Composition of the early intestinal microbiota: knowledge, knowledge gaps and the use of high-throughput sequencing to address these gaps

Standard diet and animal source influence hippocampal spatial reference learning and memory in congenic C57BL/6J mice

Background

Assessing learning and memory has become critical to evaluate brain function in health, aging or neurological disease. The hippocampus is crucially involved in these processes as illustrated by H.M.'s remarkable case and by the well-established early symptoms of Alzheimer's disease. Numerous studies have reported the impact of gut microbiota on hippocampal structure and function using pro-, pre- and antibiotics, diet manipulations, germ-free conditions or fecal transfer. However, most diet manipulations have relied on Western diet paradigms (high fat, high energy, high carbohydrates). Here, we compared the impact of two standard diets, 5K52 and 2918 (6% fat, 18% protein, 3.1kcal/g), and how they influenced hippocampal learning and memory in adult 6-month-old congenic C57BL/6J mice from two sources.

Results

Using a hippocampal-dependent task, we found that 5K52-fed mice performed consistently better than 2918-fed animals in the Barnes circular maze. These behavioral differences were accompanied with marked changes in microbiota, which correlated with spatial memory retention performance. We next tested whether 2918-induced alterations in behavior and microbiome could be rescued by 5K52 diet for 3 months. Changing the 2918 diet to 5K52 diet mid-life improved spatial learning and memory in mice. Shotgun sequencing and principal component analyses revealed significant differences at both phylum and species levels. Multivariate analyses identified Akkermansia muciniphila or Bacteroidales bacterium M11 and Faecalibaculum rodentium as the strongest correlates to spatial memory retention in mice depending on the animal source. In both settings, the observed behavioral differences only affected hippocampal-dependent performance as mice fed with either diet did similarly well on the non-spatial variant of the Y-maze.

Conclusions

In summary, these findings demonstrate the diverging effects of seemingly equivalent standard diets on hippocampal memory. Based on these results, we strongly recommend the mandatory inclusion of the diet and source of animals used in rodent behavioral studies.

Linking growth performance and carcass traits with enterotypes in Muscovy ducks

OBJECTIVE

Enterotypes (ETs) are the clustering of gut microbial community structures, which could serve as indicators of growth performance and carcass traits. However, ETs have been sparsely investigated in waterfowl. The objective of this study was to identify the ileal ETs and explore the correlation of the ETs with growth performance and carcass traits in Muscovy ducks.

METHODS

A total of 200 Muscovy ducks were randomly selected from a population of 5,000 ducks at 70-day old, weighed and slaughtered. The growth performance and carcass traits, including body weight, dressed weight and evidenced weight, dressed percentage, percentage of apparent yield, breast muscle weight, leg muscle weight, percentage of leg muscle and percentage of breast muscle, were determined. The contents of ileum were collected for the isolation of DNA and 16S rRNA gene sequencing. The ETs were identified based on the 16S rRNA gene sequencing data and the correlation of the ETs with growth performance and carcass traits was performed by Spearman correlation analysis.

RESULTS

Three ETs (ET1, ET2, and ET3) were observed in the ileal microbiota of Muscovy ducks with significant differences in number of features and α-diversity among these ETs (p<0.05). Streptococcus, Candida Arthritis, and Bacteroidetes were the presentative genus in ET1 to ET3, respectively. Correlation analysis revealed that Lactococcus and Bradyrhizobium were significantly correlated with percentage of eviscerated yield and leg muscle weight (p<0.05) while ETs were found to have a close association with percentage of eviscerated yield, leg muscle weight, and percentage of leg muscle in Muscovy ducks. However, the growth performance of ducks with different ETs did not show significant difference (p>0.05). Lactococcus were found to be significantly correlated with leg muscle weight, dressed weight, and percentage of eviscerated yield.

CONCLUSION

Our findings revealed a substantial variation in carcass traits associated with ETs in Muscovy ducks. It is implied that ETs might have the potential to serve as a valuable biomarker for assessing duck carcass traits. It would provide novel insights into the interaction of gut microbiota with growth performance and carcass traits of ducks.

Dietary Patterns, Gut Microbiota and Sports Performance in Athletes: A Narrative Review

The intestinal tract of humans harbors a dynamic and complex bacterial community known as the gut microbiota, which plays a crucial role in regulating functions such as metabolism and immunity in the human body. Numerous studies conducted in recent decades have also highlighted the significant potential of the gut microbiota in promoting human health. It is widely recognized that training and nutrition strategies are pivotal factors that allow athletes to achieve optimal performance. Consequently, there has been an increasing focus on whether training and dietary patterns influence sports performance through their impact on the gut microbiota. In this review, we aim to present the concept and primary functions of the gut microbiota, explore the relationship between exercise and the gut microbiota, and specifically examine the popular dietary patterns associated with athletes' sports performance while considering their interaction with the gut microbiota. Finally, we discuss the potential mechanisms by which dietary patterns affect sports performance from a nutritional perspective, aiming to elucidate the intricate interplay among dietary patterns, the gut microbiota, and sports performance. We have found that the precise application of specific dietary patterns (ketogenic diet, plant-based diet, high-protein diet, Mediterranean diet, and high intake of carbohydrate) can improve vascular function and reduce the risk of illness in health promotion, etc., as well as promoting recovery and controlling weight with regard to improving sports performance, etc. In conclusion, although it can be inferred that certain aspects of an athlete's ability may benefit from specific dietary patterns mediated by the gut microbiota to some extent, further high-quality clinical studies are warranted to substantiate these claims and elucidate the underlying mechanisms.

Associations of Infant Feeding, Sleep, and Weight Gain with the Toddler Gut Microbiome

This study examines how feeding, sleep, and growth during infancy impact the gut microbiome (GM) in toddlers. The research was conducted on toddlers (n = 36), born to Latina women of low-income with obesity. Their mothers completed retrospective feeding and sleeping questionnaires at 1, 6, and 12 months; at 36 months, fecal samples were collected. Sequencing of the 16S rRNA gene (V4 region) revealed that breastfeeding for at least 1 month and the introduction of solids before 6 months differentiated the GM in toddlerhood (Bray-Curtis, pseudo-F = 1.805, p = 0.018, and pseudo-F = 1.651, p = 0.044, respectively). Sleep had an effect across time; at 1 and 6 months of age, a lower proportion of nighttime sleep (relative to 24 h total sleep) was associated with a richer GM at three years of age (Shannon H = 4.395, p = 0.036 and OTU H = 5.559, p = 0.018, respectively). Toddlers experiencing rapid weight gain from birth to 6 months had lower phylogenetic diversity (Faith PD H = 3.633, p = 0.057). These findings suggest that early life nutrition, sleeping patterns, and growth rate in infancy may influence the GM composition. Further verification of these results with objective sleep data and a larger sample is needed.

Postweaning intermittent sleep deprivation enhances defensive attack in adult female mice via the microbiota-gut-brain axis

Sleep is one of the most important physiological activities in life and promotes the growth and development of an individual. In modern society, sleep deprivation (SD), especially among adolescents, has become a common phenomenon. However, long-term SD severely affected adolescents' neurodevelopment leading to abnormal behavioral phenotypes. Clinical studies indicated that sleep problems caused increased aggressive behavior in adolescents. Aggressive behavior was subordinate to social behaviors, in which defensive attack was often the last line for survival. Meanwhile, increasing studies shown that gut microbiota regulated social behaviors by affecting specific brain regions via the gut-brain axis. However, whether postweaning intermittent SD is related to defensive attack in adulthood, and if so, whether it is mediated by the microbiota-gut-brain axis are still elusive. Combined with microbial sequencing and hippocampal metabolomics, the present study mainly investigated the long-term effects of postweaning intermittent SD on defensive attack in adult mice. Our study demonstrated that postweaning intermittent SD enhanced defensive attack and impaired long-term memory formation in adult female mice. Moreover, microbial sequencing and LC-MS analysis showed that postweaning intermittent SD altered the gut microbial composition and the hippocampal metabolic profile in female mice, respectively. Our attention has been drawn to the neuroactive ligand-receptor interaction pathway and related metabolites. In conclusion, our findings provide a new perspective on the relationship of early-life SD and defensive attack in adulthood, and also highlight the importance of sleep in early-life, especially in females.

