High Potential Source for Biomass Degradation Enzyme Discovery and Environmental Aspects Revealed through Metagenomics of Indian Buffalo Rumen

Singh, Krishna M.; Reddy, Bhaskar; Patel, Dishita; Parmar, Nidhi; Patel, Anand; Patel, J. B.; Joshi, Chaitanya G.

doi:10.1155/2014/267189

Cited by 33 publications

(23 citation statements)

References 44 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In this study, the most highly represented GH family was GH2 (which comprises β-Dgalactosidase, β-glucuronidase, β-D-mannosidase, and exo-β-glucosaminidase [38]) followed by the GH43 (which includes β-xylosidase, β-1,3-xylosidase, α-L-arabinofuranosidase, arabinanase, xylanase, galactan 1, and 3-β-galactosidase). Our results are in accordance with the finding that GH3 and GH2 are the predominant GHs in the rumen of Indian buffalo [3,35,36]. GTs catalyze the binding of sugars to glycosyl groups; we found that GT2, GT4, GT27, GT5, and GT41 families were the most highly represented in the rumen of cattle-yaks.…”

Section: Discussionsupporting

confidence: 92%

“…To date, 42 unique strains of cellulase-and GH-producing bacteria have been identified [36]. GHs hydrolyze glycosidic [3]. Most of the GHs identified in our study were oligosaccharide-degrading enzymes such as cellulase, hemicellulose, and pectinase that degrade the plant cell wall to produce oligosaccharides [37].…”

Section: Discussionmentioning

confidence: 76%

“…These microorganisms can degrade the plant cell wall and fibrous substances that are converted into absorbable compounds such as proteins and volatile fatty acids (VFAs) [1,2]. One study analyzing the rumen microbiome of Indian buffalo identified 2614 contigs encoding putative degradative enzymes [3], and another reported 42 operational taxonomic units representing the rumen bacterial community of adult buffalo [4]. Microbiome profile can vary according to the developmental stage; for instance, rumen microbial community composition in cows changes markedly from birth to the age of 2 years [5].…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Characteristics and Functions of the Rumen Microbial Community of Cattle-Yak at Different Ages

Sha

Shi

et al. 2020

BioMed Research International

View full text Add to dashboard Cite

A cattle-yak, which is a hybrid between a yak (Bos grunniens) and cattle (Bos taurus), is an important livestock animal, but basic questions regarding its physiology and environmental adaptation remain unanswered. To address this issue, the present study examined the species composition and functional characteristics of rumen microorganisms in the cattle-yak of different ages (2 and 3 years old) by metagenomic analysis. We found that rumen microbial community composition was similar at the two ages. Firmicutes, Fibrobacteres, Euryarchaeota, Bacteroidetes, and Proteobacteria were the predominant phyla, with Firmicutes accounting for the highest percentage of bacteria in 2-year-old (48%) and 3-year-old (46%) animals. Bacterial species involved in lignocellulose degradation were detected in the rumen of adult cattle-yaks including Ruminococcus flavefaciens, Ruminococcus albus, Fibrobacter succinogenes, and Prevotella ruminicola, with F. succinogenes being the most abundant. A total of 145,489 genes were annotated according to the Carbohydrate-active Enzyme database, which identified glycoside hydrolases as the most highly represented enzyme family. Further functional annotation revealed specific microflora and genes in the adult rumen that are potentially related to plateau adaptability. These results could explain the heterosis of the cattle-yak and provide insight into mechanisms of physiologic adaptation in plateau animals.

show abstract

Section: Discussionsupporting

confidence: 92%

Section: Discussionmentioning

confidence: 76%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Characteristics and Functions of the Rumen Microbial Community of Cattle-Yak at Different Ages

Sha

Shi

et al. 2020

BioMed Research International

View full text Add to dashboard Cite

show abstract

“…To analyze microbial diversity, 16S rRNA amplicon-based sequencing has been widely used in various engineered or environmental samples (Hess et al, 2011;Singh et al, 2014;Chan et al, 2015;Mhuantong, Charoensawan, Kanokratana, Tangphatsornruang, & Champreda, 2015;Vishnivetskaya et al, 2015). Culture independent studies at hot springs in YNP have a long research history where the clonal library was initially used (Brock, 1967;Thiel et al, 2016).…”

Section: Microbial Diversity Analysis In Sk-ymentioning

confidence: 99%

Microbial diversity of thermophiles with biomass deconstruction potential in a foliage‐rich hot spring

Lee¹,

Goh

Chan

et al. 2018

MicrobiologyOpen

View full text Add to dashboard Cite

The ability of thermophilic microorganisms and their enzymes to decompose biomass have attracted attention due to their quick reaction time, thermostability, and decreased risk of contamination. Exploitation of efficient thermostable glycoside hydrolases (GHs) could accelerate the industrialization of biofuels and biochemicals. However, the full spectrum of thermophiles and their enzymes that are important for biomass degradation at high temperatures have not yet been thoroughly studied. We examined a Malaysian Y-shaped Sungai Klah hot spring located within a wooded area. The fallen foliage that formed a thick layer of biomass bed under the heated water of the Y-shaped Sungai Klah hot spring was an ideal environment for the discovery and analysis of microbial biomass decay communities. We sequenced the hypervariable regions of bacterial and archaeal 16S rRNA genes using total community DNA extracted from the hot spring. Data suggested that 25 phyla, 58 classes, 110 orders, 171 families, and 328 genera inhabited this hot spring. Among the detected genera, members of Acidimicrobium, Aeropyrum, Caldilinea, Caldisphaera, Chloracidobacterium, Chloroflexus, Desulfurobacterium, Fervidobacterium, Geobacillus, Meiothermus, Melioribacter, Methanothermococcus, Methanotorris, Roseiflexus, Thermoanaerobacter, Thermoanaerobacterium, Thermoanaerobaculum, and Thermosipho were the main thermophiles containing various GHs that play an important role in cellulose and hemicellulose breakdown. Collectively, the results suggest that the microbial community in this hot spring represents a good source for isolating efficient biomass degrading thermophiles and thermozymes.

show abstract

“…The intestinal microbiota of various animals, which can degrade complicated carbohydrates, is under investigation as a resource for the discovery of novel enzymes for e.g. more efficient breakdown of organic waste streams and non-food biomass for the production of biofuel [40,41]. The intestines of elephants [42], koalas [43], and termites [44] harbour microbes with a totally different capacity for polysaccharide and lignin breakdown, which could be utilized in such processes.…”

Section: What Is Being Sequenced and Which Questions Can This Answer?mentioning

confidence: 99%

Interactive functional networks in microbiota

Hornung

View full text Add to dashboard Cite

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.

show abstract

High Potential Source for Biomass Degradation Enzyme Discovery and Environmental Aspects Revealed through Metagenomics of Indian Buffalo Rumen

Cited by 33 publications

References 44 publications

Characteristics and Functions of the Rumen Microbial Community of Cattle-Yak at Different Ages

Characteristics and Functions of the Rumen Microbial Community of Cattle-Yak at Different Ages

Microbial diversity of thermophiles with biomass deconstruction potential in a foliage‐rich hot spring

Interactive functional networks in microbiota

Contact Info

Product

Resources

About