Xylan degradation, a metabolic property shared by rumen and human colonic Bacteroidetes

Dodd, Dylan; Mackie, Roderick I.; Cann, Isaac

doi:10.1111/j.1365-2958.2010.07473.x

Cited by 211 publications

(163 citation statements)

References 60 publications

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“…The relative abundance of the transcripts encoding dockerin-, cohesin-, and CBM10-like proteins indicates that cellulosomes may play a hitherto underestimated role in PCWP degradation in the rumen. The PULs were first identified as the starch utilization system (Sus) in the anaerobic human gut bacterium Bacteroides thetaiotaomicron (53) and were later expanded to include cellulose (11), xylan (54,55), and pectin (56) utilization systems in herbivore gut bacteria. The multiprotein system includes SusC (also called the TonB-dependent receptor), SusD-like proteins, SusE, SusF, SusG, and other components, among which SusC and SusDlike proteins are central to and, thus, typical of this system (10).…”

Section: Discussionmentioning

confidence: 99%

Metatranscriptomic Analyses of Plant Cell Wall Polysaccharide Degradation by Microorganisms in the Cow Rumen

Dai

Tian

et al. 2015

Appl Environ Microbiol

189

178

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gThe bovine rumen represents a highly specialized bioreactor where plant cell wall polysaccharides (PCWPs) are efficiently deconstructed via numerous enzymes produced by resident microorganisms. Although a large number of fibrolytic genes from rumen microorganisms have been identified, it remains unclear how they are expressed in a coordinated manner to efficiently degrade PCWPs. In this study, we performed a metatranscriptomic analysis of the rumen microbiomes of adult Holstein cows fed a fiber diet and obtained a total of 1,107,083 high-quality non-rRNA reads with an average length of 483 nucleotides. Transcripts encoding glycoside hydrolases (GHs) and carbohydrate binding modules (CBMs) accounted for ϳ1% and ϳ0.1% of the total non-rRNAs, respectively. The majority (ϳ98%) of the putative cellulases belonged to four GH families (i.e., GH5, GH9, GH45, and GH48) and were primarily synthesized by Ruminococcus and Fibrobacter. Notably, transcripts for GH48 cellobiohydrolases were relatively abundant compared to the abundance of transcripts for other cellulases. Two-thirds of the putative hemicellulases were of the GH10, GH11, and GH26 types and were produced by members of the genera Ruminococcus, Prevotella, and Fibrobacter. Most (ϳ82%) predicted oligosaccharide-degrading enzymes were GH1, GH2, GH3, and GH43 proteins and were from a diverse group of microorganisms. Transcripts for CBM10 and dockerin, key components of the cellulosome, were also relatively abundant. Our results provide metatranscriptomic evidence in support of the notion that members of the genera Ruminococcus, Fibrobacter, and Prevotella are predominant PCWP degraders and point to the significant contribution of GH48 cellobiohydrolases and cellulosome-like structures to efficient PCWP degradation in the cow rumen. In nature, the cow rumen represents a highly specialized bioreactor wherein plant cell wall polysaccharides (PCWPs) are efficiently deconstructed. The extraordinary efficiency results from the concerted action of various enzymes produced by rumen-resident bacteria, archaea, fungi, and protozoa. Three rumen bacteria, i.e., Ruminococcus flavefaciens, Ruminococcus albus, and Fibrobacter succinogenes, which can be isolated and cultivated in the laboratory, have been thought to serve a predominant role in the degradation of cellulosic PCWPs in this niche (1, 2). However, metagenomic quantitations based on 16S rRNA gene analysis indicate that these three species of bacteria account for only less than 5% of the total rumen microorganisms (3). In addition, Koike et al. estimated that ϳ77% of the rumen microorganisms attached to solid fibers are uncultured, as their 16S rRNA gene sequences share less than 97% similarity with those of known isolates (4).To bypass the cultivation step, metagenomic approaches involving the direct analysis of total DNA sequences have been extensively used to investigate the PCWP-degrading gastrointestinal microbes in a variety of herbivores, such as termite hindguts (5); cow (6-8), yak (9), and Svalbard reindeer (10) ...

