scholarly journals PSIX-5 Effects of live yeast on functional attributes of rumen microbiota in beef cattle

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 394-395
Author(s):  
Ibukun M Ogunade ◽  
Jerusha Lay ◽  
Kenneth Andries
Keyword(s):  
Beef Cattle ◽  
Relative Abundance ◽  
Rumen Fluid ◽  
Basal Diet ◽  
Glycoside Hydrolases ◽  
Carbohydrate Binding ◽  
Illumina Hiseq ◽  
Rumen Microbiota ◽  
Carbohydrate Binding Modules ◽  
Live Yeast

Abstract This study applied whole-metagenomics shotgun sequencing to evaluate the effects of live yeast supplementation on functional potential of rumen microbiota in beef cattle. Eight rumen-cannulated Holstein steers were assigned randomly to 1 of 2 treatments in cross-over design with two 25-d experimental periods and a 10-d wash-out between the two periods. The steers were housed in individual pens and were fed 50% concentrate and 50% red clover hay ad libitum. Dietary treatments were (1) control (CON; basal diet) and (2) yeast (YEA; basal diet plus 15 g/d of yeast product; PMI, Arden Hills, MN, USA). Rumen fluid samples were collected at 3, 6 and 9 h after feeding on the last day of each period. Sequencing was done on an Illumina HiSeq 2500. Differences in the relative abundance of taxa at the species level were analyzed using the GLIMMIX procedure of SAS using a model that included the effects of treatment, period, and their interaction. Dietary yeast supplementation increased (P < 0.05) the relative abundance of carbohydrate-fermenting bacteria, such as Ruminococcus albus, R. champanellensis, R. bromii, and R. obeum, and lactate-utilizing bacteria, such as Megasphera elsdenii, Desulfovibrio desulfuricans, and D. vulgaris. A total of 154 differentially abundant microbial genes (DAGs) were obtained (false discovery rate < 0.01). Kyoto Encyclopedia of Genes and Genomes annotation analysis of the DAGs revealed that pathways involving amino sugar and nucleotide sugar metabolism, oxidative phosphorylation, pantothenate and CoA biosynthesis, beta-alanine metabolism, and polyketide sugar unit biosynthesis were enriched in steers fed YEA. Annotation of the DAGs in carbohydrate-active enzymes database revealed that genes coding for enzymes belonging to glycoside hydrolases, glycosyltransferases, and carbohydrate binding modules were enriched in steers fed YEA. These findings confirm the efficacy of live S. cerevisiae product at reducing redox potential and increasing cellulolytic and lactate-utilizing activities in the rumen.

scholarly journals Monensin Alters the Functional and Metabolomic Profile of Rumen Microbiota in Beef Cattle

Animals ◽  
2018 ◽  
Vol 8 (11) ◽  
pp. 211 ◽  
Author(s):  
Ibukun Ogunade ◽  
Hank Schweickart ◽  
Kenneth Andries ◽  
Jerusha Lay ◽  
James Adeyemi
Keyword(s):  
Linoleic Acid ◽  
Amino Acid ◽  
Beef Cattle ◽  
Relative Abundance ◽  
Rumen Fluid ◽  
Differentially Expressed ◽  
Beef Steers ◽  
Rumen Microbiota ◽  
Rumen Microbiome ◽  
Clostridium Symbiosum

To identify differences in rumen function as a result of feeding monensin to beef cattle, rumen fluid metagenomics and metabolomics analyses were used to evaluate the functional attributes and metabolites of rumen microbiota in beef steers fed no or 200 mg/d of monensin. Eight rumen-fistulated steers were used in the study for a period of 53 days. Rumen fluid samples were collected on the last day of the experiment. Monensin increased the relative abundance of Selenomonas sp. ND2010, Prevotella dentalis, Hallella seregens, Parabacteroides distasonis, Propionispira raffinosivorans, and Prevotella brevis, but reduced the relative abundance of Robinsoniella sp. KNHs210, Butyrivibrio proteoclasticus, Clostridium botulinum, Clostridium symbiosum, Burkholderia sp. LMG29324, and Clostridium butyricum. Monensin increased the relative abundance of functional genes involved in amino acid metabolism and lipid metabolism. A total of 245 metabolites were identified. Thirty-one metabolites were found to be differentially expressed. Pathway analysis of the differentially expressed metabolites revealed upregulated metabolic pathways associated with metabolism of linoleic acid and some amino acids. These findings confirm that monensin affects rumen fermentation of forage-fed beef cattle by modulating the rumen microbiome, and by reducing amino acid degradation and biohydrogenation of linoleic acid in the rumen.

