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  1. Article ; Online: A gauge of coral physiology: re-examining temporal changes in

    Chuang, Po-Shun / Yu, Sheng-Ping / Liu, Po-Yu / Hsu, Ming-Tsung / Chiou, Yu-Jing / Lu, Chih-Ying / Tang, Sen-Lin

    ISME communications

    2024  Volume 4, Issue 1, Page(s) ycae001

    Abstract: Bacteria contribute to many physiological functions of coral holobionts, including responses to bleaching. The bacterial genus, ...

    Abstract Bacteria contribute to many physiological functions of coral holobionts, including responses to bleaching. The bacterial genus,
    Language English
    Publishing date 2024-01-12
    Publishing country England
    Document type Journal Article
    ISSN 2730-6151
    ISSN (online) 2730-6151
    DOI 10.1093/ismeco/ycae001
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Bacterial Community Shifts during Polyp Bail-Out Induction in

    Chuang, Po-Shun / Yamada, Yosuke / Liu, Po-Yu / Tang, Sen-Lin / Mitarai, Satoshi

    Microbiology spectrum

    2023  Volume 11, Issue 4, Page(s) e0025723

    Abstract: Polyp bail-out constitutes both a stress response and an asexual reproductive strategy that potentially facilitates dispersal of some scleractinian corals, including several dominant reef-building taxa in the family Pocilloporidae. Recent studies have ... ...

    Abstract Polyp bail-out constitutes both a stress response and an asexual reproductive strategy that potentially facilitates dispersal of some scleractinian corals, including several dominant reef-building taxa in the family Pocilloporidae. Recent studies have proposed that microorganisms may be involved in onset and progression of polyp bail-out. However, changes in the coral microbiome during polyp bail-out have not been investigated. In this study, we induced polyp bail-out in
    MeSH term(s) Animals ; Anthozoa/genetics ; Anthozoa/microbiology ; Coral Reefs ; Microbiota/genetics ; Gammaproteobacteria/genetics ; Rhodobacteraceae/genetics ; Myxococcales/genetics ; RNA, Ribosomal, 16S/genetics
    Chemical Substances RNA, Ribosomal, 16S
    Language English
    Publishing date 2023-06-28
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2807133-5
    ISSN 2165-0497 ; 2165-0497
    ISSN (online) 2165-0497
    ISSN 2165-0497
    DOI 10.1128/spectrum.00257-23
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Spatial and cross-seasonal patterns of coral diseases in reefs of Taiwan: high prevalence and regional variation.

    Huang, Ching-Yun / Hwang, Jiang-Shiou / Yamashiro, Hideyuki / Tang, Sen-Lin

    Diseases of aquatic organisms

    2021  Volume 146, Page(s) 145–156

    Abstract: Although research on coral diseases is increasing worldwide, it remains limited in Taiwan. Taiwan is located at the Tropic of Cancer and contains both tropical and subtropical reefs. We conducted spatial and cross-seasonal surveys in Taiwan in 2018 and ... ...

    Abstract Although research on coral diseases is increasing worldwide, it remains limited in Taiwan. Taiwan is located at the Tropic of Cancer and contains both tropical and subtropical reefs. We conducted spatial and cross-seasonal surveys in Taiwan in 2018 and identified 7 types of disease and nondisease lesions and 6 potential factors influencing coral health. The overall mean prevalence of disease and nondisease lesions varied considerably across the reef regions, and host susceptibility differed among the coral taxa. The overall mean prevalence of disease and nondisease lesions was highest in Kenting (mean ± SEM: 8.58 ± 1.81%) and lowest on the Southern Islands (2.12 ± 0.73%). Although the prevalence of diseases did not differ significantly between the seasons, cyanobacteria-related diseases-including black band disease (BBD), BBD-like syndrome, and other cyanobacterial syndromes-were slightly more prevalent in autumn than in spring. Furthermore, 3 of the potential factors influencing coral health (i.e. turf algae, bioeroding sponges, and coral bleaching) were strong predictors of disease and nondisease lesion prevalence. These results advance our understanding of coral disease ecology in Taiwan and highlight the need for further research on the correlations between diseases, hosts, and environment.
    MeSH term(s) Animals ; Anthozoa ; Cyanobacteria ; Prevalence ; Seasons ; Taiwan/epidemiology
    Language English
    Publishing date 2021-10-21
    Publishing country Germany
    Document type Journal Article
    ISSN 0177-5103
    ISSN 0177-5103
    DOI 10.3354/dao03624
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: The Novel Halovirus Hardycor1, and the Presence of Active (Induced) Proviruses in Four Haloarchaea.

    Dyall-Smith, Mike / Pfeiffer, Friedhelm / Chiang, Pei-Wen / Tang, Sen-Lin

    Genes

    2021  Volume 12, Issue 2

    Abstract: The virus Hardycor1 was isolated in 1998 and infects the ... ...

