The fecal microbiota of piglets during weaning transition and its association with piglet growth across various farm environments

This study describes the fecal microbiota from piglets reared in different living environments during the weaning transition, and presents the characteristics of microbiota associated with good growth of piglets after weaning. Fecal samples were collected pre- (d26) and post-weaning (d35) from 288 male piglets in 16 conventional indoor commercial farms located in the West of France. The changes one week after weaning on the most abundant microbial families was roughly the same in all farms: alpha diversity increased, the relative abundance of Bacteroidaceae (-61%), Christensenellaceae (-35%), Enterobacteriaceae (-42%), and Clostridiaceae (-32%) decreased, while the relative abundance of Prevotellaceae (+143%) and Lachnospiraceae (+21%) increased. Among all the collected samples, four enterotypes that were ubiquitous in all farms were identified. They could be discriminated by their respective relative abundances of Prevotella, Faecalibacterium, Roseburia, and Lachnospira, and likely corresponded to a gradual maturational shift from pre- to post-weaning microbiota. The rearing environment influenced the frequency of enterotypes, as well as the relative abundance of 6 families at d26 (including Christensenellaceae and Lactobacillaceae), and of 21 families at d35. In all farms, piglets showing the highest relative growth rate during the first three weeks after weaning, which were characterized as more robust, had a higher relative abundance of Bacteroidetes, a lower relative abundance of Proteobacteria, and showed a greater increase in Prevotella, Coprococcus, and Lachnospira in the post-weaning period. This study revealed the presence of ubiquitous enterotypes among the farms of this study, reflecting maturational stages of microbiota from a young suckling to an older cereal-eating profile. Despite significant variation in the microbial profile between farms, piglets whose growth after weaning was less disrupted were, those who had reached the more mature phenotype characterized by Prevotella the fastest.

Metagenomic insights into the diversity of carbohydrate-degrading enzymes in the yak fecal microbial community

BACKGROUND

Yaks are able to utilize the gastrointestinal microbiota to digest plant materials. Although the cellulolytic bacteria in the yak rumen have been reported, there is still limited information on the diversity of the major microorganisms and putative carbohydrate-metabolizing enzymes for the degradation of complex lignocellulosic biomass in its gut ecosystem.

RESULTS

Here, this study aimed to decode biomass-degrading genes and genomes in the yak fecal microbiota using deep metagenome sequencing. A comprehensive catalog comprising 4.5 million microbial genes from the yak feces were established based on metagenomic assemblies from 92 Gb sequencing data. We identified a full spectrum of genes encoding carbohydrate-active enzymes, three-quarters of which were assigned to highly diversified enzyme families involved in the breakdown of complex dietary carbohydrates, including 120 families of glycoside hydrolases, 25 families of polysaccharide lyases, and 15 families of carbohydrate esterases. Inference of taxonomic assignments to the carbohydrate-degrading genes revealed the major microbial contributors were Bacteroidaceae, Ruminococcaceae, Rikenellaceae, Clostridiaceae, and Prevotellaceae. Furthermore, 68 prokaryotic genomes were reconstructed and the genes encoding glycoside hydrolases involved in plant-derived polysaccharide degradation were identified in these uncultured genomes, many of which were novel species with lignocellulolytic capability.

CONCLUSIONS

Our findings shed light on a great diversity of carbohydrate-degrading enzymes in the yak gut microbial community and uncultured species, which provides a useful genetic resource for future studies on the discovery of novel enzymes for industrial applications.

Melatonin attenuates microbiota dysbiosis of jejunum in short-term sleep deprived mice

Our study demonstrated that sleep deprivation resulted in homeostasis disorder of colon. Our study goes deeper into the positive effects of melatonin on small intestinal microbiota disorder caused by sleep deprivation. We successfully established a multiplatform 72 h sleep deprivation mouse model with or without melatonin supplementation, and analyzed the change of small intestinal microbiota using high-throughput sequencing of the 16S rRNA. We found melatonin supplementation suppressed the decrease of plasma melatonin level in sleep deprivation mice. Meanwhile, melatonin supplementation improved significantly the reduction in OTU numbers and the diversity and richness of jejunal microbiota and the abundance of Bacteroidaeae and Prevotellaceae, as well as an increase in the Firmicutes-to-Bacteroidetes ratio and the content of Moraxellaceae and Aeromonadaceae in the jejunum of sleep deprived-mice. Moreover, melatonin supplementation reversed the change of metabolic pathway in sleep deprived-mice, including metabolism, signal transduction mechanisms and transcription etc, which were related to intestinal health. Furthermore, melatonin supplementation inverted the sleep deprivation-induced a decline of anti-inflammatory cytokines (IL-22) and an increase of the ROS and proinflammatory cytokines (IL-17) in jejunum. These findings suggested that melatonin, similar to a probiotics agent, can reverse sleep deprivation-induced small intestinal microbiota disorder by suppressing oxidative stress and inflammation response.

Faecal microbiota shift during weaning transition in piglets and evaluation of AO blood types as shaping factor for the bacterial community profile

The host-microbiota interplay is recognized as a key factor for the homeostatic maintenance in animals. In pigs, the weaning transition represents a drastic changes event leading to high risk of gut dysbiosis, which in most cases results in economic losses for swine industry. The blood type antigens expressed on mucosal surfaces can act as receptors for bacterial adhesion and the hypothesis of possible associations between blood groups and intestinal microbial profiles has been tested in human with contrasting results. Nevertheless, no studies testing the blood type as possible shaping factor for gut microbiota are available for pigs. The results of our previous study suggested the porcine AO blood types system as a possible factor influencing the microbiota composition. In the present study, the changes in fecal microbiota of 12 piglets were followed from 7 days after birth to 2 weeks post-weaning, testing the hypothesis that blood types may impact on its structure. No effects attributable to the difference in blood groups were detected, however, the sampling site (faeces) and the low statistical power might have masked the hypothesized impact. The data clearly showed the rearrangement of the bacterial ecosystem triggered by weaning transition; mainly consisting of a shift from a Bacteroidaceae-Enterobacteriaceae dominated community, to a Prevotellaceae-Ruminococcaceae dominated community. The functional analysis by metagenomic predictions suggested a role of the high levels of long-chain fatty acid in swine milk as energy source for Enterobacteriaceae (E. coli), in suckling piglets. This study provides a first insight for further investigations; indicating the need for larger sample size, preferably derived from intestinal mucosa, to test the potential effect of blood groups on gut microbiota profiles, and for analyses aimed at assessing the long-chain fatty acids degradation activity within the intestinal microbiota of suckling piglets, with particular attention to the role of E. coli.

Assessing the spatial and temporal variability of bacterial communities in two Bardenpho wastewater treatment systems via Illumina MiSeq sequencing

Next generation sequencing provides new insights into the diversity and ecophysiology of bacteria communities throughout wastewater treatment plants (WWTP), as well as the fate of pathogens in wastewater treatment system. In the present study, we investigated the bacterial communities and human-associated Bacteroidales (HF183) marker in two WWTPs in North America that utilize Bardenpho treatment processes. Although, most pathogens were eliminated during wastewater treatment, some pathogenic bacteria were still observed in final effluents. The HF183 genetic marker demonstrated significant reductions between influent and post-Bardenpho treated samples in each WWTP, which coincided with changes in bacteria relative abundances and community compositions. Consistent with previous studies, the major phyla in wastewater samples were predominantly comprised by Proteobacteria (with Gammaproteobacteria and Alphaproteobacteria among the top two classes), Actinobacteria, Bacteroidetes, and Firmicutes. Dominant genera were often members of Proteobacteria and Firmicutes, including several pathogens of public health concern, such as Pseudomonas, Serratia, Streptococcus, Mycobacterium and Arcobacter. Pearson correlations were calculated to observe the seasonal variation of relative abundances of gene sequences at different levels based on the monthly average temperature. These findings profile how changes in bacterial communities can function as a robust method for monitoring wastewater treatment quality and performance for public and environmental health purposes.

Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana

BACKGROUND

Gut microbiota from individuals in rural, non-industrialized societies differ from those in individuals from industrialized societies. Here, we use 16S rRNA sequencing to survey the gut bacteria of seven non-industrialized populations from Tanzania and Botswana. These include populations practicing traditional hunter-gatherer, pastoralist, and agropastoralist subsistence lifestyles and a comparative urban cohort from the greater Philadelphia region.

