scholarly journals Microbial Diversity in the EarlyIn Vivo-Formed Dental Biofilm

2016 ◽  
Vol 82 (6) ◽  
pp. 1881-1888 ◽  
Author(s):  
D. Heller ◽  
E. J. Helmerhorst ◽  
A. C. Gower ◽  
W. L. Siqueira ◽  
B. J. Paster ◽  
...  

ABSTRACTAlthough the mature dental biofilm composition is well studied, there is very little information on the earliest phase ofin vivotooth colonization. Progress in dental biofilm collection methodologies and techniques of large-scale microbial identification have made new studies in this field of oral biology feasible. The aim of this study was to characterize the temporal changes and diversity of the cultivable and noncultivable microbes in the early dental biofilm. Samples of early dental biofilm were collected from 11 healthy subjects at 0, 2, 4, and 6 h after removal of plaque and pellicle from tooth surfaces. With the semiquantitative Human Oral Microbiome Identification Microarray (HOMIM) technique, which is based on 16S rRNA sequence hybridizations, plaque samples were analyzed with the currently available 407 HOMIM microbial probes. This led to the identification of at least 92 species, with streptococci being the most abundant bacteria across all time points in all subjects. High-frequency detection was also made withHaemophilus parainfluenzae,Gemella haemolysans,Slackia exigua, andRothiaspecies. Abundance changes over time were noted forStreptococcus anginosusandStreptococcus intermedius(P= 0.02),Streptococcus mitisbv. 2 (P= 0.0002),Streptococcus oralis(P= 0.0002),Streptococcuscluster I (P= 0.003),G. haemolysans(P= 0.0005), andStenotrophomonas maltophilia(P= 0.02). Among the currently uncultivable microbiota, eight phylotypes were detected in the early stages of biofilm formation, one belonging to the candidate bacterial division TM7, which has attracted attention due to its potential association with periodontal disease.

2019 ◽  
Vol 87 (12) ◽  
Author(s):  
Yongli Bi ◽  
Qingan Xu ◽  
Lingkai Su ◽  
Jiantao Xu ◽  
Zhongfang Liu ◽  
...  

ABSTRACT We previously demonstrated that recombinant protein PAc could be administered as an anticaries vaccine. However, the relatively weak immunogenicity of PAc limits its application. In the present study, we investigated the effect of two adjuvant combinations of chitosan plus Pam3CSK4 (chitosan-Pam3CSK4) and of chitosan plus monophosphoryl lipid A (chitosan-MPL) in the immune responses to the PAc protein in vivo and in vitro. PAc-chitosan-Pam3CSK4 or PAc-chitosan-MPL promoted significantly higher PAc-specific antibody titers in serum and saliva, inhibited Streptococcus mutans colonization onto the tooth surfaces, and endowed better protection effect with significantly less caries activities than PAc alone. Chitosan-Pam3CSK4 and chitosan-MPL showed no statistically significant differences. In conclusion, our study demonstrated that the chitosan-Pam3CSK4 and chitosan-MPL combinations are promising for anticaries vaccine development.


2020 ◽  
Vol 86 (8) ◽  
Author(s):  
Wei Luo ◽  
Chao Xue ◽  
Yuzheng Zhao ◽  
Huili Zhang ◽  
Zhiming Rao ◽  
...  

ABSTRACT Blakeslea trispora is an industrial fungal species used for large-scale production of carotenoids. However, B. trispora light-regulated physiological processes, such as carotenoid biosynthesis and phototropism, are not fully understood. In this study, we isolated and characterized three photoreceptor genes, btwc-1a, btwc-1b, and btwc-1c, in B. trispora. Bioinformatics analyses of these genes and their protein sequences revealed that the functional domains (PAS/LOV [Per-ARNT-Sim/light-oxygen-voltage] domain and zinc finger structure) of the proteins have significant homology to those of other fungal blue-light regulator proteins expressed by Mucor circinelloides and Neurospora crassa. The photoreceptor proteins were synthesized by heterologous expression in Escherichia coli. The chromogenic groups consisting of flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) were detected to accompany BTWC-1 proteins by using high-performance liquid chromatography (HPLC) and fluorescence spectrometry, demonstrating that the proteins may be photosensitive. The absorbance changes of the purified BTWC-1 proteins seen under dark and light conditions indicated that they were light responsive and underwent a characteristic photocycle by light induction. Site-directed mutagenesis of the cysteine residual (Cys) in BTWC-1 did not affect the normal expression of the protein in E. coli but did lead to the loss of photocycle response, indicating that Cys represents a flavin-binding domain for photon detection. We then analyzed the functions of BTWC-1 proteins by complementing btwc-1a, btwc-1b, and btwc-1c into the counterpart knockout strains of M. circinelloides for each mcwc-1 gene. Transformation of the btwc-1a complement into mcwc-1a knockout strains restored the positive phototropism, while the addition of btwc-1c complement remedied the deficiency of carotene biosynthesis in the mcwc-1c knockout strains under conditions of illumination. These results indicate that btwc-1a and btwc-1c are involved in phototropism and light-inducible carotenogenesis. Thus, btwc-1 genes share a conserved flavin-binding domain and act as photoreceptors for control of different light transduction pathways in B. trispora. IMPORTANCE Studies have confirmed that light-regulated carotenogenesis is prevalent in filamentous fungi, especially in mucorales. However, few investigations have been done to understand photoinduced synthesis of carotenoids and related mechanisms in B. trispora, a well-known industrial microbial strains. In the present study, three photoreceptor genes in B. trispora were cloned, expressed, and characterized by bioinformatics and photoreception analyses, and then in vivo functional analyses of these genes were constructed in M. circinelloides. The results of this study will lead to a better understanding of photoreception and light-regulated carotenoid synthesis and other physiological responses in B. trispora.


