16S rRNA gene microbial analysis of the skin of fleece rot resistant and susceptible sheep

2007 ◽  
Vol 58 (7) ◽  
pp. 739 ◽  
Author(s):  
T. J. Dixon ◽  
S. I. Mortimer ◽  
B. J. Norris
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Current Knowledge ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
Bacterial Load ◽  
Molecular Genetic Analysis ◽  
Future Research ◽  
Rrna Gene ◽  
Major Interest

Fleece rot is a bacterial dermatitis that follows prolonged wetting of the sheep’s skin, and a major pre-disposing condition to body strike in the Australian Merino. Several studies have examined bacterial load of the fleece in relation to fleece rot using traditional culture-based techniques focussing on only a few bacterial species. We examined the natural bacterial diversity of the healthy sheep skin and changes that occurred in fleece-rot resistant and susceptible animals during fleece rot development. Presented is a preliminary molecular genetic analysis of the bacterial ecology of the sheep skin. Eight 16S rRNA gene libraries were constructed from susceptible and resistant sheep both before and after onset of the disease following induction by simulated rainfall. Approximately 75% of the sequences obtained in this study have not been previously identified in fleece-rot studies. Four operational taxonomic units (OTU; groups of >97% sequence similarity) of major interest were present on susceptible animals and absent from resistant animals. Data on these OTU expand current knowledge of bacteria involved in inflammation and wounding of sheep skin tissue, and provide direction for future research that may lead to new treatment options for fleece rot and body strike.

scholarly journals Cautionary tale of using 16S rRNA gene sequence similarity values in identification of human-associated bacterial species

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1929-1934 ◽  
Author(s):  
Morgane Rossi-Tamisier ◽  
Samia Benamar ◽  
Didier Raoult ◽  
Pierre-Edouard Fournier
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Bacterial Taxonomy ◽  
Associated Species

Modern bacterial taxonomy is based on a polyphasic approach that combines phenotypic and genotypic characteristics, including 16S rRNA sequence similarity. However, the 95 % (for genus) and 98.7 % (for species) sequence similarity thresholds that are currently recommended to classify bacterial isolates were defined by comparison of a limited number of bacterial species, and may not apply to many genera that contain human-associated species. For each of 158 bacterial genera containing human-associated species, we computed pairwise sequence similarities between all species that have names with standing in nomenclature and then analysed the results, considering as abnormal any similarity value lower than 95 % or greater than 98.7 %. Many of the current bacterial species with validly published names do not respect the 95 and 98.7 % thresholds, with 57.1 % of species exhibiting 16S rRNA gene sequence similarity rates ≥98.7 %, and 60.1 % of genera containing species exhibiting a 16S rRNA gene sequence similarity rate <95 %. In only 17 of the 158 genera studied (10.8 %), all species respected the 95 and 98.7 % thresholds. As we need powerful and reliable taxonomical tools, and as potential new tools such as pan-genomics have not yet been fully evaluated for taxonomic purposes, we propose to use as thresholds, genus by genus, the minimum and maximum similarity values observed among species.

scholarly journals Complementing 16S rRNA Gene Amplicon Sequencing with Total Bacterial Load To Infer Absolute Species Concentrations in the Vaginal Microbiome

mSystems ◽  
2020 ◽  
Vol 5 (2) ◽  
Author(s):  
Florencia A. Tettamanti Boshier ◽  
Sujatha Srinivasan ◽  
Anthony Lopez ◽  
Noah G. Hoffman ◽  
Sean Proll ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Relative Abundance ◽  
Bacterial Species ◽  
Bacterial Load ◽  
Amplicon Sequencing ◽  
Individual Species ◽  
Rrna Gene ◽  
Vaginal Microbiome ◽  
Bacterial Concentrations

