Early life: gut microbiota and immune development in infancy

Revolutionizing lung health: Exploring the latest breakthroughs and future prospects of synbiotic nanostructures in lung diseases

The escalating prevalence of lung diseases underscores the need for innovative therapies. Dysbiosis in human body microbiome has emerged as a significant factor in these diseases, indicating a potential role for synbiotics in restoring microbial equilibrium. However, effective delivery of synbiotics to the target site remains challenging. Here, we aim to explore suitable nanoparticles for encapsulating synbiotics tailored for applications in lung diseases. Nanoencapsulation has emerged as a prominent strategy to address the delivery challenges of synbiotics in this context. Through a comprehensive review, we assess the potential of nanoparticles in facilitating synbiotic delivery and their structural adaptability for this purpose. Our review reveals that nanoparticles such as nanocellulose, starch, and chitosan exhibit high potential for synbiotic encapsulation. These offer flexibility in structure design and synthesis, making them promising candidates for addressing delivery challenges in lung diseases. Furthermore, our analysis highlights that synbiotics, when compared to probiotics alone, demonstrate superior anti-inflammatory, antioxidant, antibacterial and anticancer activities. This review underscores the promising role of nanoparticle-encapsulated synbiotics as a targeted and effective therapeutic approach for lung diseases, contributing valuable insights into the potential of nanomedicine in revolutionizing treatment strategies for respiratory conditions, ultimately paving the way for future advancements in this field.

Multi-omics revealed rumen microbiota metabolism and host immune regulation in Tibetan sheep of different ages

The rumen microbiota and metabolites play an important role in energy metabolism and immune regulation of the host. However, the regulatory mechanism of rumen microbiota and metabolite interactions with host on Tibetan sheep's plateau adaptability is still unclear. We analyzed the ruminal microbiome and metabolome, host transcriptome and serum metabolome characteristics of Tibetan sheep at different ages. Biomarkers Butyrivibrio, Lachnospiraceae_XPB1014_group, Prevotella, and Rikenellaceae_RC9_gut_group were found in 4 months, 1.5 years, 3.5 years, and 6 years Tibetan sheep, respectively. The rumen microbial metabolites were mainly enriched in galactose metabolism, unsaturated fatty acid biosynthesis and fatty acid degradation pathways, and had significant correlation with microbiota. These metabolites further interact with mRNA, and are co-enriched in arginine and proline metabolism, metabolism of xenobiotics by cytochrome P450, propanoate metabolism, starch and sucrose metabolism, gap junction pathway. Meanwhile, serum metabolites also have a similar function, such as chemical carcinogenesis - reactive oxygen species, limonene and pinene degradation, and cutin, suberine and wax biosynthesis, thus participating in the regulation of the body's immune and energy-related metabolic processes. This study systematically revealed that rumen microbiota, metabolites, mRNA and serum metabolites of Tibetan sheep were involved in the regulation of fermentation metabolic function and immune level of Tibetan sheep at different ages, which provided a new perspective for plateau adaptability research of Tibetan sheep at different ages.

Sialic acid-based probiotic intervention in lactating mothers improves the neonatal gut microbiota and immune responses by regulating sialylated milk oligosaccharide synthesis via the gut-breast axis

Human milk oligosaccharides (HMOs) are vital milk carbohydrates that help promote the microbiota-dependent growth and immunity of infants. Sialic acid (SA) is a crucial component of sialylated milk oligosaccharides (S-MOs); however, the effects of SA supplementation in lactating mothers on S-MO biosynthesis and their breastfed infants are unknown. Probiotic intervention during pregnancy or lactation demonstrates promise for modulating the milk glycobiome. Here, we evaluated whether SA and a probiotic (Pro) mixture could increase S-MO synthesis in lactating mothers and promote the microbiota development of their breastfed neonates. The results showed that SA+Pro intervention modulated the gut microbiota and 6'-SL contents in milk of maternal rats more than the SA intervention, which promoted Lactobacillus reuteri colonization in neonates and immune development. Deficient 6'-SL in the maternal rat milk of St6gal1 knockouts (St6gal1-/-) disturbed intestinal microbial structures in their offspring, thereby impeding immune tolerance development. SA+Pro intervention in lactating St6gal1± rats compromised the allergic responses of neonates by promoting 6'-SL synthesis and the neonatal gut microbiota. Our findings from human mammary epithelial cells (MCF-10A) indicated that the GPR41-PI3K-Akt-PPAR pathway helped regulate 6'-SL synthesis in mammary glands after SA+Pro intervention through the gut - breast axis. We further validated our findings using a human-cohort study, confirming that providing SA+Pro to lactating Chinese mothers increased S-MO contents in their breast milk and promoted gut Bifidobacterium spp. and Lactobacillus spp. colonization in infants, which may help enhance immune responses. Collectively, our findings may help alter the routine supplementation practices of lactating mothers to modulate milk HMOs and promote the development of early-life gut microbiota and immunity.

Effects of probiotic supplementation in adult with atopic dermatitis: a systematic review with meta-analysis

BACKGROUND

Atopic dermatitis (AD) is one of the most common chronic inflammatory skin diseases. The effect of probiotic administration on the severity of AD in adults has shown inconsistent results.

OBJECTIVES

To determine the effectiveness of probiotic supplementation as a therapeutic tool for adult AD.

METHODS

PubMed, Scopus and Embase were systematically searched to collect data from studies in which probiotics were administered to treat adult AD.

RESULTS

Out of 413 publications, 9 papers were included in the meta-analysis. Significant differences in the ScORing Atopic Dermatitis tool favouring probiotics were observed [relative risk (RR) -5.93, 95% confidence interval (CI) -8.43 to -3.43]. Lactobacillus salivarius presented with largest effect size (RR -9.79, 95% CI -13.04 to -6.54), followed by L. acidophilus (RR -5.77, 95% CI -10.82 to -0.72) and L. plantarum (RR -3.76, 95% CI -6.36 to -1.16). No benefit was observed with L. fermentum. Based on the severity of AD, probiotics showed better results in people with moderate-to-severe AD (RR -9.12, 95% CI -12.17 to -6.08) than in individuals with mild disease (RR -2.67, 95% CI -4.67 to -0.66). Serum levels of IgE and eosinophil count remained significantly unchanged after the probiotic intervention (RR 0.25, 95% CI -0.10 to 0.60; RR -0.27, 95% CI -0.68 to 0.13, respectively).

CONCLUSIONS

Current evidence supports a role for some probiotics as a therapeutic tool for the treatment of adult AD, particularly in patients with severe AD. The efficacy of probiotics is strain specific, with L. salivarius and L. acidophilus having the largest clinical benefit. Such benefit is apparently independent of IgE levels and eosinophil count. Despite these encouraging results, the decrease in AD severity did not translate into a clinically meaningful better quality of life as assessed by the Dermatology Life Quality Index. There currently is not enough reliable data to reach conclusions about the optimal dose and duration for probiotic treatment.

Maternal vitamin D in pregnancy and infant's gut microbiota: a systematic review

Background

An infant's gut microbiome plays a vital role in their health, and various factors can impact their gut microbiota composition. This review aimed to summarize the current knowledge regarding the associations between maternal prenatal supplementation with vitamin D and the composition of infants' gut microbiota.

Method

A comprehensive systematic search was done on Web of Science, Scopus, PubMed, ScienceDirect, and Google Scholar databases without date restrictions until December 2022 using relevant keywords. All relevant original articles in English were eligible for the present review.

Results

Eight articles (two mice, three randomized clinical trials, and three cohort studies) were included in this review. The included mice studies reported that maternal prenatal vitamin D supplementation significantly affects the offspring's gut microbiome composition (such as enhancing the abundance of colonic Bacteroides). Moreover, the included cohort studies revealed a significant association between maternal supplementation with vitamin D during pregnancy and the infant's gut microbiome. However, one-third of clinical trials indicated that vitamin D levels in utero could influence the colonization of the microbial community in the infant's gut.

Conclusion

The findings of this review revealed that maternal vitamin D supplementation during pregnancy was linked to an infant's gut microbiome and could impact their gut microbiota composition. However, more studies are warranted to confirm these results.

Antibiotic use during pregnancy is linked to offspring gut microbial dysbiosis, barrier disruption, and altered immunity along the gut-lung axis

Antibiotic use during pregnancy is associated with increased asthma risk in children. Since approximately 25% of women use antibiotics during pregnancy, it is important to identify the pathways involved in this phenomenon. We investigate how mother-to-offspring transfer of antibiotic-induced gut microbial dysbiosis influences immune system development along the gut-lung axis. Using a mouse model of maternal antibiotic exposure during pregnancy, we immunophenotyped offspring in early life and after asthma induction. In early life, prenatal-antibiotic exposed offspring exhibited gut microbial dysbiosis, intestinal inflammation (increased fecal lipocalin-2 and IgA), and dysregulated intestinal ILC3 subtypes. Intestinal barrier dysfunction in the offspring was indicated by a FITC-dextran intestinal permeability assay and circulating lipopolysaccharide. This was accompanied by increased T-helper (Th)17 cell percentages in the offspring's blood and lungs in both early life and after allergy induction. Lung tissue additionally showed increased percentages of RORγt T-regulatory (Treg) cells at both time points. Our investigation of the gut-lung axis identifies early-life gut dysbiosis, intestinal inflammation, and barrier dysfunction as a possible developmental programming event promoting increased expression of RORγt in blood and lung CD4+ T cells that may contribute to increased asthma risk.

