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: Cell host & microbe

Article Title: Indoleacrylic acid produced by commensal Peptostreptococcus species suppresses inflammation

doi: 10.1016/j.chom.2017.06.007

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Bacterial strains used in this study are as follows: Clostridium butyricum ATCC 19398, Clostridium ramosum ATCC 25582, Clostridium scindens ATCC 35704, Clostridium tyrobutyricum ATCC 25755, Coprococcus comes ATCC 27758, Lachnospiraceae bacterium ATCC BAA2281, Ruminococcus gnavus ATCC 29148, Ruminococcus torques ATCC 27756, Bacteroides thetaiotaomicron ATCC 29148, Akkermansia muciniphila ATCC BAA835, Anaerotruncus colihominis DSM 17241, Blautia hansenii DSM 20583, Blautia hydrogenotrophica DSM 10507, Blautia producta DSM 2950, Catenibacterium mitsuokai DSM 15897, Clostridium aldenense DSM 19262, Clostridium asparagiforme DSM 15981, Clostridium bolteae DSM 15670, Clostridium hathewayi DSM 13479, Clostridium hiranonis DSM 13275, Clostridium lentocellum DSM 5427, Clostridium methylpentosum DSM 5476, Clostridium spiroforme DSM 1552, Clostridium symbiosum DSM 934, Dorea formicigenerans DSM 3992, Eubacterium biforme DSM 3989, Eubacterium dolichum DSM 3991, Holdemania filiformis DSM 12042, Marvinbryantia formatexigens DSM 14469, Peptostreptococcus anaerobius DSM 2949 , Peptostreptococcus russellii DSM 23041, Peptostreptococcus stomatis DSM 17678, and Ruminococcus obeum DSM 25238.

Techniques: Virus, Recombinant, Reverse Transcription, RNA Sequencing, Software