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2. The Role of Human Gut Microbe Ruminococcus gnavus in Inflammatory Diseases

Author

Kandasamy, Sasmitra, primary, Letchumanan, Vengadesh, additional, Hong, Kar Wai, additional, Chua, Kah-Ooi, additional, Ab Mutalib, Nurul Syakima, additional, Ng, Alvin Lai Oon, additional, Ming, Long Chiau, additional, Lim, Hui Xuan, additional, Thurairajasingam, Sivakumar, additional, Law, Jodi Woan-Fei, additional, and Tan, Loh Teng-Hern, additional

Published
2023
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6. Migratory behaviour is positively associated with genetic diversity in butterflies

Author

Aurora García‐Berro, Venkat Talla, Roger Vila, Hong Kar Wai, Daria Shipilina, Kok Gan Chan, Naomi E. Pierce, Niclas Backström, Gerard Talavera, National Geographic Society, Ministerio de Ciencia e Innovación (España), Museum of Comparative Zoology (US), Generalitat de Catalunya, University of Malaya, Swedish Collegium for Advanced Study, and Swedish Research Council

Subjects
demography, Evolutionary Biology, insect migration, Outbreaks, migratory connectivity, genetic diversity, population bottlenecks, Genetic diversity, Evolutionsbiologi, Migratory connectivity, Effective population size, outbreaks, Population bottlenecks, PSMC, Vanessa cardui, Genetics, effective population size, Insect migration, Ecology, Evolution, Behavior and Systematics, Demography
Abstract

Migration is typically associated with risk and uncertainty at the population level, but little is known about its cost¿benefit trade-offs at the species level. Migratory insects in particular often exhibit strong demographic fluctuations due to local bottlenecks and outbreaks. Here, we use genomic data to investigate levels of heterozygosity and long-term population size dynamics in migratory insects, as an alternative to classical local and short-term approaches such as regional field monitoring. We analyse whole-genome sequences from 97 Lepidoptera species and show that individuals of migratory species have significantly higher levels of genome-wide heterozygosity, a proxy for effective population size, than do nonmigratory species. Also, we contribute whole-genome data for one of the most emblematic insect migratory species, the painted lady butterfly (Vanessa cardui), sampled across its worldwide distributional range. This species exhibits one of the highest levels of genomic heterozygosity described in Lepidoptera (2.95 ± 0.15%). Coalescent modelling (PSMC) shows historical demographic stability in V. cardui, and high effective population size estimates of 2 -20 million individuals 10,000 years ago. The study reveals that the high risks associated with migration and local environmental fluctuations do not seem to decrease overall genetic diversity and demographic stability in migratory Lepidoptera. We propose a "compensatory" demographic model for migratory r-strategist organisms in which local bottlenecks are counterbalanced by reproductive success elsewhere within their typically large distributional ranges. Our findings highlight that the boundaries of populations are substantially different for sedentary and migratory insects, and that, in the latter, local and even regional field monitoring results may not reflect whole population dynamics. Genomic diversity patterns may elucidate key aspects of an insect's migratory nature and population dynamics at large spatiotemporal scales., This work was funded by the National Geographic Society (grant WW1-300R-18) and by the grant PID2020-117739GA-I00 from MCIN/AEI/10.13039/501100011033 to G.T., by fellowship FPU19/01593 to A.G.-B., by project LINKA20399 from the CSIC i-LINK-2021 programme to G.T., N.E.P., R.V. and N.B., by grants from the Putnam Expeditionary Fund of the Museum of Comparative Zoology to G.T. and N.E.P., by projects PID2019-107078GB-I00/MCIN/AEI/10.13039/501100011033 and 2017-SGR-991 (Generalitat de Catalunya) to R.V. and G.T., by the University of Malaya (grant H50001-A-000027) to K.G.C., by the Swedish Collegium for Advanced Science (SCAS; Natural Sciences Programme, Knut and Alice Wallenberg Foundation, Postdoc funding) to D.S., by NSF grant DEB-1541560 to N.E.P., and by the Swedish Research Council FORMAS (grant 2019-00670) to N.B., G.T. and R.V., 1 INTRODUCTION2 MATERIALS AND METHODS2.1 Heterozygosity estimates2.2 Behavioural scoring2.3 Comparative analyses2.4 Vanessa cardui sampling and sequencing2.5 Vanessa cardui reference-based assemblies2.6 Vanessa cardui demographic inference3 RESULTS3.1 Heterozygosity rates in Lepidoptera3.2 Vanessa cardui demographic history4 DISCUSSION4.1 Genomic heterozygosity, effective population size and migration4.2 Short-term migratory cost but long-term demographic stability4.3 Delimiting populations in migratory insect speciesAUTHOR CONTRIBUTIONSACKNOWLEDGEMENTSCONFLICT OF INTEREST

