scholarly journals A computational protocol to characterize elusive Candidate Phyla Radiation bacteria in oral environments using metagenomic data

2018 ◽  
Author(s):  
Peiqi Meng ◽  
Chang Lu ◽  
Xinzhe Lou ◽  
Qian Zhang ◽  
Peizeng Jia ◽  
...  
Keyword(s):  
Oral Cavity ◽  
Ribosomal Proteins ◽  
Morphological Changes ◽  
Metagenomic Data ◽  
Great Promise ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Human Oral Cavity ◽  
Candidate Phyla Radiation ◽  
Computational Protocol

AbstractSeveral studies have documented the diversity and potential pathogenic associations of organisms in the human oral cavity. Although much progress has been made in understanding the complex bacterial community inhabiting the human oral cavity, our understanding of some microorganisms is less resolved due to a variety of reasons. One such little-understood group is the candidate phyla radiation (CPR), which is a recently identified, but highly abundant group of ultrasmall bacteria with reduced genomes and unusual ribosomes. Here, we present a computational protocol for the detection of CPR organisms from metagenomic data. Our approach relies on a self-constructed dataset comprising published CPR genomic sequences as a filter to identify CPR sequences from metagenomic sequencing data. After assembly and functional prediction, the taxonomic affiliation of CPR contigs can be identified through phylogenetic analysis with publically available 16S rRNA gene and ribosomal proteins, in addition to sequence similarity analyses (e.g., average nucleotide identity calculations and contig mapping). Using this protocol, we reconstructed two draft genomes of organisms within the TM7 superphylum, that had genome sizes of 0.594 Mb and 0.678 Mb. Among the predicted functional genes of the constructed genomes, a high percentage were related to signal transduction, cell motility, and cell envelope biogenesis, which could contribute to cellular morphological changes in response to environmental cues.ImportanceCandidate phyla radiation (CPR) bacterial group is a recently identified, but highly diverse and abundant group of ultrasmall bacteria exhibiting reduced genomes and limited metabolic capacities. A number of studies have reported their potential pathogenic associations in multiple mucosal diseases including periodontitis, halitosis, and inflammatory bowel disease. However, CPR organisms are difficult to cultivate and are difficult to detect with PCR-based methods due to divergent genetic sequences. Thus, our understanding of CPR has lagged behind that of other bacterial component. Here, we used metagenomic approaches to overcome these previous barriers to CPR identification, and established a computational protocol for detection of CPR organisms from metagenomic samples. The protocol describe herein holds great promise for better understanding the potential biological functioning of CPR. Moreover, the pipeline could be applied to other organisms that are difficult to cultivate.

scholarly journals Diversity and Morphology of Members of the Phylum “Synergistetes” in Periodontal Health and Disease

2009 ◽  
Vol 75 (11) ◽  
pp. 3777-3786 ◽  
Author(s):  
S. R. Vartoukian ◽  
R. M. Palmer ◽  
W. G. Wade
Keyword(s):  
Oral Health ◽  
Oral Cavity ◽  
Positive Sample ◽  
Rrna Gene ◽  
Fish Analysis ◽  
Subgingival Plaque ◽  
Pcr Cloning ◽  
Human Oral Cavity ◽  
Health And Disease

ABSTRACT Members of the phylum “Synergistetes” have frequently been detected in the human oral cavity at sites of dental disease, but they have rarely been detected in studies of oral health. Only two oral “Synergistetes” taxa are cultivable. The aims of this study were to investigate the diversity of “Synergistetes” in the oral cavity, to establish whether “Synergistetes” taxa are more strongly associated with periodontitis than with oral health, and to visualize unculturable “Synergistetes” in situ. Sixty samples (saliva, dental plaque, and mucosal swabs) were collected from five subjects with periodontitis and five periodontally healthy controls. Using phylum-specific 16S rRNA gene primers, “Synergistetes” were identified by PCR, cloning, and sequencing of 48 clones per PCR-positive sample. Subgingival plaque samples were labeled with probes targeting rRNA of unculturable oral “Synergistetes” using fluorescent in situ hybridization (FISH). Analysis of 1,664 clones revealed 12 “Synergistetes” operational taxonomic units (OTUs) at the 99% sequence identity level, 5 of which were novel. “Synergistetes” OTU 4.2 was found in significantly more subjects with periodontitis than controls (P = 0.048) and was more abundant in subgingival plaque at diseased sites than at healthy sites in subjects with periodontitis (P = 0.019) or controls (P = 0.019). FISH analysis revealed that unculturable oral “Synergistetes” cells were large curved bacilli. The human oral cavity harbors a diverse population of “Synergistetes.” “Synergistetes” OTU 4.2 is associated with periodontitis and may have a pathogenic role.

