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Summary: Nanometa Live presents a user-friendly interface designed for real-time metagenomic data analysis and pathogen identification utilizing Oxford Nanopore Technologies’ MinION and Flongle flow cells. It offers an efficient workflow and graphical interface for the visualization and interpretation of metagenomic data as it is being generated. Key features include automated BLAST validation, streamlined handling of custom Kraken2 databases, and a simplified graphical user interface for enhanced user experience. Nanometa Live is particularly notable for its capability to run without constant internet or server access once installed, setting it apart from similar tools. It provides a comprehensive view of taxonomic composition and facilitates the detection of user-defined pathogens or other species of interest, catering to both researchers and clinicians. Availability and implementation: Nanometa Live has been implemented as a local web application using the Dash framework with Snakemake handling the data processing. The source code is freely accessible on the GitHub repository at https://github.com/FOIBioinformatics/nanometa_live and it is easily installable using Bioconda. It includes containerization support via Docker and Singularity, ensuring ease of use, reproducibility, and portability.

Summary: Nanometa Live presents a user-friendly interface designed for real-time metagenomic data analysis and pathogen identification utilizing Oxford Nanopore Technologies’ MinION and Flongle flow cells. It offers an efficient workflow and graphical interface for the visualization and interpretation of metagenomic data as it is being generated. Key features include automated BLAST validation, streamlined handling of custom Kraken2 databases, and a simplified graphical user interface for enhanced user experience. Nanometa Live is particularly notable for its capability to run without constant internet or server access once installed, setting it apart from similar tools. It provides a comprehensive view of taxonomic composition and facilitates the detection of user-defined pathogens or other species of interest, catering to both researchers and clinicians. Availability and implementation: Nanometa Live has been implemented as a local web application using the Dash framework with Snakemake handling the data processing. The source code is freely accessible on the GitHub repository at https://github.com/FOIBioinformatics/nanometa_live and it is easily installable using Bioconda. It includes containerization support via Docker and Singularity, ensuring ease of use, reproducibility, and portability.

Summary: Nanometa Live presents a user-friendly interface designed for real-time metagenomic data analysis and pathogen identification utilizing Oxford Nanopore Technologies’ MinION and Flongle flow cells. It offers an efficient workflow and graphical interface for the visualization and interpretation of metagenomic data as it is being generated. Key features include automated BLAST validation, streamlined handling of custom Kraken2 databases, and a simplified graphical user interface for enhanced user experience. Nanometa Live is particularly notable for its capability to run without constant internet or server access once installed, setting it apart from similar tools. It provides a comprehensive view of taxonomic composition and facilitates the detection of user-defined pathogens or other species of interest, catering to both researchers and clinicians. Availability and implementation: Nanometa Live has been implemented as a local web application using the Dash framework with Snakemake handling the data processing. The source code is freely accessible on the GitHub repository at https://github.com/FOIBioinformatics/nanometa_live and it is easily installable using Bioconda. It includes containerization support via Docker and Singularity, ensuring ease of use, reproducibility, and portability.

Summary: Nanometa Live presents a user-friendly interface designed for real-time metagenomic data analysis and pathogen identification utilizing Oxford Nanopore Technologies’ MinION and Flongle flow cells. It offers an efficient workflow and graphical interface for the visualization and interpretation of metagenomic data as it is being generated. Key features include automated BLAST validation, streamlined handling of custom Kraken2 databases, and a simplified graphical user interface for enhanced user experience. Nanometa Live is particularly notable for its capability to run without constant internet or server access once installed, setting it apart from similar tools. It provides a comprehensive view of taxonomic composition and facilitates the detection of user-defined pathogens or other species of interest, catering to both researchers and clinicians. Availability and implementation: Nanometa Live has been implemented as a local web application using the Dash framework with Snakemake handling the data processing. The source code is freely accessible on the GitHub repository at https://github.com/FOIBioinformatics/nanometa_live and it is easily installable using Bioconda. It includes containerization support via Docker and Singularity, ensuring ease of use, reproducibility, and portability.

Big data abound in microbiology, but the workflows designed to enable researchers to interpret data can constrain the biological questions that can be asked. Five years after anvi'o was first published, this community-led multi-omics platform is maturing into an open software ecosystem that reduces constraints in 'omics data analyses.