Rural Versus Urban Mothers' Microbiome Difference and Its Effect on Neonates: A Systematic Review

The growth and development of microorganisms are stimulated by external stimuli. Urbanization has changed the macroenvironment and individual microenvironmental factors such as smoking, alcohol, and diet, which can alter the microbiota and influence disease in the mother and child. However, the microbiome difference between rural and urban mothers and its effect on neonates have received little attention, as per sources; we have not found any systematic review. This review determined the microbiome difference between rural and urban mothers and its effect on neonates. Five studies selected based on inclusion/exclusion criteria were retrieved from PubMed, Scopus, and Embase databases, and evidence-based comparisons were made to establish the microbiome difference in rural and urban mothers and its effect on neonates. The study findings indicate that microbiome development in newborns is hindered by urbanization. Infants born to urban mothers have reduced microbial diversity, thereby having decreased protective immunity.

A systematic review and meta-analysis of the effects of long-term antibiotic use on cognitive outcomes

Antibiotics are indispensable to infection management. However, use of antibiotics can cause gut microbiota dysbiosis, which has been linked to cognitive impairment by disrupting communication between the gut microbiota and the brain. We conducted a systematic review and meta-analysis on the effects of long-term antibiotic use on cognitive outcomes. We have searched PubMed, Web of Science, Embase, Cochrane Library and Scopus for English publications before March 2023 following the PRISMA guidelines. Screening, data extraction, and quality assessment were performed in duplicate. 960 articles were screened and 16 studies which evaluated the effect of any antibiotic compared to no antibiotics or placebo were included. Case-reports, in vitro and animal studies were excluded. We found that antibiotic use was associated with worse cognitive outcomes with a pooled effect estimate of - 0.11 (95% CI - 0.15, - 0.07, Z = 5.45; P < 0.00001). Subgroup analyses performed on adult vs pediatric patients showed a similar association of antibiotic on cognition in both subgroups. Antibiotic treatment was not associated with worse cognition on subjects with existing cognitive impairment. On the other hand, antibiotic treatment on subjects with no prior cognitive impairment was associated with worse cognitive performance later in life. This calls for future well-designed and well-powered studies to investigate the impact of antibiotics on cognitive performance.

Adolescence, the Microbiota-Gut-Brain Axis, and the Emergence of Psychiatric Disorders

Second only to early life, adolescence is a period of dramatic change and growth. For the developing young adult, this occurs against a backdrop of distinct environmental challenges and stressors. A significant body of work has identified an important role for the microbiota-gut-brain (MGB) axis in the development and function of the brain. Given that the MGB axis is both highly plastic during the teenage years and vulnerable to environmental stressors, more attention needs to be drawn to its potential role in the emergence of psychiatric illnesses, many of which first manifest during adolescence. Here, we review the current literature surrounding the developing microbiome, enteric nervous system, vagus nerve, and brain during the adolescent period. We also examine preclinical and clinical research involving the MGB axis during this dynamic developmental window and argue that more research is needed to further understand the role of the MGB in the pathogenesis of brain disorders. Greater understanding of the adolescent MGB axis will open up the exciting potential for new microbial-based therapeutics for the treatment of these often-refractory psychiatric illnesses.

Preventing and Treating Colic: An Update

Infantile colic (IC) is c is a self-limiting functional gastrointestinal disorder (FGID) with a favorable natural history. Worldwide, IC has a significant impact on many newborns and their families. Although not an indication of an illness, its symptoms are wide and generic and may indicate a potentially serious underlying issue in a tiny percentage of newborns who may require a medical evaluation. The pathogenesis appears to be multifactorial implying a complex relationship between the infant and the environment. One of the most studied theories attributes a key role to the gut microbiota in the pathogenesis of IC. A variety of approaches have been suggested for the clinical management of IC, and several randomized controlled trials have been reported in the literature. Probiotics can change the host's microbiota and positively impact health. They may be able to restore balance and create a better intestinal microbiota landscape since there is mounting evidence that the gut microbial environment of colicky newborns differs from that of healthy infants. In this review, we revise the most commonly studied probiotics and mixtures to treat and prevent IC and the most recent recommendations.

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.

Circulating LPS from gut microbiota leverages stenosis-induced deep vein thrombosis in mice

OBJECTIVE AND DESIGN

An accumulating body of evidence has shown that gut microbiota is involved in regulating inflammation; however, it remains undetermined if and how gut microbiota plays an important role in modulating deep venous thrombosis (DVT), which is an inflammation-involved thrombotic event.

SUBJECTS

Mice under different treatments were used in this study.

METHODS AND TREATMENT

We induced stenosis DVT in mice by partially ligating the inferior vena cava. Mice were treated with antibiotics, prebiotics, probiotics, or inflammatory reagents to modulate inflammatory states, and their effects on the levels of circulating LPS and DVT were examined.

RESULTS

Antibiotic-treated mice or germ-free mice exhibited compromised DVT. Treatment of mice with either prebiotics or probiotics effectively suppressed DVT, which was accompanied with the downregulation of circulating LPS. Restoration of circulating LPS in these mice with a low dose of LPS was able to restore DVT. LPS-induced DVT was blocked by a TLR4 antagonist. By performing proteomic analysis, we identified TSP1 as one of the downstream effectors of circulating LPS in DVT.

CONCLUSION

These results suggest that gut microbiota may play a nonnegligible role in modulating DVT by leveraging the levels of LPS in circulation, thus shedding light on the development of gut microbiota-based strategies for preventing and treating DVT.

Disruption of the early-life microbiota alters Peyer's patch development and germinal center formation in gastrointestinal-associated lymphoid tissue

During postnatal development, both the maturing microbiome and the host immune system are susceptible to environmental perturbations such as antibiotic use. The impact of timing in which antibiotic exposure occurs was investigated by treating mice from days 5-9 with amoxicillin or azithromycin, two of the most commonly prescribed medications in children. Both early-life antibiotic regimens disrupted Peyer's patch development and immune cell abundance, with a sustained decrease in germinal center formation and diminished intestinal immunoglobulin A (IgA) production. These effects were less pronounced in adult mice. Through comparative analysis of microbial taxa, Bifidobacterium longum abundance was found to be associated with germinal center frequency. When re-introduced to antibiotic-exposed mice, B. longum partially rescued the immunological deficits. These findings suggest that early-life antibiotic use affects the development of intestinal IgA-producing B cell functions and that probiotic strains could be used to restore normal development after antibiotic exposure.

Santos I, Matijasevich A, Tovo-Rodrigues L. Sleep Duration in Adolescence and Its Prenatal, Perinatal, and Health Determinants in a Large Population-based Cohort Followed from Birth

Objective  To investigate sleep duration and its associated factors in adolescents aged 11 years from the 2004 Pelotas (Brazil) Birth Cohort Study. Methods  Sleep duration was assessed using a self-report sleep habits. Independent variables included perinatal, sociodemographic, behavioral, and health characteristics. The associations were estimated using multiple linear regression. Results  The mean sleep duration of 3,179 adolescents was 9.3 hour (SD =1.7 hour). Longer sleep duration was associated with lower socioeconomic status at birth (β: 0.37, 95% CI: 0.12; 0.61), lower mother's education level ( p  < 0.001), and being female (β: 0.19, 95% CI: 0.06; 0.33). Shorter sleep duration was associated with cesarean section delivery (β: -0.16, 95% CI: -0.31; -0.02); having classes in the morning shift (β: -1.38, 95% CI: -1.51; -1.26), and lower terciles of physical activity ( p  = 0.04). Conclusions  The mean sleep duration observed in this study was consistent with the international recommendations for this age range. Adolescents from lower income families, who are more active, study in shifts other than morning, girls, and those born through vaginal delivery presented higher sleep duration than their counterparts.

