New to science: November 2015

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 a few of the new species that have been discovered and the places they’ve been found. The full papers are available to journal subscribers, but the abstracts are free to read.

It’s the last day of November, which can only mean one thing – Christm15453932822_1c3c42dbaf_zas is just around
the corner. Whether this fills you with joy for the approaching festivities, or leaves you slightly bemused at how fast the year has gone, we’ve got a roundup of this month’s microbial discoveries just for you.

Scientists in Austria and Germany discovered two new strains of the genus Corynebacterium inside the noses of sick animals submitted to the Veterinary University in Vienna. The new species, C. tapiri and C. nasicanis, are named for the animals they were isolated from – a tapir and a dog, respectively. In another animal-related find, scientists in South Korea have found a novel species of microbe in a natural cave on Jeju Island. The strain, Rhodococcus antrifimi was isolated from dried bat dung (also known as guano).

Sea urchins are prickly underwater creatures that come in all colours, shapes and sizes. These animals, also known as sea hedgehogs, were the source of two new members of the phylum Bacteriodetes isolated by teams in Taiwan and Japan. Chryseobacterium echinoideorum came from sea urchins collected on Penghu Island, and Lutibacter holmesii was extracted from another species of sea urchin found in the Sea of Japan.

Elsewhere, in India, scientists studying the sludge from a dairy-waste treatment plant isolated and cultivated a peach-coloured colony of Rhodococcus bacteria, for which they propose the name R. lactis. Also looking at sludge, a team of Chinese researchers has discovered a new species of bacteria in a wastewater treatment plant that is able to degrade m-cresol (a phenolic compound found in creosote). The strain is named Lysinibacillus cresolivorans.

Lastly for this month, some very tiny microbes. Bacterial cells tend to be in the order of a few micrometres across – about 1/20th the width of a human hair – but some are much smaller. These cells, known as ultramicrobacteria, are around 0.2 micrometres wide. Scientists from Japan have isolated just such a species, and have aptly named it Aurantimicrobium minutum. The new species was discovered while the team was looking for bacteria that could pass through the very fine pore filters that are used for filtering microbes out of fluids.

Anand Jagatia

Image credit: Matt Chan on Flickr under CC BY-ND 2.0
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Microbe Talk: November 2015

Quantum_Dots_with_emission_maxima_in_a_10-nm_step_are_being_produced_at_PlasmaChem_in_a_kg_scaleHow could you convert the dust, leaves and cigarettes that litter the side of the road into something useful and valuable?

In this month’s podcast, we spoke to Dr Angela Murray from the University of Birmingham about using microbes to turn waste products into high-end products.

We hear about a patented technology to convert road dust into precious metal catalysts, and how cleaning up heavy metal pollution can be used to make powerful crystals called quantum dots.

Don’t forget, you can subscribe to Microbe Talk on iTunes. You can also find us on Soundcloud and Stitcher.

Anand Jagatia

Image credit: Antipoff on Wikimedia under CC BY-SA 3.0
Music: Kosmiche Slop by Anenon, Day Bird by Broke For Free, Mells by Broke for Free, Lights – And Counting by Action Davis
Sound effects (from Traffic by malupeeters, Car Engine by Pogotron, purr Tims by aivaaroo
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Q&A: Dr Tim Walker

Tim WalkerTomorrow, at the Federation of Infection Societies (FIS) 2015 conference, Dr Tim Walker will be giving the British Infection Association’s Barnett Christie lecture about his work on the genome sequencing of Mycobacterium tuberculosis. We asked him about his career and his research.

How would you describe a typical day at work?

At the moment I’ve got a job that is half-academic and half-clinical, so it really depends what day it is.

I’m a medical doctor, a Registrar in a clinical microbiology laboratory in the John Radcliffe Hospital, Oxford, training in microbiology and infectious diseases. Any clinical sample from the patients in our Trust comes to our lab and I act as the interface between the scientists and the clinicians.

In parallel, I’m carving out an academic career; I’ve done a PhD and am part of a large research group at the University of Oxford. I’m either in the laboratory working with TB strains, or at a computer looking at whole genome sequences.

Your first degree was in Politics, Philosophy and Economics. Why did you change fields?

I was very focused on humanities at school and wasn’t particularly interested in science – it was only after finishing my degree that I had to have a think about what I wanted to do for the rest of my life. On the one hand, I would have loved to have been a political philosopher, but I’m not sure I would have made much difference to anyone. I wanted to do something socially useful and medicine seemed like a reasonable way of achieving this. I was extremely fortunate; I got a place in medical school three weeks after deciding it was what I wanted to do – it was a bit of a whirlwind.

At what point did you decide to lean more towards science?

After I’d qualified and done three years of clinical work, I started to think that maybe research was the way forward. I still enjoy clinical work, but I wanted something more.  Being able to jump from one to the other was a very attractive balance and it’s turned out to be a good thing.

What’s your field of TB research?

