Clifford J. Beall

Distinct and complex bacterial profiles in human periodontitis and health revealed by 16S pyrosequencing.

Periodontitis has a polymicrobial etiology within the framework of a complex microbial ecosystem. With advances in sequencing technologies, comprehensive studies to elucidate bacterial community differences have recently become possible. We used 454 sequencing of 16S rRNA genes to compare subgingival bacterial communities from 29 periodontally healthy controls and 29 subjects with chronic periodontitis. Amplicons from both the V1-2 and V4 regions of the 16S gene were sequenced, yielding 1 393 579 sequences. They were identified by BLAST against a curated oral 16S database, and mapped to 16 phyla, 106 genera, and 596 species. 81% of sequences could be mapped to cultivated species. Differences between health- and periodontitis-associated bacterial communities were observed at all phylogenetic levels, and UniFrac and principal coordinates analysis showed distinct community profiles in health and disease. Community diversity was higher in disease, and 123 species were identified that were significantly more abundant in disease, and 53 in health. Spirochaetes, Synergistetes and Bacteroidetes were more abundant in disease, whereas the Proteobacteria were found at higher levels in healthy controls. Within the phylum Firmicutes, the class Bacilli was health-associated, whereas the Clostridia, Negativicutes and Erysipelotrichia were associated with disease. These results implicate a number of taxa that will be targets for future research. Some, such as Filifactor alocis and many Spirochetes were represented by a large fraction of sequences as compared with previously identified targets. Elucidation of these differences in community composition provides a basis for further understanding the pathogenesis of periodontitis.

Arthrin, a myofibrillar protein of insect flight muscle, is an actin-ubiquitin conjugate

Flight muscles of some insects contain a myofibrillar protein termed arthrin, which is closely related to actin (mw 43,000). Here we demonstrate that arthrin (mw 55,000) is ubiquitinated actin. We show that in Act88FM342, a flightless Drosophila mutant wherein the Act88F actin gene specifies a glu93----lys replacement, isoelectric points of both actin III and arthrin are shifted, revealing that both are encoded by the same gene. Arthrin reacts with an anti-ubiquitin antibody, which demonstrates that its extra mass results from ubiquitin ligation. Approximately one-seventh of myofibrillar actin is stably ubiquitinated, suggesting that there may be one arthrin molecule per actin-tropomyosin-troponin cooperative unit. Arthrin formation lags several hours behind that of actin III, implying that ubiquitination coincides with some aspect of myofibril assembly.

Beyond Streptococcus mutans: Dental Caries Onset Linked to Multiple Species by 16S rRNA Community Analysis

Dental caries in very young children may be severe, result in serious infection, and require general anesthesia for treatment. Dental caries results from a shift within the biofilm community specific to the tooth surface, and acidogenic species are responsible for caries. Streptococcus mutans, the most common acid producer in caries, is not always present and occurs as part of a complex microbial community. Understanding the degree to which multiple acidogenic species provide functional redundancy and resilience to caries-associated communities will be important for developing biologic interventions. In addition, microbial community interactions in health and caries pathogenesis are not well understood. The purpose of this study was to investigate bacterial community profiles associated with the onset of caries in the primary dentition. In a combination cross-sectional and longitudinal design, bacterial community profiles at progressive stages of caries and over time were examined and compared to those of health. 16S rRNA gene sequencing was used for bacterial community analysis. Streptococcus mutans was the dominant species in many, but not all, subjects with caries. Elevated levels of S. salivarius, S. sobrinus, and S. parasanguinis were also associated with caries, especially in subjects with no or low levels of S. mutans, suggesting these species are alternative pathogens, and that multiple species may need to be targeted for interventions. Veillonella, which metabolizes lactate, was associated with caries and was highly correlated with total acid producing species. Among children without previous history of caries, Veillonella, but not S. mutans or other acid-producing species, predicted future caries. Bacterial community diversity was reduced in caries as compared to health, as many species appeared to occur at lower levels or be lost as caries advanced, including the Streptococcus mitis group, Neisseria, and Streptococcus sanguinis. This may have implications for bacterial community resilience and the restoration of oral health.