Early Administration of Vancomycin Inhibits Pulmonary Embolism by Remodeling Gut Microbiota

Pulmonary embolism (PE) is a common and potentially fatal condition in the emergency department, and early identification of modifiable risk factors for prevention and management is highly desirable. Although gut dysbiosis is associated with a high incidence of venous thromboembolism, the role and mechanisms of the gut microbiome in the pathogenesis of venous thromboembolism, especially PE, remain unexplored. Here, we attempted to elucidate the benefits of the gut microbiome in the pathogenesis of PE using multiple antibiotics and fecal microbiota transplantation (FMT) for early intervention in a classical mouse model of PE. The results showed that early administration of various antibiotics (except ampicillin) could inhibit pulmonary thrombosis to a certain extent and reduced mortality in young and old mice with PE. Among them, vancomycin has the best inhibitory effect on PE. With the help of gut microbiota sequencing analysis, we found that antibiotic treatment can reshape the gut microbiota; especially vancomycin can significantly improve the gut microbiota structure in PE mice. Furthermore, FMT could transfer vancomycin-modified gut microbes into mice and inhibit the pathogenesis of PE, possibly due to increased intestinal colonization by Parasutterella. These data elucidate the underlying molecular mechanism by which early administration of vancomycin can remodel the gut microbiota to suppress PE, providing new clues for clinical optimization and development of PE prevention strategies.

A critical review of the recent concept of artificial mechanical uterus design in relation to the maternal microbiome: An Update to past researches

The microbiome in the female reproductive tract plays an essential role in immune modulation and reproductive health. However, various microbes become established during pregnancy, the balance of which plays a crucial role in embryonic development and healthy births. The contribution of disturbances in the microbiome profile to embryo health is poorly understood. A better understanding of the relationship between reproductive outcomes and the vaginal microbiota is needed to optimize the chances of healthy births. In this regards, microbiome dysbiosis refers to conditions in which the pathways of communication and balance within the normal microbiome are imbalanced due to the intrusion of pathogenic microorganisms into the reproductive system. This review summarizes the current state of knowledge on the natural human microbiome, with a focus on the natural uterine microbiome, mother-to-child transmission, dysbiosis, and the pattern of microbial change in pregnancy and parturition, and reviews the effects of artificial uterus probiotics during pregnancy. These effects can be studied in the sterile environment of an artificial uterus, and microbes with potential probiotic activity can be studied as a possible therapeutic approach. The artificial uterus is a technological device or biobag used as an incubator, allowing extracorporeal pregnancy. Establishing beneficial microbial communities within the artificial womb using probiotic species could modulate the immune system of both the fetus and the mother. The artificial womb could be used to select the best strains of probiotic species to fight infection with specific pathogens. Questions about the interactions and stability of the most appropriate probiotics, as well as dosage and duration of treatment, need to be answered before probiotics can be a clinical treatment in human pregnancy.

Gut microbial shifts by synbiotic combination of Pediococcus acidilactici and lactulose in weaned piglets challenged with Shiga toxin-producing Escherichia coli

Development of alternatives to in-feed antibiotics in the swine industry have been the focused of many pig gut microbiota studies to improve animal health. In this study, we evaluated the effects of probiotic Pediococcus acidilactici (PRO), prebiotic lactulose (PRE), and their synbiotic combination (SYN) on gut microbiota using 16S rRNA gene sequencing in weaned piglets challenged with Shiga-toxin producing Escherichia coli (STEC). Our data showed that prebiotics, probiotics and synbiotics improved the intestinal health in weaned piglets. No significant differences were observed in species richness and species diversity in weaned piglets fed prebiotics, probiotics and their synbiotic combination. However, beta diversity analysis revealed distinct clustering of the microbiota of according to dietary treatment and by oral challenge of STEC. At the phylum level, Firmicutes to Bacteroidetes ratio was lower in the dietary treatment groups than the control group. Oral supplementation of prebiotics, probiotics and synbiotics enriched the abundance of Prevotella and Roseburia. Succinivibrio was elevated in PRO group; however, Phascolarctobacterium was depleted with STEC challenge regardless of dietary treatment. Overall, our data showed that administration of synbiotics in piglets improved intestinal health through gut microbiota modulation. Our data indicated that prebiotics, probiotics and their synbiotic combination could promote intestinal health through gut microbiota modulation in weaned piglets.

Sialic acid and food allergies: The link between nutrition and immunology

Food allergies (FA), a major public health problem recognized by the World Health Organization, affect an estimated 3%-10% of adults and 8% of children worldwide. However, effective treatments for FA are still lacking. Recent advances in glycoimmunology have demonstrated the great potential of sialic acids (SAs) in the treatment of FA. SAs are a group of nine-carbon α-ketoacids usually linked to glycoproteins and glycolipids as terminal glycans. They play an essential role in modulating immune responses and may be an effective target for FA intervention. As exogenous food components, sialylated polysaccharides have anti-FA effects. In contrast, as endogenous components, SAs on immunoglobulin E and immune cell surfaces contribute to the pathogenesis of FA. Given the lack of comprehensive information on the effects of SAs on FA, we reviewed the roles of endogenous and exogenous SAs in the pathogenesis and treatment of FA. In addition, we considered the structure-function relationship of SAs to provide a theoretical basis for the development of SA-based FA treatments.

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.

Intestinal Microbiota and Sleep Inversion

Various human lifestyle and environmental factors are known to influence sleep. The number of adults and children suffering from chronic sleep disorders has grown over the past decade. Lack of sleep and impaired circadian rhythms have been proven to be associated with adverse metabolic health effects. Often, such disorders are associated with gastrointestinal tract diseases, and accompanied by dysbiosis. Significant number of studies have been conducted on animal models in recent years. They have shown the correlation between the gut microbiota and brain functions. According to these results scientists have clearly demonstrated the role of gut microbiota in regulating brain function, sleep, and behavior. The number of studies with volunteers is currently limited. The bacteria forming gut microbiota have significant impact on human health by synthesizing and secreting biologically active substances such as vitamins, essential amino acids, lipids, and others. Moreover, they have an indirect effect by modulating metabolic processes and the immune system. Changes in gut microbiota diversity occur due to the lack of sleep and shifting circadian rhythms, and it can lead to changes in the structure and function of microorganisms living in the gut. This can lead to changes in the composition and number of metabolites synthesized by these microorganisms (such as short-chain fatty acids and secondary bile acids) which contributes to the development of chronic inflammation, increased body weight and endocrine changes. This article provides the literature review on issues of interaction between gut microbiota and processes occurring during sleep.