scholarly journals Evidence of independent acquisition and adaption of ultra-small bacteria to human hosts across the highly diverse yet reduced genomes of the phylum Saccharibacteria

2018 ◽  
Author(s):  
Jeffrey S. McLean ◽  
Batbileg Bor ◽  
Thao T. To ◽  
Quanhui Liu ◽  
Kristopher A. Kerns ◽  
...  
Keyword(s):  
Oral Cavity ◽  
De Novo ◽  
Gc Content ◽  
Single Copy ◽  
Small Subunit ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Ssu Rrna Gene ◽  
Human Oral Cavity

ABSTRACTRecently, we discovered that a member of the Saccharibacteria/TM7 phylum (strain TM7x) isolated from the human oral cavity, has an ultra-small cell size (200-300nm), a highly reduced genome (705 Kbp) with limited de novo biosynthetic capabilities, and a very novel lifestyle as an obligate epibiont on the surface of another bacterium 1. There has been considerable interest in uncultivated phyla, particularly those that are now classified as the proposed candidate phyla radiation (CPR) reported to include 35 or more phyla and are estimated to make up nearly 15% of the domain Bacteria. Most members of the larger CPR group share genomic properties with Saccharibacteria including reduced genomes (<1Mbp) and lack of biosynthetic capabilities, yet to date, strain TM7x represents the only member of the CPR that has been cultivated and is one of only three CPR routinely detected in the human body. Through small subunit ribosomal RNA (SSU rRNA) gene surveys, members of the Saccharibacteria phylum are reported in many environments as well as within a diversity of host species and have been shown to increase dramatically in human oral and gut diseases. With a single copy of the 16S rRNA gene resolved on a few limited genomes, their absolute abundance is most often underestimated and their potential role in disease pathogenesis is therefore underappreciated. Despite being an obligate parasite dependent on other bacteria, six groups (G1-G6) are recognized using SSU rRNA gene phylogeny in the oral cavity alone. At present, only genomes from the G1 group, which includes related and remarkably syntenic environmental and human oral associated representatives1, have been uncovered to date. In this study we systematically captured the spectrum of known diversity in this phylum by reconstructing completely novel Class level genomes belonging to groups G3, G6 and G5 through cultivation enrichment and/or metagenomic binning from humans and mammalian rumen. Additional genomes for representatives of G1 were also obtained from modern oral plaque and ancient dental calculus. Comparative analysis revealed remarkable divergence in the host-associated members across this phylum. Within the human oral cavity alone, variation in as much as 70% of the genes from nearest oral clade (AAI 50%) as well as wide GC content variation is evident in these newly captured divergent members (G3, G5 and G6) with no environmental relatives. Comparative analyses suggest independent episodes of transmission of these TM7 groups into humans and convergent evolution of several key functions during adaptation within hosts. In addition, we provide evidence from in vivo collected samples that each of these major groups are ultra-small in size and are found attached to larger cells.

scholarly journals Description of Alloprevotella rava gen. nov., sp. nov., isolated from the human oral cavity, and reclassification of Prevotella tannerae Moore et al. 1994 as Alloprevotella tannerae gen. nov., comb. nov.

