Nicolas E. Gaultier

The microbiomes of blowflies and houseflies as bacterial transmission reservoirs

Blowflies and houseflies are mechanical vectors inhabiting synanthropic environments around the world. They feed and breed in fecal and decaying organic matter, but the microbiome they harbour and transport is largely uncharacterized. We sampled 116 individual houseflies and blowflies from varying habitats on three continents and subjected them to high-coverage, whole-genome shotgun sequencing. This allowed for genomic and metagenomic analyses of the host-associated microbiome at the species level. Both fly host species segregate based on principal coordinate analysis of their microbial communities, but they also show an overlapping core microbiome. Legs and wings displayed the largest microbial diversity and were shown to be an important route for microbial dispersion. The environmental sequencing approach presented here detected a stochastic distribution of human pathogens, such as Helicobacter pylori, thereby demonstrating the potential of flies as proxies for environmental and public health surveillance.

Ecological succession of the microbial communities of an air-conditioning cooling coil in the tropics

Air-conditioning systems harbor microorganisms, potentially spreading them to indoor environments. While air and surfaces in air-conditioning systems are periodically sampled as potential sources of indoor microbes, little is known about the dynamics of cooling coil-associated communities and their effect on the downstream airflow. Here, we conducted a 4-week time series sampling to characterize the succession of an air-conditioning duct and cooling coil after cleaning. Using an universal primer pair targeting hypervariable regions of the 16S/18S ribosomal RNA, we observed a community succession for the condensed water, with the most abundant airborne taxon Agaricomycetes fungi dominating the initial phase and Sphingomonas bacteria becoming the most prevalent taxa toward the end of the experiment. Duplicate air samples collected upstream and downstream of the coil suggest that the system does not act as ecological filter or source/sink for specific microbial taxa during the duration of the experiment.

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

Abstract 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 users 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.

Complete genome sequence of bacillus altitudinis type strain SGAir0031 isolated from tropical air collected in Singapore

ABSTRACT Bacillus altitudinis strain SGAir0031 (Firmicutes) was isolated from tropical air samples collected in Singapore. Its genome was assembled using short reads and single-molecule real-time sequencing, comprising one chromosome with 3.81 Mb and one plasmid with 32 kb. The genome consists of 3,820 protein-coding genes, 81 tRNAs, and 24 rRNAs.