Microbiome analysis of gut bacterial communities of healthy and diseased Malaysian mahseer (Tor tambroides) using 16S rRNA metagenomics approach

Aims@#The gut microbiota is referred to as an ‘extra organ’ and is critical in assisting the host in terms of nutrition and immunity. Environmental stressors could alter the gut microbial community and cause gut inflammation. This study aimed to investigate and compare the gut microbiota community between healthy and diseased Tor tambroides.@*Methodology and results@#In this study, such gut microbial alterations were explored using NGS-based 16S rDNA targeted sequencing on the Malaysian mahseer (T. tambroides). Three healthy adult and three diseased adult Malaysian mahseers (showing signs of exophthalmia, coelomic distension and petechial haemorrhage) were obtained from LTT Aquaculture Sdn Bhd. Our results revealed significant differences in microbial diversity, composition and function between both populations of T. tambroides. Alpha diversity analysis depicts lower diversity of gut microbiota composition in diseased T. tambroides as compared to the healthy group. In particular, Enterobacteriaceae, Aeromonas, Bacteroides, Vibrio and Pseudomonas were found within gut microbiota of the diseased fishes. In addition, cellulosedegrading bacteria and protease-producing bacteria were identified from the gut of T. tambroides.@*Conclusion, significance and impact of study@#Thus, our findings emphasized on the association between the alteration in gut microbiota composition and infectious abdominal dropsy (IAD) in T. tambroides. This finding is important to provide basic information for further diagnosis, prevention and treatment of intestinal diseases in fish.

Genotypic profiles of virulent genes detected among the Enterococcus faecalis, Escherichia coli, Pseudomonas aeruginosa isolated from swiftlets in Borneo

Aims@#The occurrence of multiple pathogenic Enterococcus faecalis, Escherichia coli, and Pseudomonas aeruginosa are important nosocomial and hazardous infection clinically challenge worldwide. Thus, the aim of this study was to screen for the virulent genes profiles to ascertain their prevalence in swiftlets in Borneo. @*Methodology and results@#The Enterococci, E. coli and P. aeruginosa bacteria were isolated from the swiftlets’ faeces and air inside swiftlet houses, which located in the Southern, Central and Northern regions of Borneo. The isolates were identified to the species level by 16S rRNA sequencing assay. Specific primers were designed for detection of the potential virulence genes in E. faecalis (ace, AS, efaA and gelE), E. coli (stx) and P. aeruginosa (oprL) by PCR assay. A total of 38 Enterococci, 26 of E. coli and 2 of P. aeruginosa fecal and airborne bacteria were identified. Sixty-seven percent of E. faecalis isolates were detected positive for four virulence genes, 27% possessed three (AS, efaA, gelE) genes and 6% possessed two (ace, AS) genes. There were no stx genes detected among all the E. coli isolates. The oprL gene was detected in all the P. aeruginosa isolates. @*Conclusion, significance and impact of study@#Virulence genes are important in the pathogenesis of both clinical and avian infections which considered to be a serious public health threat. The high incidence of virulence genes detection in E. faecalis and P. aeruginosa indicates these genes were widely disseminated among the bacteria found in swiftlet houses, suggesting the important issues in the pathogenesis of infections and diseases which may cause potential health risks to humans.

Distribution and prevalence of antibiotic resistant bacteria in fish farms in East Malaysia

Aims@#Aquaculture has grown tremendously in Malaysia over the past decades. However, guaranteeing aquaculture sustainability is a big challenge in terms of maintaining continuous output with a safe environment. Furthermore, the cultured species should be free from antibiotic resistance bacterial and antibiotic residue. This study aimed to monitor the existence and prevalence of antibiotic resistant bacteria associated with aquaculture farms in Sarawak.@*Methodology and results@#Samples of water, sediment and fish were collected from five aquaculture farms within Sarawak. The samples were plated on trypticase soy agar and incubated at 28 °C for 24 h. A total of 204 bacterial isolates were isolated and analysed by (GTG)5-fingerprinting to determine genetic similarity among the bacterial isolates, so that representatives could be selected from similar clonal isolates. Based on the (GTG)5 profiles, 50 representative isolates were chosen for species identification using 16S rRNA sequencing. The identified bacteria were tested against 25 antibiotics using standard disk diffusion method. The 16S rRNA analysis revealed that the isolates constitute of 14 genera of bacteria including Bacillus (38%), Exiguobacterium (16%), Enterobacter (14%), Aeromonas (6%), Acinetobacter (4%), Citrobacter (4%), Staphylococcus (4%), Achromobacter (2%), Chitinophaga (2%), Fictibacillus (2%), Plesiomonas (2%), Pseudomonas (2%), Pseudoxanthomonas (2%) and Stenotrophomonas (2%). The antibiotic resistance analysis revealed that the highest percentage of resistance was recorded against streptomycin (75.0%), followed by ampicillin (66.0%), ceftriaxone (50.0%), rifampin (43.3%), aztreonam (36.8%) and ceftazidime (31.6%). Resistance to more than two antibiotics was observed in 40.0% of isolates with an overall multiple antibiotic resistant (MAR) index ranging from 0 to 0.79. @*Conclusion, significant and impact of study@#The variability of antibiotic resistance patterns exhibited by different bacterial species suggests a dependence on selective pressures exhibited in different geographical locations. Our results show that the occurrence of MAR bacteria in an aquaculture environment with unknown history of antibiotics usage in the aquaculture system is possible, indicating a need to continuously monitor the presence of antibiotic resistant bacteria in the aquaculture system.

