Currently, it seems inconceivable to dispute the major role of microorganisms in human health or insects with endosymbionts. Although microbial endophytes were discovered long ago, little is known about the roles of plant-associated microorganisms. Some endophytes are horizontally transmitted, whereas others are seed-borne; together, they influence plant health. Beneficial endophytes can promote plant growth and yield by increasing plant resistance to biotic and abiotic stresses. Recently, the tools available to study the phytobiome have much improved, opening doors for a better understanding of the fascinating interactions taking place at the plant level. This review redefines the conceptual framework for “endophyte” and “endophytome,” focusing on the intricate dynamics of bacterial endophytomes. Systematically examining the formation pathways and profiling endophytes allows for a comprehensive exploration of the intricate dynamics governing plant-microbe interactions. Additionally, the assessment of how endophytomes are influenced by both biotic and abiotic factors provides essential insights into the adaptability and resilience of plant-associated microorganisms. Our comprehensive analysis integrates genomic insights with environmental considerations, offering a nuanced perspective on the functional roles of bacterial endophytomes. Therefore, a new, inclusive definition is essential to accurately represent the complexity of interactions within the plant microbiome as well as having the whole picture of associated concepts.

Bacterial endophytome sources, profile and dynamics—a conceptual framework

Abstract Aim: This review aims to identify the mechanistic relationships related to periodontal diseases and its possible association with changes in human milk composition and the composition and function of infants’ gut microbiome. Background: Maternal health conditions, especially inflammatory, are associated with altered human milk composition. It is not known whether maternal oral inflammatory diseases, including periodontal diseases, deleteriously affect human milk composition. Methods: A narrative review was conducted according to SANRA, the Scale for the Assessment of Narrative Review Articles, guidelines. PubMed, Google Scholar, and Cochrane database of systematic reviews were searched from September 2019 up to December 2023 using keywords such as breast/human milk, maternal health/infections, and periodontal diseases. Reference lists of relevant articles were also screened. Our primary outcome of interest was human milk composition (i.e., any changes in macronutrients, immunological components, etc.). Secondary outcomes included changes in human milk microbiome and subsequent changes in the infant gut microbiome. Outcomes were synthesized using a narrative approach where the existing evidence and current literature were summarized. No risk of bias assessment of the studies was performed in this review. Findings: The search yielded no studies investigating the relationship between periodontal diseases in nursing mothers and changes in human milk composition. However, a dose–response relationship exists between the severity of periodontal diseases and the risk of adverse pregnancy outcomes such as preterm birth. Mastitis and diabetes affected milk lipids. Immunoglobulin A (sIgA) was increased in mastitis, whereas reduced concentrations were reported in diabetes. Potential biological pathways through which periodontal diseases can negatively affect human milk composition include the systemic dissemination of inflammatory cytokines like IL-6, PGE2, and tumor necrosis factor (TNF)-β that can be up-regulated by bacterial by-products. This biological plausibility needs to be investigated, given the potentially negative impact on the quality of human milk that could be caused by periodontal inflammation. 

The unrevealed links: periodontal health, human milk composition, and infant gut microbiome dynamics

Abstract The rising incidence of pediatric-onset inflammatory bowel disease (IBD) has intensified focus on the early-life period as a critical window for prevention. Accumulating observational evidence links prenatal, perinatal, and early childhood exposures to later IBD risk. Several mechanisms underpin this relationship, including gut microbiome development, immune system maturation, epigenetic modulation, and metabolic and endocrine programming. Building on this framework, this review outlines potential intervention strategies across key developmental stages—from maternal nutrition and microbiome modulation during pregnancy to delivery-related factors such as birth mode, intrapartum antibiotic use, and early breastfeeding practices. Postnatal strategies include breastfeeding promotion, timely and diverse dietary introduction, antibiotic stewardship, and minimization of detrimental environmental exposures. Such approaches may be particularly relevant for high-risk groups, notably children born to individuals with IBD. Practical guidance is provided for families affected by IBD, alongside a discussion on how universal and risk-stratified strategies may be integrated. However, it is important to note that most of these strategies remain hypothetical, with limited validation. Emerging research areas include maternal dietary interventions, microbiome-based therapies, and the utilization of digital tools for risk monitoring. This review also addresses ethical and implementation challenges inherent to early-life prevention research and intervention. 

