Glucose metabolism by Prevotella intermedia and Prevotella nigrescens

Correlation between the structures of natural polysaccharides and their properties in regulating gut microbiota: Current understanding and beyond

Natural polysaccharides have complex structural properties and a wide range of health-promoting effects. Accumulating evidence suggests that the effects are significantly mediated through fermentation by gut microbiota. In recent years, the relationship between the structures of natural polysaccharides and their properties in regulating gut microbiota has garnered significant research attention as researchers attempt to precisely understand the role of gut microbiota in the bioactivities of natural polysaccharides. Progress in this niche, however, remains limited. In this review, we first provide an overview of current research investigating this structure-property relationship. We then present a detailed correlation analysis between the structural characteristics of 159 purified natural polysaccharides and their effects on gut microbiota reported over the past two decades. The analysis revealed that diverse gut bacteria show specific correlations with the molecular weight, glycosidic linkages, and monosaccharide composition of natural polysaccharides. Multifaceted molecular mechanisms, including carbohydrate binding, enzymatic degradation, and cross-feeding, were proposed to be collectively involved in these correlations. Finally, we offer our perspective on future studies to further improve our understanding of the relationship between polysaccharide structure and gut microbiota regulation.

Metabolic profiling of peri-implant crevicular fluid in peri-implantitis

OBJECTS

This study aims to explore the etiology of peri-implantitis by comparing the metabolic profiles in peri-implant crevicular fluid (PICF) from patients with healthy implants (PH) and those with peri-implantitis (PI).

MATERIALS AND METHODS

Fifty-six patients were enrolled in this cross-sectional study. PICF samples were collected and analyzed using both non-targeted and targeted metabolomics approaches. The relationship between metabolites and clinical indices including probing depth (PD), bleeding on probing (BOP), and marginal bone loss (MBL) was examined. Additionally, submucosal microbiota was collected and analyzed using 16S rRNA gene sequencing to elucidate the association between the metabolites and microbial communities.

RESULTS

Significant differences in metabolic profiles were observed between the PH and PI groups, with 179 distinct metabolites identified. In the PI group, specific amino acids and fatty acids were significantly elevated compared to the PH group. Organic acids including succinic acid, fructose-6-phosphate, and glucose-6-phosphate were markedly higher in the PI group, showing positive correlations with mean PD, BOP, and MBL. Metabolites that increased in the PI group positively correlated with the presence of Porphyromonas and Treponema and negatively with Streptococcus and Haemophilus.

CONCLUSIONS

This study establishes a clear association between metabolic compositions and peri-implant condition, highlighting enhanced metabolite activity in peri-implantitis. These findings open avenues for further research into metabolic mechanisms of peri-implantitis and their potential therapeutic implications.

Prevotella, a dominant bacterium in young people with stage Ⅲ periodontitis, related to the arachidonic acid metabolism pathway

OBJECTS

As periodontitis progresses, the oral microbiome changes dynamically. The aim of this study is to evaluate the dominant bacteria of adults with stage III periodontitis and investigate potential pathways related to the dominant bacteria.

MATERIALS AND METHODS

16S rRNA sequencing was carried out to detect the differences in the oral microbiome between adult with stage Ⅰ and stage Ⅲ periodontitis and find the dominant bacteria in each group. The inhibitor of the predominant pathway for stage Ⅲ periodontitis was used to investigate the role of the dominant bacteria in periodontitis in vivo and in vitro.

RESULTS

There was no significant difference in the α-diversity between the two groups. The results of β-diversity showed that the samples were divided into different groups according to the stage of periodontitis. The dominant bacteria in youths with stage Ⅲ periodontitis was Prevotella and may be related to the arachidonic acid metabolism pathway. Administration of SKF-86002 suppressed the expression of inflammation mediators in vivo and vitro.

CONCLUSIONS

Prevotella was the one dominant bacteria in young people with stage Ⅲ periodontitis and was related to the arachidonic acid metabolism pathway.

Structurally Orientated Rheological and Gut Microbiota Fermentation Property of Mannans Polysaccharides and Oligosaccharides

Three mannan polysaccharides and their oligosaccharides were investigated in terms of physicochemical characteristics and effects on gut microbiota. Oligosaccharides from guar gum had the fastest fermentation kinetics for SCFAs generation at the initial stage, while the locust bean of both polymers and oligosaccharides demonstrated the lowest SCFAs through the whole fermentation process. In contrast, konjac gum steadily increased SCFAs and reached its maximum level at 24 h fermentation, indicating its fermentation character may be associated with its rheological properties. Compared to their corresponding polysaccharides, all the oligosaccharides demonstrated a faster fermentation kinetics, followed by an enriched abundance of propionate-producing bacterial Prevotella and a decreased abundance of Megamonas and Collinsella. Meanwhile, oligosaccharides reduced the Firmicutes/Bacteroidota ratio as well as the abundance of Bacteroidetes and Escherichia-Shigella. The fermentation of konjac substrate significantly promoted the abundance of butyrate-producing bacterial Faecalibacterium. In contrast, although the fermentation of locust bean and guar gum substrates benefited Bifidobacterium abundance due to their similar structure and monosaccharides composition, the fermentation of locust bean gum led to greater Bifidobacterium than the others, which may be associated with its higher mannose composition in the molecules. Interestingly, the partial hydrolysis of the three polysaccharides slightly reduced their prebiotic function.

Symbiotic relationship between Prevotella denticola and Streptococcus mutans enhances virulence of plaque biofilms

OBJECTIVES

This study aimed to explore that whether interactions between Prevotella denticola and Streptococcus mutans could promote the establishment of hypervirulent biofilms on teeth surface and eventually influence the occurrence and development of caries.

DESIGN

Based on single-species biofilms of either P. denticola or S. mutans, and dual-species biofilms of both bacteria, we compared the virulence properties associated with cariogenicity in vitro, including carbohydrate metabolism and acid productivity, synthesis of extracellular polysaccharides, biomass and architecture of biofilms, level of enamel demineralization and expression of virulence genes associated with carbohydrate metabolism and adhesion in S. mutans.

RESULTS

The data demonstrated that, compared to single-species of above two taxa, dual-species produced lactate by metabolizing carbohydrates at a higher level during the observation period. Moreover, dual-species biofilms accrued more biomass and exhibited more dense microcolonies and abundant extracellular matrix. And it's noticeable that the level of enamel demineralization in dual-species biofilms was more augmented than that of single-species. In addition, the presence of P. denticola induced the expression of virulence genes gtfs and gbpB in S. mutans.

CONCLUSIONS

Symbiotic relationship between P. denticola and S. mutans enhances caries-associated virulence of plaque biofilms, which might provide new strategies for effective prevention and treatment of caries.

Productive and physiological implications of top-dress addition of branched-chain amino acids and arginine on lactating sows and offspring

BACKGROUND

Branched-chain amino acids (BCAAs), including L-leucine (L-Leu), L-isoleucine (L-Ile), L-valine (L-Val), and L-arginine (L-Arg), play a crucial role in mammary gland development, secretion of milk and regulation of the catabolic state and immune response of lactating sows. Furthermore, it has recently been suggested that free amino acids (AAs) can also act as microbial modulators. This study aimed at evaluating whether the supplementation of lactating sows with BCAAs (9, 4.5 and 9 g/d/sow of L-Val, L-Ile and L-Leu, respectively) and/or L-Arg (22.5 g/d/sow), above the estimated nutritional requirement, could influence the physiological and immunological parameters, microbial profile, colostrum and milk composition and performance of sows and their offspring.