Diet-microbiome-gut-brain nexus in acute and chronic brain injury

In recent years, appreciation for the gut microbiome and its relationship to human health has emerged as a facilitator of maintaining healthy physiology and a contributor to numerous human diseases. The contribution of the microbiome in modulating the gut-brain axis has gained significant attention in recent years, extensively studied in chronic brain injuries such as Epilepsy and Alzheimer’s Disease. Furthermore, there is growing evidence that gut microbiome also contributes to acute brain injuries like stroke(s) and traumatic brain injury. Microbiome-gut-brain communications are bidirectional and involve metabolite production and modulation of immune and neuronal functions. The microbiome plays two distinct roles: it beneficially modulates immune system and neuronal functions; however, abnormalities in the host’s microbiome also exacerbates neuronal damage or delays the recovery from acute injuries. After brain injury, several inflammatory changes, such as the necrosis and apoptosis of neuronal tissue, propagates downward inflammatory signals to disrupt the microbiome homeostasis; however, microbiome dysbiosis impacts the upward signaling to the brain and interferes with recovery in neuronal functions and brain health. Diet is a superlative modulator of microbiome and is known to impact the gut-brain axis, including its influence on acute and neuronal injuries. In this review, we discussed the differential microbiome changes in both acute and chronic brain injuries, as well as the therapeutic importance of modulation by diets and probiotics. We emphasize the mechanistic studies based on animal models and their translational or clinical relationship by reviewing human studies.

Power law analysis of the human milk microbiome

The human breast milk microbiome (HMM) has far reached health implications for both mothers and infants, and understanding the structure and dynamics of milk microbial communities is therefore of critical biomedical importance. Community heterogeneity, which has certain commonalities with familiar diversity but also with certain fundamental differences, is an important aspect of community structure and dynamics. Taylor's (1961) power law (TPL) (Nature, 1961) was discovered to govern the mean-variance power function relationship of population abundances and can be used to characterize population spatial aggregation (heterogeneity) and/or temporal stability. TPL was further extended to the community level to measure community spatial heterogeneity and/or temporal stability (Ma 2015, Molecular Ecology). Here, we applied TPL extensions (TPLE) to analyze the heterogeneity of the human milk microbiome by reanalyzing 12 datasets (2115 samples) of the healthy human milk microbiome. Our analysis revealed that the TPLE heterogeneity parameter (b) is rather stable across the 12 datasets, and there were approximately no statistically significant differences among ¾ of the datasets, which is consistent with the hypothesis that the heterogeneity scaling (i.e., change across individuals) of the human microbiome, including HMM, is rather stable or even constant. For this, we built a TPLE model for the pooled 12 datasets (b = 1.906), which can therefore represent the scaling rate of community-level spatial heterogeneity of HMM across individuals. Similarly, we also analyzed mixed-species ("averaged virtual species") level heterogeneity of HMM, and it was found that the mixed-species level heterogeneity was smaller than the heterogeneity at the previously mentioned community level (1.620 vs. 1.906).

Neonatal Programming of Microbiota Composition: A Plausible Idea That Is Not Supported by the Evidence

Underpinning the theory "developmental origins of health and disease" (DOHaD), evidence is accumulating to suggest that the risks of adult disease are in part programmed by exposure to environmental factors during the highly plastic "first 1,000 days of life" period. An elucidation of the mechanisms involved in this programming is challenging as it would help developing new strategies to promote adult health. The intestinal microbiome is proposed as a long-lasting memory of the neonatal environment. This proposal is supported by indisputable findings such as the concomitance of microbiota assembly and the first 1,000-day period, the influence of perinatal conditions on microbiota composition, and the impact of microbiota composition on host physiology, and is based on the widely held but unconfirmed view that the microbiota is long-lastingly shaped early in life. In this review, we examine the plausibility of the gut microbiota being programmed by the neonatal environment and evaluate the evidence for its validity. We highlight that the capacity of the pioneer bacteria to control the implantation of subsequent bacteria is supported by both theoretical principles and statistical associations, but remains to be demonstrated experimentally. In addition, our critical review of the literature on the long-term repercussions of selected neonatal modulations of the gut microbiota indicates that sustained programming of the microbiota composition by neonatal events is unlikely. This does not exclude the microbiota having a role in DOHaD due to a possible interaction with tissue and organ development during the critical windows of neonatal life.

The Connection Between Physical Exercise and Gut Microbiota: Implications for Competitive Sports Athletes

Gut microbiota refers to those microorganisms in the human digestive tract that display activities fundamental in human life. With at least 4 million different bacterial types, the gut microbiota is composed of bacteria that are present at levels sixfold greater than the total number of cells in the entire human body. Among its multiple functions, the microbiota helps promote the bioavailability of some nutrients and the metabolization of food, and protects the intestinal mucosa from the aggression of pathogenic microorganisms. Moreover, by stimulating the production of intestinal mediators able to reach the central nervous system (gut/brain axis), the gut microbiota participates in the modulation of human moods and behaviors. Several endogenous and exogenous factors can cause dysbiosis with important consequences on the composition and functions of the microbiota. Recent research underlines the importance of appropriate physical activity (such as sports), nutrition, and a healthy lifestyle to ensure the presence of a functional physiological microbiota working to maintain the health of the whole human organism. Indeed, in addition to bowel disturbances, variations in the qualitative and quantitative microbial composition of the gastrointestinal tract might have systemic negative effects. Here, we review recent studies on the effects of physical activity on gut microbiota with the aim of identifying potential mechanisms by which exercise could affect gut microbiota composition and function. Whether physical exercise of variable work intensity might reflect changes in intestinal health is analyzed.

Eucommiae cortex polysaccharides mitigate obesogenic diet-induced cognitive and social dysfunction via modulation of gut microbiota and tryptophan metabolism

Rationale: The high fat and sucrose diet, known as the obesogenic diet (OD), has been related to low-grade chronic inflammation and neurodevelopmental disorders. Emerging evidence suggests that OD influences cognitive and social function via the gut-brain axis. However, the effects of OD during adolescence on future health have been unclear. Meanwhile, the underlying mechanisms and effective interventions are not fully understood. Polysaccharides, one of the most abundant substances in the Eucommiae cortex, exhibit potential immunomodulatory and neuroprotective effects. Here, we aimed to investigate the impact of OD on adolescents, explore the modulating roles of Eucommiae cortex polysaccharides (EPs) on OD-induced behavioral dysfunction, and elucidate the underlying molecular mechanisms. Methods: In the present study, four-week-old mice were fed with OD for four weeks to simulate persistent OD in adolescents. The behavioral features were accessed by open field test and Morris water maze. The gut bacterial structure was identified by 16S rRNA gene amplicon sequencing. The gene and protein expression in colonic tissues and hippocampus were detected by qRT-PCR, immunoblotting, enzyme-linked immunosorbent assay, and immunofluorescence staining. Detection of biological metabolites in serum and hippocampal tissues was performed by widely targeted metabolomics and targeted metabolomics. Results: We found that OD-fed mice showed cognitive and social-behavioral deficits accompanied by gut dysbiosis and systematic tryptophan (Trp) metabolism disorders, which increased kynurenine (Kyn) concentration in the hippocampus. Bacteria-derived lipopolysaccharide (LPS, endotoxin) induced microglia-mediated neuroinflammation, directing the metabolism of Kyn in the hippocampus toward quinolinic acid (QA), which led to glutamate-mediated hyperactivation of mossy cells (MCs) in hippocampal hilus. Furthermore, OD impaired parvalbumin (PV) interneurons-related local circuits in the hippocampal granule cell layer. These resulted in hippocampal neurogenesis deficits and related behavioral dysfunction in mice. EPs supplementation ameliorated OD-induced gut dysbiosis, as evidenced by inhibiting the expansion of Escherichia coli (E.coli) and reducing the concentration of LPS in colonic contents and serum, thereby inhibiting the subsequent neuroinflammation. In addition, oral EPs suppressed the peripheral Kyn pathway to reduce the concentration of QA and glutamic acid in the hippocampus of OD-fed mice, thereby rescuing the glutamic acid-triggered neuroexcitotoxicity. These contributed to remodeling the rhythm of hippocampal neurogenesis and mitigated behavioral dysfunction in OD-fed mice. Conclusions: The present study addresses a gap in the understanding of neuronal dysfunction associated with OD during adolescence and provides the first evidence that EPs improved cognitive and social behavior via modulation of gut microbiota and tryptophan metabolism in adolescent mice fed with OD, which may represent novel preemptive therapy for neurodevelopmental disorders via manipulation of the tryptophan metabolite.