The unifying factor with all the work we do is Whole Genome Sequencing. We’re taking advantage of new technologies that allow us to sequence large amounts of pathogen genomes rapidly and cheaply.

The initial focus of our work was to use these technologies to better identify person-to-person TB transmission and translate that knowledge into improved public health interventions.

How will Whole Genome Sequencing make a difference in patient treatment? Where do you see this new technology leading?

I think we’re at one of the most important times in microbiology since we first started identifying and cultivating bacteria. We’re now starting to transition away from culture and base most, if not all, of our diagnostic efforts on molecular and sequencing data. TB is leading this field for a number of reasons, not least because it is a relatively slow-growing organism, so culturing creates long delays to obtaining useful clinical data.

We’re working towards a future where we’ll be able to obtain all the information needed to treat a patient and control a disease in a community from a single genomic sequence, rather than from a group of tests that each give out fragments of information.

Once we’ve achieved that it’s not hard to imagine the clinical possibilities. Genome sequencers are getting smaller and cheaper, and the software is getting faster – these can be run from a laptop, which could itself be run by a solar panel. You could take this combination and run it in a low resource setting – where most TB is – and have a point-of-care test that rapidly gives you all the results you want.

Has your medical job helped your scientific one, and vice versa?

Very much so. Because the research we do is so translational the two naturally feed into each other. As a scientist, you want to know what the clinician needs, in order to design something that is user-friendly and that will be used. You also want to create something that people are comfortable using; otherwise they’ll revert to what they’re used to.

As a clinician, your day-to-day activity throws up new questions, which you might want to address through research. If you’re completely detached from clinical medicine it can be difficult to focus on what matters.

What will you be talking about in your lecture tomorrow?

I’m going to present the work my colleagues and I have done over the last five years and how we’ve used sequencing to learn about TB transmission, species identification and drug resistance. The title of my talk is Whole Genome Sequencing of M. tuberculosis: how big a revolution? – given that I’ve said it’s possibly the biggest change in 130 years, I’d say the answer is very!

What does being invited to give this lecture mean to you?

It’s very flattering, but this work is not an individual effort; you can only do it with a large group of collaborators. We’ve got a multidisciplinary team in Oxford, but we also work with researchers elsewhere in the UK and internationally. All the research is a synthesis of thought and effort from many people.

Benjamin Thompson

Image credit: Tim Walker
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Microbes: Martian miners of the future?

ISSIn the world of ‘Emerging Tech’, asteroid mining is an idea that won’t go away. As we whittle away our resources here on Earth, many companies are looking to the orbiting lumps of rock in our Solar System as the next source of valuable metals and minerals. This isn’t as far-fetched as it might seem; for example, NASA is planning a mission to bring back a piece of asteroid and have it orbit the moon in the near future.

Rather than sending a Bruce Willis-esque miner into space to do the extracting, most of these future-gazers are envisioning robots, satellites and lasers to do the work. But might there be another way?

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Arsenic in drinking water: Detecting a silent killer

Today at the Society’s Focused Meeting on Industrial Applications of Metal–Microbe Interactions, Dr Joanne Santini spoke about her group’s research into biosensors for arsenic contamination.

In the3132110060_0a47f6733e_z 1970s, the United Nations (UN) and the World Bank led a movement to improve the quality of drinking water in Bangladesh. At the time, pathogens in dirty surface water were infecting and killing huge numbers of the country’s population, many of them children. The solution was simple – by digging down into underground sources of water and drawing it up through a tube, communities could be given access to clean, safe water. Tube wells were a cheap and effective way to prevent diseases like cholera and dysentery, and would save thousands of lives. Or so people thought.

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The JAM was packed…

CroppedLast month, the Institute for Microbiology and Infection hosted the first Junior Award for Microbiology event, organised to give early-career researchers a forum to talk about their research and network with their peers. In this post, Dr Amanda Rossiter – a Sir Henry Wellcome Postdoctoral Fellow at the University of Birmingham – tells us about the event.

Nearly every academic institution runs a seminar programme, which invites academics from across the world to present their latest research. While this is a very successful model, these programmes are predominantly aimed at senior academics. At the Institute for Microbiology and Infection (IMI), within the University of Birmingham, many junior academics recognised the lack of networking events that were aimed solely at junior academics. To help resolve this issue, I have been working with a group of microbe-lovers at the IMI on a shared vision to revolutionise the way early-career researchers interact. The vision was simple: create an event that motivates early-career researchers to network with their peers. Emphasis was placed on creating a relaxed environment, which would encourage junior microbiologists to let their ‘scientific mojos’ flow, without the intimidating presence of Professors who often, let’s face it, dominate Q&A sessions. Continue reading

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Microbe Talk Extra: Swallowed by a whale

12422148723_4522577c36_bBaleen whales are some of the largest creatures on Earth, but they feed on some of the smallest – tiny ocean-dwelling crustaceans called krill and copepods.

Smaller still are the microscopic organisms that help the whales to digest this vast quantity of prey.

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