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Supplemental Information

Supplementary materials and methods

Additional information from the materials and methods, which were shortened in the main manuscript.

DOI: 10.7287/peerj.preprints.2918v1/supp-1

Distribution of COG categories in R. ilealis CRIBT.

DOI: 10.7287/peerj.preprints.2918v1/supp-2

Organization of the L-fucose degradation gene cluster of R. ilealis CRIBT compared to similar gene clusters found in C. perfringens (strain ATCCT) and C. sordellii (strains VPI 9048 and ATCC 9714T)

In the current annotation of C. sordellii ATCC 9714T open reading frame prediction seems to be suboptimal, with a considerable amount of potentially wrong stop codons. Genes are color-coded by predicted function: transporter (green), metabolic enzyme with EC number (blue), metabolic enzyme with preliminary EC number/without assigned EC number (dark blue), transcriptional regulator (yellow), hypothetical/unknown protein (grey), protein involved in DNA processing (brown), protein involved in vitamin metabolism (light blue).

DOI: 10.7287/peerj.preprints.2918v1/supp-3

Organization of the urease gene cluster of R. ilealis CRIBT compared to similar gene clusters found in H. pylori (strain 26695) and close-relative C. sordellii (strains VPI 9048 and ATCC 9714T)

In the current annotation of C. sordellii ATCC 9714T open reading frame prediction seems to be suboptimal, with a considerable amount of potentially wrong stop codons. Genes are color-coded by predicted function: urease accessory proteins (red), transporter (green), metabolic enzyme with EC number (blue), metabolic enzyme with preliminary EC number/without assigned EC number (dark blue), transcriptional regulator (yellow), hypothetical/unknown protein (grey), protein involved in vitamin metabolism (light blue), ribosomal proteins (green).

DOI: 10.7287/peerj.preprints.2918v1/supp-4

Growth characteristics of the individual cultures used for whole-genome transcriptome analysis of R. ilealis CRIBT grown in four experimental conditions

DOI: 10.7287/peerj.preprints.2918v1/supp-5

Summary of the RNA-seq raw data analysis for whole-genome transcriptome analysis of R. ilealis CRIBT grown in four experimental conditions

DOI: 10.7287/peerj.preprints.2918v1/supp-6

Overview of the genes that were significantly upregulated during growth of R. ilealis CRIBT in the presence of glucose in comparison to at least one of the other three conditions

These three conditions included L-fucose, control (absence of additional carbon source) and FOS. Differential gene expression values that did not meet the criteria for significance (≥1.5 log2(fold change) and q value ≤0.05) are color-coded in dark-grey.

DOI: 10.7287/peerj.preprints.2918v1/supp-7

Overview of the genes that were significantly upregulated during growth of R. ilealis CRIBT in the presence of FOS in comparison to at least one of the other three conditions

These conditions included glucose, L-fucose and control (absence of additional carbon source)]. Differential gene expression values that did not meet the criteria for significance (≥1.5 log2(fold change) and q value ≤0.05) are color-coded in dark-grey.

DOI: 10.7287/peerj.preprints.2918v1/supp-8

Overview of the genes that were significantly upregulated during growth of R. ilealis CRIBT in the presence of L-fucose in comparison to at least one of the other three conditions

These conditions included glucose, FOS and control (absence of additional carbon source). Differential gene expression values that did not meet the criteria for significance (≥1.5 log2(fold change) and q value ≤0.05) are color-coded in dark-grey.

DOI: 10.7287/peerj.preprints.2918v1/supp-9

Overview of the genes that were significantly upregulated during growth of R. ilealis CRIBT in absence of a carbon source (control condition) in comparison to at least one of the other conditions

These conditions included glucose, FOS and L-fucose. Differential gene expression values that did not meet the criteria for significance (≥1.5 log2(fold change) and q value ≤0.05) are color-coded in dark-grey.

DOI: 10.7287/peerj.preprints.2918v1/supp-10

Additional Information

Competing Interests

J. Gerritsen is currently an employee of Winclove Probiotics. However, these associations do not influence our objectivity, integrity and interpretation of the results that we present in this manuscript.

Sacha A. F. T. van Hijum is an employee of NIZO, Kernhemseweg 2, 6718 ZB, Ede, the Netherlands and Vitor A.P. Martins dos Santos is an employee of LifeGlimmer GmbH, Markelstrasse 38, Berlin, Germany.

Willem M. de Vos and Hauke Smidt are Academic Editors for PeerJ.

Author Contributions

Jacoline Gerritsen conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Bastian Hornung performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Bernadette Renckens performed the experiments, analyzed the data, reviewed drafts of the paper.

Sacha A.F.T. van Hijum analyzed the data, reviewed drafts of the paper.

Vitor A.P. Martins dos Santos analyzed the data, reviewed drafts of the paper.

Ger T. Rijkers conceived and designed the experiments, analyzed the data, reviewed drafts of the paper.

Peter J. Schaap analyzed the data, reviewed drafts of the paper.

Willem M. de Vos conceived and designed the experiments, analyzed the data, reviewed drafts of the paper.

Hauke Smidt conceived and designed the experiments, analyzed the data, reviewed drafts of the paper.

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

All related data has been deposited at the European Nucleotide Archive. The raw reads for the genome of can be accessed via the accession numbers ERR366773, ERX397233, ERX397242 and ERX339449. The assembly can be accessed under LN555523-LN555524. The RNAseq data has been deposited under the numbers ERS533849- ERS533861.

Data Deposition

The following information was supplied regarding data availability:

All data has been submitted to the EBI.

Funding

This work was supported by a grant of SenterNovum (Agentschap NL), an agency of the Dutch Ministry of Economic Affairs (FND-07013). B. Hornung is supported by Wageningen University and the Wageningen Institute for Environment and Climate Research (WIMEK) through the IP/OP program Systems Biology (project KB-17-003.02-023). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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