Temporal development of the gut microbiome in early childhood from the TEDDY study

The Microbiota-Gut-Brain Axis

The importance of the gut-brain axis in maintaining homeostasis has long been appreciated. However, the past 15 yr have seen the emergence of the microbiota (the trillions of microorganisms within and on our bodies) as one of the key regulators of gut-brain function and has led to the appreciation of the importance of a distinct microbiota-gut-brain axis. This axis is gaining ever more traction in fields investigating the biological and physiological basis of psychiatric, neurodevelopmental, age-related, and neurodegenerative disorders. The microbiota and the brain communicate with each other via various routes including the immune system, tryptophan metabolism, the vagus nerve and the enteric nervous system, involving microbial metabolites such as short-chain fatty acids, branched chain amino acids, and peptidoglycans. Many factors can influence microbiota composition in early life, including infection, mode of birth delivery, use of antibiotic medications, the nature of nutritional provision, environmental stressors, and host genetics. At the other extreme of life, microbial diversity diminishes with aging. Stress, in particular, can significantly impact the microbiota-gut-brain axis at all stages of life. Much recent work has implicated the gut microbiota in many conditions including autism, anxiety, obesity, schizophrenia, Parkinson’s disease, and Alzheimer’s disease. Animal models have been paramount in linking the regulation of fundamental neural processes, such as neurogenesis and myelination, to microbiome activation of microglia. Moreover, translational human studies are ongoing and will greatly enhance the field. Future studies will focus on understanding the mechanisms underlying the microbiota-gut-brain axis and attempt to elucidate microbial-based intervention and therapeutic strategies for neuropsychiatric disorders.

Early-life factors contributing to type 1 diabetes

The incidence of type 1 diabetes has increased since the mid-twentieth century at a rate that is too rapid to be attributed to genetic predisposition alone. While the disease can occur at any age, mounting evidence from longitudinal cohort studies of at-risk children indicate that type 1 diabetes associated autoantibodies can be present from the first year of life, and that those who develop type 1 diabetes at a young age have a more aggressive form of the disease. This corroborates the hypothesis that environmental exposures in early life contribute to type 1 diabetes risk, whether related to maternal influences on the fetus during pregnancy, neonatal factors or later effects during infancy and early childhood. Studies to date show a range of environmental triggers acting at different time points, suggesting a multifactorial model of genetic and environmental factors in the pathogenesis of type 1 diabetes, which integrally involves a dialogue between the immune system and pancreatic beta cells. For example, breastfeeding may have a weak protective effect on type 1 diabetes risk, while use of an extensively hydrolysed formula does not. Additionally, exposure to being overweight pre-conception, both in utero and postnatally, is associated with increased risk of type 1 diabetes. Epidemiological, clinical and pathological studies in humans support a role for viral infections, particularly enteroviruses, in type 1 diabetes, but definitive proof is lacking. The role of the early microbiome and its perturbations in islet autoimmunity and type 1 diabetes is the subject of investigation in ongoing cohort studies. Understanding the interactions between environmental exposures and the human genome and metagenome, particularly across ethnically diverse populations, will be critical for the development of future strategies for primary prevention of type 1 diabetes.

Prenatal and postnatal contributions of the maternal microbiome on offspring programming

The maternal microbiota is positioned to regulate the development of offspring immunity, metabolism, as well as brain function and behavior. The mechanisms by which maternal microbial signals drive these processes are beginning to be elucidated. In this review, we provide a brief overview on the importance of the microbiome in brain function and behavior, define the maternal vaginal and gut microbiota as distinct influences on offspring development, and outline current concepts in microbial origins of offspring health outcomes. We propose that the maternal microbiota influences prenatal and early postnatal offspring development and health outcomes through two overlapping processes. First, during pregnancy maternal gut microbiota provide metabolites and substrates essential for fetal growth through metabolic provisioning, driving expansion and maturation of central and peripheral immune cells, and formation of neural circuits. Second, vertical transmission of maternal microbiota during birth and in the early postnatal window elicits a potent immunostimulatory effect in offspring that induces metabolic and developmental transcriptional programs, primes the immune system for subsequent microbial exposure, and provides substrates for brain metabolism. Finally, we explore the possibility that environmental factors, such as malnutrition, stress and infection, may exert programmatic effects by disrupting the functional contributions of the maternal microbiome during prenatal and postnatal development to influence offspring outcomes across the lifespan.

Comparative genomics of Bifidobacterium species isolated from marmosets and humans

The genus Bifidobacterium is purported to have beneficial consequences for human health and is a major component of many gastrointestinal probiotics. Although species of Bifidobacterium are generally at low relative frequency in the adult human gastrointestinal tract, they can constitute high proportions of the gastrointestinal communities of adult marmosets. To identify genes that might be important for the maintenance of Bifidobacterium in adult marmosets, ten strains of Bifidobacterium were isolated from the feces of seven adult marmosets, and their genomes were sequenced. There were six B. reuteri strains, two B. callitrichos strains, one B. myosotis sp. nov. and one B. tissieri sp. nov. among our isolates. Phylogenetic analysis showed that three of the four species we isolated were most closely related to B. bifidum, B. breve and B. longum, which are species found in high abundance in human infants. There were 1357 genes that were shared by at least one strain of B. reuteri, B. callitrichos, B. breve, and B. longum, and 987 genes that were found in all strains of the four species. There were 106 genes found in B. reuteri and B. callitrichos but not in human bifidobacteria, and several of these genes were involved in nutrient uptake. These pathways for nutrient uptake appeared to be specific to Bifidobacterium from New World monkeys. Additionally, the distribution of Bifidobacterium in fecal samples from captive adult marmosets constituted as much as 80% of the gut microbiome, although this was variable between individuals and colonies. We suggest that nutrient transporters may be important for the maintenance of Bifidobacterium during adulthood in marmosets.