Effects of dietary fiber on intestinal microbiota in geese evaluated by 16SrRNA gene sequencing

AIMS

The purpose of the research is to study the effects of different fiber types and sources on the intestinal flora of geese.

METHODS AND RESULTS

A total of 48 geese (males 35 days old) were divided into 4 groups, each of which included 3 replicates of 4 geese. Groups 1 to 4 were fed a diet containing 5% corn stover Crude fiber (CF, the LJ group), 8% corn stover CF (the HJ group), 5% alfalfa CF (the LM group), or 8% alfalfa CF (the HM group) respectively. After 42 days of feeding, the intestinal flora of each group was determined by 16SrRNA gene sequencing. In the duodenum, the diet supplemented with corn stover meal increased the relative abundance of Proteobacteria, Actinobacteria and Euryarchaeota, and with alfalfa as fiber source increased the relative abundance of Firmicutes, Bacteroidetes, Tenericutes and Chloroflexi. In the jejunum, Bacteroidetes, Actinobacteria, Planctomycetes, Acidobacteria, Tenericutes and Spirochetes were significantly more abundant in the corn stover group. There were no significant differences among the results for the other two fiber sources, which were fibre level in their influence where in ileum. Firmicutes, Deferribacteres and Euryarchaeota with corn stover as fiber source in the cecum were higher than the alfalfa group.

CONCLUSIONS

Different fiber sources have significant effects on goose gut microbiota. There were same flora has the same trend of change in different intestinal segments. The relative fiber source in the ileum makes the gut microbiota more sensitive to differences in fiber levels..

SIGNIFICANCE AND IMPACT OF THE STUDY

This study proved that the dietary fibre affects the intestinal flora. At the same time, different groups of dietary fibre may be used to provide the possibility to study functional roles of specific bacteria in host physiology.

The Effect of Long-Term or Repeated Use of Antibiotics in Children and Adolescents on Cognitive Impairment in Middle-Aged and Older Person(s) Adults: A Cohort Study

Objectives

We evaluated the effects of long-term/recurrent use of antibiotics in childhood on developing cognitive impairment in middle and old age from UK Biobank Database.

Methods

UK Biobank recruited participants aged 37-73 years. Cognitive impairment was ascertained by fluid intelligence questionnaire. Primary outcome was the occurrence of cognitive impairment in middle and old age. Multivariate logistic regression models were used to explore the relationship between long-term/recurrent use of antibiotics and cognitive impairment.

Results

Over 3.8-10.8 years' follow-up, 4,781 of the 35,921 participants developed cognitive impairment. The odds of cognitive impairment in middle and old age among long-term/recurrent use of antibiotics in childhood were increased by 18% compared with their counterparts (adjusted odd ratio 1.18, 95% confidence interval 1.08-1.29, p < 0.01). The effect of long-term/recurrent use of antibiotics in childhood on cognitive impairment was homogeneous across different categories of various subgroup variables such as sex, age, APOE4, ethnic groups, income before tax, smoking status, alcohol status, BMI, hypertension and diabetes but the effect of long-term/recurrent use of antibiotics in childhood was modified by the educational qualification (p-value for interaction <0.05).

Conclusion

Long-term/recurrent use of antibiotics in childhood may increase the risk of cognitive impairment in middle and old age.

Pathobionts: mechanisms of survival, expansion, and interaction with host with a focus on Clostridioides difficile

Pathobionts are opportunistic microbes that emerge as a result of perturbations in the healthy microbiome due to complex interactions of various genetic, exposomal, microbial, and host factors that lead to their selection and expansion. Their proliferations can aggravate inflammatory manifestations, trigger autoimmune diseases, and lead to severe life-threatening conditions. Current surge in microbiome research is unwinding these complex interplays between disease development and protection against pathobionts. This review summarizes the current knowledge of pathobiont emergence with a focus on Clostridioides difficile and the recent findings on the roles of immune cells such as iTreg cells, Th17 cells, innate lymphoid cells, and cytokines in protection against pathobionts. The review calls for adoption of innovative tools and cutting-edge technologies in clinical diagnostics and therapeutics to provide insights in identification and quantification of pathobionts.

Role of milk carbohydrates in intestinal health of nursery pigs: a review

Intestinal health is essential for the resistance to enteric diseases and for nutrient digestion and absorption to support growth. The intestine of nursery pigs are immature and vulnerable to external challenges, which cause negative impacts on the structure and function of the intestine. Among nutritional interventions, the benefits of milk are significant for the intestinal health of pigs. Milk coproducts have traditionally been used in starter feeds to improve the growth of nursery pigs, but their use is somewhat limited due to the high costs and potential risks of excessive lactose on the intestine. Thus, understanding a proper feeding level of milk carbohydrates is an important start of the feeding strategy. For nursery pigs, lactose is considered a highly digestible energy source compared with plant-based starch, whereas milk oligosaccharides are considered bioactive compounds modulating intestinal immunity and microbiota. Therefore, milk carbohydrates, mainly composed of lactose and oligosaccharides, have essential roles in the intestinal development and functions of nursery pigs. The proper feeding levels of lactose in starter feeds could be variable by weaning age, body weight, or genetic lines. Effects of lactose and milk oligosaccharides have been broadly studied in human health and animal production. Therefore, this review focuses on the mechanisms of lactose and milk oligosaccharides affecting intestinal maturation and functions through modulation of enterocyte proliferation, intestinal immunity, and intestinal microbiota of nursery pigs.

Fecal microbiota relationships with childhood obesity: A scoping comprehensive review

Childhood obesity is a costly burden in most regions with relevant and adverse long-term health consequences in adult life. Several studies have associated excessive body weight with a specific profile of gut microbiota. Different factors related to fecal microorganism abundance seem to contribute to childhood obesity, such as gestational weight gain, perinatal diet, antibiotic administration to the mother and/or child, birth delivery, and feeding patterns, among others. This review reports and discusses diverse factors that affect the infant intestinal microbiota with putative or possible implications on the increase of the obesity childhood rates as well as microbiota shifts associated with excessive body weight in children.

The hidden universe of human milk microbiome: origin, composition, determinants, role, and future perspectives

Although traditionally considered sterile, human milk is currently recognized as an alive ecosystem that harbors not only bacteria, but also viruses, fungi and yeasts, and minor genera, collectively known as the human milk microbiome (HMM). The seeding of HMM is a complex phenomenon whose dynamics are still a matter of research. Many factors contribute to its determination, both maternal, neonatal, environmental, and related to human milk itself. The transmission of microorganisms to the infant through breastfeeding may impact its present and future health, mainly shaping the GI tract microbiome and immune system. The existence and persistence of HMM as a conserved feature among different species may also have an evolutionary meaning, which will become apparent only in evolutionary times.

CONCLUSION

The complexities of HMM warrant further research in order to deepen our knowledge on its origin, determinants, and impact on infants' health. The practical and translational implications of research on HMM (e.g., reconstitution of donor human milk through inoculation of infant's own mother milk, modulation of HMM through maternal dietary supplementation) should not be overlooked.

WHAT IS KNOWN

• Human milk harbors a wide variety of microorganisms, ranging from bacteria to viruses, fungi and yeasts, and minor genera. • Human milk microbiome is shaped over time by many factors: maternal, neonatal, environmental, and related to human milk itself. • The transmission of microorganisms through breastfeeding may impact the infant's present and future health.

