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Shotgun Metagenomic Sequencing Reveals Functional Genes and Microbiome Associated with Bovine Digital Dermatitis.

Zinicola M, Higgins H, Lima S, Machado V, Guard C, Bicalho R - PLoS ONE (2015)

Bottom Line: Recruitment plots comparing sequences from HS, ADD and IDD samples to the genomes of specific Treponema spp., supported the presence of T. denticola and T. vincentii in ADD and IDD.Comparison of the functional composition of HS to ADD and IDD identified a significant difference in genes associated with motility/chemotaxis and iron acquisition/metabolism.We also provide evidence that the microbiome of ADD and IDD compared to that of HS had significantly higher abundance of genes associated with resistance to copper and zinc, which are commonly used in footbaths to prevent and control DD.

View Article: PubMed Central - PubMed

Affiliation: Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York, United States of America.

ABSTRACT
Metagenomic methods amplifying 16S ribosomal RNA genes have been used to describe the microbial diversity of healthy skin and lesion stages of bovine digital dermatitis (DD) and to detect critical pathogens involved with disease pathogenesis. In this study, we characterized the microbiome and for the first time, the composition of functional genes of healthy skin (HS), active (ADD) and inactive (IDD) lesion stages using a whole-genome shotgun approach. Metagenomic sequences were annotated using MG-RAST pipeline. Six phyla were identified as the most abundant. Firmicutes and Actinobacteria were the predominant bacterial phyla in the microbiome of HS, while Spirochetes, Bacteroidetes and Proteobacteria were highly abundant in ADD and IDD. T. denticola-like, T. vincentii-like and T. phagedenis-like constituted the most abundant species in ADD and IDD. Recruitment plots comparing sequences from HS, ADD and IDD samples to the genomes of specific Treponema spp., supported the presence of T. denticola and T. vincentii in ADD and IDD. Comparison of the functional composition of HS to ADD and IDD identified a significant difference in genes associated with motility/chemotaxis and iron acquisition/metabolism. We also provide evidence that the microbiome of ADD and IDD compared to that of HS had significantly higher abundance of genes associated with resistance to copper and zinc, which are commonly used in footbaths to prevent and control DD. In conclusion, the results from this study provide new insights into the HS, ADD and IDD microbiomes, improve our understanding of the disease pathogenesis and generate unprecedented knowledge regarding the functional genetic composition of the digital dermatitis microbiome.

No MeSH data available.


Related in: MedlinePlus

Normalized abundance of Treponema spp. from HS, ADD and IDD.Error bars are standard error of the mean. *P < 0.05.
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pone.0133674.g003: Normalized abundance of Treponema spp. from HS, ADD and IDD.Error bars are standard error of the mean. *P < 0.05.

Mentions: Comparison of the 12 most abundant phyla between HS, ADD and IDD are illustrated in Fig 1. Chordata, Firmicutes, Actinobacteria, Arthropoda, and Echinodermata were identified in HS as the most abundant phyla with Chordata being the most dominant phylum. Statistically significant differences at the phylum level were not identified between ADD and IDD and Chordata, Bacteroidetes, Firmicutes, Spirochaetes and Protobacteria were the most abundant phyla. The phylum Chordata, most likely bovine DNA, was more abundant (P<0.05) in HS when compared to ADD and IDD and the phylum Spirochaetes was significantly more abundant (P<0.05) in IDD when compared to HS (Fig 1). We also evaluated the phylum distribution of HS, ADD and IDD samples using a Heatmap (Fig 2). Spirochaetes and Bacteroidetes were highly prevalent in ADD and IDD samples followed by Proteobacteria and Firmicutes (Fig 2). The most dominant phyla in HS samples include Chordata, Actinobacteria and Firmicutes (Fig 2). Analysis of the normalized abundance of Treponema spp. from HS, ADD and IDD demonstrated that T. phagedenis, T. denticola, T. vincentii and T. pallidum were the most abundant Treponema spp. and were significantly more abundant (P<0.05) in ADD and IDD compared to HS samples (Fig 3). Evaluation of the Treponema spp. across ADD and IDD identified a higher abundance (P<0.05) of T. maltophilum in IDD compared to ADD (Fig 3). The heatmap showing the functional composition of HS, ADD and IDD samples is illustrated in Fig 4. Differences in functional categories were associated with motility/chemotaxis, respiration, iron acquisition, phosphorus metabolism, cell division and cell cycle and regulation and cell signaling (Fig 4).


