scholarly journals Globetrotting strangles: the unbridled national and international transmission of Streptococcus equi between horses

2021 ◽  
Author(s):  
Catriona Mitchell ◽  
Karen F. Steward ◽  
Amelia R. L. Charbonneau ◽  
Saoirse Walsh ◽  
Hayley Wilson ◽  
...  
Keyword(s):  
Type Species ◽  
Genetic Relationships ◽  
Genomic Analysis ◽  
Economic Cost ◽  
Close Relative ◽  
International Transmission ◽  
Content Type ◽  
Link Type ◽  
Streptococcus Equi ◽  
The World

The equine disease strangles, which is characterized by the formation of abscesses in the lymph nodes of the head and neck, is one of the most frequently diagnosed infectious diseases of horses around the world. The causal agent, Streptococcus equi subspecies equi , establishes a persistent infection in approximately 10 % of animals that recover from the acute disease. Such ‘carrier’ animals appear healthy and are rarely identified during routine veterinary examinations pre-purchase or transit, but can transmit S. equi to naïve animals initiating new episodes of disease. Here, we report the analysis and visualization of phylogenomic and epidemiological data for 670 isolates of S. equi recovered from 19 different countries using a new core-genome multilocus sequence typing (cgMLST) web bioresource. Genetic relationships among all 670 S. equi isolates were determined at high resolution, revealing national and international transmission events that drive this endemic disease in horse populations throughout the world. Our data argue for the recognition of the international importance of strangles by the Office International des Épizooties to highlight the health, welfare and economic cost of this disease. The Pathogenwatch cgMLST web bioresource described herein is available for tailored genomic analysis of populations of S. equi and its close relative S. equi subspecies zooepidemicus that are recovered from horses and other animals, including humans, throughout the world. This article contains data hosted by Microreact.

Roseomonas oleicola sp. nov., isolated from an oil production mixture in Yumen Oilfield, and emended description of Roseomonas frigidaquae

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Danni Wu ◽  
Hongcan Liu ◽  
Yuguang Zhou ◽  
Xiaolei Wu ◽  
Yong Nie ◽  
...  
Keyword(s):  
Type Species ◽  
Genomic Analysis ◽  
Oil Production ◽  
Gene Families ◽  
Specific Gene ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A pink, ovoid-shaped, Gram-stain-negative, strictly aerobic and motile bacterial strain, designated ROY-5-3T, was isolated from an oil production mixture from Yumen Oilfield in PR China. The strain grew at 4–42 °C (optimum, 30 °C), at pH 5–10 (optimum, 7) and with 0–5 % (w/v) NaCl (optimum, 0%). The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that ROY-5-3T belongs to the genus Roseomonas and shared the highest pairwise similarities with Roseomonas frigidaquae CW67T (98.1%), Roseomonas selenitidurans BU-1T (97.8%), Roseomonas tokyonensis K-20T (97.7%) and Roseomonas stagni HS-69T (97.3%). The average nucleotide identity and digital DNA–DNA hybridization values between ROY-5-3T and other related type strains of Roseomonas species were less than 84.08 and 28.60 %, respectively, both below the species delineation threshold. Pan-genomic analysis showed that the novel isolate ROY-5-3T shared 3265 core gene families with the four closely related type strains in Roseomonas , and the number of strain-specific gene families was 513. The major fatty acids were identified as summed feature 8 (C18 : 1 ω6c/C18 : 1 ω7c), summed feature 3 (C16 : 1 ω6c/C16 : 1 ω7c) and C16 : 0. Strain ROY-5-3T contained Q-10 as the main ubiquinone and the genomic DNA G+C content was 69.8 mol%. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol. Based on the phylogenetic, morphological, physiological, chemotaxonomic and genome analyses, strain ROY-5-3T represents a novel species of the genus Roseomonas for which the name Roseomonas oleicola sp. nov. is proposed. The type strain is ROY-5-3T (=CGMCC 1.13459T =KCTC 82484T).

scholarly journals Lichenicola cladoniae gen. nov., sp. nov., a member of the family Acetobacteraceae isolated from an Antarctic lichen

2020 ◽  
Vol 70 (11) ◽  
pp. 5918-5925 ◽  
Author(s):  
Hyun-Ju Noh ◽  
Seung Chul Shin ◽  
Yerin Park ◽  
Ahyoung Choi ◽  
Kiwoon Baek ◽  
...  
Keyword(s):  
Type Species ◽  
Genomic Analysis ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Nitrate And Nitrite

