Developmental microbial ecology of the neonatal gastrointestinal tract

Gut phages and their interactions with bacterial and mammalian hosts

The mammalian gut microbiome is a dense and diverse community of microorganisms that reside in the distal gastrointestinal tract. In recent decades, the bacterial members of the gut microbiome have been the subject of intense research. Less well studied is the large community of bacteriophages that reside in the gut, which number in the billions of viral particles per gram of feces, and consist of considerable unknown viral "dark matter." This community of gut-residing bacteriophages, called the gut "phageome," plays a central role in the gut microbiome through predation and transformation of native gut bacteria, and through interactions with their mammalian hosts. In this review, we will summarize what is known about the composition and origins of the gut phageome, as well as its role in microbiome homeostasis and host health. Furthermore, we will outline the interactions of gut phages with their bacterial and mammalian hosts, and plot a course for the mechanistic study of these systems.

Effects of Infant Formula Supplemented With Prebiotics on the Gut Microbiome, Gut Environment, Growth Parameters, and Safety and Tolerance: A Systematic Review and Meta-Analysis

CONTEXT

Prebiotics are often added to infant formulas to mimic the benefits of oligosaccharides found in human milk.

OBJECTIVE

This systematic review and meta-analysis evaluated the effects of prebiotic-supplemented cow's milk-based formula on the gut microbiota, gut environment, growth parameters, and safety and tolerance in infants ≤6 months old, compared with a standard formula or human milk comparator.

DATA SOURCES

Searches were performed in the PubMed, Embase, Cochrane Central Register of Controlled Trials, and ProQuest Dissertations & Theses databases. Articles were included that reported on randomized controlled trials, were published from inception until April 2024, and met prespecified inclusion and exclusion criteria.

DATA EXTRACTION

Outcomes included gut microbiota (eg, diversity; taxa at phylum, family, genus and species levels), gut environment (eg, pH, secretory immunoglobulin A, fecal calprotectin, fecal metabolites), growth parameters (eg, z scores), and safety and tolerance. Fixed or random effects models were used and mean differences (MDs) with 95% CIs were calculated to assess pooled effects. Risk of bias was assessed using the Cochrane Collaboration Tool (RoB 2).

DATA ANALYSIS

A total of 30 articles met inclusion criteria, with 5290 infants included. Whereas effects on Lactobacillus were inconsistent, prebiotic formula supplementation increased Bifidobacterium counts (k = 7 [MD: 0.49; 95% CI, 0.27-0.71]; I2 = 13%; P < .00001) and decreased fecal pH (k = 7 [MD: -0.39; 95% CI, -0.57 to -0.20]; I2 = 0%; P < .0001) compared with standard formula. Prebiotic formula supplementation increased total bacteria compared with human milk (MD: 0.41 [95% CI, 0.17-0.65]; I2 = 8%; P = .0006). In terms of growth parameters, weight-for-age z scores favored the prebiotic formula group compared with the human milk group (k = 2 [MD: 0.23; 95% CI, 0.04-0.42]; I2 = 7%; P = .02).

CONCLUSIONS

Prebiotic supplementation in infant formula can positively alter the gut microbiota, particularly Bifidobacterium, without negative impacts on growth. Standardized, high-quality research is needed to confirm the study findings and inform guidelines for prebiotic use in infant nutrition.

SYSTEMATIC REVIEW REGISTRATION

PROSPERO registration no. CRD42021253589.

Phenome-wide investigation of bidirectional causal relationships between major depressive disorder and common human diseases

The high comorbidity of major depressive disorder (MDD) with other diseases has been well-documented. However, the pairwise causal connections for MDD comorbid networks are poorly characterized. We performed Phenome-wide Mendelian randomization (MR) analyses to explore bidirectional causal associations between MDD (N = 807,553) and 877 common diseases from FinnGen datasets (N = 377,277). The inverse variance weighting method was the primary technique, and other methods (weighted median and MR-Egger) were used for sensitivity analyses. Our MR analyses showed that the genetic liability to MDD is causally associated with the risks of 324 disease phenotypes (average b: 0.339), including 46 psychiatric and behavioral disorders (average b: 0.618), 18 neurological diseases (average b: 0.348), 44 respiratory diseases (average b: 0.345), 40 digestive diseases (average b: 0.281), 18 circulatory diseases (average b: 0.237), 37 genitourinary diseases (average b: 0.271), 66 musculoskeletal and connective diseases (average b: 0.326), 22 endocrine diseases (average b: 0.302), and others. In a reverse analysis, a total of 51 genetic components predisposing to various diseases were causally associated with MDD risk (average b: 0.086), including 5 infectious diseases (average b: 0.056), 11 neurological diseases (average b: 0.106), 14 oncological diseases (average b: 0.108), and 5 psychiatric and behavioral disorders (average b: 0.114). Bidirectional causal associations were identified between MDD and 15 diseases. For most MR analyses, little evidence of heterogeneity and pleiotropy was detected. Our findings confirmed the extensive and significant causal role of genetic predisposition to MDD in contributing to human disease phenotypes, which were more pronounced than those seen in the reverse analysis of the causal influences of other diseases on MDD.

Relationship between frequency of yogurt consumption at 1 year of age and development at 3 years of age: The Japan Environment and Children's Study

BACKGROUND

Multiple observational studies have demonstrated the health benefits of yogurt, which are considered due to yogurt's positive effects on the gut microbiota. It is also known that the intestinal microbiota is associated with cognitive and emotional functions. Although the intake of probiotics has been reported to improve neurodevelopmental symptoms in children, no large-scale studies have examined the association of yogurt consumption in early childhood with later neurodevelopmental status. In this study, we examined the association between frequency of such consumption at 1 year of age and the children's subsequent neurodevelopmental status.

METHODS

We studied children's dietary consumption of yogurt at age 1 year and their neurodevelopment at age 3 years from data gathered from70,276 mother-child pairs enrolled in the Japan Environment and Children's Study. We collected data from pregnant women whose consent was obtained after the study was explained to them at participating facilities in the target area. Frequency of yogurt consumption was categorized into 0, 1-2, 3-4, and ≥ 5 times/week based on a questionnaire about the child's diet completed by the mother. Developmental delay was assessed using the Ages and Stages Questionnaires, Third Edition (ASQ-3™) in five domains: communication, gross motor, fine motor, problem solving, and personal-social. Using the results of the group that did not consume yogurt as a reference, multivariate logistic regression analysis was performed to compare the neurodevelopment of children according to frequency of yogurt consumption. For the covariates, items related to the socio-economic background and children's neurodevelopment were selected with reference to previous studies.

RESULTS

Consumption of yogurt 1-4 times/week was associated with a reduced risk of developmental delay in all ASQ-3 categories(adjusted odds ratios, 0.71-0.87). However, the risk of developmental delay was not necessarily reduced with yogurt consumption ≥5 times/week (adjusted odds ratios, 0.84-0.96).

CONCLUSION

Yogurt consumption habits at 1 year of age were associated with a lower risk of developmental delay at 3 years of age. However, the association was less apparent when yogurt was consumed more frequently. Possible mechanisms by which yogurt intake affects neurodevelopment include neurotransmitters produced by intestinal bacteria as well as the suppression of intestinal inflammation through improvements in the intestinal environment. Regular intake of yogurt in early childhood may have a positive association with neurodevelopment, but it is hoped that clearer links will be found in the future through intervention studies.

Unveiling the neonatal gut microbiota: exploring the influence of delivery mode on early microbial colonization and intervention strategies

Recent research has emphasized the critical importance of establishing the neonatal gut microbiota for overall health and immune system development, prompting deeper studies about the early formation of neonatal gut microbiota and its influencing factors. Various factors, including maternal and environmental factors, affect the early formation of neonatal gut microbiota, in which delivery mode has been considered as one of the most crucial influencing factors. In recent years, the increasing trend of cesarean section during childbirth has become a serious challenge for global public health. This review thoroughly analyzes the effects of vaginal delivery and cesarean section on the establishment of neonatal gut microbiota and the potential long-term impacts. In addition, we analyze and discuss interventions such as probiotics, prebiotics, vaginal seeding, fecal microbiota transplantation, and breastfeeding to address the colonization defects of the neonatal gut microbiota caused by cesarean section, aiming to provide theoretical basis for the prevention and treatment of colonization defects and related diseases in infants caused by cesarean section in clinical practice and to provide a theoretical foundation for optimizing the development of neonatal gut microbiota.

