The Predominant Oral Microbiota Is Acquired Early in an Organized Pattern

Probiotics for oral health: a critical evaluation of bacterial strains

Oral health is critical for total body health and well-being; however, little improvement in oral health status has occurred in the U.S. over the past 20 years. Tooth decay and gum disease remain highly prevalent, with more than 90% and 50% of adults suffering from these conditions, respectively. To combat this lack of improvement, alternative approaches to dental care are now being suggested. One such alternative therapy is probiotics for oral care. In the oral cavity, probiotic strains have been shown to reduce levels of oral pathogens, inhibit the formation of dental caries, and reduce the levels of bacteria that cause halitosis. However, as the oral care probiotic market expands, many products contain bacterial species and strains with no documented health benefits leading to confusion and mistrust among consumers and clinicians. This confusion is enhanced by the regulatory status of probiotic products which puts the onus of safety and efficacy on the manufacturer rather than a central regulatory body. The overarching goal of this review is to provide consumers and clinicians with documented evidence supporting (or refuting) the health benefits of oral care probiotics marketed for sale in the United States. This includes defining what constitutes an oral care probiotic product and a strain level analysis of candidate probiotics from the genera Streptococcus, Lactobacillus, Bifidobacterium, and Bacillus. Additionally, prebiotics and postbiotics will be discussed. Finally, a set of considerations for consumers and clinicians is provided to empower probiotic product decision making. Together, this review will improve understanding of oral care probiotics marketed in the US for dental professionals and consumers.

The oral microbiome and oral and upper gastrointestinal diseases

Background

Microbiomes are essential components of the human body, and their populations are substantial. Under normal circumstances, microbiomes coexist harmoniously with the human body, but disturbances in this equilibrium can lead to various diseases. The oral microbiome is involved in the occurrence and development of many oral and gastrointestinal diseases. This review focuses on the relationship between oral microbiomes and oral and upper gastrointestinal diseases, and therapeutic strategies aiming to provide valuable insights for clinical prevention and treatment.

Methods

To identify relevant studies, we conducted searches in PubMed, Google Scholar, and Web of Science using keywords such as "oral microbiome," "oral flora, " "gastrointestinal disease, " without any date restrictions. Subsequently, the retrieved publications were subject to a narrative review.

Results

In this review, we found that oral microbiomes are closely related to oral and gastrointestinal diseases such as periodontitis, dental caries, reflux esophagitis, gastritis, and upper gastrointestinal tumors (mainly the malignant ones). Oral samples like saliva and buccal mucosa are not only easy to collect, but also display superior sample stability compared to gastrointestinal tissues. Consequently, analysis of the oral microbiome could potentially serve as an efficient preliminary screening method for high-risk groups before undergoing endoscopic examination. Besides, treatments based on the oral microbiomes could aid early diagnosis and treatment of these diseases.

Conclusions

Oral microbiomes are essential to oral and gastrointestinal diseases. Therapies centered on the oral microbiomes could facilitate the early detection and management of these conditions.

Upper respiratory microbial communities of healthy populations are shaped by niche and age

Background

Alterations in upper respiratory microbiomes have been implicated in shaping host health trajectories, including by limiting mucosal pathogen colonization. However, limited comparative studies of respiratory microbiome development and functioning across age groups have been performed. Herein, we perform shotgun metagenomic sequencing paired with pathogen inhibition assays to elucidate differences in nasal and oral microbiome composition and functioning across healthy 24-month-old infant (n=229) and adult (n=100) populations.

Results

We find that beta diversity of nasal and oral microbiomes varies with age, with nasal microbiomes showing greater population-level variation compared to oral microbiomes. Infant microbiome alpha diversity was significantly lower across nasal samples and higher in oral samples, relative to adults. Accordingly, we demonstrate significant differences in genus- and species-level composition of microbiomes between sites and age groups. Antimicrobial resistome patterns likewise varied across body sites, with oral microbiomes showing higher resistance gene abundance compared to nasal microbiomes. Biosynthetic gene clusters encoding specialized metabolite production were found in higher abundance across infant oral microbiomes, relative to adults. Investigation of pathogen inhibition revealed greater inhibition of gram-negative and gram-positive bacteria by oral commensals, while nasal isolates had higher antifungal activity.

Conclusions

In summary, we identify significant differences in the microbial communities inhabiting nasal and oral cavities of healthy infants relative to adults. These findings inform our understanding of the interactions impacting respiratory microbiome composition and functioning, with important implications for host health across the lifespan.

The oral microbiome: diversity, biogeography and human health

The human oral microbiota is highly diverse and has a complex ecology, comprising bacteria, microeukaryotes, archaea and viruses. These communities have elaborate and highly structured biogeography that shapes metabolic exchange on a local scale and results from the diverse microenvironments present in the oral cavity. The oral microbiota also interfaces with the immune system of the human host and has an important role in not only the health of the oral cavity but also systemic health. In this Review, we highlight recent advances including novel insights into the biogeography of several oral niches at the species level, as well as the ecological role of candidate phyla radiation bacteria and non-bacterial members of the oral microbiome. In addition, we summarize the relationship between the oral microbiota and the pathology of oral diseases and systemic diseases. Together, these advances move the field towards a more holistic understanding of the oral microbiota and its role in health, which in turn opens the door to the study of novel preventive and therapeutic strategies.

The contribution of maternal factors to the oral microbiota of the child: Influence from early life and clinical relevance

The mother represents one of the earliest sources of microorganisms to the child, influencing the acquisition and establishment of its microbiota in early life. However, the impact of the mother on the oral microbiota of the child from early life until adulthood remains to unveil. This narrative review aims to: i) explore the maternal influence on the oral microbiota of the child, ii) summarize the similarity between the oral microbiota of mother and child over time, iii) understand possible routes for vertical transmission, and iv) comprehend the clinical significance of this process for the child. We first describe the acquisition of the oral microbiota of the child and maternal factors related to this process. We compare the similarity between the oral microbiota of mother and child throughout time, while presenting possible routes for vertical transmission. Finally, we discuss the clinical relevance of the mother in the pathophysiological outcome of the child. Overall, maternal and non-maternal factors impact the oral microbiota of the child through several mechanisms, although the consequences in the long term are still unclear. More longitudinal research is needed to unveil the importance of early-life microbiota on the future health of the infant.

Genome Mining Uncovers NRPS and PKS Clusters in Rothia dentocariosa with Inhibitory Activity against Neisseria Species

The growing global threat of antimicrobial resistance is reaching a crisis point as common bacterial infections, including those caused by pathogenic Neisseria species, are becoming increasingly untreatable. This is compelling the scientific community to search for new antimicrobial agents, taking advantage of computational mining and using whole genome sequences to discover natural products from the human microbiome with antibiotic effects. In this study, we investigated the crude extract from a Rothia dentocariosa strain with demonstrated antimicrobial activity against pathogenic Neisseria spp. by spot-on-lawn assay. The genomic DNA of the R. dentocariosa strain was sequenced, and bioinformatic evaluation was performed using antiSMASH and PRISM to search for biosynthetic gene clusters (BGCs). The crude extract with potential antimicrobial activity was run on Tricine-SDS-PAGE, and the putative peptides were characterised using liquid chromatography-tandem mass spectrometry (LC-MS). The crude extract inhibited the growth of the pathogenic Neisseria spp. Six BGCs were identified corresponding to non-ribosomal peptide synthases (NRPSs), polyketide synthases (PKSs), and ribosomally synthesised and post-translationally modified peptides. Three peptides were also identified corresponding to Actinorhodin polyketide putative beta-ketoacyl synthase 1. These findings serve as a useful reference to facilitate the research and development of NRPS and PKS as antimicrobial products against multidrug-resistant N. gonorrhoeae.