Two Gram-stain-negative, facultative anaerobic, chemoheterotrophic, pink-coloured, rod-shaped and non-motile bacterial strains, PAMC 26568 and PAMC 26569T, were isolated from an Antarctic lichen. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains PAMC 26568 and PAMC 26569T belong to the family Acetobacteraceae and the most closely related species are Gluconacetobacter takamatsuzukensis (96.1 %), Gluconacetobacter tumulisoli (95.9 %) and Gluconacetobacter sacchari (95.7 %). Phylogenomic and genomic relatedness analyses showed that strains PAMC 26568 and PAMC 26569T are clearly distinguished from other genera in the family Acetobacteraceae by average nucleotide identity values (<72.8 %) and the genome-to-genome distance values (<22.5 %). Genomic analysis revealed that strains PAMC 26568 and PAMC 26569T do not contain genes involved in atmospheric nitrogen fixation and utilization of sole carbon compounds such as methane and methanol. Instead, strains PAMC 26568 and PAMC 26569T possess genes to utilize nitrate and nitrite and certain monosaccharides and disaccharides. The major fatty acids (>10 %) are summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c; 40.3–40.4 %), C18 : 1 2OH (22.7–23.7 %) and summed feature 2 (C14 : 0 3OH and/or C16 : 1 iso I; 12.0 % in PAMC 26568). The major respiratory quinone is Q-10. The genomic DNA G+C content of PAMC 26568 and PAMC 26569T is 64.6 %. Their distinct phylogenetic position and some physiological characteristics distinguish strains PAMC 26568 and PAMC 26569T from other genera in the family Acetobacteraceae supporting the proposal of Lichenicola gen. nov., with the type species Lichenicola cladoniae sp. nov. (type strain, PAMC 26569T=KCCM 43315T=JCM 33604T).

scholarly journals Marinobacter changyiensis, sp. nov., isolated from offshore sediment

2020 ◽  
Vol 70 (5) ◽  
pp. 3004-3011 ◽  
Author(s):  
Guangyu Li ◽  
Shanshan Wang ◽  
Yingbao Gai ◽  
Xiupian Liu ◽  
Qiliang Lai ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Genomic Analysis ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Promising Alternative ◽  
Content Type ◽  
Link Type ◽  
Marine Sediment Sample ◽  
Major Respiratory Quinone

An aerobic, Gram-stain-negative bacterium, designated CLL7-20T, was isolated from a marine sediment sample from offshore of Changyi, Shandong Province, China. Cells of strain CLL7-20T were rod-shaped, motile with one or more polar flagella, and grew optimally at pH 7.0, at 28 °C and with 3 % (w/v) NaCl. The principal fatty acids of strain CLL7-20T were C16 : 0 and summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c). The main polar lipids of strain CLL7-20T were phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG) and an unidentified aminolipid (AL). Strain CLL7-20T contained Q-9 as the major respiratory quinone. The G+C content of its genomic DNA was 56.2 mol%. Phylogenetically, strain CLL7-20T branched within the genus Marinobacter , with M. daqiaonensis YCSA40T being its closest phylogenetic relative (96.7 % 16S rRNA gene sequence similarity), followed by M. sediminum R65T (96.6 %). Average nucleotide identity and in silico DNA–DNA hybridization values between strain CLL7-20T and the closest related reference strains were 73.2% and 19.8 %, respectively. On the basis of its phenotypic, phylogenetic and chemotaxonomic characteristics, we suggest that strain CLL7-20T (=MCCC 1A14855T=KCTC 72664T) is the type strain of a novel species in the genus Marinobacter , for which the name Marinobacter changyiensis sp. nov. is proposed. Based on the genomic analysis, siderophore genes were found from strain CLL7-20T, which indicate its potential as a promising alternative to chemical fertilizers in iron-limitated environments such as saline soils.

scholarly journals Cryobacterium ruanii sp. nov. and Cryobacterium breve sp. nov., isolated from glaciers

2020 ◽  
Vol 70 (3) ◽  
pp. 1918-1923 ◽  
Author(s):  
Qing Liu ◽  
Ji-Hui Tian ◽  
Hong-Can Liu ◽  
Yu-Guang Zhou ◽  
Yu-Hua Xin
Keyword(s):  
Fatty Acids ◽  
Type Strain ◽  
Type Species ◽  
Gansu Province ◽  
Polar Lipids ◽  
Close Relative ◽  
Unidentified Phospholipid ◽  
Content Type ◽  
Link Type ◽  
Unidentified Glycolipid