RESULTS

At d 41, piglets born from the sows supplemented with the AAs were heavier (P = 0.03). The BCAAs increased glucose and prolactin (P < 0.05) in the sows' serum at d 27, tended to increase immunoglobulin A (IgA) and IgM in the colostrum (P = 0.06), increased the IgA (P = 0.004) in the milk at d 20 and tended to increase lymphocyte% in the sows' blood at d 27 (P = 0.07). Furthermore, the BCAAs tended to reduce the Chao1 and Shannon microbial indices (P < 0.10) in the sows' faeces. The BCAA group was discriminated by Prevotellaceae_UCG-004, Erysipelatoclostridiaceae UCG-004, the Rikenellaceae_RC9_gut_group and Treponema berlinense. Arginine reduced piglet mortality pre- (d 7, d 14) and post-weaning (d 41) (P < 0.05). Furthermore, Arg increased the IgM in the sow serum at d 10 (P = 0.05), glucose and prolactin (P < 0.05) in the sow serum at d 27 and the monocyte percentage in the piglet blood at d 27 (P = 0.025) and their jejunal expression of NFKB2 (P = 0.035) while it reduced the expression of GPX-2 (P = 0.024). The faecal microbiota of the sows in Arg group was discriminated by Bacteroidales. The combination of BCAAs and Arg tended to increase spermine at d 27 (P = 0.099), tended to increase the Igs (IgA and IgG, P < 0.10) at d 20 in the milk, favoured the faecal colonisation of Oscillospiraceae UCG-005 and improved piglet growth.

CONCLUSION

Feeding Arg and BCAAs above the estimated requirements for milk production may be a strategy to improve sow productive performance in terms of piglet average daily gain (ADG), immune competence and survivability via modulation of the metabolism, colostrum and milk compositions and intestinal microbiota of the sows. The synergistic effect between these AAs, noticeable by the increase of Igs and spermine in the milk and in the improvement of the performance of the piglets, deserves additional investigation.

Fumarate and nitrite reduction by Prevotella nigrescens and Prevotella buccae isolated from Chronic Periodontitis patients

OBJECTIVE

This study is an investigation of anaerobic nitrite and fumarate reduction/respiration abilities of two characterised Prevotella species namely Prevotella nigrescens (SS6B) and Prevotella buccae (GS6B) isolated from the periodontal pockets of chronic periodontitis (ChP) patients.

METHODS

Isolation and identification of the periodontal bacteria from 20 patients showing clinical symptoms of ChP. Characterisation of anaerobic nitrite and fumarate reduction was done in P. nigrescens (SS6B) and P. buccae (GS6B) using reduction assays, inhibition assays with use of specific inhibitors, growth assays and enzyme activity assays. Degenerate PCR was used to detect and amplify nitrite reductase (nrfA) and fumarate reductase (frdA) gene sequences in these Prevotella isolates. In addition, molecular and in silico analysis of the amplified anaerobic reductase gene sequences was performed using NCBI conserved domain analysis, Interpro database and MegaX.

RESULTS

We provided experimental evidence for presence of active nitrite and fumarate reductase activities through enzyme activity, reduction, inhibitor and growth assays. Moreover, we were able to detect presence of 505 bps nrfA gene fragment and 400 bps frdA gene fragment in these Prevotella spp. These fragments show similarity to multiheme ammonia forming cytochrome c nitrite reductases and fumarate reductases flavoprotein subunit, respectively.

CONCLUSION

Anaerobic nitrite and fumarate respiration abilities in P. nigrescens and P. buccae isolates appear to be important for detoxification process and growth, respectively.

Presence of zoonotic black-pigmented periodontal pathogens in the oral microbiota of pet and stray cats

Black-pigmented bacteria are one of the neglected species to cause periodontal disease in cats, and they are also zoonotic agents that pose an infection risk to humans. In this study, we aimed to determine the presence of Porphyromonas gingivalis, Porphyromonas gulae and Prevotella nigrescens in the oral microbiota of pet and stray cats. Dental swab samples were taken from 25 pet cats and 25 stray cats with symptoms of periodontal disease and then investigated by multiplex polymerase chain reaction using 16S rRNA species-specific primers. As a result of the multiplex PCR analysis, P. gingivalis 3/25 (12%), P. nigrescens 1/25 (4%), P. gingivalis + P. gulae 7/25 (28%), P. gingivalis + P. nigrescens 1/25 (4%), P. gulae + P. nigrescens 1/25 (4%), and P. gingivalis + P. gulae + P. nigrescens 2/25 (8%) were molecularly typed in the pet cats. In addition, 1/25 (4%) of P. gulae and 21/25 (84%) of P. gingivalis + P. gulae were typed in the stray cats. In 10/25 (40%) pet and 3/25 (12%) stray cat samples, no bacteria were detected by molecular typing. In summary, the results provide strong evidence that black-pigmented zoonotic pathogens are associated with cat periodontal disease.

Microbial communities and metabolic pathways involved in reductive decolorization of an azo dye in a two-stage AD system

Multiple stage anaerobic system was found to be an effective strategy for reductive decolorization of azo dyes in the presence of sulfate. Bulk color removal (56-90%) was achieved concomitant with acidogenic activity in the 1st-stage reactor (R1), while organic matter removal (≤100%) and sulfate reduction (≤100%) occurred predominantly in the 2nd-stage reactor (R2). However, azo dye reduction mechanism and metabolic routes involved remain unclear. The involved microbial communities and conditions affecting the azo dye removal in a two-stage anaerobic digestion (AD) system were elucidated using amplicon sequencing (16S rRNA, fhs, dsrB and mcrA) and correlation analysis. Reductive decolorization was found to be co-metabolic and mainly associated with hydrogen-producing pathways. We also found evidence of the involvement of an azoreductase from Lactococcus lactis. Bacterial community in R1 was sensitive and shifted in the presence of the azo dye, while microorganisms in R2 were more protected. Higher diversity of syntrophic-acetate oxidizers, sulfate reducers and methanogens in R2 highlights the role of the 2nd-stage in organic matter and sulfate removals, and these communities might be involved in further transformations of the azo dye reduction products. The results improve our understanding on the role of different microbial communities in anaerobic treatment of azo dyes and can help in the design of better solutions for the treatment of textile effluents.

Genomic and phenotypic comparison of Prevotella intermedia strains possessing different virulence in vivo

Prevotella intermedia readily colonizes healthy dental biofilm and is associated with periodontal diseases. The viscous exopolysaccharide (EPS)-producing capability is known as a major virulence factor of P. intermedia 17 (Pi17). However, the inter-strain difference in P. intermedia regarding virulence-associated phenotype is not well studied. We compared in vivo virulence and whole genome sequences using five wild-type strains: ATCC 49046 (Pi49046), ATCC 15032 (Pi15032), ATCC 15033 (Pi15033), ATCC 25611 (Pi25611), and Pi17. Non-EPS producing Pi25611 was the least virulent in insect and mammalian models. Unexpectedly, Pi49046 did not produce viscous EPS but was the most virulent, followed by Pi17. Genomes of the five strains were quite similar but revealed subtle differences such as copy number variations and single nucleotide polymorphisms. Variations between strains were found in genes encoding glycosyltransferases and genes involved in the acquisition of carbohydrates and iron/haem. Based on these genetic variations, further analyses were performed. Phylogenetic and structural analyses discovered phosphoglycosyltransferases of Pi49046 and Pi17 have evolved to contain additional loops that may confer substrate specificity. Pi17, Pi15032, and Pi15033 displayed increased growth by various carbohydrates. Meanwhile, Pi49046 exhibited the highest activities for haemolysis and haem accumulation, as well as co-aggregation with Porphyromonas gingivalis harbouring fimA type II, which is more tied to periodontitis than other fimA types. Collectively, subtle genetic differences related to glycosylation and acquisition of carbohydrates and iron/haem may contribute to the diversity of virulence and phenotypic traits among P. intermedia strains. These variations may also reflect versatile strategies for within-host adaptation of P. intermedia.