The Relationship between Dietary Habits and Periodontal Pathogens in a Sample of Romanian Children and Adolescents: A Cross-Sectional Study

The role of diet in shaping oral microbiota and its potential contribution to the development of periodontal pathogens cannot be understated. This study aimed to explore the correlation between dietary habits and the prevalence of 11 periodontal pathogens among children and adolescents in Oradea, Romania. The identification of these pathogens was performed using the micro-IDent test kit, capable of detecting 11 specific periodontal pathogens. Bacterial sampling was conducted from the crevicular fluid in the morning, prior to brushing, followed by the completion of a brief questionnaire by parents. The questionnaire captured various aspects of the children's eating habits, including meal frequency, consumption of sweets, and hydration levels. The collected samples were dispatched to the laboratory for analysis, which provided insights into the abundance of microorganisms. The study encompassed 60 participants aged between 2 and 18 years, with the majority reported by their parents to have regulated meal timings, frequent sugar intake, and adequate hydration. The findings revealed significant associations between certain dietary factors and the presence of specific periodontal pathogens. Notably, the absence of breastfeeding was linked with the detection of Tannerella forsythia and Campylobacter rectus. Furthermore, frequent consumption of sweets corresponded with the presence of Capnocytophaga spp., which was particularly observed in individuals consuming sweets 2-3 times a day. Insufficient age-appropriate hydration showed an association with the prevalence of T. forsythia, Peptostreptococcus micros, and Capnocytophaga spp. In this sample, it became evident that eating habits and diet influenced the presence of several periodontal pathogens. The lack of breastfeeding was predominantly associated with positive results for T. forsythia and C. rectus, while inadequate hydration correlated more frequently with the presence of T. forsythia and P. micros. Moreover, frequent consumption of sweets was linked to the presence of Capnocytophaga spp.

Rookery through rehabilitation: Microbial community assembly in newborn harbour seals after maternal separation

Microbial community assembly remains largely unexplored in marine mammals, despite its potential importance for conservation and management. Here, neonatal microbiota assembly was studied in harbour seals (Phoca vitulina richardii) at a rehabilitation facility soon after maternal separation, through weaning, to the time of release back to their native environment. We found that the gingival and rectal communities of rehabilitated harbour seals were distinct from the microbiotas of formula and pool water, and became increasingly diverse and dissimilar over time, ultimately resembling the gingival and rectal communities of local wild harbour seals. Harbour seal microbiota assembly was compared to that of human infants, revealing the rapid emergence of host specificity and evidence of phylosymbiosis even though these harbour seals had been raised by humans. Early life prophylactic antibiotics were associated with changes in the composition of the harbour seal gingival and rectal communities and surprisingly, with transient increases in alpha diversity, perhaps because of microbiota sharing during close cohabitation with other harbour seals. Antibiotic-associated effects dissipated over time. These results suggest that while early life maternal contact may provide seeding for microbial assembly, co-housing of conspecifics during rehabilitation may help neonatal mammals achieve a healthy host-specific microbiota with features of resilience.

Establishment of tongue microbiota by 18 months of age and determinants of its microbial profile

IMPORTANCE

Understanding the development of oral microbiota early in life and the factors that influence it is important for preventing the establishment of dysbiotic oral microbiota later in life. This study demonstrates that the tongue microbiota undergoes early development from 4 to 18 months of age and converges into two types of microbiota showing indications of adult characteristics, with either S. salivarius or Neisseria-dominance. Interestingly, their divergence was strongly determined by their weaning status and the dietary frequencies of sweetened beverages, snacks, and fruits, suggesting that dietary habits during this period might influence the establishment of the oral microbiota. These findings may contribute to the development of novel preventive strategies against oral microbiota-related diseases.

Oral Microbiota: A New Insight into Cancer Progression, Diagnosis and Treatment

The polymorphic microbiome has been defined as one of the "Hallmarks of Cancer". Extensive studies have now uncovered the role of oral microbiota in cancer development and progression. Bacteria, fungi, archaea, and viruses in the oral cavity interact dynamically with the oral microenvironment to maintain the oral micro-ecological homeostasis. This complex interaction is influenced by many factors, such as maternal transmission, personal factors and environmental factors. Dysbiosis of oral microbiota can disturbed this host-microbiota interaction, leading to systemic diseases. Numerous studies have shown the potential associations between oral microbiota and a variety of cancers. However, the underlying mechanisms and therapeutic insights are still poorly understood. In this review, we mainly focus on the following aspects: (1) the factors affect oral microbiota composition and function; (2) the interaction between microenvironment and oral microbiota; (3) the role of multi-kingdom oral microbiota in human health; (4) the potential underlying mechanisms and therapeutic benefits of oral microbiota against cancer. Finally, we aim to describe the impact of oral microbiota on cancer progression and provide novel therapeutic insights into cancer prevention and treatment by targeting oral microbiota.

Social networking at the microbiome-host interface

Microbial species colonizing host ecosystems in health or disease rarely do so alone. Organisms conglomerate into dynamic heterotypic communities or biofilms in which interspecies and interkingdom interactions drive functional specialization of constituent species and shape community properties, including nososymbiocity or pathogenic potential. Cell-to-cell binding, exchange of signaling molecules, and nutritional codependencies can all contribute to the emergent properties of these communities. Spatial constraints defined by community architecture also determine overall community function. Multilayered interactions thus occur between individual pairs of organisms, and the relative impact can be determined by contextual cues. Host responses to heterotypic communities and impact on host surfaces are also driven by the collective action of the community. Additionally, the range of interspecies interactions can be extended by bacteria utilizing host cells or host diet to indirectly or directly influence the properties of other organisms and the community microenvironment. In contexts where communities transition to a dysbiotic state, their quasi-organismal nature imparts adaptability to nutritional availability and facilitates resistance to immune effectors and, moreover, exploits inflammatory and acidic microenvironments for their persistence.

Impact of breastfeeding and other early-life factors on the development of the oral microbiome

The oral cavity is home to the second most diverse microbiome in the human body. This community contributes to both oral and systemic health. Acquisition and development of the oral microbiome is a dynamic process that occurs over early life; however, data regarding longitudinal assembly of the infant oral microbiome is scarce. While numerous factors have been associated with the composition of the infant oral microbiome, early feeding practices (breastfeeding and the introduction of solids) appear to be the strongest determinants of the infant oral microbiome. In the present review, we draw together data on the maternal, infant, and environmental factors linked to the composition of the infant oral microbiome, with a focus on early nutrition. Given evidence that breastfeeding powerfully shapes the infant oral microbiome, the review explores potential mechanisms through which human milk components, including microbes, metabolites, oligosaccharides, and antimicrobial proteins, may interact with and shape the infant oral microbiome. Infancy is a unique period for the oral microbiome. By enhancing our understanding of oral microbiome assembly in early life, we may better support both oral and systemic health throughout the lifespan.

Microbial associations and transfers across the One Health Triad effects on human and animal adiposity and temperament: a protocol for an observational pilot study

Introduction

It is known that humans and pet dogs harbor microbial communities that are important regulators of health and disease. Pet dogs have been shown to promote microbial exchange between members of a household, a process that may have lasting health implications. Infancy marks a unique period of development as environmental exploration and introduction to complementary foods occur. This may lead to greater opportunities for microbial transfer between pet dogs and human infants due to a more confined shared environment, similar means of mobility, greater physical contact, and increased frequency of shared foods. This human-animal bond has led to extensive research in the areas of childhood allergies and behavioral health; however, there is a paucity in the available literature that has evaluated how this unique ecological relationship may impact both human and animal health.

Methods

Infants who reside in a household with a pet dog will be recruited from the greater Phoenix metropolitan area for this longitudinal, observational pilot study and followed through the complementary feeding period. Infant and pet dog fecal, salivary, and skin samples, as well as environmental samples from feeding areas/surfaces and main indoor play areas from both infants and pet dogs will be collected through in-home visits before (~5 mos), during (~9 mos), and after (~12 mos) the complementary feeding (CF) period. Anthropometrics, temperament, and dietary habits of both infants and pet dogs along with assessment of the home condition will also be collected. Microbial comparisons between infant and pet dog samples and evaluation of microbial changes during the CF period will be evaluated. Further, we will assess relationships between microbial composition and adiposity and temperament of both infants and pet dogs.

Discussion

The proposed observational pilot study will advance the available science by exploring how microbial communities are associated and change between infants and pet dogs before, during, and after the CF period, a unique period of human growth and development. Findings from this study will provide insights into the impact these ecological relationships have on each other and how transfer across the One Health Triad impacts human and animal health.