Published
2022

15. Additional file 6 of Bacterial microbiome of faecal samples of naked mole-rat collected from the toilet chamber

Author

Chua, Kah-Ooi, Fatima, Iqra, Lau, Yin Yin, Hong, Kar Wai, Yin, Wai-Fong, Mardaryev, Andrei, Chan, Kok-Gan, and Chang, Chien-Yi

Subjects
fluids and secretions
Abstract

Additional file 6: Figure S3. The bacterial microbiomes of faecal samples from wild individual NMRs and the toilet chamber of a laboratory NMR colony. Barplot showing the relative abundance of bacterial taxa at the rank of family.

Published
2022
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16. Additional file 5 of Bacterial microbiome of faecal samples of naked mole-rat collected from the toilet chamber

Author

Chua, Kah-Ooi, Fatima, Iqra, Lau, Yin Yin, Hong, Kar Wai, Yin, Wai-Fong, Mardaryev, Andrei, Chan, Kok-Gan, and Chang, Chien-Yi

Subjects
fluids and secretions
Abstract

Additional file 5: Figure S2. The bacterial microbiomes of faecal samples from wild individual NMRs and the toilet chamber of a laboratory NMR colony. Barplot showing the relative abundance of bacterial taxa at the rank of phylum.

Published
2022
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18. Additional file 4 of Bacterial microbiome of faecal samples of naked mole-rat collected from the toilet chamber

Author

Chua, Kah-Ooi, Fatima, Iqra, Lau, Yin Yin, Hong, Kar Wai, Yin, Wai-Fong, Mardaryev, Andrei, Chan, Kok-Gan, and Chang, Chien-Yi

Abstract

Additional file 4: Table S3. The number of 16S rRNA gene sequences in the bacterial microbiomes of faecal samples from wild individual NMRs and the toilet chamber of a laboratory NMR colony. The data for wild NMRs were obtained from previous studies (1. Debebe T, Biagi E, Soverini M, Holtze S, Hildebrandt TB, Birkemeyer C, et al. Unraveling the gut microbiome of the long-lived naked mole-rat. Sci Rep. 2017;7(1):1���9).

Published
2022
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19. Additional file 1 of Bacterial microbiome of faecal samples of naked mole-rat collected from the toilet chamber

Author

Chua, Kah-Ooi, Fatima, Iqra, Lau, Yin Yin, Hong, Kar Wai, Yin, Wai-Fong, Mardaryev, Andrei, Chan, Kok-Gan, and Chang, Chien-Yi

Subjects
fluids and secretions, digestive system diseases
Abstract

Additional file 1: Table S1. 16S rRNA gene sequences of bacteria in the microbiome of the faecal samples from the toilet chamber of the laboratory NMR colony.

