Multilocus Sequence Analysis of the Marine Bacterial Genus Tenacibaculum Suggests Parallel Evolution of Fish Pathogenicity and Endemic Colonization of Aquaculture Systems

ABSTRACTThe genusTenacibaculum, a member of the familyFlavobacteriaceae, is an abundant component of marine bacterial ecosystems that also hosts several fish pathogens, some of which are of serious concern for marine aquaculture. Here, we applied multilocus sequence analysis (MLSA) to 114 representatives of most known species in the genus and of the worldwide diversity of the major fish pathogenTenacibaculum maritimum. Recombination hampers precise phylogenetic reconstruction, but the data indicate intertwined environmental and pathogenic lineages, which suggests that pathogenicity evolved independently in several species. At lower phylogenetic levels recombination is also important, and the speciesT. maritimumconstitutes a cohesive group of isolates. Importantly, the data reveal no trace of long-distance dissemination that could be linked to international fish movements. Instead, the high number of distinct genotypes suggests an endemic distribution of strains. The MLSA scheme and the data described in this study will help in monitoringTenacibaculuminfections in marine aquaculture; we show, for instance, that isolates from tenacibaculosis outbreaks in Norwegian salmon farms are related toT. dicentrarchi, a recently described species.

Download Full-text

Mariniradius saccharolyticus gen. nov., sp. nov., a member of the family Cyclobacteriaceae isolated from marine aquaculture pond water, and emended descriptions of the genus Aquiflexum and Aquiflexum balticum

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.043919-0 ◽

2013 ◽

Vol 63 (Pt_6) ◽

pp. 2088-2094 ◽

Cited By ~ 17

Author(s):

V. Bhumika ◽

T. N. R. Srinivas ◽

K. Ravinder ◽

P. Anil Kumar

Keyword(s):

Type Species ◽

Sequence Similarity ◽

Pond Water ◽

Rrna Gene ◽

Unidentified Phospholipid ◽

Marine Aquaculture ◽

Content Type ◽

Aquaculture Pond ◽

Link Type ◽

The Family

A novel marine, Gram-stain-negative, oxidase- and catalase- positive, rod-shaped bacterium, designated strain AK6T, was isolated from marine aquaculture pond water collected in Andhra Pradesh, India. The fatty acids were dominated by iso-C15 : 0, iso-C17 : 1ω9c, iso-C15 : 1 G, iso-C17 : 0 3-OH and anteiso-C15 : 0. Strain AK6T contained MK-7 as the sole respiratory quinone and phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified phospholipid and seven unidentified lipids as polar lipids. The DNA G+C content of strain AK6T was 45.6 mol%. Phylogenetic analysis showed that strain AK6T formed a distinct branch within the family Cyclobacteriaceae and clustered with Aquiflexum balticum DSM 16537T and other members of the family Cyclobacteriaceae . 16S rRNA gene sequence analysis confirmed that Aquiflexum balticum DSM 16537T was the nearest neighbour, with pairwise sequence similarity of 90.1 %, while sequence similarity with the other members of the family was <88.5 %. Based on differentiating phenotypic characteristics and phylogenetic inference, strain AK6T is proposed as a representative of a new genus and species of the family Cyclobacteriaceae , as Mariniradius saccharolyticus gen. nov., sp. nov. The type strain of Mariniradius saccharolyticus is AK6T ( = MTCC 11279T = JCM 17389T). Emended descriptions of the genus Aquiflexum and Aquiflexum balticum are also proposed.

Download Full-text

Multilocus Sequence Analysis Reveals Genetic Diversity in Xanthomonads Associated With Poinsettia Production

Plant Disease ◽

10.1094/pdis-08-14-0867-re ◽

2015 ◽

Vol 99 (6) ◽

pp. 874-882 ◽

Cited By ~ 8

Author(s):

W. Rockey ◽

N. Potnis ◽

S. Timilsina ◽

J. C. Hong ◽

G. E. Vallad ◽

...

