Early Colonization Patterns Research Articles

Oral Cavity Microbiome Impact on Respiratory Infections Among Children.

The respiratory system, traditionally considered antiseptic, harbors a diverse and dynamic bacterial microbiome. Recent advancements in microbiome research have revealed its significant influence on both innate and adaptive immunity, particularly in the context of respiratory infections in children. This article also provides an overview of the types of bacteria that commonly affect the respiratory system, including Streptococcus pneumoniae, Moraxella catarrhalis and Haemophilus influenzae. These bacteria are prevalent in pediatric populations and significantly contribute to the development and severity of respiratory tract infections (RTIs). This review aims to evaluate the impact of the oral cavity and upper respiratory microbiome on the susceptibility and severity of respiratory infections in pediatric populations. We specifically focus on how early colonization patterns of bacteria such as Moraxella and Streptococcus contribute to the development of respiratory tract infections in children from birth through adolescence. A thorough literature review was performed, focusing on studies publishing between 2004 and 2023. The review included research exploring the role of the upper respiratory microbiome in pediatric populations, with a specific focus on children aged birth to 18 years. Emphasis was placed on microbial characterization, the modulation of immune responses in respiratory tract infections, and the potential therapeutic applications of microbiome-targeted interventions. The findings suggest that the composition and disruption of the upper respiratory microbiome significantly influence clinical outcomes in children with respiratory infections. Notably, dysbiosis in the microbiome has been linked to increased susceptibility to repeated infections, highlighting the importance of maintaining microbial balance for optimal respiratory health. Understanding the impact of oral cavity and upper respiratory microbiome could lead to improved management and prevention strategies for respiratory infections in children. This review underscores the potential of microbiome modulation, including the use of probiotics as a therapeutic approach to enhance clinical outcomes in pediatric respiratory infections.

The contribution of the gut microbiome to neurodevelopment and neuropsychiatric disorders

Bidirectional communication between the gut and brain is well recognized, with data now accruing for a specific role of the gut microbiota in that link, referred to as the microbiome-gut-brain axis. This review will discuss the emerging role of the gut microbiota in brain development and behavior. Animal studies have clearly demonstrated effects of the gut microbiota on gene expression and neurochemical metabolism impacting behavior and performance. Based on these changes, a modulating role of the gut microbiota has been demonstrated for a variety of neuropsychiatric disorders, including depression, anxiety, and movement including Parkinson's, and importantly for the pediatric population autism. Critical developmental windows that influence early behavioral outcomes have been identified that include both the prenatal environment and early postnatal colonization periods. The clearest data regarding the role of the gut microbiota on neurodevelopment and psychiatric disorders is from animal studies; however, human data have begun to emerge, including an association between early colonization patterns and cognition. The importance of understanding the contribution of the gut microbiota to the development and functioning of the nervous system lies in the potential to intervene using novel microbial-based approaches to treating neurologic conditions. While pathways of communication between the gut and brain are well established, the gut microbiome is a new component of this axis. The way in which organisms that live in the gut influence the central nervous system (CNS) and host behavior is likely to be multifactorial in origin. This includes immunologic, endocrine, and metabolic mechanisms, all of which are pathways used for other microbial-host interactions. Germ-free (GF) mice are an important model system for understanding the impact of gut microbes on development and function of the nervous system. Alternative animal model systems have further clarified the role of the gut microbiota, including antibiotic treatment, fecal transplantation, and selective gut colonization with specific microbial organisms. Recently, researchers have started to examine the human host as well. This review will examine the components of the CNS potentially influenced by the gut microbiota, and the mechanisms mediating these effects. Links between gut microbial colonization patterns and host behavior relevant to a pediatric population will be examined, highlighting important developmental windows in utero or early in development.

