Spotlight on Grants: Nickel and cobalt in Streptococcus

Each year, the Microbiology Society awards a number of grants that enable undergraduates to work on microbiological research projects during the summer vacation. Over the next few weeks, we’ll be posting a series of articles from students who were awarded Harry Smith Vacation Studentships this summer. This week is Siti Nur Amalina, a third-year student studying Biomedical Science with Medical Microbiology at Newcastle University.

Nickel and cobalt in oral bacteria S. sanguinis and S. gordonii  

FROM THE STUDENT: Siti Nur Amalina

sitiMy summer project focused on two bacterial species that live in the mouth, Streptococcus sanguinis and S. gordonii. These Gram-positive bacteria are most abundantly found in dental plaque, which is actually a community of microbes living in a biofilm on top of the enamel.

Although they are considered to be ‘commensals’, meaning they live in the oral cavity without harming/affecting the host, these species are thought to contribute to the accumulation of dental plaque and to the recruitment of pathogens, causing diseases such as dental caries and periodontitis.

This summer research project was initiated because, recently, work in the host laboratory discovered that all S. sanguinis strains contain a 70-gene cluster that is absent from S. gordonii. This cluster encodes nickel and cobalt uptake systems, as well as pathways that enable the microbes to utilise certain organic molecules. This has led to a hypothesis that these genes are important in determining the different ecological roles of S. sanguinis and S. gordonii.

The aim of my project was to try to investigate whether the two species require cobalt for growth, how much cobalt they store inside their cells, and how cobalt allows them to use different compounds for growth.

In the Oral Microbiology laboratory in Newcastle University, I was under the supervision of Dr Nicholas Jakubovics, who works closely with oral streptococci and bacterial biofilms. During the eight weeks of this summer studentship, I completed a series of different experiments with the help of others in the research group. Familiarising myself to a new laboratory environment was kind of awkward at first but everyone was really accommodating and I quickly gained confidence within a couple of weeks working in the lab. I got to learn new things daily and had first-hand experience on everything. As I was involved in planning and organising the experimental work, this made me more proactive. I could give opinions and receive feedback from the other lab members about my work.

One of the most interesting experiences was working with inductively coupled plasma mass spectrometry (ICP-MS) with Dr Emma Tarrant and Dr Kevin Waldron. We used this instrument to measure the concentration of intracellular cobalt in S. sanguinis and S. gordonii when grown in different environments. As an undergraduate student, we rarely handle advanced laboratory equipment due to the high number of students on the course and the limited tools available. Therefore, it was definitely an unforgettable experience and I believe it will be useful knowledge for me to bring into my final year.

In my opinion, summer studentships like this are extremely beneficial, as I have gained an immeasurable amount of knowledge and skills just from this short experience. During the timespan of working in the laboratory, I also got to personally observe how researchers, postgraduates and lab technicians work. It definitely has made me think more about my future plans and provided insights into what research careers looks like. So far, this research experience has been very positive for me and I am thankful to receive support from the Microbiology Society through the Harry Smith Vacation Studentship.



It has been a real pleasure to host Siti in the laboratory over the summer. Her project has provided an opportunity for us to start to explore an interesting topic that has developed from some genomic sequencing that I have done recently with collaborators at the University of Malaya in Kuala Lumpur. Coincidentally, Siti is also Malaysian so she has continued the project’s connection with Malaysia.

The goal of our work has been to understand the key differences between two closely related oral streptococci, S. sanguinis and S. gordonii. Although both species are commonly found in dental plaque, S. sanguinis is almost always present in higher numbers. It is not clear how S. sanguinis manages to outgrow S. gordonii in dental plaque and in fact previous work has shown that S. gordonii can outcompete S. sanguinis for adhesion to saliva pellicle (a protein film that forms on enamel).

Understanding why species such as S. sanguinis are such effective colonisers may potentially lead to new approaches to restrict dental plaque growth and help people maintain good oral hygiene. This project is providing the preliminary data that will hopefully start a new area of research for an enthusiastic student like Siti to explore in more detail, perhaps as a larger postgraduate research project.

To find out more about the Harry Smith Vacation Studentships, please contact

Image courtesy of the researchers
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On the Horizon: Hantaviruses

In early 2013, a man in North Wales was rushed to hospital showing symptoms of serious kidney problems. The source of his infection? His pet rats.

Tests revealed that the causative agent was a rodent virus known as Seoul virus. Epidemiological tracing showed that the virus was present in the pet rats, and also in rats at the breeding farm where they came from. The owner of the breeding colony and her spouse tested positive for antibodies against the virus, and the spouse had in fact been hospitalised in late 2011 with an unidentified viral kidney illness.

In response to this case, and the handful that have happened since, Public Health England performed blood tests of people who kept pet rats. Results showed that nearly a third of those tested contained antibodies against Seoul virus, suggesting a previous exposure to the virus. In the control group, or in groups who only occasionally came into contact with rats (pest control workers, for example) less than 3.3% of people tested positive. In 2015, an outbreak of Seoul virus in South Wales was linked to both pet rats and large-scale commercial breeding of rats for reptile food. Continue reading

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Spotlight on Grants: A search for prions in yeast

Each year, the Microbiology Society awards a number of grants that enable undergraduates to work on microbiological research projects during the summer vacation. Over the next few weeks, we’ll be posting a series of articles from students who were awarded Harry Smith Vacation Studentships this summer. This week is Alister Brown, a third-year Biomedical Science student at the University of Kent.

