“…These microhabitats are shaped by gradients that create ecological niches and determine both microbial structure and function (Figure 1A). For example, oxygen (Zheng et al, 2015;Thermann et al, 1985;Kelly and Colgan 2016;Schwerdtfeger et al, 2019) and antimicrobial concentrations decrease from the small intestine to the colon while bacterial load (Gu et al, 2013;Dieterich et al, 2018;Sender et al, 2016;Donaldson et al 2016), pH (Nugent et al, 2001;Ilhan et al, 2017), and transit time (Donaldson et al, 2016) increase, typically selecting for facultative or obligate anaerobes (Roediger 1980;Thursby and Juge 2017). Facultative anaerobes that are bile acid tolerant, such as Lactobacillaceae and Enterobacteriaceae, constitute a majority of the microflora in the small intestine (Zoetendal et al, 2012; Antibiotic-induced dysbiosis specifically decreases diversity of the gut microbiome and creates a nutrient niche vacuum that allows opportunistic pathogens to colonize and cause local infections (Dollive et al, 2013;Blaser and Falkow 2009;Chang et al, 2008).…”