Temporal development of the infant gut microbiome

The majority of organisms that inhabit the human body reside in the gut. Since babies are born with an immature immune system, they depend on a highly synchronized microbial colonization process to ensure the correct microbes are present for optimal immune function and development. In a balanced microbiome, symbiotic and commensal species outcompete pathogens for resources. They also provide a protective barrier against chemical signals and toxic metabolites. In this targeted review we will describe factors that influence the temporal development of the infant microbiome, including the mode of delivery and gestational age at birth, maternal and infant perinatal antibiotic infusions, and feeding method-breastfeeding versus formula feeding. We will close by discussing wider environmental pressures and early intimate contact, particularly between mother and child, as they play a pivotal role in early microbial acquisition and community succession in the infant.

Maternal Vertical Transmission Affecting Early-life Microbiota Development

The association of the human microbiome with health outcomes has attracted much interest toward its therapeutic manipulation. The likelihood of modulating the human microbiome in early life is high and offers great potential to exert profound effects on human development since the early microbiota shows more flexibility compared to that of adults. The human microbiota, being similar to human genetics, can be transmitted from mother to infant, providing insights into early microbiota acquisition, subsequent development, and potential opportunities for intervention. Here, we review adaptations of the maternal microbiota during pregnancy, birth, and infancy, the acquisition and succession of early-life microbiota, and highlight recent efforts to elucidate mother-to-infant microbiota transmission. We further discuss how the mother-to-infant microbial transmission is shaped; and finally we address potential directions for future studies to promote our understanding within this field.

Early life determinants induce sustainable changes in the gut microbiome of six-year-old children

While the association between early life determinants and the development of the gut microbiome composition in infancy has been widely investigated, a potential persistent influence of early life determinants on the gut microbial community after its stabilization at later childhood remains largely unknown. Therefore, we aimed to identify the association between several early life determinants and the gut microbiome composition in six-year-old children from the LISA birth cohort. A total number of 166 fecal samples were analyzed using 16S rRNA gene-based barcoding to assess bacterial diversity pattern. The bacterial profiles were investigated for their association with maternal smoking during pregnancy, mode of delivery, breastfeeding, antibiotic treatment between one and two years of age, gender and socioeconomic status (SES). While alpha and beta diversity of the infants’ gut microbiome remained unaffected, amplicon sequence variants (ASVs) annotated to Firmicutes and Actinobacteria responded to early life determinants, mostly to feeding practice and antibiotics use. ASVs associated to Bacteriodetes remained unaffected. Our findings indicate that early life determinants could have a long-term sustainable effect on the gut microflora of six-year-old children, however, associations with early life determinates are weaker than reported for infants.

The Development of the Human Microbiome: Why Moms Matter

The human body is cohabitated with trillions of commensal bacteria that are essential for our health. However, certain bacteria can also cause diseases in the human host. Before the microbiome can be attributed to disease risk and pathogenesis, normal acquisition and development of the microbiome must be understood. Here, we explore the evidence surrounding in utero microbial exposures and the significant of this exposure in the proper development of the fetal and neonatal microbiome. We further explore the development of the fetal and neonatal microbiome and its relationship to preterm birth, feeding practices, and mode of delivery, and maternal diet.

Preliminary feasibility for recruiting and retaining black and white females to provide fecal samples for longitudinal research

As the associations between the gut microbiota and numerous health outcomes become more evident, it is important to conduct longitudinal microbiome research to advance the field beyond the identification of associations. It is also necessary to include individuals who have historically been underrepresented in biomedical research in longitudinal microbiome studies to better understand and eliminate racial/ethnic health disparities. This paper describes our experiences in recruiting and retaining participants for an ongoing, longitudinal microbiome study for which the main results will be reported at a later time. This article provides preliminary evidence of the feasibility of recruiting and retaining a racially diverse sample of females (97% completion for invited participants) for longitudinal microbiome research.

The Gut Microbiota in the First Decade of Life

Appreciation of the importance of the gut microbiome is growing, and it is becoming increasingly relevant to identify preventive or therapeutic solutions targeting it. The composition and function of the gut microbiota are relatively well described for infants (less than 3 years) and adults, but have been largely overlooked in pre-school (3-6 years) and primary school-age (6-12 years) children, as well as teenagers (12-18 years). Early reports suggested that the infant microbiota would attain an adult-like structure at the age of 3 years, but recent studies have suggested that microbiota development may take longer. This development time is of key importance because there is evidence to suggest that deviations in this development may have consequences in later life. In this review, we provide an overview of current knowledge concerning the gut microbiota, its evolution, variation, and response to dietary challenges during the first decade of life with a focus on healthy pre-school and primary school-age children (up to 12 years) from various populations around the globe. This knowledge should facilitate the identification of diet-based approaches targeting individuals of this age group, to promote the development of a healthy microbiota in later life.

Dietary intake influences gut microbiota development of healthy Australian children from the age of one to two years

Early life nutrition is a vital determinant of an individual’s life-long health and also directly influences the ecological and functional development of the gut microbiota. However, there are limited longitudinal studies examining the effect of diet on the gut microbiota development in early childhood. Here, up to seven stool samples were collected from each of 48 healthy children during their second year of life, and microbiota dynamics were assessed using 16S rRNA gene amplicon sequencing. Children’s dietary information was also collected during the same period using a validated food frequency questionnaire designed for this age group, over five time points. We observed significant changes in gut microbiota community, concordant with changes in the children’s dietary pattern over the 12-month period. In particular, we found differential effects on specific Firmicutes-affiliated lineages in response to frequent intake of either processed or unprocessed foods. Additionally, the consumption of fortified milk supplemented with a Bifidobacterium probiotic and prebiotics (synbiotics) further increased the presence of Bifidobacterium spp., highlighting the potential use of synbiotics to prolong and sustain changes in these lineages and shaping the gut microbiota community in young children.

Maturation of the infant rhesus macaque gut microbiome and its role in the development of diarrheal disease

BACKGROUND

Diarrhea is the second leading cause of death in children under 5 years of age. Enhanced understanding of causal pathways, pathogenesis, and sequelae of diarrhea is urgently needed. Although the gut microbiota is believed to play a role in susceptibility to diarrheal diseases, our understanding of this association remains incomplete. Infant rhesus macaques (Macaca mulatta) are susceptible to diarrhea making them an ideal model to address this question.