Strains Sr36T and TMT4-23T were isolated from No. 1 glacier in Xinjiang Uygur Autonomous Region and Toumingmengke glacier in Gansu Province, PR China, respectively. They were Gram-stain-positive and rod-shaped micro-organisms. The optimum growth temperature of the two strains was 10–14 °C. Phylogenetic analysis showed that the two strains were related to members of the genus Cryobacterium . The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain Sr36T and its close relatives Cryobacterium luteum Hh15T, Cryobacterium aureum Hh31T, Cryobacterium levicorallinum Hh34T and Cryobacterium flavum Hh8T were 81.16–87.24 and 28.0–32.5 %, respectively. The ANI and dDDH values between strain TMT4-23T and its close relative Cryobacterium psychrotolerans 0549T were 81.16 and 22.3 %. The polar lipids of strain Sr36T were diphosphatidylglycerol, phosphatidylglycerol, one unidentified glycolipid and three unidentified lipids. The polar lipids of strain TMT4-23T were diphosphatidylglycerol, phosphatidylglycerol, one unidentified glycolipid, one unidentified phospholipid and six unidentified lipids. The major fatty acids of strain Sr36T were anteiso-C15 : 0, iso-C16 : 0, anteiso-C17 : 0 and anteiso-C15 : 1. The major fatty acids of strain TMT4-23T were anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0, anteiso-C15 : 1 and iso-C15 : 1. Both strains contained 2,4-diaminobutyric acid and their predominant menaquinone was MK-10. On the basis of the phenotypic, phylogenetic and genotypic data, two novel species Cryobacterium ruanii sp. nov. (type strain = Sr36T=CGMCC 1.9275T=NBRC 113797T) and Cryobacterium breve sp. nov. (type strain =TMT4-23T=CGMCC 1.9556T=NBRC 113800T) are proposed.

scholarly journals Prevotella hominis sp. nov., isolated from human faeces

2020 ◽  
Vol 70 (8) ◽  
pp. 4767-4773 ◽  
Author(s):  
Jong-Shian Liou ◽  
Chien-Hsun Huang ◽  
Nao Ikeyama ◽  
Ai-Yun Lee ◽  
I-Ching Chen ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
Genomic Analysis ◽  
Amino Acid Identity ◽  
Strictly Anaerobic ◽  
Content Type ◽  
Link Type ◽  
Predominant Bacterium ◽  
Species Specific

A strictly anaerobic predominant bacterium, designated as strain gm001T, was isolated from a freshly voided faecal sample collected from a healthy Taiwanese adult. Cells were Gram-stain-negative rods, non-motile and non-spore-forming. Strain gm001T was identified as a member of the genus Prevotella , and a comparison of 16S rRNA and hsp60 gene sequences revealed sequence similarities of 98.5 and 93.3 %, respectively, demonstrating that it was most closely related to the type strain of Prevotella copri . Phylogenomic tree analysis indicated that the gm001T cluster is an independent lineage of P. copri DSM 18205T. The average nucleotide identity, digital DNA‒DNA hybridization and average amino acid identity values between strain gm001T and P. copri DSM 18205T were 80.9, 28.6 and 83.8 %, respectively, which were clearly lower than the species delineation thresholds. The species-specific genes of this novel species were also identified on the basis of pan-genomic analysis. The predominant menaquinones were MK-11 and MK-12, and the predominant fatty acids were anteiso-C15 : 0, C15 : 0 and iso-C15 : 0. Acetate and succinate were produced from glucose as metabolic end products. Taken together, the results indicate that strain gm001T represents a novel species of the genus Prevotella , for which the name Prevotella hominis sp. nov. is proposed. The type strain is gm001T (=BCRC 81118T=JCM 33280T).

scholarly journals Xanthomonas euroxanthea sp. nov., a new xanthomonad species including pathogenic and non-pathogenic strains of walnut

2020 ◽  
Vol 70 (12) ◽  
pp. 6024-6031 ◽  
Author(s):  
Leonor Martins ◽  
Camila Fernandes ◽  
Jochen Blom ◽  
Nay C. Dia ◽  
Joël F. Pothier ◽  
...  
Keyword(s):  
Type Species ◽  
Juglans Regia ◽  
Genomic Analysis ◽  
Housekeeping Genes ◽  
Effector Proteins ◽  
Content Type ◽  
Type Iii ◽  
Link Type ◽  
Xanthomonas Arboricola ◽  
Walnut Leaves

