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More About Microbes: The Good, the Bad and the Downright Ugly!

Posted in: Cells and Model Organisms

In a previous article, we took a quick journey through the wonderful world of microbes. Let’s take a step back now and have a closer look at the benefits of microbes. We will also look at reasons to avoid many of them. For example, the ‘plague’ which is caused by a particularly nasty bacteria called Yersinia pestis.

It’s important to remember that while non-scientists often tend to have a negative view of bacteria, it is only a relatively small number of species that actually cause human disease (these ones are known as pathogens).

The Good Microbes!

Food Making

  • Lactic acid bacteria (from the genus Lactobacillus) are essential for making yoghurt and cheese.
  • Molds are used in the fermentation of certain cheeses, especially blue cheeses like Roquefort and Stilton.
  • Baker’s yeast is a mainstay in the bakery. It is responsible for that characteristic sweet smell you get walking past the baker early in the morning!
  • Brewer’s yeast (actually the same species as baker’s yeast). As the name suggests, you can thank yeast for your Indian pale ales, your pilsners and your pints of Guinness! Not the same yeast is in all beers, mind you. There are as many different brewers’ yeast strains as there are beers; and brewers tend to develop their own specialized yeast strains – for example: Saccharomyces carlsbergensis, a name given to one of the early brewing yeast strains used by the Danish brewer Carlsberg!


  • Does the name Alexander Fleming ring any bells? He made the accidental discovery that penicillin (produced by the fungus Penicillium notatum) kills bacteria, marking the dawn of the antibiotic era. Since this discovery, many antimicrobials have been found in bacteria and fungi.
  • Ciclosporin (also spelled as cyclosporine and modifications thereof) was originally isolated from the Tolypocladium inflatum fungus in Norway. It is one of the most important immunosuppressive drugs used to counteract organ rejection in organ transplant patients.
  • Yeast cells are used as factories to express insulin used to treat diabetes patients. Before the advent of biotechnology, insulin was isolated from the pancreases of slaughtered pigs. As you can imagine, supply was an issue, and it was also risky business in terms of disease transmission! It’s not all about yeast, though – E. coli is the most widely used bacterial species for the production of recombinant proteins in the biotechnological and pharmaceutical industry (1).
  • Probiotics.  Those pills you pop to boost your microflora are a collection of bacteria often from the Lactobacillus and Bifidobacterium genera. Probiotics aid digestion, prevent diarrhea, and may help with certain food intolerances. In fact, humans (and animals) host trillions of microbes, and it is estimated that the number of microbes is almost equal to the number of cells in our bodies!! Even though this only amounts to 1-3 % of our total body mass, the important role of microbes in human health cannot be disputed and our understanding in this area is likely to grow significantly in the future (2) .


  • Certain soil bacteria degrade organic compounds for energy, and without these, there would be no soil on earth in which to grow plants.
  • Bioremediation. Bacteria and fungi clean up oil spills and other types of environmental contamination. According to the United States Environmental Protection Agency (EPA), bioremediation is a “treatment that uses naturally occurring organisms to break down hazardous substances into less toxic or non-toxic substances” (3, 4).
  • Bacteria are important decomposers releasing nutrients back into the soil.
  • Although often forgotten about, fungi also play important roles in the environment. They are major decomposers and they are important in maintaining soil structure by virtue of their filamentous growth patterns.
  • Endophytic fungi, which form symbiotic relationships with plants, confer a range of benefits to their host, including resistance to biotic and abiotic stresses.

The Bad Microbes!

  • Food spoilage – this occurs when food deteriorates to the point where it is no longer edible. This is particularly relevant for harvested fruit and vegetables due to the enzymatic action of bacteria, yeast and molds (collectively fungi), as well as environmental factors.

And Finally…. The Ugly Microbes!

This section deals with microbial infections in plants and humans. Human infections can be split into the not-so-nice and the downright ugly (and often life-threatening)! While we don’t touch upon animal infections here, they overlap to some extent with human infections and the treatment (if available) is often the same.

Plant diseases

Microbial diseases of plants pose a threat to animal feed as well as food for human consumption.  They are responsible for major human, animal and economic losses in different parts of the world.

  • A notable historical example of such a disaster is the Great Famine of Ireland (1845-1852). This was caused by a fungus-like eukaryotic organism (Phytophthora infestans), known as potato blight in layman’s terms. This disease of potatoes caused the death of 1 million people in Ireland due to starvation during this period. This highlights the risk in relying on a single vegetable crop.
  • Today, wheat rust, caused by the Puccinia fungi, leads to serious epidemics in North and South America, Mexico and parts of Asia. Yellow rust, in particular, is a devastating seasonal disease in India, resulting in huge yield losses. Currently, a highly virulent strain known as Ug99 is spreading in Africa in the Middle East, causing up to 100 % yield losses and is feared to threaten food security worldwide if successful control measures are not found in time.

