Journal: Gut Microbes

Article Title: The mucin-degradation strategy of Ruminococcus gnavus : The importance of intramolecular trans -sialidases

doi: 10.1080/19490976.2016.1186334

Figure Lengend Snippet: Growth curves of R. gnavus ATCC 29149 and ATCC 35913 on pPGM. The growth curves represent the average growth, measured at OD600nm, of at least 3 biological replicates.

Article Snippet: Transcriptomics analyses of both ATCC 29149 and ATCC 35913 strains confirmed that the strategy utilized by R. gnavus for mucin-degradation is focused on the utilization of terminal mucin glycans.

Techniques:

Journal: Gut Microbes

Article Title: The mucin-degradation strategy of Ruminococcus gnavus : The importance of intramolecular trans -sialidases

doi: 10.1080/19490976.2016.1186334

Figure Lengend Snippet: Comparison of the distribution of glycoside hydrolases (GHs) between R. gnavus strains. GHs are represented by light gray boxes for R. gnavus ATCC 35913, striped boxed for R. gnavus ATCC 29149 and dark gray boxes for R. gnavus E1.

Article Snippet: Transcriptomics analyses of both ATCC 29149 and ATCC 35913 strains confirmed that the strategy utilized by R. gnavus for mucin-degradation is focused on the utilization of terminal mucin glycans.

Techniques:

Journal: Gut Microbes

Article Title: The mucin-degradation strategy of Ruminococcus gnavus : The importance of intramolecular trans -sialidases

doi: 10.1080/19490976.2016.1186334

Figure Lengend Snippet: Relative level of transcription of GH genes in R. gnavus ATCC 29149 (A) and ATCC 35913 (B). The transcriptomic analysis has been performed by RNASeq from R. gnavus grown in presence of pPGM and compared to Glc as sole carbon source. The relative level of transcription was expressed as the Log2 of the fold change in gene transcription and the figures showed averages of 4 biological replicates for the GH genes that exhibited increased transcription (Log2 fold change > 1). Data were analyzed by DESeq2. The significance of differential expression was determined by the Benjamini-Hochberg corrected p-values of the Wald test of the negative binomial test per each set of two conditions. The transcription level was considered significantly increased when p < 0.05 and a Log2 (fold change) >1 and significant results were labeled with *. Error bars were plotted as the standard error of the Log2 fold change.

Article Snippet: Transcriptomics analyses of both ATCC 29149 and ATCC 35913 strains confirmed that the strategy utilized by R. gnavus for mucin-degradation is focused on the utilization of terminal mucin glycans.

Techniques: Expressing, Labeling

Journal: Gut Microbes

Article Title: The mucin-degradation strategy of Ruminococcus gnavus : The importance of intramolecular trans -sialidases

doi: 10.1080/19490976.2016.1186334

Figure Lengend Snippet: The Nan locus in R. gnavus ATCC 29149 and ATCC 35913. (A) Schematic representation of the nan genetic organization in ATCC 35913. RGNV35913_01299 encodes a putative GDSL-like protein. RGNV35913_01298encodes a putative sugar isomerase involved in sialic acid catabolism. RGNV35913_01297 encodes a protein with homology with transcriptional regulators of the AraC family. The following 3 genes code for a predicted solute-binding protein (RGNV35913_01296) and two putative permeases (RGNV35913_01295 and RGNV35913_01294), components of a sugar ABC transporter. The following gene has homology with oxidoreductases from the Gfo/Idh/MocA family. The sialidase gene nanH (RGNV35913_01292) predicted to encode the GH33 enzyme comes next. Then nanE (RGNV35913_01291), which encodes a predicted ManNAc-6-P epimerase is followed by nanA (RGNV35913_01290) encoding a putative Neu5Ac lyase. nanK (RGNV35913_01289) is the last gene of the cluster, coding for a predicted ManNAc kinase. The previously described R. gnavus ATCC 29149 nan cluster shares 99.9% identity with the one present in ATCC 35913. Level of transcription of nan genes in R. gnavus ATCC 29149 (B) or ATCC 35913 (C). R. gnavus was grown in basal YCFA medium supplemented with either glucose (Glc) or mucin (pPGM) as sole carbon source. Cells were collected during the exponential phase of growth; RNA was extracted from 4 biological replicates for each carbon sources. The level of transcription of each gene was determined by RNASeq. The transcription of each gene was compared when the bacterium grew with pPGM vs. Glc using the R package DESeqx; it was considered significantly increased when the transcript was present at least twice more frequently, with a padj value (p-value adjusted for multiple testing) <=0.05 (* padj<=0.05).