Francisella noatunensis is a fastidious facultative intracellular bacterial pathogen that causes 'piscine francisellosis', a serious disease affecting both marine and fresh water farmed and wild fish worldwide. Currently two F. noatunensis subspecies are recognized, i.e. F. noatunensis subsp. noatunensis and F. noatunensis subsp. orientalis. In the present study, the taxonomy of F noatunensis was revisited using a polyphasic approach, including whole genome derived parameters such as digital DNA-DNA hybridization, whole genome average nucleotide identity (wg-ANlm), whole genome phylogenetic analysis, whole genome G+C content, metabolic fingerprinting and chemotaxonomic analyses. The results indicated that isolates belonging to F. noatunensis subsp. orientalis represent a phenotypically and genetically homogenous taxon, clearly distinguishable from F. noatunensis subsp. noatunensis that fulfils requirements for separate species status. We propose, therefore, elevation of F. noatunensis subsp. orientalis to the species rank as Francisella orientalis sp. nov. with the type strain remaining as Ehime-1T (DSM 21254(T)=LMG 24544(T)). Furthermore, we identified sufficient phenotypic and genetic differences between F. noatunensis subsp. noatunensis recovered from diseased farmed Atlantic salmon in Chile and those isolated from wild and farmed Atlantic cod in Northern Europe to warrant proposal of the Chilean as a novel F. noatunensis subspecies, i.e. Francisella noatunensis subsp. chilensis subsp. nov. with strain PQ1106(T) (CECT 9798(T)=NCTC14375(T)) as the type strain. Finally, we emend the description of F. noatunensis by including further metabolic information and the description of atypical strains.

Early-childhood biomonitoring of persistent organic pollutants (POPs) is challenging due to the logistic and ethical limitations associated with blood sampling. We investigated using faeces as a non-invasive matrix to estimate internal exposure to POPs. The concentrations of selected POPs were measured in matched plasma and faecal samples collected from 20 infants/toddlers (aged 13 +/- 4.8 months), including a repeat sample time point for 13 infants (similar to 5 months apart). We observed higher rates of POP quantification in faeces (2 g dry weight) than in plasma (0.5 mL). Among the five chemicals that had quantification frequencies over 50% in both matrices, except for HCB, log concentration in faeces (C-f) and blood (C-b) were correlated (r > 0.74, P < 0.05) for p.p'-dichlorodiphenyldichloroethylene (p,p'-DDE), 2,3', 4,4', 5-pentachlorobiphenyl (PCB118), 2,2', 3,4,4', 5'-pentachlorobiphenyl (PCB138) and 2,2', 4,4', 5,5'-pentachlorobiphenyl (PCB153). We determined faeces: plasma concentration ratios (K-fb), which can be used to estimate C-b from measurements of C-f for infants/toddlers. For a given chemical, the variation in K-fb across individuals was considerable (CV from 0.46 to 0.70). Between 5% and 50% of this variation was attributed to short-term intra-individual variability between successive faecal samples. This variability could be reduced by pooling faeces samples over several days. Some of the remaining variability was attributed to longer-term intra-individual variability, which was consistent with previously reported observations of a decrease in K-fb over the first year of life. The strong correlations between C-f and C-b demonstrate the promise of using faeces for biomonitoring of these compounds. Future research on the sources of variability in K-fb could improve the precision and utility of this technique.

Early-childhood biomonitoring of persistent organic pollutants (POPs) is challenging due to the logistic and ethical limitations associated with blood sampling. We investigated using faeces as a non-invasive matrix to estimate internal exposure to POPs. The concentrations of selected POPs were measured in matched plasma and faecal samples collected from 20 infants/toddlers (aged 13 ± 4.8 months), including a repeat sample time point for 13 infants (~ 5 months apart). We observed higher rates of POP quantification in faeces (2 g dry weight) than in plasma (0.5 mL). Among the five chemicals that had quantification frequencies over 50% in both matrices, except for HCB, log concentration in faeces (Cf) and blood (Cb) were correlated (r > 0.74, P < 0.05) for p.p′-dichlorodiphenyldichloroethylene (p,p′-DDE), 2,3′,4,4′,5-pentachlorobiphenyl (PCB118), 2,2′,3,4,4′,5′-pentachlorobiphenyl (PCB138) and 2,2′,4,4′,5,5′-pentachlorobiphenyl (PCB153). We determined faeces:plasma concentration ratios (Kfb), which can be used to estimate Cb from measurements of Cf for infants/toddlers. For a given chemical, the variation in Kfb across individuals was considerable (CV from 0.46 to 0.70). Between 5% and 50% of this variation was attributed to short-term intra-individual variability between successive faecal samples. This variability could be reduced by pooling faeces samples over several days. Some of the remaining variability was attributed to longer-term intra-individual variability, which was consistent with previously reported observations of a decrease in Kfb over the first year of life. The strong correlations between Cf and Cb demonstrate the promise of using faeces for biomonitoring of these compounds. Future research on the sources of variability in Kfb could improve the precision and utility of this technique.

