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Top 10 most downloaded papers: Access Microbiology

Top 10 most downloaded papers: Access Microbiology

Posted on June 1, 2023   by Microbiology Society

Publishing in Access Microbiology – our sound science open research platform – is free until the end of June 2023. Submit your manuscript before the end of the month to make the most of free Open Access publication.

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Access Microbiology publishes a range of sound science research, including replication studies, negative or null results, research proposals, case reports and more. We welcome work from all branches of microbiology and virology, offering fully transparent peer review.

See the top 10 most downloaded papers from 2019 to May 2023 below:

When good bacteria behave badly: a case report of Bacillus clausii sepsis in an immunocompetant adult

Isabella Princess, T. Natarajan, Siddhartha Ghosh​

Case Report

9350 full text downloads

A case report: insights into reducing plastic waste in a microbiology laboratory    

Joana Alves, Fiona A. Sargison, Hanne Stawarz, Willow B. Fox, Samuel G. Huete, Amany Hassan,​ Brian McTeir, Amy C. Pickering

Short Communication

9017 full text downloads

High SARS-CoV-2 viral load is associated with a worse clinical outcome of COVID-19 disease

María Eugenia Soria, Marta Cortón, Brenda Martínez-González, Rebeca Lobo-Vega, Lucía Vázquez-Sirvent, Rosario López-Rodríguez​, Berta Almoguera​, Ignacio Mahillo​, Pablo Mínguez, Antonio Herrero, Juan Carlos Taracido​, Alicia Macías-Valcayo, Jaime Esteban, Ricardo Fernandez-Roblas​, Ignacio Gadea, Javier Ruíz-Hornillos​, Carmen Ayuso, Celia Perales

Short Communication

8714 full text downloads

Disseminated sporotrichosis in a person with human immunodeficiency virus disease

Vhudzani Tshisevhe, Lebogang Skosana, Kagiso Motse, Tinashe Maphosa, Barend Mitton​

Case Report

8225 full text downloads

Phylogenetic diversity and activity screening of cultivable Actinobacteria isolated from marine sponges and associated environments from the western coast of India

Ulfat Baig​, Neelesh Dahanukar, Neha Shintre, Ketki Holkar​, Anagha Pund​, Uttara Lele​, Tejal Gujarathi​, Kajal Patel​, Avantika Jakati​, Ruby Singh​, Harshada Vidwans​, Vaijayanti Tamhane, Neelima Deshpande​, Milind Watve

Research Article

8223 full text downloads

Not all wavelengths are created equal: disinfection of SARS-CoV-2 using UVC radiation is wavelength-dependent

Richard M. Mariita, James W. Peterson

Short Communication

8214 full text downloads

Streptococcus lutetiensis neonatal meningitis with empyema

Allen T. Yu, Kate Shapiro​, Christy A. Beneri, Lisa S. Wilks-Gallo

Case Report

8173 full text downloads

Disinfection of methicillin-resistant Staphylococcus aureus, vancomycin-resistant Enterococcus faecium and Acinetobacter baumannii using Klaran WD array system

Richard M. Mariita, Rajul V. Randive

Short Communication

8106 full text downloads

Distribution of cycle threshold values in RT-qPCR tests during the autumn 2020 peak of the COVID-19 pandemic in the Czech Republic

Michal Koblížek, Daniela Hávová​, Karel Kopejtka, Jürgen Tomasch, Kateřina Bišová

Short Communication

8000 full text downloads

Rapid growth atypical mycobacteria infection associated with growth hormone injections: a case report

Christian David Cardozo Lomaquiz, Tamara Frontanilla, Natalia Scavone, Alba Fretes​, Nathalia Torales, María Elena Pereira​, Herminia Mino de Kaspar, Xavier Ortiz​, Renate Henning

Case Report

7992 full text downloads

Download data from 23rd May 2023

To the Himalayan marmot and beyond: new microbes discovered this month

To the Himalayan marmot and beyond: new microbes discovered this month

Posted on May 31, 2023   by Clare Baker

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

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The discovery of Cellulomonas xiejunii, Cellulomonas chengniuliangii and Cellulomonas wangsupingiae were published in International Journal of Systematic and Evolutionary Microbiology this month. While these bacteria are new to science, their source is not. You might be familiar with the Marmota himalayana, otherwise known as the Himalayan marmot, from a previous edition of ‘New to Science’. These three newly discovered microbes were also isolated from our furry friends, their intestinal contents to be exact, in Qinghai Province, PR China. Each new bacterial species is named after a professor at Shanxi Medical University in honour of their contributions to medicine. In fact, the Himalayan marmot is really carrying this edition of ‘New to Science’, as it is the source of two more novel microbes published this month. Nocardioides marmotae and Nocardioides faecalis were isolated from the faeces of M. himalayana during a study exploring the microbial diversity of Nocardioides on the Qinghai–Tibet Plateau.

