EasyMicroPlot: An Efficient and Convenient R Package in Microbiome Downstream Analysis and Visualization for Clinical Study

Advances in next-generation sequencing (NGS) have revolutionized microbial studies in many fields, especially in clinical investigation. As the second human genome, microbiota has been recognized as a new approach and perspective to understand the biological and pathologic basis of various diseases. However, massive amounts of sequencing data remain a huge challenge to researchers, especially those who are unfamiliar with microbial data analysis. The mathematic algorithm and approaches introduced from another scientific field will bring a bewildering array of computational tools and acquire higher quality of script experience. Moreover, a large cohort research together with extensive meta-data including age, body mass index (BMI), gender, medical results, and others related to subjects also aggravate this situation. Thus, it is necessary to develop an efficient and convenient software for clinical microbiome data analysis. EasyMicroPlot (EMP) package aims to provide an easy-to-use microbial analysis tool based on R platform that accomplishes the core tasks of metagenomic downstream analysis, specially designed by incorporation of popular microbial analysis and visualization used in clinical microbial studies. To illustrate how EMP works, 694 bio-samples from Guangdong Gut Microbiome Project (GGMP) were selected and analyzed with EMP package. Our analysis demonstrated the influence of dietary style on gut microbiota and proved EMP package's powerful ability and excellent convenience to address problems for this field.

The Effects of Pulsed UV Light Implementation on the Preservation Duration of Şavak Cheese Made from Raw Milk

This study aimed to investigate the effect of pulsed UV light on the the preservation of the Şavak cheese. In this study, the samples of Savak cheese (average 2 cm) that were produced from raw milk were exposed to two-sided pulsed UV light. The microbial analysis (enterobacteria, psychrophilic aerob, lactic acid, sulphate reducing bacteria, S.aureus and yeast-fungus) and chemical analysis (acidity, pH and the number of thiobarbituric acid) of şavak cheese were performed during storage time (25 days) at 4°C. According to the results, spoilage was observed in the control group after ten days, Group 1 was the best in terms of microbiological quality. When experimental samples were compared to the control group, no statistically differences were observed in terms of TBA, acidity, and pH value.

Microbial Analysis of Contact Lenses

Introduction: Contact lenses are small, thin lenses which are worn directly on the surface of the eyes. They can be worn aesthetically or to correct vision. Contact lens related eye infections can lead to serious complications such as blindness, and are associated with several risk factors such as sleeping with lenses, exposure to water, not adhering to replacement schedules, and reusing disinfecting solutions, among others. The severity of the infection may vary with the degree of pathogenicity of the microorganism. Hygiene and handling of contact lenses play a very important role. The main aim of this study is to assess the microbial analysis of contact lenses. Materials and Methods: A total of 15 lenses were collected in 2 ml sterile saline solution individually and manually agitated for five minutes. The lens was then removed using a sterile toothpick from the container. The sterile container was stored at 4°C till it was processed. 50 microliter of the sample was transferred using a pipette and inoculated on nutrient agar, blood agar and sabouraud dextrose agar. The microorganism (fungus or bacteria) were identified by standard protocol. Results and Discussion: Bacillus, Staphylococcus aureus and CONS [Coagulase Negative Staphylococci] were found in blood agar. No fungal growth was found among the samples. More importance could be given to contact lenses handling and hygiene to avoid eye related bacterial and fungal infections. Conclusion: In the present study, the total CFU (Colony Forming Unit) was found to be confluent in all the participants who wore contact lenses for 4 months compared to those who have worn contact lenses from 15 and 28 days. Only bacterial growth was seen in the culture plate. There was no fungal growth seen from the samples collected.

