Numerous important environments harbour low levels of microbial biomass, including certain human tissues, the atmosphere, plant seeds, treated drinking water, hyper-arid soils and the deep subsurface, with some environments lacking resident microbes altogether. These low microbial biomass environments pose unique challenges for standard DNA-based sequencing approaches, as the inevitability of contamination from external sources becomes a critical concern when working near the limits of detection. Likewise, lower-biomass samples can be disproportionately impacted by cross-contamination and practices suitable for handling higher-biomass samples may produce misleading results when applied to lower microbial biomass samples. This Consensus Statement outlines strategies to reduce contamination and cross-contamination, focusing on marker gene and metagenomic analyses. We also provide minimal standards for reporting contamination information and removal workflows. Considerations must be made at every study stage, from sample collection and handling through data analysis and reporting to reduce and identify contaminants. We urge researchers to adopt these recommendations when designing, implementing and reporting microbiome studies, especially those conducted in low-biomass systems.

This study aims to examine the specific relationships between gut, oral, and vaginal microbiota and the frozen embryo transfer (FET) process. Patients undergoing fertility treatment who met the inclusion criteria were included in this study. After sampling at three time points, participants were then divided into two groups: the failure group and the success group, based on whether a viable intrauterine pregnancy was confirmed. In this pilot study, we systematically examined changes in the gut, oral, and vaginal microbiota at various stages of the FET process using 16S rDNA high-throughput sequencing and investigated their respective associations with FET outcomes. Metabolomics and random forest were used for evaluating the relationship between gut microbiota and metabolites during FET. Our findings indicate that while the gut microbiota underwent the least change throughout FET, it exhibited the greatest differences between success and failure groups. The oral and vaginal microbiota exhibited significant fluctuations. However, the differences in oral microbiota between the success and failure groups changed with the FET process, while the vaginal microbiota did not show any differences. Notably, two key gut genera, Anaerococcus and Negativicoccus, were identified as genera significantly associated with FET outcomes. Additionally, specific gut microbiota and metabolite profiles displayed significant correlations with FET success, particularly highlighting the potential relevance of cystamine before FET. These findings suggest that targeting microbiota-associated metabolic pathways may serve as a potential strategy to enhance FET success rates and provide new biomarkers for clinical prediction and intervention.IMPORTANCEThis study explores the potential role of microbiota in influencing FET outcomes. Through an analysis of gut, oral, and vaginal microbiota, we observed notable differences between success and failure groups, particularly in gut microbiota. Genera such as Anaerococcus and Negativicoccus, along with associated metabolic profiles, may offer insights into underlying mechanisms. These findings contribute to a growing understanding of the interplay between microbiota and reproductive outcomes and suggest that targeting microbiota-associated metabolic pathways could be a promising direction for enhancing FET success rates. This research highlights potential biomarkers and therapeutic avenues for further exploration in fertility treatments.

To describe the microbiome of the vagina and fallopian tubes (FT) and its relation with hydrosalpinx.

Case-control study was conducted in women who underwent salpingectomy for hydrosalpinx (case) or other indications (controls). Samples were obtained during surgery and subjected to 16S rRNA amplicon sequencing, and analyses of alpha diversity and beta diversity measures were compared between sites and groups. Differential abundance of bacteria associated with vaginal dysbiosis was compared between cases and controls.

Nine women with hydrosalpinx and 23 women without hydrosalpinx were included in the study. The mean age of studied women was 41 (range: 29-54) and most (89%) were premenopausal. After in silico decontamination, only 30% of control FT samples and 10% of case FT samples had evidence of bacterial presence. The vaginal microbiome of control patients showed greater abundance of lactobacilli, whereas the vaginal microbiome of case patients contained relatively more bacterial vaginosis-associated bacteria, such as Prevotella and Atopobium. A significant difference was found in alpha and beta diversity between vaginal and FT microbiomes in control patients as FT samples were more diverse. We found that women with hydrosalpinx had a more "dysbiotic" vaginal microbiome and in women without hydrosalpinx, microbial composition within the vagina and FT differed, possibly representing two distinct ecological environments.

Women undergoing salpingectomy for various reasons harbored bacteria within their FT, while women with hydrosalpinx generally did not. This suggests that even though infection may be an underlying cause of hydrosalpinx, bacteria may not be present by the time patients require surgery.

Understanding when host-microbiome interactions are first established is crucial for comprehending normal development and identifying disease prevention strategies. Furthermore, bacterially derived metabolites play critical roles in shaping the intestinal immune system. Recent studies have demonstrated that memory T cells infiltrate human intestinal tissue early in the second trimester, suggesting that microbial components such as peptides that can prime adaptive immunity and metabolites that can influence the development and function of the immune system are also present in utero. Our previous study reported a unique fetal intestinal metabolomic profile with an abundance of several bacterially derived metabolites and aryl hydrocarbon receptor (AHR) ligands implicated in mucosal immune regulation.

In the current study, we demonstrate that a number of microbiome-associated metabolites present in the fetal intestines are also present in the placental tissue, and their abundance is different across the fetal intestine, fetal meconium, fetal placental villi, and the maternal decidua. The fetal gastrointestinal samples and maternal decidua samples show substantially higher positive correlation on the abundance of these microbial metabolites than the correlation between the fetal gastrointestinal samples and meconium samples. The expression of genes associated with the transport and signaling of some microbial metabolites is also detectable in utero.

We suggest that the microbiome-associated metabolites are maternally derived and vertically transmitted to the fetus. Notably, these bacterially derived metabolites, particularly short-chain fatty acids and secondary bile acids, are likely biologically active and functional in regulating the fetal immune system and preparing the gastrointestinal tract for postnatal microbial encounters, as the transcripts for their various receptors and carrier proteins are present in second trimester intestinal tissue through single-cell transcriptomic data. Video Abstract.