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For our next new microbe we can move away from the Himalayan marmot and on to humans. Curtanaerobium respiraculi is a novel bacterium isolated from human bronchoalveolar lavage fluid. A bronchoalveolar lavage is a procedure where a small amount of saline is introduced to the lungs through a bronchoscope, before the lung fluid is then collected and tested. It was originally believed that the lungs were a sterile environment, but in recent years it has been proven that the lungs are a low-density diversified microbial ecosystem. Next generation sequencing technology has shown that the lung microbiome is dominated by the phyla Pseudomonadota, Bacillota, Bacteroidota and the phyla of our new bacterium Actinomycetota. Our new bacterium is not only a new species within this phyla, but also a new genus.

We need to look down to the soil for our next novel microbe. Massilia agrisoli was isolated from the rhizosphere of a banana plant in Dighalgram, Magura, Bangladesh. The plant rhizosphere bacterial community is a regular feature of ‘New to Science’ and is home to many of our newly discovered microbes. The rhizosphere is the soil surrounding the root of the plant that is affected by its biological activities and is home to a community of bacteria called a microbiome. Our newly discovered microbe joins the species Massilia, which has been found in an array of ecological niches, including human clinical specimens, drinking water and even ice cores. 

Keeping to the soil and moving back to China we find our final new microbes, Geothrix fuzhouensis and Geothrix paludis. These two anaerobic, Fe(III)-reducing and gram-negative strains were isolated from paddy soils in Fujian Province, PR China. Our new microbes were found during an investigation of the diversity analysis of Fe(III) reducing bacteria in paddy soil but iron reducing bacteria have been found in various other anaerobic environments including groundwater and lake sediments.

Dynamic Soil Genes: Time and Neonicotinoid Seed Treatments Affect Agricultural Microbiomes

Dynamic Soil Genes: Time and Neonicotinoid Seed Treatments Affect Agricultural Microbiomes

Posted on May 31, 2023   by Mona Parizadeh

Mona Parizadeh takes us behind the scenes of her latest publication Soil microbial gene expression in an agricultural ecosystem varies with time and neonicotinoid seed treatments‘ published in Microbiology.

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Mona Parizadeh

My name is Mona Parizadeh. I am a postdoctoral fellow in the Arrieta lab at the University of Calgary, Canada. I specialize in microbial ecology, community ecology, computational biology, and bioinformatics. My research focuses on studying environmental effects on microbiomes, host-microbe and microbe-microbe interactions, and drivers of microbial community assembly in different environments. To address these objectives, I apply ecological theory and different high-throughput sequencing approaches, including meta-barcoding and meta-omics. During my Ph.D. under the supervision of Dr. Steven W. Kembel (Université du Québec à Montréal) and Dr. Benjamin Mimee (Agriculture and Agri-Food Canada), I studied the effects of host species, time and environmental stress and perturbations, like pesticide treatments, on microbial composition variation in agroecosystems.

Agriculture plays a critical role in feeding the growing global population. Sustainability in agriculture relies on maintaining soil quality and health, which is directly related to the diversity and dynamics of microbial communities. Soil microbial communities perform vital functions, such as nutrient cycling, and organic matter production and decomposition. Several factors influence the composition of microbial communities and gene expression patterns, including: time, soil management practices, environmental conditions, disturbances and perturbations (such as cultivation methods, drought, climate change, and pesticide treatments).

© Mona Parizadeh

A beautiful sampling day at the L’Acadie Research Sub Station of Agriculture and Agri-Food Canada, St-Jean-sur-Richelieu, Quebec. Soybean field; Mona wearing a pink cap, and her colleagues.

Neonicotinoids, also known as neonics, are a family of systemic and neuro-active insecticides widely used in recent years to control pests in both the soil and foliage. These chemicals are structurally similar to nicotine and have been predominantly employed as seed treatments in North America to control early-season insect pests in crops such as corn, soybean, and wheat. These treatments are often applied prophylactically without specific knowledge about the presence of the targeted pests. Neonicotinoid compounds are characterized by their small size and high solubility in water. Due to their systemic nature, plants absorb them from the seed coating and translocate them to various tissues and products, including guttation, nectar, and pollen. Neonicotinoids may remain active for extended periods, up to 200 days, in certain plant species. However, plants only absorb around 20% of the neonicotinoids present in the seed coating, while the remaining pesticide persists in the soil for up to three years. In recent years, neonicotinoid pesticides have gained widespread attention for their potential non-target effects on ecological communities and their functions. There has been extensive evidence that neonicotinoids affect beneficial organisms in agriculture, including insect pollinators, especially honeybees and butterflies, and soil invertebrates, such as earthworms. In response to these concerns, several regulatory measures have been implemented in various regions. In 2018, the European Union prohibited the outdoor use of several neonicotinoids. Similarly, in 2020, the United States Environmental Protection Agency banned the spray application of neonicotinoids and proposed limitations on their quantity and timing, particularly for crops in bloom. In Canada, the Quebec province implemented a requirement in 2018, mandating farmers to obtain prescriptions from agronomists before using neonicotinoids on crops. In 2021, Health Canada opted not to impose a complete ban on neonicotinoid application but instead imposed additional restrictions, such as implementing buffer zones around affected sectors and reducing the neonicotinoid seed treatment rate for certain crops like soybean and corn.

