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    Item type:Publication,
    Comparative genomics reveals insight into the phylogeny and habitat adaptation of novel Amycolatopsis species, an endophytic actinomycete associated with scab lesions on potato tubers
    (2024-01-01)
    Wannawong, Thippawan
    ;
    Mhuantong, Wuttichai
    ;
    Macharoen, Pipat
    ;
    Niemhom, Nantawan
    ;
    Sitdhipol, Jaruwan
    A novel endophytic actinomycete, strain MEP2-6<sup>T</sup>, was isolated from scab tissues of potato tubers collected from Mae Fag Mai Sub-district, San Sai District, Chiang Mai Province, Thailand. Strain MEP2-6<sup>T</sup> is a gram-positive filamentous bacteria characterized by meso-diaminopimelic acid in cell wall peptidoglycan and arabinose, galactose, glucose, and ribose in whole-cell hydrolysates. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and hydroxy-phosphatidylethanolamine were the major phospholipids, of which MK-9(H<inf>6</inf>) was the predominant menaquinone, whereas iso-C<inf>16:0</inf> and iso-C<inf>15:0</inf> were the major cellular fatty acids. The genome of the strain was 10,277,369 bp in size with a G + C content of 71.7%. The 16S rRNA gene phylogenetic and core phylogenomic analyses revealed that strain MEP2-6<sup>T</sup> was closely related to Amycolatopsis lexingtonensis NRRL B-24131<sup>T</sup> (99.4%), A. pretoriensis DSM 44654<sup>T</sup> (99.3%), and A. eburnea GLM-1<sup>T</sup> (98.9%). Notably, strain MEP2-6<sup>T</sup> displayed 91.7%, 91.8%, and 87% ANIb and 49%, 48.8%, and 35.4% dDDH to A. lexingtonensis DSM 44653<sup>T</sup> (=NRRL B-24131<sup>T</sup>), A. eburnea GLM-1<sup>T</sup>, and A. pretoriensis DSM 44654<sup>T</sup>, respectively. Based on phenotypic, chemotaxonomic, and genomic data, strain MEP2-6<sup>T</sup> could be officially assigned to a novel species within the genus Amycolatopsis, for which the name Amycolatopsis solani sp. nov. has been proposed. The type of strain is MEP2-6<sup>T</sup> (=JCM 36309<sup>T</sup> = TBRC 17632<sup>T</sup> = NBRC 116395<sup>T</sup>). Amycolatopsis solani MEP2-6<sup>T</sup> was strongly proven to be a non-phytopathogen of potato scab disease because stunting of seedlings and necrotic lesions on potato tuber slices were not observed, and there were no core biosynthetic genes associated with the BGCs of phytotoxin-inducing scab lesions. Furthermore, comparative genomics can provide a better understanding of the genetic mechanisms that enable A. solani MEP2-6<sup>T</sup> to adapt to the plant endosphere. Importantly, the strain smBGCs accommodated 33 smBGCs encoded for several bioactive compounds, which could be beneficially applied in the fields of agriculture and medicine. Consequently, strain MEP2-6<sup>T</sup> is a promising candidate as a novel biocontrol agent and antibiotic producer.
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    Molecular serotyping, virulence gene profiling and pathogenicity of Streptococcus agalactiae isolated from tilapia farms in Thailand by multiplex PCR
    (2017-06-01)
    Kannika, K.
    ;
    Pisuttharachai, D.
    ;
    Srisapoome, P.
    ;
    Wongtavatchai, J.
    ;
    Kondo, H.
    Aims: This study aimed to biotype Streptococcus agalactiae isolated from tilapia farms in Thailand based on molecular biotyping methods and to determine the correlation between the serotype and virulence of bacteria. In addition to a biotyping (serotyping) technique based on multiplex PCR of cps genes, in this study, we developed multiplex PCR typing of Group B streptococcus (GBS) virulence genes to examine three clusters of virulence genes and their correlation with the pathogenicity of S. agalactiae. The epidemiology of S. agalactiae in Thailand was analysed to provide bacterial genetic information towards a future rational vaccine strategy for tilapia culture systems. Methods and Results: Streptococcus agalactiae were isolated from diseased tilapia from different areas of Thailand. A total of 124 S. agalactiae isolates were identified by phenotypic analysis and confirmed by 16S rRNA PCR. Bacterial genotyping was conducted based on (i) molecular serotyping of the capsular polysaccharide (cps) gene cluster and (ii) virulence gene profiling using multiplex PCR analysis of 14 virulence genes (lmb, scpB, pavA, cspA, spb1, cyl, bca, rib, fbsA, fbsB, cfb, hylB, bac and pbp1A/ponA). Only serotypes Ia and III were found in this study; serotype Ia lacks the lmb, scpB and spb1 genes, whereas serotype III lacks only the bac gene. Virulence tests in juvenile Nile tilapia demonstrated a correlation between the pathogenicity of the bacteria and their virulence gene profile, with serotype III showing higher virulence than serotype Ia. Epidemiological analysis showed an almost equal distribution in all regions of Thailand, except serotype III was found predominantly in the southern areas. Conclusions: Only two serotypes of S. agalactiae were isolated from diseased tilapia in Thailand. Serotype Ia showed fewer virulence genes and lower virulence than serotype III. Both serotypes showed a similar distribution throughout Thailand. Significance and Impact of the Study: We identified two major serotypes of S. agalactiae isolates associated with the outbreak in tilapia culture in Thailand. We developed multiplex PCR assays for 14 virulence genes, which may be used to predict the pathogenicity of the isolates and track future infections. Multiplex PCR typing of the GBS virulence genes was developed and might be further used to predict the pathogenicity of S. agalactiae.