Microbe Talk: December 2014

Native ScientistIn a special, end-of-the-year podcast, Ben went to do some outside recording at the Wix School in Clapham, London, where he learnt about ‘Native Scientist’, an outreach project that goes into schools to give children a chance to learn about science research in their native language. The project was co-founded by Dr Joana Moscoso, the Society for General Microbiology’s 2014 Outreach Prize winner. We spoke to her about the project, and asked a teacher at Wix what he thought the benefits of the Native Scientist are.

Show notes:

  • Native Scientist’s homepage.
  • Our interview with Joana about her Outreach Prize win can be found here.
  • Information on the Wix School can be found here.

Benjamin Thompson

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How much might antimicrobial resistance cost? $100 trillion.

drugs-AMRToday at the Wellcome Trust’s headquarters in London, economist Jim O’Neill will launch Antimicrobial Resistance: Tackling a Crisis for the Health and Wealth of Nations, the first paper from the economic review he chairs that will investigate the growing problem of drug resistance in bacteria, viruses and parasites.

Antimicrobial resistance (AMR) has been frequently covered in the news from a scientific angle, but this paper is perhaps the first time a large-scale economic analysis has been attempted. The numbers raised in this report are staggering. Working with the analyst companies RAND Europe and KPMG, O’Neill and his team have estimated that by 2050, AMR could cause 10 million extra deaths annually and a cumulative loss to world GDP of $100 trillion.

In the scenario they describe, with microbes becoming resistant to some (if not all) drugs, the burden of AMR will not be equally shared across the globe. The paper estimates that the vast majority of AMR-related deaths will occur in Africa and Asia, with O’Neill stating that almost 2 million extra lives could be lost each year in India and that more than 1 in 4 deaths in Nigeria could be attributable to AMR by 2050.

In the paper, the team also stress that there would be serious secondary effects associated with a lack of effective drugs. In particular, they highlight four areas of modern medicine that are only possible thanks to antibiotics: caesarean sections, joint replacement, improved chemotherapy and organ transplants.

We’re yet to see the data associated with this report to understand how these numbers were calculated, and this is clearly only the first part of the overall review, so it will be interesting to see what else emerges when further papers from the review are published.

The report ends with a call for coordinated action that “… spans drug regulation and antimicrobial drug use across humans, animals and the environment…”, and describes AMR as a “… crisis that can be averted if the world takes action soon.” As Jim O’Neill himself said when launching the report, “The cost of stopping the problem is significantly lower than not stopping the problem.”

Benjamin Thompson

You can read the Review on Antimicrobial Resistance report.

Image Credit: Thinkstock/iStock
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New to Science: December Edition

GorillaEach month, the Society for General Microbiology 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.

The Christmas theme has begun to well and truly dominate every aspect of our lives, with just over two weeks to go until the big day. Here at the Society for General Microbiology, we would like to buck the trend for variety’s sake and provide you with some light reading that is not holiday-specific. After all, new species are always out there waiting to be discovered, and the fruits of busy microbiologists’ labours are showcased in this month’s New to Science.

Japanese researchers, for example, teamed up with colleagues from Gabon in central Africa to study the differences between captive and wild western lowland gorillas. They sampled the faeces of animals from Kyoto Zoo and the Moukalaba-Doudou National Park in Gabon and isolated Lactobacillus gorillae, a new addition to the over 200 Lactobacillus species found in a variety of animal intestines and fermented foods. The same strain of the bacterium was found in all the gorillas, suggesting that the microbes shared a common ancestor not too long ago.

In other primate news, an international group of scientists in Texas analysed samples of baboon placentas taken after the monkeys had suffered stillbirths. They discovered Brucella papionis, a new species that belongs to a group of bacteria associated with unsuccessful pregnancies in various animals.

At Ghent University in Belgium, a group of Czech, Belgian and French scientists isolated a new species of Acinetobacter from horse dung and named it A. gandensis. To their surprise, they also found bacteria belonging to the same species in dung samples from a horse and a cow in Lebanon and a forest pool in a natural reserve in the Czech Republic.

Beluga whales normally live in the frigid waters of the Arctic Ocean, but they are also popular in aquariums due to their characteristic white colour and expressive faces. Korean researchers investigated the faeces of one whale at the Yeosu aquarium in Busan and isolated Amphritea ceti. This group of bacteria is named after Amphritete, the wife of Poseidon in Greek mythology.

French microbiologists studying people with leptospirosis in the French overseas territory of Mayotte, near Madagascar, have isolated a new strain of Leptospira bacteria from their patients. These bacteria cause a range of diseases, from Weil’s disease to severe lung infections. The new species is called L. mayottensis after the place of its discovery.