Enrichment of Prevotella intermedia in human colorectal cancer and its additive effects with Fusobacterium nucleatum on the malignant transformation of colorectal adenomas

Background

Owing to the heterogeneity of microbiota among individuals and populations, only Fusobacterium nucleatum and Bacteroides fragilis have been reported to be enriched in colorectal cancer (CRC) in multiple studies. Thus, the discovery of additional bacteria contributing to CRC development in various populations can be expected. We aimed to identify bacteria associated with the progression of colorectal adenoma to carcinoma and determine the contribution of these bacteria to malignant transformation in patients of Han Chinese origin.

Methods

Microbiota composition was determined through 16S rRNA V3–V4 amplicon sequencing of autologous adenocarcinomas, adenomatous polyps, and non-neoplastic colon tissue samples (referred to as “tri-part samples”) in patients with CRC. Enriched taxa in adenocarcinoma tissues were identified through pairwise comparison. The abundance of candidate bacteria was quantified through genomic quantitative polymerase chain reaction (qPCR) in tissue samples from 116 patients. Associations of candidate bacteria with clinicopathological features and genomic and genetic alterations were evaluated through odds ratio tests. Additionally, the effects of candidate bacteria on CRC cell proliferation, migration, and invasion were evaluated through the co-culture of CRC cells with bacterial cells or with conditioned media from bacteria.

Results

Prevotella intermedia was overrepresented in adenocarcinomas compared with paired adenomatous polyps. Furthermore, co-abundance of P. intermedia and F. nucleatum was observed in tumor tissues. More notably, the coexistence of these two bacteria in adenocarcinomas was associated with lymph node involvement and distant metastasis. These two bacteria also exerted additive effects on the enhancement of the migration and invasion abilities of CRC cells. Finally, conditioned media from P. intermedia promoted the migration and invasion of CRC cells.

Conclusion

This report is the first to demonstrate that P. intermedia is enriched in colorectal adenocarcinoma tissues and enhances the migration and invasion abilities of CRC cells. Moreover, P. intermedia and F. nucleatum exert additive effects on the malignant transformation of colorectal adenomas into carcinomas. These findings can be used to identify patients at a high risk of malignant transformation of colorectal adenomas or metastasis of CRC, and they can accordingly be provided optimal clinical management.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12929-022-00869-0.

Targeting the succinate receptor effectively inhibits periodontitis

Periodontal disease (PD) is one of the most common inflammatory diseases in humans and is initiated by an oral microbial dysbiosis that stimulates inflammation and bone loss. Here, we report an abnormal elevation of succinate in the subgingival plaque of subjects with severe PD. Succinate activates succinate receptor-1 (SUCNR1) and stimulates inflammation. We detected SUCNR1 expression in the human and mouse periodontium and hypothesize that succinate activates SUCNR1 to accelerate periodontitis through the inflammatory response. Administration of exogenous succinate enhanced periodontal disease, whereas SUCNR1 knockout mice were protected from inflammation, oral dysbiosis, and subsequent periodontal bone loss in two different models of periodontitis. Therapeutic studies demonstrated that a SUCNR1 antagonist inhibited inflammatory events and osteoclastogenesis in vitro and reduced periodontal bone loss in vivo. Our study reveals succinate’s effect on periodontitis pathogenesis and provides a topical treatment for this disease.

Periodontitis is the most prevalent adult oral disease. Guo et al. show elevation of succinate in periodontitis, which aggravates the disease through the succinate receptor (SUCNR1). They developed a gel formulation of a small compound specifically blocking SUCNR1 to prevent and treat periodontitis by inhibiting dysbiosis, inflammation, and bone loss.

Effects of Tetrabasic Zinc Chloride on Growth Performance, Nutrient Digestibility and Fecal Microbial Community in Weaned Piglets

The study was conducted to explore the effects of tetrabasic zinc chloride (TBZC), as an alternative to zinc oxide (ZnO), on growth performance, serum indexes, and fecal microbiota of weaned piglets. A total of 108 weaned piglets (average initial body weight of 7.84 ± 0.97 kg) were randomly allocated into one of three dietary treatments with six replicate pens and six piglets per pen. The dietary treatments included a control diet (CON, negative control), a ZnO diet (CON + 1,600 mg Zn/kg from ZnO, positive control), and a TBZC diet (CON + 1,000 mg Zn/kg from TBZC). The average daily gain of pigs in the TBZC group was greater (P < 0.05) than those in CON and ZnO groups during the whole period. Piglets fed the ZnO and TBZC diets showed lower (P < 0.05) diarrhea incidence than those fed the CON diet during d 1-14 and the whole period. Piglets fed the TBZC diet had higher (P < 0.05) digestibility of crude protein and gross energy than those fed the CON diet. Serum concentrations of IGF-I and GH, as well as ALP activity, were significantly elevated (P < 0.05) in the TBZC treatment group compared to the CON group on d 14. Piglets fed the ZnO diet had greater (P < 0.05) acetate and total short-chain fatty acids concentrations, while the TBZC diet had greater (P < 0.05) fecal acetate and propionate concentrations on d 28. Moreover, TBZC supplementation significantly increased (P < 0.05) microbial α-diversity compared with the CON group. The fecal microbiota of piglets in ZnO and TBZC treatment groups tended (P = 0.08) to have greater relative abundance of Prevotellaceae compared with the CON piglets. In conclusion, TBZC acted as a suitable alternative to ZnO to reduce zinc excretion, and improve growth performance of weaned piglets.

Prevotella species as oral residents and infectious agents with potential impact on systemic conditions

Oral Prevotella are known as anaerobic commensals on oral mucosae and in dental plaques from early life onwards, including pigmented P. melaninogenica, P. nigrescens, and P. pallens and non-pigmented Prevotella species. Many Prevotella species contribute to oral inflammatory processes, being frequent findings in dysbiotic biofilms of periodontal diseases (P. intermedia, P. nigrescens), cariotic lesions (P. denticola, Alloprevotella (formerly Prevotella) tannerae), endodontic infections (P. baroniae, P. oris, P. multisaccharivorax), and other clinically relevant oral conditions. Over the years, several novel species have been recovered from the oral cavity without knowledge of their clinical relevance. Within this wide genus, virulence properties and other characteristics like biofilm formation seemingly vary in a species- and strain-dependent manner, as shown for the P. intermedia group organisms (P. aurantiaca, P. intermedia, P. nigrescens, and P. pallens). Oral Prevotella species are identified in various non-oral infections and chronic pathological conditions. Here, we have updated the knowledge of the genus Prevotella and the role of Prevotella species as residents and infectious agents of the oral cavity, as well as their detection in non-oral infections, but also gathered information on their potential link to cancers of the head and neck, and other systemic disorders.