RESULTS

We find that bacterial diversity per individual and within-population phylogenetic dissimilarity differs between Botswanan and Tanzanian populations, with Tanzania generally having higher diversity per individual and lower dissimilarity between individuals. Among subsistence groups, the gut bacteria of hunter-gatherers are phylogenetically distinct from both agropastoralists and pastoralists, but that of agropastoralists and pastoralists were not significantly different from each other. Nearly half of the Bantu-speaking agropastoralists from Botswana have gut bacteria that are very similar to the Philadelphian cohort. Based on imputed metagenomic content, US samples have a relative enrichment of genes found in pathways for degradation of several common industrial pollutants. Within two African populations, we find evidence that bacterial composition correlates with the genetic relatedness between individuals.

CONCLUSIONS

Across the cohort, similarity in bacterial presence/absence compositions between people increases with both geographic proximity and genetic relatedness, while abundance weighted bacterial composition varies more significantly with geographic proximity than with genetic relatedness.

A Microbial Signature of Psychological Distress in Irritable Bowel Syndrome

OBJECTIVE

Irritable bowel syndrome (IBS) is associated with alterations along the brain-gut-microbiota axis. Previous studies have suggested a parallel segregation of microbial features and psychological burden in IBS. This study aimed at exploring the microbial correlates of psychological distress in patients with IBS.

METHODS

Forty-eight patients with IBS (Rome III criteria, M (SD) age = 42 (15) years, 35 female, 25 diarrhea-dominant, 5 constipation-dominant, and 18 alternating-type IBS) were assessed for psychological and clinical variables with validated questionnaires, fecal samples underwent microbial 16S rRNA analyses (regions V1-2). Microbial analyses comprised examination of alpha and beta diversity, correlational analyses of bacterial abundance and comparisons among subgroups defined by thresholds of psychological and IBS symptom variables, and machine learning to identify bacterial patterns corresponding with psychological distress.

RESULTS

Thirty-one patients (65%) showed elevated psychological distress, 22 (31%) anxiety, and 10 depression (21%). Microbial beta diversity was significantly associated with distress and depression (q = .036 each, q values are p values false discovery rate-corrected for multiple testing). Depression was negatively associated with Lachnospiraceae abundance (Spearman's ρ = -0.58, q = .018). Patients exceeding thresholds of distress, anxiety, depression, and stress perception showed significantly higher abundances of Proteobacteria (q = .020-.036). Patients with anxiety were characterized by elevated Bacteroidaceae (q = .036). A signature of 148 unclassified species accounting for 3.9% of total bacterial abundance co-varied systematically with the presence of psychological distress.

CONCLUSIONS

Psychological variables significantly segregated gut microbial features, underscoring the role of brain-gut-microbiota interaction in IBS. A microbial signature corresponding with psychological distress was identified.

CLINICAL TRIAL REGISTRATION

ClinicalTrials.gov identifier NCT02536131, retrospectively registered.

Increasing dietary nitrate has no effect on cancellous bone loss or fecal microbiome in ovariectomized rats

SCOPE

Studies suggest diets rich in fruit and vegetables reduce bone loss, although the specific compounds responsible are unknown. Substrates for endogenous nitric oxide (NO) production, including organic nitrates and dietary nitrate, may support NO production in age-related conditions, including osteoporosis. We investigated the capability of dietary nitrate to improve NO bioavailability, reduce bone turnover and loss.

METHODS AND RESULTS

Six-month-old Sprague Dawley rats [30 ovariectomized (OVX) and 10 sham-operated (sham)] were randomized into three groups: (i) vehicle (water) control, (ii) low-dose nitrate (LDN, 0.1 mmol nitrate/kg bw/day), or (iii) high-dose nitrate (HDN, 1.0 mmol nitrate/kg bw/day) for three weeks. The sham received vehicle. Serum bone turnover markers; bone mass, mineral density, and quality; histomorphometric parameters; and fecal microbiome were examined. Three weeks of LDN or HDN improved NO bioavailability in a dose-dependent manner. OVX resulted in cancellous bone loss, increased bone turnover, and fecal microbiome changes. OVX increased relative abundances of Firmicutes and decreased Bacteroideceae and Alcaligenaceae. Nitrate did not affect the skeleton or fecal microbiome.

CONCLUSION

These data indicate that OVX affects the fecal microbiome and that the gut microbiome is associated with bone mass. Three weeks of nitrate supplementation does not slow bone loss or alter the fecal microbiome in OVX.

11β-hydroxysteroid dehydrogenase-1 deficiency alters the gut microbiome response to Western diet

The enzyme 11β-hydroxysteroid dehydrogenase (11β-HSD) interconverts active glucocorticoids and their intrinsically inert 11-keto forms. The type 1 isozyme, 11β-HSD1, predominantly reactivates glucocorticoids in vivo and can also metabolise bile acids. 11β-HSD1-deficient mice show altered inflammatory responses and are protected against the adverse metabolic effects of a high-fat diet. However, the impact of 11β-HSD1 on the composition of the gut microbiome has not previously been investigated. We used high-throughput 16S rDNA amplicon sequencing to characterise the gut microbiome of 11β-HSD1-deficient and C57Bl/6 control mice, fed either a standard chow diet or a cholesterol- and fat-enriched 'Western' diet. 11β-HSD1 deficiency significantly altered the composition of the gut microbiome, and did so in a diet-specific manner. On a Western diet, 11β-HSD1 deficiency increased the relative abundance of the family Bacteroidaceae, and on a chow diet, it altered relative abundance of the family Prevotellaceae Our results demonstrate that (i) genetic effects on host-microbiome interactions can depend upon diet and (ii) that alterations in the composition of the gut microbiome may contribute to the aspects of the metabolic and/or inflammatory phenotype observed with 11β-HSD1 deficiency.

Association between the presence of Treponema denticola and reduced levels of antiatherogenic high density lipoprotein in periodontitis

OBJECTIVE

Dyslipidemia, a disorder in the levels of cholesterol or lipoproteins in the plasma, is a feature of atherosclerosis, leading to cardiovascular disease. The objective of this study was to evaluate whether Tanerella forsythia and Treponema denticola are related to reduced levels of antiatherogenic high density lipoprotein (HDL).

METHOD AND MATERIALS

In this cross-sectional study, 108 patients were invited to participate. The diagnosis of chronic periodontitis and the diagnosis of adipose tissue disorders were made based on criteria previously defined. The presence of T forsythia and T denticola was detected by polymerase chain reaction.

RESULTS

A total of 61 women and 19 men with chronic periodontitis, and 18 women and 10 men without periodontitis were studied. The serum levels of total cholesterol and low density lipoprotein were similar in both groups. Inversely, the levels of triglycerides (TG) were higher in periodontitis patients compared to subjects without periodontitis (178 mg/dL vs 165 mg/dL; P < .05), and the levels of HDL were lower (44 mg/dL vs 50 mg/dL; P < .05), respectively. The presence of T denticola was associated with low levels of HDL in periodontitis patients after adjustment for possible confounders (OR, 3.03; 95% CI, 1.2-7.2).

CONCLUSION

Higher levels of TG and lower levels of HDL were associated with the presence of T denticola in chronic periodontitis. These results may suggest that the presence of T denticola could reduce the antiatherogenic potency of HDL and may increase the risk for cardiovascular disease in patients with chronic periodontitis.

First detection of endosymbiotic bacteria in biting midges Culicoides pulicaris and Culicoides punctatus, important Palaearctic vectors of bluetongue virus

Heritable bacteria have been highlighted as important components of vector biology, acting as required symbionts with an anabolic role, altering competence for disease transmission, and affecting patterns of gene flow by altering cross compatibility. In this paper, we tested eight U.K. species of Culicoides (Diptera: Ceratopogonidae) midge for the presence of five genera of endosymbiotic bacteria: Cardinium (Bacteroidales: Bacteroidaceae); Wolbachia (Rickettsiales: Rickettsiaceae); Spiroplasma (Entomoplasmatales: Spiroplasmataceae); Arsenophonus (Enterobacteriales: Enterobacteriaceae), and Rickettsia (Rickettsiales: Rickettsiaceae). Cardinium spp. were detected in both sexes of Culicoides pulicaris and Culicoides punctatus, two known vectors of bluetongue virus. Cardinium spp. were not detected in any other species, including the Culicoides obsoletus group, the main vector of bluetongue and Schmallenberg viruses in northern Europe. The other endosymbionts were not detected in any Culicoides species. The Cardinium strain detected in U.K. Culicoides species is very closely related to the Candidatus Cardinium hertigii group C, previously identified in Culicoides species in Asia. Further, we infer that the symbiont is not a sex ratio distorter and shows geographic variation in prevalence within a species. Despite its detection in several species of Culicoides that vector arboviruses worldwide, the absence of Cardinium in the C. obsoletus group suggests that infections of these symbionts may not be necessary to the arboviral vector competence of biting midges.

