though breastfeeding increases the presence of Bifidobacteria, further research with proper feeding classification is needed to prove the restoration effect on some taxa in infants after C-section.

Systematic Review Registration:

[www.crd.york.ac.uk/prospero/], identifier [CRD42021287672].

Could Weaning Remodel the Oral Microbiota Composition in Donkeys? An Exploratory Study

As the initiation point of digestion, the oral microbiome is important in maintaining oral and systemic health. However, the composition of oral microbial communities and the influence of weaning on the oral microbiota of donkey foals remains poorly characterized. The present study used buccal swab samples to determine the changes in oral microbial communities occurring at the time of weaning. A total of 20 oral swab samples were collected from two groups: preweaning donkey foals (PreW group, n = 10) and postweaning donkey foals (PostW group, n = 10). The donkey oral microbiome was analyzed by 16S rRNA gene sequencing using Illumina MiSeq. This study is the first report of the donkey oral microbiome in association with weaning. Compared to the preweaning donkeys, the oral bacteria diversity in the postweaning donkeys was increased, with a higher Simpson index. Changes in the composition of the oral microbiota between the PreW and PostW groups were observed in the present study. At the phylum level, the relative abundance of Firmicutes and Myxococcota was significantly greater in the PostW than in the PreW group. At the genus level, the Gemella, unclassified_o__Lactobacillales, and Lactobacillus were increased in the postweaning donkeys. The donkeys’ oral microbial functions were predicted using PICRUSt, and the functions related to carbohydrate metabolic pathways were significantly enriched in the oral microbiome in the PostW donkeys. In summary, the current study provides a deeper insight into the oral microbiota changes during the weaning period, and the influence of weaning together with the documented changes in diversity and composition will help us to obtain a better understanding of their long-term health impact within the oral cavities of donkey foals. However, a major limitation of the present study was that the samples were obtained from different animals in the PreW and PostW groups, which may have resulted in variability among the different individuals. Further investigation is needed to monitor the shift in oral microbes in the same individuals during the weaning period.

Effects of Probiotics on Gut Microbiomes of Extremely Preterm Infants in the Neonatal Intensive Care Unit: A Prospective Cohort Study

Background: Probiotics have been previously reported to reduce the incidence of necrotizing enterocolitis (NEC) in extremely preterm infants, but the mechanisms by which the probiotics work remain unknown. We aimed to investigate the effects of probiotics on the gut microbiota of extremely preterm infants. Methods: A prospective cohort study was conducted on 120 extremely preterm neonates (gestational age ≤ 28 weeks) between August 2019 and December 2021. All neonates were divided into the study (receiving probiotics) and the control (no probiotics) groups. Multivariate logistic regression analysis was performed to investigate the significantly different compositions of gut microbiota between these two groups. The effects of probiotics on the occurrence of NEC and late-onset sepsis were also investigated. Results: An increased abundance of Lactobacillus was noted in neonates who received the probiotics (AOR 4.33; 95% CI, 1.89-9.96, p = 0.009) when compared with the control group. Subjects in the probiotic group had significantly fewer days of total parenteral nutrition (median [interquartile range, IQR]) 29.0 (26.8-35.0) versus 35.5 (27.8-45.0), p = 0.004) than those in the control group. The probiotic group had a significantly lower rate of late-onset sepsis than the control group (47.1% versus 70.0%, p = 0.015), but the rate of NEC, duration of hospitalization and the final in-hospital mortality rates were comparable between these two groups. Conclusions: Probiotic supplementation of extremely preterm infants soon after the initiation of feeding increased the abundance of Lactobacillus. Probiotics may reduce the risk of late-onset sepsis, but further randomized controlled trials are warranted in the future.

Changes to the Gut Microbiome in Young Children Showing Early Behavioral Signs of Autism

The human gut microbiome has increasingly been associated with autism spectrum disorder (ASD), which is a neurological developmental disorder, characterized by impairments to social interaction. The ability of the gut microbiota to signal across the gut-brain-microbiota axis with metabolites, including short-chain fatty acids, impacts brain health and has been identified to play a role in the gastrointestinal and developmental symptoms affecting autistic children. The fecal microbiome of older children with ASD has repeatedly shown particular shifts in the bacterial and fungal microbial community, which are significantly different from age-matched neurotypical controls, but it is still unclear whether these characteristic shifts are detectable before diagnosis. Early microbial colonization patterns can have long-lasting effects on human health, and pre-emptive intervention may be an important mediator to more severe autism. In this study, we characterized both the microbiome and short-chain fatty acid concentrations of fecal samples from young children between 21 and 40 months who were showing early behavioral signs of ASD. The fungal richness and acetic acid concentrations were observed to be higher with increasing autism severity, and the abundance of several bacterial taxa also changed due to the severity of ASD. Bacterial diversity and SCFA concentrations were also associated with stool form, and some bacterial families were found with differential abundance according to stool firmness. An exploratory analysis of the microbiome associated with pre-emptive treatment also showed significant differences at multiple taxonomic levels. These differences may impact the microbial signaling across the gut-brain-microbiota axis and the neurological development of the children.

