Glycan processing in gut microbiomes

Rosa, Sabina Leanti La; Ostrowski, Matthew; León, Arturo Vera‐Ponce de; McKee, Lauren S.; Larsbrink, Johan; Eijsink, Vincent G. H.; Lowe, Elisabeth C.; Martens, Eric C.; Pope, Phillip B.

doi:10.1016/j.mib.2022.102143

Cited by 44 publications

(22 citation statements)

References 81 publications

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“…This also reflects differences in the strategies used for complex carbohydrate utilization by Bacteroidetes and Firmicutes. In Bacteroidetes, CAZymes are grouped within polysaccharide utilization loci (PULs) allowing disassembly of complex polysaccharides in a highly coordinated process while Firmicutes encode a lower proportional number of CAZymes that are specialized to target a few selected carbohydrates (Ndeh and Gilbert 2018 , La Rosa et al 2022 ).…”

Section: Microbial Ecology Of R Gnavus In the Huma...mentioning

confidence: 99%

Ruminococcus gnavus: friend or foe for human health

Crost

Coletto

Bell

et al. 2023

FEMS Microbiology Reviews

106

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Ruminococcus gnavus was first identified in 1974 as a strict anaerobe in the gut of healthy individuals, and for several decades, its study has been limited to specific enzymes or bacteriocins. With the advent of metagenomics, R. gnavus has been associated both positively and negatively with an increasing number of intestinal and extra-intestinal diseases from inflammatory bowel diseases to neurological disorders. This prompted renewed interest in understanding the adaptation mechanisms of R. gnavus to the gut, and the molecular mediators affecting its association with health and disease. From ca. 250 publications citing R. gnavus since 1990, 94% were published in the last 10 years. In this review, we describe the biological characterisation of R. gnavus, its occurrence in the infant and adult gut microbiota and the factors influencing its colonisation of the gastrointestinal tract; we also discuss the current state of our knowledge on its role in host health and disease. We highlight gaps in knowledge and discuss the hypothesis that differential health outcomes associated with R. gnavus in the gut are strain and niche specific.

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Section: Microbial Ecology Of R Gnavus In the Huma...mentioning

confidence: 99%

Ruminococcus gnavus: friend or foe for human health

Crost

Coletto

Bell

et al. 2023

FEMS Microbiology Reviews

106

View full text Add to dashboard Cite

show abstract

“…This percentage is likely underestimated due to the complex structures of carbohydrates ( 27 ) and the inconsistent, non-standard, and mixed use of glycan nomenclature in the literature ( 28 ). For example, pectins have alpha-rhamnoside and beta-galactan side chains, which are also found in arabinogalactans ( 27 ); beta-galactan also exists in algal polysaccharides such as carrageenans ( 7 , 27 ).…”

Section: Database Contentmentioning

confidence: 99%

dbCAN-seq update: CAZyme gene clusters and substrates in microbiomes

Zheng

Zhang

et al. 2022

Nucleic Acids Research

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Carbohydrate Active EnZymes (CAZymes) are significantly important for microbial communities to thrive in carbohydrate rich environments such as animal guts, agricultural soils, forest floors, and ocean sediments. Since 2017, microbiome sequencing and assembly have produced numerous metagenome assembled genomes (MAGs). We have updated our dbCAN-seq database (https://bcb.unl.edu/dbCAN_seq) to include the following new data and features: (i) ∼498 000 CAZymes and ∼169 000 CAZyme gene clusters (CGCs) from 9421 MAGs of four ecological (human gut, human oral, cow rumen, and marine) environments; (ii) Glycan substrates for 41 447 (24.54%) CGCs inferred by two novel approaches (dbCAN-PUL homology search and eCAMI subfamily majority voting) (the two approaches agreed on 4183 CGCs for substrate assignments); (iii) A redesigned CGC page to include the graphical display of CGC gene compositions, the alignment of query CGC and subject PUL (polysaccharide utilization loci) of dbCAN-PUL, and the eCAMI subfamily table to support the predicted substrates; (iv) A statistics page to organize all the data for easy CGC access according to substrates and taxonomic phyla; and (v) A batch download page. In summary, this updated dbCAN-seq database highlights glycan substrates predicted for CGCs from microbiomes. Future work will implement the substrate prediction function in our dbCAN2 web server.

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“…Bacteroides species are obligate anaerobes highly adapted to life in the gut as they live and grow exclusively in the gastrointestinal tracts of mammals (Ley et al , 2008). They are the foundation of the microbial food webs in the gut because they can break down a wide range of complex sugars (including dietary plant polysaccharides, host glycans, and milk oligosaccharides) that are major carbon sources (Martens et al , 2014; Schwalm III & Groisman, 2017; La Rosa et al , 2022). Nevertheless, Bacteroides species appear to experience carbon limitation in the gut because proteins and signaling molecules that accumulate upon carbon starvation are required for gut colonization (Schofield et al , 2018; Townsend II et al , 2020).…”

Section: Introductionmentioning

confidence: 99%

Gut colonization by Bacteroides requires translation by an EF‐G paralog lacking GTPase activity

et al. 2022

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Protein synthesis is crucial for cell growth and survival yet one of the most energy‐consuming cellular processes. How, then, do cells sustain protein synthesis under starvation conditions when energy is limited? To accelerate the translocation of mRNA–tRNAs through the ribosome, bacterial elongation factor G (EF‐G) hydrolyzes energy‐rich guanosine triphosphate (GTP) for every amino acid incorporated into a protein. Here, we identify an EF‐G paralog—EF‐G2—that supports translocation without hydrolyzing GTP in the gut commensal bacterium Bacteroides thetaiotaomicron. EF‐G2's singular ability to sustain protein synthesis, albeit at slow rates, is crucial for bacterial gut colonization. EF‐G2 is ~10‐fold more abundant than canonical EF‐G1 in bacteria harvested from murine ceca and, unlike EF‐G1, specifically accumulates during carbon starvation. Moreover, we uncover a 26‐residue region unique to EF‐G2 that is essential for protein synthesis, EF‐G2 dissociation from the ribosome, and responsible for the absence of GTPase activity. Our findings reveal how cells curb energy consumption while maintaining protein synthesis to advance fitness in nutrient‐fluctuating environments.

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Glycan processing in gut microbiomes

Cited by 44 publications

References 81 publications

Ruminococcus gnavus: friend or foe for human health

Ruminococcus gnavus: friend or foe for human health

dbCAN-seq update: CAZyme gene clusters and substrates in microbiomes

Gut colonization by Bacteroides requires translation by an EF‐G paralog lacking GTPase activity

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