The Anti-Elixir Triad: Non-Synced Circadian Rhythm, Gut Dysbiosis, and Telomeric Damage

Aging is an inevitable life process which is accelerated by lifestyle and environmental factors. It is an irreversible accretion of molecular and cellular damage associated with changes in the body composition and deterioration in physiological functions. Each cell (other than stem cells) reaches the limit of its ability to replicate, known as cellular or replicative senescence, and consequently, the organs lose their physiological functions, resulting in overall impairment. Other factors that promote aging include smoking, alcohol, UV rays, sleep habits, food, stress, sedentary lifestyle, and genetic abnormalities. These stress factors can alter our endogenous clock (the circadian rhythm) and the microbial commensals. As a result of the effect of these stressors, the microorganisms that generally support human physiological processes become baleful. The disturbance of natural physiology instigates many age-related pathologies, such as cardiovascular diseases, chronic obstructive pulmonary disorder, cerebrovascular diseases, opportunistic infections, high blood pressure, cancer, diabetes, kidney diseases, dementia, and Alzheimer's disease. The present review covers the three most essential processes of the circadian clock; the circadian gene mechanism and regulation, the mitotic clock (which plays a vital role in the telomere's attrition) and the gut microbiota and their metabolome that drive aging and lead to age-related pathologies. In conclusion, maintaining a synchronized circadian rhythm, a healthy gut microbiome, and telomere integrity is essential for mitigating the effects of aging and promoting longevity. The interplay among these factors underscores the importance of lifestyle choices in enhancing overall health and lifespan.

Fecal microbiota of diarrheic calves: Before, during, and after recovering from disease

BACKGROUND

It is unknown if gastrointestinal dysbiosis in diarrheic calves causes disease or is a consequence of the disease.

OBJECTIVES

Describe the fecal microbiota of calves before, during, and after recovering from diarrhea.

ANIMALS

Fifteen female Holstein calves of 0 to 21 days old from a single farm. Seven calves remained healthy throughout the study, and 8 developed diarrhea on Day 14.

METHODS

Longitudinal cohort study. Microbiota composition was characterized by amplifying the V4 region of the 16S rRNA gene.

RESULTS

Diversity (Shannon index) increased with age in healthy and diarrheic calves from Day 3 to 21, but diarrheic calves had a lower diversity on the day diarrhea was first observed (Day 14). By Day 21, diversity increased in calves that recovered from diarrhea and was not significantly different from that of their healthy counterparts (P > .05). Weighted UniFrac distance showed significant differences in the fecal microbiota between diarrheic and healthy calves at Day 14 of age (PERMANOVA, P < .05), but not before or after diarrhea (PERMANOVA, P > .05). Lactobacillus, Clostridium Sensu Stricto 1, and Collinsella were differentially abundant on Day 10 in calves that developed diarrhea on Day 14 (P < .05).

CONCLUSION AND CLINICAL IMPORTANCE

The fecal microbiota of healthy and diarrheic calves evolved similarly during the first 10 days of age but differed significantly on the day of onset of diarrhea. Enriching Lactobacillus, Clostridium Sensu Stricto 1, and Collinsella before diarrhea onset could have been contributed to the development of diarrhea.

Investigation into Critical Gut Microbes Influencing Intramuscular Fat Deposition in Min Pigs

To determine the pivotal microorganisms affecting intramuscular fat (IMF) accumulation in Min pigs and to discern the extent of the influence exerted by various intestinal segments on IMF-related traits, we sequenced 16S rRNA from the contents of six intestinal segments from a high IMF group (Group H) and a low IMF group (Group L) of Min pigs weighing 90 ± 1 kg. We then compared their diversity and disparities in bacterial genera. Group H exhibited considerably higher α diversity in the jejunum and colon than Group L (p < 0.05). When 95% confidence levels were considered, the main β diversity components for the ileum, caecum, and colon within Groups H and L exhibited absolute segregation. Accordingly, 31 differentially abundant genera across Group H were pinpointed via LEfSe and the Wilcoxon test (p < 0.05) and subsequently scrutinised based on their distribution and abundance across distinct intestinal segments and their correlation with IMF phenotypes. The abundances of Terrisporobacter, Acetitomaculum, Bacteroides, Fibrobacter, Treponema, Akkermansia, Blautia, Clostridium sensu stricto 1, Turicibacter, Subdoligranulum, the [Eubacterium] siraeum group, and dgA 11 gut groups were positively correlated with IMF content (p < 0.05), whereas those of Bacillus, the Lachnospiraceae NK4A136 group, Streptococcus, Roseburia, Solobacterium, Veillonella, Lactobacillus, the Rikenellaceae RC9 gut group, Anaerovibrio, and the Lachnospiraceae AC2044 group were negatively associated with IMF content (p < 0.05). Employing PICRUSt2 for predicting intergenic metabolic pathways that differ among intestinal microbial communities revealed that within the 95% confidence interval the colonic microbiome was enriched with the most metabolic pathways, including those related to lipid metabolism. The diversity results, bacterial genus distributions, and metabolic pathway disparities revealed the colonic segment as an influential region for IMF deposition.

The Influence of Maternal Lifestyle Factors on Human Breast Milk Microbial Composition: A Narrative Review

Human breast milk (HBM) is considered the gold standard for infant nutrition due to its optimal nutrient profile and complex composition of cellular and non-cellular components. Breastfeeding positively influences the newborn's gut microbiota and health, reducing the risk of conditions like gastrointestinal infections and chronic diseases (e.g., allergies, asthma, diabetes, and obesity). Research has revealed that HBM contains beneficial microbes that aid gut microbiota maturation through mechanisms like antimicrobial production and pathogen exclusion. The HBM microbiota composition can be affected by several factors, including gestational age, delivery mode, medical treatments, lactation stage, as well as maternal lifestyle habits (e.g., diet, physical activity, sleep quality, smoking, alcohol consumption, stress level). Particularly, lifestyle factors can play a significant role in shaping the HBM microbiota by directly modulating the microbial composition or influencing the maternal gut microbiota and influencing the HBM microbes through the enteromammary pathway. This narrative review of current findings summarized how maternal lifestyle influences HBM microbiota. While the influence of maternal diet on HBM microbiota is well-documented, indicating that dietary patterns, especially those rich in plant-based proteins and complex carbohydrates, can positively influence HBM microbiota, the impact of other lifestyle factors is poorly investigated. Maintaining a healthy lifestyle during pregnancy and breastfeeding is crucial for the health of both mother and baby. Understanding how maternal lifestyle factors influence microbial colonization of HBM, along with their interactions and impact, is key to developing new strategies that support the beneficial maturation of the infant's gut microbiota.

Probiotic Lactobacillus rhamnosus species: considerations for female reproduction and offspring health

Lactobacillus rhamnosus is a type of bacteria known as a probiotic and is often used to support the health of the digestive system and vaginal flora. This type of bacteria has an important role, showing positive effects on female reproductive biology, particularly by maintaining the balance of microorganisms in the vagina, reducing the risk of infection, and strengthening the immune system to support maternal health during pregnancy. There are also studies showing that these probiotics prevent maternal obesity and gestational diabetes. Consuming probiotics containing Lactobacillus rhamnosus strains may support the intestinal health of breastfeeding mothers, but they may also contribute to the health of offspring. Therefore, this review focuses on the current available data for examining the effects of Lactobacillus rhamnosus strains on female reproductive biology and offspring health. A systematic search was conducted in the PubMed and Web of Science databases from inception to May 2024. The search strategy was performed using keywords and MeSH (Medical Subject Headings) terms. Inconsistent ratings were resolved through discussion. This review is strengthened by multiple aspects of the methodological approach. The systematic search strategy, conducted by two independent reviewers, enabled the identification and evaluation of all relevant literature. Although there is a limited number of studies with high heterogeneity, current literature highlights the important contribution of Lactobacillus rhamnosus probiotics in enhancing female reproductive health and fertility. Furthermore, the probiotic bacteria in breast milk may also support the intestinal health of newborn, strengthen the immune system, and protect them against diseases at later ages.

Role of Gut Microbial Metabolites in Cardiovascular Diseases-Current Insights and the Road Ahead

Cardiovascular diseases (CVDs) are the leading cause of premature morbidity and mortality globally. The identification of novel risk factors contributing to CVD onset and progression has enabled an improved understanding of CVD pathophysiology. In addition to the conventional risk factors like high blood pressure, diabetes, obesity and smoking, the role of gut microbiome and intestinal microbe-derived metabolites in maintaining cardiovascular health has gained recent attention in the field of CVD pathophysiology. The human gastrointestinal tract caters to a highly diverse spectrum of microbes recognized as the gut microbiota, which are central to several physiologically significant cascades such as metabolism, nutrient absorption, and energy balance. The manipulation of the gut microbial subtleties potentially contributes to CVD, inflammation, neurodegeneration, obesity, and diabetic onset. The existing paradigm of studies suggests that the disruption of the gut microbial dynamics contributes towards CVD incidence. However, the exact mechanistic understanding of such a correlation from a signaling perspective remains elusive. This review has focused upon an in-depth characterization of gut microbial metabolites and their role in varied pathophysiological conditions, and highlights the potential molecular and signaling mechanisms governing the gut microbial metabolites in CVDs. In addition, it summarizes the existing courses of therapy in modulating the gut microbiome and its metabolites, limitations and scientific gaps in our current understanding, as well as future directions of studies involving the modulation of the gut microbiome and its metabolites, which can be undertaken to develop CVD-associated treatment options. Clarity in the understanding of the molecular interaction(s) and associations governing the gut microbiome and CVD shall potentially enable the development of novel druggable targets to ameliorate CVD in the years to come.