Keyword(s):

Sequence Analysis ◽

Leaf Spot ◽

Reference Strain ◽

Housekeeping Genes ◽

Causal Agent ◽

Multilocus Sequence Analysis ◽

Bacterial Leaf Spot ◽

The Family ◽

Systemic Infections ◽

Spot Formation

Xanthomonas axonopodis pv. poinsettiicola is traditionally identified as the primary causal agent of bacterial leaf spot on poinsettia (family Euphorbiaceae). Sixty-seven strains of xanthomonads isolated from lesions associated with several species within the family Euphorbiaceae were collected over a 64-year period. The pathogenicity of these strains was compared on several potential hosts and they were analyzed by multilocus sequence analysis (MLSA) using six housekeeping genes. The 67 Xanthomonas strains associated with poinsettia production were separated into three distinct clades based on MLSA. The first clade identified contained the X. axonopodis pv. poinsettiicola reference strain (LMG849PT). A second clade was more closely related to X. hortorum pv. pelargonii (LMG7314PT) and the third clade contained the X. codiaei type strain (LMG8678T). This analysis indicated that there may also be other closely related pathovars or species of Xanthomonas that can infect poinsettia. Strains from the three clades could not be distinguished by symptoms or virulence on poinsettia plants. Strains capable of infecting geranium were found in all three clades, although the extent of leaf spot formation and number of systemic infections were significantly less than those produced by X. hortorum pv. pelargonii strains, typically the main causal agent of bacterial leaf spot on geranium. Clade III also contained strains isolated from zebra plant (Aphelandra squarrosa, family Acanthaceae), which is a newly recognized host for X. codiaei and X. axonopodis pv. poinsettiicola. Xanthomonas leaf spot is a serious threat to poinsettia production that can be caused by several Xanthomonas spp. that can infect different ornamental plant hosts. It is imperative that growers maintain a strict sanitation program because reservoirs of inoculum can occur on a number of ornamental hosts.

Download Full-text

Multilocus Sequence Analysis of Xanthomonads Causing Bacterial Spot of Tomato and Pepper Plants Reveals Strains Generated by Recombination among Species and Recent Global Spread of Xanthomonas gardneri

Applied and Environmental Microbiology ◽

10.1128/aem.03000-14 ◽

2014 ◽

Vol 81 (4) ◽

pp. 1520-1529 ◽

Cited By ~ 38

Author(s):

Sujan Timilsina ◽

Mustafa O. Jibrin ◽

Neha Potnis ◽

Gerald V. Minsavage ◽

Misrak Kebede ◽

...

Keyword(s):

Genetic Diversity ◽

Sequence Analysis ◽

Housekeeping Genes ◽

Global Distribution ◽

Multilocus Sequence Analysis ◽

Regional Differentiation ◽

Bacterial Spot ◽

Content Type ◽

Global Spread ◽

Pathogen Populations

ABSTRACTFourXanthomonasspecies are known to cause bacterial spot of tomato and pepper, but the global distribution and genetic diversity of these species are not well understood. A collection of bacterial spot-causing strains from the Americas, Africa, Southeast Asia, and New Zealand were characterized for genetic diversity and phylogenetic relationships using multilocus sequence analysis of six housekeeping genes. By examining strains from different continents, we found unexpected phylogeographic patterns, including the global distribution of a single multilocus haplotype ofX. gardneri, possible regional differentiation inX. vesicatoria, and high species diversity on tomato in Africa. In addition, we found evidence of multiple recombination events betweenX. euvesicatoriaandX. perforans.Our results indicate that there have been shifts in the species composition of bacterial spot pathogen populations due to the global spread of dominant genotypes and that recombination between species has generated genetic diversity in these populations.

Download Full-text

Draft Genome Sequence of Neisseria mucosa Strain HSUH001, Isolated from an Aggressive Periodontal Lesion

Microbiology Resource Announcements ◽

10.1128/mra.00238-21 ◽

2021 ◽

Vol 10 (19) ◽

Author(s):

Masatoshi Yamashita ◽

Toshiyuki Nagasawa ◽

Satsuki Kato ◽

Hiroshi Miyakawa ◽

Mari Fujita ◽

...

Keyword(s):

Sequence Analysis ◽

Genome Sequence ◽

Draft Genome ◽

Draft Genome Sequence ◽

Multilocus Sequence Analysis ◽

Content Type ◽

Total Length ◽

Neisseria Mucosa

ABSTRACT We report the draft genome sequence (143 contigs, with a total length of 2,424,805 bp and an N50 value of 36,066 bp) of a bacterium isolated from an aggressive periodontal lesion in a patient. We assigned strain HSUH001 to Neisseria mucosa through a multilocus sequence analysis.

