Terminal restriction fragment length polymorphism is an “old school” reliable technique for swift microbial community screening in anaerobic digestion

The microbial community in anaerobic digestion has been analysed through microbial fingerprinting techniques, such as terminal restriction fragment length polymorphism (TRFLP), for decades. In the last decade, high-throughput 16S rRNA gene amplicon sequencing has replaced these techniques, but the time-consuming and complex nature of high-throughput techniques is a potential bottleneck for full-scale anaerobic digestion application, when monitoring community dynamics. Here, the bacterial and archaeal TRFLP profiles were compared with 16S rRNA gene amplicon profiles (Illumina platform) of 25 full-scale anaerobic digestion plants. The α-diversity analysis revealed a higher richness based on Illumina data, compared with the TRFLP data. This coincided with a clear difference in community organisation, Pareto distribution, and co-occurrence network statistics, i.e., betweenness centrality and normalised degree. The β-diversity analysis showed a similar clustering profile for the Illumina, bacterial TRFLP and archaeal TRFLP data, based on different distance measures and independent of phylogenetic identification, with pH and temperature as the two key operational parameters determining microbial community composition. The combined knowledge of temporal dynamics and projected clustering in the β-diversity profile, based on the TRFLP data, distinctly showed that TRFLP is a reliable technique for swift microbial community dynamics screening in full-scale anaerobic digestion plants

Terminal restriction fragment length polymorphism is an “old school” reliable technique for swift microbial community screening in anaerobic digestion

The microbial community in anaerobic digestion has been analysed through microbial fingerprinting techniques, such as terminal restriction fragment length polymorphism (TRFLP), for decades. In the last decade, high-throughput 16S rRNA gene amplicon sequencing has replaced these techniques, but the time-consuming and complex nature of high-throughput techniques is a potential bottleneck for full-scale anaerobic digestion application, when monitoring community dynamics. Here, the bacterial and archaeal TRFLP profiles were compared with 16S rRNA gene amplicon profiles (Illumina platform) of 25 full-scale anaerobic digestion plants. The α-diversity analysis revealed a higher richness based on Illumina data, compared with the TRFLP data. This coincided with a clear difference in community organisation, Pareto distribution, and co-occurrence network statistics, i.e., betweenness centrality and normalised degree. The β-diversity analysis showed a similar clustering profile for the Illumina, bacterial TRFLP and archaeal TRFLP data, based on different distance measures and independent of phylogenetic identification, with pH and temperature as the two key operational parameters determining microbial community composition. The combined knowledge of temporal dynamics and projected clustering in the β-diversity profile, based on the TRFLP data, distinctly showed that TRFLP is a reliable technique for swift microbial community dynamics screening in full-scale anaerobic digestion plants. © 2018, The Author(s)

Survey of aflatoxins in chillies from Pakistan produced in rural, semi-rural and urban environments

Chilli peppers from Pakistan are consumed locally and also exported. Their quality is compromised by aflatoxins (AF) contamination. AF in chillies from rural, semi-rural and urban areas of the Punjab region of Pakistan were determined. Twenty-three (52.3%), 22 (50%) and 29 (65.9%) samples from rural, semi-rural and urban areas respectively, contained levels of aflatoxins which exceeded the European Union limits of >5 µg kg-1 for AFB1 and >10 µg kg-1 for total AF that apply to spices. Mean values for AFB1 in ground samples were 23.8, 14.8 and 14.0 µg kg-1 for rural, semi-rural and urban areas, respectively. Mean total AF in ground samples were 27.7, 17.7 and 16.2 µg kg-1 from equivalent locations. Eleven (50%), 12 (54.5%) and 14 (63.6%) whole samples from rural, semi-rural and urban areas, respectively, contained total levels of AF that exceeded European Union limits. The data indicate that individual localities have particular problems. In conclusion, the concentrations were often greater than the statutory limits set by the European Union.The authors acknowledge the financial support of the Higher Education Commission, Pakistan, under Indigenous PhD fellowship 5000 batch-III (Grant Number 063-00445-Ps3-047). R.R.M.P. is grateful for the FCT framework position: Commitment to Science (C2008-UMIN-HO-CEB-2)

Fecal Enterobacteriales enrichment is associated with increased in vivo intestinal permeability in humans

Type 2 diabetes (T2D) has been linked with increased intestinal permeability, but the clinical significance of this phenomenon remains unknown. The objective of this study was to investigate the potential link between glucose control, intestinal permeability, diet and intestinal microbiota in patients with T2D. Thirty‐two males with well‐controlled T2D and 30 age‐matched male controls without diabetes were enrolled in a case–control study. Metabolic parameters, inflammatory markers, endotoxemia, and intestinal microbiota in individuals subdivided into high (HP) and normal (LP) colonic permeability groups, were the main outcomes. In T2D, the HP group had significantly higher fasting glucose (P = 0.034) and plasma nonesterified fatty acid levels (P = 0.049) compared with the LP group. Increased colonic permeability was also linked with altered abundances of selected microbial taxa. The microbiota of both T2D and control HP groups was enriched with Enterobacteriales. In conclusion, high intestinal permeability was associated with poorer fasting glucose control in T2D patients and changes in some microbial taxa in both T2D patients and nondiabetic controls. Therefore, enrichment in the gram‐negative order Enterobacteriales may characterize impaired colonic permeability prior to/independently from a disruption in glucose tolerance