This review summarizes and discusses key recent findings suggesting that microbiomes can play a role in the development and progression of osteoarthritis. Evidence supporting a gut microbiome-joint connection derived from human and animal studies is enumerated and discussed, with particular attention on the microbial and molecular basis for the development of therapeutic interventions that involve targeting the gut. Additionally, clinical data supporting the concept of a living microbiome within a diarthrodial joint are summarized. A discussion of key limitations in the current data and important technical considerations for firmly establishing the existence of a synovial joint microbial community is included.

This study is aimed at exploring the relationship between maternal weight categories, including pre-pregnancy body mass index (P-BMI) and gestational weight gain (GWG), and the composition of the infant gut microbiome in the early days of life. We recruited 71 mother-infant pairs from Kangwon National University Hospital and Bundang CHA Hospital, collecting meconium samples from the infants within the first 5 days postpartum. Using 16S ribosomal RNA gene sequencing (V3-V4 region), this study assessed microbial diversity and the relative abundance of specific bacterial taxa in these initial stool samples. Participants were categorized into groups based on maternal P-BMI and GWG, enabling a comprehensive comparison of the microbiota composition in the infants' meconium across different maternal weight metrics. Our analysis identified significant variations in the infant gut microbiome correlated with maternal weight categories. Key findings include a differential abundance of genera such as Sphingobacteriaceae, Bacillaceae, Cytophagaceae, and Alteromonadaceae across maternal P-BMI groups, whereas Moraxellaceae and Rhodospirillaceae varied across GWG groups. In the P-BMI category, infants born to overweight mothers demonstrated a higher abundance of Pseudopedobacter, and a lower abundance of Citrobacter and Lachnospira, while infants in the underweight group showed a higher abundance of Lachnospira and Weissella. In the normal weight group, Citrobacter and Pseudopedobacter were more abundant. Within the GWG category, infants in the inadequate group showed a higher abundance of Klebsiella, whereas the normal group showed a higher abundance of Holdemania. The composition of the infant gut microbiome in the early postnatal period is significantly influenced by maternal weight categories. Understanding the role of maternal weight in shaping early microbial colonization may provide insights into developing strategies to optimize infant health outcomes through targeted interventions before and during pregnancy.

Microbiome-based dietary supplements have gained attention for their role in enhancing brain development and cognitive health. The gut microbiome influences neurological functions through the gut-brain axis, impacting neurotransmitter production, immune regulation, and metabolic pathways. Dysbiosis is linked to neurological disorders such as Alzheimer's, Parkinson's, and autism spectrum disorders. This chapter explores dietary interventions targeting the microbiome, emphasising probiotics, prebiotics, and postbiotics. Additionally, AI and machine learning are transforming microbiome research by enabling personalised supplementation strategies tailored to individual gut profiles. Ethical challenges, including data privacy and algorithmic bias, are also discussed. Advances in big data analytics and predictive modelling are paving the way for precision-targeted interventions to optimise brain health. While microbiome-based therapies hold great promise, further clinical validation and regulatory frameworks are needed to ensure their efficacy and accessibility. This chapter highlights the future potential of microbiome-targeted strategies in neuroprotection and cognitive well-being.

The current discovery that the gut microbiome, which contains roughly 100 trillion microbes, affects health and disease has catalyzed a boom in multidisciplinary research efforts focused on understanding this relationship. Also, it is commonly demonstrated that the gut and the CNS are closely related in a bidirectional pathway. A balanced gut microbiome is essential for regular brain activities and emotional responses. On the other hand, the CNS regulates the majority of GI physiology. Any disruption in this bidirectional pathway led to a progression of health problems in both directions, neurological and gastrointestinal diseases. In this review, we hope to shed light on the complicated connections of the microbiome-gut-brain axis and the critical roles of gut microbiome in the early development of the brain in order to get a deeper knowledge of microbiome-mediated pathological conditions and management options through rebalancing of gut microbiome.

Psoriatic arthritis (PsA) is a chronic inflammatory disease characterized by joint inflammation and skin lesions. Recent research has underscored the critical role of gut microbiota-comprising bacteria, fungi, viruses, and archaea-in the pathogenesis and progression of PsA. This narrative review synthesizes the latest findings on the influence of gut microbiota on PsA, focusing on mechanisms such as immune modulation, microbial dysbiosis, the gut-joint axis, and its impact on treatment. Advances in high-throughput sequencing and metagenomics have revealed distinct microbial profiles associated with PsA. Studies show that individuals with PsA have a unique gut microbiota composition, differing significantly from healthy controls. Alterations in the abundance of specific bacterial taxa, including a decrease in beneficial bacteria and an increase in potentially pathogenic microbes, contribute to systemic inflammation by affecting the intestinal barrier and promoting immune responses. This review explores the impact of various factors on gut microbiota composition, including age, hygiene, comorbidities, and medication use. Additionally, it highlights the role of diet, probiotics, and fecal microbiota transplantation as promising strategies to modulate gut microbiota and alleviate PsA symptoms. The gut-skin-joint axis concept illustrates how gut microbiota influences not only gastrointestinal health but also skin and joint inflammation. Understanding the complex interplay between gut microbiota and PsA could lead to novel, microbiome-based therapeutic approaches. These insights offer hope for improved patient outcomes through targeted manipulation of the gut microbiota, enhancing both diagnosis and treatment strategies for PsA.

To investigate the specific characteristics and differences in the placental microbiome of preterm infants with and without pneumonia.

Fifty-nine infants born at 32-36 weeks' gestation were enrolled in this study. Among them, 33 developed pneumonia within 48 hours of birth, while the remaining 26 did not. Placental swabs were collected at birth for DNA extraction, from which the placental microbial composition was analyzed using a bioinformatics pipeline following PCR amplification of genetic material and subsequent sequencing of bacterial 16S rRNA.