We describe a novel species isolated from walnut (Juglans regia) which comprises non-pathogenic and pathogenic strains on walnut. The isolates, obtained from a single ornamental walnut tree showing disease symptoms, grew on yeast extract–dextrose–carbonate agar as mucoid yellow colonies characteristic of Xanthomonas species. Pathogenicity assays showed that while strain CPBF 424T causes disease in walnut, strain CPBF 367 was non-pathogenic on walnut leaves. Biolog GEN III metabolic profiles disclosed some differences between strains CPBF 367 and CPBF 424T and other xanthomonads. Multilocus sequence analysis with seven housekeeping genes (fyuA, gyrB, rpoD, atpD, dnaK, efp, glnA) grouped these strains in a distinct cluster from Xanthomonas arboricola pv. juglandis and closer to Xanthomonas prunicola and Xanthomonas arboricola pv. populi. Average nucleotide identity (ANI) analysis results displayed similarity values below 93 % to X. arboricola strains. Meanwhile ANI and digital DNA–DNA hybridization similarity values were below 89 and 50 % to non-arboricola Xanthomonas strains, respectively, revealing that they do not belong to any previously described Xanthomonas species. Furthermore, the two strains show over 98 % similarity to each other. Genomic analysis shows that strain CPBF 424T harbours a complete type III secretion system and several type III effector proteins, in contrast with strain CPBF 367, shown to be non-pathogenic in plant bioassays. Taking these data altogether, we propose that strains CPBF 367 and CPBF 424T belong to a new species herein named Xanthomonas euroxanthea sp. nov., with CPBF 424T (=LMG 31037T=CCOS 1891T=NCPPB 4675T) as the type strain.

scholarly journals Lactobacillus salitolerans sp. nov., a novel lactic acid bacterium isolated from spent mushroom substrates

2019 ◽  
Vol 69 (4) ◽  
pp. 964-969 ◽  
Author(s):  
Masanori Tohno ◽  
Yasuhiro Tanizawa ◽  
Yoichiro Kojima ◽  
Mitsuo Sakamoto ◽  
Yasukazu Nakamura ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Type Species ◽  
Sequence Similarity ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Bacterium Strain

A taxonomic study of a Gram-stain-positive, rod-shaped, non-motile, non-spore-forming, catalase-negative bacterium, strain YK43T, isolated from spent mushroom substrates stored in Nagano, Japan was performed. Growth was detected at 15–45 °C, pH 5.0–8.5, and 0–10 % (w/v) NaCl. The genomic DNA G+C content of strain YK43T was 43.6 mol%. The predominant fatty acids were C16 : 0, C18 : 1 ω9c and summed feature 8. Based on 16S rRNA gene sequence analysis, the type strains of Lactobacillus acidipiscis (sequence similarity, 97.6 %) and Lactobacillus pobuzihii (97.4 %) were most closely related to YK43T. The average nucleotide identities were 74.1 % between strain YK43T and L. acidipiscis DSM 15836T and 74.0 % between YK43T and L. pobuzihii E100301T. Based on a multilocus sequence analysis, comparative genomic analysis and a range of phenotypic and chemotaxonomic characteristics, strain YK43T represents a novel species of the genus Lactobacillus , for which the name Lactobacillus salitolerans sp. nov. is proposed. The type strain is YK43T (=JCM 31331T = DSM 103433T).

scholarly journals Dickeya oryzae sp. nov., isolated from the roots of rice

2020 ◽  
Vol 70 (7) ◽  
pp. 4171-4178 ◽  
Author(s):  
Xing Wang ◽  
Shan-Wen He ◽  
He-Bao Guo ◽  
Ji-Gang Han ◽  
kyu kyu Thin ◽  
...  
Keyword(s):  
16S Rrna ◽  
Type Species ◽  
Novel Species ◽  
Genomic Analysis ◽  
Core Gene ◽  
Phylogenomic Analysis ◽  
Rrna Gene ◽  
16S Rrna Gene Analysis ◽  
Content Type ◽  
Link Type