The above restrictions are mostly based on neonicotinoids’ effects on beneficial invertebrates since they were initially considered more toxic to invertebrates. However, as reported in our previous research, they show non-target impacts on diversity and taxonomic composition of agricultural microbiomes. Gaining insights into the dynamics of soil microbial functions when faced with disturbances is also essential for evaluating their influence on ecosystem functioning and advancing the development of sustainable agricultural practices. Therefore, we decided to study the microbial functional activities and gene expression variations following neonicotinoid seed treatments in an experimental design of a 2-year soybean/corn crop rotation that was representing real farming conditions.

As we used metatranscriptomics to study soil microbial expressed genes and active functions, many challenges arose. Obtaining high-quality microbial RNA in sufficient quantities was one of these challenges. It took us several attempts before we found the appropriate kit and protocol. We then sent the extracted RNA to Genome Quebec for sequencing. The other challenge was determining a proper, efficient and accurate data-processing approach, for which we tried various pipelines and bioinformatics tools and software. It is also important to note that when it comes to gene annotations, a consistent and universally accepted method for labeling genes is lacking in the majority of reliable public genome databases. This poses a challenge in annotating gene expression at a community level in transcriptomic and metatranscriptomic studies like ours. However, we overcame these limitations by employing various strategies, such as utilizing multiple databases and implementing thorough data-cleaning processes.

Having surmounted these limitations and challenges, our findings revealed that soil microbial gene expression is influenced by both temporal variations and neonicotinoid seed treatments. Across various time intervals, genes associated with heat shock proteins, regulatory functions (such as soil respiration), and metabolic processes (like phosphonate breakdown and enzyme catalysis) were underexpressed in response to neonicotinoid seed treatment. Conversely, genes related to photosynthesis and DNA repair were overexpressed in the presence of neonicotinoid seed treatment. These results underscore the vital influence of time and temporal dynamics in shaping soil microbial gene expression. However, although gene expression in soil microbial communities fluctuates significantly over time, these communities are either highly resilient or resistant to alterations in gene expression triggered by neonicotinoid seed treatment. This resilience could potentially be attributed to functional redundancy in the genes that are expressed, despite the significant variation in the taxonomic composition of these microbial communities that we have previously documented. Understanding these dynamics is critical for assessing the impacts of agrochemicals on soil health and ecosystem functioning.

Candida and Candidiasis 2023 – a view from Twitter

Candida and Candidiasis 2023 – a view from Twitter

Posted on May 26, 2023   by Priya Gurung

Candida and Candidiasis 2023 took place on 13–17 May 2023 at the Le Centre Sheraton Montreal Hotel, Canada. In this blog, we take a look at the highlights from Twitter.

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#Candida2023 was our biggest Focused Meeting so far, with 338 delegates from 29 countries, including countries from North and South America, Asia, Australia, Africa and Europe! The programme was filled with scientific talks and poster presentations from experts across the world in the field of Candida.

We were excited to welcome new faces and welcome back familiar faces in the Candida community together in person after five years! 





Scientific sessions

The scientific sessions at #Candida2023 were designed to give delegates a forum to discuss the latest advances in the field of Candida and spotlight the achievements of early career scientists. 






Poster sessions

The poster sessions showcased the diversity of research within the Candida community. Our delegates were able to share their work, and discuss and exchange ideas with one another, giving plenty of opportunities for early career researchers to present their work too!









Many congratulations to our poster prize winners Delavy Margot, Viola Halder and Daniel Gutzmann (not pictured)! They were awarded an Outstanding Science Prize for a scientific poster, sponsored by our flagship journal, Microbiology.



Canada Showcase and social programme

The Microbiology Society hosted our first Canada Showcase at the McGill Faculty Club. Delegates from #Candida2023 and local scientists were welcomed to network over some drinks and canapes, and to find out more about the Society from the Chief Executive, Peter Cotgrave, Society staff members, Editors and more. 




During the conference dinner, the Candida community paid tribute to Frank C. Odds. He was a mycologist and studied Candida albicans, establishing how modern researchers study fungal pathogens and the diseases they cause.



Thank you

Thank you once again to all the organisers, speakers, poster presenters and delegates who joined us at the #Candida2023 and helped make it a success! We hope you enjoyed the event as much as we did, and we look forward to welcoming you back at our future events.