Gut microbiota dysbiosis and its impact on asthma and other lung diseases: potential therapeutic approaches

The emerging field of gut-lung axis research has revealed a complex interplay between the gut microbiota and respiratory health, particularly in asthma. This review comprehensively explored the intricate relationship between these two systems, focusing on their influence on immune responses, inflammation, and the pathogenesis of respiratory diseases. Recent studies have demonstrated that gut microbiota dysbiosis can contribute to asthma onset and exacerbation, prompting investigations into therapeutic strategies to correct this imbalance. Probiotics and prebiotics, known for their ability to modulate gut microbial compositions, were discussed as potential interventions to restore immune homeostasis. The impact of antibiotics and metabolites, including short-chain fatty acids produced by the gut microbiota, on immune regulation was examined. Fecal microbiota transplantation has shown promise in various diseases, but its role in respiratory disorders is not established. Innovative approaches, including mucus transplants, inhaled probiotics, and microencapsulation strategies, have been proposed as novel therapeutic avenues. Despite challenges, including the sophisticated adaptability of microbial communities and the need for mechanistic clarity, the potential for microbiota-based interventions is considerable. Collaboration between researchers, clinicians, and other experts is essential to unravel the complexities of the gut-lung axis, paving a way for innovative strategies that could transform the management of respiratory diseases.

Alterations in the Intestinal Microbiome and Metabolic Profile of British Shorthair Kittens Fed with Milk Replacer

With the rising popularity of pet cats as companion animals, the survival of newborn kittens is often threatened by factors such as inadequate nursing, maternal behavior and blood incompatibility. These challenges require the use of milk replacers for nurturing. To investigate the effects that feeding kittens with an experimental milk replacer (EMR) have on growth and development, intestinal microbiota, immune response and nutrient metabolism, 12 British shorthair kittens were randomly divided into two groups after nursing for the first week of life. Kittens were fed queen's milk or EMR, whereby kittens fed queen's milk served as the control (CON) group. The findings revealed that the CON group exhibited superoxide dismutase (SOD) activity and total antioxidant capacity (T-AOC) (p < 0.01) on day 7. However, the EMR group had better growth performance during the later stage of the experiment (p < 0.05); the immunocompetence and antioxidant capacity of the EMR group were not significantly different from those of the CON group in the middle and late stages of the experiment, and the mean values of all the indexes were slightly better than those of the control group. Sequencing of the 16S rRNA gene in microbiota demonstrated that EMR increased the colonization of bacterial genera, including Lachnospiraceae, Enterococcus, Rothia and Ligilactobacillus. Compared to the CON group, acetate acid (p < 0.05), propionate acid (p < 0.01) and total SCFAs (p < 0.01) in the EMR group were significantly increased. Moreover, the intake of the EMR resulted in the production of distinct metabolites implicated in the metabolism of lipids and amino acids, among other nutrients, thus invigorating the associated metabolic pathways. These results elucidate the impact of administering a milk replacer on gastrointestinal health and nutrient assimilation in kittens. The study provides insights into the use of milk powder alternatives and sets the stage for future research on the formulation and effectiveness of kitten milk replacers.

Mapping the geographical distribution of the mucosa-associated gut microbiome in GI-symptomatic children with autism spectrum disorder

Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by cognitive, behavioral, and communication impairments. In the past few years, it has been proposed that alterations in the gut microbiota may contribute to an aberrant communication between the gut and brain in children with ASD. Consistent with this notion, several studies have demonstrated that children with ASD have an altered fecal microbiota compared with typically developing (TD) children. However, it is unclear where along the length of the gastrointestinal (GI) tract these alterations in microbial communities occur. In addition, the variation between specific mucosa-associated communities remains unknown. To address this gap in knowledge of the microbiome associated with ASD, biopsies from the antrum, duodenum, ileum, right colon, and rectum of children with ASD and age- and sex-matched TD children were examined by 16S rRNA sequencing. We observed an overall elevated abundance of Bacillota and Bacteroidota and a decreased abundance of Pseudomonadota in all GI tract regions of both male and female children with ASD compared with TD children. Further analysis at the genera level revealed unique differences in the microbiome in the different regions of the GI tract in children with ASD compared with TD children. We also observed sex-specific differences in the gut microbiota composition in children with ASD. These data indicate that the microbiota of children with ASD is altered in multiple regions of the GI tract and that different anatomic locations have unique alterations in mucosa-associated bacterial genera.NEW & NOTEWORTHY Analysis in stool samples has shown gut microbiota alterations in children with autism spectrum disorder (ASD) compared with typically developing (TD) children. However, it is unclear which segment(s) of the gut exhibit alterations in microbiome composition. In this study, we examined microbiota composition along the gastrointestinal (GI) tract in the stomach, duodenum, ileum, right colon, and rectum. We found site-specific and sex-specific differences in the gut microbiota of children with ASD, compared with controls.

Milk replacer feeding once or twice a day did not change the ruminal metabolomic profile and the microbial diversity of dairy calves from birth to weaning

In commercial dairy production systems, feeding calves once daily could be an alternative to reduce labor expenses. Several studies comparing once-a-day (OAD) versus twice-a-day (TAD) milk feeding systems have not evidenced differences in calf growth, rumen development, blood parameters or health scores, but effect on ruminal microbiota remains to be investigated. The objective of this study was to determine the effects of OAD or TAD on the establishment of the ruminal microbiota and its metabolic activity. Sixteen male calves (45.9 ± 5.7 kg at birth) were involved in the trial from birth to weaning (63 d). After the colostrum phase, 2 feeding programs based on a milk replacer were tested and calves were allocated to these programs on d 5. To study the establishment of the bacterial community, ruminal fluid was obtained from each calf 1 h after the morning meal at 7, 35, and 63 d of age. The ruminal metabolome was evaluated at a 7-d interval from d 1 to d 63. Ruminal microbiota and metabolite profiles were characterized by 16 S rRNA gene sequencing- and by 1H nuclear magnetic resonance spectroscopy, respectively. Our results showed that feeding milk replacer once or TAD did not change the ruminal microbiota and metabolites of dairy calves from birth to weaning. Microbial data showed that diversity and richness increased with age, suggesting a shift from a heterogeneous and less diverse community after birth (d 7) to a more diverse but homogeneous community at 35 and 63 d. These findings suggest that feeding milk OAD can be successfully applied to a calf feeding system without compromising microbial establishment and functions.

Development of systemic and mucosal immune responses against gut microbiota in early life and implications for the onset of allergies

The early microbial colonization of human mucosal surfaces is essential for the development of the host immune system. Already during pregnancy, the unborn child is prepared for the postnatal influx of commensals and pathogens via maternal antibodies, and after birth this protection is continued with antibodies in breast milk. During this critical window of time, which extends from pregnancy to the first year of life, each encounter with a microorganism can influence children's immune response and can have a lifelong impact on their life. For example, there are numerous links between the development of allergies and an altered gut microbiome. However, the exact mechanisms behind microbial influences, also extending to how viruses influence host-microbe interactions, are incompletely understood. In this review, we address the impact of infants' first microbial encounters, how the immune system develops to interact with gut microbiota, and summarize how an altered immune response could be implied in allergies.

Modulation of gut microbiome in the treatment of neurodegenerative diseases: A systematic review

BACKGROUND AND AIMS

Microbiota plays an essential role in maintaining body health, through positive influences on metabolic, defensive, and trophic processes and on intercellular communication. Imbalance in intestinal flora, with the proliferation of harmful bacterial species (dysbiosis) is consistently reported in chronic illnesses, including neurodegenerative diseases (ND). Correcting dysbiosis can have a beneficial impact on the symptoms and evolution of ND. This review examines the effects of microbiota modulation through administration of probiotics, prebiotics, symbiotics, or prebiotics' metabolites (postbiotics) in patients with ND like multiple sclerosis (MS), Alzheimer's disease (AD), Parkinson's disease (PD) and amyotrophic lateral sclerosis (ALS).

METHODS

PubMed, Web of Science, Medline databases and ClinicalTrials.gov registry searches were performed using pre-/pro-/postbiotics and ND-related terms. Further references were obtained by checking relevant articles.

