Due to the issues of species substitution and product mislabelling of beche-de-mer worldwide, this study aimed to identify the species of seven gamat-based beche-de-mer specimens from Kuah, Langkawi Island, Kedah, Malaysia based on ossicle shapes and non-protein-coding 12S mitochondrial rRNA gene sequences. In general, ossicles were well extracted from the specimens. At least eight ossicle shapes were observed i.e. large I-shaped rod, perforated plate, table, C-shaped rod, button, rosette, I-shaped rod and X-shaped rod. Except for button, I-shaped rod and X-shaped rod, the other five ossicle shapes are common in Stichopus horrens. However, the species status could not be resolved at this level due to the presence of uncommon ossicle shapes and the physical features of the specimens could not be used as supporting data as they were different from the live or unprocessed sea cucumber. In this study, 12S mitochondrial rRNA gene sequences were analysed using the Basic Local Alignment Search Tool programme for Nucleotides (blastn), resulting in the species identification of the beche-de-mer specimens as S. horrens, known locally as gamat emas (golden sea cucumber) with 96-99% similarity (an average of 98%). The phylogenetic trees based on the Neighbour-Joining method, Maximum Parsimony method and Maximum Likelihood method indicated that all 12S mitochondrial rRNA gene sequences of the beche-de-mer specimens clustered with the reference samples of S. horrens from Pangkor Laut, Pangkor Island, Perak, Malaysia, supporting the BLASTN results and confirming their species status as S. horrens. Furthermore, 10 partial 12S mitochondrial rRNA gene sequences of the reference samples and the beche-de-mer specimens of S. horrens were registered with the GenBank (Accession No.: KX879628-KX879637). Overall, the findings suggested that the species identification of the beche-de-mer specimens using 12S mitochondrial rRNA gene sequence gave better inference than ossicle-shape identification. The outcomes of this study benefit enforcement agencies in their work of monitoring and overcoming the issues of species substitution and product mislabelling of beche-de-mer or commercial dried sea cucumber in Malaysian markets as well as in global markets. � Universiti Putra Malaysia Press.

A few studies on the presence of microbes and their association in sea cucumbers can be found to date, especially in Apostichopus japonicus. However, such studies on Malaysian sea cucumbers and in the gastrointestines of the echinoderms are still lacking. Therefore, the aims of this study are to isolate and identify associated bacteria in the gastrointestines of two common species of Malaysian sea cucumbers i.e. Holothuria (Mertensiothuria) leucospilota (Brandt, 1835), the most dominant sea cucumber species in Malaysia, and Stichopus horrens Selenka, 1867, the commercial gamat species. A number of six genera of Gram-positive bacteria representing the order Bacillales and the order Micrococcales i.e. Bacillus, Brevibacillus, Lysinibacillus, Staphylococcus, Dermacoccus and Micrococcus are isolated from the gastrointestines of H. leucospilota, as suggested by the phylogenetic trees of partial 16S rRNA gene sequences. Meanwhile, three genera of Gram-positive bacteria that represent the order Bacillales i.e. Bacillus, Brevibacillus and Lysinibacillus are isolated from the gastrointestines of S. horrens. Interestingly, 60% of the bacterial species have been known to contain commercial potentials mainly as antibiotic producers, and only bacteria with commercial potentials were present in the gastrointestines of S. horrens. In contrast to that, bacteria that could be pathogenic were also present in the gastrointestines of H. leucospilota. The presence of all bacteria that have been known to contain commercial potentials in the gastrointestines of S. horrens and more diverse microbial population in H. leucospilota could be due to the higher level of antimicrobial properties in the gastrointestines of S. horrens. However, experiments on antibacterial properties of the isolates have to be done and those proven to contain commercial potential can be exploited towards the development of industrial applications in Malaysia. � Universiti Putra Malaysia Press.

