Pitfalls using tributyrin agar screening to detect lipolytic activity in metagenomic studies

The metagenomics approach is an efficient method for obtaining novel biocatalysts and useful genes from uncultured microorganisms within diverse environments. In this study, we constructed a metagenomic library using a South African deep mine biofilm sample. The library was screened forlipolytic activity using LB Tributyrin (TLB). Although we were able to identify 3 diverse esterase enzymes, we found that 70% of the obtained sequence data revealed the presence of enzymes and genes completely unrelated to that of lipolytic enzymes thereby highlighting the limitation of screening with TLB

A deep gold mine metagenome as a source of novel esterases

New sources of enzymes for biotechnological applications are continually being sought for. While diverse microbial ecosysyems have been demonstrated in the deep subsurfaces, deep mines provide easy access to these specialist communities. Therefore, the aim of this study was to assess a deep mine biofilm as a source of novel esterase enzymes. Biofilm was collected from the Beatrix Mine in South Africa, at a depth of 808 m. Assessment of the diversity revealed a group of previously uncultured bacteria and archaea. A metagenome library was screened for esterolytic activity, producing two esterolytic clones: a phospholipase patatin protein and an isochorismatase family protein. The isochorismatase family protein contained the catalytic Asp and Cys but not the Arg, which is considered as important for catalysis. The patatin showed 55% similarity to its closest relative; the patatin family protein from Plesiocystis pacifica. The expressed patatin displayed a preference for the C6 ester and was maximally active at pH 8 and 30°C. This study reported that screening of a relatively small metagenome library from the deep mine biofilm provided two esterolytic clones, which differed from their known counterparts. This indicates that the deep mine ecosystems contain an untapped resource of novel and potentially useful enzymes which may have applications in chemical syntheses.Key words: Metagenome library, functional screening, lipolytic activity, patatin, isochorismatas

Metagenomics - a guide from sampling to data analysis

Metagenomics applies a suite of genomic technologies and bioinformatics tools to directly access the genetic content of entire communities of organisms. The field of metagenomics has been responsible for substantial advances in microbial ecology, evolution, and diversity over the past 5 to 10 years, and many research laboratories are actively engaged in it now. With the growing numbers of activities also comes a plethora of methodological knowledge and expertise that should guide future developments in the field. This review summarizes the current opinions in metagenomics, and provides practical guidance and advice on sample processing, sequencing technology, assembly, binning, annotation, experimental design, statistical analysis, data storage, and data sharing. As more metagenomic datasets are generated, the availability of standardized procedures and shared data storage and analysis becomes increasingly important to ensure that output of individual projects can be assessed and compared

Tracking down carbon inputs underground from an arid zone Australian calcrete.

Freshwater ecosystems play a key role in shaping the global carbon cycle and maintaining the ecological balance that sustains biodiversity worldwide. Surficial water bodies are often interconnected with groundwater, forming a physical continuum, and their interaction has been reported as a crucial driver for organic matter (OM) inputs in groundwater systems. However, despite the growing concerns related to increasing anthropogenic pressure and effects of global change to groundwater environments, our understanding of the dynamics regulating subterranean carbon flows is still sparse. We traced carbon composition and transformations in an arid zone calcrete aquifer using a novel multidisciplinary approach that combined isotopic analyses of dissolved organic carbon (DOC) and inorganic carbon (DIC) (δ13CDOC, δ13CDIC, 14CDOC and 14CDIC) with fluorescence spectroscopy (Chromophoric Dissolved OM (CDOM) characterisation) and metabarcoding analyses (taxonomic and functional genomics on bacterial 16S rRNA). To compare dynamics linked to potential aquifer recharge processes, water samples were collected from two boreholes under contrasting rainfall: low rainfall ((LR), dry season) and high rainfall ((HR), wet season). Our isotopic results indicate limited changes and dominance of modern terrestrial carbon in the upper part (northeast) of the bore field, but correlation between HR and increased old and 13C-enriched DOC in the lower area (southwest). CDOM results show a shift from terrestrially to microbially derived compounds after rainfall in the same lower field bore, which was also sampled for microbial genetics. Functional genomic results showed increased genes coding for degradative pathways-dominated by those related to aromatic compound metabolisms-during HR. Our results indicate that rainfall leads to different responses in different parts of the bore field, with an increase in old carbon sources and microbial processing in the lower part of the field. We hypothesise that this may be due to increasing salinity, either due to mobilisation of Cl- from the soil, or infiltration from the downstream salt lake during HR. This study is the first to use a multi-technique assessment using stable and radioactive isotopes together with functional genomics to probe the principal organic biogeochemical pathways regulating an arid zone calcrete system. Further investigations involving extensive sampling from diverse groundwater ecosystems will allow better understanding of the microbiological pathways sustaining the ecological functioning of subterranean biota

