Fusobacterium hwasookii sp. nov., Isolated from a Human Periodontitis Lesion

Identification of Fusobacterium Species Using Matrix-Assisted Laser Desorption/Ionization-Time-of-Flight Mass Spectrometry by Updating ASTA CoreDB

PURPOSE

Fusobacterium species can cause infections, and associations with cancer are being increasingly reported. As their clinical significance differs, accurate identification of individual species is important. However, matrix-assisted laser desorption/ionization-time of flight mass spectrometry has not been found to be effective in identifying Fusobacterium species in previous studies. In this study, we aimed to improve the accuracy and efficacy of identifying Fusobacterium species in clinical laboratories.

MATERIALS AND METHODS

In total, 229 Fusobacterium isolates were included in this study. All isolates were identified at the species level based on nucleotide sequences of the 16S ribosomal RNA gene and/or DNA-dependent RNA polymerase β-subunit gene (rpoB). Where necessary, isolates were identified based on whole genome sequences. Among them, 47 isolates were used for updating the ASTA database, and 182 isolates were used for the validation of Fusobacterium spp. identification.

RESULTS

Fusobacterium isolates used for validation (182/182) were correctly identified at the genus level, and most (180/182) were correctly identified at the species level using the ASTA MicroIDSys system. Most of the F. nucleatum isolates (74/75) were correctly identified at the subspecies level.

CONCLUSION

The updated ASTA MicroIDSys system can identify nine species of Fusobacterium and four subspecies of F. nucleatum in good agreement. This tool can be routinely used in clinical microbiology laboratories to identify Fusobacterium species and serve as a springboard for future research.

Development of the First Tractable Genetic System for Parvimonas micra, a Ubiquitous Pathobiont in Human Dysbiotic Disease

Parvimonas micra is a Gram-positive obligate anaerobe and a typical member of the human microbiome. P. micra is among the most highly enriched species at numerous sites of mucosal dysbiotic disease and is closely associated with the development of multiple types of malignant tumors. Despite its strong association with disease, surprisingly little is known about P. micra pathobiology, which is directly attributable to its longstanding genetic intractability. To address this problem, we directly isolated a collection of P. micra strains from odontogenic abscess clinical specimens and then screened these isolates for natural competence. Amazingly, all of the P. micra clinical isolates exhibited various levels of natural competence, including the reference strain ATCC 33270. By exploiting this ability, we were able to employ cloning-independent methodologies to engineer and complement a variety of targeted chromosomal genetic mutations directly within low-passage-number clinical isolates. To develop a tractable genetic system for P. micra, we first adapted renilla-based bioluminescence for highly sensitive reporter studies. This reporter system was then applied for the development of the novel Theo+ theophylline-inducible riboswitch for tunable gene expression studies over a broad dynamic range. Finally, we demonstrate the feasibility of generating mariner-based transposon sequencing (Tn-seq) libraries for forward genetic screening in P. micra. With the availability of a highly efficient transformation protocol and the current suite of genetic tools, P. micra should now be considered a fully genetically tractable organism suitable for molecular genetic research. The methods presented here provide a clear path to investigate the understudied role of P. micra in polymicrobial infections and tumorigenesis. IMPORTANCE Parvimonas micra is among the most highly enriched species at numerous sites of mucosal dysbiotic disease and is closely associated with numerous cancers. Despite this, little is known about P. micra pathobiology, which is directly attributable to its longstanding genetic intractability. In this study, we provide the first report of P. micra natural competence and describe the only tractable genetic system for this species. The methods presented here will allow for the detailed study of P. micra and its role in infection and tumorigenesis.