Needles and Haystacks: Understanding the HBV transcriptome

Needles and Haystacks: Understanding the HBV transcriptome

Posted on May 25, 2023   by James Harris

James Harris takes us behind the scenes of his latest publication ‘An enrichment protocol and analysis pipeline for long read sequencing of the hepatitis B virus transcriptome‘ published in Journal of General Virology.


Hello I’m James Harris, a post-doctoral research fellow in Jane McKeating’s group in the Nuffield Department of Medicine, at the University of Oxford, UK.

Hepatitis B virus (HBV) infects hepatocytes in the liver with chronically infected subjects at a lifelong risk of liver fibrosis, cirrhosis or even hepatocellular carcinoma. HBV is one of the smallest known DNA viruses; its 3.2kb covalently closed circular genome (cccDNA) encodes 4 overlapping open reading frames and transcribes 6 major viral RNAs with unique 5’ transcriptional start sites that share a common 3’ terminus and poly-adenylation sequence. These transcripts translate in different frames, making interpreting the viral transcriptome from short read sequencing almost impossible.

A further complication is that HBV can integrate into the cellular chromosomal DNA. These integrants are defective and only transcribe a subset of viral RNAs transcripts that differ at their 3’ terminus. Any curative therapy will require the silencing or ablation of replicating cccDNA, however ongoing transcription from integrants makes the task of identifying successful treatments very challenging. Clearly identifying the source of viral RNAs is important for future clinical developments, and that’s what got us interested!

HBV infection efficiency in vitro is low, with large amounts of virus required to establish infection. To circumvent this, many studies use plasmid transfection to deliver HBV into cells. To allow transcription of the full repertoire of viral RNAs, the plasmid-encoded genome is overlength (1.3x) with a repetition of some loci and promoters. We compared the HBV transcriptome produced from this synthetic viral DNA construct with authentic genomes produced during infection.

Our previous work showed that HBV RNAs comprise a very small portion of the cellular transcriptome, and this is further diluted by the presence of large numbers of uninfected cells. However, we knew that our colleagues Azim Ansari and Philippa Matthews were developing an enrichment protocol to study HBV DNA in clinical samples, and thought we could apply this technique to increase the abundance of viral RNAs in our library. All we had to do was decide on our sequencing strategy…

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Finding a needle in a haystack: enriching HBV RNAs allowed us to overcome the dilution of rare viral RNAs by abundant host cell transcripts.

In late 2021 PacBio ran an online presentation with Oxford Genomics Centre to publicise the new Sequel II long read sequencing platform that would be available in the following spring. Everyone who registered for the event got a free travel mug, so of course we all signed up! In addition to their presentations, PacBio held a competition to win a free run on their brand new machine. This was a single box on their website with space for a title and 200 words. We filled it in, and got this message three days later:

SMRT Grant Winner
McKeating Group, Nuffield Department of Medicine, University of Oxford
Alternative Transcription in Hepatitis B Virus

Our sequencing strategy was decided! Sequencing entire transcripts rather than fragments solves the problem of identifying the transcripts in our library and we were delighted when our PacBio Sequel II run yielded several hundred thousand reads, allowing us to assess the abundance of spliced RNAs, and compare the infection and transfection delivery methods.

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Sequencing whole transcripts, not RNA fragments: Traditional short read methods offer great depth, but its impossible to determine what RNA transcript they originated from. This is the reason we chose to go with the PacBio platform.

Mug photo credits to the proud owner of the PacBio travel mug, Dr Peter Balfe.

Esther Ng, a talented computational biologist, worked to streamline and rewrite the conventional analysis pipelines to interrogate the unusual canonical and non-canonical (spliced) viral transcripts. We were pleasantly surprised to find broadly similar transcript patterns in both infection and transfection models, suggesting that the model systems in widespread use are not as different as we originally thought. As the cost of sequencing continues to drop, and more long-read instruments are being installed, the approach we’ve described is becoming increasingly feasible and routine (indeed our sequencing service now charges less for long-read than short-read sequencing). We set about making all the required reagents and analysis methods as transparent and accessible as possible and everything we did is available online.

We hope this enrichment, sequencing and analysis pipeline will be of interest to groups working on HBV and other viruses – the only changes needed would be to design new capture probes and work out the transcription pattern files for the analysis pipeline.

Microbe Talk: a deep dive into wastewater monitoring

Microbe Talk: a deep dive into wastewater monitoring

Posted on May 24, 2023   by Clare Baker

This month, inspired by a paper published in Microbial Genomics, Clare takes a deep dive into the method of wastewater monitoring. She speaks to Professor Steve Patterson and Dr Anne Leonard about how wastewater monitoring is a useful tool which helps us understand not only the spread of diseases like COVID-19, but also antimicrobial resistance.


You can read Professor Patterson’s paper, published in Microbial Genomics here

Music: pixabay Chill Abstract (Intention) Coma-Media

Download the transcript of the podcast here.

What’s the Quorum?

What’s the Quorum?

