Association Between Breast Milk Bacterial Communities and Establishment and Development of the Infant Gut Microbiome

Association between fat-soluble vitamins in breast milk and neonatal gut microbiome in Tibetan mother-infant dyads during the first month postnatal

The Tibetan Plateau is a high-altitude environment characterized by hypoxic conditions, strong ultraviolet rays, and significant temperature variations that affect the well-being of local residents, including mother-infant dyads. Adaptive evolution through lifestyle and dietary patterns plays an important role in nutrition during the maternal lactation period, which offers unique merits for investigation at the intersection of environmental and nutritional fields. Specifically, changes in the nutrient composition of human milk among Tibetan lactating mothers and their associated consequences for infants provide insight into early nutrition research and infant food production. In this study, the concentrations of vitamins A, D, E, and β-carotene in the human milk of Tibetan mothers, as well as the fecal microbiome profiles of their infants, were analyzed within the first month postnatal. The results showed that the fat-soluble vitamins in Tibetan human milk were at satisfactory levels, particularly during the colostrum stage, which may be attributed to the advantages of their dietary pattern and dwelling environment. Dynamic changes in the gut microbiota composition of Tibetan infants were observed, with the phyla Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria being relatively abundant. The abundance of Bifidobacterium increased as infants aged within the first month postnatal. Correlations were found between the fat-soluble vitamin composition in human milk and the characteristics of the infant gut microbiota, including alpha (α)-diversity indices and microbial abundances. These findings will help enhance the understanding of early nutrition under harsh natural conditions and will guide relevant innovations and improvements in the maternal and infant food industry.

Personalized Dietary Approaches to Optimizing Intestinal Microbial Health and Homeostasis

Diet has a profound impact in human health, which is partly driven by changes in the intestinal microbiota. Several associations between dietary intake and the intestinal microbiota composition and function have been described. Namely, the Mediterranean diet is associated with beneficial bacteria, while the intake of ultraprocessed foods is linked to dysbiosis. It is, therefore, very tempting to tailor dietary approaches to the individual needs of the microbiota; however, high-quality prospective data are lacking. Provisionally, a diet rich in fruits and vegetables and low in ultraprocessed foods is recommended to improve the intestinal microbiota composition and function.

Role of sn-2 palmitate on the development of the infant gut microbiome: A metagenomic insight

The infant gut microbiome, which develops from birth, has profound and lasting effects on human health. Its establishment in early life is influenced by events such as delivery mode and feeding type. This study examined the effects of formula milk enriched with sn-2 palmitate on the gut microbiota of healthy term infants. We conducted a 16-week comparative analysis of three feeding groups: infants receiving high sn-2 palmitate formula (n = 30), regular vegetable oil formula (n = 32), and breast milk (n = 30). Using shotgun metagenomic sequencing of fecal samples, we performed a comprehensive assessment of the gut microbiota. While overall microbial composition and diversity were comparable across groups, the functional profile of the microbiome in infants receiving sn-2 palmitate-enriched formula more closely resembled that of breastfed infants compared to the control formula group. This similarity extended to microbial species interactions, virulence gene abundance, and metabolic pathway expression patterns. In addition, sn-2 palmitate promoted the proliferation of Bifidobacterium breve and enhanced the robustness of the gut microbial ecology. Notably, the phylogenetic analysis of B. breve strains in the sn-2 palmitate group showed closer alignment with the breastfed group compared to the control group. These findings suggest that sn-2 palmitate-enriched formula may confer gut microbiota functional benefits that more closely resemble those of breast milk compared to control formula milk. This study provides scientific evidence for the development of future functional infant formulas.

Maternal immunoglobulins differentially bind a diverse bacterial community in human colostrum and the stool of breastfed neonates

In the early days, maternal immunoglobulins are essential for sustaining a balanced gut environment by influencing the interaction between the host and the microbiome. The successional establishment of the pioneer strains is an interesting topic of research where maternal immunoglobulins appear to be important. This proof-of-concept study explored the binding pattern of IgA1, IgA2, IgM, and IgG classes to a commensal bacterial in human colostrum and the stool of breastfed neonates. We used flow cytometry coupled with 16S rRNA gene sequencing in human colostrum and neonatal feces samples to characterize this Ig-microbiota association. We observed that in human colostrum samples, IgA2 and IgM bind alfa and beta Proteobacteria, which can potentially stimulate neonatal immune system development in the gut. Other immunoglobulins like IgG predominantly bind facultative anaerobes belonging to the Firmicutes phylum, reported as part of human milk microbiota and pioneer colonizers of the neonatal gut. Maternal immunoglobulins also bind a wide diversity of bacteria in the neonatal stool. For instance, IgA2 and IgM bound more members of the phylum Bacteroidetes in comparison to IgG, these Bacteroidetes and some firmicutes have been reported as late colonizers of the neonatal gut, and their presence is important due to their ability to produce important short chain fatty acids like propionate and butyrate. Our results support the current view that microbial and immunoglobulin transference is crucial for developing the neonate's immune system and individual gut microbiota.

Impact of antimicrobial exposure at delivery and siblings on early Bifidobacterium succession and allergy development up to 24 months of age

BACKGROUND

Allergic diseases such as asthma, eczema, and food allergies are rising globally. The infant gut microbiota, particularly the dominance of Bifidobacterium, shapes immune development and allergy risk. In Japan-where Bifidobacterium prevalence is notably high-longitudinal investigations focusing on the pre-weaning period, when external influences are relatively limited, remain scarce. Therefore, based on consistent hypotheses and findings from previous studies, we investigated how two important early factors-antibiotic exposure at birth and the presence of older siblings-influence the gut environment in early infancy and subsequent allergy development.

RESULTS

In a prospective cohort of 121 Japanese infants, stool samples were collected at seven time points from birth through 24 months. We quantified the relative abundances of Bifidobacterium, Bacteroides, Clostridium, and Faecalibacterium and recorded allergic outcomes at 2 years. Both antimicrobial exposure at delivery and sibling presence significantly altered gut microbiota composition and overall diversity in early infancy. Although the full cohort showed no consistent diversity or Bifidobacterium differences by allergic status, in several subgroups where these two factors were excluded, infants who had an allergy by 24 months exhibited marked shifts in early gut microbiota community structure-particularly in beta diversity-and reduced Bifidobacterium occupancy during the pre-weaning period (1-6 months) versus non-allergic peers. Moreover, infants whose gut microbiota was initially affected by these factors showed a recovery in diversity after weaning, a rebound more pronounced in non-allergic individuals.

CONCLUSIONS

These findings indicate that both the initial community configuration and its capacity to rebound after perturbation are critical determinants of allergy risk. By focusing on dynamic changes through weaning and adjusting for decisive confounders, this study refines insight beyond prior cross-sectional work. Early interventions that preserve or restore microbial diversity and Bifidobacterium dominance may therefore offer a promising strategy to mitigate allergic disease development.

Microbiome and pediatric leukemia, diabetes, and allergies: Systematic review and meta-analysis

BACKGROUND

Despite the different pathologies and genetic susceptibilities of childhood ALL, T1DM and allergies, these conditions share epidemiological risk factors related to timing of infectious exposures and acquisition of the gut microbiome in infancy. We have assessed whether lower microbiome diversity (Shannon Index) and shared genus/species profiles are associated with pediatric ALL, allergies, and T1DM.

METHODS AND FINDINGS

Literature search was performed using PubMed, Embase, Cochrane, and Web of Science databases. Case-control, meta-analyses, and cohort studies were considered for inclusion. Inclusion criteria: (i) subjects age 1-18 years at diagnosis, (ii) reports effect of microbiome measured prior to/at time of diagnosis/first intervention (iii) outcome of ALL, allergies, asthma, or T1DM, (iv) English text. Exclusion criteria: (i) age < 1 or >18 years at diagnosis, (ii) Down Syndrome-associated ALL, (iii) non-English text, (iv) reviews, pre-print, or abstracts, (v) heavily biased studies. Abstract and full text screening were performed by two independent reviewers. Data extraction was performed by one reviewer following PRISMA guidelines. Data were pooled using a random-effects model. Eighty-eight studies were included in the analysis, with seventy-seven in the qualitative analysis and 54 in the meta-analysis. Cases were found to have lower alpha-diversity than controls in ALL (SMD:-0.78, 95%CI:-1.21, -0.34), T1DM (SMD:-1.26, 95%CI:-3.49, 0.96), eczema (SMD:-0.34, 95%CI:-0.56, -0.12), atopy (SMD:-0.06, 95%CI:-0.34, 0.22), asthma (SMD:-0.37, 95%CI:-1.16, 0.42), and food allergy (SMD:-0.11, 95%CI:-0.63, 0.41).

CONCLUSIONS

These results highlight similarities in the microbiome diversity and composition of children with ALL, T1DM, and allergies. This is compatible with a common risk factor related to immune priming in infancy and highlights the gut microbiome as a potentially modifiable risk factor and preventative strategy for these childhood diseases.