2018 ◽  
Vol 84 (7) ◽  
Author(s):  
Qiang Li ◽  
Bingjian Zhang ◽  
Xiaoru Yang ◽  
Qinya Ge

ABSTRACTResearch on the microbial communities that colonize stone monuments may provide a new understanding of stone biodeterioration and microbe-induced carbonate precipitation. This work investigated the seasonal variation of microbial communities in 2016 and 2017, as well as its effects on stone monuments. We determined the bacterial and fungal compositions of 12 samples from four well-separated geographic locations by using 16S rRNA and internal transcribed spacer gene amplicon sequencing.Cyanobacteriaand Ascomycota were the predominant bacterial and fungal phyla, respectively, and differences in species abundance among our 12 samples and 2 years showed no consistent temporal or spatial trends. Alpha diversity, estimated by Shannon and Simpson indices, revealed that an increase or decrease in bacterial diversity corresponded to a decrease or increase in the fungal community from 2016 to 2017. Large-scale association analysis identified potential bacteria and fungi correlated with stone deterioration. Functional prediction revealed specific pathways and microbiota associated with stone deterioration. Moreover, a culture-dependent technique was used to identify microbial isolates involved in biodeterioration and carbonatogenesis; 64% of 85 bacterial isolates caused precipitation of carbonates in biomineralization assays. Imaging techniques including scanning electron microscopy with energy-dispersive spectroscopy, X-ray diffraction, and fluorescence imaging identified CaCO3crystals as calcite and vaterite. Although CaCO3precipitation induced by bacteria often has esthetically deleterious impacts on stone monuments, this process may potentially serve as a novel, environmentally friendly bacterial self-inoculation approach to the conservation of stone.IMPORTANCEComprehensive analyses of the microbiomes associated with the deterioration of stone monuments may contribute to the understanding of mechanisms of deterioration, as well as to the identification of potentially beneficial or undesirable microbial communities and their genomic pathways. In our study, we demonstrated thatCyanobacteriawas the predominant bacterial phylum and exhibited an increase from 2016 to 2017, whileProteobacteriashowed a decreasing trend. Apart from esthetic deterioration caused by cyanobacteria and fungi, white plaque, which is composed mainly of CaCO3and is probably induced byCrossiellaandCyanobacteria, was also considered to be another threat to stone monuments. We showed that there was no significant correlation between microbial population variation and geographic location. Specific functional genes and pathways were also enriched in particular bacterial species. The CaCO3precipitation induced by an indigenous community of carbonatogenic bacteria also provides a self-inoculation approach for the conservation of stone.


2011 ◽  
Vol 77 (22) ◽  
pp. 8009-8014 ◽  
Author(s):  
Nicole Reichardt ◽  
Andrew R. Barclay ◽  
Lawrence T. Weaver ◽  
Douglas J. Morrison