Posted on May 23, 2023   by Dr Jennifer Rattray

Dr Jennifer Rattray takes us behind the scenes of her latest publication ‘The dynamic response of quorum sensing to density is robust to signal supplementation and individual signal synthase knockouts‘ published in Microbiology.

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Fluorescence microscopy image of individual Pseudomonas aeruginosa cells tagged with a green fluorescent marker of virulence activity.

My name is Dr Jennifer Rattray, I’m a postdoctoral fellow in Global Chemical and Biological Security at Sandia National Laboratories in the United States. This work was done during my time as a National Science Foundation Graduate Research Fellow in Dr. Sam Brown’s lab at the Georgia Institute of Technology. As a microbial and evolutionary ecologist interested in emerging biological threats, I take a top-down approach to understand disease-causing agents. This means that I study complex systems as a whole and work inwards – like starting a puzzle by building the outer edges first.

Our understanding of how bacterial pathogens cause disease is ever evolving. As of now, we know that the ecological bacterial component of an infection is a complex mix of community dynamics, spatio-temporal dynamics, and behavioral dynamics, along with constant evolutionary feedback dynamics. This work focuses on the behavioral component. Thanks to a lot of hard work by molecular biologists and chemists, we know that group-dependent pathogenesis in bacteria can be controlled on the molecular level by a form of cell‐cell communication mediated by diffusible signal molecules called quorum sensing (QS). Each individual produces and responds to these diffusible signaling molecules, inferring properties of their environment and modulating the regulation of hundreds of downstream genes in response. Traditionally, QS dynamics are studied in reference to population density, hence the legal ‘quorum’ analogy. We studied QS in the context of Pseudomonas aeruginosa, a laboratory-tractable gram-negative bacterium capable of causing severe chronic illness and a major cause of acute hospital-acquired infections that represents one of the most intensely studied pathogen model systems for QS.

As microbial ecologists, to understand a system we like to first observe the system and then test the extremes to push the system to a ‘breaking’ point so that we can identify the dynamic range of behavior. A growing body of literature highlights that QS can produce more nuanced, graded responses to environmental variation, implying there is no simple threshold ‘quorum’ on either the single cell or population scale. In this paper we control the quantity and type of chemical signal and observe the population-level response by tracking expression of the virulence factor, elastase. Looking at QS dynamics across discretely controlled environments rapidly increases the amount of data required to make any conclusions, which complicates analysis. To manage this, we introduce the use of “reaction norms”, a historical concept in ecology, to reduce the dimensionality of this data and highlight its power to make broad conclusions.

One result that stuck out for us is the robustness of this behavior to multi-signal input. The two acyl-homoserine lactone (AHL) signals we used are two of the major QS signals studied by the field. Addition of both of these AHL signals to either the WT or the double AHL synthase deletion strain did not negate the ability to sense density, even those these were density-independent concentrations. The only scenario that reproducibly reduces the ability to sense density was when we flooded WT populations with not only both AHL signals, but also the lesser-studied Pseudomonas Quinolone Signal (PQS).

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Photo of a mixed media sculpture depicting these disease-causing bacteria on display at the Atlanta Science Festival, a collaboration between Rattray and Atlanta-based artist Elizabeth Porcel.

The robustness of this ability of P. aeruginosa to use QS to sense their density environment is likely a result of the interconnectedness of the multiple signal-receptor systems. Many researchers in the field are recognizing this complexity and our results call into question the use of AHL synthase deletions strains as a null model of this behavior, at least when manipulating the system. The use of reaction norms to reduce the complexity of this data also brought about a serendipitous result from this work- a potential link between divergent QS activity and antimicrobial resistance. P. aeruginosa naturally has high amounts of antimicrobial resistance and is, in general, a stubborn pathogen when it comes to treatment. Since the study, we’ve seen that different lab strains of P. aeruginosa, caused by natural microevolution in laboratory research, have reaction norms that induce at different densities indicating there is a different baseline sensitivity for sensing their environment. Efflux pump regulation, which seems to be a key difference between these lab strains, traditionally mediates antimicrobial resistance but also may impact the intracellular and extracellular concentrations of QS signals and therefore the ability of QS to act as a collective mediator of pathogenesis. A comparative study using reaction norms across laboratory strains could be an exciting intersection between signal mediated pathogenesis, antimicrobial resistance, and collective behavior.  

Plant health: an interview with Dr Andrew Armitage

Plant health: an interview with Dr Andrew Armitage

Posted on May 23, 2023   by Andrew Armitage

In this blog, we caught up with Microbiology Society member Dr Andrew Armitage from the Natural Resources Institute, University of Greenwich, about his work on plant diseases and the importance of plant health. 


What is your name, job title and institution?

My name is Andrew Armitage, and I am a Senior Research Fellow at the Natural Resources Institute, University of Greenwich.

Can you tell us a little bit about your research and why it is important?

