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Fulltext Complete chloroplast genome of Boesenbergia rotunda and a comparative analysis with members of the family Zingiberaceae

Liew YJM, Chua KO, Yong HS, Song SL, Chan KG

Rev Bras Bot, 2022;45(4):1209-1222.
PMID: 36320930 DOI: 10.1007/s40415-022-00845-w

Boesenbergia rotunda (L.) Mansf. is a medically important ginger species of the family Zingiberaceae but its genomic information on molecular phylogeny and identification is scarce. In this work, the chloroplast genome of B. rotunda was sequenced, characterized and compared to the other Zingiberaceae species to provide chloroplast genetic resources and to determine its phylogenetic position in the family. The chloroplast genome of B. rotunda was 163,817 bp in length and consisted of a large single-copy (LSC) region of 88,302 bp, a small single-copy (SSC) region of 16,023 bp and a pair of inverted repeats (IRA and IRB) of 29,746 bp each. The chloroplast genome contained 113 unique genes, including 79 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosomal RNA (rRNA) genes. Several genes had atypical start codons, while most amino acids exhibited biased usage of synonymous codons. Comparative analyses with various chloroplast genomes of Zingiberaceae taxa revealed several highly variable regions (psbK-psbI, trnT-GGU-psbD, rbcL-accD, ndhF-rpl32, and ycf1) in the LSC and SSC regions in the chloroplast genome of B. rotunda that could be utilized as molecular markers for DNA barcoding and species delimitation. Phylogenetic analyses based on shared protein-coding genes revealed that B. rotunda formed a distinct lineage with B. kingii Mood & L.M.Prince, in a subclade that also contained the genera Kaempferia and Zingiber. These findings constitute the first chloroplast genome information of B. rotunda that could be a reference for phylogenetic analysis and identification of genus Boesenbergia within the Zingiberaceae family.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s40415-022-00845-w.
Core members and differential abundance of chrysomelid microbiota in the life stages of Podontiaaffinis (Galerucinae) and adult Silanafarinosa(Cassidinae, Coleoptera)

Song SL, Yong HS, Chua KO, Eamsobhana P, Lim PE, Chan KG

Biodivers Data J, 2022;10:e87459.
PMID: 36761655 DOI: 10.3897/BDJ.10.e87459

The chrysomelid beetlesPodontiaaffinis and Silanafarinosa are members of the subfamilies Galerucinae and Cassidinae, respectively. This study, based on 16S rRNA gene-targeted metagenomics sequencing, reports the core members and differential abundance of bacterial communities in the larvae and adult beetles of P.affinis and the adult S.farinosa. Cyanobacteria/Melainabacteria group was the predominant phylum in the larvae of P.affinis, while Proteobacteria was the predominant phylum in adult P.affinis and S.farinosa. The number of Order, Family, Genus and Species OTUs in the adult stage of P.affinis was higher than that in the larval stage. The bacterial species richness of adult P.affinis was significantly higher than that of adult S.farinosa. Betaproteobacteria was the predominant class in adult P.affinis, Cyanobacteria in the larvae of P.affinis and Gammaproteobacteria in S.farinosa. The larvae and adult beetles of P.affinis and adult S.farinosahad a low number of unique and shared bacterial OTUs (> 5% relative abundance). The differences in the microbiota indicate possible differences in nutrient assimilation, host taxonomy and other stochastic processes. These findings provide new information to our understanding of the bacteria associated with specialist phytophagous chrysomelid beetles and beetles in general.
Fulltext Dataset of core and differentially abundant bacteria in various compartments of farm-cultivated and home-planted chilli plants (Capsicum frutescens)

Song SL, Lew ZX, Yong HS, Lim QH, Chai RJ

Data Brief, 2024 Jun;54:110273.
PMID: 38962198 DOI: 10.1016/j.dib.2024.110273

Chillies are members of the genus Capsicum L. (family Solanaceae). They are native to Central and South America and consist of approximately 35 species [1,2]. Among these, five species (C. annuum L., C. baccatum L., C. chinense Jacq., C. frutescens L., and C. pubescens Ruiz & Pav.) have been domesticated and are mainly cultivated for consumption as vegetables and spices. Of the domesticated chillies, C. annuum is commercially cultivated worldwide, while C. frutescens and C. chinense are mainly cultivated in American, Asian, and African countries [3]. We compared the diversity of microbiota in various compartments of farm-cultivated (FC) and home-planted (HP) chilli plants (Capsicum frutescens). Targeted 16S rRNA gene (V5-V6 region) was sequenced using the Illumina NovaSeq 6000 platform. Proteobacteria, Actinobacteriota, Acidobacteriota, Gemmatimonadota, Bacteroidota, and Firmicutes were present in all compartments of both the FC and HP plants. Proteobacteria (or Pseudomonadota) was the predominant phylum in all the compartments of both HP and FC plants, while Actinobacteriota (or Actinomycetota) was the second most abundant phylum. Most plant compartments (leaves, fruits and roots) exhibited a higher relative abundance of Proteobacteria compared to the soil samples. With few exceptions, the soil compartments (bulk and rhizospheric soils) displayed a higher relative abundance of the phyla Myxococcota, Acidobacteriota, Gemmatimonadota, Bacteroidota, Nitrospirota, Verrucomicrobiota, and Firmicutes than the plant compartments. Diversity indices revealed that the bacterial community in chili plants clustered based on both compartment and cultivation area.
Fulltext Mitochondrial Genome Supports Sibling Species of Angiostrongylus costaricensis (Nematoda: Angiostrongylidae)

Yong HS, Song SL, Eamsobhana P, Goh SY, Lim PE, Chow WL, et al.