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1214-1218 ◽  
Author(s):  
Julia Downes ◽  
Floyd E. Dewhirst ◽  
Anne C. R. Tanner ◽  
William G. Wade
Keyword(s):  
Oral Cavity ◽  
Type Strain ◽  
Type Species ◽  
Rrna Gene ◽  
The Novel ◽  
Content Type ◽  
Human Oral Cavity ◽  
Link Type ◽  
Prevotella Melaninogenica ◽  
The Family

Five strains of anaerobic, Gram-negative bacilli isolated from the human oral cavity were subjected to a comprehensive range of phenotypic and genotypic tests and were found to comprise a homogeneous group. Phylogenetic analysis of full-length 16S rRNA gene sequences showed that these strains represented a novel group within the family Prevotellaceae , and the most closely related species was Prevotella tannerae . P. tannerae and the novel taxon are deeply branched from the genus Prevotella , with sequence identities to the type strain of the type species of Prevotella , Prevotella melaninogenica , of 82.2 and 85.6 %, respectively. The novel genus Alloprevotella gen. nov. is proposed to accommodate the novel species Alloprevotella rava gen. nov., sp. nov. and the previously named Prevotella tannerae Moore et al. 1994 as Alloprevotella tannerae gen. nov., comb. nov. The type species is Alloprevotella tannerae. The type strain of Alloprevotella rava is 81/4-12T ( = DSM 22548T  = CCUG 58091T) and the type strain of Alloprevotella tannerae is ATCC 51259T  = CCUG 34292T  = CIP 104476T  = NCTC 13073T. Alloprevotella rava is weakly to moderately saccharolytic and produces moderate amounts of acetic acid and major amounts of succinic acid as end products of fermentation. Strains are sensitive to 20 % bile and hydrolyse gelatin. The principal cellular long-chain fatty acids are anteiso-C15 : 0, iso-C15 : 0, C16 : 0, iso-C17 : 0 and iso-C17 : 0 3-OH. The G+C content of the DNA of the type strain is 47 mol%.

scholarly journals Scardovia wiggsiae sp. nov., isolated from the human oral cavity and clinical material, and emended descriptions of the genus Scardovia and Scardovia inopinata

2011 ◽  
Vol 61 (1) ◽  
pp. 25-29 ◽  
Author(s):  
Julia Downes ◽  
Maria Mantzourani ◽  
David Beighton ◽  
Samuel Hooper ◽  
Melanie J. Wilson ◽  
...  
Keyword(s):  
16S Rrna ◽  
Oral Cavity ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Lipid Analysis ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Human Oral Cavity

Six strains of anaerobic, pleomorphic Gram-positive bacilli, isolated from the human oral cavity and an infected arm wound, were subjected to a comprehensive range of phenotypic and genotypic tests and were found to comprise a homogeneous group. 16S rRNA gene sequence analysis revealed that the isolates were most closely related to Scardovia inopinata CCUG 35729T (94.8–94.9 % 16S rRNA gene sequence similarity). The isolates were saccharolytic and produced acetic and lactic acids as end products of fermentation. The major fatty acids were C16 : 0 (49.8 %) and C18 : 1 ω9c (35.8 %). Polar lipid analysis revealed a variety of glycolipids, diphosphatidylglycerol, an unidentified phospholipid and an unidentified phosphoglycolipid. No respiratory quinones were detected. The peptidoglycan was of the type A4α l-Lys–Thr–Glu, with l-lysine partially replaced by l-ornithine. The DNA G+C content of one of the strains, C1A_55T , was 55 mol%. A novel species, Scardovia wiggsiae sp. nov., is proposed to accommodate the six isolates, with the type strain C1A_55T (=DSM 22547T=CCUG 58090T).

scholarly journals Site-specificity of streptococci in the oral microbiome

2021 ◽  
Author(s):  
Anthony R. McLean ◽  
Julian Torres-Morales ◽  
Gary G. Borisy ◽  
Jessica L. Mark Welch
Keyword(s):  
Oral Cavity ◽  
Related Species ◽  
Oral Microbiome ◽  
Individual Species ◽  
Rrna Gene ◽  
Site Specificity ◽  
Oral Streptococci ◽  
Closely Related Species ◽  
Streptococcus Species ◽  
Human Oral Cavity