Good correlation between the Afinion AS100 analyser and the ABX Pentra 400 analyser for the measurement of glycosylated haemoglobin and lipid levels in older adults in Durban, South Africa

Background. The Afinion AS100 analyser is a small bench-top, multi-assay, point-of-care (POC) analyser that is able to measure glycated haemoglobin (HbA1c) and lipid levels.Objective. To assess performance of the Afinion analyser compared with a reference laboratory test for the measurement of HbA1c and lipid levels.Method. The study involved men and women enrolled in a cross-sectional study, Sexual health, HIV infection and comorbidity with non-communicable diseases among Older Persons (SHIOP), which was conducted from February to May 2016. Whole blood was drawn aseptically by a trained study nurse into a serum separator gel tube and an thylenediaminetetra-acetic acid (EDTA) tube. The EDTA whole blood was used to measure HbA1c levels, and serum to measure total cholesterol (TC), high-density lipoprotein  cholesterol (HDL-C), lowdensity lipoprotein cholesterol (LDL-C) and triglyceride levels. Lin’s correlation coefficient was used to assess the agreement between the Afinion and ABX Pentra 400 analysers for each marker.Results. A total of 435 older individuals were included in the study. The proportion of HbA1c results that were correctly classified by the Afinion analyser was 92.2%. Bland-Altman analysis and linear regression analysis showed a very good agreement (correlation concordance 0.89) between the two analysers for the measurement of HbA1c. The two-way scatter plot for TC showed a substantial correlation (0.80). However, a total of 69 cholesterol results that were within the normal range on the Pentra were misclassified as abnormal on the Afinion. The readings obtained for HDL-C levels with the Afinion were shown to be slightly overestimated when compared with the Pentra. However, correlation for HDL-C on the two analysers was 0.93, indicating an almost perfect agreement. Seventy-four LDL-C results were erroneously classified as abnormal on the Afinion but were within the normal range on the Pentra, resulting in a substantial correlation of 0.75. An excellent agreement was observed between triglyceride measurements (0.99).Conclusion. This study supports the use of the Afinion AS100 analyser in POC testing for the measurement of HbA1c, triglycerides and HDL-C in a South African setting

Biological factors that place women at risk for HIV: Evidence from a large-scale clinical trial in Durban

Background: It is well documented that the mucosal linings of the female genital tract (FGT) usually provides a robust barrier that protects against sexually acquired infections. However, to the best of our knowledge there are limited South African studies that have investigated the association between damage to the mucosal linings and the acquisition of HIV infections. We hypothesize that in this cohort of women, a higher rate of HIV seroconversions will be observed for women who present with evidence of mucosal damage. Methods: We undertook a secondary analysis of the Methods for Improving Reproductive Health in Africa (MIRA) trial that assessed the effectiveness of the latex diaphragm and lubricant gel on HIV prevention among women. Participants underwent a physical examination which included a pelvic examination to detect the presence of mucosal abnormalities. During the physical examinations, the study clinicians examined the genitalia, cervix and vagina for signs of epithelial disruptions and abnormal vaginal discharge. The association between the various genital factors and HIV seroconversion was modeled using Cox proportional hazards regression analysis. Results: In this cohort of 1485 women that had enrolled to participate in the study, women that had presented with genital epithelial disruptions and abnormal vaginal discharge were shown to be at highest risk for HIV acquisition (Hazard Ratio (HR): 4.30, 95 % CI: 2.25, 8.22, p <0001, HR: 2.37, 95 % CI: 1.69, 3.33, p <0.001) respectively. In addition, the Kaplan Meier analysis showed that the highest number of seroconversions was observed in women that had disrupted genital epithelia (27 per 100/py, 95 % CI: 15.0, 50.7) and abnormal vaginal discharge (12 per 100/py, 95 % CI: 9.70, 16.7). Other significant factors included: genital signs and symptoms (HR: 1.67, 95 % CI: 1.07, 2.61, p = 0.02) and genital ulcers/sores (HR: 1.79, 95 % CI: 1.05, 3.06, p = 0.03). Conclusion: We have shown that damage to the mucosal epithelial lining increases a women's risk of HIV seroconversion. Future studies that provide an in depth understanding of the mechanisms associated with the FGT and mucosal immunity will be most valuable. An understanding of all of these mechanisms will be key in directing the advancement of products most suitable for combating HIV infection in women. Trial registration: This study was registered with ClinicalTrials.gov,number NCT00121459on the 28th February 2007