scholarly journals Combined Supplementation of Probiotics and Enzymes Improves Performance and Regulates Rumen Microbiota in Fattening Goats

2021 ◽  
Author(s):  
Jiawei Lu ◽  
Zili Chen ◽  
Qin Gao ◽  
Peizhen Li ◽  
Jingang Wang ◽  
...  
Keyword(s):  
Growth Performance ◽  
Relative Abundance ◽  
Rumen Fluid ◽  
Basal Diet ◽  
Tca Cycle ◽  
The Body ◽  
Enzyme Preparations ◽  
Rumen Microbiota ◽  
Slaughter Performance ◽  
Serum Biochemical

Abstract Background: The aim of this study was to explore the effects of growth performance, slaughter performance, serum biochemical, immune and antioxidant indexes and rumen microflora fed with a basal diet (CON group), added B. subtilis and B. licheniformis (PRO group), supplemented with B. subtilis, B. licheniformis and enzyme preparations (COM group) on fattening goats.Methods: 39 male goats were randomly divided into 4 groups with 13 individuals in each group for feed period of 80 d. Goats were fed as follows: CON diet, PRO diet with B. subtilis and B. licheniformis, and COM diet with B. subtilis, B. licheniformis and compound enzymes.Results: ADFI of COM group significantly increased compared with CON group and PRO group (P < 0.01), as well as COM group and PRO group dramatically promoted ADG versus with CON group (P < 0.05). As a consequence, the body weight of fattening goats in the COM group was predominantly higher than that in the CON group (P < 0.01). In addition, the PRO group and COM group enhanced the TNF-α (P < 0.05) and IL-10 content (P < 0.01) in the serum. No differences were observed in serum biochemical and antioxidant indexes of three groups (P > 0.05). Likewise, the GR values of PRO group and COM group were noteworthy improved in comparison with CON group (P < 0.01). The VFA contents in rumen fluid were insignificantly different (P > 0.05). COM group also enriched the relative abundance of Proteobacteria compared with CON group and PRO group (P < 0.05). Nevertheless, the relative abundance of Actinobacteria decreased of PRO group and COM group in rumen fluid microorganisms (P < 0.05). Apparently, COM group significantly enriched nitrogen metabolism, glycolysis and TCA cycle (P < 0.05), whereas nucleotides biosynthesis was notably reduced (P < 0.05).Conclusion: The combined feed of probiotics and enzymes had more profound effects than probiotics feed. Consequently, supplementation with B. subtilis and B. licheniformis and enzymes in the basal diet of fattening goats, which could improve growth performance, slaughter performance, immunity and accommodate rumen microbiota.

scholarly journals A unique combination of glycoside hydrolases in Streptococcus suis specifically and sequentially acts on host-derived αGal-epitope glycans

2020 ◽  
Vol 295 (31) ◽  
pp. 10638-10652
Author(s):  
Ping Chen ◽  
Ran Liu ◽  
Mengmeng Huang ◽  
Jinlu Zhu ◽  
Dong Wei ◽  
...  
Keyword(s):  
Wide Spectrum ◽  
Streptococcus Suis ◽  
Glycoside Hydrolases ◽  
Carbohydrate Binding ◽  
Unique Combination ◽  
Enzymatic Assays ◽  
Tracheal Epithelial Cells ◽  
Carbohydrate Binding Modules ◽  
Host Signaling ◽  
Important Host