Published
2022
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21. Insight in the quorum sensing-driven lifestyle of the non-pathogenic Agrobacterium tumefaciens 6N2 and the interactions with the yeast Meyerozyma guilliermondii

Author

Bertini, Elisa Violeta, primary, Torres, Mariela Analía, additional, Léger, Thibaut, additional, Garcia, Camille, additional, Hong, Kar-Wai, additional, Chong, Teik Min, additional, Castellanos de Figueroa, Lucía I., additional, Chan, Kok-Gan, additional, Dessaux, Yves, additional, Camadro, Jean-Michel, additional, and Nieto-Peñalver, Carlos Gabriel, additional

Published
2021
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22. Genome-wide mapping of the RNA targets of the Pseudomonas aeruginosa riboregulatory protein RsmN

Author

Romero, Manuel, Silistre, Hazel, Lovelock, Laura, Wright, Victoria J, Chan, Kok-Gan, Hong, Kar-Wai, Williams, Paul, Cámara, Miguel, and Heeb, Stephan

Subjects
Alginates, Polysaccharides, Bacterial, RNA-Binding Proteins, Gene Expression Regulation, Bacterial, Type VI Secretion Systems, Regulon, Repressor Proteins, Bacterial Proteins, Pseudomonas aeruginosa, RNA and RNA-protein complexes, RNA, Small Untranslated, RNA, Messenger, Cyclic GMP, Genome, Bacterial
Abstract

Pseudomonads typically carry multiple non-identical alleles of the post-transcriptional regulator rsmA. In Pseudomonas aeruginosa, RsmN is notable in that its structural rearrangement confers distinct and overlapping functions with RsmA. However, little is known about the specificities of RsmN for its target RNAs and overall impact on the biology of this pathogen. We purified and mapped 503 transcripts directly bound by RsmN in P. aeruginosa. About 200 of the mRNAs identified encode proteins of demonstrated function including some determining acute and chronic virulence traits. For example, RsmN reduces biofilm development both directly and indirectly via multiple pathways, involving control of Pel exopolysaccharide biosynthesis and c-di-GMP levels. The RsmN targets identified are also shared with RsmA, although deletion of rsmN generally results in less pronounced phenotypes than those observed for ΔrsmA or ΔrsmArsmNind mutants, probably as a consequence of different binding affinities. Targets newly identified for the Rsm system include the small non-coding RNA CrcZ involved in carbon catabolite repression, for which differential binding of RsmN and RsmA to specific CrcZ regions is demonstrated. The results presented here provide new insights into the intricacy of riboregulatory networks involving multiple but distinct RsmA homologues.

Published
2018

23. Genome-Wide Analysis of Targets for Post-Transcriptional Regulation by Rsm Proteins in Pseudomonas putida

Author

Huertas-Rosales, Óscar, primary, Romero, Manuel, additional, Chan, Kok-Gan, additional, Hong, Kar-Wai, additional, Cámara, Miguel, additional, Heeb, Stephan, additional, Barrientos-Moreno, Laura, additional, Molina-Henares, María Antonia, additional, Travieso, María L., additional, Ramos-González, María Isabel, additional, and Espinosa-Urgel, Manuel, additional

Published
2021
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25. Seasonal adaptations of the hypothalamo-neurohypophyseal system of the dromedary camel

Author

Alim, Fatma Zohra Djazouli, primary, Romanova, Elena V., additional, Tay, Yea-Ling, additional, Rahman, Ahmad Yamin bin Abdul, additional, Chan, Kok-Gan, additional, Hong, Kar-Wai, additional, Rogers, Mark, additional, Southey, Bruce R., additional, Greenwood, Michael P., additional, Mecawi, Andre Souza, additional, Mustafa, Mohammad Rais, additional, Mahy, Nicole, additional, Campbell, Colin, additional, Antunes-Rodrigues, José, additional, Sweedler, Jonathan V., additional, Murphy, David, additional, and Hindmarch, Charles C. T., additional

Published
2019
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28. Insights of biosurfactant producing Serratia marcescens strain W2.3 isolated from diseased tilapia fish: a draft genome analysis

Author

Chan, Xin Yue, Chang, Chien Yi, Hong, Kar Wai, Tee, Kok Keng, Yin, Wai Fong, and Chan, Kok Gan