Integration of anammox into the MBR process for main stream sewage treatment

The integration of Anaerobic ammonia oxidation (anammox) into the membrane bioreactor (MBR) process (AX-MBR) is proposed in this study to reduce operating costs. The temperature was not controlled during the study. Anammox, denitrification, and nitrification were studied in the AX-MBR for 210 days. The reactor was fed with mainstream sewage from Guilin City, China. The results showed that AX-MBR could run with reduced dissolved oxygen (DO) concentration, and COD, NH4+-N, and total nitrogen removal were maintained or improved. The microbial analysis results demonstrated that the added anammox sludge could survive in the AX-MBR, but the sludge microbial diversity decreased. Nitrospira, Candidatus Kuenenia, and Nitrosomonas dominated the anammox sludge. In a word, the AX-MBR developed in this study could treat mainstream sewage with the appropriate management, and the operation costs are expected to reduce by decreasing the amount of aeration.

Heavy Metal, Aflatoxin, Pesticide Residue, Microbial Analysis of Siddha Polyherbal Formulation Veppampoo mathirai

Aim: The polyherbal siddha formulation veppampoo Mathirai is effective in regulating blood pressure but its safety is not known. The heavy metal, aflatoxins, pesticide residue, microbial count have not been evaluated so far. The current study evaluated the above parameters. The present study was aimed to evaluate the safety parameters (heavy metal, aflatoxin, pesticide residue and microbial profile) of Veppampoo Mathirai. Materials and Methods: According to AYUSH [Ayurveda, yoga, unani, siddha, naturopathy] Pharmacopoeial laboratory for Indian medicine (PLIM) guidelines, the formulation was evaluated for its safety parameters at Noble research solutions, kolathur, Chennai, accredited with ISO 9001: 2015.Atomic Absorption Spectrometer (AAS) was used for testing heavy metals and aflatoxins were tested using Thin layer chromatography(TLC). The Pesticide residues content was estimated by GC/MS while microbial count by pour plate method. Results: The study revealed presence of heavy metals mercury, arsenic, lead and cadmium within the recommended limit as per AYUSH Pharmacopoeial Laboratory for Indian Medicine Guidelines whereas presence of Aflatoxin, pesticide residues and microbes were absent in the sample which showed the formulation Veppampoo Mathirai (VPM) was free from toxicity. Conclusion: VPM showed heavy metal content below the permissible limit as per PLIM guidelines of AYUSH. Aflatoxins and pesticide residue were not detected while the microbes and specific pathogens were absent in the current batch of VPM. Hence, the present study ensures the formulation was safe for therapeutic use.

Haematology of Birds and Microbial Analysis of Recycled Poultry Litter Treated with Graded Levels of Aluminium Sulphate (Alum)

The study was carried out at the poultry unit of the Department of Animal Science teaching and research farm, Ahmadu Bello University, Zaria to determine the Chemical and Microbial Analysis of Poultry Litter Treated with Graded Levels of Aluminium sulphate (Alum). The alum used was obtained from the Sabon-garimarket in Zaria, Kaduna State. Aluminium sulphate (alum) was applied to the wood shavings by mixing it with alum thoroughly using hands covered with hand gloves. The rates of alum application was as follows: T1 control (normal poultry litter with no alum), T2 (5% alum by kg weight of poultry litter), T3 (10% alum by kg weight of poultry litter) and T4 (15% alum by kg weight of poultry litter). Five sets of litter samples were obtained fortnightly from each pen from different locations i.e. the four corners and centre from which the microbial load were measured. At the termination of the experiment (day 56), two birds from each pen having representative weights for the group (6 birds per Treatment) were selected and 1.5ml of blood was taken via the wing vein. Haematological parameters were analyzed by an auto haemo-analyser (BC2800 vet auto haemo analyser) at the Clinical Pathology Laboratory, Faculty of Veterinary Medicine, Ahmadu Bello University, Zaria. This result shows significant (P<0.05) difference among all the parameters analysed except MCHC. The result shows a significant decrease in the total bacteria, E. coliand Salmonella spp. in the alum treated litter groups (5%, 10% and 15% alum treated litter) compared to the control group (0% alum treated litter), the mould and yeast load was significantly increased in alum treated litter groups (5%, 10% and 15% alum treated litter) compared to the control group (0% alum treated litter).The study conclude that treating recycled poultry litter with alum can reduce microbial load of the litter. Birds reared on recycled poultry litter have significantly higher haemoglobin and PCV compared to the control.