Holothuria (Mertensiothuria) leucospilota is the most abundant sea cucumber species in Malaysia. This study aimed to identify bacteria isolated from the external and internal body parts of H. leucospilota collected from the coastal water of Pangkor Island, Perak, Malaysia. A total of 26 bacterial samples were isolated using streak plate method from eight body parts of two fresh H. leucospilota specimens and from the surrounding surface sediments and seawater. Identification of the bacterial isolates was based on microscopic examination, 16S rDNA amplification and phylogenetic analysis using the neighbour-joining method. Three genera of bacteria were identified namely Vibrio, Bacillus, and Acinetobacter. The genus Vibrio was found to be the main bacterial group associated with the H. leucospilota specimens from Pangkor Island. � 2018, Malaysian Society of Applied Biology. All rights reserved.

Ragi is a traditional dry starter culture frequently used in many fermented food products in Asian countries. Ragi contains starch that can be degraded by amylases provided by bacteria and other microorganisms during fermentation in producing fermented foods. This study was carried out to isolate bacteria from ragi and to screen for their ability to hydrolyse starch. Seven bacterial colonies were isolated from ragi, with three samples showing starch hydrolysis activity. Two of the starch-degrading bacterial isolates were identified using partial 16S rRNA gene sequencing as Bacillus licheniformis with 97% and 98% similarity, and one sample identified as a lactic acid bacteria, Enterococcus faecium (98%). Isolation and identification of these bacteria from ragi can provide a promising source of amylase that can be further studied and manipulated for the development of starter culture and to improve the quality of traditional ragi-based fermented food products. � 2018, Malaysian Society of Applied Biology. All rights reserved.

The abundance of sea cucumbers (Phylum Echinodermata: Class Holothuroidea) in Malaysian waters has been gradually declining in past decades. Due to the lack of recent studies on the status of sea cucumber populations in Kudat, Sabah, Malaysia, this study was conducted. This study aimed to identify the species of a timun laut morphospecies i.e. Holothuria (Metriatyla) scabra and two gamat morphospecies i.e. Stichopus horrens and Stichopus ocellatus that were collected from Limau Limawan based on ossicle shapes and non-protein-coding 12S mitochondrial rRNA gene sequences. A number of five main ossicle shapes were microscopically identifed without microscopic size measurement i.e. rod, plate, rosette, button and table. However, a number of ossicle shapes for S. horrens and S. ocellatus recorded in the previous studies were not observed in this study and this could be due to the body deformation of the specimens. Interestingly, fve specimens of H. scabra exhibited additional ossicle shapes other than the smooth button and the table. Despite the absence of common ossicles and the presence of additional ossicle shapes, 12S mitochondrial rRNA gene sequences analysed using the Basic Local Alignment Search Tool programme for Nucleotide (blastn) resulted in the species identifcation of the specimens of morphospecies H. scabra and S. horrens as H. scabra and S. horrens; however, the specimen of morphospecies S. ocellatus was identifed only up to the genus level i.e. genus Stichopus, showing the lack of 12S mitochondrial rRNA gene sequences of S. ocellatus in the GenBank until 15 September, 2016. In total, 31 partial sequences of 12S mitochondrial rRNA gene were registered with the GenBank (Accession No.: KX913672-KX913702). The fndings also suggested that species identifcation based on 12S mitochondrial rRNA gene sequence showed better inference than the ossicle shape identifcation. In summary, the three morphospecies were morphologically and genetically verifed as H. scabra, S. horrens and S. ocellatus. Despite the fact that more specimens and more molecular techniques are required to generate better conclusive outcomes, the current fndings give better insight into the importance of morphological and molecular approaches and the present status of the timun laut species and gamat species in Kudat. � Universiti Putra Malaysia Press.