Intervention(s) in the Early-Life Period to Modulate Inflammatory Bowel Disease Risk: What Could Be the Impact?

BACKGROUND
Despite reassuring clinical safety data, thrombocytosis, anemia, lymphopenia, and liver function derangements have been observed in infants born to women with inflammatory bowel disease (IBD) treated with thiopurines and biologics. We aimed to define the prevalence, course, associations, and clinical impact of hematological and biochemical abnormalities in such infants.


METHODS
This multicenter prospective cohort study assessed clinical, hematologic, and biochemical outcomes of infants exposed to thiopurines or biologics in utero for management of maternal IBD. Liver transaminases, full blood examination, and infant thiopurine metabolites (where exposed) were taken at delivery and 6 weeks of age. Abnormal results were repeated until normalization. Infants were followed clinically by a pediatric gastroenterologist up to 2 years of age.


RESULTS
A total of 130 infants were included. Thrombocytosis and elevated alanine transaminase (ALT) were seen in over half of infants up to 6 months of age with no significant clinical impact. Elevated ALT was associated with increasing maternal C-reactive protein in second trimester, while thrombocytosis was associated with increasing maternal C-reactive protein and fecal calprotectin in third trimester. Preceding infection and vaccination were associated with an increased risk of elevated alkaline phosphatase at 3 months. In those exposed to thiopurines, increasing maternal 6-methylmercaptopurine at delivery was associated with increased ALT to 6 months.


CONCLUSIONS
Infants born to women with IBD commonly developed thrombocytosis, elevated alkaline phosphatase, and elevated ALT. These findings were associated with exposure to maternal inflammation, elevated 6-methylmercaptopurine at delivery, and infant vaccinations and infections, and had minimal clinical consequence.

Thrombocytosis and Transaminitis in Infants Born to Women With Inflammatory Bowel Disease Is Associated With Exposure to Maternal Inflammation In Utero.

The early-life period is one of microbiome establishment and immune maturation. Early-life exposures are increasingly being recognised to play an important role in IBD risk. The composition of functions of the gut microbiome in the prenatal, perinatal, and postnatal period may be crucial towards development of health or disease, including IBD, later in life. We herein present a comprehensive summary of the interplay between early-life factors and microbiome perturbations, and their association with risk of IBD. In addition, we provide an overview of host and external factors in early life that are known to impact gut microbiome maturation and exposures implicated in IBD risk. Considering the emerging concept of IBD prevention, we propose strategies to minimise maternal and offspring exposure to potentially harmful variables and recommend protective measures during pregnancy and the postpartum period. This holistic view of early-life factors and microbiome signatures among mothers and their offspring will help frame our current understanding of their importance towards IBD pathogenesis and frame the roadmap for preventive strategies.

Early-life exposures and the microbiome: implications for IBD prevention

/pdf/op02-the-breastmilk-proteomics-of-women-with-inflammatory-12khldv5.pdf

OP02 The breastmilk proteomics of women with Inflammatory Bowel Disease (IBD) and its impact on fecal calprotectin and microbiota composition in their babies

P050 A comparison of the Gut Microbiota in Pregnant Women with and without Inflammatory Bowel Disease and Their Offspring in Hong Kong and United States

Influence of Early Life Factors, including Breastmilk Composition, on the Microbiome of Infants Born to Mothers with and without Inflammatory Bowel Disease.

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OP02 The breastmilk proteomics of women with Inflammatory Bowel Disease (IBD) and its impact on fecal calprotectin and microbiota composition in their babies

P050 A comparison of the Gut Microbiota in Pregnant Women with and without Inflammatory Bowel Disease and Their Offspring in Hong Kong and United States

Influence of Early Life Factors, including Breastmilk Composition, on the Microbiome of Infants Born to Mothers with and without Inflammatory Bowel Disease.