PLoS One, 2015;10(7):e0134581.
PMID: 26230642 DOI: 10.1371/journal.pone.0134581

Angiostrongylus costaricensis is a zoonotic parasitic nematode that causes abdominal or intestinal angiostrongyliasis in humans. It is endemic to the Americas. Although the mitochondrial genome of the Brazil taxon has been published, there is no available mitochondrial genome data on the Costa Rica taxon. We report here the complete mitochondrial genome of the Costa Rica taxon and its genetic differentiation from the Brazil taxon. The whole mitochondrial genome was obtained from next-generation sequencing of genomic DNA. It had a total length of 13,652 bp, comprising 36 genes (12 protein-coding genes-PCGs, 2 rRNA and 22 tRNA genes) and a control region (A + T rich non-coding region). It is longer than that of the Brazil taxon (13,585 bp). The larger mitogenome size of the Costa Rica taxon is due to the size of the control region as the Brazil taxon has a shorter length (265 bp) than the Costa Rica taxon (318 bp). The size of 6 PCGs and the start codon for ATP6, CYTB and NAD5 genes are different between the Costa Rica and Brazil taxa. Additionally, the two taxa differ in the stop codon of 6 PCGs. Molecular phylogeny based on 12 PCGs was concordant with two rRNA, 22 tRNA and 36 mitochondrial genes. The two taxa have a genetic distance of p = 16.2% based on 12 PCGs, p = 15.3% based on 36 mitochondrial genes, p = 13.1% based on 2 rRNA genes and p = 10.7% based on 22 tRNA genes, indicating status of sibling species. The Costa Rica and Brazil taxa of A. costaricensis are proposed to be accorded specific status as members of a species complex.
Identification of AKT1 3'UTR variants in two Indian schizophrenia patients with poor executive functioning

Chow TJ, Tee SF, Loh SY, Yong HS, Abu Bakar AK, Song SL, et al.

Asian J Psychiatr, 2018 Aug;36:17-18.
PMID: 29864676 DOI: 10.1016/j.ajp.2018.05.025
Oecophyllibacter saccharovorans gen. nov. sp. nov., a bacterial symbiont of the weaver ant Oecophylla smaragdina

Chua KO, See-Too WS, Tan JY, Song SL, Yong HS, Yin WF, et al.

J Microbiol, 2020 Dec;58(12):988-997.
PMID: 33095388 DOI: 10.1007/s12275-020-0325-8

In this study, bacterial strains Ha5T, Ta1, and Jb2 were isolated from different colonies of weaver ant Oecophylla smaragdina. They were identified as bacterial symbionts of the ant belonging to family Acetobacteraceae and were distinguished as different strains based on distinctive random-amplified polymorphic DNA (RAPD) fingerprints. Cells of these bacterial strains were Gram-negative, rod-shaped, aerobic, non-motile, catalase-positive and oxidase-negative. They were able to grow at 15-37°C (optimum, 28-30°C) and in the presence of 0-1.5% (w/v) NaCl (optimum 0%). Their predominant cellular fatty acids were C18:1ω7c, C16:0, C19:0ω8c cyclo, C14:0, and C16:0 2-OH. Strains Ha5T, Ta1, and Jb2 shared highest 16S rRNA gene sequence similarity (94.56-94.63%) with Neokomagataea tanensis NBRC106556T of family Acetobacteraceae. Both 16S rRNA gene sequence-based phylogenetic analysis and core gene-based phylogenomic analysis placed them in a distinct lineage in family Acetobacteraceae. These bacterial strains shared higher than species level thresholds in multiple overall genome-relatedness indices which indicated that they belonged to the same species. In addition, they did not belong to any of the current taxa of Acetobacteraceae as they had low pairwise average nucleotide identity (< 71%), in silico DNA-DNA hybridization (< 38%) and average amino acid identity (< 67%) values with all the type members of the family. Based on these results, bacterial strains Ha5T, Ta1, and Jb2 represent a novel species of a novel genus in family Acetobacteaceae, for which we propose the name Oecophyllibacter saccharovorans gen. nov. sp. nov., and strain Ha5T as the type strain.
Fulltext Complete mitochondrial genomes and phylogenetic relationships of the genera Nephila and Trichonephila (Araneae, Araneoidea)

Yong HS, Song SL, Chua KO, Wayan Suana I, Eamsobhana P, Tan J, et al.

