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Geerlings et al. Microbiome Res Rep 2024;3:36 https://dx.doi.org/10.20517/mrr.2024.06 Page 9 of 15

Figure 4. Volcano plot comparing the transcriptional response of A. muciniphila in fermentations containing a high concentration of
GlcNAc (mid-log condition A) and mucin (condition D). Due to the high number of genes upregulated in high-GlcNAc, genes with a
-50
-log10 P-value < 1 × 10 and a log2 fold change < 2.5 that are mentioned in the text are not shown in this figure. All other differentially
expressed genes mentioned in the text are labeled here. The complete overview of differentially expressed genes and their annotation
can be found in Supplementary File 1. A. muciniphila: Akkermansia muciniphila; GlcNAc: N-acetylglucosamine.

were identified to have a protein abundance ratio higher than 10. The protein abundance ratios indicate that
in the mucin condition, most proteins involved in mucin degradation were upregulated [Supplementary
Table 3]. In contrast, in high GlcNAc medium, the proteins that were upregulated in comparison to mucin
were mainly stress-related proteins and glycosyltransferases, in line with the observations related to the
transcriptional response.

In the following sections, we focus mainly on the transcriptome data since these revealed a higher number
of differentially expressed genes than that found in the proteomics data [Supplementary Table 2]. This
suggests that cells responded to differences in medium composition by adapting its regulations over its
functional aspect, possibly minimizing differences in overall cell composition. In the following sections, we
compared the transcriptional response of exponentially growing cells (mid-log) on high GlcNAc or low
GlcNAc and mucin.

High GlcNAc induces stress response as compared to mucin
In the medium containing high GlcNAc (Condition A), several genes and complete gene clusters related to
stress responses were found to be significantly upregulated as compared to the mucin condition [Figure 4].
This includes a gene cluster encoding for an ABC transporter and phosphate ABC transporter
(Amuc_1294-1308), a gene cluster involved in the production of exopolysaccharides (Amuc_2077-