dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

Nucleic Acids Research, Год журнала: 2018, Номер 46(W1), С. W95 - W101

Опубликована: Май 4, 2018

Complex carbohydrates of plants are the main food sources animals and microbes, serve as promising renewable feedstock for biofuel biomaterial production. Carbohydrate active enzymes (CAZymes) most important complex carbohydrate metabolism. With an increasing number plant plant-associated microbial genomes metagenomes being sequenced, there is urgent need automatic tools genomic data mining CAZymes. We developed dbCAN web server in 2012 to provide a public service automated CAZyme annotation newly sequenced genomes. Here, dbCAN2 (http://cys.bios.niu.edu/dbCAN2) presented updated meta server, which integrates three state-of-the-art CAZome (all CAZymes genome) annotation: (i) HMMER search against HMM (hidden Markov model) database; (ii) DIAMOND CAZy pre-annotated sequence database (iii) Hotpep conserved short peptide database. Combining outputs removing found by only one tool can significantly improve accuracy. In addition, now also accepts nucleotide submission, offers predict physically linked gene clusters (CGCs), will be very useful online identifying putative polysaccharide utilization loci (PULs) or metagenomes.

Язык: Английский

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Gut Bacteroides species in health and disease

Gut Microbes, Год журнала: 2021, Номер 13(1)

Опубликована: Янв. 1, 2021

The functional diversity of the mammalian intestinal microbiome far exceeds that host organism, and microbial genes contribute substantially to well-being host. However, beneficial gut organisms can also be pathogenic when present in or other locations body. Among dominant bacteria are several species

Язык: Английский

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dbCAN3: automated carbohydrate-active enzyme and substrate annotation

Nucleic Acids Research, Год журнала: 2023, Номер 51(W1), С. W115 - W121

Опубликована: Май 1, 2023

Carbohydrate active enzymes (CAZymes) are made by various organisms for complex carbohydrate metabolism. Genome mining of CAZymes has become a routine data analysis in (meta-)genome projects, owing to the importance bioenergy, microbiome, nutrition, agriculture, and global carbon recycling. In 2012, dbCAN was provided as an online web server automated CAZyme annotation. dbCAN2 (https://bcb.unl.edu/dbCAN2) further developed 2018 meta combine multiple tools improved also included CGC-Finder, tool identifying gene clusters (CGCs) (meta-)genomes. We have updated dbCAN3 with following new functions components: (i) dbCAN-sub profile Hidden Markov Model database (HMMdb) substrate prediction at subfamily level; (ii) searching against experimentally characterized polysaccharide utilization loci (PULs) known glycan substates dbCAN-PUL CGC (iii) majority voting method consider all predicted from (iv) browsing visualization results on website. summary, not only inherits dbCAN2, but integrates three methods prediction.

Язык: Английский

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Bacteroidetes use thousands of enzyme combinations to break down glycans

Nature Communications, Год журнала: 2019, Номер 10(1)

Опубликована: Май 3, 2019

Abstract Unlike proteins, glycan chains are not directly encoded by DNA, but the specificity of enzymes that assemble them. Theoretical calculations have proposed an astronomical number possible isomers (> 10 12 hexasaccharides) actual diversity structures in nature is known. Bacteria Bacteroidetes phylum considered primary degraders polysaccharides and they found all ecosystems investigated. In genomes, carbohydrate-degrading (CAZymes) arranged gene clusters termed polysaccharide utilization loci (PULs). The depolymerization a given complex PULs requires bespoke enzymes; conversely, enzyme composition can provide information on structure targeted glycans. Here we group 13,537 964 genomes according to their CAZyme composition. We find collectively elaborated few thousand combinations for breakdown, suggesting global estimate much smaller than theoretical one.

Язык: Английский

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Carbohydrate-active enzymes (CAZymes) in the gut microbiome

Nature Reviews Microbiology, Год журнала: 2022, Номер 20(9), С. 542 - 556

Опубликована: Март 28, 2022

Язык: Английский

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Developing a new class of engineered live bacterial therapeutics to treat human diseases

Nature Communications, Год журнала: 2020, Номер 11(1)

Опубликована: Апрель 8, 2020

Abstract A complex interplay of metabolic and immunological mechanisms underlies many diseases that represent a substantial unmet medical need. There is an increasing appreciation the role microbes play in human health disease, evidence accumulating new class live biotherapeutics comprised engineered could address specific disease. Using tools synthetic biology, nonpathogenic bacteria can be designed to sense respond environmental signals order consume harmful compounds deliver therapeutic effectors. In this perspective, we describe considerations for design development achieve regulatory patient acceptance.