Gut microbiota changes in horses with Chlamydia

BACKGROUND

Zoonotic diseases pose a significant threat to public health. Chlamydia, as an intracellular pathogen, can colonize the intestinal tract of humans and animals, changing the gut microbiota. However, only a few studies have evaluated alterations in the gut microbiota of horses infected with Chlamydia. Therefore, this study aimed to investigate gut microbiota and serum biochemical indicators in horses with Chlamydial infection (IG) and healthy horses (HG). Fecal and blood samples were collected from 16 horses (IG: 10; HG: 6) before morning feeding for the determination of gut microbiota and serum biochemical parameters.

RESULTS

The results showed that total globulin (GLB), alanine aminotransferase (ALT), and creatine kinase (CK) levels were significantly increased in IG compared with HG. Notably, the gut microbial diversity increased in IG compared with HG. Furthermore, Moraxellaceae and Akkermanisa abundance decreased in IG, while Streptococcus, Treponema, Prevotella, and Paraprevotella abundances (13 genera of bacterial species) increased. Compared with HG, carbohydrate metabolism increased in IG while amino acid metabolism decreased. In addition, the abundance of 18 genera of bacteria was associated with the level of five serum biochemical indicators.

CONCLUSIONS

In summary, this study elucidated the influence of Chlamydia infection in horses on the gut microbiota, unraveling consequential alterations in its composition and metabolic profile. Therefore, this study improves the understanding of Chlamydia-induced intestinal infections.

Early gut microbiota intervention in premature infants: Application perspectives

BACKGROUND

Preterm birth is the leading cause of death in children under the age of five. One of the major factors contributing to the high risk of diseases and deaths in premature infants is the incomplete development of the intestinal immune system. The gut microbiota has been widely recognized as a critical factor in promoting the development and function of the intestinal immune system after birth. However, the gut microbiota of premature infants is at high risk of dysbiosis, which is highly associated with adverse effects on the development and education of the early life immune system. Early intervention can modulate the colonization and development of gut microbiota and has a long-term influence on the development of the intestinal immune system.

AIM OF REVIEW

This review aims to summarize the characterization, interconnection, and underlying mechanism of gut microbiota and intestinal innate immunity in premature infants, and to discuss the status, applicability, safety, and prospects of different intervention strategies in premature infants, thus providing an overview and outlook of the current applications and remaining gaps of early intervention strategies in premature infants.

KEY SCIENTIFIC CONCEPTS OF REVIEW

This review is focused on three key concepts. Firstly, the gut microbiota of premature infants is at high risk of dysbiosis, resulting in dysfunctional intestinal immune system processes. Secondly, contributing roles of early intervention have been observed in improving the intestinal environment and promoting gut microbiota colonization, which is significant in the development and function of gut immunity in premature infants. Thirdly, different strategies of early intervention, such as probiotics, fecal microbiota transplantation, and nutrients, show different safety, applicability, and outcome in premature infants, and the underlying mechanism is complex and poorly understood.

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

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

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

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

Assessment of infant outgrowth of cow's milk allergy in relation to the faecal microbiome and metaproteome

Previous studies provide evidence for an association between modifications of the gut microbiota in early life and the development of food allergies. We studied the faecal microbiota composition (16S rRNA gene amplicon sequencing) and faecal microbiome functionality (metaproteomics) in a cohort of 40 infants diagnosed with cow's milk allergy (CMA) when entering the study. Some of the infants showed outgrowth of CMA after 12 months, while others did not. Faecal microbiota composition of infants was analysed directly after CMA diagnosis (baseline) as well as 6 and 12 months after entering the study. The aim was to gain insight on gut microbiome parameters in relation to outgrowth of CMA. The results of this study show that microbiome differences related to outgrowth of CMA can be mainly identified at the taxonomic level of the 16S rRNA gene, and to a lesser extent at the protein-based microbial taxonomy and functional protein level. At the 16S rRNA gene level outgrowth of CMA is characterized by lower relative abundance of Lachnospiraceae at baseline and lower Bacteroidaceae at visit 12 months.

Building better barriers: how nutrition and undernutrition impact pediatric intestinal health

Chronic undernutrition is a major cause of death for children under five, leaving survivors at risk for adverse long-term consequences. This review focuses on the role of nutrients in normal intestinal development and function, from the intestinal epithelium, to the closely-associated mucosal immune system and intestinal microbiota. We examine what is known about the impacts of undernutrition on intestinal physiology, with focus again on the same systems. We provide a discussion of existing animal models of undernutrition, and review the evidence demonstrating that correcting undernutrition alone does not fully ameliorate effects on intestinal function, the microbiome, or growth. We review efforts to treat undernutrition that incorporate data indicating that improved recovery is possible with interventions focused not only on delivery of sufficient energy, macronutrients, and micronutrients, but also on efforts to correct the abnormal intestinal microbiome that is a consequence of undernutrition. Understanding of the role of the intestinal microbiome in the undernourished state and correction of the phenotype is both complex and a subject that holds great potential to improve recovery. We conclude with critical unanswered questions in the field, including the need for greater mechanistic research, improved models for the impacts of undernourishment, and new interventions that incorporate recent research gains. This review highlights the importance of understanding the mechanistic effects of undernutrition on the intestinal ecosystem to better treat and improve long-term outcomes for survivors.

A preliminary study of the salivary microbiota of young male subjects before, during, and after acute high-altitude exposure

Background

The microbial community structure in saliva differs at different altitudes. However, the impact of acute high-altitude exposure on the oral microbiota is unclear. This study explored the impact of acute high-altitude exposure on the salivary microbiome to establish a foundation for the future prevention of oral diseases. Methods. Unstimulated whole saliva samples were collected from 12 male subjects at the following three time points: one day before entering high altitude (an altitude of 350 m, pre-altitude group), seven days after arrival at high altitude (an altitude of 4,500 m, altitude group) and seven days after returning to low altitude (an altitude of 350 m, post-altitude group). Thus, a total of 36 saliva samples were obtained. 16S rRNA V3-V4 region amplicon sequencing was used to analyze the diversity and structure of the salivary microbial communities, and a network analysis was employed to investigate the relationships among salivary microorganisms. The function of these microorganisms was predicted with a Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis.

Results

In total, there were 756 operational taxonomic units (OTUs) identified, with 541, 613, and 615 OTUs identified in the pre-altitude, altitude, and post-altitude groups, respectively. Acute high-altitude exposure decreased the diversity of the salivary microbiome. Prior to acute high-altitude exposure, the microbiome mainly consisted of Proteobacteria, Firmicutes, Bacteroidetes, Fusobacteria, and Actinobacteria. After altitude exposure, the relative abundance of Streptococcus and Veillonella increased, and the relative abundance of Prevotella, Porphyromonas, and Alloprevotella decreased. The relationship among the salivary microorganisms was also affected by acute high-altitude exposure. The relative abundance of carbohydrate metabolism gene functions was upregulated, while the relative abundance of coenzyme and vitamin metabolism gene functions was downregulated.

Conclusion

Rapid high-altitude exposure decreased the biodiversity of the salivary microbiome, changing the community structure, symbiotic relationships among species, and abundance of functional genes. This suggests that the stress of acute high-altitude exposure influenced the stability of the salivary microbiome.

Modulation of bone remodeling by the gut microbiota: a new therapy for osteoporosis

The gut microbiota (GM) plays a crucial role in maintaining the overall health and well-being of the host. Recent studies have demonstrated that the GM may significantly influence bone metabolism and degenerative skeletal diseases, such as osteoporosis (OP). Interventions targeting GM modification, including probiotics or antibiotics, have been found to affect bone remodeling. This review provides a comprehensive summary of recent research on the role of GM in regulating bone remodeling and seeks to elucidate the regulatory mechanism from various perspectives, such as the interaction with the immune system, interplay with estrogen or parathyroid hormone (PTH), the impact of GM metabolites, and the effect of extracellular vesicles (EVs). Moreover, this review explores the potential of probiotics as a therapeutic approach for OP. The insights presented may contribute to the development of innovative GM-targeted therapies for OP.

Intermittent fasting protects against food allergy in a murine model via regulating gut microbiota

Background

The prevalence of food allergy (FA) is increasing. Decreases in the diversity of gut microbiota may contribute to the pathogenesis of FA by regulating IgE production of B cells. Intermittent fasting (IF) is a popular diet with the potential to regulate glucose metabolism, boosting immune memory and optimizing gut microbiota. The potential effect of long-term IF on the prevention and treatment of FA is still unknown.