Significant differences in both the alpha and beta diversities were found between the two groups (P<0.05). Proteobacteria, Firmicutes, and Actinobacteriota were identified as the predominant phyla in the placenta, while predominant identified genera included Brevundimonas, Caulobacter, Lactobacillus, and Citrobacter. There were no significant inter-group differences in the relative abundances of the predominant phyla and genera except Lactobacillus(P>0.05). Compared to infants without pneumonia, those with pneumonia demonstrated a decreased abundance of Lactobacillus, and an increased abundance of Ureaplasma and Staphylococcus (P<0.05). The relative abundance of Ureaplasma was positively correlated with that of Staphylococcus, and negatively correlation with that of Lactobacillus (P<0.05). Notably, we observed significant disparities in the metabolic pathways and phenotypes between the two groups (P<0.05).

Overall, this study suggests that alterations in the placental microbiome may be linked to the onset of pneumonia in preterm infants. Further investigations are required to elucidate the relationship between microbiota and disease pathogenesis.

As the population ages, intestinal health in the elderly has become a key area of concern, with gut microbiota dysbiosis emerging as a significant issue. This review summarizes the factors influencing dysbiosis and interventions from both traditional Chinese medicine (TCM) and Western medicine, offering a reference for future research. A comprehensive search of global databases up to March 2024 identified 617 original studies on gut microbiota dysbiosis in individuals aged 65 and older. After applying strict PRISMA guidelines, 20 articles met the inclusion criteria. Key findings are summarized in four areas: 1) the definition and mechanisms of dysbiosis, 2) evaluation tools for gut microbiota imbalance, 3) factors contributing to dysbiosis in the elderly, and 4) pharmacological treatments. Both TCM and Western medicine offer unique advantages in managing gut microbiota dysbiosis, and the choice of intervention should be tailored to the individual's condition. Future research should focus on optimizing integrated TCM and Western medicine approaches to improve outcomes for elderly patients with gut microbiota dysbiosis.

The human placenta is a unique organ that forms under specific physiological conditions and plays a crucial role in nutrient and metabolite exchange between the mother and fetus. Research on the placenta is important for understanding maternal-fetal diseases. Traditionally, the placenta was considered "sterile," but advancements in detection techniques have revealed the presence of a low level of microorganisms. This discovery challenges the traditional notion that the uterine placenta is sterile. The revelation of this truth marks a significant breakthrough in medical research, prompting more researchers to focus on this vital organ, the placenta. Placental microbial communities may originate from the oral, vaginal, and intestinal microbiota of expectant mothers. These microorganisms may reach the maternal-fetal interface, collectively shaping the placental microbiota and contributing to the composition of normal placental microbial communities. Abnormal placental microbial communities may be associated with some pregnancy complications and fetal developmental issues such as preterm birth, gestational hypertension, fetal growth restriction, and gestational diabetes mellitus. Intervention strategies targeting microbial communities, which include modulation of placental microbiota composition or function, such as probiotics, may help prevent or treat complications related to abnormal placental microbiota during pregnancy.

Periodontal disease is a risk factor for many systemic diseases such as Alzheimer's disease and adverse pregnancy outcomes. Cleft palate (CP), the most common congenital craniofacial defect, has a multifaceted etiology influenced by complex genetic and environmental risk factors such as maternal bacterial or virus infection. A prior case-control study revealed a surprisingly strong association between maternal periodontal disease and CP in offspring. However, the precise relationship remains unclear. In this study, the relationship between maternal oral pathogen and CP in offspring was studied by sonicated P. gingivalis injected intravenously and orally into pregnant mice. We investigated an obvious increasing CP (12.5%) in sonicated P. gingivalis group which had inhibited osteogenesis in mesenchyme and blocked efferocytosis in epithelium. Then glycolysis and H4K12 lactylation (H4K12la) were detected to elevate in both mouse embryonic palatal mesenchyme (MEPM) cells and macrophages under P. gingivalis exposure which further promoted the transcription of metallopeptidase domain17 (ADAM17), subsequently mediated the shedding of transforming growth factor-beta receptor 1 (TGFBR1) in MEPM cells and mer tyrosine kinase (MerTK) in macrophages and resulted in the suppression of efferocytosis and osteogenesis in palate, eventually caused abnormalities in palate fusion and ossification. The abnormal efferocytosis also led to a predominance of M1 macrophages, which indirectly inhibited palatal osteogenesis via extracellular vesicles. Furthermore, pharmacological ADAM17 inhibition could ameliorate the abnormality of P. gingivalis-induced abnormal palate development. Therefore, our study extends the knowledge of how maternal oral pathogen affects fetal palate development and provides a novel perspective to understand the pathogenesis of CP.

Humans and other animals contain multitudes of microorganisms including bacteria, fungi, and viruses, which make up a diverse microbiome. Across body sites including skin, gastrointestinal tract, and oral cavity there are distinct microbial niches that are made up of trillions of microorganisms that have co-evolved to inhabit and interact with the host. The microbiome also interacts with the changing environment. This tripartite interaction between the host, microbiome, and environment suggests microbial communities play a key role in the biological processes of the host, such as development and behaviors. Over the past two decades, emerging research continues to reveal how host and microbe interactions impact nervous system signaling and behaviors, and influence neurodevelopmental, neurological, and neurodegenerative disorders. In this review, we will describe the unique features of the maternal microbiome that exist during the perinatal period and discuss evidence for the function of the maternal microbiome in offspring development. Finally, we will discuss how the maternal environment interacts with the microbiome and nervous system development and then postulate how the maternal microbiome can modify early offspring development to have lasting influence on brain health.

In early-life, the gut microbiota is highly modifiable, being modulated by external factors such as maternal microbiota, mode of delivery, and feeding strategies. The composition of the child's gut microbiota will deeply impact the development and maturation of its immune system, with consequences for future health. As one of the main sources of microorganisms to the child, the mother represents a crucial factor in the establishment of early-life microbiota, impacting the infant's wellbeing. Recent studies have proposed that dysbiotic maternal gut microbiota could be transmitted to the offspring, influencing the development of its immunity, and leading to the development of diseases such as obesity. This paper aims to review recent findings in gut microbiota and immune system interaction in early-life, highlighting the benefits of a balanced gut microbiota in the regulation of the immune system.