Bacteria and Methanogens in the Human Microbiome: a Review of Syntrophic Interactions

Methanogens are microorganisms belonging to the Archaea domain and represent the primary source of biotic methane. Methanogens encode a series of enzymes which can convert secondary substrates into methane following three major methanogenesis pathways. Initially recognized as environmental microorganisms, methanogens have more recently been acknowledged as host-associated microorganisms after their detection and initial isolation in ruminants in the 1950s. Methanogens have also been co-detected with bacteria in various pathological situations, bringing their role as pathogens into question. Here, we review reported associations between methanogens and bacteria in physiological and pathological situations in order to understand the metabolic interactions explaining these associations. To do so, we describe the origin of the metabolites used for methanogenesis and highlight the central role of methanogens in the syntrophic process during carbon cycling. We then focus on the metabolic abilities of co-detected bacterial species described in the literature and infer from their genomes the probable mechanisms of their association with methanogens. The syntrophic interactions between bacteria and methanogens are paramount to gut homeostasis. Therefore, any dysbiosis affecting methanogens might impact human health. Thus, the monitoring of methanogens may be used as a bio-indicator of dysbiosis. Moreover, new therapeutic approaches can be developed based on their administration as probiotics. We thus insist on the importance of investigating methanogens in clinical microbiology.

Archaeal and Bacterial Content in a Two-Stage Anaerobic System for Efficient Energy Production from Agricultural Wastes

Anaerobic digestion (AD) is a microbially-driven process enabling energy production. Microorganisms are the core of anaerobic digesters and play an important role in the succession of hydrolysis, acidogenesis, acetogenesis, and methanogenesis processes. The diversity of participating microbial communities can provide new information on digester performance for biomass valorization and biofuel production. In this study anaerobic systems were used, operating under mesophilic conditions that realized biodegradation processes of waste wheat straw pretreated with NaOH-a renewable source for hydrogen and methane production. These processes could be managed and optimized for hydrogen and methane separately but combining them in a two-stage system can lead to higher yields and a positive energy balance. The aim of the study was to depict a process of biohydrogen production from lignocellulosic waste followed by a second one leading to the production of biomethane. Archaeal and bacterial consortia in a two-stage system operating with wheat straw were identified for the first time and the role of the most important representatives was elucidated. The mixed cultures were identified by the molecular-biological methods of metagenomics. The results showed that biohydrogen generation is most probably due to the presence of Proteiniphilum saccharofermentans, which was 28.2% to 45.4% of the microbial community in the first and the second bioreactor, respectively. Archaeal representatives belonging to Methanobacterium formicicum (0.71% of the community), Methanosarcina spelaei (0.03%), Methanothrix soehngenii (0.012%), and Methanobacterium beijingense (0.01%) were proven in the methane-generating reactor. The correlation between substrate degradation and biogas accumulation was calculated, together with the profile of fatty acids as intermediates produced during the processes. The hydrogen concentration in the biogas reached 14.43%, and the Methane concentration was 69%. Calculations of the energy yield during the two-stage process showed 1195.89 kWh·t-1 compared to a 361.62 kWh·t-1 cumulative yield of energy carrier for a one-stage process.

A Sodium-Translocating Module Linking Succinate Production to Formation of Membrane Potential in Prevotella bryantii

Ruminants such as cattle and sheep depend on the breakdown of carbohydrates from plant-based feedstuff, which is accomplished by the microbial community in the rumen. Roughly 40% of the members of the rumen microbiota belong to the family Prevotellaceae, which ferments sugars to organic acids such as acetate, propionate, and succinate. These substrates are important nutrients for the ruminant. In a metaproteome analysis of the rumen of cattle, proteins that are homologous to the Na⁺-translocating NADH:quinone oxidoreductase (NQR) and the quinone:fumarate reductase (QFR) were identified in different Prevotella species. Here, we show that fumarate reduction to succinate in anaerobically growing Prevotella bryantii is coupled to chemiosmotic energy conservation by a supercomplex composed of NQR and QFR. This sodium-translocating NADH:fumarate oxidoreductase (SNFR) supercomplex was enriched by blue native PAGE (BN-PAGE) and characterized by in-gel enzyme activity staining and mass spectrometry. High NADH oxidation (850 nmol min^-1mg^-1), quinone reduction (490 nmol min^-1mg^-1), and fumarate reduction (1,200 nmol min^-1mg^-1) activities, together with high expression levels, demonstrate that SNFR represents a charge-separating unit in P. bryantii. Absorption spectroscopy of SNFR exposed to different substrates revealed intramolecular electron transfer from the flavin adenine dinucleotide (FAD) cofactor in NQR to heme b cofactors in QFR. SNFR catalyzed the stoichiometric conversion of NADH and fumarate to NAD⁺ and succinate. We propose that the regeneration of NAD⁺ in P. bryantii is intimately linked to the buildup of an electrochemical gradient which powers ATP synthesis by electron transport phosphorylation. IMPORTANCE Feeding strategies for ruminants are designed to optimize nutrient efficiency for animals and to prevent energy losses like enhanced methane production. Key to this are the fermentative reactions of the rumen microbiota, dominated by Prevotella spp. We show that succinate formation by P. bryantii is coupled to NADH oxidation and sodium gradient formation by a newly described supercomplex consisting of Na⁺-translocating NADH:quinone oxidoreductase (NQR) and fumarate reductase (QFR), representing the sodium-translocating NADH:fumarate oxidoreductase (SNFR) supercomplex. SNFR is the major charge-separating module, generating an electrochemical sodium gradient in P. bryantii. Our findings offer clues to the observation that use of fumarate as feed additive does not significantly increase succinate production, or decrease methanogenesis, by the microbial community in the rumen.

Applying PICRUSt and 16S rRNA functional characterisation to predicting co-digestion strategies of various animal manures for biogas production

An estimated 25 million tons of animal manure is produced globally every year, causing considerable impact to the environment. These impacts can be managed through the use of anaerobic digestion (AD) This process achieves waste degradation through enzymatic activity, the efficiency of the AD process is directly related to microorganisms that produce these enzymes. Biomethane potential (BMP) assays remain the standard theoretical framework to pre-determine biogas yield and have been used to determine the feasibility of substrates or their combination for biogas production. However, an integrated approach that combines substrate choice and co-digestion would provide an improvement to the current predictive models. PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) addresses the limitations of assays in this regard. In this paper, the biochemical functions of horse, cow, and pig manures are predicted. A total of 135 predicted KEGG Orthologies (KOs) showed amino acids, carbohydrate, energy, lipid, and xenobiotic metabolisms in all the samples. Linear discriminant analysis (LDA) combined with the effect size measurements (LEfSe), showed that fructose, mannose, amino acid and nucleotide sugar, phosphotransferase (PST) as well as starch and sucrose metabolisms were significantly higher in horse manure samples. 36 of the KOs were related to the acidogenesis and/or acetogenesis AD stages. Extended bar plots showed that 11 significant predictions were observed for horse-cow, while 5 were predicted for horse-pig and for cow-pig manures. Based on these predictions, the AD process can be enhanced through co-digestion strategies that takes into account the predicted metabolic contributions of the manure samples. The results supported the BMP calculations for the samples in this study. Biogas yields can be improved if this combined approach is employed in routine analysis before co-digesting different substrates.

Assessment of Biolog EcoplateTM method for functional metabolic diversity of aerotolerant pig fecal microbiota

Abstract

In the last decades, gut microbiota and its role in mammal host development and health have been increasingly investigated. Metabolites produced by gut microbiota can affect intestinal homeostasis and immune system maturity and activation, and in turn, they can influence the health and growth performance of livestock. Therefore, a better understanding of the functional metabolic capability of the gut microbiota would be appreciated by the scientific community. In this study, the Biolog^TM Ecoplates technology was applied for studying the metabolic potential of the aerotolerant microbial community of pig fecal samples, evaluating the interference of different storage conditions and cell concentrations. The length of time for which a fecal sample maintained detectable and unchanged microbial metabolic activity was also investigated. Two assays aimed to evaluate differences in the metabolic activities between fresh and snap-frozen fecal samples at different dilutions and at different lengths of times of preservation at −80°C were carried out. The biodiversity and the predicted functionality of the entire bacterial community through a targeted metagenomic approach were also explored. The results highlighted that snap freezing of fecal samples preserved the metabolic activity of the microbial community when compared to fresh feces. Sample storage at −80 °C did not significantly affect the metabolic activity of the microbial community, which was stable for 150 days. Furthermore, the highest metabolic activity was detected with 1:2 to 1:5 dilutions of the stock suspension. Biolog^TM Ecoplates technology is a rapid and useful method to explore microbial communities’ metabolism in animal fecal samples contributing to investigate host animal physiology.