Methods

Two IF protocols (16 h fasting/8 h feeding and 24 h fasting/24 h feeding) were conducted on mice for 56 days, while the control mice were free to intake food (free diet group, FrD). To construct the FA model, all mice were sensitized and intragastrical challenged with ovalbumin (OVA) during the second half of IF (day 28 to day 56). Rectal temperature reduction and diarrhea were recorded to evaluate the symptoms of FA. Levels of serum IgE, IgG1, Th1/Th2 cytokines, mRNA expression of spleen T cell related transcriptional factors, and cytokines were examined. H&E, immunofluorescence, and toluidine blue staining were used to assess the structural changes of ileum villi. The composition and abundance of gut microbiota were analyzed by 16srRNA sequencing in cecum feces.

Results

The diarrhea score and rectal temperature reduction were lower in the two fasting groups compared to the FrD groups. Fasting was associated with lower levels of serum OVA-sIgE, OVA-sIgG1, interleukin (IL)-4 and IL-5, and mRNA expression of IL-4, IL-5, and IL-10 in the spleen. While no significant association was observed in interferon (IFN)-γ, tumor necrosis factor (TNF)-α, IL-6, IL-2 levels. Less mast cell infiltration in ileum was observed in the 16h/8h fasting group compared to the FrD group. ZO-1 expression in the ileum of the two fasting groups was higher in IF mice. The 24h/24h fasting reshaped the gut microbiota, with a higher abundance of Alistipes and Rikenellaceae strains compared to the other groups.

Conclusion

In an OVA-induced mice FA model, long-term IF may attenuate FA by reducing Th2 inflammation, maintaining the integrity of the intestinal epithelial barrier, and preventing gut dysbiosis.

Effects of dietary N-carbamylglutamate on rumen fermentation parameters, and bacterial community diversity of Holstein dairy cows in Tibet

Introduction

The Tibetan Plateau is characterized by low temperature and hypoxia. N-carbamylglutamic acid (NCG) can increase blood oxygen saturation, and have the potential to be used to prevent the high-altitude hypoxia stress state of cows. However, its beneficial effect on the rumen microbiota of Holstein dairy cows remains unclear.

Methods

Hence, the experiments 12 multiparous (parity ranged from 2 to 7) Holstein dairy cows (413.0 ± 42 kg) were randomly assigned to 2 treatments with 6 replicates in each treatment: basal diet (CON, control group) and basal diet plus 20 g/d/cow of NCG (NCG, experiment group), respectively. To study the effects of dietary NCG supplementation on rumen microbiota of Holstein dairy cows in Tibet. The experiment lasted for 45 days, with 15 days of pre-feeding and 30 days of formal trail period.

Results

The results showed that ruminal NH₃-N concentration in NCG group was lower (p < 0.05) than that in the CON group, while molar proportion of acetic acid and total volatile fatty acid (VFA) concentration were increased (p < 0.05) with the addition of NCG. Microbial diversity increased (p < 0.05) in NCG group, with Bacteroidetes, Firmicutes, and Patescibacteria as the most abundant phyla. The KEGG pathway analysis showed that the potential function of ruminal bacteria was mainly enriched in metabolism (carbohydrates, amino acids, lipids, energy, and nucleotides) and genetic information processing (replication, repair, and translation).

Conclusion

In conclusion, NCG can improve rumen nitrogen utilization, total VFA and acetic acid production, and increase rumen microbial diversity, all of which could make the introduced Holstein dairy cows to better adapt to the harsh environment in Tibet and improve their production performance.

Effects of prophylactic probiotics supplementation on infants born very preterm or very low birth weight

OBJECTIVE

To evaluate the effects of guideline-driven prophylactic supplementation of a multi-strain neonatal intensive care unit-specific probiotic product on infants born very preterm (VP) or very low birth weight (VLBW).

STUDY DESIGN

A prospective cohort of 125 infants born in one year after implementation who received probiotics were compared to a retrospective cohort of eligible 126 VP or VLBW infants who did not receive probiotics. The primary outcome of interest was necrotizing enterocolitis (NEC).

RESULT

The incidence of NEC decreased from 6.3 to 1.6%. After adjusting for multiple variables, there were no significant differences in primary or other outcomes of interest; odds ratio (95% confidence interval) NEC 0.27 (0.05-1.33), death 0.76 (0.26-2.21) and late-onset sepsis 0.54 (0.18-1.63). No adverse effects related to probiotics supplementation were observed.

CONCLUSION

Although nonsignificant, prophylactic probiotics supplementation in infants born VP or VLBW was associated with reduction of NEC.

Altered Faecal Microbiota Composition and Structure of Ghanaian Children with Acute Gastroenteritis

Acute gastroenteritis (AGE) is a disease of global public health importance. Recent studies show that children with AGE have an altered gut microbiota relative to non-AGE controls. Yet, how the gut microbiota differs in Ghanaian children with and without AGE remains unclear. Here, we explore the 16S rRNA gene-based faecal microbiota profiles of Ghanaian children five years of age and younger, comprising 57 AGE cases and 50 healthy controls. We found that AGE cases were associated with lower microbial diversity and altered microbial sequence profiles relative to the controls. The faecal microbiota of AGE cases was enriched for disease-associated bacterial genera, including Enterococcus, Streptococcus, and Staphylococcus. In contrast, the faecal microbiota of controls was enriched for potentially beneficial genera, including Faecalibacterium, Prevotella, Ruminococcus, and Bacteroides. Lastly, distinct microbial correlation network characteristics were observed between AGE cases and controls, thereby supporting broad differences in faecal microbiota structure. Altogether, we show that the faecal microbiota of Ghanaian children with AGE differ from controls and are enriched for bacterial genera increasingly associated with diseases.

Association of cesarean section with risk of childhood leukemia: A meta-analysis from an observational study

Recent studies suggest that children born via cesarean section (CS) are predisposed to immune-mediated diseases later in life. The association between CS and childhood leukemia was investigated in this meta-analysis of observational studies. Two researchers independently searched PubMed, Web of Science, Embase, and Cochrane Library for literature on the association between CS and childhood leukemia before February 2022. And pooled odds ratios (OR) with 95% confidence intervals (CI) were calculated to determine the link between CS and childhood leukemia. The preliminary search resulted in 1321 articles and 16 articles were finally included after screening. The primary outcome was the risk of leukemia in children born via CS versus those born vaginally. The results revealed that having a CS was associated with an increased risk of childhood leukemia compared to having vaginal section (VS) (OR = 1.07, 95% CI: 1.02-1.13, p = 0.01), especially for acute lymphoblastic leukemia (ALL) (OR = 1.09, 95% CI: 1.03-1.16, p = 0.004). Children delivered via elective CS had a higher risk of ALL (OR = 1.18, 95% CI: 1.07-1.31, p = 0.001), but emergency CS did not. It is worth noting that neither emergency CS nor elective CS were found to be associated with acute myeloid leukemia. Compared to VS, CS increased the risk of leukemia in children, with elective CS significantly increasing ALL risk.

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

BACKGROUND

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

RESULTS

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

CONCLUSIONS

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

Compound probiotics can improve intestinal health by affecting the gut microbiota of broilers

Probiotics, as a widely used additive, have played a unique advantage in replacing antibiotic products. As a result, the probiotic effects on broiler development, intestinal flora, intestinal barrier, and immunity were assessed by this investigation. Four hundred and eighty 1-day-old Arbor Acres broilers were randomly allotted to 4 groups of 5 replicates with 24 broilers each. The control was fed only a basal corn-soybean meal diet. Probiotics I, probiotics II, and probiotics III were fed basal diet and 1, 5, and 10 g/kg compound probiotics (Lactobacillus casei: Lactobacillus acidophilus: Bifidobacterium = 1:1:2), respectively. We found that broilers in the compound probiotic group exhibited better growth performance and carcass characteristics compared with control, especially among probiotics III group. The intestinal barrier-related genes relative expression of Claudin, Occludin, MUC2, and ZO-1 mRNA in the probiotic group increased at 21 and 42 d compared with control, especially among probiotics III group (P < 0.05). The early gut immune-related genes (TLR2, TLR4, IL-1β, and IL-2) mRNA increased compared with control, while the trend at 42 d was completely opposite to that in the earlier stage (P < 0.05). Among them, probiotics III group showed the most significant changes compared to probiotics II group and probiotics I group. Select probiotics III group and control group for 16S rDNA amplicon sequencing analysis. The 16S rDNA amplicon sequencing results demonstrated that probiotics increased the relative abundance of beneficial microbes such as o_Bacteroidales, f_Rikenellaceae, and g_Alistipes and improved the cecum's gut microbiota of 42-day-old broilers. Additionally, adding the probiotics decreased the relative abundance of harmful microbes such as Proteobacteria. PICRUSt2 functional analysis revealed that most proteins were enriched in DNA replication, transcription, and glycolysis processes. Therefore, this study can provide theoretical reference value for probiotics to improve production performance, improve intestinal barrier, immunity, intestinal flora of broilers, and the application of probiotics.

