A synbiotic intervention modulates meta-omics signatures of gut redox potential and acidity in elective caesarean born infants.

Background The compromised gut microbiome that results from C-section birth has been hypothesized as a risk factor for the development of non-communicable diseases (NCD). In a double-blind randomized controlled study, 153 infants born by elective C-section received an infant formula supplemented with either synbiotic, prebiotics, or unsupplemented from birth until 4 months old. Vaginally born infants were included as a reference group. Stool samples were collected from day 3 till week 22. Multi-omics were deployed to investigate the impact of mode of delivery and nutrition on the development of the infant gut microbiome, and uncover putative biological mechanisms underlying the role of a compromised microbiome as a risk factor for NCD. Results As early as day 3, infants born vaginally presented a hypoxic and acidic gut environment characterized by an enrichment of strict anaerobes (Bifidobacteriaceae). Infants born by C-section presented the hallmark of a compromised microbiome driven by an enrichment of Enterobacteriaceae. This was associated with meta-omics signatures characteristic of a microbiome adapted to a more oxygen-rich gut environment, enriched with genes associated with reactive oxygen species metabolism and lipopolysaccharide biosynthesis, and depleted in genes involved in the metabolism of milk carbohydrates. The synbiotic formula modulated expression of microbial genes involved in (oligo)saccharide metabolism, which emulates the eco-physiological gut environment observed in vaginally born infants. The resulting hypoxic and acidic milieu prevented the establishment of a compromised microbiome. Conclusions This study deciphers the putative functional hallmarks of a compromised microbiome acquired during C-section birth, and the impact of nutrition that may counteract disturbed microbiome development. Trial registration The study was registered in the Dutch Trial Register (Number: 2838 ) on 4th April 2011

STUDI KASUS LINGUSQL: APLIKASI TRANSAKSI PERDAGANGAN SAHAM

Proses pengembangan perangkat lunak yang ideal selalu mensyaratkan pengujian yang menyeluruh untuk memperoleh hasil perangkat lunak yang memiliki tingkat kebenaran tertentu. Namun pada prakteknya pengujian secara menyeluruh sangat jarang dilakukan karena membutuhkan sumber daya waktu dan biaya yang banyak. LinguSQL adalah sebuah tool pengembangan eksperimen yang mengintegrasikan proses pengujian secara whitebox dan blackbox ke dalam aktifitas pembuatan kodenya. Paper ini memaparkan penerapan LinguSQL dalam pengembangan studi kasus sebuah aplikasi transaksi perdagangan saham. Penerapan LinguSQL pada studi kasus yang cukup kompleks diharapkan akan menampilkan keuntungan konsep pengujian secara menyeluruh serta, dalam konteks implementasi tool, menunjukkan bagian-bagian yang masih perlu dikembangkan lebih lanjut. The ideal process software development always requires thorough testing to obtain the software that has a certain degree of truth. However, in practice very rarely thorough testing done because it requires so much resources of time and cost. LinguSQL is an experimental tool that integrates the development process is whitebox and blackbox testing in manufacturing activity code. This paper describes the implementastion of LinguSQL in the development of a stock trading application case study. Implementation of LinguSQL on a complex case study will show the expected benefit of testing the concept a thorough and in the context of the implementation tool, showing the parts that still need to be developed further

MetaLIMS, a simple open-source laboratory information management system for small metagenomic labs

Background: As the cost of sequencing continues to fall, smaller groups increasingly initiate and manage larger sequencing projects and take on the complexity of data storage for high volumes of samples. This has created a need for low-cost laboratory information management systems (LIMS) that contain flexible fields to accommodate the unique nature of individual labs. Many labs do not have a dedicated information technology position, so LIMS must also be easy to setup and maintain with minimal technical proficiency. Findings: MetaLIMS is a free and open-source web-based application available via GitHub. The focus of MetaLIMS is to store sample metadata prior to sequencing and analysis pipelines. Initially designed for environmental metagenomics labs, in addition to storing generic sample collection information and DNA/RNA processing information, the user can also add fields specific to the user's lab. MetaLIMS can also produce a basic sequencing submission form compatible with the proprietary Clarity LIMS system used by some sequencing facilities. To help ease the technical burden associated with web deployment, MetaLIMS options the use of commercial web hosting combined with MetaLIMS bash scripts for ease of setup. Conclusions: MetaLIMS overcomes key challenges common in LIMS by giving labs access to a low-cost and open-source tool that also has the flexibility to meet individual lab needs and an option for easy deployment. By making the web application open source and hosting it on GitHub, we hope to encourage the community to build upon MetaLIMS, making it more robust and tailored to the needs of more researchers.MOE (Min. of Education, S’pore)Published versio

Genome sequence of Prosthecochloris sp. strain HL-130-GSB from the phylum Chlorobi

The genome of the green sulfur bacterium Prosthecochloris sp. strain HL-130-GSB, isolated from a cyanobacterial mat obtained from Hot Lake, a saline meromictic lake in Washington, USA, comprises 2,437,774 bp in a single contig. The genome is predicted to encode 2,565 proteins and contain 47 tRNA genes and 2 rRNA operons.Published versio

Draft genome sequence of Klebsiella pneumoniae strain KP-1

Klebsiella pneumoniae is ubiquitous in the environment and is a member of a three-species biofilm model. We compared the genome sequence of an environmental isolate, K. pneumoniae strain KP-1, to those of two clinical strains (NTUH-K2044 and MGH 78578). KP-1 possesses strain-specific prophage sequences that distinguish it from the clinical strains.Published versio