In-Silico Detection of Oral Prokaryotic Species With Highly Similar 16S rRNA Sequence Segments Using Different Primer Pairs

Although clustering by operational taxonomic units (OTUs) is widely used in the oral microbial literature, no research has specifically evaluated the extent of the limitations of this sequence clustering-based method in the oral microbiome. Consequently, our objectives were to: 1) evaluate in-silico the coverage of a set of previously selected primer pairs to detect oral species having 16S rRNA sequence segments with ≥97% similarity; 2) describe oral species with highly similar sequence segments and determine whether they belong to distinct genera or other higher taxonomic ranks. Thirty-nine primer pairs were employed to obtain the in-silico amplicons from the complete genomes of 186 bacterial and 135 archaeal species. Each fasta file for the same primer pair was inserted as subject and query in BLASTN for obtaining the similarity percentage between amplicons belonging to different oral species. Amplicons with 100% alignment coverage of the query sequences and with an amplicon similarity value ≥97% (ASI97) were selected. For each primer, the species coverage with no ASI97 (SC-NASI97) was calculated. Based on the SC-NASI97 parameter, the best primer pairs were OP_F053-KP_R020 for bacteria (region V1-V3; primer pair position for Escherichia coli J01859.1: 9-356); KP_F018-KP_R002 for archaea (V4; undefined-532); and OP_F114-KP_R031 for both (V3-V5; 340-801). Around 80% of the oral-bacteria and oral-archaea species analyzed had an ASI97 with at least one other species. These very similar species play different roles in the oral microbiota and belong to bacterial genera such as Campylobacter, Rothia, Streptococcus and Tannerella, and archaeal genera such as Halovivax, Methanosarcina and Methanosalsum. Moreover, ~20% and ~30% of these two-by-two similarity relationships were established between species from different bacterial and archaeal genera, respectively. Even taxa from distinct families, orders, and classes could be grouped in the same possible OTU. Consequently, regardless of the primer pair used, sequence clustering with a 97% similarity provides an inaccurate description of oral-bacterial and oral-archaeal species, which can greatly affect microbial diversity parameters. As a result, OTU clustering conditions the credibility of associations between some oral species and certain health and disease conditions. This significantly limits the comparability of the microbial diversity findings reported in oral microbiome literature.

Comparison of the oral microbial composition between healthy individuals and periodontitis patients in different oral sampling sites using 16S metagenome profiling

Purpose

The purpose of this study was to compare the microbial composition of 3 types of oral samples through 16S metagenomic sequencing to determine how to resolve some sampling issues that occur during the collection of sub-gingival plaque samples.

Methods

In total, 20 subjects were recruited. In both the healthy and periodontitis groups, samples of saliva and supra-gingival plaque were collected. Additionally, in the periodontitis group, sub-gingival plaque samples were collected from the deepest periodontal pocket. After DNA extraction from each sample, polymerase chain reaction amplification was performed on the V3-V4 hypervariable region on the 16S rRNA gene, followed by metagenomic sequencing and a bioinformatics analysis.

Results

When comparing the healthy and periodontitis groups in terms of alpha-diversity, the saliva samples demonstrated much more substantial differences in bacterial diversity than the supra-gingival plaque samples. Moreover, in a comparison between the samples in the case group, the diversity score of the saliva samples was higher than that of the supra-gingival plaque samples, and it was similar to that of the sub-gingival plaque samples. In the beta-diversity analysis, the sub-gingival plaque samples exhibited a clustering pattern similar to that of the periodontitis group. Bacterial relative abundance analysis at the species level indicated lower relative frequencies of bacteria in the healthy group than in the periodontitis group. A statistically significant difference in frequency was observed in the saliva samples for specific pathogenic species (Porphyromonas gingivalis, Treponema denticola, and Prevotella intermedia). The saliva samples exhibited a similar relative richness of bacterial communities to that of sub-gingival plaque samples.

Conclusions

In this 16S oral microbiome study, we confirmed that saliva samples had a microbial composition that was more similar to that of sub-gingival plaque samples than to that of supra-gingival plaque samples within the periodontitis group.