The geriatric population, comprising ages 65 and above, encounters distinct health obstacles because of physiological changes and heightened vulnerability to diseases. New technologies are being investigated to tackle the intricate health requirements of this population. Recent advancements in probiotics and nanotechnology offer promising strategies to enhance geriatric health by improving nutrient absorption, modulating gut microbiota, and delivering targeted therapeutic agents. Probiotics play a crucial role in maintaining gut homeostasis, reducing inflammation, and supporting metabolic functions. However, challenges such as limited viability and efficacy in harsh gastrointestinal conditions hinder their therapeutic potential. Advanced nanotechnology can overcome these constraints by enhancing the efficacy of probiotics through nano-encapsulation, controlled delivery, and improvement of bioavailability. This review explores the synergistic potential of probiotics and advanced nanotechnology in addressing age-related health concerns. It highlights key developments in probiotic formulations, nano-based delivery systems, and their combined impact on gut health, immunity, and neuroprotection. The convergence of probiotics and nanotechnology represents a novel and transformative approach to promoting healthy aging, paving the way for innovative therapeutic interventions.

The intestinal microbiota has major influence on human physiology and modulates health and disease. Complex host-microbe interactions regulate various homeostatic processes, including metabolism and immune function, while disturbances in microbiota composition (dysbiosis) are associated with a plethora of human diseases and are believed to modulate disease initiation, progression and therapy response. The vast complexity of the human microbiota and its metabolic output represents a great challenge in unraveling the molecular basis of host-microbe interactions in specific physiological contexts. To increase our understanding of these interactions, functional microbiota research using animal models in a reductionistic setting are essential. In the dynamic landscape of gut microbiota research, the use of germ-free and gnotobiotic mouse technology, in which causal disease-driving mechanisms can be dissected, represents a pivotal investigative tool for functional microbiota research in health and disease, in which causal disease-driving mechanisms can be dissected. A better understanding of the health-modulating functions of the microbiota opens perspectives for improved therapies in many diseases. In this review, we discuss practical considerations for the design and execution of germ-free and gnotobiotic experiments, including considerations around germ-free rederivation and housing conditions, route and timing of microbial administration, and dosing protocols. This comprehensive overview aims to provide researchers with valuable insights for improved experimental design in the field of functional microbiota research.

Recurrent pregnancy loss (RPL) involves multiple consecutive miscarriages in early pregnancy, affecting a significant number of Indian women and placing substantial physical and emotional stress on expecting couples. This expert consensus aims to highlight probiotics as a promising option for enhancing fertility and supporting successful pregnancy outcomes, offering hope to individuals and couples affected by RPL. A group of fourteen experts with diverse expertise in gynecology, obstetrics, and fertility from across India gathered between June 29 and June 30, 2024. According to the experts, advanced maternal age emerges as an independent risk factor for miscarriage, with increased risks among older Indian women. The major contributors to RPL include thyroid disease and polycystic ovarian disease. Experts emphasize that the vaginal microbiome dysbiosis, characterized by the reduced dominance of Lactobacilli, is associated with adverse pregnancy outcome, such as preterm birth, early pregnancy loss, and increased events of RPL. Oral probiotic supplementation, particularly strains like L. acidophilus and L. rhamnosus, may improve embryo implantation, reduce miscarriage risk, and support pregnancy maintenance. A healthy lifestyle choice and minimal use of antibiotics are important in creating a positive reproductive outcome. The present expert opinion supports the potential benefits of probiotics, particularly Lactobacillus species, in managing RPL and improving reproductive outcomes. By promoting a balanced microbiota, reducing inflammation, and modulating immune responses, probiotics may play a critical role in enhancing reproductive success.

Childhood is a multifactorial disease, and recent research highlights the influence of early-life microbial communities in shaping disease risk. This review explores the roles of the gut and respiratory microbiota in asthma development, emphasizing the importance of early microbial exposure. The gut microbiota has been particularly well studied, with certain taxa like Faecalibacterium and Bifidobacterium linked to asthma protection, whereas short-chain fatty acids produced by gut microbes support immune tolerance through the gut-lung axis. In contrast, the respiratory microbiota, though low in biomass, shows consistent associations between early bacterial colonization by Streptococcus, Moraxella, and Haemophilus and increased asthma risk. The review also addresses the emerging roles of the skin microbiota and environmental fungi in asthma, though findings remain inconsistent. Timing is a critical factor, with early-life disruptions, such as antibiotic use, potentially leading to increased asthma risk. Despite significant advances, there are still unresolved questions about the long-term consequences of early microbial perturbations, particularly regarding whether microbial dysbiosis is a cause or consequence of asthma. This review integrates current findings, highlighting the need for deeper investigation into cross-organ interactions and early microbial exposures to understand childhood asthma pathophysiology.

The neonatal microbiome has been the focus of considerable research over the past two decades and studies have added fascinating information in terms of early microbial patterns and how these relate to various disease processes. One difficulty with the interpretation of these relationships is that such data is associative and provides little in terms of proof of causality or the underpinning mechanisms. Integrating microbiome data with other omics such as the proteome, inflammatory mediators, and the metabolome is an emerging approach to address this gap. Here we discuss these omics, their integration, and how they can be applied to improve our understanding, treatment, and prevention of disease. IMPACT: This review introduces the concept of multiomics in neonatology and how emerging technologies can be integrated improve understanding, treatment, and prevention of disease. We highlight considerations for performing multiomic research in neonates and the need for validation in separate cohorts and/or relevant model systems. We summarise how the use of multiomics is expanding and lay out steps to bring this to the clinic to enable precision medicine.