Effects of Sarawak local salts and commercial sodium chloride on biofilm formation of Vibrio cholerae

Aims@#Bacterial biofilms can be defined as a community of microorganisms in which cells adhere to one another on a surface and are embedded in a protective matrix of lipids, nucleic acids, proteins and polysaccharides. Biofilm produced by Vibrio cholerae represents a significant threat to food safety, as they can lead to the transmission of diseases. Hence, the purpose of this study is to review the effect of different types of sodium chloride on minimum biofilm eradication concentration (MBEC) and morphology of biofilm formation of Vibrio cholerae. @*Methodology and results@#In this study, V. cholerae biofilm was treated with four different types of sodium chloride; ‘Bario’ salt, ‘Bakelalan’ salt, commercial sodium chloride and laboratory sodium chloride. By using MBEC test, the concentration of sodium chloride needed to eradicate the biofilm of V. cholerae was determined. Based on the result obtained, commercial sodium chloride and laboratory sodium chloride showed the highest anti-biofilm activity against the biofilm of V. cholerae at 500 mg/mL concentration while no complete eradication of V. cholerae biofilm was achieved when treated with Sarawak local salts (‘Bario’ salt and ‘Bakelalan’ salt). However, noticeable inhibitions of bacterial growth were seen at the highest concentration of local salts. @*Conclusion, significance and impact of study@#Commercial sodium chloride and laboratory sodium chloride showed a better anti-biofilm activity towards the V. cholerae biofilm formation as compared to the local salts. Thus, commercial sodium chloride and laboratory sodium chloride can be an effective anti-biofilm agent to mitigate the biofilm formation of V. cholerae. Further studies can be done to determine the MBEC values of other pathogenic bacteria against commercial and laboratory sodium chloride.

Production of pigments by Rhodotorula mucilaginosa

Aims@#Pigments have a large and growing market in the world. Drawbacks in their production such as raw materials availability and low productivity prompt the search for fermentation routes for industrial production. A carotenoid-producing yeast identified as Rhodotorula mucilaginosa was isolated in our laboratory. The aim of this study was to investigate the growth and carotenoid production capacity of the yeast.@*Methodology and results@#A cost-effective substrate of sago starch hydrolysate (SSH) derived from sago fiber waste was used for the fermentation. The fermentation was carried out for 96 h at 27 °C in batch mode. The biomass produced during 5 days of fermentation was 9.6 g/L, which contained a carotenoid concentration of 8.1 mg/L and a specific yield of 845.9 g/g.@*Conclusion, significance and impact of study@#The results demonstrated the capacity of R. mucilaginosa yeast to produce carotenoids and its potential for larger-scale production.

Isolation and characterisation of Arbuscular mycorrhizal (AM) fungi spores from selected plant roots and their rhizosphere soil environment

Aims@#Arbuscular mycorrhizal (AM) fungi or previously known as the vesicular-arbuscular mycorrhizal (VAM) fungi, is a type of endomycorrhiza that closely associates with most species of plants. Meanwhile, they significantly improve the nutrients uptake in exchange of photosynthates and decrease the stress caused by both biotic and abiotic factors through symbiosis relationship. However, the understanding of indigenous AM fungi species present in its host plants are comparatively inadequate, hence this research study concentrated on indigenous AM fungi population in some selected plants that contribute to agricultural sector in Malaysia and phytochemical properties of soil that affect the colonization rate of AM fungi.@*Methodology and results@#Bamboo, banana, coconut, sugarcane, papaya, lemongrass, pandan and tapioca plant were selected in this study. The soil and plant roots were sampled and the fungi spores were extracted by applying Wet sieves and decantation techniques then further purified by sucrose density centrifugation. Genera Glomus, Funneliformis, Rhizophagus, Acaulospora and Dentiscutata were isolated and Glomus was determined as the dominant genera followed by Acaulospora in these selected plants. Soil pH were found to be significantly affecting the AM fungi population and the root colonization percentage of AM fungi in the plants analysed.@*Conclusion, significance and impact of study@#From this study, tapioca recorded the highest percentage of AM fungi root colonization rate with 20.00% in root while banana recorded the lowest rate of 3.33% only. Based on this study, tapioca is recommended for the propagation of AM fungi for biofertilizer usage in agricultural sector in future.