RESULTS

Although few compared to animal studies, the human studies generally show positive effects on disease-specific symptoms, overall health, metabolic parameters, on oxidative stress and immunological markers. Therapy with probiotics in various forms (mixtures of bacterial strains, fecal microbiota transplant, diets rich in fermented foods) exert favorable effects on patients' mental health, cognition, and quality of life, targeting pathogenetic ND mechanisms and inducing reparatory mechanisms at the cellular level. More encouraging results have been observed in prebiotic/postbiotic therapy in some ND.

CONCLUSIONS

The effects of probiotic-related interventions depend on the patients' ND stage and pre-existing allopathic medication. Further studies on larger cohorts and long term comprehensive neuropsychiatric, metabolic, biochemical testing, and neuroimaging monitoring are necessary to optimize therapeutic protocols in ND.

A Meta-analysis of the Effect of Probiotic Lactobacillus sp. as Immunomodulating Inflammatory Responses

Lactobacillus sp. is considered an indispensable probiotic, and this probiotic has an effective role in maintaining the immune system. We evaluated the effect of the probiotic Lactobacillus sp. on modulating inflammation in several cases. In collecting the literature, we used databases from the Web of Science, the Cochrane Central Register of Controlled Trials, PubMed, and Embase. Studies that met the inclusion criteria were analyzed using Review Manager (version 5.4). A p-value of <0.05 of the total effect is considered statistically significant. Finally, 1895 references were retrieved and 20 were included in the meta-analysis. This meta-analysis suggested that most cases in this study were healthy elderly who received treatment with Lactobacillus sp. Lactobacillus sp. has a positive effect on B cells, eosinophils, IgE, NK cells, TNF-α, and IL-10. Lactobacillus could regulate the immune system by modulating inflammation in the healthy elderly.

Relationship between maternal consumption of fermented foods and the development of the offspring at the age of 3 years: The Japan Environment and Children's Study

BACKGROUND

It is well known that maternal diet affects the development of offspring. Herein, the relationship between maternal intake of fermented foods during pregnancy and offspring development was investigated.

METHODS

The diet of 103,060 pregnant women at >4 months of gestation who were enrolled in the Japan Environment and Children's Study was analyzed. Their intake levels of fermented soybeans (miso and natto), yogurt, and cheese were investigated. The developmental status of the offspring at 3 years of age was assessed using the Ages and Stages Questionnaires (ASQ-3). Multivariable logistic regression analysis was performed to determine the risk of maternal intake levels of the fermented foods associated with subsequent developmental delay in the offspring.

RESULTS

Intake of cheese was associated with a reduced risk of child developmental delay in all intake level groups from the second quartile onward. Intakes of miso and yogurt were associated with a reduced risk of developmental delay in communication skills in the fourth quartile. There was no association between intake of natto and developmental delay.

CONCLUSION

Maternal consumption of fermented foods during pregnancy may reduce the risk of later developmental delay in offspring. It is therefore important to review the mother's diet for fermented foods during pregnancy. However, further studies are warranted to evaluate the factors influencing the association between diet and offspring development.

MAIT cells monitor intestinal dysbiosis and contribute to host protection during colitis

Intestinal inflammation shifts microbiota composition and metabolism. How the host monitors and responds to such changes remains unclear. Here, we describe a protective mechanism by which mucosal-associated invariant T (MAIT) cells detect microbiota metabolites produced upon intestinal inflammation and promote tissue repair. At steady state, MAIT ligands derived from the riboflavin biosynthesis pathway were produced by aerotolerant bacteria residing in the colonic mucosa. Experimental colitis triggered luminal expansion of riboflavin-producing bacteria, leading to increased production of MAIT ligands. Modulation of intestinal oxygen levels suggested a role for oxygen in inducing MAIT ligand production. MAIT ligands produced in the colon rapidly crossed the intestinal barrier and activated MAIT cells, which expressed tissue-repair genes and produced barrier-promoting mediators during colitis. Mice lacking MAIT cells were more susceptible to colitis and colitis-driven colorectal cancer. Thus, MAIT cells are sensitive to a bacterial metabolic pathway indicative of intestinal inflammation.

Establishment and perturbation of human gut microbiome: common trends and variations between Indian and global populations

Human gut microbial species are crucial for dietary metabolism and biosynthesis of micronutrients. Digested products are utilised by the host as well as several gut bacterial species. These species are influenced by various factors such as diet, age, geographical location, and ethnicity. India is home to the largest human population in the world. It is spread across diverse ecological and geographical locations. With variable dietary habits and lifestyles, Indians have unique gut microbial composition. This review captures contrasting and common trends of gut bacterial community establishment in infants (born through different modes of delivery), and how that bacterial community manifests itself along infancy, through old age between Indian and global populations. Because dysbiosis of the gut community structure is associated with various diseases, this review also highlights the common and unique bacterial species associated with various communicable as well as noncommunicable diseases such as diarrhoea, amoebiasis, malnutrition, type 2 diabetes, obesity, colorectal cancer, inflammatory bowel disease, and gut inflammation and damage to the brain in the global and Indian population.

A successional shift enhances stability in ant symbiont communities

Throughout succession, communities undergo structural shifts, which can alter the relative abundances of species and how they interact. It is frequently asserted that these alterations beget stability, i.e. that succession selects for communities better able to resist perturbations. Yet, whether and how alterations of network structure affect stability during succession in complex communities is rarely studied in natural ecosystems. Here, we explore how network attributes influence stability of different successional stages of a natural network: symbiotic arthropod communities forming food webs inside red wood ant nests. We determined the abundance of 16 functional groups within the symbiont community across 51 host nests in the beginning and end stages of succession. Nest age was the main driver of the compositional shifts: symbiont communities in old nests contained more even species abundance distributions and a greater proportion of specialists. Based on the abundance data, we reconstructed interaction matrices and food webs of the symbiont community for each nest. We showed that the enhanced community evenness in old nests leads to an augmented food web stability in all but the largest symbiont communities. Overall, this study demonstrates that succession begets stability in a natural ecological network by making the community more even.

Unraveling the Microbiome-Human Body Axis: A Comprehensive Examination of Therapeutic Strategies, Interactions and Implications

This review scrutinizes the intricate interplay between the microbiome and the human body, exploring its multifaceted dimensions and far-reaching implications. The human microbiome, comprising diverse microbial communities inhabiting various anatomical niches, is increasingly recognized as a critical determinant of human health and disease. Through an extensive examination of current research, this review elucidates the dynamic interactions between the microbiome and host physiology across multiple organ systems. Key topics include the establishment and maintenance of microbiota diversity, the influence of host factors on microbial composition, and the bidirectional communication pathways between microbiota and host cells. Furthermore, we delve into the functional implications of microbiome dysbiosis in disease states, emphasizing its role in shaping immune responses, metabolic processes, and neurological functions. Additionally, this review discusses emerging therapeutic strategies aimed at modulating the microbiome to restore host-microbe homeostasis and promote health. Microbiota fecal transplantation represents a groundbreaking therapeutic approach in the management of dysbiosis-related diseases, offering a promising avenue for restoring microbial balance within the gut ecosystem. This innovative therapy involves the transfer of fecal microbiota from a healthy donor to an individual suffering from dysbiosis, aiming to replenish beneficial microbial populations and mitigate pathological imbalances. By synthesizing findings from diverse fields, this review offers valuable insights into the complex relationship between the microbiome and the human body, highlighting avenues for future research and clinical interventions.

Antibiotics Use and Its Effects on the Establishment of Feeding Tolerance in Preterm Neonates

OBJECTIVE

Antibiotics are one of the most widely used medications in today's neonatal intensive care units. Indiscriminate antibiotic usage persists in preterm newborns who are symptomatic due to factors linked to prematurity rather than being septic. Previous studies in older infants suggest that prior antibiotic administration is associated with possible dysmotility and microbial dysbiosis in the intestinal tract. We hypothesize that early antibiotic administration impacts high-risk preterm infants' tolerance to enteral feeding advancement.

STUDY DESIGN

As part of the Routine Early Antibiotic Use in SymptOmatic Preterm Neonates study, symptomatic preterm newborns without maternal infection risk factors were randomized to receive or not receive antibiotics, with C1 receiving antibiotics and C2 not. Of the 55 newborns that underwent pragmatic randomization, 28 preterm neonates in group C1 received antibiotics.

RESULTS

The premature neonates in the randomized groups who received antibiotics and those who did not showed no differences in sustained feeding tolerance.

CONCLUSION

Our investigation of the risk of feeding issues in babies who get antibiotics early in life revealed no differences between neonates who received antibiotics and those who did not when the randomized controlled trial data alone was reviewed. Given the sample sizes, it is uncertain if the preceding analysis is powerful enough to detect differences (a significant percentage of neonates who were randomly assigned to NOT get antibiotics subsequently received early treatment due to changing clinical conditions). This affirms the requirement for a meticulously designed prospective randomized study.