A novel Gram-stain-negative strain, designated ZYY5T, was isolated from rice roots. Results of 16S rRNA gene analysis indicated that strain ZYY5T was a member of the genus Dickeya , with a highest similarity to Dickeya zeae DSM 18068T (98.5%). The major fatty acids were summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), C16:0 and summed feature 8 (C18:1 ω7c and/or C18:1 ω6c). Multi-locus sequence analysis using five concatenated genes (16S rRNA, atpD, infB, recA and gyrB) and phylogenomic analysis based on 2940 core gene sequences showed that strain ZYY5T formed a robust cluster with strains EC1, ZJU1202, DZ2Q, NCPPB 3531 and CSL RW192, while separated from the other strains of D. zeae . The orthologous average nucleotide identity (ANI) and digital DNA–DNAhybridization (dDDH) values among these six strains ranged from 96.8–99.9% and 73.7–99.8%, which supported that they were belonged to the same species. However, strain ZYY5T shared 58.4 of dDDH and 94.5% of ANI values with type strain D. zeae DSM 18068T, which were lower than the proposed species boundary cut-off for dDDH and ANI. The genomic analysis revealed that strain ZYY5T contained virulence-associated genes, which is same as the phylogenetic-related strains of the genus Dickeya . Based on the results of the polyphasic approaches, we propose that strain ZYY5T represents a novel species in the genus Dickeya , for which the name Dickeya oryzae sp. nov. (=JCM 33020 T=ACCC 61554 T) is proposed. Strains EC1, ZJU1202, DZ2Q, NCPPB 3531 and CSL RW192 should also be classified in the same genomospecies of D. oryzae same as ZYY5T.

Streptomyces spirodelae sp. nov., isolated from duckweed

2021 ◽  
Vol 71 (11) ◽  
Author(s):  
Yuparat Saimee ◽  
Kannika Duangmal
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Genomic Analysis ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Unidentified Phospholipid ◽  
Content Type ◽  
Link Type ◽  
Diamino Acid

A novel actinobacterium, designated strain DW4-2T, was isolated from duckweed (Spirodela sp.) collected from an agricultural pond in Kasetsart University, Bangkok, Thailand. The morphological, chemotaxonomic and phylogenetic characteristics were consistent with its classification in the genus Streptomyces . Strain DW4-2T showed the highest 16S rRNA gene sequence similarity values to Streptomyces qinglanensis DSM 42035T (98.5 %), S treptomyces smyrnaeus DSM 42105T (98.4 %) and Streptomyces oryzae S16-07T (98.4 %). Digital DNA–DNA hydridization and average nucleotide identity values between the genome sequences of strain DW4-2T with S. qinglanensis DSM 42035T (29.8 and 87.8 %), S. smyrnaeus DSM 42105T (33.1 and 89.0 %) and S. oryzae S16-07T (33.0 and 88.9 %) were below the thresholds of 70 and 95–96 % for prokaryotic conspecific assignation. Chemotaxonomic data revealed that strain DW4-2T possessed MK-9(H6) and MK-9(H8) as the predominant menaquinones. It contained ll -diaminopimelic acid as the diagnostic diamino acid and glucose, ribose and trace amount of madurose in whole-cell sugars. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, an unidentified aminolipid, an unidentified lipid and an unidentified phospholipid. The predominant cellular fatty acids were anteiso-C17 : 0, anteiso-C15 : 0 and iso-C16 : 0. The genomic DNA size of the strain DW4-2T was 7 310 765 bp with DNA G+C content 71.0 mol%. Genomic analysis of the genome indicated that the strain DW4-2T had the potential to produce bioactive compounds. On the basis of these genotypic and phenotypic data, it is supported that strain DW4-2T represents a novel species of the genus Streptomyces , for which the name Streptomyces spirodelae sp. nov. is proposed. The type strain is strain DW4-2T (=TBRC 13095T=NBRC 114803T).

Yersinia occitanica is a later heterotypic synonym of Yersinia kristensenii subsp. rochesterensis and elevation of Yersinia kristensenii subsp. rochesterensis to species status

2021 ◽  
Author(s):  
Scott Van Nguyen ◽  
Scott A. Cunningham ◽  
Patricio Jeraldo ◽  
Anthony Tran ◽  
Robin Patel
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Genomic Analysis ◽  
Average Nucleotide Identity ◽  
Species Status ◽  
Content Type ◽  
Link Type ◽  
Type Strains ◽  
Genomic Relatedness

The taxonomic position of Yersinia kristensenii subsp. rochesterensis and Yersinia occitanica was re-evaluated by genomic analysis. Average nucleotide identity (ANI), digital DNA–DNA hybridization values, and phylogenetic analyses of the type strains indicate that Y. kristensenii subsp. rochesterensis and Y. occitanica are the same genospecies. Additionally, the overall genomic relatedness index (OGRI) values reveal that Y. kristensenii subsp. rochesterensis should be elevated to species status as Yersinia rochesterensis sp. nov.

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