In vivo effectiveness of silicone gel sheets as barriers at the inner microgap between a prosthetic abutment and an external-hexagon implant platform

PURPOSE

Bacterial penetration and colonization of the microgap at the implant-abutment interface have been reported in several studies. The aim of this study was to evaluate the effectiveness of placing a silicone membrane between the abutment and the implant platform in an attempt to seal the interface.

MATERIALS AND METHODS

A total of 15 external-hex implants were placed in 10 patients with clinically healthy peri-implant tissues, and all of the patients had ceramic prosthetic crowns. Samples were collected from the microgaps before, 30 days after, and 90 days after insertion of a silicone membrane. Bacterial DNA was extracted and submitted in triplicate to polymerase chain reaction using primers specific for four peri-implant pathogens: Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia, and Tannerella forsythia.

RESULTS

In the initial samples, a positivity of 52% was found, which was different from that found in samples collected after 30 days (32%) and 90 days (27%) after insertion of the membrane.

CONCLUSION

It was evident that the silicone membrane reduced, but did not prevent, penetration of these species into external-hex implants.

Fecal microbiota in early rheumatoid arthritis

OBJECTIVE

To compare the composition of intestinal microbiota of patients with early rheumatoid arthritis (RA) or fibromyalgia (FM), fecal samples were collected from 51 patients with RA and 50 with FM.

METHODS

RA patients fulfilled the RA criteria of the American College of Rheumatology, and duration of their disease was < or = 6 months. Only nonhospitalized patients from outpatient care were included. Patients having extreme diets or previous disease modifying antirheumatic drug or glucocorticoid medication were excluded, as were those taking antibiotics or having gastroenteritis for at least 2 months prior to sampling. Fecal bacterial composition was analyzed with a method based on flow cytometry, 16S rRNA hybridization, and DNA-staining. A set of 8 oligonucleotide probes was used.

RESULTS

In comparison to patients with FM, the RA patients had significantly less bifidobacteria and bacteria of the Bacteroides-Porphyromonas-Prevotella group, Bacteroides fragilis subgroup, and Eubacterium rectale--Clostridium coccoides group. Results from the 8 probes showed a significant overall difference between the 2 patient groups, indicating widespread microbial differences.

CONCLUSION

These findings support the hypothesis that intestinal microbes participate in the etiopathogenesis of RA.

16S rRNA-based assays for quantitative detection of universal, human-, cow-, and dog-specific fecal Bacteroidales: a Bayesian approach

We report the design and validation of new TaqMan((R)) assays for microbial source tracking based on the amplification of fecal 16S rRNA marker sequences from uncultured cells of the order Bacteroidales. The assays were developed for the detection and enumeration of non-point source input of fecal pollution to watersheds. The quantitative "universal"Bacteroidales assay BacUni-UCD detected all tested stool samples from human volunteers (18 out of 18), cat (7 out of 7), dog (8 out of 8), seagull (10/10), cow (8/8), horse (8/8), and wastewater effluent (14/14). The human assay BacHum-UCD discriminated fully between human and cow stool samples but did not detect all stool samples from human volunteers (12/18). In addition, there was 12.5% detection of dog stool (1/8), but no cross-reactivity with cat, horse, or seagull fecal samples. In contrast, all wastewater samples were positive for the BacHum-UCD marker, supporting its designation as 100% sensitive for mixed-human source identification. The cow-specific assay BacCow-UCD fully discriminated between cow and human stool samples. There was 38% detection of horse stool (3/8), but no cross-specificity with any of the other animal stool samples tested. The dog assay BacCan-UCD discriminated fully between dog and cow stool or seagull guano samples and detected 62.5% stool samples from dogs (5/8). There was some cross-reactivity with 22.2% detection of human stool (4/18), 14.3% detection of cat stool (1/7), and 28.6% detection of wastewater samples (4/14). After validation using stool samples, single-blind tests were used to further demonstrate the efficacy of the developed markers; all assays were sensitive, reproducible, and accurate in the quantification of mixed fecal sources present in aqueous samples. Finally, the new assays were compared with previously published sequences, which showed the new methodologies to be more specific and sensitive. Using Bayes' Theorem, we calculated the conditional probability that the four assays would correctly identify general and host-specific fecal pollution in a specific watershed in California for which 73 water samples had been analyzed. Such an approach allows for a direct comparison of the efficacy of different MST methods, including those based on library-dependent methodologies. For the universal marker BacUni-UCD, the probability that fecal pollution is present when the marker is detected was 1.00; the probability that host-specific pollution is present was 0.98, 0.84, and 0.89 for the human assay HF160F, the cow assay BacCow-UCD, and the dog assay BacCan-UCD, respectively. The application of these markers should provide meaningful information to assist with efforts to identify and control sources of fecal pollution to impaired watersheds.

Persistently high levels of periodontal pathogens associated with preterm pregnancy outcome

BACKGROUND

Few studies examining the association between periodontal diseases and preterm birth have explored the underlying microbial and antibody responses associated with oral infection.

METHODS

A nested case-control study was performed using data from a recent interventional trial following the delayed-treatment control group of 31 subjects with periodontal diseases. The levels of eight oral bacteria and the maternal immunoglobulin G (IgG) responses in serum to these bacteria were measured at antepartum and postpartum visits to determine the relationship to cases (preterm delivery <37 weeks' gestation) and controls (term delivery).

RESULTS

Antepartum, the levels of periodontal pathogens tended to be higher in the preterm (case group) deliveries compared to the term deliveries (control group). Maternal anti-Porphyromonas gingivalis IgG was significantly lower in the preterm group compared to the term group (P = 0.028). Postpartum, levels of P. gingivalis, Tannerella forsythia, Prevotella intermedia, and Prevotella nigrescens were statistically significantly higher in preterm births compared to term deliveries, adjusting for baseline levels. The joint effects of red and orange microbial clusters were significantly higher in the preterm group compared to the term group.

CONCLUSIONS

High levels of periodontal pathogens and low maternal IgG antibody response to periodontal bacteria during pregnancy are associated with an increased risk for preterm delivery. Further studies elucidating the role of the microbial load and maternal immune response as related to pregnancy outcome seem merited.

Longitudinal Study of the Association Between Smoking as a Periodontitis Risk and Salivary Biomarkers Related to Periodontitis

BACKGROUND

Insufficient data exist regarding the long-term influence of lifestyle factors including smoking on periodontal health. The objective of this study was to examine the prospective association between smoking and periodontal disease progression and the effects of smoking on salivary biomarkers related to periodontitis.

METHODS

Probing depth (PD) was measured at health checkups of workers in 1999 and 2003; additionally, lifestyle information was obtained through a questionnaire. In 2003, 219 of 256 (86%) workers examined at baseline completed PD measurements; saliva samples were also collected. Change in PD was used for assessment of periodontitis progression when three or more sites displayed an increase of >or=2 mm over 4 years. Salivary biomarker levels were determined by real-time polymerase chain reaction and enzyme assay. Statistical methods included bivariate and multivariate regression analyses.

RESULTS

In the multiple logistic model, in which lifestyle-related factors served as independent variables, significant variables were current smoking and hours of sleep; respective odds ratios were 2.3 and 2.1. Additionally, 38.5% of periodontal disease progression was attributable to current smoking. Moreover, pack-years of smoking showed a dose-response relationship with disease progression. Levels of salivary markers including prostaglandin E(2), lactoferrin, albumin, aspartate aminotransferase, lactate dehydrogenase, and alkaline phosphatase were significantly lower in current smokers than in non-current smokers. However, no meaningful differences in the proportions of six periodontal pathogens were observed between current and non-current smokers.