CORE: A Phylogenetically-Curated 16S rDNA Database of the Core Oral Microbiome

Comparing bacterial 16S rDNA sequences to GenBank and other large public databases via BLAST often provides results of little use for identification and taxonomic assignment of the organisms of interest. The human microbiome, and in particular the oral microbiome, includes many taxa, and accurate identification of sequence data is essential for studies of these communities. For this purpose, a phylogenetically curated 16S rDNA database of the core oral microbiome, CORE, was developed. The goal was to include a comprehensive and minimally redundant representation of the bacteria that regularly reside in the human oral cavity with computationally robust classification at the level of species and genus. Clades of cultivated and uncultivated taxa were formed based on sequence analyses using multiple criteria, including maximum-likelihood-based topology and bootstrap support, genetic distance, and previous naming. A number of classification inconsistencies for previously named species, especially at the level of genus, were resolved. The performance of the CORE database for identifying clinical sequences was compared to that of three publicly available databases, GenBank nr/nt, RDP and HOMD, using a set of sequencing reads that had not been used in creation of the database. CORE offered improved performance compared to other public databases for identification of human oral bacterial 16S sequences by a number of criteria. In addition, the CORE database and phylogenetic tree provide a framework for measures of community divergence, and the focused size of the database offers advantages of efficiency for BLAST searching of large datasets. The CORE database is available as a searchable interface and for download at http://microbiome.osu.edu.

Functional Nonequivalence of Drosophila Actin Isoforms

We show that different Drosophila actinisoforms are not interchangeable. We sequenced the sixgenes that encode conventional Drosophilaactins and found that they specify amino acidreplacements in 27 of 376 positions. To test the significance ofthese changes we used directed mutagenesis to introduce10 such conversions, independently, into the Act88Fflight muscle-specific actin gene. We challenged these variant actins to replace the nativeprotein by transforming germline chromosomes of aDrosophila strain lacking flight muscle actin.Only one of the 10 reproducibly perturbed myofibrillarfunction, demonstrating that most isoform-specific aminoacid replacements are of minor significance. In order toestablish the consequences of multiple amino acidreplacements, we substituted portions of theDrosophila Act88F actin gene with correspondingregions of genes encoding other isoforms. Only one offive constructs tested engendered normally functioningflight muscles, and the severity of myofibrillar defects correlated with the number of replacementswithin the chimeric genes. Finally, we completelyconverted the flight muscle actin-encoding gene to onespecifying a nonmuscle isoform, a change entailing atotal of 18 amino acid replacements. Transformationof flies with this construct resulted in disruption offlight muscle structure and function. We conclude thatactin isoform sequences are not equivalent and that effects of the amino acid replacements,while minor individually, collectively confer uniqueproperties.

Genetic approaches to myofibril form and function in Drosophila

Myofibrils, the contractile organelles of muscle, are apt subjects for studies on the formation and function of actomyosin networks. Molecular genetic approaches are advancing our understanding of myofibril structure and assembly, and may offer a novel and useful approach for investigating the crossbridge cycle. We review recent progress in Drosophila.

Diversity and genomic insights into the uncultured Chloroflexi from the human microbiota.