Diversity of the Tryptophanase Gene and Its Evolutionary Implications in Living Organisms

Tryptophanase encoded by the gene tnaA is a pyridoxal phosphate-dependent enzyme that catalyses the conversion of tryptophan to indole, which is commonly used as an intra- and interspecies signalling molecule, particularly by microbes. However, the production of indole is rare in eukaryotic organisms. A nucleotide and protein database search revealed tnaA is commonly reported in various Gram-negative bacteria, but that only a few Gram-positive bacteria and archaea possess the gene. The presence of tnaA in eukaryotes, particularly protozoans and marine organisms, demonstrates the importance of this gene in the animal kingdom. Here, we document the distribution of tnaA and its acquisition and expansion among different taxonomic groups, many of which are usually categorized as non-indole producers. This study provides an opportunity to understand the intriguing role played by tnaA, and its distribution among various types of organisms.

Paenibacillus oralis sp. nov., Isolated from Human Subgingival Dental Plaque of Gingivitis Lesion

A Gram-stain-negative, facultative anaerobic, spore-forming, motile, and rod-shaped bacterium, strain ChDC PVNT-B20^T, was isolated from the human subgingival dental plaque of a gingivitis lesion. Phylogenetic analysis based on the 16S ribosomal RNA gene (16S rDNA) showed that the strain belonged to the genus Paenibacillus. BLAST analysis of 16S rDNA sequence of the strain displayed high identity to those of Paenibacillus faecis DSM 23593^T (97.7% similarity) and Paenibacillus macerans ATCC 8244^T (97.6% similarity). Draft genome of strain ChDC PVNT-B20^T was composed of 8,112,407 bp. The DNA G+C content of the strain was 51.3 mol%. Average nucleotide identity values between strain ChDC PVNT-B20^T and P. faecis DSM 23593^T or P. macerans ATCC 8244^T were 75.71% and 91.5%, respectively. Genome-to-genome distance values between strain ChDC PVNT-B20^T and P. faecis DSM 23593^T or P. macerans ATCC 8244^T were 21.6% (19.3-24.0%) and 44.9% (42.3-47.4%), respectively. Major cellular fatty acids of strain ChDC PVNT-B20^T were anteiso-C_15:0 (43.4%), C_16:0 (16.6%), iso-C_16:0 (14.4%), and anteiso-C_17:0 (12.4%). The sole respiratory quinone of the strain was menaqinone-7. Major polar lipids of the strain were phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), and one unidentified glycolipid (GL). Minor polar lipids were one unidentified aminolipid (AL), one unidentified phospholipid (PL), and three unidentified lipids (L1-L3). Based on these results, strain ChDC PVNT-B20^T is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus oralis sp. nov. is proposed. Type strain is ChDC PVNT-B20^T (= KCOM 3021^T = JCM 33462 ^T).

Streptococcus koreensis sp. nov., Isolated from Human Subgingival Dental Plaque of Periodontitis Lesion

A novel facultative anaerobic, Gram-stain-positive coccus, strain JS71^T, was isolated from the human subgingival dental plaque of a periodontitis lesion. Phylogenetic analysis based on the 16S ribosomal RNA gene (16S rDNA) revealed that the strain belonged to the genus Streptococcus. The 16S rDNA sequence had high similarity with Streptococcus rubneri DSM 26920^T (98.6%), Streptococcus parasanguinis ATCC 15912^T (98.5%), and Streptococcus australis CCUG 45919^T (98.3%). The genome of strain JS71^T was 2,009,592 bp in length. The DNA G+C content of the strain was 42.1 mol%. Average nucleotide identity values between strain JS71^T and S. rubneri DSM 26920^T, S. parasanguinis ATCC 15912^T, and S. australis CCUG 45919^T were 88.9%, 80.8%, and 92.4%, respectively. Genome-to-genome distance values between strain JS71^TS. rubneri DSM 26920^T, S. parasanguinis ATCC 15912^T, and S. australis CCUG 45919^T were 36.5% (34-39%), 26.3% (23.9-28.7%), and 48.0% (45.4-50.6%), respectively. The major fatty acids of the strain were C_16:0 (39.7%), C_{18:1 ω6c}/C_{18:1 ω7c} (15.5%), and C_18:0 (10.4%). Based on these results, strain JS71^T (= KCOM 2890^T = JCM 33454^T) should be a novel species of the genus Streptococcus, for which the name Streptococcus koreensis sp. nov. is proposed.