KEY POINTS

· Defining feeding tolerance for the first time in neonates.. · Patients from the REASON trial were evaluated.. · Preterm neonates were the focus of this study..

Castration alters the ileum microbiota of Holstein bulls and promotes beef flavor compounds

BACKGROUND

In the beef industry, bull calves are usually castrated to improve flavor and meat quality; however, this can reduce their growth and slaughter performance. The gut microbiota is known to exert a significant influence on growth and slaughter performance. However, there is a paucity of research investigating the impact of castration on gut microbiota composition and its subsequent effects on slaughter performance and meat flavor.

RESULT

The objective of this study was to examine the processes via which castration hinders slaughter productivity and enhances meat quality. Bull and castrated calves were maintained under the same management conditions, and at slaughter, meat quality was assessed, and ileum and epithelial tissue samples were obtained. The research employed metagenomic sequencing and non-targeted metabolomics techniques to investigate the makeup of the microbiota and identify differential metabolites. The findings of this study revealed the Carcass weight and eye muscle area /carcass weight in the bull group were significantly higher than those in the steer group. There were no significant differences in the length, width, and crypt depth of the ileum villi between the two groups. A total of 53 flavor compounds were identified in the two groups of beef, of which 16 were significantly higher in the steer group than in the bull group, and 5 were significantly higher in the bull group than in the steer group. In addition, bacteria, Eukaryota, and virus species were significantly separated between the two groups. The lipid metabolism pathways of α-linolenic acid, linoleic acid, and unsaturated fatty acids were significantly enriched in the Steers group. Compared with the steer group, the organic system pathway is significantly enriched in the bull group. The study also found that five metabolites (LPC (0:0/20:3), LPC (20:3/0:0), LPE (0:0/22:5), LPE (22:5/0:0), D-Mannosamine), and three species (s_Cloning_vector_Hsp70_LexA-HP1, s_Bacteroides_Coprophilus_CAG: 333, and s_Clostridium_nexile-CAG: 348) interfere with each other and collectively have a positive impact on the flavor compounds of beef.

CONCLUSIONS

These findings provide a basic understanding that under the same management conditions, castration does indeed reduce the slaughter performance of bulls and improve the flavor of beef. Microorganisms and metabolites contribute to these changes through interactions.

From womb to world: mapping gut microbiota-related health literacy among Italian mothers, a cross-sectional study

BACKGROUND

The gut microbiota is a key determinant of long-term health. Promoting maternal health literacy may enhance children well-being. Aim of the present study was to assess gut microbiota-related health literacy of Italian women and identify potential gaps in awareness.

METHODS

A cross-sectional survey study was conducted using an online questionnaire (17 questions) on determinants and long-term impact of infant gut microbiota. The survey targeted Italian pregnant women and mothers of children under 2 years old, and was distributed through various social media channels between September 28th and November 15th, 2022. A total score was calculated as the sum of positive answers. Data on demographics, pregnancy status, and pre-existing knowledge of the infant gut microbiota were also collected. Descriptive and inferential statistics were applied.

RESULTS

The questionnaire was completed by 1076 women. Median total score was 9 [7-11]. The 81.7% of respondents declared prior knowledge of the gut microbiota. The internet was among the most commonly cited primary sources of information. Independent predictors of total score were having a university degree (B = 0.656, p = 0.002) and prior knowledge (B = 2.246, p < 0.001). Conversely, older age was associated with lower total scores (B = -0.092, p < 0.001). The least known determinants of infant gut microbiota were gestational BMI, prematurity, mode of delivery and NICU stay. Pregnant women failed to recognize the role of breastfeeding in the development of infant gut microbiota more frequently than non-pregnant women. The 97.5% of participants reported increased interest in the gut microbiota, with heightened interest associated with prior knowledge.

CONCLUSIONS

Our study revealed a moderate level of knowledge about infant gut microbiota among respondents, emphasizing the positive impact of prior knowledge on understanding and interest. Targeted educational interventions are needed to address awareness gaps, especially concerning the influence of breastfeeding on infant gut microbiota. Healthcare providers have the potential to enhance women's knowledge and awareness of this topic.

Change in the Gut Microbiota of Lactating Sows and Their Piglets by Inclusion of Dietary Spray-Dried Plasma in Sow Diets

This study aimed to investigate the effects of dietary spray-dried plasma (SDP) on the gut microbiota of lactating sows and their piglets. A total of 12 sows were randomly assigned to one of two dietary treatment groups in a completely randomized design. The treatments were a sow diet based on corn and soybean meal (CON), and a CON diet with an added 1% SDP. The sows were fed the dietary treatments from d 30 before farrowing to weaning (d 28). The fecal samples of three sows from each treatment and two of their randomly selected piglets were collected to verify their fecal microbiota. There were no differences in the alpha diversity and distinct clustering of the microbial communities in the sows and their piglets when SDP was added to the sow diets from late gestation to weaning. The fecal microbiota of the lactating sows and their piglets showed a higher relative abundance of the phylum Bacteroidota and genus Lactobacillus and Ruminococcus and showed a lower relative abundance of the phylum Bacillota and genus Bacteroides, Escherichia/Shigella, and Clostridium in the sows fed the SDP diet than those fed the CON diet. Overall, these results show that the addition of SDP to the sow diet during lactation altered the gut environment with positive microbial composition changes. These results were similar in the nursing piglets, suggesting that the control of the sow diets during lactation may contribute to the intestinal health and growth in piglets after weaning.

Early-life ruminal microbiome-derived indole-3-carboxaldehyde and prostaglandin D2 are effective promoters of rumen development

BACKGROUND

The function of diverse ruminal microbes is tightly linked to rumen development and host physiology. The system of ruminal microbes is an excellent model to clarify the fundamental ecological relationships among complex nutrient-microbiome-host interactions. Here, neonatal lambs are introduced to different dietary regimes to investigate the influences of early-life crosstalk between nutrients and microbiome on rumen development.

RESULTS

We find starchy corn-soybean starter-fed lambs exhibit the thickest ruminal epithelia and fiber-rich alfalfa hay-fed lambs have the thickest rumen muscle. Metabolome and metagenome data reveal that indole-3-carboxaldehyde (3-IAld) and prostaglandin D2 (PGD2) are the top characteristic ruminal metabolites associated with ruminal epithelial and muscular development, which depend on the enhanced ruminal microbial synthesis potential of 3-IAld and PGD2. Moreover, microbial culture experiment first demonstrates that Bifidobacterium pseudolongum is able to convert tryptophan into 3-IAld and Candida albicans is a key producer for PGD2. Transcriptome sequencing of the ruminal epithelia and smooth muscle shows that ruminal epithelial and muscular development is accompanied by Wnt and Ca2+ signaling pathway activation. Primary cell cultures further confirm that 3-IAld promotes ruminal epithelial cell proliferation depending on AhR-wnt/β-catenin signaling pathway and PGD2 accelerates ruminal smooth muscle cell proliferation via Ca2+ signaling pathway. Furthermore, we find that 3-IAld and PGD2 infusion promote ruminal epithelial and musculature development in lambs.

CONCLUSIONS

This study demonstrates that early-life ruminal microbiome-derived 3-IAld and PGD2 are effective promoters of rumen development, which enhances our understanding of nutrient-microbiome-host interactions in early life.

The role of the gut microbiome in gastrointestinal cancers

The gut microbiota present in the human digestive system is incredibly varied and is home to trillions of microorganisms. The gut microbiome is shaped at birth, while numerous genetic, dietary, and environmental variables primarily influence the microbiome composition. The importance of gut microbiota on host health is becoming more widely acknowledged. Digestion, intestinal permeability, and immunological and metabolism responses can all be affected by changes in the composition and function of the gut microbiota. There is mounting evidence that the microbial population's complex traits are important biomarkers and indicators of patient outcomes in cancer and its therapies. Numerous studies have demonstrated that changed commensal gut microorganisms contribute to the development and spread of cancer through various routes. Despite the ongoing controversy surrounding the gut microbiome and gastrointestinal cancer, accumulating evidence points to a potentially far more intricate connection than a simple cause-and-effect relationship. SIMPLE SUMMARY: Due to their high frequency and fatality rate, gastrointestinal cancers are regarded as a severe public health issue with complex medical and economic burdens. The gut microbiota may directly or indirectly interact with existing therapies like immunotherapy and chemotherapy, affecting how well a treatment works. The gut microbiome influences the immune response's activity, function, and development. Generally, certain gut bacteria impact the antitumor actions during cancer by creating particular metabolites or triggering T-cell responses. Yet, certain bacterial species have been found to promote cellular proliferation and metastasis in cancer, and comprehending these interactions in the context of cancer may help identify possible treatment targets. Notwithstanding the improvements in the field, additional research is still required to comprehend the underlying processes, examine the effects on existing therapies, and pinpoint certain bacteria and immune cells that can cause this interaction.