Oral microbial communities in children, caregivers, and associations with salivary biomeasures and environmental tobacco smoke exposure

Human oral microbial communities are diverse, with implications for oral and systemic health. Oral microbial communities change over time; thus, it is important to understand how healthy versus dysbiotic oral microbiomes differ, especially within and between families. There is also a need to understand how the oral microbiome composition is changed within an individual including by factors such as environmental tobacco smoke (ETS) exposure, metabolic regulation, inflammation, and antioxidant potential. Using archived saliva samples collected from caregivers and children during a 90-month follow-up assessment in a longitudinal study of child development in the context of rural poverty, we used 16S rRNA gene sequencing to determine the salivary microbiome. A total of 724 saliva samples were available, 448 of which were from caregiver/child dyads, an additional 70 from children and 206 from adults. We compared children's and caregivers' oral microbiomes, performed "stomatotype" analyses, and examined microbial relations with concentrations of salivary markers associated with ETS exposure, metabolic regulation, inflammation, and antioxidant potential (i.e., salivary cotinine, adiponectin, C-reactive protein, and uric acid) assayed from the same biospecimens. Our results indicate that children and caregivers share much of their oral microbiome diversity, but there are distinct differences. Microbiomes from intrafamily individuals are more similar than microbiomes from nonfamily individuals, with child/caregiver dyad explaining 52% of overall microbial variation. Notably, children harbor fewer potential pathogens than caregivers, and participants' microbiomes clustered into two groups, with major differences being driven by Streptococcus spp. Differences in salivary microbiome composition associated with ETS exposure, and taxa associated with salivary analytes representing potential associations between antioxidant potential, metabolic regulation, and the oral microbiome. IMPORTANCE The human oral cavity is a multi-environment habitat that harbors a diversity of microorganisms. This oral microbiome is often transmitted between cohabitating individuals, which may associate oral and systemic health within family members. Furthermore, family social ecology plays a significant role in childhood development, which may be associated with lifelong health outcomes. In this study, we collected saliva from children and their caregivers and used 16S rRNA gene sequencing to characterize their oral microbiomes. We also analyzed salivary biomeasures of environmental tobacco smoke exposure, metabolic regulation, inflammation, and antioxidant potential. We show there are differences in individuals' oral microbiomes mainly due to Streptococcus spp. that family members share much of their microbes, and several bacterial taxa associate with the selected salivary biomeasures. Our results suggest there are large-scale oral microbiome patterns, and there are likely relationships between oral microbiomes and the social ecology of families.

The Relationship between Age, Gender, BMI, Diet, Salivary pH and Periodontal Pathogenic Bacteria in Children and Adolescents: A Cross-Sectional Study

The oral microbiome can be influenced by many factors and its dysbiosis can have negative effects on oral and general health. The purpose of this study was to analyze the intensity of 11 periodontal pathogenic microorganisms identified in the oral cavity of a sample of children and adolescents from Oradea, Romania and to investigate the association of some variables (age, gender, body mass index, diet, and salivary pH) with the identified microorganisms. The cross-sectional study was conducted on a group of clinically healthy patients under the age of 18 years from Oradea, Romania. For the analysis of the periodontal pathogens, the micro-IDent kit was used, which determines 11 bacterial markers for periodontitis and peri-implantitis. The kit is based on the polymerase chain reaction (PCR). Bacterial sampling was carried out according to the manufacturer's instructions. A total of 60 children (23 male, 37 female) were included in this study, and were divided into three different age categories. No statistically significant results were identified for gender. However statistically significant results were obtained for other variables. Positive results for Prevotella intermedia and Bacteroides forsythus were associated with ages between 13 and 18 years, while positive results for Capnocytophaga spp. were associated with ages between 2 and 5 years. Positive results for Prevotella intermedia, Bacteroides forsythus, Peptostreptococcus micros, Campylobacter rectus and Eikenella corodens were associated with an overweight BMI. Negative results for Prevotella intermedia and Eikenella corodens were associated with a natural diet in the first 6 months of life. Positive results for Fusobacterium nucleatum and Campylobacter rectus were associated with an acidic salivary pH. In this study, the identified periodontal pathogens were associated with age, body mass index, diet in the first 6 months of life, and salivary pH.

Evaluating Alterations of the Oral Microbiome and Its Link to Oral Cancer among Betel Quid Chewers: Prospecting Reversal through Probiotic Intervention

Areca nut and slaked lime, with or without tobacco wrapped in Piper betle leaf, prepared as betel quid, is extensively consumed as a masticatory product in many countries across the world. Betel Quid can promote the malignant transformation of oral lesions as well as trigger benign cellular and molecular changes. In the oral cavity, it causes changes at the compositional level in oral microbiota called dysbiosis. This dysbiosis may play an important role in Oral Cancer in betel quid chewers. The abnormal presence and increase of bacteria Fusobacterium nucleatum, Capnocytophaga gingivalis, Prevotella melaninogenica, Peptostreptococcus sp., Porphyromonas gingivalis, and Streptococcus mitis in saliva and/or other oral sites of the cancer patients has attracted frequent attention for its association with oral cancer development. In the present review, the authors have analysed the literature reports to revisit the oncogenic potential of betel quid and oral microbiome alterations, evaluating the potential of oral microbiota both as a driver and biomarker of oral cancer. The authors have also shared a perspective that the restoration of local microbiota can become a potentially therapeutic or prophylactic strategy for the delay or reversal of lip and oral cavity cancers, especially in high-risk population groups.

Initial oral microbiota and the impact of delivery mode and feeding practices in 0 to 2 month-old infants

The aim of this study was to describe the initial oral microbiota and how delivery mode and feeding practices impact its diversity in 0-2-month-old infants. This was a cross-sectional study that consisted of one collection of saliva samples from 0-2-month infants at baseline. Ten pairs of mothers and infants were selected. Medical health history, pregnancy, birth, feeding practices (breastfeeding or milk formula), and infant health status was obtained. Pooled microbial samples were obtained from the oral surfaces using a sterile cotton swab. Infants did not receive any breast milk before sampling. After collection, each swab was analyzed through microbiological culture-based procedures, using selective mediums. Cultures were analyzed for the presence of Streptococci, Lactobacillus, Staphylococcus, Enterobacterium , and Candida albicans . Twenty percent of the samples were serially diluted (10-2) to assess the number of bacteria expressed as CFU. Bacillota was the leading phylogenetic group in the infant's pooled microbial sample. The most prevalent genera were Streptococcus, Lactobacillus , and Staphylococcus . Two participants had a positive growth of Candida albicans . The association between genus group, type of delivery, and feeding practices was not statistically significant (p > 0.05). Lactobacillus genus was frequently present in the cesarean delivery group but with slightly higher counts in a vaginal delivery study subject. Exclusively breastfed infants showed presence of Streptococcus, Lactobacillus, Staphylococcus . The oral microbiome in infants (0-2 month-old) is highly heterogeneous and dynamic. Microbiota composition seems to be impacted by mode of delivery, with slight differences among groups. Breastmilk appears as an essential factor in maintaining the oral microbiome's stability and diversity.

Parents with periodontitis drive the early acquisition of dysbiotic microbiomes in their offspring

AIM

To evaluate the microbial colonization in different dentition phases on individuals from 0 to 18 years of age belonging to families with a history of periodontitis compared to descendants of periodontally healthy parents.

MATERIALS AND METHODS

The offspring of subjects with periodontitis ('Perio' group) and the offspring of periodontally healthy subjects ('Healthy' group), matched for gender and age, were included in this cross-sectional study and divided according to the dentition phase: pre-dentate, primary, mixed and permanent. The patients were clinically assessed, and their saliva was collected. DNA was extracted, and V1-V3 and V4-V5 regions of the 16S rRNA gene were sequenced.

RESULTS

Fifty children of parents with periodontitis and 50 from healthy parents were included in the study and divided according to the dentition phase: pre-dentate (n = 5/group), primary dentition (n = 15/group), mixed dentition (n = 15/group) and permanent dentition (n = 15/group) in each group. The microbiome composition was different between dentitions for both groups. Children of the Perio group presented a microbial diversity different from that of the Healthy group in mixed and permanent dentitions. The more intense shift in the community occurred between primary and mixed dentition in the Perio group, while the transition between mixed and permanent dentition was the period with greater changes in the microbiome for the Healthy group. Furthermore, a pathogen-rich environment-higher prevalence and abundance of periodontitis-associated species such as Prevotella spp., Selenomonas spp., Leptotrichia spp., Filifactor alocis, Prevotella intermedia, Treponema denticola and Tannerella forsythia- was observed in the Perio group.

CONCLUSIONS

The parents' periodontal status significantly affects the microbiome composition of their offspring from an early age. The mixed dentition was the phase associated with establishing a dysbiotic and pathogen-rich microbiome in descendants of parents with periodontitis.

The microbiota of pregnant women with SARS-CoV-2 and their infants

BACKGROUND

Infants receive their first bacteria from their birthing parent. This newly acquired microbiome plays a pivotal role in developing a robust immune system, the cornerstone of long-term health.