RESULTS

The maturation of the infant rhesus macaque gut microbiome throughout the first 8 months of life occurs in a similar pattern as that described for human infants. Moreover, the microbiome of the captive reared infant rhesus macaque more closely resembles that of human infants in the developing world than in the western world. Importantly, prior to disease onset, the gut microbiome of infants that later develop diarrhea is enriched in pathways of immunomodulatory metabolite synthesis, while those of infants that remain asymptomatic are enriched in pathways for short-chain fatty acid production. We identify Prevotella strains that are more abundant at 1 month in infants that later develop diarrhea. At 8 months, the microbiomes of animals that experience diarrhea show increased abundance of Campylobacter and a reduction in Helicobacter macacae.

CONCLUSION

The composition of the microbial community could provide a phenotypic marker of an infant's susceptibility to diarrheal disease. Given the significant physiological and immunological similarities between human and nonhuman primates, these findings provide potential markers of susceptibility to diarrhea that could be modulated to improve infant health, especially in the developing world.

Pancreas–Microbiota Cross Talk in Health and Disease

The pancreas controls metabolism through endocrine and exocrine functions. Pancreatic diseases comprise a spectrum of mild to life-threatening conditions, including acute and chronic pancreatitis, diabetes, and pancreatic cancer, which affect endocrine and exocrine pancreatic function and impose a substantial disease burden on individuals. Increasing experimental evidence demonstrates that the intestinal microbiota has an important impact on pancreatic function and diseases. This influence may be conferred by bacterial metabolites, such as short-chain fatty acids, or the modulation of immune responses. In turn, pancreatic factors, such as the excretion of antimicrobials, might have a substantial impact on the composition and functional properties of the gut microbiota. Here, we summarize experimental and clinical approaches used to untie the intricate pancreas–microbiota cross talk. Future advances will allow clinicians to manipulate the intestinal microbiota and guide patient management in pancreatic diseases.

Gut microbes, ageing & organ function: a chameleon in modern biology?

All species, including humans, are cohabited by a myriad of microbial species, which massively influences body function in a diet‐, exercise‐ and age‐dependent manner. The microbiome composition differs between individuals, partly due to the polymorphic immune system, as well as the environment, making the microbe–host interplay unique in each one of us. Ageing is a gradual loss of function in part due to reduced repair mechanisms and accumulation of tissue damage through mechanisms largely unknown. Accumulating evidence suggests that our indigenous microbes, a known major regulator of human physiology, are also connected to regulate the ageing process through signalling pathways and metabolites though the biological mechanisms are unknown. At an ageing meeting in Singapore in 2018, investigators discussed the current understanding of microbe regulation and its impact on healthy ageing. This review summarizes the highlights from the meeting and conveys some of the new ideas that emerged around gut microbes and the biology of ageing. While highly speculative, an idea emerged in which gut microbes constantly respond and evolve to environmental cues, as part of an ageing process, thus serving as a second messenger to support and attenuate organ decline in a diet‐, gender‐ and age‐dependent manner.

What Pediatricians Should Know Before Studying Gut Microbiota

Billions of microorganisms, or “microbiota”, inhabit the gut and affect its homeostasis, influencing, and sometimes causing if altered, a multitude of diseases. The genomes of the microbes that form the gut ecosystem should be summed to the human genome to form the hologenome due to their influence on human physiology; hence the term “microbiome” is commonly used to refer to the genetic make-up and gene–gene interactions of microbes. This review attempts to provide insight into this recently discovered vital organ of the human body, which has yet to be fully explored. We herein discuss the rhythm and shaping of the microbiome at birth and during the first years leading up to adolescence. Furthermore, important issues to consider for conducting a reliable microbiome study including study design, inclusion/exclusion criteria, sample collection, storage, and variability of different sampling methods as well as the basic terminology of molecular approaches, data analysis, and clinical interpretation of results are addressed. This basic knowledge aims to provide the pediatricians with a key tool to avoid data dispersion and pitfalls during child microbiota study.

Genetic risk for autoimmunity is associated with distinct changes in the human gut microbiome

Susceptibility to many human autoimmune diseases is under strong genetic control by class II human leukocyte antigen (HLA) allele combinations. These genes remain by far the greatest risk factors in the development of type 1 diabetes and celiac disease. Despite this, little is known about HLA influences on the composition of the human gut microbiome, a potential source of environmental influence on disease. Here, using a general population cohort from the All Babies in Southeast Sweden study, we report that genetic risk for developing type 1 diabetes autoimmunity is associated with distinct changes in the gut microbiome. Both the core microbiome and beta diversity differ with HLA risk group and genotype. In addition, protective HLA haplotypes are associated with bacterial genera Intestinibacter and Romboutsia. Thus, general population cohorts are valuable in identifying potential environmental triggers or protective factors for autoimmune diseases that may otherwise be masked by strong genetic control.

Gut microbiome dysbiosis and increased intestinal permeability in children with islet autoimmunity and type 1 diabetes: A prospective cohort study

AIMS/HYPOTHESIS

To investigate the longitudinal relationship between the gut microbiome, circulating short chain fatty acids (SCFAs) and intestinal permeability in children with islet autoimmunity or type 1 diabetes and controls.

METHODS

We analyzed the gut bacterial microbiome, plasma SCFAs, small intestinal permeability and dietary intake in 47 children with islet autoimmunity or recent-onset type 1 diabetes and in 41 unrelated or sibling controls over a median (range) of 13 (2-34) months follow-up.

RESULTS

Children with multiple islet autoantibodies (≥2 IA) or type 1 diabetes had gut microbiome dysbiosis. Anti-inflammatory Prevotella and Butyricimonas genera were less abundant and these changes were not explained by differences in diet. Small intestinal permeability measured by blood lactulose:rhamnose ratio was higher in type 1 diabetes. Children with ≥2 IA who progressed to type 1 diabetes (progressors), compared to those who did not progress, had higher intestinal permeability (mean [SE] difference +5.14 [2.0], 95% confidence interval [CI] 1.21, 9.07, P = .006), lower within-sample (alpha) microbial diversity (31.3 [11.2], 95% CI 9.3, 53.3, P = .005), and lower abundance of SCFA-producing bacteria. Alpha diversity (observed richness) correlated with plasma acetate levels in all groups combined (regression coefficient [SE] 0.57 [0.21], 95% CI 0.15, 0.99 P = .008).