PETR: A novel peristaltic mixed tubular bioreactor simulating human colonic conditions

A novel bioreactor simulating human colonic conditions for in vitro cultivation of intestinal microbiota is presented. The PEristaltic mixed Tubular bioReactor (PETR) is modular designed and periodically kneaded to simulate intestinal peristalsis. The reactor is introduced, characterized from a bioprocess engineer's perspective and discussed in its ability to mimic colon conditions. PETR provides physiological temperature and appropriate anaerobic conditions, simulates intestinal peristalsis, and has a mean residence time of 32.8 ± 0.8 h comparable to the adult human colon. The single-tube design enables a time-constant and longitudinally progressive pH gradient from 5.5 to 7.0. Using a dialysis liquid containing high molecular weight polyethylene glycol, the integrated dialysis system efficiently absorbs short chain fatty acids (up to 60%) and water (on average 850 mL d-1 ). Cultivation of a typical gut bacterium (Bifidobacterium animalis) was performed to demonstrate the applicability for controlled microbiota cultivation. PETR is unique in combining simulation of the entire colon, peristaltic mixing, dialytic water and metabolite absorption, and a progressive pH gradient in a single-tube design. PETR is a further step to precise replication of colonic conditions in vitro for reliable and reproducible microbiota research, such as studying the effect of food compounds, prebiotics or probiotics, or the development and treatment of infections with enteric pathogens, but also for further medical applications such as drug delivery studies or to study the effect of drugs on and their degradation by the microbiota.

Microbiota of pregnancy, placenta and newborns in the third trimester: A randomized controlled study

Microbiota in pregnant time is vital to healthy of pregnant women and their offspring. However, few study evaluate the composition of the microbiota of health pregnancy, placenta and their newborns at different stages and the origin of the placental microbiota. Samples were obtained from a total of 31 pregnant individuals and their offspring, analyzing by 16S rRNA amplicon sequencing of the V4 region to evaluate the composition and variation of them. We found that the microbiota of pregnant individuals changes in the third trimester. The placental microbiota has its own specific dominant microbiota. The placental microbiota is correlated with the pregnancy microbiota in the gut and vagina at 32-34 weeks but not at full term. The gut microbiota in newborns changes over the first 14 days.

Fermented Mare Milk and Its Microorganisms for Human Consumption and Health

Mare milk is consumed by approximatively 30 million people in the world. In countries in Asia and East Europe, mare milk is mainly consumed as source of fermented products, called koumiss, airag or chigee, alcoholic beverages obtained by means of a culture of bacteria and lactose-fermenting yeasts. Recent research concerning mare milk and its derivatives deals mainly with their potential employment for human health. Studies about the isolation and characterization of Lactobacillus spp. and yeasts from koumiss have been aimed at assessing the potential functional properties of these micro-organisms and to find their employment for the industrial processing of mare milk. The aim of this literature review is to summarize recent research about microorganisms in fermented mare milk products and their potential functional properties.

Swine Gastrointestinal Microbiota and the Effects of Dietary Amino Acids on Its Composition and Metabolism

Many researchers consider gut microbiota (trillions of microorganisms) an endogenous organ of its animal host, which confers a vast genetic diversity in providing the host with essential biological functions. Particularly, the gut microbiota regulates not only gut tissue structure but also gut health and gut functionality. This paper first summarized those common bacterial species (dominated by the Firmicutes, Bacteroidota, and Proteobacteria phyla) in swine gut and then briefly discussed their roles in swine nutrition and health, which include roles in nutrient metabolism, pathogen exclusion, and immunity modulation. Secondly, the current knowledge on how dietary nutrients and feed additives affect the gut bacterial composition and nutrient metabolism in pigs was discussed. Finally, how dietary amino acids affect the relative abundances and metabolism of bacteria in the swine gut was reviewed. Tryptophan supplementation promotes the growth of beneficial bacteria and suppresses pathogens, while arginine metabolism affects nitrogen recycling, impacting gut immune response and health. Glutamate and glutamine supplementations elevate the levels of beneficial bacteria and mitigate pathogenic ones. It was concluded that nutritional strategies to manipulate gut microbial ecosystems are useful measures to optimize gut health and gut functions. For example, providing pigs with nutrients that promote the growth of Lactobacillus and Bifidobacterium can lead to better gut health and growth performance, especially when dietary protein is limited. Further research to establish the mechanistic cause-and-effect relationships between amino acids and the dynamics of gut microbiota will allow swine producers to reap the greatest return on their feed investment.

Dietary fiber pectin: challenges and potential anti-inflammatory benefits for preterms and newborns

Pectins, a class of dietary fibers abundant in vegetables and fruits, have drawn considerable interest due to their potential anti-inflammatory properties. Numerous studies have indicated that incorporating pectins into infant formula could be a safe strategy for alleviating infant regurgitation and diarrhea. Moreover, pectins have been shown to modulate cytokine production, macrophage activity, and NF-kB expression, all contributing to their anti-inflammatory effects. Despite this promising evidence, the exact mechanisms through which pectins exert these functions and how their structural characteristics influence these processes remain largely unexplored. This knowledge is particularly significant in the context of gut inflammation in developing preterm babies, a critical aspect of necrotizing enterocolitis (NEC), and in children and adults dealing with inflammatory bowel disease (IBD). Our mini review aims to provide an up-to-date compilation of relevant research on the effects of pectin on gut immune responses, specifically focusing on preterms and newborns. By shedding light on the underlying mechanisms and implications of pectin-mediated anti-inflammatory properties, this review seeks to advance our knowledge in this area and pave the way for future research and potential therapeutic interventions.

A comprehensive diversity analysis on the gut microbiomes of ASD patients: from alpha, beta to gamma diversities

Autism spectrum disorder (ASD) is estimated to influence as many as 1% children worldwide, but its etiology is still unclear. It has been suggested that gut microbiomes play an important role in regulating abnormal behaviors associated with ASD. A de facto standard analysis on the microbiome-associated diseases has been diversity analysis, and nevertheless, existing studies on ASD-microbiome relationship have not produced a consensus. Here, we perform a comprehensive analysis of the diversity changes associated with ASD involving alpha-, beta-, and gamma-diversity metrics, based on 8 published data sets consisting of 898 ASD samples and 467 healthy controls (HC) from 16S-rRNA sequencing. Our findings include: (i) In terms of alpha-diversity, in approximately 1/3 of the studies cases, ASD patients exhibited significantly higher alpha-diversity than the HC, which seems to be consistent with the "1/3 conjecture" of diversity-disease relationship (DDR). (ii) In terms of beta-diversity, the AKP (Anna Karenina principle) that predict all healthy microbiomes should be similar, and every diseased microbiome should be dissimilar in its own way seems to be true in approximately 1/2 to 3/4 studies cases. (iii) In terms of gamma-diversity, the DAR (diversity-area relationship) modeling suggests that ASD patients seem to have large diversity-area scaling parameter than the HC, which is consistent with the AKP results. However, the MAD (maximum accrual diversity) and RIP (ratio of individual to population diversity) parameters did not suggest significant differences between ASD patients and HC. Throughout the study, we adopted Hill numbers to measure diversity, which stratified the diversity measures in terms of the rarity-commonness-dominance spectrum. It appears that the differences between ASD patients and HC are more propounding on rare-species side than on dominant-species side. Finally, we discuss the apparent inconsistent diversity-ASD relationships among different case studies and postulate that the relationships are not monotonic.

Insights into the Microbial Composition of Intratumoral, Reproductive Tract, and Gut Microbiota in Ovarian Cancer Patients

According to the latest global cancer data, ovarian cancer is the deadliest among all gynecological malignant tumors and ranks fifth in terms of mortality. Its etiology and pathogenesis are unknown, and the 5-year survival rate of patients with advanced ovarian cancer is only 40% (Sung et al. CA Cancer J Clin 71:209-49, 2021). Recent research has shown that the human microbiota plays a crucial role in the development and progression of tumors, including ovarian cancer. Numerous studies have highlighted the complex connections between the reproductive tract microbiota, intestinal microbiota, and ovarian cancer (Jacobson et al. PeerJ 9:e11574, 2021). Therefore, this chapter will delve into composition, function, and the correlation between microbiota and immunity in the field of ovarian cancer microbiota, as well as the potential of bacteria in therapeutics and diagnostics of ovarian cancer.

