is sometimes yes, sometimes no. Analysis at the strain level is difficult, but different
strains of the same species can have quite different properties. Nevertheless, there is
increasing evidence that exposure to soil organisms is relevant.
The composition of the gut microbiome is strongly influenced by diet. For
example, rural African villagers have strains of Xylanibacter, and Treponema that
are entirely absent from the guts of European children, and indicate an ability to use
indigestible carbohydrates such as xylane, xylose, and carboxymethylcellulose that
are present in a diet rich in roots and tubers (De Filippo et al. 2010). From where did
the African children acquire these organisms? An experiment with caterpillars provides a clue. The microbiome of caterpillars does not resemble that of the leaves on
which they feed. The caterpillars are not endeavouring to become leaves. Rather,
their microbiome resembles that of the soil beneath the plant, where organisms that
can digest the leaves are found (Hannula et al. 2019). It is probable that the African
communities picked up organisms that digest the foods they eat from the soil in
which the food was grown.
18.4.8.1 Fermented Foods
Moreover, in the absence of refrigerators fermentation by environmental organisms
was inevitable, and in scavenged meat or fallen fruit the process would have begun
before the food was gathered. This would increase exposure to the organisms from
the soil capable of metabolizing the food in question. Learning to control these
fermentation processes involving bacteria (e.g. lactic fermentation), yeast (alcoholic
beverages), or moulds (oncom, tempeh) so as to develop palatable non-toxic storage
options was a crucial cultural advance. Analyses of residues in pottery reveal that
fermented beverages containing alcohol were in use at least 9000 years ago
(McGovern et al. 2004) and probably a great deal earlier (McGovern 2009). These
techniques, together with lactic fermentation of vegetables (Sauerkraut, Kimchi etc.)
and olives (Benitez-Cabello et al. 2016) or fermentation of meat, add nutritional
supplements such as vitamins and lactoferrin (Swain et al. 2014; Leroy et al. 2013;
Selhub et al. 2014; Breidt et al. 2013). Moreover, fermented foods provide microbiological diversity as well as bioactive peptides and phytochemicals such as
flavonoids that modulate the intestinal microbiota (Lu et al. 2013). Microbiota
from foods can transiently colonise the gut (David et al. 2014), and since there are
relatively few organisms in the ileum, ingested organisms can form a significant
percentage of the organisms present at this site, or even transiently outnumber the
resident ones (Derrien et al. 2015). This is important because the ileum is where
mucosal dendritic cells sample the gut contents and “inform” the immune system
about the antigenic repertoire of gut contents (Schulz and Pabst 2013).
These points raise interesting issues for modern humans. Even when we do eat
fermented foods, these are mostly fermented in controlled factory conditions, so we
take in few fermenting organisms from the natural environment. How many
European citizens have encountered the soil in which bananas, dates, or pineapples
were grown? Are we failing to pick up organisms that we require for the inactivation
18 Darwinian Medicine: We Evolved to Require Continuing Contact with the. . .
347
strains of the same species can have quite different properties. Nevertheless, there is
increasing evidence that exposure to soil organisms is relevant.
The composition of the gut microbiome is strongly influenced by diet. For
example, rural African villagers have strains of Xylanibacter, and Treponema that
are entirely absent from the guts of European children, and indicate an ability to use
indigestible carbohydrates such as xylane, xylose, and carboxymethylcellulose that
are present in a diet rich in roots and tubers (De Filippo et al. 2010). From where did
the African children acquire these organisms? An experiment with caterpillars provides a clue. The microbiome of caterpillars does not resemble that of the leaves on
which they feed. The caterpillars are not endeavouring to become leaves. Rather,
their microbiome resembles that of the soil beneath the plant, where organisms that
can digest the leaves are found (Hannula et al. 2019). It is probable that the African
communities picked up organisms that digest the foods they eat from the soil in
which the food was grown.
18.4.8.1 Fermented Foods
Moreover, in the absence of refrigerators fermentation by environmental organisms
was inevitable, and in scavenged meat or fallen fruit the process would have begun
before the food was gathered. This would increase exposure to the organisms from
the soil capable of metabolizing the food in question. Learning to control these
fermentation processes involving bacteria (e.g. lactic fermentation), yeast (alcoholic
beverages), or moulds (oncom, tempeh) so as to develop palatable non-toxic storage
options was a crucial cultural advance. Analyses of residues in pottery reveal that
fermented beverages containing alcohol were in use at least 9000 years ago
(McGovern et al. 2004) and probably a great deal earlier (McGovern 2009). These
techniques, together with lactic fermentation of vegetables (Sauerkraut, Kimchi etc.)
and olives (Benitez-Cabello et al. 2016) or fermentation of meat, add nutritional
supplements such as vitamins and lactoferrin (Swain et al. 2014; Leroy et al. 2013;
Selhub et al. 2014; Breidt et al. 2013). Moreover, fermented foods provide microbiological diversity as well as bioactive peptides and phytochemicals such as
flavonoids that modulate the intestinal microbiota (Lu et al. 2013). Microbiota
from foods can transiently colonise the gut (David et al. 2014), and since there are
relatively few organisms in the ileum, ingested organisms can form a significant
percentage of the organisms present at this site, or even transiently outnumber the
resident ones (Derrien et al. 2015). This is important because the ileum is where
mucosal dendritic cells sample the gut contents and “inform” the immune system
about the antigenic repertoire of gut contents (Schulz and Pabst 2013).
These points raise interesting issues for modern humans. Even when we do eat
fermented foods, these are mostly fermented in controlled factory conditions, so we
take in few fermenting organisms from the natural environment. How many
European citizens have encountered the soil in which bananas, dates, or pineapples
were grown? Are we failing to pick up organisms that we require for the inactivation
18 Darwinian Medicine: We Evolved to Require Continuing Contact with the. . .
347