ABSTRACTThe human intestinal microbiota is a complex biological system comprising a vast repertoire of microbes with considerable metabolic activity relevant to both bacterial growth and host health. Greater strides have been made in the analysis of microbial diversity than in the measurement of functional activity, particularlyin vivo. Stable isotope probing offers a new approach by coupling measurements of metabolic activity with microbial identification. Using a low-enrichment labeling strategyin vitro, this study has identified metabolically active bacterial groups via magnetic-bead capture methodology and stable isotope ratio analysis. Using five probes (EUB338, Bac303, Bif164, EREC482, and Clep866), changes in the activities of key intestinal microbial groups were successfully measured by exploiting tracers ofde novoRNA synthesis. Perturbation of the nutrient source with oligofructose generated changes in the activity of bifidobacteria as expected, but also in theBacteroides-Prevotellagroup, theEubacterium rectale-Clostridium coccoidesgroup, and theClostridium leptumsubgroup. Changes in activity were also observed in response to the medium type. This study suggests that changes in the functional activity of the gut microbiota can be assessed using tracers ofde novonucleic acid synthesis combined with measurement of low isotopic enrichment in 16S rRNA. Such tracers potentially limit substrate bias because they are universally available to bacteria. This low-enrichment labeling approach does not depend on the commercial availability of specific labeled substrates and can be easily translated toin vivoprobing experiments of the functional activity of the microbiota in the human gut.


2020 ◽  
Vol 86 (13) ◽  
Author(s):  
Yunpeng Yang ◽  
Huan Zhang ◽  
Nannan Lang ◽  
Lu Zhang ◽  
Changsheng Chai ◽  
...  

ABSTRACT Small RNAs (sRNAs) are crucial regulatory molecules in organisms and are well-known not only for their roles in the control of diverse crucial biological processes but also for their value in regulation rewiring. However, to date, in Gram-positive anaerobic solventogenic clostridia (a group of important industrial bacteria with exceptional substrate and product diversity), sRNAs remain minimally explored, and thus there is a lack of detailed understanding regarding these important molecules and their use as targets for genetic improvement. Here, we performed large-scale phenotypic screens of a transposon-mediated mutant library of Clostridium acetobutylicum, a typical solventogenic clostridial species, and discovered a novel sRNA (sr8384) that functions as a crucial regulator of cell growth. Comparative transcriptomic data combined with genetic and biochemical analyses revealed that sr8384 acts as a pleiotropic regulator and controls multiple targets that are associated with crucial biological processes through direct or indirect interactions. Notably, the in vivo expression level of sr8384 determined the cell growth rate, thereby affecting the solvent titer and productivity. These findings indicate the importance of the sr8384-mediated regulatory network in C. acetobutylicum. Furthermore, a homolog of sr8384 was discovered and proven to be functional in another important Clostridium species, C. beijerinckii, suggesting the potential broad role of this sRNA in clostridia. Our work showcases a previously unknown potent and complex role of sRNAs in clostridia, providing new opportunities for understanding and engineering these anaerobes. IMPORTANCE The uses of sRNAs as new resources for functional studies and strain modifications are promising strategies in microorganisms. However, these crucial regulatory molecules have hardly been explored in industrially important solventogenic clostridia. Here, we identified sr8384 as a novel determinant sRNA controlling the cell growth of solventogenic Clostridium acetobutylicum. Based on a detailed functional analysis, we further reveal the pleiotropic function of sr8384 and its multiple direct and indirect crucial targets, which represents a valuable source for understanding and optimizing this anaerobe. Of note, manipulation of this sRNA achieves improved cell growth and solvent synthesis. Our findings provide a new perspective for future studies on regulatory sRNAs in clostridia.


mSphere ◽  
2020 ◽  
Vol 5 (5) ◽  
Author(s):  
Brayon J. Fremin ◽  
Ami S. Bhatt

ABSTRACT Ribosome profiling (Ribo-Seq) is a powerful method to study translation in bacteria. However, Ribo-Seq signal can be observed across RNAs that one would not expect to be bound by ribosomes. For example, Escherichia coli Ribo-Seq libraries also capture reads from most noncoding RNAs (ncRNAs). While some of these ncRNAs may overlap coding regions, this alone does not explain the majority of observed signal across ncRNAs. These fragments of ncRNAs in Ribo-Seq data pass all size selection steps of the Ribo-Seq protocol and survive hours of micrococcal nuclease (MNase) treatment. In this work, we specifically focus on Ribo-Seq signal across ncRNAs and provide evidence to suggest that RNA structure, as opposed to ribosome binding, protects them from degradation and allows them to persist in the Ribo-Seq sequencing library preparation. By inspecting these “contaminant reads” in bacterial Ribo-Seq, we show that data previously disregarded in bacterial Ribo-Seq experiments may, in fact, be used to gain partial information regarding the in vivo secondary structure of ncRNAs. IMPORTANCE Structured ncRNAs are pivotal mediators of bioregulation in bacteria, and their functions are often reliant on their specific structures. Here, we first inspect Ribo-Seq reads across noncoding regions, identifying contaminant reads in these libraries. We observe that contaminant reads in bacterial Ribo-Seq experiments that are often disregarded, in fact, strongly overlap with structured regions of ncRNAs. We then perform several bioinformatic analyses to determine why these contaminant reads may persist in Ribo-Seq libraries. Finally, we highlight some structured RNA contaminants in Ribo-Seq and support the hypothesis that structures in the RNA protect them from MNase digestion. We conclude that researchers should be cautious when interpreting Ribo-Seq signal as coding without considering signal distribution. These findings also may enable us to partially resolve RNA structures, identify novel structured RNAs, and elucidate RNA structure-function relationships in bacteria at a large scale and in vivo through the reanalysis of existing Ribo-Seq data sets.