Not-So-Nice Microbial Infections

Now let’s look at a few examples of human infections which are ugly, but not life-threatening.  With proper treatment they rarely cause long-term complications:

  • Bacterial infections such as urinary tract infections (UTIs), are caused by E. coli. They are uncomfortable and often need antibiotic treatment. You may feel miserable if you have a UTI, but luckily they are not usually life-threatening.
  • Bacterial infections caused by Staphylococcus aureus include boils, cellulitis (a painful skin infection), abscesses, toxic shock syndrome, pneumonia, wound infections and food poisoning. These infections are also usually treatable as long as the bacteria is susceptible to antibiotics, and treatment often involves a combination of antibiotics and drainage of the infected area.
  • Streptococcal bacteria cause a variety of infections in the body, including pneumonia, meningitis, ear infections, and strep throat.
  • Yeast and fungal infections – oral and genital thrush caused by the yeast Candida albicans, ringworm infections such as athlete’s foot and jock itch (caused by dermatophytic fungi) are itchy and downright uncomfortable but are treated effectively and fast, often using over-the-counter topical antifungals.
  • Sexually transmitted infections (STIs) – When speaking of STIs, you might think virus first, but bacteria are also responsible for STIs. This group of nasties encompasses anything from chlamydia (caused by the bacterium Chlamydia trachomatis) to gonorrhea (caused by the bacterium Neisseria gonorrhoeae) to syphilis (caused by the bacterium Treponema pallidum), to name a few. Luckily, the majority of STIs are treatable but early treatment is essential to avoid ugly complications.

Now let’s look at some of the downright nasty, often contagious, life-threatening infections, which at the very least lead to long-term complications. Such infections are often refractory to antibiotic treatments or treatments have limited effectiveness.

Life Threatening Bacterial Infections

  • Antibiotic-resistant, so-called superbug bacteria, such as MRSA (methicillin-resistant Staphylococcus aureus). Many of these infections occur in healthcare settings (so-called nosocomial infections) and are difficult to treat due to bacterial resistance to many commonly used antibiotics.
  • Necrotizing fasciitis, better known as flesh-eating disease, is a rare bacterial infection of the deeper layers of skin that rapidly spreads to subcutaneous tissue. It is a severe disease of sudden onset and is probably one of the ugliest bacterial diseases known. It is often caused by MRSA and is treatable through a combination of IV antibiotics and surgical removal of heavily infected tissue. Mortality rates are very high.
  • The bacterium Neisseria meningitides is the main cause of bacterial meningitis in children and adolescents. This is an acute infection of the protective membranes (the meninges) of the brain and spinal cord. It causes developmental impairments and mortality in about 10% of cases. It is treatable, but early treatment is imperative and mortality rates remain high with death occurring in 5-15 % cases, despite treatment.

Life Threatening Infections Yeast and Fungal Infections

  • Invasive or systemic fungal infections are on the rise in parallel with improvements in modern medicine. As counterintuitive as it might sound, modern immunosuppressive treatments in organ transplant recipients, powerful chemotherapeutic regimens, and cutting edge surgical procedures are among some of the biggest contributing factors to the rise in invasive fungal infections caused by opportunistic species such as the mold Aspergillus fumigatus and the yeasts Candida albicans and Cryptococcus neoformans.
  • Species of fungi that are otherwise considered harmless and are kept in check by the immune system of healthy individuals pose major threats to critically ill and immunocompromised patients. Burn patients, HIV patients and those with congenital immunodeficiencies are also at risk.
  • Treatments exist but many carry undesirable side effects and drug resistance often hampers the use of available treatments.

So that is it for a snapshot of the good, bad and ugly microbes. Stay tuned for more exciting articles in this series!


1. Russo,E. (2003) Special Report: The birth of biotechnology. Nature, 421, 456–457.
2. Gilbert,J.A., Quinn,R.A., Debelius,J., Xu,Z.Z., Morton,J., Garg,N., Jansson,J.K., Dorrestein,P.C. and Knight,R. (2016) Microbiome-wide association studies link dynamic microbial consortia to disease. Nature, 535, 94–103.
4. EPA A Citizen’s Guide to Bioremediation.

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Image Credit: John Voo


  1. karenarabella on April 10, 2020 at 7:22 pm

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  2. DJ on April 1, 2020 at 5:49 am

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