My group focusses on how fungal pathogens cause disease on crops. Pathogens are locked in an evolutionary arms race with their host. We use genomics to study pathogen evolution and how closely-related fungi adapt to cause diseases on different hosts. This allows us to understand how plants are resistant/susceptible to particular fungi, to support crop breeding programmes. Playing genomic games of spot-the-difference between fungi can also identify unique regions of the genome to develop novel diagnostic assays for crop disease. We can also use these genomic approaches to investigate how groups of fungi have evolved fungicide resistance, and are investigating how plant disease may be controlled by beneficial microbes such as viruses and other fungi.

Why is plant health so important?

Losses to food production from plant disease could feed millions of people across the planet every year. These impacts are felt greatest in regions of the world subject to the greatest pressures from climate change and expanding populations.

Fungal plant diseases form a major component of these losses, and impact crops at all stages between planting in the field and our forks. In the field we see soilborne infections of root systems preventing establishment of seed, or later wilting and killing of our crops. We see wind-blown spores landing on leaves, leading to leaf infections progressively reducing photosynthetic potential, and reduced yields. Upon harvest we see latent crop infections creeping in and rotting our foods in transit or storage. On top of all of this, we may observe mycotoxin contamination from undetected fungi posing risks to human health and leading to food shipments needing to be destroyed.

We need to take an active approach to breeding crops more resistant to disease, while investing in new strategies to control pathogens (including greater use of biological control agents), and monitoring pathogen spread to prevent new diseases establishing in response to a changing climate.

How do plants benefit people?

Plants save our lives every day. They provide the air we breathe and the food we eat. They furnish our Green Planet, underpinning food webs and providing habitats that shape our ecosystems.

What is the biggest threat to plant health?

We face a number of major agricultural challenges when feeding the world. Fungal diseases such as wheat and rice devastate staple crops, whilst we also see spreading of pandemics such as Panama disease of banana. Viral diseases have major impacts upon subsistence crops of cassava and yam in regions such as Africa. Whereas emerging bacterial diseases such as Xyella pose threats to food production and the environment across Europe. Researchers and Plant Health agencies need to respond quickly in an ever-changing landscape as climate change shifts the borders on what diseases are found where.

What do you enjoy most about your work?

A career in research is a great path for anyone inquisitive. It allows us to keep learning and keep asking questions.

Why did you choose to study plant science?

I originally studied Ecology as a degree, before moving into genomics and molecular biology over an MRes, PhD and PostDoc. Understanding how organisms interact with one another and understanding how populations of a species differ in the field is fascinating. Being able to look at the genetic basis of these differences and the interactions between organisms is even better.

If you weren’t a scientist, what would you be doing?

A teacher would be an interesting career. I love passing on knowledge alongside active research and get a lot of satisfaction from lecturing.

Global Accessibility Awareness Day: an interview with Tanya Horne

Global Accessibility Awareness Day: an interview with Tanya Horne

Posted on May 18, 2023   by Tanya Horne

Global Accessibility Awareness Day is celebrated today, 18 May, and its purpose is to get everyone talking, thinking and learning about global accessibility. To mark this day, we interviewed Microbiology Society member Tanya Horne about her experience of navigating academia with a disability and the importance of accessibility.  

Could you tell us about yourself?

My name is Tanya, and I have a growing love for all things bacteriophage and phage defence systems, especially how happily (or not!) they co-exist when you throw in a lot of other mobile genetic elements and defences. This can have profound implications for horizontal gene flow, and by extension pose huge challenges to human health such as antimicrobial resistance. I’m currently exploring these themes as a PhD student based within the Institute of Infection, Veterinary and Ecological Sciences at the University of Liverpool.

I was diagnosed with ovarian cancer during the first year of my PhD. The side effects of the treatment I received will affect every day of my life, forever, which of course has a big impact on my day-to-day as a postgraduate researcher. I am always very happy to chat about this, and grateful to the Society for inviting me to help raise awareness around accessibility.

It’s Global Accessibility Awareness Day on 18 May 2023; will you be doing anything to raise awareness? 

I will be spending the day working on my PhD project, trying to be thankful that I’m currently well enough to be able to sit at a lab bench, and very much hoping that this interview will help raise awareness of this important issue.



As someone studying microbiology who has recently gone through a cancer diagnosis, could you tell us about some of the challenges you have faced?

It’s been an extremely challenging time. As a result of my treatment, I suffer from joint and pelvic pain that can be severe. I also have to manage the symptoms of cancer induced early menopause as best I can; this has included a lot of memory impairment, which has been very frustrating and difficult to manage alongside a very technically challenging PhD! I’ve adapted as best I can in the lab by working as efficiently as possible on days when the pain is less severe and taking adequate rest when needed. Through trial and error, I’ve also found effective methods to minimise physical discomfort and cognitive impairment. These tend to be simple and timeworn: regular walks, mnemonics, having a regular routine, etc.

