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Metagenomic Analysis of the Rumen Microbiome of Steers with Wheat-Induced Frothy Bloat.

Pitta DW, Pinchak WE, Indugu N, Vecchiarelli B, Sinha R, Fulford JD - Front Microbiol (2016)

Bottom Line: Assignment of contigs to CaZy database revealed a greater diversity of Glycosyl Hydrolases dominated by oligosaccharide breaking enzymes (>70%) in non-bloated samples.However, the abundance and diversity of CaZymes were greatly reduced in bloated samples indicating the disruption of carbohydrate metabolism.We conclude that mild to moderate frothy bloat results from tradeoffs both within and between microbial domains due to greater competition for substrates that are of limited availability as a result of biofilm formation.

View Article: PubMed Central - PubMed

Affiliation: Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania Kennett Square, PA, USA.

ABSTRACT
Frothy bloat is a serious metabolic disorder that affects stocker cattle grazing hard red winter wheat forage in the Southern Great Plains causing reduced performance, morbidity, and mortality. We hypothesize that a microbial dysbiosis develops in the rumen microbiome of stocker cattle when grazing on high quality winter wheat pasture that predisposes them to frothy bloat risk. In this study, rumen contents were harvested from six cannulated steers grazing hard red winter wheat (three with bloat score "2" and three with bloat score "0"), extracted for genomic DNA and subjected to 16S rDNA and shotgun sequencing on 454/Roche platform. Approximately 1.5 million reads were sequenced, assembled and assigned for phylogenetic and functional annotations. Bacteria predominated up to 84% of the sequences while archaea contributed to nearly 5% of the sequences. The abundance of archaea was higher in bloated animals (P < 0.05) and dominated by Methanobrevibacter. Predominant bacterial phyla were Firmicutes (65%), Actinobacteria (13%), Bacteroidetes (10%), and Proteobacteria (6%) across all samples. Genera from Firmicutes such as Clostridium, Eubacterium, and Butyrivibrio increased (P < 0.05) while Prevotella from Bacteroidetes decreased in bloated samples. Co-occurrence analysis revealed syntrophic associations between bacteria and archaea in non-bloated samples, however; such interactions faded in bloated samples. Functional annotations of assembled reads to Subsystems database revealed the abundance of several metabolic pathways, with carbohydrate and protein metabolism well represented. Assignment of contigs to CaZy database revealed a greater diversity of Glycosyl Hydrolases dominated by oligosaccharide breaking enzymes (>70%) in non-bloated samples. However, the abundance and diversity of CaZymes were greatly reduced in bloated samples indicating the disruption of carbohydrate metabolism. We conclude that mild to moderate frothy bloat results from tradeoffs both within and between microbial domains due to greater competition for substrates that are of limited availability as a result of biofilm formation.

No MeSH data available.


Related in: MedlinePlus

Analysis of co-occurrence among the most abundant bacterial and archaeal lineages scored using the Dice index for bloated and non-bloated rumen samples respectively. Co-occurrence is shown by the color code (navy blue, high co-occurrence; sky blue, moderate co-occurrence; green, low co-occurrence) at the bottom.
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Figure 2: Analysis of co-occurrence among the most abundant bacterial and archaeal lineages scored using the Dice index for bloated and non-bloated rumen samples respectively. Co-occurrence is shown by the color code (navy blue, high co-occurrence; sky blue, moderate co-occurrence; green, low co-occurrence) at the bottom.

Mentions: As rumen microbes work cohesively to perform various metabolic activities in the rumen, we sought to determine the associative interactions between bacteria and archaea present in bloated and non-bloated samples using co-occurrence analysis based on the Dice index (Figure 2). For this analysis, we selected the most abundant genera (>0.01%) from both bacterial and archaeal communities. In total, we had six genera from Actinobacteria, two genera from Bacteroidetes and 14 genera from Firmicutes and 11 genera from Euryachaeota. Associations were presented for non-bloated and bloated samples (Figure 2). Co-occurrence is shown by the color code (navy blue, high co-occurrence; sky blue, moderate co-occurrence; green, low co-occurrence).