Subjects
Nucleotide sequencing -- Research -- Genetic aspects, Virulence (Microbiology) -- Genetic aspects -- Research, Gene expression -- Genetic aspects -- Research, Nocardia corallina -- Research, DNA sequencing -- Research -- Genetic aspects, Genetic transcription -- Research -- Genetic aspects, Tilapia -- Genetic aspects -- Research
Abstract

Background Serratia marcescens is an opportunistic bacterial pathogen with broad range of host ranging from vertebrates, invertebrates and plants. S. marcescens strain W2.3 was isolated from a diseased tilapia fish and it was suspected to be the causal agent for the fish disease as virulence genes were found within its genome. In this study, for the first time, the genome sequences of S. marcescens strain W2.3 were sequenced using the Illumina MiSeq platform. Result Several virulent factors of S. marcescens such as serrawettin, a biosurfactant, has been reported to be regulated by N-acyl homoserine lactone (AHL)-based quorum sensing (QS). In our previous studies, an unusual AHL with long acyl side chain was detected from this isolate suggesting the possibility of novel virulence factors regulation. This evokes our interest in the genome of this bacterial strain and hereby we present the draft genome of S. marcescens W2.3, which carries the serrawettin production gene, swrA and the AHL-based QS transcriptional regulator gene, luxR which is an orphan luxR. Conclusion With the availability of the whole genome sequences of S. marcescens W2.3, this will pave the way for the study of the QS-mediated genes expression in this bacterium. Keywords: Serratia marcescens, Biosurfactant, Serrawettin, Quorum sensing, N-acyl homoserine lactone, swrA, Next generation sequencing technology, Author(s): Xin Yue Chan[sup.1] , Chien Yi Chang[sup.2,3] , Kar Wai Hong[sup.1] , Kok Keng Tee[sup.4] , Wai Fong Yin[sup.1] and Kok Gan Chan[sup.1,2,5] Background Serratia marcescens is common microorganism [...]

Published
2013
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29. The complete genome sequence of Ensifer meliloti strain CCMM B554 (FSM-MA), a highly effective nitrogen-fixing microsymbiont of Medicago truncatula Gaertn

Author

Nagymihály, Marianna, primary, Vásarhelyi, Bálint M., additional, Barrière, Quentin, additional, Chong, Teik-Min, additional, Bálint, Balázs, additional, Bihari, Péter, additional, Hong, Kar-Wai, additional, Horváth, Balázs, additional, Ibijbijen, Jamal, additional, Amar, Mohammed, additional, Farkas, Attila, additional, Kondorosi, Éva, additional, Chan, Kok-Gan, additional, Gruber, Véronique, additional, Ratet, Pascal, additional, Mergaert, Peter, additional, and Kereszt, Attila, additional

Published
2017
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45. Insights of biosurfactant producing Serratia marcescens strain W2.3 isolated from diseased tilapia fish: a draft genome analysis

Author

Chan, Xin Yue, Chang, Chien Yi, Hong, Kar Wai, Tee, Kok Keng, Yin, Wai Fong, Chan, Kok Gan, Chan, Xin Yue, Chang, Chien Yi, Hong, Kar Wai, Tee, Kok Keng, Yin, Wai Fong, and Chan, Kok Gan

Abstract

Background Serratia marcescens is an opportunistic bacterial pathogen with broad range of host ranging from vertebrates, invertebrates and plants. S. marcescens strain W2.3 was isolated from a diseased tilapia fish and it was suspected to be the causal agent for the fish disease as virulence genes were found within its genome. In this study, for the first time, the genome sequences of S. marcescens strain W2.3 were sequenced using the Illumina MiSeq platform. Result Several virulent factors of S. marcescens such as serrawettin, a biosurfactant, has been reported to be regulated by N-acyl homoserine lactone (AHL)-based quorum sensing (QS). In our previous studies, an unusual AHL with long acyl side chain was detected from this isolate suggesting the possibility of novel virulence factors regulation. This evokes our interest in the genome of this bacterial strain and hereby we present the draft genome of S. marcescens W2.3, which carries the serrawettin production gene, swrA and the AHL-based QS transcriptional regulator gene, luxR which is an orphan luxR. Conclusion With the availability of the whole genome sequences of S. marcescens W2.3, this will pave the way for the study of the QS-mediated genes expression in this bacterium.