Lautropia dentalis sp. nov., Isolated from Human Dental Plaque of a Gingivitis Lesion

A novel Gram-stain-negative, motile, and facultative anaerobic coccus, strain ChDC F240^T was isolated from human subgingival dental plaque of a gingivitis lesion. The phylogenetic analysis based on the 16S ribosomal RNA gene (16S rDNA) sequence showed that the strain belonged to the genus Lautropia. 16S rDNA of strain ChDC F240^T had the highest similarity to that of Lautropia mirabilis ATCC 51599^T (98.8%). Major cellular fatty acids of strain ChDC F240^T were C_16:0 (43.9%) and C_16:1ω6C/C_16:1ω7C (38.1%). Draft genome of the strain was 3,834,139 bp in length and the G+C content was 65.0 mol%. Average nucleotide identity and genome-to-genome distance values between strain ChDC F240^T and L. mirabilis ATCC 51599 ^T were 81.99% and 28.50% (26.1-30.9%), respectively. These results reveal that strain ChDC F240^T is a novel species within the genus Lautropia, for which the name Lautropia dentalis sp. nov. is proposed; type strain is ChDC F240^T (= KCOM 2505^T = JCM 33297^T).

Lachnoanaerobaculum gingivalis sp. nov., Isolated from Human Subgingival Dental Plaque of a Gingivitis Lesion

A novel Gram-stain-positive, obligately anaerobic, spore-forming rod, designated strain ChDC B114^T, was isolated from a human dental plaque of a gingivitis lesion. The strain was characterized by polyphasic taxonomic analysis to identify it at the species level. The 16S ribosomal RNA gene (16S rDNA) sequence analysis revealed that the strain belongs to the genus Lachnoanaerobaculum. The percent similarity of the 16S rDNA of the strain was closest to the homologous gene sequence of Lachnoanaerobaculum orale N1^T (98.5%) and Lachnoanaerobaculum saburreum CCUG 28089^T (97.6%). The major fatty acids of strain ChDC B114^T were C_16:0 (30.7%), C_14:0 (17.7%), iso-C_19:0 (14.9%), and C_17:0 2OH (12.0%). The draft genome of strain ChDC B114^T was 3,097,953 bp in length. The G+C content of the strain was 35.9 mol %. Average nucleotide identity values between strain ChDC B114^T and L. orale N1^T and L. saburreum CCUG 28089^T were 83.2% and 82.0%, respectively. Genome-to-genome distance values between strain ChDC B114^T and L. orale N1^T and L. saburreum CCUG 28089^T were 26.8% (24.5-29.3%) and 26.30% (24.0-28.8%), respectively. Based on these results, strain ChDC B114^T (= KCOM 2030^T = JCM 33452^T) should be classified as a novel species of genus Lachnoanaerobaculum, for which the name Lachnoanaerobaculum gingivalis sp. nov. is proposed.

Streptococcus chosunense sp. nov., Isolated from Human Postoperative Maxillary Cyst

A novel facultative anaerobic, non-spore forming, non-motile, and Gram-stain-positive coccus, designated strain ChDC B353^T, was isolated from human postoperative maxillary cyst. The 16S ribosomal RNA gene (16S rDNA) sequence of the strain was most closely related to those of Streptococcus pseudopneumoniae ATCC BAA-960^T (99.4%), Streptococcus mitis NCTC 12261^T (99.3%), and Streptococcus pneumoniae NCTC 7465^T (99.2%). The major fatty acids of the strain were C_16:0 (43.2%) and C_{18:1 ω6c}/C_{18:1 ω7c} (20.2%). The genome of strain ChDC B353^T was composed of 1,902,053 bps. The DNA G+C content of the strain was 40.2 mol%. Average nucleotide identity (ANI) values between strain ChDC B353^T and S. pseudopneumoniae ATCC BAA-960^T, S. mitis NCTC 12261^T, and S. pneumoniae NCTC 7465^T were 91.9%, 93.5%, and 91.3%, respectively. Genome-to-genome distance (GGD) values between strain ChDC B353^T and S. pseudopneumoniae ATCC BAA-960^T, S. mitis NCTC 12261^T, or S. pneumoniae NCTC 7465^T were 46.6% (44.0-49.2%), 53.2% (50.5-55.9%), and 46.0% (43.5-48.7%), respectively. The threshold values of ANI and GGD for species discrimination are 95-96% and 70%, respectively. These results reveal that strain ChDC B353^T (= KCOM 1699^T = JCM 33453^T) is a novel species belonging to genus Streptococcus, for which a name of Streptococcus chosunense sp. nov. is proposed.