Maternal vitamin D deficiency aggravates the dysbiosis of gut microbiota by affecting intestinal barrier function and inflammation in obese male offspring mice

OBJECTIVES

The colonization of gut microbiota during early life may play a critical role in the progression of metabolic syndrome in adulthood. Targeting gut-based genes in the barrier function, inflammation, and lipid transportation are potential therapies for obesity. Therefore, this study focused on whether maternal deficient vitamin D (VD) intake could aggravate the dysbiosis of gut microbiota by affecting the expressions of these genes in the ileum and colon of obese male offspring mice.

METHODS

Four-week-old female C57 BL/6 J mice were fed normal (VD-C) or VD-deficient (VD-D) reproductive diets throughout pregnancy and lactation (n = 15/group). Weaning male pups (n = 10/group) were fed either a high-fat (HFD; VD-C-HFD, VD-D-HFD) or normal-fat diet (control) for 16 wk. All biologic samples were obtained after the mice were anesthetized by cervical dislocation. Subsequently, the compositions of the gut microbiota in cecal contents were analyzed using 16 S ribosomal RNA sequencing. Messenger RNA expression in the ileum and colon was determined using real-time reverse transcription-polymerase chain reaction. The distributions of ZO-1 and Claudin-1 were determined using immunohistochemistry testing.

RESULTS

Maternal deficient VD intake significantly aggravated the dysbiosis of gut microbiota persisting into adulthood from phylum to genus levels in the cecal contents among obese male offspring mice. This aggravation led to significantly depleted Bacteroidetes and Verrucomicrobia (Akkermansia, Alliprevotella, and Bacteroides), with higher relative abundance of Firmicutes (Lactobacillus, Lachnoclostridium, Romboutsia, and Ruminiclostridium_9) and Firmicutes/Bacteroidetes. The gene expressions of proinflammatory cytokines (Ccl2, Ccl4 and interleukin-1β) and lipid transportation molecules (Ffar3, Fabp4, and Fabp1) were higher, and the levels of intestinal barrier function (Occludin, ZO-1, and Claudin-1) were lower in the VD-D-HFD group than those in the VD-C-HFD group. Furthermore, there were significant correlations between the dysbiosis of intestinal microbials and expressions of genes related to barrier function, inflammation, and lipid transportation in the ileum and/or colon.

CONCLUSIONS

Maternal VD deficiency during pregnancy and lactation could aggravate the dysbiosis of gut microbiota to affect the progression of obesity among male offspring, which might be regulated by genes associated with barrier function, inflammation, and lipid transportation. So early life appropriate VD intake could play a significant role in preventing later obesity.

[Diversity and functional prediction of gut microbiota in children with autism spectrum disorder]

OBJECTIVES

To study the structure and diversity of gut microbiota in children with autism spectrum disorder (ASD), and to predict the metabolic function of gut microbiota.

METHODS

Fecal samples were collected from 30 ASD children (ASD group) and 20 typically developing (TD) children (TD group). Genomic DNA was extracted, the 16S rDNA V4 region was amplified by PCR, and Illumina NovaSeq6000 platform was used for high-throughput sequencing. The composition and distribution characteristics of gut microbiota were analyzed for the two groups, and the metabolic function of gut microbiota was predicted.

RESULTS

There were no significant differences in alpha diversity indices (Chao1, Shannon, and Simpson) of gut microbiota between the ASD and TD groups (P>0.05). At the phylum and class levels, there was no significant difference in the structure of gut microbiota between the two groups (P>0.05). Compared with the TD group, the ASD group had significantly higher abundance of Megamonas, Barnesiella, Dialister, Megasphaera, Ruminococcus_torques_group, and Fusobacterium at the genus level (P<0.05). Functional prediction analysis showed that compared with the TD group, the ASD group had a significantly lower abundance of the gut microbiota with the metabolic functions such as tryptophan degradation, glutamate degradation, and butyrate production (P<0.05) and a significantly higher abundance of the gut microbiota with the metabolic function of GABA degradation (P<0.05).

CONCLUSIONS

There is no significant difference in the alpha diversity of gut microbiota between ASD children and TD children, while there are differences in the composition of species at the genus level and the metabolic functions of gut microbiota.

Infant feeding practice and gastrointestinal tolerance: a real-world, multi-country, cross-sectional observational study

BACKGROUND

Signs of feeding intolerance, such as gastrointestinal (GI) symptoms, are frequently observed in otherwise healthy formula-fed infants in the first months of life. The primary objective of this observational study was to examine GI tolerance in formula-fed infants (FFI) vs. breastfed infants (BFI) in a real-world setting with a secondary objective being the comparison of infants fed formula with pre- and/or probiotics (FFI_PP) and those fed formula without any pre- and/or probiotics (FFI_noPP) as well as BFI.

METHODS

A six-country, cross-sectional study in full-term exclusively/predominantly FFI (n = 2036) and BFI (n = 760) aged 6-16 weeks was conducted using the validated Infant Gastrointestinal Symptom Questionnaire (IGSQ) and a Feeding Practice and Gut Comfort Questionnaire.

RESULTS

The IGSQ composite score in FFI was non-inferior compared to BFI (mean difference [95%CI]: 0.17 [-0.34, 0.67]; non-inferiority p-value < 0.0001) and scores for BFI and FFI were below the threshold of 23, indicating no GI discomfort. Adjusted mean IGSQ scores ± SE were similar in FFI_PP (22.1 ± 0.2) and BFI (22.3 ± 0.3) while FFI_noPP (23.4 ± 0.3) was significantly higher and above 23 indicating some GI discomfort (mean differences [95%CI] FFI_noPP minus FFI_PP and FFI_noPP minus BFI were 1.28 [0.57, 1.98] and 1.09 [0.38, 1.80], respectively; both p < 0.01). Hard stools and difficulty in passing stool were more common in FFI compared to BFI (p < 0.01) but were less common in FFI_PP compared to FFI_noPP (p < 0.01). FFI_PP showed significantly less crying than FFI_noPP and was similar to BFI. Significantly fewer physician-confirmed colic episodes (Rome IV criteria) were reported in FFI_PP compared with FFI_noPP or BFI.

CONCLUSIONS

In this real-world observational study, FFI had non-inferior overall GI tolerance compared to BFI. Within FFI, infants receiving formulas with pre- and/or probiotics had a better GI tolerance, improved stooling and less infantile colic compared to those receiving formula without any pre- and/or probiotics and were more similar to BFI.

TRIAL REGISTRATION

NCT03703583, 12/10/2018 ( https://clinicaltrials.gov/ct2/show/NCT03703583 ).

Enterococci as Intestinal Microbiota: Investigation of Characteristics and Probiotic Potential in Isolates from Adults and Breast-Fed Infants

Enterococci act as symbionts in human gastrointestinal tract. The present study aimed to evaluate the characteristics of fecal enterococci isolated from infants and adults, and to compare them to the known probiotic bacteria, including lactobacilli species and E. faecalis Symbioflor 1. In total, sporadic distribution of virulence genes was detected among the studied enterococci. Furthermore, the frequency of genes encoding for sex pheromones (ccf and cob), collagen adhesion (ace), cell wall adhesion (efaAfs), and gelatinase (gelE) was observed to be significantly higher in those isolates obtained from infants compared to those obtained from adults. Although the ability of biofilm formation was found in all isolates, the strong biofilm formation was observed in enterococci from infants and strong correlation was observed between the capacities to form biofilm and attachment to Caco-2 cells. Cell-free culture supernatant showed some inhibitory effects on indicator strains, which were related to the production of organic acids (against P. aeruginosa and enteropathogenic E. coli) or both organic acids and proteinaceous antimicrobial agents (against L. monocytogenes and E. faecalis). Approximately, 79% and 71% of the isolates showed strong inhibitory effects on P. aeruginosa and L. monocytogenes, respectively. Unlike lactobacilli, enterococcal cell-free supernatants had no toxicity on intestinal cells. In conclusion, this study shows that some enterococcal isolates obtained from fecal microbiota have characteristics, which are comparable with the known probiotic bacteria. Therefore, these isolates should be considered to find probiotic candidate. The proteinaceous identity of antimicrobial substances derived from these isolates highlighted the probable contribution of bacteriocins into this issue.

Maternal prenatal immunity, neonatal trained immunity, and early airway microbiota shape childhood asthma development

BACKGROUND

The path to childhood asthma is thought to initiate in utero and be further promoted by postnatal exposures. However, the underlying mechanisms remain underexplored. We hypothesized that prenatal maternal immune dysfunction associated with increased childhood asthma risk (revealed by low IFN-γ:IL-13 secretion during the third trimester of pregnancy) alters neonatal immune training through epigenetic mechanisms and promotes early-life airway colonization by asthmagenic microbiota.

METHODS

We examined epigenetic, immunologic, and microbial features potentially related to maternal prenatal immunity (IFN-γ:IL-13 ratio) and childhood asthma in a birth cohort of mother-child dyads sampled pre-, peri-, and postnatally (N = 155). Epigenome-wide DNA methylation and cytokine production were assessed in cord blood mononuclear cells (CBMC) by array profiling and ELISA, respectively. Nasopharyngeal microbiome composition was characterized at age 2-36 months by 16S rRNA sequencing.