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46. Insights of biosurfactant producing Serratia marcescens strain W2.3 isolated from diseased tilapia fish: a draft genome analysis

Author

Chan, Xin Yue, Chang, Chien Yi, Hong, Kar Wai, Tee, Kok Keng, Yin, Wai Fong, Chan, Kok Gan, Chan, Xin Yue, Chang, Chien Yi, Hong, Kar Wai, Tee, Kok Keng, Yin, Wai Fong, and Chan, Kok Gan

Abstract

Background Serratia marcescens is an opportunistic bacterial pathogen with broad range of host ranging from vertebrates, invertebrates and plants. S. marcescens strain W2.3 was isolated from a diseased tilapia fish and it was suspected to be the causal agent for the fish disease as virulence genes were found within its genome. In this study, for the first time, the genome sequences of S. marcescens strain W2.3 were sequenced using the Illumina MiSeq platform. Result Several virulent factors of S. marcescens such as serrawettin, a biosurfactant, has been reported to be regulated by N-acyl homoserine lactone (AHL)-based quorum sensing (QS). In our previous studies, an unusual AHL with long acyl side chain was detected from this isolate suggesting the possibility of novel virulence factors regulation. This evokes our interest in the genome of this bacterial strain and hereby we present the draft genome of S. marcescens W2.3, which carries the serrawettin production gene, swrA and the AHL-based QS transcriptional regulator gene, luxR which is an orphan luxR. Conclusion With the availability of the whole genome sequences of S. marcescens W2.3, this will pave the way for the study of the QS-mediated genes expression in this bacterium.

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47. Insights of biosurfactant producing Serratia marcescens strain W2.3 isolated from diseased tilapia fish: a draft genome analysis

Author

Chan, Xin Yue, Chang, Chien Yi, Hong, Kar Wai, Tee, Kok Keng, Yin, Wai Fong, Chan, Kok Gan, Chan, Xin Yue, Chang, Chien Yi, Hong, Kar Wai, Tee, Kok Keng, Yin, Wai Fong, and Chan, Kok Gan

Abstract

Background Serratia marcescens is an opportunistic bacterial pathogen with broad range of host ranging from vertebrates, invertebrates and plants. S. marcescens strain W2.3 was isolated from a diseased tilapia fish and it was suspected to be the causal agent for the fish disease as virulence genes were found within its genome. In this study, for the first time, the genome sequences of S. marcescens strain W2.3 were sequenced using the Illumina MiSeq platform. Result Several virulent factors of S. marcescens such as serrawettin, a biosurfactant, has been reported to be regulated by N-acyl homoserine lactone (AHL)-based quorum sensing (QS). In our previous studies, an unusual AHL with long acyl side chain was detected from this isolate suggesting the possibility of novel virulence factors regulation. This evokes our interest in the genome of this bacterial strain and hereby we present the draft genome of S. marcescens W2.3, which carries the serrawettin production gene, swrA and the AHL-based QS transcriptional regulator gene, luxR which is an orphan luxR. Conclusion With the availability of the whole genome sequences of S. marcescens W2.3, this will pave the way for the study of the QS-mediated genes expression in this bacterium.

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48. Insights of biosurfactant producing Serratia marcescens strain W2.3 isolated from diseased tilapia fish: a draft genome analysis

Author

Chan, Xin Yue, Chang, Chien Yi, Hong, Kar Wai, Tee, Kok Keng, Yin, Wai Fong, Chan, Kok Gan, Chan, Xin Yue, Chang, Chien Yi, Hong, Kar Wai, Tee, Kok Keng, Yin, Wai Fong, and Chan, Kok Gan