The vaginal microbiome of healthy women is dominated by Lactobacillus spp. A variety of illnesses, such as vaginosis, sexually transmitted infections (STIs), failed implantation, premature birth (PTB), and preterm pre-labor membrane rupture, are brought on by an unbalanced microbiota. Pregnancy is associated with a decrease in the metabolic capacity of the vaginal resident microbiome, which is consistent with a change to a less complex Lactobacillus-dominated microbiome. Age, race, sexual intercourse, smoking, IUD, contraception, lifestyle, and diet all affect the makeup of the vaginal microbiome. Moreover, physiological events including menarche, the menstrual cycle, pregnancy, menopause, and other hormonal changes have an impact on the vaginal microbiome. The vaginal microbiome is significantly disrupted by the menstrual cycle, with significant changes toward a more varied microbiota occurring around menstruation. Several major factors maintain or disrupt the vaginal microbiome including ethnic group, menstruation cycle, and pregnancy which are discussed in this section. In the index pregnancy, the vaginal microbiota of women who had already given birth, or had just experienced an induced or spontaneous abortion, was qualitatively and quantitatively different from that of women who were having their first child. Early pregnancy vaginal microbiome depletion is a risk factor for early pregnancy miscarriage. Although, early pregnancy miscarriage is not always caused by a high bacterial diversity and quantity of lactobacilli. Lactobacillus protects against pathogens through the production of antibacterial compounds such as lactic acid and bacteriocins.

The gut microbiota has been increasingly recognised as a critical determinant of human health, influencing a wide range of physiological processes. A healthy gut microbiota is essential for maintaining metabolic, immune, and gastrointestinal homeostasis, contributing to overall well-being. Alterations in its composition and functionality, often referred to as microbial dysbiosis, are strongly associated with the development of gut-related and systemic diseases. The gut microbiota synthesises several components and interacts with epithelial cell receptors, influencing processes that extend beyond nutritional status to the pathogenesis of diseases such as obesity, which extend beyond their known contribution to nutritional status. Therefore, this state-of-the-art review synthesises findings from recent studies on the composition, functions, and influencing factors of the gut microbiota, with a focus on its role in obesity. A systematic search of peer-reviewed literature was conducted to ensure comprehensive coverage, while expert insights are incorporated to discuss emerging research directions and future perspectives in the field.

This study aimed to scrutinize variations in the intestinal microbiota of neonatal dogs born through natural birth versus elective cesarean section, focusing on evaluating the influence of vaginal seeding on the microbiota of cesarean-born neonates. Samples were collected from cesarean-sectioned females before anesthesia and from naturally birthing females during prodrome signs, along with neonates at eight time points from birth to 15 days of age. In the cesarean section group, seeding was performed in half of the neonates (cesarean section seeding group; seeding consisted of gently rubbing the gauze, obtained from the mother's vagina, onto the mouths, faces, and bodies of the newborns), while the other half underwent microbiological sample collection without seeding (cesarean section group). Another group (normal birth group) consisted of naturally born neonates. Microbiota analysis included counting for enterobacteria, Staphylococcus spp., and Streptococcus spp. The results suggested that vertical transmission played a crucial role, but the method of birth did not emerge as the primary determinant of observed differences. Under study conditions, vaginal seeding failed to effectively modulate the microbiota of neonates born through elective cesarean section. Further investigations into the gut-brain axis are suggested for understanding factors influencing the initial development of the canine intestinal microbiota in neonates born through different delivery routes.

Antibiotics are widely used during pregnancy. Recent epidemiological studies suggest that maternal exposure to antibiotics during pregnancy is associated with increased risks of various diseases in offspring; host-microbiome interactions are considered to be involved in pathogenesis, as antibiotic-induced perturbations (dysbiosis) of the maternal microbiome can be transmitted to offspring. We reviewed the current status of antibiotic usage during pregnancy, transmission of maternal antibiotic-induced dysbiosis to offspring, and several diseases in offspring reported to be associated with maternal antibiotic exposure. Antibiotics must be properly used when necessary. While the adverse effect of maternal antibiotic exposure during pregnancy on the health of offspring has been demonstrated by several studies, more robust clinical evidence is necessary to define the best practice for antibiotic use during pregnancy. Epidemiologic studies have limitations in establishing causal links beyond associations; animal studies provide benefits in examining these links, however, microbiomes, gestation courses, and aging vary between host species. Understanding the underlying mechanisms of epidemiologic findings as well as the healthy microbiome during pregnancy and early life in humans would contribute to developing future microbial interventions for restoring antibiotic-induced dysbiosis during pregnancy.

The mouth houses the second largest diversity of microorganisms in the body, harboring more than 700 bacterial species colonizing the soft mucosa and hard tooth surfaces. Microbes are the cause of several health-related problems, such as dental carries, gingivitis, periodontitis, etc., in the mouth across different age groups and socioeconomic/demographic groups. Oral infections are major health problems that affect the standard of living. Compromised oral health is related to chronic conditions and systemic disorders. Microbes responsible for dental caries are acid-producing and aciduric Gram-positive bacteria (Streptococci, Lactobacilli). Gram-negative bacteria (Porphyromonas, Prevotella, Actinobacillus, and Fusobacterium) capable of growing in anaerobic environments are responsible for periodontal diseases. Due to the high prevalence of oral diseases, negative effects associated with the use of antimicrobial agents and increased antibiotic resistance in oral pathogens, suitable alternative methods (effective, economical and safe) to suppress microbes disturbing oral health need to be adopted. Side effects associated with the chemical antimicrobial agents are vomiting, diarrhea and tooth staining. Several researchers have studied the antimicrobial properties of plant extracts and phytochemicals and have used them as indigenous practices to control several infections. Therefore, phytochemicals extracted from plants can be suitable alternatives. This review focuses on the various phytochemical/plant extracts suppressing the growth of oral pathogens either by preventing their attachment to the surfaces or by preventing biofilm formation or other mechanisms.