RESULTS

Maternal prenatal immune status related to methylome profiles in neonates born to non-asthmatic mothers. A module of differentially methylated CpG sites enriched for microbe-responsive elements was associated with childhood asthma. In vitro responsiveness to microbial products was impaired in CBMCs from neonates born to mothers with the lowest IFN-γ:IL-13 ratio, suggesting defective neonatal innate immunity in those who developed asthma during childhood. These infants exhibited a distinct pattern of upper airway microbiota development characterized by early-life colonization by Haemophilus that transitioned to a Moraxella-dominated microbiota by age 36 months.

CONCLUSIONS

Maternal prenatal immune status shapes asthma development in her child by altering the epigenome and trained innate immunity at birth, and is associated with pathologic upper airway microbial colonization in early life.

Microecosystem of yak rumen on the Qinghai-Tibetan Plateau is stable and is unaffected by soil or grass microbiota

The rumen of livestock grazing on the Qinghai-Tibetan Plateau (QTP) acts as a transfer station for the circulation of soil, grass, faecal mineral elements and nutrients. Whether the microorganisms from the soil and grass could circulate through livestock rumen and excreted faeces. We studied the structural composition and interactive networks of microbiomes (bacteria and fungi) in soil, grass, and grazing yaks (rumen and faeces) on the QTP by using 16S rRNA gene and internally transcribed spacer (ITS) sequencing technology and to calculate the contribution rate of microorganisms from one habitat to another habitat using SourceTracker analysis. The meta-co-occurrence network revealed that soil, grass, rumen, and faeces comprise four independent habitats. The bacterial and fungal composition was significantly different in these four habitats. Soil microbiota showed the highest alpha diversity and microbial network complexity. Rumen microbiota demonstrated the highest microbial network stability and synergy, while grass endophytes showed the lowest microbial network complexity, stability, and synergy. According to the SourceTracker model, grass contributes 0.02% to the rumen microbes of yaks, while soil microorganisms do not circulate in the rumen. The soil and grass microbiota originating from faeces were 4.5% and 1.2%, respectively. The contribution of soil to grass was found to be 1.1%. Overall, the rumen microbiota of yaks is relatively stable and is only minimally influenced by the microbiota inhabiting the environment under natural grazing conditions. However, the contribution of yaks to soil and grass microbiota is relatively high when compared with the contribution of soil and grass to yaks microbiota.

Dynamic alterations in yak (Bos grunniens) rumen microbiome in response to seasonal variations in diet

Rumen microorganisms play important roles in the healthy growth of yaks. This study investigated changes in yak rumen microbiome during natural grazing at the warm seasons and supplementary feeding at cold seasons. High-throughput sequencing of 16S rRNA and metagenome analysis were conducted to investigate the structures and functions of yak rumen microbial communities. The results indicated that Bacteroidetes and Firmicutes were the most abundant phyla. In addition, Bacteroidetes might play a more important role than Firmicutes during the supplementary feeding stage (spring and winter), but less during natural grazing stage (summer and autumn). KEGG analysis showed that the amino sugar and nucleotide sugar metabolism, glycolysis/gluconeogenesis, pyruvate metabolism, starch and sucrose metabolism, and fructose and mannose metabolism were the main pathways in the microbial community, which were significantly different between seasons. The carbohydrate-active enzymes (CAZyme) annotation revealed that cellulose was an important carbon source for microorganisms in yak rumen. Glycoside hydrolases (GHs) were the most abundant class of CAZymes, followed by glycosyl transferases (GTs), which were important to digestion of oil, cellulose, and hemicellulose in food. These results contribute to the understanding of microbial components and functions in yak rumen.

Response of Ruminal Microbiota-Host Gene Interaction to High-Altitude Environments in Tibetan Sheep

Altitude is the main external environmental pressure affecting the production performance of Tibetan sheep, and the adaptive evolution of many years has formed a certain response mechanism. However, there are few reports on the response of ruminal microbiota and host genomes of Tibetan sheep to high-altitude environments. Here, we conducted an integrated analysis of volatile fatty acids (VFAs), microbial diversity (16S rRNA), epithelial morphology, and epithelial transcriptome in the rumen of Tibetan sheep at different altitudes to understand the changes in ruminal microbiota−host interaction in response to high altitude. The differences in the nutritional quality of forage at different altitudes, especially the differences in fiber content (ADF/NDF), led to changes in rumen VFAs of Tibetan sheep, in which the A/P value (acetic acid/propionic acid) was significantly decreased (p < 0.05). In addition, the concentrations of IgA and IgG in Middle-altitude (MA) and High-altitude Tibetan sheep (HA) were significantly increased (p < 0.05), while the concentrations of IgM were significantly increased in MA (p < 0.05). Morphological results showed that the width of the rumen papilla and the thickness of the basal layer increased significantly in HA Tibetan sheep (p < 0.05). The 16S rRNA analysis found that the rumen microbial diversity of Tibetan sheep gradually decreased with increasing altitude, and there were some differences in phylum- and genus-level microbes at the three altitudes. RDA analysis found that the abundance of the Rikenellaceae RC9 gut group and the Ruminococcaceae NK4A214 group increased with altitudes. Furthermore, a functional analysis of the KEGG microbial database found the “lipid metabolism” function of HA Tibetan sheep to be significantly enriched. WGCNA revealed that five gene modules were enriched in “energy production and conversion”, “lipid transport and metabolism”, and “defense mechanisms”, and cooperated with microbiota to regulate rumen fermentation and epithelial immune barrier function, so as to improve the metabolism and immune level of Tibetan sheep at high altitude.

Composition and diverse differences of intestinal microbiota in ulcerative colitis patients

Objective

To explore the composition of the intestinal microbiota in ulcerative colitis (UC) patients and to identify differences in the microbiota between patients with active disease and those in remission.

Methods

Between September 2020 and June 2021, we enrolled into our study, and collected stool samples from, patients with active UC or in remission and healthy control subjects. The diagnosis of UC was based on clinical, endoscopic, radiological, and histological findings. The composition of the intestinal microbiota was determined by sequencing of the 16S rRNA V3–V4 region and by bioinformatic methods. The functional composition of the intestinal microbiota was predicted using PICRUSt 2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) software.

Results

We found that the intestinal flora was significantly less rich and diverse in UC patients than in healthy control subjects. Beta diversity analysis revealed notable differences in the intestinal flora compositions among the three groups, but there was no statistical difference in alpha diversity between UC patients with active disease and those in remission. At the phylum level, the relative abundances of Proteobacteria and Patescibacteria were significantly higher, and the relative abundances of Desulfobacterota and Verrucomicrobiota were lower, in UC patients with active disease than in the healthy control group. Higher levels of potential pathogens and lower levels of butyrate-producing bacteria were also detected in UC patients with active disease. Linear discriminant analysis Effect Size (LefSe) revealed that 71 bacterial taxa could serve as biomarkers, with 26 biomarkers at the genus level. In addition, network analysis showed that there was a positive correlation between Roseburia and Lachnospira. Functional predictions indicated that gene functions involving the metabolism of some substances, such as methane, lipopolysaccharide, geraniol, and ansamycins, were significantly different among the three groups.

Conclusion

The richness and diversity of the intestinal microbiota differed significantly among the three groups. Richness describes the state of being rich in number of intestinal bacteria, whereas diversity is the number of different species of intestinal bacteria. Different bacterial taxa could be used as biomarkers, expanding our understanding of the relationship between the intestinal microbiota microenvironment and UC in the future.

Gut microbiota in women with gestational diabetes mellitus has potential impact on metabolism in pregnant mice and their offspring

Studies have shown that gestational diabetes mellitus (GDM) is closely related to abnormalities in the gut microbiota, and the offspring of these women have an increased risk of diabetes. There is no direct evidence of whether bacteria in women with GDM colonize the intestinal tract of offspring and cause hyperglycemia. In this fecal microbiota transplantation (FMT), pregnant mouse model study, two groups of germ-free (GF) mice after FMT showed different colonization patterns of gut microbiota and phenotype. Compared with the control group (healthy-FMT), we found in the GDM-FMT group as a lower relative abundance of Akkermansia and Faecalibacterium; a lower content of short-chain fatty acids and naringenin in feces; an elevated blood glucose; an inflammatory factor expression (TNF-α, CXCL-15, and IL-6), and a hepatic fat deposition. In addition, the influence of the gut microbiota continued in offspring. The gut microbiota of the offspring of GDM-FMT mice was still different from that of the control group as a lower relative abundance of Akkermansia and Parvibacter; and a higher relative abundance of bacteria such as Oscillibacter, Romboutsia, and Harryflintia. In addition, the offspring of GDM-FMT mice had higher body weight and blood glucose levels than the control offspring.