WHAT IS NEW

• We provide an overview on human milk microbiome, hopefully encouraging physicians to consider it among the other better-known breastfeeding benefits. • Further studies, with standardized and rigorous study designs to enhance accuracy and reproducibility of the results, are needed to deepen our knowledge of the human milk microbiota and its role in newborn and infant's health.

The First 1000 Days: Assembly of the Neonatal Microbiome and Its Impact on Health Outcomes

Early life microbial colonization is critical for the development of the immune system, postnatal growth, and long-term health and disease. The dynamic and nascent microbiomes of children are highly individualized and are characterized by low bacterial diversity. Any disruptions in microbial colonization can contribute to shifts in normal microbial colonization that persist past the first 1000 days of life and result in intestinal dysbiosis. Here, we focus on microbiome-host interactions during fetal, newborn, and infant microbiome development. We summarize the roles of bacterial communities in fetal development and adverse health outcomes due to dysbiosis. We also discuss how internal and external factors program the microbiome's metabolic machinery as it evolves into an adult-like microbiome. Finally, we discuss the limits of current studies and future directions. Studies on the early-life microbiome will be critical for a better understanding of childhood health and diseases, as well as restorative methods for the prevention and treatment of diseases in adulthood.

Cross-talk between immune system and microbiota in COVID-19

INTRODUCTION

Human gut microbiota plays a crucial role in providing protective responses against pathogens, particularly by regulating immune system homeostasis. There is a reciprocal interaction between the gut and lung microbiota, called the gut-lung axis (GLA). Any alteration in the gut microbiota or their metabolites can cause immune dysregulation, which can impair the antiviral activity of the immune system against respiratory viruses such as severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2.

AREAS COVERED

This narrative review mainly outlines emerging data on the mechanisms underlying the interactions between the immune system and intestinal microbial dysbiosis, which is caused by an imbalance in the levels of essential metabolites. The authors will also discuss the role of probiotics in restoring the balance of the gut microbiota and modulation of cytokine storm.

EXPERT OPINION

Microbiota-derived signals regulate the immune system and protect different tissues during severe viral respiratory infections. The GLA's equilibration could help manage the mortality and morbidity rates associated with SARS-CoV-2 infection.

The Role of Microbiota in Infant Health: From Early Life to Adulthood

From early life to adulthood, the microbiota play a crucial role in the health of the infant. The microbiota in early life are not only a key regulator of infant health but also associated with long-term health. Pregnancy to early life is the golden time for the establishment of the infant microbiota, which is affected by both environmental and genetic factors. Recently, there is an explosion of the studies on the role of microbiota in human diseases, but the application to disease or health is relatively limited because many aspects of human microbiota remain controversial, especially about the infant microbiota. Therefore, a critical and conclusive review is necessary to understand fully the relationship between the microbiota and the health of infant. In this article, we introduce in detail the role of microbiota in the infant from pregnancy to early life to long-term health. The main contents of this article include the relationship between the maternal microbiota and adverse pregnancy outcomes, the establishment of the neonatal microbiota during perinatal period and early life, the composition of the infant gut microbiota, the prediction of the microbiota for long-term health, and the future study directions of microbiota.

Longitudinal Multi-Omics Study of a Mother-Infant Dyad from Breastfeeding to Weaning: An Individualized Approach to Understand the Interactions Among Diet, Fecal Metabolome and Microbiota Composition

The development of the human gut microbiota is characterized by a dynamic sequence of events from birth to adulthood, which make the gut microbiota unique for everyone. Its composition and metabolism may play a critical role in the intestinal homeostasis and health. We propose a study on a single mother-infant dyad to follow the dynamics of an infant fecal microbiota and metabolome changes in relation to breast milk composition during the lactation period and evaluate the changes induced by introduction of complementary food during the weaning period. Nuclear Magnetic Resonance (NMR)-based metabolomics was performed on breast milk and, together with 16S RNA targeted-metagenomics analysis, also on infant stool samples of a mother-infant dyad collected over a period running from the exclusive breastfeeding diet to weaning. Breast milk samples and neonatal stool samples were collected from the 4th to the 10th month of life. Both specimens were collected from day 103 to day 175, while from day 219-268 only stool samples were examined. An exploratory and a predictive analysis were carried out by means of Common component and specific weight analysis and multi-block partial least squares discriminant analysis, respectively. Stools collected during breastfeeding and during a mixed fruit/breastfeeding diet were characterized by high levels of fucosyl-oligosaccharides and glycolysis intermediates, including succinate and formate. The transition to a semi-solid food diet was characterized by several changes in fecal parameters: increase in short-chain fatty acids (SCFAs) levels, including acetate, propionate and butyrate, dissapearance of HMOs and the shift in the community composition, mainly occurring within the Firmicutes phylum. The variations in the fecal metabolome reflected the infant's diet transition, while the composition of the microbiota followed a more complex and still unstable behavior.

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

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

The Influence of Cesarean Section on the Composition and Development of Gut Microbiota During the First 3 Months of Life

The intestinal microbiota has emerged as a critical regulator of growth and development in the early postnatal period of life. Cesarean section (CS) delivery is one of the strongest disrupting factors of the normal colonization process and has been reported as a risk factor for disorders in later life. In this study, we dynamically and longitudinally evaluated the impact of CS on the initial colonization pattern and development of gut microbiota by 16 healthy Chinese infants with fecal samples collected at 9 time points (day 5, day 8, day 11, week 2, week 4, week 6, week 7, month 2, and month 3) during the first 3 months of life. The V3–V4 regions of 16S rRNA gene were analyzed by Illumina sequencing. In comparison with vaginally delivered (VD) infants, infants born by CS showed decreased relative abundance of Bacteroides and Parabacteroides and enrichment of Clostridium_sensu_stricto_1, Enterococcus, Klebsiella, Clostridioides, and Veillonella. Most interestingly, Firmicutes/Bacteroidetes ratio was found to be significantly higher in the CS group than in the VD group from day 5 until month 3. Besides, the results of microbial functions showed that the VD group harbored significantly higher levels of functional genes in vitamin B6 metabolism at day 5, day 8, week 2, week 4, week 6, week 7, month 2, and month 3 and taurine and hypotaurine metabolism at day 5, while the phosphotransferase system and starch and sucrose metabolism involved functional genes were plentiful in the CS group at day 11, week 2, week 4, week 6, week 7, and month 2 and at week 2, week 7, and month 2, respectively. Our results establish a new evidence that CS affected the composition and development of gut microbiota in the first 3 months and provide a novel insight into strategies for CS-related disorders in later life.

Protocol of the Snuggle Bug/Acurrucadito Study: a longitudinal study investigating the influences of sleep-wake patterns and gut microbiome development in infancy on rapid weight gain, an early risk factor for obesity

BACKGROUND

Overweight, obesity, and associated comorbidities are a pressing global issue among children of all ages, particularly among low-income populations. Rapid weight gain (RWG) in the first 6 months of infancy contributes to childhood obesity. Suboptimal sleep-wake patterns and gut microbiota (GM) have also been associated with childhood obesity, but little is known about their influences on early infant RWG. Sleep may alter the GM and infant metabolism, and ultimately impact obesity; however, data on the interaction between sleep-wake patterns and GM development on infant growth are scarce. In this study, we aim to investigate associations of infant sleep-wake patterns and GM development with RWG at 6 months and weight gain at 12 months. We also aim to evaluate whether temporal interactions exist between infant sleep-wake patterns and GM, and if these relations influence RWG.