Язык: Английский

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Division of labor in honey bee gut microbiota for plant polysaccharide digestion

Proceedings of the National Academy of Sciences, Год журнала: 2019, Номер 116(51), С. 25909 - 25916

Опубликована: Ноя. 27, 2019

Bees acquire carbohydrates from nectar and lipids; amino acids pollen, which also contains polysaccharides including cellulose, hemicellulose, pectin. These potential energy sources could be degraded fermented through microbial enzymatic activity, resulting in short chain fatty available to hosts. However, the contributions of individual microbiota members polysaccharide digestion have remained unclear. Through analysis bacterial isolate genomes a metagenome honey bee gut microbiota, we identify that Bifidobacterium Gilliamella are principal degraders hemicellulose Both show extensive strain-level diversity gene repertoires linked digestion. Strains bees possess more such genes than strains bumble bees. In Bifidobacterium, encoding carbohydrate-active enzymes colocated within loci devoted utilization, as Bacteroides human gut. Carbohydrate-active enzyme-encoding expressions up-regulated response particular hemicelluloses both vitro vivo. Metabolomic analyses document experimentally colonized by different generate distinctive metabolomic profiles, with enrichment for specific monosaccharides, corresponding predictions genomic data. The other 3 core species clusters (Snodgrassella 2 Lactobacillus clusters) few or no Together, these findings indicate strain composition hosts determines metabolic capabilities potentially affects host nutrition. Furthermore, niche specialization revealed our study may promote overall community stability microbiomes

Язык: Английский

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Potential of Pectins to Beneficially Modulate the Gut Microbiota Depends on Their Structural Properties

Frontiers in Microbiology, Год журнала: 2019, Номер 10

Опубликована: Фев. 14, 2019

Pectins are plant cell-wall polysaccharides which can be utilized by commensal bacteria in the gut, exhibiting beneficial properties for host. Knowledge of impact pectins on intestinal bacterial communities is insufficient and limited to a few types pectins. This study characterized relationship between structural their potential modulate composition activity gut microbiota way. For this purpose we performed vitro fermentations nine structurally diverse from citrus fruits sugar beet, pectic derivative, rhamnogalacturonan I (RGI), using TIM-2 colon model. The during was assessed 16S rRNA gene amplicon sequencing. Both general pectin-specific changes were observed relative abundances numerous taxa time-dependent Bacterial populations associated with human health, such as Faecalibacterium prausnitzii, Coprococcus, Ruminococcus, Dorea, Blautia, Oscillospira, Sutterella, Bifidobacterium, Christensenellaceae, Prevotella copri, Bacteroides spp. either increased or decreased depending substrate, suggesting that these controlled different main features linked pectin-mediated shifts included degree esterification, neutral sugars, distribution homogalacturonan fractions, branching, presence amide groups. Cumulative production total short chain fatty acids propionate largest high methoxyl Thus, indicates microbial specifically modulated identifies pectin molecules alterations. knowledge used define preferred dietary pectins, targeting bacteria, favoring more balanced gut.

Язык: Английский

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Mini‐review: Phytoplankton‐derived polysaccharides in the marine environment and their interactions with heterotrophic bacteria

Environmental Microbiology, Год журнала: 2018, Номер 20(8), С. 2671 - 2685

Опубликована: Июль 20, 2018

Summary Within the wealth of molecules constituting marine dissolved organic matter, carbohydrates make up largest coherent and quantifiable fraction. Their main sources are from primary producers, which release large amounts photosynthetic products – mainly polysaccharides directly into surrounding water via passive active exudation. The carbon other nutrients derived these photosynthates enrich ‘phycosphere’ attract heterotrophic bacteria. rapid uptake remineralization free monosaccharides by bacteria account for barely detectable levels compounds. By contrast, combined can reach high concentrations, especially during phytoplankton blooms. Polysaccharides too to be taken bacteria, instead requiring hydrolytic cleavage smaller oligo‐ or monomers with a suitable set exoenzymes. diverse various taxa is generally interpreted as deposition excess material. However, likely also fulfil distinct, yet not fully understood functions, inferred their modulation in terms quality quantity when becomes nutrient limited exposed This minireview summarizes current knowledge regarding exudation composition phytoplankton‐derived exopolysaccharides acquisition compounds

Язык: Английский

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The effects of different dietary fiber pectin structures on the gastrointestinal immune barrier: impact via gut microbiota and direct effects on immune cells

Experimental & Molecular Medicine, Год журнала: 2020, Номер 52(9), С. 1364 - 1376

Опубликована: Сен. 1, 2020

Abstract Pectins are dietary fibers with different structural characteristics. Specific pectin structures can influence the gastrointestinal immune barrier by directly interacting cells or impacting intestinal microbiota. The impact of strongly depends on specific characteristics pectin; for example, degree methyl-esterification, acetylation and rhamnogalacturonan I II neutral side chains. Here, we review interactions barrier. effects include strengthening mucus layer, enhancing epithelial integrity, activating inhibiting dendritic cell macrophage responses. direct interaction pectins may be governed through pattern recognition receptors, such as Toll-like receptors 2 4 Galectin-3. In addition, stimulate diversity abundance beneficial microbial communities. Furthermore, enhanced short-chain fatty acids. Moreover, enhance favoring adhesion commensal bacteria pathogens to cells. Current data illustrate that a powerful fiber manage prevent several inflammatory conditions, but additional human studies molecules well-defined urgently needed.

Язык: Английский

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