Key points

• Freezing of samples can preserve the functional activity of the aerotolerant microbial community for 150 days.

• The concentration of microbial cells strongly influences metabolic activity detection.

• Sequencing coupled with the Biolog^TMEcoplates could be a strategy to evaluate the metabolic potential of the microbiota of the fecal sample.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-021-11449-x.

Cultivation of the gut bacterium Prevotella copri DSM 18205T using glucose and xylose as carbon sources

Prevotella copri DSM18205T is a human gut bacterium, suggested as a next-generation probiotic. To utilize it as such, it is, however, necessary to grow the species in a reproducible manner. Prevotella copri has previously been reported to be highly sensitive to oxygen, and hence difficult to isolate and cultivate. This study presents successful batch cultivation strategies for viable strain inoculations and growth in both serum bottles and a stirred tank bioreactor (STR), without the use of an anaerobic chamber, as long as the cells were kept in the exponential growth phase. A low headspace volume in the STR was important to reach high cell density. P. copri utilized xylose cultivated in Peptone Yeast Xylose medium (PYX medium), resulting in a comparable growth rate and metabolite production as in Peptone Yeast Glucose medium (PYG medium) in batch cultivations at pH 7.2.Up to 5 g/L of the carbon source was consumed, leading to the production of succinic acid, acetic acid, and formic acid, and cell densities (OD620 nm ) in the range 6-7.5. The highest yield of produced succinic acid was 0.63 ± 0.05 g/g glucose in PYG medium cultivations and 0.88 ± 0.06 g/g xylose in PYX medium cultivations.

Live Yeast or Live Yeast Combined with Zinc Oxide Enhanced Growth Performance, Antioxidative Capacity, Immunoglobulins and Gut Health in Nursery Pigs

This study aimed to investigate the effects of dietary LY or LY combined with ZnO supplementation on performance and gut health in nursery pigs. 192 Duroc × Landrace × Yorkshire piglets (weaned on d 32 of the age with 9.2 ± 1.7 kg BW) were allocated into four treatments with eight replicate pens, six piglets per pen. The treatments included a basal diet as control (CTR), an antibiotic plus ZnO diet (CTC-ZnO, basal diet + 75 mg/kg of chlortetracycline + ZnO (2000 mg/kg from d 1 to 14, 160 mg/kg from d 15 to 28)), a LY diet (LY, basal diet + 2 g/kg LY), and a LY plus ZnO diet (LY-ZnO, basal diet + 1 g/kg LY + ZnO). The results showed that pigs fed LY or LY-ZnO had increased (p < 0.05) average daily gain, serum IgA, IgG, superoxide dismutase, fecal butyric acid, and total volatile fatty acid concentrations, as well as decreased (p < 0.05) feed conversion ratio and diarrhea rate compared with CTR. In conclusion, pigs fed diets with LY or LY combined with ZnO had similar improvement to the use of antibiotics and ZnO in performance, antioxidant status, immunoglobulins, and gut health in nursery pigs.

Introduction of Colonic and Fecal Microbiota From an Adult Pig Differently Affects the Growth, Gut Health, Intestinal Microbiota and Blood Metabolome of Newborn Piglets

Microbiota transplantation is a rapid and effective method for changing and reshaping the intestinal microbiota and metabolic profile in humans and animals. This study compared the different influences of the introduction of fecal microbes and colonic microbes from a fat, adult pig in newborn pigs. Both colonic microbiota transplantation (CMT) and fecal microbiota transplantation (FMT) promoted growth and improved gut functions in suckling pigs up to weaning. FMT was more beneficial for body weight gain and body fat deposition in piglets, while CMT was more beneficial for intestinal health and mucosal immunity. 16S rDNA sequence analysis indicated that both CMT and FMT significantly increased the abundances of beneficial or functional bacteria, such as Lactobacillus and Prevotella_2 genera, in the piglets, and reduced the abundances of harmful bacteria, such as Escherichia-Shigella. Blood metabolome analysis showed that transplantation, especially FMT, enhanced lipid metabolism in piglets. In addition, while CMT also changed amino acid metabolism and increased anti-inflammatory metabolites such as 3-indoleacetic acid and 3-indolepropionic acid in piglets, FMT did not. Of note, FMT damaged the intestinal barrier of piglets to a certain extent and increased the levels of inflammatory factors in the blood that are potentially harmful to the health of pigs. Taken together, these results suggested that intestinal and fecal microbiota transplantations elicited similar but different physiological effects on young animals, so the application of microbiota transplantation in animal production requires the careful selection and evaluation of source bacteria.

The structure of microbial populations in Nelore GIT reveals inter-dependency of methanogens in feces and rumen

Background

The success of different species of ruminants in the colonization of a diverse range of environments is due to their ability to digest and absorb nutrients from cellulose, a complex polysaccharide found in leaves and grass. Ruminants rely on a complex and diverse microbial community, or microbiota, in a unique compartment known as the rumen to break down this polysaccharide. Changes in microbial populations of the rumen can affect the host’s development, health, and productivity. However, accessing the rumen is stressful for the animal. Therefore, the development and use of alternative sampling methods are needed if this technique is to be routinely used in cattle breeding. To this end, we tested if the fecal microbiome could be used as a proxy for the rumen microbiome due to its accessibility. We investigated the taxonomic composition, diversity and inter-relations of two different GIT compartments, rumen and feces, of 26 Nelore (Bos indicus) bulls, using Next Generation Sequencing (NGS) metabarcoding of bacteria, archaea and ciliate protozoa.

Results

We identified 4265 Amplicon Sequence Variants (ASVs) from bacteria, 571 from archaea, and 107 from protozoa, of which 143 (96 bacteria and 47 archaea) were found common between both microbiomes. The most prominent bacterial phyla identified were Bacteroidetes (41.48%) and Firmicutes (56.86%) in the ruminal and fecal microbiomes, respectively, with Prevotella and Ruminococcaceae UCG-005 the most relatively abundant genera identified in each microbiome. The most abundant archaeal phylum identified was Euryarchaeota, of which Methanobrevibacter gottschalkii, a methanogen, was the prevalent archaeal species identified in both microbiomes. Protozoa were found exclusively identified in the rumen with Bozasella/Triplumaria being the most frequent genus identified. Co-occurrence among ruminal and fecal ASVs reinforces the relationship of microorganisms within a biological niche. Furthermore, the co-occurrence of shared archaeal ASVs between microbiomes indicates a dependency of the predominant fecal methanogen population on the rumen population.

Conclusions

Co-occurring microorganisms were identified within the rumen and fecal microbiomes, which revealed a strong association and inter-dependency between bacterial, archaeal and protozoan populations of the same microbiome. The archaeal ASVs identified as co-occurring between GIT compartments corresponded to the methanogenic genera Methanobrevibacter and Methanosphaera and represented 26.34% of the overall archaeal sequencesdiversity in the rumen and 42.73% in feces. Considering that these archaeal ASVs corresponded to a significant part of the overall diversity of both microbiomes, which is much higher if one includes the interactions of these co-occurring with other rumen archaea ASVs, we suggest that fecal methanogens could be used as a proxy of ruminal methanogens.