METHODS

The Snuggle Bug/ Acurrucadito study is an observational, longitudinal study investigating whether 24-h, actigraphy-assessed, sleep-wake patterns and GM development are associated with RWG among infants in their first year. Based on the Ecological Model of Growth, we propose a novel conceptual framework to incorporate sleep-wake patterns and the GM as metabolic contributors for RWG in the context of maternal-infant interactions, and familial and socio-physical environments. In total, 192 mother-infant pairs will be recruited, and sleep-wake patterns and GM development assessed at 3 and 8 weeks, and 3, 6, 9, and 12 months postpartum. Covariates including maternal and child characteristics, family and environmental factors, feeding practices and dietary intake of infants and mothers, and stool-derived metabolome and exfoliome data will be assessed. The study will apply machine learning techniques combined with logistic time-varying effect models to capture infant growth and aid in elucidating the dynamic associations between study variables and RWG.

DISCUSSION

Repeated, valid, and objective assessment at clinically and developmentally meaningful intervals will provide robust measures of longitudinal sleep, GM, and growth. Project findings will provide evidence for future interventions to prevent RWG in infancy and subsequent obesity. The work also may spur the development of evidence-based guidelines to address modifiable factors that influence sleep-wake and GM development and prevent childhood obesity.

Breast milk nutrients driving intestinal epithelial layer maturation via Wnt and Notch signaling: Implications for necrotizing enterocolitis

Necrotizing enterocolitis (NEC) is an often lethal, inflammatory disease of the preterm intestine. The underdeveloped immune system plays an important role; however, the initial trigger for NEC development is likely a damaged intestinal epithelial layer. We hypothesize that due to incomplete maturation of different epithelial cell lineages, nutrients and bacteria are able to damage the epithelial cells and cause the (immature) inflammatory response, food intolerance and malabsorption seen in NEC. Intestinal organoid research has shown that maturation of intestinal epithelial cell lineages is orchestrated by two key signaling pathways: Wnt and Notch. In NEC, these pathways are dysregulated by hyperactivation of Toll-like-receptor-4. Breastfeeding decreases the risk of developing NEC compared to formula milk. Here, we review the intricate link between breast milk components, Wnt and Notch signaling and intestinal epithelial maturation. We argue that (nutritional) interventions regulating these pathways may decrease the risk of NEC development in preterm infants.

The First Report of Bacteroides fragilis and Bacteroides thetaiotaomicron Relative Abundance in Obese Iranian Population

Background and Objectives: Obesity is a multifactorial disorder, and gut microbiota has a fundamental role in its pathophysiology. Bacteroides spp. has significant roles in gut microbiota- host interactions that determine health and disease development. Since the gut microbiota pattern changes based on different criteria in each population, we studied the abundance of two important Bacteroides strains, Bacteroides fragilis, and Bacteroides thetaiotaomicron, in Iranian obese and normal-weight subjects for the first time. Methods: In this study, 100 participants were recruited and classified based on their body mass index (BMI). The subjects were divided into normal (average BMI, 22.37 kg/m2) and obese (average BMI, 29.10 kg/m2) groups. Bacterial DNA was extracted from the samples, and quantitative polymerase chain reaction (qPCR) was conducted based on 16s rDNA universal primers. Finally, the correlation between bacterial abundance and obesity was investigated. Results: The results of qPCR showed that the relative abundance means of B. fragilis in normal weight and obese subjects was 8.68 × 1012 and 9.27 × 1012 cfu/mL, respectively. Also, the relative abundance mean of B. thetaiotaomicron in normal weight and obese subjects was 2.32 × 1012 and 5.39 × 1012 cfu/mL, respectively. Although obese subjects had more B. fragilis and B. thetaiotaomicron abundance compared to subjects with normal weight, no significant difference was identified between relative abundance of B. fragilis (P = 0.79) and B. thetaiotaomicron (P = 0.18) in the two groups. Conclusions: Although obese subjects had more B. fragilis and B. thetaiotaomicron abundance compared to normal-weight subjects, no significant difference was identified between the two groups. Since Bacteroides spp. have significant role in gut microbiota-host interaction, determination of their abundance in obesity development and targeting restoration of gut microbiota pattern could be valuable in controlling obesity. In this regard, dietary intervention could be based on determination of gut microbiota pattern in certain populations.

Gut Microbiota And Inflammatory Disorders

The gut has been colonized with bacteria, fungi, viruses, archaea, eukarya. The human and bacterial cells are found in a 1:1 ratio, while the variance in the diversity of gut microbiota may result in Dysbiosis. Gut dysbiosis may result in various pathological manifestations. Beneficial gut microbiota may synthesize short-chain fatty acids like acetate, butyrate, propionate, while -gram-negative organisms are the primary source of LPS, a potent pro-inflammatory mediator. Both gut microbiota and microbial products may be involved in immunomodulation as well as inflammation. Prebiotics and probiotics are being explored as therapeutic agents against various inflammatory and autoimmune disorders. Here we discuss the molecular mechanisms involved in gut bacteria-mediated modulation of various inflammatory and autoimmune disorders.

Microbial Glycoside Hydrolases in the First Year of Life: An Analysis Review on Their Presence and Importance in Infant Gut

The first year of life is a crucial period during which the composition and functionality of the gut microbiota develop to stabilize and resemble that of adults. Throughout this process, the gut microbiota has been found to contribute to the maturation of the immune system, in gastrointestinal physiology, in cognitive advancement and in metabolic regulation. Breastfeeding, the “golden standard of infant nutrition,” is a cornerstone during this period, not only for its direct effect but also due to its indirect effect through the modulation of gut microbiota. Human milk is known to contain indigestible carbohydrates, termed human milk oligosaccharides (HMOs), that are utilized by intestinal microorganisms. Bacteria that degrade HMOs like Bifidobacterium longum subsp. infantis, Bifidobacterium bifidum, and Bifidobacterium breve dominate the infant gut microbiota during breastfeeding. A number of carbohydrate active enzymes have been found and identified in the infant gut, thus supporting the hypothesis that these bacteria are able to degrade HMOs. It is suggested that via resource-sharing and cross-feeding, the initial utilization of HMOs drives the interplay within the intestinal microbial communities. This is of pronounced importance since these communities promote healthy development and some of their species also persist in the adult microbiome. The emerging production and accessibility to metagenomic data make it increasingly possible to unravel the metabolic capacity of entire ecosystems. Such insights can increase understanding of how the gut microbiota in infants is assembled and makes it a possible target to support healthy growth. In this manuscript, we discuss the co-occurrence and function of carbohydrate active enzymes relevant to HMO utilization in the first year of life, based on publicly available metagenomic data. We compare the enzyme profiles of breastfed children throughout the first year of life to those of formula-fed infants.

Faecal microbiota transplantation in endocrine diseases and obesity

The prevalence of type 1 (T1D) and type 2 diabetes mellitus (T2D) has greatly increased worldwide over the last century. Although the exact pathophysiology of both these conditions is distinct and still largely unknown, T1D as well as T2D, have been linked to distinct perturbations of the gut microbiome. Faecal microbiota transplantation (FMT) is a potent, and if performed well, a safe method to modulate the composition of the gut microbiome and thus positively influences the course of these hyperglycaemic conditions in humans. In this review, we provide an overview of how FMT is commonly performed and summarise how this procedure may reduce the insulin-resistance driving T2D, and the underlying auto-immunity driving T1D. Insights derived from FMT studies in T1D and T2D may help identify beneficial microbiota and associated metabolites that may serve as future treatments for these conditions.