2018 ◽  
Vol 84 (17) ◽  
Author(s):  
Na Li ◽  
Ren-Lei Tong ◽  
Li Yao ◽  
Qing Chen ◽  
Xin Yan ◽  
...  

ABSTRACTThe herbicide dicamba is initially demethylated to 3,6-dichlorosalicylate (3,6-DCSA) inRhizorhabdus dicambivoransNdbn-20 and is subsequently 5-hydroxylated to 3,6-dichlorogentisate (3,6-DCGA). In the present study, two glutathione-dependent 3,6-DCGA dehalogenases, DsmH1 and DsmH2, were identified in strain Ndbn-20. DsmH2 shared a low identity (only 31%) with the tetrachlorohydroquinone (TCHQ) dehalogenase PcpC fromSphingobium chlorophenolicumATCC 39723, while DsmH1 shared a high identity (79%) with PcpC. In the phylogenetic tree of related glutathioneS-transferases (GSTs), DsmH1 and DsmH2, together with PcpC and the 2,5-dichlorohydroquinone dehalogenase LinD, formed a separate clade. DsmH1 and DsmH2 were synthesized inEscherichia coliBL21 and purified as His-tagged enzymes. Both enzymes required glutathione (GSH) as a cofactor and could 6-dechlorinate 3,6-DCGA to 3-chlorogentisatein vitro. DsmH2 had a significantly higher catalytic efficiency toward 3,6-DCGA than DsmH1. Transcription and disruption analysis revealed that DsmH2 but not DsmH1 was responsible for the 6-dechlorination of 3,6-DCGA in strain Ndbn-20in vivo. Furthermore, we propose a novel eta class of GSTs to accommodate the four bacterial dehalogenases PcpC, LinD, DsmH1, and DsmH2.IMPORTANCEDicamba is an important herbicide, and its use and leakage into the environment have dramatically increased since the large-scale planting of genetically modified (GM) dicamba-resistant crops in 2015. However, the complete catabolic pathway of dicamba has remained unknown, which limits ecotoxicological studies of this herbicide. Our previous study revealed that 3,6-DCGA was an intermediate of dicamba degradation in strain Ndbn-20. In this study, we identified two glutathione-dependent 3,6-DCGA dehalogenases, DsmH1 and DsmH2, and demonstrated that DsmH2 is physiologically responsible for the 6-dechlorination of 3,6-DCGA in strain Ndbn-20. GSTs play an important role in the detoxification and degradation of a variety of endogenous and exogenous toxic compounds. On the basis of their sequence identities, phylogenetic status, and functions, the four bacterial GSH-dependent dehalogenases (PcpC, LinD, DsmH1, and DsmH2) were reclassified as a new eta class of GSTs. This study helps us to elucidate the microbial catabolism of dicamba and enhances our understanding of the diversity and functions of GSTs.


Author(s):  
Ioannis Fragkioudakis ◽  
Marcello P. Riggio ◽  
Danae Anastasia Apatzidou

In the mid-1960s the microbial aetiology of periodontal diseases was introduced based on classical experimental gingivitis studies . Since then, numerous studies have addressed the fundamental role that oral microbiota plays in the initiation and progression of periodontal diseases. Recent advances in laboratory identification techniques have contributed to a better understanding of the complexity of the oral microbiome in both health and disease. Modern culture-independent methods such as human oral microbial identification microarray and next-generation sequencing have been used to identify a wide variety of microbial taxa residing in the gingival sulcus and the periodontal pocket. The first theory of the ‘non-specific plaque’ hypothesis gave rise to the ‘ecological plaque’ hypothesis and more recently to the ‘polymicrobial synergy and dysbiosis hypothesis’. Periodontitis is now considered to be a multimicrobial inflammatory disease in which the various bacterial species within the dental biofilm are in a dysbiotic state and this imbalance favours the establishment of chronic inflammatory conditions and ultimately the destruction of tooth-supporting tissues. Apart from the known putative periodontal pathogens, the whole biofilm community is now considered to play a role in the establishment of inflammation and the initiation and progression of periodontitis in a susceptible host. Treatment is unlikely to eliminate putative pathogens but, when it is thoroughly performed it has the potential to establish a healthy ecosystem by altering the microbial community in numbers and composition and also contribute to the maturation of the host immune response.