Effect of live yeast Saccharomyces cerevisiae supplementation on the performance and cecum microbial profile of suckling piglets

One mechanism through which S. cerevisiae may improve the performance of pigs is by altering the composition of the gut microbiota, a response that may be enhanced by early postnatal supplementation of probiotics. To test this hypothesis, newborn piglets (16 piglets/group) were treated with either S. cerevisiae yeast (5 x 109 cfu/pig: Low) or (2.5 x 1010 cfu/piglet: High) or equivalent volume of sterile water (Control) by oral gavage every other day starting from day 1 of age until weaning (28±1 days of age). Piglet body weight was recorded on days 1, 3, 7, 10, 17, 24 and 28 and average daily gain (ADG) calculated for the total period. At weaning, piglets were euthanized to collect cecum content for microbial profiling by sequencing of the 16S rRNA gene. ADG was higher in both Low and High yeast groups than in Control group (P<0.05). Alpha diversity analyses indicated a more diverse microbiota in the Control group compared with Low yeast group; the High yeast being intermediate (P < 0.01). Similarly, Beta diversity analyses indicated differences among treatments (P = 0.03), mainly between Low yeast and Control groups (P = 0.02). The sparse Partial Least Squares Discriminant Analysis (sPLS-DA) indicated that Control group was discriminated by a higher abundance of Veillonella, Dorea, Oscillospira and Clostridium; Low yeast treated pigs by higher Blautia, Collinsella and Eubacterium; and High yeast treated pigs by higher Eubacterium, Anaerostipes, Parabacteroides, Mogibacterium and Phascolarctobacterium. Partial Least Squares (PLS) analysis showed that piglet ADG was positively correlated with genus Prevotella in High yeast group. Yeast supplementation significantly affected microbial diversity in cecal contents of suckling piglets associated with an improvement of short chain fatty acid producing bacteria in a dose-dependent manner. In conclusion, yeast treatment improved piglet performance and shaped the piglet cecum microbiota composition in a dose dependent way.

Occurrence and Function of the Na+-Translocating NADH:Quinone Oxidoreductase in Prevotella spp

Strictly anaerobic Prevotella spp. are characterized by their vast metabolic potential. As members of the Prevotellaceae family, they represent the most abundant organisms in the rumen and are typically found in monogastrics such as pigs and humans. Within their largely anoxic habitats, these bacteria are considered to rely primarily on fermentation for energy conservation. A recent study of the rumen microbiome identified multiple subunits of the Na⁺-translocating NADH:quinone oxidoreductase (NQR) belonging to different Prevotella spp. Commonly, the NQR is associated with biochemical energy generation by respiration. The existence of this Na⁺ pump in Prevotella spp. may indicate an important role for electrochemical Na⁺ gradients in their anaerobic metabolism. However, detailed information about the potential activity of the NQR in Prevotella spp. is not available. Here, the presence of a functioning NQR in the strictly anaerobic model organism P. bryantii B₁4 was verified by conducting mass spectrometric, biochemical, and kinetic experiments. Our findings propose that P. bryantii B₁4 and other Prevotella spp. retrieved from the rumen operate a respiratory NQR together with a fumarate reductase which suggests that these ruminal bacteria utilize a sodium motive force generated during respiratory NADH:fumarate oxidoreduction.

Physiology and central carbon metabolism of the gut bacterium Prevotella copri

The human gut microbiota is a crucial factor for the host's physiology with respect to health and disease. Metagenomic shotgun sequencing of microbial gut communities revealed that Prevotella copri is one of the most important players in the gastrointestinal tract of many individuals. Because of the importance of this bacterium we analyzed the growth behavior and the central metabolic pathways of P. copri. Bioinformatic data, transcriptome profiling and enzyme activity measurements indicated that the major pathways are based on glycolysis and succinate production from fumarate. In addition, pyruvate can be degraded to acetate and formate. Electron transport phosphorylation depends on fumarate respiration with NADH and reduced ferredoxin as electron donors. In contrast to Bacteroides vulgatus, P. copri showed a more pronounced dependency on the addition of CO₂ or bicarbonate for biomass formation, which is a remarkable difference between P. copri and Bacteroides spp. with important implication in the context of gut microbial competition. The analysis of substrate consumption and product concentrations from many P. copri cultures with different optical densities allowed a prediction of the carbon and electron flow in the central metabolism and a detailed calculation of growth yields as well as carbon and redox balances.

Population-Genomic Insights into Variation in Prevotella intermedia and Prevotella nigrescens Isolates and Its Association with Periodontal Disease

High-throughput sequencing has helped to reveal the close relationship between Prevotella and periodontal disease, but the roles of subspecies diversity and genomic variation within this genus in periodontal diseases still need to be investigated. We performed a comparative genome analysis of 48 Prevotella intermedia and Prevotella nigrescens isolates that from the same cohort of subjects to identify the main drivers of their pathogenicity and adaptation to different environments. The comparisons were done between two species and between disease and health based on pooled sequences. The results showed that both P. intermedia and P. nigrescens have highly dynamic genomes and can take up various exogenous factors through horizontal gene transfer. The major differences between disease-derived and health-derived samples of P. intermedia and P. nigrescens were factors related to genome modification and recombination, indicating that the Prevotella isolates from disease sites may be more capable of genomic reconstruction. We also identified genetic elements specific to each sample, and found that disease groups had more unique virulence factors related to capsule and lipopolysaccharide synthesis, secretion systems, proteinases, and toxins, suggesting that strains from disease sites may have more specific virulence, particularly for P. intermedia. The differentially represented pathways between samples from disease and health were related to energy metabolism, carbohydrate and lipid metabolism, and amino acid metabolism, consistent with data from the whole subgingival microbiome in periodontal disease and health. Disease-derived samples had gained or lost several metabolic genes compared to healthy-derived samples, which could be linked with the difference in virulence performance between diseased and healthy sample groups. Our findings suggest that P. intermedia and P. nigrescens may serve as “crucial substances” in subgingival plaque, which may reflect changes in microbial and environmental dynamics in subgingival microbial ecosystems. This provides insight into the potential of P. intermedia and P. nigrescens as new predictive biomarkers and targets for effective interventions in periodontal disease.

Recovering hydrogen production performance of upflow anaerobic sludge blanket reactor (UASBR) fed with galactose via repeated heat treatment strategy

This study evaluated the effect of repeated heat treatment towards the enhancement of hydrogen fermentation from galactose in an upflow anaerobic sludge blanket reactor with the hydraulic retention time of 6h and the operation temperature of 37°C. The hydrogen production rate (HPR) and hydrogen yield (HY) gradually increased up to 9.1L/L/d and 1.1mol/mol galactose, respectively, until the 33rd day of operation. When heat treatment at 80°C for 30min was applied, hydrogen production performance was enhanced by 37% with the enrichment of hydrogen producing bacteria population. The HPR and HY were achieved at 12.5L/L/d and 1.5mol/mol hexose, respectively, during further 30 cycles of reactor operation. The repeated heat treatment would be a viable strategy to warrant reliable continuous hydrogen production using mixed culture.

