Insights into microbial community structure and diversity in oil palm waste compost

Empty fruit bunch (EFB) and palm oil mill effluent (POME) are the major wastes generated by the oil palm industry in Malaysia. The practice of EFB and POME digester sludge co-composting has shown positive results, both in mitigating otherwise environmentally damaging waste streams and in producing a useful product (compost) from these streams. In this study, the bacterial ecosystems of 12 week-old EFB-POME co-compost and POME biogas sludge from Felda Maokil, Johor were analysed using 16S metagenome sequencing. Over 10 phyla were detected with Chloroflexi being the predominant phylum, representing approximately 53% of compost and 23% of the POME microbiome reads. The main bacterial lineage found in compost and POME was Anaerolinaceae (Chloroflexi) with 30% and 18% of the total gene fragments, respectively. The significant differences between compost and POME communities were abundances of Syntrophobacter, Sulfuricurvum, and Coprococcus. No methanogens were identified due to the bias of general 16S primers to eubacteria. The preponderance of anaerobic species in the compost, and high abundance of secondary metabolite fermenting bacteria is due to an extended composting time, with anaerobic collapse of the pile in the tropical heat. Predictive functional profiles of the metagenomes using 16S rRNA marker genes suggest the presence of enzymes involved in polysaccharide degradation such as glucoamylase, endoglucanase, arabinofuranosidase, all of which were strongly active in POME. Eubacterial species associated with cellulytic methanogenesis were present in both samples

Gut microbiota metagenomics in aquaculture: factors influencing gut microbiome and its physiological role in fish

Fish gut microbiome confers various effects to the host fish; this includes overall size, metabolism, feeding behaviour and immune response in the fish. The emergence of antimicrobial-resistant (AMR) bacteria and hard to cure fish diseases warrant the possible utilization of gut microbes that exhibits a positive effect on the fish and thus lead to the usage of these microbes as probiotics. The widespread and systematic use of antibiotics has led to severe biological and ecological problems, especially the development of antibiotic resistance that affects the gut microbiota of aquatic organisms. Probiotics are proposed as an effective and environmentally friendly alternative to antibiotics, known as beneficial microbes. At the same time, prebiotics are considered beneficial to the host's health and growth by decreasing the prevalence of intestinal pathogens and/or changing the development of bacterial metabolites related to health. Uprise of sequencing technology and the development of intricate bioinformatics tools has provided a way to study these gut microbes through metagenomic analysis. From various metagenomic studies, ample of information was obtained; such information includes the effect of the gut microbiome on the physiology of fish, gut microbe composition of different fish, factors affecting the gut microbial composition of the fish and the immunological effect of gut microbes in fish; such this information related to the fish gut microbiome, their function and their importance in aquaculture is discussed in this review

Kesediaan pensyarah teknikal terhadap pelaksanaan School Enterprise di kolej vokasional wilayah Utara

Pelaksanaan School Enterprise merupakan salah satu aktiviti pendidikan berteraskan bidang keusahawanan yang dijalankan di Kolej Vokasional pada masa ini. Program School Enterprise yang dilaksanakan di Kolej Vokasional juga merupakan salah satu elemen pengajaran dan pembelajaran yang memberikan peluang kepada para pensyarah dan pelajar khususnya untuk melalui pengalaman sebenar dalam dunia perniagaan serta mengaplikasikan konsep dan teori pendekatan perniagaan yang dipelajari ke situasi yang sebenar. Para pensyarah dilihat sebagai individu yang bertanggungjawab dalam menjayakan pelaksanaan School Enterprise ini. Oleh itu, kajian ini dijalankan bagi mengenal pasti tahap kesediaan para pensyarah dalam pelaksanaan School Enterprise di empat buah Kolej Vokasional Wilayah Utara Semenanjung iaitu KV Alor Setar, KV Sungai Petani 2, KV Arau dan KV Kangar. Persepsi terhadap kesediaan para pensyarah dilihat daripada aspek pengetahuan, amalan dan kemahiran. Seramai 100 orang para pensyarah daripada empat buah Kolej Vokasional Wilayah Utara dipilih secara rawak bagi menjawab soal selidik yang diberikan. Analisis data ini melibatkan skor min dan sisihan piawai untuk menentukan skor min serta ANOVA untuk mencari perbezaan pada aspek yang dikehendaki. Didapati purata skor min kesediaan pensyarah KV di Wilayah Utara daripada aspek amalan (min=3.97) dan pengetahuan (min=3.796) serta kemahiran (min=3.821) adalah tinggi. Hal ini menunjukkan persepsi tahap kesediaan para pensyarah daripada sudut pengetahuan, amalan dan kemahiran berada pada tahap yang tinggi terhadap pelaksanaan School Enterprise. Hal ini disebabkan kebanyakan pensyarah KV telah bersedia melaksanakan program School Enterprise namun terdapat kekangan seperti bebanan tugas dan kerja di KV yang memaksa para pensyarah mendominasikan tugas pentadbiran berbanding program yang berkisarkan pada keusahawanan ini. Kesimpulannya, kajian ini menunjukkan tidak terdapat perbezaan yang signifikan mengenai kesediaan pensyarah teknikal terhadap pelaksanaan School Enterprise di Kolej Vokasional Wilayah Utara

Efficient extraction of small and large RNAs in bacteria for excellent total RNA sequencing and comprehensive transcriptome analysis.