The Gut Microbiome as a Key Determinant of the Heritability of Body Mass Index

The pathogenesis of obesity is complex and incompletely understood, with an underlying interplay between our genetic architecture and obesogenic environment. The public understanding of the development of obesity is shrouded in myths with widespread societal misconceptions. Body Mass Index (BMI) is a highly heritable trait. However, despite reports from recent genome-wide association studies, only a small proportion of the overall heritability of BMI is known to be lurking within the human genome. Other non-genetic heritable traits may contribute to BMI. The gut microbiome is an excellent candidate, implicating complex interlinks with hypothalamic control of appetite and metabolism via entero-endocrine, autonomic, and neuro-humeral pathways. The neonatal gut microbiome derived from the mother via transgenerational transmission (vaginal delivery and breastfeeding) tends to have a permanence within the gut. Conversely, non-maternally derived gut microbiota manifest mutability that responds to changes in lifestyle and diet. We should all strive to optimize our lifestyles and ensure a diet that is replete with varied and unprocessed plant-based foods to establish and nurture a healthy gut microbiome. Women of reproductive age should optimize their gut microbiome, particularly pre-conception, ante- and postnatally to enable the establishment of a healthy neonatal gut microbiome in their offspring. Finally, we should redouble our efforts to educate the populace on the pathogenesis of obesity, and the role of heritable (but modifiable) factors such as the gut microbiome. Such renewed understanding and insights would help to promote the widespread adoption of healthy lifestyles and diets, and facilitate a transition from our current dispassionate and stigmatized societal approach towards people living with obesity towards one that is epitomized by understanding, support, and compassion.

Phage diversity in human breast milk: a systematic review

Breast milk is not sterile. The microbiome in human milk serves as a crucial source of early gut microbes for infants, directly impacting the host's health. This microbiome includes bacteria, viruses, archaea, and fungi. Bacteriophages, as key components of the virome, continually prey on bacterial hosts, thereby influencing the development of early gut microbial communities. Pertinent records from various databases, including EMBASE, Cochrane Library, PubMed, and Web of Science, were comprehensively reviewed against inclusion criteria up to March 24, 2025. A checklist was employed to assess the risk of bias in the selected studies. After screening a total of 635 records, we included 5 studies with 182 women and 251 samples. Seven families of bacteriophages were identified, primarily Herelleviridae, Myoviridae, Podoviridae, Siphoviridae, Caudoviridales, Microviridae, and Inoviridae. Their abundance varies at different stages of lactation and can be vertically transmitted through breastfeeding. However, due to the limited number of studies and methodological differences, it is not yet possible to determine which maternal and infant characteristics influence the abundance of these bacteriophages.

CONCLUSION

Human milk contains abundant bacteriophages that bind to specific bacterial hosts and are transmitted vertically from mother to infant, collectively shaping the infant's gut microbiome. Conducting more longitudinal studies on mother-infant pairs will help better determine the composition of bacteriophages in human milk and their functional impact on infant development.

WHAT IS KNOWN

• Human milk is a source of diverse microbes, including bacteriophages, that contribute to the establishment of the infant gut microbiome. • Bacteriophages can influence bacterial populations by infecting specific bacterial hosts.

WHAT IS NEW

• Human milk harbors abundant and diverse bacteriophages that are vertically transmitted from mother to infant. • Current evidence underscores the need for longitudinal studies to clarify the role of milk-derived bacteriophages in shaping infant gut microbiota and development.

Gut-immune-brain interactions during neurodevelopment: from a brain-centric to a multisystem perspective

BACKGROUND

Neurodevelopmental disorders (NDDs) and epileptic syndromes are complex neurological conditions linked by shared abnormal neurobiological processes. Existing therapies mostly target symptoms, rather than addressing the underlying causes of the disease, leaving a burden of unmet clinical needs.

MAIN BODY

Emerging evidence suggests a significant role for the gut microbiota and associated immune responses in influencing brain development and function, changing the paradigm of a brain-centric origin of NDDs. This review discusses the pivotal interactions within the gut-immune-brain axis, highlighting how microbial dysbiosis and immune signaling contribute to neurological pathologies. We also explore the potential of microbial management and immunomodulation as novel therapeutic avenues, emphasizing the need for a shift towards addressing the root causes of these disorders rather than just their symptoms.

CONCLUSIONS

This integrated perspective offers new insights into the biological underpinnings of NDDs and epilepsy, proposing innovative biomarkers and therapeutic strategies.

Gut Microbiota Dysbiosis: Pathogenesis, Diseases, Prevention, and Therapy

Dysbiosis refers to the disruption of the gut microbiota balance and is the pathological basis of various diseases. The main pathogenic mechanisms include impaired intestinal mucosal barrier function, inflammation activation, immune dysregulation, and metabolic abnormalities. These mechanisms involve dysfunctions in the gut-brain axis, gut-liver axis, and others to cause broader effects. Although the association between diseases caused by dysbiosis has been extensively studied, many questions remain regarding the specific pathogenic mechanisms and treatment strategies. This review begins by examining the causes of gut microbiota dysbiosis and summarizes the potential mechanisms of representative diseases caused by microbiota imbalance. It integrates clinical evidence to explore preventive and therapeutic strategies targeting gut microbiota dysregulation, emphasizing the importance of understanding gut microbiota dysbiosis. Finally, we summarized the development of artificial intelligence (AI) in the gut microbiota research and suggested that it will play a critical role in future studies on gut dysbiosis. The research combining multiomics technologies and AI will further uncover the complex mechanisms of gut microbiota dysbiosis. It will drive the development of personalized treatment strategies.

Pavlik Harness Treatment for Infantile Hip Dysplasia Lowers Breastfeeding Self-efficacy

INTRODUCTION

Breastfeeding is recommended exclusively until at least 6 months of age by the American Academy of Pediatrics. For mothers of children with hip dysplasia (DDH), Pavlik harness treatment may impact breastfeeding. The aim of this study was to assess how Pavlik harness treatment may impact breastfeeding by evaluating patient-reported outcomes (PRO) associated with breastfeeding.

METHODS

This was a prospective cohort study of mothers of patients treated in a Pavlik harness for DDH at <3 months of age. Controls were recruited from patients evaluated for DDH who had normal ultrasounds. Patients with neuromuscular/developmental conditions were excluded. The validated beginning breastfeeding survey-cumulative (BBS-C), breastfeeding self-efficacy scale-short form (BSES-SF), and patient health questionnaire-8 (PHQ8) were administered to mothers at the initial clinic appointment and 2, 4, 6 weeks postbaseline.

RESULTS

A total of 29 cases and 29 controls were enrolled. There were no differences in baseline demographics or socioeconomic/educational status between maternal cohorts. There were similarly no differences in demographics or birth characteristics between children except presenting age was lower in the DDH cohort (30.7±22.1 vs. 58.7±21.4 d, P<0.001). PROs were similar at enrollment. Six weeks after harness initiation, 76% of the DDH cohort were still breastfeeding (vs. 89% of controls, P=0.303), and 52% (vs. 77%, P=0.052) reported breastfeeding >80% of the time. Mothers of 13% of DDH patients reported that the Pavlik usually/always negatively impacted their breastfeeding ability at 6 weeks. The DDH cohort had lower BBS-C problem scores at 4 (17.6±6.4 vs. 20.8±3.7, P=0.045) and 6 weeks (17.2±6.2 vs. 20.2±3.3, P=0.029). BSES-SF scores were additionally lower among the DDH group at 2 (47.6±11.8 vs. 54.1±10.2, P=0.047) and 4 weeks (48.5±13.0 vs. 55.6±10.3, P=0.040). There were no differences in PHQ-8 scores.

CONCLUSION

Pavlik harness treatment for DDH was associated with lower patient-reported breastfeeding efficacy PROs. Pavlik harness treatment did not lead to earlier breastfeeding cessation 6 weeks after harness initiation. Lower breastfeeding efficacy for these mothers may justify early education regarding effective breastfeeding methods in a harness.

LEVEL OF EVIDENCE

Level II-prospective therapeutic cohort study.

Breast milk stabilizes bacterial communities in the large intestine even after weaning

The development and maintenance of a balanced microbiota is crucial for human health. Milk contains immune factors that not only protect offspring from infectious diseases but also play an important role in promoting the development and maintenance of the microbiota. However, the persisting effects of milk-derived immune factors on the maintenance of the microbiota after weaning have not been carefully examined. In this study, a cross-fostering model was employed using immunocompetent (IC) and immunodeficient (ID) mice in which one-half of the pups born from two dams were replaced. As a result, breast milk from the IC dam (IC milk) affected the development of the microbiota during lactation and maintained it even after weaning in the large intestine of the ID pups. The large intestinal microbiota of ID pups raised on IC milk remained similar to that of normal IC pups. Under normal conditions, the genus Mucispirillum was closely associated with other bacteria, forming a diverse bacterial community in the large intestine. In the small intestine, there were no differences in the microbiota before weaning, regardless of whether IC or ID milk was consumed. By contrast, significant differences were observed in the small intestinal microbiota between IC and ID mice after weaning; however, this was dependent on the immune-related characteristics of offspring (rather than milk-derived immune factors). These results indicate that breast milk plays an important role in the large (not small) intestine of offspring to create and maintain a diverse microbiota with a balanced bacterial network even after weaning.