ABSTRACT Whereas 16S rRNA gene amplicon sequencing quantifies relative abundances of bacterial taxa, variation in total bacterial load between samples restricts its ability to reflect absolute concentrations of individual bacterial species. Quantitative PCR (qPCR) can quantify individual species, but it is not practical to develop a suite of qPCR assays for every bacterium present in a diverse sample. We sought to determine the accuracy of an inferred measure of bacterial concentration using total bacterial load and relative abundance. We analyzed 1,320 samples from 20 women with a history of frequent bacterial vaginosis who self-collected vaginal swabs daily over 60 days. We inferred bacterial concentrations by taking the product of species relative abundance (assessed by 16S rRNA gene amplicon sequencing) and bacterial load (measured by broad-range 16S rRNA gene qPCR). Log10-converted inferred concentrations correlated with targeted qPCR (r = 0. 935, P < 2.2e–16) for seven key bacterial species. The mean inferred concentration error varied across bacteria, with rarer bacteria associated with larger errors. A total of 92% of the >0.5-log10 errors occurred when the relative abundance was <10%. Many errors occurred during early bacterial expansion from or late contraction to low abundance. When the relative abundance of a species is >10%, inferred concentrations are reliable proxies for targeted qPCR in the vaginal microbiome. However, targeted qPCR is required to capture bacteria at low relative abundance and is preferable for characterizing growth and decay kinetics of single species. IMPORTANCE Microbiome studies primarily use 16S rRNA gene amplicon sequencing to assess the relative abundance of bacterial taxa in a community. However, these measurements do not accurately reflect absolute taxon concentrations. We sought to determine whether the product of species’ relative abundance and total bacterial load measured by broad-range qPCR is an accurate proxy for individual species’ concentrations, as measured by taxon-specific qPCR assays. Overall, the inferred bacterial concentrations were a reasonable proxy of species-specific qPCR values, particularly when bacteria are present at a higher relative abundance. This approach offers an opportunity to assess the concentrations of bacterial species and how they change in a community over time without developing individual qPCR assays for each taxon.

scholarly journals Kordiimonas gwangyangensis gen. nov., sp. nov., a marine bacterium isolated from marine sediments that forms a distinct phyletic lineage (Kordiimonadales ord. nov.) in the ‘Alphaproteobacteria’

2005 ◽  
Vol 55 (5) ◽  
pp. 2033-2037 ◽  
Author(s):  
Kae Kyoung Kwon ◽  
Hee-Soon Lee ◽  
Sung Hyun Yang ◽  
Sang-Jin Kim
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Marine Bacterium ◽  
Enrichment Culture ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
Carbon Sources ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Respiratory Quinone

A marine bacterium, designated strain GW14-5T, capable of degrading high-molecular-mass polycyclic aromatic hydrocarbons was isolated from the sediments of Gwangyang Bay, Republic of Korea, after enrichment culture for 2 years with a mixture of benzo[a]pyrene and pyrene. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate forms a phyletic lineage that is distinct from the seven known orders within the ‘Alphaproteobacteria’. 16S rRNA gene sequence similarity of strain GW14-5T to all recognized bacterial species was not greater than 92 %. The dominant fatty acids of the isolate were i-17 : 1 (46·2 %), i-15 : 0 (15·1 %) and i-17 : 0 (12·6 %). The major respiratory quinone was MK-5, and the DNA G+C content was 39·3 mol%. Cells of strain GW14-5T were Gram-negative, motile, catalase-positive, oxidase-positive and weakly halophilic. Glucose, N-acetylglucosamine and maltose were utilized as sole carbon sources. The strain was positive for β-glucosidase activity. Optimal growth of strain GW14-5T was at pH 7·0 and 37–40 °C and required the presence of 2 % (w/v) NaCl. On the basis of this evidence, strain GW14-5T represents a novel genus and species in the ‘Alphaproteobacteria’ for which the name Kordiimonas gwangyangensis gen. nov., sp. nov. is proposed. The novel order Kordiimonadales is proposed for the distinct phyletic line represented by the genus Kordiimonas. The type strain is GW14-5T (=KCCM 42021T=JCM 12864T).

scholarly journals Complementing 16S rRNA gene amplicon sequencing with estimates of total bacterial load to infer absolute species concentrations in the vaginal microbiome

2019 ◽  
Author(s):  
Florencia Tettamanti Boshier ◽  
Sujatha Srinivasan ◽  
Anthony Lopez ◽  
Noah G. Hoffman ◽  
Sean Proll ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Vaginosis ◽  
Relative Abundance ◽  
Bacterial Species ◽  
Bacterial Load ◽  
Amplicon Sequencing ◽  
Individual Species ◽  
Rrna Gene ◽  
Associated Bacteria