CONCLUSIONS

Smoking exerted the greatest influence on periodontitis risk among lifestyle factors. Smoking may suppress the host-defense system, which may promote periodontal disease progression.

Competitive metagenomic DNA hybridization identifies host-specific microbial genetic markers in cow fecal samples

Several PCR methods have recently been developed to identify fecal contamination in surface waters. In all cases, researchers have relied on one gene or one microorganism for selection of host-specific markers. Here we describe the application of a genome fragment enrichment (GFE) method to identify host-specific genetic markers from fecal microbial community DNA. As a proof of concept, bovine fecal DNA was challenged against a porcine fecal DNA background to select for bovine-specific DNA sequences. Bioinformatic analyses of 380 bovine enriched metagenomic sequences indicated a preponderance of Bacteroidales-like regions predicted to encode membrane-associated and secreted proteins. Oligonucleotide primers capable of annealing to select Bacteroidales-like bovine GFE sequences exhibited extremely high specificity (>99%) in PCR assays with total fecal DNAs from 279 different animal sources. These primers also demonstrated a broad distribution of corresponding genetic markers (81% positive) among 148 different bovine sources. These data demonstrate that direct metagenomic DNA analysis by the competitive solution hybridization approach described is an efficient method for identifying potentially useful fecal genetic markers and for characterizing differences between environmental microbial communities.

Periodontal infections and coronary heart disease: role of periodontal bacteria and importance of total pathogen burden in the Coronary Event and Periodontal Disease (CORODONT) study

BACKGROUND

Chronic inflammation from any source is associated with increased cardiovascular risk. Periodontitis is a possible trigger of chronic inflammation. We investigated the possible association between periodontitis and coronary heart disease (CHD), focusing on microbiological aspects.

METHODS

A total of 789 subjects (263 patients with angiographically confirmed, stable CHD and 526 population-based, age- and sex-matched controls without a history of CHD) were included in the Coronary Event and Periodontal Disease (CORODONT) study. Subgingival biofilm samples were analyzed for periodontal pathogens Actinobacillus actinomycetemcomitans, Tannerella forsythensis, Porphyromonas gingivalis, Prevotella intermedia, and Treponema denticola using DNA-DNA hybridization. The need for periodontal treatment in each subject was assessed using the Community Periodontal Index of Treatment Needs (CPITN). The main outcome measures included total periodontal pathogen burden, number of the various periodontal pathogens in the subgingival biofilm, and periodontal treatment needs (according to the CPITN).

RESULTS

In multivariable analyses, we found a statistically significant association between the periodontal pathogen burden (log10 of the sum of all pathogens) (odds ratio [OR], 1.92; 95% confidence interval [CI], 1.34-2.74; P<.001) or the number of A actinomycetemcomitans in periodontal pockets (log10) (OR, 2.70; 95% CI, 1.79-4.07; P<.001) and the presence of CHD. In addition, a statistically significant association between an increase in mean CPITN score by 1 and the presence of CHD (OR, 1.67; 95% CI, 1.08-2.58; P = .02) was observed.

CONCLUSIONS

Our findings suggest an association between periodontitis and presence of CHD. Periodontal pathogen burden, and particularly infection with A actinomycetemcomitans, may be of special importance.

Endosymbiotic Bacteroidales bacteria of the flagellated protist Pseudotrichonympha grassii in the gut of the termite Coptotermes formosanus

A unique lineage of bacteria belonging to the order Bacteroidales was identified as an intracellular endosymbiont of the protist Pseudotrichonympha grassii (Parabasalia, Hypermastigea) in the gut of the termite Coptotermes formosanus. We identified the 16S rRNA, gyrB, elongation factor Tu, and groEL gene sequences in the endosymbiont and detected a very low level of sequence divergence (<0.9% of the nucleotides) in the endosymbiont population within and among protist cells. The Bacteroidales endosymbiont sequence was affiliated with a cluster comprising only sequences from termite gut bacteria and was not closely related to sequences identified for members of the Bacteroidales attached to the cell surfaces of other gut protists. Transmission electron microscopy showed that there were numerous rod-shaped bacteria in the cytoplasm of the host protist, and we detected the endosymbiont by fluorescence in situ hybridization (FISH) with an oligonucleotide probe specific for the 16S rRNA gene identified. Quantification of the abundance of the Bacteroidales endosymbiont by sequence-specific cleavage of rRNA with RNase H and FISH cell counting revealed, surprisingly, that the endosymbiont accounted for 82% of the total bacterial rRNA and 71% of the total bacterial cells in the gut community. The genetically nearly homogeneous endosymbionts of Pseudotrichonympha were very abundant in the gut symbiotic community of the termite.

Identification of periodontal pathogens in atherosclerotic vessels

BACKGROUND

Epidemiological studies have shown that periodontitis may be associated with presence of atherosclerosis. DNA from periodontal pathogens has been detected in atherosclerotic lesions, but viable oral bacteria have not yet been isolated from atherosclerotic plaques. The purpose of the present study was to determine if viable oral bacteria could be isolated from atherosclerotic lesions and if DNA from periodontal pathogens could be detected by use of polymerase chain reaction (PCR) techniques.

METHODS

Seventy-nine specimens of atherosclerotic plaque removed from carotid or femoral arteries during surgery were immediately transferred to reduced transport fluid and brought to the laboratory. The calcified tissue was meticulously cut into fine pieces and used for cultivation of Porphyromonas gingivalis, Prevotella intermedia, P. nigrescens, Campylobacter rectus, Actinobacillus actinomycetemcomitans, Tannerella forsythensis, and oral streptococci. The material from 24 of the specimens was homogenized, DNA was extracted, and PCR amplification of 16S rDNA with universal and specific primers was carried out. Finally, the PCR products were sequenced.

RESULTS

None of the samples yielded growth of the oral bacteria under investigation. In all the 24 specimens bacterial DNA was detected and likewise DNA of P. intermedia was found in the samples. P. nigrescens and P. gingivalis were found sporadically.

CONCLUSIONS

Viable oral bacteria could not be isolated from the atheromas, but the data confirm that DNA of periodontal pathogens can be detected in atherosclerotic plaques. However, the finding that DNA from P. intermedia constantly occured in the examined samples was new. Further studies may focus on the simultaneous occurrence of identical clones of this species in subgingival plaque and atherosclerotic plaques.

Loop-mediated isothermal amplification method for rapid detection of the periodontopathic bacteria Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola

Loop-mediated isothermal amplification (LAMP), a novel nucleic acid amplification method, was developed for the rapid detection of the major periodontal pathogens Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola. The LAMP method amplifies DNA with high specificity, efficiency, and rapidity under isothermal conditions using a set of four specially designed primers and a DNA polymerase with strand displacement activity. In this study, we initially designed the primers for LAMP assays to detect these bacteria and evaluated the specificity and sensitivity of these assays. The specificities of the primers for these bacteria were examined using various oral bacteria and various reaction times. The lower detection limits of the 60-min LAMP reaction without loop primers were 1 microg/tube for P. gingivalis, 10 fg/tube for T. forsythia, and 1 ng/tube for T. denticola. Addition of the loop primers for each bacterium improved the detection specificities and sensitivities by several magnitudes. Furthermore, LAMP assays were applied to the rapid detection of these periodontal pathogens in clinical specimens, and the results were compared with those of conventional PCR detection. The results of the LAMP assays corresponded to those of conventional PCR assays. These results indicate that the LAMP assay is an extremely rapid, highly sensitive, specific method. This method is very useful for the rapid detection of periodontopathic bacteria and the diagnosis of periodontal disease.

