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.

Otariodibacter oris gen. nov., sp. nov., a member of the family Pasteurellaceae isolated from the oral cavity of pinnipeds

2012 ◽  
Vol 62 (Pt_11) ◽  
pp. 2572-2578 ◽  
Author(s):  
Mie Johanne Hansen ◽  
Mads Frost Bertelsen ◽  
Henrik Christensen ◽  
Anders Miki Bojesen ◽  
Magne Bisgaard
Keyword(s):  
16S Rrna ◽  
Oral Cavity ◽  
Related Species ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Quinone Profile ◽  
The Family

A total of 27 bacterial isolates from California sea lions and a walrus tentatively classified within the family Pasteurellaceae was further characterized by genotypic and phenotypic tests. Phylogenetic analysis of partial 16S rRNA and rpoB gene sequences showed that the isolates investigated formed a monophyletic group, tentatively designated Bisgaard taxon 57. According to 16S rRNA gene sequences, the most closely related species with a validly published name was Bisgaardia hudsonensis and the most closely related species based on rpoB sequence comparison was Pasteurella multocida subsp. multocida; highest similarities between the isolates and the type strains of B. hudsonensis and P. multocida subsp. multocida were 95.0 and 88.2%. respectively. All isolates of Bisgaard taxon 57 exhibit the phenotypic characters of the family Pasteurellaceae . Members of Bisgaard taxon 57 can be separated from existing genera of the Pasteurellaceae by the following tests: positive reactions for catalase, oxidase, Voges–Proskauer and indole; no X- or V-factor dependency; and acid production from l-arabinose (slow), l-fucose, maltose and trehalose, but not from dulcitol, d-mannitol, d-mannose or sucrose. The main fatty acids of Bisgaard taxon 57 (CCUG 59994T) are C14 : 0, C16 : 0, C16 : 1ω7c and the summed feature C14 : 0 3-OH/iso-C16 : 1 I. This fatty acid profile is characteristic of members of the Pasteurellaceae . The quinone profile of Bisgaard taxon 57 (DSM 23800T) was similar to that of other genera in the Pasteurellaceae . The DNA G+C content of strain Baika1T is 36.2 mol%, which is at the lower end of the range for members of the family Pasteurellaceae . On the basis of both phylogenetic and phenotypic evidence, it is proposed that members of Bisgaard taxon 57 should be classified as representatives of a novel species in a new genus, Otariodibacter oris gen. nov., sp. nov. The type strain of Otariodibacter oris is Baika1T ( = CCUG 59994T = DSM 23800T), which was isolated from the oral cavity of a healthy California sea lion in Copenhagen Zoo, Denmark, in 2007.

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 Wickerhamiella allomyrinae f.a., sp. nov., a yeast species isolated from the gut of the rhinoceros beetle Allomyrina dichotoma

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3856-3861 ◽  
Author(s):  
Yong-Cheng Ren ◽  
Yun Wang ◽  
Liang Chen ◽  
Tao Ke ◽  
Feng-Li Hui
Keyword(s):  
Related Species ◽  
Nature Reserve ◽  
Yeast Species ◽  
Novel Species ◽  
Sequence Divergence ◽  
Rrna Gene ◽  
The Novel ◽  
Closely Related Species ◽  
Rhinoceros Beetle ◽  
Lsu Rrna Gene

Two strains representing Wickerhamiella allomyrinae f.a., sp. nov. were isolated from the gut of Allomyrina dichotoma (Coleoptera: Scarabeidae) collected from the Baotianman National Nature Reserve, Nanyan, Henan Province, China. Sequence analyses of the D1/D2 domains of the LSU rRNA gene revealed that this novel species was located in the Wickerhamiella clade (Saccharomycetes, Saccharomycetales), with three described species of the genus Candida, namely Candida musiphila, Candida spandovensis and Candida sergipensis, as the most closely related species. The novel species differed from these three species by 9.3–9.8 % sequence divergence (35–45 nt substitutions) in the D1/D2 sequences. The species could also be distinguished from the closely related species, C. musiphila, C. spandovensis and C. sergipensis, by growth on vitamin-free medium and at 37 °C. The type strain is Wickerhamiella allomyrinae sp. nov. NYNU 13920T ( = CICC 33031T = CBS 13167T).

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%.

Molecular identification of animal isolates ofEchinococcus granulosusfrom Iran using four mitochondrial genes

2011 ◽  
Vol 86 (4) ◽  
pp. 485-492 ◽  
Author(s):  
M. Rostami Nejad ◽  
N. Taghipour ◽  
Z. Nochi ◽  
E. Nazemalhosseini Mojarad ◽  
S.R. Mohebbi ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Related Species ◽  
Mitochondrial Genes ◽  
12S Rrna ◽  
Rrna Gene ◽  
Sequence Evolution ◽  
Closely Related Species ◽  
12S Rrna Gene ◽  
Complete Sequences ◽  
Animal Isolates

AbstractMitochondrial genes have more power than nuclear genes in reconstructing phylogenetic relationships among closely related species because of their faster sequence evolution. The aim of this study was to use the complete or near-complete sequences from three mitochondrial genes (cox1,nad1andatp6) and partial sequences of the 12S rRNA gene to infer relationships among isolates ofEchinococcus granulosusfrom Iran. Two hundred and twenty-nine isolates ofE. granulosuswere collected from cattle, camels, sheep, buffalo and goats from different geographical areas. Most individuals were found to possess the G1 genotype but some of the camel samples belonged to the G6 genotype. Newly designed primers forcox1,nad1andatp6genes amplified bands of 1830, 708 and 1157 bp for the G1 genotype and 1856, 705, 1054 bp for the G6 genotype, respectively. The result of this survey showed thatatp6andnad1genes are good molecular markers for identifyingE. granulosusisolates from a range of hosts in Iran.