RESULTS

We demonstrated that the gut, vaginal, and oral microbial diversity of pregnant women with SARS-CoV-2 infection is reduced, and women with early infections exhibit a different vaginal microbiota composition at the time of delivery compared to their healthy control counterparts. Accordingly, a low relative abundance of two Streptococcus sequence variants (SV) was predictive of infants born to pregnant women with SARS-CoV-2 infection.

CONCLUSIONS

Our data suggest that SARS-CoV-2 infections during pregnancy, particularly early infections, are associated with lasting changes in the microbiome of pregnant women, compromising the initial microbial seed of their infant. Our results highlight the importance of further exploring the impact of SARS-CoV-2 on the infant's microbiome-dependent immune programming. Video Abstract.

Discovery of phosphorylated lantibiotics with proimmune activity that regulate the oral microbiome

Lantibiotics are ribosomally synthesized and posttranslationally modified peptides (RiPPs) that are produced by bacteria. Interest in this group of natural products is increasing rapidly as alternatives to conventional antibiotics. Some human microbiome-derived commensals produce lantibiotics to impair pathogens' colonization and promote healthy microbiomes. Streptococcus salivarius is one of the first commensal microbes to colonize the human oral cavity and gastrointestinal tract, and its biosynthesis of RiPPs, called salivaricins, has been shown to inhibit the growth of oral pathogens. Herein, we report on a phosphorylated class of three related RiPPs, collectively referred to as salivaricin 10, that exhibit proimmune activity and targeted antimicrobial properties against known oral pathogens and multispecies biofilms. Strikingly, the immunomodulatory activities observed include upregulation of neutrophil-mediated phagocytosis, promotion of antiinflammatory M2 macrophage polarization, and stimulation of neutrophil chemotaxis-these activities have been attributed to the phosphorylation site identified on the N-terminal region of the peptides. Salivaricin 10 peptides were determined to be produced by S. salivarius strains found in healthy human subjects, and their dual bactericidal/antibiofilm and immunoregulatory activity may provide new means to effectively target infectious pathogens while maintaining important oral microbiota.

Development of the oral resistome during the first decade of life

Antibiotic overuse has promoted the spread of antimicrobial resistance (AMR) with significant health and economic consequences. Genome sequencing reveals the widespread presence of antimicrobial resistance genes (ARGs) in diverse microbial environments. Hence, surveillance of resistance reservoirs, like the rarely explored oral microbiome, is necessary to combat AMR. Here, we characterise the development of the paediatric oral resistome and investigate its role in dental caries in 221 twin children (124 females and 97 males) sampled at three time points over the first decade of life. From 530 oral metagenomes, we identify 309 ARGs, which significantly cluster by age, with host genetic effects detected from infancy onwards. Our results suggest potential mobilisation of ARGs increases with age as the AMR associated mobile genetic element, Tn916 transposase was co-located with more species and ARGs in older children. We find a depletion of ARGs and species in dental caries compared to health. This trend reverses in restored teeth. Here we show the paediatric oral resistome is an inherent and dynamic component of the oral microbiome, with a potential role in transmission of AMR and dysbiosis.

Tolerance to intraoral biofilms and their effectiveness in improving mouth dryness and modifying oral microbiota in patients with primary Sjögren's syndrome: "Predelfi study"

INTRODUCTION

Primary Sjögren's syndrome (pSS) is a systemic autoimmune disease characterized by exocrine gland dysfunction. No therapeutic strategy is sufficient on its own for the management of dry mouth and therapeutic innovations are required.

METHODS

This Predelfi study was a single-center, prospective, comparative, randomized, double-blind, cross-over controlled study with the primary objective of assessing the tolerance to and effectiveness of two adhesive biofilms (containing prebiotics and, sodium alginate, respectively) in patients with pSS and hyposialia (#NCT04206826 in ClinicalTrials.gov). Secondary objectives were to obtain initial data regarding the clinical effectiveness of such biofilms in the improvement of signs and symptoms related to dry mouth and potential changes in the oral microbiota. Ten pSS patients with pSS were included (9 females and 1 male) with a mean age of 58.1 ± 14.0 years.

RESULTS AND DISCUSSION

Tolerance to the prebiotic and sodium alginate biofilms was assessed by the patients (visual analog scale [VAS] score 66.7 and 87.6, respectively) and the practitioner (90 and 100, respectively). The absolute changes in the VAS scores at the start and end of each treatment period highlighted an improvement in mouth dryness for the sodium alginate versus the prebiotic biofilm. The VAS scores for other parameters (mouth burning sensation; taste alteration; chewing; swallowing and speech difficulties) remained globally comparable between the two groups. Unstimulated salivary flow showed no changes regardless of the biofilm used. Regarding the oral microbiota, the sodium alginate biofilm increased the abundance of the Treponema genus, whereas the use of the prebiotic biofilm as the first treatment increased the abundance of the genera Veillonella and Prevotella. Nevertheless, the prebiotic biofilm appeared to stimulate "milder" genera with regard to periodontal infections. Furthermore, pre-treatment with the prebiotic biofilm prevented the emergence of the Treponema genus induced by subsequent treatment with the sodium alginate biofilm, suggesting a potential protective effect.

Pseudomonadota in the oral cavity: a glimpse into the environment-human nexus

The phylum Pseudomonadota is amongst the most represented in the environment, with a comparatively lower prevalence in the human oral cavity. The ubiquity of Pseudomonadota and the fact that the oral cavity is the most likely entry portal of bacteria from external sources underlie the need to better understand its occurrence in the interface environment-humans. Yet, the relevance oral Pseudomonadota is largely underexplored in the scientific literature, a gap that this review aims at addressing by making, for the first time, an overview of the diversity and ecology of Pseudomonadota in the oral cavity. The screening of scientific literature and human microbiome databases unveiled 1328 reports of Pseudomonadota in the oral cavity. Most of these belonged to the classes Beta- and Gammaproteobacteria, mainly to the families Neisseriaceae, Campylobacteriaceae, and Pasteurelaceae. Others also regularly reported include genera such as Enterobacter, Klebsiella, Acinetobacter, Escherichia, Burkholderia, or Citrobacter, whose members have high potential to acquire virulence and antibiotic resistance genes. This review provides evidence that clinically relevant environmental Pseudomonadota may colonize humans via oral cavity. The need for further investigation about Pseudomonadota at the environment-oral cavity interface and their role as vectors potentially involved in virulence and antibiotic resistance transmission is demonstrated. KEY POINTS: • Neisseriaceae, Campylobacteriaceae, and Pasteurelaceae are part of the core oral microbiome • Enterobacteriaceae, Acinetobacter, or Burkholderia are frequent in the oral microbiome • Gut dysbiosis may be associated with colonization by ubiquitous oral Pseudomonadota.

Evaluating the ecological hypothesis: early life salivary microbiome assembly predicts dental caries in a longitudinal case-control study

BACKGROUND

Early childhood caries (ECC)-dental caries (cavities) occurring in primary teeth up to age 6 years-is a prevalent childhood oral disease with a microbial etiology. Streptococcus mutans was previously considered a primary cause, but recent research promotes the ecologic hypothesis, in which a dysbiosis in the oral microbial community leads to caries. In this incident, density sampled case-control study of 189 children followed from 2 months to 5 years, we use the salivary bacteriome to (1) prospectively test the ecological hypothesis of ECC in salivary bacteriome communities and (2) identify co-occurring salivary bacterial communities predicting future ECC.

RESULTS

Supervised classification of future ECC case status using salivary samples from age 12 months using bacteriome-wide data (AUC-ROC 0.78 95% CI (0.71-0.85)) predicts future ECC status before S. mutans can be detected. Dirichlet multinomial community state typing and co-occurrence network analysis identified similar robust and replicable groups of co-occurring taxa. Mean relative abundance of a Haemophilus parainfluenzae/Neisseria/Fusobacterium periodonticum group was lower in future ECC cases (0.14) than controls (0.23, P value < 0.001) in pre-incident visits, positively correlated with saliva pH (Pearson rho = 0.33, P value < 0.001) and reduced in individuals who had acquired S. mutans by the next study visit (0.13) versus those who did not (0.20, P value < 0.01). In a subset of whole genome shotgun sequenced samples (n = 30), case plaque had higher abundances of antibiotic production and resistance gene orthologs, including a major facilitator superfamily multidrug resistance transporter (MFS DHA2 family PBH value = 1.9 × 10-28), lantibiotic transport system permease protein (PBH value = 6.0 × 10-6) and bacitracin synthase I (PBH value = 5.6 × 10-6). The oxidative phosphorylation KEGG pathway was enriched in case plaque (PBH value = 1.2 × 10-8), while the ABC transporter pathway was depleted (PBH value = 3.6 × 10-3).

