Metagenomic analysis of buffalo rumen microbiome: Effect of roughage diet on Dormancy and Sporulation genes

Singh, Krishna M.; Reddy, Bhaskar; Patel, Amrutlal K.; Panchasara, H. H.; Parmar, Nidhi; Shah, Tejas; Bhatt, Vaibhav D.; Joshi, Chaitanya G.

doi:10.1016/j.mgene.2014.01.005

Cited by 24 publications

(20 citation statements)

References 30 publications

(29 reference statements)

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“…This observation was also recapitulated in our findings for both platforms. Additionally, the 16S rDNA-based taxonomic composition of bacterial communities retrieved here is in accordance with other shotgun metagenomic datasets sequenced on the Ion Torrent platform ( Patel et al, 2014 ; Pitta et al, 2015 ; Singh et al, 2014 ).…”

Section: Discussionsupporting

confidence: 83%

A comparison of rumen microbial profiles in dairy cows as retrieved by 454 Roche and Ion Torrent (PGM) sequencing platforms

Indugu

Bittinger

Kumar

et al. 2016

PeerJ

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Next generation sequencing (NGS) technology is a widely accepted tool used by microbial ecologists to explore complex microbial communities in different ecosystems. As new NGS platforms continue to become available, it becomes imperative to compare data obtained from different platforms and analyze their effect on microbial community structure. In the present study, we compared sequencing data from both the 454 and Ion Torrent (PGM) platforms on the same DNA samples obtained from the rumen of dairy cows during their transition period. Despite the substantial difference in the number of reads, error rate and length of reads among both platforms, we identified similar community composition between the two data sets. Procrustes analysis revealed similar correlations (M2 = 0.319; P = 0.001) in the microbial community composition between the two platforms. Both platforms revealed the abundance of the same bacterial phyla which were Bacteroidetes and Firmicutes; however, PGM recovered an additional four phyla. Comparisons made at the genus level by each platforms revealed differences in only a few genera such as Prevotella, Ruminococcus, Succiniclasticum and Treponema (p < 0.05; chi square test). Collectively, we conclude that the output generated from PGM and 454 yielded concurrent results, provided stringent bioinformatics pipelines are employed.

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Section: Discussionsupporting

confidence: 83%

A comparison of rumen microbial profiles in dairy cows as retrieved by 454 Roche and Ion Torrent (PGM) sequencing platforms

Indugu

Bittinger

Kumar

et al. 2016

PeerJ

View full text Add to dashboard Cite

show abstract

“…This observation was also recapitulated in our findings for both platforms. Additionally, the 16S rDNA-based taxonomic composition of bacterial communities retrieved here is in accordance with other shotgun metagenomic datasets sequenced on the Ion Torrent platform (Patel et al, 2014;unpublished data Pitta;Singh et al, 2014).…”

Section: Ruminal Bacterial Diversity Dynamicssupporting

confidence: 84%

Peer Review #1 of "A comparison of rumen microbial profiles in dairy cows as retrieved by 454 Roche and Ion Torrent (PGM) sequencing platforms (v0.1)"

Joshi¹

2016

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Next generation sequencing (NGS) technology is a widely accepted tool used by microbial ecologists to explore complex microbial communities in different ecosystems. As new NGS platforms continue to become available, it becomes imperative to compare data obtained from different platforms and analyze their effect on microbial community structure. In the present study, we compared sequencing data from both the 454 and Ion Torrent (PGM) platforms on the same DNA samples obtained from the rumen of dairy cows during their transition period. Despite the substantial difference in the number of reads, error rate and length of reads among both platforms, we identified similar community composition between the two data sets. Procrustes analysis revealed similar correlations (M 2 = 0.319; P = 0.001) in the microbial community composition between the two platforms. Both platforms revealed the abundance of the same bacterial phyla which were Bacteroidetes, Firmicutes and Proteobacteria, however, PGM recovered an additional four phyla. Comparisons made at the genus level by each platforms revealed differences in only a few genera such as Prevotella, Ruminococcus, Succiniclasticum and Treponema (p < 0.05; chi square test). Collectively, we conclude that the output generated from PGM and 454 yielded concurrent results, provided stringent bioinformatics pipelines are employed.

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“…Initially, the most widely used NGS method in the identification of rumen communities and its functional mechanisms was based on 454-pyrosequencing ( Mccann et al, 2014 ; Weimer, 2015 ; Güllert et al, 2016 ; Kala et al, 2017 ). Nowadays, other NGS approaches like Illumina TM , and Ion Torrent TM have also been employed to investigate these communities ( Singh et al, 2014 ; Mao et al, 2015 ; Pitta et al, 2016 ; Comtet-Marre et al, 2017 ).…”

Section: Introductionmentioning

confidence: 99%

The Planktonic Core Microbiome and Core Functions in the Cattle Rumen by Next Generation Sequencing

Wirth

Kádár²,

Kakuk

et al. 2018

Front. Microbiol.

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The cow rumen harbors a great variety of diverse microbes, which form a complex, organized community. Understanding the behavior of this multifarious network is crucial in improving ruminant nutrient use efficiency. The aim of this study was to expand our knowledge by examining 10 Holstein dairy cow rumen fluid fraction whole metagenome and transcriptome datasets. DNA and mRNA sequence data, generated by Ion Torrent, was subjected to quality control and filtering before analysis for core elements. The taxonomic core microbiome consisted of 48 genera belonging to Bacteria (47) and Archaea (1). The genus Prevotella predominated the planktonic core community. Core functional groups were identified using co-occurrence analysis and resulted in 587 genes, from which 62 could be assigned to metabolic functions. Although this was a minimal functional core, it revealed key enzymes participating in various metabolic processes. A diverse and rich collection of enzymes involved in carbohydrate metabolism and other functions were identified. Transcripts coding for enzymes active in methanogenesis made up 1% of the core functions. The genera associated with the core enzyme functions were also identified. Linking genera to functions showed that the main metabolic pathways are primarily provided by Bacteria and several genera may serve as a “back-up” team for the central functions. The key actors in most essential metabolic routes belong to the genus Prevotella. Confirming earlier studies, the genus Methanobrevibacter carries out the overwhelming majority of rumen methanogenesis and therefore methane emission mitigation seems conceivable via targeting the hydrogenotrophic methanogenesis.

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Metagenomic analysis of buffalo rumen microbiome: Effect of roughage diet on Dormancy and Sporulation genes

Cited by 24 publications

References 30 publications

A comparison of rumen microbial profiles in dairy cows as retrieved by 454 Roche and Ion Torrent (PGM) sequencing platforms

A comparison of rumen microbial profiles in dairy cows as retrieved by 454 Roche and Ion Torrent (PGM) sequencing platforms

Peer Review #1 of "A comparison of rumen microbial profiles in dairy cows as retrieved by 454 Roche and Ion Torrent (PGM) sequencing platforms (v0.1)"

The Planktonic Core Microbiome and Core Functions in the Cattle Rumen by Next Generation Sequencing

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