and cure diseases. For example, there is evidence that societies in Egypt and Rome
topically applied mouldy bread to wounds to prevent infections. Presumably, the
fungal species that were growing on the bread were producing antimicrobials that
inhibited the proliferation of pathogenic microbes (Gould 2016). Famously, Alexander Fleming serendipitously showed that fungi could make such compounds by
leaving agar plates growing a bacteria, called Staphylococcus, uncovered whilst
away on holiday. He noticed that a contaminating fungus, called Penicillium
notatum, created bacteria-free zones wherever it was growing, suggesting that the
fungus was producing a potent antibacterial which he named penicillin (Fleming
1929). Penicillin was the first modern antibiotic to be mass-produced and was hugely
important during World War II when it was used to treat the infected wounds of
injured soldiers (Dias et al. 2012). Around the same time that Fleming discovered
penicillin, a scientist called Selman Waksman was studying a phylum of bacteria
called Actinobacteria. Waksman observed that many actinobacterial species isolated
from soil could selectively inhibit the growth of other microorganisms when they
were grown together in the laboratory (Hopwood 2007). This finding led to a
systematic search for actinobacterial isolates that could kill disease-causing bacteria
and fungi. This, in turn, resulted in the isolation of several clinically useful antibiotics, including streptomycin which is produced by the bacterial species Streptomyces griseus and can be used to treat a variety of bacterial infections, including
tuberculosis (Schatz et al. 1944). Currently, the phylum Actinobacteria is responsible for producing over half of all clinically useful antibiotics (Hopwood 2007; van
der Meij et al. 2017; Devine et al. 2017). Genome sequencing has also revealed that
many isolates have the genetic potential to produce a huge diversity of different
natural products that may demonstrate novel activities and could also be exploited in
the future.
Thus, microbially produced antibiotics have been instrumental in reducing
human mortality throughout history, but particularly over the last century when
they became widely prescribed in the clinic. However, it is not only humans that
have exploited the products of microbial competition to prevent infection and
disease. In fact, an increasing number of organisms with markedly distinct natural
histories are being found to accumulate microbial species that produce antimicrobial
compounds. These microbes, in turn, are being shown to protect their hosts against
infections caused by parasitic and pathogenic microorganisms.
23.2 The Microbiome
Almost all organisms, at some stage during their lifecycle, interact extensively with a
complex community of microorganisms which make use of host resources and are
acquired from the host’s environment. These diverse microbial assemblages, their
collective genomes as well as the host habitat, are collectively referred to as an
organism’s microbiome (Marchesi and Ravel 2015). Advances in nucleic acid
sequencing technologies have enabled us to investigate the composition and function
498
S. Worsley
topically applied mouldy bread to wounds to prevent infections. Presumably, the
fungal species that were growing on the bread were producing antimicrobials that
inhibited the proliferation of pathogenic microbes (Gould 2016). Famously, Alexander Fleming serendipitously showed that fungi could make such compounds by
leaving agar plates growing a bacteria, called Staphylococcus, uncovered whilst
away on holiday. He noticed that a contaminating fungus, called Penicillium
notatum, created bacteria-free zones wherever it was growing, suggesting that the
fungus was producing a potent antibacterial which he named penicillin (Fleming
1929). Penicillin was the first modern antibiotic to be mass-produced and was hugely
important during World War II when it was used to treat the infected wounds of
injured soldiers (Dias et al. 2012). Around the same time that Fleming discovered
penicillin, a scientist called Selman Waksman was studying a phylum of bacteria
called Actinobacteria. Waksman observed that many actinobacterial species isolated
from soil could selectively inhibit the growth of other microorganisms when they
were grown together in the laboratory (Hopwood 2007). This finding led to a
systematic search for actinobacterial isolates that could kill disease-causing bacteria
and fungi. This, in turn, resulted in the isolation of several clinically useful antibiotics, including streptomycin which is produced by the bacterial species Streptomyces griseus and can be used to treat a variety of bacterial infections, including
tuberculosis (Schatz et al. 1944). Currently, the phylum Actinobacteria is responsible for producing over half of all clinically useful antibiotics (Hopwood 2007; van
der Meij et al. 2017; Devine et al. 2017). Genome sequencing has also revealed that
many isolates have the genetic potential to produce a huge diversity of different
natural products that may demonstrate novel activities and could also be exploited in
the future.
Thus, microbially produced antibiotics have been instrumental in reducing
human mortality throughout history, but particularly over the last century when
they became widely prescribed in the clinic. However, it is not only humans that
have exploited the products of microbial competition to prevent infection and
disease. In fact, an increasing number of organisms with markedly distinct natural
histories are being found to accumulate microbial species that produce antimicrobial
compounds. These microbes, in turn, are being shown to protect their hosts against
infections caused by parasitic and pathogenic microorganisms.
23.2 The Microbiome
Almost all organisms, at some stage during their lifecycle, interact extensively with a
complex community of microorganisms which make use of host resources and are
acquired from the host’s environment. These diverse microbial assemblages, their
collective genomes as well as the host habitat, are collectively referred to as an
organism’s microbiome (Marchesi and Ravel 2015). Advances in nucleic acid
sequencing technologies have enabled us to investigate the composition and function
498
S. Worsley