Disease-associated Microorganisms Research Articles

Mechanical abrasion stimulation: Altered epidermal mucus composition and microbial community in grass carp (Ctenopharyngodon idella)

In modern high-density farming, seasonal change, fishing, transportation, and other conditions easily cause mechanical abrasion of fish skin. This leads to alterations in the material balance of the epidermal mucus composition of fish, preventing normal immune function. Subsequently, the risk of disease increases. In this study, grass carp (Ctenopharyngodon idella) was used as an object to investigate immune-related enzyme activities, structural characteristics, and physiological changes of its epidermal mucous cells caused by mechanical abrasion. Furthermore, we explored the changes in body surface mucus composition and microbial community diversity and structure. Our results showed that mechanical abrasion stimulation, significantly changed the activities of immune-related enzymes, such as lysozyme (LZM), alkaline phosphatase (AKP), and acid phosphatase (ACP) were within 24 h (P < 0.05). Their levels gradually recovered after 48 h. In contrast, no significant change was observed in superoxide dismutase (SOD) levels. The number of mucous cells increased, especially those of type I and type II mucous cells in the dorsal skin, which were significantly increased (P < 0.05). Meanwhile, the stimulation changed the metabolites composition of the fish epidermal mucus in the short term, upregulating 12-OPDA, indole, quinic acid and GSH, which are beneficial to antibacterial and anti-inflammatory, and downregulating L-saccharopine, L-2-aminoadipic acid, spermine, GSSG and ribose 5-phosphate, which disrupt protein synthesis, energy production and DNA synthesis. Additionally, these metabolite changes further affect the composition of microorganism communities, rising the abundance of certain disease-associated microorganisms, such as Acidovorax, Rhizobiaceae, Aurantimicrobium, and Leifsonia, which increases the risk of disease in fish. The findings of the present study provide a deeper understanding of the role of mucus as a component of the immune system in fish and provide a scientific basis for effective grass carp culture management and disease control.

Нутритивная поддержка у детей с внебольничными пневмониями

The nutritional status (NS) of a patient with an acute infectious disease often determines its course and prognosis. One of the factors involved in the formation and maintenance of NS is the state of the microbiome of various loci of the macroorganism. Such an integrated approach to the treatment of lower respiratory tract infections in pediatric practice has not been studied. Objective. Optimization of dietary therapy of children over 3 years old with out-of-hospital pneumonia based on the study of NS. Patients and methods. Eighty children (3–10 years old, 43 girls and 37 boys) hospitalized with out-of-hospital pneumonia of moderate severity in the children's infectious diseases department of the Khimki Regional Hospital were examined. The main group (40 children) received Resource® Clinutren® Junior product throughout hospitalization, the comparison group (40 children) received a standard diet. Additionally, the physical development of patients was assessed using the World Health Organization AnthroPlus program, Nutrishional Risk Screening (NRI). Bioimpedanceometry was performed daily (active cell mass (ACM) and fat mass were determined). The gut microbiome was examined by 16S genome sequencing before and after antibiotic therapy. Results. Protein metabolism disorders were recorded in 88.7% of children with out-of-hospital pneumonia in the acute febrile period according to bioimpedanceometry. By the time of discharge in children who received general-age nutrition, the decrease of ACM index remained in 57% of cases (23/40 of the comparison group). The use of Resource® Clinutren® Junior in children in the acute febrile period leads to the recovery of ACM already on the second day from the beginning of diet therapy. From the second day of observation, reliable differences between the number of children with normalization of temperature and appetite in the main group and the comparison group (57.5% &amp; 25%, p &lt; 0.01) were registered. Normalization of temperature was achieved in all children of the main group by the 4th day of hospitalization, in all children of the comparison group – by the 5th day. Normalization of appetite by the time of discharge was achieved in all patients of the main group and in 97.5% of patients of the comparison group. The duration of productive cough in the main group was shorter than in the experimental group (Me in the main group was 3 (IQR 2–4) days, in the comparison group – 4 (IQR 3–5.25) days. In the main group of patients who took specialized nutrition Resource® Clinutren® Junior, we observed a rarer development of antibiotic-associated syndrome (ASS) symptoms (45% &amp; 55%) and rapid relief of its manifestations (reduction of abdominal bloating in 47.5% of patients, reduction of diarrheal syndrome in 70% of cases). Analysis of 16S sequencing data demonstrated a more rapid recovery of beta diversity by reducing the proportion of diseaseassociated microorganisms. Conclusions. Connection of Resource® Clinutren® Junior product in the acute febrile period of out-of-hospital pneumonia in children 3 years and older from the first days of the disease leads to faster relief of the main symptoms of the disease, prevents the development of AAS due to normalization of protein metabolism indicators and restoration of intestinal microbiome. Key words: Resource® Clinutren® Junior, nutritional status, nutritional deficiency, nutritional support, bioimpedanceometry