2019 ◽  
Vol 85 (6) ◽  
Author(s):  
Yi-Ywan M. Chen ◽  
Yi-Chien Chiang ◽  
Tzu-Ying Tseng ◽  
Hui-Yu Wu ◽  
Yueh-Ying Chen ◽  
...  

ABSTRACTStreptococcus sanguinis, dominant in the oral microbiome, is the only known streptococcal species possessing apilgene cluster for the biosynthesis of type IV pili (Tfp). Although this cluster is commonly present in the genome ofS. sanguinis, most of the strains do not express Tfp-mediated twitching motility. Thus, this study was designed to investigate the biological functions encoded by the cluster in the twitching-negative strainS. sanguinisSK36. We found that the cluster was transcribed as an operon, with three promoters located 5′ to the cluster and one in the intergenic region between SSA_2307 and SSA_2305. Studies using promoter-catfusion strains revealed that the transcription of the cluster was mainly driven by the distal 5′ promoter, which is located more than 800 bases 5′ to the first gene of the cluster, SSA_2318. Optimal expression of the cluster occurred at the early stationary growth phase in a CcpA-dependent manner, although a CcpA-binding consensus is absent in the promoter region. Expression of the cluster resulted in a short hairlike surface structure under transmission electron microscopy. Deletion of the putative pilin genes (SSA_2313 to SSA_2315) abolished the biosynthesis of this structure and significantly reduced the adherence of SK36 to HeLa and SCC-4 cells. Mutations in thepilgenes downregulated biofilm formation byS. sanguinisSK36. Taken together, the results demonstrate that Tfp of SK36 are important for host cell adherence, but not for motility, and that expression of thepilcluster is subject to complex regulation.IMPORTANCEThe proteins and assembly machinery of the type IV pili (Tfp) are conserved throughout bacteria and archaea, and yet the function of this surface structure differs from species to species and even from strain to strain. As seen inStreptococcus sanguinisSK36, the expression of the Tfp gene cluster results in a hairlike surface structure that is much shorter than the typical Tfp. This pilus is essential for the adherence of SK36 but is not involved in motility. Being a member of the highly diverse dental biofilm, perhapsS. sanguiniscould more effectively utilize this structure to adhere to host cells and to interact with other microbes within the same niche.


2016 ◽  
Vol 60 (9) ◽  
pp. 5331-5336 ◽  
Author(s):  
M. O. Faruk Khan ◽  
Jennifer Keiser ◽  
P. N. A. Amoyaw ◽  
Mohammad F. Hossain ◽  
Mireille Vargas ◽  
...  

ABSTRACTPraziquantel (PZQ) is the only drug available for the treatment of schistosomiasis, and since its large-scale use might be associated with the onset of resistance, new antischistosomal drugs should be developed. A series of 26 synthetic tetraazamacrocyclic derivatives and their metal complexes were synthesized, characterized, and screened for antischistosomal activity by application of a phased screening program. The compounds were first screened against newly transformed schistosomula (NTS) of harvestedSchistosoma mansonicercariae, then against adult worms, and finally,in vivousing the mouse model ofS. mansoniinfection. At a concentration of 33 μM, incubation with a total of 12 compounds resulted in the mortality of NTS at the 62% to 100% level. Five of these showing 100% inhibition of viability of NTS at 10 μM were selected for further screening for determination of the 50 inhibitory concentrations (IC50s) against both NTS and adult worms. Against NTS, all 5 compounds showed IC50s comparable to the IC50of the standard drug, PZQ (0.87 to 9.65 μM for the 5 compounds versus 2.20 μM for PZQ). Three of these, which are the bisquinoline derivative of cyclen and its Fe2+and Mn2+complexes, showed micromolar IC50s (1.62 μM, 1.34 μM, and 4.12 μM, respectively, versus 0.10 μM for PZQ) against adult worms.In vivo, the worm burden reductions were 12.3%, 88.4%, and 74.5%, respectively, at a single oral dose of 400 mg/kg of body weight. The Fe2+complex exhibited activityin vivocomparable to that of PZQ, pointing to the discovery of a novel drug lead for schistosomiasis.


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