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Pilot study for master’s degree leads to PhD

19 April 2024 | Story André Damons | Photo Supplied

A pilot study for his master’s degree not only ignited Dr Milton Mogotsi’s passion but he was also inspired by the fact that this was a newly emerging field of research in the discipline of virology at the time. This eventually led to him pursuing a PhD and ing on his research.

Dr Mogotsi graduated on Thursday (18 April) with the degree Doctor of Philosophy with specialisation in Virology during the Faculty of Health Sciences at the University of the Free State (UFS) autumn graduation ceremonies. Prof Martin Nyaga, Head of the Next Generation Sequencing Unit (UFS-NGS) and an associate professor in the Division of Virology, was his promotor and Prof Trudi O’Neill from the Department of Microbiology and Biochemistry his co-promotor.

“It feels great! It was exhausting and overwhelming at times, but that light at the end of the tunnel will start to be brighter. I feel so proud of myself and very free. Nothing beats that liberating feeling that I have successfully completed a doctoral degree and now a new chapter of my life begins. I believe this post-PhD period is an excellent time for reflecting on my attributes and revising my CV, and with a PhD degree under my belt, I look forward to an abundance of opportunities that will soon open up,” says Dr Mogotsi after graduating.

Research

According to him, he was first introduced into this research concept when he was doing his master’s degree in microbiology. “Although it was more of a pilot study aiming to assess the feasibility of conducting this type of research on a larger scale, we made some interesting findings which we published in an international journal.

“I obtained my degree with distinction, receiving an award for Best Master’s Dissertation in Microbiology. The findings of this research really ignited my passion, and I was also inspired by the fact that this was a newly emerging field of research in the discipline of virology at the time, and of course in my master’s research there were some gaps and limitations which needed to be addressed. I then took a decision to pursue a PhD and expand on that research, and working with new-born babies is always enjoyable,” says Dr Mogotsi.

With his thesis titled “Longitudinal characterisation of the enteric virome of infants from the Free State, South Africa, using viral metagenomics”, Dr Mogotsi’s research aimed to characterise the total assemblage of all viruses that colonise the gastrointestinal tract of newborns, often referred to as the gut virome, using metagenomics.

“We know that the human gut undergoes some changes as the new-born baby becomes exposed to the numerous microorganisms, such as viruses, from the immediate environment. This once-in-a-lifetime occurrence can have life-long effects on the health and disease state of humans. Viral intestinal infections are among the leading causes of childhood hospitalisations and deaths, especially in Africa, and infants are at a greater risk of suffering severe illnesses due to their immature immune system,” he explains.

According to him, previous research had focused more on the investigating the population of bacteria present in the gut of new-borns, therefore, there’s a huge knowledge gap about viruses colonising this part of the human body. In South Africa, more attention has been on assessing the effectiveness of currently available vaccines and surveillance of specific disease-causing viruses such as rotavirus.

The research he was conducting, he continues, therefore, sought to characterise all intestinal viruses in healthy new-borns individuals, their source of origin, the changes in diversity and composition occurring over time, as well as their potential implications on the health of infants. “The findings of my study have provided more insights into what is known or new viruses are colonising the infants’ gut, as well as their evolution over time”, he adds.

PhD journey

Even though he had to put his PhD on hold for a year due to COVID-19, but with the resilience, persistence, and his ability to clear the roadblocks that were in his way, he managed to complete it. He also credits his supportive mentors and a community of colleagues and friends for their unwavering support throughout his academic journey.

“After a year-long delay, I was able to go ahead with the project and everything went well from sample collection and sample processing in the lab. The challenging part was analysing and interpreting the data as this involved advanced bioinformatics, but in the end, I was able to find solutions and make sense out of the results I got. The study was a great success with two publications in peer-reviewed international journals emanating from this study.

“Furthermore, I had an opportunity to present my research in local and international conferences. I have been to Ghana, Nigeria and Indonesia. Locally, I presented in a conference in Johannesburg and in Cape Town. More exciting was participating in the Three Minute Thesis (3MT) competition in which I emerged victorious, winning the National 3MT competition. The other award I received was from the Faculty of Health Sciences Research Forum, winning the Dr Lehlohonolo Mathengtheng Trophy for best PhD presentation”, says Dr Mogotsi.

Motivation

Dr Mogotsi says the fact that he comes from the township and received his secondary education from a township school always kept him motivated. He is well aware that there are many who look up to him, who are also inspired by what he has achieved.

“More importantly, my supervisor, Prof Nyaga, was very supportive and he is very active in his research field with genuine interest in student projects, while making time to provide adequate supervision and mentorship. His high standards of ensuring that students graduate with a strong publication record is commendable.”