Whole-Genome Sequencing of Lactobacillus johnsonii MT4, a Novel Strain Isolated from the Oral Cavity of C57BL/6 Mice

Lactobacillus johnsonii strain MT4, isolated from the oral cavity of C57BL/6 mice, elicits antimicrobial activity against disease-associated microorganisms. Short-read sequencing of the whole genome revealed a single genome of 1,883,026 bp, with a GC content of 34.4%, and no plasmids.

The Efficiency of Photodynamic Therapy in the Bacterial Decontamination of Periodontal Pockets and Its Impact on the Patient.

Research in the field of periodontal disease continues to focus on disease-associated microorganisms, as the microbial plaque and the host immune responses are considered to be important causative factors, that are highly responsible for the progression of this disease. The purpose of this article is to compare the reduction in the number of specific periodontopathogens in two test groups according to different therapeutic approaches in periodontal disease and to show possible differences. This article is based on a prospective clinical study involving eighteen subjects with forty-four average periodontal pockets assigned to study groups treated by two different methods, SRP and SRP followed by a single PDT application. Efficiency in removing specific bacterial species was evaluated by PCR testing, at baseline and immediately after treatment. The hypothesis that using SRP + aPDT results in an increased decontamination potential was confirmed statistically, when all five specific bacterial pathogens were investigated together. When the pathogens were considered separately, two of the five microorganisms tested were significantly lower in the SRP + PDT group (p &lt; 0.00), and important germ counts reductions were also observed for the other three. There is also a statistically significant relation between the pain at 48 h postoperatively and the type of treatment the patients received, as resulted from the Questionnaire Form. Our results demonstrate that aPDT, as an adjunctive treatment to conservative mechanical cleaning of root surfaces at sites affected by periodontitis, represents an effective tool in terms of reducing specific periodontopathogen germs.

A CRISPR/Cas12a-based photothermal platform for the portable detection of citrus-associated Alternaria genes using a thermometer

The outbreak of citrus brown spot because of Alternaria is one of the most destructive citrus diseases. Additionally, Alternaria species produce highly toxic mycotoxins. Mass screening is a valid method to control the spread of Alternaria. Morphological analysis and polymerase chain reaction combined with gene-sequencing technique are the most commonly used techniques for detecting Alternaria. However, they are limited by either low convenience and accuracy or low instrument accessibility and high cost. To balance the convenience, accuracy, test availability, and low cost, we develop a CRISPR/Cas12a-based photothermal platform for the portable detection of Alternaria genes using a thermometer. Using this platform, the Alternaria genes from the synthetic sequences and cultured fungus of citrus, tomato, and apple can be detected using a thermometer with a detection limit of 1.5 pM. With the aid of the CRISPR/Cas12a system, citrus-associated Alternaria can be specifically differentiated from other citrus disease-associated microorganisms. When the photothermal platform is applied to analyze the citrus fruit samples collected in the field, good-consistency results are obtained with the gene-sequencing technology. The excellent performance of this portable method shows that it can be applied to screen for Alternaria in resource-poor settings.

Fecal bacterial communities of wild black capuchin monkeys (Sapajus nigritus) from the Atlantic Forest biome in Southern Brazil are divergent from those of other non-human primates.