This preliminary study aimed to identify a commercial gamat species, Stichopus horrens Selenka, 1867, and a timun laut species, Holothuria (Mertensiothuria) leucospilota (Brandt, 1835), from Pangkor Island, Perak, Malaysia, employing morphological techniques based on the shape of the ossicles and molecular techniques based on the cytochrome c oxidase I (COI) mitochondrial DNA (mtDNA) gene. In Malaysia, a gamat is defined as a sea cucumber species of the family Stichopodidae with medicinal value, and timun laut refers to non-gamat species. S. horrens is very popular on Pangkor Island as a main ingredient in the traditional production of air gamat and minyak gamat, while H. leucospilota is the most abundant species in Malaysia. In contrast to previous studies, internal body parts (the respiratory tree and gastrointestine) were examined in this study to obtain better inferences based on morphology. The results showed that there were no ossicles present in the gastrointestine of H. leucospilota, and this characteristic is suggested as a unique diagnostic marker for the timun laut species. In addition, the presence of Y-shaped rods in the respiratory tree of S. horrens subsequently supported the potential to use internal body parts to identify the gamat species. Phylogenetic analysis of the COI mtDNA gene of the sea cucumber specimens using the neighbour-joining method and maximum likelihood methods further confirmed the species status of H. leucospilota and S. horrens from Pangkor Island, Perak, Malaysia. The COI mtDNA gene sequences were registered with GenBank, National Center for Biotechnology Information (NCBI), US National Library of Medicine (GenBank accession no.: KC405565-KC405568). Although additional specimens from various localities will be required to produce more conclusive results, the current findings provide better insight into the importance of complementary approaches involving morphological and molecular techniques in the identification of the two Malaysian sea cucumber species. � Penerbit Universiti Sains Malaysia, 2015.

This study aimed to resolve the taxonomic status of a morphologically undetermined sea cucumber species of order Apodida from Malaysia (GenBank accession no.: FJ223867) using partial 16S mitochondrial rRNA gene sequences and subsequently to determine the validity of morphological taxonomy of Holothuria species into its current subgenera. The undetermined species clustered with all taxa of Holothuria in previous study. Phylogenetic analyses using maximum parsimony and Bayesian methods suggest that the undetermined species was genetically closer to Holothuria (Lessonothuria) pardalis and Holothuria (Acanthotrapeza) coluber; and its position in both phylogenetic trees further suggests its status as a Holothuria taxon. Subgenera of Holothuria, Merthensiothuria and Metriatyla are monophyletic with strong bootstrap supports and posterior probabilities of clades, thus strengthening their morphological taxonomies. Nonetheless, the non-monophyly of subgenera of Halodeima, Microthele and Platyperona suggests a requirement for their taxonomic revisions using integrative taxonomy. The status of Holothuria (Halodeima) edulis subgroups in the maximum parsimony and Bayesian trees is indistinct and further taxonomic revisions are necessary. In terms of sister relationship, both phylogenetic trees suggest that subgenus Holothuria is a sister taxon of subgenus Roweothuria while the other sister relationships were unclear due to the undetermined species, paraphyly and polyphyly of a number of subgenera. Further studies with more specimens of genus Holothuria from broader geographical locations and various mtDNA genes along with morphological approaches may facilitate to provide better insights into the molecular phylogeny of subgenera of Holothuria.

This study aimed at documenting species richness and distribution of sea cucumbers (Phylum Echinodermata: Class Holothuroidea) in Malaysia. Sea cucumber collections were conducted from August 2004 until November 2011 from several study sites in Peninsular Malaysia and Sabah. A total of fifty two morphospecies of sea cucumbers from four orders comprising of 12 genera were documented. Thirty eight species were recorded for Sabah, followed by 24 species for Peninsular Malaysia, and 10 species were recorded in both regions. However, nine species required further taxonomic works for their identification. Of the 15 Actinopyga species recorded, 14 species were from Sabah and one species was from Peninsular Malaysia. The order Aspidochirotida in general, and genus Holothuria in particular were the dominant taxa. Holothuria (Mertensiothuria) leucospilota (Brandt, 1835) is the dominant species in Malaysia as it was observed and documented at all collection sites. Future studies on the species richness of sea cucumbers are required in Sarawak marine waters and the molecular phylogeny of the sea cucumbers in order to obtain a better understanding of the evolutionary relationships between the sea cucumbers of Malaysia. � Universiti Putra Malaysia Press.