Cesarean section changes neonatal gut colonization

Delivery by means of cesarean section has been associated with increased risk of childhood immune-mediated diseases, suggesting a role of early bacterial colonization patterns for immune maturation. We sought to describe the influence of delivery method on gut and airway colonization patterns in the first year of life in the Copenhagen Prospective Studies on Asthma in Childhood2010 (COPSAC2010) birth cohort. Seven hundred children from the COPSAC2010 birth cohort participated in this analysis. Fecal samples were collected at age 1week, 1month, and 1year, and hypopharyngeal aspirates were collected at age 1week, 1month, and 3months and cultured for bacteria. Detailed information on delivery method, intrapartum antibiotics, and lifestyle factors was obtained by personal interviews. Seventy-eight percent of the children were born by means of natural delivery, 12% by means of emergency cesarean section, and 9% by means of elective cesarean section. Birth by means of cesarean section was significantly associated with colonization of the intestinal tract by Citrobacter freundii, Clostridium species, Enterobacter cloacae, Enterococcus faecalis, Klebsiella oxytoca, Klebsiella pneumoniae, and Staphylococcus aureus at age 1week, whereas colonization by Escherichia coli was associated with natural birth. At age 1month, these differences were less prominent, and at age 1year, they were not apparent, which was confirmed by means of multivariate data-driven partial least squares analyses. The initial airway microbiota was unaffected by birth method. Delivery by means of cesarean section was associated with early colonization patterns of the neonatal gut but not of the airways. The differences normalized within the first year of life. We speculate that microbial derangements, as indicated in our study, can demonstrate a possible link between delivery by means of cesarean section and immune-mediated disease.

Spore Density Determines Infection Strategy by the Plant Pathogenic Fungus Plectosphaerella cucumerina.

Necrotrophic and biotrophic pathogens are resisted by different plant defenses. While necrotrophic pathogens are sensitive to jasmonic acid (JA)-dependent resistance, biotrophic pathogens are resisted by salicylic acid (SA)- and reactive oxygen species (ROS)-dependent resistance. Although many pathogens switch from biotrophy to necrotrophy during infection, little is known about the signals triggering this transition. This study is based on the observation that the early colonization pattern and symptom development by the ascomycete pathogen Plectosphaerella cucumerina (P. cucumerina) vary between inoculation methods. Using the Arabidopsis (Arabidopsis thaliana) defense response as a proxy for infection strategy, we examined whether P. cucumerina alternates between hemibiotrophic and necrotrophic lifestyles, depending on initial spore density and distribution on the leaf surface. Untargeted metabolome analysis revealed profound differences in metabolic defense signatures upon different inoculation methods. Quantification of JA and SA, marker gene expression, and cell death confirmed that infection from high spore densities activates JA-dependent defenses with excessive cell death, while infection from low spore densities induces SA-dependent defenses with lower levels of cell death. Phenotyping of Arabidopsis mutants in JA, SA, and ROS signaling confirmed that P. cucumerina is differentially resisted by JA- and SA/ROS-dependent defenses, depending on initial spore density and distribution on the leaf. Furthermore, in situ staining for early callose deposition at the infection sites revealed that necrotrophy by P. cucumerina is associated with elevated host defense. We conclude that P. cucumerina adapts to early-acting plant defenses by switching from a hemibiotrophic to a necrotrophic infection program, thereby gaining an advantage of immunity-related cell death in the host.

Driving Factors in the Colonization of Oceania: Developing Island-Level Statistical Models to Test Competing Hypotheses

Migration is a key driver of human cultural and genetic evolution, with recent theoretical advances calling for work to accurately identify factors behind early colonization patterns. However, inferring prehistoric migration strategies is a controversial field of inquiry that largely relies on interpreting settlement chronologies and constructing plausible narratives around environmental factors. Model selection approaches, along with new statistical models that match the dynamic nature of colonization, offers a more rigorous framework to test competing theories. We demonstrate the utility of this approach by developing an Island-Level Model of Colonization adapted from epidemiology in a Bayesian model-selection framework. Using model selection techniques, we assess competing colonization theories of Near and Remote Oceania, showing that models of exploration angles and risk performed considerably better than models using inter-island distance, suggesting early seafarers were already adept at long-distance travel. These results are robust after artificially increasing the uncertainty around settlement times. We show how decades of thinking on colonization strategies can be brought together and assessed in one statistical framework, providing us with greater interpretive power to understand a fundamental feature of our past.