Article Snippet: Transcriptomics analyses of both ATCC 29149 and ATCC 35913 strains confirmed that the strategy utilized by R. gnavus for mucin-degradation is focused on the utilization of terminal mucin glycans.

Techniques: Binding Assay

Journal: Gut Microbes

Article Title: The mucin-degradation strategy of Ruminococcus gnavus : The importance of intramolecular trans -sialidases

doi: 10.1080/19490976.2016.1186334

Figure Lengend Snippet: Proposed pathways for the catabolism of sialic acid in R. gnavus ATCC 29149 and ATCC 35913. Rg NanH releases 2,7-anhydro-Neu5Ac from α2–3 linked sialylated substrates. (A) It can be hypothesized that 2,7-anhydro-Neu5Ac is transported inside the bacterium via a 2,7-anhydro-Neu5Ac-specific ABC transporter composed of a solute-binding protein (RUMGNA_02698 in ATCC 29149;RGNV35913_01296 in ATCC 35913) and two putative permeases (RUMGNA_02697 and RUMGNA_02696 in ATCC 29149; RGNV35913_01295 and RGNV35913_01294 in ATCC 35913) and then hydrolyzed into Neu5Ac, possibly by the action of RUMGNA_02701 or RGNV35913_01299, before being catabolized into GlcNAc-6-P following the traditional pathway by the successive action of NanA (Neu5Ac lyase), NanK (ManNAc kinase) and NanE (ManNAc-6-P epimerase). (B) Alternatively, both 2,7-anhydro-Neu5Ac and Neu5Ac could enter the cells via the ABC transporter but NanA would either be inactive or specific for 2,7-anhydro-Neu5Ac, explaining the absence of growth of the bacteria on sialic acid.

Article Snippet: Transcriptomics analyses of both ATCC 29149 and ATCC 35913 strains confirmed that the strategy utilized by R. gnavus for mucin-degradation is focused on the utilization of terminal mucin glycans.

Techniques: Binding Assay

Journal: eLife

Article Title: Interrogating the recognition landscape of a conserved HIV-specific TCR reveals distinct bacterial peptide cross-reactivity

doi: 10.7554/eLife.58128

Figure Lengend Snippet: ( A ) Ten non-redundant ('nr') database-mined HdH peptides with close homology to S. newyorkensis peptide (Mic 1/HdH1) were tested in an IFN-γ based ELISpot assays using an AGA1-expressing T cell clone. Peptide concentration (Molar (M)) is denoted on the X-axis and the numbers of Spot Forming Cells (SFC) per 500 cell input is displayed on the Y-axis. Responses to the KF11 epitope are noted in red. Assays were performed in duplicate (technical repeats) on two separate occasions using different peptide stock dilutions and following re-stimulation and resting of T cell clone 1.2 (biological repeats), with one representative shown here. Error bars corresponding to the Standard Error of the Mean (SEM) reported. Test peptide IDs, their origins and sequence identities are specified in Table 2. ( B ) Binding of the HdH peptides to HLA-B*57:01, assessed in the UV-mediated peptide exchange sandwich ELISA assay. The Y-axis denotes average absorbance readings at 450 nm and the X-axis denotes test peptides. The background corresponding to the no peptide rescue (nr) control is denoted in grey (also illustrated across the samples by grey hatching). Assays were performed in duplicate (technical repeats) on two separate occasions using different peptide stock dilutions (biological repeats, n = 2), with one representative shown here. Error bars corresponding to the Standard Error of the Mean (SEM) are reported. Test peptide IDs, their origins and sequence identities are specified in Table 2. ( C ) Summary of evolved peptide motifs recognised by the AGA1 TCR. Recognition beyond the original KAFSPEVIPMF (KF11) index motif is exemplified initially by the diverse peptide sequences retrieved during repeated rounds of AGA1 TCR-mediated peptide selection, with a Seq2Logo motif reported for the top 20 Round 3 evolved peptide libraries. Following evaluation of 'nr'-database derived peptides in T cell functional assays, peptides that elicited the strongest functional responses - in this case, a S. newyorkensis -derived haloacid dehydrogenase peptide -allowed further refinement of database-led search motifs and identification of related peptide that were functionally recognized by AGA1 TCR-expressing T cell clones. Amino acids shared between KF11 and the S. newyorkensis -derived Mic1/HdH1 peptide is illustrated in the smaller right panel (pink shading). ( D ) Recognition of bacterial cell lysates from S. newyorkensis (Mic 1), C. orthopsilosis (Mic 2), O. uli (Mic 3) and R. gnavus (control) by AGA1-expressing T cell clones 1.1 and 1.2 was tested using an IFN-γ based ELISpot assay. Bacterial cell lysates (20μg/mL) were incubated with cytokine-matured HLA-B*57:01 positive HL60 cells for 7 hours, following which T cell responses were evaluated. PMA (10ng/mL) was included as a positive control, and the background control comprised HL60 cells incubated with T cells only. Lysate identity is denoted on the X-axes and the numbers of Spot Forming Cells (SFC) per 500 cell input are displayed on the Y-axes. Assays were performed in duplicate (technical repeats, n = 2) on two separate occasions (biological repeats, n = 2) using fresh lysate stock dilutions and following re-stimulation and resting of T cell clones 1.1 and 1.2. One representative is shown. Figure 4—source data 1. AGA1+ T cell clone 1.2 recognition of 'nr' mined HdH peptides_ELISpot data. Figure 4—source data 2. UV-exchange HLA-B*57:01 peptide binding ELISA data for HdH peptides. Figure 4—source data 3. Recognition of S. newyorkensis bacterial lysates by AGA1+ T cell clones 1.1 and 1.2_ELISpot data.