Patterns of microbial distribution are determined by as-yet poorly understood rules governing where microbes can grow and thrive. Therefore, a detailed understanding of where bacteria localize is necessary to advance microbial ecology and microbiome-based therapeutics. The site-specialist hypothesis predicts that most microbes in the human oral cavity have a primary habitat within the mouth where they are most abundant. We asked whether this hypothesis accurately describes the distribution of the members of the genus Streptococcus, a clinically relevant taxon that dominates most oral sites. Prior analysis of 16S rRNA gene sequencing data indicated that some oral Streptococcus clades are site-specialists while others may be generalists. However, within complex microbial populations composed of numerous closely-related species and strains, such as the oral streptococci, genome-scale analysis is necessary to provide the resolution to discriminate closely related taxa with distinct functional roles. Here we assess whether individual species within this genus are generalists using publicly available genomic sequence data that provides species-level resolution. We chose a set of high-quality representative genomes for Streptococcus species from the human oral microbiome. Onto these genomes, we mapped short-read metagenomic sequences from supragingival plaque, tongue dorsum, and other sites in the oral cavity. We found that every reliably detectable Streptococcus species in the human oral cavity was a site-specialist and that even closely related species such as S. mitis, S. oralis, and S. infantis specialized in different sites. These findings indicate that closely related bacteria can have distinct habitat distributions in the absence of dispersal limitation and under similar environmental conditions and immune regimes. These three species also share substantially the same species-specific core genes indicating that neither taxonomy nor gene content are clear predictors of site-specialization. Site-specificity may instead be influenced by subtle characteristics such as nucleotide-level divergences within conserved genes.

scholarly journals Veillonellae: Beyond Bridging Species in Oral Biofilm Ecology

2021 ◽  
Vol 2 ◽  
Author(s):  
Peng Zhou ◽  
Daniel Manoil ◽  
Georgios N. Belibasakis ◽  
Georgios A. Kotsakis
Keyword(s):  
Oral Cavity ◽  
Bacterial Species ◽  
Oral Microbiome ◽  
Future Research ◽  
Great Promise ◽  
Large Species ◽  
Oral Biofilm ◽  
Human Oral Cavity ◽  
Oral Biofilms ◽  
Polymicrobial Disease

The genus Veillonella comprises 16 characterized species, among which eight are commonly found in the human oral cavity. The high abundance of Veillonella species in the microbiome of both supra- and sub-gingival biofilms, and their interdependent relationship with a multitude of other bacterial species, suggest veillonellae to play an important role in oral biofilm ecology. Development of oral biofilms relies on an incremental coaggregation process between early, bridging and later bacterial colonizers, ultimately forming multispecies communities. As early colonizer and bridging species, veillonellae are critical in guiding the development of multispecies communities in the human oral microenvironment. Their ability to establish mutualistic relationships with other members of the oral microbiome has emerged as a crucial factor that may contribute to health equilibrium. Here, we review the general characteristics, taxonomy, physiology, genomic and genetics of veillonellae, as well as their bridging role in the development of oral biofilms. We further discuss the role of Veillonella spp. as potential “accessory pathogens” in the human oral cavity, capable of supporting colonization by other, more pathogenic species. The relationship between Veillonella spp. and dental caries, periodontitis, and peri-implantitis is also recapitulated in this review. We finally highlight areas of future research required to better understand the intergeneric signaling employed by veillonellae during their bridging activities and interspecies mutualism. With the recent discoveries of large species and strain-specific variation within the genus in biological and virulence characteristics, the study of Veillonella as an example of highly adaptive microorganisms that indirectly participates in dysbiosis holds great promise for broadening our understanding of polymicrobial disease pathogenesis.

scholarly journals Microbial Community Analysis with Ribosomal Gene Fragments from Shotgun Metagenomes