The development of the fetal immune response is a highly complex process. In the present review, we describe the development of the fetal immune response and the role of the maternal gut bacteria in this process. In contrast to the previous belief that the fetal immune response is inert, it is now thought that the fetal immune response is uniquely tolerant to maternal and allo-antigens, but able to respond to infectious agents, such as bacteria. This is accomplished by the development of T cells toward regulatory T cells rather than toward effector T cells, but also by the presence of functional innate immune cells, such as monocytes and NK cells. Moreover, in fetuses there is different programming of CD8 + T cells and memory T cells toward innate immune cells rather than to adaptive immune cells. The maternal gut bacteria are important in shaping the fetal immune response by producing bacterial products and metabolites that pass the placenta into the fetus and influence development of the fetal immune response. Insight into how and when these products affect the fetal immune response may open new treatment options with pre- or probiotics to affect the maternal gut bacteria and therewith the fetal immune response.

The prevalence of gestational diabetes mellitus (GDM), a condition that is widespread globally, is increasing. The relationship between the gut microbiota and GDM has been a subject of research for nearly two decades, yet there has been no bibliometric analysis of this correlation. This study aimed to use bibliometrics to explore the relationship between the gut microbiota and GDM, highlighting emerging trends and current research hotspots in this field.

A total of 394 papers were included in the analysis. China emerged as the preeminent nation in terms of the number of publications on the subject, with 128 papers (32.49%), whereas the United States had the most significant impact, with 4,874 citations. The University of Queensland emerged as the most prolific institution, contributing 18 publications. Marloes Dekker Nitert was the most active author with 16 publications, and Omry Koren garnered the most citations, totaling 154. The journal Nutrients published the most studies (28 publications, 7.11%), whereas PLoS One was the most commonly co-cited journal, with a total of 805 citations. With respect to keywords, research focuses can be divided into 4 clusters, namely, "the interrelationship between the gut microbiota and pregnancy, childbirth," "the relationship between adverse metabolic outcomes and GDM," "the gut microbiota composition and metabolic mechanisms" and "microbiota and ecological imbalance." Key areas of focus include the interactions between the gut microbiota and individuals with GDM, as well as the formation and inheritance of the gut microbiota. Increasing attention has been given to the impact of probiotic supplementation on metabolism and pregnancy outcomes in GDM patients. Moreover, ongoing research is exploring the potential of the gut microbiota as a biomarker for GDM. These topics represent both current and future directions in this field.

This study provides a comprehensive knowledge map of the gut microbiota and GDM, highlights key research areas, and outlines potential future directions.

The early colonization and establishment of the microbiome in newborns is a crucial step in the development of the immune system and host metabolism. However, the exact timing of initial microbial colonization remains a subject of ongoing debate. While numerous studies have attempted to determine the presence or absence of intrauterine bacteria, the majority of them have drawn conclusions based on sequencing data from maternal or infant samples taken at a single time point. In this study, we aimed to investigate the microbial population in amniotic fluid (AF) from the second trimester until the time of delivery using multiple microbiological methods.

AF samples were collected during the second trimester (19-21 gestational weeks) and at the time of delivery. Cohort 1 included 51 women who underwent the term and elective cesarean section, with both their second trimester and delivery AF samples (n = 55, respectively) analyzed. Cohort 2 contained 22 women who experienced infection-related adverse pregnancy outcomes (including preterm birth, histological chorioamnionitis, and stillbirth), with only their second trimester AF samples (n = 24) examined. Additionally, multiple procedural negative controls and technical positive controls were applied to this study to remove potential contamination. Microbial profiles were assessed through cultivation, quantitative real-time polymerase chain reaction, 16S ribosomal RNA gene sequencing, and cytokine analysis.

In cohort 1, the bacterial load and community structure in the second trimester AF samples were indistinguishable from negative controls. Although marginally higher bacterial loads and different bacterial communities were observed in the delivery AF samples compared to negative controls, these bacterial DNA were not considered biologically functional due to the absence of maternal inflammatory responses. In cohort 2, the bacterial load and community structure of the second trimester AF samples differed significantly from those of negative controls, with Ureaplasma and Lactobacillus identified as the most prevalent genera against negative controls.

Our study demonstrates that no microorganisms were detected in the AF of healthy pregnancies from the second trimester to the delivery. The presence of Ureaplasma and Lactobacillus in the second trimester AF may be associated with infection-related adverse pregnancy outcomes. Video Abstract.

The first 1, 000 days of life, from the fetal stage of a woman's pregnancy to 2 years of age after the baby is born, is a critical period for microbial colonization of the body and development of the immune system. The immune system and microbiota exhibit great plasticity at this stage and play a crucial role in subsequent development and future health. Two-way communication and interaction between immune system and microbiota is helpful to maintain human microecological balance and immune homeostasis. Currently, there is a growing interest in the important role of the microbiota in the newborn, and it is believed that the absence or dysbiosis of human commensal microbiota early in life can have lasting health consequences. Thus, this paper summarizes research advances in the establishment of the oral and intestinal microbiome and immune system in early life, emphasizing the substantial impact of microbiota diversity in the prenatal and early postnatal periods, and summarizes that maternal microbes, mode of delivery, feeding practices, antibiotics, probiotics, and the environment shape the oral and intestinal microbiota of infants in the first 1, 000 days of life and their association with the immune system.

For years, the placenta was believed to be sterile, but recent studies reveal it hosts a unique microbiome. Despite these findings, significant questions remain about the origins of the placental microbiome and its effects on pregnancy and fetal health. Some studies suggest it may originate from the vaginal tract, while others indicate that oral bacteria can enter the maternal bloodstream and seed the placenta. However, research analyzing the vaginal, oral, and placental microbiomes within the same cohort is lacking. Additionally, it's unclear whether the placental microbiome differs between healthy pregnancies and those with complications like preterm birth (PTB), which remains a leading cause of neonatal morbidity and mortality worldwide.

