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

Jose, V. Lyju; Thulasi, A.; More, Ravi Prabhakar; Arumugaperumal, Arun

doi:10.1186/s13568-016-0310-0

Cited by 67 publications

(56 citation statements)

References 40 publications

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“…In Gir cattle rumen, cellulolytic and xylan degrading fibrolytic enzymes (GH5, GH9, GH11, GH16 & GH45) were highly expressed in the solid fraction when the animals were provided 100% roughage in their diet. Interestingly, our findings are in accordance with previous studies of different cattle breeds [20,66,74], although they were fed with different diets which is rich in fibres. However, our findings diverse from those reported in buffalo [22] probably because of differential host-microbiota interaction since one is cattle and another is buffalo.…”

Section: Discussionsupporting

confidence: 92%

“…Rumen harbours a unique consortium of microbes which has been evolved into a complex and efficient system of lignocellulose degradation. This panel of enzymes are collectively known as Carbohydrate-Active enZYmes (CAZymes) and have been studied in cattle and buffalo rumen [20,21,68,74]. However, it is crucial to understand the expression of such enzymes under different dietary regimes, especially in animals who thrive on high roughage diet.…”

Section: Introductionmentioning

confidence: 99%

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Microbiota composition, gene pool and its expression in Gir cattle (Bos indicus) rumen under different forage diets using metagenomic and metatranscriptomic approaches

Pandit

Hinsu

Patel

et al. 2018

Systematic and Applied Microbiology

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Zebu (Bos indicus) is a domestic cattle species originating from the Indian subcontinent and now widely domesticated on several continents. In this study, we were particularly interested in understanding the functionally active rumen microbiota of an important Zebu breed, the Gir, under different dietary regimes. Metagenomic and metatranscriptomic data were compared at various taxonomic levels to elucidate the differential microbial population and its functional dynamics in Gir cattle rumen under different roughage dietary regimes. Different proportions of roughage rather than the type of roughage (dry or green) modulated microbiome composition and the expression of its gene pool. Fibre degrading bacteria (i.e. Clostridium, Ruminococcus, Eubacterium, Butyrivibrio, Bacillus and Roseburia) were higher in the solid fraction of rumen (P<0.01) compared to the liquid fraction, whereas bacteria considered to be utilizers of the degraded product (i.e. Prevotella, Bacteroides, Parabacteroides, Paludibacter and Victivallis) were dominant in the liquid fraction (P<0.05). Likewise, expression of fibre degrading enzymes and related carbohydrate binding modules (CBMs) occurred in the solid fraction. When metagenomic and metatranscriptomic data were compared, it was found that some genera and species were transcriptionally more active, although they were in low abundance, making an important contribution to fibre degradation and its further metabolism in the rumen. This study also identified some of the transcriptionally active genera, such as Caldicellulosiruptor and Paludibacter, whose potential has been less-explored in rumen. Overall, the comparison of metagenomic shotgun and metatranscriptomic sequencing appeared to be a much richer source of information compared to conventional metagenomic analysis.

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Section: Discussionsupporting

confidence: 92%

Section: Introductionmentioning

confidence: 99%

Microbiota composition, gene pool and its expression in Gir cattle (Bos indicus) rumen under different forage diets using metagenomic and metatranscriptomic approaches

Pandit

Hinsu

Patel

et al. 2018

Systematic and Applied Microbiology

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“…The high abundance of GH78 has been also found in the microbial communities of elephant feces [13] and cow rumen [25]. The other debranching enzymes, such as β-xylosidase, α-L-arabinofuranosidase, and α-glucuronidase, which play a crucial role in depolymerization of hemicellulose [26], were also identi ed and represented by the genes assigned to the families GH51, GH54, and GH67. For the hemicellulose-degrading enzymes, the genes belonging to the most abundant family GH28 were coding for polygalacturonases involved in pectin digestion [27].…”

Section: Diversity Of Carbohydrate-degrading Enzymes and Microbial Comentioning

confidence: 93%

“…The other two Firmicutes families, Ruminococcaceae and Clostridiaceae, possessed some well-studied cellulolytic organisms, which have been experimentally veri ed in ruminants and pigs, such as Ruminococcus albus, R. avefaciens, Clostridium longisporum and C. herbivorans [10,30]. The four bacteria families (Bacteroidaceae, Prevotellaceae, Ruminococcaceae, and Clostridiaceae) dominated in the yak fecal microbiome have also been detected as the main producers for CAZymes in the cattle rumen microbiome [26]. However, the Fibrobacteres bacteria, which are important degraders of cellulose and are often highly abundant in the bovine rumen [31,32], were found to be lowly abundant in the yak fecal microbiome (Additional le 3).…”