Gut microbiota are influenced by factors such as diet, habitat, and social contact, which directly affect the host's health. Studies related to gut microbiota in non-human primates are increasing worldwide. However, little remains known about the gut bacterial composition in wild Brazilian monkeys. Therefore, we studied the fecal microbiota composition of wild black capuchin monkey (Sapajus nigritus) (n=10) populations from two different Atlantic Forest biome fragments (five individuals per fragment) in south Brazil. The bacterial community was identified via the high-throughput sequencing and partial amplification of the 16S rRNA gene (V4 region) using an Ion Personal Genome Machine (PGMTM) System. In contrast to other studies involving monkey microbiota, which have generally reported the phyla Firmicutes and Bacteroidetes as predominant, black capuchin monkeys showed a high relative abundance of Proteobacteria ( = 80.54%), followed by Firmicutes ( = 12.14%), Actinobacteria ( = 4.60%), and Bacteriodetes ( = 1.31%). This observed particularity may have been influenced by anthropogenic actions related to the wild habitat and/or diet specific to the Brazilian biome's characteristics and/or monkey foraging behavior. Comparisons of species richness (Chao1) and diversity indices (Simpson and InvSimpson) showed no significant differences between the two groups of monkeys. Interestingly, PICRUSt2 analysis revealed that metabolic pathways present in the bacterial communities were associated with xenobiotic biodegradation and the biosynthesis of secondary metabolites, which may suggest positive effects on monkey health and conservation in this anthropogenic habitat. Infectious disease-associated microorganisms were also observed in the samples. The present study provides information about the bacterial population and metabolic functions present in fecal microbiota, which may contribute to a better understanding of the ecology and biology of black capuchin monkeys living in forest fragments within the Atlantic Forest biome in southern Brazil. Additionally, the present study demonstrates that the fecal bacterial communities of wild black capuchin monkeys in this area are divergent from those of other wild non-human primates.

Dendrobium officinale Kimura et Migo and American ginseng mixture: A Chinese herbal formulation for gut microbiota modulation.

Dendrobium officinale Kimura et Migo (D. officinale) is a famous traditional Chinese medicine (TCM). A mixture of D. officinale and American ginseng has been shown to enhance cell-mediated immunity, humoral immunity, and monocyte/macrophage functions in mice. Here, the effects of a D. officinale and American ginseng mixture on the structure of gut microbial community in dogs were examined using high-throughput 16S rRNA gene amplicon sequencing. The data revealed that while the mixture did not change the diversity of gut microbial community significantly, differences among individuals were significantly reduced. Furthermore, the mixture-responsive operational taxonomic units (OTUs) exhibited a phase-dependent expression pattern. Fifty-five OTUs were found to exhibit a mixture-induced expression pattern, among which one third were short-chain fatty acid (SCFA)-producing genera and the others were probiotic genera included Lactobacillus spp., Sutterella, Alistipes, Anaerovorax, Bilophila, Coprococcus, Gordonibacter, Oscillibacter, among others. By contrast, 36% of the OTUs exhibiting a mixture-repressed expression pattern were disease-associated microorganisms, and six genera, namely Actinomyces, Escherichia/Shigella, Fusobacterium, Slackia, Streptococcus and Solobacterium, were associated with cancer. In addition, five genera were closely associated with diabetes, namely Collinsella, Rothia, Howardella, Slackia and Intestinibacter. Our results indicate that this D. officinale and American ginseng mixture may be used as a prebiotic agent to enhance SCFA-producing genera and prevent gut dysbiosis.

The balance of metagenomic elements shapes the skin microbiome in acne and health.

Studies have emphasized the importance of disease-associated microorganisms in perturbed communities, however, the protective roles of commensals are largely under recognized and poorly understood. Using acne as a model disease, we investigated the determinants of the overall virulence property of the skin microbiota when disease- and health-associated organisms coexist in the community. By ultra-deep metagenomic shotgun sequencing, we revealed higher relative abundances of propionibacteria and Propionibacterium acnes phage in healthy skin. In acne patients, the microbiome composition at the species level and at P. acnes strain level was more diverse than in healthy individuals, with enriched virulence-associated factors and reduced abundance of metabolic synthesis genes. Based on the abundance profiles of the metagenomic elements, we constructed a quantitative prediction model, which classified the clinical states of the host skin with high accuracy in both our study cohort (85%) and an independent sample set (86%). Our results suggest that the balance between metagenomic elements, not the mere presence of disease-associated strains, shapes the overall virulence property of the skin microbiota. This study provides new insights into the microbial mechanism of acne pathogenesis and suggests probiotic and phage therapies as potential acne treatments to modulate the skin microbiota and to maintain skin health.