Achieving caloric goal in postoperative management of CHD surgery

BACKGROUND

This study investigated the prevalence of malnutrition, time to achieve caloric goals, and nutritional risk factors after surgery for CHD in a cardiac ICU.

METHOD

This retrospective study included patients with CHD (1 month-18 years old) undergoing open-heart surgery (2021-2022). We recorded nutritional status, body mass index-for-age z-score, weight-for-length/height z-score, cardiopulmonary bypass and aortic cross-clamp time, Paediatric Risk of Mortality-3 score, Paediatric Logistic Organ Dysfunction-2 score, vasoactive inotropic score, total duration of mechanical ventilation, length of stay in the cardiac ICU, mortality, and time to achieve caloric goals.

RESULTS

Of the 75 included patients, malnutrition was detected in 17% (n= 8) based on the body mass index-for-age z-score and in 35% (n= 10) based on the weight-for-length/height z-score. Sex, mortality, cardiopulmonary bypass and aortic cross-clamp time, Paediatric Risk of Mortality-3, Paediatric Logistic Organ Dysfunction-2, and vasoactive inotropic score, duration of mechanical ventilation, and length of cardiac ICU stay were similar between patients with and without malnutrition. Patients who achieved caloric goals on the fourth day and those who achieved them beyond the fourth day showed statistical differences in mortality, maximum vasoactive inotropic score, duration of mechanical ventilation, cardiopulmonary bypass and aortic cross-clamp time, Paediatric Risk of Mortality-3, Paediatric Logistic Organ Dysfunction-2, and length of cardiac ICU and hospital stay (p< 0.05). Logit regression analysis indicated that the duration of mechanical ventilation, Paediatric Logistic Organ Dysfunction-2 and Paediatric Risk of Mortality-3 score was a risk factor for achieving caloric goals (p< 0.05).

CONCLUSIONS

Malnutrition is prevalent in patients with CHD, and concomitant organ failure and duration of mechanical ventilation play important roles in achieving postoperative caloric goals.

Human Milk Microbiome from Polish Women Giving Birth via Vaginal Delivery-Pilot Study

The human milk (HM) microbiome is variable and depends on maternal, perinatal, and cultural-environmental factors. The diversity of the HM microbiome is crucial in the development of the child. The aim of the study was to assess the prevalence of bacteria (using culture-based methods) of Polish women with normal BMI, giving birth on time through vaginal delivery.

METHODS

The research material consisted of human milk and swabs from the areola and nipple, before and after breastfeeding, derived from Polish women (n = 86). Classic culture methods were used to obtain multiple bacteria. Species identification of the grown colonies was performed using MALDI TOF MS (Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry).

RESULTS

120 species of bacteria were isolated, mainly from the genus Streptococcus and Staphylococcus. Species specific only to human milk were identified (belonging to the following genera: Microbacterium, Shewanella, Psychrobacter, Aeromonas, Serratia, Buttiauxella, Lactobacillus, Bifidobacterium) as well as species specific only to areola and nipple swabs after breastfeeding (Acinetobacter lactucae, Moraxella catarrhalis, Corynebacterium pseudodiphtheriticum, Corynebacterium propinquim). It was confirmed that most species were present in all tested materials collected from one patient.

CONCLUSIONS

The analysis carried out showed the presence of bacteria in the human milk of Polish women, including strains of lactic acid bacteria. The human milk microbiota may significantly influence the formation of the infant's intestinal microbiota, including some key genera, i.e., Lactobacillus, Bifidobacterium, and Limosilactobacillus, which were also isolated from the tested samples. The data presented here provide new data on culturable bacterial species isolated from breast milk from Polish women giving birth via vaginal delivery and potential routes of transmission from the neonate's oral cavity.

Comparative Analysis of Gut Microbiota Diversity Across Different Digestive Tract Sites in Ningxiang Pigs

BACKGROUND

Microbial communities in the gastrointestinal tract play a critical role in nutrient absorption, metabolism, and overall health of animals. Understanding the structure and function of tissue-specific microbial communities in Ningxiang pigs is essential for optimizing their growth, development, and nutritional efficiency. However, the diversity and functional roles of microbiota in different nutrient absorption tissues remain underexplored.

METHODS

We collected samples from four key nutrient absorption tissues (NFC: Cecal Content, NFI: Ileal Content, NFL: Colonic Content, NFG: Gastric Content, N = 6) of Ningxiang pigs and performed 16S rRNA gene sequencing to analyze microbial community composition. Bioinformatics analyses included alpha and beta diversity assessments, linear discriminant analysis effect size (LEfSe) for biomarker identification, and PICRUSt2-based functional prediction. Comparative metabolic abundance analysis was conducted to explore functional differences among tissues.

RESULTS

Alpha diversity indices (ACE, Chao1, Simpson, and Shannon) revealed significant differences in microbial richness and evenness among the four tissues. At the phylum level, Firmicutes dominated the microbiota, while Bacteroidota was prominent in NFC and NFL. LEfSe analysis identified tissue-specific dominant microbial groups, such as f_Prevotellaceae in NFC, o_Lactobacillales in NFG, f_Clostridiaceae in NFI, and f_Muribaculaceae in NFL. Functional profiling using PICRUSt2 showed that the microbiota was primarily involved in organismal systems (e.g., aging, digestion), cellular processes (e.g., cell growth, transport), environmental information processing (e.g., signaling), genetic information processing (e.g., transcription, translation), and metabolic regulation (e.g., amino acid and carbohydrate metabolism). Comparative metabolic abundance analysis highlighted distinct functional profiles across tissues, with significant differences observed in pathways related to the immune system, energy metabolism, lipid metabolism, transcriptional and translational regulation, and aging.

CONCLUSIONS

Our findings demonstrate that tissue-specific microbial communities in Ningxiang pigs exhibit distinct structural and functional characteristics, which are closely associated with nutrient absorption and metabolic regulation. These results provide valuable insights into the roles of microbiota in the growth and health of Ningxiang pigs and pave the way for future studies on microbe-mediated nutritional interventions.

Harnessing the Potential of Human Breast Milk to Boost Intestinal Permeability for Nanoparticles and Macromolecules

The intricate interplay between human breast milk, nanoparticles, and macromolecules holds promise for innovative nutritional delivery strategies. Compared to bovine milk and infant formula, this study explores human breast milk's role in modulating intestinal permeability and its impact on nanoparticle and macromolecule transport. Comparative analysis with bovine milk and infant formula reveals significant elevations in permeability with human breast milk, accompanied by a decrease in transepithelial electrical resistance, suggesting enhanced paracellular transport. Mechanistically, human breast milk reduces Zonula occludens-1 levels, suggesting a regulatory role in intestinal barrier function. Through in vitro and ex vivo evaluations, we aim to understand better the mechanisms behind enhanced permeability and how human breast milk affects nanoparticle physicochemical properties, potentially modulating their behavior. Specifically, human breast milk improves the intestinal permeability of liposomes in a porcine intestinal model, with associated changes in the composition of milk proteins corona related to liposome charge. These findings underscore the unexploited potential of human breast milk in facilitating transport across the intestinal barrier, offering novel avenues for human nutritional delivery and therapeutic interventions.

Culture-Independent Species-Level Taxonomic and Functional Characterisation of Bacteroides, the Core Bacterial Genus Within Reptile Guts

The genus Bacteroides is a widespread and abundant bacterial taxon associated with gut microbiotas. Species within Bacteroides fill many niches, including as mutualists, commensals and pathogens for their hosts. Within many reptiles, Bacteroides is a dominant, 'core' gut bacterium that sometimes exhibits increased abundance in times of food scarcity, such as during hibernation. Here, we take a two-pronged approach to better characterise Bacteroides populations in reptile guts. Firstly, we leverage published 16S rRNA gene sequence datasets to determine the species-level distributions of Bacteroides members in reptile hosts. Secondly, we mine publicly available metagenomes to extract data for Bacteroides from reptiles, birds, amphibians and mammals, to compare the functional potential of Bacteroides in different host taxa. The 16S rRNA gene analyses revealed that B. acidifaciens is the most common Bacteroides species in reptile guts, and that different orders of reptiles differ in which Bacteroides species they harbour. The taxonomy of Bacteroides species recovered from metagenomic assembly did not differ between reptile orders or substantially across birds, amphibians and mammals. Metagenome-assembled genomes for Bacteroides species were marginally more related when their hosts were more closely related, with reptile hosts in particular harbouring markedly more unique Bacteroides MAGs compared to other hosts. Our findings indicate that hosts harbour similar profiles of Bacteroides species across broad comparisons, but with some differences between reptile groups, and that Bacteroides appears to perform largely similar roles in vertebrate host guts regardless of host relatedness.