Effects of Broad Bean Diet on the Growth Performance, Muscle Characteristics, Antioxidant Capacity, and Intestinal Health of Nile Tilapia (Oreochromis niloticus)

Four crisping diets were designed to conduct a feeding experiment to investigate the use of broad bean in the formulated feed of Nile tilapia and optimize its use. The growth performance, muscle characteristics, antioxidant capacity, and intestinal health of Nile tilapia with an initial body weight of 617.32 ± 1.64 g were evaluated after being fed with different diets for 90 days. The results showed no adverse effect on the growth performance of Nile tilapia fed with broad bean diets. Contrastingly, some improvements were found in WGR and SGR, but a lower FCR was obtained. The supplementation of broad beans weakened the antioxidant capacity of fish but did not influence liver health and the immune system. Increasing the amount of broad bean addition can increase muscle quality values, and an embrittling functional package being added to the diet can also improve muscle hardness, adhesiveness, and chewiness of Nile tilapia muscle. In addition, the crisping functional package can be applied to tilapia crisping formulated feed, which helps to improve the integrity of the intestinal tissue structure and optimize the intestinal microbiota of Nile tilapia. The final achievement of this study is to provide a theoretical reference for optimizing the breeding technology of crispy Nile tilapia and developing a specialized crisping diet for the species.

What are patterns of rise and decline?

The notions of change, such as birth, death, growth, evolution and longevity, extend across reality, including biological, cultural and societal phenomena. Patterns of change describe how success and composition of every entity, from species to societies, vary across time. Languages develop into new languages, music and fashion continuously evolve, economies rise and decline, ecological and societal crises come and go. A common way to perceive and analyse change processes is through patterns of rise and decline, the ubiquitous, often distinctively unimodal trajectories describing life histories of various entities. These patterns come in different shapes and are measured according to varying definitions. Depending on how they are measured, patterns of rise and decline can reveal, emphasize, mask or obscure important dynamics in natural and cultural phenomena. Importantly, the variations of how dynamics are measured can be vast, making it impossible to directly compare patterns of rise and decline across fields of science. Standardized analysis of these patterns has the potential to uncover important but overlooked commonalities across natural phenomena and potentially help us catch the onset of dramatic shifts in entities' state, from catastrophic crashes in success to gradual emergence of new entities. We provide a framework for standardized recognizing, characterizing and comparing patterns of change by combining understanding of dynamics across fields of science. Our toolkit aims at enhancing understanding of the most general tendencies of change, through two complementary perspectives: dynamics of emergence and dynamics of success. We gather comparable cases and data from different research fields and summarize open research questions that can help us understand the universal principles, perception-biases and field-specific tendencies in patterns of rise and decline of entities in nature.

Early Colonization of the Intestinal Microbiome of Neonatal Piglets Is Influenced by the Maternal Microbiome

The intestinal microbiome plays a crucial role in animal health and growth by interacting with the host, inhibiting pathogenic microbial colonization, and regulating immunity. This study investigated dynamic changes in the fecal microbial composition of piglets from birth through weaning and the relationship between the piglet fecal microbiome and sows. Feces, skin, neonatal oral cavity, and vaginal samples were collected from eight sows and sixty-three piglets, and 16S genome sequencing was performed. The results revealed that Firmicutes, Bacteroidetes, and Proteobacteria dominated the piglet microbiome in the early stages, and Firmicutes and Bacteroidetes were crucial for maintaining a balance in the intestinal microbiome during nursing. The abundance of Christensenellaceae_R-7_group, Succinivibrio, and Prevotella increased in weaned piglets fed solid feed. Analysis of the microbiome from sows to piglets indicated a shift in the microbiome colonizing piglet intestines, which became a significant constituent of the piglet intestinal microbiome. This study supports the theory that the neonatal intestinal microbiome is vertically transmitted from the mother. Further research is required to integrate factors related to sows, piglets, and their environments to gain a better understanding of the early establishment of the intestinal microbiome in piglets.

Secretory-IgA binding to intestinal microbiota attenuates inflammatory reactions as the intestinal barrier of preterm infants matures

Previous work has shown that Secretory-IgA (SIgA) binding to the intestinal microbiota is variable and may regulate host inflammatory bowel responses. Nevertheless, the impact of the SIgA functional binding to the microbiota remains largely unknown in preterm infants whose immature epithelial barriers make them particularly susceptible to inflammation. Here, we investigated SIgA binding to intestinal microbiota isolated from stools of preterm infants <33 weeks gestation with various levels of intestinal permeability. We found that SIgA binding to intestinal microbiota attenuates inflammatory reactions in preterm infants. We also observed a significant correlation between SIgA affinity to the microbiota and the infant's intestinal barrier maturation. Still, SIgA affinity was not associated with developing host defenses, such as the production of mucus and inflammatory calprotectin protein, but it depended on the microbiota shifts as the intestinal barrier matures. In conclusion, we reported an association between the SIgA functional binding to the microbiota and the maturity of the preterm infant's intestinal barrier, indicating that the pattern of SIgA coating is altered as the intestinal barrier matures.

The Maternal Microbiome and Gestational Diabetes Mellitus: Cause and Effect

Gestational diabetes mellitus (GDM) is a growing public health concern that affects many pregnancies globally. The condition is associated with adverse maternal and neonatal outcomes including gestational hypertension, preeclampsia, placental abruption, preterm birth, stillbirth, and fetal growth restriction. In the long-term, mothers and children have an increased risk of developing metabolic diseases such as type 2 diabetes and cardiovascular disease. Accumulating evidence suggest that alterations in the maternal microbiome may play a role in the pathogenesis of GDM and adverse pregnancy outcomes. This review describes changes in the maternal microbiome during the physiological adaptations of pregnancy, GDM and adverse maternal and neonatal outcomes. Findings from this review highlight the importance of understanding the link between the maternal microbiome and GDM. Furthermore, new therapeutic approaches to prevent or better manage GDM are discussed. Further research and clinical trials are necessary to fully realize the therapeutic potential of the maternal microbiome and translate these findings into clinical practice.

High-Throughput Sequencing Reveals a Dynamic Bacterial Linkage between the Captive White Rhinoceros and Its Environment

Soil is an essential part of the animal habitat and has a large diversity of microbiota, while the animal body was colonized by a complex bacterial community; so far, the relationship between the animal host microbial community and the soil microbial ecosystem remains largely unknown. In this study, 15 white rhinoceros from three different captive grounds were selected and the bacterial community of the gut, skin, and environment of these rhinoceros were analyzed by 16S rRNA sequencing technology. Our results showed that Firmicutes and Bacteroidota were the predominant phyla in the gut microbiome, whereas skin and environment samples share similar microbiome profiles and are dominated by the phyla of Actinobacteriota, Chloroflexi, and Proteobacteria. Although the bacterial composition of the gut differs from that of the skin and environment, the Venn diagrams showed that there were 22 phyla and 186 genera shared by all the gut, skin, and environmental microbes in white rhinoceroses. Further cooccurrence network analysis indicated a bacterial linkage based on a complex interaction was established by the bacterial communities from the three different niches. In addition, beta diversity and bacterial composition analysis showed that both the captive ground and host ages induced shifts in the microbial composition of white rhinoceroses, which suggested that the bacterial linkage between the captive white rhinoceros and its environment is dynamic. Overall, our data contribute to a better understanding of the bacterial community of the captive white rhinoceros, especially for the relationship between the environment and animal bacterial communities. IMPORTANCE The white rhinoceros is one of the world's most endangered mammals. The microbial population plays a key role in animal health and welfare; however, studies regarding the microbial communities of the white rhinoceros are relatively limited. As the white rhinoceros has a common behavior of mud baths and thus is in direct contact with the environment, a relationship between the animal microbial community and the soil microbial ecosystem appears possible, but it remains unclear. Here, we described the characteristics and interaction of bacterial communities of the white rhinoceros in three different niches, including gut, skin, and environment. We also analyzed the effects of captive ground and age on the composition of the bacterial community. Our findings highlighted the relationship among the three niches and may have important implications for the conservation and management of this threatened species.

Mechanisms and regulation of defensins in host defense

As a family of cationic host defense peptides, defensins are mainly synthesized by Paneth cells, neutrophils, and epithelial cells, contributing to host defense. Their biological functions in innate immunity, as well as their structure and activity relationships, along with their mechanisms of action and therapeutic potential, have been of great interest in recent years. To highlight the key research into the role of defensins in human and animal health, we first describe their research history, structural features, evolution, and antimicrobial mechanisms. Next, we cover the role of defensins in immune homeostasis, chemotaxis, mucosal barrier function, gut microbiota regulation, intestinal development and regulation of cell death. Further, we discuss their clinical relevance and therapeutic potential in various diseases, including infectious disease, inflammatory bowel disease, diabetes and obesity, chronic inflammatory lung disease, periodontitis and cancer. Finally, we summarize the current knowledge regarding the nutrient-dependent regulation of defensins, including fatty acids, amino acids, microelements, plant extracts, and probiotics, while considering the clinical application of such regulation. Together, the review summarizes the various biological functions, mechanism of actions and potential clinical significance of defensins, along with the challenges in developing defensins-based therapy, thus providing crucial insights into their biology and potential clinical utility.