Many microbial phyla that are widely distributed in open environments have few or no representatives within animal-associated microbiota. Among them, the Chloroflexi comprises taxonomically and physiologically diverse lineages adapted to a wide range of aquatic and terrestrial habitats. A distinct group of uncultured chloroflexi related to free-living anaerobic Anaerolineae inhabits the mammalian gastrointestinal tract and includes low-abundance human oral bacteria that appear to proliferate in periodontitis. Using a single-cell genomics approach, we obtained the first draft genomic reconstruction for these organisms and compared their inferred metabolic potential with free-living chloroflexi. Genomic data suggest that oral chloroflexi are anaerobic heterotrophs, encoding abundant carbohydrate transport and metabolism functionalities, similar to those seen in environmental Anaerolineae isolates. The presence of genes for a unique phosphotransferase system and N-acetylglucosamine metabolism suggests an important ecological niche for oral chloroflexi in scavenging material from lysed bacterial cells and the human tissue. The inferred ability to produce sialic acid for cell membrane decoration may enable them to evade the host defence system and colonize the subgingival space. As with other low abundance but persistent members of the microbiota, discerning community and host factors that influence the proliferation of oral chloroflexi may help understand the emergence of oral pathogens and the microbiota dynamics in health and disease states.

Multiple Single-Cell Genomes Provide Insight into Functions of Uncultured Deltaproteobacteria in the Human Oral Cavity

Despite a long history of investigation, many bacteria associated with the human oral cavity have yet to be cultured. Studies that correlate the presence or abundance of uncultured species with oral health or disease highlight the importance of these community members. Thus, we sequenced several single-cell genomic amplicons from Desulfobulbus and Desulfovibrio (class Deltaproteobacteria) to better understand their function within the human oral community and their association with periodontitis, as well as other systemic diseases. Genomic data from oral Desulfobulbus and Desulfovibrio species were compared to other available deltaproteobacterial genomes, including from a subset of host-associated species. While both groups share a large number of genes with other environmental Deltaproteobacteria genomes, they encode a wide array of unique genes that appear to function in survival in a host environment. Many of these genes are similar to virulence and host adaptation factors of known human pathogens, suggesting that the oral Deltaproteobacteria have the potential to play a role in the etiology of periodontal disease.

Single Cell Genomics of Uncultured, Health-Associated Tannerella BU063 (Oral Taxon 286) and Comparison to the Closely Related Pathogen Tannerella forsythia

The uncultivated bacterium Tannerella BU063 (oral taxon 286) is the closest relative to the periodontal pathogen Tannerella forsythia, but is not disease-associated itself. Using a single cell genomics approach, we isolated 12 individual BU063 cells by flow cytometry, and we amplified and sequenced their genomes. Comparative analyses of the assembled genomic scaffolds and their gene contents allowed us to study the diversity of this taxon within the oral community of a single human donor that provided the sample. Eight different BU063 genotypes were represented, all about 5% divergent at the nucleotide level. There were 2 pairs of cells and one group of three that were more highly identical, and may represent clonal populations. We did pooled assemblies on the nearly identical genomes to increase the assembled genomic coverage. The presence of a set of 66 “core” housekeeping genes showed that two of the single cell assemblies and the assembly derived from the three putatively identical cells were essentially complete. As expected, the genome of BU063 is more similar to Tannerella forsythia than any other known genome, although there are significant differences, including a 44% difference in gene content, changes in metabolic pathways, loss of synteny, and an 8–9% difference in GC content. Several identified virulence genes of T. forsythia are not found in BU063 including karilysin, prtH, and bspA. The absence of these genes may explain the lack of periodontal pathogenesis by this species and provides a new foundation to further understand the genome evolution and mechanisms of bacterial-host interaction in closely related oral microbes with different pathogenicity potential.

From genes to tensile forces: genetic dissection of contractile protein assembly and function in Drosophila melanogaster

Summary Myofibrils, the contractile organelles of skeletal muscle, are highly ordered and precisely regulated actomyosin networks. Investigations of myofibril assembly are revealing the cellular mechanisms by which contractile components are arranged and regulated. In order to facilitate this research we have developed formal molecdar genetics for myofibrillar proteins of Drosophila flight muscle. Presently, mutations can be used systematically to perturb or eliminate any of the classical myofibrillar proteins within these fibers, and the in vivo consequences can be conveniently ev.aluated using protein electrophoresis, electron microscopy, or by assaying flight performance. Here we review some recent progress.