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

Indugu, Nagaraju; Bittinger, Kyle; Kumar, Sanjay; Vecchiarelli, Bonnie; Pitta, Dipti

doi:10.7717/peerj.1599

Cited by 17 publications

(12 citation statements)

References 39 publications

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“…Although the endocrine, metabolic, physiologic, and molecular adaptations occurring in dairy cows around the peripartal period are reasonably well-described (Loor et al, 2013), there are few published studies (Lima et al, 2015; Pitta et al, 2014a; Indugu et al, 2016) that have evaluated the shifts in the ruminal microbiota composition during this period. More importantly, there is a knowledge gap on the changes occurring in the functional properties of the ruminal microbiota during the transition into lactation and their correlation with phenotypic measures of animal performance traits, such as milk production and composition.…”

Section: Introductionmentioning

confidence: 99%

Linking Peripartal Dynamics of Ruminal Microbiota to Dietary Changes and Production Parameters

et al. 2017

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During the peripartal period, proper acclimatization of rumen microorganisms to variations in nutritional management can facilitate the transition into lactation. This study characterized the temporal shifts in the composition and functional properties of ruminal microbiota during the periparturient period in dairy cows subjected to a typical two-tiered feeding management approach. Ruminal digesta samples from eight multiparous fistulated Holstein cows were collected on days −14, −7, 10, 20, and 28 relative to parturition. High-throughput Illumina sequencing of the V4 region of the bacterial 16S rRNA gene revealed distinct clustering patterns between pre- and postpartal ruminal microbiota. During the prepartal period, when the voluntary dry matter intake was lower, we observed strikingly lower inter-animal variations in the composition of the ruminal microbiota. Genera Ruminococcus and Butyrivibrio, which are considered major fibrolytic rumen dwellers, were overrepresented in the prepartal rumen ecosystem. In contrast, increased postpartal voluntary DMI was associated with enrichment of bacterial genera mainly consisting of proteolytic, amylolytic, and lactate-producer species (including Prevotella, Streptococcus, and Lactobacillus). These, together with the postpartal enrichment of energy metabolism pathways, suggested a degree of acclimatization of the ruminal microbiota to harvest energy from the carbohydrate-dense lactation diet. In addition, correlations between ruminal microbiota and parameters such as milk yield and milk composition underscored the metabolic contribution of this microbial community to the cow's performance and production.

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Section: Introductionmentioning

confidence: 99%

Linking Peripartal Dynamics of Ruminal Microbiota to Dietary Changes and Production Parameters

et al. 2017

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“…The Qiagen GeneReader shares many of the same advantages and disadvantages as the Illumina MiSeq platform at a potentially lower cost per gigabase sequenced. Both the Roche 454 and Ion Torrent systems offer superior read lengths (on average, 700 and 400 bp, respectively) compared with the other short-read sequencers (Indugu et al, 2016), but suffer similar drawbacks including insertion and deletion (indel) errors and monopolymer regions. The Roche 454 platform has been unable to compete with other platforms in terms of yield and cost and was discontinued in 2016.…”

Section: Ngs Technologies To Sequence Microbial Genomesmentioning

confidence: 99%

“…Nevertheless, as NGS platforms continue to evolve, become more affordable, and able to accommodate larger sample sizes, different omic approaches may be integrated to understand the mechanistic basis of microbial feed fermentation in the rumen. Further, optimizing sequencing conditions and developing robust bioinformatic pipelines compatible for any NGS platform are needed to avoid inconsistencies between NGS-based microbial studies (Loman et al, 2012;Salipante et al, 2014;Indugu et al, 2016).…”

Section: Commonly Used Ngs-based Approaches To Characterize the Rumenmentioning

confidence: 99%

Symposium review: Understanding diet–microbe interactions to enhance productivity of dairy cows

Pitta

Indugu

Baker

et al. 2018

Journal of Dairy Science

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Ruminants are dependent on the microbiota (bacteria, protozoa, archaea, and fungi) that inhabit the reticulo-rumen for digestion of feedstuffs. Nearly 70% of energy and 50% of protein requirements for dairy cows are met by microbial fermentation in the rumen, emphasizing the need to characterize the role of microbes in feed breakdown and nutrient utilization. Over the past 2 decades, next-generation sequencing technologies have allowed for rapid expansion of knowledge concerning microbial populations and alterations in response to forages, concentrates, supplements, and probiotics in the rumen. Advances in gene sequencing and emerging bioinformatic tools have allowed for increased throughput of data to aid in our understanding of the functional relevance of microbial genomes. In particular, metagenomics can identify specific genes involved in metabolic pathways, and metatranscriptomics can describe the transcriptional activity of microbial genes. These powerful approaches help untangle the complex interactions between microbes and dietary nutrients so that we can more fully understand the physiology of feed digestion in the rumen. Application of genomics-based approaches offers promise in unraveling microbial niches and respective gene repertoires to potentiate fiber and nonfiber carbohydrate digestion, microbial protein synthesis, and healthy biohydrogenation. New information on microbial genomics and interactions with dietary components will more clearly define pathways in the rumen to positively influence milk yield and components.

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Section: Introductionmentioning

confidence: 99%

“…Within microbiome research, most attention has been directed toward the bacterial communities inhabiting the fish farm environment or within the fish intestine (Indugu, Bittinger, Kumar, Vecchiarelli, & Pitta, 2016;Sun et al, 2016;Wu et al, 2016Wu et al, , 2017. For example, Stephens et al (2016) Although several studies are available which treat the bacterial communities of the fish intestine and the fish farm separately, few studies have focused on the interactions between the fish intestinal microbiomes of fish (such as Crucian Asia) and their surrounding fish farm environment.…”

Section: Introductionmentioning

confidence: 99%

Microorganism's adaptation of Crucian carp may closely relate to its living environments

et al. 2018

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The relationship between the internal microbiome of an individual organism and that of its external environment has been little investigated in freshwater ecosystems. Thus, this is an area of interest in freshwater fish biology. Along with the genotype of the fish host, external environment plays an important role in determining the composition of the internal microbiome. Here, we characterized the variability of the microbiome of wild Crucian carp (Carassius auratus), along with those of their surrounding environments (water and mud). We found that each environment had distinct bacterial communities, with varying composition and structure. The primary bacterial phyla identified in the Crucian carp gut were Fusobacteria and Proteobacteria (90% of all bacterial phyla identified); the primary genera identified were Cetobacterium, Aeromonas, and Plesiomonas (85% of all bacterial phyla identified). We identified 1,739 operational taxonomic units (OTUs) in the Crucian carp gut, 1,703 in water, and 5,322 in mud. Each environment had unique OTUs, but the fewest unique OTUs (97) were found in the Crucian carp gut. There were significant differences in the relative abundances of different bacterial phyla in the different environments. It may be that only bacterial phyla vital for efficient fish function (e.g., immune response or metabolism), such as Fusobacteria and Proteobacteria, are retained in the Crucian carp gut.

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

Cited by 17 publications

References 39 publications

Linking Peripartal Dynamics of Ruminal Microbiota to Dietary Changes and Production Parameters

Linking Peripartal Dynamics of Ruminal Microbiota to Dietary Changes and Production Parameters

Symposium review: Understanding diet–microbe interactions to enhance productivity of dairy cows

Microorganism's adaptation of Crucian carp may closely relate to its living environments

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