Shotgun Metagenomic Sequencing Reveals Functional Genes and Microbiome Associated with Bovine Digital Dermatitis.

Zinicola M, Higgins H, Lima S, Machado V, Guard C, Bicalho R - PLoS ONE (2015)

Normalized abundance of Treponema spp. from HS, ADD and IDD.Error bars are standard error of the mean. *P < 0.05.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4508036&req=5

pone.0133674.g003: Normalized abundance of Treponema spp. from HS, ADD and IDD.Error bars are standard error of the mean. *P < 0.05.
Mentions: Comparison of the 12 most abundant phyla between HS, ADD and IDD are illustrated in Fig 1. Chordata, Firmicutes, Actinobacteria, Arthropoda, and Echinodermata were identified in HS as the most abundant phyla with Chordata being the most dominant phylum. Statistically significant differences at the phylum level were not identified between ADD and IDD and Chordata, Bacteroidetes, Firmicutes, Spirochaetes and Protobacteria were the most abundant phyla. The phylum Chordata, most likely bovine DNA, was more abundant (P<0.05) in HS when compared to ADD and IDD and the phylum Spirochaetes was significantly more abundant (P<0.05) in IDD when compared to HS (Fig 1). We also evaluated the phylum distribution of HS, ADD and IDD samples using a Heatmap (Fig 2). Spirochaetes and Bacteroidetes were highly prevalent in ADD and IDD samples followed by Proteobacteria and Firmicutes (Fig 2). The most dominant phyla in HS samples include Chordata, Actinobacteria and Firmicutes (Fig 2). Analysis of the normalized abundance of Treponema spp. from HS, ADD and IDD demonstrated that T. phagedenis, T. denticola, T. vincentii and T. pallidum were the most abundant Treponema spp. and were significantly more abundant (P<0.05) in ADD and IDD compared to HS samples (Fig 3). Evaluation of the Treponema spp. across ADD and IDD identified a higher abundance (P<0.05) of T. maltophilum in IDD compared to ADD (Fig 3). The heatmap showing the functional composition of HS, ADD and IDD samples is illustrated in Fig 4. Differences in functional categories were associated with motility/chemotaxis, respiration, iron acquisition, phosphorus metabolism, cell division and cell cycle and regulation and cell signaling (Fig 4).

Bottom Line: Recruitment plots comparing sequences from HS, ADD and IDD samples to the genomes of specific Treponema spp., supported the presence of T. denticola and T. vincentii in ADD and IDD.Comparison of the functional composition of HS to ADD and IDD identified a significant difference in genes associated with motility/chemotaxis and iron acquisition/metabolism.We also provide evidence that the microbiome of ADD and IDD compared to that of HS had significantly higher abundance of genes associated with resistance to copper and zinc, which are commonly used in footbaths to prevent and control DD.

View Article: PubMed Central - PubMed

Affiliation: Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York, United States of America.

ABSTRACT
Metagenomic methods amplifying 16S ribosomal RNA genes have been used to describe the microbial diversity of healthy skin and lesion stages of bovine digital dermatitis (DD) and to detect critical pathogens involved with disease pathogenesis. In this study, we characterized the microbiome and for the first time, the composition of functional genes of healthy skin (HS), active (ADD) and inactive (IDD) lesion stages using a whole-genome shotgun approach. Metagenomic sequences were annotated using MG-RAST pipeline. Six phyla were identified as the most abundant. Firmicutes and Actinobacteria were the predominant bacterial phyla in the microbiome of HS, while Spirochetes, Bacteroidetes and Proteobacteria were highly abundant in ADD and IDD. T. denticola-like, T. vincentii-like and T. phagedenis-like constituted the most abundant species in ADD and IDD. Recruitment plots comparing sequences from HS, ADD and IDD samples to the genomes of specific Treponema spp., supported the presence of T. denticola and T. vincentii in ADD and IDD. Comparison of the functional composition of HS to ADD and IDD identified a significant difference in genes associated with motility/chemotaxis and iron acquisition/metabolism. We also provide evidence that the microbiome of ADD and IDD compared to that of HS had significantly higher abundance of genes associated with resistance to copper and zinc, which are commonly used in footbaths to prevent and control DD. In conclusion, the results from this study provide new insights into the HS, ADD and IDD microbiomes, improve our understanding of the disease pathogenesis and generate unprecedented knowledge regarding the functional genetic composition of the digital dermatitis microbiome.

No MeSH data available.


Related in: MedlinePlus