Exposure to polycyclic aromatic hydrocarbons (PAHs) has been associated with adverse health outcomes. Concentrations of urinary PAH metabolites (OH-PAHs) provide an integrated measure of human exposure to PAHs but measurement of urinary OH-PAHs has not been done in Australia and rarely in Vietnam, where air pollution is of concern. In this study, we assessed exposure to PAHs in 16 participants living in Brisbane, Australia and Hanoi, Vietnam, with 4 participants travelling between the two cities during the monitoring period. A total of 312 first morning urine samples were collected over 10 weeks and were analysed for nine OH-PAHs. Concentrations of the urinary OH-PAHs were 2–10 times higher in participants from Hanoi than those from Brisbane. For example, the median concentrations of 1-hydroxypyrene were 292 pg/mL in Hanoi, compared to 64 pg/mL in Brisbane. For participants travelling from Brisbane to Hanoi and back, differences in exposure to PAHs in these two cities resulted in corresponding changes of urinary OH-PAH concentrations, demonstrating that the more polluted environment in Hanoi was likely the source for higher PAH exposure there.

Human half-lives of PentaBDE congeners have been estimated from the decline in serum concentrations measured over a 6-12 month period for a population of exchange students moving from North America to Australia. Australian serum PBDE concentrations are typically between 5 -10 times lower than in North America and we can therefore hypothesize that if the biological half-life is sufficiently short we would observe a decline in serum concentration with length of residence in Australia. Thirty students were recruited over a period of 3 years from whom serum were archived every 2 months during their stay in Australia. Australian residents (n=22) were also sampled longitudinally to estimate general population background levels. All serum samples were analyzed by gas chromatography high resolution mass spectrometry. Key findings confirmed that BDE-47 concentrations in the Australians (median 2.3;

Persistent, lipophilic organochlorine pesticides (OCPs) such as dichlorodiphenyltrichloroethane (DDT), hexachlorocyclohexanes (HCHs), dieldrin, chlordanes, hexachlorobenzene (HCB) and mirex are known to accumulate in human samples [1, 2]. Persistent OCPs are among the chemicals that are covered under the Stockholm Convention on persistent organic pollutants [3]. Exceptions to this include relatively less lipophillic compounds like HCH (KOW<10^5). In Australia, OCPs such as DDT and HCHs were introduced in the 1940s. This followed a period of widespread use until the 1970s when recognition of risks related to OCPs resulted in reduced use and their ultimate ban in the 1980s. Mirex, however, remained in very restricted use in Northern Australia for treatment of one species of termites (the Giant Termite (Mastotermes darwinensis)) but this use was phased out in 2007.

Human polybrominated diphenyl ether (PBDE) exposure occurs through a range of pathways including: ingestion of dust including hand-to-mouth contact; inhalation (air/particulate matter); and ingestion via food including the unique nutrition sources of human milk and placental transfer. While inhalation has been deemed a minor source of exposure, ingestion of food and dust make greater contributions to overall PBDE body burden with intake via dust reported to be much higher in infants than in adults. PBDEs have been detected in samples of human milk, blood serum, cord blood, and adipose tissue worldwide. Concentrations have been found to be highest in populations from North America, followed by Australia, Europe, and Asia. While factors such as gender and parity may not affect concentrations, occupational exposure and age (infants and children) are associated with higher PBDE concentrations. In contrast to “traditional” persistent organic pollutants, there is an inverse relationship between PBDE body burden and age. Predicted body burden calculated using available information on intake and elimination rates of BFRs appears to underestimate measured human body burden data obtained through analysis of BFRs in blood or human milk. This may be due to unknown exposure or inaccurate elimination data. Further exposure studies should focus on younger age groups and an investigation of human PBDE half-lives.

Polyfluoroalkyl chemicals (PFCs) have been used worldwide for more than 50 years in a wide variety of industrial and consumer products. Limited data exist on human exposure to PFCs in the Southern Hemisphere. Human blood serum collected in southeast Queensland, Australia, in 2006−2007 from 2420 donors was pooled according to age (cord blood, 0−0.5, 0.6−1, 1.1−1.5, 1.6−2, 2.1−2.5, 2.6−3, 3.1−3.5, 3.6−4, 4.1−6, 6.1−9, 9.1−12, 12.1−15, 16−30, 31−45, 46−60, and >60 years) and gender and was analyzed for eight PFCs. Across all pools, perfluorooctane sulfonate (PFOS) was detected at the highest mean concentration (15.2 ng/mL) followed by perfluorooctanoate (PFOA, 6.4 ng/mL), perfluorohexane sulfonate (PFHxS, 3.1 ng/mL), perfluorononanoate (PFNA, 0.8 ng/mL), 2-(N-methyl-perfluorooctance sulfonamide) acetate (Me-PFOSA-AcOH, 0.66 ng/mL), and perfluorodecanoate (PFDeA, 0.29 ng/mL). Perfluorooctane sulfonamide was detected in only 24% of the pools, and 2-(N-ethylperfluorooctane sulfonamide) acetate was detected in only one. PFOS concentrations were significantly higher in pools from adult males than from adult females (p = 0.002); no gender differences were apparent in the pools from children (<12 years old). The highest mean concentrations of PFOA, PFHxS, PFNA, PFDeA, and Me-PFOSA-AcOH were found in children <15 years, while PFOS was highest in adults >60 years. Investigation into the sources and exposure pathways in Australia, in particular for children, is necessary as well as continued biomonitoring to determine the potential effects on human concentrations as a result of changes in the PFC manufacturing practices, including the cessation of production of several PFCs.

