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Chapter 6 : The Niche of

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Abstract:

This chapter presents an overview of the habitats where can be isolated. It reviews some of the data that characterize the boundaries of its broad ecological niche. The genus is not as genetically diverse as once thought and contains only three named species: , , and . The frequency of gene flow among the phylogenetic lineages and the phylogenetic scale at which it is occurring suggest that boundaries to gene flow among species are minimal and also that clades may not occupy entirely different ecological niches. The chapter discusses the niche of . A human host typically harbors two or three genotypes, and together these genotypes represent the majority of the cells to be found in a sample. First, nine or more genotypes may be detected in a sample at a single point in time. Second, selective plating reveals the presence of genotypes that exist at very low frequencies. Finally, the number of samples that contain rare genotypes also indicates that there may be a rather large pool of genotypes. The high densities of in sand led many to speculate that, as in the tropics and subtropics, is an environmental organism even in some of the coldest temperate regions. is widespread among warm-blooded animals and humans, and the dynamics of its colonization of the gastrointestinal (GI) tract is dependent on a number of host and microbial determinants.

Citation: Alm E, Walk S, Gordon D. 2011. The Niche of , p 69-89. In Walk S, Feng P (ed), Population Genetics of Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555817114.ch6

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Figures

Image of Figure 1.
Figure 1.

Graphical representation of CCs of as determined by eBURST. Central circle denotes the ancestor of the CC: ST10 (A) and ST95 (B). Each dot denotes an ST, and the size of the dot indicates the number of representatives of the ST in the database (http://mlst.ucc.ie).

Citation: Alm E, Walk S, Gordon D. 2011. The Niche of , p 69-89. In Walk S, Feng P (ed), Population Genetics of Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555817114.ch6
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Image of Figure 2.
Figure 2.

The frequency distribution of the number of genotypes recovered per individual host. Data are for isolates from humans ( ) and wild boars ( ).

Citation: Alm E, Walk S, Gordon D. 2011. The Niche of , p 69-89. In Walk S, Feng P (ed), Population Genetics of Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555817114.ch6
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Image of Figure 3.
Figure 3.

The relative abundance of the genotypes recovered from four human hosts ( ). The total number of isolated colonies analyzed for each person () was 175.

Citation: Alm E, Walk S, Gordon D. 2011. The Niche of , p 69-89. In Walk S, Feng P (ed), Population Genetics of Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555817114.ch6
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Figure 4.

The relative frequency of strains of the four main phylogroups recovered from people living in different cities. Data are from references and .

Citation: Alm E, Walk S, Gordon D. 2011. The Niche of , p 69-89. In Walk S, Feng P (ed), Population Genetics of Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555817114.ch6
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Tables

Generic image for table
Table 1.

Phylogenetically incongruent housekeeping loci of and

Citation: Alm E, Walk S, Gordon D. 2011. The Niche of , p 69-89. In Walk S, Feng P (ed), Population Genetics of Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555817114.ch6

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