Chapter 19

Microbiomics

The great increase in DNA sequencing capability over the past couple of decades

has given a tremendous impetus to the study of bacterial ecosystems, termed the

microbiome (cf. Sect. 17.8), and it is now not only possible to obtain a comprehen-

sive snapshot of microbial genomes but also follow how they vary temporally and

spatially. ¹ Analysis of microbial genomes presents some challenges slightly different

from those raised by eukaryotic genomes. ²

Even a genetically homogeneous population of bacteria can show considerable

phenotypic variation due to environmental conditions that are continually changing,

sometimes rapidly. ³ Bioinformatics analyses have already yielded interesting rela-

tionships between genome and phenotype, such as a correlation between codon bias

and prokaryotic physiology. ⁴

Great practical interest is attached to the human microbiome (which mostly resides

in the gastrointestinal tract) because of its links to good health. ⁵ It is perhaps well

known nowadays that the number of individual microbial cells in a typical human

being exceeds the number of proper cells by about an order of magnitude. The impor-

tance of these guests in processing ingested nutrients can scarcely be overestimated,

not only in our own species but also in, for example, ruminants, which could not

otherwise digest cellulose. A less well-known example is the primitive wood-eating

termite Kalotermes schwarzii. Seemingly paradoxically, although its diet is wood it

cannot itself digest wood. It relies on a huge population of perhaps 30–40 different

species of microörganisms in its gut to break down the wood. These microörganisms

are in turn dependent on other symbionts. For example, one of the gut microörgan-

isms is the protozoan Mixotricha paradoxa. Its whole surface is covered with two

types of spirochaete bacteria beating in rhythm to propel it along. Each spirochaete

1 Costello et al. (2009).

2 Liò (2003).

3 Smits et al. (2006); see also Kempes et al. (2012).

4 Carbone et al. (2005).

5 Jackson and Golden (1970), Canny and McCormick (2008), Nishihara (2010), Hooper et al.

(2012), Cryan and Dinan (2012), Le Chatelier et al. (2013), and Montiel-Castro et al. (2013).

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https://doi.org/10.1007/978-3-030-45607-8_19

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