Sci Rep, 2021 May 21;11(1):10680.
PMID: 34021208 DOI: 10.1038/s41598-021-90162-1

Spiders of the genera Nephila and Trichonephila are large orb-weaving spiders. In view of the lack of study on the mitogenome of these genera, and the conflicting systematic status, we sequenced (by next generation sequencing) and annotated the complete mitogenomes of N. pilipes, T. antipodiana and T. vitiana (previously N. vitiana) to determine their features and phylogenetic relationship. Most of the tRNAs have aberrant clover-leaf secondary structure. Based on 13 protein-coding genes (PCGs) and 15 mitochondrial genes (13 PCGs and two rRNA genes), Nephila and Trichonephila form a clade distinctly separated from the other araneid subfamilies/genera. T. antipodiana forms a lineage with T. vitiana in the subclade containing also T. clavata, while N. pilipes forms a sister clade to Trichonephila. The taxon vitiana is therefore a member of the genus Trichonephila and not Nephila as currently recognized. Studies on the mitogenomes of other Nephila and Trichonephila species and related taxa are needed to provide a potentially more robust phylogeny and systematics.
Fulltext Fecal Calprotectin in Parkinson's Disease and Multiple System Atrophy

Hor JW, Lim SY, Khor ES, Chong KK, Song SL, Ibrahim NM, et al.

J Mov Disord, 2021 Dec 24.
PMID: 34937162 DOI: 10.14802/jmd.21085

Objective: Converging evidence suggests that intestinal inflammation is involved in the pathogenesis of neurodegenerative diseases. Previous studies on fecal calprotectin in Parkinson's disease (PD) were limited by small sample sizes, and literature regarding intestinal inflammation in multiple system atrophy (MSA) is very scarce. We investigated the levels of fecal calprotectin, a marker of intestinal inflammation, in PD and MSA.
Methods: We recruited 169 subjects (71 PD, 38 MSA, and 60 age-similar nonneurological controls). Clinico-demographic data were collected. PD and MSA were subtyped and the severity assessed using the MDS-UPDRS and UMSARS, respectively. Fecal calprotectin and blood immune markers were analyzed.
Results: Compared to controls (median: 35.7 [IQR: 114.2] μg/g), fecal calprotectin was significantly elevated in PD (median: 95.6 [IQR: 162.1] μg/g, p = 0.003) and even higher in MSA (median: 129.5 [IQR: 373.8] μg/g, p = 0.002). A significant interaction effect with age was observed; between-group differences were significant only in older subjects (i.e., ≥ 61 years) and became more apparent with increasing age. A total of 28.9% of MSA and 18.3% of PD patients had highly abnormal fecal calprotectin levels (≥ 250 μg/g); however, this difference was only significant for MSA compared to controls. Fecal calprotectin correlated moderately with selected blood immune markers in PD, but not with clinical features of PD or MSA.
Conclusions: Elevated fecal calprotectin suggests a role for intestinal inflammation in PD and MSA. A more complete understanding of gut immune alterations could open up new avenues of research and treatment for these debilitating diseases.
Altered gut microbiome and metabolome in patients with multiple system atrophy

Tan AH, Chong CW, Song SL, Teh CSJ, Yap IKS, Loke MF, et al.

Mov Disord, 2018 01;33(1):174-176.
PMID: 29083071 DOI: 10.1002/mds.27203
Gut Microbial Ecosystem in Parkinson Disease: New Clinicobiological Insights from Multi-Omics

Tan AH, Chong CW, Lim SY, Yap IKS, Teh CSJ, Loke MF, et al.

Ann Neurol, 2021 03;89(3):546-559.
PMID: 33274480 DOI: 10.1002/ana.25982

OBJECTIVE: Gut microbiome alterations in Parkinson disease (PD) have been reported repeatedly, but their functional relevance remains unclear. Fecal metabolomics, which provide a functional readout of microbial activity, have scarcely been investigated. We investigated fecal microbiome and metabolome alterations in PD, and their clinical relevance.
METHODS: Two hundred subjects (104 patients, 96 controls) underwent extensive clinical phenotyping. Stool samples were analyzed using 16S rRNA gene sequencing. Fecal metabolomics were performed using two platforms, nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography-mass spectrometry.
RESULTS: Fecal microbiome and metabolome composition in PD was significantly different from controls, with the largest effect size seen in NMR-based metabolome. Microbiome and NMR-based metabolome compositional differences remained significant after comprehensive confounder analyses. Differentially abundant fecal metabolite features and predicted functional changes in PD versus controls included bioactive molecules with putative neuroprotective effects (eg, short chain fatty acids [SCFAs], ubiquinones, and salicylate) and other compounds increasingly implicated in neurodegeneration (eg, ceramides, sphingosine, and trimethylamine N-oxide). In the PD group, cognitive impairment, low body mass index (BMI), frailty, constipation, and low physical activity were associated with fecal metabolome compositional differences. Notably, low SCFAs in PD were significantly associated with poorer cognition and low BMI. Lower butyrate levels correlated with worse postural instability-gait disorder scores.
INTERPRETATION: Gut microbial function is altered in PD, characterized by differentially abundant metabolic features that provide important biological insights into gut-brain pathophysiology. Their clinical relevance further supports a role for microbial metabolites as potential targets for the development of new biomarkers and therapies in PD. ANN NEUROL 2021;89:546-559.