Section: Diversity Of Carbohydrate-degrading Enzymes and Microbial Comentioning

confidence: 95%

Metagenomic insights into the diversity of carbohydrate-degrading enzymes in the yak fecal microbial community

Gong

Zhou

Luo

et al. 2020

Preprint

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Background: Yaks are able to utilize the gastrointestinal microbiota to digest plant materials. Although the cellulolytic bacteria in the yak rumen have been reported, there is still limited information on the diversity of the major microorganisms and putative carbohydrate-metabolizing enzymes for the degradation of complex lignocellulosic biomass in its gut ecosystem. Results: Here, this study aimed to decode biomass-degrading genes and genomes in the yak fecal microbiota using deep metagenome sequencing. A comprehensive catalog comprising 4.5 million microbial genes from the yak feces were established based on metagenomic assemblies from 92 Gb sequencing data. We identified a full spectrum of genes encoding carbohydrate-active enzymes, three-quarters of which were assigned to highly diversified enzyme families involved in the breakdown of complex dietary carbohydrates, including 120 families of glycoside hydrolases, 25 families of polysaccharide lyases, and 15 families of carbohydrate esterases. Inference of taxonomic assignments to the carbohydrate-degrading genes revealed the major microbial contributors were Bacteroidaceae, Ruminococcaceae, Rikenellaceae, Clostridiaceae, and Prevotellaceae. Furthermore, 68 prokaryotic genomes were reconstructed and the genes encoding glycoside hydrolases involved in plant-derived polysaccharide degradation were identified in these uncultured genomes, many of which were novel species with lignocellulolytic capability. Conclusions: Our findings shed light on a great diversity of carbohydrate-degrading enzymes in the yak gut microbial community and uncultured species, which provides a useful genetic resource for future studies on the discovery of novel enzymes for industrial applications.

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“…Microbial ecology in cows and other ruminants has been investigated using 16S ribosomal RNA (rRNA) genes as molecular markers [426,427], the sheep rumen microbial metatranscriptome has been investigated [428], and in cows specialized and general microbial functions have been examined [423,[429][430][431][432][433][434]. Understanding the mechanisms that influence cow rumen methanogenesis requires community-level analysis of active metabolic functions, however, a comprehensive analysis of dietdependent effects on the functional landscape of the rumen microbiota is lacking.…”

Section: Introductionmentioning

confidence: 99%

Interactive functional networks in microbiota

Hornung

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Humans are not autonomous entities. We are all living in a complex environment, interacting not only with our peers, but as true holobionts we are also very much in interaction with our coexisting microbial ecosystems living on and especially within us, in the intestine. Intestinal microorganisms, often collectively referred to as intestinal microbiota, contribute significantly to our daily energy uptake by breaking down complex carbohydrates into simple sugars, which are fermented to short-chain fatty acids and subsequently absorbed by human cells. They also have an impact on our immune system, by suppressing or enhancing the growth of malevolent and beneficial microbes. Our lifestyle can have a large influence on this ecosystem. What and how much we consume can tip the ecological balance in the intestine. A "western diet" containing mainly processed food will have a different effect on our health than a balanced diet fortified with pre-and probiotics. In recent years, new technologies have emerged, which made a more detailed understanding of microbial communities and ecosystems feasible. This includes progress in the sequencing of PCR-amplified phylogenetic marker genes as well as the collective microbial metagenome and metatranscriptome, allowing us to determine with an increasing level of detail, which microbial species are in the microbiota, understand what these microorganisms do and how they respond to changes in lifestyle and diet. These new technologies also include the use of synthetic and in vitro systems, which allow us to study the impact of substrates and addition of specific microbes to microbial communities at a high level of detail, and enable us to gather quantitative data for modelling purposes. Here we will review the current state of microbiome research, summarizing the computational methodologies in this area, and highlighting possible outcomes for personalized nutrition and medicine. [301]). The researchers in the microbiome field need to be aware that this hype can also happen to the microbiome [302, 303]. Current microbiome research aims to overcome some of these challenges. Obesity research is likely to contribute in the close future to a better understanding of the underlying mechanisms, and the 4P medicine might partially become achievable in not too distant future, leading to better health and combating epidemics like obesity. Chapter 3: Genomic and functional analysis of Romboutsia ilealis CRIB T reveals adaptation to the small intestine.

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

Cited by 67 publications

References 40 publications

Microbiota composition, gene pool and its expression in Gir cattle (Bos indicus) rumen under different forage diets using metagenomic and metatranscriptomic approaches

Microbiota composition, gene pool and its expression in Gir cattle (Bos indicus) rumen under different forage diets using metagenomic and metatranscriptomic approaches

Metagenomic insights into the diversity of carbohydrate-degrading enzymes in the yak fecal microbial community

Interactive functional networks in microbiota

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