Insights into Butyrate Production in a Controlled Fermentation System via Gene Predictions

Butyrate is a common fatty acid produced in important fermentative systems, such as the human/animal gut and other H₂ production systems. Despite its importance, there is little information on the partnerships between butyrate producers and other bacteria. The objective of this work was to uncover butyrate-producing microbial communities and possible metabolic routes in a controlled fermentation system aimed at butyrate production. The butyrogenic reactor was operated at 37°C and pH 5.5 with a hydraulic retention time of 31 h and a low hydrogen partial pressure (PH₂). High-throughput sequencing and metagenome functional prediction from 16S rRNA data showed that butyrate production pathways and microbial communities were different during batch (closed) and continuous-mode operation. Lactobacillaceae, Lachnospiraceae, and Enterococcaceae were the most abundant phylotypes in the closed system without PH₂ control, whereas Prevotellaceae, Ruminococcaceae, and Actinomycetaceae were the most abundant phylotypes under continuous operation at low PH₂. Putative butyrate producers identified in our system were from Prevotellaceae, Clostridiaceae, Ruminococcaceae, and Lactobacillaceae. Metagenome prediction analysis suggests that nonbutyrogenic microorganisms influenced butyrate production by generating butyrate precursors such as acetate, lactate, and succinate. 16S rRNA gene analysis suggested that, in the reactor, a partnership between identified butyrogenic microorganisms and succinate (i.e., Actinomycetaceae), acetate (i.e., Ruminococcaceae and Actinomycetaceae), and lactate producers (i.e., Ruminococcaceae and Lactobacillaceae) took place under continuous-flow operation at low PH₂. IMPORTANCE This study demonstrates how bioinformatics tools, such as metagenome functional prediction from 16S rRNA genes, can help understand biological systems and reveal microbial interactions in controlled systems (e.g., bioreactors). Results obtained from controlled systems are easier to interpret than those from human/animal studies because observed changes may be specifically attributed to the design conditions imposed on the system. Bioinformatics analysis allowed us to identify potential butyrogenic phylotypes and associated butyrate metabolism pathways when we systematically varied the PH₂ in a carefully controlled fermentation system. Our insights may be adapted to butyrate production studies in biohydrogen systems and gut models, since butyrate is a main product and a crucial fatty acid in human/animal colon health.

The use of bacteriophages to biocontrol oral biofilms

Infections induced by oral biofilms include caries, as well as periodontal, and peri-implant disease, and may influence quality of life, systemic health, and expenditure. As bacterial biofilms are highly resistant and resilient to conventional antibacterial therapy, it has been difficult to combat these infections. An innovative alternative to the biocontrol of oral biofilms could be to use bacteriophages or phages, the viruses of bacteria, which are specific, non-toxic, self-proliferating, and can penetrate into biofilms. Phages for Actinomyces naeslundii, Aggregatibacter actinomycetemcomitans, Enterococcus faecalis, Fusobacterium nucleatum, Lactobacillus spp., Neisseria spp., Streptococcus spp., and Veillonella spp. have been isolated and characterised. Recombinant phage enzymes (lysins) have been shown to lyse A. naeslundii and Streptococcus spp. However, only a tiny fraction of available phages and their lysins have been explored so far. The unique properties of phages and their lysins make them promising but challenging antimicrobials. The genetics and biology of phages have to be further explored in order to determine the most effective way of applying them. Studying the effect of phages and lysins on multispecies biofilms should pave the way for microbiota engineering and microbiota-based therapy.

Breakdown of albumin and haemalbumin by the cysteine protease interpain A, an albuminase of Prevotella intermedia

BACKGROUND

Prevotella intermedia is a Gram-negative black-pigmenting oral anaerobe associated with periodontitis in humans, and has a haem requirement for growth, survival and virulence. It produces an iron porphyrin-containing pigment comprising monomeric iron (III) protoporphyrin IX (Fe(III)PPIX.OH; haematin). The bacterium expresses a 90-kDa cysteine protease termed interpain A (InpA) which both oxidizes and subsequently degrades haemoglobin, releasing haem. However, it is not known whether the enzyme may play a role in degrading other haem-carrying plasma proteins present in the gingival sulcus or periodontal pocket from which to derive haem. This study evaluated the ability of InpA to degrade apo- and haem-complexed albumin.

RESULTS

Albumin breakdown was examined over a range of pH and in the presence of reducing agent; conditions which prevail in sub- and supra-gingival plaque. InpA digested haemalbumin more efficiently than apoalbumin, especially under reducing conditions at pH 7.5. Under these conditions InpA was able to substantially degrade the albumin component of whole human plasma.

CONCLUSIONS

The data point to InpA as an efficient "albuminase" with the ability to degrade the minor fraction of haem-bound albumin in plasma. InpA may thus contribute significantly to haem acquisition by P. intermedia under conditions of low redox potential and higher pH in the inflamed gingival crevice and diseased periodontal pocket where haem availability is tightly controlled by the host.

Real-time monitoring of the metabolic activity of periodontopathic bacteria

Bacterial metabolic activity is associated with the onset and progression mechanisms of oral biofilm-mediated disease; however, at present no method to monitor bacterial metabolism exists, especially for periodontopathic bacteria. Therefore, we aimed to establish a novel method for monitoring the metabolic activity of periodontopathic bacteria, Porphyromonas gingivalis (Pg), Prevotella intermedia (Pi) and Fusobacterium nucleatum (Fn), as well as Streptococcus mutans (Sm) for comparison. The method is based on the dye resazurin, which is converted to the fluorescent molecule resorufin by reducing molecules derived from bacterial metabolism. Additionally, the effects of antimicrobial substances on bacterial metabolic activity were evaluated using this method. When bacterial suspensions were incubated with tryptone, glutamate, aspartate or glucose in the presence of resazurin, the fluorescence intensity increased over time by these bacterial metabolic reactions, indicating that this method can be used to monitor the metabolic activity of periodontopathic bacteria. Chlorhexidine showed the 50% inhibitory concentration (IC50) of 15-49 μg/ml for tryptone metabolism by Pg, Pi, and Fn, and 7.1-18 μg/ml for glucose metabolism by Pi and Sm. The IC50s for cetylpyridinium chloride and sodium dodecyl sulfate were 0.8-2.1 and 28-44 μg/ml, respectively for all bacteria examined. Fluoride had no effect except the IC50 of 640 μg/ml for Sm, while minocycline hydrochloride had no effect on any of the bacteria. The present study established the method for real-time monitoring of the metabolic activity of periodontopathic bacteria, and the method might be useful for evaluating the effects of antimicrobial substances on the bacterial metabolic activity.

In vitro effects of N-acetyl cysteine alone and in combination with antibiotics on Prevotella intermedia

N-acetyl cysteine (NAC) is an antioxidant that possesses anti-inflammatory activities in tissues. In the field of dentistry, NAC was demonstrated to prevent the expression of LPS-induced inflammatory mediators in phagocytic cells and gingival fibroblasts during the inflammatory process, but the effect of NAC on oral pathogens has been rarely studied. Here, we examined the effect of NAC against planktonic and biofilm cells of Prevotella intermedia, a major oral pathogen. NAC showed antibacterial activity against the planktonic P. intermedia with MIC value of 3 mg/ml and significantly decreased biofilm formation by the bacterium even at sub MIC. NAC did not affect the antibiotic susceptibility of planktonic P. intermedia, showing indifference (fractional inhibitory concentration index of 0.5-4) results against the bacterium in combination with ampicillin, ciprofloxacin, tetracycline or metronidazole. On the other hand, viability of the pre-established bacterial biofilm exposed to the antibiotics except metronidazole was increased in the presence of NAC. Collectively, NAC may be used for prevention of the biofilm formation by P. intermedia rather than eradication of the pre-established bacterial biofilm. Further studies are required to explore antibacterial and anti-biofilm activity of NAC against mixed population of oral bacteria and its modulatory effect on antibiotics used for oral infectious diseases.