Symbiosis, the mutually beneficial co-operation of two or more organisms, is a concept many of us may be familiar with from the plant and animal kingdoms. Groups of microbes that enter such symbiotic relationships are sometimes known as consortia. Chinese researchers investigated microbial consortia at a biogas production facility belonging to the Modern Farming Corporation in Hebei province, near Beijing. They isolated Clostridium huakuii from several of the consortia in the biogas reactor. In Tianjin, just across the provincial border, a fish-farming pond yielded Colwellia aquaemaris. Continuing the farming theme (and the northeast Chinese theme), Comamonas serinivorans was isolated from wheat compost in the neighbouring Shandong province.

Microbiologists also ventured further afield in their search for new species. A Chinese team isolated Sphingobacterium gobiense from soil in the Gobi desert in Central Asia, while looking for bacteria resistant to the aridity and heat of the desert. At the other end of the spectrum, Korean researchers ventured to Antarctica and discovered Granulosicoccus marinus in seawater collected just off the coast of the Antarctic peninsula.

These are just a few of the new species described this month; you can see the full list on the IJSEM website. The staff of the Society for General Microbiology and its journals would like to conclude this final New to Science of 2014 by wishing you a merry Christmas and a happy New Year. Look out for us again in 2015!

Jon Fuhrmann

Image Credit: lambda_x on Flickr under CC BY-ND 2.0.
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World AIDS Day 2014

Red ribbon at the White House to commemorate World AIDS Day

A red ribbon, the symbol of solidarity of people living with AIDS, is displayed on the North Portico of the White House.

1 December is World AIDS Day, highlighting the fight against this global pandemic. AIDS, or Acquired Immunodeficiency Syndrome, has killed over 39 million people worldwide since 1981, and some 35 million people are currently estimated to be living with the disease.

AIDS is considered a major challenge of modern public health – indeed, World AIDS Day was the first global health day and has been held every year since 1988. Since 2011, the theme has been ‘Getting to Zero’, referring to the World Health Organisation’s joint goals of ‘Zero new HIV infections. Zero deaths from AIDS-related illness. Zero discrimination’.

AIDS is caused by the Human Immunodeficiency Virus (HIV). HIV is a lentivirus, a group of viruses that cause long-term, chronic diseases with long incubation periods. HIV infects cells such as CD4+ cells that are part of the human immune system, reducing their number and rendering the body increasingly susceptible to infection. As a result, other illnesses and cancers, such as tuberculosis or HIV-associated Kaposi’s sarcoma, occur more frequently as the disease progresses.

There are two types of HIV, both of which are thought to have spread to humans from monkeys and apes. They are mutations of the Simian Immunodeficiency Virus (SIV), which has existed for over 30,000 years. Two strains of SIV that infect chimpanzees and sooty mangabeys, respectively, mutated to infect humans in the early 20th century; these mutations are known as HIV subtype 1 and 2, respectively. Subtype 1 is by far the more widespread and virulent, although many HIV tests also test for subtype 2.

The initial stage of HIV infection is called acute retroviral syndrome. It tends to occur in the first few weeks after infection and usually involves flu-like symptoms. As the infection progresses, common signs include swollen lymph nodes, weight loss and frequent fevers or diarrhoea. The most advanced stage of HIV infection is known as AIDS; at this stage, severe diseases such as tuberculosis and meningitis become increasingly likely and life expectancy decreases rapidly.

HIV can be transmitted via sexual contact, exposure to infected blood, or from mother to child during pregnancy, birth or breastfeeding. Other bodily fluids such as saliva, sweat, tears or vomit cannot cause infection unless they are contaminated with blood.

The most frequent mode of HIV transmission is through unprotected sex with an infected person. Worldwide, the majority of infections occur as a result of heterosexual contact, although men who have sex with men (MSM) tend to be proportionally more at risk in high-income countries. For example, nearly two thirds of new HIV infections in the USA in 2009 were in MSM.

Blood-borne infection can result from needle-sharing for intravenous drug use and injections or blood transfusions with unsterilised equipment. Transfusions of infected blood are a particularly important risk factor, with over 90% of such transfusions resulting in the recipient contracting HIV.

Transmission from mother to child is the least common of the three main modes of transmission. However, it accounts for 9 of every 10 HIV cases in children.

There is currently no known cure or vaccine for AIDS. Depending on how early the disease is diagnosed, it can be managed with a ‘cocktail’ of drugs called antiretrovirals. These can slow down the progression of the disease to final-stage AIDS and lower the risk of death. They also lower the risk of common HIV-related infections such as tuberculosis and can improve mental and physical well-being.

If antiretroviral drugs are used soon after infection with HIV, patient life expectancies near the national average are possible. This is a significant improvement over the average post-infection survival time for those not taking antiretrovirals, which is estimated to be around 11 years.