Deciphering the tripartite interaction of urbanized environment, gut microbiome and cardio-metabolic disease

The world is experiencing a sudden surge in urban population, especially in developing Asian and African countries. Consequently, the global burden of cardio-metabolic disease (CMD) is also rising owing to gut microbiome dysbiosis due to urbanization factors such as mode of birth, breastfeeding, diet, environmental pollutants, and soil exposure. Dysbiotic gut microbiome indicated by altered Firmicutes to Bacteroides ratio and loss of beneficial short-chain fatty acids-producing bacteria such as Prevotella, and Ruminococcus may disrupt host-intestinal homeostasis by altering host immune response, gut barrier integrity, and microbial metabolism through altered T-regulatory cells/T-helper cells balance, activation of pattern recognition receptors and toll-like receptors, decreased mucus production, elevated level of trimethylamine-oxide and primary bile acids. This leads to a pro-inflammatory gut characterized by increased pro-inflammatory cytokines such as tumour necrosis factor-α, interleukin-2, Interferon-ϒ and elevated levels of metabolites or metabolic endotoxemia due to leaky gut formation. These pathophysiological characteristics are associated with an increased risk of cardio-metabolic disease. This review aims to comprehensively elucidate the effect of urbanization on gut microbiome-driven cardio-metabolic disease. Additionally, it discusses targeting the gut microbiome and its associated pathways via strategies such as diet and lifestyle modulation, probiotics, prebiotics intake, etc., for the prevention and treatment of disease which can potentially be integrated into clinical and professional healthcare settings.

Practical concepts and strategies for early diagnosis and management of eosinophilic gastrointestinal disorders in East-Asian children

Eosinophilic gastrointestinal disorders (EGIDs) are emerging as significant concerns in the Korean pediatric population and transitioning from rare to more commonly diagnosed conditions. This review discusses the increasing prevalence of EGID among children and adolescents and highlights the complexities involved in its diagnosis and management. This review begins with a thorough examination of the diverse clinical presentations of EGIDs in Korean children, with a special focus on common gastrointestinal symptoms such as abdominal pain, diarrhea, and bloody stool. Additionally, we explored extraintestinal manifestations, including growth failure, malnutrition, and associated allergic comorbidities, highlighting their importance in the clinical landscape of EGIDs. Because of its subtle and overlapping symptoms with those of other gastrointestinal disorders, EGID is frequently underdiagnosed. Addressing this challenge requires maintaining a high index of suspicion and employing a comprehensive diagnostic approach to differentiating EGID from functional gastrointestinal disorders and other inflammatory or systemic diseases such as inflammatory bowel disease. The optimal management of EGID requires a collaborative multidisciplinary strategy that includes dietary management, regular monitoring, and tailored medical interventions. This review emphasizes the importance of proactive patient and caregiver education and regular follow-ups to improve long-term outcomes in affected children. Enhanced awareness among healthcare providers and better educational resources for families are critical for the early identification and effective management of EGID among pediatric patients.

Harnessing the Farm Effect: Microbial Products for the Treatment and Prevention of Asthma Throughout Life

It has long been appreciated that farm exposure early in life protects individuals from allergic asthma. Understanding what component(s) of this exposure is responsible for this protection is crucial to understanding allergic asthma pathogenesis and developing strategies to prevent or treat allergic asthma. In this review, we introduce the concept of Farm-Friends, or specific microbes associated with both a farm environment and protection from allergic asthma. We review the mechanism(s) by which these Farm-Friends suppress allergic inflammation, with a focus on the molecule(s) produced by these Farm-Friends. Finally, we discuss the relevance of Farm-Friend administration (oral vs. inhaled) for preventing the development and severity of allergic asthma throughout childhood and adulthood. By developing a fuller understanding of which Farm-Friends modulate host immunity, a greater wealth of prophylactic and therapeutic options becomes available to counter the current allergy epidemic.

Infant feeding and criticality in children

BACKGROUND

Data support the protective effects of human breast milk (HBM) feeding in acute illness but little is known about the impact of HBM feeding on the criticality of infants.

AIM

To explore the relationship between early HBM feeding and severity of illness and recovery in critically ill children requiring intubation and mechanical ventilation for acute respiratory failure (ARF).

STUDY DESIGN

Prospective cohort study of mothers of patients aged 1-36 months who participated in the acute and follow-up phases of the Randomized Evaluation of Sedation Titration for Respiratory Failure (RESTORE) clinical trial. Participants completed a survey describing HBM dose fed during their infant's first month of life.

RESULTS

Of 138 patients, 70 (51%) received exclusive HBM feedings (90%-100% total feeds) and 68 (49%) did not. We found no group differences in severity of illness on paediatric intensive care unit (PICU) admission or severity of paediatric acute respiratory distress syndrome (PARDS) within the first 24-48 h of intubation/mechanical ventilation (Pediatric Risk of Mortality [PRISM] III-12 score median: 5 vs. 5, p = .88; moderate/severe PARDS: 53% vs. 54%, p = .63). While median time to recovery from ARF was reduced by 1 day in patients who received exclusive HBM feedings, the difference between groups was not statistically significant (median 1.5 vs. 2.6 days, hazard ratio 1.40 [95% confidence interval, 0.99-1.97], p = .06).

CONCLUSIONS

Human breast milk dose was not associated with severity of illness on PICU admission in children requiring mechanical ventilation for ARF.

RELEVANCE TO CLINICAL PRACTICE

Data support the protective effects of HBM during acute illness and data from this study support a clinically important reduction in time to recovery of ARF. Paediatric nurses should continue to champion HBM feeding to advance improvements in infant health.

A menu for microbes: unraveling appetite regulation and weight dynamics through the microbiota-brain connection across the lifespan

Appetite, as the internal drive for food intake, is often dysregulated in a broad spectrum of conditions associated with over- and under-nutrition across the lifespan. Appetite regulation is a complex, integrative process comprising psychological and behavioral events, peripheral and metabolic inputs, and central neurotransmitter and metabolic interactions. The microbiota-gut-brain axis has emerged as a critical mediator of multiple physiological processes, including energy metabolism, brain function, and behavior. Therefore, the role of the microbiota-gut-brain axis in appetite and obesity is receiving increased attention. Omics approaches such as genomics, epigenomics, transcriptomics, proteomics, and metabolomics in appetite and weight regulation offer new opportunities for featuring obesity phenotypes. Furthermore, gut-microbiota-targeted approaches such as pre-, pro-, post-, and synbiotic, personalized nutrition, and fecal microbiota transplantation are novel avenues for precision treatments. The aim of this narrative review is 1) to provide an overview of the role of the microbiota-gut-brain axis in appetite regulation across the lifespan and 2) to discuss the potential of omics and gut microbiota-targeted approaches to deepen understanding of appetite regulation and obesity.

Gut microbiota alterations in golden snub-nosed monkeys during food shortage and parturition-nursing periods

Adopting unique survival strategies during spring food shortages and simultaneous parturition and nursing is crucial for golden snub-nosed monkeys. Social behaviors, such as altruism within one-male units (OMUs), are decisive for family health, but the role of microbiota in regulating these behaviors remains unknown. We conducted the gut microbiota from members of 10 OMUs using 16S RNA sequencing technology. We found that in adult males, gut microbiota diversity significantly decreased in food shortages and parturition-nursing period. Meanwhile, there was a notable reduction in 12 metabolism-related pathways, including those related to carbohydrates, amino acids, and lipid. The gut microbiota of adult male monkeys shifts from being enriched with the genera Akkermansia in winter to the genera norank Muribaculaceae in spring. This transition alters the pathways for nutrient acquisition, thereby reducing the consumption of stored energy. In contrast, other OMU members (adult females and subadults) did not experience adverse effects on the metabolic functions of their gut microbiota during the food-scarce spring, which is also a critical period for parturition and lactation in adult females. This study elucidates the co-evolution of altruistic behavior and gut microbiota in Sichuan snub-nosed monkeys, insights into the interaction mechanisms between mammalian microbiota and survival strategies.

Human Milk Microbiota Across Lactation Stages and Free Glutamate Concentrations in Healthy Ecuadorian Women

Background/Objectives: There is limited information on human milk (HM) microbiome composition and function in Latin America. Also, interactions between HM constituents and its microbiome have received partial attention. Objective: To characterize the HM microbiota composition considering lactation stages (colostrum, transition, and mature HM) and free glutamate concentrations in Ecuadorian mothers. Methods: We recruited 20 mothers that gave birth to normal full-term babies and donated colostrum, transition, and mature milk. Samples were assessed by 16S rRNA gene sequencing by Oxford Nanopore Technologies (ONT). Free glutamate concentrations were measured by proton nuclear magnetic resonance (NMR) spectroscopy. Results: For each lactation stage and in order of frequency, the majority of ASVs were assigned to Staphylococcus, Streptococcus, (Firmicutes); Escherichia, Acinetobacter, (Proteobacteria); Corynebacterium, Lactobacillus, Cutibacterium, (Actinobacteriota); Chryseobacterium, and Flavobacterium (Bacteroidota). Alfa diversity was similar in HM samples and tended to be higher in milk intended for male infants. We observed significant differences in qualitative β-diversity metrics between samples with low and high glutamate concentrations. Functional predictions of HM microbiota demonstrated the presence of polyamine biosynthesis II super pathway in samples with high glutamate concentrations. Conclusions: The core bacterial components of the HM microbiota in Ecuadorian women were similar to those reported from different parts of the world, with variations at the genus level. Free glutamate dynamics in HM need to be studied considering maternal production and bacterial metabolism to better understand HM composition for optimal infant nutrition.