CONCLUSIONS

Early-life bacterial interactions predisposed children to ECC, supporting a time-dependent interpretation of the ecological hypothesis. Bacterial communities which assemble before 12 months of age can promote or inhibit an ecological succession to S. mutans dominance and cariogenesis. Intragenera competitions and intergenera cooperation between oral taxa may shape the emergence of these communities, providing points for preventive interventions. Video Abstract.

Microbiota of preterm infant develops over time along with the first teeth eruption

Objective

The temporal growth of the infant microbiome in the early years of life influences short- and long-term infant health. The aim of this longitudinal study was to investigate bacterial dynamics in the microbiome of preterm infants during tooth eruption.

Methods

Saliva samples from normally delivered (n = 24) and preterm infants (n = 31) were collected 30 days after birth and after the eruption of two primary mandibular incisors. Based on Illumina MiSeq Sequencing of the 16S rRNA gene, the dynamic microbial changes of newborns at two-time points were investigated. Meanwhile, the Human Oral Microbiome Database was adopted for assigning taxonomy.

Results

Using alpha and beta diversity analyses, different shift patterns of microbiome structures in preterm and healthy participants and bacterial diversity over time were observed. The relative abundance and shifts trend, along with the two lower primary central incisors eruption, of core oral flora varies in full-term and preterm groups, including Gemella spp., Rothia mucilaginosa, Veillonella atypica, etc. Several microorganisms colonize later in the oral microbiome development of premature babies, such as Gemella spp. In addition to teeth eruption, the growth of the saliva microbiome in preterm infants could be influenced by breastfeeding durations and birth weight.

Conclusion

This study provided insights into how the oral microbiota changes during tooth eruption in preterm infants and how the colonization of the oral cavity with bacteria in preterm infants differs significantly from that in full-term infants.

The dynamic communities of oral microbiome in neonates

The oral microbiome, associated with both oral disease and systemic disease, is in dynamic status along the whole life, and many factors including maternal microbiomes could impact the oral microbiome. While fewer studies have been conducted to study the characteristics of the oral microbiome in neonates and the associated maternal factors. Hence, we collected the microbiome of 15 mother-infant pairs across multiple body sites from birth up to 4 days postpartum and used high-throughput sequencing to characterize the microbiomes in mothers and their neonates. The oral microbiome in the neonates changed obviously during the 4 days after birth. Many bacteria originating from the vagina, skin, and environment disappeared in oral cavity over time, such as Prevotella bivia and Prevotella jejuni. Meanwhile, Staphylococcus epidermidis RP62A phage SP-beta, predominate bacterium in maternal skin microbiome and Streptococcus unclassified, main bacterium in vaginal microbiome, obviously increased in neonatal oral microbiome as time went on. Interestingly, as time progressed, the composition of the oral microbiome in the neonates was more similar to that of the milk microbiome in their mothers. Moreover, we found that the changes in the predominant bacteria in the neonates were in line with those in the neonates exposed to the environment. Together, these data described the sharp dynamics of the oral microbiome in neonates and the importance of maternal efforts in the development of the neonatal microbiome.

Comparative genomics of Rothia species reveals diversity in novel biosynthetic gene clusters and ecological adaptation to different eukaryotic hosts and host niches

Rothia species are understudied members of the phylum Actinobacteria and prevalent colonizers of the human and animal upper respiratory tract and oral cavity. The oral cavity, including the palatine tonsils, is colonized by a complex microbial community, which compete for resources, actively suppress competitors and influence host physiology. We analysed genomic data from 43 new porcine Rothia isolates, together with 112 publicly available draft genome sequences of Rothia isolates from humans, animals and the environment. In all Rothia genomes, we identified biosynthetic gene clusters predicted to produce antibiotic non-ribosomal peptides, iron scavenging siderophores and other secondary metabolites that modulate microbe-microbe and potentially microbe-host interactions. In vitro overlay inhibition assays corroborated the hypothesis that specific strains produce natural antibiotics. Rothia genomes encode a large number of carbohydrate-active enzymes (CAZy), with varying CAZy activities among the species found in different hosts, host niches and environments. These findings reveal competition mechanisms and metabolic specializations linked to ecological adaptation of Rothia species in different hosts.

Changes in Oral Microbial Diversity in a Piglet Model of Traumatic Brain Injury

Dynamic changes in the oral microbiome have gained attention due to their potential diagnostic role in neurological diseases such as Alzheimer's disease and Parkinson's disease. Traumatic brain injury (TBI) is a leading cause of death and disability in the United States, but no studies have examined the changes in oral microbiome during the acute stage of TBI using a clinically translational pig model. Crossbred piglets (4-5 weeks old, male) underwent either a controlled cortical impact (TBI, n = 6) or sham surgery (sham, n = 6). The oral microbiome parameters were quantified from the upper and lower gingiva, both buccal mucosa, and floor of the mouth pre-surgery and 1, 3, and 7 days post-surgery (PS) using the 16S rRNA gene. Faith's phylogenetic diversity was significantly lower in the TBI piglets at 7 days PS compared to those of sham, and beta diversity at 1, 3, and 7 days PS was significantly different between TBI and sham piglets. However, no significant changes in the taxonomic composition of the oral microbiome were observed following TBI compared to sham. Further studies are needed to investigate the potential diagnostic role of the oral microbiome during the chronic stage of TBI with a larger number of subjects.

A complete guide to human microbiomes: Body niches, transmission, development, dysbiosis, and restoration

Humans are supra-organisms co-evolved with microbial communities (Prokaryotic and Eukaryotic), named the microbiome. These microbiomes supply essential ecosystem services that play critical roles in human health. A loss of indigenous microbes through modern lifestyles leads to microbial extinctions, associated with many diseases and epidemics. This narrative review conforms a complete guide to the human holobiont-comprising the host and all its symbiont populations- summarizes the latest and most significant research findings in human microbiome. It pretends to be a comprehensive resource in the field, describing all human body niches and their dominant microbial taxa while discussing common perturbations on microbial homeostasis, impacts of urbanization and restoration and humanitarian efforts to preserve good microbes from extinction.

A Pilot Study on Donor Human Milk Microbiota: A Comparison with Preterm Human Milk Microbiota and the Effect of Pasteurization

Human milk (HM) is the best feeding option for preterm infants; however, when mother’s own milk (MOM) is not available, pasteurized donor human milk (DHM) is the best alternative. In this study, we profiled DHM microbiota (19 samples) using 16S rRNA amplicon sequencing and compared its compositional features with the MOM microbiota (14 samples) from mothers who delivered prematurely (PT-MOM). As a secondary study aim, we assessed the specific effect of pasteurization on the characteristics of the DHM microbiota. DHM showed significantly higher alpha diversity and significant segregation from PT-MOM. Compositionally, the PT-MOM microbiota had a significantly higher proportion of Staphylococcus than DHM, with Streptococcus tending to be and Pseudomonas being significantly overrepresented in DHM compared with the PT-MOM samples. Furthermore, pasteurization affected the HM microbiota structure, with a trend towards greater biodiversity and some compositional differences following pasteurization. This pilot study provided further evidence on the HM microbial ecosystem, demonstrating that the DHM microbiota differs from the PT-MOM microbiota, possibly due to inherent differences between HM donors and mothers delivering prematurely, and that pasteurization per se impacts the HM microbiota. Knowledge about HM microbiota needs to be acquired by investigating the effect of DHM processing to develop strategies aimed at improving DHM quality while guaranteeing its microbiological safety.

Neisseria genes required for persistence identified via in vivo screening of a transposon mutant library

The mechanisms used by human adapted commensal Neisseria to shape and maintain a niche in their host are poorly defined. These organisms are common members of the mucosal microbiota and share many putative host interaction factors with Neisseria meningitidis and Neisseria gonorrhoeae. Evaluating the role of these shared factors during host carriage may provide insight into bacterial mechanisms driving both commensalism and asymptomatic infection across the genus. We identified host interaction factors required for niche development and maintenance through in vivo screening of a transposon mutant library of Neisseria musculi, a commensal of wild-caught mice which persistently and asymptomatically colonizes the oral cavity and gut of CAST/EiJ and A/J mice. Approximately 500 candidate genes involved in long-term host interaction were identified. These included homologs of putative N. meningitidis and N. gonorrhoeae virulence factors which have been shown to modulate host interactions in vitro. Importantly, many candidate genes have no assigned function, illustrating how much remains to be learned about Neisseria persistence. Many genes of unknown function are conserved in human adapted Neisseria species; they are likely to provide a gateway for understanding the mechanisms allowing pathogenic and commensal Neisseria to establish and maintain a niche in their natural hosts. Validation of a subset of candidate genes confirmed a role for a polysaccharide capsule in N. musculi persistence but not colonization. Our findings highlight the potential utility of the Neisseria musculi-mouse model as a tool for studying the pathogenic Neisseria; our work represents a first step towards the identification of novel host interaction factors conserved across the genus.