Whereas 16S rRNA gene amplicon sequencing quantifies relative abundances of bacterial taxa, variation in total bacterial load between samples restricts its ability to reflect absolute concentration of individual species. Quantitative PCR (qPCR) can quantify individual species, but it is not practical to develop a suite of qPCR assays for every bacterium present in a diverse sample. We analyzed 1320 samples from 20 women with a history of frequent bacterial vaginosis, who self-collected vaginal swabs daily over 60 days. We inferred bacterial concentrations by taking the product of species relative abundance (assessed by 16S rRNA gene amplicon sequencing) and total bacterial load (measured by broad-range 16S rRNA gene qPCR). Log10-converted inferred concentrations correlated with targeted qPCR (r = 0. 935, p<2.2e-16) for seven key bacterial species. The mean inferred concentration error varied across bacteria, with rarer bacterial vaginosis-associated bacteria associated with larger errors. 92% of errors >0.5 log10 occurred when relative abundance was <10%. Many errors occurred during early bacterial expansion or late contraction. When relative abundance of a species is >10%, inferred concentrations are reliable proxies for targeted qPCR. However, targeted qPCR is required to capture bacteria at low relative abundance, particularly with BV-associated bacteria during the early onset of bacterial vaginosis.

Pontibacter rubellus sp. nov., and Pontibacter situs sp. nov. bacteria isolated from soil

2021 ◽  
Author(s):  
Soohyun Maeng ◽  
Yuna Park ◽  
Tuvshinzaya Damdintogtokh ◽  
Hyejin Oh ◽  
Minji Bang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Bacterial Species ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Major Polar Lipid ◽  
Respiratory Quinone ◽  
Distinct Lineage

Abstract Gram-stain-negative, aerobic, non-flagellated strains 172403-2T and BT310T were isolated from the soil collected in Pyeongchang city and Uijeongbu city, Korea. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strains 172403-2T and BT310T formed a distinct lineage within the family Hymenobacteraceae (order Chitinophagales, class Chitinophagia) and were most closely related to members of the genus Pontibacter, Pontibacter chitinilyticus 17gy-14T (95.7%), and Pontibacter populi HLY7-15T (97.1% 16S rRNA gene sequence similarity) respectively. The optimal growth of strains 172403-2T and BT310T occurred at pH 7.0, in the absence of NaCl, and 25°C and 30°C, respectively. The predominant cellular fatty acids were iso-C15:0 and summed feature 4 (iso-C17:1 I / anteiso-C17:1 B). The major respiratory quinone of the two strains was MK-7. The major polar lipid of the two strains was phosphatidylethanolamine. Biochemical, chemotaxonomic and phylogenetic analyses indicated that strains 172403-2T and BT310T represent novel bacterial species within the genus Pontibacter, for which the names Pontibacter rubellus and Pontibacter situs are proposed. The type strains of Pontibacter rubellus and Pontibacter situs are 172403-2T and BT310T, respectively.

scholarly journals Microvirga Amygdalina sp. nov., and Microvirga Alba sp. nov., Two New Species Isolated from Soil in South Korea

2021 ◽  
Author(s):  
Hyejin Oh ◽  
Myungkyum Kim ◽  
Sathiyaraj Sriniva
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
South Korea ◽  
Type Strain ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Cellular Fatty Acids

Abstract Two novel Gram-stain-negative, aerobic, rod-shaped, circular, convex, light-pink and white-coloured bacterial strains BT291T and BT350T were isolated from soil collected in Uijeongbu city (37° 44′ 55″ N, 127° 2′ 20″ E) and Jeju island (33° 22′ 48″ N, 126° 31′ 48″ E), respectively, South Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains BT291T and BT350T belong to a distinct lineage within the genus Microvirga (family Methylobacteriaceae, order Rhizobiales, class Alpha Proteobacteria, phylum Proteobacteria, kingdom Bacteria). The 16S rRNA gene sequence similarity between the two strains BT291T and BT350T was 97.4 %. The two strains were found to have the same quinone system, with Q-10 as the major respiratory quinone. The major polar lipids of strains BT291T and BT350T were phosphatidylethanolamine (PE), diphosphatydilglycerol (DPG), phosphatidylcholine (PC) and phosphatidylglycerol (PG). The major cellular fatty acids of strain BT291T were C18:1 ω7c (58.2 %) and cyclo-C19:0 ω8c (25.7 %). The major cellular fatty acids of strain BT350T were C18:1 ω7c (38.5 %) and cyclo-C19:0 ω8c (27.7 %). Based on the polyphasic analysis (phylogenetic, chemotaxonomic and biochemical), strains BT291T and BT350T can be suggested as two novel bacterial species within the genus Microvirga and the proposed names are Microvirga amygdalina and Microvirga alba, respectively. The type strain of Microvirga amygdalina is BT291T (= KCTC 72368T = NBRC 114845T) and the type strain of Microvirga alba is BT350T (= KCTC 72385T = NBRC 114848T).

