Bacteriocin production by Actinobacillus actinomycetemcomitans isolated from the oral cavity of humans with periodontal disease, periodontally healthy subjects and marmosets

Biogeography of Bacterial Communities and Specialized Metabolism in Human Aerodigestive Tract Microbiomes

The aerodigestive tract (ADT) is the primary portal through which pathogens and other invading microbes enter the body. As the direct interface with the environment, we hypothesize that the ADT microbiota possess biosynthetic gene clusters (BGCs) for antibiotics and other specialized metabolites to compete with both endogenous and exogenous microbes. From 1,214 bacterial genomes, representing 136 genera and 387 species that colonize the ADT, we identified 3,895 BGCs. To determine the distribution of BGCs and bacteria in different ADT sites, we aligned 1,424 metagenomes, from nine different ADT sites, onto the predicted BGCs. We show that alpha diversity varies across the ADT and that each site is associated with distinct bacterial communities and BGCs. We identify specific BGC families enriched in the buccal mucosa, external naris, gingiva, and tongue dorsum despite these sites harboring closely related bacteria. We reveal BGC enrichment patterns indicative of the ecology at each site. For instance, aryl polyene and resorcinol BGCs are enriched in the gingiva and tongue, which are colonized by many anaerobes. In addition, we find that streptococci colonizing the tongue and cheek possess different ribosomally synthesized and posttranslationally modified peptide BGCs. Finally, we highlight bacterial genera with BGCs but are underexplored for specialized metabolism and demonstrate the bioactivity of Actinomyces against other bacteria, including human pathogens. Together, our results demonstrate that specialized metabolism in the ADT is extensive and that by exploring these microbiomes further, we will better understand the ecology and biogeography of this system and identify new bioactive natural products.

IMPORTANCE Bacteria produce specialized metabolites to compete with other microbes. Though the biological activities of many specialized metabolites have been determined, our understanding of their ecology is limited, particularly within the human microbiome. As the aerodigestive tract (ADT) faces the external environment, bacteria colonizing this tract must compete both among themselves and with invading microbes, including human pathogens. We analyzed the genomes of ADT bacteria to identify biosynthetic gene clusters (BGCs) for specialized metabolites. We found that the majority of ADT BGCs are uncharacterized and the metabolites they encode are unknown. We mapped the distribution of BGCs across the ADT and determined that each site is associated with its own distinct bacterial community and BGCs. By further characterizing these BGCs, we will inform our understanding of ecology and biogeography across the ADT, and we may uncover new specialized metabolites, including antibiotics.

Metabolites of the Oral Microbiome: Important Mediators of Multi-Kingdom Interactions

The oral cavity hosts over 700 different microbial species that produce a rich reservoir of bioactive metabolites critical to oral health maintenance. Over the last two decades, new insights into the oral microbiome and its importance in health and disease have emerged mainly due to the discovery of new oral microbial species using next-generation sequencing (NGS). This advancement has revolutionized the documentation of unique microbial profiles associated with different niches and health/disease states within the oral cavity and the relation of the oral bacteria to systemic diseases. However, less work has been done to identify and characterize the unique oral microbial metabolites that play critical roles in maintaining equilibrium between the various oral microbial species and their human hosts. This article discusses the most significant microbial metabolites produced by these diverse communities of oral bacteria that can either foster health or contribute to disease. Finally, we shed light on how advances in genomics and genome mining can provide a high throughput platform for discovering novel bioactive metabolites derived from the human oral microbiome to tackle emerging human infections and systemic diseases.

Bacteriocin-mediated interactions within and between coexisting species

Bacteriocins are bacteriocidal toxins released by almost all bacteria. They are thought to have a narrow range of killing, but as bacteriocin-mediated interactions have been rarely studied at biologically relevant scales, whether this narrow range of action falls mostly within or mostly between coexisting species in natural communities is an open question with important ecological and evolutionary implications. In a previous study, we systematically sampled Xenorhabdus bacteria along a hillside and found evidence for genotypic variability and bacteriocin-mediated interactions within Xenorhabdus bovienii and X. koppenhoeferi colonies that were collected only a few meters apart. In contrast, colonies that were isolated from the same soil sample were always genetically similar and showed no inhibitions. Here, we conducted pairwise growth-inhibition assays within and between seven X. bovienii and five X. koppenhoeferi colonies that were isolated from different soil samples; all seven X. bovienii colonies and at least three of the X. koppenhoeferi have been distinguished as distinct genotypes based on coarse-grain genomic markers. We found signatures for both conspecific and heterospecific bacteriocin inhibitions in this natural community of Xenorhabdus bacteria, but intraspecific inhibitions were significantly more common than interspecific inhibitions. These results suggest that bacteriocins have a major role in intraspecific competition in nature, but also suggest that bacterocins are important in mediating interspecific interactions among coexisting species in natural communities.