CONCLUSIONS/INTERPRETATION

Children with ≥2 IA who progress to diabetes, like those with recent-onset diabetes, have gut microbiome dysbiosis associated with increased intestinal permeability. Interventions that expand gut microbial diversity, in particular SCFA-producing bacteria, may have a role to decrease progression to diabetes in children at-risk.

The gut microbiota in type 1 diabetes: friend or foe?

PURPOSE OF REVIEW

Evidence is mounting that disturbances in the gut microbiota play a role in the rising incidence of type 1 diabetes (T1D) and new technologies are expanding our ability to understand microbial function and host interactions. Longitudinal data from large cohorts of children at risk of T1D are nor solidifying our understanding of the function of the microbiota in this disease.

RECENT FINDINGS

Although taxonomic changes in the gut microbiota associated with T1D are relatively modest, a functional defect in production of short-chain fatty acids (SCFAs) remains as a unifying feature across multiple studies and populations. Dysbiosis of the microbiota in T1D has been linked to decreased gut barrier and exocrine pancreas function. We explore factors contributing to the disturbed microbiota in T1D such as infant diet, probiotic use and genetic risk linked to defective immune regulation. We also discuss the interplay between immunotherapy, the gut immune response and the microbiota.

SUMMARY

Functional alterations in the microbiota are linked to pathogenesis of T1D and these findings provide a rationale for future investigations aimed at establishing a healthy microbiota and promoting SCFA production and prevention of T1D.

Celiac disease: should we care about microbes?

The prevalence of celiac disease (CeD) has increased in the last decades, suggesting a role for environmental factors in addition to gluten. Several cohort studies have shown that different gastrointestinal infections increase CeD risk. However, the mechanisms by which microbes participate in CeD have remained elusive. Recently, with the use of animal models, both viral and bacterial opportunistic pathogens were shown to induce immune activation relevant for CeD. The hypothesis that viral and/or bacterial infections can contribute to immune activation and breakdown of tolerance toward gluten in genetically susceptible individuals is therefore reinforced. Here, we discuss the evidence regarding the role of microbes in promoting CeD and the specific pathways triggered by microbes that could participate in CeD pathogenesis. Understanding these pathways will allow us to develop optimal microbiota-modulating strategies to help prevent CeD.

Gut microbiota composition is associated with temperament traits in infants

BACKGROUND

One of the key behavioral phenotypes in infancy are different temperament traits, and certain early life temperament traits have been shown to precede later mental health problems. Differences in the gut microbiota composition (GMC) have been suggested to link with neurodevelopment. For example, toddler temperament traits have been found to associate with differences in GMC; however, studies in infants are lacking although infancy is a rapid period of neurodevelopment as well as GM development. Thus, we aimed to investigate association between infant GMC and temperament.

METHODS

The study population (n = 301, 53% boys) was drawn from the FinnBrain Birth Cohort Study. Stool samples were collected from the 2.5-month-old infants and sequenced with 16S Illumina MiSeq platform. GMC taxonomic composition (at Genus and OTU level), observed sample clusters, diversity and richness were investigated in relation to the maternal reports of Infant Behavior Questionnaire -Revised (IBQ-R) at the age of 6 months.

RESULTS

Three sample clusters (Bifidobacterium/Enterobacteriaceae, Bacteroides, V. Dispar) based on GMC were identified, of which Bifidobacterium/Enterobacteriaceae-cluster presented with higher scores on the IBQ-R main dimension regulation and its subscale duration of orienting compared to Bacteroides-cluster. The clusters associated with temperament in a sex-dependent manner. The IBQ-R main dimension surgency (positive emotionality) was associated positively both with genus Bifidobacterium and Streptococcus. Alpha diversity had a negative association with negative emotionality and fear reactivity.

CONCLUSION

This is the first study demonstrating associations, but not causal connections, between GMC and temperament in young infants in a prospective design.

To start or not: Factors to consider when implementing routine probiotic use in the NICU

Supplementation of probiotics to very low birth weight (VLBW) infants has been extensively studied, with multiple meta-analyses reporting probiotics decrease the risk of necrotizing enterocolitis (NEC) and death. Despite availability of this evidence, the decision to initiate routine probiotic supplementation to preterm infants continues to be a complex one. There are uncertainties regarding the use of probiotics, including selecting the appropriate product, dose and target population. Additionally, availability of specific probiotic products and regulatory oversight varies by country, raising concerns regarding the safety and efficacy of specific probiotic products. In this review, we summarize the latest evidence on probiotic use in preterm infants and discuss considerations that may help guide clinicians who are considering routine probiotic supplementation.

Current understanding of the role of gut dysbiosis in type 1 diabetes

Type 1 diabetes (T1D) is a chronic autoimmune disorder that results from destruction of the insulin-producing pancreatic β-cells. The disease mainly affects juveniles. Changes in the composition of the gut microbiota (dysbiosis) and changes in the properties of the gut barrier have been documented in T1D subjects. Because these factors affect immune system functions, they are likely to play a role in disease pathogenesis. However, their exact role is currently not fully understood and is under intensive investigation. In this article we discuss recent advancements depicting the role of intestinal dysbiosis on immunity and autoimmunity in T1D. We also discuss therapies aimed at maintaining a healthy gut barrier as prevention strategies for T1D.

Timescales of gut microbiome dynamics

Vast communities of microorganisms inhabit the gastrointestinal tracts of humans and other animals. Understanding their initial development, fluctuations in composition, stability over long times, and responses to transient perturbations - in other words their dynamics - is important both for gaining basic insights into these ecosystems and for rationally manipulating them for therapeutic ends. Gut microbiome dynamics, however, remain poorly understood. We review here studies of gut microbiome dynamics in the presence and absence of external perturbations, noting especially the long timescales associated with overall stability and the short timescales associated with various underlying biological processes. Integrating these disparate timescales, we suggest, is an important goal for future work and is necessary for developing a predictive understanding of microbiome dynamics.

