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Page 8 of 15 Geerlings et al. Microbiome Res Rep 2024;3:36 https://dx.doi.org/10.20517/mrr.2024.06

Figure 3. Volcano plot comparing the transcriptional response of A. muciniphila in fermentations containing a high concentration of
GlcNAc (mid-log condition A) and a low concentration of GlcNAc (mid-log condition C). The differentially expressed genes mentioned
in the text are labeled here, as well as highly differentiated genes annotated as hypothetical proteins in italics. The complete overview of
differentially expressed genes and their annotation can be found in Supplementary File 1. A. muciniphila: Akkermansia muciniphila; GlcNAc:
N-acetylglucosamine.

condition A (high GlcNAc) and condition C (low GlcNAc) (252 differentially expressed genes) [Figure 3].

A higher concentration of GlcNAc showed significantly higher expression of a glycosyltransferase cluster
(Amuc_1139 until Amuc_1142) and genes possibly involved in exopolysaccharide or capsular
polysaccharide production (Amuc_2077 until Amuc_2079). Furthermore, a higher concentration of
GlcNAc led to overexpression of genes involved in stress response, including an anaerobic ribonucleoside
triphosphate reductase cluster (Amuc_0860 until Amuc_0862), NAD(P)-dependent oxidoreductase
(Amuc_0777), rubrerythrin (Amuc_2056), catalase (Amuc_2070), glutamate decarboxylase (Amuc_0372),
and molecular chaperones DnaK (Amuc_1406), HtpG (Amuc_2002), and GroES (Amuc_1407). In low
GlcNAc, many genes encoding hypothetical proteins were found among the upregulated genes. However,
lactoylglutathione lyase (Amuc_1878), glutamate dehydrogenase (Amuc_2051), and phosphate ABC
transporter permease protein PstA (Amuc_1304) were significantly upregulated in this condition as
compared to high GlcNAc.

Proteomic and transcriptomic response of A. muciniphila in glucose/GlcNAc vs. mucin
Cultivating A. muciniphila in food-grade medium where mucin is substituted for a mixture of glucose and
GlcNAc may induce transcriptional and translational changes that affect its physiology. Using the proteome
data, we compared mid-log condition A (high GlcNAc) and condition D (mucin). In total, 116 proteins