Global Investigations of Fusobacterium nucleatum in Human Colorectal Cancer

Colorectal cancer (CRC) is the third most prevalent cancer and second in terms of mortality. Emerging evidence from recent studies suggests a potential role of Fusobacterium nucleatum in the development of CRC. In this article, we review studies from different geographical regions examining the association between F. nucleatum and CRC, the detection methods and the tumorigenic mechanisms. Furthermore, we discuss the potential clinical impact of F. nucleatum in CRC and suggest future study directions.

Prevotella koreensis sp. nov., Isolated from Human Subgingival Dental Plaque of Periodontitis Lesion

A novel Gram-negative, obligately anaerobic, non-motile, non-spore forming, and rod-shaped bacterium, designated strain JS262^T, was isolated from human subgingival plaque of periodontitis lesion and was characterized by polyphasic taxonomic analysis. Comparison of 16S ribosomal RNA gene (16S rDNA) sequence revealed that the strain belonged to the genus Prevotella. The percent similarity of 16S rDNA of strain JS262^T was closest to those of Prevotella buccae ATCC 33574^T (89.1%) and Prevotella shahii JCM 12083^T (88.9%). The major fatty acids of strain JS262^T were C_16:0 (29.2%), iso-C_15:0 (19.2%), and anteiso-C_15:0 (16.9%). Complete genome of strain JS262^T was 2,691,540 bp in length and the G+C content was 43.9 mol%. Average nucleotide identity and genome-to-genome distance values between strain JS262^T and P. buccae ATCC 33574^T or P. loescheii DSM 19665^T were > 70.4% and > 30.1%, respectively. On the basis of these data, a novel Prevotella species is proposed: Prevotella koreensis sp. nov. The type strain of P. koreensis is JS262^T (= KCOM 3155^T = JCM 33298^T).

Streptococcus periodonticum sp. nov., Isolated from Human Subgingival Dental Plaque of Periodontitis Lesion

A novel facultative anaerobic and Gram-stain-positive coccus, designated strain ChDC F135^T, was isolated from human subgingival dental plaque of periodontitis lesion and was characterized by polyphasic taxonomic analysis. The 16S rRNA gene (16S rDNA) sequence of strain ChDC F135^T was closest to that of Streptococcus sinensis HKU4^T (98.2%), followed by Streptococcus intermedia SK54^T (97.0%), Streptococcus constellatus NCTC11325^T (96.0%), and Streptococcus anginosus NCTC 10713^T (95.7%). In contrast, phylogenetic analysis based on the superoxide dismutase gene (sodA) and the RNA polymerase beta-subunit gene (rpoB) showed that the nucleotide sequence similarities of strain ChDC F135^T were highly similar to the corresponding genes of S. anginosus NCTC 10713^T (99.2% and 97.6%, respectively), S. constellatus NCTC11325^T (87.8% and 91.4%, respectively), and S. intermedia SK54^T (85.8% and 91.2%, respectively) rather than those of S. sinensis HKU4^T (80.5% and 82.6%). The complete genome of strain ChDC F135^T consisted of 1,901,251 bp and the G+C content was 38.9 mol %. Average nucleotide identity value between strain ChDC F135^T and S. sinensis HKU4^T or S. anginosus NCTC 10713^T were 75.7% and 95.6%, respectively. The C_14:0 composition of the cellular fatty acids of strain ChDC F135^T (32.8%) was different from that of S. intermedia (6-8%), S. constellatus (6-13%), and S. anginosus (13-20%). Based on the results of phylogenetic and phenotypic analysis, strain ChDC F135^T (= KCOM 2412^T = JCM 33300^T) was classified as a type strain of a novel species of the genus Streptococcus, for which we proposed the name Streptococcus periodonticum sp. nov.