Past, Present, and Future Research on the Lung Microbiome in Inflammatory Airway Disease

COPD, asthma, and cystic fibrosis (CF) are obstructive lung diseases with distinct pathophysiologies and clinical phenotypes. In this paper, we highlight recent advances in our understanding of relationships between clinical phenotypes, host inflammatory response, and lung microbiota in these diseases. Although COPD, asthma, and CF largely have distinct lung microbiota and inflammatory profiles, certain commonalities exist. In all three of these lung diseases, and in healthy persons, anaerobic taxa that are typically associated with oral microbiota (eg, Prevotella species, Veillonella species) are present in the airways and associated with increased host inflammatory response. Similarly, across all three diseases, members of the Proteobacteria phylum are associated with more advanced disease. Finally, we highlight challenges in translating these findings into advances in clinical care, including continued knowledge gaps regarding the causal relationships between host inflammatory response, lung microbiota, medication effects, and clinical phenotypes.

Dysbiosis associated with acute helminth infections in herbivorous youngstock - observations and implications

A plethora of data points towards a role of the gastrointestinal (GI) microbiota of neonatal and young vertebrates in supporting the development and regulation of the host immune system. However, knowledge of the impact that infections by GI helminths exert on the developing microbiota of juvenile hosts is, thus far, limited. This study investigates, for the first time, the associations between acute infections by GI helminths and the faecal microbial and metabolic profiles of a cohort of equine youngstock, prior to and following treatment with parasiticides (ivermectin). We observed that high versus low parasite burdens (measured via parasite egg counts in faecal samples) were associated with specific compositional alterations of the developing microbiome; in particular, the faecal microbiota of animals with heavy worm infection burdens was characterised by lower microbial richness, and alterations to the relative abundances of bacterial taxa with immune-modulatory functions. Amino acids and glucose were increased in faecal samples from the same cohort, which indicated the likely occurrence of intestinal malabsorption. These data support the hypothesis that GI helminth infections in young livestock are associated with significant alterations to the GI microbiota, which may impact on both metabolism and development of acquired immunity. This knowledge will direct future studies aimed to identify the long-term impact of infection-induced alterations of the GI microbiota in young livestock.

Microbiota-derived acetate protects against respiratory syncytial virus infection through a GPR43-type 1 interferon response

Severe respiratory syncytial virus (RSV) infection is a major cause of morbidity and mortality in infants <2 years-old. Here we describe that high-fiber diet protects mice from RSV infection. This effect was dependent on intestinal microbiota and production of acetate. Oral administration of acetate mediated interferon-β (IFN-β) response by increasing expression of interferon-stimulated genes in the lung. These effects were associated with reduction of viral load and pulmonary inflammation in RSV-infected mice. Type 1 IFN signaling via the IFN-1 receptor (IFNAR) was essential for acetate antiviral activity in pulmonary epithelial cell lines and for the acetate protective effect in RSV-infected mice. Activation of Gpr43 in pulmonary epithelial cells reduced virus-induced cytotoxicity and promoted antiviral effects through IFN-β response. The effect of acetate on RSV infection was abolished in Gpr43^−/− mice. Our findings reveal antiviral effects of acetate involving IFN-β in lung epithelial cells and engagement of GPR43 and IFNAR.

Dietary fibers and SCFAs can exert a protective effect against respiratory syncytial virus (RSV). Here, the authors report that microbiota-derived acetate protects mice against RSV infection via GPR43- mediated type 1 interferon response induction in the lungs.

Patterned progression of gut microbiota associated with necrotizing enterocolitis and late onset sepsis in preterm infants: a prospective study in a Chinese neonatal intensive care unit

Necrotizing enterocolitis (NEC) and late-onset sepsis (LOS) are two common premature birth complications with high morbidity and mortality. Recent studies in Europe and America have linked gut microbiota dysbiosis to their etiology. However, similar studies in Asian populations remain scant. In this pilot study, we profiled gut microbiota of 24 Chinese preterm infants from birth till death or discharge from NICU. Four of them developed NEC and three developed LOS. Unexpectedly, we detected highly-diversified microbiota with similar compositions in all patients shortly after birth. However, as patients aged, the microbial diversities in case groups differed significantly from that of the control group. These differences emerged after the third day of life and persisted throughout the course of both NEC and LOS. Using a Zero-Inflated Beta Regression Model with Random Effects (ZIBR), we detected higher Bacillus (p = 0.032) and Solibacillus (p = 0.047) before the onset of NEC and LOS. During NEC progression, Enterococcus, Streptococcus and Peptoclostridium were the dominant genera while during LOS progression; Klebsiella was the only dominant genus that was also detected by the diagnostic hemoculture. These results warrant further studies to identify causative microbial patterns and underlying mechanisms.

Human Milk Oligosaccharide Composition Is Associated With Excessive Weight Gain During Exclusive Breastfeeding-An Explorative Study