In this study, we performed 16S rRNA gene sequencing to investigate the composition of the oral and placental microbiome in samples collected from 18 women who experienced PTB and 36 matched controls who delivered at term (TB), all of whom were part of the Molecular Signature in Pregnancy (MSP) study. We leveraged on the multisite microbiome sampling from the MSP participants and on our previously published vaginal microbiome data to investigate the potential origins of the placental microbiome and assess whether its composition varies between healthy and complicated pregnancies.

Our analysis revealed distinct profiles in the oral microbiome of PTB subjects compared to those who delivered at term. Specifically, we observed an increased abundance of Treponema maltophilum, Bacteroides sp, Mollicutes, Prevotella buccae, Leptotrichia, Prevotella_sp_Alloprevotella, in the PTB group. Importantly, Treponema maltophilum species showed higher abundance in the PTB group during the second trimester, suggesting its potential use as biomarkers. When we assessed the placenta microbiome composition, we found that Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria were the most dominant phyla. Interestingly, microorganisms such as Ureaplasma urealyticum were more abundant in PTB placenta samples. Our findings suggest that the placenta microbiome could originate from the oral or vaginal cavities, with a notable increase in the crosstalk between the vaginal and placental sites in cases of PTB. Specifically, our data revealed that in PTB cases, the placental microbiome exhibited a closer resemblance to the vaginal microbiome, whereas in term pregnancies, the placental microbiome was similar to the oral microbiome.

The complex gut microbiome influences host aging and plays an important role in the manifestation of age-related diseases. Restoring a healthy gut microbiome via Fecal Microbiota Transplantation (FMT) is receiving extensive consideration to therapeutically transfer healthy longevity. Herein, we comprehensively review the benefits of gut microbial rejuvenation - via FMT - to promote healthy aging, with few studies documenting life length properties. This review explores how preconditioning donors via standard - lifestyle and pharmacological - antiaging interventions reshape gut microbiome, with the resulting benefits being also FMT-transferable. Finally, we expose the current clinical uses of FMT in the context of aging therapy and address FMT challenges - regulatory landscape, protocol standardization, and health risks - that require refinement to effectively utilize microbiome interventions in the elderly.

Recent evidence challenging the notion of a sterile intrauterine environment has sparked research into the origins and effects of fetal microbiota on immunity development during gestation. Rhesus macaques (RMs) serve as valuable nonhuman primate models due to their similarities to humans in development, placental structure, and immune response. In this study, metagenomic analysis was applied to the placenta, umbilical cord, spleen, gastrointestinal tissues of an unborn RM fetus, and the maternal intestine, revealing the diversity and functionality of microbes in these tissues. Additionally, gut metagenomic data of adult Rhesus macaques from our previous study, along with data from a human fetus obtained from public databases, were included for comparison. We observed substantial microbial sharing between the mother and fetus, with the microbial composition of the placenta and umbilical cord more closely resembling that of the fetal organs than the maternal intestine. Notably, compared with other adult RMs, there was a clear convergence between maternal and fetal microbiota, alongside distinct differences between the microbiota of adults and the fetus, which underscores the unique microbial profiles in fetal environments. Furthermore, the fetal microbiota displayed a less developed carbohydrate metabolism capacity than adult RMs. It also shared antibiotic resistance genes with both maternal and adult RM microbiomes, indicating potential vertical transmission. Comparative analysis of the metagenomes between the RM fetus and a human fetus revealed significant differences in microbial composition and genes, yet also showed similarities in certain abundant microbiota. Collectively, our results contribute to a more comprehensive understanding of the intrauterine microbial environment in macaques.

This study aimed to preliminarily explore the composition and diversity of intestinal bacteria in Erinaceus amurensis during breeding period, aiding in the field rescue and population conservation efforts of Erinaceus amurensis. This also provides foundational data for further research on the prevention and screening of Emerging Zoonotic Infectious Diseases and the experimental animalization of wild Erinaceus amurensis. Between April and July 2023, we collected 13 fresh fecal samples from Erinaceus amurensis at the Sishan Forest Farm in Jidong County, Heilongjiang Province, situated within the Wandashan Mountain range. Utilizing metagenomic sequencing technology, we conducted a comparative analysis of the gut microbiota composition and diversity in wild Erinaceus amurensis across different genders and between adult and fetal individuals within the same habitat. Our results revealed significant differences (P < 0.01) in the classification and diversity of gut microbiota between genders and between adult and fetal Erinaceus amurensis. Specifically, the dominant bacterial groups in the gut of Erinaceus amurensis were Pseudomonas, Proteobacteria, and Enterobacteriaceae. In male and female Erinaceus amurensis, the dominant bacterial groups were Pseudomonas, Bacteroides, and Firmicutes, with variations in bacterial abundance and diversity. While male and female Erinaceus amurensis exhibited similar microbial compositions, they displayed significant differences in specific bacterial classifications. The dominant bacterial group in fetal Erinaceus amurensis was Proteobacteria, which demonstrated lower diversity and abundance compared to the adult group. Furthermore, the types and abundance of pathogenic or opportunistic pathogens in the gut of fetal Erinaceus amurensis and male Erinaceus amurensis were higher than those in female Erinaceus amurensis. The analysis of experimental results indicates that Erinaceus amurensis in this region either have or are at risk of developing inflammation related to the intestinal and urinary tracts, as well as skin-related issues. Consequently, it is advised that forestry and wildlife conservation personnel in this area prioritize treatment against these specific pathogens when conducting rescue operations for Erinaceus amurensis in the wild.

This Mendelian randomisation (MR) study endeavoured to delineate the causal relationship between periodontitis and adverse pregnancy outcomes (APOs), encompassing low birthweight (LBW), pre-term birth (PTB), stillbirth, miscarriage, and gestational hypertension (GH).

Utilising genetic instruments for periodontitis (acute and chronic periodontitis) from the Genome-Wide Association Study (GWAS) database among individuals of European descent, this study explored the causal relationship with adverse pregnancy outcomes, and vice versa. The Inverse Variance Weighted (IVW) method was employed as the primary analytical approach to assess causality, with MR-Egger serving as a sensitivity analysis method.