Complementary Feeding and Infant Gut Microbiota: A Narrative Review

Background: The complementary feeding period, spanning from 6 to 24 months of age, marks the transition from an exclusive liquid diet in infants to a dietary pattern requiring the introduction of solid foods to meet nutritional demands. Complementary feeding coincides with other critical development windows, including the maturation of the gut microbiome. However, the effects of specific solid foods on gut microbiota and the subsequent influence on health outcomes require further investigation. Methods: This narrative review analyzes published research from January 2004 to October 2024 and aims to summarize the current evidence of the effects of complementary feeding on the infant gut microbiota. Results: A total of 43 studies were included in this review. Overall, multiple studies reported an increase in alpha-diversity after solid food introduction. Bifidobacteriaceae is the predominant bacterial family during the first 6 months of life, shifting to Lachnospiraceae, Ruminococcaceae, and Clostridium spp. after the introduction of solid foods. The timing of solid food introduction may also influence gut microbiota, though results were inconclusive. The effect of individual dietary components on the gut microbiota was conflicting, with limited evidence to make inferences. Conclusions: Because of variations in study design, dietary intake quantification, and minimal follow-up, a lack of conclusive evidence exists describing the relationship between complementary feeding and gut microbiota outcomes in infants. Future research to describe these relationships should focus on the impact of individual foods on microbial diversity and maturation, as well as the relationship between microbiota and infant health outcomes.

A Systematic Review and Meta-Analysis of 16S rRNA and Cancer Microbiome Atlas Datasets to Characterize Microbiota Signatures in Normal Breast, Mastitis, and Breast Cancer

The breast tissue microbiome has been increasingly recognized as a potential contributor to breast cancer development and progression. However, inconsistencies in microbial composition across studies have hindered the identification of definitive microbial signatures. We conducted a systematic review and meta-analysis of 11 studies using 16S rRNA sequencing to characterize the bacterial microbiome in 1260 fresh breast tissue samples, including normal, mastitis-affected, benign, cancer-adjacent, and cancerous tissues. Studies published until 31 December 2023 were included if they analyzed human breast tissue using Illumina short-read 16S rRNA sequencing with sufficient metadata, while non-human samples, non-breast tissues, non-English articles, and those lacking metadata or using alternative sequencing methods were excluded. We also incorporated microbiome data from The Cancer Genome Atlas breast cancer (TCGA-BRCA) cohort to enhance our analyses. Our meta-analysis identified Proteobacteria, Firmicutes, Actinobacteriota, and Bacteroidota as the dominant phyla in breast tissue, with Staphylococcus and Corynebacterium frequently detected across studies. While microbial diversity was similar between cancer and cancer-adjacent tissues, they both exhibited a lower diversity compared to normal and mastitis-affected tissues. Variability in bacterial genera was observed across primer sets and studies, emphasizing the need for standardized methodologies in microbiome research. An analysis of TCGA-BRCA data confirmed the dominance of Staphylococcus and Corynebacterium, which was associated with breast cancer proliferation-related gene expression programs. Notably, high Staphylococcus abundance was associated with a 4.1-fold increased mortality risk. These findings underscore the potential clinical relevance of the breast microbiome in tumor progression and emphasize the importance of methodological consistency. Future studies to establish causal relationships, elucidate underlying mechanisms, and assess microbiome-targeted interventions are warranted.

MultiTax-human: an extensive and high-resolution human-related full-length 16S rRNA reference database and taxonomy

Considering that the human microbiota plays a critical role in health and disease, an accurate and high-resolution taxonomic classification is thus essential for meaningful microbiome analysis. In this study, we developed an automatic system, named MultiTax pipeline, for generating de novo taxonomy from full-length 16S rRNA sequences using the Genome Taxonomy Database and other existing reference databases. We first constructed the MultiTax-human database, a high-resolution resource specifically designed for human microbiome research and clinical applications. The database includes 842,649 high-quality full-length 16S rRNA sequences, extracted from multiple public repositories and human-related studies, offering a comprehensive and accurate portrayal of the human microbiome. To validate the MultiTax-human database, we profiled the human microbiome across various body sites, identified core microbial taxa, and tested its performance using an independent data set. Additionally, the database is equipped with a user-friendly web interface for easy querying and data exploration. The MultiTax-human database is poised to serve as a valuable tool for researchers, enhancing the precision of human microbiome studies and advancing our understanding of its impact on human health and diseases.IMPORTANCEUnderstanding the human microbiome, the collection of microorganisms in and on our bodies, is essential for advancing health research. Current methods often lack precision and consistency, hindering our ability to study these microorganisms effectively. Our study presents the MultiTax-human database, a high-resolution reference tool specifically designed for human microbiome research. By integrating data from multiple sources and employing advanced classification techniques, this database offers an accurate and detailed map of the human microbiome. This resource enhances the ability of researchers and clinicians to explore the roles of microorganisms in health and disease, potentially leading to improved diagnostics, treatments, and insights into various medical conditions.

Maternal OM-85 administration alleviates offspring allergic airway inflammation by downregulating IL-33/ILC2 axis

BACKGROUND

Type 2 innate lymphoid cells (ILC2s) are essential for maintaining immune regulation and promoting tissue homeostasis in allergic asthma. How the development of gut microbiota on neonatal ILC2s influences allergic airway inflammation remains unclear. Here we focus on offspring ILC2 development in the context of alterations in maternal gut microbiota.

METHODS

C57BL/6 maternal mice were gavaged with OM-85 during pregnancy and/or lactation, ILC2-driven allergic airway inflammation in the OVA-sensitized adult offspring was observed. ILC2 development in offspring early life were investigated using recombinant (r)IL-33, rIL-25 and Bromodeoxyuridine in the vivo experiments. Further ILC2 promoting factors- IL-33 and IL-25 production in offspring early life were analysed. Finally, we examined the changes in gut microbiota and its metabolites in both dams and pups, and explored the effects of short-chain fatty acids (SCFAs) on IL-33 expression and secretion.

RESULTS

Maternal OM-85 administration restrained ILC2-driven allergic airway inflammation in the OVA-sensitized adult offspring. During ILC2 development in offspring early life, maternal OM-85 administration suppressed IL-33 and IL-25 production to inhibit ILC2 expansion and ILC2 responsiveness to alarmins, and infantile ILC2s could persist into adulthood. Maternal OM-85 administration increased SCFAs in breast milk and SCFA-producing gut probiotics (predominant Bacteroides and Blautia) in offspring, especially during pregnancy and lactation. SCFAs down-regulated IL-33 expression and reduced IL-33 secretion by inhibited gasdermin D (GSDMD) formation.

CONCLUSION

Maternal OM-85 administration restrains ILC2-driven allergic airway inflammation in adult offspring by increasing offspring intestinal SCFAs to modulate ILC2 development at an early stage, demonstrating that the transgenerational effects of maternal OM-85 exposure on offspring innate immunity.

Individual and Combined Effects of 2'-Fucosyllactose and Bifidobacterium longum subsp. infantis on the Gut Microbiota Composition of Piglets

BACKGROUND

Human milk is a source of oligosaccharides that promote the growth of beneficial bacteria, including Bifidobacterium longum subsp. infantis, which can utilize human milk oligosaccharides.

OBJECTIVES

To evaluate the individual and combined effects of 2'-fucosyllactose (2'-FL), B. infantis Bi-26 (Bi-26) on piglet gut microbiota composition, and short-chain fatty acid (SCFA) concentrations.

METHODS

Intact male pigs (n = 63) had ad libitum access to milk replacer without (control; CON) or with 1.0 g/L 2'-FL (FL) from postnatal day 2 to 34/35. Pigs were further stratified to receive either 12% glycerol or 109 CFU/d Bi-26 in glycerol (BI and FLBI). Gut microbiota and SCFA concentrations were determined in ascending colon contents (AC) and rectal contents (RC) by 16S ribosomal ribonucleic acid gene sequencing and gas chromatography, respectively. Microbiota composition and functional profiles were analyzed using QIIME 2 and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States-2 (PICRUSt2).

RESULTS

Supplementation of 2'-FL increased valerate concentration in AC (P = 0.03) and tended to modulate the overall bacterial composition in RC (P = 0.06). Compared with CON, 2'-FL alone increased the acetate concentration in AC (P < 0.05). The addition of Bi-26 decreased Shannon indices and reduced propionate and butyrate concentrations in AC (P < 0.05). Bi-26 alone affected the relative abundances of several bacterial amplicon sequence variants (ASVs) in AC and RC, including the ASVs identified as Phocaeicola (Bacteroides) vulgatus and Faecalibacterium prausnitzii. Additionally, 2'-FL and Bi-26 individually increased the relative abundances of 9 PICRUSt2-predicted metabolic pathways related to fatty acid and lipid biosynthesis or carboxylate degradation/secondary metabolite degradation in the RC; however, these effects were negated, and the values were identical to the CON group when 2'-FL and Bi-26 were supplemented together.