Nearly 12 million people were receiving antiretroviral cocktails in low- and middle-income countries in 2013; 750,000 of them children. The treatment of children is lagging behind, with 24% of HIV-positive children receiving treatment compared to 38% of adults.

Condoms are the main weapon in the fight against AIDS, reducing the likelihood of HIV transmission to below 1% per year. Other measures such as spermicides, gels and male circumcision have been reported to reduce transmission rates in sub-Saharan Africa, but condoms – along with large-scale education and counselling programmes – remain by far the dominant measure to stop the HIV pandemic.

Antiretroviral treatment can effectively prevent the transmission of HIV. It can be used as a preventative measure by an infected person, reducing the likelihood of sexual transmission by up to 96%, or by non-infected people to minimise their risk of contracting the virus. Non-infected people can also receive treatment immediately after suspected exposure to HIV.

The risk of HIV being transmitted from mother to child can be minimised – but not eliminated – if the mother receives antiretroviral drugs during pregnancy and her baby receives them in the first 18 months after birth. Over two thirds of HIV-positive mothers and their babies now receive antiviral treatment in low- and middle-income countries, and this statistic is steadily rising.

As of 2013, new HIV infections have declined by a third since 2001 – in children, they have declined by more than half. The availability and cost of antiretroviral therapy in low- and middle-income countries has improved considerably, and the number of AIDS-related deaths has dropped accordingly. These statistics justify the WHO’s ‘Closing the Gap’ theme, a contrast to earlier themes such as ‘Children Living in a World with AIDS’ or ‘I Care. Do You?’.

Each year, the White House commemorates World AIDS Day by hanging a ribbon outside the building. This became the first such symbol to decorate the building since Abraham Lincoln’s times. It is thanks to the work of countless people around the world that we are making progress in the fight against AIDS, giving hope to the millions of people living with HIV.

Jon Fuhrmann

Image Credit: Ted Eytan on Flickr under CC BY-SA 2.0.
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Microbe Talk: November 2014

521724789New York’s Central Park is huge. This iconic rectangle of greenery, 2.5 miles long and 0.5 miles wide, receives 40 million human visitors annually and is home to hundreds of species of animals and insects, and over 25,000 trees. But what of the world beneath the soil? How many microbes are living beneath the different environments found in the park?

A recent paper, published in Proceedings of the Royal Society B, has investigated the below-ground microbial diversity in Central Park. We spoke to Dr Kelly Ramirez, the study’s lead author, who is currently working as a Postdoctoral Researcher at the Netherlands Institute of Ecology. Kelly told us how she went about searching for microbes in the park, and how many new species were uncovered.

Show notes:

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

Benjamin Thompson

Image Credit: Thinkstock
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Not to be underestimated: nematodes learn to avoid smelly bacteria

C elegans

C. elegans nematodes (black) on a background of E. coli.

There are many examples of remarkable intelligence from the animal kingdom: chimpanzees can learn sign language and use tools to gather food; elephants have been known to perform basic maths; and a Border Collie named Chaser knows over 1,000 different toys by name. These remarkable feats are generally associated with mammals; more primitive organisms are rarely considered to be particularly intelligent.

However, this is unjustified – take Caenorhabditis elegans, for example. This nematode (or roundworm) consists of only about 1,000 cells and has no brain, although nearly a third of the cells in its body are neurons responsible for transmitting information around the body. Despite its very simple anatomy, researchers at Rockefeller University in New York found that C. elegans is capable of “learning” which chemical signals are associated with harmful bacteria. They believe that the nematodes’ ability to learn is associated with their olfactory neurons – that is, their sense of smell.

C. elegans usually lives in soil, an environment abundant in bacteria; some, such as Escherichia coli, are a food source for the nematodes, while others are harmful to them. To study the nematodes’ ability to learn from experiences, the scientists looked at how ‘naive’ nematodes – raised without exposure to harmful bacteria – responded to a choice between moving towards edible E. coli or towards pathogens. Having not had the opportunity to learn that pathogens are harmful and not a source of food, roughly equal numbers of these nematodes moved towards the pathogens and towards the E. coli. Repeating the experiment with nematodes that had previously been exposed to pathogens, the researchers found that almost all of them avoided the pathogens and moved towards the safe food source. These results suggest that odour recognition is not instinctive, but can be learned through exposure to harmful bacteria.

The learning ability of C. elegans is now being used to evaluate the pathogenicity of different bacterial strains. Euan Scott, a PhD student at the University of Southampton, is using the nematodes to model how likely the various bacteria are to cause infection and disease in humans. He is presenting his work at the Society for General Microbiology’s Focused Meeting in London today.

