290
19
Microbiomics
is clamped to the surface by another bacterium, and within it are at least three further
species of bacteria that help to digest the wood.
Efforts to investigate this microbial richness seem to have been disproportion-
ately small with respect to its evident importance for the maintenance of a healthy
organism. A corollary of this relative neglect has been the rather casual attitude of
medicine towards this indispensable miniature ecosystem. For example, antibiotics
are frequently prescribed to eliminate a bacterial infection of the “main” organism,
heedless of the devastation that the antibiotics are likely to inflict on gastrointestinal
microbial diversity, with the likelihood of consequential ill health. Of similar con-
cern is the well-nigh endemic use of certain herbicides, the residues of which that
remain in food destined for human consumption may have deleterious effects on the
gut microbes. 6
Nevertheless, progress in metagenomics has led to a great improvement in knowl-
edge and understanding of the human gut microbiome. 7 Very recently the metabolism
of many thousand human gut microörganisms has been reconstructed; 8 this will well
serve the development of personalized medicine.
References
Altamirano Á, Saa P, Garrido D (2020) Inferring composition and function of the human gut
microbiome in time and space: a review of genome-scale metabolic modelling tools. Comput
Struct Biotechnol J 18:3897–3904
Canny GO, McCormick BA (2008) Bacteria in the intestine, helpful residents or enemies from
within? Infect Community 76:3360–3373
Carbone A, Képès F, Zinovyev A (2005) Codon bias signatures, organization of microorganisms in
codon space, and lifestyle. Molec Biol Ecol 22:547–561
Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R (2009) Bacterial community
variation in human body habitats across space and time. Science 326:1694–1697
Cryan JF, Dinan TG (2012) Mind-altering microorganisms: the impact of the gut microbiota on
brain and behaviour. Nat Rev Neurosci 13:701–712
Heinken A et al. (2023) Genome-scale metabolic reconstruction of 7,302 human microorganisms
for personalized medicine. Nat Biotechnol (in press)
Hooper LV, Littman DR, Macpherson AJ (2012) Interactions between the microbiota and the
immune system. Science 336:1268–1273
Jackson AA, Golden MHN (1970) The human rumen. Lancet (7 October):764–767
Kempes CP, Dutkiewicz S, Follows MJ (2012) Growth, metabolic partitioning, and the size of
microorganisms. Proc Natl Acad Sci USA 109:495–500
Le Chatelier E et al (2013) Richness of human gut microbiome correlates with metabolic markers.
Nature 500:541–546
Liò P (2003) Statistical bioinformatics methods in microbial genome analysis. BioEssays 25:266–
273
6 Samsel and Seneff (2013).
7 Altamirano et al. (2020).
8 Heinken et al. (2023).