Infections by many bacterial pathogens rely on their ability to degrade host glycans by producing glycoside hydrolases (GHs). Here, we discovered a conserved multifunctional GH, SsGalNagA, containing a unique combination of two family 32 carbohydrate-binding modules (CBM), a GH16 domain and a GH20 domain, in the zoonotic pathogen Streptococcus suis 05ZYH33. Enzymatic assays revealed that the SsCBM-GH16 domain displays endo-(β1,4)-galactosidase activity specifically toward the host-derived αGal epitope Gal(α1,3)Gal(β1,4)Glc(NAc)-R, whereas the SsGH20 domain has a wide spectrum of exo-β-N-acetylhexosaminidase activities, including exo-(β1,3)-N-acetylglucosaminidase activity, and employs this activity to act in tandem with SsCBM-GH16 on the αGal-epitope glycan. Further, we found that the CBM32 domain adjacent to the SsGH16 domain is indispensable for SsGH16 catalytic activity. Surface plasmon resonance experiments uncovered that both CBM32 domains specifically bind to αGal-epitope glycan, and together they had a KD of 3.5 mm toward a pentasaccharide αGal-epitope glycan. Cell-binding and αGal epitope removal assays revealed that SsGalNagA efficiently binds to both swine erythrocytes and tracheal epithelial cells and removes the αGal epitope from these cells, suggesting that SsGalNagA functions in nutrient acquisition or alters host signaling in S. suis. Both binding and removal activities were blocked by an αGal-epitope glycan. SsGalNagA is the first enzyme reported to sequentially act on a glycan containing the αGal epitope. These findings shed detailed light on the evolution of GHs and an important host-pathogen interaction.

scholarly journals Enzymatic Adaptation of Bifidobacterium bifidum to Host Glycans, Viewed from Glycoside Hydrolyases and Carbohydrate-Binding Modules

2020 ◽  
Vol 8 (4) ◽  
pp. 481 ◽  
Author(s):  
Toshihiko Katoh ◽  
Miriam N. Ojima ◽  
Mikiyasu Sakanaka ◽  
Hisashi Ashida ◽  
Aina Gotoh ◽  
...  
Keyword(s):  
Carbon Sources ◽  
Bifidobacterium Bifidum ◽  
Glycoside Hydrolases ◽  
Altruistic Behavior ◽  
Carbohydrate Binding ◽  
Human Gut ◽  
Genetic Characteristics ◽  
Beneficial Effects ◽  
Carbohydrate Binding Modules ◽  
Enzymatic Machinery

Certain species of the genus Bifidobacterium represent human symbionts. Many studies have shown that the establishment of symbiosis with such bifidobacterial species confers various beneficial effects on human health. Among the more than ten (sub)species of human gut-associated Bifidobacterium that have significantly varied genetic characteristics at the species level, Bifidobacterium bifidum is unique in that it is found in the intestines of a wide age group, ranging from infants to adults. This species is likely to have adapted to efficiently degrade host-derived carbohydrate chains, such as human milk oligosaccharides (HMOs) and mucin O-glycans, which enabled the longitudinal colonization of intestines. The ability of this species to assimilate various host glycans can be attributed to the possession of an adequate set of extracellular glycoside hydrolases (GHs). Importantly, the polypeptides of those glycosidases frequently contain carbohydrate-binding modules (CBMs) with deduced affinities to the target glycans, which is also a distinct characteristic of this species among members of human gut-associated bifidobacteria. This review firstly describes the prevalence and distribution of B. bifidum in the human gut and then explains the enzymatic machinery that B. bifidum has developed for host glycan degradation by referring to the functions of GHs and CBMs. Finally, we show the data of co-culture experiments using host-derived glycans as carbon sources, which underpin the interesting altruistic behavior of this species as a cross-feeder.

scholarly journals Metatranscriptomic Analysis of Sub-Acute Ruminal Acidosis in Beef Cattle

Animals ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 232 ◽  
Author(s):  
Ibukun Ogunade ◽  
Andres Pech-Cervantes ◽  
Hank Schweickart
Keyword(s):  
Beef Cattle ◽  
Rumen Fluid ◽  
Control Diet ◽  
Bacterial Biofilm ◽  
Ruminal Bacteria ◽  
Subacute Ruminal Acidosis ◽  
Rumen Microbiota ◽  
Ruminal Acidosis ◽  
Rrna Sequencing ◽  
Illumina Hiseq4000

