Microbial and Carbohydrate Active Enzyme profile of buffalo rumen metagenome and their alteration in response to variation in the diet

Patel, Dishita; Patel, Amrutlal K.; Parmar, Nidhi; Shah, Tejas; Patel, J. B.; Pandya, P.R.; Joshi, Chaitanya G.

doi:10.1016/j.gene.2014.05.003

Cited by 85 publications

(58 citation statements)

References 24 publications

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“…A previous report indicated that the relative abundance of Prevotella in the caecum tended to increase linearly in rabbits that drank acidified drinking water29. Consistent with our findings, adding barley acidified with citric acid increased the in vitro relative abundance of Prevotella 30, which is a polysaccharide-degrading bacterial genus23. Together, these findings suggest that adding organic acids to a liquid diet and maintaining a low pH may represent a feasible strategy for rearing pre-weaned dairy calves.…”

Section: Discussionsupporting

confidence: 91%

“…Such an elevated abundance of Parabacteroides may have been related to the relatively larger quantities of amino acids and monosaccharides observed in the rumen of the PWM-fed dairy calves. Moreover, feeding calves with UBM elevated the relative abundance in the rumen (both mucosa and digesta) of the genus Fibrobacter, which is responsible for the degradation of dietary fibre and polysaccharides, and this result was likely related to the lack of antibiotics in the UBM2223. Therefore, more volatile fatty acids and monosaccharides may have been produced in the rumen of dairy calves fed UBM.…”

Section: Discussionmentioning

confidence: 99%

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Influence of dairy by-product waste milk on the microbiomes of different gastrointestinal tract components in pre-weaned dairy calves

Deng

Wang

Zou

et al. 2017

Sci Rep

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The community structure of colonised bacteria in the gastrointestinal tracts (GITs) of pre-weaned calves is affected by extrinsic factors, such as the genetics and diet of the calves; however, the dietary impact is not fully understood and warrants further research. Our study revealed that a total of 6, 5, 2 and 10 bacterial genera showed biologically significant differences in the GITs of pre-weaned calves fed four waste-milk diets: acidified waste milk, pasteurised waste milk, untreated bulk milk, and untreated waste milk, respectively. Specifically, generic biomarkers were observed in the rumen (e.g., Bifidobacterium, Parabacteroides, Fibrobacter, Clostridium, etc.), caecum (e.g., Faecalibacterium, Oxalobacter, Odoribacter, etc.) and colon (e.g., Megamonas, Comamonas, Stenotrophomonas, etc.) but not in the faeces. In addition, the predicted metabolic pathways showed that the expression of genes related to metabolic diseases was increased in the calves fed untreated waste milk, which indicated that untreated waste milk is not a suitable liquid diet for pre-weaned calves. This is the first study to demonstrate how different types of waste milk fed to pre-weaned calves affect the community structure of colonised bacteria, and the results may provide insights for the intentional adjustment of diets and gastrointestinal bacterial communities.

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Section: Discussionsupporting

confidence: 91%

Section: Discussionmentioning

confidence: 99%

Influence of dairy by-product waste milk on the microbiomes of different gastrointestinal tract components in pre-weaned dairy calves

Deng

Wang

Zou

et al. 2017

Sci Rep

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“…Out of 135 CAZy families that are reported in the CAZy database till date, 96 families were represented by cattle rumen metagenome. Patel et al (2014) reported 72 families of GHs from the buffalo rumen ecosystem. The substantially large number of enzymes from the GH family (96 families) in our study could be either due to the difference in NGS sequencing platform or the modifications in the analysis pipe line.…”

Section: Discussionmentioning

confidence: 99%

Metagenomic insights into the rumen microbial fibrolytic enzymes in Indian crossbred cattle fed finger millet straw

Jose

Thulasi

et al. 2017

AMB Expr

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The rumen is a unique natural habitat, exhibiting an unparalleled genetic resource of fibrolytic enzymes of microbial origin that degrade plant polysaccharides. The objectives of this study were to identify the principal plant cell wall-degrading enzymes and the taxonomic profile of rumen microbial communities that are associated with it. The cattle rumen microflora and the carbohydrate-active enzymes were functionally classified through a whole metagenomic sequencing approach. Analysis of the assembled sequences by the Carbohydrate-active enzyme analysis Toolkit identified the candidate genes encoding fibrolytic enzymes belonging to different classes of glycoside hydrolases(11,010 contigs), glycosyltransferases (6366 contigs), carbohydrate esterases (4945 contigs), carbohydrate-binding modules (1975 contigs), polysaccharide lyases (480 contigs), and auxiliary activities (115 contigs). Phylogenetic analysis of CAZyme encoding contigs revealed that a significant proportion of CAZymes were contributed by bacteria belonging to genera Prevotella, Bacteroides, Fibrobacter, Clostridium, and Ruminococcus. The results indicated that the cattle rumen microbiome and the CAZymes are highly complex, structurally similar but compositionally distinct from other ruminants. The unique characteristics of rumen microbiota and the enzymes produced by resident microbes provide opportunities to improve the feed conversion efficiency in ruminants and serve as a reservoir of industrially important enzymes for cellulosic biofuel production.Electronic supplementary materialThe online version of this article (doi:10.1186/s13568-016-0310-0) contains supplementary material, which is available to authorized users.

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“…Knowledge of the environmental parameters underlying samples may aid in the selection of suitable screen targets and substrates for metagenomic functional screening (Taupp, Mewis et al 2011). For example, clone libraries from the bovine rumen metagenome are a logical source for carbohydrate active enzymes (CAZymes) (Patel, Patel et al 2014). The rumen microbiome provides a rich source of enzymes that digest complex plant oligosaccharides given the natural diet of the host.…”

Section: Sampling Metagenomes: Random or Intuitivementioning

confidence: 99%

“…Glycosyl hydrolases Buffalo rumen High-throughput sequencing (Patel, Patel et al 2014) Glycosyl hydrolases Elephant feces High-throughput sequencing (Ilmberger, Gullert et al 2014) Carbohydrate active enzymes Leaf-cutter ant fungus garden High-throughput sequencing (Suen, Scott et al 2010) Glycosyl hydrolases Wallaby High-throughput sequencing, Sanger sequencing (Pope, Denman et al 2010) Antibiotic resistance genes Hen feces High-throughput sequencing (Videnska, Rahman et al 2014) Glycosyl hydrolases Termite hindgut Sanger sequencing, PCR (Warnecke, Luginbuhl et al 2007) …”

mentioning

confidence: 99%

Contemporary molecular tools in microbial ecology and their application to advancing biotechnology

Rashid

Stingl

2015

Biotechnology Advances

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Microbial and Carbohydrate Active Enzyme profile of buffalo rumen metagenome and their alteration in response to variation in the diet

Cited by 85 publications

References 24 publications

Influence of dairy by-product waste milk on the microbiomes of different gastrointestinal tract components in pre-weaned dairy calves

Influence of dairy by-product waste milk on the microbiomes of different gastrointestinal tract components in pre-weaned dairy calves

Metagenomic insights into the rumen microbial fibrolytic enzymes in Indian crossbred cattle fed finger millet straw

Contemporary molecular tools in microbial ecology and their application to advancing biotechnology

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