Article Snippet: Strain, strain background ( Ruminococcus gnavus) , Ruminococcus gnavus , DSMZ-German Collection of Microorganisms and Cell Cultures GmbH , CC55_001C , Bacterial cultures for generation of lysates (20 μg/mL).

Techniques: Enzyme-linked Immunospot, Expressing, Concentration Assay, Sequencing, Binding Assay, Sandwich ELISA, Control, Selection, Derivative Assay, Functional Assay, Clone Assay, Incubation, Positive Control, Enzyme-linked Immunosorbent Assay

Journal: eLife

Article Title: Interrogating the recognition landscape of a conserved HIV-specific TCR reveals distinct bacterial peptide cross-reactivity

doi: 10.7554/eLife.58128

Figure Lengend Snippet:

Article Snippet: Strain, strain background ( Ruminococcus gnavus) , Ruminococcus gnavus , DSMZ-German Collection of Microorganisms and Cell Cultures GmbH , CC55_001C , Bacterial cultures for generation of lysates (20 μg/mL).

Techniques: Construct, Recombinant, Plasmid Preparation, Sequencing, Software, Functional Assay, Flow Cytometry, Enzyme-linked Immunospot, Positive Control, Bicinchoninic Acid Protein Assay, Expressing, Enzyme-linked Immunosorbent Assay

Journal: iScience

Article Title: Identification of proteotoxic and proteoprotective bacteria that non-specifically affect proteins associated with neurodegenerative diseases

doi: 10.1016/j.isci.2024.110828

Figure Lengend Snippet:

Article Snippet: Ruminococcus gnavus , BEI Resources , HM-1056.

Techniques: Virus, Recombinant, Membrane, Western Blot, Software

Journal: Gut Microbiome

Article Title: Establishment and perturbation of human gut microbiome: common trends and variations between Indian and global populations

doi: 10.1017/gmb.2024.6

Figure Lengend Snippet: Common and/or unique trends observed between gut microbiome of Indian and global populations in noncommunicable and communicable diseases

Article Snippet: Inflammatory bowel diseases , USA , Non–IBD = 27, UC = 38, CD = 67 , 27.5 years (mean) , WGS , Illumina HiSeq2500 , s–E. coli, Ruminococcus torques and Ruminococcus gnavus , Faecalibacterium prausnitzii, and Roseburia hominis , Lloyd–Price et al. ( ) .

Techniques: Sequencing, Control, In Situ, Hybridization, Flow Cytometry, Real-time Polymerase Chain Reaction, Amplification, Denaturing Gradient Gel Electrophoresis, Software, Shotgun Sequencing, Infection, Functional Assay