The Neisseria genus contains many genetically related commensals of animals and humans, and two human pathogens, Neisseria gonorrhoeae and Neisseria meningitidis. The mechanisms allowing commensal Neisseria to maintain a niche in their host is little understood. To identify genes required for persistence, we screened a library of transposon mutants of Neisseria musculi, a commensal of wild-caught mice, in CAST/EiJ mice, which persistently and asymptomatically colonizes. Approximately 500 candidate host interaction genes were identified. A subset of these are homologs of N. meningitidis and N. gonorrhoeae genes known to modulate pathogen-host interactions in vitro. Many candidate genes have no known function, demonstrating how much remains to be learned about N. musculi niche maintenance. As many genes of unknown function are conserved in human adapted Neisseria, they provide a gateway for understanding Neisseria persistence mechanisms in general.

Study of oral microbiota diversity among groups of families originally from different countries

The diversity of oral microbiota is affected by diets habits, gender, age, ethnic group, and environment. The acquisition of oral microbiota and the role of family on oral microbiota development is poorly understood. This study aims to characterize and compare the oral bacterial microbiota among families using 16S rRNA gene sequencing. This work was conducted in Jeddah city from 2020 to 2021, in which four families composed of 20 members of different ethnicity and lifestyle were recruited. After the collection of saliva samples, the DNA was extracted and processed for 16S rRNA gene metagenomics sequencing. Among 378 OUTs generated, 39 (10.3%) were unique in group A, 13 (3.4%) unique in group B, and 11 (2.9%) were unique in groups C and D. We observed a significant variation at the level of top abundance phylum (14), families (23), genera (24), and species (22) of bacteria among family members. Within family groups, different bacterial species were reported to be more dominant among certain family members than the other; Prevotella melaninogenica, Prevotella histicola and Haemophilus parainfluenzae, Veillonella atypica, Porphyromonas pasteri and Haemophilus pittmaniae were more dominant in parents of some families than the other family member. In summary, this study highlights the precise and perceptible association of oral microbial between family members. Our findings documented the clustering of certain bacterial species in family groups, supporting the role of community in the development of oral microbiota.

Maturation of the oral microbiota during primary teeth eruption: a longitudinal, preliminary study

Introduction

Oral microbiota that established in the early years of life may influence the child’s oral health in the long term. Until now, no consensus is reached about whether the development of the oral microbiota is more related with age increase or more with teeth eruption.

Objective

To analyze the microbiota development of both saliva and supragingival plaque during the gradual eruption of primary teeth in caries-free infants and toddlers.

Methods

Saliva and plaque samples were collected at five and four dentition states, respectively, and were identified by bacterial 16S rRNA gene sequencing.

Results

During the longitudinal observation, the saliva ecosystem seemed more complex and dynamic than the plaque, with larger bacteria quantity and more significantly varied species over time. About 70% of the initial colonized OTUs in plaque persisted until the completion of the primary dentition. Transient bacteria were mostly detected in the early saliva and plaque microbiota, which came from the environment and other sites of the human body. Microbial diversity in both saliva and plaque varied greatly from pre-dentition to full eruption of eight anterior teeth, but not during the eruption of primary molars.

Conclusion

Oral bacterial development follows an ordered sequence during the primary teeth eruption. ‘Fully eruption of all primary anterior teeth’ is a critical stage in this process.

Exclusively Breastfed Infant Microbiota Develops over Time and Is Associated with Human Milk Oligosaccharide Intakes

Temporal development of maternal and infant microbiomes during early life impacts short- and long-term infant health. This study aimed to characterize bacterial dynamics within maternal faecal, human milk (HM), infant oral, and infant faecal samples during the exclusive breastfeeding period and to document associations between human milk oligosaccharide (HMO) intakes and infant oral and faecal bacterial profiles. Maternal and infant samples (n = 10) were collected at 2−5, 30, 60, 90 and 120 days postpartum and the full-length 16S ribosomal RNA (rRNA) gene was sequenced. Nineteen HMOs were quantitated using high-performance liquid chromatography. Bacterial profiles were unique to each sample type and changed significantly over time, with a large degree of intra- and inter-individual variation in all sample types. Beta diversity was stable over time within infant faecal, maternal faecal and HM samples, however, the infant oral microbiota at day 2−5 significantly differed from all other time points (all p < 0.02). HMO concentrations and intakes significantly differed over time, and HMO intakes showed differential associations with taxa observed in infant oral and faecal samples. The direct clinical relevance of this, however, is unknown. Regardless, future studies should account for intakes of HMOs when modelling the impact of HM on infant growth, as it may have implications for infant microbiota development.

High-Level Acquisition of Maternal Oral Bacteria in Formula-Fed Infant Oral Microbiota

The influx of maternal oral microbes is considered to play an important role in the acquisition and development of infant oral microbiota. In this study, we examined tongue swab samples from 448 mother-infant pairs at 4-month checkups. The bacterial composition of each sample was determined using PacBio single-molecule long-read sequencing of the full-length 16S rRNA gene and the amplicon sequence variant (ASV) approach. Although the infant oral microbiota was distinctly different from the mother oral microbiota, ASVs shared with their biological mother accounted for a median relative abundance of 9.7% (range of 0.0 to 99.3%), which was significantly higher than that of ASVs shared with unrelated mothers. This shared abundance was strongly associated with the feeding method of infants rather than their delivery mode or antibiotic exposure, and formula-fed infants had higher shared abundance than exclusively breastfed infants. Our study presents strain-level evidence for mother-to-infant transmission of oral bacteria and suggests that colonization of maternal oral bacteria is higher in formula-fed infants. IMPORTANCE Acquisition of oral bacteria during infancy can affect the subsequent formation of stable oral microbiota. This study focused on the mother-to-infant transmission of oral bacteria, a major acquisition route of infant oral microbiota, and demonstrated that most infants acquired oral bacteria from their biological mother even at the single-nucleotide level. Our results also indicated that the occupancies of maternal oral bacteria in infant oral microbiota were associated with the feeding methods of infants. These data could increase understanding of the early development of oral microbiota in infants and its potential associations with oral microbiota-related diseases.

Temporal development of the infant oral microbiome

The human oral microbiome is becoming recognized as playing roles in health and disease well beyond the oral cavity over the lifetime of the individual. The oral microbiome is hypothesized to result from specific colonization events followed by a reproducible and ordered development of complex bacterial communities. Colonization events, proliferation, succession and subsequent community development are dependent on a range of host and environmental factors, most notably the neonate diet. It is now becoming apparent that early childhood and prenatal influences can have long term effects on the development of human oral microbiomes. In this review, the temporal development of the infant human oral microbiome is examined, with the effects of prenatal and postnatal influences and the roles of specific bacteria. Dietary and environmental factors, especially breastfeeding, have a significant influence on the development of the infant oral microbiome. The evidence available regarding the roles and functions of early colonizing bacteria is still limited, and gaps in knowledge where further research is needed to elucidate these specific roles in relation to health and disease still exist.

Isolation and Identification of Potential Probiotic Bacteria from Human Milk

Breast milk was long considered a sterile environment, but now it is known to harbor many bacteria that will shape the newborn microbiota. The benefits of breastfeeding to newborn health are, on some level, related to the presence of beneficial bacteria in human milk. Therefore, this study aims to investigate and isolate potential probiotics present in human milk that might be associated with improved health in infants, being potential candidates to be used in simulated human milk formula. Milk samples of 24 healthy mothers were collected at three time points: 30 min (colostrum), 5-9 days (transitional milk), and 25-30 days (mature milk) postpartum. Samples were evaluated by culturing, and the isolated bacteria were identified by MALDI-TOF MS and 16S DNA sequencing. In vitro screening for probiotics properties was performed, and the potential probiotics were mono-associated with germ-free mice to evaluate their ability to colonize the gastrointestinal tract. The microorganisms were submitted to the spray-drying process to check their viability for a potential simulated milk formula production. Seventy-seven bacteria were isolated from breast milk pertaining to four bacterial genera (Staphylococcus, Streptococcus, Leuconostoc, and Lacticaseibacillus). Four potential probiotics were selected: Lacticaseibacillus rhamnosus (n = 2) and Leuconostoc mesenteroides (n = 2). Isolates were able to colonize the gastrointestinal tract of germ-free mice and remained viable after the spray-drying process. In conclusion, breast milk harbors a unique microbiota with beneficial microorganisms that will impact the newborn gut colonization, being an essential source of probiotic candidates to be used in a formula of simulated maternal milk.