A search for prions in Saccharomyces yeast


Prions are a special class of protein that can exist in two forms: normal and misfolded. Misfolded prions can act as infectious agents and have been linked to brain diseases such as human Creutzfeldt-Jakob disease and mad cow disease (bovine spongiform encephalopathy).

alister-brown-kent-1Not all prions cause disease though, as is the case with yeasts, where several different prions have been described. My research in the Kent Fungal Group has focused on studying prions in different species of yeasts and how they affect the ‘infected’ host cells. While one yeast species, baker’s yeast or Saccharomyces cerevisiae, has been studied extensively regarding this and all manner of other topics, other species of Saccharomyces have received far less attention.

I set out to identify suspected prion proteins in three different Saccharomyces species, first by looking at amino acid sequences using a computer program called PAPA. This predicts ‘prion-domains’ in proteins that are typically rich in certain amino acids. From this point I aimed to investigate the effect that prions have on yeast, including the ability to utilise different carbon sources for energy, resistance to salt stress and to antibiotics. This was achieved by “prion-curing” the cells – chemically inhibiting the activity of proteins essential for spreading yeast prions from cell-to-cell. Continue reading

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New to science: September 2016

Each month, the Microbiology Society publishes the International Journal of Systematic and Evolutionary Microbiology (IJSEM), which details newly discovered species of bacteria, fungi and protists. Here are a few of the new species that have been discovered and the places they’ve been found. 

A team of researchers from China has discovered a novel Actinobacterium in the mouths of Chinese cobras, which is one of the most common venomous snakes in Hong Kong. They name the species Tsukamurella serpentis. Elsewhere in China, another team has isolated the Proteobacterium Paracoccus acridae from the Chinese grasshopper. The insect was captured from a deserted cropland, crushed, and put on an agar medium for colonies to grow.

Some of of my favourites this month came from animals with fantastic names. Campylobacter geochelonis was isolated from the western Hermann’s tortoise (Latin name Testudo hermanni hermanni). The new bacterial species Neisseria musculi came from the oral cavity of a wild house mouse. And the bacterium Lutimaribacter marinisteallae came from an unidentified organism, referred to simply as ‘a starfish of China’.


Continue reading

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How is the hepatitis C-like hepacivirus of horses transmitted?

In 2011, a new virus was identified in dogs that were suffering from respiratory disease. Analysis revealed that this virus – at the time named canine hepacivirus (CHV) – was the closest known relative of the human virus hepatitis C (HCV), which infects millions of people across the world and can cause serious liver problems.

Previously, HCV and its relatives were believed to be limited to humans and chimpanzees, so the discovery of a virus that infected another species was exciting for researchers. It opened up the possibility that canine hepacivirus could be used as a model to understand how HCV infects humans.

However, further searches in other dogs failed to detect any more of the virus, suggesting that canines weren’t CHV’s natural host after all. CHV-like viruses were subsequently identified in horses, while an almost identical match was found in horse blood serum in New Zealand, raising the possibility that this virus is one that can infect not just dogs, but a variety of non-primate species. The virus has since been named nonprimate hepacivirus (NPHV) to reflect this.

Continue reading

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Drumming up disease? Anthrax and African drum hides


In 2006, a man in Scotland died from the first case of anthrax in Britain for 32 years. Then, in 2008, a man in London was fatally infected with the same disease. The properties of both men were sealed up while the authorities investigated where the anthrax spores had come from. The source in both cases? West African drums, made from animal hides.

Anthrax is very rare in the UK, but it is relatively common in livestock and wild animals in other parts of the world. The disease is caused by the bacterium Bacillus anthracis, which is found naturally in soil where it produces hardy spores that can lay dormant for decades. Anthrax isn’t contagious, but it’s these spores that make it so dangerous as a biological weapon – as in the 2001 anthrax attacks in the US, or the warfare testing that contaminated Gruinard Island in Scotland for almost 60 years.

If anthrax spores enter an animal or human, they can germinate to become active cells that rapidly multiply and spew out toxins, causing serious illness. Cutaneous anthrax (caused by spore entry through the skin) leads to painful sores and blisters, while inhalation anthrax causes flu-like symptoms and can lead to patients coughing up blood and haemorrhaging.

Human anthrax is usually caught by contact with contaminated animals or products. In fact, in the 1800s, anthrax was known as woolsorter’s disease, because people working with wool frequently became sick after inhaling spores. The risk of this happening in the UK today is very low, because animals with the disease are quickly spotted and dealt with. But spores can still be present on animal products from places where anthrax is more common, such as the animal hides used to make the drums in the two recent UK cases. Continue reading

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Nations and leaders commit to tackle antimicrobial resistance

Over the last few months there has been a plethora of commitment at the highest level across the world to working together to tackle antimicrobial resistance (AMR).

Firstly, at the G7 Ise-Shima Summit in Japan on 26 and 27 May 2016, world leaders recognised the serious impact that AMR could have on their economies and committed to taking action. The group emphasised the importance of promoting R&D and innovation in this area and agreed to take concrete actions, laid out in the G7 Ise-Shima Vision for Global Health. This view was reiterated at the G20 summit in China on 5 September, where leaders affirmed the need to fight AMR in an inclusive manner by developing evidence-based ways to prevent and mitigate its spread, and by unlocking R&D into new and existing antimicrobials.

Finally, at the United Nations (UN) General Assembly on 21 September, all 193 member nations agreed to sign a landmark declaration to fight the growing threat of AMR. This is only the fourth time in history that a UN health declaration has been signed and this, alongside the commitment shown from the G7 and G20 leaders, are important steps on the road to a global solution. Continue reading

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