2015 ◽  
Vol 82 (1) ◽  
pp. 157-166 ◽  
Author(s):  
Jiarong Guo ◽  
James R. Cole ◽  
Qingpeng Zhang ◽  
C. Titus Brown ◽  
James M. Tiedje
Keyword(s):  
Community Analysis ◽  
Rrna Genes ◽  
Metagenomic Data ◽  
Rrna Gene ◽  
Processing Unit ◽  
Metagenomic Sequencing ◽  
Ssu Rrna ◽  
Variable Regions ◽  
Content Type ◽  
Central Processing

ABSTRACTShotgun metagenomic sequencing does not depend on gene-targeted primers or PCR amplification; thus, it is not affected by primer bias or chimeras. However, searching rRNA genes from large shotgun Illumina data sets is computationally expensive, and no approach exists for unsupervised community analysis of small-subunit (SSU) rRNA gene fragments retrieved from shotgun data. We present a pipeline, SSUsearch, to achieve the faster identification of short-subunit rRNA gene fragments and enabled unsupervised community analysis with shotgun data. It also includes classification and copy number correction, and the output can be used by traditional amplicon analysis platforms. Shotgun metagenome data using this pipeline yielded higher diversity estimates than amplicon data but retained the grouping of samples in ordination analyses. We applied this pipeline to soil samples with paired shotgun and amplicon data and confirmed bias againstVerrucomicrobiain a commonly used V6-V8 primer set, as well as discovering likely bias againstActinobacteriaand forVerrucomicrobiain a commonly used V4 primer set. This pipeline can utilize all variable regions in SSU rRNA and also can be applied to large-subunit (LSU) rRNA genes for confirmation of community structure. The pipeline can scale to handle large amounts of soil metagenomic data (5 Gb memory and 5 central processing unit hours to process 38 Gb [1 lane] of trimmed Illumina HiSeq2500 data) and is freely available athttps://github.com/dib-lab/SSUsearchunder a BSD license.

scholarly journals Molecular profiling of microbiota in human oral cavity, stomach and intestine

2018 ◽  
Author(s):  
Qianqian Liu ◽  
Feizhou Zhu ◽  
Liyu Chen ◽  
Meihua Xu ◽  
Jianwei Chen ◽  
...  
Keyword(s):  
16S Rrna ◽  
Oral Cavity ◽  
16S Rrna Gene ◽  
Gastric Juice ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Rrna Gene ◽  
Human Oral Cavity ◽  
Stool Microbiota ◽  
The 16S Rrna Gene

The microbiota in the human gut is not only a complicated microecological system but also plays important roles in both health and disease. In order to understand the roles of these gut bacteria, we determined the distribution of microbiota in different regions of the gut by sequencing the 16S rRNA gene V4 region of the bacteria in the saliva, gastric juice, and stool of healthy individuals. The 16S rRNA gene V3-V5 region sequences of saliva and stool microbiota were obtained from Human Microbiome Project (HMP) and the V4 sequence was obtained from the V3-V5 sequences by a program designed by Perl language. We found that the microbiota of the gastric juice is more similar to those in the saliva rather than that in the stool. The frequency of some taxa was significantly different among the three groups with the Streptococcus, Veillonella, Oribacterium, Selenomonas, Actinomyces, and Granulicatella most abundant in the saliva; the Prevotella, Neisseria, Actinobacillus, Treponema, and Helicobacter most abundant in the gastric juice; and the Bacteroides, Parabacteroides, Faecalibacterium, Sutterella, Ruminococcus, Oscillospira and Phascolarctobacterium most abundant in the stool. In addition, results from PICRUSt analyses suggest that the functions of microbiota in the gastric juice are more similar as those in the saliva than in the stool. Moreover, we also found that the membrane transport of the microbiota in the saliva is higher than that in the stool and gastric juice. To our knowledge, this is the first comprehensive comparison of microbiota in the human oral cavity, stomach, and intestine.

scholarly journals Genomic and phenotypic description of Streptococcus resistens sp. nov., Streptococcus buccae sp. nov. and Streptococcus mediterraneus sp. nov., three new members of the Streptococcus genus isolated from the human oral cavity

