Proteomics and metabolomics analyses of Streptococcus agalactiae isolates from human and animal sources

Abstract

Streptococcus agalactiae (S. agalactiae), group B Streptococcus (GBS), a major cause of infection in a wide variety of diseases, have been compared in different human and animal sources. We aimed to compare the bacterial proteome and metabolome profiles of human and animal S. agalactiae strains to delineate biological interactions relevant to infection. With the innovative advancement in mass spectrometry, a comparative result between both strains provided a solid impression of different responses to the host. For instance, stress-related proteins (Asp23/Gls24 family envelope stress response protein and heat shock protein 70), which play a role in the survival of GBS under extreme environmental conditions or during treatment, are highly expressed in human and animal strains. One human strain contains ꞵ-lactamase (serine hydrolase) and biofilm regulatory protein (lytR), which are important virulence regulators and potential targets for the design of novel antimicrobials. Another human strain contains the aminoglycosides-resistance bifunctional AAC/APH (A0A0U2QMQ5) protein, which confers resistance to almost all clinically used aminoglycosides. Fifteen different metabolites were annotated between the two groups. L-aspartic acid, ureidopropionic acid, adenosine monophosphate, L-tryptophan, and guanosine monophosphate were annotated at higher levels in human strains. Butyric acid, fumaric acid, isoleucine, leucine, and hippuric acid have been found in both human and animal strains. Certain metabolites were uniquely expressed in animal strains, with fold changes greater than 2. For example, putrescine modulates biofilm formation. Overall, this study provides biological insights into the substantial possible bacterial response reflected in its macromolecular production, either at the proteomic or metabolomic level.

Figure 1

(A) Most abundant protein classes identified in human S. agalactiae strains, x axis shows number of proteins involved in the pathway, Y axis shows KEGG pathway. This figure was created using the KEGG database developed by Kanehisa Laboratories (www.kegg.jp/kegg/kegg1.html). (B) T-test with a p-value of 0.05 and FDR = 1% between proteins in human and animals S. agalactiae strains, red dots represent significant protein between both groups. (C) Partial least squares—discriminant analysis (PLS-DA) showing differences in proteome profile between both experimental groups. Both first and second components discriminate human and animals S. agalactiae proteome strains by 69.1%. (D) Clustering heatmap showing protein abundance of human and animals S. agalactiae strains. X axis represents samples with clear separation in proteome abundances of both strains. The Y axis represents gene symbol of protein. Scale represents scaled data. Heatmap is generated using the ggplot 2 package for the statistical programming language R (Version 3.4.3, https://ggplot2.tidyverse.org). (E) Volcano plot showing significantly dysregulated proteins between both strains. X axis represents log2 fold change differences of human/ animal where onefold change differences was set as a cutoff value. Y axis represents − log 10 of q value.

Figure 2

(A) Proteome comparison between human and animals S. agalactiae strains. Number of proteins identified in human strains were 1090; from them 1009 identified by TrEMBL and 81 by SwissProt, while the number of proteins identified in animal strains were 859; from them 847 identified by Tremble and 12 by SwissProt. Shared proteins between the two groups were 176 by TrEMBL and 1 by SwissProt. (B) Metabolome comparison between human and animals S. agalactiae strains. Number of metabolites identified were 240 and 243 in human and animal strains; respectively, from them 237 were shared.

Figure 3

(A) Variable importance in projection (VIP) scores obtained from the OPLS-DA showing top 15 discriminating metabolites between human and animal S. agalactiae strains, (B) Metabolome heatmap showing differences in the metabolites abundance (scaled) annotated between human and animal S. agalactiae strains. X axis represents samples and Y axis represents metabolite. Heatmap is generated using the ggplot 2 package for the statistical programming language R (Version 3.4.3, https://ggplot2.tidyverse.org).