Download Full-text

Isolation of Potentially Novel Brucella spp. from Frogs

Applied and Environmental Microbiology ◽

10.1128/aem.07509-11 ◽

2012 ◽

Vol 78 (10) ◽

pp. 3753-3755 ◽

Cited By ~ 51

Author(s):

Tobias Eisenberg ◽

Hans-Peter Hamann ◽

Ute Kaim ◽

Karen Schlez ◽

Helga Seeger ◽

...

Keyword(s):

Sequence Analysis ◽

16S Rrna ◽

16S Rrna Sequencing ◽

Multilocus Sequence Analysis ◽

Ochrobactrum Anthropi ◽

Bacterial Isolates ◽

Content Type ◽

Zoonotic Pathogens ◽

Rrna Sequencing ◽

Close Relationship

ABSTRACTBacterial isolates from frogs were phenotypically identified asOchrobactrum anthropi, but 16S rRNA sequencing showed up to 100% identity withBrucella inopinata. Further analysis ofrecA,omp2a,omp2b,bcsp31, and IS711and multilocus sequence analysis (MLSA) verified a close relationship withBrucella, suggesting the isolates may actually represent novel members of this growing genus of zoonotic pathogens.

Download Full-text

Multilocus sequence analysis of root nodule isolates from Lotus arabicus (Senegal), Lotus creticus, Argyrolobium uniflorum and Medicago sativa (Tunisia) and description of Ensifer numidicus sp. nov. and Ensifer garamanticus sp. nov.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.012088-0 ◽

2010 ◽

Vol 60 (3) ◽

pp. 664-674 ◽

Cited By ~ 61

Author(s):

C. Merabet ◽

M. Martens ◽

M. Mahdhi ◽

F. Zakhia ◽

A. Sy ◽

...

Keyword(s):

Sequence Analysis ◽

Medicago Sativa ◽

Type Strain ◽

Gene Sequence ◽

Sequence Similarity ◽

Phylogenetic Reconstruction ◽

Housekeeping Genes ◽

Multilocus Sequence Analysis ◽

Rrna Gene ◽

Reconstruction Method

Nine isolates from Argyrolobium uniflorum, Lotus creticus, Medicago sativa (Tunisia) and Lotus arabicus (Senegal) were analysed by multilocus sequence analysis (MLSA) of five housekeeping genes (recA, atpD, glnA, gltA and thrC), the 16S rRNA gene and the nodulation gene nodA. Analysis of the individual and concatenated gene sequences demonstrated that the nine new strains constituted three stable, well-supported (bootstrap and gene sequence similarity values) monophyletic clusters, A, B and C, all belonging to the branch of the genus Ensifer, regardless of the phylogenetic reconstruction method used (maximum likelihood, maximum-parsimony, neighbour-joining). The three groups were further characterized by API 100 auxanographic tests, host specificity and nodA gene sequence analysis. On the basis of these data, clusters A and C are suggested as representing two novel species within the genus Ensifer, for which the names Ensifer numidicus sp. nov. (type strain ORS 1407T=LMG 24690T=CIP 109850T) and Ensifer garamanticus sp. nov. (type strain ORS 1400T=LMG 24692T=CIP 109916T) are proposed. The cluster B strains were assigned to Ensifer adhaerens genomovar A.

Download Full-text

Multilocus Sequence Analysis of Phylogroup 1 and 2 Oral Treponeme Strains

Applied and Environmental Microbiology ◽

10.1128/aem.02499-16 ◽

2016 ◽

Vol 83 (3) ◽

Cited By ~ 4

Author(s):

Yong-Biao Huo ◽

Yuki Chan ◽

Donnabella C. Lacap-Bugler ◽

Sisu Mo ◽

Patrick C. Y. Woo ◽

...