Background: Some infants experience excessive weight gain during exclusive breastfeeding. The cause is unknown, but variation in human milk composition might play a role. Several human milk koligosaccharides (HMOs) have been associated with growth velocity in breastfed infants, and it has been suggested that the mechanism could be through an effect on infant gut microbiota composition. Objective: The purpose of this exploratory study was to evaluate if HMO composition was different in milk fed to infants with excessive weight gain compared to infants with normal weight gain. Furthermore, we aimed to examine if HMO composition was associated with growth velocity and change in body composition and if there were maternal determinants of HMO composition. Materials and Methods: We recruited 13 high weight-gain (HW) and 17 normal weight-gain (NW) breastfed infants, collected human milk and anthropometry data at 5 and 9 months, and analyzed HMO composition by high performance liquid chromatography. Results: In the HW group eight out of 11 infants received milk from secretor mothers and in the NW group 15 out of 17. Comparing milk from Secretor mothers only, four HMO's were significantly different between the HW and NW group at 5 months and two remained significant at 9 months. Total HMO concentrations as well as total HMO-bound fucose at 5 months were positively associated with both fat mass index (FMI) and weight velocity from 0 to 5 months (all p < 0.025). 2'-fucosyllactose (2'-FL) was positively associated with weight velocity from 0 to 5 months and FMI at 5 months. In contrast, lacto-N-neotetraose was lower in the HW group (p = 0.012) and negatively associated with height-for-age Z-scores (p = 0.008), weight velocity from 0 to 5 months (p = 0.009) and FMI (p = 0.033). Maternal BMI at 5 months was negatively associated with 6'-sialyllactose and sialyl-lacto-N-tetraose (LSTb) and positively with 2'-FL, total HMO and total HMO-bound fucose (all p ≤ 0.03). Conclusion: In a small cohort, we found significantly different HMO concentrations in milk to exclusively breastfed infants with excessive weight gain, suggesting that some HMOs, including 2'-FL, which is the most abundant HMO and currently added to some infant formula, could be part of the cause for the excessive weight gain.

Combining integrated systems-biology approaches with intervention-based experimental design provides a higher-resolution path forward for microbiome research

The Hooks et al. review of microbiota-gut-brain (MGB) literature provides a constructive criticism of the general approaches encompassing MGB research. This commentary extends their review by: (a) highlighting capabilities of advanced systems-biology “-omics” techniques for microbiome research and (b) recommending that combining these high-resolution techniques with intervention-based experimental design may be the path forward for future MGB research.

Type 1 Diabetes: an Association Between Autoimmunity, the Dynamics of Gut Amyloid-producing E. coli and Their Phages

The etiopathogenesis of type 1 diabetes (T1D), a common autoimmune disorder, is not completely understood. Recent studies suggested the gut microbiome plays a role in T1D. We have used public longitudinal microbiome data from T1D patients to analyze amyloid-producing bacterial composition and found a significant association between initially high amyloid-producing Escherichia coli abundance, subsequent E. coli depletion prior to seroconversion, and T1D development. In children who presented seroconversion or developed T1D, we observed an increase in the E. coli phage/E. coli ratio prior to E. coli depletion, suggesting that the decrease in E. coli was due to prophage activation. Evaluation of the role of phages in amyloid release from E. coli biofilms in vitro suggested an indirect role of the bacterial phages in the modulation of host immunity. This study for the first time suggests that amyloid-producing E. coli, their phages, and bacteria-derived amyloid might be involved in pro-diabetic pathway activation in children at risk for T1D.

Reduced genetic potential for butyrate fermentation in the gut microbiome of infants who develop allergic sensitization

BACKGROUND

Allergic disease is the most frequent chronic health issue in children and has been linked to early-life gut microbiome dysbiosis. Many lines of evidence suggest that microbially derived short-chain fatty acids, and particularly butyrate, can promote immune tolerance.

OBJECTIVE

We sought to determine whether bacterial butyrate production in the gut during early infancy is protective against the development of atopic disease in children.

METHODS

We used shotgun metagenomic analysis to determine whether dysbiosis in butyrate fermentation could be identified in human infants, before their developing allergic disease.

RESULTS

We found that the microbiome of infants who went on to develop allergic sensitization later in childhood lacked genes encoding key enzymes for carbohydrate breakdown and butyrate production.

CONCLUSIONS

Our findings support the importance of microbial carbohydrate metabolism during early infancy in protecting against the development of allergies.

Characterizing a Murine Model for Astrovirus Using Viral Isolates from Persistently Infected Immunocompromised Mice

Human astroviruses are single-stranded RNA enteric viruses that cause a spectrum of disease ranging from asymptomatic infection to systemic extragastrointestinal spread; however, they are among the least-characterized enteric viruses, and there is a lack of a well-characterized small animal model. Finding that immunocompromised mice were resistant to human astrovirus infection via multiple routes of inoculation, our studies aimed to determine whether murine astrovirus (MuAstV) could be used to model human astrovirus disease. We experimentally infected wild-type mice with MuAstV isolated from immunocompromised mice and found that the virus was detected throughout the gastrointestinal tract, including the stomach, but was not associated with diarrhea. The virus was also detected in the lung. Although virus levels were higher in recently weaned mice, the levels were similar in male and female adult mice. Using two distinct viruses isolated from different immunocompromised mouse strains, we observed virus strain-specific differences in the duration of infection (3 versus 10 weeks) in wild-type mice, indicating that the within-host immune pressure from donor mice shaped the virus kinetics in immunocompetent recipient hosts. Both virus strains elicited minimal pathology and a lack of sustained immunity. In summary, MuAstV represents a useful model for studying asymptomatic human infection and gaining insight into the astrovirus pathogenesis and immunity.IMPORTANCE Astroviruses are widespread in both birds and mammals; however, little is known about the pathogenesis and the immune response to the virus due to the lack of a well-characterized small-animal model. Here we describe two distinct strains of murine astrovirus that cause infections in immunocompetent mice that mirror aspects of asymptomatic human infections, including minimal pathology and short-lived immunity. However, we noted that the duration of infection differed greatly between the strains, highlighting an important facet of these viruses that was not previously appreciated. The ubiquitous nature and diversity of murine astroviruses coupled with the continuous likelihood of reinfection raise the possibility of viral interference with other mouse models of disease.

Microbiome and type 1 diabetes

The steep increase in the incidence of type 1 diabetes (T1D), in the Western world after World War II, cannot be explained solely by genetic factors but implies that this rise must be due to crucial interactions between predisposing genes and environmental changes. Three parallel phenomena in early childhood – the dynamic development of the immune system, maturation of the gut microbiome, and the appearance of the first T1D-associated autoantibodies – raise the question whether these phenomena might reflect causative relationships. Plenty of novel data on the role of the microbiome in the development of T1D has been published over recent years and this review summarizes recent findings regarding the associations between islet autoimmunity, T1D, and the intestinal microbiota.

