scholarly journals The Human Oral Microbiome

2010 ◽  
Vol 192 (19) ◽  
pp. 5002-5017 ◽  
Author(s):  
Floyd E. Dewhirst ◽  
Tuste Chen ◽  
Jacques Izard ◽  
Bruce J. Paster ◽  
Anne C. R. Tanner ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Species Level ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Oral Microbiota ◽  
16S Rrna Gene Sequences ◽  
Culture Independent ◽  
Health And Disease

ABSTRACT The human oral cavity contains a number of different habitats, including the teeth, gingival sulcus, tongue, cheeks, hard and soft palates, and tonsils, which are colonized by bacteria. The oral microbiome is comprised of over 600 prevalent taxa at the species level, with distinct subsets predominating at different habitats. The oral microbiome has been extensively characterized by cultivation and culture-independent molecular methods such as 16S rRNA cloning. Unfortunately, the vast majority of unnamed oral taxa are referenced by clone numbers or 16S rRNA GenBank accession numbers, often without taxonomic anchors. The first aim of this research was to collect 16S rRNA gene sequences into a curated phylogeny-based database, the Human Oral Microbiome Database (HOMD), and make it web accessible (www.homd.org ). The HOMD includes 619 taxa in 13 phyla, as follows: Actinobacteria, Bacteroidetes, Chlamydiae, Chloroflexi, Euryarchaeota, Firmicutes, Fusobacteria, Proteobacteria, Spirochaetes, SR1, Synergistetes, Tenericutes, and TM7. The second aim was to analyze 36,043 16S rRNA gene clones isolated from studies of the oral microbiota to determine the relative abundance of taxa and identify novel candidate taxa. The analysis identified 1,179 taxa, of which 24% were named, 8% were cultivated but unnamed, and 68% were uncultivated phylotypes. Upon validation, 434 novel, nonsingleton taxa will be added to the HOMD. The number of taxa needed to account for 90%, 95%, or 99% of the clones examined is 259, 413, and 875, respectively. The HOMD is the first curated description of a human-associated microbiome and provides tools for use in understanding the role of the microbiome in health and disease.

Isolation and Identification of Thermo-Acidophilic Bacteria from Orchards in China

2010 ◽  
Vol 73 (2) ◽  
pp. 390-394 ◽  
Author(s):  
YING WANG ◽  
TIANLI YUE ◽  
YAHONG YUAN ◽  
ZHENPENG GAO
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Species Level ◽  
Shaanxi Province ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Isolation And Identification ◽  
Acidophilic Bacteria ◽  
Different Strains

Eight strains of thermo-acidophilic bacteria have been isolated from apple orchards in Shaanxi Province, China. The isolated strains were identified at the species level by comparing 16S rRNA gene sequences. It was found that all strains could be assigned to two genera. The strain YL-5 belonged to Alicyclobacillus, and other isolates belonged to Bacillus. The enzymatic patterns by the API ZYM system showed very significant differences between 12 strains of Alicyclobacillus and 8 strains of Bacillus. The ability of guaiacol production varied among different strains.

scholarly journals New insights into human nostril microbiome from the expanded Human Oral Microbiome Database (eHOMD): a resource for the microbiome of the human aerodigestive tract

2018 ◽  
Author(s):  
Isabel F. Escapa ◽  
Tsute Chen ◽  
Yanmei Huang ◽  
Prasad Gajare ◽  
Floyd E. Dewhirst ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Clinical Relevance ◽  
Species Level ◽  
Aerodigestive Tract ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Minimum Entropy ◽  
Nasal Passages ◽  
Vital Resource