Keyword(s):

Sequence Analysis ◽

16S Rrna ◽

Periodontal Diseases ◽

Genetic Relationships ◽

Species Level ◽

Multilocus Sequence Analysis ◽

Species Differentiation ◽

Treponema Denticola ◽

Rrna Gene ◽

Content Type

ABSTRACT More than 75 “species-level” phylotypes of spirochete bacteria belonging to the genus Treponema reside within the human oral cavity. The majority of these oral treponeme phylotypes correspond to as-yet-uncultivated taxa or strains of uncertain standing in taxonomy. Here, we analyze phylogenetic and taxonomic relationships between oral treponeme strains using a multilocus sequence analysis (MLSA) scheme based on the highly conserved 16S rRNA, pyrH, recA, and flaA genes. We utilized this MLSA scheme to analyze genetic data from a curated collection of oral treponeme strains (n = 71) of diverse geographical origins. This comprises phylogroup 1 (n = 23) and phylogroup 2 (n = 48) treponeme strains, including all relevant American Type Culture Collection reference strains. The taxonomy of all strains was confirmed or inferred via the analysis of ca. 1,450-bp 16S rRNA gene sequences using a combination of bioinformatic and phylogenetic approaches. Taxonomic and phylogenetic relationships between the respective treponeme strains were further investigated by analyzing individual and concatenated flaA (1,074-nucleotide [nt]), recA (1,377-nt), and pyrH (696-nt) gene sequence data sets. Our data confirmed the species differentiation between Treponema denticola (n = 41) and Treponema putidum (n = 7) strains. Notably, our results clearly supported the differentiation of the 23 phylogroup 1 treponeme strains into five distinct “species-level” phylotypes. These respectively corresponded to “Treponema vincentii” (n = 11), Treponema medium (n = 1), “Treponema sinensis” (Treponema sp. IA; n = 4), Treponema sp. IB (n = 3), and Treponema sp. IC (n = 4). In conclusion, our MLSA-based approach can be used to effectively discriminate oral treponeme taxa, confirm taxonomic assignment, and enable the delineation of species boundaries with high confidence. IMPORTANCE Periodontal diseases are caused by persistent polymicrobial biofilm infections of the gums and underlying tooth-supporting structures and have a complex and variable etiology. Although Treponema denticola is strongly associated with periodontal diseases, the etiological roles of other treponeme species/phylotypes are less well defined. This is due to a paucity of formal species descriptions and a poor understanding of genetic relationships between oral treponeme taxa. Our study directly addresses these issues. It represents one of the most comprehensive analyses of oral treponeme strains performed to date, including isolates from North America, Europe, and Asia. We envisage that our results will greatly facilitate future metagenomic efforts aimed at characterizing the clinical distributions of oral treponeme species/phylotypes, helping investigators to establish a more detailed understanding of their etiological roles in periodontal diseases and other infectious diseases. Our results are also directly relevant to various polymicrobial tissue infections in animals, which also involve treponeme populations.

Download Full-text

Differentiation of Xylella fastidiosa Strains via Multilocus Sequence Analysis of Environmentally Mediated Genes (MLSA-E)

Applied and Environmental Microbiology ◽

10.1128/aem.06679-11 ◽

2011 ◽

Vol 78 (5) ◽

pp. 1385-1396 ◽

Cited By ~ 22

Author(s):

Jennifer K. Parker ◽

Justin C. Havird ◽

Leonardo De La Fuente

Keyword(s):

Sequence Analysis ◽

Genetic Variability ◽

Xylella Fastidiosa ◽

Genetic Relationships ◽

Phylogenetic Analyses ◽

Housekeeping Genes ◽

The United States ◽

Multilocus Sequence Analysis ◽

Biological Traits ◽

Content Type

ABSTRACTIsolates of the plant pathogenXylella fastidiosaare genetically very similar, but studies on their biological traits have indicated differences in virulence and infection symptomatology. Taxonomic analyses have identified several subspecies, and phylogenetic analyses of housekeeping genes have shown broad host-based genetic differences; however, results are still inconclusive for genetic differentiation of isolates within subspecies. This study employs multilocus sequence analysis of environmentally mediated genes (MLSA-E; genes influenced by environmental factors) to investigateX. fastidiosarelationships and differentiate isolates with low genetic variability. Potential environmentally mediated genes, including host colonization and survival genes related to infection establishment, were identifieda priori. The ratio of the rate of nonsynonymous substitutions to the rate of synonymous substitutions (dN/dS) was calculated to select genes that may be under increased positive selection compared to previously studied housekeeping genes. Nine genes were sequenced from 54X. fastidiosaisolates infecting different host plants across the United States. Results of maximum likelihood (ML) and Bayesian phylogenetic (BP) analyses are in agreement with knownX. fastidiosasubspecies clades but show novel within-subspecies differentiation, including geographic differentiation, and provide additional information regarding host-based isolate variation and specificity.dN/dSratios of environmentally mediated genes, though <1 due to high sequence similarity, are significantly greater than housekeeping genedN/dSratios and correlate with increased sequence variability. MLSA-E can more precisely resolve relationships between closely related bacterial strains with low genetic variability, such asX. fastidiosaisolates. Discovering the genetic relationships betweenX. fastidiosaisolates will provide new insights into the epidemiology of populations ofX. fastidiosa, allowing improved disease management in economically important crops.