Normal vaginal flora in chimpanzees (Pan troglodytes): qualitative and quantitative study

Lactobacilli are the predominant microorganisms in the vaginal flora of human beings, and are known to play an important role in protecting them from genital infections. On the other hand, the composition of the vaginal flora differs among laboratory animal species, and lactobacilli are not the predominant vaginal microorganism in many laboratory animals. We speculated that the vaginal flora of chimpanzees would be more similar to those of human beings than to those of other animal species, because chimpanzees are phylogenetically close to human beings, and their reproductive physiology is similar to that of human beings. To clarify our speculation, we examined the development of the vaginal flora in chimpanzees (Pan troglodytes). Streptococci, lactobacilli, and members of the family Bacteroidaceae were the most predominant bacteria in the vagina of mature chimpanzees (9 to 22 years old). During development of the vaginal flora of chimpanzees, the total number of bacteria increased with age and reached a plateau just before sexual maturity (5 to 7 years of age; juvenile period). Lactobacilli were already one of the predominant bacteria before sexual maturity. In mature chimpanzees, the total number of bacteria (aerobes and anaerobes) in the vagina was highest during the swelling phase of the menstrual cycle. During the swelling phase in mature chimpanzees, streptococci, lactobacilli, and Bacteroidaceae were the most frequently isolated (100%) organisms, and the total number of organisms recovered from vaginal specimens from these three groups was the highest. In mature chimpanzees in which the number of bacteria was the highest, lactobacilli were the predominant bacteria. Taken together, these results suggest that these three bacterial groups (streptococci, lactobacilli, and Bacteroidaceae) are indigenous to the vagina of chimpanzees, and chimpanzees would be the most suitable laboratory animals for studying the role of lactobacilli in the vagina of human beings.

Qualitative and quantitative differences in normal vaginal flora of conventionally reared mice, rats, hamsters, rabbits, and dogs

We examined quantitatively the vaginal flora of conventionally reared mice, rats, hamsters, rabbits and dogs, species that are widely used as laboratory animals. Vaginal specimens were examined according to the method of analyzing intestinal flora (Mitsuoka's procedure). The total number of bacteria (aerobes and anaerobes) and the prevalence of specific bacteria were determined. The total number of bacteria was highest during estrus and lowest during diestrus or anestrus in mice, rats, hamsters, and dogs. The most predominant bacteria during estrus were streptococci in mice; gram-negative rods (GNR), streptococci, and members of the family Bacteroidaceae in rats; GNR, Bacteroidaceae and gram-positive anaerobic cocci in hamsters, and Bacteroidaceae in dogs. The increase in the total number of bacteria during estrus was caused by an increase of predominant bacteria in the vagina. Aerobes were more predominant than anaerobes in mice, and number of aerobes was comparable to that of anaerobes in rats and dogs. On the other hand, in hamsters, anaerobes were more predominant than aerobes and the total number of bacteria was highest among the laboratory animals (mice, rats, hamsters, rabbits, and dogs). However, in rabbits, bacteria were not isolated from about 90% of the vaginal specimens. Rabbits do not have cyclic reproductive stages and are usually in precoital status in the laboratory. In precoital rabbits, vaginal epithelium manifests few signs of secretion. Therefore, we suspect that the vaginal environment in precoital rabbits is comparable to that during diestrus or anestrus in mice, rats, hamsters, and dogs. These results suggest that the vaginal flora of laboratory animals is influenced by the estrous cycle, and probably by mucous secretion. Our data imply that vaginal flora differ among laboratory animals species, and researchers need to take into consideration the estrous cycle of laboratory animals when studying their vaginal flora.

Exploring prokaryotic diversity in the genomic era

Our understanding of prokaryote biology from study of pure cultures and genome sequencing has been limited by a pronounced sampling bias towards four bacterial phyla - Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes - out of 35 bacterial and 18 archaeal phylum-level lineages. This bias is beginning to be rectified by the use of phylogenetically directed isolation strategies and by directly accessing microbial genomes from environmental samples.

[Comparative antibiotic susceptibility in vitro of microbial isolates from patients with complications after gastrectomy for stomach carcinoma and from contents of their large intestine]

Antibiotic susceptibility of the main isolates from the large intestine contents and pathological substrates of 12 patients after gastroectomy for stomach carcinoma was studied. Three of them developed esophagoenterostomy incompetence, 4 had intraabdominal abscesses and in 5 infection of the operation wound was stated. In all, 30 isolates of enterobacteria, 28 isolates of enterococci and 38 isolates of bacteroides were tested. Antibiotic susceptibility of the isolates from various sources was practically identical, which showed that before surgical operations for stomach carcinoma it was necessary that data on the patients intestine microbiocenosis and antibioticograms of the main isolates should be available to correct severe dysbiotic disorders.

[Non-sporulating anaerobic bacteria and anastomosis failure in patients with gastric carcinoma]

Cases of anastomosis suture failure within the period from 1977 to 1987 and from 1988 to 1998 in 139 patients after various surgical operations for gastric carcinoma were analyzed. Infection in the cases of the anastomosis sUture failure at the early terms was mainly due to representatives of Enterobacteriaceae and at the later terms the failure was mainly due to non-sporulating anaerobes belonging to Bacteroidaceae. The data are indicative of the fact that the use of antimicrobials requires a differential approach.

Age and disease related changes in intestinal bacterial populations assessed by cell culture, 16S rRNA abundance, and community cellular fatty acid profiles

BACKGROUND

The normal intestinal microflora plays an important role in host metabolism and provides a natural defence mechanism against invading pathogens. Although the microbiota in adults has been extensively studied, little is known of the changes that occur in the microflora with aging. These may have important consequences in elderly people, many of whom are receiving antibiotic therapy and who are most susceptible to intestinal dysbiosis.

AIMS

To characterise the major groups of faecal bacteria in subjects of different ages using a combination of cultural, molecular, and chemotaxonomic approaches.

METHODS

Comparative microbiological studies were made on four different subject groups: children (16 months to seven years, n=10), adults (21-34 years, n=7), healthy elderly subjects (67-88 years, n=5), and geriatric patients (68-73 years, n=4) diagnosed with Clostridium difficile diarrhoea. Selected faecal bacteria were investigated using viable counting procedures, 16S ribosomal RNA (rRNA) abundance measurements, and the occurrence of specific signature fatty acids in whole community fatty acid methyl ester profiles.

RESULTS

The principal microbiological difference between adults and children was the occurrence of higher numbers of enterobacteria in the latter group, as determined by viable counts (p<0.05) and 16S rRNA (p<0.01) measurements. Moreover, a greater proportion of children's faecal rRNA was hybridised by the three probes (bifidobacteria, enterobacteria, bacteroides-porphyromonas-prevotella) used in the study, indicating a less developed gut microbiota. Species diversity was also markedly lower in the Clostridium difficile associated diarrhoea group, which was characterised by high numbers of facultative anaerobes and low levels of bifidobacteria and bacteroides. Although it was a considerably less sensitive diagnostic tool, cellular fatty acid analysis correlated with viable bacterial counts and 16S rRNA measurements in a number of bacteria, including bacteroides.

CONCLUSIONS

Polyphasic analysis of faecal bacteria showed that significant structural changes occur in the microbiota with aging, and this was especially evident with respect to putatively protective bifidobacteria. Reductions in these organisms in the large bowel may be related to increased disease risk in elderly people.

Effect of dietary short-chain fructooligosaccharides on the cecal microflora in gastrectomized rats

Total gastric resection is known to lead to changes in the microflora in the whole gastrointestinal tract. Dietary short-chain fructooligosaccharides (Sc-FOS) have been shown to also induce a change in the microflora in the large bowel by promoting an increase in the numbers of Bifidobacterium and Lactobacillus which have beneficial effects on the host. In the present study, 4-week-old male Sprague-Dawley rats received total gastrectomy or laparotomy, and each of these surgically treated groups was randomly divided into two experimental diet groups and given a 7.5% Sc-FOS diet or control diet. Enumeration and identification of the cecal bacteria was performed by using selective and non-selective media. In the gastrectomized rats, the total bacterial count, and the counts of Bacteroidaceae and Enterobacteriaceae were higher than those in the sham-operated rats. Sc-FOS promoted an increase in the numbers of Bifidobacterium and Lactobacillus, In the rats fed on the Sc-FOS diet, the predominant type of bacteria was Lactobacillus and in the rats fed on the control diet, it was Bacteroidaceae irrespective of gastrectomy. We confirmed that both gastrectomy and dietary Sc-FOS changed the composition of cecal microflora in the rats. Dietary Sc-FOS in the gastrectomized rats increased the proportions of Lactobacillus relative to other types of bacteria to levels similar to those seen in healthy normal rats, and decreased the proportion of Bacteroidaceae.