Spiteful Interactions in a natural population of the bacterium Xenorhabdus bovienii

An individual behaves spitefully when it harms itself in the act of harming other individuals. One of the clearest potential examples of spite is the costly production and release of toxins called bacteriocins. Bacteriocins are toxins produced by bacteria that can kill closely related strains of the same species. Theoretical work has predicted that bacteriocin-mediated interactions could play an important role in maintaining local genetic and/or species diversity, but these interactions have not been studied at biologically relevant scales in nature. Here we studied toxin production and among-strain inhibitions in a natural population of Xenorhabdus bovienii. We found genetic differences and inhibitions between colonies that were collected only a few meters apart. These results suggest that spite exists in natural populations of bacteria.

Production of antagonistic substance by Eikenella corrodens isolated from the oral cavity of human beings with and without periodontal disease

AIMS

Antagonistic abilities may confer ecological advantages for micro-organisms in competitive ecosystems. However, reports regarding this phenomenon in Eikenella corrodens are not available.

METHODS AND RESULTS

Nineteen E. corrodens strains, isolated from the oral cavity of human beings without periodontal disease (n = 5) and with aggressive (n = 9) and chronic (n = 5) periodontitis, as well as a reference strain (E. corrodens ATCC23834), were evaluated for antagonistic activity. The following indicators were used: Porphyromonas gingivalis FDC381, Prevotella intermedia ATCC25611, Actinomyces israelii ATCC12102, Eubacterium lentum ATCC25559, Peptostreptococcus anaerobius ATCC27337, Actinobacillus actinomycetemcomitans FDCY4, Fusobacterium nucleatum ATCC10953, Streptococcus sanguinis ATCC10557, Streptococcus uberis ATCC9927, Streptococcus mutans IM/UFRJ, Staphylococcus aureus ATCC33591 and Candida albicans ATCC18804. All the strains showed antagonism against at least one of the indicator strains. This phenomenon was more frequently observed for strains isolated from patients with chronic periodontitis (36.4%), than those from healthy subjects (20.6%) and those with aggressive periodontitis (10.8%).

CONCLUSIONS

The heterogeneous antagonistic spectrum exhibited by E. corrodens isolates suggests their ability to produce more than one antagonistic substance, whose ecological relevance is yet to be demonstrated.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first description of antagonistic compound production by E. corrodens and its relationships with the clinical status of the patients.

Purification and partial characterization of a bacteriocin produced by Eikenella corrodens

AIMS

The purpose of this study was to purify and characterize a bacteriocin produced by Eikenella corrodens A32E2.

METHODS AND RESULTS

Peptostreptococcus anaerobius ATCC27337 was used as indicator strain in antagonistic assays for bacteriocin-producing E. corrodens A32E2. Protein extraction was influenced by pH and buffer composition. The protein was active in the pH range 6-8. Inhibitory activity was lost by both heating and treatment with proteolytic enzymes and decreased with organic solvents. The substance is rather unstable but maintains 100% of its activity after being exposed to acetone and when stored at -70 degrees C. The antagonistic substance was first precipitated by ammonium sulfate and further partially purified by Mono-Q FPLC and C-18 HPLC. Mass spectrometry analysis showed that the molecular mass was 23 625 Da, and the sequence obtained for the N-terminus was: Met-Asn-Phe-Asp-Glu-Lys-Val-Gly-Lys-Val-X-Phe-Lys-Val-Gly-Asp.

CONCLUSIONS

The evidence presented in this study supports the idea that an antagonistic substance produced by E. corrodens A32E2 isolated from a periodontal diseased site is a novel bacteriocin, which we designate corrodecin.

SIGNIFICANCE AND IMPACT OF THE STUDY

We anticipated that corrodecin might play an important role at the periodontal site. This compound could also be attractive in biotechnological applications as an interesting tool for oral ecosystem control.

Influence of abiotic factors on the bacteriocinogenic activity of Actinobacillus actinomycetemcomitans

We evaluated the influence of abiotic factors on antagonistic activity of Actinobacillus actinomycetemcomitans strains isolated from periodontal pockets and two reference strains (ATCC 29523 and FDC Y4). Antagonistic assays were performed by the overlayer method on tryptic soy agar (TSA), brain heart infusion agar, thioglycollate agar and brucella agar, added with yeast extract and supplemented (S) or not with L-cystine and sodium bicarbonate. Iso-, auto-, and heteroantagonism against a wide range of indicator strains were assayed. The influence of incubation atmosphere (anaerobic chamber, anaerobic and candle jars) and pH (5.0 to 11.0) was also evaluated. Autoantagonism was not observed. TSA-S was shown to be the most adequate medium for antagonistic activity expression. The widest spectrum of heteroantagonistic activity was also observed on TSA-S. The incubation atmosphere affected only the isoantagonistic activity expression. Only at pH 8.0 did A. actinomycetemcomitans express bacteriocinogenic activity. The lack of standardized methodology to detect antagonistic activity can lead to discrepant results and can make data difficult to be compared. This study provides information on abiotic factors that influence bacteriocinogenic activity expression and suggests adequate culture conditions for testing A. actinomycetemcomitans bacteriocin production, contributing to the establishment of a reproducible and reliable methodology.