Cohort profile: Finnish Health and Early Life Microbiota (HELMi) longitudinal birth cohort

PURPOSE

HELMi (Health and Early Life Microbiota) is a longitudinal, prospective general population birth cohort, set up to identify environmental, lifestyle and genetic factors that modify the intestinal microbiota development in the first years of life and their relation to child health and well-being.

PARTICIPANTS

The HELMi cohort consists of 1055 healthy term infants born in 2016-2018 mainly at the capital region of Finland and their parents. The intestinal microbiota development of the infants is characterised based on nine, strategically selected, faecal samples and connected to extensive online questionnaire-collected metadata at weekly to monthly intervals focusing on the diet, other exposures and family's lifestyle as well as the health and growth of the child. Motor and cognitive developmental screening takes place at 18 months. Infant's DNA sample, mother's breast milk sample and both parent's spot faecal samples have been collected.

FINDINGS TO DATE

The mean age of the mothers was 32.8 (SD 4.1) and fathers/coparents 34.8 (5.3) years at the time of enrolment. Seventeen percentage (n=180) of the infants were born by caesarean section. Just under half (49%) were firstborns; 50.7% were males. At 3 months of age, 86% of the babies were exclusively breastfed and 2% exclusively formula-fed.

FUTURE PLANS

The current follow-up from pregnancy to first 24 months will be completed in March 2020, totalling to over 10 000 biological samples and over 50 000 questionnaire entries. The results are expected to identify environmental and host factors that affect early gut microbiota development and health, and hence give indications of how to prevent or reverse microbiota perturbations in infancy. This prospective cohort will be followed up further to identify how the early microbiota relates to later health outcomes, especially weight gain, infections and allergic and other chronic diseases.

TRIAL REGISTRATION NUMBER

NCT03996304; Pre-results.

Dynamic signatures of gut microbiota and influences of delivery and feeding modes during the first 6 months of life

The gut microbiota of infants changes over time and is affected by various factors during early life. However, rarely have studies explored the gut microbiota development and affecting factors in the Chinese infant population. We enrolled 102 infants and collected stool samples from them at birth, 42 days, 3 mo, and 6 mo after delivery to characterize the microbiota signatures and the effects of different factors that modulate the gut microbiota diversity, composition, and function over time. DNA extracted from the bacteria in the stool samples was subjected to high-throughput sequencing and bioinformatics analysis. Microbial richness and diversity increased significantly during the first 6 mo of life. Beneficial microbes such as Bifidobacterium, Lactobacillus, and Blautia were found to be increased in the infant's gut at 6 mo, while pathological bacteria such as Escherichia-Shigella, Enterobacter, Staphylococcus, and Klebsiella decreased over time. The changes in the infant delivery mode and infant-feeding mode only produced changes in the microbial composition, whereas changes in bacterial richness, diversity and effects sizes on the microbial architecture were all time dependent. A comparison of infant delivery modes conveyed a decrease in abundance of Bacteroidetes over time in the gut of infants born via C-section, while the Bifidobacterium was the most dominant genus in the vaginal delivery group. The gut microbiota of infants changed extensively during the first 6 mo of life. Delivery and feeding modes were strong factors that significantly affected microbial architecture and functions.

Gut microbiome analysis by post: Evaluation of the optimal method to collect stool samples from infants within a national cohort study

Background

Understanding the role of the gut microbiome is pivotal for the future development of therapies for the prevention and management of autoimmune conditions such as type 1 diabetes when sampling during early life may be particularly important. The current standard methods for collecting gut microbiome samples for research is to extract fresh samples or freeze samples immediately after collection. This is often impractical however for population-based studies. The aim of this study was to determine the optimal method for the stabilization of stool bacterial DNA obtained from nappies and transported by post in ambient conditions to the research centre for a national birth cohort study.

Methods

Four methods to collect samples were compared to immediate freezing of samples: 1) collecting faeces onto a swab which was immediately frozen, 2) using a commercially available kit with stabilisation solution (OMNIgene•GUT kit) at ambient temperature, 3) collecting onto a swab and 4) collecting into a sterile plain tube. Samples 3) and 4) were returned to the laboratory by post at ambient temperatures. A Bland Altman analysis was used to assess the agreement between the different methods and the frozen standard.

Results

Stool samples were collected by parents. For samples transported in ambient conditions, the limits of agreement showed that the OMNIgene•GUT kit had the narrowest 95% limits of agreement with the frozen standard as measured by the number of operational taxonomic units and the Shannon diversity index.

Conclusions

All methods assessed for preserving samples collected from nappies at a distance and delivered by post for gut microbiome analysis showed variation / disagreement from the frozen standard. Overall, the OMNIgene•GUT kit preserved the samples with minimal changes compared to other methods and was practical for parents to use.

Factors influencing the gut microbiome in children: from infancy to childhood

The human microbiota plays a crucial role in educating the immune system and influencing host health right since birth. Various maternal factors along with the vertical microbial transfer from the mother, as well as the horizontal environmental transmission and internal factors relating to the infant, play a crucial role in modulating the gut microbiota. The early life microflora is highly unstable and undergoes dynamic changes during the first few years, converging towards a more stabilized adult microbiota by co-evolving with the host by the age of 3-4 years. Microbiota studies have underlined the role of dysbiosis in developing several metabolic disorders like obesity, diabetes and immune-related disorders like asthma, to name a few. Thus, understanding early life microbial composition and various factors affecting the microbial community will provide a platform for developing strategies/techniques to maintain host health by restoring gut microbial flora. This review focuses on the factors that affect the microbial composition of the foetus in utero, during birth, infancy through childhood.