Download Full-text

Multilocus sequence analysis of the family Halomonadaceae

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.032938-0 ◽

2012 ◽

Vol 62 (Pt_3) ◽

pp. 520-538 ◽

Cited By ~ 67

Author(s):

Rafael R. de la Haba ◽

M. Carmen Márquez ◽

R. Thane Papke ◽

Antonio Ventosa

Keyword(s):

Phylogenetic Analysis ◽

Sequence Analysis ◽

16S Rrna ◽

Halophilic Bacteria ◽

Multilocus Sequence Analysis ◽

23S Rrna ◽

Rrna Gene ◽

The Family ◽

Micro Organisms ◽

The Impact

Multilocus sequence analysis (MLSA) protocols have been developed for species circumscription for many taxa. However, at present, no studies based on MLSA have been performed within any moderately halophilic bacterial group. To test the usefulness of MLSA with these kinds of micro-organisms, the family Halomonadaceae, which includes mainly halophilic bacteria, was chosen as a model. This family comprises ten genera with validly published names and 85 species of environmental, biotechnological and clinical interest. In some cases, the phylogenetic relationships between members of this family, based on 16S rRNA gene sequence comparisons, are not clear and a deep phylogenetic analysis using several housekeeping genes seemed appropriate. Here, MLSA was applied using the 16S rRNA, 23S rRNA, atpA, gyrB, rpoD and secA genes for species of the family Halomonadaceae. Phylogenetic trees based on the individual and concatenated gene sequences revealed that the family Halomonadaceae formed a monophyletic group of micro-organisms within the order Oceanospirillales. With the exception of the genera Halomonas and Modicisalibacter, all other genera within this family were phylogenetically coherent. Five of the six studied genes (16S rRNA, 23S rRNA, gyrB, rpoD and secA) showed a consistent evolutionary history. However, the results obtained with the atpA gene were different; thus, this gene may not be considered useful as an individual gene phylogenetic marker within this family. The phylogenetic methods produced variable results, with those generated from the maximum-likelihood and neighbour-joining algorithms being more similar than those obtained by maximum-parsimony methods. Horizontal gene transfer (HGT) plays an important evolutionary role in the family Halomonadaceae; however, the impact of recombination events in the phylogenetic analysis was minimized by concatenating the six loci, which agreed with the current taxonomic scheme for this family. Finally, the findings of this study also indicated that the 16S rRNA, gyrB and rpoD genes were the most suitable genes for future taxonomic studies using MLSA within the family Halomonadaceae.

Download Full-text

Draft Genome Sequence of Mycolicibacterium sp. Strain NCC-Tsukiji, Isolated from Blood Culture of a Patient with Malignant Lymphoma

Microbiology Resource Announcements ◽

10.1128/mra.01575-18 ◽

2019 ◽

Vol 8 (14) ◽

Cited By ~ 1

Author(s):

Hanako Fukano ◽

Mitsunori Yoshida ◽

Michi Shouji ◽

Shunsuke Hatta ◽

Dai Maruyama ◽

...

Keyword(s):

Sequence Analysis ◽

Blood Culture ◽

Malignant Lymphoma ◽

Genome Sequence ◽

Draft Genome ◽

Draft Genome Sequence ◽

Multilocus Sequence Analysis ◽

Lymphoma Patient ◽

Content Type

A nonidentifiable mycolicibacterium was isolated from a malignant lymphoma patient treated with intensive chemoimmunotherapy. Multilocus sequence analysis showed that this isolate was close to “Mycolicibacterium (Mycobacterium) ratisbonense,” but the details of this species were still unknown.

Download Full-text