CONCLUSIONS

2'-FL and Bi-26 added to milk replacer exerted distinct influences on gut bacterial composition and metabolic function, and 2'-FL alone increased specific SCFA concentrations, demonstrating its prebiotic potential.

Gut Microbiota: An Important Participant in Childhood Obesity

Increasing prevalence of childhood obesity has emerged as a critical global public health concern. Recent studies have challenged the previous belief that obesity was solely a result of excessive caloric intake. Alterations in early-life gut microbiota can contribute to childhood obesity through their influence on nutrient absorption and metabolism, initiation of inflammatory responses, and regulation of gut-brain communication. The gut microbiota is increasingly acknowledged to play a crucial role in human health, as certain beneficial bacteria have been scientifically proven to possess the capacity to reduce body fat content and enhance intestinal barrier function and their metabolic products to exhibit anti-inflammatory effect. Examples of such microbes include bifidobacteria, Akkermansia muciniphila, and Lactobacillus reuteri. In contrast, an increase in Enterobacteriaceae and propionate-producing bacteria (Prevotellaceae and Veillonellaceae) has been implicated in the induction of low-grade systemic inflammation and disturbances in lipid metabolism, which can predispose individuals to obesity. Studies have demonstrated that modulating the gut microbiota through diet, lifestyle changes, prebiotics, probiotics, or fecal microbiota transplantation may contribute to gut homeostasis and the management of obesity and its associated comorbidities. This review aimed to elucidate the impact of alterations in gut microbiota composition during early life on childhood obesity and explores the mechanisms by which gut microbiota contributes to the pathogenesis of obesity and specifically focused on recent advances in using short-chain fatty acids for regulating gut microbiota and ameliorating obesity. Additionally, it aimed to discuss the therapeutic strategies for childhood obesity from the perspective of gut microbiota, aiming to provide a theoretical foundation for interventions targeting pediatric obesity based on gut microbiota.

Maternal stress in the early postpartum period is associated with alterations in human milk microbiome composition

BACKGROUND

Maternal stress is associated with negative early-life development and (mental)health outcomes. There is recent evidence that maternal stress in the postpartum period impacts the nutrient composition of human milk (HM). However, it is currently not known whether maternal stress is associated with changes in the HM microbiome during the critical early postpartum period.

METHODS

In this prospective observational cohort study, lactating women were recruited into a high-stress (HS, n = 23) and control (CTL, n = 69) group. The HS group included mothers with infants hospitalized for at least two days. Maternal stress was assessed using validated questionnaires and cortisol concentrations in hair, saliva and HM. HM was collected at days 10 and 24 and its microbiome was analyzed using 16 s rRNA sequencing. HM bacterial composition was compared between study groups and their correlation with maternal stress levels, maternal characteristics and infant outcomes was determined.

RESULTS

HM microbiome β-diversity differed significantly between study groups, with HS mothers displaying decreased abundance of Streptococcus, Gemella, and Veillonella, and increased levels of Staphylococcus, Corynebacterium and Acinetobacter compared to the control group. While the strongest correlation of β-diversity was with stress, HM microbiome β-diversity also correlated significantly with maternal education level and infant sex. No correlation between HM microbiome composition and HM cortisol concentrations was found.

CONCLUSIONS

This study demonstrates stress-associated alterations in the early HM microbiome that could potentially contribute to early gut colonization and subsequent (mental)health outcomes. Future research is needed to elucidate the physiological significance of these changes for infant development and health.

Gut-X axis

Recent advances in understanding the modulatory functions of gut and gut microbiota on human diseases facilitated our focused attention on the contribution of the gut to the pathophysiological alterations of many extraintestinal organs, including the liver, heart, brain, lungs, kidneys, bone, skin, reproductive, and endocrine systems. In this review, we applied the "gut-X axis" concept to describe the linkages between the gut and other organs and discussed the latest findings related to the "gut-X axis," including the underlying modulatory mechanisms and potential clinical intervention strategies.

Maternal Roughage Sources Influence the Gastrointestinal Development of Goat Kids by Modulating the Colonization of Gastrointestinal Microbiota

During pregnancy and lactation, maternal nutrition is linked to the full development of offspring and may have long-term or lifelong effects. However, the influence of the doe's diet on the gastrointestinal (GI) tract of young kids remains largely unexplored. Therefore, we investigated the effects of doe roughage sources (alfalfa hay, AH, or corn straw, CS) during pregnancy and lactation on kid growth, GI morphology, barrier function, metabolism, immunity, and microbiome composition. The results indicate that, compared with the CS group, does fed an AH diet had significantly higher feed intake (p < 0.01). However, CS-fed does exhibited higher neutral detergent fiber (NDF) digestibility (p < 0.05). There were no significant differences in animal (doe or kid) weight among the groups (p > 0.05). In the rumen of goat kids, the AH group exhibited a higher papillae width and increased levels of interleukin-10 (IL-10) compared with the CS group (p < 0.05). In the jejunum of goat kids, the AH group showed a higher villus-height-to-crypt-depth (VH/CD) ratio, as well as elevated levels of secretory immunoglobulin A (SIgA), immunoglobulin G (IgG), IL-10, acetate, and total volatile fatty acids (TVFAs), when compared with the CS group (p < 0.05). Transcriptome analysis revealed that the source of roughage in does was associated with changes in the GI transcriptome of the kids. Differentially expressed genes (DEGs) in the rumen were mainly associated with tissue development and immune regulation, while the DEGs in the jejunum were mainly associated with the regulation of transferase activity. Spearman correlation analyses indicated significant associations between GI DEGs and phenotypic indicators related to GI development, immunity, and metabolism. LEfSe analysis identified 14 rumen microbial biomarkers and 6 jejunum microbial biomarkers. Notably, these microorganisms were also enriched in the rumen or day 28 milk of the does. Further microbial composition analysis revealed significant correlations between the rumen and milk microbiomes of does and the rumen or jejunum microbiomes of kids. Association analyses indicated that microbial biomarkers interact with host genes, thereby affecting the development and function of the GI system. Additionally, correlation analyses revealed significant association between milk metabolites and the rumen and jejunum microbiomes of kids. This study demonstrated that maternal diet significantly influences the development of microbial ecosystems in offspring by modulating microbial communities and metabolite composition. The early colonization of GI microorganisms is crucial for the structural development, barrier function, immune capacity, and microbial metabolic activity of the GI system.

Preventive effects of kefir on colon tumor development in Wistar rats: gut microbiota critical role

To clarify the effects of kefir in critical periods of development in adult diseases, we study the effects of kefir intake during early life on gut microbiota and prevention of colorectal carcinogenesis in adulthood. Lactating Wistar rats were divided into three groups: control (C), kefir lactation (KL), and kefir puberty (KP) groups. The C and KP groups received 1 mL of water/day; KL dams received kefir milk daily (108 CFU/mL) during lactation. After weaning (postnatal day 21), KP pups received kefir treatment until 60 days. At 67 days old, colorectal carcinogenesis was induced through intraperitoneal injection of 1, 2-dimethylhydrazine. The gut microbiota composition were analyzed by 16S rRNA gene sequencing and DESeq2 (differential abundance method), revealing significant differences in bacterial abundances between the kefir consumption periods. Maternal kefir intake strong anticancer power, suppressed tumors in adult offspring and reduced the relative risk of offspring tumor development. The gut microbiota in cecal samples of the KL group was enriched with Lactobacillus, Romboutsia, and Blautia. In contrast, control animals were enriched with Acinetobacter. The administration of kefir during critical periods of development, with emphasis on lactation, affected the gut microbial community structure to promote host benefits. Pearson analysis indicated positive correlation between tumor number with IL-1 levels. Therefore, the probiotic fermented food intake in early life may be effective as chemopreventive potential against colon tumor development, especially in lactation period.

Unveiling early-life microbial colonization profile through characterizing low-biomass maternal-infant microbiomes by 2bRAD-M

Introduction

The microbial composition of human breast milk and infant meconium offers critical insights into the early microbial colonization profile, and it greatly contributes to the infant's immune system and long-term health outcomes. However, analyzing these samples often faces technical challenges and limitations of low-resolution using conventional approaches due to their low microbial biomass.

Methods

Here, we employed the type IIB restriction enzymes site-associated DNA sequencing for microbiome (2bRAD-M) as a reduced metagenomics method to address these issues and profile species-level microbial composition. We collected breast milk samples, maternal feces, and infant meconium, comparing the results from 2bRAD-M with those from both commonly used 16S rRNA amplicon sequencing and the gold-standard whole metagenomics sequencing (WMS).

Results

The accuracy and robustness of 2bRAD-M were demonstrated through its consistently high correlation of microbial individual abundance and low whole-community-level distance with the paired WMS samples. Moreover, 2bRAD-M enabled us to identify clinical variables associated with infant microbiota variations and significant changes in microbial diversity across different lactation stages of breast milk.