Subacute ruminal acidosis (SARA) is a metabolic disease of ruminants characterized by low pH, with significant impacts on rumen microbial activity, and animal productivity and health. Microbial changes during subacute ruminal acidosis have previously been analyzed using quantitative PCR and 16S rRNA sequencing, which do not reveal the actual activity of the rumen microbial population. Here, we report the functional activity of the rumen microbiota during subacute ruminal acidosis. Eight rumen-cannulated Holstein steers were assigned randomly to acidosis-inducing or control diet. Rumen fluid samples were taken at 0, 3, 6, and 9 h relative to feeding from both treatments on the challenge day. A metatranscriptome library was prepared from RNA extracted from the samples and the sequencing of the metatranscriptome library was performed on Illumina HiSeq4000 following a 2 × 150 bp index run. Cellulolytic ruminal bacteria including Fibrobacter succinogenes, Ruminococcus albus, and R. bicirculans were reduced by an induced acidotic challenge. Up to 68 functional genes were differentially expressed between the two treatments. Genes mapped to carbohydrate, amino acid, energy, vitamin and co-factor metabolism pathways, and bacterial biofilm formation pathways were enriched in beef cattle challenged with sub-acute acidosis. This study reveals transcriptionally active taxa and metabolic pathways of rumen microbiota during induced acidotic challenge.

scholarly journals Cloning, purification, crystallization and preliminary X-ray studies of a carbohydrate-binding module (CBM_E1) derived from sugarcane soil metagenome

2014 ◽  
Vol 70 (9) ◽  
pp. 1232-1235 ◽  
Author(s):  
Bruna Medeia Campos ◽  
Thabata Maria Alvarez ◽  
Marcelo Vizona Liberato ◽  
Igor Polikarpov ◽  
Harry J. Gilbert ◽  
...  
Keyword(s):  
Fossil Fuels ◽  
Plant Biomass ◽  
Metagenomic Library ◽  
Glycoside Hydrolases ◽  
Diffusion Method ◽  
Carbohydrate Binding ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
Carbohydrate Binding Modules

In recent years, owing to the growing global demand for energy, dependence on fossil fuels, limited natural resources and environmental pollution, biofuels have attracted great interest as a source of renewable energy. However, the production of biofuels from plant biomass is still considered to be an expensive technology. In this context, the study of carbohydrate-binding modules (CBMs), which are involved in guiding the catalytic domains of glycoside hydrolases for polysaccharide degradation, is attracting growing attention. Aiming at the identification of new CBMs, a sugarcane soil metagenomic library was analyzed and an uncharacterized CBM (CBM_E1) was identified. In this study, CBM_E1 was expressed, purified and crystallized. X-ray diffraction data were collected to 1.95 Å resolution. The crystals, which were obtained by the sitting-drop vapour-diffusion method, belonged to space groupI23, with unit-cell parametersa=b=c= 88.07 Å.

scholarly journals Genome Sequencing and Carbohydrate-Active Enzyme (CAZyme) Repertoire of the White Rot Fungus Flammulina elastica

2018 ◽  
Vol 19 (8) ◽  
pp. 2379 ◽  
Author(s):  
Young-Jin Park ◽  
Yong-Un Jeong ◽  
Won-Sik Kong
Keyword(s):  
Gene Prediction ◽  
Gc Content ◽  
Industrial Applications ◽  
Fungal Species ◽  
Amino Acid Sequences ◽  
Glycoside Hydrolases ◽  
White Rot ◽  
White Rot Fungus ◽  
Carbohydrate Binding ◽  
Carbohydrate Binding Modules