scholarly journals Microvirga Terrestris sp. nov., and Microvirga Arvi sp. nov., Two Novel Species Isolated From Soil in South Korea

2021 ◽  
Author(s):  
Tuvshinzaya Damdintogtokh ◽  
Yuna Park ◽  
Soohyun Maeng ◽  
Hye Jin Oh ◽  
Minji Bang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
South Korea ◽  
Type Strain ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Respiratory Quinone ◽  
Distinct Lineage

Abstract Two novel Gram-stain-negative, aerobic, rod shaped bacterial strains BT290T and BT689T were isolated from soil collected in South Korea. Colony morphologies of both strains were circular and convex while the colors of BT290T and BT689T were light-pink and white, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that BT290T and BT689T belong to a distinct lineage within the genus Microvirga (family Methylobacteriaceae, order Rhizobiales, class Alphaproteobacteria, phylum Proteobacteria, kingdom Bacteria). The 16S rRNA gene sequence similarity between two strains was 97.9 %. Both strains had the similar quinone system, with ubiquinone 10 (Q-10) as the major respiratory quinone. The major polar lipids of strains BT290T and BT689T were phosphatidylethanolamine (PE), diphosphatydilglycerol (DPG), phosphatidylcholine (PC) and phosphatydilglycerol (PG). The major cellular fatty acids of strain BT290T were C18:1 ω7c (58.2 %) and C16:0 (17.7 %), while those of strain BT689T were C18:1 ω7c (61.8 %) and C16:0 (10.8 %).On the bases of polyphasic analysis (phylogenetic, chemotaxonomic and biochemical), strains BT290T and BT689T can be suggested as novel bacterial species within the genus Microvirga and the proposed names are Microvirga terrestris and Microvirga arvi, respectively. The type strain of Microvirga terrestris is BT290T (= KCTC 72367T=NBRC 114844T) and the type strain of Microvirga arvi is BT689T (= KACC 22016T = NBRC 114858T), respectively.

scholarly journals Microvirga Jeongseonensis Sp. Nov., New Species Isolated From Soil in South Korea

2021 ◽  
Author(s):  
Soohyun Maeng ◽  
Yuna Park ◽  
Hyejin Oh ◽  
Minji Bang ◽  
Jigden Baigalmaa ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
South Korea ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Respiratory Quinone

Abstract A novel Gram-stain-negative, aerobic, rod-shaped, convex, and light pink-colored strain BT688T was isolated from a soil sample collected in Jeongseon city, South Korea. Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain BT688T belongs to a distinct lineage within the genus Microvirga (family Methylobacteriaceae, order Rhizobiales, class Alpha Proteobacteria, phylum Proteobacteria). The 16S rRNA gene sequence similarity between strain BT688T and Microvirga aerilata 5420S-16T was 98.5%. Strain BT688T had Q-10 as a major respiratory quinone and the major polar lipids of strain BT688T was diphosphatidilglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), and phosphatidylcholine (PC). The major cellular fatty acids of strain BT688T were C18:1 ω7c (76.0%) and summed feature 3 (9.6%).Based on the polyphasic characteristics, strain BT688T can be suggested as a novel bacterial species within the genus Microvirga and the proposed name is Microvirga jeongseonensis. The type strain of Microvirga jeongseonensis is BT688T (= KCTC XXXXT=NBRC 114857 T).

Microbulbifer marinus sp. nov. and Microbulbifer yueqingensis sp. nov., isolated from marine sediment

2012 ◽  
Vol 62 (Pt_3) ◽  
pp. 505-510 ◽  
Author(s):  
Dong-Sheng Zhang ◽  
Ying-Yi Huo ◽  
Xue-Wei Xu ◽  
Yue-Hong Wu ◽  
Chun-Sheng Wang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
Tween 80 ◽  
Threshold Value ◽  
Rrna Gene ◽  
Optimum Growth Temperature ◽  
Ph Range ◽  
Type Strains

