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Mucosal surfaces are the primary zones where animals meet their environment, and thus also the main points of entry for pathogenic microorganisms. The mucus layer is heavily colonized by bacteria, including many symbionts that contribute additional genetic and metabolic potential to the host (1, 2). Bacterial symbionts associated with a variety of other host surfaces also provide goods and services, e.g., nutrients (3–6), bioluminescence (7, 8), and antibiotics (9, 10). These resident symbionts benefit from increased nutrient availability (5, 11–13)

Within the mucus, the predominant macromolecules are the large (up to 106–109 Da) mucin glycoproteins. The amino acid backbone of these proteins incorporates tandem repeats of exposed hydrophobic regions alternating with blocks bearing extensive O-linked glycosylation (17). Hundreds of variable, branched, negatively charged glycan chains extend 0.5–5 nm from the peptide core outward into the surrounding environment (17, 18). Other proteins, DNA, and cellular debris also are present. Continual secretion and shedding of mucins maintain a protective mucus layer from 10–700 µm thick depending on species and body location (19–22).

By offering both structure and nutrients, mucus layers commonly support higher bacterial concentrations than the surrounding environment (11, 23). Of necessity, hosts use a variety of mechanisms to limit microbial colonization (24–27). Secretions produced by the underlying epithelium influence the composition of this microbiota (12, 27, 28).

the mucus layer, already considered part of the innate immune system and known to provide physical and biochemical antimicrobial defenses (18, 27, 67)

The mucus layer is dynamic. Mucins are secreted continually by the underlying epithelium while mucus is sloughed continually from the outer surface. As a result, there is an ongoing turnover of both the bacterial and phage populations in the mucus layer.