Effect of breast milk with or without bacteria on infant gut microbiota

BACKGROUND

The breast milk microbiome could be a source of infant intestinal microbiota. Several studies have found that some breast milk is extremely low in bacteria or is even sterile. There are limited studies on the effect of milk without bacteria on the infant gut microbiota. The purpose of this study was to investigate the gut microbiota of infants fed with bacterial milk or sterile milk. Meanwhile, we attempted to find the cause of undetectable bacteria in milk.

METHODS

A total of 17 healthy pregnant women and 17 infants were enrolled in this study. Fecal samples were collected from full-term pregnant women. Milk samples and infant fecal samples were collected on the 14th postnatal day. Breast milk and fecal samples were examined using 16S rRNA sequencing technology. Pregnant women and infants were grouped according to milk with or without bacteria. To compare the differences in gut microbiota and clinical characteristics between groups.

RESULTS

Bacteria were detected in 11 breast milk samples, and the bacterial detection rate was 64.7%. Infants fed with bacterial milk showed higher Shannon index and Simpson index (P = 0.020, P = 0.048), and their relative abundance of Lachnospirales, Lachnospiraceae and Eggerthellaceae was markedly higher. In addition, there were more bacterial associations in the co-occurrence network of infants fed with bacterial milk. Pregnant women with sterile and bacterial breast milk showed no significant differences in their clinical characteristics, and microbial composition and diversity.

CONCLUSIONS

Some breast milk from healthy postpartum women failed to be sequenced due to low microbial DNA quantities or is sterile. Research is needed to explore the reasons for this phenomenon. Infants fed with bacterial milk had higher Alpha diversity and more complex microbiota networks. These findings provide novel insight into milk microbiota and infant gut microbiota.

Very Preterm Children Gut Microbiota Comparison at the Neonatal Period of 1 Month and 3.5 Years of Life

Prematurity is a risk factor for dysbiosis of the gut microbiota due to particular birth conditions and frequent prolonged hospitalization of neonates. Although gut microbiota colonization after birth and its establishment during the hospitalization period have been studied in preterm infants, data on gut microbiota following discharge, particularly during early childhood, are scarce. The present study investigated the relationship between gut microbiota at 1 month after birth (hospitalization period) and 3.5 years of age in 159 preterm children belonging to the French EPIFLORE prospective observational cohort study. Analysis using bacterial 16S rRNA gene sequencing showed that the gut microbiota of preterm neonates at 1 month was highly variable and characterized by six distinct enterotypes. In contrast, the gut microbiota of the same children at 3.5 years of age showed less variability, with only two discrete enterotypes. An absence of association between enterotypes at 1 month and 3.5 years of age was observed. While the alpha diversity of gut microbiota significantly increased between 1 month and 3.5 years of age, for both alpha and beta diversities, there was no correlation between the 1-month and 3.5-years time points. Comparison at 3.5 years between children born either preterm (n = 159) or full-term (n = 200) showed no differences in terms of enterotypes, but preterm children harbored a lower Shannon diversity index and a different overall composition of microbiota than full-term children. This study suggests that the characteristics of the early gut microbiota of preterm children are not predictive of the microbial community composition at 3.5 years of age. However, the impact of gestational age is still noticeable on the gut microbiota up to 3.5 years of age.

Fecal amine metabolite analysis before onset of severe necrotizing enterocolitis in preterm infants: a prospective case-control study

Infants developing necrotizing enterocolitis (NEC) have a different metabolomic profile compared to controls. The potential of specific metabolomics, i.e. amino acids and amino alcohols (AAA), as early diagnostic biomarkers for NEC is largely unexplored. In this multicenter prospective case-control study, longitudinally collected fecal samples from preterm infants (born <30 weeks of gestation) from 1-3 days before diagnosis of severe NEC (Bell's stage IIIA/IIIB), were analyzed by targeted high-performance liquid chromatography (HPLC). Control samples were collected from gestational and postnatal age-matched infants. Thirty-one NEC cases (15 NEC IIIA;16 NEC IIIB) with 1:1 matched controls were included. Preclinical samples of infants with NEC were characterized by five increased essential amino acids-isoleucine, leucine, methionine, phenylalanine and valine. Lysine and ethanolamine ratios were lower prior to NEC, compared to control samples. A multivariate model was rendered based on isoleucine, lysine, ethanolamine, tryptophan and ornithine, modestly discriminating cases from controls (AUC 0.67; p < 0.001). Targeted HPLC pointed to several specific AAA alterations in samples collected 1-3 days before NEC onset, compared to controls. Whether this reflects metabolic alterations and has a role in early biomarker development for NEC, has yet to be elucidated.