Metagenomic Analysis of the Rumen Microbiome of Steers with Wheat-Induced Frothy Bloat.

Pitta DW, Pinchak WE, Indugu N, Vecchiarelli B, Sinha R, Fulford JD - Front Microbiol (2016)

Analysis of co-occurrence among the most abundant bacterial and archaeal lineages scored using the Dice index for bloated and non-bloated rumen samples respectively. Co-occurrence is shown by the color code (navy blue, high co-occurrence; sky blue, moderate co-occurrence; green, low co-occurrence) at the bottom.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4863135&req=5

Figure 2: Analysis of co-occurrence among the most abundant bacterial and archaeal lineages scored using the Dice index for bloated and non-bloated rumen samples respectively. Co-occurrence is shown by the color code (navy blue, high co-occurrence; sky blue, moderate co-occurrence; green, low co-occurrence) at the bottom.
Mentions: As rumen microbes work cohesively to perform various metabolic activities in the rumen, we sought to determine the associative interactions between bacteria and archaea present in bloated and non-bloated samples using co-occurrence analysis based on the Dice index (Figure 2). For this analysis, we selected the most abundant genera (>0.01%) from both bacterial and archaeal communities. In total, we had six genera from Actinobacteria, two genera from Bacteroidetes and 14 genera from Firmicutes and 11 genera from Euryachaeota. Associations were presented for non-bloated and bloated samples (Figure 2). Co-occurrence is shown by the color code (navy blue, high co-occurrence; sky blue, moderate co-occurrence; green, low co-occurrence).

Bottom Line: Assignment of contigs to CaZy database revealed a greater diversity of Glycosyl Hydrolases dominated by oligosaccharide breaking enzymes (>70%) in non-bloated samples.However, the abundance and diversity of CaZymes were greatly reduced in bloated samples indicating the disruption of carbohydrate metabolism.We conclude that mild to moderate frothy bloat results from tradeoffs both within and between microbial domains due to greater competition for substrates that are of limited availability as a result of biofilm formation.

View Article: PubMed Central - PubMed

Affiliation: Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania Kennett Square, PA, USA.

ABSTRACT
Frothy bloat is a serious metabolic disorder that affects stocker cattle grazing hard red winter wheat forage in the Southern Great Plains causing reduced performance, morbidity, and mortality. We hypothesize that a microbial dysbiosis develops in the rumen microbiome of stocker cattle when grazing on high quality winter wheat pasture that predisposes them to frothy bloat risk. In this study, rumen contents were harvested from six cannulated steers grazing hard red winter wheat (three with bloat score "2" and three with bloat score "0"), extracted for genomic DNA and subjected to 16S rDNA and shotgun sequencing on 454/Roche platform. Approximately 1.5 million reads were sequenced, assembled and assigned for phylogenetic and functional annotations. Bacteria predominated up to 84% of the sequences while archaea contributed to nearly 5% of the sequences. The abundance of archaea was higher in bloated animals (P < 0.05) and dominated by Methanobrevibacter. Predominant bacterial phyla were Firmicutes (65%), Actinobacteria (13%), Bacteroidetes (10%), and Proteobacteria (6%) across all samples. Genera from Firmicutes such as Clostridium, Eubacterium, and Butyrivibrio increased (P < 0.05) while Prevotella from Bacteroidetes decreased in bloated samples. Co-occurrence analysis revealed syntrophic associations between bacteria and archaea in non-bloated samples, however; such interactions faded in bloated samples. Functional annotations of assembled reads to Subsystems database revealed the abundance of several metabolic pathways, with carbohydrate and protein metabolism well represented. Assignment of contigs to CaZy database revealed a greater diversity of Glycosyl Hydrolases dominated by oligosaccharide breaking enzymes (>70%) in non-bloated samples. However, the abundance and diversity of CaZymes were greatly reduced in bloated samples indicating the disruption of carbohydrate metabolism. We conclude that mild to moderate frothy bloat results from tradeoffs both within and between microbial domains due to greater competition for substrates that are of limited availability as a result of biofilm formation.

No MeSH data available.


Related in: MedlinePlus