ABSTRACTThe expanded Human Oral Microbiome Database (eHOMD) is a comprehensive microbiome database for sites along the human aerodigestive tract that revealed new insights into the nostril microbiome. The eHOMD provides well-curated 16S rRNA gene reference sequences linked to available genomes and enables assignment of species-level taxonomy to most NextGeneration sequences derived from diverse aerodigestive tract sites, including the nasal passages, sinuses, throat, esophagus and mouth. Using Minimum Entropy Decomposition coupled with the RDP Classifier and our eHOMD V1-V3 training set, we reanalyzed 16S rRNA V1-V3 sequences from the nostrils of 210 Human Microbiome Project participants at the species level revealing four key insights. First, we discovered that Lawsonella clevelandensis, a recently named bacterium, and Neisseriaceae [G-1] HMT-174, a previously unrecognized bacterium, are common in adult nostrils. Second, just 19 species accounted for 90% of the total sequences from all participants. Third, one of these 19 belonged to a currently uncultivated genus. Fourth, for 94% of the participants, two to ten species constituted 90% of their sequences, indicating nostril microbiome may be represented by limited consortia. These insights highlight the strengths of the nostril microbiome as a model system for studying interspecies interactions and microbiome function. Also, in this cohort, three common nasal species (Dolosigranulum pigrum and two Corynebacterium species) showed positive differential abundance when the pathobiont Staphylococcus aureus was absent, generating hypotheses regarding colonization resistance. By facilitating species-level taxonomic assignment to microbes from the human aerodigestive tract, the eHOMD is a vital resource enhancing clinical relevance of microbiome studies.IMPORTANCEThe eHOMD (ehomd.org) is a valuable resource for researchers, from basic to clinical, who study the microbiomes, and the individual microbes, in health and disease of body sites in the human aerodigestive tract, which includes the nasal passages, sinuses, throat, esophagus and mouth, and the lower respiratory tract. The eHOMD is an actively curated, web-based, open-access resource. eHOMD provides the following: (1) species-level taxonomy based on grouping 16S rRNA gene sequences at 98.5% identity, (2) a systematic naming scheme for unnamed and/or uncultivated microbial taxa, (3) reference genomes to facilitate metagenomic, metatranscriptomic and proteomic studies and (4) convenient cross-links to other databases (e.g., PubMed and Entrez). By facilitating the assignment of species names to sequences, the eHOMD is a vital resource for enhancing the clinical relevance of 16S rRNA gene-based microbiome studies, as well as metagenomic studies.

Identification of genus Campylobacter up to species level using internal features of 16S rRNA gene sequences

2016 ◽  
Vol 31 (3) ◽  
pp. 187-196
Author(s):  
ManasaSri Muralidharan ◽  
Avantika Ghosh ◽  
Nirjara Singhvi ◽  
P. S. Dhanaraj ◽  
Rup Lal ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Species Level ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences

scholarly journals Cellulolytic Bacteria in the Foregut of the Dromedary Camel (Camelus dromedarius)

2012 ◽  
Vol 78 (24) ◽  
pp. 8836-8839 ◽  
Author(s):  
Anjas A. Samsudin ◽  
André-Denis G. Wright ◽  
Rafat Al Jassim
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Species Level ◽  
Neutral Detergent Fiber ◽  
Dromedary Camel ◽  
Rrna Gene ◽  
Cellulolytic Bacteria ◽  
16S Rrna Gene Sequences ◽  
Dromedary Camels ◽  
Operational Taxonomic Units

ABSTRACTForegut digesta from five feral dromedary camels were inoculated into three different enrichment media: cotton thread, filter paper, and neutral detergent fiber. A total of 283 16S rRNA gene sequences were assigned to 33 operational taxonomic units by using 99% species-level identity. LIBSHUFF revealed significant differences in the community composition across all three libraries.

scholarly journals Site- and Taxa-Specific Disease-Associated Oral Microbial Structures Distinguish Inflammatory Bowel Diseases

2021 ◽  
Author(s):  
Hari K Somineni ◽  
Jordan H Weitzner ◽  
Suresh Venkateswaran ◽  
Anne Dodd ◽  
Jarod Prince ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Oral Microbiome ◽  
Spatial And Temporal Variation ◽  
Rrna Gene ◽  
Oral Microbiota ◽  
Microbial Composition ◽  
Healthy Control ◽  
Inflammatory Bowel ◽  
A Site

Abstract Background The gut and oral microbiome have independently been shown to be associated with inflammatory bowel disease (IBD). However, it is not known to what extent gut and oral microbial disease markers converge in terms of their composition in IBD. Further, the spatial and temporal variation within the oral microenvironments of IBD remain to be elucidated. Patients and Methods We used a prospectively recruited cohort of patients with IBD (n = 47) and unrelated healthy control patients (n = 18) to examine the spatial and temporal distribution of microbiota within the various oral microenvironments, represented by saliva, tongue, buccal mucosa, and plaque, and compared them with stool. Microbiome characterization was performed using 16S rRNA gene sequencing. Results The oral microbiome displayed IBD-associated dysbiosis, in a site- and taxa-specific manner. Plaque samples depicted a relatively severe degree of dysbiosis, and the disease-associated dysbiotic bacterial groups were predominantly the members of the phylum Firmicutes. Our 16S rRNA gene analyses show that oral microbiota can distinguish patients with IBD from healthy control patients, with salivary microbiota performing the best, closely matched by stool and other oral sites. Longitudinal profiles of microbial composition suggest that some taxa are more consistently perturbed than others, preferentially in a site-dependent fashion. Conclusions Collectively, these data indicate the potential of using oral microbial profiles in screening and monitoring patients with IBD. Furthermore, these results support the importance of spatial and longitudinal microbiome sampling to interpret disease-associated dysbiotic states and eventually to gain insights into disease pathogenesis.