Two Gram-negative, aerobic strains, Y215T and Y226T, were isolated from sediment from Yueqing Bay, Zhejiang Province, China. The two novel strains were both positive for oxidase activity, nitrate reduction, and aesculin and casein decomposition, but negative for gelatin and tyrosine decomposition. Catalase activity, and starch and Tween 80 decomposition differed between the two strains. Cells of both novel strains were rod-shaped in young cultures and ovoid in older cultures. Optimum NaCl concentration and pH range for growth of both strains were 2.0–3.0 % (w/v) and 7.0–8.0, respectively, whereas the optimum growth temperature for strain Y215T (25–30 °C) was lower than that for strain Y226T (30–37 °C). The genomic DNA G+C contents of strains Y215T and Y226T were 54.0 and 56.7 mol%, respectively. The major fatty acids in both isolates were iso-C15 : 0 and iso-C17 : 1ω9c, which was also the case in the reference strains apart from Microbulbifer salipaludis, which possessed C18 : 1ω7c as the predominant fatty acid. The predominant isoprenoid quinone was Q-8 and the major polar lipids of both strains were phosphatidylethanolamine, phosphatidylglycerol and an unknown glycolipid. Both strains had highest 16S rRNA gene sequence similarity to members of the genus Microbulbifer. Strain Y215T was closely related to the type strains of Microbulbifer maritimus (97.6 %) and Microbulbifer donghaiensis (97.5 %), whereas strain Y226T was closely related to the type strain of M. salipaludis (97.6 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strains Y215T and Y226T fell into two separate clusters. The DNA–DNA relatedness values of strain Y215T with M. maritimus TF-17T and M. donghaiensis CN85T were 34.1 and 32.8 %, respectively, whereas that between strain Y226T and M. salipaludis SM-1T was 38.0 %; these values are significantly lower than the threshold value for the delineation of bacterial species. On the basis of their distinct taxonomic characteristics, the two isolates represent two novel species of the genus Microbulbifer, for which the names Microbulbifer marinus sp. nov. and Microbulbifer yueqingensis sp. nov. are proposed; the type strains are Y215T ( = CGMCC 1.10657T = JCM 17211T) and Y226T ( = CGMCC 1.10658T = JCM 17212T), respectively.

scholarly journals Erythrobacter spongiae sp. nov., isolated from marine sponge

2019 ◽  
Vol 69 (4) ◽  
pp. 1111-1116 ◽  
Author(s):  
Lingping Zhuang ◽  
Binbin Lin ◽  
Li Xu ◽  
Guoqiang Li ◽  
Chang-Jer Wu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Hydrolysis Of ◽  
Distinct Phylogenetic Lineage

A taxonomic study was carried out on strain HN-E23T, which was isolated from sponge collected from Yangpu Bay, Hainan, China. Cells of strain HN-E23T were Gram-stain-negative, non-motile, orange-yellow-pigmented, short rods, that could grow at 10–40 °C (optimum, 28 °C), at pH 5–11 (optimun, pH 7) and in 0.5–12 % (w/v) NaCl (optimum, 3 %). This isolate was positive for oxidase, catalase, and the hydrolysis of aesculin, but negative for indole production and the reduction of nitrate. The phylogenetic tree based on 16S rRNA gene sequences revealed that strain HN-E23T formed a distinct phylogenetic lineage within the cluster comprising Erythrobacter strains. Strain HN-E23T shared the highest 16S rRNA gene sequence similarity to Erythrobacter aquimixticola JSSK-14T (97.2 %), followed by Erythrobacter atlanticus s21-N3T (96.6 %), Erythrobacter luteus KA37T (96.5 %) and Erythrobacter citreus RE35F/1T (96.4 %). The digital DNA–DNA hybridization (dDDH) and the average nucleotide identity (ANI) values between strain HN-E23T and JSSK-14T were 18.8 and 74.9 %, respectively. The dDDH and ANI values are below the standard cut-off criteria for delineation of bacterial species. The dominant fatty acids were summed feature 8 (C18 : 1ω7c/ω6c), C16 : 0 and summed feature 3 (C16 : 1ω7c/ω6c). The major polar lipids comprised phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid, an unidentified glycolipid and six unidentified lipids. The respiratory lipoquinone was identified as Q-10. The G+C content of the genomic DNA was 65.5 mol%. Based on the phenotypic and phylogenetic data, strain HN-E23T represents a novel species of the genus Erythrobacter , for which the name Erythrobacter spongiae sp. nov. is proposed, with the type strain HN-E23T (=MCCC 1K03331T=LMG 30457T).

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