Next-generation sequencing (NGS) of the Flammulina elastica (wood-rotting basidiomycete) genome was performed to identify carbohydrate-active enzymes (CAZymes). The resulting assembly (31 kmer) revealed a total length of 35,045,521 bp (49.7% GC content). Using the AUGUSTUS tool, 12,536 total gene structures were predicted by ab initio gene prediction. An analysis of orthologs revealed that 6806 groups contained at least one F. elastica protein. Among the 12,536 predicted genes, F. elastica contained 24 species-specific genes, of which 17 genes were paralogous. CAZymes are divided into five classes: glycoside hydrolases (GHs), carbohydrate esterases (CEs), polysaccharide lyases (PLs), glycosyltransferases (GTs), and auxiliary activities (AA). In the present study, annotation of the predicted amino acid sequences from F. elastica genes using the dbCAN CAZyme database revealed 508 CAZymes, including 82 AAs, 218 GHs, 89 GTs, 18 PLs, 59 CEs, and 42 carbohydrate binding modules in the F. elastica genome. Although the CAZyme repertoire of F. elastica was similar to those of other fungal species, the total number of GTs in F. elastica was larger than those of other basidiomycetes. This genome information elucidates newly identified wood-degrading machinery in F. elastica, offers opportunities to better understand this fungus, and presents possibilities for more detailed studies on lignocellulosic biomass degradation that may lead to future biotechnological and industrial applications.

scholarly journals The modular architecture of Cellvibrio japonicus mannanases in glycoside hydrolase families 5 and 26 points to differences in their role in mannan degradation

2003 ◽  
Vol 371 (3) ◽  
pp. 1027-1043 ◽  
Author(s):  
Deborah HOGG ◽  
Gavin PELL ◽  
Paul DUPREE ◽  
Florence GOUBET ◽  
Susana M. MARTÍN-ORÚE ◽  
...  
Keyword(s):  
Glycoside Hydrolase ◽  
Plant Cell Wall ◽  
Catalytic Domain ◽  
Glycoside Hydrolases ◽  
Crystalline Cellulose ◽  
Carbohydrate Binding ◽  
Molecular Architecture ◽  
Catalytic Domains ◽  
Carbohydrate Binding Modules ◽  
Cellvibrio Japonicus

β-1,4-Mannanases (mannanases), which hydrolyse mannans and glucomannans, are located in glycoside hydrolase families (GHs) 5 and 26. To investigate whether there are fundamental differences in the molecular architecture and biochemical properties of GH5 and GH26 mannanases, four genes encoding these enzymes were isolated from Cellvibrio japonicus and the encoded glycoside hydrolases were characterized. The four genes, man5A, man5B, man5C and man26B, encode the mannanases Man5A, Man5B, Man5C and Man26B, respectively. Man26B consists of an N-terminal signal peptide linked via an extended serine-rich region to a GH26 catalytic domain. Man5A, Man5B and Man5C contain GH5 catalytic domains and non-catalytic carbohydrate-binding modules (CBMs) belonging to families 2a, 5 and 10; Man5C in addition contains a module defined as X4 of unknown function. The family 10 and 2a CBMs bound to crystalline cellulose and ivory nut crystalline mannan, displaying very similar properties to the corresponding family 10 and 2a CBMs from Cellvibrio cellulases and xylanases. CBM5 bound weakly to these crystalline polysaccharides. The catalytic domains of Man5A, Man5B and Man26B hydrolysed galactomannan and glucomannan, but displayed no activity against crystalline mannan or cellulosic substrates. Although Man5C was less active against glucomannan and galactomannan than the other mannanases, it did attack crystalline ivory nut mannan. All the enzymes exhibited classic endo-activity producing a mixture of oligosaccharides during the initial phase of the reaction, although their mode of action against manno-oligosaccharides and glucomannan indicated differences in the topology of the respective substrate-binding sites. This report points to a different role for GH5 and GH26 mannanases from C. japonicus. We propose that as the GH5 enzymes contain CBMs that bind crystalline polysaccharides, these enzymes are likely to target mannans that are integral to the plant cell wall, while GH26 mannanases, which lack CBMs and rapidly release mannose from polysaccharides and oligosaccharides, target the storage polysaccharide galactomannan and manno-oligosaccharides.

scholarly journals Comparative Genomic Analysis of Bifidobacterium Catenulatum Reveal the Genetic Divergence of its Two Subspecies from Infant and Adult Gut