Infancy Dietary Patterns, Development, and Health: An Extensive Narrative Review

Correct dietary patterns are important for a child’s health from birth to adulthood. Understanding a child’s health as a state of entire physical, mental, and social well-being is essential. However, reaching adulthood in a complete health proper state is determined by feeding and dietary habits during preconception, pregnancy, or children infancy. Different factors, such as the mother’s lifestyle, culture, or socioeconomic status, are crucial during all these phases. In this review, we aimed to assess the long-term associations between infancy dietary patterns and health and their influence on development and growth. To reach this objective, a consensus critical review was carried out using primary sources such as scientific articles, and secondary bibliographic indexes, databases, and web pages. PubMed, SciELO, and Google Scholar were the tools used to complete this research. We found that high-income countries promote high-calorie foods and, consequently, obesity problems among children are rising. However, undernutrition is a global health issue concerning children in low- and middle-income countries; thus, parental socioeconomic status in early life is essential to children’s health and development, showing that biological, social, and environmental influences are increased risk factors for chronic diseases. This narrative review is aimed to collect evidence for early nutritional intervention and future disease prevention.

Gut Microbiome Changes Occurring with Norovirus Infection and Recovery in Infants Enrolled in a Longitudinal Birth Cohort in Leon, Nicaragua

Noroviruses are associated with one fifth of diarrheal illnesses globally and are not yet preventable with vaccines. Little is known about the effects of norovirus infection on infant gut microbiome health, which has a demonstrated role in protecting hosts from pathogens and a possible role in oral vaccine performance. In this study, we characterized infant gut microbiome changes occurring with norovirus-associated acute gastroenteritis (AGE) and the extent of recovery. Metagenomic sequencing was performed on the stools of five infants participating in a longitudinal birth cohort study conducted in León, Nicaragua. Taxonomic and functional diversities of gut microbiomes were profiled at time points before, during, and after norovirus infection. Initially, the gut microbiomes resembled those of breastfeeding infants, rich in probiotic species. When disturbed by AGE, Gammaproteobacteria dominated, particularly Pseudomonas species. Alpha diversity increased but the genes involved in carbohydrate metabolism and glycan biosynthesis decreased. After the symptoms subsided, the gut microbiomes rebounded with their taxonomic and functional communities resembling those of the pre-infection microbiomes. In this study, during disruptive norovirus-associated AGE, the gut microbiome was temporarily altered, returning to a pre-infection composition a median of 58 days later. Our study provides new insights for developing probiotic treatments and furthering our understanding of the role that episodes of AGE have in shaping the infant gut microbiome, their long-term outcomes, and implications for oral vaccine effectiveness.

Babies, Bugs, and Barriers: Dietary Modulation of Intestinal Barrier Function in Early Life

The intestinal barrier is essential in early life to prevent infection, inflammation, and food allergies. It consists of microbiota, a mucus layer, an epithelial layer, and the immune system. Microbial metabolites, the mucus, antimicrobial peptides, and secretory immunoglobulin A (sIgA) protect the intestinal mucosa against infection. The complex interplay between these functionalities of the intestinal barrier is crucial in early life by supporting homeostasis, development of the intestinal immune system, and long-term gut health. Exclusive breastfeeding is highly recommended during the first 6 months. When breastfeeding is not possible, milk-based infant formulas are the only safe alternative. Breast milk contains many bioactive components that help to establish the intestinal microbiota and influence the development of the intestinal epithelium and the immune system. Importantly, breastfeeding lowers the risk for intestinal and respiratory tract infections. Here we review all aspects of intestinal barrier function and the nutritional components that impact its functionality in early life, such as micronutrients, bioactive milk proteins, milk lipids, and human milk oligosaccharides. These components are present in breast milk and can be added to milk-based infant formulas to support gut health and immunity. Expected final online publication date for the Annual Review of Nutrition, Volume 42 is August 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Synbiotic containing extensively hydrolyzed formula improves gastrointestinal and atopic symptom severity, growth, caregiver quality of life, and hospital-related healthcare use in infants with cow's milk allergy

Background

Healthy gut microbiota is important for prognosis in cow's milk allergy (CMA). The application of synbiotics (specific pre‐ and probiotics) in extensively hydrolyzed formulae (eHFs) is a relatively new concept.

Aims

To evaluate a synbiotic‐containing, whey‐based eHF (SeHF) with galacto‐oligosaccharides, fructo‐oligosaccharides, and bifidobacterium breve M‐16V in infants with CMA.

Materials and Methods

A 31‐day one‐arm pilot study in 29 infants with CMA (mean age 30.8 weeks [SD 11]) was undertaken, with outcomes including gastrointestinal tolerance, atopic dermatitis symptoms, dietary intake, growth, SeHF acceptability, caregiver quality of life, and hospital‐related healthcare use.

Results

Significant improvements (p < .05) in the severity of abdominal pain (in 57%), burping (in 46%), flatulence (in 79%), constipation (in 14%), rhinitis (41%), and itchy eyes (73%), as well as atopic dermatitis in those with severe baseline symptoms (PO‐SCORAD^© reduction: 34.7–18.2 (p = .003), n = 6) were observed over time. Growth and caregiver quality of life scores significantly increased (+26.7%, p < .05) over time. Hospital visits and medications significantly reduced (−1.61 and −2.23, respectively, p < .005) in the 6 months after SeHF initiation.

Discussion

In this small, single‐arm, pilot study, the use of SeHF enhanced the management of infants with non‐IgE mediated CMA who were already established on eHF. Conclusion: Whilst this study adds to the evidence base for the use of SeHF in CMA, further robust research to explore the longer‐term benefits of synbiotics, specifically the blend used in this study, for the clinical management of infants with CMA is warranted.

Alterations in the Gut Microbiota of Tibetan Patients With Echinococcosis

There are two main types of echinococcosis, namely alveolar echinococcosis (AE) and cystic echinococcosis (CE). They are zoonotic parasitic diseases caused by the metacestodes of Echinococcus multilocularis and Echinococcus granulosus. In order to explore the gut microbiome composition of patients with echinococcosis, we analyzed fecal samples of seven patients with AE, six patients with CE, and 13 healthy individuals from the Qinghai-Tibetan Plateau, China. Using metagenomic next-generation sequencing, we identified fecal bacteria in the patients with AE and CE. The gut microbiota was analyzed by next-generation metagenomic sequencing (mNGS) to compare patients with either AE or CE against healthy individuals. We found there were some differences between them in abundant bacteria. Our results led to five findings: (1) Between patients with echinococcosis and healthy individuals, the differential bacteria were from four phyla: Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria. (2) Rothia mucilaginosa, Veillonella dispar, Veillonella atypica, Streptococcus parasanguinis, Streptococcus salivarius, and Alistipes finegoldii were abundant in the feces of patients with AE. (3) Bacteroides dorei, Parabacteroides distasonis, Escherichia sp_E4742, and Methanobrevibacter smithii were abundant in the feces of the patients with CE. (4) At the phylum and class level, compared to the AE group, the healthy group was characterized by higher numbers of Actinobacteria. (5) At the family level, Lachnospiraceae and Eubacteriaceae were more abundant in the feces of healthy individuals than in AE patients. The genera Coprococcus, Eubacterium, and Bilophia were more abundant in the healthy group, while the genus Rothia was more abundant in the AE group. The results of this study enrich our understanding of the gut microbiome composition of patients with AE and CE in the Qinghai-Tibetan Plateau.

Effects of Altitude on the Digestion Performance, Serum Antioxidative Characteristics, Rumen Fermentation Parameters, and Rumen Bacteria of Sanhe Heifers

The production efficiency of dairy cows is affected by altitude, with lower efficiency reported at higher altitudes. However, only a few studies have investigated the digestion performance, serum antioxidative characteristics, rumen fermentation performance, and rumen bacteria of Sanhe heifers at different altitudes. Therefore, in this study, we explored the effects of altitude on these aspects of Sanhe heifers. We evaluated the effects of altitude on the apparent digestibility of nutrients, serum antioxidative characteristics, rumen fermentation parameters, and rumen bacteria in Sanhe heifers. Twenty Sanhe heifers from the same herd and managed with the same practice were used. However, the heifers were from two regions in China: 10 were fed in Hulunbuir City, Inner Mongolia Autonomous Region (119°57'E, 47°17'N; approximately 700 m altitude, named LA) and 10 were fed in Lhasa City, Tibet Autonomous Region (91°06'E, 29°36'N; approximately 3,750 m altitude, named HA). The dry matter intake (DMI), average daily gain (ADG), and DMI/ADG ratio were higher (p < 0.05) in LA than in HA heifers, whereas the apparent total tract digestibility of dry matter, ether extract, and crude proteins were higher (p < 0.05) in the HA group. Compared with LA heifers, the HA heifers showed decreased (p < 0.05) serum concentrations of superoxide dismutase and glutathione peroxidase and increased serum concentration of hydrogen peroxide (p < 0.05). Altitude did not significantly affect the volatile fatty acid concentration in the rumen, but HA presented a lower acetate-to-propionate ratio than LA. The 16S rRNA gene sequencing data showed that altitude significantly affected the rumen microbial composition. At the phylum level, the HA heifers presented a lower relative abundance of Actinobacteria (p < 0.05) and higher relative abundance of Spirochaetae (p < 0.05) than the LA heifers. The correlation analysis revealed that the operational taxonomic units belonging to the genus Prevotella_1 were correlated (p < 0.05) with altitude and DMI. The results indicate that altitude can influence the apparent digestibility of nutrients, serum antioxidant capacity, rumen fermentation, and rumen bacteria composition of Sanhe heifers. The study provides insights into the adaptation mechanism of Sanhe heifers to high-altitude areas.