Phenotypic and genotypic characterization of antimicrobial resistant Escherichia coli isolated from ready-to-eat food in Singapore using disk diffusion, broth microdilution and whole genome sequencing methods

This study aimed to determine the antimicrobial resistance (AMR) profiles of Escherichia coli isolated from ready-to-eat (RTE) food sold in retail food premises in Singapore. In this study, a total of 99 E. coli isolates from poultry-based dishes (n = 77) and fish-based dishes (n = 22), obtained between 2009 and 2014, were included for disk diffusion testing. Of the 99 isolates, 24 (24.2%) were resistant to at least one antimicrobial agent. These isolates were then subjected to broth microdilution testing against 33 antimicrobial agents, including beta-lactams, aminoglycosides, tetracycline, fluoroquinolones and polymyxin E (also known as colistin) to determine the minimum inhibitory concentration (MIC) of isolates. Finally, whole genome sequence (WGS) was carried out on the strains in order to correlate resistant phenotypes to putative antimicrobial-related genes. Of the 24 isolates, 15 (62.5%) were found to be resistant to three or more classes of antimicrobials and thus were defined as multidrug resistant strains. Two isolates (8.3%) were confirmed as Extended-Spectrum Beta-Lactamase (ESBL)-producing E. coli by double-disk synergy test. Based on WGS data, online analysis tool ResFinder detected 7 classes of AMR genes and resistance-related chromosomal point mutations in 19 of the 24 E. coli isolates. Prediction of AMR using WGS data was evaluated for six antimicrobials including ampicillin, chloramphenicol, colistin, fluoroquinolones, tetracycline and trimethoprim. By analyzing the WGS contigs using BLASTn and KmerFinder, quinolone resistance genes, ESBL genes and transferable colistin resistance gene mcr-1 and mcr-5 were determined to be located on plasmids, which could pose a greater risk of AMR transfer among bacteria. Mutations were detected in four isolates within genes previously shown to confer resistance to quinolones (gyrA and parE) and tetracycline (rrsB). This study showed the presence of AMR E. coli isolates in RTE food, and raises a concern on the possible transmission of AMR bacteria from food to humans.Nanyang Technological UniversityNational Environmental Agency (NEA)This study was supported by the National Environment Agency (NEA) and Nanyang Technological University Research Initiative. Authors would like to thank Man Ling Chau and Ramona Alikiiteaga Gutiérrez for manuscript vetting, and thank Food Hygiene team members in the Environmental Health Institute of NEA for providing isolates and experimental guidance

Large-scale mitogenomics enables insights into Schizophora (Diptera) radiation and population diversity

True flies are insects of the order Diptera and encompass one of the most diverse groups of animals on Earth. Within dipterans, Schizophora represents a recent radiation of insects that was used as a model to develop a pipeline for generating complete mitogenomes using various sequencing platforms and strategies. 91 mitogenomes from 32 different species were sequenced and assembled with high fidelity, using amplicon, whole genome shotgun or single molecule sequencing approaches. Based on the novel mitogenomes, we estimate the origin of Schizophora within the Cretaceous-Paleogene (K-Pg) boundary, about 68.3 Ma. Detailed analyses of the blowfly family (Calliphoridae) place its origin at 22 Ma, concomitant with the radiation of grazing mammals. The emergence of ectoparasitism within calliphorids was dated 6.95 Ma for the screwworm fly and 2.3 Ma for the Australian sheep blowfly. Varying population histories were observed for the blowfly Chrysomya megacephala and the housefly Musca domestica samples in our dataset. Whereas blowflies (n = 50) appear to have undergone selective sweeps and/or severe bottlenecks in the New World, houseflies (n = 14) display variation among populations from different zoogeographical zones and low levels of gene flow. The reported high-throughput mitogenomics approach for insects enables new insights into schizophoran diversity and population history of flies.Published versio

Whole-genome sequencing of Aspergillus terreus species complex

Aspergillus terreus species complex is an opportunistic fungal pathogen increasingly implicated in invasive infection, as well as chronic respiratory disease. Currently, an understanding of A. terreus pathogenicity is impeded by a limited number of whole-genome sequences of this fungal pathogen. We here describe a high-quality whole-genome assembly of European A. terreus clinical isolate M6925, derived by single-molecule real-time sequencing with short-read polishing

Complete genome sequence of Streptomyces sp. strain SGAir0924, an actinobacterium isolated from outdoor air in Singapore

Streptomyces sp. strain SGAir0924 was isolated from outdoor air collected in Singapore. Its genome was assembled using long reads generated by single-molecule real-time sequencing. The final assembly had one chromosome of 7.65 Mb and three plasmids with an average length of 142 kb. The genome contained 6,825 protein-coding genes, 68 tRNAs, and 18 rRNAs.MOE (Min. of Education, S’pore)Published versio

Complete genome sequence of Brevundimonas sp. strain SGAir0440, isolated from indoor air in Singapore

Brevundimonas sp. strain SGAir0440 was isolated from indoor air samples collected in Singapore. Its genome was assembled using single-molecule real-time sequencing data, resulting in one circular chromosome with a length of 3.1 Mbp. The genome consists of 3,033 protein-coding genes, 48 tRNAs, and 6 rRNA operons.MOE (Min. of Education, S’pore)Published versio