Polyphasic characterization of four species of Pseudanabaena (Oscillatoriales, Cyanobacteria) from China and insights into polyphyletic divergence within the Pseudanabaena genus

Phytotaxa ◽  
2015 ◽  
Vol 192 (1) ◽  
pp. 1 ◽  
Author(s):  
Gongliang Yu ◽  
Mengling Zhu ◽  
Youxin Chen ◽  
Qianqian Pan ◽  
Wenbo Chai ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Extreme Environments ◽  
Rrna Gene ◽  
Main Stream ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Polyphasic Characterization ◽  
Taxonomic Studies

Current cyanobacterial taxonomic studies are mainly performed through polyphasic characterization at the genus and/or species levels. In this study, eleven Pseudanabaena strains isolated in China were taxonomically and phylogenetically evaluated by investigating several characteristics, including morphological features, cellular ultrastructures, pigment composition, and 16S rRNA gene sequences. The strains were identified as four morphospecies, namely, Pseudanabaena mucicola, P. galeata, P. limnetica, and P. minima. The cellular ultrastructures of these species showed that peripheral thylakoids with 4‒8 parallel layers were parietally distributed. Phylogenetic results based on 16S rRNA gene sequences indicated that most of the Pseudanabaena strains used in this study, including the eleven from China and three Pseudanabaena catenata strains from GenBank, gathered into one large cluster that represents the core of the genus Pseudanabaena. Several Pseudanabaena species/strains that represent different extreme environments were phylogenetically located outside the main stream cluster and should be removed under the genus Pseudanabaena on the basis of the role of the main stream species. Limnothrix strains were divided into two clades, and the taxonomic solution for these clades was discussed. This study is the first to report on the morphology and phylogeny of Pseudanabaena species in China, providing new insights into the taxonomy of the genera Pseudanabaena and Limnothrix.

scholarly journals Novel high-resolution targeted sequencing of the cervicovaginal microbiome

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Karolina M. Andralojc ◽  
Mariano A. Molina ◽  
Mengjie Qiu ◽  
Bram Spruijtenburg ◽  
Menno Rasing ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Species Level ◽  
Rrna Gene ◽  
High Grade ◽  
Cervical Lesions ◽  
Health And Disease ◽  
Rrna Gene Sequencing

Abstract Background The cervicovaginal microbiome (CVM) plays a significant role in women’s cervical health and disease. Microbial alterations at the species level and characteristic community state types (CST) have been associated with acquisition and persistence of high-risk human papillomavirus (hrHPV) infections that may result in progression of cervical lesions to malignancy. Current sequencing methods, especially most commonly used multiplex 16S rRNA gene sequencing, struggle to fully clarify these changes because they generally fail to provide sufficient taxonomic resolution to adequately perform species-level associative studies. To improve CVM species designation, we designed a novel sequencing tool targeting microbes at the species taxonomic rank and examined its potential for profiling the CVM. Results We introduce an accessible and practical circular probe-based RNA sequencing (CiRNAseq) technology with the potential to profile and quantify the CVM. In vitro and in silico validations demonstrate that CiRNAseq can distinctively detect species in a mock mixed microbial environment, with the output data reflecting its ability to estimate microbes’ abundance. Moreover, compared to 16S rRNA gene sequencing, CiRNAseq provides equivalent results but with improved sequencing sensitivity. Analyses of a cohort of cervical smears from hrHPV-negative women versus hrHPV-positive women with high-grade cervical intraepithelial neoplasia confirmed known differences in CST occurring in the CVM of women with hrHPV-induced lesions. The technique also revealed variations in microbial diversity and abundance in the CVM of hrHPV-positive women when compared to hrHPV-negative women. Conclusions CiRNAseq is a promising tool for studying the interplay between the CVM and hrHPV in cervical carcinogenesis. This technology could provide a better understanding of cervicovaginal CST and microbial species during health and disease, prompting the discovery of biomarkers, additional to hrHPV, that can help detect high-grade cervical lesions.

scholarly journals High-resolution ISR amplicon sequencing reveals personalized oral microbiome

2018 ◽  
Author(s):  
Chiranjit Mukherjee ◽  
Clifford J. Beall ◽  
Ann L. Griffen ◽  
Eugene J. Leys
Keyword(s):  
High Resolution ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Cost Effective ◽  
Amplicon Sequencing ◽  
Species Level ◽  
Rrna Gene ◽  
Oral Microbiota ◽  
Community Fingerprinting