Discussion

This study underscores the importance of employing 2bRAD-M in future large-scale and longitudinal studies on maternal and infant microbiomes, thereby enhancing our understanding of microbial colonization in early life stages and demonstrating further translational potential.

Human milk oligosaccharides: bridging the gap in intestinal microbiota between mothers and infants

Breast milk is an essential source of infant nutrition. It is also a vital determinant of the structure and function of the infant intestinal microbial community, and it connects the mother and infant intestinal microbiota. Human milk oligosaccharides (HMOs) are a critical component in breast milk. HMOs can reach the baby's colon entirely from milk and become a fermentable substrate for some intestinal microorganisms. HMOs can enhance intestinal mucosal barrier function and affect the intestinal function of the host through immune function, which has a therapeutic effect on specific infant intestinal diseases, such as necrotizing enterocolitis. In addition, changes in infant intestinal microbiota can reflect the maternal intestinal microbiota. HMOs are a link between the maternal intestinal microbiota and infant intestinal microbiota. HMOs affect the intestinal microbiota of infants and are related to the maternal milk microbiota. Through breastfeeding, maternal microbiota and HMOs jointly affect infant intestinal bacteria. Therefore, HMOs positively influence the establishment and balance of the infant microbial community, which is vital to ensure infant intestinal function. Therefore, HMOs can be used as a supplement and alternative therapy for infant intestinal diseases.

How maternal factors shape the immune system of breastfed infants to alleviate food allergy: A systematic and updated review

What infants eat early in life may shape the immune system and have long-standing consequences on the health of the host during later life. In the early months post-birth, breast milk serves as the exclusive and optimal nourishment for infants, facilitating crucial molecular exchanges between mother and infant. Recent advances have uncovered that some maternal factors influence breastfed infant outcomes, including the risk of food allergy (FA). To date, accumulated data show that breastfed infants have a lower risk of FA. However, the issue remains disputed, some reported preventive allergy effects, while others did not confirm such effects, or if identified, protective effects were limited to early childhood. The disputed outcomes may be attributed to the maternal status, as it determines the compounds of the breast milk that breastfed infants are exposed to. In this review, we first detail the compounds in breast milk and their roles in infant FA. Then, we present maternal factors resulting in alterations in breast milk compounds, such as maternal health status, maternal diet intake, and maternal food allergen intake, which subsequently impact FA in breastfed infants. Finally, we analyze how these compounds in breast milk alleviated the infant FA by mother-to-infant transmission. Altogether, the mechanisms are primarily linked to the synergetic and direct effects of compounds in breast milk, via promoting the colonization of gut microbiota and the development of the immune system in infants.

Interactions with alloparents are associated with the diversity of infant skin and fecal bacterial communities in Chicago, United States

INTRODUCTION

Social interactions shape the infant microbiome by providing opportunities for caregivers to spread bacteria through physical contact. With most research focused on the impact of maternal-infant contact on the infant gut microbiome, it is unclear how alloparents (i.e., caregivers other than the parents) influence the bacterial communities of infant body sites that are frequently contacted during bouts of caregiving, including the skin.

METHODS

To begin to understand how allocare may influence the diversity of the infant microbiome, detailed questionnaire data on infant-alloparent relationships and specific allocare behaviors were coupled with skin and fecal microbiome samples (four body sites) from 48 infants living in Chicago, United States.

RESULTS

Data from 16S rRNA gene amplicon sequencing indicated that infant skin and fecal bacterial diversity showed strong associations (positive and negative) to having female adult alloparents. Alloparental feeding and co-sleeping displayed stronger associations to infant bacterial diversity compared to playing or holding. The associations with allocare behaviors differed in magnitude and direction across infant body sites. Bacterial relative abundances varied by infant-alloparent relationship and breastfeeding status.

CONCLUSION

This study provides some of the first evidence of an association between allocare and infant skin and fecal bacterial diversity. The results suggest that infants' exposure to bacteria from the social environment may vary based on infant-alloparent relationships and allocare behaviors. Since the microbiome influences immune system development, variation in allocare that impacts the diversity of infant bacterial communities may be an underexplored dimension of the social determinants of health in early life.

Feeding Expressed Breast Milk Alters the Microbial Network of Breast Milk and Increases Breast Milk Microbiome Diversity over Time

Breastfeeding supplies nutrition, immunity, and hormonal cues to infants. Feeding expressed breast milk may result in de-phased milk production and feeding times, which distort the real-time circadian cues carried by breast milk. We hypothesized that providing expressed breast milk alters the microbiotas of both breast milk and the infant's gut. To test this hypothesis, we analyzed the microbiota of serial breast milk and infant fecal samples obtained from 14 mother-infant dyads who were lactating, half of which were providing expressed breast milk. Infant fecal microbiota showed lower α-diversity than breast milk microbiota. Bacterial amplicon sequence variant sharing occurred between breast milk and infant feces with no feeding group differences. However, the age-dependent gain in breast milk α-diversity was only significant in the expressed breast milk group and not in the direct breastfeeding group, suggesting that decreased contact with the infant's mouth influences the milk microbiota. Trending lower connectivity was also noted with breast milk microbes in the direct breastfeeding group, consistent with regular perturbations of the developing baby's oral microbiota by latching on the breast. The results of this preliminary study urge further research to independently confirm the effects of providing expressed breast milk and their health significance.

Human milk microbiota and oligosaccharides in colostrum and mature milk: comparison and correlation

Background

The interaction between the human breast milk microbiota and human milk oligosaccharides (HMOs) plays a crucial role in the healthy growth and development of infants. We aimed to clarify the link between the breast milk microbiota and HMOs at two stages of lactation.

Methods

The microbiota and HMOs of 20 colostrum samples (C group, 1-5 days postpartum) and 20 mature milk samples (S group, 42 days postpartum) collected from postpartum mothers were analyzed using 16S rRNA gene high-throughput sequencing and high-performance liquid chromatography-tandem mass spectrometry.

Result

The total average HMO content was significantly higher in the C group than in the S group (6.76 ± 1.40 g/L vs. 10.27 ± 2.00 g/L, p < 0.05). Among the HMOs, the average values of 2'-fucosyllactose (2'-FL, 1.64 ± 1.54 g/L vs. 3.03 ± 1.79 g/L), 3'-sialyllactose (3'-SL, 0.10 ± 0.02 g/L vs. 0.21 ± 0.06), 6'-SL (0.22 ± 0.09 g/L vs. 0.33 ± 0.11 g/L), and lacto-N-triaose 2 (LNT2, 0.03 ± 0.01 g/L vs. 0.16 ± 0.08 g/L) were significantly lower in the S group than in the C group (p < 0.05), while that of 3'-FL was significantly higher in the S group than in the C group (1.35 ± 1.00 g/L vs. 0.41 ± 0.43 g/L, p < 0.05). The diversity and structure of the microbiota in the S and C groups were also significantly different (p < 0.05). Comparative analysis of the microbial communities revealed that Proteobacteria and Firmicutes were the most abundant phyla, in both groups, with the keystone species (Serratia, Streptococcus and Staphylococcus) of breast milk closely interacting with HMOs, including 3'-SL, 6'-SL, and LNT2. In PICRUSt2 functional prediction analysis, the S group exhibited significant reduction in the expression of genes involved in several infectious disease pathways.

Discussion

Our findings support the recognition of human milk as a synbiotic comprising beneficial bacteria and prebiotic HMOs.

Wise Roles and Future Visionary Endeavors of Current Emperor: Advancing Dynamic Methods for Longitudinal Microbiome Meta-Omics Data in Personalized and Precision Medicine

Understanding the etiological complexity of diseases requires identifying biomarkers longitudinally associated with specific phenotypes. Advanced sequencing tools generate dynamic microbiome data, providing insights into microbial community functions and their impact on health. This review aims to explore the current roles and future visionary endeavors of dynamic methods for integrating longitudinal microbiome multi-omics data in personalized and precision medicine. This work seeks to synthesize existing research, propose best practices, and highlight innovative techniques. The development and application of advanced dynamic methods, including the unified analytical frameworks and deep learning tools in artificial intelligence, are critically examined. Aggregating data on microbes, metabolites, genes, and other entities offers profound insights into the interactions among microorganisms, host physiology, and external stimuli. Despite progress, the absence of gold standards for validating analytical protocols and data resources of various longitudinal multi-omics studies remains a significant challenge. The interdependence of workflow steps critically affects overall outcomes. This work provides a comprehensive roadmap for best practices, addressing current challenges with advanced dynamic methods. The review underscores the biological effects of clinical, experimental, and analytical protocol settings on outcomes. Establishing consensus on dynamic microbiome inter-studies and advancing reliable analytical protocols are pivotal for the future of personalized and precision medicine.