Streptococcus gwangjuense sp. nov., Isolated from Human Pericoronitis

A novel facultative anaerobic, Gram-stain-negative coccus, designated strain ChDC B345^T, was isolated from human pericoronitis lesion and was characterized by polyphasic taxonomic analysis. The 16S ribosomal RNA gene (16S rDNA) sequence revealed that the strain belonged to the genus Streptococcus. The 16S rDNA sequence of strain ChDC B345^T was most closely related to those of  Streptococcus mitis NCTC 12261^T (99.5%) and Streptococcus pseudopneumoniae ATCC BAA-960^T (99.5%). Complete genome of strain ChDC B345^T was 1,972,471 bp in length and the G + C content was 40.2 mol%. Average nucleotide identity values between strain ChDC B345^T and S. pseudopneumoniae ATCC BAA-960^T or S. mitis NCTC 12261^T were 92.17% and 93.63%, respectively. Genome-to-genome distance values between strain ChDC B345^T and S. pseudopneumoniae ATCC BAA-960^T or S. mitis NCTC 12261^T were 47.8% (45.2-50.4%) and 53.0% (51.0-56.4%), respectively. Based on these results, strain ChDC B345^T (= KCOM 1679^T= JCM 33299^T) should be classified as a novel species of genus Streptococcus, for which we propose the name Streptococcus gwangjuense sp. nov.

Fusobacterium pseudoperiodonticum sp. nov., Isolated from the Human Oral Cavity

In the present study, three strains (ChDC F213^T, ChDC F251, and ChDC F267) were classified as novel species of genus Fusobacterium based on average nucleotide identity (ANI) and genome-to-genome distance (GGD) analysis and chemotaxonomic characterization. 16S rDNA sequences of strains ChDC F213^T, ChDC F251, and ChDC F267 were highly similar to that of F. periodonticum ATCC 33693^T (99.6, 99.4, and 99.4%, respectively). ANI and GGD values of the three isolates with F. periodonticum ATCC 33693^T ranged from 92.5 to 92.6% and 47.7 to 48.2%, respectively. Considering that threshold of ANI and GGD values for bacterial species discrimination are 95-96% and 70%, respectively, these results indicate that the three isolates represent a novel Fusobacterium species. DNA G + C contents of the three isolates were 28.0 mol% each. Cellular fatty acid analysis of these strains revealed that C_14:0, C_16:0, and C_16:1 ω6c/C_16:1 ω7c were major fatty acids. Therefore, these three strains are novel species belonging to genus Fusobacterium. Strain ChDC F213^T (= KCOM 1259^T = KCTC 5677^T = JCM 33009^T) is the type strain of a novel species of genus Fusobacterium, for which a name of Fusobacterium pseudoperiodonticum sp. nov. is proposed.

Role of SCFAs in gut microbiome and glycolysis for colorectal cancer therapy

Increased risk of colorectal cancer (CRC) is associated with altered intestinal microbiota as well as short-chain fatty acids (SCFAs) reduction of output The energy source of colon cells relies mainly on three SCFAs, namely butyrate (BT), propionate, and acetate, while CRC transformed cells rely mainly on aerobic glycolysis to provide energy. This review summarizes recent research results for dysregulated glucose metabolism of SCFAs, which could be initiated by gut microbiome of CRC. Moreover, the relationship between SCFA transporters and glycolysis, which may correlate with the initiation and progression of CRC, are also discussed. Additionally, this review explores the linkage of BT to transport of SCFAs expressions between normal and cancerous colonocyte cell growth for tumorigenesis inhibition in CRC. Furthermore, the link between gut microbiota and SCFAs in the metabolism of CRC, in addition, the proteins and genes related to SCFAs-mediated signaling pathways, coupled with their correlation with the initiation and progression of CRC are also discussed. Therefore, targeting the SCFA transporters to regulate lactate generation and export of BT, as well as applying SCFAs or gut microbiota and natural compounds for chemoprevention may be clinically useful for CRCs treatment. Future research should focus on the combination these therapeutic agents with metabolic inhibitors to effectively target the tumor SCFAs and regulate the bacterial ecology for activation of potent anticancer effect, which may provide more effective application prospect for CRC therapy.