My Doctoral Training Programme, lab mates and supervisors Professor Heather Allison and Professor Jay Hinton are very supportive, which makes a big difference. For example, my DTP provided paid sick leave for 12 weeks – at the time, this gave me one less thing to worry about and enabled me to concentrate fully on surgery and recovery. They also later approved my application for a funded extension, which means I can better pace myself through the last two years of my studies, better safeguarding my health and ensuring I reach my full potential despite cancer.

Overall, despite the obstacles, I’d say things are working very well at present and that I’m making good progress.

What are some of the access requirements people living with a cancer diagnosis might need as a result of their diagnosis that others may not have considered?

I think this is hugely variable – someone’s requirements will depend on lots of different factors including their age, general health, and treatment status. I also think their requirements are likely to change over time – again, depending on lots of different factors. My own requirements can change day to day.

Although I much prefer to attend meetings and conferences in person, I think it’s wonderful that remote attendance is now much more available – and the norm – than ever. It’s very reassuring to know that if I’m ever immunocompromised again, I can still safely take part in our weekly lab meetings in this way. Heather and Jay will also regularly ask me whether there’s anything more they can be doing to support me, which is wonderful – there’s no better way to ensure you’re maximizing support and accessibility for a student post cancer diagnosis than asking them what they need rather than making assumptions.

Is there anything you wish you had known before your diagnosis that would have made going back to the lab easier post diagnosis?

I had no idea until fairly recently that The Equality Act considers a diagnosis of cancer as a disability, and that this meant I had the right to request reasonable adjustments and support. This was despite being very proactive and seeking support upon my return to the lab from a wide range of university staff and departments. Had I known, I would have been able to access specialised support and advice which I’m certain would have enabled my return to go much more smoothly. I now spread awareness of this as best I can in the hope that future students in my position will have a much easier time than I did.

The uncomfortable truth is that the university was completely unprepared for my situation and didn’t know how to support a student with a cancer diagnosis – there was simply no roadmap in place, and although of course people were sympathetic and wanted to help, no one seemed to know what this should look like. I was told more than once that if I were a staff member, there would be a plan and a system of support in place. Well, with respect, that’s not good enough. Students aren’t immune to cancer; the sad fact is that there will be more diagnosed after me, and they need to be as well supported as staff.

We must do better – and I include myself in that. I hadn’t given any of these issues much thought until I found myself in that situation. Now that I have thought about it deeply, I of course recognise the immense challenges, not least funding, that stand in the way of truly universally accessible lab facilities such as adjustable height benches and equipment. It’s not something we can fix overnight, and is something that will require wholescale, long-term cultural change as well as financial investment.

Thankfully, Microbiology is intrinsically more accessible to work in than a lot of other biological sciences. Whatever I’m working on can usually be popped in the cold room or freezer if I suddenly develop pain, and I can get on with some computer-based work – from home if needed – until it passes. I’m mindful that if I were working with larger, more complex organisms with say a feeding schedule or other needs, that probably wouldn’t be the case!

Is there any advice that you would give to other people living with a cancer diagnosis who are working in (or hoping to work in) science?

My advice, particularly to those newly diagnosed, would be this: be mindful of how all of this is going to impact you psychologically. Practical considerations such as access requirements and working adjustments are of course an essential consideration, but it’s largely underappreciated just how heavy a toll cancer takes on your mental health. This is especially true after you’ve finished with treatment. The unfortunate fact is that it’s never really over, and the vast majority of other people with a cancer diagnosis that I’ve spoken to say the period after treatment ends was by far the toughest time for them, mentally. The good news is that you can do things to help prepare you for, and mitigate, this impact. Seek as much support as you can, even if you don’t think you’ll need it. For example, Macmillan Cancer Support provide free, rapid access therapy sessions that I would strongly recommend to everyone in this position.

Do you think more needs to be done to support people living with a cancer diagnosis studying or working in science?

Yes, absolutely! With that in mind, alongside a fellow PhD student from another Institute, I’ve revived the University’s Cancer Support Network to help provide informal peer support. We meet once a month, and our conversations make me feel much less alone.

Studying for a PhD is inherently difficult, and challenging – as it is supposed to be. During this process, life goes on of course: we will all experience some type of ill health, which for some of us will be a critical illness. This will have a huge, direct impact on your PhD work, because both the PhD and the illness are all encompassing by their very nature – there is no escaping this. You may also be far from home and family too, which will make this situation even tougher.

If you’re a PI (or in another position of leadership) and wondering how you can support an ECR through cancer or something else very difficult, one of the very best ways you can do this is by fostering an inclusive, supportive community in your lab and wider department. I am incredibly lucky – a lot of hard work had already gone into this long before I jointed the Microbiology Department here in Liverpool, and I have benefited from this enormously. To be clear: if not for this community, and the leaders within it with a holistic approach to mentorship and supervision, I doubt my PhD would have survived my diagnosis.

When and why did you first become interested in microbiology?

