**8. Changes in the gut microbiome under PN**

The microbial communities within the gut contain vast numbers of microorganisms from the domains of bacteria, archeae, yeasts and fungi, protists, and

virus. The number of individual microbial cells rivals that of the human host and contains upwards of 150 fold the genetic content of the mammalian host [89]. The bacterial population, which accounts for >99% of all microbial DNA, contains trillions of organisms from numerous phyla, including *Firmicutes*, *Bacteroidetes,* and *Actinobacteria*. The basic role of the microbes in digestion is to breakdown nutrients and to synthesize novel compounds—including short chain fatty acids (SCFAs) and vitamins, including vitamin K and numerous B vitamins. Intestinal colonizers play complex roles in gut colonization and community establishment, creating barriers to intruding pathobionts and serve the host through modification of secreted molecules, including bile acids, and consumption of secreted glycoproteins. *O*-glycosylated mucin glycoproteins secreted by the host serve both as nutrients for the microorganisms and as a substrate for colonization by *Akkermansia muciniphila*, *Bacteroides thetaiotaomicron*, and *Bacteroides fragilis* [89].

PN challenges the host with a unique set of circumstances. On one hand, elemental nutrients are plentiful in the bloodstream, yet the physiology required for host adaptation are bypassed. From a gastrointestinal standpoint, lack of central intake only occurs during hibernation and prolonged fasting or starvation. These circumstances are associated with catabolism. However, the goal of PN is to prevent catabolism and drive stable metabolic homeostasis or anabolism. Given the close interdependence of the gut microbiome and diet, it is unsurprising that the primary driver of microbial community structure is host nutrition [90]. Resident got colonizers are adapted to metabolize the breakdown of indigestible fiber and play important roles in coordinating host responses to dietary intake, influencing incretins, bile acid pools, and gut enterohormones [91]. Some of these hormones have direct effects on the pancreatic islet and acinar cells (GLP-1, secretin), liver homeostasis (FGF15/19), and gall bladder (CCK).

Given that *Firmicutes* are efficient degraders of dietary carbohydrate, this phylum is decreased under PN while increased relative abundance of *Proteobacteria* are frequently observed [92]. *Proteobacteria* can digest alternate food sources, such as amino acids and various host secretions, making them more resilient in a fasted or starved state. Prior work showed that elemental nutrients from PN enter the gut lumen in low abundance through the use of tracers and that these nutrients are utilized by resident *Enterobacteriaceae* [93]. Since PN reaches the lumen, it is perhaps unsurprising that dirurnal variations in host metabolism may also influence gut community structure, even in the absence of dietary intake. Leone et al. demonstrated that the intestinal microbiome oscillates in composition over 24-h circadian rhythms, regardless of whether the host is enterally fed or PN [79]. This finding further illustrates the role of the diet, host, and combined metabolites in shaping and selecting for gut microbial community members.

In the absence of enteral feeding, pathogens may proliferate in the setting of PN due to decreased commensal nutrition that would usually lead to an ecology capable of outcompeting with them. Under PN feeding *Proteobacteria* blooms include many pathogens such as *E. coli, Salmonella, Yersinia, Helicobacter,* and *Vibrio* [92, 94]. In addition to providing competitive exclusion, other beneficial bacteria, including *Bacteroides fragilis*, are decreased. The presence of *B. fragilis* can support sIgA release [95]. The problematic changes in gut microbiome communities occur in concert with a loss of gut barrier, innate, and adaptive immune responses which can render the gut susceptible to a source of infection. Fecal microbiome transplantation (FMT) have demonstrated PN microbiome communities alone can decrease gut inflammation and decrease tight junction protein expression when placed into enterally fed previously germ-free animals [93].

In addition to bacteria, PN also reduces resistance to fungal pathogens, such as *Candida albicans* [96]. While *C. albicans* is found in healthy humans, it can become virulent in the gut and oral cavity, eventually entering systemic circulation, and causing disease. Experimental inoculation of *C. albicans* during PN results in increased gut translocation systemic infection of *C. albicans* compared with control animals [97]. As with bacteria, it is likely that changes in innate and adaptive immune arms underscore the increased susceptibility to otherwise harmless gut microbes [40, 98].