Early-life cytomegalovirus infection is associated with gut microbiota perturbations and increased risk of atopy

BACKGROUND

The "old friends" hypothesis posits that reduced exposure to previously ubiquitous microorganisms is one factor involved in the increased rates of allergic diseases. Cytomegalovirus (CMV) may be one of the "old friends" hypothesized to help prevent allergic diseases. We sought to elucidate whether early-life CMV infection is associated with childhood atopy via perturbations of the gut microbiota.

METHODS

Participants were recruited from a population-based birth cohort (CHILD study) and followed prospectively until age 5 years in four Canadian cities. A total of 928 participants provided stool microbiome data, urine for CMV testing, skin prick tests, and questionnaire-based detailed environmental exposures. Cytomegalovirus infection was assessed in the first year of life while the main outcome was defined by persistent sensitization to any allergen at ages 1, 3, and 5 years.

RESULTS

Early CMV infection was associated with increased beta and decreased alpha diversity of the gut microbiota. Both changes in diversity measures and early CMV infection were associated with persistent allergic sensitization at age 5 years (aOR = 2.08; 95% CI: 1, 4.33). Mediation analysis demonstrated that perturbation of gut microbial composition explains 30% of the association.

CONCLUSIONS

Early-life CMV infection is associated with an alteration in the intestinal microbiota, which mediates the effect of the infection on childhood atopy. This work indicates that preventing CMV infection would not put children at increased risk of developing atopy. Rather, a CMV vaccine, in addition to preventing CMV-associated morbidity and mortality, might reduce the risk of childhood allergic diseases.

Gut Microbiota Implications for Health and Welfare in Farm Animals: A Review

Simple Summary

Farm animal health and welfare have been paid increasing concern in the world, which is generally assessed by the measurements of physical health, immune response, behavior, and physiological indicators, such as stress-related hormone, cortisone, and norepinephrine. Gut microbiota as a “forgotten organ” has been reported for its great influence on the host phenotypes through the immune, neural, and endocrine pathways to affect the host health and behavior. In addition, fecal microbiota transplantation as a novel approach is applied to regulating the composition and function of the recipient farm animals. In this review, we summarized recent studies that gut microbiota influenced health, immunity, behavior, and stress response, as well as the progress of fecal microbiota transplantation in farm animals. The review will provide new insights into the measurement of farm animal health and welfare concerning gut microbiota, and the implication of fecal microbiota transplantation to improve productivity, health, and welfare. Above all, this review suggests that gut microbiota is a promising field to evaluate and improve animal welfare.

Abstract

In the past few decades, farm animal health and welfare have been paid increasing concern worldwide. Farm animal health and welfare are generally assessed by the measurements of physical health, immune response, behavior, and physiological indicators. The gut microbiota has been reported to have a great influence on host phenotypes, possibly via the immune processes, neural functions, and endocrine pathways, thereby influencing host phenotypes. However, there are few reviews regarding farm animals’ health and welfare status concerning the gut microbiota. In this point of view, (1) we reviewed recent studies showing that gut microbiota (higher alpha diversity, beneficial composition, and positive functions) effectively influenced health characteristics, immunity, behaviors, and stress response in farm animals (such as pigs, chickens, and cows), which would provide a novel approach to measure and evaluate the health status and welfare of farm animals. In addition, fecal microbiota transplantation (FMT) as one of the methods can modulate the recipient individual’s gut microbiota to realize the expected phenotype. Further, (2) we highlighted the application of FMT on the improvement of the production performance, the reduction in disease and abnormal behavior, as well as the attenuation of stress in farm animals. It is concluded that the gut microbiota can be scientifically used to assess and improve the welfare of farm animals. Moreover, FMT may be a helpful strategy to reduce abnormal behavior and improve stress adaption, as well as the treatment of disease for farm animals. This review suggests that gut microbiota is a promising field to evaluate and improve animal welfare.

Genetic factors of functional traits

Selection of functional traits is a challenge for researchers, but an increasingly necessary objective due to the growing concern regarding animal welfare and overcoming the problems of reducing antibiotic use in rabbit production without undermining the animals’ productivity. The aim of this review is to discuss the genetic control of resistance to diseases, longevity and variability of birth weight within a litter, or litter size variability at birth within doe, describing the selection programmes and the first results from a multi-omics analysis of resistance/susceptibility to diseases. The heritability is around 0.13 for longevity, 0.01 for uniformity in birth weight, 0.09 for litter size variability and around 0.11 for disease resistance. Genetic correlations between functional traits and production traits are mostly no different from zero, or are moderately favourable in some cases. Six selection programmes developed in three countries are reviewed. Line foundation with high pressure for selection or divergent selection experiments are different methodologies used, and favourable responses to selection have been achieved. Genomics studies have revealed associations in regions related to immune system functionality and stress in lines selected for litter size variability. Knowledge of the role of gut microbiota in the rabbit’s immune response is very limited. A multi-omics approach can help determine the microbial mechanisms in regulation immunity genes of the host.

Association of infant antibiotic exposure and risk of childhood asthma: A meta-analysis

Background

Infant antibiotic exposure may be associated with childhood asthma development.

Objective

To examine and detail this association considering potential confounders.

Study design

PubMed, EMBASE, Web of Science, and the Cochrane Library were searched for publications from January 2011 to March 2021. Eligible studies were independently reviewed to extract data and assess quality. Random effect model was used to pool odds ratio (OR) and corresponding 95% confidence intervals (CIs).

Results

A total of 52 studies were included. The association of infant antibiotic exposure and childhood asthma was statistically significant for overall analysis (OR, 1.37; 95% CI, 1.29-1.45) and for studies that addressed reverse causation (RC) and confounding by indication (CbI) (1.19; 95% CI, 1.11-1.28). Significance remained after stratification by adjustment for maternal antibiotic exposure, medical consultation, sex, smoke exposure, parental allergy, birth weight, and delivery mode. In detailed analyses, macrolides (OR, 1.56; 95% CI, 1.31-1.86), antibiotic course≥5 (OR, 1.79; 95% CI, 1.36-2.36), exposure within 1 week of birth (OR, 1.82; 95% CI, 1.34-2.47), asthma developed among 1-3 years (OR, 1.84; 95% CI, 1.63-2.08), short time lag between exposure and asthma onset (OR, 2.05; 95% CI, 1.91-2.20), persistent asthma (OR, 2.61; 95% CI, 1.49-4.59), and atopic asthma (OR, 2.14; 95% CI, 1.58-2.90) showed higher pooled estimates.

Conclusion

Infant antibiotic exposure is associated with increased risk of childhood asthma considering confounding, and the association varied with different settings of exposure and outcomes. This highlights the need for prevention of asthma after early antibiotic exposure. Heterogeneity among studies called for caution when interpretation.

Characteristics of Surgical Necrotizing Enterocolitis: Is It Different from Medical Necrotizing Enterocolitis? A Single-Center Retrospective Study

(1) Background: Necrotizing enterocolitis (NEC) is one of the leading causes of death in newborns despite improvements in the care of critically ill neonates. Approximately 50–70% of the cases are managed by medical therapy. However, the remaining patients require surgical intervention. The purpose of our study was to analyze the factors associated with patients requiring surgical treatment compared to patients requiring only medical treatment; (2) Method: Patients diagnosed with necrotizing enterocolitis over a period of 14 years (January 2003–December 2016) in a single tertiary referral children’s hospital were retrospectively enrolled. Demographics and clinical data were collected through the medical record and were analyzed using Pearson’s χ2 test, t-tests, and linear regression; (3) Results: A total of 189 NEC patients were analyzed. In the surgical NEC group, gestational age was lower (p = 0.018), body weight at birth was lower (p = 0.034), comorbidity with respiratory distress syndrome (RDS) was higher (p = 0.005), the days of antibiotic use were greater (p = 0.014), the percentage of breast milk feeding was lower (p = 0.001), and the length of hospital stay was longer (p < 0.000). The in-hospital mortality between the two groups was not significantly different (p = 0.196). In multivariate logistic analysis, breast milk feeding remained less associated with surgical NEC (OR = 0.366, 95% CI: 0.164–0.817), whereas the length of hospital stay was more associated with surgical NEC (OR = 1.010, 95% CI: 1.001–1.019); (4) Conclusion: Comparing medical and surgical NEC, a significantly lower percentage of surgical NEC patients were fed breast milk and their hospital stays were longer.