    Abstract The virus Hardycor1 was isolated in 1998 and infects the haloarchaeon
    Language English
    Publishing date 2021-01-23
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2527218-4
    ISSN 2073-4425 ; 2073-4425
    ISSN (online) 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes12020149
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Genome Sequence of Hardyhisp2, a Gammapleolipovirus Infecting Haloarcula hispanica.

    Dyall-Smith, Mike / Pfeiffer, Friedhelm / Chiang, Pei-Wen / Tang, Sen-Lin

    Microbiology resource announcements

    2021  Volume 10, Issue 19

    Abstract: Hardyhisp2 virus infects the halophilic ... ...

    Abstract Hardyhisp2 virus infects the halophilic archaeon
    Language English
    Publishing date 2021-05-13
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/MRA.00226-21
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: High-Quality Genome Sequences of Two Octocoral-Associated Bacteria, Endozoicomonas euniceicola EF212

    Chiou, Yu-Jing / Chen, Yu-Hsiang / Chiang, Pei-Wen / Chen, Hsing-Ju / Tang, Sen-Lin

    Microbiology resource announcements

    2022  Volume 12, Issue 1, Page(s) e0087722

    Abstract: Endozoicomonas euniceicola ... ...

    Abstract Endozoicomonas euniceicola EF212
    Language English
    Publishing date 2022-12-21
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/mra.00877-22
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Reciprocal transplant experiment reveals multiple factors influencing changes in coral microbial communities across climate zones.

    Chan, Ya-Fan / Chen, Yu-Hsiang / Yu, Sheng-Ping / Chen, Hsing-Ju / Nozawa, Yoko / Tang, Sen-Lin

    The Science of the total environment

    2023  Volume 907, Page(s) 167929

    Abstract: Previous studies have demonstrated the influence of external factors (environmental factors and the coral host factors) on the community structure of coral-associated bacteria. However, the internal factors, e.g. the interaction within the bacterial ... ...

    Abstract Previous studies have demonstrated the influence of external factors (environmental factors and the coral host factors) on the community structure of coral-associated bacteria. However, the internal factors, e.g. the interaction within the bacterial community or bacteria itself, have often been overlooked in studies of the coral microbiome. Hence, we performed a reciprocal transplant of corals between two different climate zones to examine the resultant alterations in coral-associated bacterial communities. The findings highlight the significance of environmental factors, host selection, and highly resilient bacteria in shaping the coral microbial composition. The results support that coral species consistently harbor specific predominant bacterial groups influenced by host selection, while locations display unique bacterial taxa due to environmental variations. The transplantation of corals into new environments leads to a gradual shift in the bacterial community, from initially resembling that of the native location to eventually resembling that of the transplanted location, emphasizing the crucial role of bacterial community composition for coral survival under changing ambient conditions. Furthermore, highly resilient bacteria that persisted throughout the reciprocal transplant experiment demonstrated their adaptability to environmental and host changes, suggesting the presence of robust adaptation or resistance mechanisms in bacterial communities. Genetic adaptations within the prevalent bacterial group, Endozoicomonas, were also observed, suggesting variations in resilience and adaptation capabilities among different phylotypes. This study highlights the need to conduct further investigations into the coral-associated bacteria themselves, as they may hold some key insights into understanding the dynamics of coral-associated microbial communities. These data also highlight some key species of coral-associated bacteria which could benefit coral in response to alterations in ambient environment.
    MeSH term(s) Animals ; Anthozoa/microbiology ; Microbiota ; Bacteria ; Climate ; Coral Reefs
    Language English
    Publishing date 2023-10-18
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 121506-1
    ISSN 1879-1026 ; 0048-9697
    ISSN (online) 1879-1026
    ISSN 0048-9697
    DOI 10.1016/j.scitotenv.2023.167929
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: The Novel Halovirus Hardycor1, and the Presence of Active (Induced) Proviruses in Four Haloarchaea

    Dyall-Smith, Mike / Pfeiffer, Friedhelm / Chiang, Pei-Wen / Tang, Sen-Lin

    Genes. 2021 Jan. 23, v. 12, no. 2

    2021  

    Abstract: The virus Hardycor1 was isolated in 1998 and infects the haloarchaeon Halorubrum coriense. DNA from a frozen stock (HC1) was sequenced and the viral genome found to be 45,142 bp of dsDNA, probably having redundant, circularly permuted termini. The genome ...