2021 ◽  
Author(s):  
Jiaqi Liu ◽  
Weicheng Li ◽  
Caiqing Yao ◽  
Jie Yu ◽  
Heping Zhang
Keyword(s):  
Genetic Divergence ◽  
Gc Content ◽  
Genomic Analysis ◽  
Glycoside Hydrolases ◽  
Comparative Genomic ◽  
Carbohydrate Binding ◽  
Functional Difference ◽  
Carbohydrate Utilization ◽  
Carbohydrate Binding Modules ◽  
Genomic Studies

Abstract Background: Bifidobacterium catenulatum, which includes two subspecies that B. catenulatum subsp. kashiwanohense and B. catenulatum subsp. catenulatum are usually from infant and adult gut respectively, while the genomic studies of functional difference and genetic divergence in them have been rarely reported. In this study, we analyzed 16 B. catenulatum strains through comparative genomics, including two novel sequenced strains. Results: A phylogenetic tree based on 785 core genes indicated that the two subspecies of B. catenulatum were significantly separated and confirmed their colonizing bias in infants and adults. Comparison of general genomic characteristics revealed that the two subspecies had significantly different genomic sizes but similar GC content. Functional annotations found that they peculiarly differ in utilization of carbohydrates and amino acid. Among them, we found that carbohydrate metabolism seems to play an important role in the divergence because of their carbohydrate-active enzymes (CAZyme) present two different clustering patterns. B. catenulatum subsp. kashiwanohense have functional genes that specifically adapted to the infant gut for glycoside hydrolases 95 (GH95) and carbohydrate-binding modules 51 (CBM51), which specifically participated in the metabolism of Human Milk Oligosaccharides (HMOs), and specific genes fuc that related to HMOs were also detected. While B. catenulatum subsp. catenulatum rich in GH3 and glycosyltransferases 4 (GT4) tended to metabolize plant-derived glycan that may help it metabolize more complex carbohydrates (eg. xylan) in the adult intestine. Conclusions: Our findings revealed genomic evidence of carbohydrate utilization bias which may be a key leading to the genetic divergence of two subspecies of B. catenulatum.

scholarly journals Metagenomic analysis reveals rumen microbiota alteration of the yak at different stages of growth

2021 ◽  
Author(s):  
Li Wang ◽  
Li Juan ◽  
Ahmad Aboragah ◽  
Mingfeng Jiang ◽  
Juan J. Loor
Keyword(s):  
Glycoside Hydrolase ◽  
Age Groups ◽  
Carbohydrate Binding ◽  
The Tibetan Plateau ◽  
Tissue Slices ◽  
Rumen Microbiota ◽  
Stages Of Growth ◽  
Ruminant Species ◽  
Cazy Database ◽  
Carbohydrate Binding Modules

Abstract The Yak (Bos grunniens) is a unique ruminant species that is crucially important to agriculture in the Tibetan plateau. Variation of microorganism communities in the yak rumen is of great interest because of possible links to environmentally and economically important traits. In this study, we performed histological and microbial analyses of the yak rumen at 5 stages of growth: 1 day, 20 days, 60 days, 15 months, and 5 years of age. Tissue slices and metagenomics sequencing were used. The rumen index increased gradually from 1 day to 5 years of age. These were significant differences in rumen index between the 60d, 15m, and 5y group (p < 0.05). Compared with other time points, the thickness of muscularis along with length and width of rumen papillae at 60 d,15 m, and 5 years of age increased and differed (p < 0.05), respectively. At the phylum level, Bacteroidetes and Firmicutes were the phyla with the highest abundance in all the age groups. A total of 115,401 genes were annotated on the CAZy database. Glycoside Hydrolase (GH) had the highest relative abundance, followed by Glycosyl Transferase (GT), and Carbohydrate-binding Modules (CBM). There were significant variations for the microbial species and CAZys within the five groups. Taken together, the morphology and microbiota in the yak rumen changed at various stages of growth and likely played a significant role in the absorption of nutrients. This study provides new insights into the function of yak rumen microbiota and physiologic adaptations in plateau animals.

Sign in / Sign up

Export Citation Format

Share Document