Distinct gut microbiome patterns associate with consensus molecular subtypes of colorectal cancer

Colorectal cancer (CRC) is a heterogeneous disease and recent advances in subtype classification have successfully stratified the disease using molecular profiling. The contribution of bacterial species to CRC development is increasingly acknowledged, and here, we sought to analyse CRC microbiomes and relate them to tumour consensus molecular subtypes (CMS), in order to better understand the relationship between bacterial species and the molecular mechanisms associated with CRC subtypes. We classified 34 tumours into CRC subtypes using RNA-sequencing derived gene expression and determined relative abundances of bacterial taxonomic groups using 16S rRNA amplicon metabarcoding. 16S rRNA analysis showed enrichment of Fusobacteria and Bacteroidetes, and decreased levels of Firmicutes and Proteobacteria in CMS1. A more detailed analysis of bacterial taxa using non-human RNA-sequencing reads uncovered distinct bacterial communities associated with each molecular subtype. The most highly enriched species associated with CMS1 included Fusobacterium hwasookii and Porphyromonas gingivalis. CMS2 was enriched for Selenomas and Prevotella species, while CMS3 had few significant associations. Targeted quantitative PCR validated these findings and also showed an enrichment of Fusobacterium nucleatum, Parvimonas micra and Peptostreptococcus stomatis in CMS1. In this study, we have successfully associated individual bacterial species to CRC subtypes for the first time.

Genome-Based Reclassification of Fusobacterium nucleatum Subspecies at the Species Level

Fusobacterium nucleatum is classified as four subspecies, subsp. nucleatum, polymorphum, vincentii, and animalis, based on DNA-DNA hybridization (DDH) patterns, phenotypic characteristics, and/or multilocus sequence analysis (MLSA). The gold standards for classification of bacterial species are DDH and 16S ribosomal RNA gene (16S rDNA) sequence homology. The thresholds of DDH and 16S rDNA similarity for delineation of bacterial species have been suggested to be >70 and 98.65%, respectively. Average nucleotide identity (ANI) and genome-to-genome distance (GGD) analysis based on genome sequences were recently introduced as a replacement for DDH to delineate bacterial species with ANI (95-96%) and GGD (70%) threshold values. In a previous study, F. hwasookii was classified as a new species based on MLSA and DDH results. 16S rDNA similarity between F. hwasookii type strain and F. nucleatum subspecies type strains was higher than that between F. nucleatum subspecies type strains. Therefore, it is possible that the four F. nucleatum subspecies can be classified as Fusobacterium species. In this study, we performed ANI and GGD analyses using the genome sequences of 36 F. nucleatum, five F. hwasookii, and one Fusobacterium periodonticum strain to determine whether the four F. nucleatum subspecies could be classified as species using OrthoANI and ANI web-based softwares provided by ChunLab and Kostas lab, respectively, and GGD calculator offered by German Collection of Microorganisms and Cell Cultures. ANI values calculated from OrthoANI and ANI calculators between the type strains of F. nucleatum subspecies ranged from 89.80 to 92.97 and from 90.40 to 91.90%, respectively. GGD values between the type strains of F. nucleatum subspecies ranged from 42.3 to 46.0%. ANI and GGD values among strains belonging to the same F. nucleatum subspecies, subsp. nucleatum, subsp. polymorphum, subsp. vincentii, and subsp. animalis were >96 and >68.2%, respectively. These results strongly suggest that F. nucleatum subsp. nucleatum, subsp. polymorphum, subsp. vincentii, and subsp. animalis should be classified as F. nucleatum, F. polymorphum, F. vincentii, and F. animalis, respectively.