As a coordinator of wet lab activities at the UFS-NGS Unit, Dr Mogotsi is currently involved in several projects as the unit is a World Health Organisation Collaborating Center for Vaccine Preventable Diseases and Pathogen Genomics. They are doing collaborative projects with several partners across the continent on the genomic surveillance of enteric viruses such as rotavirus, norovirus, sapovirus, astrovirus and adenoviruses.

News Archive

Bloemfontein's quality of tap water compares very favourably with bottled water

2009-08-04

The quality of the drinking water of five suburbs in Bloemfontein is at least as good as or better than bottled water. This is the result of a standard and chemical bacterial analysis done by the University of the Free State’s (UFS) Centre for Environmental Management in collaboration with the Institute for Groundwater Studies (IGS).

Five samples were taken from tap water sources in the suburbs of Universitas, Brandwag, Bain’s Vlei, Langenhoven Park and Bayswater and 15 samples were taken of different brands of still and unflavoured bottled water. The samples were analysed at the laboratory of the IGS, while the interpretation of the analysis was done by the Centre for Environmental Management.

“We wanted to evaluate the difference in quality for human consumption between tap water and that of the different brands of bottled water,” said Prof. Maitland Seaman, Head of the Centre for Environmental Management.

“With the exception of two samples produced by multinational companies at their plants in South Africa, the different brands of bottled water used for the study were produced by South African companies, including a local small-scale Bloemfontein producer,” said Prof. Seaman.

According to the labels, the sources of the water vary from pure spring water, to partial reverse osmosis (as an aid to standardise salt, i.e. mineral, content), to only reverse osmosis (to remove salts). (Reverse osmosis is a process in which water is forced under pressure through a pipe with minute pores through which water passes but no – or very low concentrations of – salts pass.)

According to Prof. Seaman, the analysis revealed some interesting findings, such as:

• It is generally accepted that drinking water should have an acceptable level of salt content, as the body needs salts. Most mineral contents were relatively higher in the tap water samples than the bottled water samples and were very much within the acceptable range of drinkable water quality. One of the bottled samples, however, had a very low mineral content, as the water was produced by reverse osmosis, as stated on the bottle. While reverse osmosis is used by various producers, most producers use it as an aid, not as a single method to remove nearly all the salts. Drinking only such water over a prolonged period may probably have a negative effect on the human physiology.

• The pH values of the tap water samples (8,12–8,40) were found to be slightly higher (slightly alkaline), like in all south-eastern Free State rivers (from where the water is sourced) than the pH of most of the bottled water samples, most of which are sourced and/or treated in other areas. Two brands of bottled water were found to have relatively low pH levels (both 4,5, i.e. acidic) as indicated on their bottles and as confirmed by the IGS analysis. The health implication of this range of pH is not significant.

• The analysis showed differences in the mineral content given on the labels of most of the water bottles compared to that found by IGS analysis. The possibility of seasonal fluctuation in content, depending on various factors, is expected and most of the bottling companies also indicate this on their labels. What was a rather interesting finding was that two pairs of bottled water brands claimed exactly the same mineral content but appeared under different brand names and were also priced differently. In each case, one of the pair was a well-known house brand, and the other obviously the original producer. In one of these paired cases, the house brand stated that the water was spring water, while the other (identical) “original” brand stated that it was spring water treated by reverse osmosis and oxygen-enriched.

• Nitrate (NO3) levels were uniformly low except in one bottled sample, suggesting a low (non-threatening) level of organic pollution in the source water. Otherwise, none of the water showed any sign of pollution.

• The bacterial analysis confirmed the absence of any traces of coliforms or E.coli in any of the samples, as was also indicated by the bottling companies. This is very reassuring. What is not known is how all these waters were sterilised, which could be anything from irradiation to chlorine or ozone treatment.

• The price of the different brands of bottled water, each containing 500 ml of still water, ranged between R3,99 and R8,99, with R5,03 being the average price. A comparison between the least expensive and the most expensive bottles of water indicated no significant difference in quality. In fact, discrepancies were observed in the most expensive bottle in that the amount of Calcium (Ca) claimed to be present in it was found to be significantly different from what the analysis indicated (29,6 mg/l versus 0,92 mg/l). The alkalinity (CaCO3 mg/l) indicated on the bottle was also found to differ considerably (83 mg/l versus 9,4 mg/l). The concentration of Total Dissolved Salts (TDS) was not given on the product.

“The preference for bottled water as compared to Bloemfontein’s tap water from a qualitative perspective as well as the price discrepancy is unjustifiable. The environmental footprint of bottled water is also large. Sourcing, treating, bottling, packaging and transporting, to mention but a few of the steps involved in the processing of bottled water, entail a huge carbon footprint, as well as a large water footprint, because it also requires water for treating and rinsing to process bottled water,” said Prof. Seaman.

Media Release
Lacea Loader
Deputy Director: Media Liaison
Tel: 051 401 2584
Cell: 083 645 2454
E-mail: loaderl.stg@ufs.ac.za
3 August 2009

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