The c-di-AMP signaling system influences stress tolerance and biofilm formation of Streptococcus mitis

Streptococcus mitis is a commensal bacterial species of the oral cavity, with the potential for opportunistic pathogenesis. For successful colonization, S. mitis must be able to adhere to surfaces of the oral cavity and survive and adapt to frequently changing environmental conditions. Cyclic-di-AMP (c-di-AMP) is a nucleotide second messenger, involved in the regulation of stress responses and biofilm formation in several bacterial species. Cyclic-di-AMP is produced by diadenylate cyclases and degraded by phosphodiesterases. We have previously shown that in S. mitis, one diadenylate cyclase (CdaA) and at least two phosphodiesterases (Pde1 and Pde2) regulate the intracellular concentration of c-di-AMP. In this study, we utilized S. mitis deletion mutants of cdaA, pde1, and pde2 to analyze the role of c-di-AMP signaling in various stress responses, biofilm formation, and adhesion to eukaryotic cells. Here, we demonstrate that the Δpde1 mutant displayed a tendency toward increased susceptibility to acetic acid at pH 4.0. Deletion of cdaA increases auto-aggregation of S. mitis but reduces biofilm formation on an abiotic surface. These phenotypes are more pronounced under acidic extracellular conditions. Inactivation of pde1 or pde2 reduced the tolerance to ciprofloxacin, and UV radiation and the Δpde1 mutant was more susceptible to Triton X-100, indicating a role for c-di-AMP signaling in responses to DNA damage and cell membrane perturbation. Finally, the Δpde2 mutant displayed a tendency toward a reduced ability to adhere to oral keratinocytes. Taken together, our results indicate an important role for c-di-AMP signaling in cellular processes important for colonization of the mouth.

In vitro models of gut digestion across childhood: current developments, challenges and future trends

The human digestion is a multi-step and multi-compartment process essential for human health, at the heart of many issues raised by academics, the medical world and industrials from the food, nutrition and pharma fields. In the first years of life, major dietary changes occur and are concomitant with an evolution of the whole child digestive tract anatomy and physiology, including colonization of gut microbiota. All these phenomena are influenced by child exposure to environmental compounds, such as drugs (especially antibiotics) and food pollutants, but also childhood infections. Due to obvious ethical, regulatory and technical limitations, in vivo approaches in animal and human are more and more restricted to favor complementary in vitro approaches. This review summarizes current knowledge on the evolution of child gut physiology from birth to 3 years old regarding physicochemical, mechanical and microbial parameters. Then, all the available in vitro models of the child digestive tract are described, ranging from the simplest static mono-compartmental systems to the most sophisticated dynamic and multi-compartmental models, and mimicking from the oral phase to the colon compartment. Lastly, we detail the main applications of child gut models in nutritional, pharmaceutical and microbiological studies and discuss the limitations and challenges facing this field of research.

How does the early life environment influence the oral microbiome and determine oral health outcomes in childhood?

The first 1000 days of life, from conception to 2 years, are a critical window for the influence of environmental exposures on the assembly of the oral microbiome, which is the precursor to dental caries (decay), one of the most prevalent microbially induced disorders worldwide. While it is known that the human microbiome is susceptible to environmental exposures, there is limited understanding of the impact of prenatal and early childhood exposures on the oral microbiome trajectory and oral health. A barrier has been the lack of technology to directly measure the foetal "exposome", which includes nutritional and toxic exposures crossing the placenta. Another barrier has been the lack of statistical methods to account for the high dimensional data generated by-omic assays. Through identifying which early life exposures influence the oral microbiome and modify oral health, these findings can be translated into interventions to reduce dental decay prevalence.

Maternal milk microbiota and oligosaccharides contribute to the infant gut microbiota assembly

Breastfeeding protects against diseases, with potential mechanisms driving this being human milk oligosaccharides (HMOs) and the seeding of milk-associated bacteria in the infant gut. In a cohort of 34 mother-infant dyads we analyzed the microbiota and HMO profiles in breast milk samples and infant's feces. The microbiota in foremilk and hindmilk samples of breast milk was compositionally similar, however hindmilk had higher bacterial load and absolute abundance of oral-associated bacteria, but a lower absolute abundance of skin-associated Staphylococcus spp. The microbial communities within both milk and infant's feces changed significantly over the lactation period. On average 33% and 23% of the bacterial taxa detected in infant's feces were shared with the corresponding mother's milk at 5 and 9 months of age, respectively, with Streptococcus, Veillonella and Bifidobacterium spp. among the most frequently shared. The predominant HMOs in feces associated with the infant's fecal microbiota, and the dominating infant species B. longum ssp. infantis and B. bifidum correlated inversely with HMOs. Our results show that breast milk microbiota changes over time and within a feeding session, likely due to transfer of infant oral bacteria during breastfeeding and suggest that milk-associated bacteria and HMOs direct the assembly of the infant gut microbiota.

Shaped by the epithelium - postnatal immune mechanisms of oral homeostasis

The first encounter of mucosal barriers with the microbiota initiates host-microbiota feedback loops instructing the tailored development of both the immune system and microbiota at each mucosal site. Once established, balanced immunological interactions enable symbiotic relationships with the microbiota in adult life. This process has been extensively investigated in the mammalian monolayer epithelium-covered intestine and lung mucosae; however, the postnatal mechanisms engaged by the oral mucosa to establish homeostasis are currently being discovered. Here, we discuss the early life dialogue between the oral mucosa and the microbiota, with particular emphasis on the central role the multilayer epithelium plays to protect the oral mucosa. These intricate and unique postnatal immunological processes shape oral homeostasis, which can potentially affect buccal and systemic health in adult life.

Multiple Brain Abscesses of Odontogenic Origin. May Oral Microbiota Affect Their Development? A Review of the Current Literature

In the last few years, the role of oral microbiota in the setting of oral diseases such as caries, periodontal disease, oral cancer and systemic infections, including rheumatoid arthritis, cardiovascular disease and brain abscess (BA), has attracted the attention of physicians and researchers. Approximately 5–7% of all BAs have an odontogenic origin, representing an important pathological systemic condition with a high morbidity and mortality. A systematic search of two databases (Pubmed and Ovid EMBASE) was performed for studies published up to 5 January 2021, reporting multiple BAs attributed to an odontogenic origin. According to PRISMA guidelines, we included a total of 16 papers reporting multiple BAs due to odontogenic infections. The aim of this review is to investigate the treatment modality and the clinical outcome of patients with multiple BAs due to odontogenic infections, as well as to identify the most common pathogens involved in this pathological status and their role, in the oral microbiota, in the onset of oral infections. A multidisciplinary approach is essential in the management of multiple BAs. Further studies are required to understand better the role of microbiota in the development of multiple BAs.

Developmental trajectory of the healthy human gut microbiota during the first 5 years of life

The gut is inhabited by a densely populated ecosystem, the gut microbiota, that is established at birth. However, the succession by which different bacteria are incorporated into the gut microbiota is still relatively unknown. Here, we analyze the microbiota from 471 Swedish children followed from birth to 5 years of age, collecting samples after 4 and 12 months and at 3 and 5 years of age as well as from their mothers at birth using 16S rRNA gene profiling. We also compare their microbiota to an adult Swedish population. Genera follow 4 different colonization patterns during establishment where Methanobrevibacter and Christensenellaceae colonize late and do not reached adult levels at 5 years. These late colonizers correlate with increased alpha diversity in both children and adults. By following the children through age-specific community types, we observe that children have individual dynamics in the gut microbiota development trajectory.