The primary analytical method employed in this study, IVW, did not reveal any impact of periodontitis (acute and chronic periodontitis) on PTB, stillbirth, miscarriage, and gestational hypertension, and vice versa. Heterogeneity testing using the MR-Egger method confirmed the null causal hypothesis, with odds ratios (OR) approximating 1, and P-values exceeding 0.05. Notably, the results from the IVW analysis (OR 1.410, CI 1.039-1.915, P-value 0.028) indicate statistically significant evidence supporting a causal relationship between chronic periodontitis and LBW. However, caution is advised in interpreting the causal relationship, considering the non-significant P-values obtained from other methods.

Within the limitations of this MR study, the findings do not support the influence of periodontitis on LBW, PTB, stillbirth, miscarriage, and GH, nor vice versa.

Previously believed sterile, the placenta hosts distinct microbial species across various locations. This study aims to elucidate the temporal and spatial variations of placental microbiota throughout gestation, addressing gaps in current understanding.

A case-control study at a single-center compared microbial profiles in pregnant women delivering preterm (<37 weeks) or at term (>37 weeks) across placental sites: basal plate, fetal membranes, and placental villous. Microbial abundance and diversity were evaluated using QIIME and the R package "Phyloseq," while Q-PCR with specific primers validated absolute abundance in samples.

We found no alteration in bacterial communities based on delivery mode across all samples. Q-PCR detected low-abundance bacteria, notably enriched in preterm samples, especially in early preterm cases. Throughout gestation, bacterial composition varied, with increasing levels of Proteobacteria and Firmicutes observed in the placenta. Significant differences in bacterial profiles were noted across locations and gestational stages, with Ralstonia insidiosa consistently present in the basal plate throughout gestation. Species-specific Q-PCR confirmed the presence of Ralstonia and revealed an inverse relationship between Streptococcus agalactiae and pregnancy progression.

The placenta hosts its own microbiome, with distinct profiles observed between term and preterm samples. Further research is needed to clarify the impact of bacterial dysbiosis on preterm birth and develop methods to distinguish pathological bacteria from the natural microbiome.

This review examines the longstanding debate of nature and intrauterine environmental challenges that shapes human development and behavior, with a special focus on the influence of maternal prenatal gut microbes. Recent research has revealed the critical role of the gut microbiome in human neurodevelopment, and evidence suggest that maternal microbiota can impact fetal gene and microenvironment composition, as well as immunophysiology and neurochemical responses. Furthermore, intrauterine neuroepigenetic regulation may be influenced by maternal microbiota, capable of having long-lasting effects on offspring behavior and cognition. By examining the complex relationship between maternal prenatal gut microbes and human development, this review highlights the importance of early-life environmental factors in shaping neurodevelopment and cognition.

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.

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.

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.

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

Premature infants are more prone to brain injuries owing to incomplete nervous system development and poor adaptation outside the mother's body. Without timely intervention, premature infants with brain injuries often develop intellectual disabilities, causing significant burdens on families and the society. Multiple studies have shown that gut dysbiosis can affect the nervous system, and vice versa. This study aimed to explore the changes in gut microbiota of typical premature infants and those with brain injuries on the third and seventh days after birth using 16 S rRNA technology.

Fecal samples from typical premature infants (non-brain injury group, n = 17) and those with brain injuries (brain injury group, n = 21) were collected on days 1, 3, and 7 after birth for 16 S rRNA sequencing. Alpha diversity analysis was used to evaluate the diversity of gut microbiome. LEfSe and DESeq2 were used to analyze of the microorganisms' characteristics and differentiate the microorganisms between the two groups.

At the phylum level, Firmicutes, Proteobacteria, and Actinobacteria were the dominant flora in both groups. At the genus level, the proportion of Enterococcus in fecal samples of the brain injury group was higher than that of the non-brain injury group on day three after birth; however, the opposite was observed on day seven. Rothia and Lactobacillales were characteristic bacteria of the non-brain injury group on days three and seven after birth, whereas Enterococcus and Bifidobacteria were characteristic bacteria of the brain injury group on days three and seven after birth, respectively. Three days after birth, the Shannon and Simpson indices of the non-brain injury group were significantly higher than those of the brain injury group.

Premature infants with brain injuries have a unique gut microbiota that is different from that of typical premature infants, indicating correlation between brain injuries and gut microbiota.

Despite many decades of research, the exact etiology of pre-eclampsia (PE) remains unknown. Several etiopathologies have been suggested, including the role of the placental microbiota. However, the existence of placental microbiota and its possible contribution to pregnancy complications, particularly PE has remained controversial.

The present study was designed to identify different microbes that co-exist the placenta of women with early- and late-onset PE.

Thirty age-matched normotensive and early-onset as well as age-matched normotensive and late-onset pre-eclamptic women respectively, were recruited. After obtaining an informed consent, the placental tissues were obtained through caesarian section with sterile and standardized clinical procedures. DNA was extracted from each tissue and microbiome analysis was conducted using a targeted 16 S analysis and the reads were analyzed with bioinformatics.

There was a significance difference between the blood pressure of early-/late-onset PE compared with age-matched normotensive controls, respectively. In addition, the reads from placencental samples were classified as belonging to the phyla, Actinobacteria, Firmicutes, Bacteroidetes, Proteobacteria, with Proteobacteria dominated by the classes Pseudomonadales and Gammaproteobacteria with smaller amounts of Actinobacteria and Bacteroidetes. There was no significant difference between the placental bacterial species of early-/late-onset PE compared with age-matched normotensive controls, respectively. Further analysis found no correlation between bacterial species and early- or late-onset PE.

The present results demonstrate a low biomass of bacterial species, which might further indicate that the placental samples had very low levels of bacteria species and there is no correlation between the bacterial composition and early- or late-onset PE.