Introduction Polybrominated diphenyl ethers (PBDEs) are considered to be a cost effective and efficient way to reduce the possibility of product ignition and inhibit the spread of fire, thereby limiting harm caused by fires. PBDEs are incorporated into a wide variety of manufactured products and are now considered an ubiquitous contaminant found worldwide in biological and environmental samples . In comparison to “traditional” persistent organic pollutants (POPs), the exposure modes of PBDEs in humans are less well defined, although dietary sources, inhalation (air/particulate matter) and dust ingestion have been reported 2-4. Limited investigations of population specific factors such as age or gender and PBDE concentrations report: no conclusive correlation by age in adults ; higher concentrations in children ; similar concentrations in maternal and cord blood ; and no gender differences . After preliminary findings of higher PBDE concentrations in children than in adults in Australia11 we sought to investigate at what age the PBDE concentrations peaked in an effort to focus exposure studies. This investigation involved the collection of blood samples from young age groups and the development of a simple model to predict PBDE concentrations by age in Australia.

Introduction Polybrominated diphenyl ethers (PBDEs) are considered to be a cost effective and efficient way to reduce the possibility of product ignition and inhibit the spread of fire, thereby limiting harm caused by fires. PBDEs are incorporated into a wide variety of manufactured products and are now considered an ubiquitous contaminant found worldwide in biological and environmental samples1 . In comparison to “traditional” persistent organic pollutants (POPs), the exposure modes of PBDEs in humans are less well defined, although dietary sources, inhalation (air/particulate matter) and dust ingestion have been reported 2-4. Limited investigations of population specific factors such as age or gender and PBDE concentrations report: no conclusive correlation by age in adults; higher concentrations in children ; similar concentrations in maternal and cord blood; and no gender differences. After preliminary findings of higher PBDE concentrations in children than in adults in Australia11 we sought to investigate at what age the PBDE concentrations peaked in an effort to focus exposure studies. This investigation involved the collection of blood samples from young age groups and the development of a simple model to predict PBDE concentrations by age in Australia.

The increasing accessibility and use of microarrays in transcriptomics has accentuated the need for purpose-designed storage and analysis tools. Here we present UPSC-BASE, a database for analysis and storage of Populus DNA microarray data. A microarray analysis pipeline has also been established to allow consistent and efficient analysis (from small to large scale) of samples in various experimental designs. A range of optimized experimental protocols is provided for each step in generating the data. Within UPSC-BASE, researchers can perform standard and advanced microarray analysis procedures in a user-friendly environment. Background corrections, normalizations, quality-control tools, visualizations, hypothesis tests and export tools are provided without requirements for expert-level knowledge. Although the database has been developed primarily for handling Populus DNA microarrays, most of the tools are generic and can be used for other types of microarray. UPSC-BASE is also a repository of Populus microarray information, providing data from 21 experiments on a total of 407 microarray hybridizations in the public domain of the database. There are also an additional 10 experiments containing 347 hybridizations, where the automatically analysed data are searchable., QC 20100525

The genetic nature of tree adaptation to drought stress was examined by utilizing variation in the drought response of a full-sib second generation (F-2) mapping population from a cross between Populus trichocarpa (93-968) and P. deltoides Bart (ILL-129) and known to be highly divergent for a vast range of phenotypic traits. We combined phenotyping, quantitative trait loci (QTL) analysis and microarray experiments to demonstrate that 'genetical genomics' can be used to provide information on adaptation at the species level. The grandparents and F-2 population were subjected to soil drying, and contrasting responses to drought across genotypes, including leaf coloration, expansion and abscission, were observed, and QTL for these traits mapped. A subset of extreme genotypes exhibiting extreme sensitivity and insensitivity to drought on the basis of leaf abscission were defined, and microarray experiments conducted on these genotypes and the grandparent species. The extreme genotype groups induced a different set of genes: 215 and 125 genes differed in their expression response between groups in control and drought, respectively, suggesting species adaptation at the gene expression level. Co-location of differentially expressed genes with drought-specific and drought-responsive QTLs was examined, and these may represent candidate genes contributing to the variation in drought response., QC 20100525