Scott uses laboratory-grown, naive nematodes and places them near E. coli patches laced with harmful bacteria. Rather than having to choose between pathogens and safe food, the nematodes now have to learn that their food contains harmful substances. The theory underlying his experiments is that more dangerous bacteria elicit stronger aversive reactions in C. elegans, meaning that more of them will learn to abandon the food patch in search of alternative food sources. Scott is also investigating how the nematodes’ fertility changes when they spend time near pathogens. If the number of eggs were to be directly related to exposure to harmful bacteria, this would be useful for determining the pathogenicity of bacteria.

Knowing how harmful different strains of bacteria are – and which genes cause their pathogenicity – will hopefully translate into human medicine and inform future antibacterial drugs and treatment methods.

The other important aspect of Scott’s research is that while we know which neurons are activated in C. elegans in response to odours, it is not clearly understood how exactly the learning process takes place. He thinks that decoding the learning process of nematodes could mark an important step in understanding how more complex organisms such as humans form memories.

Euan Scott’s work on nematode-based pathogenicity models is just one of many cutting-edge research projects showcased at the Society for General Microbiology’s Focused Meeting in London. To stay up to date on our future events, visit our website.

Jon Fuhrmann

Image Source: Niharb on Flickr under CC BY-NC-ND 2.0.
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New to Science: November Edition

Wine: New to Science in MicrobiologyEach month, the Society for General Microbiology 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 subscribersbut the abstracts are free to read.

As supermarkets and the media never fail to remind us, the festive season has arrived – whether we like it or not. Fortunately, this is also an opportunity to relax a little and enjoy quality time with those dear to us. More often than not, a sophisticated tipple is served at such social occasions – much to the joy of the wine industry.

French wine producers, in particular, are pleased with the outcome of the 2014 harvest and are predicting that this will have been a good wine year. Their Greek counterparts are less optimistic: difficult weather conditions throughout the growing and harvesting seasons saw production drop by 15%. A team of microbiologists from Greek universities also took an interest in their country’s wine output, albeit for a different reason. They studied grapes from a vineyard in the Nemea region and isolated a new species of bacterium, Weissella uvarum.

In other parts of the world, fermented grape juice is less of a staple at the dining-room table. Researchers at Chung-Ang University in Seoul studied a dish called myeolchi-jeot, a traditional Korean dish made from fermented anchovies, and identified the bacterium Salimicrobium jeotgali. Sugarcane juice, meanwhile, is a popular drink across Southeast Asia. A Thai team isolated Wickerhamiella siamensis, a species of yeast that grows on the leaves of sugarcane plants without damaging them.

Another species of Wickerhamiella bacteria, W. allomyrinae, was discovered in the gut of a rhinoceros beetle by Chinese scientists. Since these beetles feed on sugarcane plants, the bacterium was likely consumed by the specimen just before it was studied by the researchers.

Elsewhere in the animal kingdom, Japanese researchers isolated a previously unknown species of Streptococcus from the oral cavity of an African elephant. They named it S. oriloxodontae, after ‘oris’ (Greek for ‘mouth’) and ‘loxodontae’, the scientific name of the African elephant. Danish and German scientists studied Syrian and European hamsters and isolated two new genera of bacteria, both in the Pasteurellaceae family. They named them Mesocricetibacter intestinalis and Cricetibacter osteomyelitidis, respectively.

As they are wont to do, a number of microbiologists have also been travelling to far-flung places in pursuit of their quest to introduce hitherto unknown microbes to science. In Bijie in southern China, Thermomonas carbonis was isolated from soil inside a coal mine. A team from Korea scaled the country’s tallest mountain, Hallasan, to isolate Aneurinibacillus soli from a soil sample collected at 1,950m above sea level. A different group discovered Pedobacter pituitosus at the Wibong waterfalls, less than 200 miles to the north.

American and Korean researchers teamed up to explore the Juan de Fuca Ridge off the coasts of the northwestern USA and British Columbia in Canada. Here, they discovered Thermococcus paralvinellae and T. cleftensis, two heat-loving species of bacteria that thrive in the low-oxygen conditions of hydrothermal vents. Over 5,000 miles to the southwest, a Japanese team isolated Psychrobium conchae from the Iheya North hydrothermal field off the eponymous island in Okinawa, Japan.

To get our loyal readers into the spirit for next month’s Christmas edition, we conclude this issue of New to Science with a microbe that was discovered near the closest fully functional settlement to the North Pole. A group of scientists from Wuhan University in China discovered Terrimonas arctica in a sample of the frozen soil near Ny-Ålesund in the Svalbard archipelago.

These are just a few of the new species described this month; you can see the full list on the IJSEM website. We’ll be back again next month with a host of new ones  look out for us then!

Jon Fuhrmann

Image credit: Paul Lieberwirth on Flickr under CC BY-NC-ND 2.0.
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