BACKGROUND: Next-generation transcriptome sequencing (RNA-Seq) has become the standard practice for studying gene splicing, mutations and changes in gene expression to obtain valuable, accurate biological conclusions. However, obtaining good sequencing coverage and depth to study these is impeded by the difficulties of obtaining high quality total RNA with minimal genomic DNA contamination. With this in mind, we evaluated the performance of Phenol-free total RNA purification kit (Amresco) in comparison with TRI Reagent (MRC) and RNeasy Mini (Qiagen) for the extraction of total RNA of Pseudomonas aeruginosa which was grown in glucose-supplemented (control) and polyethylene-supplemented (growth-limiting condition) minimal medium. All three extraction methods were coupled with an in-house DNase I treatment before the yield, integrity and size distribution of the purified RNA were assessed. RNA samples extracted with the best extraction kit were then sequenced using the Illumina HiSeq 2000 platform. RESULTS: TRI Reagent gave the lowest yield enriched with small RNAs (sRNAs), while RNeasy gave moderate yield of good quality RNA with trace amounts of sRNAs. The Phenol-free kit, on the other hand, gave the highest yield and the best quality RNA (RIN value of 9.85 ± 0.3) with good amounts of sRNAs. Subsequent bioinformatic analysis of the sequencing data revealed that 5435 coding genes, 452 sRNAs and 7 potential novel intergenic sRNAs were detected, indicating excellent sequencing coverage across RNA size ranges. In addition, detection of low abundance transcripts and consistency of their expression profiles across replicates from the same conditions demonstrated the reproducibility of the RNA extraction technique. CONCLUSIONS: Amresco\u27s Phenol-free Total RNA purification kit coupled with DNase I treatment yielded the highest quality RNAs containing good ratios of high and low molecular weight transcripts with minimal genomic DNA. These RNA extracts gave excellent non-biased sequencing coverage useful for comprehensive total transcriptome sequencing and analysis. Furthermore, our findings would be useful for those interested in studying both coding and non-coding RNAs from precious bacterial samples cultivated in growth-limiting condition, in a single sequencing run

Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage

Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we use meta-genomic analysis of untreated sewage to characterize the bacterial resistome from 79 sites in 60 countries. We find systematic differences in abundance and diversity of AMR genes between Europe/North-America/Oceania and Africa/Asia/South-America. Antimicrobial use data and bacterial taxonomy only explains a minor part of the AMR variation that we observe. We find no evidence for cross-selection between antimicrobial classes, or for effect of air travel between sites. However, AMR gene abundance strongly correlates with socio-economic, health and environmental factors, which we use to predict AMR gene abundances in all countries in the world. Our findings suggest that global AMR gene diversity and abundance vary by region, and that improving sanitation and health could potentially limit the global burden of AMR. We propose metagenomic analysis of sewage as an ethically acceptable and economically feasible approach for continuous global surveillance and prediction of AMR.Peer reviewe

Setting a baseline for global urban virome surveillance in sewage

The rapid development of megacities, and their growing connectedness across the world is becoming a distinct driver for emerging disease outbreaks. Early detection of unusual disease emergence and spread should therefore include such cities as part of risk-based surveillance. A catch-all metagenomic sequencing approach of urban sewage could potentially provide an unbiased insight into the dynamics of viral pathogens circulating in a community irrespective of access to care, a potential which already has been proven for the surveillance of poliovirus. Here, we present a detailed characterization of sewage viromes from a snapshot of 81 high density urban areas across the globe, including in-depth assessment of potential biases, as a proof of concept for catch-all viral pathogen surveillance. We show the ability to detect a wide range of viruses and geographical and seasonal differences for specific viral groups. Our findings offer a cross-sectional baseline for further research in viral surveillance from urban sewage samples and place previous studies in a global perspective

Investigation on raspberry Pi Microcontroller as digital processing controller in back to back converter

This paper is about, the investigation of the Raspberry Pi as a microcontroller for back-to-back converter. The Matlab-Simulink is used as the communication medium between the software and the microcontroller and at the same time, controllers have been developed based on the mathematical formulas in the MATLAB. Three types of controllers have been designed and simulated which are voltage, current and power controllers with the PID and Hysteresis control mechanism in order to see the respond to the given reference signals at the converter output. Two of controllers, which are the voltage and current controls have been tested in hardware setup that consists of single phase diode bridge, 3-phase inverter and a resistive load. Those tests have shown, the Raspberry Pi is managed to generate the gate signals for the converter which respond to the controller without any programming code written in the Matlab