Gastrointestinal perforations and associated risk factors in children after liver transplantation

In this study, possible risk factors of gastrointestinal perforations (GIP) that increase mortality after liver transplantation in children were investigated. One hundred and thirty-one pediatric patients who underwent 139 liver transplants between January 2016 and February 2020 were evaluated retrospectively based on preoperative and surgical data. Furthermore, cases with biliary atresia, which constitute 26.7% (35) of the patients, were compared within themselves and with other groups. It was found that the cases that developed perforations were younger, lower in weight, and had higher number of surgeries than those who did not, while the mortality and morbidity rates were higher in these patients. When cases with biliary atresia were analyzed within themselves, no significant difference was found between perforated biliary atresia and non-perforated cases in terms of age, weight, and previous surgery. When biliary atresia and other etiologies were compared, biliary atresia cases were found to be transplanted at a younger age, at a lower weight, and this group had a higher risk for perforation. Early laparotomy should be performed in order to reduce mortality in GIPs. Patients that are younger, underweight, previously operated, and using mesh must be closely monitored.

Unravelling the potential of gut microbiota in sustaining brain health and their current prospective towards development of neurotherapeutics

Increasing incidences of neurological disorders, such as Parkinson's disease (PD), multiple sclerosis (MS), Alzheimer's disease (AD) and amyotrophic lateral sclerosis (ALS) are being reported, but an insight into their pathology remains elusive. Findings have suggested that gut microbiota play a major role in regulating brain functions through the gut-brain axis. A unique bidirectional communication between gut microbiota and maintenance of brain health could play a pivotal role in regulating incidences of neurodegenerative diseases. Contrarily, the present life style with changing food habits and disturbed circadian rhythm may contribute to gut homeostatic imbalance and dysbiosis leading to progression of several neurological disorders. Therefore, dysbiosis, as a primary factor behind intestinal disorders, may also augment inflammation, intestinal and blood-brain barrier permeability through microbiota-gut-brain axis. This review primarily focuses on the gut-brain axis functions, specific gut microbial population, metabolites produced by gut microbiota, their role in regulating various metabolic processes and role of gut microbiota towards development of neurodegenerative diseases. However, several studies have reported a decrease in abundance of a specific gut microbial population and a corresponding increase in other microbial family, with few findings revealing some contradictions. Reports also showed that colonization of gut microbiota isolated from patients suffering from neurodegenerative disease leads to the development of enhance pathological outcomes in animal models. Hence, a systematic understanding of the dominant role of specific gut microbiome towards development of different neurodegenerative diseases could possibly provide novel insight into the use of probiotics and microbial transplantation as a substitute approach for treating/preventing such health maladies.

Anti-Inflammatory and Immunomodulatory Effects of Probiotics in Gut Inflammation: A Door to the Body

Hosting millions of microorganisms, the digestive tract is the primary and most important part of bacterial colonization. On one side, in cases of opportunistic invasion, the abundant bacterial population inside intestinal tissues may face potential health problems such as inflammation and infections. Therefore, the immune system has evolved to sustain the host-microbiota symbiotic relationship. On the other hand, to maintain host immune homeostasis, the intestinal microflora often exerts an immunoregulatory function that cannot be ignored. A field of great interest is the association of either microbiota or probiotics with the immune system concerning clinical uses. This microbial community regulates some of the host's metabolic and physiological functions and drives early-life immune system maturation, contributing to their homeostasis throughout life. Changes in gut microbiota can occur through modification in function, composition (dysbiosis), or microbiota-host interplays. Studies on animals and humans show that probiotics can have a pivotal effect on the modulation of immune and inflammatory mechanisms; however, the precise mechanisms have not yet been well defined. Diet, age, BMI (body mass index), medications, and stress may confound the benefits of probiotic intake. In addition to host gut functions (permeability and physiology), all these agents have profound implications for the gut microbiome composition. The use of probiotics could improve the gut microbial population, increase mucus-secretion, and prevent the destruction of tight junction proteins by decreasing the number of lipopolysaccharides (LPSs). When LPS binds endothelial cells to toll-like receptors (TLR 2, 4), dendritic cells and macrophage cells are activated, and inflammatory markers are increased. Furthermore, a decrease in gut dysbiosis and intestinal leakage after probiotic therapy may minimize the development of inflammatory biomarkers and blunt unnecessary activation of the immune system. In turn, probiotics improve the differentiation of T-cells against Th2 and development of Th2 cytokines such as IL-4 and IL-10. The present narrative review explores the interactions between gut microflora/probiotics and the immune system starting from the general perspective of a biological plausibility to get to the in vitro and in vivo demonstrations of a probiotic-based approach up to the possible uses for novel therapeutic strategies.

When a Neonate Is Born, So Is a Microbiota

In recent years, the role of human microbiota as a short- and long-term health promoter and modulator has been affirmed and progressively strengthened. In the course of one’s life, each subject is colonized by a great number of bacteria, which constitute its specific and individual microbiota. Human bacterial colonization starts during fetal life, in opposition to the previous paradigm of the “sterile womb”. Placenta, amniotic fluid, cord blood and fetal tissues each have their own specific microbiota, influenced by maternal health and habits and having a decisive influence on pregnancy outcome and offspring outcome. The maternal microbiota, especially that colonizing the genital system, starts to influence the outcome of pregnancy already before conception, modulating fertility and the success rate of fertilization, even in the case of assisted reproduction techniques. During the perinatal period, neonatal microbiota seems influenced by delivery mode, drug administration and many other conditions. Special attention must be reserved for early neonatal nutrition, because breastfeeding allows the transmission of a specific and unique lactobiome able to modulate and positively affect the neonatal gut microbiota. Our narrative review aims to investigate the currently identified pre- and peri-natal factors influencing neonatal microbiota, before conception, during pregnancy, pre- and post-delivery, since the early microbiota influences the whole life of each subject.

Metagenomic analysis of the gut microbiome composition associated with vitamin D supplementation in Taiwanese infants

Early childhood is a critical stage for the foundation and development of the gut microbiome, large amounts of essential nutrients are required such as vitamin D. Vitamin D plays an important role in regulating calcium homeostasis, and deficiency can impair bone mineralization. In addition, most people know that breastfeeding is advocated to be the best thing for a newborn; however, exclusively breastfeeding infants are not easily able to absorb an adequate amount of vitamin D from breast milk. Understanding the effects of vitamin D supplementation on gut microbiome can improve the knowledge of infant health and development. A total of 62 fecal sample from healthy infants were collected in Taiwan. Of the 62 infants, 31 were exclusively breastfed infants and 31 were mixed- or formula-fed infants. For each feeding type, one subgroup of infants received 400 IU of vitamin D per day, and the remaining infants received a placebo. In total, there are 15 breastfed and 20 formula-fed infants with additional vitamin D supplementation, and 16 breastfed and 11 formula-fed infants belong to control group, respectively. We performed a comparative metagenomic analysis to investigate the distribution and diversity of infant gut microbiota among different types of feeding regimes with and without vitamin D supplementation. Our results reveal that the characteristics of infant gut microbiota not only depend on the feeding types but also on nutrients intake, and demonstrated that the vitamin D plays an important role in modulating the infant gut microbiota, especially increase the proportion of probiotics in breast-fed infants.

Crosstalk between PPARs and gut microbiota in NAFLD

Nonalcoholic fatty liver disease (NAFLD) has become the most common liver disorder in both China and worldwide. It ranges from simple steatosis and progresses over time to nonalcoholic steatohepatitis (NASH), advanced liver fibrosis, cirrhosis, or hepatocellular carcinoma(HCC). Furthermore, NAFLD and its complications impose a huge health burden to society. The microbiota is widely connected and plays an active role in human physiology and pathology, and it is a hidden 'organ' in determining the state of the host, in terms of homeostasis, or disease. Peroxisome proliferator-activated receptors (PPARs) are members of the nuclear receptorsuperfamily and can regulate multiple pathways involved in metabolism, and serve as effective targets forthe treatment of many types of metabolic syndromes, including NAFLD. The purpose of this review is to integrate related articles on gut microbiota, PPARs and NAFLD, and present a balanced overview on how the microbiota can possibly influence the development of NAFLD through PPARs.