White adipose tissue undergoes browning during preweaning period in association with microbiota formation in mice

Beige adipocytes are transiently induced during early postnatal period in mice. Previous studies have suggested that, unlike in adults, the induction is independent of the sympathetic nerve activity; however, the mechanism is yet unknown. Here, we showed that beige adipocytes are induced during the preweaning period in association with the formation of microbiota in mice. Alteration of gut microbiota composition in preweaning mice by maternal treatment with antibiotics or high-fat diet feeding substantially suppressed WAT browning. The suppression was also found in pups transplanted cecal microbiota from pups of high-fat diet-fed dams. These treatments reduced the hepatic expression of genes involved in bile acid synthesis and the serum bile acids level. The abundance of Porphyromonadaceae and Ruminococcaceae in microbiota showed a positive and negative correlation with the induction of beige adipocytes, respectively. This finding may provide comprehensive understanding of the association between gut microbiota and adipose tissue development in the neonatal period.

Faecal Microbiota Characterisation of Potamochoerus porcus Living in a Controlled Environment

Intestinal bacteria establish a specific relationship with the host animal, which causes the acquisition of gut microbiota with a unique composition classified as the enterotype. As the name suggests, the Red River Hog is a wild member of the pig family living in Africa, in particular through the West and Central African rainforest. To date, very few studies have analysed the gut microbiota of Red River Hogs (RRHs) both housed under controlled conditions and in wild habitats. This study analysed the intestinal microbiota and the distribution of Bifidobacterium species in five Red River Hog (RRH) individuals (four adults and one juvenile), hosted in two different modern zoological gardens (Parco Natura Viva, Verona, and Bioparco, Rome) with the aim of disentangling the possible effects of captive different lifestyle and host genetics. Faecal samples were collected and studied both for bifidobacterial counts and isolation by means of culture-dependent method and for total microbiota analysis through the high-quality sequences of the V3-V4 region of bacterial 16S rRNA. Results showed a host-specific bifidobacterial species distribution. Indeed, B. boum and B. thermoacidophilum were found only in Verona RRHs, whereas B. porcinum species were isolated only in Rome RRHs. These bifidobacterial species are also typical of pigs. Bifidobacterial counts were about 10⁶ CFU/g in faecal samples of all the individuals, with the only exception for the juvenile subject, showing 10⁷ CFU/g. As in human beings, in RRHs a higher count of bifidobacteria was also found in the young subject compared with adults. Furthermore, the microbiota of RRHs showed qualitative differences. Indeed, Firmicutes was found to be the dominant phylum in Verona RRHs whereas Bacteroidetes was the most represented in Roma RRHs. At order level, Oscillospirales and Spirochaetales were the most represented in Verona RRHs compared with Rome RRHs, where Bacteroidales dominated over the other taxa. Finally, at the family level, RRHs from the two sites showed the presence of the same families, but with different levels of abundance. Our results highlight that the intestinal microbiota seems to reflect the lifestyle (i.e., the diet), whereas age and host genetics are the driving factors for the bifidobacterial population.

The role of the microbiome on fish mucosal immunity under changing environments

The environment is crucial for fish as their mucosal surfaces face continuous challenges in the water. Fish mucosal surfaces harbor the microbiome and mucosal immunity. Changes in the environment could affect the microbiome, thus altering mucosal immunity. Homeostasis between the microbiome and mucosal immunity is crucial for the overall health of fish. To date, very few studies have investigated mucosal immunity and its interaction with the microbiome in response to environmental changes. Based on the existing studies, we can infer that environmental factors can modulate the microbiome and mucosal immunity. However, we need to retrospectively examine the existing literature to investigate the possible interaction between the microbiome and mucosal immunity under specific environmental conditions. In this review, we summarize the existing literature on the effects of environmental changes on the fish microbiome and mucosal immunity. This review mainly focuses on temperature, salinity, dissolved oxygen, pH, and photoperiod. We also point out a gap in the literature and provide directions to go further in this research field. In-depth knowledge about mucosal immunity-microbiome interaction will also improve aquaculture practices by reducing loss during environmental stressful conditions.

Impact of Gut Microbiota on Host Aggression: Potential Applications for Therapeutic Interventions Early in Development

Aggression in the animal kingdom is a necessary component of life; however, certain forms of aggression, especially in humans, are pathological behaviors that are detrimental to society. Animal models have been used to study a number of factors, including brain morphology, neuropeptides, alcohol consumption, and early life circumstances, to unravel the mechanisms underlying aggression. These animal models have shown validity as experimental models. Moreover, recent studies using mouse, dog, hamster, and drosophila models have indicated that aggression may be affected by the "microbiota-gut-brain axis." Disturbing the gut microbiota of pregnant animals increases aggression in their offspring. In addition, behavioral analyses using germ-free mice have shown that manipulating the intestinal microbiota during early development suppresses aggression. These studies suggest that treating the host gut microbiota during early development is critical. However, few clinical studies have investigated gut-microbiota-targeted treatments with aggression as a primary endpoint. This review aims to clarify the effects of gut microbiota on aggression and discusses the therapeutic potential of regulating human aggression by intervening in gut microbiota.

Maternal effects drive intestinal development beginning in the embryonic period on the basis of maternal immune and microbial transfer in chickens

BACKGROUND

Nutrition drives immunity and health in animals, and maternal immunity benefits offspring. In our previous study, a nutritional intervention strategy was found to promote the immunity of hens, which subsequently improved immunity and growth in offspring chicks. Maternal effects clearly exist, but how are mothers' immune advantages transferred to their offspring, and how do they benefit them?

RESULTS

Here, we traced the beneficial effects back to the process of egg formation in the reproductive system, and we focused on the embryonic intestinal transcriptome and development, as well as on maternal microbial transfer in offspring. We found that maternal nutritional intervention benefits maternal immunity, egg hatching, and offspring growth. The results of protein and gene quantitative assays showed that the transfer of immune factors into egg whites and yolks depends on maternal levels. Histological observations indicated that the promotion of offspring intestinal development begins in the embryonic period. Microbiota analyses suggested that maternal microbes transfer to the embryonic gut from the magnum to the egg white. Transcriptome analyses revealed that offspring embryonic intestinal transcriptome shifts are related to development and immunity. Moreover, correlation analyses showed that the embryonic gut microbiota is correlated with the intestinal transcriptome and development.

CONCLUSIONS

This study suggests that maternal immunity positively influences offspring intestinal immunity establishment and intestinal development beginning in the embryonic period. Adaptive maternal effects might be accomplished via the transfer of relatively large amounts of maternal immune factors and by shaping of the reproductive system microbiota by strong maternal immunity. Moreover, reproductive system microbes may be useful resources for the promotion of animal health. Video Abstract.

Immunity orchestrates a bridge in gut-brain axis of neurodegenerative diseases

Neurodegenerative diseases, in particular for Alzheimer's disease (AD), Parkinson's disease (PD) and Multiple sclerosis (MS), are a category of diseases with progressive loss of neuronal structure or function (encompassing neuronal death) leading to neuronal dysfunction, whereas the underlying pathogenesis remains to be clarified. As the microbiological ecosystem of the intestinal microbiome serves as the second genome of the human body, it is strongly implicated as an essential element in the initiation and/or progression of neurodegenerative diseases. Nevertheless, the precise underlying principles of how the intestinal microflora impact on neurodegenerative diseases via gut-brain axis by modulating the immune function are still poorly characterized. Consequently, an overview of initiating the development of neurodegenerative diseases and the contribution of intestinal microflora on immune function is discussed in this review.

Gut microbiota-mediated metabolism of green tea catechins and the biological consequences: An updated review

Multiple beneficial effects have been attributed to green tea catechins (GTCs). However, the bioavailability of GTCs is generally low, with only a small portion directly absorbed in the small intestine. The majority of ingested GTCs reaches the large intestinal lumen, and are extensively degraded via biotransformation by gut microbiota, forming many low-molecular-weight metabolites such as phenyl-γ-valerolactones, phenolic acids, butyrate, and acetate. This process not only improves the overall bioavailability of GTC-derived metabolites but also enriches the biological activities of GTCs. Therefore, the intra- and inter-individual differences in human gut microbiota as well as the resulting biological contribution of microbial metabolites are crucial for the ultimate health benefits. In this review, the microbial degradation of major GTCs was characterized and an overview of the in vitro models used for GTC metabolism was summarized. The intra- and inter-individual differences of human gut microbiota composition and the resulting divergence in the metabolic patterns of GTCs were highlighted. Moreover, the potential beneficial effects of GTCs and their gut microbial metabolites were also discussed. Overall, the microbial metabolites of GTCs with higher bioavailability and bioactive potency are key factors for the observed beneficial effects of GTCs and green tea consumption.