Metagenomic analysis reveals presence of Treponema denticola in a tissue biopsy of the Iceman.

Ancient hominoid genome studies can be regarded by definition as metagenomic analyses since they represent a mixture of both hominoid and microbial sequences in an environment. Here, we report the molecular detection of the oral spirochete Treponema denticola in ancient human tissue biopsies of the Iceman, a 5,300-year-old Copper Age natural ice mummy. Initially, the metagenomic data of the Iceman’s genomic survey was screened for bacterial ribosomal RNA (rRNA) specific reads. Through ranking the reads by abundance a relatively high number of rRNA reads most similar to T. denticola was detected. Mapping of the metagenome sequences against the T. denticola genome revealed additional reads most similar to this opportunistic pathogen. The DNA damage pattern of specifically mapped reads suggests an ancient origin of these sequences. The haematogenous spread of bacteria of the oral microbiome often reported in the recent literature could already explain the presence of metagenomic reads specific for T. denticola in the Iceman’s bone biopsy. We extended, however, our survey to an Iceman gingival tissue sample and a mouth swab sample and could thereby detect T. denticola and Porphyrimonas gingivalis, another important member of the human commensal oral microflora. Taken together, this study clearly underlines the opportunity to detect disease-associated microorganisms when applying metagenomics- enabled approaches on datasets of ancient human remains.

Periodontal disease-associated micro-organisms in peri-menopausal and post-menopausal women using or not using hormone replacement therapy. A two-year follow-up study

BackgroundDespite conflicting results on the use of hormone replacement therapy (HRT) there is no doubt that many women benefit from it. Women using HRT are known to be more health conscious in general with putative positive implications in the mouth. However, we observed recently in our cohort hardly any difference in oral health status between HRT-users and non-users. There are only a few studies about HRT and oral microbiota. We hypothesized that counts of periodontal micro-organisms are lower in health-conscious HRT-users than non-users.MethodsTwo-year open follow-up study was conducted on originally 200 HRT-users and 200 non-users from age cohorts of 50-58 years. After clinical examination pooled subgingival plaque samples were taken for polymerase chain reaction analyses. The results of finally 135 women meeting the inclusion criteria were analyzed with cross-tabulation and chi-square test. Explanatory factors were studied by step-wise logistic regression analysis.ResultsIn HRT group, the numbers of positive samples for Porphyromonas gingivalis (P. gingivalis, p < 0.07), Prevotella intermedia (P. intermedia, p < 0.05)and Tannerella forsythia (T. forsythia, p < 0.01) decreased in women with ≥ 4-mm-deep pockets. Respectively in HRT users with ≥ 6-mm-deep pockets the numbers of positive samples for P. gingivalis (p < 0.05) and T. forsythia (p < 0.01) were decreased. No corresponding differences were observed in the non-HRT group. In logistic regression, the existence of deep periodontal pockets explained the majority of cases harboring specific micro-organisms in both groups.ConclusionAlthough use of HRT did not correlate with periodontal health status, HRT led to decreasing numbers of positive samples of the periodontal pathogens P. gingivalis and T. forsythia. Further studies with longer observation time are needed to observe the clinical relevance of the results.

Some disease-associated microorganisms on plants in Irian Jaya, Indonesia

A checklist is given of the fungi, bacteria, viruses and algae recorded on diseased plants in Irian Jaya during surveys in 1992 and 1993

Some Disease-Associated Microorganisms on Plants in the Western Province of Papua New Guinea.