Lichen colonization patterns show minor effects of dispersal distance at landscape scale

The role of dispersal in controlling the distribution of species at landscape scale (102–104 m) is still a matter of dispute. Here, we use the early colonization pattern of 23 epiphytic lichen species in a former tree‐less heathland landscape (170 km2) to test three hypotheses on how a landscape is colonized: A) mainly by long‐distance dispersal (LDD), B) by rare LDD events followed by limited local dispersal, and C) mainly by limited dispersal, resulting in a colonization front. The study system consisted of a chronosequence of 94 habitat patches constituting 0.4% of the landscape area, with a minimum inter‐site distance of 0.2 km. We used generalized linear mixed models with Bayesian inference to test predictions from the hypotheses. When age of sites and habitat area were accounted for, additional effects of geographical position of sites (distance from old sites, distance‐dependent relative propagule pressure, and distance from border of study area) on the probability of colonization by lichen species were small. Furthermore, species richness of sites did not depend on geographical position, either. Our results support a colonization process mainly governed by LDD at landscape scale, and that local stepwise colonization was not important. We argue that passively dispersed species with numerous small propagules tend to exhibit patchy populations with extensive dispersal at the landscape scale, rather than behaving like classical metapopulations.

Do early colonization patterns of periphytic ciliate fauna reveal environmental quality status in coastal waters?

The feasibility for developing a protocol to assess marine water quality based on early colonization features of periphytic ciliate fauna was studied in coastal waters of the Yellow Sea, northern China. The ciliate communities with 3-28-day ages were collected monthly at four stations with a spatial gradient of environmental stress from August 2011 to July 2012. The spatial patterns of both early (3-7 days) and mature (>10 days) communities of the ciliates represented significant differences among the four stations, and were significantly correlated with environmental variables, especially nutrients and chemical oxygen demand (COD). Seven and eight dominant species were significantly correlated with nutrients or COD within the early and mature communities, respectively. The species richness indices were strongly correlated with nutrients, especially in mature communities. These findings suggest that it is possible to assess the status of water quality using early colonization features of periphytic ciliate fauna in coastal waters.

Infant B cell memory and gut bacterial colonization

Under normal conditions, the gut microbiota confers health benefits for the host. The microbiota aids in the nutrient processing and contributes to the construction of the intestinal epithelial barrier. Furthermore, animal models demonstrate the importance of stimulation from gut bacteria for a proper maturation of the immune system. In this addendum, we summarize our recent study1 in which we demonstrate that colonization with Escherichia coli and bifidobacteria in the first 2 months of life was related to higher numbers of CD27-positive memory B cells later in infancy. The numbers of total B cells or CD5+CD20+ B cells, on the other hand, were not related to the bacterial colonization pattern. Thus, the gut microbiota might affect the B cell maturation also in humans, and our study indicates that an early colonization pattern that includes E. coli and bifidobacteria might promote this maturation early in life.

Bacterial colonization immediately after installation on oral titanium implants

Information on bacterial colonization immediately after dental implant insertion is limited. (1) To assess the early colonization on titanium implants immediately after placement and throughout the first 12 post-surgical weeks, (2) to compare the microbiota at interproximal subgingival implant and adjacent tooth sites. Subgingival plaque samples from implant and neighbouring teeth were studied by checkerboard DNA-DNA hybridization before surgery, 30 min after implant placement, and 1, 2, 4, 8, and 12 weeks after surgery. Comparing bacterial loads at implant sites between 30 min after placement with 1-week data showed that only the levels of Veillonella parvula (P<0.05) differed with higher loads at week 1 post-surgically. Week 12 data demonstrated significantly higher bacterial loads for 15/40 species at tooth sites compared with pre-surgery (P-values varying between 0.05 and 0.01). Between the period immediately after surgery and 12 weeks at implant sites, 29/40 species was more commonly found at 12 weeks. Included among these bacteria at implant sites were Porphyromonas gingivalis (P<0.05), Tannerella forsythia, (P<0.01), and Treponema denticola (P<0.001). Immediately post-surgery 5.9% of implants, and 26.2% of teeth, and at week 12, 15% of implants, and 39.1% of teeth harbored Staphylococcus aureus. Comparing tooth and implant sites, significantly higher bacterial loads were found at tooth sites for 27/40 species after 30 min following implant placement. This difference increased to 35/40 species at 12 weeks post-surgically. Bacterial colonization occurred within 30 min after implant placement. Early colonization patterns differed between implant and tooth surfaces.