Salivary Microbiome Variation in Early Childhood Caries of Children 3-6 Years of Age and Its Association With Iron Deficiency Anemia and Extrinsic Black Stain

ECC is a common clinical manifestation of the oral cavity in childhood and Iron deficiency-anemia (IDA) is a high-risk factor but extrinsic black stain on the tooth surface is a protective factor for caries. There is limited information about oral microecological change in early children who suffer from ECC with IDA and extrinsic black stain (BS). This study enrolled 136 children aged 3-6 years. Dental caries and teeth BS were examined. Saliva was collected for 16S rRNA gene and fingertip blood were for Hemoglobin test. There are 93 ECC including 13 with IDA (IDA ECC) and 80 without IDA (NIDA ECC) and 43 caries free (CF) including 17 with BS (BSCF) and 26 without BS (NBS CF). Statistical analysis of microbiota data showed differences of the oral flora in different groups. The oral flora of the IDA ECC group had a high diversity, while the BSCF group had a low diversity. The bacterial genera Bacillus, Moraxella, and Rhodococcus were enriched in the IDA ECC while Neisseria was enriched in the NIDA ECC. Neisseria only exhibited high abundance in the BSCF, and the remaining genera exhibited high abundance in the NBSCF. Interestingly, the BSCF had the same trend as the NIDA ECC, and the opposite trend was observed with IDA ECC. We established random forest classifier using these biomarkers to predict disease outcomes. The random forest classifier achieved the best accuracy in predicting the outcome of caries, anemia and black stain using seven, one and eight biomarkers, respectively; and the accuracies of the classifiers were 93.35%, 94.62% and 95.23%, respectively. Our selected biomarkers can achieve good prediction, suggesting their potential clinical implications.

The Oral Microbiome in Periodontal Health

The estimation of oral microbiome (OM) taxonomic composition in periodontally healthy individuals can often be biased because the clinically periodontally healthy subjects for evaluation can already experience dysbiosis. Usually, they are included just based on the absence of clinical signs of periodontitis. Additionally, the age of subjects is used to be higher to correspond well with tested groups of patients with chronic periodontitis, a disorder typically associated with aging. However, the dysbiosis of the OM precedes the clinical signs of the disease by many months or even years. The absence of periodontal pockets thus does not necessarily mean also good periodontal health and the obtained image of "healthy OM" can be distorted.To overcome this bias, we taxonomically characterized the OM in almost a hundred young students of dentistry with precise oral hygiene and no signs of periodontal disease. We compared the results with the OM composition of older periodontally healthy individuals and also a group of patients with severe periodontitis (aggressive periodontitis according to former classification system). The clustering analysis revealed not only two compact clearly separated clusters corresponding to each state of health, but also a group of samples forming an overlap between both well-pronounced states. Additionally, in the cluster of periodontally healthy samples, few outliers with atypical OM and two major stomatotypes could be distinguished, differing in the prevalence and relative abundance of two main bacterial genera: Streptococcus and Veillonella. We hypothesize that the two stomatotypes could represent the microbial succession from periodontal health to starting dysbiosis. The old and young periodontally healthy subjects do not cluster separately but a trend of the OM in older subjects to periodontitis is visible. Several bacterial genera were identified to be typically more abundant in older periodontally healthy subjects.

Acquisition and establishment of the oral microbiota

Acquisition and establishment of the oral microbiota occur in a dynamic process over various stages and involve close and continuous interactions with the host and its environment. In the present review, we discuss the stages of this process in chronological order. We start with the prenatal period and address the following questions: ‘Is the fetus exposed to maternal microbiota during pregnancy?’ and ‘If so, what is the potential role of this exposure?’ We comment on recent reports of finding bacterial DNA in placenta during pregnancies, and provide current views on the potential functions of prenatal microbial encounters. Next, we discuss the physiological adaptations that take place in the newborn during the birth process and the effect of this phase of life on the acquisition of the oral microbiota. Is it really just exposure to maternal vaginal microbes that results in the difference between vaginally and Cesarian section‐born infants? Then, we review the postnatal phase, in which we focus on transmission of microbes, the intraoral niche specificity, the effects of the host behavior and environment, as well as the role of genetic background of the host on shaping the oral microbial ecosystem. We discuss the changes in oral microbiota during the transition from deciduous to permanent dentition and during puberty. We also address the finite knowledge on colonization of the oral cavity by microbes other than the bacterial component. Finally, we identify the main outstanding questions that limit our understanding of the acquisition and establishment of a healthy microbiome at an individual level.

Acquisition of oral microbiota is driven by environment, not host genetics

BACKGROUND

The oral microbiota is acquired very early, but the factors shaping its acquisition are not well understood. Previous studies comparing monozygotic (MZ) and dizygotic (DZ) twins have suggested that host genetics plays a role. However, all twins share an equal portion of their parent's genome, so this model is not informative for studying parent-to-child transmission. We used a novel study design that allowed us to directly examine the genetics of transmission by comparing the oral microbiota of biological versus adoptive mother-child dyads.

RESULTS

No difference was observed in how closely oral bacterial community profiles matched for adoptive versus biological mother-child pairs, indicating little if any effect of host genetics on the fidelity of transmission. Both adopted and biologic children more closely resembled their own mother as compared to unrelated women, supporting the role of contact and environment. Mother-child strain similarity increased with the age of the child, ruling out early effects of host genetic influence that are lost over time. No effect on the fidelity of mother-child strain sharing from vaginal birth or breast feeding was seen. Analysis of extended families showed that fathers and mothers were equally similar to their children, and that cohabitating couples showed even greater strain similarity than mother-child pairs. These findings support the role of contact and shared environment, and age, but not genetics, as determinants of microbial transmission, and were consistent at both species and strain level resolutions, and across multiple oral habitats. In addition, analysis of individual species all showed similar results.

CONCLUSIONS

The host is clearly active in shaping the composition of the oral microbiome, since only a few of the many bacterial species in the larger environment are capable of colonizing the human oral cavity. Our findings suggest that these host mechanisms are universally shared among humans, since no effect of genetic relatedness on fidelity of microbial transmission could be detected. Instead our findings point towards contact and shared environment being the driving factors of microbial transmission, with a unique combination of these factors ultimately shaping the highly personalized human oral microbiome. Video abstract.

A novel sialic acid-binding adhesin present in multiple species contributes to the pathogenesis of Infective endocarditis

Bacterial binding to platelets is a key step in the development of infective endocarditis (IE). Sialic acid, a common terminal carbohydrate on host glycans, is the major receptor for streptococci on platelets. So far, all defined interactions between streptococci and sialic acid on platelets are mediated by serine-rich repeat proteins (SRRPs). However, we identified Streptococcus oralis subsp. oralis IE-isolates that bind sialic acid but lack SRRPs. In addition to binding sialic acid, some SRRP^- isolates also bind the cryptic receptor β-1,4-linked galactose through a yet unknown mechanism. Using comparative genomics, we identified a novel sialic acid-binding adhesin, here named AsaA (associated with sialic acid adhesion A), present in IE-isolates lacking SRRPs. We demonstrated that S. oralis subsp. oralis AsaA is required for binding to platelets in a sialic acid-dependent manner. AsaA comprises a non-repeat region (NRR), consisting of a FIVAR/CBM and two Siglec-like and Unique domains, followed by 31 DUF1542 domains. When recombinantly expressed, Siglec-like and Unique domains competitively inhibited binding of S. oralis subsp. oralis and directly interacted with sialic acid on platelets. We further demonstrated that AsaA impacts the pathogenesis of S. oralis subsp. oralis in a rabbit model of IE. Additionally, we found AsaA orthologues in other IE-causing species and demonstrated that the NRR of AsaA from Gemella haemolysans blocked binding of S. oralis subsp. oralis, suggesting that AsaA contributes to the pathogenesis of multiple IE-causing species. Finally, our findings provide evidence that sialic acid is a key factor for bacterial-platelets interactions in a broader range of species than previously appreciated, highlighting its potential as a therapeutic target.

Infective endocarditis (IE) is typically a bacterial infection of the heart valves that causes high mortality. Infective endocarditis can affect people with preexisting lesions on their heart valves (Subacute IE). These lesions contain platelets and other host factors to which bacteria can bind. Growth of bacteria and accumulation of host factors results in heart failure. Therefore, the ability of bacteria to bind platelets is key to the development of IE. Here, we identified a novel bacterial protein, AsaA, which helps bacteria bind to platelets and contributes to the development of disease. Although this virulence factor was characterized in Streptococcus oralis, a leading cause of IE, we demonstrated that AsaA is also present in several other IE-causing bacterial species and is likely relevant to their ability to cause disease. We showed that AsaA binds to sialic acid, a terminal sugar present on platelets, thereby demonstrating that sialic acid serves as a receptor for a wider range of IE-causing bacteria than previously appreciated, highlighting its potential as a therapeutic target.