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 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 Burkholderia phytofirmans sp. nov., a novel plant-associated bacterium with plant-beneficial properties

2005 ◽  
Vol 55 (3) ◽  
pp. 1187-1192 ◽  
Author(s):  
A. Sessitsch ◽  
T. Coenye ◽  
A. V. Sturz ◽  
P. Vandamme ◽  
E. Ait Barka ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Related Species ◽  
Sequence Data ◽  
Single Species ◽  
Homoserine Lactone ◽  
Plant Production ◽  
Cell Protein ◽  
Rrna Gene ◽  
Closely Related Species ◽  
Beneficial Bacterium

A Gram-negative, non-sporulating, rod-shaped, motile bacterium, with a single polar flagellum, designated strain PsJNT, was isolated from surface-sterilized onion roots. This isolate proved to be a highly effective plant-beneficial bacterium, and was able to establish rhizosphere and endophytic populations associated with various plants. Seven related strains were recovered from Dutch soils. Based on 16S rRNA gene sequence data, strain PsJNT and the Dutch strains were identified as representing a member of the genus Burkholderia, as they were closely related to Burkholderia fungorum (98·7 %) and Burkholderia phenazinium (98·5 %). Analysis of whole-cell protein profiles and DNA–DNA hybridization experiments confirmed that all eight strains belonged to a single species. Strain PsJNT had a DNA G+C content of 61·0 mol%. Only low levels of DNA–DNA hybridization to closely related species were found. Qualitative and quantitative differences in fatty acid composition between strain PsJNT and closely related species were identified. The predominant fatty acids in strain PsJNT were 16 : 0, 18 : 1ω7c and summed feature 3 (comprising 16 : 1ω7c and/or iso-15 : 0 2-OH). Isolate PsJNT showed high 1-aminocyclopropane-1-carboxylate deaminase activity and is therefore able to lower the ethylene level in a developing or stressed plant. Production of the quorum-sensing signal compound 3-hydroxy-C8-homoserine lactone was detected. Based on the results of this polyphasic taxonomic study, strain PsJNT and the seven Dutch isolates are considered to represent a single, novel species, for which the name Burkholderia phytofirmans sp. nov. is proposed. The type strain is strain PsJNT (=LMG 22146T=CCUG 49060T).

scholarly journals Pseudonocardia mongoliensis sp. nov. and Pseudonocardia khuvsgulensis sp. nov., isolated from soil

2011 ◽  
Vol 61 (4) ◽  
pp. 747-756 ◽  
Author(s):  
Ismet Ara ◽  
Baljinova Tsetseg ◽  
Damdinsuren Daram ◽  
Manabu Suto ◽  
Katsuhiko Ando
Keyword(s):  
Related Species ◽  
Type Strain ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Closely Related Species ◽  
Whole Cell ◽  
Hybridization Data ◽  
Physiological And Biochemical Characteristics ◽  
Phenotypic Tests ◽  
Physiological And Biochemical

Two actinomycetes, designated MN08-A0270T and MN08-A0297T, were isolated from soil from the area around Khuvsgul Lake, Khuvsgul province, Mongolia, and subjected to phenotypic and genotypic characterization. They produced well-developed, branched substrate hyphae and, similar to closely related species of the genus Pseudonocardia, produced zigzag-shaped aerial hyphae by acropetal budding and blastospores. A comparative analysis of 16S rRNA gene sequences indicated that strains MN08-A0270T and MN08-A0297T formed two distinct clades within the genus Pseudonocardia and were respectively most closely related to Pseudonocardia yunnanensis NBRC 15681T (97.3 % similarity) and Pseudonocardia thermophila IMSNU 20112T (97.1 %). Chemotaxonomic characteristics, including cell-wall diaminopimelic acid, whole-cell sugars, fatty acid components and major menaquinones, suggested that the two organisms belonged to the genus Pseudonocardia. Strains MN08-A0270T and MN08-A0297T could be differentiated from each other and from closely related species of the genus Pseudonocardia by physiological and biochemical characteristics, predominant fatty acids, menaquinones and whole-cell sugar components. Combined with the results of a broad range of phenotypic tests and DNA–DNA hybridization data and phylogenetic analysis, these results support the conclusion that these strains represent two novel species of the genus Pseudonocardia, for which we propose the names Pseudonocardia mongoliensis sp. nov. (type strain MN08-A0270T  = NBRC 105885T  = VTCC D9-25T) and Pseudonocardia khuvsgulensis sp. nov. (type strain MN08-A0297T  = NBRC 105886T  = VTCC D9-26T).

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