Bacterial Colonization on Titanium, Hydroxyapatite, and Amalgam Surfaces in vivo

A study was conducted to evaluate qualitative and quantitative differences in bacterial colonization on titanium, hydroxyapatite, and amalgam surfaces in vivo. Six healthy adult individuals participated in the study. Two pieces each of titanium, hydroxyapatite, and amalgam of similar size were placed in cobalt-chromium splints and kept intra-orally in each individual for 10 min, and 1, 3, 6, 24, and 72 hrs. After removal of the splints, the pieces were rinsed in PBS and transferred to transport medium. After being vortexed, the samples were inoculated on selective and non-selective media for analyses of various facultative and anaerobic bacteria. During the experiment, total viable count increased on all surfaces. The investigated bacterial groups constituted, on average, approximately 60 to 99% of the total viable count on all three types of surfaces in each of the experiments, except in the 10-minute samples, when they constituted around 20 to 30%. Various streptococcal species predominated and usually constituted > 50% of total viable count. Similar colonization patterns of Streptococcus spp., Actinomyces naeslundii, Neisseria spp., Hemophilus parainfluenzae, Fusobacterium spp., and black-pigmented Prevotella spp. were seen at all three types of surfaces. No significant differences among the materials regarding colonization of investigated bacteria were found during the study period. This study failed to show any qualitative and quantitative differences in bacterial colonization among these materials. Titanium, hydroxyapatite, and amalgam do not seem to have a marked influence on the early colonization pattern in vivo.

Enhanced settlement on microtopographical high points by the intertidal red alga Halosaccion glandiforme

The early colonization patterns of the red alga Halosaccion glandiforme (Gmel.) were examined on artificial substrata cast from molds of both real (e.g. barnacles) and model surfaces with and without surface “roughness” at the scale of 100–1,200 µm. Settlement over a 3‐d period was always at least 35 times higher on rough substrata than on smooth substrata. This difference was due to the high (84–98%) settlement of spores on the tips of individual small‐scale surface projections (i.e. the roughness elements). An outplanting experiment suggested that the greater abundance of sporelings on the tips of surface projections resulted from settlement processes rather than differential postsettlement mortality. When sporeling densities were compared at larger spatial scales (e.g. areas near the base of the substrata vs. areas near the top), they varied greatly on smooth substrata, with highest densities found near surface transitions (e.g. corners and edges). On rough surfaces, the sporelings were more evenly distributed among the various areas. Thus, smaller scale features (i.e. 100–1,200 µm) of the surface appear to be more important than larger scale features (1–2 cm) in determining the settlement of H. glandiforme.

Early Colonization Patterns of Diatoms and Protozoa in Fourteen Fresh‐water Lakes1

ABSTRACT. Polyurethane substrates were anchored near the surface of 14 lakes in the northern tip of the lower peninsula of Michigan. I wo substrates were removed from each take and taken to the laboratory after 1, 3, 6, 15, and 21 days of exposure. At the laboratory, one substrate was used for determining the number of species of diatoms and the other for protozoa. A cluster analysis of the matrix of Jaccard's coefficients for all diatom samples from all lakes showed that virtually all samples from any given lake consistently clustered together. This indicates that, with respect to species occurrence, distinct and compositionally stable diatom assemblages formed on the substrates in fewer than 21 days. Analysis of all protozoan samples from all lakes did not show such clustering, however, and the correspondence of clusters for protozoan and diatom communities for the 14 lakes was not particularly good. This suggests that the link between the two groups at the species level is not particularly strong during the early phases of artificial substrate colonization.