I’m a big reader – after devouring everything by Richard Dawkins and Jared Diamond during my commutes and lunch breaks, I somehow found my way to Martin J. Blaser’s Missing Microbes and Ed Yong’s I Contain Multitudes. This sparked the desire to return to education and pursue a degree in life sciences.

A short time later, during my time at college working towards this, I therefore made time to listen to a lecture by a guest speaker from the University of Liverpool – as fate would have it, this speaker would be one of my future PhD supervisors, Jay. Jay’s lecture helped me see beyond the pages of those popular science books, offering instead a glimpse into the actual day to day life and research priorities of Microbiologists at the University of Liverpool. This led to an intern week in his lab that summer, at the end of which I knew I’d found my calling.

If you hadn’t gone into science, what career path do you think you would you have chosen?

I’m a bit unusual in that I had a career in politics, which I found very rewarding, prior to my undergraduate degree in Microbiology, which I obtained in my mid-30s. I’ve always wanted to be a scientist for as long as I can remember, but had to take a detour as my high school didn’t allow me to take STEM related A Levels. Refusing to give up on that ambition and pursuing it via a Foundation Year later in life was one of the best decisions I’ve ever made – I can’t imagine doing anything else, now.

Could you tell us why you decided to join the Society?

I was awarded a Society Undergraduate of the Year Award in 2019, which came with 12 months free membership – I’ve renewed it every year since. During my time as an undergraduate, I was strongly encouraged to join by ECR members of the labs I worked in, as well as my supervisors. After they took the time to explain how much the Society did to support its members, for example through initiatives like travel grants, membership was a no brainer. Of course, I’m now one of those ECR members encouraging current undergraduates to sign up!

International Day Against Homophobia, Biphobia and Transphobia: Anonymous Blog

International Day Against Homophobia, Biphobia and Transphobia: Anonymous Blog

Posted on May 17, 2023   by Anonymous

International Day Against Homophobia, Biphobia and Transphobia is an annual awareness day which takes place on 17 May to draw attention to the violence and discrimination faced by LGBTQ+ communities around the world. This year, our members organised an LGBTQ+ Networking Event during Annual Conference 2023 and so, to celebrate this important day, an attendee has written a review of the networking event.

LGBTQ+ social.jpg
The Microbiology Society Members Panel, organisers of the LGBTQ+ event


The Microbiology Society hosted an LGBTQ+ event during this year’s Annual Conference, and I’m writing this in an attempt to express how important it was. I’ve been a member of the Society for way over a decade but I only decided to join the Champions scheme when I realised the commitment of the Microbiology Society to changing culture. It might not seem like much, but hosting this type of event during a conference that invites researchers from all over the world can really make a significant impact.

I signed up to the event slightly hesitant about actually turning up. I thought I would decide based on how I felt during the conference. I regularly attend LGBTQ+ events, which always make me feel very welcome and seen, but I wasn’t sure what to expect from an event organised by a professional society with international reach. At the moment of writing it is still unfortunately unsafe for me to publicly “come out”, or as my therapist would say, “invite others in” in a public forum. I felt anxious about safety and the possible consequences of exposing part of myself that I keep away from my professional life. You might think that in this day and age being queer is not something people should fear embracing in a learned environment. Unfortunately, we still experience different types of bullying and discrimination, sometimes in the form of inappropriate comments, ostracising, and other damaging behaviours. If we also add the fact that we all have different characteristics, backgrounds, and lived experiences that drift from heteronormativity, exposing one more layer of the cake of intersectional beings we are can feel very daunting.

I did feel anxious in anticipation. But that feeling was quickly replaced by excitement as I started to engage with colleagues during the conference. It was clear to me that the Society was providing a wonderful opportunity by empowering us to connect, build our network, and have our own safe space; without being exclusive towards our ally friends, having queer spaces creates a completely different dynamic in which we can feel safer and (more) comfortable being ourselves.

I made my decision and walked to the event, still slightly worried, but with the conviction that I was taking an important step in merging my two worlds.

The event itself was really fun! It was in a little colourful café (with delicious food!). I could chat with old friends and met new colleagues that I hope I will get a chance to collaborate with in the future. There were introductions from the organisers and a suggestion for a fun ice-breaking activity, but the truth is that everyone was happily chatting to each other as if we were old friends catching up after a long time. It felt like the welcoming environment I’ve known from other non-professional LGBTQ+ events.

I was happily surprised to meet people in different career paths and stages. It’s not easy to find examples of queer people in STEM that have leadership roles, and I certainly didn’t personally know anyone in microbiology. Hosting events like this one can widen our view and open doors. I had conversations with colleagues that I wouldn’t have been able to have in any other setting, which gave me a feeling that somehow I could have a future doing what I love.

I’m hoping one day we won’t need safe spaces, but until then, I’m proud of my colleagues and to be a Champion of the Microbiology Society. I can’t wait for the next one!

Microbiome: From Research and Innovation to Market