Abstract

Background Serratia marcescens is an opportunistic bacterial pathogen with broad range of host ranging from vertebrates, invertebrates and plants. S. marcescens strain W2.3 was isolated from a diseased tilapia fish and it was suspected to be the causal agent for the fish disease as virulence genes were found within its genome. In this study, for the first time, the genome sequences of S. marcescens strain W2.3 were sequenced using the Illumina MiSeq platform. Result Several virulent factors of S. marcescens such as serrawettin, a biosurfactant, has been reported to be regulated by N-acyl homoserine lactone (AHL)-based quorum sensing (QS). In our previous studies, an unusual AHL with long acyl side chain was detected from this isolate suggesting the possibility of novel virulence factors regulation. This evokes our interest in the genome of this bacterial strain and hereby we present the draft genome of S. marcescens W2.3, which carries the serrawettin production gene, swrA and the AHL-based QS transcriptional regulator gene, luxR which is an orphan luxR. Conclusion With the availability of the whole genome sequences of S. marcescens W2.3, this will pave the way for the study of the QS-mediated genes expression in this bacterium.

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49. Insights of biosurfactant producing Serratia marcescens strain W2.3 isolated from diseased tilapia fish: a draft genome analysis

Author

Chan, Xin Yue, Chang, Chien Yi, Hong, Kar Wai, Tee, Kok Keng, Yin, Wai Fong, Chan, Kok Gan, Chan, Xin Yue, Chang, Chien Yi, Hong, Kar Wai, Tee, Kok Keng, Yin, Wai Fong, and Chan, Kok Gan

Abstract

Background Serratia marcescens is an opportunistic bacterial pathogen with broad range of host ranging from vertebrates, invertebrates and plants. S. marcescens strain W2.3 was isolated from a diseased tilapia fish and it was suspected to be the causal agent for the fish disease as virulence genes were found within its genome. In this study, for the first time, the genome sequences of S. marcescens strain W2.3 were sequenced using the Illumina MiSeq platform. Result Several virulent factors of S. marcescens such as serrawettin, a biosurfactant, has been reported to be regulated by N-acyl homoserine lactone (AHL)-based quorum sensing (QS). In our previous studies, an unusual AHL with long acyl side chain was detected from this isolate suggesting the possibility of novel virulence factors regulation. This evokes our interest in the genome of this bacterial strain and hereby we present the draft genome of S. marcescens W2.3, which carries the serrawettin production gene, swrA and the AHL-based QS transcriptional regulator gene, luxR which is an orphan luxR. Conclusion With the availability of the whole genome sequences of S. marcescens W2.3, this will pave the way for the study of the QS-mediated genes expression in this bacterium.

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50. Whole genome sequencing enables the characterization of BurI, a LuxI homologue of Burkholderia cepacia strain GG4.

Author

How KY, Hong KW, and Chan KG

Abstract

Quorum sensing is a mechanism for regulating proteobacterial gene expression in response to changes in cell population. In proteobacteria, N-acyl homoserine lactone (AHL) appears to be the most widely used signalling molecules in mediating, among others, the production of extracellular virulence factors for survival. In this work, the genome of B. cepacia strain GG4, a plasmid-free strain capable of AHL synthesis was explored. In silico analysis of the 6.6 Mb complete genome revealed the presence of a LuxI homologue which correspond to Type I quorum sensing. Here, we report the molecular cloning and characterization of this LuxI homologue, designated as BurI. This 609 bp gene was cloned and overexpressed in Escherichia coli BL21(DE3). The purified protein was approximately 25 kDa and is highly similar to several autoinducer proteins of the LuxI family among Burkholderia species. To verify the AHL synthesis activity of this protein, high resolution liquid chromatography-mass spectrometry analysis revealed the production of 3-oxo-hexanoylhomoserine lactone, N-octanoylhomoserine lactone and 3-hydroxy-octanoylhomoserine lactone from induced E. coli BL21 harboring the recombinant BurI. Our data show, for the first time, the cloning and characterization of the LuxI homologue from B. cepacia strain GG4 and confirmation of its AHL synthesis activity.

Published
2015
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