Chitinolytic bacteria in the minke whale forestomach

Minke whales consume large amounts of pelagic crustaceans. Digestion of the prey is initiated by indigenous bacteria in a rumen-like forestomach system. A major structural component of the crustacean exoskeleton is chitin, the beta-1,4-linked polymer of N-acetyl-D-glucosamine. The exoskeletons appear to dissolve completely in the non-glandular forestomach. Bacteria in the forestomach fluid of six krill-eating minke whales were enumerated and isolated using an anaerobic habitat-simulating culture medium. Median viable population densities ranged between 6.0 x 10(6) and 9.9 x 10(9) bacterial cells per mL forestomach fluid. Bacterial isolates (n = 44) cultured from the forestomach fluid of one minke whale mainly resembled strains of Eubacterium (25%), Streptococcus (18%), Clostridium (14%), and Bacteroides (11%). As much as 12% of the bacterial isolates were chitinolytic, while beta-N-acetylglucosaminidase activity was demonstrated in 54% of the isolates, and utilisation of N-acetyl-D-glucosamine was observed in 73%. The chitinolytic isolates resembled strains of Bacteroides, Bacteroidaceae, Clostridium, and Streptococcus. Scanning and transmission electron microscopy of partly digested krill from the minke whale forestomach revealed bacteria close to and inside the chitinous exoskeleton. The bacterial chitinase may act on the chitinous crustacean exoskeletons, thereby allowing other bacteria access to the nutritious soft inner tissues of the prey, and thus initiating its degradation and fermentation.

In vitro utilization of amylopectin and high-amylose maize (Amylomaize) starch granules by human colonic bacteria

It has been well established that a certain amount of ingested starch can escape digestion in the human small intestine and consequently enters the large intestine, where it may serve as a carbon source for bacterial fermentation. Thirty-eight types of human colonic bacteria were screened for their capacity to utilize soluble starch, gelatinized amylopectin maize starch, and high-amylose maize starch granules by measuring the clear zones on starch agar plates. The six cultures which produced clear zones on amylopectin maize starch- containing plates were selected for further studies for utilization of amylopectin maize starch and high-amylose maize starch granules A (amylose; Sigma) and B (Culture Pro 958N). Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) was used to detect bacterial starch-degrading enzymes. It was demonstrated that Bifidobacterium spp., Bacteroides spp., Fusobacterium spp., and strains of Eubacterium, Clostridium, Streptococcus, and Propionibacterium could hydrolyze the gelatinized amylopectin maize starch, while only Bifidobacterium spp. and Clostridium butyricum could efficiently utilize high-amylose maize starch granules. In fact, C. butyricum and Bifidobacterium spp. had higher specific growth rates in the autoclaved medium containing high-amylose maize starch granules and hydrolyzed 80 and 40% of the amylose, respectively. Starch-degrading enzymes were cell bound on Bifidobacterium and Bacteroides cells and were extracellular for C. butyricum. Active staining for starch-degrading enzymes on SDS-PAGE gels showed that the Bifidobacterium cells produced several starch-degrading enzymes with high relative molecular (M(r)) weights (>160,000), medium-sized relative molecular weights (>66,000), and low relative molecular weights (<66,000). It was concluded that Bifidobacterium spp. and C. butyricum degraded and utilized granules of amylomaize starch.

Clinical spectrum of bacteroidaceae in a tertiary care hospital

Members of Bacteroidaceae family are the most commonly isolated anaerobic pathogens in humans. This study summarises our experience of isolation and antimicrobial susceptibility pattern of these anaerobes from diverse clinical infections in a tertiary care hospital. Over a period of 5 years, 611 samples were received for anaerobic culture. Of these, 53 specimens yielded 62 anaerobic isolates. Thirty of the 62 isolates (48.4%) belonged to Bacteroidacea family obtained from 29 patients. They comprised of 14 (14/32; 43.7%) Prevotella spp., 13 (13/32; 40.6%) Bacteroides spp., 3 (3/32; 9.3%) Porphyromonas spp and Fusobacterium (2/32; 6.2%). In 14 of 27 patients (48%) the infection was polymicrobial. All the isolated strains were sensitive to metronidazole. This study highlights need for adopting anaerobic culture technique as a routine diagnostic procedure and constant monitoring of antimicrobial susceptibility of all anaerobic isolates.

Porphyromonas gingivalis prevalence related to other micro-organisms in adult refractory periodontitis

Forty-six adult periodontal patients, selected on the basis of clinical examination, and 46 adult healthy subjects were examined. The subgingival plaque samples from one inflammatory and one non-inflammatory site of each periodontal patient were studied to determine Porphyromonas gingivalis prevalence related to other periodontal micro-organisms and to periodontal tissue destruction. The results showed Porphyromonas gingivalis as the main pathogenic micro-organism isolated in the inflammatory sites together with Bacteroides forsythus. Peptostreptococcus sp., Actinomyces sp. and Prevotella sp. were found as a normal oral flora in the healthy subjects. Fusobacterium nucleatum, Prevotella intermedia, Campylobacter rectus and Eikenella corrodens were detected both in inflammatory and in non-inflammatory sites of periodontal patients as well as in the healthy subjects.

Prevalence of nim genes in anaerobic/facultative anaerobic bacteria isolated in South Africa

This study investigated the prevalence of nim genes (proposed to encode a 5-nitroimidazole resistance product) in 64 anaerobic/facultative anaerobic bacteria. Employing universal nim gene primers, 458-bp amplified fragments were recorded as presumptive positives in 22/64 strains at an annealing temperature of 52 degrees C and 15/64 strains at 62 degrees C, of which seven were propionibacteria. DNA sequencing confirmed the presence of nimA genes in Propionibacterium spp. (five strains), Actinomyces odontolyticus (one strain), Prevotella bivia (one strain) and Clostridium bifermentans (one strain) and nimB genes from five strains of Bacteroides fragilis. nimA genes were predominant in propionibacteria indicating a potential nimA gene source in anaerobic environments.

Subgingival microflora associated with nifedipine-induced gingival overgrowth

The purpose of this study was to examine the composition of subgingival plaque of 140 periodontal lesions in 35 patients with cardiovascular disorders who were administered nifedipine and manifested nifedipine-induced gingival overgrowth (GO). Age was inversely associated with the GO. Plaque index and bleeding index showed a significant association with GO, while nifedipine dosage and duration of nifedipine therapy were not found to be significant predictors of GO. The gingival inflammation as expressed in the logistic regression model by the interaction term color x tone was found to be significantly associated with the GO. Statistically significant differences between the groups of comparable probing depth and different degrees of GO were detected for Propionibacterium acnes, Capnocytophaga gingivalis, Capnocytophaga ochracea, Capnocytophaga sputigena, Bacteroides gracilis, Fusobacterium mortiferum, Fusobacterium nucleatum, Fusobacterium varium and Selenomonas sputigena in deep and enlarged lesions. Significantly more frequently isolated were the bacterial species Eubacterium alactolyticum, Campylobacter concisus, C. gingivalis, C. ochracea, C. sputigena, F. mortiferum, F. nucleatum, and F. varium from the more enlarged lesions (GO >3).

Microbiota of health, gingivitis, and initial periodontitis

This study compared the subgingival microbiota in periodontal health, gingivitis and initial periodontitis using predominant culture and a DNA probe, checkerboard hybridization method. 56 healthy adult subjects with minimal periodontal attachment loss were clinically monitored at 3-month intervals for 12 months. More sites demonstrated small increments of attachment loss than attachment gain over the monitoring period. Sites, from 17 subjects, showing > or = 1.5 mm periodontal attachment loss during monitoring were sampled as active lesions for microbial analysis. Twelve subjects demonstrated interproximal lesions, and 5 subjects had attachment loss at buccal sites (recession). Cultural studies identified Bacteroides forsythus, Campylobacter rectus, and Selenomonas noxia as the predominant species associated with active interproximal lesions (9 subjects), whereas Actinomyces naeslundii, and Streptococcus oralis, were the dominant species colonizing buccal active sites. A. naeslundii, Campylobacter gracilis, and B. forsythus (at lower levels than active sites) were the dominant species cultured from gingivitis (10 subjects). Health-associated species (10 subjects) included Streptococcus oralis, A. naeslundii, and Actinomyces gerencseriae. DNA probe data identified higher mean levels of B. forsythus and C. rectus with active (7 subjects) compared to inactive periodontitis sites. Porphyromonas gingivalis and Actinobacillus actinomycetemcomitans were detected infrequently. Cluster analysis of the cultural microbiota grouped 8/9 active interproximal lesions in one subcluster characterized by a mostly gram-negative microbiota, including B. forsythus and C. rectus. The data suggest that B. forsythus C. rectus and S. noxia were major species characterizing sites converting from periodontal health to disease. The differences in location and microbiota of interproximal and buccal active sites suggested that different mechanisms may be involved in increased attachment loss.