Aflatoxin B1 in chilies from the Punjab region, Pakistan

The occurrence of aflatoxin B1 (AFB1) in chilies from Pakistan was determined by using HPLC in work undertaken in Pakistan.Whole (n=22) and powdered (n=22) chilies were analyzed. Sixteen (73.0%) and 19 (86.4%) samples of whole and ground chilies, respectively, were contaminated. The mean concentration in powdered chilies (32.20 μg/kg) was higher statistically than in whole chilies (24.69 μg/kg). Concentrations ranged from 0.00 to 89.56 μg/ kg for powdered chilies, compared with 0.00–96.3 μg/kg for whole chilies. The limits of detection and quantification were 0.05 μg/kg and 0.53 μg/kg, respectively. The concentrations were high in general and greater than the statutory limit set by the European Union. There is considerable scope for improvements in chili production in Pakistan.Higher Education Commission, PakistanFundação para a Ciência e a Tecnologia (FCT

Assessment of Protective Clothing Used by Chemical Industry Workers in Pakistan

Protective clothing serves as a barrier against many hazards faced by workers in the industry. This study aimed to investigate the performance of locally manufactured clothing used by workers in the chemical industries in Pakistan. The construction parameters were determined using international test procedures for all samples. Then, these were assessed for their chemical resistance behavior after various laundering intervals, following the ISO 6530:2005 test method. After the investigation, it was observed that the collected samples failed to meet the minimum criteria for penetration and repellency through their structure. The samples were unable to repel a minimum of 95% liquid chemical and penetrated it more than 5%, even at zero wash. These conditions worsened with each washing interval. Clothing materials should always be checked for their performance before use to protect workers at workplace

Effect of laser irradiation on cell function and its implications in Raman spectroscopy

Lasers are instrumental in advanced bioimaging and Raman spectroscopy. However, they are also well known for their destructive effects on living organisms, leading to concerns about the adverse effects of laser technologies. To implement Raman spectroscopy for cell analysis and manipulation, such as Raman activated cell sorting, it is crucial to identify non-destructive conditions for living cells. Here, we evaluated quantitatively the effect of 532 nm laser irradiation on bacterial cell fate and growth at the single-cell level. Using a purpose-built microfluidic platform, we were able to quantify the growth characteristics i.e. specific growth rate and lag time of individual cells as well as the survival rate of a population in conjunction with Raman spectroscopy. Representative Gram-negative and Gram-positive species show a similar trend in response to laser irradiation dose. Laser irradiation could compromise physiological function of cells and the degree of destruction is both dose and strain dependent, ranging from reduced cell growth to a complete loss of cell metabolic activity and finally to physical disintegration. Gram-positive bacterial cells are more susceptible than Gram-negative bacterial strains to irradiation-induced damage. By directly correlating Raman acquisition with single cell growth characteristics, we provide evidence of non-destructive characteristics of Raman spectroscopy on individual bacterial cells. However, while strong Raman signals can be obtained without causing cell death, the variety of responses from different strains and from individual cells justify careful evaluation of Raman acquisition conditions if cell viability is critical

Impact of a nurse‐led enhanced monitoring, management and contact tracing intervention for chronic hepatitis B in England, 2015‐2017

Around 200,000 people live with chronic hepatitis B in England. Despite national guidance on identification and management of cases and their close contacts, testing rates of close contacts is as low as 43% in high prevalence areas of London. Our study aimed to determine whether a nurse‐led enhanced management and contact tracing of chronically infected individuals improved testing uptake, vaccination and onward referral of close contacts. The study was conducted across Greater Manchester and East of England regions between October 2015 and July 2017. All HBV chronically infected individuals registered with a GP and their close contacts were eligible for recruitment. The proportion of contacts who were tested, vaccinated and referred where appropriate were compared before and after the nurse‐led intervention. Baseline and outcome information was collected using questionnaires. The intervention improved case referral rates by an additional 14% (from 86% (88/102 cases) to 99.7%; 648/650 cases). The proportion of contacts tested increased from 34% to 72%‐94% with 18 new cases of HBV diagnosed. Amongst close contacts tested, vaccination rates of at least three doses increased from 77% (43/56) to 93% (452/491) during the study. Our study has shown that nurse‐led enhanced management greatly improves identification, testing and vaccination of close contacts. The identification of new acute and chronic cases is likely to make the intervention cost effective and local health commissioners should consider providing a nurse‐led service as part of hepatitis B care pathways

Putative antimicrobial peptides within bacterial proteomes affect bacterial predominance: a network analysis perspective

The predominance of bacterial taxa in the gut, was examined in view of the putative antimicrobial peptide sequences (AMPs) within their proteomes. The working assumption was that compatible bacteria would share homology and thus immunity to their putative AMPs, while competing taxa would have dissimilarities in their proteome-hidden AMPs. A network–based method (“Bacterial Wars”) was developed to handle sequence similarities of predicted AMPs among UniProt-derived protein sequences from different bacterial taxa, while a resulting parameter (“Die” score) suggested which taxa would prevail in a defined microbiome. T he working hypothesis was examined by correlating the calculated Die scores, to the abundance of bacterial taxa from gut microbiomes from different states of health and disease. Eleven publicly available 16S rRNA datasets and a dataset from a full shotgun metagenomics served for the analysis. The overall conclusion was that AMPs encrypted within bacterial proteomes affected the predominance of bacterial taxa in chemospheres