2021 ◽  
Author(s):  
Sabrina Naud ◽  
Issam Hasni ◽  
Sara Bellali ◽  
Hoang Thong Kieu ◽  
Cheikh Ibrahima Lo ◽  
...  
Keyword(s):  
New Species ◽  
Oral Cavity ◽  
Rpob Gene ◽  
Genome Comparison ◽  
Rrna Gene ◽  
New Members ◽  
Human Oral Cavity ◽  
Genomic Studies ◽  
The 16S Rrna Gene

Abstract Phenotypic, phylogenetic and genomic studies were carried out on three unidentified Gram-stain positive, facultative anaerobic, and cocci-shaped bacteria isolated from the human oral cavity. The 16S rRNA gene of strains Marseille-P5794 T , Marseille-P6264 T and Marseille-P7376 T exhibited a sequence identity of 99,41%, 99.67% and 97.88%, respectively with Streptococcus cristatus, their closest phylogenetic relative with standing in nomenclature. Moreover, the rpoB gene sequence of strains Marseille-P5794 T and Marseille-P6264 T shared a similarity level with 96.1%, and 95.9% with Streptococcus cristatus whereas strain Marseille-P7376 T shared a 93.98% identity with Streptococcus sanguinis. Whole genome comparison of strains Marseille-P5794 T , Marseille-P6264 T and Marseille-P7376 T with their phylogenetic neighbours were under the threshold values set to define new species using digital DNA-DNA hybridization and Orthologous Average Nucleotide Identity. The taxonogenomics analysis thus allowed the classification of these strains as new species within the Streptococcus genus named Streptoccocus resistens sp. nov. Strain Marseille-P5794 T (=CSUR P5794 = CECT9902), Streptococcus buccae sp. nov. Strain Marseille-P6264 T (=CSUR P6264 = CECT9910) and Streptococcus mediterraneus sp. nov. Strain Marseille-P7376 (=CSUR P7376 = CECT30035).

scholarly journals Anomalous phylogenetic behavior of ribosomal proteins in metagenome assembled genomes

2019 ◽  
Author(s):  
Sriram G. Garg ◽  
Nils Kapust ◽  
Weili Lin ◽  
Fernando D. K. Tria ◽  
Shijulal Nelson-Sathi ◽  
...  
Keyword(s):  
Ribosomal Proteins ◽  
Gc Content ◽  
Eukaryotic Cell ◽  
Gene Content ◽  
Metagenomic Data ◽  
Genome Sequences ◽  
Taxonomic Assignment ◽  
Candidate Phyla Radiation ◽  
Domain Level

SummaryMetagenomic studies have claimed the existence of novel lineages with unprecedented properties never before observed in prokaryotes. Such lineages include Asgard archaea1–3, which are purported to represent archaea with eukaryotic cell complexity, and the Candidate Phyla Radiation (CPR), a novel domain level taxon erected solely on the basis of metagenomic data4. However, it has escaped the attention of most biologists that these metagenomic sequences are not assembled into genomes by sequence overlap, as for cultured archaea and bacteria. Instead, short contigs are sorted into computer files by a process called binning in which they receive taxonomic assignment on the basis of sequence properties like GC content, dinucleotide frequencies, and stoichiometric co-occurrence across samples. Consequently, they are not genome sequences as we know them, reflecting the gene content of real organisms. Rather they are metagenome assembled genomes (MAGs). Debates that Asgard data are contaminated with individual eukaryotic sequences5–7 are overshadowed by the more pressing issue that no evidence exists to indicate that any sequences in binned Asgard MAGs actually stem from the same chromosome, as opposed to simply stemming from the same environment. Here we show that Asgard and CPR MAGs fail spectacularly to meet the most basic phylogenetic criterion8 fulfilled by genome sequences of all cultured prokaryotes investigated to date: the ribosomal proteins of Asgard and CPR MAGs do not share common evolutionary histories. Their phylogenetic behavior is anomalous to a degree never observed with genomes of real organisms. CPR and Asgard MAGs are binning artefacts, assembled from environments where up to 90% of the DNA is from dead cells9–12. Asgard and CPR MAGs are unnatural constructs, genome-like patchworks of genes that have been stitched together into computer files by binning.

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