Fungi and some other microorganisms that cause plant disease or are associated with diseases of plants in the Western Province of Papua New Guinea are listed. Eight are new records for Papua New Guinea. Severity of some of the important diseases is discussed.

Repeated subgingival oxygen irrigations in untreated periodontal patients

The aim of this study was to assess the effect of repeated subgingival oxygen irrigations in previously untreated deep periodontal pockets. 112 pockets > or = 4 mm were selected in 14 subjects. Probing attachment level and bleeding on probing were recorded, as well as the presence of disease-associated micro-organisms within the pocket. Subsequently, the pockets were irrigated with gaseous oxygen 1 x a week during a continuous 8-week period. Irrigations with nitrogen served as control. The re-evaluation of all clinical and microbiological parameters at the end of study revealed that repeated oxygen insufflations resulted in a significant clinical improvement of the periodontal baseline conditions superior to the one found in the control.

Some Disease-Associated Microorganisms on Plants of Cape York Peninsula and Torres Strait Islands.

Fungi and some other micro-organisms that cause plant disease or are associated with diseased plants on Cape York Peninsula and Torres Strait islands are listed.

Subgingival irrigation in the maintenance phase of periodontal therapy

Abstract The purpose of this study was to evaluate the effect of subgingival scaling versus subgingival pocket irrigation with 0.1% chlorhexidine or saline controls on the repopulation of subgingival periodontal sites with disease-associated micro-organisms following a single procedure of scaling and root planing. Additionally, pertinent clinical parameters (attachment level, plaque index, bleeding on probing) were also recorded. 375 sites in 30 individuals with previously untreated periodontal disease were thoroughly scaled and subsequently either rescaled, irrigated, or not treated at all for the following 6 months at 1-month intervals. The results show that the initial scaling and root planing procedure led to significant clinical and microbiological improvements in all experimental groups. These improvements were maintained in all but the untreated sites. Based on the observed clinical and microbiological changes, subgingival irrigation of periodontal pockets at 1-month intervals was equally effective as scaling and root planing performed at the same pace. 0.1% chlorhexidine however, being used as test irrigant, was not more effective than saline controls.

Subgingival irrigation in the maintenance phase of periodontal therapy

Abstract The purpose of this study was to evaluate the effect of subgingival scaling versus subgingival pocket irrigation with 0.1% chlorhexidine or saline controls on the repopulation of subgingival periodontal sites with disease-associated micro-organisms following a single procedure of scaling and root planing. Additionally, pertinent clinical parameters (attachment level, plaque index, bleeding on probing) were also recorded. 375 sites in 30 individuals with previously untreated periodontal disease were thoroughly scaled and subsequently either rescaled, irrigated, or not treated at all for the following 6 months at 1-month intervals. The results show that the initial scaling and root planing procedure led to significant clinical and microbiological improvements in all experimental groups. These improvements were maintained in all but the untreated sites. Based on the observed clinical and microbiological changes, subgingival irrigation of periodontal pockets at 1-month intervals was equally effective as scaling and root planing performed at the same pace. 0.1% chlorhexidine however, being used as test irrigant, was not more effective than saline controls.

Subgingival irrigation in the maintenance phase of periodontal therapy

The purpose of this study was to evaluate the effect of subgingival scaling versus subgingival pocket irrigation with 0.1% chlorhexidine or saline controls on the repopulation of subgingival periodontal sites with disease-associated micro-organisms following a single procedure of scaling and root planing. Additionally, pertinent clinical parameters (attachment level, plaque index, bleeding on probing) were also recorded. 375 sites in 30 individuals with previously untreated periodontal disease were thoroughly scaled and subsequently either rescaled, irrigated, or not treated at all for the following 6 months at 1-month intervals. The results show that the initial scaling and root planing procedure led to significant clinical and microbiological improvements in all experimental groups. These improvements were maintained in all but the untreated sites. Based on the observed clinical and microbiological changes, subgingival irrigation of periodontal pockets at 1-month intervals was equally effective as scaling and root planing performed at the same pace. 0.1% chlorhexidine however, being used as test irrigant, was not more effective than saline controls.

Humoral immune response to selected subgingival plaque microorganisms in insulin-dependent diabetic children.