Changes in normal vaginal flora of African green monkeys (Cercopithecus aethiops) during the menstrual cycle

Changes in normal vaginal flora of African green monkeys associated with the estrous cycle were examined by the swab method. Bacteroidaceae, corynebacteria, and streptococci were predominant throughout the whole estrous cycle, although individual differences were great. It was also clear that all bacterial species tended to decrease in the menstrual phase. Lactobacilli, the most predominant bacteria in the normal vagina of humans, were detected only in very low numbers in the African green monkey, suggesting that the normal vagina of the African green monkey has a different ecosystem from that of normal human vaginal flora.

Microbial findings of deep peri-implant bone defects

The objective of this study was to examine inflammatory tissue in deep peri-implant bone pockets (> 5 mm) for anaerobic bacteria colonization. The peri-implant inflammatory tissue of bone defects from 12 edentulous patients with 18 unsuccessful implants (IMZ type) was removed after surgical opening of the defects. After grinding the tissue with glass beads in nutrient solution, an aliquot of the suspension was plated and incubated on appropriate culture media. The quantitative and qualitative distribution of bacteria as a function of the tissue dry weight was determined (cell count/mg dry weight). The mean total cell count was 67 x 10(3) cells/mg dry weight. The following bacteria dominated: species of the family Bacteroidaceae (Prevotella intermedia, Prevotella buccae, Prevotella oralis, Prevotella melaninogenica, Prevotella denticola); Actinobacillus actinomycetemcomitans; Fusobacterium nucleatum; Capnocytophaga spp; and Eikenella corrodens. Bacteroidaceae and Actinobacillus actinomycetemcomitans were found particularly frequently. The increased colonization of these bacteria in deep peri-implant bone pockets is consistent with the currently held view of advanced periodontal lesions, whereby certain pathogens grow at a disproportionate rate in comparison with the total bacteria count under specific circumstances.

Human root caries: microbiota of a limited number of root caries lesions

The microbiota of root caries lesions of different grades of severity were studied. Fourteen lesions were examined. The experimental design of the study allowed correlation of histopathologically distinguishable stages with specific and distinct microbial populations. Dentin samples were ground in a sterile mortar and cultured anaerobically on nonselective Columbia blood agar plates supplemented with 5% hemolyzed human blood and on media selective for Lactobacillus spp. and streptococci. The cultivable microbiota were quantitatively speciated using Rapid ID 32A, Rapid ID 32 Strep, API 20 Strep, APIZYM, and API50 CH tests and SDS-PAG electrophoresis. In initial as well as in advanced lesions gram-positive bacteria accounted for approximately 90% of the CFUt. The proportion of Actinomyces, and in particular A. naeslundii was significantly higher (p < 0.05) in initial lesions than in advanced lesions. In contrast, the percentage of Streptococcus and especially S. mutans was higher (p < 0.05) in advanced than in initial lesions. Surprisingly low (0.8% of the CFUt) was the percentage of lactobacilli in advanced lesions. Gram-negative bacteria formed a minor part of the microbiota in both initial and advanced lesions. Among the gram-negative isolates, Prevotella, Selenomonas, and Bacteroides spp. were most noticeable. In advanced lesions, only the outermost layer of 0.5 mm thickness was populated by a high number of bacteria; the following segments harbored a negligible number of bacteria only. It is concluded that root caries is a continuous destruction process which is restricted to a subsurface zone of limited depth. The necrotic dentin is successively worn away, leading to a saucer-shaped cavitation which is repopulated by plaque. The creation of cavitations favors an aciduric flora. This might explain the succession of bacterial populations observed during the destruction process.

Environmental microbial contamination. Pilot study in a dental surgery

Environmental contamination by bacterial aerosols occurs every day in the dental surgery. The aim of this study was to determine bacterial levels in five different areas of a dental surgery during ultrasonic scaling procedures using bacterial cultures. Two areas with markedly different amounts of infective aerosols were identified. The role of the air conditioning system was also assessed. There was evidence that the air conditioning system could act as a vehicle for the transmission of microorganisms.

Clinical and microbiological changes associated with the use of 4 adjunctive systemically administered agents in the treatment of periodontal infections

The purpose of the present investigation was to assess the effects of periodontal surgery and 4 systemically administered agents, Augmentin, tetracycline, ibuprofen or a placebo on clinical and microbiological parameters of periodontal disease. 98 subjects were monitored at 2-month intervals at 6 sites per tooth for clinical parameters. Subgingival plaque samples were taken from the mesial surface of each tooth at each visit and evaluated for their content of 14 subgingival species using DNA probes and a colony lift method. 40 subjects who exhibited loss of attachment > 2.5 mm at 1 or more sites during longitudinal monitoring were treated using modified Widman flap surgery at sites with probing pocket depth > 4 mm, subgingival scaling at all other sites and were randomly assigned 1 of the 4 agents. Treatment was completed within 30 days during which time the subject took the assigned agent. Overall, subjects exhibited a mean attachment level "gain" of 0.34 +/- 0.10 mm (SEM) and a mean pocket depth reduction of 0.62 +/- 0.09 mm 10 +/- 4 months post-therapy. However, certain subjects in each treatment group showed a poor response. Subjects receiving antibiotics exhibited significantly more attachment level "gain" (0.57 +/- 0.15 mm, SEM) than subjects receiving either ibuprofen or a placebo (0.02 +/- 0.10). The differences between Augmentin and tetracycline groups were not significant, nor were the differences between ibuprofen and placebo. 10 months post-therapy, there was a reduction in the number of sites colonized in any subject group by detectable levels (10(3)) of P. gingivalis. Species showing similar reductions were B. forsythus, P. intermedia and P. micros. Subjects receiving systemically administered antibiotics had a significant increase in the proportion of sites colonized by C. ochracea coupled with a greater decrease in the number of sites colonized by P. gingivalis, B. forsythus, P. intermedia and P. micros post-therapy than subjects not receiving antibiotics. The results of this investigation indicate that adjunctive systemic antibiotics increase periodontal attachment "gain" and decrease the levels of some suspected periodontal pathogens in subjects with evidence of current disease progression.

Activity of ampicillin/sulbactam, ticarcillin/clavulanate, clarithromycin, and eleven other antimicrobial agents against anaerobic bacteria isolated from infections in children

The activity of 14 antimicrobial agents against 253 clinical isolates of anaerobic bacteria from pediatric infections was assessed by the agar dilution method. Fifty-eight percent of the isolates were from intraabdominal sites. The drugs tested were ampicillin/sulbactam, ticarcillin/clavulanate, ampicillin, sulbactam, piperacillin, cefoxitin, cefotaxime, cefoperazone/sulbactam, clarithromycin, azithromycin, erythromycin, clindamycin, metronidazole, and chloramphenicol. Ticarcillin/clavulanate was active against all isolates. Clarithromycin was the most active macrolide; combination of this agent with its 14-hydroxy metabolite did not result in synergy. Sixty-two percent of Bacteroides fragilis group isolates, 13% of B. fragilis isolates, and 22% of peptostreptococcal isolates were resistant to clindamycin at a concentration of 4 micrograms/mL. The distribution of these strains in clinical specimens and the patterns of antimicrobial susceptibility documented were different from the findings for isolates from adults in the Los Angeles area.

Isolation and characteristics of a wheatbran-degrading Butyrivibrio from human faeces

Screening over 100 isolates from human faeces for cellulolytic activity led to the isolation of a weakly cellulolytic anaerobic, curved, motile bacterium which produced H2, lactate and butyrate from wheatbran. The mol% of G + C in the DNA was 39-42. These properties, together with the Gram-positive cell wall ultrastructure and SDS-PAGE profile, are consistent with the genus Butyrivibrio. The isolate is believed to be the most active wheatbran-degrading bacterium so far described.