AbstractBackground:Sequencing of the 16S rRNA gene has been the standard for studying the composition of microbial communities. While it allows identification of bacteria at the level of species, it does not usually provide sufficient information to resolve at the sub-species level. Species-level resolution is not adequate for studies of transmission or stability, or for exploring subspecies variation in disease association. Current approaches using whole metagenome shotgun sequencing require very high coverage that can be cost-prohibitive and computationally challenging for diverse communities. Thus there is a need for high-resolution, yet cost-effective, high-throughput methods for characterizing microbial communities.Results:Significant improvement in resolution for amplicon-based bacterial community analysis was achieved by combining amplicon sequencing of a high-diversity marker gene, the ribosomal operon ISR, with a probabilistic error modeling algorithm, DADA2. The resolving power of this new approach was compared to that of both standard and high-resolution 16S-based approaches using a set of longitudinal subgingival plaque samples. The ISR strategy achieved a 5.2-fold increase in community richness compared to reference-based 16S rRNA gene analysis, and showed 100% accuracy in predicting the correct source of a clinical sample. Individuals’ microbial communities were highly personalized, and although they exhibited some drift in membership and levels over time, that difference was always smaller than the differences between any two subjects, even after one year. The construction of an ISR database from publicly available genomic sequences allowed us to explore genomic variationwithinspecies, resulting in the identification of multiple variants of the ISR for most species.Conclusions:The ISR approach resulted in significantly improved resolution of communities, and revealed a highly personalized, stable human oral microbiota. Multiple ISR types were observed for all species examined, demonstrating a high level of subspecies variation in the oral microbiota. The approach is high-throughput, high-resolution yet cost-effective, allowing subspecies-level community fingerprinting at a cost comparable to that of 16S rRNA gene amplicon sequencing. It will be useful for a range of applications that require high-resolution identification of organisms, including microbial tracking, community fingerprinting, and potentially for identification of virulence-associated strains.

scholarly journals New Insights into Human Nostril Microbiome from the Expanded Human Oral Microbiome Database (eHOMD): a Resource for the Microbiome of the Human Aerodigestive Tract

mSystems ◽  
2018 ◽  
Vol 3 (6) ◽  
Author(s):  
Isabel F. Escapa ◽  
Tsute Chen ◽  
Yanmei Huang ◽  
Prasad Gajare ◽  
Floyd E. Dewhirst ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Clinical Relevance ◽  
Species Level ◽  
Aerodigestive Tract ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Content Type ◽  
Nasal Passages ◽  
Vital Resource

ABSTRACT The expanded Human Oral Microbiome Database (eHOMD) is a comprehensive microbiome database for sites along the human aerodigestive tract that revealed new insights into the nostril microbiome. The eHOMD provides well-curated 16S rRNA gene reference sequences linked to available genomes and enables assignment of species-level taxonomy to most next-generation sequences derived from diverse aerodigestive tract sites, including the nasal passages, sinuses, throat, esophagus, and mouth. Using minimum entropy decomposition coupled with the RDP Classifier and our eHOMD V1-V3 training set, we reanalyzed 16S rRNA V1-V3 sequences from the nostrils of 210 Human Microbiome Project participants at the species level, revealing four key insights. First, we discovered that Lawsonella clevelandensis, a recently named bacterium, and Neisseriaceae [G-1] HMT-174, a previously unrecognized bacterium, are common in adult nostrils. Second, just 19 species accounted for 90% of the total sequences from all participants. Third, 1 of these 19 species belonged to a currently uncultivated genus. Fourth, for 94% of the participants, 2 to 10 species constituted 90% of their sequences, indicating that the nostril microbiome may be represented by limited consortia. These insights highlight the strengths of the nostril microbiome as a model system for studying interspecies interactions and microbiome function. Also, in this cohort, three common nasal species (Dolosigranulum pigrum and two Corynebacterium species) showed positive differential abundance when the pathobiont Staphylococcus aureus was absent, generating hypotheses regarding colonization resistance. By facilitating species-level taxonomic assignment to microbes from the human aerodigestive tract, the eHOMD is a vital resource enhancing clinical relevance of microbiome studies. IMPORTANCE The eHOMD (http://www.ehomd.org) is a valuable resource for researchers, from basic to clinical, who study the microbiomes and the individual microbes in body sites in the human aerodigestive tract, which includes the nasal passages, sinuses, throat, esophagus, and mouth, and the lower respiratory tract, in health and disease. The eHOMD is an actively curated, web-based, open-access resource. eHOMD provides the following: (i) species-level taxonomy based on grouping 16S rRNA gene sequences at 98.5% identity, (ii) a systematic naming scheme for unnamed and/or uncultivated microbial taxa, (iii) reference genomes to facilitate metagenomic, metatranscriptomic, and proteomic studies and (iv) convenient cross-links to other databases (e.g., PubMed and Entrez). By facilitating the assignment of species names to sequences, the eHOMD is a vital resource for enhancing the clinical relevance of 16S rRNA gene-based microbiome studies, as well as metagenomic studies.

Sign in / Sign up

Export Citation Format

Share Document