Functional gene profiling through metaRNAseq approach reveals diet-dependent variation in rumen microbiota of buffalo (Bubalus bubalis)

Hinsu, Ankit T.; Parmar, Nidhi; Nathani, Neelam M.; Pandit, Ramesh; Patel, Anand; Patel, Amrutlal K.; Joshi, Chaitanya G.

doi:10.1016/j.anaerobe.2017.02.021

Cited by 13 publications

(9 citation statements)

References 62 publications

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“…These differences among the liquid and solid fraction identified in the MT dataset, and to a lesser extent in MG, suggested that there is a special role of specific bacteria in the fibre degradation and subsequent fermentation of released building blocks of different plant polymers. This results are in accordance with previous studies of rumen [15,48,53,67,78]. The shift in the microbial population observed during the different diet treatments suggested that different rumen bacteria show a preference for specific substrates and their abundance changes accordingly.…”

Section: Discussionsupporting

confidence: 92%

“…The primary role of the ruminal bacteria is to degrade the plant polysaccharides using potent hydrolytic enzymes. Our previous studies with different breeds of buffaloes [42,47] and cattle [15] revealed that glycosyl hydrolases (GH) is the actively engaged CAZy family in the rumen microbes. 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.…”

Section: Discussionmentioning

confidence: 99%

“…For metatranscriptome sequencing, RNA was extracted using RNeasy Mini Kit (Qiagen, Germany) according to manufacturer's instructions with a few modifications in solid fraction samples. These modifications has been described in our previous study [15]. Quantity and quality of RNA was estimated using Qubit following the manufacturer's instructions.…”

Section: Dna and Rna Isolationmentioning

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: Discussionmentioning

confidence: 99%

Section: Dna and Rna Isolationmentioning

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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“…Studies that decipher the community composition of anaerobic sludge has also been conducted by many research groups across the world (Guo et al, 2015; Sun et al, 2015; Ferrentino et al, 2016; Ju et al, 2016) but the studies conducting the detailed investigation of taxonomic as well as functional composition of pre- and post-treated anaerobic sludge are very few. Researchers have used different sequencing depths ranging from 0.1 GB to 3.3 GB to study functional composition using the Ion-torrent platform (Joshi et al, 2014; Patel et al, 2014; Rua et al, 2015; Hinsu et al, 2017; Motooka et al, 2017). Here, we employed ∼1 GB sequencing depth for shotgun metagenomic sequencing to inspect the microbial shifts in pre- and post-treated sludge along with their functional alterations.…”

Section: Discussionmentioning

confidence: 99%

Unraveling the Microbial Interactions and Metabolic Potentials in Pre- and Post-treated Sludge from a Wastewater Treatment Plant Using Metagenomic Studies

2017

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Sewage waste represents an ecosystem of complex and interactive microbial consortia which proliferate with different kinetics according to their individual genetic as well as metabolic potential. We performed metagenomic shotgun sequencing on Ion-Torrent platform, to explore the microbial community structure, their biological interactions and associated functional capacity of pre-treated/raw sludge (RS) and post-treated/dried sludge (DS) of wastewater treatment plant. Bacterial phylotypes belonging to Epsilonproteobacteria (∼45.80%) dominated the RS with relatively few Archaea (∼1.94%) whereas DS has the dominance of beta- (30.23%) and delta- (13.38%) classes of Proteobacteria with relatively greater abundance of Archaea (∼7.18%). In particular, Epsilonproteobacteria appears as a primary energy source in RS and sulfur-reducing bacteria with methanogens seems to be in the potential syntrophic association in DS. These interactions could be ultimately responsible for carrying out amino-acid degradation, aromatic compound degradation and degradation of propionate and butyrate in DS. Our data also reveal the presence of key genes in the sludge microbial community responsible for degradation of polycyclic aromatic hydrocarbons. Potential pathogenic microbes and genes for the virulence factors were found to be relatively abundant in RS which clearly reflect the necessity of treatment of RS. After treatment, potential pathogens load was reduced, indicating the sludge hygienisation in DS. Additionally, the interactions found in this study would reveal the biological and environmental cooperation among microbial communities for domestic wastewater treatment.

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“…Utilizing metatranscriptomics for the study of eukaryotic derived activity in mixed communities has many advantages (Marmeisse et al, 2017 ); particularly due to the syntrophic interactions that occur between anaerobic fungi and other rumen microbes (see section Metabolomics). Recently, a number of studies have used metatranscriptomics to examine the rumen microbial community (Qi et al, 2011 ; Wang et al, 2011 ; Poulsen et al, 2013 ; Dai et al, 2014 ; Kamke et al, 2016 ; Li F., et al, 2016 ; Comtet-Marre et al, 2017 ; Hinsu et al, 2017 ; Li and Guan, 2017 ). However, very few of these studies identified significant numbers of anaerobic fungal transcripts in their results.…”

Section: Transcriptomicsmentioning

confidence: 99%

PCR and Omics Based Techniques to Study the Diversity, Ecology and Biology of Anaerobic Fungi: Insights, Challenges and Opportunities

et al. 2017

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Anaerobic fungi (phylum Neocallimastigomycota) are common inhabitants of the digestive tract of mammalian herbivores, and in the rumen, can account for up to 20% of the microbial biomass. Anaerobic fungi play a primary role in the degradation of lignocellulosic plant material. They also have a syntrophic interaction with methanogenic archaea, which increases their fiber degradation activity. To date, nine anaerobic fungal genera have been described, with further novel taxonomic groupings known to exist based on culture-independent molecular surveys. However, the true extent of their diversity may be even more extensively underestimated as anaerobic fungi continue being discovered in yet unexplored gut and non-gut environments. Additionally many studies are now known to have used primers that provide incomplete coverage of the Neocallimastigomycota. For ecological studies the internal transcribed spacer 1 region (ITS1) has been the taxonomic marker of choice, but due to various limitations the large subunit rRNA (LSU) is now being increasingly used. How the continued expansion of our knowledge regarding anaerobic fungal diversity will impact on our understanding of their biology and ecological role remains unclear; particularly as it is becoming apparent that anaerobic fungi display niche differentiation. As a consequence, there is a need to move beyond the broad generalization of anaerobic fungi as fiber-degraders, and explore the fundamental differences that underpin their ability to exist in distinct ecological niches. Application of genomics, transcriptomics, proteomics and metabolomics to their study in pure/mixed cultures and environmental samples will be invaluable in this process. To date the genomes and transcriptomes of several characterized anaerobic fungal isolates have been successfully generated. In contrast, the application of proteomics and metabolomics to anaerobic fungal analysis is still in its infancy. A central problem for all analyses, however, is the limited functional annotation of anaerobic fungal sequence data. There is therefore an urgent need to expand information held within publicly available reference databases. Once this challenge is overcome, along with improved sample collection and extraction, the application of these techniques will be key in furthering our understanding of the ecological role and impact of anaerobic fungi in the wide range of environments they inhabit.

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Functional gene profiling through metaRNAseq approach reveals diet-dependent variation in rumen microbiota of buffalo (Bubalus bubalis)

Cited by 13 publications

References 62 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

Unraveling the Microbial Interactions and Metabolic Potentials in Pre- and Post-treated Sludge from a Wastewater Treatment Plant Using Metagenomic Studies

PCR and Omics Based Techniques to Study the Diversity, Ecology and Biology of Anaerobic Fungi: Insights, Challenges and Opportunities

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