Screening and characterisation of two Pseudomonas aeruginosa from aquaculture and water environment

Aims@#Pseudomonas has been associated with diseases occurring in people with weakened or compromised immune system after exposure to contaminated water. The diseases are commonly treated with antibiotics. However, the bacteria had developed resistances to commonly used antibiotics making treatment a difficult task. Therefore, the continuous surveillance of susceptibility of Pseudomonas especially for the human pathogen P. aeruginosa to commonly clinical and aquaculture farming used antibiotics is important to ensure that serious infections remain susceptible to those antibiotics.@*Methodology and results@#In this study, the bacteria were screened from water, sediment and fish from rivers and aquaculture farms around Kuching, Sarawak. A total number of 38 presumptive P. aeruginosa were isolated using CHROMagar TM Pseudomonas and subjected to a series of biochemical tests. Out of all the isolates tested, only two isolates designated as AS-R10(S) and BK2-OLT2(S) fulfilled the biochemical characteristics of P. aeruginosa. 16S rRNA gene sequencing further confirmed these two isolates as P. aeruginosa based on their 100% similarity with P. aeruginosa strain GD1 and P. aeruginosa strain PA1201 in NCBI database. These two isolates were tested for their susceptibilities against nine common antibiotics used in both clinical and aquaculture farming nowadays: imipenem, piperacillin, meropenem, amikacin, gentamicin, ciprofloxacin, ceftazidime, tobramycin and norfloxacin according to CLSI standard using disk diffusion method.@*Conclusion, significance and impact of study@#The two isolates exhibited total susceptibility to all the antibiotics analysed, suggesting the effectiveness of the antimicrobial agents towards P. aeruginosa isolated from aquaculture and water environment in the study area.

In Vitro Antagonism of Phytophthora capsici And Fusarium solani by Bacterial Isolates from Sarawak

Aims: Phytophthora capsici and Fusarium solani are common fungal pathogens causing severe diseases that lead to economic loss in pepper industry, especially in Sarawak. In response to the infections, chemical approach is more common; nevertheless, biological control is more favorable to control fungal pathogens. Biological control approach greatly reduces the problems associated with chemical applications and it restores balance of the natural environment. Here we present the ongoing work to study the action of antagonistic bacteria, Bacillus sp. and Pseudomonas sp., that produce volatile and non-volatile antifungal compounds against P. capsici and F. solani on pepper plants. Methodology and results: A total of seven bacterial candidates were isolated from different locations and tested for their antagonistic properties against P. capsici and F. solani in a dual culture assay and extracellular metabolite test. Extracellular hydrolytic enzymes production was also monitored and followed by genotypic indentification. Preliminary antagonism tests indicated that bacterial isolate Pep3 and Pep4 inhibit up to 50% of the growth of P. capsici and F. solani as compared to the control. Subsequent investigation on extracellular hydrolytic enzyme production revealed that both bacterial isolates are capable of secreting hydrolytic enzymes. Microscopic and genotypic analyses identified the bacterial isolates Pep3 as Bacillus amyloliquefaciens (KJ461444) and Pep4 as Pseudomonas pachastrellae (KM460937). Conclusion, significance and impact of study: B. Amyloliquefaciens (KJ461444) and P. pachastrellae (KM460937) inhibited the growth of P. capsici and F. solani thus reflecting the potential of the produced metabolites to be purified and used in combating plant pathogenic fungi.

Genomic Diversity of Cholera Outbreak Strains in East Malaysia

Thirty one Vibrio cholera isolates recovered from cholera outbreak in Bintulu, Sarawak (Malaysia) were detected with the presence of ctx gene by using specific PCR. These isolates were further characterized and differentiated by using the Enterobacterial Repetitive Intergenic Consensus PCR (ERIC-PCR) and BOX-PCR to determine their genomic fingerprints. The specific PCR result confirmed the identities of 27 isolates out of 31 as pathogenic V. cholerae. The ERIC-PCR generated several genetic profiles consisting of 4-6 bands with sizes in the range of 100 to 600 bp, while the BOX-PCR produced profiles numbering 2-7 bands in the sizes between 200 to 1000 bp. Based on the dendrogram generated from the DNA fingerprinting profiles (ERIC-PCR and BOX-PCR), all of the isolates can be divided into 2 main clusters that is further divided into 2 sub-clusters. The low genetic diversity of the isolates indicated the outbreak of V. cholerae in the study area was due to the contamination from a single or few sources of V. cholerae.

Community Awareness and Attitudes towards Influenza Outbreak and Prevention in Serian, Sarawak

To date, there has been no systematic research that investigates the rural community awareness and attitudes towards pandemic influenza H1N1 and its prevention measures in the context of Sarawak. There is also no systematic study about whether the initiatives to educate the public undertaken by the government and other agencies have empowered the rural communities to practice an effective self-care within the context of community, that assist to curb the potential spread of this disease. Our research aims to address these limitations. In this paper, we report a survey finding about the awareness and attitudes of the Serian community with regard to this area of research interest. We also investigate the relevant sources of information that the community relies on in understanding about the influenza and how it can spread. Overall, the outcomes of the survey reveal that a majority of our respondents has a relatively low level of knowledge and awareness particularly about the characteristics of the illness and how H1N1 virus can transmit. With regard to prevention measures, a majority of them reported good understanding and awareness about the effective self-care practices that can help to curb the potential spread of the influenza. The top five sources to obtain information about the influenza were: information from family, relatives, friends or neighbours; radio; TV; newspapers; and government health talk seminar or campaigns. The research outcomes can offer pragmatic contributions that can benefit the health campaigners and policy makers.