Comparative genome analysis of Prevotella intermedia strain isolated from infected root canal reveals features related to pathogenicity and adaptation

Background

Many species of the genus Prevotella are pathogens that cause oral diseases. Prevotella intermedia is known to cause various oral disorders e.g. periodontal disease, periapical periodontitis and noma as well as colonize in the respiratory tract and be associated with cystic fibrosis and chronic bronchitis. It is of clinical significance to identify the main drive of its various adaptation and pathogenicity. In order to explore the intra-species genetic differences among strains of Prevotella intermedia of different niches, we isolated a strain Prevotella intermedia ZT from the infected root canal of a Chinese patient with periapical periodontitis and gained a draft genome sequence. We annotated the genome and compared it with the genomes of other taxa in the genus Prevotella.

Results

The raw data set, consisting of approximately 65X-coverage reads, was trimmed and assembled into contigs from which 2165 ORFs were predicted. The comparison of the Prevotella intermedia ZT genome sequence with the published genome sequence of Prevotella intermedia 17 and Prevotella intermedia ATCC25611 revealed that ~14% of the genes were strain-specific. The Preveotella intermedia strains share a set of conserved genes contributing to its adaptation and pathogenic and possess strain-specific genes especially those involved in adhesion and secreting bacteriocin. The Prevotella intermedia ZT shares similar gene content with other taxa of genus Prevotella. The genomes of the genus Prevotella is highly dynamic with relative conserved parts: on average, about half of the genes in one Prevotella genome were not included in another genome of the different Prevotella species. The degree of conservation varied with different pathways: the ability of amino acid biosynthesis varied greatly with species but the pathway of cell wall components biosynthesis were nearly constant. Phylogenetic tree shows that the taxa from different niches are scarcely distributed among clades.

Conclusions

Prevotella intermedia ZT belongs to a genus marked with highly dynamic genomes. The specific genes of Prevotella intermedia indicate that adhesion, competing with surrounding microbes and horizontal gene transfer are the main drive of the evolution of Prevotella intermedia.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1272-3) contains supplementary material, which is available to authorized users.

Evidence of mutualism between two periodontal pathogens: co-operative haem acquisition by the HmuY haemophore of Porphyromonas gingivalis and the cysteine protease interpain A (InpA) of Prevotella intermedia

Haem (iron protoporphyrin IX) is both an essential growth factor and a virulence regulator of the periodontal pathogens Porphyromonas gingivalis and Prevotella intermedia, which acquire it through the proteolytic degradation of haemoglobin and other haem-carrying plasma proteins. The haem-binding lipoprotein HmuY haemophore and the gingipain proteases of P. gingivalis form a unique synthrophic system responsible for capture of haem from haemoglobin and methaemalbumin. In this system, methaemoglobin is formed from oxyhaemoglobin by the activities of gingipain proteases and serves as a facile substrate from which HmuY can capture haem. This study examined the possibility of cooperation between HmuY and the cysteine protease interpain A (InpA) of Pr. intermedia in the haem acquisition process. Using UV-visible spectroscopy and polyacrylamide gel electrophoresis, HmuY was demonstrated to be resistant to proteolysis and so able to cooperate with InpA to extract haem from haemoglobin, which was proteolytically converted to methaemoglobin by the protease. Spectroscopic pH titrations showed that both the iron(II) and iron(III) protoporphyrin IX-HmuY complexes were stable over the pH range 4-10, demonstrating that the haemophore could function over a range of pH that may be encountered in the dental plaque biofilm. This is the first demonstration of a bacterial haemophore working in conjunction with a protease from another bacterial species to acquire haem from haemoglobin and may represent mutualism between P. gingivalis and Pr. intermedia co-inhabiting the periodontal pocket.

Role of the cysteine protease interpain A of Prevotella intermedia in breakdown and release of haem from haemoglobin

The gram-negative oral anaerobe Prevotella intermedia forms an iron(III) protoporphyrin IX pigment from haemoglobin. The bacterium expresses a 90 kDa cysteine protease, InpA (interpain A), a homologue of Streptococcus pyogenes streptopain (SpeB). The role of InpA in haemoglobin breakdown and haem release was investigated. At pH 7.5, InpA mediated oxidation of oxyhaemoglobin to hydroxymethaemoglobin [in which the haem iron is oxidized to the Fe(III) state and which carries OH- as the sixth co-ordinate ligand] by limited proteolysis of globin chains as indicated by SDS/PAGE and MALDI (matrix-assisted laser-desorption ionization)-TOF (time-of-flight) analysis. Prolonged incubation at pH 7.5 did not result in further haemoglobin protein breakdown, but in the formation of a haemoglobin haemichrome (where the haem Fe atom is co-ordinated by another amino acid ligand in addition to the proximal histidine residue) resistant to degradation by InpA. InpA-mediated haem release from hydroxymethaemoglobin-agarose was minimal compared with trypsin at pH 7.5. At pH 6.0, InpA increased oxidation at a rate greater than auto-oxidation, producing aquomethaemoglobin (with water as sixth co-ordinate ligand), and resulted in its complete breakdown and haem loss. Aquomethaemoglobin proteolysis and haem release was prevented by blocking haem dissociation by ligation with azide, whereas InpA proteolysis of haem-free globin was rapid, even at pH 7.5. Both oxidation of oxyhaemoglobin and breakdown of methaemoglobin by InpA were inhibited by the cysteine protease inhibitor E-64 [trans-epoxysuccinyl-L-leucylamido-(4-guanidino)butane]. In summary, we conclude that InpA may play a central role in haem acquisition by mediating oxyhaemoglobin oxidation, and by degrading aquomethaemoglobin in which haem-globin affinity is weakened under acidic conditions.

Degradation of human hemoglobin by Prevotella intermedia

In this study, the ability of Prevotella intermedia, an obligate anaerobic rod, to degrade human hemoglobin was determined by SDS-PAGE and the degradation was quantified by scanning densitometry. Both bacterial cells and culture supernatants degraded hemoglobin. The hemoglobin degradation by P. intermedia was time-dependent, heat sensitive, pH related and was not influenced by iron restriction. Inhibition studies demonstrated that a cysteine protease might be involved in hemoglobin degradation and this protease might require metal ions for its activity and it might be thiol-requiring and trypsin-inducible. The results indicate that P. intermedia is capable to release heme from hemoglobin, hence provide a source of iron for its proliferation.

The haem pigment of the oral anaerobes Prevotella nigrescens and Prevotella intermedia is composed of iron(III) protoporphyrin IX in the monomeric form

The haem pigment of Porphyromonas gingivalis is composed of micro -oxo bishaem, [Fe(III)PPIX](2)O, but the nature of that generated by Prevotella species has not been established. Mössbauer, Raman and UV-visible spectrophotometry were used to characterize the haem pigment of Prevotella intermedia and Prevotella nigrescens. Mössbauer and Raman spectroscopy revealed the major haem species to be monomeric iron protoporphyrin IX, Fe(III)PPIX.OH (haematin). The terminal growth pH of both species on blood agar was between 5.8 and 6.0, which favours the formation and maintenance of monomeric Fe(III)PPIX.OH. Incubation of Pr. nigrescens and Pr. intermedia with oxyhaemoglobin at pH 6.5 resulted in formation of aquomethaemoglobin which was degraded to generate Fe(III)PPIX.OH which in turn became cell-associated, whilst incubation at pH 7.5 resulted in formation of [Fe(III)PPIX](2)O. It is concluded that both Prevotella species degrade oxyhaemoglobin to form [Fe(III)PPIX](2)O as an intermediate, which is converted to Fe(III)PPIX.OH through a depression in pH. The low pH encourages cell-surface deposition of insoluble Fe(III)PPIX.OH which would act as a barrier against oxygen and reactive oxygen species, and also protect against H(2)O(2) through its inherent catalase activity.