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Section: Discussionmentioning

confidence: 99%

Metatranscriptomic Analyses of Plant Cell Wall Polysaccharide Degradation by Microorganisms in the Cow Rumen

Dai

Tian

et al. 2015

Appl Environ Microbiol

189

178

View full text Add to dashboard Cite

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“…The species of Gammaproteobacteria relating to Azotobacter chroococcum were reported to produce indole and other antifungal antibiotics (Gowariker et al 2009). In addition, many Bacteroides species are known to be xylanolytic (Dodd et al 2011) and produce fatty acids such as acetate and succinate as the fermentation products (Shah 1992). Bacteroides eggerthii, the closest relative of one of the large OTUs in the Wheat bran 18 library, is a representative of such Bacteroides species.…”

Section: Analysis Of Bacterial Communities By the Molecular Techniquesmentioning

confidence: 99%

Development of anaerobic bacterial community consisted of diverse clostridial species during biological soil disinfestation amended with plant biomass

Mowlick

Hirota²,

Takehara

et al. 2012

Soil Science and Plant Nutrition

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Biological soil disinfestation (BSD) using plant biomass incorporation is an effective method and a good alternative to chemical fumigants for controlling soil-borne plant pathogens. In this study the bacterial communities in pot soil treated with three different BSD conditions (without plant biomass and with Brassica juncea L. plants or bran of wheat, Triticum aestivum L.) were analyzed using mainly molecular techniques. Earlier dropping of redox potential of both biomass-treated soils indicated rapid development of anaerobic conditions in the soil. The population of Fusarium oxysporum F. pathogen incorporated in the soil at the start was decreased considerably during the treatment, and the number of culturable anaerobic bacteria increased in both biomass-treated soils. Rather high concentrations of acetate and butyrate were detected from the biomass-treated soils. The polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis for the V3 region of 16S rRNA gene sequences revealed that the profiles of both biomass-treated soils were initially represented by similar and dominant groups, many of which were closely related to the species in the classes Clostridia and Bacilli of the phylum Firmicutes. Based on the clone library analysis, the control soil samples showed diverse bacterial groups with a few number of anaerobic clones. In contrast, for both biomass-treated libraries, clones belonging to the class Clostridia, a strictly anaerobic spore-forming bacterial group, appeared exceedingly dominant. The clostridial group detected was composed of phylogenetically diverse members, and it seemed likely that the diverse clostridial species were responsible for suppression of pathogens by making various compounds including volatile fatty acids and other compounds during anaerobic decomposition of plant biomass.

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“…Indeed, xylan's application in the pharmaceutical field has been studied mainly for colon-targeted drug delivery. When administered by the oral route, this polysaccharide is only degradable at the ascendant and transversal colon region due to the presence of bacteria that produce and excrete xylanases into the gastrointestinal tract [5,6]. However, its use as a raw material for the production of drug delivery systems has emerged in the recent literature [7,8].…”

Section: Introductionmentioning

confidence: 99%

Leads from Physical, Chemical, and Thermal Characterization on Cytotoxic Effects of Xylan-Based Microparticles

et al. 2015

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Interfacial cross-linking (ICL) has been considered a feasible technique to produce polysaccharide-based microparticles (PbMs), even though only a few studies have been concerned with their biocompatibility. In this work, PbMs were prepared by the ICL method and characterized in regard to their in vitro biocompatibility, chemical linkages, and physical and thermal properties. First, the cell viability assay revealed that PbMs toxicity was concentration-dependent. Then, it was observed that the toxicity may be related to the way in which the binding occurred, and not exclusively to the stoichiometry between the polymer and the cross-linking agent. Moreover, the PbMs biosafety was predicted by the use of physicochemical procedures, which were able to identify unbound cross-linking agent residues and also to reveal the improvement of their thermal stability. Accordingly, this work suggests a step-by-step physicochemical procedure able to predict potential toxicity from micro-structured devices produced by polysaccharides. Likewise, the use of PbMs as a drug carrier should be cautiously considered.

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Xylan degradation, a metabolic property shared by rumen and human colonic Bacteroidetes

Cited by 211 publications

References 60 publications

Metatranscriptomic Analyses of Plant Cell Wall Polysaccharide Degradation by Microorganisms in the Cow Rumen

Metatranscriptomic Analyses of Plant Cell Wall Polysaccharide Degradation by Microorganisms in the Cow Rumen

Development of anaerobic bacterial community consisted of diverse clostridial species during biological soil disinfestation amended with plant biomass

Leads from Physical, Chemical, and Thermal Characterization on Cytotoxic Effects of Xylan-Based Microparticles

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