    Abstract The virus Hardycor1 was isolated in 1998 and infects the haloarchaeon Halorubrum coriense. DNA from a frozen stock (HC1) was sequenced and the viral genome found to be 45,142 bp of dsDNA, probably having redundant, circularly permuted termini. The genome showed little similarity (BLASTn) to known viruses. Only twenty-two of the 53 (41%) predicted proteins were significantly similar to sequences in the NCBI nr protein database (E-value ≤ 10⁻¹⁵). Six caudovirus-like proteins were encoded, including large subunit terminase (TerL), major capsid protein (Mcp) and tape measure protein (Tmp). Hardycor1 was predicted to be a siphovirus (VIRFAM). No close relationship to other viruses was found using phylogenetic tree reconstructions based on TerL and Mcp. Unexpectedly, the sequenced virus stock HC1 also revealed two induced proviruses of the host: a siphovirus (Humcor1) and a pleolipovirus (Humcor2). A re-examination of other similarly sequenced, archival virus stocks revealed induced proviruses of Haloferax volcanii, Haloferax gibbonsii and Haloarcula hispanica, three of which were pleolipoviruses. One provirus (Halfvol2) of Hfx. volcanii showed little similarity (BLASTn) to known viruses and probably represents a novel virus group. The attP sequences of many pleolipoproviruses were found to be embedded in a newly detected coding sequence, split in the provirus state, that spans between genes for integrase and a downstream CxxC-motif protein. This gene might play an important role in regulation of the temperate state.
    Keywords DNA ; Haloarcula ; Haloferax volcanii ; coat proteins ; databases ; genes ; integrases ; phylogeny ; proviruses ; terminase ; viral genome
    Language English
    Dates of publication 2021-0123
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 2527218-4
    ISSN 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes12020149
    Database NAL-Catalogue (AGRICOLA)

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  9. Article ; Online: Taxonomy based performance metrics for evaluating taxonomic assignment methods.

    Chen, Chung-Yen / Tang, Sen-Lin / Chou, Seng-Cho T

    BMC bioinformatics

    2019  Volume 20, Issue 1, Page(s) 310

    Abstract: Background: Metagenomics experiments often make inferences about microbial communities by sequencing 16S and 18S rRNA, and taxonomic assignment is a fundamental step in such studies. This paper addresses the weaknesses in two types of metrics commonly ... ...

    Abstract Background: Metagenomics experiments often make inferences about microbial communities by sequencing 16S and 18S rRNA, and taxonomic assignment is a fundamental step in such studies. This paper addresses the weaknesses in two types of metrics commonly used by previous studies for measuring the performance of existing taxonomic assignment methods: Sequence count based metrics and Binary error measurement. These metrics made performance evaluation results biased, less informative and mutually incomparable.
    Results: We investigated weaknesses in two types of metrics and proposed new performance metrics including Average Taxonomy Distance (ATD) and ATD_by_Taxa, together with the visualized ATD plot.
    Conclusions: By comparing the evaluation results from four popular taxonomic assignment methods across three test data sets, we found the new metrics more robust, informative and comparable.
    MeSH term(s) Bacteria/genetics ; Classification/methods ; Databases, Genetic ; Metagenomics/methods ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics
    Chemical Substances RNA, Ribosomal, 16S ; RNA, Ribosomal, 18S
    Language English
    Publishing date 2019-06-11
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041484-5
    ISSN 1471-2105 ; 1471-2105
    ISSN (online) 1471-2105
    ISSN 1471-2105
    DOI 10.1186/s12859-019-2896-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: IMPARO: inferring microbial interactions through parameter optimisation.

    Vidanaarachchi, Rajith / Shaw, Marnie / Tang, Sen-Lin / Halgamuge, Saman

    BMC molecular and cell biology

    2020  Volume 21, Issue Suppl 1, Page(s) 34

    Abstract: Background: Microbial Interaction Networks (MINs) provide important information for understanding bacterial communities. MINs can be inferred by examining microbial abundance profiles. Abundance profiles are often interpreted with the Lotka Volterra ... ...

    Abstract Background: Microbial Interaction Networks (MINs) provide important information for understanding bacterial communities. MINs can be inferred by examining microbial abundance profiles. Abundance profiles are often interpreted with the Lotka Volterra model in research. However existing research fails to consider a biologically meaningful underlying mathematical model for MINs or to address the possibility of multiple solutions.
    Results: In this paper we present IMPARO, a method for inferring microbial interactions through parameter optimisation. We use biologically meaningful models for both the abundance profile, as well as the MIN. We show how multiple MINs could be inferred with similar reconstructed abundance profile accuracy, and argue that a unique solution is not always satisfactory. Using our method, we successfully inferred clear interactions in the gut microbiome which have been previously observed in in-vitro experiments.
    Conclusions: IMPARO was used to successfully infer microbial interactions in human microbiome samples as well as in a varied set of simulated data. The work also highlights the importance of considering multiple solutions for MINs.
    MeSH term(s) Algorithms ; Bacteria/metabolism ; Data Accuracy ; Feces/microbiology ; Female ; Gastrointestinal Microbiome ; Healthy Volunteers ; Humans ; Male ; Microbial Interactions/physiology ; Models, Biological
    Language English
    Publishing date 2020-08-19
    Publishing country England
    Document type Journal Article
    ISSN 2661-8850
    ISSN (online) 2661-8850
    DOI 10.1186/s12860-020-00269-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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