Review of the Relationships Between Human Gut Microbiome, Diet, and Obesity

Obesity is a complex disease that increases the risk of other pathologies. Its prevention and long-term weight loss maintenance are problematic. Gut microbiome is considered a potential obesity modulator. The objective of the present study was to summarize recent findings regarding the relationships between obesity, gut microbiota, and diet (vegetable/animal proteins, high-fat diets, restriction of carbohydrates), with an emphasis on dietary fiber and resistant starch. The composition of the human gut microbiome and the methods of its quantification are described. Products of the gut microbiome metabolism, such as short-chain fatty acids and secondary bile acids, and their effects on the gut microbiota, intestinal barrier function and immune homeostasis are discussed in the context of obesity. The importance of dietary fiber and resistant starch is emphasized as far as effects of the host diet on the composition and function of the gut microbiome are concerned. The complex relationships between human gut microbiome and obesity are finally summarized.

Research focus and emerging trends of the gut microbiome and infant: a bibliometric analysis from 2004 to 2024

Background

Over the past two decades, gut microbiota has demonstrated unprecedented potential in human diseases and health. The gut microbiota in early life is crucial for later health outcomes. This study aims to reveal the knowledge collaboration network, research hotspots, and explore the emerging trends in the fields of infant and gut microbiome using bibliometric analysis.

Method

We searched the literature on infant and gut microbiome in the Web of Science Core Collection (WOSCC) database from 2004 to 2024. CiteSpace V (version: 6.3.R1) and VOSview (version: 1.6.20) were used to display the top authors, journals, institutions, countries, authors, keywords, co-cited articles, and potential trends.

Results

A total of 9,899 documents were retrieved from the Web of Science Core Collection. The United States, China, and Italy were the three most productive countries with 3,163, 1,510, and 660 publications. The University of California System was the most prolific institution (524 publications). Van Sinderen, Douwe from University College Cork of Ireland was the most impactful author. Many studies have focused on atopic dermatitis (AD), necrotizing enterocolitis (NEC), as well as the immune mechanisms and microbial treatments for these diseases, such as probiotic strains mixtures and human milk oligosaccharides (HMOs). The mother-to-infant microbiome transmission, chain fatty acids, and butyrate maybe the emerging trends.

Conclusion

This study provided an overview of the knowledge structure of infant and gut microbiome, as well as a reference for future research.

The microbiota: a key regulator of health, productivity, and reproductive success in mammals

The microbiota, intensely intertwined with mammalian physiology, significantly impacts health, productivity, and reproductive functions. The normal microbiota interacts with the host through the following key mechanisms: acting as a protective barrier against pathogens, maintain mucosal barrier integrity, assisting in nutrient metabolism, and modulating of the immune response. Therefore, supporting growth and development of host, and providing protection against pathogens and toxic substances. The microbiota significantly influences brain development and behavior, as demonstrated by comprehensive findings from controlled laboratory experiments and human clinical studies. The prospects suggested that gut microbiome influence neurodevelopmental processes, modulate stress responses, and affect cognitive function through the gut-brain axis. Microbiota in the gastrointestinal tract of farm animals break down and ferment the ingested feed into nutrients, utilize to produce meat and milk. Among the beneficial by-products of gut microbiota, short-chain fatty acids (SCFAs) are particularly noteworthy for their substantial role in disease prevention and the promotion of various productive aspects in mammals. The microbiota plays a pivotal role in the reproductive hormonal systems of mammals, boosting reproductive performance in both sexes and fostering the maternal-infant connection, thereby becoming a crucial factor in sustaining mammalian existence. The microbiota is a critical factor influencing reproductive success and production traits in mammals. A well-balanced microbiome improves nutrient absorption and metabolic efficiency, leading to better growth rates, increased milk production, and enhanced overall health. Additionally, it regulates key reproductive hormones like estrogen and progesterone, which are essential for successful conception and pregnancy. Understanding the role of gut microbiota offers valuable insights for optimizing breeding and improving production outcomes, contributing to advancements in agriculture and veterinary medicine. This study emphasizes the critical ecological roles of mammalian microbiota, highlighting their essential contributions to health, productivity, and reproductive success. By integrating human and veterinary perspectives, it demonstrates how microbial communities enhance immune function, metabolic processes, and hormonal regulation across species, offering insights that benefit both clinical and agricultural advancements.

Time-varying ambient air pollution exposure is associated with gut microbiome variation in the first 2 years of life

The infant gut microbiome matures greatly in the first year of life. Ambient air pollution (AAP) exposure is associated with the infant gut microbiome. However, whether time-varying AAP influences infant gut microbiome variation is rarely investigated. This study aimed to investigate the effects of PM2.5, PM10, and O3 on infant gut microbiome variation longitudinally. Demographic information, stool samples, and AAP exposure concentrations were collected at 6, 12, 24 months from infants. Gut microbiome was processed and analyzed using 16S rRNA V3-V4 gene regions. AAP exposure concentrations were calculated using the China High Air Pollutants (CHAP) database. Multiple pollutant models were used to assess the mixed effects of PM2.5, PM10, and O3 on infant gut microbiome variation. Infants' gut microbiomes at 6, 12, 24 months old had significant differences in alpha diversity, beta diversity, and community composition. PM2.5 and O3 respectively explained 6.3% and 5.3% of the differences in community composition for 24-month-old infants. Single pollutant exposure and multiple pollutant exposure in different periods were both associated with alpha diversity indices and specific gut microbial phyla and genera. AAP was more associated with infant gut microbial alpha diversity indices, phyla variations, and genera variations at 12-24 months than 6-12 months. Multiple pollutant exposure in 0-2 lag months showed negative correlations with 12-24 months variation in Escherichia-Shigella (β = -0.854, 95%CI: 1.398 to -0.310) and Enterococcus (β = -0.979, 95%CI: 1.429 to -0.530). This study highlighted that time-varying PM2.5, PM10, and O3 synergistically influenced the variation of alpha diversity and abundance of gut microbial taxa in infants. Further research is needed to explore the effects and mechanisms of other environmental exposures on infant gut microbiome variation.

Non-nutritional use of human milk as a therapeutic agent in neonates: Brain, gut, and immunologic targets

Human milk (HM) exposure improves short- and long-term outcomes for infants due to a complex milieu of bioactive, stem cell, anti-inflammatory, anti-microbial, and nutritive components. Given this remarkable biologic fluid, non-nutritional utilization of HM as a targeted therapeutic is being explored in pre-clinical and clinical studies. This article describes recent research pertinent to non-nutritional uses of HM for neurologic, gastrointestinal, and infectious pathologies in neonates, as well as future directions.

Isolation and evaluation of Pediococcus acidilactici YH-15 from cat milk: Potential probiotic effects and antimicrobial properties

The study aimed to screen for the possible presence of lactic acid bacteria (LAB) in cat milk in order to evaluate their probiotic properties. The isolates were characterized by biochemical identification, morphological tests and 16S rDNA sequencing. Afterward, gastrointestinal passage, in vitro safety and probiotic properties were evaluated. The results showed that the isolates had 10 strains of Pediococcus acidilactici permitted in the feed additive catalog. The high survival rate in the acid and bile salt resistance test reflected the good strain tolerance of the isolates to the simulated gastrointestinal conditions of the host in vitro. The mean inhibitory diameters of the 10 strains against chloramphenicol and tetracycline were 23.6 mm and 17.4 mm, respectively; none of the hemolytic tests showed α/β hemolytic ring. The bacteriostatic test showed that P. acidilactici YH-9, YH-14 and YH-15 had inhibitory effects on four common pathogenic bacteria, including Escherichia coli, Salmonella typhimurium, Staphylococcus aureus and Streptococcus. The adhesion test showed that P. acidilactici YH-15 had good adhesion to HT-29 cells. Based on these results, we concluded that P. acidilactici YH-15 extracted from cat milk has potential application as a clinical probiotic therapy and health care product.

Infant formula with added Lacticaseibacillus rhamnosus GG supported adequate growth and was well tolerated in healthy term infants: a randomized controlled trial

Introduction

Lacticaseibacillus rhamnosus GG (LGG) is a well-studied probiotic with a history of safe use.

Methods

In this double-blind, prospective study, growth and tolerance were evaluated in healthy term infants randomized to: marketed, routine intact cow's milk protein-based formula (Control, n = 172) or a similar investigational formula with added LGG (INV-LGG, n = 179; 106 CFU LGG®/g powder) from 14 to 120 days of age. Anthropometrics, stool characteristics, fussiness, and gassiness were evaluated through Day 120. Medically confirmed adverse events were recorded throughout the study period. The primary outcome was rate of weight gain from Day 14-120.

Results

Of 351 infants enrolled, 275 completed (Control, n = 131; INV-LGG, n = 144). No significant group differences in rate of weight gain from Day 14-120 were detected. Study formula acceptance and tolerance was good with no significant differences in study discontinuation due to study formula or parent-reported gassiness, stool frequency, or stool consistency; however mean fussiness relative to normal was significantly lower for INV-LGG vs Control at Days 60 and 90.

Discussion

In healthy term infants, a routine intact cow's milk protein-based formula with added LGG supported adequate growth and was well tolerated. Further studies are needed to evaluate potential benefits for fussiness and efficacy outcomes.

Clinical Trial Registration

Clinicaltrials.gov, identifier (NCT01897922).

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.