Comparing Alternative Breast Milk Feeding Questions to U.S. Breastfeeding Surveillance Questions

Background: Most mothers in the United States express their milk, which is then bottle fed to their infants. The National Immunization Survey (NIS), used to report national breastfeeding prevalence, asks about infant breast milk consumption, regardless of whether it is consumed at the mother's breast or from a bottle. The NIS data are often erroneously interpreted, however, to mean prevalence of at-the-breast feeding. We hypothesized that over half of infants classified as breastfed at 3, 6, and 12 months by the NIS questions would also be consuming expressed breast milk. Materials and Methods: A convenience sample of 456 mothers of infants 19-35 months of age recruited through ResearchMatch.org completed an online infant-feeding questionnaire. The questionnaire included both the NIS questions and more-detailed questions about feeding mode, distinguishing between at-the-breast and bottle. Results: Based on responses of our sample to the NIS questions, it could be interpreted that 74%, 64%, and 39% of mother-infant dyads were at-the-breast feeding at 3, 6, and 12 months, respectively. However, at each time point, most infants consumed at least some breast milk from a bottle. As infants got older, the proportion of breast milk consumed from a bottle increased. Conclusions: In this U.S. sample, the predominant breast milk feeding style involves both at-the-breast and expressed breast milk feeding. Future research and national surveillance should consider including separate measures of maternal breast milk expression and infant consumption of expressed breast milk to enable meaningful exploration of maternal and infant outcomes associated with these asynchronous behaviors.

Whole genome metagenomic analysis of the gut microbiome of differently fed infants identifies differences in microbial composition and functional genes, including an absent CRISPR/Cas9 gene in the formula-fed cohort

BACKGROUND

Advancements in sequencing capabilities have enhanced the study of the human microbiome. There are limited studies focused on the gastro-intestinal (gut) microbiome of infants, particularly the impact of diet between breast-fed (BF) versus formula-fed (FF). It is unclear what effect, if any, early feeding has on short-term or long-term composition and function of the gut microbiome.

RESULTS

Using a shotgun metagenomics approach, differences in the gut microbiome between BF (n = 10) and FF (n = 5) infants were detected. A Jaccard distance principle coordinate analysis was able to cluster BF versus FF infants based on the presence or absence of species identified in their gut microbiome. Thirty-two genera were identified as statistically different in the gut microbiome sequenced between BF and FF infants. Furthermore, the computational workflow identified 371 bacterial genes that were statistically different between the BF and FF cohorts in abundance. Only seven genes were lower in abundance (or absent) in the FF cohort compared to the BF cohort, including CRISPR/Cas9; whereas, the remaining candidates, including autotransporter adhesins, were higher in abundance in the FF cohort compared to BF cohort.

CONCLUSIONS

These studies demonstrated that FF infants have, at an early age, a significantly different gut microbiome with potential implications for function of the fecal microbiota. Interactions between the fecal microbiota and host hinted at here have been linked to numerous diseases. Determining whether these non-abundant or more abundant genes have biological consequence related to infant feeding may aid in understanding the adult gut microbiome, and the pathogenesis of obesity.

Cutibacterium avidum is phylogenetically diverse with a subpopulation being adapted to the infant gut

The infant gut harbors a diverse microbial community consisting of several taxa whose persistence depends on adaptation to the ecosystem. In healthy breast-fed infants, the gut microbiota is dominated by Bifidobacterium spp.. Cutibacterium avidum is among the initial colonizers, however, the phylogenetic relationship of infant fecal isolates to isolates from other body sites, and C. avidum carbon utilization related to the infant gut ecosystem have been little investigated. In this study, we investigated the phylogenetic and phenotypic diversity of 28 C. avidum strains, including 16 strains isolated from feces of healthy infants. We investigated the in vitro capacity of C. avidum infant isolates to degrade and consume carbon sources present in the infant gut, and metabolic interactions of C. avidum with infant associated Bifidobacterium longum subsp. infantis and Bifidobacterium bifidum. Isolates of C. avidum showed genetic heterogeneity. C. avidum consumed d- and l-lactate, glycerol, glucose, galactose, N-acetyl-d-glucosamine and maltodextrins. Alpha-galactosidase- and β-glucuronidase activity were a trait of a group of non-hemolytic strains, which were mostly isolated from infant feces. Beta-glucuronidase activity correlated with the ability to ferment glucuronic acid. Co-cultivation with B. infantis and B. bifidum enhanced C. avidum growth and production of propionate, confirming metabolic cross-feeding. This study highlights the phylogenetic and functional diversity of C. avidum, their role as secondary glycan degraders and propionate producers, and suggests adaptation of a subpopulation to the infant gut.

Breast milk alkylglycerols sustain beige adipocytes through adipose tissue macrophages

Prevalence of obesity among infants and children below 5 years of age is rising dramatically, and early childhood obesity is a forerunner of obesity and obesity-associated diseases in adulthood. Childhood obesity is hence one of the most serious public health challenges today. Here, we have identified a mother-to-child lipid signaling that protects from obesity. We have found that breast milk-specific lipid species, so-called alkylglycerol-type (AKG-type) ether lipids, which are absent from infant formula and adult-type diets, maintain beige adipose tissue (BeAT) in the infant and impede the transformation of BeAT into lipid-storing white adipose tissue (WAT). Breast milk AKGs are metabolized by adipose tissue macrophages (ATMs) to platelet-activating factor (PAF), which ultimately activates IL-6/STAT3 signaling in adipocytes and triggers BeAT development in the infant. Accordingly, lack of AKG intake in infancy leads to a premature loss of BeAT and increases fat accumulation. AKG signaling is specific for infants and is inactivated in adulthood. However, in obese adipose tissue, ATMs regain their ability to metabolize AKGs, which reduces obesity. In summary, AKGs are specific lipid signals of breast milk that are essential for healthy adipose tissue development.

Biologically inspired approaches to enhance human organoid complexity

Organoids are complex three-dimensional in vitro organ-like model systems. Human organoids, which are derived from human pluripotent stem cells or primary human donor tissue, have been used to address fundamental questions about human development, stem cell biology and organ regeneration. Focus has now shifted towards implementation of organoids for biological discovery and advancing existing systems to more faithfully recapitulate the native organ. This work has highlighted significant unknowns in human biology and has invigorated new exploration into the cellular makeup of human organs during development and in the adult - work that is crucial for providing appropriate benchmarks for organoid systems. In this Review, we discuss efforts to characterize human organ cellular complexity and attempts to make organoid models more realistic through co-culture, transplantation and bioengineering approaches.