Transcriptional profiling of coaggregation interactions between Streptococcus gordonii and Veillonella parvula by Dual RNA-Seq

Abstract

Many oral bacteria form macroscopic clumps known as coaggregates when mixed with a different species. It is thought that these cell-cell interactions are critical for the formation of mixed-species biofilms such as dental plaque. Here, we assessed the impact of coaggregation between two key initial colonizers of dental plaque, Streptococcus gordonii and Veillonella parvula , on gene expression in each partner. These species were shown to coaggregate in buffer or human saliva. To monitor gene regulation, coaggregates were formed in human saliva and, after 30 minutes, whole-transcriptomes were extracted for sequencing and Dual RNA-Seq analysis. In total, 272 genes were regulated in V. parvula , including 39 genes in oxidoreductase processes. In S. gordonii , there was a high degree of inter-sample variation. Nevertheless, 69 genes were identified as potentially regulated by coaggregation, including two phosphotransferase system transporters and several other genes involved in carbohydrate metabolism. Overall, these data indicate that responses of V. parvula to coaggregation with S. gordonii are dominated by oxidative stress-related processes, whereas S. gordonii responses are more focussed on carbohydrate metabolism. We hypothesize that these responses may reflect changes in the local microenvironment in biofilms when S. gordonii or V. parvula immigrate into the system.

Spatial scale in analysis of the dental plaque microbiome

“…Chemical interaction among oral biofilm members may be either synergistic or antagonistic 97 . Although secreted molecules have the potential to exert their effects over long distances due to the dispersive effect of diffusion, we include these interactions in our discussion of microscale inputs because, in practice, the close apposition of microbial cells 98 and the dense extrapolymeric matrix greatly restrict the diffusion of molecules within dental plaque biofilms 99 . In contrast to human gut microbial communities, in which inferred co‐occurrence patterns and known metabolic capacities suggest high levels of competition for overlapping resources that result in niche partitioning, there is strong evidence for metabolic cooperation in dental plaque communities 100 .…”

Iron Supplementation Eliminates Antagonistic Interactions Between Root-Associated Bacteria

“…We developed a rapid and reproducible assay to monitor microbe-microbe interactions based on cell viability as an alternative to technically involved methods, such as metagenomic RNAseq or microbial capture in microdroplets (Jackman et al, 2019;Mutha et al, 2019). We adapted an established agar plate based assay used to monitor cell-cell interactions in Saccharomyces cerevisiae (Abelson et al, 1990;Liu et al, 2019).…”

Omics and interspecies interaction

“…Similarly to its partner species, P. gingivalis, S. gordonii is one of the few oral bacterial species for which transcriptomics analyses have been performed to elucidate its transcriptional response to the presence of other microbial species. Two recent studies by the same group examined, via RNA sequencing, how coaggregation (for 30 minutes) of S. gordonii with F. nucleatum 45 or V. parvula 46 dependence on environmental arginine, the availability of which is limited in dental biofilms. 50…”

“…The majority of studies vary greatly in experimental design, as follows: (1) RNASeq analysis of the response of Porphyromonas gingivalis to Candida albicans hyphae after 1 hour of aerobic coincubation in rich medium 40 ; (2) RNASeq analysis of the responses of P. gingivalis and Acinetobacter baumannii to each other after 3 hours of aerobic coincubation as a pellet in phosphate‐buffered saline 35 ; (3) RNASeq analysis of the responses of P. gingivalis to Streptococcus gordonii during a time course of 0, 5, 30, 120, 240, and 360 minutes of aerobic coincubation as a pellet in phosphate‐buffered saline 34 ; (4) RNASeq analysis of mutual responses between different P. gingivalis strains and a 5‐species oral community ( Actinomyces naeslundii , Campylobacter gracilis , Fusobacterium nucleatum , Streptococcus mitis , and Veillonella parvula ) after a time course of 0, 1, 3, and 9 days of anaerobic incubation as biofilm in artificial crevicular fluid 41 ; (5) microarrray analysis of the responses of P. gingivalis to a 5‐species oral community comprising Aggregatibacter actinomycetemcomitans ( Aa ), A. naeslundii , F. nucleatum , Streptococcus oralis , and V. parvula ) after 4 days of anaerobic incubation as biofilm in rich medium 42 ; (6) microarray analysis of the responses of P. gingivalis and Treponema denticola to each other after 4 days of anaerobic coincubation as batch culture in rich medium 43 ; (7) RNASeq analysis of the responses of S. gordonii and (a) F. nucleatum or (b) V . parvula to each other after 30 minutes of coaggregation in saliva 45,46 ; (8) RNASeq analysis of the response of S. gordonii to C. albicans hyphae after 1 hour of coaggregation in various media 47 ; (9) microarray analysis of the responses of S. gordonii to C. albicans hyphae after 30 minutes of aerobic coincubation as a pellet in rich medium 48 ; (10) microarray analysis of the responses of S. gordonii to A. naeslundii after 3 hours of aerobic coaggregation in chemically defined medium 49 ; (11) RNASeq analysis of the responses of Streptococcus mutans and A. actinomycetemcomitans to each other after a time course of 0, 4, 6, 8, 10, 12, and 24 hours of anaerobic incubation as biofilm in artificial saliva 55 ; (12) RNASeq analysis of the response of S. mutans to C. albicans hyphae after 24 hours of aerobic (5% CO 2 ) incubation as biofilm in rich medium 79 —this study has corresponding proteomic information; (13) RNASeq analysis of the response of S. mutans to C. albicans hyphae after 42 hours of aerobic (5% CO 2 ) incubation as biofilm in rich medium 53 ; (14) microarray analysis of the response of S. mutans to C. albicans hyphae after a time course of 6, 10, and 24 hours of aerobic (5% CO 2 ) incubation as biofilm in rich medium 54 ; (15) microarray analysis of the responses of S. mutans to S. mitis after 24 hours of anaerobic incubation as biofilm in chemically defined medium containing 1% sucrose 56 ; (16) microarray analyses of the responses of T. denticola to S. gordonii , S. sanguinis , F. nucleatum , P. intermedia , T. forsythia , or P. gingivalis after 5 hours of anaerobic incubation as pellets in rich medium 44 …”

“…Similarly to its partner species, P. gingivalis , S. gordonii is one of the few oral bacterial species for which transcriptomics analyses have been performed to elucidate its transcriptional response to the presence of other microbial species. Two recent studies by the same group examined, via RNA sequencing, how coaggregation (for 30 minutes) of S. gordonii with F. nucleatum 45 or V. parvula 46 affects the respective transcriptomes. Saliva‐mediated binding to F. nucleatum led to the induction of pathways related to DNA and amino acid metabolism and suppression of phosphotransferase system‐mediated galactose and lactose uptake in S. gordonii .…”