Profiling Tryptophan Catabolites of Human Gut Microbiota and Acute-Phase Protein Levels in Neonatal Dried Blood Specimens

National screening programs use dried blood specimens to detect metabolic disorders or aberrant protein functions that are not clinically evident in the neonatal period. Similarly, gut microbiota metabolites and immunological acute-phase proteins may reveal latent immune aberrations. Microbial metabolites interact with xenobiotic receptors (i.e., aryl hydrocarbon and pregnane-X) to maintain gastrointestinal tissue health, supported by acute-phase proteins, functioning as sensors of microbial immunomodulation and homeostasis. The delivery (vaginal or cesarean section) shapes the microbial colonization, which substantially modulates both the immune system’s response and mucosal homeostasis. This study profiled microbial metabolites of the kynurenine and tryptophan pathway and acute-phase proteins in 134 neonatal dried blood specimens. We newly established neonatal blood levels of microbial xenobiotic receptors ligands (i.e., indole-3-aldehyde, indole-3-butyric acid, and indole-3-acetamide) on the second day of life. Furthermore, we observed diverse microbial metabolic profiles in neonates born vaginally and via cesarean section, potentially due to microbial immunomodulatory influence. In summary, these findings suggest the supportive role of human gut microbiota in developing and maintaining immune system homeostasis.

Significance of the Gut Microbiome for Viral Diarrheal and Extra-Intestinal Diseases

The composition of the mammalian gut microbiome is very important for the health and disease of the host. Significant correlations of particular gut microbiota with host immune responsiveness and various infectious and noninfectious host conditions, such as chronic enteric infections, type 2 diabetes, obesity, asthma, and neurological diseases, have been uncovered. Recently, research has moved on to exploring the causalities of such relationships. The metabolites of gut microbiota and those of the host are considered in a ‘holobiontic’ way. It turns out that the host’s diet is a major determinant of the composition of the gut microbiome and its metabolites. Animal models of bacterial and viral intestinal infections have been developed to explore the interrelationships of diet, gut microbiome, and health/disease phenotypes of the host. Dietary fibers can act as prebiotics, and certain bacterial species support the host’s wellbeing as probiotics. In cases of Clostridioides difficile-associated antibiotic-resistant chronic diarrhea, transplantation of fecal microbiomes has sometimes cured the disease. Future research will concentrate on the definition of microbial/host/diet interrelationships which will inform rationales for improving host conditions, in particular in relation to optimization of immune responses to childhood vaccines.

Medicinal Plants, Phytochemicals, and Their Impacts on the Maturation of the Gastrointestinal Tract

The gastrointestinal tract (GIT) is the first point of contact for ingested substances and thus represents a direct interface with the external environment. Apart from food processing, this interface plays a significant role in immunity and contributes to the wellbeing of individuals through the brain-gut-microbiota axis. The transition of life from the in utero environment, to suckling and subsequent weaning has to be matched by phased development and maturation of the GIT; from an amniotic fluid occupancy during gestation, to the milk in the suckling state and ultimately solid food ingestion at weaning. This phased maturation of the GIT can be affected by intrinsic and extrinsic factors, including diet. Despite the increasing dietary inclusion of medicinal plants and phytochemicals for health benefits, a dearth of studies addresses their impact on gut maturation. In this review we focus on some recent findings mainly on the positive impact of medicinal plants and phytochemicals in inducing precocious maturation of the GIT, not only in humans but in pertinent animals. We also discuss Paneth cells as mediators and potential markers of GIT maturation.

Review: The development of the gastrointestinal tract microbiota and intervention in neonatal ruminants

The complex microbiome colonizing the gastrointestinal tract (GIT) of ruminants plays an important role in the development of the immune system, nutrient absorption and metabolism. Hence, understanding GIT microbiota colonization in neonatal ruminants has positive impacts on host health and productivity. Microbes rapidly colonize the GIT after birth and gradually develop into a complex microbial community, which allows the possibility of GIT microbiome manipulation to enhance newborn health and growth and perhaps induce lasting effects in adult ruminants. This paper reviews recent advances in understanding how host-microbiome interactions affect the GIT development and health of neonatal ruminants. Following initial GIT microbiome colonization, continuous exposure to host-specific microorganisms is necessary for GIT development and immune system maturation. Furthermore, the early GIT microbial community structure is significantly affected by early life events, such as maternal microbiota exposure, dietary changes, age and the addition of prebiotics, probiotics and synbiotics, supporting the idea of microbial programming in early life. However, the time window in which interventions can optimally improve production and reduce gastrointestinal disease as well as the role of key host-specific microbiota constituents and host immune regulation requires further study.

Maturation of the preterm gastrointestinal tract can be defined by host and microbial markers for digestion and barrier defense

Functionality of the gastrointestinal tract is essential for growth and development of newborns. Preterm infants have an immature gastrointestinal tract, which is a major challenge in neonatal care. This study aims to improve the understanding of gastrointestinal functionality and maturation during the early life of preterm infants by means of gastrointestinal enzyme activity assays and metaproteomics. In this single-center, observational study, preterm infants born between 24 and 33 weeks (n = 40) and term infants born between 37 and 42 weeks (n = 3), who were admitted to Isala (Zwolle, the Netherlands), were studied. Enzyme activity analyses identified active proteases in gastric aspirates of preterm infants. Metaproteomics revealed human milk, digestive and immunological proteins in gastric aspirates of preterm infants and feces of preterm and term infants. The fecal proteome of preterm infants was deprived of gastrointestinal barrier-related proteins during the first six postnatal weeks compared to term infants. In preterm infants, bacterial oxidative stress proteins were increased compared to term infants and higher birth weight correlated to higher relative abundance of bifidobacterial proteins in postnatal week 3 to 6. Our findings indicate that gastrointestinal and beneficial microbial proteins involved in gastrointestinal maturity are associated with gestational and postnatal age.

Effects of Dietary Supplementation of Recombinant Plectasin on Growth Performance, Intestinal Health and Innate Immunity Response in Broilers

The present study was conducted to evaluate the effects of dietary supplementation of recombinant plectasin (Ple) on the growth performance, intestinal health, and serum immune parameters in broilers. A total of 288 1-day-old male broilers (Arbor Acres) were randomly allotted to four dietary treatments including the basal diet (NC) and basal diet supplemented with 10 mg enramycin/kg (PC), 100 mg Ple/kg (LPle), and 200 mg Ple/kg (HPle) diets. The results indicated Ple increased (P < 0.01) average daily gain and decreased (P ≤ 0.02) feed to gain ratio of broilers. In addition, the supplementation of Ple in the diets increased (P ≤ 0.01) duodenal lipase (day 21) and trypsin (day 42) activities compared with the NC group. Similar as the supplementation of enramycin, Ple also increased villus height and decreased crypt depth in jejunum (day 21), and thus the villus height to crypt depth ratio (P < 0.01) was increased compared to the NC group on day 42. The serum immunoglobulin M (days 21 and 42), immunoglobulin G (day 42), complement 3 (day 21), and complement 4 (days 21 and 42) were significantly increased (P ≤ 0.02) due to the supplementation of Ple and enramycin, while the concentration of malondialdehyde in jejunum was decreased (P < 0.01) in PC, LPle, and HPle groups on day 21 compared with those in the NC group. Furthermore, Ple reduced (P < 0.01) Escherichia coli and total aerobic bacteria population in ileum and cecum of birds on days 21 and 42. These results indicate that the recombinant plectasin has beneficial effects on growth performance, intestinal health, and innate immunity in broilers.

Comparison of Gut Microbiota of Yaks From Different Geographical Regions

Gut microbiota are closely linked to host health and adaptability to different geographical environments. However, information on the influence of different geographical conditions on the intestinal microbiota of yaks is limited. In this study, 18 yak fecal samples were collected from three regions of China, namely Shangri-la, Lhasa, and Yushu, and were analyzed via high-throughput sequencing. The alpha diversity, as measured by the Shannon, ACE, and Chao indices, was the highest in the Shangri-la samples. Principal coordinate analysis detected significant differences in the composition of the intestinal microbiota of yaks from different regions. A total of six phyla, 21 families, and 29 genera were identified in the fecal samples. The dominant phyla in the samples were Firmicutes and Bacteroidetes, and the most abundant family was Ruminococcaceae. In addition, Ruminococcaceae_UCG-005 was the predominant genus and was more abundant in Yushu samples than in other samples. However, the predicted functional gene composition of the gut microbiota of yaks from different regions was similar. Our results revealed that geographical conditions influence the diversity and composition of the intestinal microbiota of yaks.

Breast milk urea as a nitrogen source for urease positive Bifidobacterium infantis

Human milk stimulates a health-promoting gut microbiome in infants. However, it is unclear how the microbiota salvages and processes its required nitrogen from breast milk. Human milk nitrogen sources such as urea could contribute to the composition of this early life microbiome. Urea is abundant in human milk, representing a large part of the non-protein nitrogen (NPN). We found that B. longum subsp. infantis (ATCC17930) can use urea as a main source of nitrogen for growth in synthetic medium and enzyme activity was induced by the presence of urea in the medium. We furthermore confirmed the expression of both urease protein subunits and accessory proteins of B. longum subsp. infantis through proteomics. To the same end, metagenome data were mined for urease-related genes. It was found that the breastfed infant's microbiome possessed more urease-related genes than formula fed infants (51.4:22.1; 2.3-fold increase). Bifidobacteria provided a total of 106 of urease subunit alpha alignments, found only in breastfed infants. These experiments show how an important gut commensal that colonizes the infant intestine can metabolize urea. The results presented herein further indicate how dietary nitrogen can determine bacterial metabolism in the neonate gut and shape the overall microbiome.