Periodontopathogens in elderly Chinese with different periodontal disease experience

If an etiological relationship exists between destructive periodontal disease and putative periodontopathogens, they would be expected to have a very low prevalence in periodontally healthy elderly persons. To test this hypothesis, 2 subgroups of elderly, rural Chinese (a periodontally "best" and a "worst" group, each comprising 15 persons) were identified in 1990 from a cohort aged 55-69 years, examined in 1984. Assessment of changes in periodontal status over the 6-year period were possible by comparing detailed clinical recordings performed by the same examinator. Subgingival microbial samples were taken at the mesial aspects of an upper central incisor and a lower canine and examined for the presence of Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia group, Prevotella melaninogenica group, Capnocytophaga, Selenomonas, Campylobacter rectus as well as predominant Streptococcus and Actinomyces species. During the 6 years prior to microbiological sampling, persons in the "best" group had lost an average of 1.21 +/- 0.48 mm attachment, while persons in the "worst" group had lost an average of 1.60 +/- 0.94 mm. The latter group had lost 53.3 teeth, predominantly for periodontal reasons, in contrast to 1.8 teeth lost in the "best" group. "Best" persons did not differ from "worst" persons with respect to the occurrence of the putative periopathogens, total viable count, and total streptococcal and Actinomyces recovery. Similarly, sites which had experienced an attachment loss > or = 2 mm during the 6-year period did not differ microbiologically from sites with less attachment loss. It is concluded that subgingival microbial characterization does not allow for a distinction between elderly individuals with markedly different periodontal disease experiences.

Human root caries: microbiota in plaque covering sound, carious and arrested carious root surfaces

The plaque microbiota covering sound or carious root surfaces were studied and compared with that covering arrested root caries lesions. From each of these categories five extracted teeth were examined. The experimental design of the study allowed us to relate the qualitative and quantitative microbial composition to the degree of integrity of the root surface. Plaque was sampled by a newly developed 'mowing' technique. Plaque samples were cultured anaerobically on nonselective Columbia blood agar plates supplemented with 5% hemolyzed human blood and on media selective for Lactobacillus spp. and streptococci of the mutans group. The cultivable microbiota were quantitatively speciated using Rapid ID 32A, Rapid ID 32 Strep, API 20 Strep, API ZYM, and API 50 CH tests and SDS-PAG electrophoresis. Regardless of the state of mineralization, the microbiota on all surfaces resembled marginal plaque associated with gingivitis. In addition to the gram-positive predominant facultative anaerobic genera Streptococcus, Staphylococcus, Lactobacillus and Actinomyces, gram-negative anaerobes, predominantly Bacteroides, Prevotella, Selenomonas, Fusobacterium, Leptotrichia, and Capnocytophaga, showed the highest isolation frequencies. On all surfaces Actinomyces spp. predominated, with streptococci and lactobacilli forming a minor part of the microbiota. With respect to the detected proportions of anaerobes, microaerophiles, Actinomyces naeslundii, Prevotella buccae and Selenomonas dianae, significant differences were observed between the three categories of root surfaces. The total CFU's on both caries-free and caries-active surfaces were significantly higher than on arrested lesions. In general, the results support a polymicrobial etiology for caries initiation on root surfaces, with A. naeslundii, Capnocytophaga spp., and Prevotella spp. making specific contributions to the processes of cementum and dentin breakdown.

Progress in the identification of nonmotile Bacteroidaceae from dental plaque

Over the last decade, biochemical and chemical analyses have been used widely to study the intrageneric structure of Bacteroidaceae. New chromogenic substrates (e.g., naphthylamide-linked compounds) and fluorogenic substrates (e.g., 4-methylumbelliferyl or 7-amido-4-methyl-coumarin compounds) can be used to identify certain species within a few hours under aerobic conditions. Clarification of the taxonomy of many oral anaerobic species that are now considered important putative periodontal pathogens has permitted the development of panels of both polyclonal and monoclonal antibodies for their detection. Similarly, both DNA and RNA gene probes, derived through nucleic acid sequence analysis, have been constructed for several species; many such probes are now commercially available. In the long term, the application of these techniques will lead to a better understanding of the distribution, transmission, and ecological and clinical importance of many species that have hitherto remained poorly characterized.

Natural distribution of 5 bacteria associated with periodontal disease

The purpose of this study was to determine the prevalence and distribution of 5 bacterial pathogens in subgingival plaque, their relationship with each other and probing depth. Plaque was collected from 6905 sites in 938 subjects. A bacterial concentration fluorescence immunoassay and bacterial specific monoclonal antibodies were used to determine the presence and level of P. gingivalis (Pg), A. actinomycetemcomitans (Aa), P. intermedia (Pi), E. corrodens (Ec) and F. nucleatum (Fn) in each plaque sample. The prevalence in subjects was lowest for Pg (32%) and highest for Ec (49%). The site-based frequency distribution of these bacterial species ranged from 10.3% for Pg to 18.7% for Ec. Pi and Ec were the bacterial combination most often found together in a subject (27.2%). While 64.0% of the sites were without any of the 5 bacterial species evaluated, 20.2% had only 1 of the 5 bacterial species evaluated. The remaining 15.8% of sites had at least 2 bacteria species present. There was a general linear association of the detection level of bacterial species and probing depth. The odds ratios were 3.9 (Pg), 3.0 (Aa), 4.0 (Pi), 2.7 (Ec) and 2.8 (Fn) of finding high levels of these bacterial pathogens at > 5 mm probing depth (p < or = 0.01). Mean probing depth at molar sites without a specific bacteria was greater (p < or = 0.01) in subjects with a specific bacterium compared to molar sites in subjects without the bacteria.(ABSTRACT TRUNCATED AT 250 WORDS)

Endocarditis caused by a Leptotrichia buccalis-like bacterium in a patient with a prosthetic aortic valve

The isolation of a Leptotrichia buccalis-like bacterium from the blood of a patient with endocarditis associated with a prosthetic aortic valve is reported. The organism was isolated from different blood cultures. It was similar but not completely identical to Leptotrichia buccalis. The microbiological identification was confirmed independently by three laboratories, including two reference institutions. The case and the characteristics of the microorganism are reported.

Black-pigmented gram-negative anaerobes in periodontitis

Black-pigmented Gram-negative anaerobes have been associated with periodontal disease and tooth loss since they were first isolated by Burdon in 1928. Porphyromonas gingivalis, which is usually not isolated from children, adolescents or adults with no periodontal breakdown, has been recognized as one of the most important periodontopathogens. Its presence is strongly correlated with deep periodontal pockets, which are assumed to be its main habitat. Correlations have been shown also with attachment loss, clinical inflammation and serum antibody levels, indicating an aetiological role in the periodontal disease. Their pathogenicity in animal models resembling periodontal disease is documented. They are frequently isolated from periodontal abscesses. The relationship between Prevotella intermedia and periodontal disease is not clear. It is frequently isolated from advanced periodontitis, often as the only black-pigmented Gram-negative anaerobic species; however, the prevalence in adults with no periodontal breakdown is high. It is found frequently in periodontal abscesses and in acute necrotizing and ulcerative gingivitis. Serogroup I is found predominantly in deep periodontal pockets, whereas all serogroups (I-III) are found in shallow pockets and gingivitis. No conclusive difference in pathogenicity between serogroups has been found. Pr. melaninogenica, Pr. denticola and Pr. loescheii are frequently found in the gingival crevice in preschool children and other age groups with gingivitis, but are seldom found in deep periodontal pockets.

Black-pigmented gram-negative anaerobes in genito-urinary tract and pelvic infections

Black-pigmented Gram-negative anaerobes are part of the normal vaginal flora and contribute to a range of superficial and deep genital infections. Prevotella melaninogenica is found in moderate numbers (10(4-6) cfu/g) in healthy women; the numbers and detection rates increase in anaerobic vaginosis (where it may be a significant contributor to changed microbial metabolic activity that gives the signs and symptoms of this condition) and in other vaginal infective conditions. Pr. melaninogenica is also part of the mixed flora in deep pelvic infections: endometritis, post-partum and post-abortal uterine infections; salpingitis and tubo-ovarian abscesses; PID and pelvic abscesses. Porphyromonas asaccharolytica is probably not a vaginal commensal, but may be isolated from patients with vaginal or pelvic disease. It is more specifically associated with superficial abscesses (e.g. Bartholin's abscess) and ulcers of the genitalia and perineum. P. asaccharolytica was the commonest species isolated from men with genital ulcers of various primary causes and ranging in severity from superficial balanitis/balanoposthitis to synergic gangrene.