Juvenile diabetics have been shown to have an increased susceptibility to gingivitis and periodontitis following puberty. However, little data are available on changes in the microbial flora that occur at the onset of puberty. This study was performed to determine if antibacterial antibody titers to selected periodontal disease-associated microorganisms might be helpful in revealing changes in plaque flora at the onset and conclusion of puberty. Sera was obtained from 35 subjects (ages 7 to 18 years) selected from a population of insulin-dependent diabetics. The subjects were given a thorough medical examination which included an assessment of sexual maturation and a dental examination which included the recording of onset and magnitude of bleeding according to the papillary bleeding score. Antibody titers to A. naeslundii (AN), B. intermedius (BI), B. gingivalis (BG), F. nucleatum (FN), A. actinomycetemcomitans (AA), C. ochracea (CO) and T. denticola (TD) were determined using the microELISA. Stratification of antibody titers by age groups (less than or equal to 12 years, 12 to 15 years, greater than 15 years) revealed that titers to AN increased significantly (P less than 0.025, ANOVA) and progressively (P less than 0.05, regression analysis) with increasing age. In contrast, the titers to FN were maximal in the under 12 year group and decreased with age (ANOVA, P less than 0.05; regression analysis, P less than 0.05). There were no significant variations in titers observed for the other microorganisms. Stratification by sexual maturity revealed a similar progressive decrease of the titer to FN (ANOVA, P less than 0.05; regression analysis, P less than 0.005).(ABSTRACT TRUNCATED AT 250 WORDS)

The effects of periodontal therapy on serum antibody (IgG) levels to plaque microorganisms.

The influence of periodontal therapy on serum antibody titers to selected periodontal disease-associated microorganisms was assessed in 23 patients having chronic inflammatory periodontal disease (CIPD). The immunoglobulin G (IgG) titers were determined by the microELISA technique in serum samples obtained prior to treatment; following a hygienic phase which included scaling, root planing, and oral hygiene instruction; following surgical treatment; and one year and two years following hygienic phase (maintenance phase). Considerable individual variability existed in the magnitude of immune response to specific bacterial preparations. Significant reductions in the mean antibody titers were seen to A. viscosus, S. sanguis, F. nucleatum, S. sputigena, B. gingivalis, B. intermedius, B. melaninogenicus, T. vincentii, and T. denticola by the end of the second year of maintenance. There was no consistent response to Capnocytophaga. When individual patient responses were examined, 6 of the 23 were found to have elevated titers to at least one of the microorganisms in the interval between pretreatment and the end of the hygienic phase; however, in all but one case, the titers at the end of the second year of maintenance were below pretreatment levels. Antibody levels to bacteria such as S. sanguis were modified during therapy. This would indicate that immune responses to microbes not generally considered to be "periodontal pathogens" may be modified by adjuvant activity associated with subgingival plaque or changes in the environment of the sulcus and that subsequent changes in titer do not necessarily reflect a role of that microorganism in the disease process.

Local Antibody Responses in Periodontal Diseases.

The relationship between local and systemic host antibody responses, colonization of subgingival plaque by periodontal disease-associated microorganisms and the progression of periodontal disease was assessed in 61 patients. Serum antibody levels to a battery of oral microorganisms were determined by an enzyme-linked immunosorbent assay (ELISA), and an organism to which each patient exhibited a significantly elevated IgG response was chosen for further study. To detect the presence of the specific microorganism, plaque samples were obtained and examined using a seroELISA. Static crevicular fluid (SCF) samples were also obtained from all teeth and analyzed for IgG antibody to the homologous organism. A modification of the standard ELISA using biotin and avidin allowed a 5- to 10-fold increase in sensitivity for detection of IgG antibody in serum and SCF. Comparison of the distribution of elevated SCF antibody and the presence of the corresponding microorganism in each patient showed that the proportion of agreement was 54 to 78% in the samples. Schematic representation of the temporal relationship between the organism, the host response and disease activity were prepared to explain the results obtained in investigations of these parameters and to provide a testable hypothetical framework for future studies.